Novel High-Quality Amoeba Genomes Reveal Widespread Codon Usage Mismatch Between Giant Viruses and Their Hosts.

The need for high-quality protist genomes has prevented in-depth computational and experimental studies of giant virus-host interactions. In addition, our current knowledge of host range is highly biased due to the few hosts used to isolate novel giant viruses. This study presents 6 high-quality amoeba genomes from known and potential giant virus hosts belonging to 2 distinct eukaryotic clades: Amoebozoa and Discoba.

Toward Automated Preprocessing of Untargeted LC-MS-Based Metabolomics Feature Lists from Human Biofluids.

Maximizing the extraction of true, high-quality, nonredundant features from biofluids analyzed via LC-MS systems is challenging. Here, the R packages IPO and AutoTuner were used to optimize XCMS parameter settings for the retrieval of metabolite or lipid features in both ionization modes from either faecal or urine samples from two cohorts ( = 621). The feature lists obtained were compared with those where the parameter values were selected manually.

Measuring the uptake of clinic-based HIV treatment and prevention services following HIV testing and referral at private pharmacies in Kenya.

Background: Despite their ubiquity across sub-Saharan Africa, private pharmacies are underutilized for HIV service delivery beyond the sale of HIV self-test kits. To understand what uptake of HIV prevention and treatment services might look like if private pharmacies offered clients free HIV self-testing and referral to clinic-based HIV services, we conducted a pilot study in Kenya.

Methods: At 20 private pharmacies in Kisumu County, Kenya, pharmacy clients (≥ 18 years) purchasing sexual health-related products (e.

Working with technical purity: simulation of red tattoo pigment metabolism by online-liquid chromatography-electrochemistry-mass spectrometry.

Tattooing is a popular form of body art that has evolved from ancient times into being part of modern society. The understanding of biotransformation processes of coloring tattoo pigments in human skin is limited although skin reactions to tattoos with unknown culprits occur. Electrochemistry coupled to mass spectrometry (EC-MS) has widely been used as a tool for a purely instrumental approach to simulating the enzymatic biotransformation of xenobiotics.

A sedimentary ancient DNA perspective on human and carnivore persistence through the Late Pleistocene in El Mirón Cave, Spain.

Caves are primary sites for studying human and animal subsistence patterns and genetic ancestry throughout the Palaeolithic. Iberia served as a critical human and animal refugium in Europe during the Last Glacial Maximum (LGM), 26.5 to 19 thousand years before the present (cal kya).

Effect of improving food security on parenting practices and caregiver-adolescent relationships: qualitative findings of an income-generating agricultural intervention in rural Kenya.

Background: Despite the recognised links between food insecurity and parenting, few studies have evaluated the perceived impacts of livelihood or food security interventions on parental practices, intra-household functioning, adolescent behaviour and psychosocial outcomes in HIV-affected households in sub-Saharan Africa.

Aims: The study aimed to understand the perceived effects of food security on parenting practices and how this was experienced by both adolescent girls (aged 13-19 years) and their caregivers in rural Kenya.

Method: We conducted semi-structured, individual interviews with 62 caregiver-adolescent dyads who were participants in the adolescent (NCT03741634), a sub-study of adolescent girls and caregivers with a household member participating in the agricultural and finance intervention trial (NCT01548599).

pH-FISH: coupled microscale analysis of microbial identity and acid-base metabolism in complex biofilm samples.

Background: Correlative structural and chemical imaging of biofilms allows for the combined analysis of microbial identity and metabolism at the microscale. Here, we developed pH-FISH, a method that combines pH ratiometry with fluorescence in situ hybridization (FISH) in structurally intact biofilms for the coupled investigation of microbial acid metabolism and biofilm composition. Careful biofilm handling and modified sample preparation procedures for FISH allowed preservation of the three-dimensional biofilm structure throughout all processing and imaging steps.

Effectiveness of influenza vaccination in preventing confirmed influenza cases and hospitalizations in Northern Spain, 2023/24 season: A population-based test-negative case-control study.

Objective: We estimated the influenza vaccination effectiveness (IVE) in preventing medical consultations and hospitalizations due to influenza during the 2023/24 season.

Methods: Two test-negative case-control studies analyzed patients who consulted primary healthcare or were hospitalized for respiratory symptoms and were tested for influenza by PCR in the 2023/24 season in Navarre, Spain. Influenza vaccination status in the current and previous seasons was compared between confirmed influenza cases and test-negative controls.

Elevated CO Increased Antibiotic Resistomes in Seed Endophytes: Evidence from a Free-Air CO Enrichment (FACE) Experiment.

Climate warming affects antibiotic resistance genes (ARGs) in soil and the plant microbiome, including seed endophytes. Seeds act as vectors for ARG dissemination in the soil-plant system, but the impact of elevated CO on seed resistomes remains poorly understood. Here, a free-air CO enrichment system was used to examine the impact of elevated CO on seed-associated ARGs and seed endophytic bacteria and fungi.

Gut microbiota genome features associated with brain injury in extremely premature infants.

Severe brain damage is common among premature infants, and the gut microbiota has been implicated in its pathology. Although the order of colonizing bacteria is well described, the mechanisms underlying aberrant assembly of the gut microbiota remain elusive. Here, we employed long-read nanopore sequencing to assess abundances of microbial species and their functional genomic potential in stool samples from a cohort of 30 extremely premature infants.

Asymptomatic carriage of intestinal protists is common in children in Lusaka Province, Zambia.

Background: PCR-based screenings on the presence of diarrhoea-causing intestinal protist species are limited in Zambia, resulting in inaccurate current prevalence and epidemiological data. Sensitive PCR-based methods are particularly well suited for detecting subclinical infections in apparently healthy carriers.

Methodology: In this prospective cross-sectional study, we investigated the occurrence of the most common intestinal protists in an apparently healthy paediatric population (5-18 years) in Lusaka Province, Zambia.

Ecology meets reproductive medicine in HIV prevention: the case for geography-informed approaches for bacterial vaginosis in Africa.

Purpose Of Review: Women in Africa bear the burden of the HIV epidemic, which has been associated with the high prevalence of bacterial vaginosis (BV) in the region. However, little progress has been made in finding an effective cure for BV. Drawing on advances in microbiome-directed therapies for gastrointestinal disorders, similar live-biotherapeutic based approaches for BV treatment are being evaluated.

Resilience and emergence of pneumococcal serotypes and lineages in adults post-PCV13 in Spain: A multicentre study.

Background: Streptococcus pneumoniae causes invasive pneumococcal disease (IPD) in adults. The introduction of pneumococcal conjugate vaccines (PCVs) has reduced vaccine serotypes but has also led to the rise of non-vaccine serotypes. The aim of this study was to analyse pneumococcal lineages and their association with recent changes in IPD among adults in Spain.

Free-Ranging Wolves (Canis lupus) are Natural Reservoirs of Intestinal Microeukaryotes of Public Health Significance in Southwestern Europe.

Introduction: Intestinal microeukaryote parasites are major contributors to the burden of diarrhoea in humans and domestic animals, but their epidemiology in wildlife is not fully understood. We investigated the frequency, genetic diversity and zoonotic potential of protists of animal and public health significance in free-ranging grey wolf (Canis lupus) populations in south-western Europe.

Methods: Individually formed faecal samples collected from necropsied wolves or scat trails in Italy (n = 47), Portugal (n = 43) and Spain (n = 225) during the period 2011-2023 were retrospectively analysed using molecular (PCR and Sanger sequencing) methods.

Characteristics of putative keystones in the healthy adult human gut microbiota as determined by correlation network analysis.

Keystone species are thought to play a critical role in determining the structure and function of microbial communities. As they are important candidates for microbiome-targeted interventions, the identification and characterization of keystones is a pressing research goal. Both empirical as well as computational approaches to identify keystones have been proposed, and in particular correlation network analysis is frequently utilized to interrogate sequencing-based microbiome data.

Training Social Network-Central Fishermen in Western Kenya to Distribute HIV Self-Test Kits and Health Facility Referral Vouchers.

Low HIV testing among men, particularly highly mobile fishermen, is a persistent challenge. The Owete study (NCT#04772469) used social network-central men (Promoters) to promote testing and linkage to HIV services among social networks of fishermen in western Kenya. The Promoters and fishermen networks were randomised to intervention or control arms.

Screening great ape museum specimens for DNA viruses.

Natural history museum collections harbour a record of wild species from the past centuries, providing a unique opportunity to study animals as well as their infectious agents. Thousands of great ape specimens are kept in these collections, and could become an important resource for studying the evolution of DNA viruses. Their genetic material is likely to be preserved in dry museum specimens, as reported previously for monkeypox virus genomes from historical orangutan specimens.

Soil fungi remain active and invest in storage compounds during drought independent of future climate conditions.

Microbial growth is central to soil carbon cycling. However, how microbial communities grow under climate change is still largely unexplored. Here we use a unique field experiment simulating future climate conditions (increased atmospheric CO and temperature) and drought concomitantly and investigate impacts on soil microbial activity.

Typhi Haplotype 58 biofilm formation and genetic variation in isolates from typhoid fever patients with gallstones in an endemic setting in Kenya.

Although typhoid fever has largely been eliminated in high-income countries, it remains a major global public health concern especially among low- and middle-income countries. The causative agent, serovar Typhi ( Typhi), is a human restricted pathogen with a limited capacity to replicate outside the human host. Human carriers, 90% of whom have gallstones in their gallbladder, continue to shed the pathogen for an ill-defined period of time after treatment.

Soil microbiomes show consistent and predictable responses to extreme events.

Increasing extreme climatic events threaten the functioning of terrestrial ecosystems. Because soil microbes govern key biogeochemical processes, understanding their response to climate extremes is crucial in predicting the consequences for ecosystem functioning. Here we subjected soils from 30 grasslands across Europe to four contrasting extreme climatic events under common controlled conditions (drought, flood, freezing and heat), and compared the response of soil microbial communities and their functioning with those of undisturbed soils.

Two Sporadic Cases of Legionellosis Associated with the Use of Domestic Ultrasonic Humidifiers.

Two sporadic cases of legionellosis occurring in consecutive years were confirmed by positive antigenuria to serogroup 1 in individuals with limited mobility who were confined to their homes. Both cases had a history of using ultrasonic humidifiers and of low exposure to other possible sources of infection. This study was conducted through an expanded epidemiological survey and home inspection.

Renewing Our Focus on Vulnerable Populations Among People Living with HIV.

The global HIV landscape has changed over the past few decades, with great milestones achieved in both HIV treatment and prevention [...

The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration.

Many human-targeted drugs alter the gut microbiome, leading to implications for host health. However, the mechanisms underlying these effects are not well known. Here we combined quantitative microbiome profiling, long-read metagenomics, stable isotope probing and single-cell chemical imaging to investigate the impact of two widely prescribed drugs on the gut microbiome.

A respiro-fermentative strategy to survive nanoxia in Acidobacterium capsulatum.

Microbial soil habitats are characterized by rapid shifts in substrate and nutrient availabilities, as well as chemical and physical parameters. One such parameter that can vary in soil is oxygen; thus, microbial survival is dependent on adaptation to this substrate. To better understand the metabolic abilities and adaptive strategies to oxygen-deprived environments, we combined genomics with transcriptomics of a model organism, Acidobacterium capsulatum, to explore the effect of decreasing, environmentally relevant oxygen concentrations.