Observed Mask Wearing and Presence of SARS-CoV-2 in School Wastewater, San Diego County, CA, 2022.

To test the association between directly observed school masking behaviors and the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in school wastewater. We randomly sampled a subset of schools participating in a translational study on the effectiveness of passive wastewater surveillance in nonresidential K‒12 settings in San Diego County. Trained observers conducted biweekly systematic observations of masking behaviors between March 2 and May 27, 2022.

Gut microbiota and derived metabolites mediate obstructive sleep apnea induced atherosclerosis.

Obstructive sleep apnea (OSA) is characterized by intermittent hypoxia/hypercapnia (IHC), affects predominantly obese individuals, and increases atherosclerosis risk. Since we and others have implicated gut microbiota and metabolites in atherogenesis, we dissected their contributions to OSA-induced atherosclerosis. Atherosclerotic lesions were compared between conventionally-reared specific pathogen free (SPF) and germ-free (GF) Apoe mice following a high fat high cholesterol diet (HFHC), with and without IHC conditions.

The International Space Station has a unique and extreme microbial and chemical environment driven by use patterns.

Space habitation provides unique challenges in built environments isolated from Earth. We produced a 3D map of the microbes and metabolites throughout the United States Orbital Segment (USOS) of the International Space Station (ISS) with 803 samples collected during space flight, including controls. We find that the use of each of the nine sampled modules within the ISS strongly drives the microbiology and chemistry of the habitat.

Human Untargeted Metabolomics in High-Throughput Gut Microbiome Research: Ethanol vs Methanol.

Untargeted metabolomics is frequently performed on human fecal samples in conjunction with sequencing to unravel the gut microbiome functionality. As sample collection efforts are rapidly expanding, with individuals often collecting specimens at home, metabolomics experiments should adapt to accommodate the safety and needs of bulk off-site collections and improve high throughput. Here, we show that a 95% ethanol, safe to be shipped and handled, extraction part of the Matrix Method pipeline recovers comparable amounts of metabolites as a validated 50% methanol extraction, preserving metabolic profile differences between investigated subjects.

To Impute or Not To Impute in Untargeted Metabolomics─That is the Compositional Question.

Untargeted metabolomics often produce large datasets with missing values. These missing values are derived from biological or technical factors and can undermine statistical analyses and lead to biased biological interpretations. Imputation methods, such as -Nearest Neighbors (kNN) and Random Forest (RF) regression, are commonly used, but their effects vary depending on the type of missing data, e.

SARS-CoV-2 infectivity can be modulated through bacterial grooming of the glycocalyx.

The gastrointestinal (GI) tract is a site of replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and GI symptoms are often reported by patients. SARS-CoV-2 cell entry depends upon heparan sulfate (HS) proteoglycans, which commensal bacteria that bathe the human mucosa are known to modify. To explore human gut HS-modifying bacterial abundances and how their presence may impact SARS-CoV-2 infection, we developed a task-based analysis of proteoglycan degradation on large-scale shotgun metagenomic data.

ChIP provides 10-fold microbial DNA enrichment from tissue while minimizing bias.

Background: Host DNA depletion is a critical tool for accessing the microbiomes of samples that have a small amount of microbial DNA contained in a high host background. Of critical practical importance is the ability to identify microbial DNA sequences in frozen tissue specimens. Here, we compare four existing commercial methods and two newly introduced methods involving chromatin immunoprecipitation (ChIP) on frozen human and pig intestinal biopsies.

Community assembly modeling of microbial evolution within Barrett's esophagus and esophageal adenocarcinoma.

Mathematical modeling of somatic evolution, a process impacting both host cells and microbial communities in the human body, can capture important dynamics driving carcinogenesis. Here we considered models for esophageal adenocarcinoma (EAC), a cancer that has dramatically increased in incidence over the past few decades in Western populations, with high case fatality rates due to late-stage diagnoses. Despite advancements in genomic analyses of the precursor Barrett's esophagus (BE), prevention of late-stage EAC remains a significant clinical challenge.

Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data.

As next-generation sequencing technologies produce deeper genome coverages at lower costs, there is a critical need for reliable computational host DNA removal in metagenomic data. We find that insufficient host filtration using prior human genome references can introduce false sex biases and inadvertently permit flow-through of host-specific DNA during bioinformatic analyses, which could be exploited for individual identification. To address these issues, we introduce and benchmark three host filtration methods of varying throughput, with concomitant applications across low biomass samples such as skin and high microbial biomass datasets including fecal samples.

Medication use is associated with distinct microbial features in anxiety and depression.

This study investigated the relationship between gut microbiota and neuropsychiatric disorders (NPDs), specifically anxiety disorder (ANXD) and/or major depressive disorder (MDD), as defined by Diagnostic and Statistical Manual of Mental Disorders (DSM)-IV or V criteria. The study also examined the influence of medication use, particularly antidepressants and/or anxiolytics, classified through the Anatomical Therapeutic Chemical (ATC) Classification System, on the gut microbiota. Both 16S rRNA gene amplicon sequencing (16S) and shallow shotgun sequencing (WGS) were performed on DNA extracted from 666 fecal samples from the Tulsa-1000 and Neurocomputational Mechanisms of Affiliation and Personality Study Center for Biomedical Research Excellence (NeuroMAP CoBRE) cohorts.

Consuming a modified Mediterranean ketogenic diet reverses the peripheral lipid signature of Alzheimer's disease in humans.

Background: Alzheimer's disease (AD) is a major neurodegenerative disorder with significant environmental factors, including diet and lifestyle, influencing its onset and progression. Although previous studies have suggested that certain diets may reduce the incidence of AD, the underlying mechanisms remain unclear.

Method: In this post-hoc analysis of a randomized crossover study of 20 elderly adults, we investigated the effects of a modified Mediterranean ketogenic diet (MMKD) on the plasma lipidome in the context of AD biomarkers, analyzing 784 lipid species across 47 classes using a targeted lipidomics platform.

Evidence for microbially-mediated tradeoffs between growth and defense throughout coral evolution.

Background: Evolutionary tradeoffs between life-history strategies are important in animal evolution. Because microbes can influence multiple aspects of host physiology, including growth rate and susceptibility to disease or stress, changes in animal-microbial symbioses have the potential to mediate life-history tradeoffs. Scleractinian corals provide a biodiverse, data-rich, and ecologically-relevant host system to explore this idea.

Anthelmintic Treatment Reveals Sex-Dependent Worm-Gut Microbiota Interactions.

Gastrointestinal helminths interact with the gut microbiota in ways that shape microbiota structure and function, but these effects are highly inconsistent across studies. One factor that may help explain variation in parasite-microbiota interactions is host sex since helminths can induce sex-specific changes in feeding behaviour and diet that might cascade to shape gut microbial communities. We tested this idea using an anthelmintic treatment experiment in wild Grant's gazelles (Nanger granti).

TEMPTED: time-informed dimensionality reduction for longitudinal microbiome studies.

Longitudinal studies are crucial for understanding complex microbiome dynamics and their link to health. We introduce TEMPoral TEnsor Decomposition (TEMPTED), a time-informed dimensionality reduction method for high-dimensional longitudinal data that treats time as a continuous variable, effectively characterizing temporal information and handling varying temporal sampling. TEMPTED captures key microbial dynamics, facilitates beta-diversity analysis, and enhances reproducibility by transferring learned representations to new data.

The mouth of America: the oral microbiome profile of the US population.

Importance: The oral microbiome is increasingly recognized to play key roles in human health and disease; yet, population-representative characterizations are lacking.

Objective: Characterize the composition, diversity, and correlates of the oral microbiome among US adults.

Design: Cross-sectional population-representative survey.

The oral microbiome and all-cause mortality in the US population.

Importance: Poor oral health, including periodontal disease, is associated with oral microbiome changes and increased mortality risk. However, no large studies have evaluated whether the oral microbiome is directly associated with mortality.

Objective: To evaluate whether measures of the oral microbiome is prospectively associated with all-cause mortality.

Antibody Levels from High-Throughput Variant-Specific SARS-CoV-2 Anti-Spike IgG and ACE2 Neutralization Assays Correlate with COVID Infection Risk in a Large Population.

Background: SARS-CoV-2 antibody levels have been proposed as a correlate of protection (CoP) from infection. Yet, large-scale prospective studies of cost-effective scalable antibody measures as predictors of infection under real-world conditions are limited. We examined whether antibody levels measured using high-throughput variant-specific SARS-CoV-2 anti-spike immunoglobulin G (IgG) and ACE2-neutralization assays correlate with cell-based neutralizing antibody (NAb) measurements, and whether they can serve as a reasonable CoP from SARS-CoV-2 infection.

Gut Microbiota and Derived Metabolites Mediate Obstructive Sleep Apnea Induced Atherosclerosis.

Background: Obstructive sleep apnea (OSA) is characterized by intermittent hypoxia/hypercapnia (IHC), affects predominantly obese individuals, and increases atherosclerosis risk. Since we and others have implicated gut microbiota and metabolites in atherogenesis, we dissected their contributions to OSA-induced atherosclerosis.

Results: Atherosclerotic lesions were compared between conventionally-reared specific pathogen free (SPF) and germ-free (GF) mice following a high fat high cholesterol diet (HFHC), with and without IHC conditions.

The microbiome diversifies -acyl lipid pools - including short-chain fatty acid-derived compounds.

-acyl lipids are important mediators of several biological processes including immune function and stress response. To enhance the detection of -acyl lipids with untargeted mass spectrometry-based metabolomics, we created a reference spectral library retrieving -acyl lipid patterns from 2,700 public datasets, identifying 851 -acyl lipids that were detected 356,542 times. 777 are not documented in lipid structural databases, with 18% of these derived from short-chain fatty acids and found in the digestive tract and other organs.

Comparative gut microbiome research through the lens of ecology: theoretical considerations and best practices.

Comparative approaches in animal gut microbiome research have revealed patterns of phylosymbiosis, dietary and physiological convergences, and environment-host interactions. However, most large-scale comparative studies, especially those that are highly cited, have focused on mammals, and efforts to integrate comparative approaches with existing ecological frameworks are lacking. While mammals serve as useful model organisms, developing generalised principles of how animal gut microbiomes are shaped and how these microbiomes interact bidirectionally with host ecology and evolution requires a more complete sampling of the animal kingdom.