mSystems

Wastewater-based surveillance (WBS) is widely used to monitor respiratory viruses, yet uncertainties remain regarding how viral RNA concentrations in wastewater reflect infection dynamics. Specifically, diurnal variation in shedding and RNA losses during in-sewer transport can impact measured signals. We conducted a field study in a 5-km trunk sewer (travel time of one hour). Wastewater was sampled at the sewer inlet and outlet using autosamplers collecting time-proportional one-hour composite s...

The ongoing COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires a significant, coordinated public health response. Assessing case density and spread of infection is critical and relies largely on clinical testing data. However, clinical testing suffers from known limitations, including test availability and a bias towards enumerating only symptomatic individuals. Wastewater-based epidemiology (WBE) has gained widespread support as a potential complem...

Wastewater surveillance of SARS-CoV-2 has become an attractive tool for combating the spread of COVID-19 by assessing the presence or levels of the virus shed in a population. However, the methods to quantify viral RNA and to link those quantities to the level of infection within the community vary. In this study, we sought to identify and optimize scalable methods for recovery of viral nucleic acids from wastewater and attempted to use a constitutive member of the gut virome, human-specific crA...

Wastewater-based epidemiology (WBE) may be useful for informing public health response to viral diseases like COVID-19 caused by SARS-CoV-2. We quantified SARS-CoV-2 RNA in wastewater influent and primary settled solids in two wastewater treatment plants to inform the pre-analytical and analytical approaches, and to assess whether influent or solids harbored more viral targets. The primary settled solids samples resulted in higher SARS-CoV-2 detection frequencies than the corresponding influent ...

Clinical staging diagnosis and progression tracking for ulcerative colitis (UC) is challenging as poor patient compliance of endoscopic biopsy, we aimed to explore a non-invasive integrative biochemical index to quantitative track and monitor pathological activity. Here we perform a study that integrates bile acid metabolomic profiling, metagenomic sequencing and clinical monitoring on serum and feacal samples from 24 active-state UC patients, 25 remission-state UC patients and 20 healthy volunt...

BackgroundCrohns disease (CD), ulcerative colitis (UC) and pouchitis are multifactorial and chronic inflammatory diseases of the gastrointestinal tract, termed together as inflammatory bowel diseases (IBD). Pouchitis develops in former patients with UC after total proctocolectomy and ileal pouch-anal anastomosis ("pouch surgery") and is characterized by inflammation of the previously normal small intestine comprising the pouch. It has been extensively shown that broad taxonomic and functional al...

BackgroundGlobally, ulcerative colitis (UC) is the most common form of intestinal inflammation, which is believed to be the result of a deregulated immune system response to commensal microbiota in a genetically susceptible host. Multicellular organisms rely heavily on their commensal symbiotic microbiota, whose composition is closely related to intrinsic local characteristics and regulated or modified by environmental factors. In the present study we aim to describe the unknown gut microbiota o...

Wastewater-based epidemiology provides an approach for assessing the prevalence of pathogens such as COVID-19 in a sewer service area. In this study, SARS-CoV-2 RNA was measured serially in 44 wastewater treatment plants of varying service capacities comprising approximately 67% of the population of Minnesota, from September 2020 through December 2022. We employed linear regression models to establish a predictive relationship between the weekly SARS-CoV-2 RNA concentrations in wastewater and cl...

ObjectiveEvidence on the association between the gut microbiome and metabolic conditions has been increasing during the past decades. Unlike the straightforward identification of beneficial non-pathogenic bacteria as a potential probiotic for clinical use, the analysis of gut microbiome diversity is more complex and required a better understanding of various measures. We aim to summarize an elaborated list of gut microbiome diversity measures. DesignSystematic search was conducted in three data...

BackgroundInflammatory bowel disease (IBD) is a set of conditions characterized by non-infectious chronic inflammation of the gastrointestinal tract. These primarily include Crohns disease (CD), ulcerative colitis (UC) and indeterminate colitis. Fecal microbiota transplantation (FMT) has proven to be an effective treatment for some patients with active UC. There is currently no procedure allowing to predict the patients response and to select the most adequate donor(s). AimInvestigate microbiom...

BackgroundBlastocystis, the most prevalent eukaryotic gut microbe in humans, has a global distribution. Studies have linked its presence with distinct gut microbiome and metabolome profiles compared to those where the organism is absent. However, the in vivo effect of antibiotics on Blastocystis and the surrounding gut microbiome remains understudied. This case study aimed to explore how antibiotic consumption influences the presence of Blastocystis and the subsequent changes in the gut microbio...

Exposure to Clostridioides difficile can result in asymptomatic carriage or infection with symptoms ranging from mild diarrhea to fulminant pseudomembranous colitis. A reliable diagnostic approach for C. difficile infection (CDI) remains controversial. Accurate diagnosis is paramount not only for patient management but also for epidemiology and disease research. Here, we characterized gut microbial compositions and a broad panel of innate and adaptive immunological markers in 243 well-characteri...

BackgroundDespite recent efforts, a single factor underlying the gut microbiota dysbiosis in intestinal diseases is not identified. We hypothesized that compromised intestinal barrier (CIB) could lead to increased host-derived contents including human cells in the gut, change its physio-metabolic properties, and globally alter gut microbiota and their metabolic capacities. ResultsConsistently, we found human DNA contents (HDCs), calculated as the percentage of metagenomic sequencing reads mappe...

ObjectiveThe gut microbiome is thought to play an important role in the development of colorectal cancer (CRC). However, as the gut microbiome varies widely based on diet, we sought to investigate the gut microbiome changes in patients with CRC in a South Asian population. DesignThe gut microbiome was assessed by 16s metagenomic sequencing targeting the V4 hypervariable region of the bacterial 16S rRNA in stool samples (n=112) and colonic tissue (n=36) in 112 individuals. Of these had CRC (n=24...

BackgroundDysbiosis of gut microbial community is associated with the pathogenesis of CD and may serve as a promising non-invasive diagnostic tool. We aimed to compare the performances of the microbial markers of different biological levels by conducting a multidimensional analysis on the microbial metagenomes of CD. MethodsWe collected fecal metagenomic datasets generated from eight cohorts that altogether include 870 CD patients and 548 healthy controls. The microbial alterations in CD patien...

Anastomotic leakage (AL) is a frequent and potentially life-threatening postoperative complication in patients undergoing colorectal surgery with a multifactorial yet unknown pathophysiology. In the present study, we aimed to unravel AL etiology and intestinal anastomotic healing (AH) physiology focusing on both host epithelial and gut microbial components. We make use of patients-related samples and two high throughput next generation sequencing analysis approaches, including anastomotic tissue...

Severe acute malnutrition (SAM) constitutes the leading risk for childhood mortality worldwide. Butyrate, a critical metabolite for mucosal immunity produced by anaerobic gut microbes, has been found to be dramatically depleted in children experiencing fatal outcomes related to SAM. However, the association between butyrate depletion and gut microbiota alteration has not yet been fully explored. Here, we performed a large group-matched case-control study in children aged 0-59 months in Mali. We ...

Wastewater monitoring enables non-invasive, population-scale tracking of community infections independent of healthcare-seeking behavior and clinical diagnosis. Metagenomic sequencing extends this capability by enabling broad, pathogen-agnostic detection, genomic characterization, and identification of novel or unexpected threats. Here, we present data from CASPER (the Coalition for Agnostic Sequencing of Pathogens from Environmental Reservoirs), a U.S.-based wastewater metagenomic sequencing ne...

The COVID-19 pandemic is spreading globally with high disparity in the susceptibility of the disease severity. Identification of the key underlying factors for this disparity is highly warranted. Here we describe constructing a proteomic risk score based on 20 blood proteomic biomarkers which predict the progression to severe COVID-19. We demonstrate that in our own cohort of 990 individuals without infection, this proteomic risk score is positively associated with proinflammatory cytokines main...

We characterize variant diversity, amino acid mutation frequency, functionality and associations with COVID-19 infections in one of the largest datasets of SARS-CoV-2 genome sequences collected from wastewater in the New York metropolitan area. Variant diversity differed within parts of the New York City sewershed and between wastewater sludge and influent samples. P314L, D614G and T3255I occurred in >95% of wastewater samples. Enhanced infectivity, transmissibility and escape from antibody neut...