Dose-response and type-dependent effects of antiviral drugs in anaerobic digestion of waste-activated sludge for biogas production.

In the context of the COVID-19 pandemic, antiviral drugs (AVDs) were heavily excreted into wastewater and subsequently enriched in sewage sludge due to their widespread use. The potential ecological risks of AVDs have attracted increasing attention, but information on the effects of AVDs on sludge anaerobic digestion (AD) is limited. In this study, two typical AVDs (lamivudine and ritonavir) were selected to investigate the responses of AD to AVDs by biochemical methane potential tests. The results indicated that the effects of AVDs on methane production from sludge AD were dose- and type-dependent. The increased ritonavir concentration (0.05-50 mg/kg TS) contributed to an 11.27-49.43% increase in methane production compared with the control. However, methane production was significantly decreased at high lamivudine doses (50 mg/kg TS). Correspondingly, bacteria related to acidification were affected when exposed to lamivudine and ritonavir. Acetoclastic and hydrotropic methanogens were inhibited at a high lamivudine dose, while ritonavir enriched methylotrophic and hydrotropic methanogens. Based on the analysis of intermediate metabolites, the inhibition of lamivudine and the promotion of ritonavir on acidification and methanation were confirmed. In addition, the existence of AVDs could affect sludge properties. Sludge solubilization was inhibited when exposed to lamivudine and enhanced by ritonavir, perhaps caused by their different structures and physicochemical properties. Moreover, lamivudine and ritonavir could be partially degraded by AD, but 50.2-68.8% of AVDs remained in digested sludge, implying environmental risks.

Biodegradation of COVID19 antibiotic; azithromycin and its impact on soil microbial community in the presence of phenolic waste and with temperature variation.

The increase in using antibiotics, especially Azithromycin have increased steadily since the beginning of COVID19 pandemic. This increase has led to its presence in water systems which consequently led to its presence upon using this water for irrigation. The aim of the present work is to study the impact of irrigation using Azithromycin containing water on soil microbial community and its catabolic activity in the presence of phenolic wastes as compost. Wild berry, red grapes, pomegranate, and spent tea waste were added to soil and the degradation was monitored after 5 and 7 days at ambient and high temperatures. The results obtained show that at 30 °C, soil microbial community collectively was able to degrade Azithromycin, while at 40 °C, addition of spent tea as compost was needed to reach higher degradation. To ensure that the degradation was biotic and depended on degradation by indigenous microflora, a 25 kGy irradiation dose was used to kill the microorganisms in the soil and this was used as negative control. The residual antibiotic was assayed using UV spectroscopy and High Performance Liquid Chromatography (HPLC). Indication of Azithromycin presence was studied using Fourier Transform Infrared Spectroscopy (FTIR) peaks and the same pattern was obtained using the 3 used detection methods, the ability to assign the peaks even in the presence of soil and not to have any overlaps, gives the chance to study this result in depth to prepare IR based sensor for quick sensing of antibiotic in environmental samples.

Native microbiomes in danger: Could One Health help to cope with this threat to global health

Planetary health faces an emergency associated with global change. Climate change, the increase in world population and urban concentration, the hyperintensification of productive systems, and the associated changes in land use, among other factors, are generating a risky substrate for global health deterioration. The emergence of the coronavirus disease 2019 pandemic is an example of the problems that this situation can provoke. Several researchers and health professionals have addressed the role of microorganisms, particularly bacteria, in promoting global health, mainly in the past decades. However, global change has contributed to the extinction of a wide array of bacterial species and the disruption of microbial communities that support the homeostasis of humans, animals, and the environment. The need to protect the diversity and richness of native microbiomes in biotic and abiotic environments is crucial but has been frequently underestimated. The "One Health" approach, based on integrating traditionally unconnected fields such as human, animal, and environmental health, could provide a helpful framework to face this challenge. Anyway, drastic political decisions will be needed to tackle this global health crisis, in which the preservation of native microbial resources plays a critical role, even in preventing the risk of a new pandemic. This review aims to explain the importance of native microbiomes in biotic and abiotic ecosystems and the need to consider bacterial extinction as a crucial problem that could be addressed under a One Health approachCopyright © Zunino

The upper respiratory tract microbiome and its role in human health: barrier function.

The human respiratory tract is a complex system characterized by a series of niches colonized with specific microbial communities. Until recently, researchers were mostly interested in lung microbiomes associated with acute and chronic infections. The upper respiratory tract microbiota has gained attention during COVID-19 (COronaVIrus Disease 2019) pandemic because it was suspected to influence the course and the outcome of viral infections. Aim. In this two-part review (see part 1, Pul'monologiya. 2022;32 (5): 745-754), we summarize current knowledge of the microbial communities at each upper respiratory tract location, considering the proposed barrier function of the respiratory microbiome. Conclusion. Based on the evidence presented in this review, we can see how the respiratory microbiome is involved in the pathogenesis of viral respiratory infections, including SARS-CoV-2 (Severe Acute Respiratory Syndrome CoronaVirus 2).Copyright © Starikova E.V. et al., 2022.

Assessment of residual chlorine in soil microbial community using metagenomics

Chlorine-containing disinfectants have been widely used around the world for the prevention and control of the COVID-19 pandemic. However, at present, little is known about the impact of residual chlorine on the soil micro-ecological environment. Herein, we treated an experimental soil-plant-microbiome microcosm system by continuous irrigation with a low concentration of chlorine-containing water, and then analyzed the influence on the soil microbial community using metagenomics. After 14-d continuous chlorine treatment, there were no significant lasting effect on soil microbial community diversity and composition either in the rhizosphere or in bulk soil. Although metabolic functions of the rhizosphere microbial community were affected slightly by continuous chlorine treatment, it recovered to the original status. The abundance of several resistance genes changed by 7 d and recovered by 14 d. According to our results, the chlorine residue resulting from daily disinfection may present a slight long-term effect on plant growth (shoot length and fresh weight) and soil micro-ecology. In general, our study assisted with environmental risk assessments relating to the application ofchlorine-containing disinfectants and minimization of risks to the environment during disease control, such as COVID-19. © 2022, Higher Education Press.

Performance and microbial community features of tidal-flow biochar-amended constructed wetlands treating sodium dodecyl sulfate (SDS)-containing greywater

A large quantity of surfactants (e.g., sodium dodecyl sulfate (SDS)) are discharged along with greywater especially during the COVID-19 pandemic, while information on the treatment of surfactant-containing greywater using eco-friendly constructed wetlands (CWs) and the impact of surfactants on CW systems has rarely been reported. In the present study, lab-scale CWs amended with a biochar substrate and operated in tidal flow (TF) mode were used to treat SDS-containing greywater. The results showed that the biochar-amended CWs removed NH4+-N significantly better (18.2–37.9%) than the gravel-only CWs (2.5–24.6%) but removed phosphorus (P) and COD less efficiently, and the feeding of SDS at 50 and 100 mg/L led to a notable decrease in N removal. TF not only notably improved the pollutant removal performance but also effectively eliminated SDS stress in the CWs (NH4+-N removal of 67.1–72.1%). Mean SDS removal efficiencies of 75.3–79.3% were obtained in the CWs. TF mode altered the microbial community structure and metabolic pattern and enhanced the abundance of functional bacteria related to N and P removal in the CWs. The bacterial community shifted considerably with SDS feeding, resulting in higher species diversity and more intensive co-occurrence network relationships. TF-CWs filled with composite substrates are highly feasible and promising for the treatment of SDS-containing greywater.

The research progress, hotspots, challenges and outlooks of solid-phase denitrification process.

Nitrogen pollution is one of the main reasons for water eutrophication. The difficulty of nitrogen removal in low-carbon wastewater poses a huge potential threat to the ecological environment and human health. As a clean biological nitrogen removal process, solid-phase denitrification (SPD) was proposed for long-term operation of low-carbon wastewater. In this paper, the progress, hotspots, and challenges of the SPD process based on different solid carbon sources (SCSs) are reviewed. Compared with synthetic SCS and natural SCS, blended SCSs have more application potential and have achieved pilot-scale application. Differences in SCSs will lead to changes in the enrichment of hydrolytic microorganisms and hydrolytic genes, which indirectly affect denitrification performance. Moreover, the denitrification performance of the SPD process is also affected by the physical and chemical properties of SCSs, pH of wastewater, hydraulic retention time, filling ratio, and temperature. In addition, the strengthening of the SPD process is an inevitable trend. The strengthening measures including SCSs modification and coupled electrochemical technology are regarded as the current research hotspots. It is worth noting that the outbreak of the COVID-19 epidemic has led to the increase of disinfection by-products and antibiotics in wastewater, which makes the SPD process face challenges. Finally, this review proposes prospects to provide a theoretical basis for promoting the efficient application of the SPD process and coping with the challenge of the COVID-19 epidemic.

Enrichment of antibiotic resistant genes and pathogens in face masks from coastal environments.

Face masks (FMs) are essential to limit the spread of the coronavirus during pandemic, a considerable of which are accumulated on the coast. However, limited is known about the microbial profile in the biofilm of the face masks (so-called plastisphere) and the impacts of face masks on the surrounding environments. We herein performed face mask exposures to coastal sediments and characterized the microbial community and the antibiotic resistome. We detected 64 antibiotic-resistance genes (ARGs) and 12 mobile gene elements (MGEs) in the plastisphere. Significant enrichments were found in the relative abundance of total ARGs in the plastisphere compared to the sediments. In detail, the relative abundance of tetracycline, multidrug, macrolide-lincosamide-streptogramin B (MLSB), and phenicol-resistant genes had increased by 5-10 times. Moreover, the relative abundance of specific hydrocarbonoclastic bacteria (e.g., Polycyclovorans sp.), pathogens (e.g., Pseudomonas oleovorans), and total MGEs significantly increased in the sediments after face mask exposure, which was congruent with the alteration of pH value and metal concentrations in the microcosms. Our study demonstrated the negative impacts of FMs on coastal environments regardless of the profiles of ARGs or pathogens. These findings improved the understanding of the ecological risks of face masks and underlined the importance of beach cleaning.

An investigation into the aging of disposable face masks in landfill leachate

Due to the excessive use of disposable face masks during the COVID-19 pandemic, their accumulation has posed a great threat to the environment. In this study, we explored the fate of masks after being disposed in landfill. We simulated the possible process that masks would experience, including the exposure to sunlight before being covered and the contact with landfill leachate. After exposure to UV radiation, all three mask layers exhibited abrasions and fractures on the surface and became unstable with the increased UV radiation duration showed aging process. The alterations in chemical groups of masks as well as the lower mechanical strength of masks after UV weathering were detected to prove the happened aging process. Then it was found that the aging of masks in landfill leachate was further accelerated compared to these processes occurring in deionized water. Furthermore, the carbonyl index and isotacticity of the mask samples after aging for 30 days in leachate were higher than those of pristine materials, especially for those endured longer UV radiation. Similarly, the weight and tensile strength of the aged masks were also found lower than the original samples. Masks were likely to release more microparticles and high concentration of metal elements into leachate than deionized water after UV radiation and aging. After being exposed to UV radiation for 48 h, the concentration of released particles in leachate was 39.45 muL/L after 1 day and then grew to 309.45 muL/L after 30 days of aging. Seven elements (Al, Cr, Cu, Zn, Cd, Sb and Pb) were detected in leachate and the concentration of this metal elements increased with the longer aging time. The findings of this study can advance our understanding of the fate of disposable masks in the landfill and develop the strategy to address this challenge in waste management. Copyright © 2023 Elsevier B.V.

The upper respiratory tract microbiome and its role in human health: biotopes and variability

Human respiratory tract is a complex system with a specific microbiological profile. Until recently, researchers were mostly interested in lung microbial communities associated with acute and chronic infections. The upper respiratory tract microbiota has gained attention during COVID-19 pandemic as it was proposed to be one of the factors affecting the course and the outcome of viral infections. The aim. In this review, we summarized the current knowledge about microbial communities in each section of the upper respiratory tract, considering the proposed barrier function of the respiratory microbiome. Conclusion. The facts provided in the first part of this review give a modern perspective on the structure of microbial communities of each part of the upper respiratory tract and factors that affect their variability. Copyright © 2022 Medical Education. All rights reserved.

Artificial intelligence-based approaches for traditional fermented alcoholic beverages' development: review and prospect.

Traditional fermented alcoholic beverages (TFABs) have gained widespread acceptance and enjoyed great popularity for centuries. COVID-19 pandemics lead to the surge in health demand for diet, thus TFABs once again attract increased focus for the health benefits. Though the production technology is quite mature, food companies and research institutions are looking for transformative innovation in TFABs to make healthy, nutritious offerings that give a competitive advantage in current beverage market. The implementation of intelligent platforms enables companies and researchers to gather, store and analyze data in a more convenient way. The development of data collection methods contributed to the big data environment of TFABs, providing a fresh perspective that helps brewers to observe and improve the production steps. Among data analytical tools, Artificial Intelligence (AI) is considered to be one of the most promising methodological approaches for big data analytics and decision-making of automated production, and machine learning (ML) is an important method to fulfill the goal. This review describes the development trends and challenges of TFABs in big data era and summarize the application of AI-based methods in TFABs. Finally, we provide perspectives on the potential research directions of new frontiers in application of AI approaches in the supply chain of TFABs.

A RARE CASE OF ANTINEUTROPHIL CYTOPLASMIC ANTIBODIES (ANCA)-ASSOCIATED VASCULITIS IN THE SETTING OF COVID-19 INFECTION

SESSION TITLE: Management of COVID-19-Induced Complications SESSION TYPE: Rapid Fire Case Reports PRESENTED ON: 10/19/2022 12:45 pm - 1:45 pm INTRODUCTION: Anti-neutrophil cytoplasmic antibody-associated vasculitis (ANCA-AV) is an autoimmune mediated inflammation of small and medium sized vessel walls. The occurrence of this autoimmune vasculitis is typically associated with underlying infection, medications, and genetic predisposition.(1) The objective of this case report is to describe a rare presentation of ANCA-AV in the setting of COVID-19 infection. CASE PRESENTATION: A 67-year-old male presented to the hospital with a three-week history of cough productive of brown sputum, epistaxis, fatigue, decreased appetite, and unintentional weight loss. During the previous week, he experienced worsening dyspnea and bilateral lower extremity swelling. On physical examination, he was hypoxic requiring 4L of supplemental oxygen to maintain saturations greater than 90%. Diffuse and bilateral wheezes were heard on auscultation of his lungs. A tender petechial rash was dispersed over his limbs, trunk, oropharynx, and nasopharynx. A basic metabolic panel revealed a mild, acute renal impairment. Urinalysis showed new onset proteinuria and hemoglobinuria. Nasopharyngeal swab was positive for SARS-COV-2. Contrast-enhanced computed tomography of the chest revealed diffuse, bilateral ground glass opacities and interstitial changes. Therapy with piperacillin-tazobactam was started for presumed superimposed bacterial community acquired pneumonia in the setting of COVID-19 infection. On day three of hospitalization, the petechial rash progressed to hemorrhagic blisters. His oral petechiae were now ulcerated. A punch biopsy of the affected skin showed leukocytoclastic vasculitis. Anti-Proteinase 3 (PR3) antibodies were positive. Subsequent renal biopsy showed pauci-immune focal necrotizing crescentic glomerulonephritis consistent with ANCA-AV. Therapy with intravenous pulse dose corticosteroids led to improvement in his rash and body aches, and he was discharged home on oral steroids ten days after admission. DISCUSSION: This report describes a rare case of ANCA-AV in the setting of recent COVID-19 infection. Differentiation of ANCA-AV, bacterial and COVID-19 pneumonia can be challenging on chest imaging alone.(1) New onset renal impairment, hematuria, proteinuria and the presence of the petechial rash were suspicious for co-existing ANCA-AV in this patient. COVID-19- associated cytokine storm and formation of neutrophil extracellular traps (NETs) is postulated to be the underlying cause.(1-3) NETs present myeloperoxidase (MPO) and PR3 antigens to the immune system. Formation of auto-antibodies to MPO and PR3 lead to the development of ANCA-AV. The findings of NETs on kidney biopsy specimens in patients with ANCA-AV supports this hypothesis.(1,2) CONCLUSIONS: To avoid the misdiagnosis of COVID-19-induced vasculitis, a low threshold to investigate co-existing vasculitis in patients with COVID-19 and associated clinical findings is highly recommended. Reference #1: Izci Duran T, Turkmen E, Dilek M, Sayarlioglu H, Arik N. ANCA-associated vasculitis after COVID-19. Rheumatol Int. 2021;41(8):1523-1529. Reference #2: Uppal NN, Kello N, Shah HH, et al. De Novo ANCA-Associated Vasculitis With Glomerulonephritis in COVID-19. Kidney Int Rep. 2020;5(11):2079-2083. Reference #3: Cobilinschi C, Cobilinschi C, Constantinescu A, Draniceanu I, Ionescu R. New-Onset ANCA-Associated Vasculitis in a Patient with SARS-COV2. Balkan Med J. 2021;38(5):318-320. DISCLOSURES: No relevant relationships by Andrei Hastings No relevant relationships by Jason Lane No relevant relationships by Tanya Marshall No relevant relationships by Palak Rath No relevant relationships by Sterling Shriber No relevant relationships by inderprit Singh No relevant relationships by Samuel Wiles

Ecological restoration for the Liangtan river by Rotating biological contactors combined with hybrid constructed wetlands

Rotating biological contactors (RBCs) were first used as pretreatment units for hybrid constructed wetlands (HCWs) in practical engineering to treat polluted river water. The experimental results during 2019–2021, except the period of global COVID-19 pandemic (January to April, November and December in 2020), indicated the average removal efficiencies of ammonia nitrogen (NH4+–N), total phosphorous (TP), and chemical oxygen demand (COD) were 95.06%, 41.03%, and 45.46%, which met the Chinese Environmental Quality Standards Ⅰ, Ⅲ, Ⅳ (CEQS Ⅰ, Ⅲ, Ⅳ), respectively. RBCs and HCWs had synergistic and complementary effects on purification efficiency, especially on nitrogen removal. The remarkable nitrification efficiency of RBCs was not influenced by temperature and influent loads. The relative abundances of microorganisms at HCWs in cold seasons were comparable to that in warm seasons, which promoted the recovery of decontamination efficiency after overwintering. These results support RBCs combined with HCWs (R-HCWs) is an effective polluted river purification process, providing a new perspective on water ecological restoration.

Smartphones as an Ecological Niche of Microorganisms: Microbial Activities, Assembly, and Opportunistic Pathogens.

Smartphone usage and contact frequency are unprecedentedly high in this era, and they affect humans mentally and physically. However, the characteristics of the microorganisms associated with smartphones and smartphone hygiene habits remain unclear. In this study, using various culture-independent techniques, including high-throughput sequencing, real-time quantitative PCR (RT-qPCR), the ATP bioluminescence system, and electron microscopy, we investigated the structure, assembly, quantity, and dynamic metabolic activity of the bacterial community on smartphone surfaces and the user's dominant and nondominant hands. We found that smartphone microbiotas are more similar to the nondominant hand microbiotas than the dominant hand microbiotas and show significantly decreased phylogenetic diversity and stronger deterministic processes than the hand microbiota. Significant interindividual microbiota differences were observed, contributing to an average owner identification accuracy of 70.6% using smartphone microbiota. Furthermore, it is estimated that approximately 1.75 × 106 bacteria (2.24 × 104/cm2) exist on the touchscreen of a single smartphone, and microbial activities remain stable for at least 48 h. Scanning electron microscopy detected large fragments harboring microorganisms, suggesting that smartphone microbiotas live on the secreta or other substances, e.g., human cell debris and food debris. Fortunately, simple smartphone cleaning/hygiene could significantly reduce the bacterial load. Taken together, our results demonstrate that smartphone surfaces not only are a reservoir of microbes but also provide an ecological niche in which microbiotas, particularly opportunistic pathogens, can survive, be active, and even grow. IMPORTANCE Currently, people spend an average of 4.2 h per day on their smartphones. Due to the COVID-19 pandemic, this figure may still be increasing. The high frequency of smartphone usage may allow microbes, particularly pathogens, to attach to-and even survive on-phone surfaces, potentially causing adverse effects on humans. We employed various culture-independent techniques in this study to evaluate the microbiological features and hygiene of smartphones, including community assembly, bacterial load, and activity. Our data showed that deterministic processes drive smartphone microbiota assembly and that approximately 1.75 × 106 bacteria exist on a single smartphone touchscreen, with activities being stable for at least 48 h. Fortunately, simple smartphone cleaning/hygiene could significantly reduce the bacterial load. This work expands our understanding of the microbial ecology of smartphone surfaces and might facilitate the development of electronic device cleaning/hygiene guidelines to support public health.

In Situ Genomics and Transcriptomics of SAR202 Subclusters Revealed Subtle Distinct Activities in Deep-Sea Water.

Deep-sea water columns are enriched with SAR202 that may conduct detrital matter degradation. There are several subclusters in SAR202, but their subtle differences in geochemical cycles are largely unknown, particularly for their in situ activities in the marine deep zone. Deep-sea DNA/RNA samples obtained from 12 continuous time periods over two days by in situ nucleic acid collection apparatus were used to re-evaluate the ecological functions of each SAR202 subcluster at a depth of ~1000 m in the South China Sea (SCS). Phylogenomics of 32 new SAR202 genomes from the SCS and western Pacific revealed their distribution in five subclusters. Metatranscriptomics analysis showed that the subclusters II and III were the dominant SAR202 groups with higher transcriptional activities in the SCS deep-sea zone than other subclusters. The analyses of functional gene expression further indicated that SAR202 subclusters II and III might be involved in different metabolic pathways in the deep-sea environment. The SAR202 subcluster III might take part in the degradation of deep-sea aromatic compounds. Time-course metagenomics and metatranscriptomics data did not show metabolic correlation of subclusters II and III over two days, suggesting diversified ecological functions of SAR202 subclusters under different organic inputs from the overlying water column. Collectively, our results indicate that the SAR202 subclusters play different roles in organic degradation and have probably undergone subtle and gradual adaptive evolution in the dynamic environment of the deep ocean.

MICROBIOME AND THE NEW CORONAVIRUS INFECTION (COVID-19)

The new coronavirus infection has been the leading public health problem in all countries for the past two years, causing enormous social and economic damage. The pathogenesis of COVID-19 infection continues to be studied, where the role of microflora of the respiratory and gastrointestinal tract (GIT) is considered to be important. The «intestine-lungs» functional axis, which ensures the interaction of the microbial communities of the respiratory tract and GIT, plays an important role in the immunopathogenesis of the COVID-19 infection, the development of inflammatory reaction in lung tissue and its subsequent restoration, as well as the formation of secondary bacterial complications. The intestinal infection with SARS-CoV-2 virus causes significant changes in the diversity and functional activity of intestine microbiota affecting negatively on the immune response patterns and maintenance of the colonization resistance of the mucous membranes. Summarizing the presented data of scientific publications on the problem of microbiome changes with the new coronavirus infection and the role of the «intestine-lungs» functional axis, the search for the modulation of the intestinal/respiratory microbiome seems promising with the purpose of not only preventing the progression of the disease, but also reducing of the duration of the disease and the severity of the symptoms of lung and GIT injury, as well as post-COVID symptoms prevention.

Targeting current and future threats: recent methodological trends in environmental antimicrobial resistance research and their relationships to risk assessment

Antimicrobial resistance (AMR) is a growing public health threat. Improved surveillance of AMR's genetic indicators in environmental reservoirs should lead to a more comprehensive understanding of the problem at a global scale, as with SARS-CoV-2 monitoring in sewage. However, the "best" monitoring approach is unclear. Some scientific works have emphasized monitoring for the abundance of already-known antimicrobial resistance genes (ARGs);others have emphasized monitoring for the potential of new ARGs to arise. The goal of this study was to examine which methods were employed by highly-cited papers studying AMR in environmental engineering and agricultural systems, thus providing insight into current and future methodological trends for monitoring ARGs. We searched recent (2018-2020) literature documenting AMR in five environmental matrices: wastewater, surface water, drinking water, stormwater, and livestock manure. We selected the most highly-cited papers across these matrices (89 papers from 17 809 initial results) and categorized them as using targeted methods (e.g., qPCR), non-targeted methods (e.g., shotgun metagenomics), or both. More than 80% of papers employed targeted methods. Only 33% employed non-targeted methods, and the use of targeted versus non-targeted methods varied by environmental matrix. We posit that improving AMR surveillance in environmental reservoirs requires assessing risk, and that different monitoring approaches imply different objectives for risk assessment. Targeted methods are appropriate for quantifying known threats, particularly in environmental matrices where direct human exposure is likely (e.g., drinking water). However, long-term studies employing non-targeted methods are needed to provide an understanding of how frequently new threats (i.e., novel ARGs) arise.

COVID-19: DIARRHEA, INFLAMMATION AND INTESTINAL MICROBIOTA

Introduction: Increased inflammatory cytokines has been observed in COVID-19 patients and there is evidence showing an alteration in gut-microbiota composition. SARS-CoV-2 can cause gastrointestinal symptoms, such as diarrhea. Evidence of an altered gut-microbiota composition and cytokines levels in COVID-19 diarrhea patients is lacking. Objectives: To compare serum cytokine levels and gut microbiota between COVID-19 diarrhea (D-COVID- 19) and non-diarrhea (NonD-COVID-19) patients and non- COVID-19 controls (HC). Material and methods: We included 143 hospitalized COVID-19 patients (positive quantitative reverse transcription PCR) in a single University Hospital, and 53 ambulatory HC (negative rapid serological test) were included. Blood and stool samples were collected at hospital admission in COVID-19 patients and at the time of HC recruitment. 27- pro and anti-inflammatory cytokines (Bio-Plex Pro™, Bio- Rad) were measured. Gut microbiota composition and diversity profiles were characterized by sequencing the 16S rRNA gene V3-V4 region amplified using DNA extracted from stool samples. Bioinformatics analysis was performed with QIIME2 software. First, we compare cytokine levels between COVID- 19 and HC and then COVID-19 with and without diarrhea. All comparisons were adjusted for age, sex, and BMI with linear regression. Results: The mean age in COVID-19 patients was 54 +/- 15 years (F=50%) and 52 +/- 8 (F=62%) for HC. Diarrhea was present in 19 (13.29%) of COVID-19 patients. COVID-19 patients had significative higher levels of: IL- 1ra, IL-2, IL-6, IL-7, IL-8, IL-13, IP-10 and PDGF-bb. Significant lower values of: IL-9, FGF -basic, MIP-1β, TNF-α were observed in D-COVID-19 compared to NonD-COVID-19. COVID-19 patients had a significant reduction of bacterial species (p=0.0001), and diversity and complexity of the bacterial community (Shannon's index) (p=0.0001) compared to the HC. There was no difference between D-COVID-19 and NonD-COVID-19. There were also changes in the composition of the microbiota associated with COVID-19. At the phylum level, COVID-19 patients showed a significant decrease in Actinobacteria and Firmicutes, and an increase in Bacteroidetes. At species level, an increase of 4 species of the genus Bacteroides was observed in COVID-19 patients. 31 very diverse bacterial species were found, all decreased in D-COVID-19. Conclusions: An alteration in serum cytokine levels was observed between COVID-19 and HC. D-COVID-19 had a decrease in some proinflammatory cytokines. A significant decrease in richness and species diversity of gutmicrobiota was observed in COVID-19 patients compared to HC, but no significant differences were observed between D-COVID-19 and NonD-COVID-19. However, in D-COVID- 19, a decrease in some bacterial species was observed.(Table Presented)(Figure Presented)

METAGENOMIC INTERROGATION OF RESPIRATORY AND GUT MICROBIAL COMMUNITIES, HOST IMMUNE RESPONSE, AND RISK OF SEVERE COVID-19

Background: Human-associated microbial communities have been linked to host immune response to respiratory viral infections. Prior investigations have observed shifts in the composition of the gut or respiratory microbiome in severe COVID-19. However, there has been no comprehensive metagenomic evaluation of the interaction between lower respiratory and gut microbiomes and host immune factors in COVID-19. Methods: From April 2020 to May 2021, we prospectively enrolled 153 hospitalized patients with mild (n=12), moderate (n=65), and severe (n=76) COVID-19 infection categorized using established clinical criteria. We longitudinally collected stool (n=270) for metagenomic profiling, and in a subset, we generated comprehensive host-microbiome-molecular profiles by collecting sputum metagenomes (n=87 participants with 212 samples) and blood cytokine levels (n=109 with 181 samples) weekly until hospital discharge. We performed omnibus testing of overall gut and respiratory community structure, species-level differential abundance testing using mixed effects modeling accounting for repeated sampling, hierarchical clustering of paired gut and respiratory metagenomic profiles, and multi-omic machine learning classification of disease severity. Results: Patients with severe COVID-19 tended to be older, were more frequently male, had higher rates of overweight/obesity, and a greater mean Charlson Comorbidity Index. Patients with severe COVID-19 infection had significantly decreased stool and respiratory microbiome a-diversity irrespective of antibiotic administration. COVID severity accounted for a small proportion of variance in stool (R2=2.4%, p=0.002) and sputum (R2=4.4%, p= 0.03) profiles. Hierarchical clustering of paired gut and respiratory samples from patients with severe COVID revealed the joint expansion of oral-typical taxa typically present during systemic inflammation (i.e., increases in Streptococcus and Peptostreptococus spp. in both gut and sputum). A pro-inflammatory milieu defined by a composite elevation of circulating plasma cytokines (e.g., IL-6, TNF-a, and IL-29 among others) were linked to broad microbial excursions in community structure for both stool and sputum as measured by Bray-Curtis distances. A random forest classifier incorporating either stool or sputum taxonomic features and accounting for age, sex, body mass index, and recent antibiotic use achieved excellent classification of biospecimens from patients with severe vs. non-severe COVID patients (AUROC > 0.80). Conclusions: Alterations of the gut and respiratory microbiome were associated with differences in host immune response and COVID-19 disease severity. Further studies are needed to identify the potential role of human-associated microbial communities as a biomarker for poor patient outcomes in COVID-19 who may warrant escalated levels of care.(Figure Presented) Fig. 1. (A) Using unsupervised feature selection (species abundance > 0.001) inclusive of taxa differentially abundant by non-parametric Wilcoxon rank-sum testing (nominal p-value < 0.05), (B) we performed random forest classification using a twice-repeated 5-fold crossvalidation scheme to predict COVID-19 disease severity from shotgun metagenomic stool profiles (C) yielding an AUROC of 0.91.