bluuebunny/crossref_metadata_2025 huggingface dataset:
Benthic visual adaptation by fine-tuning light sensitivity in Japanese flounder (Paralichthys olivaceus)
Authors: Zhang Zhengrui , Liu Yuezhong , Zhang Wei , Du Xinxin , Liu Jinxiang
Published: October 2022

The habitat occupied by flatfish fry differs considerably in light regime from that of the adult. The diversity of opsins and their expression patterns appear greatest for flatfishes to experience variable light environments. Yet, opsin repertoires and expression patterns in this group of fishes are poorly described. To understand how the visual system has adapted to such changes, we unveil that Japanese flounder (Paralichthys olivaceus) has a visual system adapted to a benthic environment by fine-tuning paralogous opsins (SWS2A and RH2) for wavelength shift and regulated expression. P. olivaceus express five basic opsin genes (M/LWS, SWS1, SWS2, RH1 and RH2) and gene-specific duplications were observed in RH2 and SWS2 paralogues. The expression of the three short-wavelength sensitive genes, SWS2Aα, SWS2Aβ, and SWS2B, is significantly elevated at the benthic stages, especially in SWS2Aβ a striking expression change is observed. The four middle-wavelength sensitive genes exhibit divergent expressions, the expression of RH2A-1 and RH2A-2 increased, while that of RH2B-1 and RH2B-2 decreased significantly from pelagic to benthic stage, especially RH2A-2. At present, changes at a total of 26 sites are known to have modified the λmax of various visual pigments during vertebrate evolution. Thus, these tuning site variations in our P. olivaceus are suspected to cause a green-shift in the λmax of SWS2Aα pigments and blue-shift in that of in RH2A-2. Together, our results suggest that RH2 and SWS2 opsin repertoires serve to optimize visual function under variable light environments by gene family duplications, differential expressions, and maximum absorption wavelength (λmax) variations.
Eukaryotic diversity of marine biofouling from coastal to offshore areas
Authors: Portas Aurélie , Quillien Nolwenn , Culioli Gérald , Briand Jean-François
Published: October 2022

Marine biofouling communities, including biofilms, are composed of many eukaryotes with high taxonomic and functional diversities. However, molecular characterization of eukaryotic diversity of marine biofouling has been barely developed due to the only recent interest in research areas such as marine renewable energies, antifouling technologies, or plastic pollution. The aim of this study was to compare the diversity and taxonomic composition of biofouling through different metabarcoding approaches used to detect the widest range of taxa from samples collected in several contrasted marine environments (French Atlantic and Mediterranean coasts). Thus, we assessed four DNA extraction methods and six primers pairs targeting the 18S rDNA gene (including the V1-V2, V4TAR, V4UNI, V7 and V9 regions) and the COI gene, the latter with two databases (BOLD and MIDORI). In addition the influence of primers selection was analyzed at three sites to compare geographic variations in eukaryotic diversity. Although none of the extraction methods greatly altered the community diversity or composition. we have observed that eukaryotic biofouling community diversity and structure varied depending on primers pairs, reference databases and sites. 18S rDNA regions allowed the detection of more taxa at the species level, including microeukaryotes, while the COI recovered more ASVs, but with a large proportion that remained taxonomically unassigned probably because BOLD and MIDORI specifically targeted metazoans. Interestingly, the spatial pattern obtained with both COI and 18S rDNA markers were similar showing that spatial selection occurred throughout a wide diversity of eukaryotic taxa. These results encouraged the use of these two complementary markers for future metabarcoding investigations but also highlighted the relevance of completing databases to enhance the identification of biofouling eukaryotes.
Tracing the depth-dependent changes in organic carbon and nutrient fluxes using high-resolution 228Ra profiles in the upper East Sea (Japan Sea)
Authors: Cho Hyung-Mi , Han Yongjin , Kim Young-Il , Baek Cheolmin , Kim Guebuem
Published: October 2022

Vertical profiles of 228Ra (half-life: 5.75 years) in the ocean provide valuable information on water mixing and ages of the upper ocean. However, its application is hampered by extremely low levels of 228Ra in the deep ocean. In this study, we measured high-resolution 228Ra/226Ra ratio profiles (>21 depths) in the East Sea (Japan Sea) by mooring Mn-fiber. Using the measured 228Ra profile from 228Ra/226Ra ratios and 226Ra activities, together with other previously published data, we estimated the vertical eddy diffusivity (8.7–9.6 cm2 s-1) in the permanent thermocline and water ages (10–15 years) in the upper 500–1000 m range. The estimated decomposition rate of organic carbon based on oxygen utilization rates using Ra-ages between 100 and 1000 m was 4.4 ± 0.8 mol C m-2 yr-1. Our results show that ~50% of the upward nutrients through 100 m support export production, and that dissolved organic carbon accounts for ~20% of carbon export. This 228Ra approach provides a holistic understanding of carbon and nutrient cycles in the ocean.
Interaction between seawater carbon dioxide dynamics and stratification in shallow coastal waters: A preliminary study based on a weekly validated three-dimensional ecological model
Authors: Xiong Bing , Yano Shinichiro , Komai Katsuaki , Saito Naoki , Komori Hiroto , Chi Baixin , Hao Lin , Nakayama Keisuke
Published: October 2022

Shallow coastal waters (SCWs) have attracted wide attention in recent years due to their strong carbon sequestration capacity. However, the complex carbon dioxide (CO2) dynamics in the water column makes it difficult to estimate the air–water CO2 fluxes (FCO2) accurately. We developed a numerical model of CO2 dynamics in water based on field measurements for a typical stratified semi-enclosed shallow bay: the Yatsushiro Sea, Japan. The developed model showed an excellent ability to reproduce the stratification and CO2 dynamics of the Yatsushiro Sea. Through numerical model simulations, we analyzed the annual CO2 dynamics in the Yatsushiro Sea in 2018. The results show that the effect of stratification on the CO2 dynamics in seawater varies greatly depending on the distance from the estuary and the period. In the estuarine region, stratification manifests itself throughout the year by promoting the maintenance of a high partial pressure of CO2 (pCO2) in surface waters, resulting in surface pCO2 being higher than atmospheric pCO2 for up to 40 days during the flood period (average surface pCO2 of 539.94 µatm). In contrast, in areas farther from the estuary, stratification mainly acts to promote the maintenance of high pCO2 in surface waters during periods of high freshwater influence. Then changes to a lower surface pCO2 before the freshwater influence leads towards complete dissipation. Finally, we estimated the FCO2 of the Yatsushiro Sea in 2018, and the results showed that the Yatsushiro Sea was a sink area for atmospheric CO2 in 2018 (−1.70 mmol/m2/day).
Multi-event modeling of true reproductive states of individual female right whales provides new insights into their decline
Authors: Reed Joshua , New Leslie , Corkeron Peter , Harcourt Robert
Published: October 2022

Abundance and population trends of Critically Endangered North Atlantic right whales (Eubalaena glacialis, NARW) have been estimated using mark-recapture analyses where an individual’s state is based upon set delineations of age, using historical estimates of age at first reproduction. Here we assigned individual females to states based upon their reproductive experience, rather than age. We developed a Bayesian mark-recapture-recovery model to investigate how survival, recapture, site-fidelity and dead-recovery probabilities vary for female NARW in different states, using data collected from 1977-2018. States were assigned as calves for individuals in their first year; pre-breeder for individuals greater than one year of age who had yet to produce a calf, or breeder if an individual had reproduced. A decline in abundance of female NARW was seen starting in 2014, with 185 females declining yearly to 142 by 2018. The largest decline was seen in breeding females, with 72 estimated to be alive at the beginning of 2018, while female pre-breeder abundance plateaued at around 70 between 2011- 2018. Females born from 2000 onwards had an average 4% (95% CI:0.03-0.06) chance of transitioning from pre-breeder to breeder, compared to 8% (95%CI:0.06-0.1) for females born prior. This reduction in transition rate from non-breeder to breeder for the current cohort resulted in breeding females declining to 51% of the female population by 2018. We show that a collapse in fecundity of breeding females, and the failure of pre-breeders to start breeding, is an important factor in understanding the current decline in abundance of the NARW.
Biological properties of Cu-bearing and Ag-bearing titanium-based alloys and their surface modifications: A review of antibacterial aspect
Authors: Ma Yidan , Yan Jiao , Yan Tingting , Wang Qiang , Bao Zhifan , Yi Zhe
Published: October 2022

The use of titanium dental implants to replace missing teeth represents an important field of daily dental practice worldwide, which is highly reliable for long-term survival and success rates. However, titanium dental implants still have intrinsic problems that cannot meet the clinical requirements. Improving the performance of implants is an increasingly important area of dental research to reduce infection rates. Improved properties can be achieved by two main methods: 1) the overall change in the materials by changing the elemental composition and 2) surface modifications. This review provides an overview of various titanium-based alloys that have been employed to achieve a higher survival rate of implantation by adding elements or modifying the surface, with a special focus on their antibacterial applications. Recent developments in titanium-based alloys containing various antibacterial agents have been described in detail, including Cu-bearing, Ag-bearing, and Zr-bearing Ti alloys. Moreover, the applications of bioactive coatings and 3D printing materials with antibacterial properties are reviewed. This review aims to highlight the antibacterial challenges associated with titanium-based alloys to promote the further development and clinical application of antibacterial alloys.
Establishment of a ccRCC patient-derived chick chorioallantoic membrane model for drug testing
Authors: Charbonneau Martine , Harper Kelly , Brochu-Gaudreau Karine , Perreault Alexis , McDonald Patrick P. , Ekindi-Ndongo Nadia , Jeldres Claudio , Dubois Claire M.
Published: October 2022

Clear cell renal cell carcinoma (ccRCC) is an aggressive subtype of renal cell carcinoma accounting for the majority of deaths in kidney cancer patients. Advanced ccRCC has a high mortality rate as most patients progress and develop resistance to currently approved targeted therapies, highlighting the ongoing need for adequate drug testing models to develop novel therapies. Current animal models are expensive and time-consuming. In this study, we investigated the use of the chick chorioallantoic membrane (CAM), a rapid and cost-effective model, as a complementary drug testing model for ccRCC. Our results indicated that tumor samples from ccRCC patients can be successfully cultivated on the chick chorioallantoic membrane (CAM) within 7 days while retaining their histopathological characteristics. Furthermore, treatment of ccRCC xenografts with sunitinib, a tyrosine kinase inhibitor used for the treatment of metastatic RCC, allowed us to evaluate differential responses of individual patients. Our results indicate that the CAM model is a complementary in vivo model that allows for rapid and cost-effective evaluation of ccRCC patient response to drug therapy. Therefore, this model has the potential to become a useful platform for preclinical evaluation of new targeted therapies for the treatment of ccRCC.
Biological variation and reference change value of the estimated glomerular filtration rate in humans: A systematic review and meta-analysis
Authors: Thöni Stefanie , Keller Felix , Denicolò Sara , Buchwinkler Lukas , Mayer Gert
Published: October 2022

Background

Knowledge of the biological variation of serum or plasma creatinine (Cr) and the estimated glomerular filtration rate (eGFR) is important for understanding disease dynamics in Chronic Kidney Disease (CKD). The aim of our study was to determine the magnitude of random fluctuation of eGFR by determining its reference change value (RCV).

Methods

We performed a systematic review and meta-analysis of studies on biological variation of Cr. Relevant studies were identified by systematic literature search on PubMed. Additional studies were retrieved from the European Federation of Clinical Chemistry and Laboratory Medicine (EFLM) Biological Variation Database. Random-effects meta-analysis was conducted to derive an overall estimate of intra-individual variation of creatinine (CVICr). Based on our estimate of CVICr and RCV for Cr, the RCV for the eGFR was determined.

Results

Among identified studies, 37 met our inclusion criteria. Meta-analysis of all studies yielded a CVICr of 5.2% (95% confidence interval [CI] 4.6–5.8%), however high between-study heterogeneity (I2 = 82.3%) was found. Exclusion of outliers led to a significant reduction of heterogeneity while still including 85% of all studies and resulted in a slightly lower CVICr of 5.0% (95% CI 4.7–5.4%). Assuming an analytical variation of CVA 1.1%, we found an overall RCV for eGFR of ±16.5%. After exclusion of outlier studies, we found a minimum conservative RCV for eGFR of ±12.5%.

Conclusion

The RCV of the eGFR represents a valuable tool for clinicians to discern true changes in kidney function from random fluctuation.
Prognostication in inflammatory bowel disease
Authors: Spencer Elizabeth A. , Agrawal Manasi , Jess Tine
Published: October 2022

Personalized care in inflammatory bowel diseases (IBD) hinges on parsing the heterogeneity of IBD patients through prognostication of their disease course and therapeutic response to allow for tailor-made treatment and monitoring strategies to optimize care. Herein we review the currently available predictors of outcomes in IBD and those on the both near and far horizons. We additionally discuss the importance of worldwide collaborative efforts and tools to support clinical use of these prognostication tools.
Biomarkers for differentiation of coronavirus disease 2019 or extracorporeal membrane oxygenation related inflammation and bacterial/fungal infections in critically ill patients: A prospective observational study
Authors: Weiss-Tessbach Matthias , Ratzinger Franz , Obermueller Markus , Burgmann Heinz , Staudinger Thomas , Robak Oliver , Schmid Monika , Roessler Bernhard , Jilma Bernd , Kussmann Manuel , Traby Ludwig
Published: October 2022

Secondary infections in coronavirus disease 2019 (COVID-19) patients are difficult to distinguish from inflammation associated with COVID-19 and/or extracorporeal membrane oxygenation (ECMO). Therefore, highly specific and sensitive biomarkers are needed to identify patients in whom antimicrobial therapy can be safely withheld. In this prospective monocentric study, 66 COVID-19 patients admitted to the intensive care unit (ICU) for ECMO evaluation were included. A total of 46 (70%) patients with secondary infections were identified by using broad microbiological and virological panels and standardized diagnostic criteria. Various laboratory parameters including C-reactive protein (CRP), interleukin (IL)-6, procalcitonin (PCT), and IL-10 were determined at time of study inclusion. The best test performance for differentiating bacterial/fungal secondary infections and COVID-19 and/or ECMO associated inflammation was achieved by IL-10 (ROC-AUC 0.84) and a multivariant step-wise regression model including CRP, IL-6, PCT, and IL-10 (ROC-AUC 0.93). Data obtained in the present study highlights the use of IL-10 to differentiate secondary bacterial/fungal infections from COVID-19 and/or ECMO associated inflammation in severely ill COVID-19 patients.
Diagnostic performance of the Qiaprep amp Viral RNA UM kit for the detection of COVID-19 compared to RT-PCR
Authors: Becerril Vargas Eduardo , Cojuc-Konigsberg Gabriel , Braverman-Poyastro Alan , Armendáriz Mendoza Erick , Mujica Sánchez Mario Alberto , García Colín María Del Carmen , Chávez Morales Hansel Hugo , Aguirre Pineda José Nicolás , Ibarra Cobas Luis Carlos
Published: October 2022

Background

RT-PCR is the currently recommended laboratory method for diagnosing acute SARS-CoV-2 infection. Nevertheless, to carry out this assay, numerous manual steps are necessary, but they are long lasting and error-prone. A new sample preparation solution was launched, the Qiaprep & amp Viral RNA UM kit, that combines a short, liquid-based sample preparation with one-step RT-PCR amplification and detection of SARS-CoV-2. Such alternative allows reducing the handling of samples and obtaining a result in a shorter period of time. The objective of the study was to compare the performance of the kit with RT-PCR.

Methods

A prospective trial was carried out in the clinical microbiology laboratory of a tertiary care hospital. The pharyngeal and nasopharyngeal swabs included in the study were taken from patients who underwent medical consultation because compatible COVID-19 symptoms. Samples were processed simultaneously for the reference RT-PCR and by the QIA P&A kit.

Results

190 samples were included in the clinical trial. The reference RT-PCR method indicated that 125 (66%) samples, out of the 190, were positive. The QIA P&A kit showed 112 positive samples for SARS-CoV-2. The QIA P&A kit has a sensitivity of 86% to detect SARS-CoV-2 and a 100% specificity, the positive predictive value was of 96%, the negative predictive value 78%, and the obtained Kappa value was 0,76. QIA P&A kit showed a lower mean cycle threshold compared with the diagnostic standard, with a statistically significant difference (p < 0.05).

Conclusion

The QIA P&A kit has an acceptable, yet not optimal performance for sample preparation and amplification of SARS-CoV-2 and further studying is required for it to be validated as a cost-effective, rapid diagnostic method for detecting infections.
A non-functional 5′ ALK fusion validated at the RNA level as a classical EML4-ALK that responds well to the novel ALK inhibitor ensartinib: A case report
Authors: Yang Hong , Li Haojing , Fang Yu , Li Zhijun , Zhu Jianhua , Liu Huan , Lu Chao , Zhang Xiaoyan , Ma Tonghui , Zhang Cuiying
Published: October 2022

Background

Currently, many targeted drugs are approved for treatment of ALK fusion non-small cell lung cancer. However, it has been previously assumed that patients with 5′ non-oncogenic kinase (5′ NOK) fusion detected by DNA next-generation sequencing (NGS) would not benefit from ALK inhibitors because of lack of an intact kinase domain.

Case description

A novel 5′ NOK fusion form, ALK-CYP27C1 (A19:C5), was detected by DNA NGS in surgical tissue specimens of a patient with recurrent lung adenosquamous carcinoma. The patient achieved 29 months of progression-free survival with ensartinib treatment. The results of RNA NGS from the same operative tissue identified EML4-ALK (E13:A20) fusion variant type I.

Conclusion

This is the first case to provide real-world evidence of effective treatment of a patient with the 5′ NOK fusion form at the DNA level but functional EML4-ALK at the RNA level, illustrating the need for RNA testing in 5′ NOK patients.
Artificial rearing alters intestinal microbiota and induces inflammatory response in piglets
Authors: Han Qi , Zhang Xiaohong , Nian Haoyang , Liu Honggui , Li Xiang , Zhang Runxiang , Bao Jun
Published: October 2022

With the ongoing genetic selection for high prolificacy in sow lines and the improvements in environment and farm management, litter size has increased in recent years. Artificial rearing is becoming widely used to raise the surplus piglets in pig industry. This study aimed to investigate the changes that happened in the morphology, microbiota, mucosal barrier function, and transcriptome caused by artificial rearing in piglet colon. Two hundred and forty newborn piglets were randomly assigned into three treatments, sow rearing until weaning (CON group), artificial rearing from day 21 (AR21 group), and artificial rearing from day 7 (AR7 group). On day 35, the piglets were euthanized to collect colon samples. The results showed that the artificially reared-piglets displayed increased pre-weaning diarrhea incidence and reduced growth performance. Artificial rearing changed the diversity and structure of colonic microbiota and increased relative abundance of harmful bacteria, such as Escherichia-Shigella. In addition, the morphological disruption was observed in AR7 group, which was coincided with decreased tight junction proteins and goblet cell numbers. Moreover, the expression of TNFSF11, TNF-α, IL-1β, TLR2, TLR4, MyD88, NF-κB, COX-2, PTGEs, iNOS, IL-2, IL-6, IL-17A, and IFN-γ was upregulated in the colon of the artificially reared-piglets, while the expression of IL-1Ra and IκBα was downregulated, indicating that artificial rearing induced inflammatory response through the activation of NF-κB pathway. Furthermore, artificial rearing regulated SLC family members, which affected solute transport and destroyed intestinal homeostasis. In conclusion, artificial rearing caused microbiota alteration, morphology disruption, the destruction of mucosal barrier function, and inflammatory response, and thus, led to subsequent increased diarrhea incidence and reduced growth performance.
Co-analysis of cucumber rhizosphere metabolites and microbial PLFAs under excessive fertilization in solar greenhouse
Authors: Wang Shuang , Bian Ting , Wu Tong , Zhang Yidi , Awais Muhammad , Fu Hongdan , Sun Zhouping
Published: October 2022

Fertilizer application is the most common measure in agricultural production, which can promote the productivity of crops such as cucumbers, but the problem of excessive fertilization occurs frequently in solar greenhouses. However, the effects of fertilization levels on cucumber rhizosphere soil microbes and metabolites and their relationships are still unclear. In order to determine how fertilization levels affect the rhizosphere microenvironment, we set up four treatments in the solar greenhouse: no-fertilization (N0P0K0), normal fertilization (N1P1K1), slight excessive fertilization (N2P2K2), and extreme excessive fertilization (N3P3K3). The results showed that fertilization treatments significantly increased cucumber yield compared to no-fertilization, but, the yield of N3P3K3 was significantly lower than that of N1P1K1 and N2P2K2. Fertilization levels had significant effects on rhizosphere microorganisms, and pH, NH4+-N and AP were the main environmental factors that affected the changes in microbial communities. The total PLFAs, the percentages of fungi and arbuscular mycorrhizal fungi (AMF) were significantly reduced and bacteria percentage was significantly increased in N3P3K3 compared to other fertilization treatments. Differential metabolites under different fertilization levels were mainly organic acids, esters and sugars. Soil phenols with autotoxic effect under fertilization treatments were higher than that of N0P0K0. In addition, compared with soil organic acids and alkanes of N0P0K0, N2P2K2 was significantly increased, and N3P3K3 was not significantly different. This suggested that cucumber could maintain microbial communities by secreting beneficial metabolites under slight excessive fertilization (N2P2K2). But under extremely excessive fertilization (N3P3K3), the self-regulating ability of cucumber plants and rhizosphere soil was insufficient to cope with high salt stress. Furthermore, co-occurrence network showed that 16:1ω5c (AMF) was positively correlated with 2-palmitoylglycerol, hentriacontane, 11-octadecenoic acid, decane,4-methyl- and d-trehalose, and negatively correlated with 9-octadecenoic acid at different fertilization levels. This indicated that the beneficial microorganisms in the cucumber rhizosphere soil promoted with beneficial metabolites and antagonized with harmful metabolites. But with the deepening of overfertilization, the content of beneficial microorganisms and metabolites decreased. The study provided new insights into the interaction of plant rhizosphere soil metabolites and soil microbiomes under the different fertilization levels.
Random sampling associated with microbial profiling leads to overestimated stochasticity inference in community assembly
Authors: Ma Kai , Tu Qichao
Published: October 2022

Revealing the mechanisms governing the complex community assembly over space and time is a central issue in ecology. Null models have been developed to quantitatively disentangle the relative importance of deterministic vs. stochastic processes in structuring the compositional variations of biological communities. Similar approaches have been recently extended to the field of microbial ecology. However, the profiling of highly diverse biological communities (e.g., microbial communities) is severely influenced by random sampling issues, leading to undersampled community profiles and overestimated β-diversity, which may further affect stochasticity inference in community assembly. By implementing simulated datasets, this study demonstrate that microbial stochasticity inference is also affected due to random sampling issues associated with microbial profiling. The effects on microbial stochasticity inference for the whole community and the abundant subcommunities were different using different randomization methods in generating null communities. The stochasticity of rare subcommunities, however, was persistently overestimated irrespective of which randomization method was used. Comparatively, the stochastic ratio approach was more sensitive to random sampling issues, whereas the Raup–Crick metric was more affected by randomization methods. As more studies begin to focus on the mechanisms governing abundant and rare subcommunities, we urge cautions be taken for microbial stochasticity inference based on β-diversity, especially for rare subcommunities. Randomization methods to generate null communities shall also be carefully selected. When necessary, the cutoff used for judging the relative importance of deterministic vs. stochastic processes shall be redefined.
Hepatitis E genotype 3 genome: A comprehensive analysis of entropy, motif conservation, relevant mutations, and clade-associated polymorphisms
Authors: Muñoz-Chimeno Milagros , Rodriguez-Paredes Vanessa , García-Lugo Maira Alejandra , Avellon Ana
Published: October 2022

Hepatitis E virus genotype 3 (HEV-3) is an EU/EEA emergent zoonosis. HEV-3 clades/subtypes have been described. Its genome contains ORF1, which encodes nonstructural proteins for virus replication, ORF2, the capsid protein, and ORF3, a multifunctional protein involved in virion pathogenesis. The study aims with respect to HEV-3 are to: (1) calculate genome entropy (excluding hypervariable region); (2) analyze the described motifs/mutations; (3) characterize clade/subtype genome polymorphisms. Seven hundred and five sequences from the GenBank database were used. The highest entropies were identified in zoonotic genotypes (HEV-3 and HEV-4) with respect to HEV-1 in X domain, RdRp, ORF2, and ORF3. There were statistically significant differences in the entropy between proteins, protease and ORF3 being the most variable and Y domain being the most conserved. Methyltransferase and Y domain motifs were completely conserved. By contrast, essential protease H581 residue and catalytic dyad exhibited amino acid changes in 1.8% and 0.4% of sequences, respectively. Several X domain amino acids were associated with clades. We found sequences with mutations in all helicase motifs except number IV. Helicase mutations related to increased virulence and/or fulminant hepatitis were frequent, the 1,110 residue being a typical HEV-3e and HEV-3f-A2 polymorphism. RdRp motifs III, V, VII also had high mutation rates. Motif III included residues that are polymorphisms of HEV-3e (F1449) and HEV-3 m (D1451). RdRp ribavirin resistance mutations were frequent, mainly 1479I (67.4, 100% in HEV-3efglmk) and 1634R/K (10.0%, almost 100% in HEV-3e). With respect to ORF2, 19/27 neutralization epitopes had mutations. The S80 residue in ORF3 presented mutations in 3.5% of cases. Amino acids in the ORF3-PSAP motif had high substitution rates, being more frequent in the first PSAP (44.8%) than in the second (1.5%). This is the first comprehensive analysis of the HEV-3 genome, aimed at improving our knowledge of the genome, and establishing the basis for future genotype-to-phenotype analysis, given that viral features associated with severity have not been explored in depth. Our results demonstrate there are important genetic differences in the studied genomes that sometimes affect significant viral structures, and constitute clade/subtype polymorphisms that may affect the clinical course or treatment efficacy.
Ambroxol for the treatment of COVID-19 among hospitalized patients: A multicenter retrospective cohort study
Authors: Lu Yun , Yang Qing-qing , Zhuo Lin , Yang Kun , Kou Hao , Gao Su-yu , Hu Wen , Jiang Qiao-li , Li Wen-jing , Wu Dong-fang , Sun Feng , Cheng Hong , Zhan Siyan
Published: October 2022

Ambroxol is a commonly used mucolytic agent principally used to treat respiratory diseases, which may have a role as adjunctive therapy for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection, but there is lack of evidence about its effectiveness on coronavirus disease-2019 (COVID-19) patients. To study the association between ambroxol use and clinical outcomes among hospitalized patients of COVID-19 infection. We conducted a multicenter retrospective cohort study involving 3,111 patients with confirmed SARS-CoV-2 infection from three hospitals in Wuhan from 19 December 2019 to 15 April 2020, and the primary outcome was in-hospital mortality. COVID-19 patients were classified into ambroxol and non-ambroxol groups based on the administration of ambroxol during hospitalization. Two analyses including propensity score matching (PSM) to obtain a 1:1 balanced cohort and logistic regression were used to control for confounding factors. The average age of 3,111 patients was 57.55 ± 14.93 years old, 127 of them died during hospitalization, and 924 of them used ambroxol. Treatment with ambroxol did not have a significant effect on in-hospital mortality of COVID-19 patients when compared with non-ambroxol in PSM model after adjusting for confounders (8.0% vs. 3.5%, adjusted OR, 1.03 [95% CI, 0.54–1.97], p = 0.936). Adverse events such as nausea/vomiting, headache, and rash were comparable between the two groups. Our results suggest that the use of ambroxol is not significantly associated with in-hospital mortality in COVID-19 patients, which provides evidence for evaluating the effects of ambroxol on COVID-19 patient outcomes and may be helpful for physicians considering medication alternatives for COVID-19 patients.
Rapid microbiological diagnosis based on 16S rRNA gene sequencing: A comparison of bacterial composition in diabetic foot infections and contralateral intact skin
Authors: Huang Ying , Xiao Zhizhou , Cao Ying , Gao Fang , Fu Yingyu , Zou Mengchen , Luo Xiangrong , Jiang Ya , Xue Yaoming
Published: October 2022

Diabetic foot infections (DFIs) represent a frequent complication of diabetes and a major cause of amputations. This study aimed to evaluate the utility of 16S rRNA gene sequencing for the rapid microbiological diagnosis of DFIs and to consistently characterize the microbiome of chronic diabetic foot ulcers (DFUs) and intact skin. Wound samples were collected by ulcer swabbing and tissue biopsy, and paired swabs of intact skin were collected from 10 patients with DFIs (five were moderately infected, and the other five were severely infected). Samples were analyzed by conventional culture and using Personal Genome Machine (PGM) 16S rRNA sequencing technology. The results showed that PGM technology detected significantly more bacterial genera (66.1 vs. 1.5 per wound sample, p < 0.001); more obligate anaerobes (52.5 vs. 0%, p < 0.001) and more polymicrobial infections (100.0 vs. 55.0%, p < 0.01) than conventional cultures. There was no statistically significant difference in bacterial richness, diversity or composition between the wound swabs and tissues (p > 0.05). The bacterial community on intact skin was significantly more diverse than that in DFUs (Chao1 value, p < 0.05; Shannon index value, p < 0.001). Gram-positive bacteria (67.6%) and aerobes (59.2%) were predominant in contralateral intact skin, while Gram-negative bacteria (63.3%) and obligate anaerobes (50.6%) were the most ubiquitous in DFUs. The most differentially abundant taxon in skin was Bacillales, while Bacteroidia was the bacterial taxon most representative of DFUs. Moreover, Fusobacterium (ρ = 0.80, p < 0.01) and Proteus (ρ = 0.78, p < 0.01) were significantly correlated with the duration of DFIs. In conclusion, PGM 16S rRNA sequencing technology could be a potentially useful technique for the rapid microbiological diagnosis of DFIs. Wound swabbing may be sufficient for sampling bacterial pathogens in DFIs compared with biopsy which is an invasive technique. The empirical use of broad-spectrum antibiotics covering Gram-negative obligate anaerobes should be considered for the treatment of moderate or severe DFIs.
Efficient elimination of RNA mycoviruses in aspergillus species using RdRp-inhibitors ribavirin and 2’-C-methylribonucleoside derivatives
Authors: Ikeda Ayano , Chiba Yuto , Kuroki Misa , Urayama Syun-ichi , Hagiwara Daisuke
Published: October 2022

RNA viruses in fungi (mycoviruses) are model systems for understanding the relationships between eukaryotic microorganisms and RNA viruses. To reveal the effects of mycoviruses on host fungi, it is essential to compare the phenotypes between isogenic fungal isolates with or without RNA virus infection. Since active entry machinery for RNA mycoviruses has never been identified, introducing mycoviruses to fungi is a difficult and time-consuming process. Therefore, most studies have tried to generate virus-free isolates from infected strains by eliminating the mycovirus. However, methods of elimination have not been evaluated in a quantitative and comparative manner. In this study, we established a method to remove mycoviruses from host cells using the antiviral drugs ribavirin, 2′-C-methylcytidine (2CMC), 2′-C-methyladenosine (2CMA), and 7d2CMA, and compared the efficiency of removal in virus-infected strains of Aspergillus fumigatus. The results indicated that treatment with the drugs removed RNA viruses of diverse proportions in the families Chrysoviridae, Mitoviridae, Partitiviridae, Polymycoviridae, and an unclassified RNA virus group. Viruses belonging to Narnaviridae were hardly eliminated by these antiviral treatments when they were the sole infectious agents. We found that 2CMC showed activity against a wider range of RNA mycoviruses compared to ribavirin, 2CMA, and 7d2CMA, although 7d2CMA also efficiently removed dsRNA viruses from the families Chrysoviridae, Partitiviridae, and Polymycoviridae. These results indicated that removal of mycoviruses depends on the specific viral species and antiviral drug. This is the first report demonstrating a preferential antiviral effect against mycoviruses, which will enhance research on microbial RNA viruses and support their elimination from economically important fungi such as edible mushrooms.
In vivo evidence of the prevents DSS-induced colitis of Lactiplantibacillus plantarum L15
Authors: Wang Zengbo , Yang Liu , Tang Hongwei , Zhang Kangyong , Chen Qingxue , Liu Caihua , Guo Yanan , Li Minghao , Guo Zengwang , Li Bailiang
Published: October 2022

Ulcerative colitis (UC) is challenging to treat and severely impacts patients and families. A previous study reported immunomodulatory and reduction of pro-inflammatory properties for the Lactiplantibacillus plantarum L15. This study aimed to analyze the preventive properties and mechanistic actions in an in vivo colitis model. The histopathological alteration, inflammation cytokines, and intestinal barrier function were analyzed. Subsequently, the cecal gut microbiota contents and products from different groups were detected. Finally, gene expressions related to the NF-κB signaling process were evaluated. L. plantarum L15 significantly decreased disease activity index (DAI), myeloperoxidase activity (MPO), pro-inflammatory cytokine (TNF-α, IL-1β, and IL-6) level, and increased weight change, colon length, and production of inflammation-suppressing cytokines. Furthermore, this strain supplementation substantially increased ZO-1, Occludin, and Claudin-1, and MUC2 mRNA expression levels with a corresponding decrease in serum lipopolysaccharide and D-lactic acid contents. In addition, L. plantarum L15 improved gut microbiota composition and increased short-chain fatty acid (SCFAs) in the colon content, which significantly reduced the transfer of NF-κB p65 to the nucleus. Our findings provide a theoretical basis for L. plantarum L15 as a preventive candidate for UC.
Effects of laccase and lactic acid bacteria on the fermentation quality, nutrient composition, enzymatic hydrolysis, and bacterial community of alfalfa silage
Authors: Bao Xueyan , Feng Haoran , Guo Gang , Huo Wenjie , Li Qinghong , Xu Qingfang , Liu Qiang , Wang Cong , Chen Lei
Published: October 2022

Ensiling has long been as a mainstream technology of preserving forage for ruminant production. This study investigated the effects of bioaugmented ensiling with laccase and Pediococcus pentosaceus on the fermentation quality, nutritive value, enzymatic hydrolysis, and bacterial community of alfalfa. The application of laccase and Pediococcus pentosaceus combination was more potent in modulating the fermentation quality of silage than laccase and Pediococcus pentosaceus alone, as indicated by higher lactic acid contents and lactic acid to acetic acid ratios, and lower pH, dry matter losses, and ammonia nitrogen contents. Moreover, treatments with additive enhanced protein preservation and structural carbohydrate degradation, while increasing true protein and water-soluble carbohydrate contents. By promoting lignin degradation, treatments containing laccase further facilitated the release of sugars from cellulose compared with treatment with Pediococcus pentosaceus alone. The additive treatments reduced the bacterial diversity and optimized the bacterial community composition of silage, with an increase in the relative abundance of desirable Lactobacillus and a decrease in the relative abundance of undesirable Enterobacter and Klebsiella. PICRUSt functional prediction based on Kyoto Encyclopedia of Genes and Genomes (KEGG) databases revealed that PL and LPL treatments increased the metabolism of membrane transport, carbohydrate, and terpenoids and polyketides related to fermentation activities. It can be concluded that bioaugmented ensiling with laccase and Pediococcus pentosaceus combination can be an effective and practical strategy to improve silage fermentation and nutrient preservation of alfalfa silage.
Bacteroides abundance drives birth mode dependent infant gut microbiota developmental trajectories
Authors: Matharu Dollwin , Ponsero Alise J. , Dikareva Evgenia , Korpela Katri , Kolho Kaija-Leena , de Vos Willem M. , Salonen Anne
Published: October 2022

Background and aims

Birth mode and other early life factors affect a newborn's microbial colonization with potential long-term health effects. Individual variations in early life gut microbiota development, especially their effects on the functional repertoire of microbiota, are still poorly characterized. This study aims to provide new insights into the gut microbiome developmental trajectories during the first year of life.

Methods

Our study comprised 78 term infants sampled at 3 weeks, 3 months, 6 months, and 12 months (n = 280 total samples), and their mothers were sampled in late pregnancy (n = 50). Fecal DNA was subjected to shotgun metagenomic sequencing. Infant samples were studied for taxonomic and functional maturation, and maternal microbiota was used as a reference. Hierarchical clustering on taxonomic profiles was used to identify the main microbiota developmental trajectories in the infants, and their associations with perinatal and postnatal factors were assessed.

Results

In line with previous studies, infant microbiota composition showed increased alpha diversity and decreased beta diversity by age, converging toward an adult-like profile. However, we did not observe an increase in functional alpha diversity, which was stable and comparable with the mother samples throughout all the sampling points. Using a de novo clustering approach, two main infant microbiota clusters driven by Bacteroidaceae and Clostridiaceae emerged at each time point. The clusters were associated with birth mode and their functions differed mainly in terms of biosynthetic and carbohydrate degradation pathways, some of which consistently differed between the clusters for all the time points. The longitudinal analysis indicated three main microbiota developmental trajectories, with the majority of the infants retaining their characteristic cluster until 1 year. As many as 40% of vaginally delivered infants were grouped with infants delivered by C-section due to their clear and persistent depletion in Bacteroides. Intrapartum antibiotics, any perinatal or postnatal factors, maternal microbiota composition, or other maternal factors did not explain the depletion in Bacteroides in the subset of vaginally born infants.

Conclusion

Our study provides an enhanced understanding of the compositional and functional early life gut microbiota trajectories, opening avenues for investigating elusive causes that influence non-typical microbiota development.
Identifying individual-specific microbial DNA fingerprints from skin microbiomes
Authors: Zheng Yiluan , Shi Jianlu , Chen Qi , Deng Chao , Yang Fan , Wang Ying
Published: October 2022

Skin is an important ecosystem that links the human body and the external environment. Previous studies have shown that the skin microbial community could remain stable, even after long-term exposure to the external environment. In this study, we explore two questions: Do there exist strains or genetic variants in skin microorganisms that are individual-specific, temporally stable, and body site-independent? And if so, whether such microorganismal genetic variants could be used as markers, called “fingerprints” in our study, to identify donors? We proposed a framework to capture individual-specific DNA microbial fingerprints from skin metagenomic sequencing data. The fingerprints are identified on the frequency of 31-mers free from reference genomes and sequence alignments. The 616 metagenomic samples from 17 skin sites at 3-time points from 12 healthy individuals from Integrative Human Microbiome Project were adopted. Ultimately, one contig for each individual is assembled as a fingerprint. And results showed that 89.78% of the skin samples despite body sites could identify their donors correctly. It is observed that 10 out of 12 individual-specific fingerprints could be aligned to Cutibacterium acnes. Our study proves that the identified fingerprints are temporally stable, body site-independent, and individual-specific, and can identify their donors with enough accuracy. The source code of the genetic identification framework is freely available at https://github.com/Ying-Lab/skin_fingerprint.
Multiple evidences reveal new species and a new record of smelly Gymnopus (Agaricales, Omphalotaceae) from China
Authors: Hu Jia-Jun , Song Li-Ru , Tuo Yong-Lan , Zhao Gui-Ping , Yue Lei , Zhang Bo , Li Yu
Published: October 2022

Gymnopus sect. Impudicae is a poorly studied group around the world. However, it is well known for its pungent smell—a total of five species from China belonging to sect. Impudicae were recorded, and included four species new to science—G. epiphyllus, G. cystidiosus, G. subdensilamellatus, and G. subpolyphyllus—which were delimited and proposed based on morphological and molecular evidences, and one new record from Henan, Jiangxi, and Gansu Province, China—G. densilamellatus. Detailed descriptions and illustrations were presented as well as comparisons to similar species. Phylogenetic analysis inferred from the ITS and nLSU dataset supported the Gymnopus as a monophyletic genus which was defined by Oliveira et al., and the novel species grouped as separate lineages within it. A Key to the reported species of Gymnopus sect. Impudicae is also provided.
Assessment of antibiotic treatment on Anopheles darlingi survival and susceptibility to Plasmodium vivax
Authors: Santos Najara Akira Costa dos , Magi Felipe Neves , Andrade Alice Oliveira , Bastos Alessandra da Silva , Pereira Soraya dos Santos , Medeiros Jansen Fernandes , Araujo Maisa da Silva
Published: October 2022

Antibiotic treatment has been used to enhance anopheline susceptibility to Plasmodium infection, because bacterial microbiota play a fundamental role in modulating the vector competence of mosquitoes that transmit Plasmodium parasites. However, few studies have examined the impact of antibiotic treatments on Plasmodium vivax sporogonic development in neotropical anopheline mosquitoes. Herein, we assessed the impact of antibiotic treatment on P. vivax development and survival in Anopheles darlingi, the main vector of malaria in the Amazon region. Female mosquitoes were treated continuously with antibiotics to impact the gut bacterial load and then tested for prevalence, infection intensity, and survival in comparison with untreated mosquitoes. Antibiotic-fed mosquitoes had not dramatic impact on P. vivax development previously observed in P. falciparum. However, antibiotic treatment increases mosquito survival, which is known to increase vectorial capacity. These findings raise questions about the effect of antibiotics on P. vivax development and survival in An. darlingi.
A resistome survey across hundreds of freshwater bacterial communities reveals the impacts of veterinary and human antibiotics use
Authors: Kraemer Susanne A. , Barbosa da Costa Naila , Oliva Anais , Huot Yannick , Walsh David A.
Published: October 2022

Our decreasing ability to fight bacterial infections is a major health concern. It is arising due to the evolution of antimicrobial resistance (AMR) in response to the mis- and overuse of antibiotics in both human and veterinary medicine. Lakes integrate watershed processes and thus may act as receptors and reservoirs of antibiotic resistance genes (ARGs) introduced into the watershed by human activities. The resistome – the diversity of ARGs – under varying anthropogenic watershed pressures has been previously studied either focused on few select genes or few lakes. Here, we link the resistome of ~350 lakes sampled across Canada to human watershed activity, trophic status, as well as point sources of ARG pollution including wastewater treatment plants and hospitals in the watershed. A high percentage of the resistance genes detected was either unimpacted by human activity or highly prevalent in pristine lakes, highlighting the role of AMR in microbial ecology in aquatic systems, as well as a pool of genes available for potential horizontal gene transfer to pathogenic species. Nonetheless, watershed agricultural and pasture area significantly impacted the resistome. Moreover, the number of hospitals and the population density in a watershed, the volume of wastewater entering the lake, as well as the fraction of manure applied in the watershed as fertilizer significantly impacted ARG diversity. Together, these findings indicate that lake resistomes are regularly stocked with resistance genes evolved in the context of both veterinary and human antibiotics use and represent reservoirs of ARGs that require further monitoring.