title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=840 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Struo2: efficient metagenome profiling database construction for ever-expanding microbial genome datasets link: https://peerj.com/articles/12198 last-modified: 2021-09-16 description: Mapping metagenome reads to reference databases is the standard approach for assessing microbial taxonomic and functional diversity from metagenomic data. However, public reference databases often lack recently generated genomic data such as metagenome-assembled genomes (MAGs), which can limit the sensitivity of read-mapping approaches. We previously developed the Struo pipeline in order to provide a straight-forward method for constructing custom databases; however, the pipeline does not scale well enough to cope with the ever-increasing number of publicly available microbial genomes. Moreover, the pipeline does not allow for efficient database updating as new data are generated. To address these issues, we developed Struo2, which is >3.5 fold faster than Struo at database generation and can also efficiently update existing databases. We also provide custom Kraken2, Bracken, and HUMAnN3 databases that can be easily updated with new genomes and/or individual gene sequences. Efficient database updating, coupled with our pre-generated databases, enables “assembly-enhanced” profiling, which increases database comprehensiveness via inclusion of native genomic content. Inclusion of newly generated genomic content can greatly increase database comprehensiveness, especially for understudied biomes, which will enable more accurate assessments of microbiome diversity. creator: Nicholas D. Youngblut creator: Ruth E. Ley uri: https://doi.org/10.7717/peerj.12198 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Youngblut and Ley title: Investigation and molecular identification of Eimeria sp. sampled from captive forest musk deer link: https://peerj.com/articles/11751 last-modified: 2021-09-15 description: Forest musk deer (Moschus berezovskii) is an endangered, protected species in China. Intestinal coccidiosis is a significant problem for captive forest musk deer. However, there are few reports on the prevalence and molecular characteristics of Eimeria sp. in forest musk deer. We sought to investigate the prevalence of Eimeria sp. in forest musk deer in the Sichuan and Shaanxi provinces in China. We also investigated the molecular characteristics of Eimeria sp. by analyzing the 18S rRNA gene. We collected a total of 328 fecal samples from forest musk deer on seven farms throughout the Sichuan and Shaanxi provinces. We extracted this parasite’s DNA and used this as a template for nested PCR amplification. The 18S rRNA gene fragment was associated with the plasmid vector, and these products were introduced into Escherichia coli (DH5α). The cultured bacterial solution was used as a PCR reaction template for identification purposes. We collected 328 fecal samples from forest musk deer in Lixian (n = 54), Maoxian (n = 52), Ma’erkang (n = 49), Dujiangyan (n = 55), Hanyuan (n = 41), Luding (n = 36) and Weinan (n = 41). One hundred ninety-eight (60.37%) fecal samples tested positive for Eimeria sp. . In our analysis of the 18S rRNA gene we found 34 types of Eimeria sp. with a similarity of 90.5–100%. We constructed a phylogenetic tree based on the parasite’s 18S rRNA gene sequence. Our findings indicated that the Eimeria sp. that parasitized the intestinal tract of forest musk deer was closely related to Eimeria alabamensis from Bos taurus and Eimeria ahsata from Ovis aries. To the best of our knowledge, ours was the first investigation and molecular identification of Eimeria sp. sampled from captive forest musk deer in China. Our results provide epidemiological data for the monitoring and prevention of Eimeria sp. in captive forest musk deer. creator: Ziwei Ren creator: Dong Yu creator: Wei Zhao creator: Yan Luo creator: Jianguo Cheng creator: Yin Wang creator: Zexiao Yang creator: Xueping Yao creator: Wei Yang creator: Xi Wu creator: Yimeng Li uri: https://doi.org/10.7717/peerj.11751 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Ren et al. title: Public perception of ecosystem services provided by the Mediterranean mussel Mytilus galloprovincialis related to anthropogenic activities link: https://peerj.com/articles/11975 last-modified: 2021-09-15 description: BackgroundMussels provide many ecosystem services as habitat, food, water filtration and recreational fishing. However, mussels are vulnerable to anthropogenic pressures such as harvesting or trampling, among others. In this frame, it would be paramount to engage society in marine conservation and improving its awareness about environmental policies. The first step lies in properly assessing what is the perception and concerns of society about marine ecosystems. Our study aims to fill this gap by examining public perception of services provided by Mytilus galloprovincialis, its state of conservation and the factors (including anthropogenic activities) shaping mussel beds.MethodsThis study is based on a face-to-face survey consisting of seven open-ended and seven multiple-choice questions of 404 people conducted in 2019 at different shores in the North Portuguese coast. The influence of respondent profile in terms of age, education, gender and place of residence was also assessed.ResultsMost of the participants in our survey (74%) considered that mussels contributed to human well-being and life quality; however, only 31% considered that mussels provide us with many benefits. Regarding the perceived state of mussel services, most of the respondents asserted that mussel services (purification of seawater, habitat, food for other species) worsened in the last 10 years. In contrast, the service as human food was perceived as in an identical state and scientific and traditional knowledge was the only service perceived in a better state. Concerning the state of mussel beds, most of the participants perceived it as good (45%) but a similar percentage (41%) asserted ignoring it. When considering the influence of different factors on mussel beds, only environmental management was considered as having a positive impact by a higher percentage of respondents. The majority of the participants considered that factors included in the questionnaire contributed to worsen mussel beds, ranging between 51% for coastal erosion and 90% for pollution. Education level and age were the main socio-economic factors driving public awareness about the importance of mussel services, its state of conservation and the factors shaping mussel beds.DiscussionResults showed that perception about the importance of mussels for human well-being and the quantity of delivered benefits increased with the education level. Moreover, older people perceived human food as the most important service offered by mussels. Therefore, our results suggest that mussels are mainly known as food resource; however, most of the people ignore their relevant ecological role and the many other benefits that mussels provide. Thus, it is necessary to actively engage society about importance of mussel beds. As M. galloprovincialis is a relevant economic resource, our data could improve the diffusion of knowledge among citizens, stakeholders and scientists, contributing to its sustainability. creator: Veiga Puri creator: Moreira Juan creator: Ramos-Oliveira Catarina creator: Sampaio Leandro creator: Marcos Rubal uri: https://doi.org/10.7717/peerj.11975 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 et al. title: The impact of peer review on the contribution potential of scientific papers link: https://peerj.com/articles/11999 last-modified: 2021-09-15 description: The peer-reviewing process has long been regarded as an indispensable tool in ensuring the quality of a scientific publication. While previous studies have tried to understand the process as a whole, not much effort has been devoted to investigating the determinants and impacts of the content of the peer review itself. This study leverages open data from nearly 5,000 PeerJ publications that were eventually accepted. Using sentiment analysis, Latent Dirichlet Allocation (LDA) topic modeling, mixed linear regression models, and logit regression models, we examine how the peer-reviewing process influences the acceptance timeline and contribution potential of manuscripts, and what modifications were typically made to manuscripts prior to publication. In an open review paradigm, our findings indicate that peer reviewers’ choice to reveal their names in lieu of remaining anonymous may be associated with more positive sentiment in their review, implying possible social pressure from name association. We also conduct a taxonomy of the manuscript modifications during a revision, studying the words added in response to peer reviewer feedback. This study provides insights into the content of peer reviews and the subsequent modifications authors make to their manuscripts. creator: Akira Matsui creator: Emily Chen creator: Yunwen Wang creator: Emilio Ferrara uri: https://doi.org/10.7717/peerj.11999 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Matsui et al. title: Post-fire dynamics of ectomycorrhizal fungal communities in a Scots pine (Pinus sylvestris L.) forest of Poland link: https://peerj.com/articles/12076 last-modified: 2021-09-15 description: BackgroundGlobal warming and drying have markedly enhanced in most forests the risk of fires across the world, which can affect the taxonomic and functional composition of key tree-associated organisms such as ectomycorrhizal (ECM) fungi. The present study was conducted to characterise the alterations in the extent of root ECM colonisation, the ECM fungal communities, and their exploration types (i.e., indicator of ECM soil foraging strategies) in regenerated pines within a burned site as compared with an unburned site (five years after the fire event) in the Forest District Myszyniec, Poland.MethodsTo assess the ECM fungal communities of burned and control sites, soil soil-root monoliths were collected from the study sites in September 2019. A total of 96 soil subsamples were collected for soil analysis and mycorrhizal assessment (6 trees × 2 sites × 4 study plots × 2 microsites (north and south) = 96 subsamples).ResultsThe percentage of root ECM colonisation was significantly lower in the burned site in comparison with the unburned (control) site. However, the ECM species richness did not differ between the control and burned sites. The identified ECM species in both sites were Imleria badia, Thelephora terrestris, Russula paludosa, R. badia, R. turci, R. vesca, Lactarius plumbeus, Phialocephala fortinii, and Hyaloscypha variabilis. The most frequent species in the burned and control sites were I. badia and T. terrestris, respectively. The relative abundances of contact, medium-distance smooth and long-distance exploration types in the burned site were significantly different from the control site, dominated by the medium-distance exploration type in both sites. The abundance of the long-distance exploration type in the burned site was markedly greater (27%) than that of the control site (14%), suggesting that the fire event had favoured this ECM foraging strategy. The results demonstrated that the fire led to reduced ECM colonisation of Scots pine trees in the burned site whereas the species richness was not affected, which can be attributed to degrees of fire-resistance in the ECM species, survival of ECM propagules in deeper soil layers, and/or continuous entry of spores/propagules of the ECM fungi from the adjacent forests via wind, water run-off or animals. creator: Jacek Olchowik creator: Dorota Hilszczańska creator: Marcin Studnicki creator: Tadeusz Malewski creator: Khalil Kariman creator: Zbigniew Borowski uri: https://doi.org/10.7717/peerj.12076 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Olchowik et al. title: Compositional distinction of gut microbiota between Han Chinese and Tibetan populations with liver cirrhosis link: https://peerj.com/articles/12142 last-modified: 2021-09-15 description: BackgroundLiver cirrhosis (LC) is caused by numerous chronic liver diseases and its complications are associated with qualitative and quantitative alterations of the gut microbiota. Previous studies have revealed the characteristics of gut microbiota in Han Chinese patients with LC and different compositions of gut microbiota were reported between the Tibetan and Han Chinese populations. This study was designed to evaluate the unique features of the gut microbiota of Tibetans and compare the differences of gut microbiota between Tibetan and Han Chinese patients with LC.MethodsThirty-six patients with liver cirrhosis and nineteen healthy volunteers, from both Tibetan and Han Chinese populations, were enrolled and fecal samples were collected for 16S rRNA gene sequencing analyses.ResultsSignificant differences were found in the gut microbiota of healthy volunteers and between Tibetan and Han Chinese patients with LC. In the Han Chinese patients with cirrhosis (HLC) group the relative abundances of the phylum Bacteroidetes was significantly reduced (P < 0.001), whereas in the Tibetan patients with cirrhosis (TLC) group Firmicutes and Actinobacteria were highly enriched (P = 0.01 and 0.03, respectively). At the genus level, the relative abundances of Anaerostipes (P < 0.001), Bifidobacterium (P = 0.03), and Blautia (P = 0.004) were prevalent, while Alloprevotella, Dorea, Prevotella_2, Prevotella_7 and Prevotella_9 were decreased in the TLC group compared to the HLC group (P < 0.01).ConclusionOur findings showed how the intestinal bacterial community shifted in Tibetan patients with cirrhosis. creator: Hui Huan creator: Tao Ren creator: Li Xu creator: Hong Hu creator: Chao Liu uri: https://doi.org/10.7717/peerj.12142 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Huan et al. title: Construction of competing endogenous RNA interaction network as prognostic markers in metastatic melanoma link: https://peerj.com/articles/12143 last-modified: 2021-09-15 description: Malignant melanoma (MM) is a malignant tumor originating from melanocytes, with high aggressiveness, high metastasis and extremely poor prognosis. MM accounts for 4% of skin cancers and 80% of mortality, and the median survival of patients with metastatic melanoma is only about 6 months, with a five-year survival rate of less than 10%. In recent years, the incidence of melanoma has gradually increased and has become one of the serious diseases that endanger human health. Competitive endogenous RNA (ceRNA) is the main model of the mechanism by which long chain non-coding RNAs (lncRNAs) play a regulatory role in the disease. LncRNAs can act as a “sponge”, competitively attracting small RNAs (micoRNAs; miRNAs), thus interfering with miRNA function, and affect the expression of target gene messenger RNAs (mRNAs), ultimately promoting tumorigenesis and progression. Bioinformatics analysis can identify potentially prognostic and therapeutically relevant differentially expressed genes in MM, finding lncRNAs, miRNAs and mRNAs that are interconnected through the ceRNA network, providing further insight into gene regulation and prognosis of metastatic melanoma. Weighted co-expression networks were used to identify lncRNA and mRNA modules associated with the metastatic phenotype, as well as the co-expression genes contained in the modules. A total of 17 lncRNAs, six miRNAs, and 11 mRNAs were used to construct a ceRNA interaction network that plays a regulatory role in metastatic melanoma patients. The prognostic risk model was used as a sorter to classify the survival prognosis of melanoma patients. Four groups of ceRNA interaction triplets were finally obtained, which miR-3662 might has potential implication for the treatment of metaststic melanoma patients, and futher experiments confirmed the regulating relationship and phenotype of this assumption. This study provides new targets to regulate metastatic process, predict metastatic potential and indicates that the miR-3662 can be used in the treatment of melanoma. creator: Zan He creator: Zijuan Xin creator: Yongfei Peng creator: Hua Zhao creator: Xiangdong Fang uri: https://doi.org/10.7717/peerj.12143 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 He et al. title: A randomized trial to evaluate the impact of copra meal hydrolysate on gastrointestinal symptoms and gut microbiome link: https://peerj.com/articles/12158 last-modified: 2021-09-15 description: The impact of copra meal hydrolysate (CMH) on gut health was assessed by conducting a double-blinded, placebo-controlled study. Sixty healthy adult participants, aged 18–40 years were assigned to daily consume 3 g of CMH, 5 g of CMH or placebo in the form of drink powder for 21 days. Consumption of CMH at 3 g/d improved defecating conditions by reducing stool size and also relieved flatulence and bloating symptoms. Fecal samples were collected serially at the baseline before treatment, after the treatment and after a 2-week washout period. The gut microbiomes were similar among the treatment groups, with microbial community changes observed within the groups. Intake of CMH at 3 g/d led to increase microbial diversity and richness. Reduction of the ratio between Firmicutes to Bacteroidetes was observed, although it was not significantly different between the groups. The 3 g/d CMH treatment increased beneficial microbes in the group of fiber-degrading bacteria, especially human colonic Bacteroidetes, while induction of Bifidobacteriaceae was observed after the washout period. Intake of CMH led to increase lactic acid production, while 3 g/d supplement promoted the present of immunoglobulin A (IgA) in stool samples. The 3 g daily dose of CMH led to the potentially beneficial effects on gut health for healthy individuals. creator: Witida Sathitkowitchai creator: Narissara Suratannon creator: Suttipun Keawsompong creator: Wanlapa Weerapakorn creator: Preecha Patumcharoenpol creator: Sunee Nitisinprasert creator: Massalin Nakphaichit uri: https://doi.org/10.7717/peerj.12158 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Sathitkowitchai et al. title: Novel ACE2 protein interactions relevant to COVID-19 predicted by evolutionary rate correlations link: https://peerj.com/articles/12159 last-modified: 2021-09-15 description: Angiotensin-converting enzyme 2 (ACE2) is the cell receptor that the coronavirus SARS-CoV-2 binds to and uses to enter and infect human cells. COVID-19, the pandemic disease caused by the coronavirus, involves diverse pathologies beyond those of a respiratory disease, including micro-thrombosis (micro-clotting), cytokine storms, and inflammatory responses affecting many organ systems. Longer-term chronic illness can persist for many months, often well after the pathogen is no longer detected. A better understanding of the proteins that ACE2 interacts with can reveal information relevant to these disease manifestations and possible avenues for treatment. We have undertaken an approach to predict candidate ACE2 interacting proteins which uses evolutionary inference to identify a set of mammalian proteins that “coevolve” with ACE2. The approach, called evolutionary rate correlation (ERC), detects proteins that show highly correlated evolutionary rates during mammalian evolution. Such proteins are candidates for biological interactions with the ACE2 receptor. The approach has uncovered a number of key ACE2 protein interactions of potential relevance to COVID-19 pathologies. Some proteins have previously been reported to be associated with severe COVID-19, but are not currently known to interact with ACE2, while additional predicted novel ACE2 interactors are of potential relevance to the disease. Using reciprocal rankings of protein ERCs, we have identified strongly interconnected ACE2 associated protein networks relevant to COVID-19 pathologies. ACE2 has clear connections to coagulation pathway proteins, such as Coagulation Factor V and fibrinogen components FGA, FGB, and FGG, the latter possibly mediated through ACE2 connections to Clusterin (which clears misfolded extracellular proteins) and GPR141 (whose functions are relatively unknown). ACE2 also connects to proteins involved in cytokine signaling and immune response (e.g. XCR1, IFNAR2 and TLR8), and to Androgen Receptor (AR). The ERC prescreening approach has elucidated possible functions for relatively uncharacterized proteins and possible new functions for well-characterized ones. Suggestions are made for the validation of ERC-predicted ACE2 protein interactions. We propose that ACE2 has novel protein interactions that are disrupted during SARS-CoV-2 infection, contributing to the spectrum of COVID-19 pathologies. creator: Austin A. Varela creator: Sammy Cheng creator: John H. Werren uri: https://doi.org/10.7717/peerj.12159 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Varela et al. title: Integrative bioinformatics and experimental analysis revealed down-regulated CDC42EP3 as a novel prognostic target for ovarian cancer and its roles in immune infiltration link: https://peerj.com/articles/12171 last-modified: 2021-09-15 description: Ovarian cancer is a significant clinical challenge as no effective treatments are available to enhance patient survival. Recently, N6-methyladenosine (m6A) RNA modification has been demonstrated to play a pivotal role in tumorigenesis and progression. However, the roles of m6A target genes in ovarian cancer haven’t been clearly illustrated. In this study, we presented a comprehensive bioinformatics and in vitro analysis to evaluate the roles of m6A target genes. Cell division cycle 42 effector protein 3 (CDC42EP3), one probable m6A target gene, was identified to be down-regulated in ovarian cancer tissues and cells. Meanwhile, quantitative PCR (qPCR) and western blot were used to confirm the down-regulated CDC42EP3 in ovarian cancer cells A2780 and TOV112D. The biological function of CDC42EP3 in ovarian cancer was further validated with several algorithms, such as PrognoScan, K-M plotter, LinkedOmics and TISIDB. These findings indicated that lower expression of CDC42EP3 was correlated with poor prognosis in patients with ovarian cancer. In addition, CDC42EP3 expression was significantly associated with a diverse range of tumor-infiltrating immune cells, including natural killer cells (NK), T central memory cells (Tcm), T gamma delta cells (Tgd), etc. Taken together, this study uncovered the potential roles of m6A target gene CDC42EP3 in the regulation of immune microenvironment in the ovarian cancer, and identified CDC42EP3 as a novel prognostic target. creator: Yuanliang Yan creator: Qiuju Liang creator: Zhijie Xu creator: Qiaoli Yi uri: https://doi.org/10.7717/peerj.12171 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yan et al.