KEGG Orthology Research Articles

A draft genome assembly of “Cas” (Psidium friedrichsthalianum (O. Berg) Nied.): an indigenous crop of Costa Rica untapped

Psidium friedrichsthalianum (O. Berg) Nied. is a tropical tree species in the Myrtaceae family, natively distributed from southern Mexico to eastern Venezuela and Ecuador and commonly known as "Cas'', "Costa Rican guava" or “Sour Guava”. The “Cas” produces a fruit with a rather distinctive acidic flavor and has bioactive compounds with biological potential equal or greater than common Guava; is considered an indigenous crop in Costa Rica with characteristics as a functional food untapped. This species has not been completely domesticated, and can be found in home gardens, paddocks, small groups, and, more recently, in small and medium sized plantations. Also, the plantations of this species do not have technical and scientific support or agronomic promotion from industry, nor are there genetic resources or germplasm readily available to farmers. This limits its commercial development and the implementation of selection or genetic improvement programs. In this study, we present the first draft assembly of the Cas genome using PacBio long reads and the Canu assembly pipeline. Our draft assembly has a total length of 417.64 Mb, with 24 440 contigs and a N50 contig size of 21.3 Kb. Structural annotation resulted in 59 036 gene models. Functional annotation was conducted against the non-redundant set of genes from the KEGG database. Of the 52 422 complete genes models, 15.55% (8 153) presented homology with KEGG orthologs. The genes found in our Cas draft assembly were compared to those found in Eucalyptus grandis W. Hill. in the KEGG repository. According to the KEGG pathway assignments, 33 isoforms were annotated as part of the flavonoid biosynthetic pathway. In addition, 19 isoforms were annotated as part of phenylpropanoid biosynthetic pathway. The results of this study provide an overview of the first draft of the Cas genome assembly using PacBio long reads. This new genomic resource represents the basis for exploring the genetic potential of this crop with characteristics as a functional food.

Fc fragment of immunoglobulin G receptor IIa (FCGR2A) as a new potential prognostic biomarker of esophageal squamous cell carcinoma.

Fc fragment of immunoglobulin G receptor IIa (FCGR2A) as a new potential prognostic biomarker of esophageal squamous cell carcinoma.

Cultivation and Genomic Characterization of the Bile Bacterial Species From Cholecystitis Patients.

The microbes in human bile are closely related to gallbladder health and other potential disorders. Although the bile microbial community has been investigated by recent studies using amplicon or metagenomic sequencing technologies, the genomic information of the microbial species resident in bile is rarely reported. Herein, we isolated 138 bacterial colonies from the fresh bile specimens of four cholecystitis patients using a culturome approach and genomically characterized 35 non-redundant strains using whole-genome shotgun sequencing. The bile bacterial isolates spanned 3 classes, 6 orders, 10 families, and 14 genera, of which the members of Enterococcus, Escherichia–Shigella, Lysinibacillus, and Enterobacter frequently appeared. Genomic analysis identified three species, including Providencia sp. D135, Psychrobacter sp. D093, and Vibrio sp. D074, which are not represented in existing reference genome databases. Based on the genome data, the functional capacity between bile and gut isolates was compared. The bile strains encoded 5,488 KEGG orthologs, of which 4.9% were specific to the gut strains, including the enzymes involved in biofilm formation, two-component systems, and quorum-sensing pathways. A total of 472 antibiotic resistance genes (ARGs) were identified from the bile genomes including multidrug resistance proteins (42.6%), fluoroquinolone resistance proteins (12.3%), aminoglycoside resistance proteins (9.1%), and β-lactamase (7.2%). Moreover, in vitro experiments showed that some bile bacteria have the capabilities for bile salt deconjugation or biotransformation (of primary bile acids into secondary bile acids). Although the physiological or pathological significance of these bacteria needs further exploration, our works expanded knowledge about the genome, diversity, and function of human bile bacteria.

Oligosaccharides and Microbiota in Human Milk Are Interrelated at 3 Months Postpartum in a Cohort of Women with a High Prevalence of Gestational Impaired Glucose Tolerance

BackgroundHuman milk is a rich source of human milk oligosaccharides (HMOs) and bacteria. It is unclear how these components interact within the breast microenvironment. ObjectivesThe objectives were first, to investigate the association between maternal characteristics and HMOs, and second, to assess the association between HMOs and microbial community composition and predicted function in milk from women with high rates of gestational glucose intolerance. MethodsThis was an exploratory analysis of a previously completed prospective cohort study (NCT01405547) where milk samples (n = 107) were collected at 3 mo postpartum. Milk microbiota composition was analyzed by V4-16S ribosomal RNA gene sequencing and HMOs by rapid high-throughput HPLC. Data were stratified and analyzed by maternal secretor status phenotype and associations between HMOs and microbiota were determined using linear regression models (ɑ-diversity), Adonis (B-diversity), Poisson regression models (differential abundance), and general linear models (predicted microbial function). ResultsPrepregnancy BMI, race, and frequency of direct breastfeeding, but not gestational glucose intolerance, were found to be significantly associated with a number of HMOs among secretors and non-secretors. Fucosyllacto-N-hexaose was negatively associated with microbial richness (Chao1) among secretors [B-estimate (SE): −9.3 × 102 (3.4 × 102); P= 0.0082] and difucosyllacto-N-hexaose was negatively associated with microbiota diversity (Shannon index) [−1.7 (0.78); P= 0.029] among secretors. Lacto-N-neotetraose (LNnT) was associated with both microbial B-diversity (weighted UniFrac R2= 0.040, P= 0.036) and KEGG ortholog B-diversity (Bray-Curtis R2= 0.039, P= 0.043) in secretors. Additionally, difucosyllactose in secretors and disialyllacto-N-hexaose and LNnT in non-secretors were associated with enrichment of predicted microbial genes encoding for metabolism- and infection-related pathways (P-false discovery rate < 0.1). ConclusionsHMOs are associated with the microbial composition and predicted microbial functions in human milk at 3 mo postpartum. Further research is needed to investigate the role these relations play in maternal and infant health.

Microbiome Profiling Using Shotgun Metagenomic Sequencing Identified Unique Microorganisms in COVID-19 Patients With Altered Gut Microbiota

COVID-19 is mainly associated with respiratory distress syndrome, but a subset of patients often present gastrointestinal (GI) symptoms. Imbalances of gut microbiota have been previously linked to respiratory virus infection. Understanding how the gut–lung axis affects the progression of COVID-19 can provide a novel framework for therapies and management. In this study, we examined the gut microbiota of patients with COVID-19 (n = 47) and compared it to healthy controls (n = 19). Using shotgun metagenomic sequencing, we have identified four microorganisms unique in COVID-19 patients, namely Streptococcus thermophilus, Bacteroides oleiciplenus, Fusobacterium ulcerans, and Prevotella bivia. The abundances of Bacteroides stercoris, B. vulgatus, B. massiliensis, Bifidobacterium longum, Streptococcus thermophilus, Lachnospiraceae bacterium 5163FAA, Prevotella bivia, Erysipelotrichaceae bacterium 6145, and Erysipelotrichaceae bacterium 2244A were enriched in COVID-19 patients, whereas the abundances of Clostridium nexile, Streptococcus salivarius, Coprococcus catus, Eubacterium hallii, Enterobacter aerogenes, and Adlercreutzia equolifaciens were decreased (p < 0.05). The relative abundance of butyrate-producing Roseburia inulinivorans is evidently depleted in COVID-19 patients, while the relative abundances of Paraprevotella sp. and the probiotic Streptococcus thermophilus were increased. We further identified 30 KEGG orthology (KO) modules overrepresented, with 7 increasing and 23 decreasing modules. Notably, 15 optimal microbial markers were identified using the random forest model to have strong diagnostic potential in distinguishing COVID-19. Based on Spearman’s correlation, eight species were associated with eight clinical indices. Moreover, the increased abundance of Bacteroidetes and decreased abundance of Firmicutes were also found across clinical types of COVID-19. Our findings suggest that the alterations of gut microbiota in patients with COVID-19 may influence disease severity. Our COVID-19 classifier, which was cross-regionally verified, provides a proof of concept that a set of microbial species markers can distinguish the presence of COVID-19.

Subsoiling and conversion to conservation tillage enriched nitrogen cycling bacterial communities in sandy soils under long-term maize monoculture

Desertification degrades soil health and severely reduces crop productivity. Conventional tillage practices can amplify these problems in arid and semi-arid regions. For semi-arid regions in Inner Mongolia, China, the effects of introducing different tillage practices such as subsoiling (SS), straw mulching (SM), and no-tillage (NT) on otherwise long-term conventional tilled maize monoculture systems, were examined in the context of sandy soil bacterial and archaeal community diversity. Results showed that after three to four years of introduction, subsoiling and conversion to conservation tillage practices had no immediate effect on the alpha-diversity of the soil microbial communities. The beta-diversity of the soil microbial communities was less affected by the introduced tillage practices than by the growing season conditions, soil moisture, total nitrogen, soil macro-aggregate, and organic matter. Importantly, the introduced tillage practices had a notable effect on soil microbial communities associated with nitrogen (N) cycling processes, especially N fixation, nitrate reduction, nitrification, and denitrification. In particular, several years of tillage change from long-term conventional tillage enhanced the abundance of KEGG orthologs (KOs) associated with N fixation function involving species in Rhodoplanes, Nitrospira, Skermanella, and Rhizobium according to PICURSt prediction. Rhodoplanes spp. are involved in nitrate reduction and denitrification processes, and Nitrospira spp. associated with nitrite oxidization. We conclude that, for maize monoculture systems in semi-arid sandy soils, the soil bacterial and archaeal communities associated with many beneficial N cycling processes can be significantly impacted by only three to four years of introduced conservation and subsoiling tillage practices.

Subterranean Microbiome Affiliations of Plantain (Musa spp.) Under Diverse Agroecologies of Western and Central Africa

Plantain (Musa spp.) is a staple food crop and an important source of income for millions of smallholder farmers in sub-Saharan Africa (SSA). However, there is a paucity of knowledge on soil microbial diversity in agroecologies where plantains are grown. Microbial diversity that increases plant performance with multi-trophic interactions involving resiliency to environmental constraints is greatly needed. For this purpose, the bacterial and fungal communities of plantain fields in high rainfall forests (HR) and derived savannas (SV) were studied using Illumina MiSeq for 16S rDNA and ITS amplicon deep sequencing. Microbial richness (α- and β-diversity), operational taxonomic units, and Simpson and Shannon–Wiener indexes (observed species (Sobs), Chao, ACE; P < 0.05) suggested that there were significant differences between HR and SV agroecologies among the most abundant bacterial communities, and some specific dynamic response observed from fungal communities. Proteobacteria formed the predominant bacterial phylum (43.7%) succeeded by Firmicutes (24.7%), and Bacteroidetes (17.6%). Ascomycota, Basidiomycota, and Zygomycota were the three most dominant fungal phyla in both agroecologies. The results also revealed an immense array of beneficial microbes in the roots and rhizosphere of plantain, including Acinetobacter, Bacillus, and Pseudomonas spp. COG and KEGG Orthology database depicted significant variations in the functional attributes of microbes found in the rhizosphere to roots. This result indicates that the different agroecologies and host habitats differentially support the dynamic microbial profile and that helps in altering the structure in the rhizosphere zone for the sake of promoting synergistic host-microbe interactions particularly under resource-poor conditions of SSA.

Cross-Sectional Study on the Gut Microbiome of Parkinson's Disease Patients in Central China.

Gastrointestinal dysfunction plays an important role in the occurrence and development of Parkinson’s disease (PD). This study investigates the composition of the gut microbiome using shotgun metagenomic sequencing in PD patients in central China. Fecal samples from 39 PD patients (PD group) and the corresponding 39 healthy spouses of the patients (SP) were collected for shotgun metagenomics sequencing. Results showed a significantly altered microbial composition in the PD patients. Bilophila wadsworthia enrichment was found in the gut microbiome of PD patients, which has not been reported in previous studies. The random forest (RF) model, which identifies differences in microbiomes, reliably discriminated patients with PD from controls; the area under the receiver operating characteristic curve was 0.803. Further analysis of the microbiome and clinical symptoms showed that Klebsiella and Parasutterella were positively correlated with the duration and severity of PD, whereas hydrogen-generating Prevotella was negatively correlated with disease severity. The Cluster of Orthologous Groups of protein database, the KEGG Orthology database, and the carbohydrate-active enzymes of gene-category analysis showed that branched-chain amino acid–related proteins were significantly increased, and GH43 was significantly reduced in the PD group. Functional analysis of the metagenome confirmed differences in microbiome metabolism in the PD group related to short-chain fatty acid precursor metabolism.

OrtSuite: from genomes to prediction of microbial interactions within targeted ecosystem processes.

The high complexity found in microbial communities makes the identification of microbial interactions challenging. To address this challenge, we present OrtSuite, a flexible workflow to predict putative microbial interactions based on genomic content of microbial communities and targeted to specific ecosystem processes. The pipeline is composed of three user-friendly bash commands. OrtSuite combines ortholog clustering with genome annotation strategies limited to user-defined sets of functions allowing for hypothesis-driven data analysis such as assessing microbial interactions in specific ecosystems. OrtSuite matched, on average, 96% of experimentally verified KEGG orthologs involved in benzoate degradation in a known group of benzoate degraders. We evaluated the identification of putative synergistic species interactions using the sequenced genomes of an independent study that had previously proposed potential species interactions in benzoate degradation. OrtSuite is an easy-to-use workflow that allows for rapid functional annotation based on a user-curated database and can easily be extended to ecosystem processes where connections between genes and reactions are known. OrtSuite is an open-source software available at https://github.com/mdsufz/OrtSuite.

High throughput sequencing-based analysis of the soil bacterial community structure and functions of Tamarix shrubs in the lower reaches of the Tarim River.

Tamarix is a dominant species in the Tarim River Basin, the longest inland river in China. Tamarix plays an important role in the ecological restoration of this region. In this study, to investigate the soil bacterial community diversity in Tamarix shrubs, we collected soil samples from the inside and edge of the canopy and the edge of nebkhas and non-nebkhas Tamarix shrubs located near the Yingsu section in the lower reaches of Tarim River. High throughput sequencing technology was employed to discern the composition and function of soil bacterial communities in nebkhas and non-nebkhas Tamarix shrubs. Besides, the physicochemical properties of soil and the spatial distribution characteristics of soil bacteria and their correlation were analyzed. The outcomes of this analysis demonstrated that different parts of Tamarix shrubs had significantly different effects on soil pH, total K (TK), available K (AK), ammonium N (NH4+), and available P (AP) values (P < 0.05), but not on soil moisture (SWC), total salt (TDS), electrical conductivity (EC), organic matter (OM), total N (TN), total P (TP), and nitrate N (NO3−) values. The soil bacterial communities identified in Tamarix shrubs were categorized into two kingdoms, 71 phyla, 161 classes, 345 orders, 473 families, and 702 genera. Halobacterota, unidentified bacteria, and Proteobacteria were found to be dominant phyla. The correlation between the soil physicochemical factors and soil bacterial community was analyzed, and as per the outcomes OM, AK, AP, EC, and NH4+ were found to primarily affect the structure of the soil bacterial community. SWC, TK and pH were positively correlated with each other, but negatively correlated with other soil factors. At the phyla level, a significantly positive correlation was observed between the Halobacterota and AP, OM as well as Bacteroidota and AK (P < 0.01), but a significantly negative correlation was observed between the Chloroflexi and AK, EC (P < 0.01). The PICRUSt software was employed to predict the functional genes. A total of 6,195 KEGG ortholog genes were obtained. The function of soil bacteria was annotated, and six metabolic pathways in level 1, 41 metabolic pathways in level 2, and 307 metabolic pathways in level 3 were enriched, among which the functional gene related to metabolism, genetic information processing, and environmental information processing was found to have the dominant advantage. The results showed that the nebkhas and canopy of Tamarix shrubs had a certain enrichment effect on soil nutrients content, and bacterial abundance and significant effects on the structure and function of the soil bacterial community.

PD62-08 DIFFERENCES IN THE GUT MICROBIOME COMPOSITION BETWEEN MEN WITH ERECTILE DYSFUNCTION AND A MATCHED COHORT: A PILOT STUDY

You have accessJournal of UrologySexual Function/Dysfunction: Basic Research & Pathophysiology (PD62)1 Sep 2021PD62-08 DIFFERENCES IN THE GUT MICROBIOME COMPOSITION BETWEEN MEN WITH ERECTILE DYSFUNCTION AND A MATCHED COHORT: A PILOT STUDY Mahdi Osman, Farouk El-Khatib, Jeanie Nguyen, Edward Choi, Joshua Randolph, Guruduth Banavar, Ying Cai, Pedro Moura, Nan Shen, Ryan Toma, Momchilo Vuyisich, Nathalie Yafi, and Faysal Yafi Mahdi OsmanMahdi Osman More articles by this author , Farouk El-KhatibFarouk El-Khatib More articles by this author , Jeanie NguyenJeanie Nguyen More articles by this author , Edward ChoiEdward Choi More articles by this author , Joshua RandolphJoshua Randolph More articles by this author , Guruduth BanavarGuruduth Banavar More articles by this author , Ying CaiYing Cai More articles by this author , Pedro MouraPedro Moura More articles by this author , Nan ShenNan Shen More articles by this author , Ryan TomaRyan Toma More articles by this author , Momchilo VuyisichMomchilo Vuyisich More articles by this author , Nathalie YafiNathalie Yafi More articles by this author , and Faysal YafiFaysal Yafi More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000002099.08AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: The gut microbiome (GM) plays an important role in human health, ranging from supplying essential nutrients, synthesizing vitamin K, to promoting angiogenesis and enteric nerve function. It has also been recently associated with a variety of chronic health conditions. To date, however, there have been no studies that have attempted to establish any association between the GM and erectile dysfunction (ED). As such, we sought to analyze stool samples from patients with ED and compare them to matched controls for differences in their GM. METHODS: We collected stool samples from 37 patients with ED and matched them with 37 controls. All samples were processed by a third-party company, Viome Inc. The samples were analyzed by metatranscriptome sequencing which allows for data to show both the taxonomy of the microbiome and its KEGG orthology (KO). We compared richness, prevalence and expression of the taxa and KOs between the ED and control groups. RESULTS: There were 224 species (16.85%) with significantly differential prevalence and 135 species (10.31%) with significantly differential expression. There were 565 KOs (10.42%) with significantly differential prevalence and 653 KOs (12.05%) with significantly differential expression. Richness is the number of microbial species detected in a sample. Diversity assesses the abundance and evenness of a species to assess how diverse an individual sample is. The ED group demonstrated significantly lower taxonomic richness and diversity, p= 1.33 x 10^-5 (see figure below). CONCLUSIONS: This is the first study to look at associations between the GM and ED. Patients with ED have significantly lower taxonomic richness and diversity. Further analyses are needed to better understand the implications of these findings and uncover potential targets for early targeted treatment or prevention of ED. Source of Funding: microbiome analysis kits were provided by Viome, Inc © 2021 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 206Issue Supplement 3September 2021Page: e1075-e1075 Advertisement Copyright & Permissions© 2021 by American Urological Association Education and Research, Inc.MetricsAuthor Information Mahdi Osman More articles by this author Farouk El-Khatib More articles by this author Jeanie Nguyen More articles by this author Edward Choi More articles by this author Joshua Randolph More articles by this author Guruduth Banavar More articles by this author Ying Cai More articles by this author Pedro Moura More articles by this author Nan Shen More articles by this author Ryan Toma More articles by this author Momchilo Vuyisich More articles by this author Nathalie Yafi More articles by this author Faysal Yafi More articles by this author Expand All Advertisement Loading ...

KEGG mapping tools for uncovering hidden features in biological data.

In contrast to artificial intelligence and machine learning approaches, KEGG (https://www.kegg.jp) has relied on human intelligence to develop "models" of biological systems, especially in the form of KEGG pathway maps that are manually created by capturing knowledge from published literature. The KEGG models can then be used in biological big data analysis, for example, for uncovering systemic functions of an organism hidden in its genome sequence through the simple procedure of KEGG mapping. Here we present an updated version of KEGG Mapper, a suite of KEGG mapping tools reported previously (Kanehisa and Sato, Protein Sci 2020; 29:28-35), together with the new versions of the KEGG pathway map viewer and the BRITE hierarchy viewer. Significant enhancements have been made for BRITE mapping, where the mapping result can be examined by manipulation of hierarchical trees, such as pruning and zooming. The tree manipulation feature has also been implemented in the taxonomy mapping tool for linking KO (KEGG Orthology) groups and modules to phenotypes.

Compositional profile of mucosal bacteriome of smokers and smokeless tobacco users.

Smoked, and especially smokeless, tobacco are major causes of oral cancer globally. Here, we examine the oral bacteriome of smokers and of smokeless tobacco users, in comparison to healthy controls, using 16S rRNA gene sequencing. Oral swab samples were collected from smokers, smokeless tobacco users, and healthy controls (n = 44). Microbial DNA was extracted and the 16S rRNA gene profiled using the Illumina MiSeq platform. Sequencing reads were processed using DADA2, and taxonomical classification was performed using the phylogenetic placement method. Differentially abundant taxa were identified using DESeq2, while functional metagenomes based on KEGG orthology abundance were inferred using LIMMA. A significantly higher microbial diversity was observed in smokeless tobacco users and smokers relative to controls (P < 0.05). Compositional differences in microbial communities were observed in all comparisons with healthy controls (PERMANOVA P < 0.05) but not between smokers and smokeless tobacco users. Levels of Fusobacterium spp., Saccharibacterium spp., and members of Shuttleworthia were elevated in smokers when compared to controls (BH adj P < 0.01). In addition, the relative abundance of three bacterial taxa belonging to genera Fusobacterium spp., Catonella, and Fretibacterium spp. was significantly increased in smokeless tobacco users relative to controls (BH adj P < 0.01). Major functional pathways significantly increased in smokeless tobacco users relative to both controls, and smokers were similar and involved amino acid metabolism including glutamate and aspartate biosynthesis and degradation (log FC > 1.5; BH adj P < 0.01). A distinct taxonomic and functional profile of oral microbiome in smokers and smokeless tobacco users as compared to healthy controls implicates a significant role of microbes and their metabolites in diseases associated with tobacco use including oral cancer. Future efforts in preventive, diagnostic, curative, and prognostic strategies for diseases associated with tobacco use in smokers and smokeless tobacco users could incorporate the oral microbiome.

The Raw Milk Microbiota from Semi-Subsistence Farms Characteristics by NGS Analysis Method.

The aim of this study was to analyze the microbiome of raw milk obtained from three semi-subsistence farms (A, B, and C) located in the Kuyavian-Pomeranian Voivodeship in Poland. The composition of drinking milk was assessed on the basis of 16S rRNA gene sequencing using the Ion Torrent platform. Based on the conducted research, significant changes in the composition of the milk microbiome were found depending on its place of origin. Bacteria belonging to the Bacillus (17.0%), Corynebacterium (12.0%) and Escherichia-Shigella (11.0%) genera were dominant in the milk collected from farm A. In the case of the milk from farm B, the dominant bacteria belonged to the Acinetobacter genus (21.0%), whereas in the sample from farm C, Escherichia-Shigella (24.8%) and Bacillus (10.3%) dominated the microbiome. An analysis was performed using the PICRUSt tool (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) in order to generate a profile of genes responsible for bacterial metabolism. The conducted analysis confirmed the diversity of the profile of genes responsible for bacterial metabolism in all the tested samples. On the other hand, simultaneous analysis of six KEGG Orthologs (KO), which participated in beta-lactam resistance responsible for antibiotic resistance of bacteria, demonstrated that there is no significant relationship between the predicted occurrence of these orthologs and the place of existence of microorganisms. Therefore, it can be supposed that bacterial resistance to beta-lactam antibiotics occurs regardless of the environmental niche, and that the antibiotic resistance maintained in the population is a factor that shapes the functional structure of the microbial consortia.

Association Between Gut Microbiota and Symptomatic Hand Osteoarthritis: Data From the Xiangya Osteoarthritis Study.

ObjectiveSystemic inflammatory factors have been implicated in symptomatic hand osteoarthritis (OA). Gut microbiome dysbiosis promotes systemic inflammation. The aim of this study was to examine the association between the gut microbiome and the presence of symptomatic hand OA in a population‐based study.MethodsStudy participants were subjects of the Xiangya Osteoarthritis Study, a community‐based observational study conducted in the Hunan Province of China. Symptomatic hand OA was defined as the presence of both symptoms and radiographic OA in the same hand. The gut microbiome was analyzed using 16S ribosomal RNA gene sequencing in stool samples. We examined the relation of α‐diversity, β‐diversity, relative abundance of taxa, and potential bacterial functional pathways to symptomatic hand OA.ResultsA total of 1,388 participants (mean age 61.3 years, 57.4% women) were included in the study, of whom 72 had symptomatic hand OA (prevalence of symptomatic hand OA 5.2%). Beta‐diversity of the gut microbiome, but not α‐diversity, was significantly associated with the presence of symptomatic hand OA (P = 0.003). Higher relative abundance of the genera Bilophila and Desulfovibrio as well as lower relative abundance of the genus Roseburia was associated with symptomatic hand OA. Most functional pathways (i.e., those annotated in the KEGG Ortholog hierarchy) that were observed to be altered in participants with symptomatic hand OA belonged to the amino acid, carbohydrate, and lipid metabolic pathways.ConclusionThis large, population‐based study provides the first evidence that alterations in the composition of the gut microbiome were observed among study participants who had symptomatic hand OA, and a low relative abundance of Roseburia but high relative abundance of Bilophila and Desulfovibrio at the genus level were associated with prevalent symptomatic hand OA. These findings may help investigators understand the role of the microbiome in the development of symptomatic hand OA and could contribute to potential translational opportunities.

Transcriptome-level assessment of the impact of deformed wing virus on honey bee larvae

Deformed wing virus (DWV) prevalence is high in honey bee (Apis mellifera) populations. The virus infects honey bees through vertical and horizontal transmission, leading to behavioural changes, wing deformity, and early mortality. To better understand the impacts of viral infection in the larval stage of honey bees, artificially reared honey bee larvae were infected with DWV (1.55 × 1010 copies/per larva). No significant mortality occurred in infected honey bee larvae, while the survival rates decreased significantly at the pupal stage. Examination of DWV replication revealed that viral replication began at 2 days post inoculation (d.p.i.), increased dramatically to 4 d.p.i., and then continuously increased in the pupal stage. To better understand the impact of DWV on the larval stage, DWV-infected and control groups were subjected to transcriptomic analysis at 4 d.p.i. Two hundred fifty-five differentially expressed genes (DEGs) (fold change ≥ 2 or ≤ -2) were identified. Of these DEGs, 168 genes were downregulated, and 87 genes were upregulated. Gene Ontology (GO) analysis showed that 141 DEGs (55.3%) were categorized into molecular functions, cellular components and biological processes. One hundred eleven genes (38 upregulated and 73 downregulated) were annotated by KO (KEGG Orthology) pathway mapping and involved metabolic pathways, biosynthesis of secondary metabolites and glycine, serine and threonine metabolism pathways. Validation of DEGs was performed, and the related gene expression levels showed a similar tendency to the DEG predictions at 4 d.p.i.; cell wall integrity and stress response component 1 (wsc1), cuticular protein and myo-inositol 2-dehydrogenase (iolG) were significantly upregulated, and small conductance calcium-activated potassium channel protein (SK) was significantly downregulated at 4 d.p.i. Related gene expression levels at different d.p.i. revealed that these DEGs were significantly regulated from the larval stage to the pupal stage, indicating the potential impacts of gene expression levels from the larval to the pupal stages. Taken together, DWV infection in the honey bee larval stage potentially influences the gene expression levels from larvae to pupae and reduces the survival rate of the pupal stage. This information emphasizes the consequences of DWV prevalence in honey bee larvae for apiculture.

Identification of Microbiota Biomarkers With Orthologous Gene Annotation for Type 2 Diabetes.

Type 2 diabetes (T2D) is a systematic chronic metabolic condition with abnormal sugar metabolism dysfunction, and its complications are the most harmful to human beings and may be life-threatening after long-term durations. Considering the high incidence and severity at late stage, researchers have been focusing on the identification of specific biomarkers and potential drug targets for T2D at the genomic, epigenomic, and transcriptomic levels. Microbes participate in the pathogenesis of multiple metabolic diseases including diabetes. However, the related studies are still non-systematic and lack the functional exploration on identified microbes. To fill this gap between gut microbiome and diabetes study, we first introduced eggNOG database and KEGG ORTHOLOGY (KO) database for orthologous (protein/gene) annotation of microbiota. Two datasets with these annotations were employed, which were analyzed by multiple machine-learning models for identifying significant microbiota biomarkers of T2D. The powerful feature selection method, Max-Relevance and Min-Redundancy (mRMR), was first applied to the datasets, resulting in a feature list for each dataset. Then, the list was fed into the incremental feature selection (IFS), incorporating support vector machine (SVM) as the classification algorithm, to extract essential annotations and build efficient classifiers. This study not only revealed potential pathological factors for diabetes at the microbiome level but also provided us new candidates for drug development against diabetes.

The Single-Molecule Long-Read Sequencing of Intestine After Soy Meal-Induced Enteritis in Juvenile Pearl Gentian Grouper, Epinephelus fuscoguttatus♀ × Epinephelus lanceolatus♂

Intestinal inflammatory disease induced by excessive soy protein substitutions for fish meal (FM) protein is a common phenomenon. The pearl gentian grouper, Epinephelus fuscoguttatus♀ × Epinephelus lanceolatus♂, a marine fish with important economical and nutritional values, exhibited a similar problem. As far as we know, there are no reports on the full-length transcriptome of the pearl gentian grouper. In the present study, seven isonitrogenous and isolipidic (10% lipid) diets were prepared and fed to fish for 10 weeks. The water volume in each barrel was about 1 m3, using natural light and temperature. The results showed that 40% dietary soy proteins significantly negatively affected the growth performance of the pearl gentian grouper. Compared to the FM control, the content of immunoglobulin M and the enzyme activities of glutathione reductase, glutathione peroxidase, and total superoxide dismutase in the intestine significantly increased; the content of malondialdehyde in the intestine significantly decreased; and the enzyme activities of alanine transaminase and aspartate transaminase in the liver significantly increased. A library composed of seven different treated distal intestine tissues, including the FM control group, 20% soybean meal substitute for FM (SBM20), SBM40, 20% soybean protein concentrate (SPC20), SPC40, 20% fermented soybean meal substitute for FM (FSBM20), and FSBM40, was constructed and sequenced using PacBio single-molecule real-time (SMRT) and the RNA-Seq technology. As a whole, this study obtained 420,006 full-length non-chimeric (FLNC) reads. After error correction, sequence clustering, and redundancy, 82,351 transcripts with high quality were obtained. In addition, a total of 77,815 transcripts were annotated in seven databases (non-redundant protein sequences, non-redundant nucleotide sequences, Protein family, Clusters of Orthologous Groups of proteins, Gene Ontology, Swiss-Prot, and KEGG Orthology). Also, 49,093 long non-coding RNAs (lncRNAs) and 141,702 simple sequence repeats were identified. Based on full-length transcriptome sequencing, the present study found that the Toll-like receptor/nuclear factor kappa-B signaling pathway plays an important role in the development of SBM- and FSBM-induced enteritis. SPC-induced enteritis is mainly accompanied by a general imbalance of the nutrition absorption-related signaling pathways, which only affects a small part of the immune-related signaling pathways. This study supplies new and valuable reference transcripts, which would better facilitate further research on the pearl gentian grouper.

Accurate annotation of protein coding sequences with IDTAXA.

The observed diversity of protein coding sequences continues to increase far more rapidly than knowledge of their functions, making classification algorithms essential for assigning a function to proteins using only their sequence. Most pipelines for annotating proteins rely on searches for homologous sequences in databases of previously annotated proteins using BLAST or HMMER. Here, we develop a new approach for classifying proteins into a taxonomy of functions and demonstrate its utility for genome annotation. Our algorithm, IDTAXA, was more accurate than BLAST or HMMER at assigning sequences to KEGG ortholog groups. Moreover, IDTAXA correctly avoided classifying sequences with novel functions to existing groups, which is a common error mode for classification approaches that rely on E-values as a proxy for confidence. We demonstrate IDTAXA’s utility for annotating eukaryotic and prokaryotic genomes by assigning functions to proteins within a multi-level ontology and applied IDTAXA to detect genome contamination in eukaryotic genomes. Finally, we re-annotated 8604 microbial genomes with known antibiotic resistance phenotypes to discover two novel associations between proteins and antibiotic resistance. IDTAXA is available as a web tool (http://DECIPHER.codes/Classification.html) or as part of the open source DECIPHER R package from Bioconductor.

Proposal of Carbonactinosporaceae fam. nov. within the class Actinomycetia. Reclassification of Streptomyces thermoautotrophicus as Carbonactinospora thermoautotrophica gen. nov., comb. nov

Streptomyces thermoautotrophicus UBT1T has been suggested to merit generic status due to its phylogenetic placement and distinctive phenotypes among Actinomycetia. To evaluate whether ‘S. thermoautotrophicus’ represents a higher taxonomic rank, ‘S. thermoautotrophicus’ strains UBT1T and H1 were compared to Actinomycetia using 16S rRNA gene sequences and comparative genome analyses. The UBT1T and H1 genomes each contain at least two different 16S rRNA sequences, which are closely related to those of Acidothermus cellulolyticus (order Acidothermales). In multigene-based phylogenomic trees, UBT1T and H1 typically formed a sister group to the Streptosporangiales-Acidothermales clade. The Average Amino Acid Identity, Percentage of Conserved Proteins, and whole-genome Average Nucleotide Identity (Alignment Fraction) values were ≤58.5%, ≤48%, ≤75.5% (0.3) between ‘S. thermoautotrophicus’ and Streptosporangiales members, all below the respective thresholds for delineating genera. The values for genomics comparisons between strains UBT1T and H1 with Acidothermales, as well as members of the genus Streptomyces, were even lower. A review of the ‘S. thermoautotrophicus’ proteomic profiles and KEGG orthology demonstrated that UBT1T and H1 present pronounced differences, both tested and predicted, in phenotypic and chemotaxonomic characteristics compared to its sister clades and Streptomyces. The distinct phylogenetic position and the combination of genotypic and phenotypic characteristics justify the proposal of Carbonactinospora gen. nov., with the type species Carbonactinospora thermoautotrophica comb. nov. (type strain UBT1T, = DSM 100163T = KCTC 49540T) belonging to Carbonactinosporaceae fam. nov. within Actinomycetia.