RNA Gene Sequence Data Research Articles

Crohn's Disease-Associated Pathogenic Mutation in the Manganese Transporter ZIP8 Shifts the Ileal and Rectal Mucosal Microbiota Implicating Aberrant Bile Acid Metabolism.

A pathogenic mutation in the manganese transporter ZIP8 (A391T; rs13107325) increases the risk of Crohn's disease. ZIP8 regulates manganese homeostasis and given the shared need for metals between the host and resident microbes, there has been significant interest in alterations of the microbiome in carriers of ZIP8 A391T. Prior studies have not examined the ileal microbiome despite associations between ileal disease and ZIP8 A391T. Here, we used the Pediatric Risk Stratification Study (RISK) cohort to perform a secondary analysis of 16S ribosomal RNA gene sequencing data obtained from ileal and rectal mucosa to study associations between ZIP8 A391T carrier status and microbiota composition. We found sequence variants mapping to Veillonella were decreased in the ileal mucosa of ZIP8 A391T carriers. Prior human studies have demonstrated the sensitivity of Veillonella to bile acid abundance. We therefore hypothesized that bile acid homeostasis is differentially regulated in carriers of ZIP8 A391T. Using a mouse model of ZIP8 A391T, we demonstrate an increase in total bile acids in the liver and stool and decreased fibroblast growth factor 15 (Fgf15) signaling, consistent with our hypothesis. We confirmed dysregulation of FGF19 in the 1000IBD cohort, finding that plasma FGF19 levels are lower in ZIP8 A391T carriers with ileocolonic Crohn's disease. In the search for genotype-specific therapeutic paradigms for patients with Crohn's disease, these data suggest targeting the FGF19 pathway in ZIP8 A391T carriers. Aberrant bile acid metabolism may precede development of Crohn's disease and prioritize study of the interactions between manganese homeostasis, bile acid metabolism and signaling, and complicated ileal Crohn's disease.

Real-time PCR-based quantitative microbiome profiling elucidates the microbial dynamic succession in backslopping fermentation of Taiwanese pickled cabbage.

Microbiota succession determines the flavor and quality of fermented foods. Quantitative PCR-based quantitative microbiome profiling (QMP) has been applied broadly for microbial analysis from absolute abundance perspectives, transforming microbiota ratios into counts by normalizing 16S ribosomal RNA (16S rRNA) gene sequencing data with gene copies quantified by quantitative PCR. However, the application of QMP in fermented foods is still limited. QMP elucidated microbial succession of Taiwanese pickled cabbage. In the spontaneous first-round fermentation (FR), the 16S rRNA gene copies of total bacteria increased from 6.1 to 10 log copies mL-1. The dominant lactic acid bacteria genera were successively Lactococcus, Leuconostoc and Lactiplantibacillus. Despite the decrease in the proportion of Lactococcus during the succession, the absolute abundance of Lactococcus still increased. In the backslopping second-round fermentation (SR), the total bacteria 16S rRNA gene copies increased from 7.6 to 9.9 log copies mL-1. The addition of backslopping starter and vinegar rapidly led to a homogenous microbial community dominated by Lactiplantibacillus. The proportion of Lactiplantibacillus remained consistently around 90% during SR, whereas its absolute abundance exhibited a continuous increase. In SR without vinegar, Leuconostoc consistently dominated the fermentation. The present study highlights that compositional analysis would misinterpret microbial dynamics, whereas QMP reflected the real succession profiles and unveiled the essential role of vinegar in promoting Lactiplantibacillus dominance in backslopping fermentation of Taiwanese pickled cabbage. Quantitative microbiome profiling (QMP) was found to be a more promising approach for the detailed observation of microbiome succession in food fermentation compared to compositional analysis. © 2024 Society of Chemical Industry.

Specific gut microbiome signature predicts hepatitis B virus-related hepatocellular carcinoma patients with microvascular invasion

Background We aimed to assess differences in intestinal microflora between patients with operable hepatitis B virus-related hepatocellular carcinoma (HBV-HCC) with microvascular invasion (MVI) and those without MVI. Additionally, we investigated the potential of the microbiome as a non-invasive biomarker for patients with MVI. Methods We analyzed the preoperative gut microbiomes (GMs) of two groups, the MVI (n = 46) and non-MVI (n = 56) groups, using 16S ribosomal RNA gene sequencing data. At the operational taxonomic unit level, we employed random forest models to predict MVI risk and validated the results in independent validation cohorts [MVI group (n = 17) and non-MVI group (n = 15)]. Results β diversity analysis, utilizing weighted UniFrac distances, revealed a significant difference between the MVI and non-MVI groups, as indicated by non-metric multidimensional scaling and principal coordinate analysis. We also observed a significant correlation between the characteristic intestinal microbial communities at the genus level and their main functions. Nine optimal microbial markers were identified, with an area under the curve of 79.76% between 46 MVI and 56 non-MVI samples and 79.80% in the independent verification group. Conclusion This pioneering analysis of the GM in patients with operable HBV-HCC with and without MVI opens new avenues for treating HBV-HCC with MVI. We successfully established a diagnostic model and independently verified microbial markers for patients with MVI. As preoperative targeted biomarkers, GM holds potential as a non-invasive tool for patients with HBV-HCC with MVI.

Association of the gut microbiota with clinical variables in obese and lean Emirati subjects.

Growing evidence supports the role of gut microbiota in obesity, yet exact associations remain largely unknown. Specifically, very little is known about this association in the Emirati population. We explored differences in gut microbiota composition, particularly the Firmicutes/Bacteroidetes (F/B) ratio, between 43 obese and 31 lean adult Emirate counterparts, and its association with obesity markers, by using V3-V4 regions of 16 S ribosomal RNA gene sequencing data. Furthermore, we collected anthropometric and biochemical data. The two major phyla in obese and lean groups were Firmicutes and Bacteroidetes. We observed a significantly lower alpha diversity (Shannon index) in obese subjects and a significant difference in beta diversity and phylum and genus levels between the two groups. The obese group had higher abundances of Verrucomicrobia and Saccharibacteira and lower abundances of Lentisphaerae. Acidaminococcus and Lachnospira were more abundant in obese subjects and positively correlated with adiposity markers. No correlations were found between the gut microbiota and biochemical variables, such as fasting blood sugar, total cholesterol, HDL cholesterol, LDL cholesterol, and triglycerides. We reveal significant differences in the gut microbiota between obese and lean adult Emiratis and an association between certain microbial genera of the gut microbiota and obesity. A better understanding of the interactions between gut microbes, diet, lifestyle, and health is warranted.

Modulation of gut microbiota alleviates cerebral ischemia/reperfusion injury in rats by inhibiting M1 polarization of microglia.

Gut microbiota affects the gut-brain axis; hence, the modulation of the microbiota has been proposed as a potential therapeutic strategy for cerebral ischemia/reperfusion injury (CIRI). However, the role and mechanism of the gut microbiota in regulating microglial polarization during CIRI remain poorly understood. Herein, using a middle cerebral artery occlusion and reperfusion (MCAO/R) rat model, we evaluated changes in the gut microbiota after CIRI and the potential effects of fecal microbiota transplant (FMT) on the brain. Rats underwent either MCAO/R or sham surgery, and then they received FMT (started 3days later; continued for 10days). 2,3,5-Triphenyltetrazolium chloride staining, neurological outcome scale, and Fluoro-Jade C staining showed that MCAO/R induced cerebral infarction, neurological deficits, and neuronal degeneration. In addition, immunohistochemistry or real-time PCR assay showed increased expression levels of M1-macrophage markers-TNF-α, IL-1β, IL-6, and iNOS-in the rats following MCAO/R. Our finding suggests that microglial M1 polarization is involved in CIRI. 16S ribosomal RNA gene sequencing data revealed an imbalance in the gut microbiota of MCAO/R animals. In contrast, FMT reversed this MCAO/R-induced imbalance in the gut microbiota and ameliorated nerve injury. In addition, FMT prevented the upregulation in the ERK and NF-κB pathways, which reversed the M2-to-M1 microglial shift 10days after MCAO/R injury in rats. Our primary data showed that the modulation of the gut microbiota can attenuate CIRI in rats by inhibiting microglial M1 polarization through the ERK and NF-κB pathways. However, an understanding of the underlying mechanism requires further study.

Abstract 3044: Integrative gut microbiome analysis of human and mouse prostate cancer

Abstract Gut microbes are intricately involved in maintaining normal physiology and homeostasis and have become a major area of study to determine their relevance in human disease. In cancer, alterations to gut microbiota has been associated to resistance to chemo- and immuno-therapy, whereas supplementation with specific taxa improves antitumor treatment responses. Mouse models have been essential to study disease biology and drug discovery. However, mice are fundamentally quite different from humans, thus, questions have arisen regarding their utility as pertinent tools to study microbial influences and their impact on human disease. To address these questions, we have performed a cross-species comparative analysis of the fecal microbiota from a human cohort of prostate cancer patients and a preclinical mouse model of prostate cancer. Microbiota composition was determined by 16s RNA gene sequencing on stool samples from tumor-bearing prostate-specific conditional Pten-knockout and disease-free wildtype mice and 16s RNA gene sequencing data from a human cohort of patients with suspected prostate cancer was used. Human cases were assigned to no cancer and cancer groups based on diagnosis from prostate biopsy and as low-risk (negative biopsy of Gleason grade <3) or high-risk (Gleason grade ≥3). Community composition differed significantly between stool samples of cancer and disease-free individuals in mice but not humans. Operational taxonomic units (OTUs) corresponding to taxa associated with cancer in both mice and humans included Odoribacter spp. and Desulfovibrio spp. Comparing the profiles predicted with Tax4Fun revealed KEGG metabolic pathways associated prostate cancer. Pathways enriched in cancer bearing-mice and that are also associated in patients with prostate cancer included folate biosynthesis, biotin metabolism and ubiquinone & other terpenoid-quinone biosynthesis. Carbon metabolism was a pathway discordant between high-risk prostate cancer patients and cancer bearing mice. Although the basal composition of gut microbes differed between humans and mice, the functional microbiome showed greater similarities. Our cross-species comparative analysis shows that gut microbial dysbiosis is connected to prostate cancer provides additional insights into the biological processes involved. This study provides additional data that may help to bridge the gap between humans and mice. Citation Format: Chisato Wakamori, Marco A. De Velasco, Yurie Kura, Naomi Ando, Noriko Sako, Kazutoshi Fujita, Kazuko Sakai, Makoto Matsushita, Eri Banno, Yasunori Mori, Masahiro Nozawa, Mitsuhisa Nishimoto, Kazuhiro Yoshimura, Norio Nonomura, Kazuto Nishio, Hirotsugu Uemura. Integrative gut microbiome analysis of human and mouse prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3044.

Morphology, morphogenesis and molecular phylogeny of a novel saline soil ciliate, Urosoma quadrinucleatum n. sp. (Ciliophora, Hypotrichia)

The morphology and morphogenesis of a new saline soil hypotrichous ciliate, Urosoma quadrinucleatum n. sp., collected from northwestern China, were studied based on live observations and protargol stained specimens. The new species is characterized as follows: size in vivo 90–130 × 20–30 μm; body outline elongate-elliptical with both ends broadly rounded; four macronuclear nodules; cortical granules present; paroral in front of endoral; usually 16 frontal-ventral-transverse cirri. Urosoma quadrinucleatum n. sp. has almost the same morphogenetic characteristics as its congeners U. gigantea and U. salmastra, and differs from other three congeners whose morphogenesis is known in the formation of the frontal-ventral-transverse cirral anlagen as well as the development of marginal and dorsal kineties anlagen. The sequence differences among U. quadrinucleatum n. sp. and other Urosoma species further support the validity of the present organism as novel species. Further, U. quadrinucleatum n. sp. clusters with U. salmastra in the phylogenetic analyses based on small subunit ribosomal RNA gene (SSU rDNA) sequence data.

1419. Matters of the Heart: A Scoping Review Toward Better Management‌ ‌of‌ Nontuberculous‌ ‌Mycobacterial‌ ‌Infections of‌ Cardiac ‌Devices‌

Abstract Background Medical device infections caused by nontuberculous mycobacteria (NTM) are increasingly reported in the literature. Management is complex and often guided by expert opinion, in the absence of evidence-based guidelines. Methods We searched available databases for reports of‌ implantable‌ cardiac device-related‌ (ICDR) infections with NTM. We collected patient-level characteristics, microbiological, and treatment data, and used univariate analysis to correlate with reported outcome, which we defined as death, treatment failure, relapse after treatment completion, cure, and treatment completion. Results Of 2573 potential eligible articles, 68 articles were included, representing 112 patients. The average patient age was 61 years, and 6% of patients were immunocompromised. Of 12 species reported, 65% were rapid growers, with M. fortuitum most common. Prosthetic heart valves and pacemaker/automatic implantable cardiac devices (AICD) were the most commonly reported infected devices (45% and 37%, respectively). Diagnosis was often delayed, and confirmed with culture (62%, 41% blood cultures) and 16s ribosomal RNA gene sequencing data (14%) of cases. Antimicrobial susceptibility was available in 55% of cases. 70% of patients received >2 antibiotics and, of these, 41% included a macrolide. Devices were removed for 65% of patients, more commonly if the infected deice was a pacemaker or AICD than another type of cardiac device (86% vs 56%, p=0.02). 67% of patients with prosthetic valves underwent valve replacement. Compared with those who did not have their device removed, patients who underwent device removal were less likely to die (23% vs 48%, p=0.02) and more likely to have favorable outcomes (68% vs 28%, p=0.002). Conclusion Reports of ICRD NTM infections were common, and suspicion should be high even for those without immunocompromising condition. Determining outcome was challenging and should be standardized to provide an evidence base for better management. In our analysis, patients who underwent device removal had improved survival, suggesting either that comorbidity precluded device removal and/or that removal may be an essential part of the management. Disclosures All Authors: No reported disclosures.

Phylogeny of the anaerobic ciliate genus Sonderia (Protista: Ciliophora: Plagiopylea), including the description of three novel species and a brief revision of the genus.

Anaerobic protists in general, and ciliates in particular, are important components of anoxic or hypoxic environments, however, their diversity remains underestimated. Sonderia is a poorly studied genus that is distributed worldwide and is commonly found in anaerobic environments. In the present study, the taxonomy and phylogeny of three new species, namely Sonderia aposinuata sp. nov., Sonderia paramacrochilus sp. nov. and Sonderia steini sp. nov., collected from China, were investigated based on microscopic observations and SSU rRNA gene sequencing methods. Sonderia aposinuata sp. nov. is diagnosed mainly by having a relatively large body size, a crescent-shaped oral opening, numerous slender extrusomes, one suture on the ventral side and two on the dorsal side, and a buccal cavity that occupies the anterior third of the cell. Sonderia paramacrochilus sp. nov. closely resembles S. macrochilus but differs mainly by its oral opening being located closer to the anterior cell margin and its spindle-shaped extrusomes. Sonderia steini sp. nov. is a freshwater species that can be recognized by its shallow buccal cavity, sparsely distributed rod-shaped extrusomes, and having 68-79 monokinetidal somatic kineties that form sutures on both sides of the body. Phylogenetic analyses based on small subunit ribosomal RNA (SSU rRNA) gene sequence data support the monophyly of the family Sonderiidae, however, Sonderia is paraphyletic. The genus Sonderia is briefly revised and a key to the identification of species belonging to this genus is supplied.

Meta-analysis of larvae of the black soldier fly (Hermetia illucens) microbiota based on 16S rRNA gene amplicon sequencing.

Black soldier fly larvae (BSFL) belong to the most widely reared insects as an alternative protein source at industrial scale. Bacteria in the larval gut can provide benefits for the animal, though some bacteria can also be pathogenic for the insect. Accurate characterization of the BSFL microbiota is important for the production of BSFL in terms of yield and microbiological safety. In this study, 16S ribosomal RNA gene sequence data sets from 11 studies were re-analysed to gain better insights in the BSFL gut microbiota, potential factors that influence their composition, and differences between the gut and the whole larvae microbiota. A core gut microbiota was found consisting of members of Enterococcus, Klebsiella, Morganella, Providencia, and Scrofimicrobium. Further, the factors ‘Study’, ‘Age’ and ‘Feed’ (i.e. rearing substrate of the larvae) significantly affected the microbiota gut composition. When compared to whole larvae, a significantly lower diversity was found for gut samples, suggesting that the larvae harboured additional microbes on their cuticle or in the insect body. Universal choices in insect sample type, primer selection and bio-informatics analysis pipeline can strengthen future meta-analyses and improve our understanding of the BSFL gut microbiota towards the optimization of insect rearing conditions and substrates.

New contributions to the Cyrtophoria ciliates (Protista, Ciliophora): Establishment of new taxa and phylogenetic analyses using two ribosomal genes.

Periphytic ciliates play a vital role in the material cycle and energy flow of microbial food web, however, their taxonomy and biodiversity are inadequately studied given their high species richness. Two new and one little known species, viz. Derouxella lembodes gen. et sp. nov., Cyrtophoron multivacuolatum sp. nov., and Cyrtophoron apsheronica Aliev, 1991, collected from coastal waters of China, were investigated using modern methods. Derouxella gen. nov. can be recognized by having dorsoventrally flattened body, a podite, one fragmented preoral kinety, two parallel circumoral kineties, and somatic kineties progressively shortened from right to left. Morphological classification and phylogenetic analyses based on nuclear small subunit ribosomal RNA (nSSU rRNA) and mitochondrial small subunit ribosomal RNA (mtSSU rRNA) gene sequence data inferred that Derouxella gen. nov. occupies an intermediate position between Hartmannulidae and Dysteriidae. Cyrtophoron multivacuolatum sp. nov. is characterized by large body size, the numbers of somatic kineties and nematodesmal rods, and having numerous contractile vacuoles. The genus Cyrtophoron and the poorly known species C. apsheronica were redefined. Even with the addition of newly obtained nSSU rRNA and mtSSU rRNA gene sequencesof Cyrtophoron, the family Chlamydodontidae was still recovered as a monophyletic group, the monophyly of Cyrtophoron was supported too.

Analysis of Fecal Microbiota Dynamics in Lupus-Prone Mice using a Simple, Cost-Effective DNA Isolation Method.

Gut microbiota has an important role in educating the immune system. This relationship is extremely important for understanding autoimmune diseases that are not only driven by genetic factors, but also environmental factors that can trigger the onset and/or worsen the disease course. A previously published study on the dynamics of the gut microbiota in lupus-prone MRL/lpr female mice showed how changes of the gut microbiota can alter disease progression. Here, a protocol is described for extracting representative samples from the gut microbiota for studies of autoimmunity. Microbiota samples are collected from the anus and processed, from which the DNA is extracted using a phenol-chloroform method and purified by alcohol precipitation. After PCR is performed, purified amplicons are sequenced using a Next Generation Sequencing platform at Argonne National Laboratory. Finally, the 16S ribosomal RNA gene sequencing data is analyzed. As an example, data obtained from gut microbiota comparisons of MRL/lpr mice with or without CX3CR1 are shown. Results showed significant differences in genera containing pathogenic bacteria such as those in the phylum Proteobacteria, as well as the genus Bifidobacterium, which is considered part of the healthy commensal microbiota. In summary, this simple, cost-effective DNA isolation method is reliable and can help the investigation of gut microbiota changes associated with autoimmune diseases.

AXIOME3: Automation, eXtension, and Integration Of Microbial Ecology.

BackgroundAdvances in high-throughput sequencing accessibility have democratized small subunit ribosomal RNA gene sequence data collection, coincident with an increasing availability of computational tools for sequence data processing, multivariate statistics, and data visualization. However, existing tools often require programming ability and frequent user intervention that may not be suitable for fast-paced and large-scale data analysis by end user microbiologists who are unfamiliar with the Linux command line environment or who prefer interactions with a GUI. Here we present AXIOME3, which is a completely redeveloped AXIOME pipeline that streamlines small subunit ribosomal RNA data analysis by managing QIIME2, R, and Python-associated analyses through an interactive web interface.FindingsAXIOME3 comes with web GUI to improve usability by simplifying configuration processes and task status tracking. Internally, it uses an automated pipeline that is wrapped around QIIME2 to generate a range of outputs including amplicon sequence variant tables, taxonomic classifications, phylogenetic trees, biodiversity metrics, and ordinations. The extension module for AXIOME3 provides advanced data visualization tools such as principal coordinate analysis, bubble plots, and triplot ordinations that can be used to visualize interactions between a distance matrix, amplicon sequence variant taxonomy, and sample metadata.ConclusionsBecause repeat analysis of small subunit ribosomal RNA amplicon sequence data is challenging for those who have limited experience in command line environments, AXIOME3 now offers rapid and user-friendly options within an automated pipeline, with advanced data visualization tools and the ability for users to incorporate additional analyses easily through extension. AXIOME3 is completely open source (https://github.com/neufeld/AXIOME3, https://github.com/neufeld/AXIOME3-GUI), and researchers are encouraged to modify and redistribute the package.

Database Mining to Unravel the Ecology of the Phylum Chloroflexi in Methanogenic Full Scale Bioreactors.

Although microbial communities of anaerobic bioreactors have been extensively studied using DNA-based tools, there are still several knowledge gaps regarding the microbiology of the process, in particular integration of all generated data is still limited. One understudied core phylum within anaerobic bioreactors is the phylum Chloroflexi, despite being one of the most abundant groups in anaerobic reactors. In order to address the abundance, diversity and phylogeny of this group in full-scale methanogenic reactors globally distributed, a compilation of 16S ribosomal RNA gene sequence data from 62 full-scale methanogenic reactors studied worldwide, fed either with wastewater treatment anaerobic reactors (WTARs) or solid-waste treatment anaerobic reactors (STARs), was performed. One of the barriers to overcome was comparing data generated using different primer sets and different sequencing platforms. The sequence analysis revealed that the average abundance of Chloroflexi in WTARs was higher than in STARs. Four genera belonging to the Anaerolineae class dominated both WTARs and STARs but the core populations were different. According to the phylogenetic analysis, most of the sequences formed clusters with no cultured representatives. The Anaerolineae class was more abundant in reactors with granular biomass than in reactors with disperse biomass supporting the hypothesis that Anaerolineae play an important role in granule formation and structure due to their filamentous morphology. Cross-study comparisons can be fruitfully used to understand the complexity of the anaerobic digestion process. However, more efforts are needed to standardize protocols and report metadata information.

Vitamin D metabolites and the gut microbiome in older men

The vitamin D receptor is highly expressed in the gastrointestinal tract where it transacts gene expression. With current limited understanding of the interactions between the gut microbiome and vitamin D, we conduct a cross-sectional analysis of 567 older men quantifying serum vitamin D metabolites using LC-MSMS and defining stool sub-Operational Taxonomic Units from16S ribosomal RNA gene sequencing data. Faith’s Phylogenetic Diversity and non-redundant covariate analyses reveal that the serum 1,25(OH)2D level explains 5% of variance in α-diversity. In β-diversity analyses using unweighted UniFrac, 1,25(OH)2D is the strongest factor assessed, explaining 2% of variance. Random forest analyses identify 12 taxa, 11 in the phylum Firmicutes, eight of which are positively associated with either 1,25(OH)2D and/or the hormone-to-prohormone [1,25(OH)2D/25(OH)D] “activation ratio.” Men with higher levels of 1,25(OH)2D and higher activation ratios, but not 25(OH)D itself, are more likely to possess butyrate producing bacteria that are associated with better gut microbial health.

Gut Microbiota and Risk of Persistent Nonalcoholic Fatty Liver Diseases.

Gut dysbiosis is regarded as a pathogenetic factor of nonalcoholic fatty liver disease (NAFLD), but its role in NAFLD persistence is unknown. We investigated the influence of the gut microbiota on persistent NAFLD. This cohort study included 766 subjects with 16S ribosomal RNA (rRNA) gene sequencing data from fecal samples at baseline who underwent repeated health check-up examinations. Fatty liver was determined using ultrasound at baseline and follow-up. Participants were categorized into four groups: none (control), developed, regressed, or persistent NAFLD. The persistent NAFLD group had lower richness compared with the control group. Significant differences were also found in both non-phylogenic and phylogenic beta diversity measures according to NAFLD persistence. Pairwise comparisons indicated that taxa abundance mainly differed between the control and persistent NAFLD groups. A relative high abundance of Fusobacteria and low abundance of genera Oscillospira and Ruminococcus of the family Ruminococcaceae and genus Coprococcus of the family Lachnospiraceae were found in the persistent NAFLD group. Based on the functional predictions, pathways related to primary and secondary bile acid biosynthesis were highly detected in the persistent NAFLD group compared with the control group. These findings support that the composition of the gut microbiome associated with dysregulation of bile acid biosynthetic pathways may contribute to the persistence of NAFLD. This is the first cohort study to demonstrate the influence of microbiota on persistent NAFLD. Our findings may help identify potential targets for therapeutic intervention in NAFLD.

Integrated taxonomy combining morphological and molecular biological analyses of soil nematodes from maritime Antarctica

Nematodes are one of the key organisms in the terrestrial ecosystems of Antarctica. Their exceptional cryptobiotic adaptations against freezing and desiccation stress have attracted significant research attention. However, even today, relatively little is known about the biology of nematodes across this continent, especially in terms of their biodiversity and distribution. To address such fundamental research areas, correct classification of Antarctic nematodes is a necessary underpinning. Until recently, morphological examination has been the only established method available, and this remains challenging even for experts. Advances in molecular biological techniques now provide a complementary approach to nematode classification, but as yet have largely not been applied to the Antarctic fauna. In this study we initiate development of cataloguing of Antarctic nematodes using both morphological and molecular information from individual worms. We collected nematode samples from islands in maritime Antarctica (Signy, Adelaide and Leonie Islands; a latitudinal range between the South Orkney Islands and Marguerite Bay), and classified them by DNA sequence obtained from morphologically-determined samples. We obtained small subunit ribosomal RNA gene (SSU rDNA) sequence data from seven major maritime Antarctic nematode species, which will permit future identification of these species without the requirement for detailed morphological taxonomic analyses. We also trialled the application of molecular analyses to morphologically unidentified samples from King George Island, thereby obtaining support for our approach through the identification of samples with identical sequences. This approach provides baseline information for future studies of Antarctic nematodes.

The Relationship between Platelet Count and Host Gut Microbiota: A Population-Based Retrospective Cross-Sectional Study.

Platelet count reflects the severity and prognosis of multiple diseases. Additionally, alterations in gut microbiota have been linked to several chronic diseases. The purpose of this study was to investigate the association between gut microbiota and platelet count. We selected 1268 subjects with fecal 16S RNA gene sequencing data from a Healthcare Screening Center cohort. Based on the third quartile of platelets (277 × 109/L), we compared the gut microbiota between the upper quartile (n = 321) and lower three quartiles groups (n = 947). The upper quartile group had lower alpha diversity based on observed amplicon sequence variants (q = 0.004) and phylogenetic index (q < 0.001) than the lower three quartiles group. Significant differences were also found in the weighted UniFrac distance (q = 0.001) and Jaccard dissimilarity (q = 0.047) beta diversity measures between the two groups. Compared with the lower three quartiles group, the upper quartile group exhibited decreased relative abundances of the genus Faecalibacterium, which was also inversely correlated with the platelet count. Increased platelet count was associated with reduced diversity in gut microbiota and lower abundances of Faecalibacterium with beneficial gut bacteria spices F. prausnitzii, suggesting that an increased platelet count, even within normal range, may adversely affect gut microbial diversity and composition.

CCMP: Software-as-a-service approach for fully-automated microbiome profiling

Microbiome profiling holds great promise for the development of novel disease biomarkers and therapeutics. Next-generation sequencing is currently the preferred method for microbiome data collection and multiple standardized tools, packages, and pipelines have been developed for the purpose of raw data processing and microbial annotation. However, these currently available pipelines come with entry-level barriers such as high-performance hardware, software installation, and sequential command-line scripting that often deter end-users. We thus created Cloud Computing for Microbiome Profiling (CCMP, https://ccmp.usc.edu), a public cloud-based web tool which combines the analytical power of current microbiome analysis platforms with a user-friendly interface. CCMP is a free-of-charge software-as-a-service (SaaS) that simplifies user experience by enabling users to complete their analysis in a single step, uploading raw sequencing data files. Once users upload 16S ribosomal RNA gene sequence data, our pipeline performs taxonomic annotation, abundance profiling, and statistical tests to report microbiota signatures altered by diseases or experimental conditions. CCMP took a 125 gigabyte (GB) input of 16S ribosomal RNA gene sequence data from 1052 specimens in FASTQ format and reported figures and tables of taxonomic annotations, statistical tests, α and β diversity calculations, and principal coordinate analyses within 21 h. CCMP is the first fully-automated web interface that integrates three key solutions for large-scale data analysis: cloud computing, fast file transfer technology, and microbiome analysis tools. As a reliable platform that supplies consistent microbiome analysis, CCMP will advance microbiome research by making effortful bioinformatics easily accessible to public.

New insight into the species diversity and life cycles of rust fungi (Pucciniales) affecting bioenergy switchgrass (Panicum virgatum) in the Eastern and Central United States

Research was undertaken to clarify the taxonomic identity of leaf rust (Pucciniales) fungi on bioenergy switchgrass in the Eastern and Central U.S. We integrated internal transcribed spacer 2 (ITS2) and partial 28S ribosomal RNA gene sequence data from collections taken from cultivated switchgrass and herbarium specimens, including purported aecial and telial states of Puccinia graminicola and Puccinia pammelii. Maximum likelihood and Bayesian analyses revealed four monophyletic clades: Puccinia emaculata sensu stricto (s.s.), P. pammelii, P. graminicola, and Puccinia novopanici. Results also indicated that P. emaculata s.s. was not affecting cultivated, bioenergy switchgrass. Aecidium pammelii and P. pammelii were distinct phylogenetically from P. emaculata s.s. and grouped within a well-supported clade, demonstrating aecial-telial host alternation for P. pammelii between Euphorbia corollata and switchgrass. Aecidium stillingiae on queen’s delight (Stillingia sylvatica)—a purported aecial state host for P. graminicola—shared identical sequences with the recently described species Puccinia pascua. The latter fungus, however, was recovered within a subclade of P. graminicola. Hence, queen’s delight likely is not an aecial host to P. graminicola s.s. Additional molecular studies are warranted to determine species boundaries within the P. graminicola complex. The majority of contemporary collections from cultivated switchgrass were recognized as P. novopanici. Collectively, bioenergy switchgrass is host to at least three phylogenetically distinct species, presenting a significant challenge to the future selection and breeding of switchgrass with improved rust resistance.