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Bibliography on: Metagenomics

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ESP: PubMed Auto Bibliography 05 Jun 2020 at 01:32 Created: 

Metagenomics

While genomics is the study of DNA extracted from individuals — individual cells, tissues, or organisms — metagenomics is a more recent refinement that analyzes samples of pooled DNA taken from the environment, not from an individual. Like genomics, metagenomic methods have great potential in many areas of biology, but none so much as in providing access to the hitherto invisible world of unculturable microbes, often estimated to comprise 90% or more of bacterial species and, in some ecosystems, the bulk of the biomass. A recent describes how this new science of metagenomics is beginning to reveal the secrets of our microbial world: The opportunity that stands before microbiologists today is akin to a reinvention of the microscope in the expanse of research questions it opens to investigation. Metagenomics provides a new way of examining the microbial world that not only will transform modern microbiology but has the potential to revolutionize understanding of the entire living world. In metagenomics, the power of genomic analysis is applied to entire communities of microbes, bypassing the need to isolate and culture individual bacterial community members.

Created with PubMed® Query: metagenomic OR metagenomics OR metagenome NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

RevDate: 2020-06-04

Wang S, Yan Z, Wang P, et al (2020)

Comparative metagenomics reveals the microbial diversity and metabolic potentials in the sediments and surrounding seawaters of Qinhuangdao mariculture area.

PloS one, 15(6):e0234128 pii:PONE-D-20-07771.

Qinhuangdao coastal area is an important mariculture area in North China. Microbial communities play an important role in driving biogeochemical cycle and energy flow. It is necessary to identify the microbial communities and their functions in the coastal mariculture area of Qinhuangdao. In this study, the microbial community compositions and their metabolic potentials in the sediments and their surrounding seawaters of Qinhuangdao mariculture area were uncovered by the 16S rRNA gene amplicon sequencing and metagenomic shotgun sequencing approaches. The results of amplicon sequencing showed that Gammaproteobacteria and Alphaproteobacteria were predominant classes. Our datasets showed a clear shift in microbial taxonomic groups and the metabolic pathways in the sediments and surrounding seawaters. Metagenomic analysis showed that purine metabolism, ABC transporters, and pyrimidine metabolism were the most abundant pathways. Genes related to two-component system, TCA cycle and nitrogen metabolism exhibited higher abundance in sediments compared with those in seawaters. The presence of cadmium-resistant genes and ABC transporters suggested the ability of microorganisms to resist the toxicity of cadmium. In summary, this study provides comprehensive and significant differential signatures in the microbial community and metabolic pathways in Qinhuangdao mariculture area, and can develop effective microbial indicators to monitor mariculture area in the future.

RevDate: 2020-06-04

Wang H, Lu Z, Bao Y, et al (2020)

Clinical diagnostic application of metagenomic next-generation sequencing in children with severe nonresponding pneumonia.

PloS one, 15(6):e0232610 pii:PONE-D-19-30910.

Pneumonia is one of the most important causes of morbidity and mortality in children. Identification and characterization of pathogens that cause infections are crucial for accurate treatment and accelerated recovery. However, in most cases, the causative agent cannot be identified, which is partly due to the limited spectrum of pathogens covered by current diagnostics based on nucleic acid amplification. Therefore, in this study, we explored the application of metagenomic next-generation sequencing (mNGS) for the diagnosis of children with severe pneumonia. From April to July 2017, 32 hospitalized children with severe nonresponding pneumonia in Shenzhen Children's Hospital were included in this study. Blood tests were conducted immediately after hospitalization to assess cell counts and inflammatory markers, oropharyngeal swabs were collected to identify common pathogens by qPCR and culture. After bronchoscopy, bronchoalveolar lavage fluid (BALF) samples were collected for further pathogen identification using standardized diagnostic tests and mNGS. Blood tests were normal in 3 of the 32 children. In 9 oropharyngeal swabs, bacterial pathogens were detected, in 5 of these Mycoplasma pneumoniae was detected. Adenovirus was detected in 5 BALF samples, using the Direct Immunofluorescence Assay (DFA). In 15 cases, no common pathogens were found in BALF samples, using the current standard diagnostic tests, while in all 32 BALFs, pathogens were identified using mNGS, including adenovirus, Mycoplasma pneumoniae, Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, cytomegalovirus and bocavirus. This study shows that, with mNGS, the sensitivity of detection of the causative pathogens in children with severe nonresponding pneumonia is significantly improved. In addition, mNGS gives more strain specific information, helps to identify new pathogens and could potentially help to trace and control outbreaks. In this study, we have shown that it is possible to have the results within 24 hours, making the application of mNGS feasible for clinical diagnostics.

RevDate: 2020-06-04

Zhang Q, Yu K, Li S, et al (2020)

gutMEGA: a database of the human gut MEtaGenome Atlas.

Briefings in bioinformatics pii:5851266 [Epub ahead of print].

The gut microbiota plays important roles in human health through regulating both physiological homeostasis and disease emergence. The accumulation of metagenomic sequencing studies enables us to better understand the temporal and spatial variations of the gut microbiota under different physiological and pathological conditions. However, it is inconvenient for scientists to query and retrieve published data; thus, a comprehensive resource for the quantitative gut metagenome is urgently needed. In this study, we developed gut MEtaGenome Atlas (gutMEGA), a well-annotated comprehensive database, to curate and host published quantitative gut microbiota datasets from Homo sapiens. By carefully curating the gut microbiota composition, phenotypes and experimental information, gutMEGA finally integrated 59 132 quantification events for 6457 taxa at seven different levels (kingdom, phylum, class, order, family, genus and species) under 776 conditions. Moreover, with various browsing and search functions, gutMEGA provides a fast and simple way for users to obtain the relative abundances of intestinal microbes among phenotypes. Overall, gutMEGA is a convenient and comprehensive resource for gut metagenome research, which can be freely accessed at http://gutmega.omicsbio.info.

RevDate: 2020-06-04

Rodriguez-R LM, Tsementzi D, Luo C, et al (2020)

Iterative Subtractive Binning of Freshwater Chronoseries Metagenomes Identifies over 400 Novel Species and their Ecologic Preferences.

Environmental microbiology [Epub ahead of print].

Recent advances in sequencing technology and bioinformatic pipelines have allowed unprecedented access to the genomes of yet-uncultivated microorganisms from diverse environments. However, the catalogue of freshwater genomes remains limited, and most genome recovery attempts in freshwater ecosystems have only targeted specific taxa. Here, we present a genome recovery pipeline incorporating iterative subtractive binning, and apply it to a time series of 100 metagenomic datasets from seven connected lakes and estuaries along the Chattahoochee River (Southeastern USA). Our set of Metagenome-Assembled Genomes (MAGs) represents >400 yet-unnamed genomospecies, substantially increasing the number of high-quality MAGs from freshwater lakes. We propose names for two novel species: 'Candidatus Elulimicrobium humile' ('Ca. Elulimicrobiota', 'Patescibacteria') and 'Candidatus Aquidulcis frankliniae' ('Chloroflexi'). Collectively, our MAGs represented about half of the total microbial community at any sampling point. To evaluate the prevalence of these genomospecies in the chronoseries, we introduce methodologies to estimate relative abundance and habitat preference that control for uneven genome quality and sample representation. We demonstrate high degrees of habitat-specialization and endemicity for most genomospecies in the Chattahoochee lakes. Wider ecological ranges characterized smaller genomes with higher coding densities, indicating an overall advantage of smaller, more compact genomes for cosmopolitan distributions. This article is protected by copyright. All rights reserved.

RevDate: 2020-06-04

Fishman JA (2020)

Prevention of infection in xenotransplantation: Designated pathogen-free swine in the safety equation.

Xenotransplantation [Epub ahead of print].

Post-transplantation infections are common. In immunosuppressed human xenograft recipients, infection is most likely to be due to the same pathogens seen in human allotransplantation. However, organisms derived from swine and transmitted with xenografts have the potential to cause novel infections in xenograft recipients. The specific organisms likely to cause infection or "xenosis" are unknown but are postulated to be like those causing infection in allograft recipients. On this basis, theoretical exclusion criteria have been developed to guide the development of source animal herds. Herds developed based on the exclusion of potential human pathogens have been termed "designated pathogen-free" (DPF). Lists of potential pathogens will require revision with changing epidemiology of infection in swine worldwide and clinical experience. Development of new microbiological assays is required both for animal screening and in clinical diagnosis should infections occur. Genetic modifications of swine have the potential to eliminate certain infectious agents such as the porcine endogenous retrovirus; infectious complications of such modifications have not been observed. Unexpected, off target effects of genetic modifications require further study. Monitoring for infection in asymptomatic recipients is important to define infectious risks which are unknown in the absence of clinical trials data. Advanced microbiological techniques may be applied to diagnose and prevent infection in xenograft recipients.

RevDate: 2020-06-04

Emiola A, Zhou W, J Oh (2020)

Metagenomic growth rate inferences of strains in situ.

Science advances, 6(17):eaaz2299 pii:aaz2299.

We developed a method for strain-level metagenomic estimation of growth rate (SMEG) for inferring growth rates of bacterial subspecies, or strains, from complex metagenomic samples. We applied our method, which is based on both reference strains and de novo approaches, to different gut metagenomic datasets, accurately identifying an outbreak-associated Escherichia coli strain and a previously unidentified association of an Akkermansia muciniphila strain in cancer immunotherapy responders. SMEG resolves strain-specific growth rates from mixtures of commensal or pathogenic strains to provide new insights into microbial interactions and disease associations at the strain level. SMEG is available for download at https://github.com/ohlab/SMEG.

RevDate: 2020-06-04

Zhao Z, Baltar F, GJ Herndl (2020)

Linking extracellular enzymes to phylogeny indicates a predominantly particle-associated lifestyle of deep-sea prokaryotes.

Science advances, 6(16):eaaz4354 pii:aaz4354.

Heterotrophic prokaryotes express extracellular hydrolytic enzymes to cleave large organic molecules before taking up the hydrolyzed products. According to foraging theory, extracellular enzymes should be cell associated in dilute systems such as deep sea habitats, but secreted into the surrounding medium in diffusion-limited systems. However, extracellular enzymes in the deep sea are found mainly dissolved in ambient water rather than cell associated. In order to resolve this paradox, we conducted a global survey of peptidases and carbohydrate-active enzymes (CAZymes), two key enzyme groups initiating organic matter assimilation, in an integrated metagenomics, metatranscriptomics, and metaproteomics approach. The abundance, percentage, and diversity of genes encoding secretory processes, i.e., dissolved enzymes, consistently increased from epipelagic to bathypelagic waters, indicating that organic matter cleavage, and hence prokaryotic metabolism, is mediated mainly by particle-associated prokaryotes releasing their extracellular enzymes into diffusion-limited particles in the bathypelagic realm.

RevDate: 2020-06-04

Carrión O, Gibson L, Elias DMO, et al (2020)

Diversity of isoprene-degrading bacteria in phyllosphere and soil communities from a high isoprene-emitting environment: a Malaysian oil palm plantation.

Microbiome, 8(1):81 pii:10.1186/s40168-020-00860-7.

BACKGROUND: Isoprene is the most abundantly produced biogenic volatile organic compound (BVOC) on Earth, with annual global emissions almost equal to those of methane. Despite its importance in atmospheric chemistry and climate, little is known about the biological degradation of isoprene in the environment. The largest source of isoprene is terrestrial plants, and oil palms, the cultivation of which is expanding rapidly, are among the highest isoprene-producing trees.

RESULTS: DNA stable isotope probing (DNA-SIP) to study the microbial isoprene-degrading community associated with oil palm trees revealed novel genera of isoprene-utilising bacteria including Novosphingobium, Pelomonas, Rhodoblastus, Sphingomonas and Zoogloea in both oil palm soils and on leaves. Amplicon sequencing of isoA genes, which encode the α-subunit of the isoprene monooxygenase (IsoMO), a key enzyme in isoprene metabolism, confirmed that oil palm trees harbour a novel diversity of isoA sequences. In addition, metagenome-assembled genomes (MAGs) were reconstructed from oil palm soil and leaf metagenomes and putative isoprene degradation genes were identified. Analysis of unenriched metagenomes showed that isoA-containing bacteria are more abundant in soils than in the oil palm phyllosphere.

CONCLUSION: This study greatly expands the known diversity of bacteria that can metabolise isoprene and contributes to a better understanding of the biological degradation of this important but neglected climate-active gas. Video abstract.

RevDate: 2020-06-04

Yang YJ, Chen PC, Lai FP, et al (2020)

Probiotics-Containing Yogurt Ingestion and H. pylori Eradication Can Restore Fecal Faecalibacterium prausnitzii Dysbiosis in H. pylori-Infected Children.

Biomedicines, 8(6): pii:biomedicines8060146.

This study investigated the compositional differences in fecal microbiota between children with and without H. pylori infection and tested whether probiotics-containing yogurt and bacterial eradication improve H. pylori-related dysbiosis. Ten H. pylori-infected children and 10 controls ingested probiotics-containing yogurt for 4 weeks. Ten-day triple therapy plus yogurt was given to the infected children on the 4th week. Fecal samples were collected at enrollment, after yogurt ingestion, and 4 weeks after successful H. pylori eradication for cytokines and microbiota analysis using ELISA and metagenomic sequencing of the V4 region of the 16S rRNA gene, respectively. The results showed H. pylori-infected children had significantly higher levels of fecal TGF-β1 than those who were not infected. Eight of 295 significantly altered OTUs in the H. pylori-infected children were identified. Among them, the abundance of F. prausnitzii was significantly lower in the H. pylori-infected children, and then increased after yogurt ingestion and successful bacterial eradication. We further confirmed probiotics promoted F. prausnitzii growth in vitro and in ex vivo using real-time PCR. Moreover, F. prausnitzii supernatant significantly ameliorated lipopolysaccharide-induced IL-8 in HT-29 cells. In conclusions, Probiotics-containing yogurt ingestion and H. pylori eradication can restore the decrease of fecal F. prausnitzii in H. pylori-infected children.

RevDate: 2020-06-04

Haudum C, Lindheim L, Ascani A, et al (2020)

Impact of Short-Term Isoflavone Intervention in Polycystic Ovary Syndrome (PCOS) Patients on Microbiota Composition and Metagenomics.

Nutrients, 12(6): pii:nu12061622.

BACKGROUND: Polycystic ovary syndrome (PCOS) affects 5-20% of women of reproductive age worldwide and is associated with disorders of glucose metabolism. Hormone and metabolic signaling may be influenced by phytoestrogens, such as isoflavones. Their endocrine effects may modify symptom penetrance in PCOS. Equol is one of the most active isoflavone metabolites, produced by intestinal bacteria, and acts as a selective estrogen receptor modulator.

METHOD: In this interventional study of clinical and biochemical characterization, urine isoflavone levels were measured in PCOS and control women before and three days after a defined isoflavone intervention via soy milk. In this interventional study, bacterial equol production was evaluated using the log(equol: daidzein ratio) and microbiome, metabolic, and predicted metagenome analyses were performed.

RESULTS: After isoflavone intervention, predicted stool metagenomic pathways, microbial alpha diversity, and glucose homeostasis in PCOS improved resembling the profile of the control group at baseline. In the whole cohort, larger equol production was associated with lower androgen as well as fertility markers.

CONCLUSION: The dynamics in our metabolic, microbiome, and predicted metagenomic profiles underline the importance of external phytohormones on PCOS characteristics and a potential therapeutic approach or prebiotic in the future.

RevDate: 2020-05-20
CmpDate: 2020-05-20

Collevatti RG, Novaes E, Silva-Junior OB, et al (2019)

A genome-wide scan shows evidence for local adaptation in a widespread keystone Neotropical forest tree.

Heredity, 123(2):117-137.

The role of natural selection in shaping patterns of diversity is still poorly understood in the Neotropics. We carried out the first genome-wide population genomics study in a Neotropical tree, Handroanthus impetiginosus (Bignoniaceae), sampling 75,838 SNPs by sequence capture in 128 individuals across 13 populations. We found evidences for local adaptation using Bayesian correlations of allele frequency and environmental variables (32 loci in 27 genes) complemented by an analysis of selective sweeps and genetic hitchhiking events using SweepFinder2 (81 loci in 47 genes). Fifteen genes were identified by both approaches. By accounting for population genetic structure, we also found 14 loci with selection signal in a STRUCTURE-defined lineage comprising individuals from five populations, using Outflank. All approaches pinpointed highly diverse and structurally conserved genes affecting plant development and primary metabolic processes. Spatial interpolation forecasted differences in the expected allele frequencies at loci under selection over time, suggesting that H. impetiginosus may track its habitat during climate changes. However, local adaptation through natural selection may also take place, allowing species persistence due to niche evolution. A high genetic differentiation was seen among the H. impetiginosus populations, which, together with the limited power of the experiment, constrains the improved detection of other types of soft selective forces, such as background, balanced, and purifying selection. Small differences in allele frequency distribution among widespread populations and the low number of loci with detectable adaptive sweeps advocate for a polygenic model of adaptation involving a potentially large number of small genome-wide effects.

RevDate: 2020-06-03

Shi Z, Liu C, Yang H, et al (2020)

Fur Seal Feces-Associated Circular DNA Virus Identified in Pigs in Anhui, China.

Virologica Sinica pii:10.1007/s12250-020-00232-3 [Epub ahead of print].

Fur seal feces-associated circular DNA virus (FSfaCV) is an unclassified circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA virus that has been detected in mammals (fur seals and pigs). The biology and epidemiology of the virus remain largely unknown. To investigate the virus diversity among pigs in Anhui Province, China, we pooled 600 nasal samples in 2017 and detected viruses using viral metagenomic methods. From the assembled contigs, 12 showed notably high nucleotide acid sequence similarities to the genome sequences of FSfaCVs. Based on these sequences, a full-length genome sequence of the virus was then obtained using overlapping PCR and sequencing, and the virus was designated as FSfaCV-CHN (GenBank No. MK462122). This virus shared 91.3% and 90.9% genome-wide nucleotide sequence similarities with the New Zealand fur seal strain FSfaCV-as50 and the Japanese pig strain FSfaCV-JPN1, respectively. It also clustered with the two previously identified FSfaCVs in a unique branch in the phylogenetic tree based on the open reading frame 2 (ORF2), Rep-coding gene, and the genome of the reference CRESS DNA viruses. Further epidemiological investigation using samples collected in 2018 showed that the overall positive rate for the virus was 56.4% (111/197) in Anhui Province. This is the first report of FSfaCVs identified in pigs in China, and further epidemiological studies are warranted to evaluate the influence of the virus on pigs.

RevDate: 2020-06-03

Tan SC, Chong CW, Yap IKS, et al (2020)

Comparative assessment of faecal microbial composition and metabonome of swine, farmers and human control.

Scientific reports, 10(1):8997 pii:10.1038/s41598-020-65891-4.

The gastrointestinal tract of humans and swine consist of a wide range of bacteria which interact with hosts metabolism. Due to the differences in co-evolution and co-adaptation, a large fraction of the gut microbiome is host-specific. In this study, we evaluated the effect of close human-animal interaction to the faecal metagenome and metabonome of swine, farmer and human control. Three distinct clusters were observed based on T-RFLP-derived faecal microbial composition. However, 16S-inferred faecal microbiota and metabolic profiles showed that only human control was significantly different from the swine (P < 0.05). The metabonome of farmers and human controls were highly similar. Notably, higher trimethylamine N-oxide (TMAO) and butyrate were detected in human control and swine, respectively. The relative abundance of TMAO was positively correlated with Prevotella copri. Overall, we compared and established the relationship between the metabolites and microbiota composition of swine, farmers and human control. Based on the data obtained, we deduced that long term occupational exposure to swine and farm environment had affected the gut bacterial composition of farmers. Nonetheless, the effect was less prominent in the metabolite profiles, suggesting the gut bacteria expressed high functional plasticity and are therefore resilience to the level of community shift detected.

RevDate: 2020-06-03

Ma S, Qin J, Hao Y, et al (2020)

Association of gut microbiota composition and function with an aged rat model of senile osteoporosis using 16S rRNA and metagenomic sequencing analysis.

Aging, 12: pii:103293 [Epub ahead of print].

Recently, more interest has been paid to the association between bone mass and gut microecological dysbiosis. The results of clinical studies comparing gut microbiota (GM) in osteoporosis patients have been inconsistent due to different inclusion and exclusion criteria. To date, the association between the GM and senile osteoporosis remains poorly understood. Here, we utilized an aged rat model (22 months old) of senile osteoporosis to study the association of the composition and function of the GM with osteoporosis by 16S rRNA and metagenomic sequencing. The results showed that there was a significant reduction in alpha diversity and the F/B (Firmicutes/Bacteroidetes) ratio in aged rats. At the genus level, the enrichment of Helicobacter was potentially related to osteoporosis as a risk factor. Metagenomics results based on two databases indicated that shifts in the GM contribute to senile osteoporosis through metabolic pathways and subsequent immune disorders. In conclusion, our study reveals the association of gut microbiota composition and function with senile osteoporosis in an aged rat model in a brand new way, and variations in the GM might contribute to senile osteoporosis through metabolic pathways.

RevDate: 2020-06-03

Sánchez-Reyes A, Bretón-Deval L, Mangelson H, et al (2020)

Draft genome sequence of "Candidatus Afipia apatlaquensis" sp. nov., IBT-C3, a potential strain for decolorization of textile dyes.

BMC research notes, 13(1):265 pii:10.1186/s13104-020-05117-y.

OBJECTIVES: In order to characterize a river-associated, enriched microbiome capable of degrading an anthraquinone dye from the oil blue family, as well as assessing its functional potential, we performed a taxa-specific metagenomic deconvolution analysis based on contact probability maps at the chromosomal level. This study will allow associating the genomic content of "Candidatus Afipia apatlaquensis" strain IBT-C3 with its phenotypic potential in the context of bioremediation of textile dyes. We anticipate that this resource will be very useful in comparative genomic clinical studies, contributing to understanding the genomic basis of Afipia pathogenicity.

DATA DESCRIPTION: Here, we report the first draft genome sequence of "Candidatus Afipia apatlaquensis" sp. nov., strain IBT-C3, obtained by deconvolution of a textile-dye degrader microbiome in Mexico. The genome composite was deconvoluted using a Hi-C proximity ligation method. Whole-genome-based comparisons and phylogenomics reconstruction indicate that strain IBT-C3 represents a new species of the genus Afipia. The assembly completeness was 92.5% with 5,604,749 bp in length and 60.72% G+C content. The genome complement of IBT-C3 suggests a functional potential for decolorization of textile dyes, contrasting with previous reports of Afipia genus focused on its pathogenic potential.

RevDate: 2020-06-03

Ierardi E, Losurdo G, Mileti A, et al (2020)

The Puzzle of Coccoid Forms of Helicobacter pylori: Beyond Basic Science.

Antibiotics (Basel, Switzerland), 9(6): pii:antibiotics9060293.

Helicobacter pylori (H. pylori) may enter a non-replicative, non-culturable, low metabolically active state, the so-called coccoid form, to survive in extreme environmental conditions. Since coccoid forms are not susceptible to antibiotics, they could represent a cause of therapy failure even in the absence of antibiotic resistance, i.e., relapse within one year. Furthermore, coccoid forms may colonize and infect the gastric mucosa in animal models and induce specific antibodies in animals and humans. Their detection is hard, since they are not culturable. Techniques, such as electron microscopy, polymerase chain reaction, loop-mediated isothermal amplification, flow cytometry and metagenomics, are promising even if current evidence is limited. Among the options for the treatment, some strategies have been suggested, such as a very high proton pump inhibitor dose, high-dose dual therapy, N-acetycysteine, linolenic acid and vonoprazan. These clinical, diagnostic and therapeutic uncertainties will represent fascinating challenges in the future.

RevDate: 2020-06-03

Koike Y, Kuwatsuka S, Nishimoto K, et al (2020)

Skin Mycobiome of Psoriasis Patients is Retained during Treatment with TNF and IL-17 Inhibitors.

International journal of molecular sciences, 21(11): pii:ijms21113892.

BACKGROUND: Biological treatment relieves refractory skin lesions in patients with psoriasis; however, changes in the fungal microbiome (the mycobiome) on the skin are unclear.

METHODS: The skin mycobiome of psoriasis patients treated with TNF inhibitors (TNFi, n = 5) and IL-17 inhibitors (IL-17i, n = 7) was compared with that of patients not receiving systemic therapy (n = 7). Skin swab samples were collected from non-lesional post-auricular areas. Fungal DNA was sequenced by ITS1 metagenomic analysis and taxonomic classification was performed.

RESULTS: An average of 37543 reads/sample were analyzed and fungi belonging to 31 genera were detected. The genus Malassezia accounted for >90% of reads in 7/7 samples from the no-therapy group, 4/5 from the TNFi group, and 5/7 from the IL-17i group. Biodiversity was low in those three groups. Few members of the genus trichophyton were detected; the genus Candida was not detected at all. Among the Malassezia species, M. restricta was the major species in 6/7 samples from the no-therapy group, 4/5 from the TNFi group, and 5/7 from the IL-17i group whose the other largest species revealed M. globosa.

CONCLUSIONS: The mycobiome is retained on post-auricular skin during systemic treatment with TNF and IL-17 inhibitors.

RevDate: 2020-06-03
CmpDate: 2020-06-03

Sun F, Wang C, Chen L, et al (2020)

The intestinal bacterial community of healthy and diseased animals and its association with the aquaculture environment.

Applied microbiology and biotechnology, 104(2):775-783.

Although increasing levels of attention have been targeted towards aquaculture-associated bacteria, the bacterial community of animal intestines and its relationship with the aquaculture environment need to be further investigated. In this study, we used high-throughput sequencing to analyze the bacterial community of pond water, sediment, and the intestines of diseased and healthy animals. Our data showed that Proteobacteria, Firmicutes, Cyanobacteria, and Bacteroidetes were the dominant taxa of bacteria across all samples and accounted for more than 90% of the total sequence. Difference analysis and Venn diagrams showed that most of the intestinal bacterial OTUs (operational taxonomic units) of diseased and healthy animals were the same as those of sediment and water, indicating that the aquaculture environment was the main source of intestinal bacteria. Compared with healthy animals, a considerable reduction of OTUs was evident in diseased animals. Welch's t test showed that the dominant bacterial taxa in sediment, water, and animal intestine were significantly different (p < 0.05) and each had its own unique dominant microorganisms. In addition, differences between the intestinal bacteria of healthy and diseased animals were represented by potential probiotics and pathogens, such as Bacillus, Vibrio, Oceanobacillus, and Lactococcus. Principal component analysis (PcoA) showed that a similar environment shaped a similar microbial structure. There was a large difference in the spectrum of intestinal bacteria in diseased animals; furthermore, the spectrum of intestinal bacteria in diseased animals was very different from the environment than in healthy animals. This study provides a theoretical basis for a relationship between the intestinal bacteria of healthy and diseased animals and the environment and provides guidance for environmental regulation and disease prevention in aquaculture areas.

RevDate: 2020-06-02

Wang MX, Lin L, Chen YD, et al (2020)

Evodiamine has therapeutic efficacy in ulcerative colitis by increasing Lactobacillus acidophilus levels and acetate production.

Pharmacological research pii:S1043-6618(20)31286-X [Epub ahead of print].

Emerging evidence implicates gut microbiota have an important role in ulcerative colitis (UC). Previous study indicated that Evodiamine (EVO) can alleviate colitis through downregulating inflammatory pathways. However, specific relationship between EVO-treated colitis relief and regulation of gut microbiota is still unclear. Here, our goal was to determine the potential role of gut microbiota in the relief of UC by EVO. By using pathology-related indicators, 16S rRNA sequencing and metabolomics profiling, we assessed the pharmacological effect of EVO on dextran sulfate sodium (DSS)-induced colitis rats as well as on the change of gut microbiota and metabolism. Fecal derived from EVO-treated rats was transplanted into colitis rats to verify the effect of EVO on gut microbiota, and 'driver bacteria' was found and validated by 16S rRNA sequencing, metagenome and qRT-PCR. The effect of Lactobacillus acidophilus (L. acidophilus) was investigated by vivo experiment, microbiota analysis, Short-chain fatty acids (SCFAs) quantification and colon transcriptomics. EVO reduced the susceptibility to DSS-induced destruction of epithelial integrity and severe inflammatory response, and regulated the gut microbiota and metabolites. Fecal Microbiota Transplantation (FMT) alleviated DSS-induced colitis, increased the abundance of L. acidophilus and the level of acetate. Furthermore, gavaged with L. acidophilus reduced pro-inflammatory cytokines, promoted the increase of goblet cells and the secretion of antimicrobial peptides, regulated the ratio of Firmicutes/Bacteroidetes and increased the level of acetate. Our results indicated that EVO mitigation of DSS-induced colitis is associated with increased in L. acidophilus and protective acetate production, which may be a promising strategy for treating UC.

RevDate: 2020-06-02

Ma S, Qin J, Hao Y, et al (2020)

Structural and functional changes of gut microbiota in ovariectomized rats and their correlations with altered bone mass.

Aging, 12: pii:103290 [Epub ahead of print].

As a critical factor involved in the maintenance of physiological homeostasis, the gut microbiota (GM) reportedly plays a key role in bone development. To date, the association between the GM and steroid deficiency-induced osteoporosis remains poorly understood. Forty female Sprague Dawley rats were divided into an ovariectomy (OVX) or control group. We performed 16S rRNA and metagenome sequencing, to compare diversity, taxonomic differences, and functional genes. The GM composition did not change in the control group and the number of operational taxonomic units increased significantly following ovariectomy. Alpha diversity, determined by ACE estimator, CHAO estimator, the Shannon index, and the Simpson index showed an increasing trend after ovariectomy. Samples in the OVX group were well clustered both pre- and post-ovariectomy, as demonstrated by principal coordinate 1 (PC1) and PC2. Functional genes of GM, including those involved in synthesis and metabolism of carbohydrates and nucleotides, microbial structure, and heme, as well as hemin uptake and utilization, increased at the early stage of osteoporosis. We observed that Ruminococcus flavefaciens exhibited the greatest variation in abundance among the GM and this was also associated with osteoclastic indicators and the estrobolome. Specific changes in fecal microbiota are associated with the pathogenesis of steroid deficiency-induced osteoporosis.

RevDate: 2020-06-02

Douglas GM, Maffei VJ, Zaneveld JR, et al (2020)

PICRUSt2 for prediction of metagenome functions.

RevDate: 2020-06-02

Geng S, Fu W, Chen W, et al (2020)

Effects of an external magnetic field on microbial functional genes and metabolism of activated sludge based on metagenomic sequencing.

Scientific reports, 10(1):8818 pii:10.1038/s41598-020-65795-3.

This study explored the effect of 70-mT magnetic field on wastewater treatment capacity for activated sludge in long-term laboratory-scale experiments. Metagenomic sequencing were conducted based on Illumina HiSeq 2000 platform after DNA extraction of the activated sludge. Then the effect of the magnetic field on the microbial unigene and metabolic pathways in activated sludge was investigated. As a result, higher pollutant removal was observed at 70 mT, with which the elimination of total nitrogen (TN) was the most effective. Functional genes annotated based on eggNOG database showed that unigenes related to information storage and processing were enhanced by the magnetic field. For CAZy classification, category such as glycosyl transferases was more abundant in the reactor with magnetic field, which has been shown to promote the entire energy supply pathway. Additionally, in the KEGG categories, unigenes related to signaling molecules and interaction were significantly inhibited. Through the enrichment analysis of the nitrogen metabolism pathway, the magnetic field inhibited anabolic nitrate reduction by significantly inhibiting enzymes such as [EC:1.7.7.2], [EC:1.7.7.1], [EC:3.5.5.1], [EC:1.4.1.2] and [EC:4.2.1.1], which are related to the improvement of the denitrification ability. This study can provide insight for future research on the response mechanism of activated sludge to magnetic fields.

RevDate: 2020-06-02

Roach TNF, Little M, Arts MGI, et al (2020)

A multiomic analysis of in situ coral-turf algal interactions.

Proceedings of the National Academy of Sciences of the United States of America pii:1915455117 [Epub ahead of print].

Viruses, microbes, and host macroorganisms form ecological units called holobionts. Here, a combination of metagenomic sequencing, metabolomic profiling, and epifluorescence microscopy was used to investigate how the different components of the holobiont including bacteria, viruses, and their associated metabolites mediate ecological interactions between corals and turf algae. The data demonstrate that there was a microbial assemblage unique to the coral-turf algae interface displaying higher microbial abundances and larger microbial cells. This was consistent with previous studies showing that turf algae exudates feed interface and coral-associated microbial communities, often at the detriment of the coral. Further supporting this hypothesis, when the metabolites were assigned a nominal oxidation state of carbon (NOSC), we found that the turf algal metabolites were significantly more reduced (i.e., have higher potential energy) compared to the corals and interfaces. The algae feeding hypothesis was further supported when the ecological outcomes of interactions (e.g., whether coral was winning or losing) were considered. For example, coral holobionts losing the competition with turf algae had higher Bacteroidetes-to-Firmicutes ratios and an elevated abundance of genes involved in bacterial growth and division. These changes were similar to trends observed in the obese human gut microbiome, where overfeeding of the microbiome creates a dysbiosis detrimental to the long-term health of the metazoan host. Together these results show that there are specific biogeochemical changes at coral-turf algal interfaces that predict the competitive outcomes between holobionts and are consistent with algal exudates feeding coral-associated microbes.

RevDate: 2020-06-02

Chu W, Han Q, Xu J, et al (2020)

Metagenomic analysis identified microbiome alterations and pathological association between intestinal microbiota and polycystic ovary syndrome.

Fertility and sterility, 113(6):1286-1298.e4.

OBJECTIVE: To identify different microbial species in women with polycystic ovary syndrome (PCOS) and reveal a possible relationship between gut dysbiosis and pathological changes.

DESIGN: Cross-sectional study.

SETTING: Academic institution.

PATIENT(S): Reproductive-aged women with PCOS (n = 14) and controls (n = 14) from the Centre for Reproductive Medicine.

INTERVENTION(S): Shotgun metagenomic sequencing on fecal samples from patients, and clinical parameters (including body mass index, endocrine hormone levels, and glycemia level) gathered for correlation analysis.

MAIN OUTCOME MEASURE(S): Identification of different gut microbial strains and relativity between microbiota and clinical parameters.

RESULT(S): We found several microbial strains were statistically significantly more abundant in the PCOS group, including Parabacteroides merdae, Bacteroides fragilis, and strains of Escherichia and Shigella, whereas Faecalibacterium prausnitzii was enriched in the control group. Metagenomic species (MGS) analysis revealed that the microbes of the PCOS group were negatively correlated with those of the control group. Of note, we observed a positive correlation between MGS relevant to PCOS and endocrine disorders, including body mass index and elevated levels of serum testosterone, luteinizing hormone, and antimüllerian hormone. Functional alterations, reflected by Kyoto Encyclopedia of Genes and Genomes orthologues, could imply potential mechanisms of microbial involvement in the developmental progress of PCOS.

CONCLUSION(S): Our findings suggest an intimate association and potential mechanisms linking microbial dysbiosis and the pathophysiologic changes of PCOS. We address the importance of monitoring and modulating microbial composition and functional shifts in future clinical practice.

RevDate: 2020-06-02

Zhong H, Lehtovirta-Morley L, Liu J, et al (2020)

Novel insights into the Thaumarchaeota in the deepest oceans: their metabolism and potential adaptation mechanisms.

Microbiome, 8(1):78 pii:10.1186/s40168-020-00849-2.

BACKGROUND: Marine Group I (MGI) Thaumarchaeota, which play key roles in the global biogeochemical cycling of nitrogen and carbon (ammonia oxidizers), thrive in the aphotic deep sea with massive populations. Recent studies have revealed that MGI Thaumarchaeota were present in the deepest part of oceans-the hadal zone (depth > 6000 m, consisting almost entirely of trenches), with the predominant phylotype being distinct from that in the "shallower" deep sea. However, little is known about the metabolism and distribution of these ammonia oxidizers in the hadal water.

RESULTS: In this study, metagenomic data were obtained from 0-10,500 m deep seawater samples from the Mariana Trench. The distribution patterns of Thaumarchaeota derived from metagenomics and 16S rRNA gene sequencing were in line with that reported in previous studies: abundance of Thaumarchaeota peaked in bathypelagic zone (depth 1000-4000 m) and the predominant clade shifted in the hadal zone. Several metagenome-assembled thaumarchaeotal genomes were recovered, including a near-complete one representing the dominant hadal phylotype of MGI. Using comparative genomics, we predict that unexpected genes involved in bioenergetics, including two distinct ATP synthase genes (predicted to be coupled with H+ and Na+ respectively), and genes horizontally transferred from other extremophiles, such as those encoding putative di-myo-inositol-phosphate (DIP) synthases, might significantly contribute to the success of this hadal clade under the extreme condition. We also found that hadal MGI have the genetic potential to import a far higher range of organic compounds than their shallower water counterparts. Despite this trait, hadal MDI ammonia oxidation and carbon fixation genes are highly transcribed providing evidence they are likely autotrophic, contributing to the primary production in the aphotic deep sea.

CONCLUSIONS: Our study reveals potentially novel adaptation mechanisms of deep-sea thaumarchaeotal clades and suggests key functions of deep-sea Thaumarchaeota in carbon and nitrogen cycling. Video Abstract.

RevDate: 2020-06-02

Cao S, Zhang W, Ding W, et al (2020)

Correction to: Structure and function of the Arctic and Antarctic marine microbiota as revealed by metagenomics.

Microbiome, 8(1):77 pii:10.1186/s40168-020-00871-4.

An amendment to this paper has been published and can be accessed via the original article.

RevDate: 2020-06-02

Moon K, Jeon JH, Kang I, et al (2020)

Freshwater viral metagenome reveals novel and functional phage-borne antibiotic resistance genes.

Microbiome, 8(1):75 pii:10.1186/s40168-020-00863-4.

BACKGROUND: Antibiotic resistance developed by bacteria is a significant threat to global health. Antibiotic resistance genes (ARGs) spread across different bacterial populations through multiple dissemination routes, including horizontal gene transfer mediated by bacteriophages. ARGs carried by bacteriophages are considered especially threatening due to their prolonged persistence in the environment, fast replication rates, and ability to infect diverse bacterial hosts. Several studies employing qPCR and viral metagenomics have shown that viral fraction and viral sequence reads in clinical and environmental samples carry many ARGs. However, only a few ARGs have been found in viral contigs assembled from metagenome reads, with most of these genes lacking effective antibiotic resistance phenotypes. Owing to the wide application of viral metagenomics, nevertheless, different classes of ARGs are being continuously found in viral metagenomes acquired from diverse environments. As such, the presence and functionality of ARGs encoded by bacteriophages remain up for debate.

RESULTS: We evaluated ARGs excavated from viral contigs recovered from urban surface water viral metagenome data. In virome reads and contigs, diverse ARGs, including polymyxin resistance genes, multidrug efflux proteins, and β-lactamases, were identified. In particular, when a lenient threshold of e value of ≤ 1 × e-5 and query coverage of ≥ 60% were employed in the Resfams database, the novel β-lactamases blaHRV-1 and blaHRVM-1 were found. These genes had unique sequences, forming distinct clades of class A and subclass B3 β-lactamases, respectively. Minimum inhibitory concentration analyses for E. coli strains harboring blaHRV-1 and blaHRVM-1 and catalytic kinetics of purified HRV-1 and HRVM-1 showed reduced susceptibility to penicillin, narrow- and extended-spectrum cephalosporins, and carbapenems. These genes were also found in bacterial metagenomes, indicating that they were harbored by actively infecting phages.

CONCLUSION: Our results showed that viruses in the environment carry as-yet-unreported functional ARGs, albeit in small quantities. We thereby suggest that environmental bacteriophages could be reservoirs of widely variable, unknown ARGs that could be disseminated via virus-host interactions. Video abstract.

RevDate: 2020-06-02

Costa OYA, de Hollander M, Pijl A, et al (2020)

Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer.

Microbiome, 8(1):76 pii:10.1186/s40168-020-00836-7.

BACKGROUND: Cultivation-independent methods, including metagenomics, are tools for the exploration and discovery of biotechnological compounds produced by microbes in natural environments. Glycoside hydrolases (GHs) enzymes are extremely desired and important in the industry of production for goods and biofuel and removal of problematic biofilms and exopolysaccharide (EPS). Biofilms and EPS are complex, requiring a wide range of enzymes for a complete degradation. The aim of this study was to identify potential GH microbial producers and GH genes with biotechnological potential, using EPS-complex structure (WH15EPS) of Acidobacteria Granulicella sp. strain WH15 as an enrichment factor, in cultivation-independent and cultivation-dependent methods. We performed stable isotope probing (SIP) combined with metagenomics on topsoil litter amended with WH15EPS and coupled solid culture-EPS amended medium with metagenomics.

RESULTS: SIP metagenome analysis of the soil litter demonstrated that phyla Proteobacteria, Actinobacteria, Acidobacteria, and Planctomycetes were the most abundant in WH15EPS amended and unamended treatments. The enrichment cultures in solid culture medium coupled to metagenomics demonstrated an enrichment in Proteobacteria, and the metagenome assembly of this enrichment cultures resulted in 4 metagenome-assembled genomes (MAGs) of microbes with low identity (42-86%) to known microorganisms. Among all carbohydrate-active enzymes (CAZymes) retrieved genes, glycoside transferase (GT) was the most abundant family, either in culture-independent or culture-based metagenome datasets. Within the glycoside hydrolases (GHs), GH13 was the most abundant family in both metagenome datasets. In the "heavy" fraction of the culture-independent metagenome SIP dataset, GH109 (α-N-acetylgalactosaminidases), GH117 (agarases), GH50 (agarases), GH32 (invertases and inulinases), GH17 (endoglucanases), and GH71 (mutanases) families were more abundant in comparison with the controls. Those GH families are affiliated to microorganism that are probably capable to degrade WH15EPS and potentially applicable for biofilm deconstruction. Subsequent in culture-based metagenome, the assembled 4 MAGs (unclassified Proteobacteria) also contained GH families of interest, involving mannosidases, lysozymes, galactosidases, and chitinases.

CONCLUSIONS: We demonstrated that functional diversity induced by the presence of WH15EPS in both culture-independent and culture-dependent approaches was enriched in GHs, such as amylases and endoglucanases that could be applied in chemical, pharmaceutical, and food industrial sectors. Furthermore, WH15EPS may be used for the investigation and isolation of yet unknown taxa, such as unclassified Proteobacteria and Planctomycetes, increasing the number of current cultured bacterial representatives with potential biotechnological traits. Video Abstract.

RevDate: 2020-06-02

Xue F, Wang Y, Zhao Y, et al (2020)

Ruminal Methanogenic Responses to the Thiamine Supplementation in High-Concentrate Diets.

Animals : an open access journal from MDPI, 10(6): pii:ani10060935.

BACKGROUND: Thiamine supplementation in high-concentrate diets (HC) was confirmed to attenuate ruminal subacute acidosis through promoting carbohydrate metabolism, however, whether thiamine supplementation in HC impacts methane metabolism is still unclear. Therefore, in the present study, thiamine was supplemented in the high-concentrate diets to investigate its effects on ruminal methanogens and methanogenesis process.

METHODS: an in vitro fermentation experiment which included three treatments: control diet (CON, concentrate/forage = 4:6; DM basis), high-concentrate diet (HC, concentrate/forage = 6:4; DM basis) and high-concentrate diet supplemented with thiamine (HCT, concentrate/forage = 6:4, DM basis; thiamine supplementation content = 180 mg/kg DM) was conducted. Each treatment concluded with four repeats, with three bottles in each repeat. The in vitro fermentation was sustained for 48h each time and repeated three times. At the end of fermentation, fermentable parameters, ruminal bacteria and methanogens community were measured.

RESULTS: HC significantly decreased ruminal pH, thiamine and acetate content, while significantly increasing propionate content compared with CON (p < 0.05). Conversely, thiamine supplementation significantly increased ruminal pH, acetate while significantly decreasing propionate content compared with HC treatment (p < 0.05). No significant difference of ruminal methanogens abundances among three treatments was observed. Thiamine supplementation significantly decreased methane production compared with CON, while no significant change was found in HCT compared with HC.

CONCLUSION: thiamine supplementation in the high-concentrate diet (HC) could efficiently reduce CH4 emissions compared with high-forage diets while without causing ruminal metabolic disorders compared with HC treatment. This study demonstrated that supplementation of proper thiamine in concentrate diets could be an effective nutritional strategy to decrease CH4 production in dairy cows.

RevDate: 2020-06-01

Wei Y, Wu Y, Zhang L, et al (2020)

Genome recovery and metatranscriptomic confirmation of functional acetate-oxidizing bacteria from enriched anaerobic biogas digesters.

Environmental pollution (Barking, Essex : 1987), 265(Pt B):114843 pii:S0269-7491(20)31337-3 [Epub ahead of print].

In many cases, it is difficult to isolate the key microbial organisms from their communities present in natural environments. Metagenomic methods can recover near-complete genomes of the dominant microbial organisms in communities, and metatrancriptomic data could further reveal important genes and pathways related to their functions. In this study, three draft genomes of Clostridium ultunense-like bacteria were recovered based on metagenomic analyses, which is an essential syntrophic acetate-oxidizing bacteria (SAOB) member for maintaining high methane production in high-ammonium biogas digesters but difficult to isolate from its syntrophic partners. Firstly, syntrophic acetate-oxidizing bacteria in a microbial community series were enriched from a biogas digester by adding sodium acetate in the medium. Global analyses of C. ultunense suggested that it would combine the pyruvate-serine-glycine pathway and part of the Wood-Ljungdahl pathway for syntrophic acetate oxidization. Moreover, metatranscriptomic analyses showed that all of the genes of the proposed syntrophic acetate-oxidizing pathway present in the genome were actively transcribed in the microbiota. The functional bacterial enrichment and refined assembly method identify rare microbial genome in complex natural microbiota, which help to recover the syntrophic acetate-oxidizing pathway in C. ultunense strains in this study.

RevDate: 2020-06-01

Asad F, Anwar H, Yassine HM, et al (2020)

White Button Mushroom, Agaricus bisporus (Agaricomycetes), and a Probiotics Mixture Supplementation Correct Dyslipidemia without Influencing the Colon Microbiome Profile in Hypercholesterolemic Rats.

International journal of medicinal mushrooms, 22(3):235-244.

Consumption of foods rich in dietary fiber has attracted considerable attention for lowering blood cholesterol and triglycerides through attenuation of gut microbiome. Diets rich in fiber may provide substrates for microbes to digest and proliferate. In response, products of microbial digestion enter systemic circulation and support host energy homeostasis. In the present study, rats with hypercholesterolemia (HC) were supplemented with probiotics (PB) and Agaricus bisporus mushroom to examine the antidyslipidemia effects. Forty adult rats were divided into five treatment groups. The rats in the control group were fed only a chow maintenance diet (CON; n = 8), whereas an atherogenic diet (chow diet supplemented with 1.5% cholesterol and 0.5% cholic acid) was offered to the remaining rats to induce hypercholesterolemia (HC group; n = 32). Rats developed HC following a 24-day continuous supplementation with the atherogenic diet. From day 25 onward, the HC group was further divided into HC-CON, HC-PB (supplemented with PB at 1 mg/rat/day), HC-AB (supplemented with A. bisporus at 5% of diet), and HC-AB.PB (supplemented with both A. bisporus and PB). After 6 weeks of supplementation, rats were killed to collect blood to determine serum lipid profile, oxidative stress, and for metagenomics analysis of colon contents. Results showed that all supplementations corrected HC-induced oxidative stress. Furthermore, A. bisporus supplementation corrected HC-induced dyslipidemia (P ≤ .05). Blautia and Bifidobacterium were the most dominant bacterial genera in HC-AB and HC-PB groups, respectively. Phylum Firmicutes and class Clostridia predominantly occupied the gut microbiome in all groups. However, no significant differences were observed in microbiome diversity and clustering patterns among study groups. In conclusion, supplementation of A. bisporus mushroom and probiotics can lower oxidative stress and dyslipidemia with partial effects on the phylogenetic makeup in the gut microbiome.

RevDate: 2020-06-01

Wang JP, Xu YC, Hou JQ, et al (2020)

Effects of Dietary Fat Profile on Gut Microbiota in Valproate Animal Model of Autism.

Frontiers in medicine, 7:151.

Autism spectrum disorder (ASD) is a developmental disability which may cause significant social, communication, and behavioral challenges. Besides certain essential symptoms, a lot of ASD individuals also suffer the comorbidity of gut microbiota dysbiosis, which possibly causes a variety of gastrointestinal (GI) difficulties. Interestingly, evidence has indicated that behavioral output may be modulated through the communication between the central nervous system and gut microbiota via the gut-brain axis. Polyunsaturated fatty acids (PUFAs) and n-3 fatty acids (n-3 PUFA) are structurally and functionally crucial components for the brain, and the state of n-3 PUFAs also affects the gut microbiota. However, how varying intake ratios of n-3/n6 PUFAs affect the gut microbiota composition in ASDs is not well-understood. Pregnant female Wistar rats with intraperitoneal administration of valproate acid (VPA) at embryonic day (E) 12.5 and their male offspring were grouped and fed three diets: a control chow (VPA group), omega-3 deficient (A group), and n-3/n6 (1:5) diet (B group). The diet of pregnant female Wistar rats with intraperitoneal administration of saline and their male offspring was a control chow (normal group). Microbial composition and species abundance were investigated accordingly by the 16S rRNA gene-based metagenomics analysis on the fecal samples. Results showed that fecal microbial abundance was decreased because of VPA administration in the period of pregnancy, and the changing pattern of gut microbiota was similar to that reported in ASD patients. Furthermore, the n-3/n6 (1:5) diet increased the fecal microbial abundance and decreased the elevated Firmicutes. In conclusion, n-3/n6 PUFAs (1:5) diet supplementation may alter gut microbiota composition in VPA-exposed rats. This study put forward a new strategy for the intervention and treatment of autism by n-3/n-6 PUFAs ratio supplementation intakes.

RevDate: 2020-06-01

Chen XY, Fan HN, Zhang HK, et al (2020)

Rewiring of Microbiota Networks in Erosive Inflammation of the Stomach and Small Bowel.

Frontiers in bioengineering and biotechnology, 8:299.

The development of non-invasive, inexpensive, and effective early diagnosis tests for gastric and small-bowel lesions is an urgent requirement. The introduction of magnetically guided capsule endoscopy (MGCE) has aided examination of the small bowel for diagnoses. However, the distribution of the fecal microbiome in abnormal erosions of the stomach and small bowel remains unclear. Herein, alternations in the fecal microbiome in three groups [normal, small-bowel inflammation, and chronic gastritis (CG)] were analyzed by metagenomics and our well-developed method [individual-specific edge-network analysis (iENA)]. In addition to the dominant microbiota identified by the conventional differential analysis, iENA could recognize novel network biomarkers of microbiome communities, such as the genus Bacteroide in CG and small-bowel inflammation. Combined with differential network analysis, the network-hub microbiota within rewired microbiota networks revealed high-ranked iENA microbiota markers, which were disease specific and had particular pathogenic functions. Our findings illuminate the components of the fecal microbiome and the importance of specific bacteria in CG and small-bowel erosions, and could be employed to develop preventive and non-invasive therapeutic strategies.

RevDate: 2020-06-01

Duan J, Meng X, Liu S, et al (2020)

Gut Microbiota Composition Associated With Clostridium difficile-Positive Diarrhea and C. difficile Type in ICU Patients.

Frontiers in cellular and infection microbiology, 10:190.

The gut microbiota composition of intensive care unit (ICU) patients suffering from Clostridium difficile-positive diarrhea (CDpD) is poorly understood. This prospective study aims to use 16S rDNA (and metagenome) sequencing to compare the microbiota composition of 58 (and 5) ICU patients with CDpD (CDpD group), 33 (and 4) ICU patients with C. difficile-negative diarrhea (CDnD group), and 21 (and 5) healthy control subjects (control group), as well as CDpD patients in the A+B+ (N = 34; A/B: C. difficile TcdA/B), A-B+ (N = 7), and A-B- (N = 17) subgroups. For 16S rDNA data, OTU clustering (tool: UPARSE), taxonomic assignment (tool: RDP classifier), α-diversity, and β-diversity analyses (tool: QIIME) were conducted. For metagenome data, metagenome assembly (tool: SOAPdenovo), gene calling (tools: MetaGeneMark, CD-HIT, and SoapAligner), unigene alignment (tool: DIAMOND), taxon difference analysis (tool: Metastats), and gene annotation (tool: DIAMOND) were performed. The microbial diversity of the CDpD group was lower than that of the CDnD and control groups. The abundances of 10 taxa (e.g., Deferribacteres, Cryptomycota, Acetothermia) were significantly higher in the CDpD group than in the CDnD group. The abundances of Saccharomycetes and Clostridia were significantly lower in CDpD in comparison with control. Some taxa were significantly different between the A+B+ and A-B- subgroups. CDpD might relate to a decrease in beneficial taxa (i.e., Saccharomycetes and Clostridia) and an increase in harmful taxa (e.g., Deferribacteres, Cryptomycota, Acetothermia) in gut microbiota of ICU patients. C. difficile toxin type might be slightly associated with gut microbiota composition.

RevDate: 2020-06-01

Wang Q, Wang K, Zhang Y, et al (2020)

Neonatal Ureaplasma parvum meningitis: a case report and literature review.

Translational pediatrics, 9(2):174-179.

Ureaplasma parvum (U. parvum) is common commensal in the female genitourinary tract. Despite U. parvum has been associated with chorioamnionitis, abortion, prematurity and perinatal complications, the invasive central nervous system (CNS) infection is rare in neonates. Diagnosis of U. parvum meningitis can be difficult for the atypical presentations and sterile cultures by conventional methods. Metagenomic next-generation sequencing (mNGS) could identify a broad range of human pathogens in a target-independent manner. Here, we performed mNGS to search for the infectious etiology in a term infant presenting with fever and seizure. U. parvum genome was identified by mNGS and further confirmed by PCR in the same cerebrospinal fluid (CSF) sample. As the quick and timely diagnosis, the baby was successfully treated with erythromycin for 4 weeks without complication. The clinical follow-up has showed that the physical and mental development are normal. In conclusion, mNGS may a promising diagnostic technology for U. parvum meningitis. As mNGS is able to identify diverse microbes in a single run, it could be a useful strategy to detection the clinical causative pathogens with atypical features in neonates.

RevDate: 2020-06-01

Sharma P, Rani J, Chauhan C, et al (2020)

Altered Gut Microbiota and Immunity Defines Plasmodium vivax Survival in Anopheles stephensi.

Frontiers in immunology, 11:609.

Blood-feeding enriched gut-microbiota boosts mosquitoes' anti-Plasmodium immunity. Here, we ask how Plasmodium vivax alters gut-microbiota, anti-Plasmodial immunity, and impacts tripartite Plasmodium-mosquito-microbiota interactions in the gut lumen. We used a metagenomics and RNAseq strategy to address these questions. In naïve mosquitoes, Elizabethkingia meningitis and Pseudomonas spp. are the dominant bacteria and blood-feeding leads to a heightened detection of Elizabethkingia, Pseudomonas and Serratia 16S rRNA. A parallel RNAseq analysis of blood-fed midguts also shows the presence of Elizabethkingia-related transcripts. After, P. vivax infected blood-meal, however, we do not detect bacterial 16S rRNA until circa 36 h. Intriguingly, the transcriptional expression of a selected array of antimicrobial arsenal cecropins 1-2, defensin-1, and gambicin remained low during the first 36 h-a time frame when ookinetes/early oocysts invaded the gut. We conclude during the preinvasive phase, P. vivax outcompetes midgut-microbiota. This microbial suppression likely negates the impact of mosquito immunity which in turn may enhance the survival of P. vivax. Detection of sequences matching to mosquito-associated Wolbachia opens a new inquiry for its exploration as an agent for "paratransgenesis-based" mosquito control.

RevDate: 2020-06-01

van Grinsven S, Sinninghe Damsté JS, Harrison J, et al (2020)

Impact of Electron Acceptor Availability on Methane-Influenced Microorganisms in an Enrichment Culture Obtained From a Stratified Lake.

Frontiers in microbiology, 11:715.

Methanotrophs are of major importance in limiting methane emissions from lakes. They are known to preferably inhabit the oxycline of stratified water columns, often assumed due to an intolerance to atmospheric oxygen concentrations, but little is known on the response of methanotrophs to different oxygen concentrations as well as their preference for different electron acceptors. In this study, we enriched a methanotroph of the Methylobacter genus from the oxycline and the anoxic water column of a stratified lake, which was also present in the oxic water column in the winter. We tested the response of this Methylobacter-dominated enrichment culture to different electron acceptors, i.e., oxygen, nitrate, sulfate, and humic substances, and found that, in contrast to earlier results with water column incubations, oxygen was the preferred electron acceptor, leading to methane oxidation rates of 45-72 pmol cell-1 day-1. Despite the general assumption of methanotrophs preferring microaerobic conditions, methane oxidation was most efficient under high oxygen concentrations (>600 μM). Low (<30 μM) oxygen concentrations still supported methane oxidation, but no methane oxidation was observed with trace oxygen concentrations (<9 μM) or under anoxic conditions. Remarkably, the presence of nitrate stimulated methane oxidation rates under oxic conditions, raising the methane oxidation rates by 50% when compared to oxic incubations with ammonium. Under anoxic conditions, no net methane consumption was observed; however, methanotroph abundances were two to three times higher in incubations with nitrate and sulfate compared to anoxic incubations with ammonium as the nitrogen source. Metagenomic sequencing revealed the absence of a complete denitrification pathway in the dominant methanotroph Methylobacter, but the most abundant methylotroph Methylotenera seemed capable of denitrification, which can possibly play a role in the enhanced methane oxidation rates under nitrate-rich conditions.

RevDate: 2020-06-01

Garcia MO, Templer PH, Sorensen PO, et al (2020)

Soil Microbes Trade-Off Biogeochemical Cycling for Stress Tolerance Traits in Response to Year-Round Climate Change.

Frontiers in microbiology, 11:616.

Winter air temperatures are rising faster than summer air temperatures in high-latitude forests, increasing the frequency of soil freeze/thaw events in winter. To determine how climate warming and soil freeze/thaw cycles affect soil microbial communities and the ecosystem processes they drive, we leveraged the Climate Change across Seasons Experiment (CCASE) at the Hubbard Brook Experimental Forest in the northeastern United States, where replicate field plots receive one of three climate treatments: warming (+5°C above ambient in the growing season), warming in the growing season + winter freeze/thaw cycles (+5°C above ambient +4 freeze/thaw cycles during winter), and no treatment. Soil samples were taken from plots at six time points throughout the growing season and subjected to amplicon (rDNA) and metagenome sequencing. We found that soil fungal and bacterial community composition were affected by changes in soil temperature, where the taxonomic composition of microbial communities shifted more with the combination of growing-season warming and increased frequency of soil freeze/thaw cycles in winter than with warming alone. Warming increased the relative abundance of brown rot fungi and plant pathogens but decreased that of arbuscular mycorrhizal fungi, all of which recovered under combined growing-season warming and soil freeze/thaw cycles in winter. The abundance of animal parasites increased significantly under combined warming and freeze/thaw cycles. We also found that warming and soil freeze/thaw cycles suppressed bacterial taxa with the genetic potential for carbon (i.e., cellulose) decomposition and soil nitrogen cycling, such as N fixation and the final steps of denitrification. These new soil communities had higher genetic capacity for stress tolerance and lower genetic capacity to grow or reproduce, relative to the communities exposed to warming in the growing season alone. Our observations suggest that initial suppression of biogeochemical cycling with year-round climate change may be linked to the emergence of taxa that trade-off growth for stress tolerance traits.

RevDate: 2020-06-01

Chun X, Zhao YS, Xin Y, et al (2020)

[Soil phosphorus forms and phosphorus solubilizing bacteria distribution after restoration from seriously burning in Greater Khingan Mountain areas, China].

Ying yong sheng tai xue bao = The journal of applied ecology, 31(2):388-398.

To understand the contents of various phosphorus forms, phosphorus solubilizing bacte-rial community structure and the relationship between them in soils after restoration from the seriously burning, we collected soil samples from artificial restoration (Pinus sylvestris var. mongolica plantation, Larix gmelinii plantation), artificial accelerated natural restoration (secondary forest) and natural restoration (natural secondary forest) stands in Greater Khingan Mountain area. Using methods of Sui et al. modified from Hedley phosphorus fractionation, we measured the contents of different phosphorus forms in rhizosphere soil and bulk soil (0-10, 10-20 cm). Abundances of phosphorus solubilizing bacteria were quantified by high-throughput sequencing method. The results showed that the contents of H2O-Pi, NaHCO3-Pi and NaHCO3-Poin 0-10 cm bulk soil and NaHCO3-Po in rhizosphere soil followed the order of L. gmelinii plantation : P. sylvestris var. mongolica plantation : natural secondary forest : secondary forest. The contents of H2O-Pi, NaHCO3-Pi, NaHCO3-Po in 10-20 cm bulk soil and H2O-Pi, NaHCO3-Pi in rhizosphere soil followed the order of L. gmelinii plantation : P. sylvestris var. mongolica plantation : secondary forest : natural secondary forest. The ratios of contents of H2O-Pi, NaHCO3-Pi and NaHCO3-Po in rhizosphere to those in bulk soil (R/S) were higher than 1 in all forest stands. The moderately labile NaOH-P included NaOH-Pi and NaOH-Po. The content of NaOH-P was in order of L. gmelinii plantation : natural secondary forest : secondary forest : P. sylvestris var. mongolica plantation in 0-10 cm layer of bulk and rhizosphere soil, and ranked as L. gmelinii plantation : P. sylvestris var. mongolica plantation : secondary forest : natural secondary forest in 10-20 cm layer of bulk soil. There was rhizosphere effect of NaOH-P in the soil. The stable HCl-P included HCl-Pi and HCl-Po. The content of HCl-P followed the order of L. gmelinii plantation : natural secondary forest : P. sylvestris var. mongolica plantation : secondary forest in 0-10 cm layer of bulk soil,and ranked as L. gmelinii plantation : P. sylvestris var. mongolica plantation : natural secondary forest : secondary forest in the 10-20 cm layer. The content of residual-P in the soil was not sensitive to restoration methods. Bradyrhizobium, Streptomyces, Burkholderia and Bacillus were the main phosphorus solubilizing bacteria across all forest stands. The abundances of phosphorus solubilizing bacteria in soil of L. gmelinii plantation and P. sylvestris var. mongolica plantation were significantly higher than that of secondary forest and natural secondary forest. Results of redundancy analysis showed that the correlation between phosphorus solubilizing bacteria and various phosphorus forms was different. Our results showed that artificial afforestation was more conducive in improving the availability of phosphorus in soil and the abundance of phosphorus solubilizing bacteria.

RevDate: 2020-06-01

Gutiérrez-Repiso C, Moreno-Indias I, Martín-Núñez GM, et al (2020)

Mucosa-associated microbiota in the jejunum of patients with morbid obesity: alterations in states of insulin resistance and metformin treatment.

Surgery for obesity and related diseases : official journal of the American Society for Bariatric Surgery pii:S1550-7289(20)30192-1 [Epub ahead of print].

BACKGROUND: Stool samples have been widely used to evaluate gut microbiota; however, little is known about the composition of human small intestinal microbiota and the alterations provoked by insulin resistance.

OBJECTIVE: To describe the composition of jejunal microbiota in morbidly obese patients, as well as its link with insulin resistance and metformin treatment.

SETTING: Virgen de la Victoria University Hospital and Regional University Hospital, Málaga, Spain.

METHODS: Jejunal biopsies from 46 morbidly obese patients were analyzed by next-generation sequencing method. Patients were classified in the following 3 groups: low homeostasis model assessment of insulin resistance index (HOMA-IR) value, high HOMA-IR value, and metformin-treated type 2 diabetes patients (T2D-metf).

RESULTS: Richness (q = .011) together with Proteobacteria (W = 2), Fusobacteria (W = 2), and Bacteroidetes (W = 1) phyla were significantly higher in high HOMA-IR compared with low HOMA-IR group. At family level, several differences were found between low HOMA-IR and T2D-metf group, being the most important the higher abundance of Halomonadacea in T2D-metf group (W = 22). PICRUSt analysis showed that predicted genes involved in trimethylamine-N-oxide biosynthesis pathway could be increased in jejunal microbiota of T2D-metf group compared with the low HOMA-IR group, while indole biosynthesis pathway could be increased in the low HOMA-IR group compared with the high HOMA-IR group.

CONCLUSION: An increase in richness and an enrichment in Proteobacteria, Fusobacteria, and Bacteroidetes was observed in jejunal from morbidly obese patients with high insulin resistance. Halomonadaceae family was significantly increased in metformin-treated patients. Functional analysis of predicted metagenome suggests that trimethylamine-N-oxide biosynthesis pathway could be increased in the jejunal microbiota of T2D-meft group, while indole biosynthesis pathway could be increased in low HOMA-IR group. These results contribute to the increase in the scarce knowledge about the mucosal microbiota of the hardly accessible small intestine.

RevDate: 2020-06-01

Zheng J, Hoffman KL, Chen JS, et al (2020)

Dietary inflammatory potential in relation to the gut microbiome: results from a cross-sectional study.

The British journal of nutrition pii:S0007114520001853 [Epub ahead of print].

Diet has direct and indirect effects on health through inflammation and the gut microbiome. We investigated total dietary inflammatory potential via the literature-derived index (DII®) with gut microbiota diversity, composition, and function. In cancer-free patient volunteers initially approached at colonoscopy and healthy volunteers recruited from the medical center community, we assessed 16S rDNA in all subjects who provided dietary assessments and stool samples (n=101) and the gut metagenome in a subset of patients with residual fasting blood samples (n=34). Associations of energy-adjusted DII scores with microbial diversity and composition were examined using linear regression, permutational multivariate analysis of variance, and linear discriminant analysis. Spearman correlation was used to evaluate associations of species and pathways with DII and circulating inflammatory markers. Alpha- and beta-diversity did not significantly differ across DII levels; however, Ruminococcus torques, Eubacterium nodatum, Acidaminococcus intestini, and Clostridium leptum were more abundant in the most pro-inflammatory diet group, while Akkermansia muciniphila was enriched in the most anti-inflammatory diet group. With adjustment for age and BMI, R. torques, E. nodatum, A. intestini remained significantly associated with a more pro-inflammatory diet. In the metagenomic and fasting blood subset, A. intestini was correlated with circulating PAI-1, a pro-inflammatory marker (rho=0.40), but no associations remained significant upon correction for multiple testing. An index reflecting overall inflammatory potential of the diet was associated with specific microbes, but not overall diversity of the gut microbiome in our study. Findings from this preliminary study warrant further research in larger samples and prospective cohorts.

RevDate: 2020-04-27
CmpDate: 2020-04-27

Leavitt J, N Saleh (2019)

The Microbiome and Colorectal Cancer: Current Clinical Trials.

Oncology (Williston Park, N.Y.), 33(2):78.

RevDate: 2020-05-30

Li J, Zhong H, Ramayo-Caldas Y, et al (2020)

A catalog of microbial genes from the bovine rumen unveils a specialized and diverse biomass-degrading environment.

GigaScience, 9(6):.

BACKGROUND: The rumen microbiota provides essential services to its host and, through its role in ruminant production, contributes to human nutrition and food security. A thorough knowledge of the genetic potential of rumen microbes will provide opportunities for improving the sustainability of ruminant production systems. The availability of gene reference catalogs from gut microbiomes has advanced the understanding of the role of the microbiota in health and disease in humans and other mammals. In this work, we established a catalog of reference prokaryote genes from the bovine rumen.

RESULTS: Using deep metagenome sequencing we identified 13,825,880 non-redundant prokaryote genes from the bovine rumen. Compared to human, pig, and mouse gut metagenome catalogs, the rumen is larger and richer in functions and microbial species associated with the degradation of plant cell wall material and production of methane. Genes encoding enzymes catalyzing the breakdown of plant polysaccharides showed a particularly high richness that is otherwise impossible to infer from available genomes or shallow metagenomics sequencing. The catalog expands the dataset of carbohydrate-degrading enzymes described in the rumen. Using an independent dataset from a group of 77 cattle fed 4 common dietary regimes, we found that only <0.1% of genes were shared by all animals, which contrast with a large overlap for functions, i.e., 63% for KEGG functions. Different diets induced differences in the relative abundance rather than the presence or absence of genes, which explains the great adaptability of cattle to rapidly adjust to dietary changes.

CONCLUSIONS: These data bring new insights into functions, carbohydrate-degrading enzymes, and microbes of the rumen to complement the available information on microbial genomes. The catalog is a significant biological resource enabling deeper understanding of phenotypes and biological processes and will be expanded as new data are made available.

RevDate: 2020-05-30

Zhang AN, Hou CJ, Negi M, et al (2020)

Online searching platform for antibiotic resistome in bacterial tree of life and global habitats.

FEMS microbiology ecology pii:5849002 [Epub ahead of print].

BACKGROUND: Metagenomic analysis reveals that antibiotic-resistance genes (ARGs) are widely distributed in both human-associated and non-human-associated habitats. However, it is difficult to equally compare ARGs between samples without a standard method.

METHODS: Here, we constructed a comprehensive profile of the distribution of potential ARGs in bacterial tree of life and global habitats by investigating ARGs in about 55,000 bacterial genomes, 16,000 bacterial plasmid sequences, 3,000 bacterial integron sequences, and 850 metagenomes using a standard pipeline.

RESULTS: We found that more than 80% of all known ARGs are not carried by any plasmid or integron sequences. Among potential mobile ARGs, tetracycline and beta-lactam resistance genes (such as tetA, tetM, and class A beta-lactamase gene) distribute in multiple pathogens across bacterial phyla, indicating their clinical relevance and importance. We showed that class 1 integrases (intI1) display a poor linear relationship with total ARGs in both non-human-associated and human-associated environments. Furthermore, both total ARGs and intI1 genes show little correlation to the degree of anthropogenicity. These observations highlight the needs to differentiate ARGs of high clinical relevance. We publish this profile on an online platform (ARGs-OSP, http://args-osp.herokuapp.com/) as valuable resources for the most challenging topics in this field, such as the risk, evolution, and emergence of ARGs.

RevDate: 2020-05-30

Morozova OV, Alekseeva AE, Sashina TA, et al (2020)

Phylodynamics of G4P[8] and G2P[4] strains of rotavirus A isolated in Russia in 2017 based on full-genome analyses.

Virus genes pii:10.1007/s11262-020-01771-3 [Epub ahead of print].

Rotavirus A is a dynamically evolving pathogen causing acute gastroenteritis in children during the first years of life. In the present study, we conducted a phylodynamic analysis based on the complete sequences of 11 segments of rotaviruses with the G4P[8] and G2P[4] genotypes isolated in Russia in 2017. Since rotavirus has a segmented genome, our analysis was performed using the Bayesian approach based on separate samples of nucleotide sequences for each gene of the strains studied. For the strain with the genotype G4P[8], the most likely geographical locations of the nearest common ancestor were Russia (VP7, VP4, VP6), China (VP1), Thailand (VP3), Belgium (NSP1), Hungary (VP2, NSP2, NSP3), Italy (NSP4) and Japan (NSP5). For the strain with the G2P[4] genotype, India (VP7, VP4, VP6, NSP1, NSP4), Malawi (VP2, NSP2, NSP3), Australia (VP1), Italy (NSP5) and Bangladesh (VP3). The closest common ancestor of the strain with the genotype G4P[8] circulated in 2001-2012, depending on the gene being analyzed. For the strain with the G2P[4] genotype, the closest common ancestor dates from 2006 to 2013.

RevDate: 2020-05-30

Vollmar S, Wellmann R, Borda-Molina D, et al (2020)

The Gut Microbial Architecture of Efficiency Traits in the Domestic Poultry Model Species Japanese Quail (Coturnix japonica) Assessed by Mixed Linear Models.

G3 (Bethesda, Md.) pii:g3.120.401424 [Epub ahead of print].

It is well known that mammals and avian gut microbiota compositions are shaped by the host genomes and affect quantitative traits. The microbial architecture describes the impact of the microbiota composition on quantitative trait variation and the number and effect distribution of microbiota features. In the present study the gut microbial architecture of feed-related traits phosphorus and calcium utilization, daily gain, feed intake and feed per gain ratio in the domestic poultry model species Japanese quail were assessed by mixed linear models. The ileum microbiota composition was characterized by 16S rRNA amplicon sequencing techniques of growing individuals. The microbiability of the traits was on a similar level as the narrow sense heritability and was highly significant except for calcium utilization. The animal microbial correlation of the traits was substantial. Microbiome-wide association analyses revealed several traits associated and highly significant microbiota features, both on the bacteria genera as well as on the operational taxonomic unit level. Most features were significant for more than one trait, which explained the high microbial correlations. It can be concluded that the traits are polymicrobial determined with some microbiota features with larger effects and many with small effects. The results are important for the development of hologenomic selection schemes for feed-related traits in avian breeding programs that are targeting the host genome and the metagenome simultaneously.

RevDate: 2020-05-30

Kitamura K, Shionoya H, Terato K, et al (2020)

Comment on: 'Metagenome-wide association study of gut microbiome revealed novel aetiology of rheumatoid arthritis in the Japanese population' by Kishikawa et al.

RevDate: 2020-05-30

Kishikawa T, Maeda Y, Nii T, et al (2020)

The positive correlation between Porphyromonas gingivalis and Prevotella spp. Response to: 'Comment on 'Metagenome-wide association study of gut microbiome revealed novel aetiology of rheumatoid arthritis in the Japanese population' by Kishikawa et al.' by Kitamura et al.

Annals of the rheumatic diseases pii:annrheumdis-2020-217897 [Epub ahead of print].

RevDate: 2020-05-30

Zlitni S, Bishara A, Moss EL, et al (2020)

Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale.

Genome medicine, 12(1):50 pii:10.1186/s13073-020-00747-0.

BACKGROUND: Populations of closely related microbial strains can be simultaneously present in bacterial communities such as the human gut microbiome. We recently developed a de novo genome assembly approach that uses read cloud sequencing to provide more complete microbial genome drafts, enabling precise differentiation and tracking of strain-level dynamics across metagenomic samples. In this case study, we present a proof-of-concept using read cloud sequencing to describe bacterial strain diversity in the gut microbiome of one hematopoietic cell transplantation patient over a 2-month time course and highlight temporal strain variation of gut microbes during therapy. The treatment was accompanied by diet changes and administration of multiple immunosuppressants and antimicrobials.

METHODS: We conducted short-read and read cloud metagenomic sequencing of DNA extracted from four longitudinal stool samples collected during the course of treatment of one hematopoietic cell transplantation (HCT) patient. After applying read cloud metagenomic assembly to discover strain-level sequence variants in these complex microbiome samples, we performed metatranscriptomic analysis to investigate differential expression of antibiotic resistance genes. Finally, we validated predictions from the genomic and metatranscriptomic findings through in vitro antibiotic susceptibility testing and whole genome sequencing of isolates derived from the patient stool samples.

RESULTS: During the 56-day longitudinal time course that was studied, the patient's microbiome was profoundly disrupted and eventually dominated by Bacteroides caccae. Comparative analysis of B. caccae genomes obtained using read cloud sequencing together with metagenomic RNA sequencing allowed us to identify differences in substrain populations over time. Based on this, we predicted that particular mobile element integrations likely resulted in increased antibiotic resistance, which we further supported using in vitro antibiotic susceptibility testing.

CONCLUSIONS: We find read cloud assembly to be useful in identifying key structural genomic strain variants within a metagenomic sample. These strains have fluctuating relative abundance over relatively short time periods in human microbiomes. We also find specific structural genomic variations that are associated with increased antibiotic resistance over the course of clinical treatment.

RevDate: 2020-05-30

Pearman WS, Freed NE, OK Silander (2020)

Testing the advantages and disadvantages of short- and long- read eukaryotic metagenomics using simulated reads.

BMC bioinformatics, 21(1):220 pii:10.1186/s12859-020-3528-4.

BACKGROUND: The first step in understanding ecological community diversity and dynamics is quantifying community membership. An increasingly common method for doing so is through metagenomics. Because of the rapidly increasing popularity of this approach, a large number of computational tools and pipelines are available for analysing metagenomic data. However, the majority of these tools have been designed and benchmarked using highly accurate short read data (i.e. Illumina), with few studies benchmarking classification accuracy for long error-prone reads (PacBio or Oxford Nanopore). In addition, few tools have been benchmarked for non-microbial communities.

RESULTS: Here we compare simulated long reads from Oxford Nanopore and Pacific Biosciences (PacBio) with high accuracy Illumina read sets to systematically investigate the effects of sequence length and taxon type on classification accuracy for metagenomic data from both microbial and non-microbial communities. We show that very generally, classification accuracy is far lower for non-microbial communities, even at low taxonomic resolution (e.g. family rather than genus). We then show that for two popular taxonomic classifiers, long reads can significantly increase classification accuracy, and this is most pronounced for non-microbial communities.

CONCLUSIONS: This work provides insight on the expected accuracy for metagenomic analyses for different taxonomic groups, and establishes the point at which read length becomes more important than error rate for assigning the correct taxon.

RevDate: 2020-05-29

Shah SHJ, Malik AH, Zhang B, et al (2020)

Metagenomic analysis of relative abundance and diversity of bacterial microbiota in Bemisia tabaci infesting cotton crop in Pakistan.

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases pii:S1567-1348(20)30212-4 [Epub ahead of print].

B. tabaci species complex are among the world's most devastating agricultural pests causing economic losses by direct feeding and more importantly by transmitting plant viruses like cotton leaf curl disease (CLCuD) associated viruses to cultivated cotton in Pakistan. Taxonomic diversity of B. tabaci associated bacterial communities using NGS techniques so far is reported from insects grown on artificial diet under lab conditions. In this study 16S rDNA metagenome sequencing analysis was used to characterize bacterial compositions in wild adult B. tabaci infesting cultivated cotton in eight major cotton growing districts of southern Punjab, Pakistan. We have identified 50 known and 7 unknown genera of bacteria belonging to 10 phyla, 20 classes, 30 orders and 40 families. Beta diversity analysis of our data sets reveal that whiteflies infesting cotton in geographically distinct locations had similar bacterial diversity. These results for the first time provide insights into the microbiome diversity of wild type whiteflies infesting a cultivated crop.

RevDate: 2020-05-29

Uberos J (2020)

Perinatal microbiota: review of its importance in newborn health.

Archivos argentinos de pediatria, 118(3):e265-e270.

The use of metagenomics in the study of gut bacterial ecosystems has helped to define a standard, functional genetic profile in newborn infants, so that a bacterial ecosystem will be deemed more "normal" the more similar its functional genetic profile is to a standard. The development of a specific functional enterotype in the first days of life after birth is critical for the priming of the immune system with certain bacterial antigens. Regardless of whether the first gut bacteria are acquired before or just after birth, the newborn microbiota will result from the symbiosis with the environmental microbial flora, especially with the bacterial flora of the mother. The type of delivery, the administration of perinatal antibiotics, the environment, and nutritional exposure, especially breastfeeding, have demonstrated an important relationship with the prevalent gut microbiome.

RevDate: 2020-05-29

Xie J, Yu R, Qi J, et al (2020)

Pectin and inulin stimulated the mucus formation at a similar level: An omics-based comparative analysis.

Journal of food science [Epub ahead of print].

Mucin 2 (MUC2) is the skeleton of colonic mucus that comprises the physical intestinal barrier. Different dietary polysaccharides may affect colonic mucus at different extents. The effect of pectin on MUC2 production is contradictory. To investigate whether and how pectin affected hosts' colonic mucus, the amount of MUC2 in colon, the cecal, mucosal microbiota, and metabolites profiles were analyzed and compared with inulin. The results showed pectin stimulated the production of MUC2 at a similar level to inulin. Both interventions increased the abundance of cecal Lachnospira and Christensenellaceae_R-7_group, and enhanced the production of specific metabolites including soyasapogenol B 24-O-b-d-glucoside, lucyoside Q, trans-EKODE-(E)-Ib, and 1,26-dicaffeoylhexacosanediol. Additionally, pectin increased the relative abundance (RA) of cecal Lactobacillus, and induced less RA of potentially harmful bacteria such as Helicobacter in mucosal microbiota than inulin. In conclusion, we first reported that pectin and inulin stimulated the mucus formation at a similar level. Two genera of cecal bacteria and four metabolites may play an important role in enhancing the production of MUC2. Moreover, the MUC2 production may be unrelated to several traditional health-beneficial bacteria; pectin possibly performed as good as or better than the inulin in rats' gut.

RevDate: 2020-05-29

Brealey JC, Leitão HG, van der Valk T, et al (2020)

Dental calculus as a tool to study the evolution of the mammalian oral microbiome.

Molecular biology and evolution pii:5848415 [Epub ahead of print].

Dental calculus, the calcified form of the mammalian oral microbial plaque biofilm, is a rich source of oral microbiome, host and dietary biomolecules and is well preserved in museum and archaeological specimens. Despite its wide presence in mammals, to date, dental calculus has primarily been used to study primate microbiome evolution. We establish dental calculus as a valuable tool for the study of non-human host microbiome evolution, by using shotgun metagenomics to characterise the taxonomic and functional composition of the oral microbiome in species as diverse as gorillas, bears and reindeer. We detect oral pathogens in individuals with evidence of oral disease, assemble near-complete bacterial genomes from historical specimens, characterise antibiotic resistance genes, reconstruct components of the host diet and recover host genetic profiles. Our work demonstrates that metagenomic analyses of dental calculus can be performed on a diverse range of mammalian species, which will allow the study of oral microbiome and pathogen evolution from a comparative perspective. As dental calculus is readily preserved through time, it can also facilitate the quantification of the impact of anthropogenic changes on wildlife and the environment.

RevDate: 2020-05-29

Jian X, Zhu Y, Ouyang J, et al (2020)

Alterations of gut microbiome accelerate multiple myeloma progression by increasing the relative abundances of nitrogen-recycling bacteria.

Microbiome, 8(1):74 pii:10.1186/s40168-020-00854-5.

BACKGROUND: Gut microbiome alterations are closely related to human health and linked to a variety of diseases. Although great efforts have been made to understand the risk factors for multiple myeloma (MM), little is known about the role of the gut microbiome and alterations of its metabolic functions in the development of MM.

RESULTS: Here, in a cohort of newly diagnosed patients with MM and healthy controls (HCs), significant differences in metagenomic composition were discovered, for the first time, with higher bacterial diversity in MM. Specifically, nitrogen-recycling bacteria such as Klebsiella and Streptococcus were significantly enriched in MM. Also, the bacteria enriched in MM were significantly correlated with the host metabolome, suggesting strong metabolic interactions between microbes and the host. In addition, the MM-enriched bacteria likely result from the regulation of urea nitrogen accumulated during MM progression. Furthermore, by performing fecal microbiota transplantation (FMT) into 5TGM1 mice, we proposed a mechanistic explanation for the interaction between MM-enriched bacteria and MM progression via recycling urea nitrogen. Further experiments validated that Klebsiella pneumoniae promoted MM progression via de novo synthesis of glutamine in mice and that the mice fed with glutamine-deficient diet exhibited slower MM progression.

CONCLUSIONS: Overall, our findings unveil a novel function of the altered gut microbiome in accelerating the malignant progression of MM and open new avenues for novel treatment strategies via manipulation of the intestinal microbiota of MM patients. Video abstract.

RevDate: 2020-05-29

Li Z, Tian J, Lai Y, et al (2020)

Puffer Fish Gut Microbiota Studies Revealed Unique Bacterial Co-Occurrence Patterns and New Insights on Tetrodotoxin Producers.

Marine drugs, 18(5): pii:md18050278.

Tetrodotoxin (TTX) is a potent neurotoxin isolated mainly from toxic puffer fish. To date, the TTX biosynthetic mechanism inside its hosts remains unresolved. Here, we hypothesize the TTX synthesis relies on the host gut microbiota, including the neglected non-culturable bacteria. In these studies, we collected the gut contents from 5 puffer fish species of the genus Takifugu including one suspected hybrid species for gut microbiota study by 16S rRNA amplicon metagenomics approach. Their gut samples were divided into toxic and non-toxic groups based on the TTX concentrations in the livers detected by LC-MS/MS. Bacterial diversity studies showed that gut microbiota structures were significantly different between toxic and non-toxic species. Vibrio and Cyanobacteria centered at the gut bacterial co-occurrence network, suggesting their importance in TTX biosynthesis. The results of PICRUSt2 metagenomic prediction and gene set enrichment analysis provided new support of arginine-precursor required in TTX biosynthesis. This is the first study to profile the gut microbiota in toxic and non-toxic puffer fish species by 16S rRNA amplicon metagenomic approach, defining significant microbial co-occurrence patterns in their gut environment. Our data supported the proposed biosynthesis of TTX inside the hosts by their gut bacterial symbionts using arginine as a precursor.

RevDate: 2020-05-29

Bilal M, Rasheed T, Mehmood S, et al (2020)

Mitigation of environmentally-related hazardous pollutants from water matrices using nanostructured materials - A review.

Chemosphere, 253:126770.

An unprecedented rise in population growth and rapid worldwide industrial development are associated with the increasing discharge of a range of toxic and baleful compounds. These toxic pollutants including dyes, endocrine-disrupters, heavy metals, personal care products, and pharmaceuticals are destructing nature's balance and intensifying environmental toxicity at a disquieting rate. Therefore, finding better, novel and more environmentally sound approaches for wastewater remediation are of great importance. Nanoscale materials have opened up some new horizons in various fields of science and technology. Among a range of treatment technologies, nanostructured materials have recently received incredible interest as an emerging platform for wastewater remediation owing to their exceptional surface-area-to-volume ratio, unique electrical and chemical properties, quantum size effects, high scalability, and tunable surface functionalities. An array of nanomaterials including noble metal-based nanostructures, transition metal oxide nanomaterials, carbon-based nanomaterials, carbon nanotubes, and graphene/graphene oxide nanomaterials to their novel nanocomposites and nanoconjugates have been attempted as the promising catalysts to overcome environmental dilemmas. In this review, we summarized recent advances in nanostructured materials that are particularly engineered for the remediation of environmental contaminants. The toxicity of various classes of relevant tailored nanomaterials towards human health and the ecosystem along with perspectives is also presented. In our opinion, an overview of the up-to-date advancements on this emerging topic may provide new ideas and thoughts for engineering low-cost and highly-efficient nanostructured materials for the abatement of recalcitrant pollutants for a sustainable environment.

RevDate: 2020-05-28

Fontaine SS, KD Kohl (2020)

The gut microbiota of invasive bullfrog tadpoles responds more rapidly to temperature than a non-invasive congener.

Molecular ecology [Epub ahead of print].

Environmental temperature can alter the composition, diversity, and function of ectothermic vertebrate gut microbial communities, which may result in negative consequences for host physiology, or conversely, increase phenotypic plasticity and persistence in harsh conditions. The magnitude of either of these effects will depend on the length of time animals are exposed to extreme temperatures, and how quickly the composition and function of the gut microbiota can respond to temperature change. However, the temporal effects of temperature on gut microbiota are currently unknown. Here, we investigated the length of time required for increased temperature to alter the composition of gut bacterial communities in tadpoles of two frog species, the green frog, Lithobates clamitans, and its congener, the globally invasive American bullfrog, L. catesbeianus. We also explored the potential functional consequences of these changes by comparing predicted metagenomic profiles across temperature treatments at the last experimental time point. Bullfrog-associated microbial communities were more plastic than those of the green frog. Specifically, bullfrog communities were altered by increased temperature within hours, while green frog communities took multiple days to exhibit significant changes. Further, over ten times more bullfrog bacterial functional pathways were temperature-dependent compared to the green frog. These results support our hypothesis that bullfrog gut microbial communities would respond more rapidly to temperature change, potentially bolstering their ability to exploit novel environments. More broadly, we have revealed that even short-term increases in environmental temperature, expected to occur frequently under global climate change, can alter the gut microbiota of ectothermic vertebrates.

RevDate: 2020-05-28

Zhang S, Yuan J, W Guo (2020)

Metagenomic insights into microbial characterizations in explaining the distinction of biofilter performance during start-up.

Biodegradation pii:10.1007/s10532-020-09902-1 [Epub ahead of print].

As an effective alternative for dissolved nitrogen removal, biofilter closely associates its treatment performance to structural and/or operational conditions. In this study, a set of four different biofilters including MAVF (mature aerated vertical flow), NAVF (new aerated vertical flow), NVF (new non-aerated vertical flow), and BHF (baffled non-aerated horizontal flow) were employed to purify low C/N ratio (3.8) domestic wastewater. All the filters were packed with round ceramsite operated under varying hydraulic loading rates (HLRs) of 0.024-0.18 m/day. During the start-up, both the physicochemical and microbial characterizations were investigated. It was found that, carbon and nitrogen could achieve ideal removal in MAVF once added with further sedimentation, while phosphorus displayed an unsatisfactory sequestration in any of the four filters probably due to the high inflow load and/or lack of alternate anaerobic/aerobic conditions. Filter clustering based on percent removal and removal rate constant displayed a consistent pattern, which was similar to that based on taxa of phylum from 16S rRNA sequencing, or phylum/genus/species from shotgun metagenomic sequencing although there were obvious distinctions in taxa compositions among direct comparison. Meanwhile, gene function annotation revealed that filter clustering based on metabolic pathways was consistent with that based on purification performance. These consistencies might imply that the treatment performance was mainly determined by microbial degradation. The enrichment of specific functional microbes responsible for the degradation of certain pollutants, such as carbohydrates, matched well with the defined purification performance.

RevDate: 2020-05-28

Kumar A, A Dubey (2020)

Rhizosphere microbiome: Engineering bacterial competitiveness for enhancing crop production.

Journal of advanced research, 24:337-352 pii:S2090-1232(20)30077-1.

Plants in nature are constantly exposed to a variety of abiotic and biotic stresses which limits their growth and production. Enhancing crop yield and production to feed exponentially growing global population in a sustainable manner by reduced chemical fertilization and agrochemicals will be a big challenge. Recently, the targeted application of beneficial plant microbiome and their cocktails to counteract abiotic and biotic stress is gaining momentum and becomes an exciting frontier of research. Advances in next generation sequencing (NGS) platform, gene editing technologies, metagenomics and bioinformatics approaches allows us to unravel the entangled webs of interactions of holobionts and core microbiomes for efficiently deploying the microbiome to increase crops nutrient acquisition and resistance to abiotic and biotic stress. In this review, we focused on shaping rhizosphere microbiome of susceptible host plant from resistant plant which comprises of specific type of microbial community with multiple potential benefits and targeted CRISPR/Cas9 based strategies for the manipulation of susceptibility genes in crop plants for improving plant health. This review is significant in providing first-hand information to improve fundamental understanding of the process which helps in shaping rhizosphere microbiome.

RevDate: 2020-05-28

Liang G, Zhao C, Zhang H, et al (2020)

The stepwise assembly of the neonatal virome is modulated by breastfeeding.

Nature, 581(7809):470-474.

The gut of healthy human neonates is usually devoid of viruses at birth, but quickly becomes colonized, which-in some cases-leads to gastrointestinal disorders1-4. Here we show that the assembly of the viral community in neonates takes place in distinct steps. Fluorescent staining of virus-like particles purified from infant meconium or early stool samples shows few or no particles, but by one month of life particle numbers increase to 109 per gram, and these numbers seem to persist throughout life5-7. We investigated the origin of these viral populations using shotgun metagenomic sequencing of virus-enriched preparations and whole microbial communities, followed by targeted microbiological analyses. Results indicate that, early after birth, pioneer bacteria colonize the infant gut and by one month prophages induced from these bacteria provide the predominant population of virus-like particles. By four months of life, identifiable viruses that replicate in human cells become more prominent. Multiple human viruses were more abundant in stool samples from babies who were exclusively fed on formula milk compared with those fed partially or fully on breast milk, paralleling reports that breast milk can be protective against viral infections8-10. Bacteriophage populations also differed depending on whether or not the infant was breastfed. We show that the colonization of the infant gut is stepwise, first mainly by temperate bacteriophages induced from pioneer bacteria, and later by viruses that replicate in human cells; this second phase is modulated by breastfeeding.

RevDate: 2020-05-28

Polster SP, Sharma A, Tanes C, et al (2020)

Permissive microbiome characterizes human subjects with a neurovascular disease cavernous angioma.

Nature communications, 11(1):2659 pii:10.1038/s41467-020-16436-w.

Cavernous angiomas (CA) are common vascular anomalies causing brain hemorrhage. Based on mouse studies, roles of gram-negative bacteria and altered intestinal homeostasis have been implicated in CA pathogenesis, and pilot study had suggested potential microbiome differences between non-CA and CA individuals based on 16S rRNA gene sequencing. We here assess microbiome differences in a larger cohort of human subjects with and without CA, and among subjects with different clinical features, and conduct more definitive microbial analyses using metagenomic shotgun sequencing. Relative abundance of distinct bacterial species in CA patients is shown, consistent with postulated permissive microbiome driving CA lesion genesis via lipopolysaccharide signaling, in humans as in mice. Other microbiome differences are related to CA clinical behavior. Weighted combinations of microbiome signatures and plasma inflammatory biomarkers enhance associations with disease severity and hemorrhage. This is the first demonstration of a sensitive and specific diagnostic microbiome in a human neurovascular disease.

RevDate: 2020-05-28

Joseph G, Zhang B, Harrison SH, et al (2020)

Microbial community dynamics during anaerobic co-digestion of corn stover and swine manure at different solid content, carbon to nitrogen ratio and effluent volumetric percentages.

Journal of environmental science and health. Part A, Toxic/hazardous substances & environmental engineering [Epub ahead of print].

The methane production and the microbial community dynamics of thermophilic anaerobic co-digestion (AD) of corn stover, swine manure and effluent were conducted at total solid (TS) content of 5%, 10% and 15%, the carbon to nitrogen ratio (C/N) of 20, 30 and 40 and the effluent volumetric percentage (EVP) of 20%, 40% and 60%. For batches with 5% TS, the highest methane yield of 238.5-283.1 mL g-1 volatile solid (VS) and the specific methane productivity of 138.5-152.2 mL g-1 initial VS were obtained at the C/N ratios of 20 and 30. For the mixtures with 10% and 15% TS, the highest methane yield was 341.9 mL g-1 VS and 351.2 mL g-1 VS, respectively, when the C/N ratio of 20% and 60% EVP conditions were maintained. Co-digestion of swine manure with corn stover caused an obvious shift in microbial population, in which the archaeal population changed from 0.3% to 2.8% and the bacterial community changed from 97.2% to 99.7%. The experimental batches with the highest relative abundance of the archaeal population (2.00% of total microbial population for 5% TS, 1.74% for 10% TS and 2.76% for 15% TS) had the highest rate of methanogenesis subsequently enhancing methane production (283.08 mL g-1 VS for 5% TS, 341.91 mL g-1 VS for 10% TS and 351.23 mL g-1 VS for 15% TS). The results of microbiome analysis enabled understanding the key populations in biomethane generation.

RevDate: 2020-05-27

Lin WH, Chen CC, Sheu YT, et al (2020)

Growth inhibition of sulfate-reducing bacteria for trichloroethylene dechlorination enhancement.

Environmental research, 187:109629 pii:S0013-9351(20)30522-3 [Epub ahead of print].

Trichloroethylene (TCE) is a frequently found organic contaminant in polluted-groundwater. In this microcosm study, effects of hydrogen-producing bacteria [Clostridium butyricum (Clostridium sp.)] and inhibitor of sulfate-reducing bacteria (SRB) addition on the enhancement of TCE dechlorination were evaluated. Results indicate that Clostridium sp. supplement could effectively enhance TCE reductive dechlorination (97.4% of TCE removal) due to increased hydrogen concentration and Dehalococcoides (DHC) populations (increased to 1 × 104 gene copies/L). However, addition of Clostridium sp. also caused the increase in dsrA (dissimilatory sulfide reductase subunit A) (increased to 2 × 108 gene copies/L), and thus, part of the hydrogen was consumed by SRB, which would limit the effective application of hydrogen by DHC. Control of Clostridium sp. addition is a necessity to minimize the adverse impact of Clostridium sp. on DHC growth. Ferric citrate caused the slight raise of the oxidation-reduction state, which resulted in growth inhibition of SRB. Molybdate addition inhibited the growth of SRB, and thus, the dsrA concentrations (dropped from 4 × 107 to 9 × 105 gene copies/L) and sulfate reduction efficiency were decreased. Increased DHC populations (increased from 8 × 103 to 1 × 105 gene copies/L) were due to increased available hydrogen (increased from 0 to 2 mg/L), which enhanced TCE dechlorination (99.3% TCE removal). Metagenomic analyses show that a significant microbial diversity was detected in microcosms with different treatments. Clostridium sp., ferric citrate, and molybdate addition caused a decreased SRB communities and increased fatty acid production microbial communities (increased from 4.9% to 20.2%), which would be beneficial to the hydrogen production and TCE dechlorination processes.

RevDate: 2020-05-27

Monaghan TM, Sloan TJ, Stockdale SR, et al (2020)

Metagenomics reveals impact of geography and acute diarrheal disease on the Central Indian human gut microbiome.

Gut microbes [Epub ahead of print].

BACKGROUND: The Central Indian gut microbiome remains grossly understudied. Herein, we sought to investigate the burden of antimicrobial resistance and diarrheal diseases, particularly Clostridioides difficile, in rural-agricultural and urban populations in Central India, where there is widespread unregulated antibiotic use. We utilized shotgun metagenomics to comprehensively characterize the bacterial and viral fractions of the gut microbiome and their encoded functions in 105 participants.

RESULTS: We observed distinct rural-urban differences in bacterial and viral populations, with geography exhibiting a greater influence than diarrheal status. Clostridioides difficile disease was more commonly observed in urban subjects, and their microbiomes were enriched in metabolic pathways relating to the metabolism of industrial compounds and genes encoding resistance to 3rd generation cephalosporins and carbapenems. By linking phages present in the microbiome to their bacterial hosts through CRISPR spacers, phage variation could be directly related to shifts in bacterial populations, with the auxiliary metabolic potential of rural-associated phages enriched for carbon and amino acid energy metabolism.

CONCLUSIONS: We report distinct differences in antimicrobial resistance gene profiles, enrichment of metabolic pathways and phage composition between rural and urban populations, as well as a higher burden of Clostridioides difficile disease in the urban population. Our results reveal that geography is the key driver of variation in urban and rural Indian microbiomes, with acute diarrheal disease, including C. difficile disease exerting a lesser impact. Future studies will be required to understand the potential role of dietary, cultural, and genetic factors in contributing to microbiome differences between rural and urban populations.

RevDate: 2020-05-27

Wang J, Dai W, Li J, et al (2020)

PaCRISPR: a server for predicting and visualizing anti-CRISPR proteins.

Nucleic acids research pii:5847774 [Epub ahead of print].

Anti-CRISPRs are widespread amongst bacteriophage and promote bacteriophage infection by inactivating the bacterial host's CRISPR-Cas defence system. Identifying and characterizing anti-CRISPR proteins opens an avenue to explore and control CRISPR-Cas machineries for the development of new CRISPR-Cas based biotechnological and therapeutic tools. Past studies have identified anti-CRISPRs in several model phage genomes, but a challenge exists to comprehensively screen for anti-CRISPRs accurately and efficiently from genome and metagenome sequence data. Here, we have developed an ensemble learning based predictor, PaCRISPR, to accurately identify anti-CRISPRs from protein datasets derived from genome and metagenome sequencing projects. PaCRISPR employs different types of feature recognition united within an ensemble framework. Extensive cross-validation and independent tests show that PaCRISPR achieves a significantly more accurate performance compared with homology-based baseline predictors and an existing toolkit. The performance of PaCRISPR was further validated in discovering anti-CRISPRs that were not part of the training for PaCRISPR, but which were recently demonstrated to function as anti-CRISPRs for phage infections. Data visualization on anti-CRISPR relationships, highlighting sequence similarity and phylogenetic considerations, is part of the output from the PaCRISPR toolkit, which is freely available at http://pacrispr.erc.monash.edu/.

RevDate: 2020-05-27

Sung JJY, NCH Poon (2020)

Artificial intelligence in gastroenterology: where are we heading?.

Frontiers of medicine pii:10.1007/s11684-020-0742-4 [Epub ahead of print].

Artificial intelligence (AI) is coming to medicine in a big wave. From making diagnosis in various medical conditions, following the latest advancements in scientific literature, suggesting appropriate therapies, to predicting prognosis and outcome of diseases and conditions, AI is offering unprecedented possibilities to improve care for patients. Gastroenterology is a field that AI can make a significant impact. This is partly because the diagnosis of gastrointestinal conditions relies a lot on image-based investigations and procedures (endoscopy and radiology). AI-assisted image analysis can make accurate assessment and provide more information than conventional analysis. AI integration of genomic, epigenetic, and metagenomic data may offer new classifications of gastrointestinal cancers and suggest optimal personalized treatments. In managing relapsing and remitting diseases such as inflammatory bowel disease, irritable bowel syndrome, and peptic ulcer bleeding, convoluted neural network may formulate models to predict disease outcome, enhancing treatment efficacy. AI and surgical robots can also assist surgeons in conducting gastrointestinal operations. While the advancement and new opportunities are exciting, the responsibility and liability issues of AI-assisted diagnosis and management need much deliberations.

RevDate: 2020-05-27

Guizzo MG, Neupane S, Kucera M, et al (2020)

Poor Unstable Midgut Microbiome of Hard Ticks Contrasts With Abundant and Stable Monospecific Microbiome in Ovaries.

Frontiers in cellular and infection microbiology, 10:211.

Culture-independent metagenomic methodologies have enabled detection and identification of microorganisms in various biological systems and often revealed complex and unknown microbiomes. In many organisms, the microbiome outnumbers the host cells and greatly affects the host biology and fitness. Ticks are hematophagous ectoparasites with a wide host range. They vector a number of human and animal pathogens and also directly cause major economic losses in livestock. Although several reports on a tick midgut microbiota show a diverse bacterial community, in most cases the size of the bacterial population has not been determined. In this study, the microbiome was quantified in the midgut and ovaries of the ticks Ixodes ricinus and Rhipicephalus microplus before, during, and after blood feeding. Although the size of bacterial community in the midgut fluctuated with blood feeding, it was overall extremely low in comparison to that of other hematophagous arthropods. In addition, the tick ovarian microbiome of both tick species exceeded the midgut 16S rDNA copy numbers by several orders of magnitude. This indicates that the ratio of a tick midgut/ovary microbiome represents an exception to the general biology of other metazoans. In addition to the very low abundance, the tick midgut diversity in I. ricinus was variable and that is in contrast to that found in the tick ovary. The ovary of I. ricinus had a very low bacterial diversity and a very high and stable bacterial abundance with the dominant endosymbiont, Midichloria sp. The elucidation of this aspect of tick biology highlights a unique tissue-specific microbial-invertebrate host interaction.

RevDate: 2020-05-27

Antonaru LA, Cardona T, Larkum AWD, et al (2020)

Global distribution of a chlorophyll f cyanobacterial marker.

The ISME journal pii:10.1038/s41396-020-0670-y [Epub ahead of print].

Some cyanobacteria use light outside the visible spectrum for oxygenic photosynthesis. The far-red light (FRL) region is made accessible through a complex acclimation process that involves the formation of new phycobilisomes and photosystems containing chlorophyll f. Diverse cyanobacteria ranging from unicellular to branched-filamentous forms show this response. These organisms have been isolated from shaded environments such as microbial mats, soil, rock, and stromatolites. However, the full spread of chlorophyll f-containing species in nature is still unknown. Currently, discovering new chlorophyll f cyanobacteria involves lengthy incubation times under selective far-red light. We have used a marker gene to detect chlorophyll f organisms in environmental samples and metagenomic data. This marker, apcE2, encodes a phycobilisome linker associated with FRL-photosynthesis. By focusing on a far-red motif within the sequence, degenerate PCR and BLAST searches can effectively discriminate against the normal chlorophyll a-associated apcE. Even short recovered sequences carry enough information for phylogenetic placement. Markers of chlorophyll f photosynthesis were found in metagenomic datasets from diverse environments around the globe, including cyanobacterial symbionts, hypersaline lakes, corals, and the Arctic/Antarctic regions. This additional information enabled higher phylogenetic resolution supporting the hypothesis that vertical descent, as opposed to horizontal gene transfer, is largely responsible for this phenotype's distribution.

RevDate: 2020-05-27

Ruff WE, Greiling TM, MA Kriegel (2020)

Host-microbiota interactions in immune-mediated diseases.

Nature reviews. Microbiology pii:10.1038/s41579-020-0367-2 [Epub ahead of print].

Host-microbiota interactions are fundamental for the development of the immune system. Drastic changes in modern environments and lifestyles have led to an imbalance of this evolutionarily ancient process, coinciding with a steep rise in immune-mediated diseases such as autoimmune, allergic and chronic inflammatory disorders. There is an urgent need to better understand these diseases in the context of mucosal and skin microbiota. This Review discusses the mechanisms of how the microbiota contributes to the predisposition, initiation and perpetuation of immune-mediated diseases in the context of a genetically prone host. It is timely owing to the wealth of new studies that recently contributed to this field, ranging from metagenomic studies in humans and mechanistic studies of host-microorganism interactions in gnotobiotic models and in vitro systems, to molecular mechanisms with broader implications across immune-mediated diseases. We focus on the general principles, such as breaches in immune tolerance and barriers, leading to the promotion of immune-mediated diseases by gut, oral and skin microbiota. Lastly, the therapeutic avenues that either target the microbiota, the barrier surfaces or the host immune system to restore tolerance and homeostasis will be explored.

RevDate: 2020-05-27

Lee SM, Kim N, Yoon H, et al (2020)

Compositional and Functional Changes in the Gut Microbiota in Irritable Bowel Syndrome Patients.

Gut and liver pii:gnl19379 [Epub ahead of print].

Background/Aims: This study aimed to characterize the changes in the gut microbiota of irritable bowel syndrome (IBS) patients and to investigate the consequent alterations in bacterial functions. Methods: We performed 16S rRNA metagenomic sequencing and a phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analyses using fecal samples from control (n=12) and diarrhea-dominant IBS patients (n=7). Results: The samples were clustered by the principal coordinates analysis depending on the presence of IBS (p=0.003). In the IBS patients, the abundances of Acidaminococcaceae, Sutterellaceae, and Desulfovibrionaceae were significantly increased, while those of Enterococcaceae, Leuconostocaceae, Clostridiaceae, Peptostreptococcaceae, and Lachnospiraceae were significantly decreased. The PICRUSt results indicated that two orthologues involved in secondary bile acid biosynthesis were significantly decreased in IBS patients. Modules involved in multidrug resistance, lipopolysaccharide biosynthesis, the reductive citrate cycle, and the citrate cycle were significantly increased in the IBS patients. In contrast, modules involved in cationic antimicrobial peptide resistance, and some transport systems were more abundant in controls than in IBS patients. Conclusions: Changes in the gut microbiota composition in IBS patients lead to alterations in bacterial functions, such as bile acid transformation and the induction of inflammation, which is a known pathophysiological mechanism of IBS.

RevDate: 2020-05-27

Geballa-Koukoulas K, Boudjemaa H, Andreani J, et al (2020)

Comparative Genomics Unveils Regionalized Evolution of the Faustovirus Genomes.

Viruses, 12(5): pii:v12050577.

Faustovirus is a recently discovered genus of large DNA virus infecting the amoeba Vermamoeba vermiformis, which is phylogenetically related to Asfarviridae. To better understand the diversity and evolution of this viral group, we sequenced six novel Faustovirus strains, mined published metagenomic datasets and performed a comparative genomic analysis. Genomic sequences revealed three consistent phylogenetic groups, within which genetic diversity was moderate. The comparison of the major capsid protein (MCP) genes unveiled between 13 and 18 type-I introns that likely evolved through a still-active birth and death process mediated by intron-encoded homing endonucleases that began before the Faustovirus radiation. Genome-wide alignments indicated that despite genomes retaining high levels of gene collinearity, the central region containing the MCP gene together with the extremities of the chromosomes evolved at a faster rate due to increased indel accumulation and local rearrangements. The fluctuation of the nucleotide composition along the Faustovirus (FV) genomes is mostly imprinted by the consistent nucleotide bias of coding sequences and provided no evidence for a single DNA replication origin like in circular bacterial genomes.

RevDate: 2020-05-27

Elokil AA, Abouelezz KFM, Ahmad HI, et al (2020)

Investigation of the Impacts of Antibiotic Exposure on the Diversity of the Gut Microbiota in Chicks.

Animals : an open access journal from MDPI, 10(5): pii:ani10050896.

The dynamic microbiota in chickens can be affected by exposure to antibiotics, which may alter the composition and substrate availability of functional pathways. Here, 120 Jing Hong chicks at 30 days of age were randomly divided into four treatments totaling seven experimental groups: control chicks not exposed to antibiotics; and chicks exposed to enrofloxacin, diclazuril, and their mixture at 1:1 for 14 days and then not exposed for a withdrawal period of 15 days. Fecal samples were collected from the 7 groups at 8 time-points (exposure to 4 antibiotics and 4 withdrawal periods) to perform in-depth 16S rRNA sequencing of the gut microbiota. Taxon-independent analysis showed that the groups had significantly distinct microbial compositions (p < 0.01). Based on the microbial composition, as compared with the control group, the abundances of the phyla Firmicutes, Actinobacteria, Thermi, and Verrucomicrobia, as well as the families Lactobacillus, Lactococcus, S24-7, and Corynebacterium, were decreased in the antibiotic-exposed chicks (p < 0.01). Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analyses revealed significant differences in microbiota metabolite pathways due to the genera of the antibiotic-responsive microbes (p < 0.01), especially the pathways relating to cell growth and death, immune system diseases, carbohydrate metabolism, and nucleotide metabolism. Oral treatment with enrofloxacin, diclazuril, and their mixture modified the gut microbiota composition and the microbial metabolic profiles in chickens, with persistent effects (during the withdrawal period) that prevented the return to the original community and led to the formation of a new community.

RevDate: 2020-05-27

Kim SI, Kang N, Leem S, et al (2020)

Metagenomic Analysis of Serum Microbe-Derived Extracellular Vesicles and Diagnostic Models to Differentiate Ovarian Cancer and Benign Ovarian Tumor.

Cancers, 12(5): pii:cancers12051309.

We aimed to develop a diagnostic model identifying ovarian cancer (OC) from benign ovarian tumors using metagenomic data from serum microbe-derived extracellular vesicles (EVs). We obtained serum samples from 166 patients with pathologically confirmed OC and 76 patients with benign ovarian tumors. For model construction and validation, samples were randomly divided into training and test sets in the ratio 2:1. Isolation of microbial EVs from serum samples of the patients and 16S rDNA amplicon sequencing were carried out. Metagenomic and clinicopathologic data-based OC diagnostic models were constructed in the training set and then validated in the test set. There were significant differences in the metagenomic profiles between the OC and benign ovarian tumor groups; specifically, genus Acinetobacter was significantly more abundant in the OC group. More importantly, Acinetobacter was the only common genus identified by seven different statistical analysis methods. Among the various metagenomic and clinicopathologic data-based OC diagnostic models, the model consisting of age, serum CA-125 levels, and relative abundance of Acinetobacter showed the best diagnostic performance with the area under the receiver operating characteristic curve of 0.898 and 0.846 in the training and test sets, respectively. Thus, our findings establish a metagenomic analysis of serum microbe-derived EVs as a potential tool for the diagnosis of OC.

RevDate: 2020-05-27
CmpDate: 2020-05-27

Davis JJ, Wattam AR, Aziz RK, et al (2020)

The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities.

Nucleic acids research, 48(D1):D606-D612.

The PathoSystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center funded by the National Institute of Allergy and Infectious Diseases (https://www.patricbrc.org). PATRIC supports bioinformatic analyses of all bacteria with a special emphasis on pathogens, offering a rich comparative analysis environment that provides users with access to over 250 000 uniformly annotated and publicly available genomes with curated metadata. PATRIC offers web-based visualization and comparative analysis tools, a private workspace in which users can analyze their own data in the context of the public collections, services that streamline complex bioinformatic workflows and command-line tools for bulk data analysis. Over the past several years, as genomic and other omics-related experiments have become more cost-effective and widespread, we have observed considerable growth in the usage of and demand for easy-to-use, publicly available bioinformatic tools and services. Here we report the recent updates to the PATRIC resource, including new web-based comparative analysis tools, eight new services and the release of a command-line interface to access, query and analyze data.

RevDate: 2020-05-27
CmpDate: 2020-05-27

Mollerup S, Asplund M, Friis-Nielsen J, et al (2019)

High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach.

The Journal of infectious diseases, 220(8):1312-1324.

BACKGROUND: Viruses and other infectious agents cause more than 15% of human cancer cases. High-throughput sequencing-based studies of virus-cancer associations have mainly focused on cancer transcriptome data.

METHODS: In this study, we applied a diverse selection of presequencing enrichment methods targeting all major viral groups, to characterize the viruses present in 197 samples from 18 sample types of cancerous origin. Using high-throughput sequencing, we generated 710 datasets constituting 57 billion sequencing reads.

RESULTS: Detailed in silico investigation of the viral content, including exclusion of viral artefacts, from de novo assembled contigs and individual sequencing reads yielded a map of the viruses detected. Our data reveal a virome dominated by papillomaviruses, anelloviruses, herpesviruses, and parvoviruses. More than half of the included samples contained 1 or more viruses; however, no link between specific viruses and cancer types were found.

CONCLUSIONS: Our study sheds light on viral presence in cancers and provides highly relevant virome data for future reference.

RevDate: 2020-05-27
CmpDate: 2020-05-27

Yates JR (3rd) (2019)

Proteomics of Communities: Metaproteomics.

Journal of proteome research, 18(6):2359.

RevDate: 2020-05-27
CmpDate: 2020-05-27

Zhang X, D Figeys (2019)

Perspective and Guidelines for Metaproteomics in Microbiome Studies.

Journal of proteome research, 18(6):2370-2380.

The microbiome is emerging as a prominent factor affecting human health, and its dysbiosis is associated with various diseases. Compositional profiling of microbiome is increasingly being supplemented with functional characterization. Metaproteomics is intrinsically focused on functional changes and therefore will be an important tool in those studies of the human microbiome. In the past decade, development of new experimental and bioinformatic approaches for metaproteomics has enabled large-scale human metaproteomic studies. However, challenges still exist, and there remains a lack of standardizations and guidelines for properly performing metaproteomic studies on human microbiome. Herein, we provide a perspective of recent developments, the challenges faced, and the future directions of metaproteomics and its applications. In addition, we propose a set of guidelines/recommendations for performing and reporting the results from metaproteomic experiments for the study of human microbiomes. We anticipate that these guidelines will be optimized further as more metaproteomic questions are raised and addressed, and metaproteomic applications are published, so that they are eventually recognized and applied in the field.

RevDate: 2020-05-27
CmpDate: 2020-05-27

Langer SG, Gabris C, Einfalt D, et al (2019)

Different response of bacteria, archaea and fungi to process parameters in nine full-scale anaerobic digesters.

Microbial biotechnology, 12(6):1210-1225.

Biogas production is a biotechnological process realized by complex bacterial, archaeal and likely fungal communities. Their composition was assessed in nine full-scale biogas plants with distinctly differing feedstock input and process parameters. This study investigated the actually active microbial community members by using a comprehensive sequencing approach based on ribosomal 16S and 28S rRNA fragments. The prevailing taxonomical units of each respective community were subsequently linked to process parameters. Ribosomal rRNA of bacteria, archaea and fungi, respectively, showed different compositions with respect to process parameters and supplied feedstocks: (i) bacterial communities were affected by the key factors temperature and ammonium concentration; (ii) composition of archaea was mainly related to process temperature; and (iii) relative abundance of fungi was linked to feedstocks supplied to the digesters. Anaerobic digesters with a high methane yield showed remarkably similar bacterial communities regarding identified taxonomic families. Although archaeal communities differed strongly on genus level from each other, the respective digesters still showed high methane yields. Functional redundancy of the archaeal communities may explain this effect. 28S rRNA sequences of fungi in all nine full-scale anaerobic digesters were primarily classified as facultative anaerobic Ascomycota and Basidiomycota. Since the presence of ribosomal 28S rRNA indicates that fungi may be active in the biogas digesters, further research should be carried out to examine to which extent they are important players in anaerobic digestion processes.

RevDate: 2020-05-27
CmpDate: 2020-05-27

Mediavilla O, Geml J, Olaizola J, et al (2019)

Effect of forest fire prevention treatments on bacterial communities associated with productive Boletus edulis sites.

Microbial biotechnology, 12(6):1188-1198.

Cistus ladanifer scrublands, traditionally considered as unproductive, have nonetheless been observed to produce large quantities of king bolete (Boletus edulis) fruitbodies. These pyrophytic scrublands are prone to wildfires, which severely affect fungi, hence the need for fire prevention in producing C. ladanifer scrublands. In addition, B. edulis productions have severely decreased in the last years. A deeper understanding of the B. edulis life cycle and of biotic and abiotic factors influencing sporocarp formation is needed to implement management practices that facilitate B. edulis production. For example, some bacteria likely are involved in sporocarp production, representing a key part in the triple symbiosis (plant-fungus-bacteria). In this study, we used soil DNA metabarcoding in C. ladanifer scrublands to (i) assess the effect of site history and fire prevention treatment on bacterial richness and community composition; (ii) test if there was any correlation between various taxonomic groups of bacteria and mycelial biomass and sporocarp production of B. edulis; and to (iii) identify indicator bacteria associated with the most productive B. edulis sites. Our results show that site history drives bacterial richness and community composition, while fire prevention treatments have a weaker, but still detectable effect, particularly in the senescent plots. Sporocarp production correlated positively with genera in Verrucomicrobia. Several genera, e.g. Azospirillum and Gemmatimonas, were identified as indicators of the most productive sites, suggesting a potential biological role in B. edulis fructification. This study provides a better understanding of the triple symbiosis (plant-fungus-bacteria) involved in C. ladanifer-B. edulis systems.

RevDate: 2020-05-27
CmpDate: 2020-05-27

Bergsveinson J, Perry BJ, Simpson GL, et al (2019)

Spatial analysis of a hydrocarbon waste-remediating landfarm demonstrates influence of management practices on bacterial and fungal community structure.

Microbial biotechnology, 12(6):1199-1209.

Cultivation of dedicated soil plots called 'landfarms' is an effective technology for bioremediation of hydrocarbon waste generated by various industrial practices. To understand the influence of soil conditions on landfarm microbial communities, analysis of bacterial and fungal community structure using next-generation sequencing at different sections and depths was performed across a hydrocarbon-waste landfarm in Regina, Saskatchewan, Canada. While a core set of hydrocarbon-associated bacterial and fungal taxa are present throughout the landfarm, unique bacterial and fungal operational taxonomic units are differentially abundant at sections within the landfarm, which correlate with differences in soil physiochemical properties and management practices. Increased frequency of waste application resulted in strong positive correlations between bacterial community assemblages and elevated amounts of oil, grease and F3 - F4 hydrocarbon fractions. In areas of standing water and lower application of hydrocarbon, microbial community structure correlated with soil pH, trace nutrients and metals. Overall, diversity and structure of bacterial communities remain relatively stable across the landfarm, while in contrast, fungal community structure appears more responsive to soil oxygen conditions. Results are consistent with the hypothesis that years of bioremediation activity have shaped microbial communities; however, several management practices can be undertaken to increase efficiency of remediation, including the removal of standing water and soil tilling across the landfarm.

RevDate: 2020-05-26

Yang H, Gan D, Li Y, et al (2020)

Quyushengxin Formula Causes Differences in Bacterial and Phage Composition in Ulcerative Colitis Patients.

Evidence-based complementary and alternative medicine : eCAM, 2020:5859023.

Background: Ulcerative colitis (UC) is a chronic inflammatory disease that affects the colon and the rectum. Recently, some studies have shown that microorganisms in the gut play important roles in many chronic diseases such as UC.

Methods: To study the candidate viruses and bacteria involved in UC and to investigate the therapeutic mechanism of Quyushengxin formula (QYSX) in UC patients, metagenomic sequencing was performed on the feces from healthy donors and UC patients before and after QYSX treatment.

Results: QYSX improved the symptoms of UC. In all participants, Caudovirales and Herpesvirales were the most dominant viruses. The abundance of Caudovirales in UC patients was significantly higher than that in the normal controls, while QYSX restored Caudovirales abundance. Furthermore, the abundance of crAssphage was enhanced in UC patients compared with the normal control, while the diversity was then decreased after QYSX treatment. However, there was no significant difference (P > 0.05). Additionally, other non-crAssphage bacteriophages including phiST, SP-10, and phi17:2 were higher in UC patients and QYSX decreased these viruses, while the trends of MED4-213, P-HM1, and P-HM2 were adverse. Interestingly, PhiDP23.1 was only found in UC patients before and after QYSX treatment. In addition, Bifidobacterium, Bacteroidetes, Prevotellaceae, Actinobacteria, and Corynebacteriales were the biomarkers in UC patients after QYSX treatment due to their high abundance. GO terms and KEGG analysis showed that the identified gut microbiome was involved in many biological processes and pathways.

Conclusions: QYSX could regulate disordered gut microbiome and phages, indicating that QYSX has great therapeutic potential for UC.

RevDate: 2020-05-26

Shang J, Y Sun (2020)

CHEER: hierarCHical taxonomic classification for viral mEtagEnomic data via deep leaRning.

Methods (San Diego, Calif.) pii:S1046-2023(19)30268-3 [Epub ahead of print].

The fast accumulation of viral metagenomic data has contributed significantly to new RNA virus discovery. However, the short read size, complex composition, and large data size can all make taxonomic analysis difficult. In particular, commonly used alignment-based methods are not ideal choices for detecting new viral species. In this work, we present a novel hierarchical classification model named CHEER, which can conduct read-level taxonomic classification from order to genus for new species. By combining k-mer embedding-based encoding, hierarchically organized CNNs, and carefully trained rejection layer, CHEER is able to assign correct taxonomic labels for reads from new species. We tested CHEER on both simulated and real sequencing data. The results show that CHEER can achieve higher accuracy than popular alignment-based and alignment-free taxonomic assignment tools. The source code, scripts, and pre-trained parameters for CHEER are available via GitHub:https://github.com/KennthShang/CHEER.

RevDate: 2020-05-26

Young F, Rogers S, DL Robertson (2020)

Predicting host taxonomic information from viral genomes: A comparison of feature representations.

PLoS computational biology, 16(5):e1007894 pii:PCOMPBIOL-D-19-01489 [Epub ahead of print].

The rise in metagenomics has led to an exponential growth in virus discovery. However, the majority of these new virus sequences have no assigned host. Current machine learning approaches to predicting virus host interactions have a tendency to focus on nucleotide features, ignoring other representations of genomic information. Here we investigate the predictive potential of features generated from four different 'levels' of viral genome representation: nucleotide, amino acid, amino acid properties and protein domains. This more fully exploits the biological information present in the virus genomes. Over a hundred and eighty binary datasets for infecting versus non-infecting viruses at all taxonomic ranks of both eukaryote and prokaryote hosts were compiled. The viral genomes were converted into the four different levels of genome representation and twenty feature sets were generated by extracting k-mer compositions and predicted protein domains. We trained and tested Support Vector Machine, SVM, classifiers to compare the predictive capacity of each of these feature sets for each dataset. Our results show that all levels of genome representation are consistently predictive of host taxonomy and that prediction k-mer composition improves with increasing k-mer length for all k-mer based features. Using a phylogenetically aware holdout method, we demonstrate that the predictive feature sets contain signals reflecting both the evolutionary relationship between the viruses infecting related hosts, and host-mimicry. Our results demonstrate that incorporating a range of complementary features, generated purely from virus genome sequences, leads to improved accuracy for a range of virus host prediction tasks enabling computational assignment of host taxonomic information.

RevDate: 2020-05-26

Pasolli E, De Filippis F, Mauriello IE, et al (2020)

Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome.

Nature communications, 11(1):2610 pii:10.1038/s41467-020-16438-8.

Lactic acid bacteria (LAB) are fundamental in the production of fermented foods and several strains are regarded as probiotics. Large quantities of live LAB are consumed within fermented foods, but it is not yet known to what extent the LAB we ingest become members of the gut microbiome. By analysis of 9445 metagenomes from human samples, we demonstrate that the prevalence and abundance of LAB species in stool samples is generally low and linked to age, lifestyle, and geography, with Streptococcus thermophilus and Lactococcus lactis being most prevalent. Moreover, we identify genome-based differences between food and gut microbes by considering 666 metagenome-assembled genomes (MAGs) newly reconstructed from fermented food microbiomes along with 154,723 human MAGs and 193,078 reference genomes. Our large-scale genome-wide analysis demonstrates that closely related LAB strains occur in both food and gut environments and provides unprecedented evidence that fermented foods can be indeed regarded as a possible source of LAB for the gut microbiome.

RevDate: 2020-05-26

Timsit E, McMullen C, Amat S, et al (2020)

Respiratory Bacterial Microbiota in Cattle: From Development to Modulation to Enhance Respiratory Health.

The Veterinary clinics of North America. Food animal practice, 36(2):297-320.

The respiratory tract of cattle is colonized by complex bacterial ecosystems also known as bacterial microbiotas. These microbiotas evolve over time and are shaped by numerous factors, including maternal vaginal microbiota, environment, age, diet, parenteral antimicrobials, and stressful events. The resulting microbiota can be diverse and enriched with known beneficial bacteria that can provide colonization resistance against bacterial pathogens or, on the contrary, with opportunistic pathogens that can predispose cattle to respiratory disease. The respiratory microbiota can be modulated by nonantimicrobial approaches to promote health, creating new potential strategies for prevention and treatment of bovine respiratory disease.

RevDate: 2020-05-26

Rubel MA, Abbas A, Taylor LJ, et al (2020)

Lifestyle and the presence of helminths is associated with gut microbiome composition in Cameroonians.

Genome biology, 21(1):122 pii:10.1186/s13059-020-02020-4.

BACKGROUND: African populations provide a unique opportunity to interrogate host-microbe co-evolution and its impact on adaptive phenotypes due to their genomic, phenotypic, and cultural diversity. We integrate gut microbiome 16S rRNA amplicon and shotgun metagenomic sequence data with quantification of pathogen burden and measures of immune parameters for 575 ethnically diverse Africans from Cameroon. Subjects followed pastoralist, agropastoralist, and hunter-gatherer lifestyles and were compared to an urban US population from Philadelphia.

RESULTS: We observe significant differences in gut microbiome composition across populations that correlate with subsistence strategy and country. After these, the variable most strongly associated with gut microbiome structure in Cameroonians is the presence of gut parasites. Hunter-gatherers have high frequencies of parasites relative to agropastoralists and pastoralists. Ascaris lumbricoides, Necator americanus, Trichuris trichiura, and Strongyloides stercoralis soil-transmitted helminths ("ANTS" parasites) significantly co-occur, and increased frequency of gut parasites correlates with increased gut microbial diversity. Gut microbiome composition predicts ANTS positivity with 80% accuracy. Colonization with ANTS, in turn, is associated with elevated levels of TH1, TH2, and proinflammatory cytokines, indicating an association with multiple immune mechanisms. The unprecedented size of this dataset allowed interrogation of additional questions-for example, we find that Fulani pastoralists, who consume high levels of milk, possess an enrichment of gut bacteria that catabolize galactose, an end product of lactose metabolism, and of bacteria that metabolize lipids.

CONCLUSIONS: These data document associations of bacterial microbiota and eukaryotic parasites with each other and with host immune responses; each of these is further correlated with subsistence practices.

RevDate: 2020-05-26

Chakraborty S, Mandal J, Cheng X, et al (2020)

Diurnal Timing Dependent Alterations in Gut Microbial Composition Are Synchronously Linked to Salt-Sensitive Hypertension and Renal Damage.

Hypertension (Dallas, Tex. : 1979) [Epub ahead of print].

Alterations of diurnal rhythms of blood pressure (BP) and reshaping of gut microbiota are both independently associated with hypertension. However, the relationships between biorhythms of BP and gut microbial composition are unknown. We hypothesized that diurnal timing-associated alterations of microbial compositions are synchronous with diurnal rhythmicity, dip in BP, and renal function. To test this hypothesis, Dahl salt-sensitive (S) rats on low- and high-salt diets were examined for time of day effects on gut microbiota, BP, and indicators of renal damage. Major shifts in night and day patterns of specific groups of microbiota were observed between the dark (active) and light (rest) phases, which correlated with diurnal rhythmicity of BP. The diurnal abundance of Firmicutes, Bacteroidetes, and Actinobacteria were independently associated with BP. Discrete bacterial taxa were observed to correlate independently or interactively with one or more of the following 3 factors: (1) BP rhythm, (2) dietary salt, and (3) dip in BP. Phylogenetic Investigation of Communities revealed diurnal timing effects on microbial pathways, characterized by upregulated biosynthetic processes during the active phase of host, and upregulated degradation pathways of metabolites in the resting phase. Additional metagenomics functional pathways with rhythm variations were noted for aromatic amino acid metabolism and taurine metabolism. These diurnal timing dependent changes in microbiota, their functional pathways, and BP dip were associated with concerted effects of the levels of renal lipocalin 2 and kidney injury molecule-1 expression. These data provide evidence for a firm and concerted diurnal timing effects of BP, renal damage, and select microbial communities.

RevDate: 2020-05-26
CmpDate: 2020-05-26

Banskar S, Detzner AA, Juarez-Rodriguez MD, et al (2019)

The Pglyrp1-Regulated Microbiome Enhances Experimental Allergic Asthma.

Journal of immunology (Baltimore, Md. : 1950), 203(12):3113-3125.

Changes in intestinal or respiratory microbiomes in infants correlate with increased incidence of asthma, but the causative role of microbiome in the susceptibility to asthma and the host genes that regulate these changes in microbiome are mostly unknown. In this study, we show that decreased responsiveness to allergic asthma in Pglyrp1-/- mice (lacking bactericidal peptidoglycan recognition protein 1) could be transferred to germ-free wild-type mice by colonization of mothers and newborns with microbiota from Pglyrp1-/- mice. These colonized mice had decreased airway resistance and fewer inflammatory cells, less severe histopathology, and lower levels of IgE and proallergic cytokines and chemokines in the lungs. This microbiome-dependent decreased responsiveness to asthma was most pronounced in colonized germ-free BALB/c mice (genetically predisposed to asthma), only partially evident in outbred germ-free Swiss Webster mice, and marginal in conventional BALB/c mice following depletion of microbiome with antibiotics. Mice with a low asthmatic response colonized with microbiota from Pglyrp1-/- mice had increased abundance of Bacteroidetes and decreased abundance of Firmicutes, Tenericutes, Deferribacteres, and Spirochaetes in the feces and increased abundance of Pasteurella in the oropharynx. These changes in bacterial abundance in the feces and oropharynx correlated with lower asthmatic responses in the lungs. Thus, our results show that Pglyrp1 enhances allergic asthmatic responses primarily through its effect on the host intestinal microbiome and identify several bacteria that may increase or decrease sensitivity to asthma. This effect of microbiome is strong in asthma-prone BALB/c mice and weak in asthma-resistant outbred mice and requires germ-free conditions before colonization with microbiota from Pglyrp1-/- mice.

RevDate: 2020-04-21
CmpDate: 2020-04-21

Liao B, Yan X, Zhang J, et al (2019)

Microbial community composition in alpine lake sediments from the Hengduan Mountains.

MicrobiologyOpen, 8(9):e00832.

Microbial communities in sediments play an important role in alpine lake ecosystems. However, the microbial diversity and community composition of alpine lake sediments from the Hengduan Mountains remain largely unknown. Therefore, based on the Illumina MiSeq platform, high-throughput sequencing analysis of the 16S rRNA gene was performed on 15 alpine lake sediments collected at different locations in the Hengduan Mountains. The abundance-based coverage estimate (ACE), Chao1, and Shannon indices indicated that the microbial abundance and diversity of these sediments were high. There are some differences in the composition of microbial communities among sediments. However, in general, Proteobacteria accounted for the largest proportion of all sediments (22.3%-67.6%) and was the dominant phylum. Followed by Bacteroidetes, Acidobacteria, Chloroflexi, and Planctomycetes. In addition, the operational taxonomic unit (OTU) interactions network had modular structures and suggested more cooperation than competition in the microbial community. Besides, we also found that temperature has a significant contribution to the sample-environment relationship. This study revealed the diversity and composition of microbial communities in alpine lake sediments from the Hengduan Mountains, and describe the correlation between microbial community structure and different environmental variables.

RevDate: 2020-05-25

Mishra P, Tulsani NJ, Jakhesara SJ, et al (2020)

Exploring the eukaryotic diversity in rumen of Indian camel (Camelus dromedarius) using 18S rRNA amplicon sequencing.

Archives of microbiology pii:10.1007/s00203-020-01897-w [Epub ahead of print].

In addition to a wide variety of anaerobic and facultative anaerobic bacteria, camel rumen also harbors a diverse of eukaryotic organisms. In the present study, the eukaryotic communities of camel rumen were characterized using 18S rRNA amplicon sequencing. Metagenomic DNA was isolated from rumen samples of fourteen adult Bikaneri and Kachchhi breeds of camel fed different diets containing Jowar, Bajra, Maize, and Guar. Illumina sequencing generated 27,161,904 number of reads corresponding to 1543 total operational taxonomic units (OTUs). Taxonomic classification of community metagenome sequences from all the samples revealed the presence of 92 genera belonging to 16 different divisions, out of which Ciliophora (73%), Fungi (13%) and Streptophyta (9%) were found to be the most dominant. Notably, the abundance of Ciliophora was significantly higher in the case of Guar feed, while Fungi was significantly higher in the case of Maize feed, indicating the influence of cellulose and hemicellulose content of feedstuff on the composition of eukaryotes. The results suggest that the camel rumen eukaryotes are highly dynamic and depend on the type of diet given to the animal. Pearson's correlation analysis suggested the ciliate protozoa and fungi were negatively correlated with each other. To the best of our knowledge, this is first systematic study to characterize camel rumen eukaryotes, which has provided newer information regarding eukaryotic diversity patterns amongst camel fed on different diets.

RevDate: 2020-05-25

Carr VR, Shkoporov A, Hill C, et al (2020)

Probing the Mobilome: Discoveries in the Dynamic Microbiome.

Trends in microbiology pii:S0966-842X(20)30128-1 [Epub ahead of print].

There has been an explosion of metagenomic data representing human, animal, and environmental microbiomes. This provides an unprecedented opportunity for comparative and longitudinal studies of many functional aspects of the microbiome that go beyond taxonomic classification, such as profiling genetic determinants of antimicrobial resistance, interactions with the host, potentially clinically relevant functions, and the role of mobile genetic elements (MGEs). One of the most important but least studied of these aspects are the MGEs, collectively referred to as the 'mobilome'. Here we elaborate on the benefits and limitations of using different metagenomic protocols, discuss the relative merits of various sequencing technologies, and highlight relevant bioinformatics tools and pipelines to predict the presence of MGEs and their microbial hosts.

RevDate: 2020-05-25

Pan S, R Chen (2020)

Metaproteomic analysis of human gut microbiome in digestive and metabolic diseases.

Advances in clinical chemistry, 97:1-12.

Metaproteomics, as a subfield of proteomics, has quickly emerged as a pivotal tool for global characterization of a microbiome system at a functional level. It has been increasingly applied in studying human digestive and metabolic diseases, and provides information-rich data to identify the dysbiosis of human gut microbiome related to healthy or disease states to elucidate the molecular events underlying host-microbiota interplays. While significant technical challenges still exist, this emerging technology has been demonstrated to provide essential information in interrogating functional changes in the human gut microbiome, complementary to metagenomics and metatranscriptomics. This chapter overviews the overall metaproteomic work flow and its recent applications in studying human gut microbiome relevant to digestive and metabolic diseases.

RevDate: 2020-05-25

Ding L, Zhao Y, Li X, et al (2020)

Early diagnosis and appropriate respiratory support for Mycoplasma pneumoniae pneumonia associated acute respiratory distress syndrome in young and adult patients: a case series from two centers.

BMC infectious diseases, 20(1):367 pii:10.1186/s12879-020-05085-5.

BACKGROUND: Mycoplasma pneumoniae (M. pneumoniae) is one of the most common causes of community acquired pneumonia (CAP). Establishing an early diagnosis of M. pneumoniae pneumonia in patients with acute respiratory distress syndrome (ARDS) may have important therapeutic implications.

METHODS: We describe diagnosis and management of M. pneumoniae pneumonia induced ARDS in a case series of adults and youth hospitalized with radiographically confirmed CAP prospectively enrolled in an observational cohort study in two university teaching hospitals, from November 2017 to October 2019.

RESULTS: In all 10 patients, early and rapid diagnosis for severe M. pneumoniae pneumonia with ARDS was achieved with polymerase chain reaction (PCR) or metagenomic next-generation sequencing (mNGS) testing of samples from the lower respiratory tract or pleural effusion. The average PaO2/FiO2 of all patients was 180 mmHg. Of the 10 cases, 4 cases had moderate ARDS (100 mmHg ≤ PaO2/FiO2 < 200 mmHg) and 3 cases had severe ARDS (PaO2/FiO2 < 100 mmHg). High flow nasal cannula (HFNC) was applied in all patients, though only two patients were sufficiently supported with HFNC. Invasive mechanical ventilation (IMV) was required in 5 patients. High resistance (median 15 L/cmH2O/s) and low compliance (median 38 ml/cmH2O) was observed in 4 cases. In these 4 cases, recruitment maneuvers (RM) were applied, with 1 patient demonstrating no response to RM. Prone positioning were applied in 4 cases. Two cases needed ECMO support with median support duration of 5.5 days. No patient in our case series received corticosteroid therapy. All patients were survived and were discharged from hospital.

CONCLUSIONS: Early and rapid diagnosis of severe M. pneumoniae pneumonia with ARDS can be achieved with PCR/mNGS tests in samples from the lower respiratory tract or pleural effusion. In our case series, half of M. pneumoniae pneumonia induced ARDS cases were adequately supported with HFNC or NIV, while half of cases required intubation. RM and prone position were effective in 30% of intubated cases, and 20% needed ECMO support. When early anti-mycoplasmal antibiotics were given together with sufficient respiratory support, the survival rate was high with no need for corticosteroid use.

RevDate: 2020-05-25

Gao LY, Xu GR, TJ Dai (2020)

Precision diagnosis and therapy of a case of brain abscesses associated with asymptomatic pulmonary arteriovenous fistulas.

BMC infectious diseases, 20(1):370 pii:10.1186/s12879-020-05092-6.

BACKGROUND: Brain abscesses, a severe infectious disease of the CNS, are usually caused by a variety of different pathogens, which include Streptococcus intermedius (S. intermedius). Pulmonary arteriovenous fistulas (PAVFs), characterized by abnormal direct communication between pulmonary artery and vein, are a rare underlying cause of brain abscesses.

CASE PRESENTATION: The patient was a previous healthy 55-year-old man who presented with 5 days of headache and fever. Cerebral magnetic resonance imaging (MRI) suggested a brain abscess. Thoracic CT scan and angiography demonstrated PAVFs. Aiding by metagenomic next-generation sequencing (mNGS) of the cerebrospinal fluid (CSF) sample which identified S. intermedius as the causative pathogen, the patient was switched to the single therapy of large dose of penicillin G and was cured precisely and economically.

CONCLUSIONS: It is an alternative way to perform mNGS to identify causative pathogens in patients with brain abscesses especially when the results of traditional bacterial culture were negative. Further thoracic CT or pulmonary angiography should also be undertaken to rule out PAVFs as the potential cause of brain abscess if the patient without any known premorbid history.

RevDate: 2020-02-24
CmpDate: 2020-02-24

Ni YH (2019)

Bugs to debug? The exploration of gut microbiome in human health and diseases.

Journal of the Formosan Medical Association = Taiwan yi zhi, 118 Suppl 1:S1-S2.

RevDate: 2020-05-24

Davies N, O'Sullivan JM, Plank LD, et al (2020)

Gut Microbial Predictors of Type 2 Diabetes Remission Following Bariatric Surgery.

Obesity surgery pii:10.1007/s11695-020-04684-0 [Epub ahead of print].

PURPOSE: Distinct anatomical rearrangements of the gastrointestinal tract achieved by various types of bariatric surgery cause changes in nutrient intake and gut microbiota. The contribution of such gut microbiota changes to remission of type 2 diabetes (T2D) remains unclear.

AIM: We examined gut microbiota changes following banded Roux-en-Y gastric bypass (RYGB) or sleeve gastrectomy (SG) in a randomised study, in relation to T2D remission.

MATERIALS AND METHODS: Whole-metagenome shotgun sequencing was carried out on paired stool samples at pre- and 1-year post-surgery collected from 44 participants with T2D randomised to banded Roux-en-Y gastric bypass (RYGB) or sleeve gastrectomy (SG). Taxonomic composition and predicted functional potential of the gut bacteria were identified using HUMANn2, and annotated using MetaCyc. Five-day dietary records (analysed using FoodWorks v8.0), body weight and diabetes status were recorded at both time points.

RESULTS: RYGB participants had higher percentage excess weight loss than SG (p = 0.01), even though dietary intake was similar at 1-year post-surgery. Similar proportions achieved diabetes remission (HbA1c < 48 mmol/mol without medications) after either RYGB (68%) or SG (59%). RYGB resulted in increased abundances of Firmicutes and Proteobacteria, while SG resulted in increased Bacteroidetes. Pre-surgery, an increased abundance of Eubacteriaceae (p = 0.01) and Alistipes putredinis (p = 0.01) was observed in those who went on to remit from T2D post-surgery. Following surgery, Lachnospiraceae (p = 0.04) and Roseburia (p = 0.01) species were more abundant in those who had achieved T2D remission.

CONCLUSIONS: Specific stool bacterial taxa may signal likelihood of T2D remission after bariatric surgery which is potentially mediated by increases in Lachnospiraceae and Roseburia.

RevDate: 2020-05-24

Sun H, Yang G, Cao R, et al (2020)

Expression and characterization of a novel glycoside hydrolase family 46 chitosanase identified from marine mud metagenome.

International journal of biological macromolecules pii:S0141-8130(20)33299-2 [Epub ahead of print].

A novel chitosanase gene, csn4, was identified through function-based screening of a marine mud metagenomic library. The encoded protein, named CSN4, which belonged to glycoside hydrolase family 46, showed its maximum identity (79%) with Methylobacter tundripaludum peptidoglycan-binding protein. CSN4 was expressed in Escherichia coli and purified. It displayed maximal activity at 30 °C and pH 7. A weakly-alkaline solution strongly inhibited the activity. The enzymatic activity was enhanced by addition of Mn2+ or Co2+. CSN4 exhibited strict substrate specificity for chitosan, and the activity was enhanced by increasing the degree of deacetylation. Thin-layer chromatography and electrospray ionization-mass spectrometry showed that CSN4 displayed an endo-type cleavage pattern, hydrolyzing chitosan mainly into (GlcN)2, (GlcN)3 and (GlcN)4. The novel characteristics of the chitosanase CSN4 make it a potential candidate to produce chitooligosaccharides from chitosan in industry.

RevDate: 2020-05-23

Ishizawa H, Kuroda M, Inoue D, et al (2020)

Community dynamics of duckweed-associated bacteria upon inoculation of plant growth-promoting bacteria.

FEMS microbiology ecology pii:5843272 [Epub ahead of print].

Plant growth-promoting bacteria (PGPB) have recently been demonstrated as a promising agent to improve wastewater treatment and biomass production efficiency of duckweed hydrocultures. For their reliable use in aqueous environments, this study analyzed the plant colonization dynamics of PGPB and its ecological consequence on the entire duckweed-associated bacterial communities. A PGPB strain, Aquitalea magnusonii H3, was inoculated to duckweed at different cell densities or timings in the presence of three environmental bacterial communities. The results showed that strain H3 improved duckweed growth by 11.7-32.1% in five out of nine experiments. Quantitative-PCR and amplicon sequencing analyses showed that strain H3 successfully colonized duckweed after 1 and 3 d of inoculations in all cultivation tests. However, it significantly decreased in numbers after 7 d, and similar bacterial communities were observed on duckweed regardless of H3 inoculation. Predicted metagenome analysis suggested that genes related to bacterial chemotactic motility and surface attachment system are consistently enriched through community assembly on duckweed. Taken together, strain H3 dominantly colonized duckweed for a short period and improved duckweed growth. However, the inoculation of the PGPB did not have a lasting impact due to the strong resilience of natural duckweed microbiome.

RevDate: 2020-05-23

Krishnaswamy VG, Aishwarya S, TM Kathawala (2020)

Extrication of the Microbial Interactions of Activated Sludge Used in the Textile Effluent Treatment of Anaerobic Reactor Through Metagenomic Profiling.

Current microbiology pii:10.1007/s00284-020-02020-4 [Epub ahead of print].

Industrial effluents are potential threats to water bodies owing to the chemicals they contain to create pollution. Activated sludge effluents represent an ecosystem of multifaceted and interactive microbial consortia that flourish with different genetic as well as metabolic potential. This study is applied to a nanopore sequencing to understand the microbial organisms involved in degradation pathways, and their interaction among them. The taxonomic profile determined the occurrence of Proteobacteria, Actinobacteria, Terrabacteria, bacteria, and Firmicutes with the dominance of Burkholderiales. Burkholderia pseudomallei was found to be 13.79% of the classified reads. The Gene ontology evaluation revealed that mobile elements and tRNA genes were the predominant genetic composition of the community with 16% of the total genes. The functional annotation of genes ensured the presence of genes encoding various types of RNA, homo and heteromultimeric proteins and pseudogenes as well. Pathways that involved in effluent treatment such as amines, aromatic, organic, and aromatic compound degradation were also illustrated. Amino acyl tRNA charging, signal transduction, and hormone degradation were the pathways that are identified to be common in all the organisms of the activated sludge. The study elaborated on the xenobiotic degradation that is exclusive of the predominant Burkholderiales and the interaction of them in the community as a whole. The present study revealed the genes, proteins, and the pathways of the activated sludge microbiome which will enhance the perceptions of the core mechanisms of effluent degradation.

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ESP Quick Facts

ESP Origins

In the early 1990's, Robert Robbins was a faculty member at Johns Hopkins, where he directed the informatics core of GDB — the human gene-mapping database of the international human genome project. To share papers with colleagues around the world, he set up a small paper-sharing section on his personal web page. This small project evolved into The Electronic Scholarly Publishing Project.

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In 1995, Robbins became the VP/IT of the Fred Hutchinson Cancer Research Center in Seattle, WA. Soon after arriving in Seattle, Robbins secured funding, through the ELSI component of the US Human Genome Project, to create the original ESP.ORG web site, with the formal goal of providing free, world-wide access to the literature of classical genetics.

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Although the methods of molecular biology can seem almost magical to the uninitiated, the original techniques of classical genetics are readily appreciated by one and all: cross individuals that differ in some inherited trait, collect all of the progeny, score their attributes, and propose mechanisms to explain the patterns of inheritance observed.

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Usage of the site grew rapidly and has remained high. Faculty began to use the site for their assigned readings. Other on-line publishers, ranging from The New York Times to Nature referenced ESP materials in their own publications. Nobel laureates (e.g., Joshua Lederberg) regularly used the site and even wrote to suggest changes and improvements.

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When the site began, no journals were making their early content available in digital format. As a result, ESP was obliged to digitize classic literature before it could be made available. For many important papers — such as Mendel's original paper or the first genetic map — ESP had to produce entirely new typeset versions of the works, if they were to be available in a high-quality format.

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