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Bibliography on: Metagenomics

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ESP: PubMed Auto Bibliography 20 Jul 2019 at 07:44 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: 2019-07-19

Cuypers L, Thijssen M, Shakibzadeh A, et al (2019)

Signature of natural resistance in NS3 protease revealed by deep sequencing of HCV strains circulating in Iran.

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases pii:S1567-1348(19)30184-4 [Epub ahead of print].

A tremendous upscale of screening and treatment strategies is required to achieve elimination of the hepatitis C virus (HCV) in Iran by 2030. Among treated patients, at least 5-10% is expected to experience treatment failure. To efficiently retreat cases with prior exposure to NS5A and NS5B drugs, knowledge on the natural prevalence of NS3 resistance is key. The NS3 region of 32 samples from sixteen Iranian HCV patients, among which 6 injecting drug users, was amplified and subjected to deep sequencing. Amplification and sequencing were successful in 29 samples. The reads were assembled to consensus sequences and showed that 6 patients were infected with HCV1a (37.5%), 7 with HCV1b (43.8%) and 3 with HCV3a (18.7%). Nucleotide identities were shared for >97% between intra-host sequences. Two patients were infected with natural resistant viruses, of which one solely comprising low frequency variants. Inferred phylogenies showed that Iranian sequences clustered together for HCV1a and HCV1b, while for HCV3a a potential recombination event was detected. We firstly report the use of deep sequencing for HCV in Iran, demonstrate the use of NS3 inhibitors as salvage therapy in case of retreatment and stress the importance for Iran to prioritize drug users for screening and treatment.

RevDate: 2019-07-19

Ruprecht C, Bönisch F, Ilmberger N, et al (2019)

High level production of flavonoid rhamnosides by metagenome-derived Glycosyltransferase C in Escherichia coli utilizing dextrins of starch as a single carbon source.

Metabolic engineering pii:S1096-7176(19)30080-1 [Epub ahead of print].

Flavonoids exert a wide variety of biological functions that are highly attractive for the pharmaceutical and healthcare industries. However, their application is often limited by low water solubility and poor bioavailability, which can generally be relieved through glycosylation. Glycosyltransferase C (GtfC), a metagenome-derived, bacterial glycosyltransferase, was used to produce novel and rare rhamnosides of various flavonoids, including chrysin, diosmetin, biochanin A, and hesperetin. Some of them are to our knowledge firstly described within this work. In our study we deployed a new metabolic engineering approach to increase the rhamnosylation rate in Escherichia coli whole cell biotransformations. The coupling of maltodextrin metabolism to glycosylation was developed in E. coli MG1655 with the model substrate hesperetin. The process proved to be highly dependent on the availability of maltodextrins. Maximal production was achieved by the deletion of the phosphoglucomutase (pgm) and UTP-glucose-1-phosphate uridyltransferase (galU) genes and simultaneous overexpression of the dTDP-rhamnose synthesis genes (rmlABCD) as well as glucan 1,4-alpha-maltohexaosidase for increased maltodextrin degradation next to GtfC in E. coli UHH_CR5-A. These modifications resulted in a 3.2-fold increase of hesperetin rhamnosides compared to E. coli MG1655 expressing GtfC in 24 h batch fermentations. Furthermore, E. coli UHH-CR_5-A was able to produce a final product titer of 2.4 g/L of hesperetin-3'-O-rhamnoside after 48 h. To show the versatility of the engineered E. coli strain, biotransformations of quercetin and kaempferol were performed, leading to production of 4.3 g/L quercitrin and 1.9 g/L afzelin in a 48 h time period, respectively. So far, these are the highest published yields of flavonoid rhamnosylation using a biotransformation approach. These results clearly demonstrate the high potential of the engineered E. coli production host as a platform for the high level biotransformation of flavonoid rhamnosides.

RevDate: 2019-07-19

Mcgeoch MA, Latombe G, Andrew NR, et al (2019)

Measuring continuous compositional change using decline and decay in zeta diversity.

Ecology [Epub ahead of print].

Incidence, or compositional, matrices are generated for a broad range of research applications in biology. Zeta diversity provides a common currency and conceptual framework that links incidence-based metrics with multiple patterns of interest in biology, ecology and biodiversity science. It quantifies the variation in species (or OTU) composition of multiple assemblages (or cases) in space or time, to capture the contribution of the full suite of narrow, intermediate and wide-ranging species to biotic heterogeneity. Here we provide a conceptual framework for the application and interpretation of patterns of continuous change in compositional diversity using zeta diversity. This includes consideration of the survey design context, and the multiple ways in which zeta diversity decline and decay can be used to examine and test turnover in the identity of elements across space and time. We introduce the zeta ratio-based retention rate curve to quantify rates of compositional change. We illustrate these applications using 11 empirical datasets from a broad range of taxa, scales and levels of biological organisation - from DNA molecules and microbes to communities and interaction networks - including one of the original data sets used to express compositional change and distance decay in ecology. We show (i) how different sample selection schemes used during the calculation of compositional change are appropriate for different data types and questions, (ii) how higher orders of zeta may in some cases better detect shifts and transitions, and (iii) the relative roles of rare versus common species in driving patterns of compositional change. By exploring the application of zeta diversity decline and decay, including the retention rate, across this broad range of contexts, we demonstrate its application for understanding continuous turnover in biological systems. This article is protected by copyright. All rights reserved.

RevDate: 2019-07-19

Getachew B, Reyes RE, Davies DL, et al (2019)

Moxidectin Effects on Gut Microbiota of Wistar-Kyoto Rats: Relevance to Depressive-Like Behavior.

Clinical pharmacology and translational medicine, 3(1):134-142.

Background/Aims: The prevalent comorbidity between neuropsychiatric and gastrointestinal (GI) disorders is believed to be significantly influenced by gut microbiota (GM). GM may also play a substantial role in comorbidity between substance abuse (e.g. Alcohol Use Disorder, AUD) and depression. The anti-parasitic drug Moxidectin (MOX) has been reported to reduce alcohol intake in male and female mice. This effect is purported to be centrally mediated with a significant contribution linked to purinergic, P2X4 purinergic receptors. However, MOX's effects on GM in animal models of depression is not known.

Methods: Adult male Wistar Kyoto (WKY) rats (5/group) were injected intraperitoneally (i.p.) once daily for 7 days with MOX (2.5mg/kg), or saline as control group. On day 8, approximately 20 h after the last MOX injection, animals were sacrificed, intestinal stools were collected and stored at -80°C DNA was extracted from the samples for 16S rRNA gene-based GM analysis using 16S Metagenomics application.

Results: At taxa and species level, MOX affected a number of bacteria including a 30-fold increase in Bifidobacterium cholerium, a bacterium with a strong ability to degrade carbohydrates that resist digestion in the small intestine. There was a minimum of 2-fold increase in: five probiotic species of Lactobacillus, butyrate-forming Rosburia Facies and Butyrivibro proteovlasticus. In contrast, MOX depleted 11 species, including 2 species of Ruminoccus, which are positively associated with severity of irritable bowel syndrome, and 4 species of Provettela, which are closely associated with depressive-like behavior.

Conclusion: Thus, MOX enhanced probiotic species, and suppressed the opportunistic pathogens. Since overall effect of MOX appears to be promoting GM associated with mood enhancement (e.g. Bifidobacterium and Lactobacillus) and suppressing GM associated with inflammation (e.g. Ruminoccus), potential antidepressant and anti-inflammatory effects of MOX in suitable animal models should be investigated.

RevDate: 2019-07-19

Anonymous (2019)

Correction: Metagenomics in ophthalmology: current findings and future prospectives.

BMJ open ophthalmology, 4(1):e000248corr1 pii:bmjophth-2018-000248corr1.

[This corrects the article DOI: 10.1136/bmjophth-2018-000248.].

RevDate: 2019-07-19

Chang WS, Pettersson JH, Le Lay C, et al (2019)

Novel hepatitis D-like agents in vertebrates and invertebrates.

Virus evolution, 5(2):vez021 pii:vez021.

Hepatitis delta virus (HDV) is the smallest known RNA virus, encoding a single protein. Until recently, HDV had only been identified in humans, where it is strongly associated with co-infection with hepatitis B virus (HBV). However, the recent discovery of HDV-like viruses in metagenomic samples from birds and snakes suggests that this virus has a far longer evolutionary history. Herein, using additional meta-transcriptomic data, we show that highly divergent HDV-like viruses are also present in fish, amphibians, and invertebrates, with PCR and Sanger sequencing confirming the presence of the invertebrate HDV-like viruses. Notably, the novel viruses identified here share genomic features characteristic of HDV, such as a circular genome of only approximately 1.7 kb in length, and self-complementary, unbranched rod-like structures. Coiled-coil domains, leucine zippers, conserved residues with essential biological functions, and isoelectronic points similar to those in the human hepatitis delta virus antigens (HDAgs) were also identified in the putative non-human viruses. Importantly, none of these novel HDV-like viruses were associated with hepadnavirus infection, supporting the idea that the HDV-HBV association may be specific to humans. Collectively, these data not only broaden our understanding of the diversity and host range of HDV, but also shed light on its origin and evolutionary history.

RevDate: 2019-07-19

Fahsbender E, Altan E, Estrada M, et al (2019)

Lyon-IARC Polyomavirus DNA in Feces of Diarrheic Cats.

Microbiology resource announcements, 8(29): pii:8/29/e00550-19.

A viral metagenomic analysis of feces from an unexplained outbreak of feline diarrhea revealed the presence of Lyon-IARC polyomavirus (LIPyV) DNA. LIPyV, whose genome was originally sequenced from swabs of human skin, was fecally shed by three out of five diarrheic cats.

RevDate: 2019-07-19

Carissimi C, Laudadio I, Palone F, et al (2019)

Functional analysis of gut microbiota and immunoinflammation in children with autism spectrum disorders.

Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver pii:S1590-8658(19)30663-2 [Epub ahead of print].

BACKGROUND AND AIMS: Recent evidence implicates gut microbiota (GM) and immune alterations in autism spectrum disorders (ASD). We assess GM profile and peripheral levels of immunological, neuronal and bacterial molecules in ASD children and controls. Alarmin HMGB1 was explored as a non-invasive biomarker to monitor gastrointestinal (GI) symptoms.

METHODS: Thirty ASD children and 14 controls entered into the study. GM metagenomic analysis was performed for 16 ASD patients and 7 controls. GM functional profile was assessed by GO term analysis. Blood levels of IL-1β, TNFα, TGFβ, IL-10, INFγ, IL-8, lipopolysaccharide, Neurotensin, Sortilin1 and GSSG/GSH ratio were analyzed in all subjects by ELISA. Fecal HMGB1 was analyzed by Western blot.

RESULTS: We observed a significant decrease in bacterial diversity. Furthermore, 82 GO terms underrepresented in ASD. Four of them pointed at 3,3 phenylpropionate catabolism and were imputable to Escherichia coli (E. coli) group. Serum levels of TNFα, TGFβ, NT, and SORT-1 increased in ASD patients. Fecal levels of HMGB1 correlated with GI sign severity in ASD children.

CONCLUSIONS: We suggest that a decrease of E. coli might affect the propionate catabolism in ASD. We report occurrence of peripheral inflammation in ASD children. We propose fecal HMGB1 as a non-invasive biomarker to detect GI symptoms.

RevDate: 2019-07-18

Reddy KR, Rai RK, Green SJ, et al (2019)

Effect of temperature on methane oxidation and community composition in landfill cover soil.

Journal of industrial microbiology & biotechnology pii:10.1007/s10295-019-02217-y [Epub ahead of print].

Municipal solid waste (MSW) landfills are the third largest anthropogenic source of methane (CH4) emissions in the United States. The majority of CH4 generated in landfills is converted to carbon dioxide (CO2) by CH4-oxidizing bacteria (MOB) present in the landfill cover soil, whose activity is controlled by various environmental factors including temperature. As landfill temperature can fluctuate substantially seasonally, rates of CH4 oxidation can also vary, and this could lead to incomplete oxidation. This study aims at analyzing the effect of temperature on CH4 oxidation potential and microbial community structure of methanotrophs in laboratory-based studies of landfill cover soil and cultivated consortia. Soil and enrichment cultures were incubated at temperatures ranging from 6 to 70 °C, and rates of CH4 oxidation were measured, and the microbial community structure was analyzed using 16S rRNA gene amplicon sequencing and shotgun metagenome sequencing. CH4 oxidation occurred at temperatures from 6 to 50 °C in soil microcosm tests, and 6-40 °C in enrichment culture batch tests; maximum rates of oxidation were obtained at 30 °C. A corresponding shift in the soil microbiota was observed, with a transition from putative psychrophilic to thermophilic methanotrophs with increasing incubation temperature. A strong shift in methanotrophic community structure was observed above 30 °C. At temperatures up to 30 °C, methanotrophs from the genus Methylobacter were dominant in soils and enrichment cultures; at a temperature of 40 °C, putative thermophilic methanotrophs from the genus Methylocaldum become dominant. Maximum rate measurements of nearly 195 μg CH4 g-1 day-1 were observed in soil incubations, while observed maximum rates in enrichments were significantly lower, likely as a result of diffusion limitations. This study demonstrates that temperature is a critical factor affecting rates of landfill soil CH4 oxidation in vitro and that changing rates of CH4 oxidation are in part driven by changes in methylotroph community structure.

RevDate: 2019-07-18

Huang Z, Zhang C, Hu D, et al (2019)

Diagnosis of osteoarticular tuberculosis via metagenomic next-generation sequencing: A case report.

Experimental and therapeutic medicine, 18(2):1184-1188.

Osteoarticular tuberculosis (OAT) may cause severe complications and disability. Due to its indolent nature, OAT is difficult to diagnose in the early stages. Diagnosis by conventional culture is time-consuming and insensitive, and polymerase chain reaction-based molecular diagnostic methods are incapable of excluding co-infections. Metagenomic next-generation sequencing (mNGS) may identify a broad spectrum of microorganisms, including Mycobacterium, bacteria and fungi, in clinical specimens. Therefore, the diagnosis of OAT may be rapidly performed using mNGS. The present study reports on a case of OAT. The patient presented with right knee swelling and pain for 1 year; his C-reactive protein levels and erythrocyte sedimentation rate were markedly elevated. Although multiple pre-operative cultures were negative, mNGS was finally used to successfully detect the underlying pathogen. The result was confirmed by other molecular biology methods and Mycobacterium culture. Anti-tuberculosis therapy was administered accordingly and the patient finally recovered. In conclusion mNGS, with the ability to detect Mycobacterium and other microorganisms in a single assay, is an emerging approach for rapidly and accurately diagnosing OAT. This method may provide significant support to guide physicians in selecting the appropriate pharmacotherapy and surgical treatments.

RevDate: 2019-07-18

Tripathi BM, Kim HM, Jung JY, et al (2019)

Distinct Taxonomic and Functional Profiles of the Microbiome Associated With Different Soil Horizons of a Moist Tussock Tundra in Alaska.

Frontiers in microbiology, 10:1442.

Permafrost-underlain tundra soils in Northern Hemisphere are one of the largest reservoirs of terrestrial carbon, which are highly sensitive to microbial decomposition due to climate warming. However, knowledge about the taxonomy and functions of microbiome residing in different horizons of permafrost-underlain tundra soils is still limited. Here we compared the taxonomic and functional composition of microbiome between different horizons of soil cores from a moist tussock tundra ecosystem in Council, Alaska, using 16S rRNA gene and shotgun metagenomic sequencing. The composition, diversity, and functions of microbiome varied significantly between soil horizons, with top soil horizon harboring more diverse communities than sub-soil horizons. The vertical gradient in soil physico-chemical parameters were strongly associated with composition of microbial communities across permafrost soil horizons; however, a large fraction of the variation in microbial communities remained unexplained. The genes associated with carbon mineralization were more abundant in top soil horizon, while genes involved in acetogenesis, fermentation, methane metabolism (methanogenesis and methanotrophy), and N cycling were dominant in sub-soil horizons. The results of phylogenetic null modeling analysis showed that stochastic processes strongly influenced the composition of the microbiome in different soil horizons, except the bacterial community composition in top soil horizon, which was largely governed by homogeneous selection. Our study expands the knowledge on the structure and functional potential of microbiome associated with different horizons of permafrost soil, which could be useful in understanding the effects of environmental change on microbial responses in tundra ecosystems.

RevDate: 2019-07-18

Krüger K, Chafee M, Ben Francis T, et al (2019)

In marine Bacteroidetes the bulk of glycan degradation during algae blooms is mediated by few clades using a restricted set of genes.

The ISME journal pii:10.1038/s41396-019-0476-y [Epub ahead of print].

We investigated Bacteroidetes during spring algae blooms in the southern North Sea in 2010-2012 using a time series of 38 deeply sequenced metagenomes. Initial partitioning yielded 6455 bins, from which we extracted 3101 metagenome-assembled genomes (MAGs) including 1286 Bacteroidetes MAGs covering ~120 mostly uncultivated species. We identified 13 dominant, recurrent Bacteroidetes clades carrying a restricted set of conserved polysaccharide utilization loci (PULs) that likely mediate the bulk of bacteroidetal algal polysaccharide degradation. The majority of PULs were predicted to target the diatom storage polysaccharide laminarin, alpha-glucans, alpha-mannose-rich substrates, and sulfated xylans. Metaproteomics at 14 selected points in time revealed expression of SusC-like proteins from PULs targeting all of these substrates. Analyses of abundant key players and their PUL repertoires over time furthermore suggested that fewer and simpler polysaccharides dominated early bloom stages, and that more complex polysaccharides became available as blooms progressed.

RevDate: 2019-07-18

Mallick H, Franzosa EA, Mclver LJ, et al (2019)

Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences.

Nature communications, 10(1):3136 pii:10.1038/s41467-019-10927-1.

Microbial community metabolomics, particularly in the human gut, are beginning to provide a new route to identify functions and ecology disrupted in disease. However, these data can be costly and difficult to obtain at scale, while amplicon or shotgun metagenomic sequencing data are readily available for populations of many thousands. Here, we describe a computational approach to predict potentially unobserved metabolites in new microbial communities, given a model trained on paired metabolomes and metagenomes from the environment of interest. Focusing on two independent human gut microbiome datasets, we demonstrate that our framework successfully recovers community metabolic trends for more than 50% of associated metabolites. Similar accuracy is maintained using amplicon profiles of coral-associated, murine gut, and human vaginal microbiomes. We also provide an expected performance score to guide application of the model in new samples. Our results thus demonstrate that this 'predictive metabolomic' approach can aid in experimental design and provide useful insights into the thousands of community profiles for which only metagenomes are currently available.

RevDate: 2019-07-18

Li T, Mbala-Kingebeni P, Naccache SN, et al (2019)

Metagenomic Next-Generation Sequencing of the 2014 Ebola Virus Disease Outbreak in the Democratic Republic of the Congo.

Journal of clinical microbiology pii:JCM.00827-19 [Epub ahead of print].

We applied metagenomic next-generation sequencing (mNGS) to detect Zaire Ebola virus (EBOV) and other potential pathogens from whole blood samples from 70 patients with suspected Ebola hemorrhagic fever during a 2014 outbreak in Boende, Democratic Republic of the Congo (DRC) and correlated these findings with clinical symptoms. 20 of 31 patients (64.5%) tested in Kinshasa, DRC, were EBOV positive by quantitative RT-PCR (qRT-PCR). Despite partial degradation of sample RNA during shipping and handling, mNGS followed by EBOV-specific capture probe enrichment in a US genomics laboratory identified EBOV reads in 22 of 70 samples (31.4%), versus 21 of 70 (30.0%) EBOV-positive samples by repeat qRT-PCR (overall concordance = 87.1%). Reads from P. falciparum (malaria) were detected in 21 patients, of which at least 9 (42.9%) were co-infected with EBOV. Other positive viral detections include hepatitis B virus (n=2), human pegivirus 1 (n=2), Epstein-Barr virus (n=9), and Orungo virus (n=1), a virus in the Reoviridae family. The patient with Orungo virus infection presented with an acute febrile illness and died rapidly from massive hemorrhage and dehydration. Although the patient blood sample was negative by EBOV qRT-PCR testing, identification of viral reads by mNGS confirmed the presence of EBOV co-infection. In total, 9 new EBOV genomes (3 complete genomes, and an additional 6 ≥50% complete) were assembled. Relaxed molecular clock phylogenetic analysis demonstrated a molecular evolutionary rate for the Boende strain 4-10X slower than that of other Ebola lineages. These results demonstrate the utility of mNGS in broad-based pathogen detection and outbreak surveillance.

RevDate: 2019-07-18

Pan H, Guo R, Ju Y, et al (2019)

A single bacterium restores the microbiome dysbiosis to protect bones from destruction in a rat model of rheumatoid arthritis.

Microbiome, 7(1):107 pii:10.1186/s40168-019-0719-1.

BACKGROUND: Early treatment is key for optimizing the therapeutic success of drugs, and the current initiating treatment that blocks the progression of bone destruction during the pre-arthritic stages remains unsatisfactory. The microbial disorder in rheumatoid arthritis (RA) patients is significantly reversed with effective treatment. Modulating aberrant gut microbiomes into a healthy state is a potential therapeutic approach for preventing bone damage.

RESULTS: By using metagenomic shotgun sequencing and a metagenome-wide association study, we assessed the effect of Lactobacillus casei (L. casei) on the induction of arthritis as well as on the associated gut microbiota and immune disorders in adjuvant-induced arthritis (AIA) rats. Treatment of AIA rats with L. casei inhibited joint swelling, lowered arthritis scores, and prevented bone destruction. Along with the relief of arthritis symptoms, dysbiosis in the microbiome of arthritic rats was significantly reduced after L. casei intervention. The relative abundance of AIA-decreased Lactobacillus strains, including Lactobacillus hominis, Lactobacillus reuteri, and Lactobacillus vaginalis, were restored to normal and Lactobacillus acidophilus was upregulated by the administration of L. casei to the AIA rats. Moreover, L. casei downregulated the expression of pro-inflammatory cytokines, which are closely linked to the effect of the L. casei treatment-associated microbes. Functionally, the maintenance of the redox balance of oxidative stress was involved in the improvement in the L. casei-treated AIA rats.

CONCLUSION: A single bacterium, L. casei (ATCC334), was able to significantly suppress the induction of AIA and protect bones from destruction in AIA rats by restoring the microbiome dysbiosis in the gut, indicating that using probiotics may be a promising strategy for treating RA, especially in the early stage of the disease.

RevDate: 2019-07-18

Cai YL, Cao Y, Fan XZ, et al (2019)

[Microbiome analysis of diabetic foot osteomyelitis by metagenome sequencing technology].

Zhonghua yi xue za zhi, 99(26):2057-2061.

Objective: To analyze the microbiome of diabetic foot osteomyelitis (DFO) by means of metagenome sequencing and provide evidence for identification of pathogenic bacteria in DFO. Methods: A total of 5 patients (3 males and 2 females) with DFO hospitalized at the Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University were enrolled and infected bone specimens were obtained between September 2016 and April 2017. The mean age was (55.8±9.5) years. Metagenome sequencing was performed to explore the characteristics of microbiome, and compared with the results of 16S rRNA sequencing. Results: The results of metagenome sequencing showed that DFO contained diverse microorganism. Totally, 22 dominant species were obtained, Klebsiella pneumoniae (69.66%) was the most abundant, followed by Veillonella parvula (36.93%) and Prevotella intermedia (34.19%). Compared with the 16S rRNA sequencing, metagenome sequencing could obtain more species information on the basis of fewer samples. At the genus level, both sequencing techniques suggested the most dominant pathogen in DFO was anaerobe. All bone specimens had polymicrobial communities. Conclusions: More microecological diversity and abundance of DFO can be found by using metagenome sequencing. At the species level, more bacteria, even bacterial strains can be identified by metagenome sequencing. At the genus level, the most abundant bacteria is anaerobe, however, at the species level, it is facultative anaerobe.

RevDate: 2019-07-17

Shah A, Crawford D, Burger D, et al (2019)

Effects of Antibiotic Therapy in Primary Sclerosing Cholangitis with and without Inflammatory Bowel Disease: A Systematic Review and Meta-Analysis.

Seminars in liver disease [Epub ahead of print].

The authors conducted a systematic review and meta-analysis to assess the effect of antibiotic therapy in primary sclerosing cholangitis (PSC). Effect of antibiotic therapy on Mayo PSC Risk Score (MRS), serum alkaline phosphatase (ALP), total serum bilirubin (TSB), and adverse events (AEs) rates were calculated and expressed as standardized difference of means or proportions. Five studies including 124 PSC patients who received antibiotics were included. Overall, antibiotic treatment was associated with a statistically significant reduction in ALP, MRS, and TSB by 33.2, 36.1, and 28.8%, respectively. ALP reduction was greatest for vancomycin (65.6%, p < 0.002) and smallest with metronidazole (22.7%, p = 0.18). Overall, 8.9% (95% confidence interval: 3.9-13.9) of patients had AEs severe enough to discontinue antibiotic therapy. In PSC patients, antibiotic treatment results in a significant improvement in markers of cholestasis and MRS. Antibiotics, particularly vancomycin, may have a positive effect on PSC either via direct effects on the microbiome or via host-mediated mechanisms.

RevDate: 2019-07-17

Haas S, Desai DK, LaRoche J, et al (2019)

Geomicrobiology of the Carbon, Nitrogen and Sulfur Cycles in Powell Lake: A Permanently Stratified Water Column Containing Ancient Seawater.

Environmental microbiology [Epub ahead of print].

We present the first geomicrobiological characterization of the meromictic water column of Powell Lake (British Columbia, Canada), a former fjord which has been stably stratified since the last glacial period. Its deepest layers (300-350 m) retain isolated, relict seawater from that period. Fine-scale vertical profiling of the water chemistry and microbial communities allowed subdivision of the water column into distinct geomicrobiological zones. These zones were further characterized by phylogenetic and functional marker genes from amplicon and shotgun metagenome sequencing. Binning of metagenomic reads allowed the linkage of function to specific taxonomic groups. Statistical analyses (ANOSIM, Bray-Curtis similarity) confirmed that the microbial community structure followed closely the geochemical zonation. Yet, our characterization of the genetic potential relevant to carbon, nitrogen and sulfur cycling of each zone revealed unexpected features, including potential for facultative anaerobic methylotrophy, nitrogen fixation despite high ammonium concentrations and potential micro-aerobic nitrifiers within the chemocline. At the oxic-suboxic interface, facultative anaerobic potential was found in the widespread freshwater lineage acI (Actinobacteria), suggesting intriguing ecophysiological similarities to the marine SAR11. Evolutionary divergent lineages among diverse phyla were identified in the ancient seawater zone and may indicate novel adaptations to this unusual environment. This article is protected by copyright. All rights reserved.

RevDate: 2019-07-17

Stres B, L Kronegger (2019)

Shift in the paradigm towards next-generation microbiology.

FEMS microbiology letters pii:5533319 [Epub ahead of print].

In this work, the position of contemporary microbiology is considered from the perspective of scientific success, and a list of historical points and lessons learned from the fields of medical microbiology, microbial ecology and systems biology are presented. In addition, patterns in the development of top-down research topics that emerged over time as well as overlapping ideas and personnel, which are the first signs of trans-domain research activities in the fields of metagenomics, metaproteomics, metatranscriptomics and metabolomics, are explored through analysis of the publication networks of 28.654 papers using the computer programme Pajek. The current state of affairs is defined, and the need for meta-analyses to leverage publication biases in the field of microbiology is put forward as a very important emerging field of microbiology, especially since microbiology is progressively dealing with multiscale systems. Consequently, the need for cross-fertilisation with other fields/disciplines instead of 'more microbiology' is needed to advance the field of microbiology as such. The reader is directed to consider how novel technologies, the introduction of big data approaches and artificial intelligence have transformed microbiology into a multi-scale field and initiated a shift away from its history of mostly manual work and towards a largely technology-, data- and statistics-driven discipline that is often coupled with automation and modelling.

RevDate: 2019-07-17

Hitch TCA, Edwards JE, RA Gilbert (2019)

Metatranscriptomics reveals mycoviral populations in the ovine rumen.

FEMS microbiology letters pii:5533320 [Epub ahead of print].

The rumen is known to contain DNA based viruses, although it is not known whether RNA based viruses that infect fungi (mycoviruses) are also present. Analysis of publicly available rumen metatranscriptome sequence data from sheep rumen samples (n = 20) was used to assess whether RNA based viruses exist within the ovine rumen. A total of 2,466 unique RNA viral contigs were identified that had homology to 9 viral families. The Partitiviridae was the most consistently observed mycoviral family. High variation in the abundance of each detected mycovirus suggests that rumen mycoviral populations vary greatly between individual sheep. Functional analysis of the genes within the assembled mycoviral contigs, suggests that the mycoviruses detected had simple genomes, often only carrying the machinery required for replication. The fungal population of the ovine rumen was also assessed using metagenomics data from the same samples, and was consistently dominated by the phyla Ascomycota and Basidomycota. The strictly anaerobic phyla, Neocallimastigomycota, were also present in all samples but at a low abundance. This preliminary investigation has provided clear evidence that mycoviruses with RNA genomes exist in the rumen, with further in-depth studies now required to characterise this mycoviral community and determine their role in the rumen.

RevDate: 2019-07-19

Gallon P, Parekh M, Ferrari S, et al (2019)

Metagenomics in ophthalmology: Hypothesis or real prospective?.

Biotechnology reports (Amsterdam, Netherlands), 23:e00355 pii:e00355.

Metagenomic analysis was originally associated with the studies of genetic material from environmental samples. But, with the advent of the Human Microbiome Project, it has now been applied in clinical practices. The ocular surface (OS) is the most exposed part of the eye, colonized by several microbial communities (both, OS and environmental) that contribute to the maintenance of the physiological state. Limited knowledge has been acquired on these microbes due to the limitations of conventional diagnostic methods. Emerging fields of research are focusing on Next Generation Sequencing (NGS) technologies to obtain reliable information on the OS microbiome. Currently only pre-specified pathogens can be detected by conventional culture-based techniques or Polymerase Chain Reaction (PCR), but there are conditions to state whether metagenomics could revolutionize the diagnosis of ocular diseases. The aim of this review is to provide an updated overview of the studies involving NGS technology for OS microbiome.

RevDate: 2019-07-17

Lefeuvre P, Martin DP, Elena SF, et al (2019)

Evolution and ecology of plant viruses.

Nature reviews. Microbiology pii:10.1038/s41579-019-0232-3 [Epub ahead of print].

The discovery of the first non-cellular infectious agent, later determined to be tobacco mosaic virus, paved the way for the field of virology. In the ensuing decades, research focused on discovering and eliminating viral threats to plant and animal health. However, recent conceptual and methodological revolutions have made it clear that viruses are not merely agents of destruction but essential components of global ecosystems. As plants make up over 80% of the biomass on Earth, plant viruses likely have a larger impact on ecosystem stability and function than viruses of other kingdoms. Besides preventing overgrowth of genetically homogeneous plant populations such as crop plants, some plant viruses might also promote the adaptation of their hosts to changing environments. However, estimates of the extent and frequencies of such mutualistic interactions remain controversial. In this Review, we focus on the origins of plant viruses and the evolution of interactions between these viruses and both their hosts and transmission vectors. We also identify currently unknown aspects of plant virus ecology and evolution that are of practical importance and that should be resolvable in the near future through viral metagenomics.

RevDate: 2019-07-17

Macher JN, Speksnijder A, Choo LQ, et al (2019)

Uncovering bacterial and functional diversity in macroinvertebrate mitochondrial-metagenomic datasets by differential centrifugation.

Scientific reports, 9(1):10257 pii:10.1038/s41598-019-46717-4.

PCR-free techniques such as meta-mitogenomics (MMG) can recover taxonomic composition of macroinvertebrate communities, but suffer from low efficiency, as >90% of sequencing data is mostly uninformative due to the great abundance of nuclear DNA that cannot be identified with current reference databases. Current MMG studies do not routinely check data for information on macroinvertebrate-associated bacteria and gene functions. However, this could greatly increase the efficiency of MMG studies by revealing yet overlooked diversity within ecosystems and making currently unused data available for ecological studies. By analysing six 'mock' communities, each containing three macroinvertebrate taxa, we tested whether this additional data on bacterial taxa and functional potential of communities can be extracted from MMG datasets. Further, we tested whether differential centrifugation, which is known to greatly increase efficiency of macroinvertebrate MMG studies by enriching for mitochondria, impacts on the inferred bacterial community composition. Our results show that macroinvertebrate MMG datasets contain a high number of mostly endosymbiont bacterial taxa and associated gene functions. Centrifugation reduced both the absolute and relative abundance of highly abundant Gammaproteobacteria, thereby facilitating detection of rare taxa and functions. When analysing both taxa and gene functions, the number of features obtained from the MMG dataset increased 31-fold ('enriched') respectively 234-fold ('not enriched'). We conclude that analysing MMG datasets for bacteria and gene functions greatly increases the amount of information available and facilitates the use of shotgun metagenomic techniques for future studies on biodiversity.

RevDate: 2019-07-17

Boscaro V, Husnik F, Vannini C, et al (2019)

Symbionts of the ciliate Euplotes: diversity, patterns and potential as models for bacteria-eukaryote endosymbioses.

Proceedings. Biological sciences, 286(1907):20190693.

Endosymbioses between bacteria and eukaryotes are enormously important in ecology and evolution, and as such are intensely studied. Despite this, the range of investigated hosts is narrow in the context of the whole eukaryotic tree of life: most of the information pertains to animal hosts, while most of the diversity is found in unicellular protists. A prominent case study is the ciliate Euplotes, which has repeatedly taken up the bacterium Polynucleobacter from the environment, triggering its transformation into obligate endosymbiont. This multiple origin makes the relationship an excellent model to understand recent symbioses, but Euplotes may host bacteria other than Polynucleobacter, and a more detailed knowledge of these additional interactions is needed in order to correctly interpret the system. Here, we present the first systematic survey of Euplotes endosymbionts, adopting a classical as well as a metagenomic approach, and review the state of knowledge. The emerging picture is indeed quite complex, with some Euplotes harbouring rich, stable prokaryotic communities not unlike those of multicellular animals. We provide insights into the distribution, evolution and diversity of these symbionts (including the establishment of six novel bacterial taxa), and outline differences and similarities with the most well-understood group of eukaryotic hosts: insects.

RevDate: 2019-07-16

Million M, Gaudin M, Melenotte C, et al (2019)

Metagenomic Analysis of Microdissected Valvular Tissue for Etiologic Diagnosis of Blood Culture Negative Endocarditis.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America pii:5532606 [Epub ahead of print].

BACKGROUND: Etiological diagnosis is one of the keys to therapeutic adaptation and improved prognosis, particularly for infections such as endocarditis. In blood-culture negative endocarditis (BCNE), 22% of cases remain undiagnosed despite an updated comprehensive syndromic approach prompting us to develop a new diagnostic approach.

METHODS: Eleven valves of 10 BCNE patients were analyzed using a method combining human RNA bait-depletion followed by phi29 DNA polymerase-based multiple displacement amplification and shotgun DNA sequencing. An additional case, in which the microbe was serendipitously visualized by immunofluorescence, was analyzed by the same method, but after laser capture microdissection (LCM).

RESULTS: Background DNA prevents any diagnosis in the cases analyzed without microdissection because majority sequences were contaminants. Moraxella sequences were dramatically enriched in the stained microdissected region of the additional case. A consensus genome sequence of 2.4Mbp covering more than 94% of the Moraxella osloensis KSH reference genome was reconstructed with a 234X average coverage. Several antibiotic resistance genes were observed. Etiological diagnosis was confirmed by western blot and specific PCR with sequencing on a different valve sample.

CONCLUSION: Microdissection could be a key to the metagenomic diagnosis of infectious diseases when a microbe is visualized but remains unidentified despite an updated optimal approach. M. osloensis should be tested in blood-culture negative endocarditis.

RevDate: 2019-07-18

Wang S, Li N, Li N, et al (2019)

A Comparative Analysis of Biosynthetic Gene Clusters in Lean and Obese Humans.

BioMed research international, 2019:6361320.

Obesity is intrinsically linked with the gut microbiome, and studies have identified several obesity-associated microbes. The microbe-microbe interactions can alter the composition of the microbial community and influence host health by producing secondary metabolites (SMs). However, the contribution of these SMs in the prevention and treatment of obesity has been largely ignored. We identified several SM-encoding biosynthetic gene clusters (BGCs) from the metagenomic data of lean and obese individuals and found significant association between some BGCs, including those that produce hitherto unknown SM, and obesity. In addition, the mean abundance of BGCs was positively correlated with obesity, consistent with the lower taxonomic diversity in the gut microbiota of obese individuals. By comparing the BGCs of known SM between obese and nonobese samples, we found that menaquinone produced by Enterobacter cloacae showed the highest correlation with BMI, in agreement with a recent study on human adipose tissue composition. Furthermore, an obesity-related nonribosomal peptide synthetase (NRPS) was negatively associated with Bacteroidetes, indicating that the SMs produced by intestinal microbes in obese individuals can change the microbiome structure. This is the first systemic study of the association between gut microbiome BGCs and obesity and provides new insights into the causes of obesity.

RevDate: 2019-07-18

Trubl G, Roux S, Solonenko N, et al (2019)

Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils.

PeerJ, 7:e7265 pii:7265.

Soils impact global carbon cycling and their resident microbes are critical to their biogeochemical processing and ecosystem outputs. Based on studies in marine systems, viruses infecting soil microbes likely modulate host activities via mortality, horizontal gene transfer, and metabolic control. However, their roles remain largely unexplored due to technical challenges with separating, isolating, and extracting DNA from viruses in soils. Some of these challenges have been overcome by using whole genome amplification methods and while these have allowed insights into the identities of soil viruses and their genomes, their inherit biases have prevented meaningful ecological interpretations. Here we experimentally optimized steps for generating quantitatively-amplified viral metagenomes to better capture both ssDNA and dsDNA viruses across three distinct soil habitats along a permafrost thaw gradient. First, we assessed differing DNA extraction methods (PowerSoil, Wizard mini columns, and cetyl trimethylammonium bromide) for quantity and quality of viral DNA. This established PowerSoil as best for yield and quality of DNA from our samples, though ∼1/3 of the viral populations captured by each extraction kit were unique, suggesting appreciable differential biases among DNA extraction kits. Second, we evaluated the impact of purifying viral particles after resuspension (by cesium chloride gradients; CsCl) and of viral lysis method (heat vs bead-beating) on the resultant viromes. DNA yields after CsCl particle-purification were largely non-detectable, while unpurified samples yielded 1-2-fold more DNA after lysis by heat than by bead-beating. Virome quality was assessed by the number and size of metagenome-assembled viral contigs, which showed no increase after CsCl-purification, but did from heat lysis relative to bead-beating. We also evaluated sample preparation protocols for ssDNA virus recovery. In both CsCl-purified and non-purified samples, ssDNA viruses were successfully recovered by using the Accel-NGS 1S Plus Library Kit. While ssDNA viruses were identified in all three soil types, none were identified in the samples that used bead-beating, suggesting this lysis method may impact recovery. Further, 13 ssDNA vOTUs were identified compared to 582 dsDNA vOTUs, and the ssDNA vOTUs only accounted for ∼4% of the assembled reads, implying dsDNA viruses were dominant in these samples. This optimized approach was combined with the previously published viral resuspension protocol into a sample-to-virome protocol for soils now available at protocols.io, where community feedback creates 'living' protocols. This collective approach will be particularly valuable given the high physicochemical variability of soils, which will may require considerable soil type-specific optimization. This optimized protocol provides a starting place for developing quantitatively-amplified viromic datasets and will help enable viral ecogenomic studies on organic-rich soils.

RevDate: 2019-07-18

Li C, Tan X, Bai J, et al (2019)

A survey of the sperm whale (Physeter catodon) commensal microbiome.

PeerJ, 7:e7257 pii:7257.

Background: Mammalian commensal microbiota play important roles in the health of its host. In comparison to terrestrial mammals, commensal microbiota of marine mammals is mainly focused on the composition and function of skin and gut microbiota, with less attention paid to the health impact of bacteria and viruses. Previous studies on sperm whales (Physeter catodon) have affirmed their important phylogenetic position; however, studies on their commensal microbiota have not been published, due to difficulty in sample collection.

Methods: Here, we sequenced the metagenomes of blood, muscle and fecal samples from a stranded sperm whale using the BGISEQ-500 platform. We compared the diversity and abundance of microbiomes from three different tissues and tried to search pathogenic bacterial and virulence genes probably related to the health of the sperm whale. We also performed 16S rDNA sequencing of the fecal sample to compare to published gut metagenome data from other marine mammals.

Results: Our results demonstrated notable differences in species richness and abundance in the three samples. Extensive bacteria, including Enterococcus faecium, Fusobacterium nucleatum, Pseudomonas aeruginosa, Streptococcus anginosus, Streptococcus pneumoniae, and Streptococcus suis, and five toxigenic Clostridium species usually associated with infection, were found in the three samples. We also found the taxa composition of sperm whale gut microbiota was similar to that of other whales, suggesting co-evolution with its host. This study is the first report of the sperm whale gut microbiome, and provides a foundation for the pathogen detection and health assessment of the sperm whale.

RevDate: 2019-07-16

Ji BW, Sheth RU, Dixit PD, et al (2019)

Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling.

Nature methods pii:10.1038/s41592-019-0467-y [Epub ahead of print].

Metagenomic sequencing has enabled detailed investigation of diverse microbial communities, but understanding their spatiotemporal variability remains an important challenge. Here, we present decomposition of variance using replicate sampling (DIVERS), a method based on replicate sampling and spike-in sequencing. The method quantifies the contributions of temporal dynamics, spatial sampling variability, and technical noise to the variances and covariances of absolute bacterial abundances. We applied DIVERS to investigate a high-resolution time series of the human gut microbiome and a spatial survey of a soil bacterial community in Manhattan's Central Park. Our analysis showed that in the gut, technical noise dominated the abundance variability for nearly half of the detected taxa. DIVERS also revealed substantial spatial heterogeneity of gut microbiota, and high temporal covariances of taxa within the Bacteroidetes phylum. In the soil community, spatial variability primarily contributed to abundance fluctuations at short time scales (weeks), while temporal variability dominated at longer time scales (several months).

RevDate: 2019-07-16

Holck J, Djajadi DT, Brask J, et al (2019)

Novel xylanolytic triple domain enzyme targeted at feruloylated arabinoxylan degradation.

Enzyme and microbial technology, 129:109353.

A three catalytic domain multi-enzyme; a CE1 ferulic acid esterase, a GH62 α-l-arabinofuranosidase and a GH10 β-d-1,4-xylanase was identified in a metagenome obtained from wastewater treatment sludge. The capability of the CE1-GH62-GH10 multi-enzyme to degrade arabinoxylan was investigated to examine the hypothesis that CE1-GH62-GH10 would degrade arabinoxylan more efficiently than the corresponding equimolar mix of the individual enzymes. CE1-GH62-GH10 efficiently catalyzed the production of xylopyranose, xylobiose, xylotriose, arabinofuranose and ferulic acid (FA) when incubated with insoluble wheat arabinoxylan (WAX-I) (kcat = 20.8 ± 2.6 s-1). Surprisingly, in an equimolar mix of the individual enzymes a similar kcat towards WAX-I was observed (kcat = 17.3 ± 3.8 s-1). Similarly, when assayed on complex plant biomass the activity was comparable between CE1-GH62-GH10 and an equimolar mix of the individual enzymes. This suggests that from a hydrolytic point of view a CE1-GH62-GH10 multi-enzyme is not an advantage. Determination of the melting temperatures for CE1-GH62-GH10 (71.0 ± 0.05 °C) and CE1 (69.9 ± 0.02), GH62 (65.7 ± 0.06) and GH10 (71 ± 0.05 °C) indicates that CE1 and GH62 are less stable as single domain enzymes. This conclusion was corroborated by the findings that CE1 lost ˜50% activity within 2 h, while GH62 retained ˜50% activity after 24 h, whereas CE1-GH62-GH10 and GH10 retained ˜50% activity for 72 h. GH62-GH10, when appended to each other, displayed a higher specificity constant (kcat/Km = 0.3 s-1 mg-1 ml) than the individual GH10 (kcat/Km = 0.12 s-1 ± 0.02 mg-1 ml) indicating a synergistic action between the two. Surprisingly, CE1-GH62, displayed a 2-fold lower kcat towards WAX-I than GH62, which might be due to the presence of a putative carbohydrate binding module appended to CE1 at the N-terminal. Both CE1 and CE1-GH62 released insignificant amounts of FA from WAX-I, but FA was released from WAX-I when both CE1 and GH10 were present, which might be due to GH10 releasing soluble oligosaccharides that CE1 can utilize as substrate. CE1 also displayed activity towards solubilized 5-O-trans-feruloyl-α-l-Araf (kcat = 36.35 s-1). This suggests that CE1 preferably acts on soluble oligosaccharides.

RevDate: 2019-07-16

Chen J, McIlroy SE, Archana A, et al (2019)

A pollution gradient contributes to the taxonomic, functional, and resistome diversity of microbial communities in marine sediments.

Microbiome, 7(1):104 pii:10.1186/s40168-019-0714-6.

BACKGROUND: Coastal marine environments are one of the most productive ecosystems on Earth. However, anthropogenic impacts exert significant pressure on coastal marine biodiversity, contributing to functional shifts in microbial communities and human health risk factors. However, relatively little is known about the impact of eutrophication-human-derived nutrient pollution-on the marine microbial biosphere.

RESULTS: Here, we tested the hypothesis that benthic microbial diversity and function varies along a pollution gradient, with a focus on human pathogens and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG annotation revealed that zinc, lead, total volatile solids, and ammonia nitrogen were correlated with microbial diversity and function. We propose several microbes, including Planctomycetes and sulfate-reducing microbes as candidates to reflect pollution concentration. Annotation of antibiotic resistance genes showed that the highest abundance of efflux pumps was found at the most polluted site, corroborating the relationship between pollution and human health risk factors. This result suggests that sediments at polluted sites harbor microbes with a higher capacity to reduce intracellular levels of antibiotics, heavy metals, or other environmental contaminants.

CONCLUSIONS: Our findings suggest a correlation between pollution and the marine sediment microbiome and provide insight into the role of high-turnover microbial communities as well as potential pathogenic organisms as real-time indicators of water quality, with implications for human health and demonstrate the inner functional shifts contributed by the microcommunities.

RevDate: 2019-07-18

You X, Einson JE, Lopez-Pena CL, et al (2017)

Food-grade cationic antimicrobial ε-polylysine transiently alters the gut microbial community and predicted metagenome function in CD-1 mice.

NPJ science of food, 1:8 pii:6.

Diet is an important factor influencing the composition and function of the gut microbiome, but the effect of antimicrobial agents present within foods is currently not understood. In this study, we investigated the effect of the food-grade cationic antimicrobial ε-polylysine on the gut microbiome structure and predicted metagenomic function in a mouse model. The relative abundances of predominant phyla and genera, as well as the overall community structure, were perturbed in response to the incorporation of dietary ε-polylysine. Unexpectedly, this modification to the gut microbiome was experienced transiently and resolved to the initial basal composition at the final sampling point. In addition, a differential non-random assembly was observed in the microbiomes characterized from male and female co-housed animals, although their perturbation trajectories in response to diet remain consistent. In conclusion, antimicrobial ε-polylysine incorporated into food systems transiently alters gut microbial communities in mice, as well as their predicted function. This indicates a dynamic but resilient microbiome that adapts to microbial-active dietary components.

RevDate: 2019-07-19

Wang J, Khokhar I, Ren C, et al (2019)

Characterization and 16S metagenomic analysis of organophosphorus flame retardants degrading consortia.

Journal of hazardous materials, 380:120881 pii:S0304-3894(19)30834-9 [Epub ahead of print].

Three bacterial consortia, named YC-SY1, YC-BJ1 and YC-GZ1, were enriched from different areas of China. Bacterial consortia YC-SY1, YC-BJ1 and YC-GZ1 could efficiently degrade triphenyl phosphate (TPhP) (100 mg/L) by approximately 79.4%, 99.8% and 99.6%, tricresyl phosphate (TCrP) by 90.6%, 91.9% and 96.3%, respectively, within 4 days. And they could retain high degrading efficiency under a broad range of temperature (15-40 ℃), pH (6.0-10.0) and salinity (0-4%). A total of 10 bacterial isolates were selected and investigated their degradation capacity. Among these isolates, two were significantly superior to the others. Strain Rhodococcus sp. YC-JH2 could utilize TPhP (50 mg/L) as sole carbon source for growth with 37.36% degradation within 7 days. Strain Sphingopyxis sp. YC-JH3 could efficiently degrade 96.2% of TPhP (50 mg/L) within 7 days, except that no cell growth was observed. Combined with 16S diversity analysis, our results suggest that the effective components of three bacterial consortia responsible for TPhP and TCrP degradation were almost the same, that is, bacteria capable of degrading TPhP and TCrP are limited, in this study, the most efficient component is Sphingopyxis. This study provides abundant microorganism sources for research on organophosphorus flame retardants (OPFRs) metabolism and bioremediation towards OPFRs-contaminated environments.

RevDate: 2019-07-19

Han L, Cai L, Zhang H, et al (2019)

Development of antibiotic resistance genes in soils with ten successive treatments of chlortetracycline and ciprofloxacin.

Environmental pollution (Barking, Essex : 1987), 253:152-160 pii:S0269-7491(19)31504-0 [Epub ahead of print].

Antibiotic contamination caused by the long-term use of organic manure (OM) in greenhouse agricultural soils poses potential detrimental effects to the soil environment. By applying OM containing chlortetracycline (CTC) and/or ciprofloxacin (CIP) ten times in soil under laboratory conditions, we investigated the dissipation and accumulation characteristics of CTC and CIP in the soil, the changes in the microbial pollution-induced community tolerance (PICT), and the diversity and abundance of antibiotic resistance genes (ARGs) in the soil microbiome. The dissipation of CTC was rapid while CIP was accumulated in repeatedly treated soils; further, CIP could inhibit the dissipation of CTC. Meanwhile, the PICT to CTC and/or CIP significantly increased up to 15.0-fold after ten successive treatments compared to that in the first treatment. As the treatment frequency increased, significant upward trends in the abundances of tetracycline resistance genes tetA(G), tetX2, tetX, tetG, tetA(33), tetA, tetW, and tetA(P), fluoroquinolone resistance gene qnrA6, and multiple resistance gene mexF were revealed by both metagenomic and qPCR analyses. The findings demonstrated that repeated treatments with CTC and/or CIP can alter the dissipation rate, promote an increase in PICT to CTC and/or CIP, and increase the ARGs abundance in steps.

RevDate: 2019-07-15

Martini VP, Krieger N, Glogauer A, et al (2019)

Structure solution and analyses of the first true lipase obtained from metagenomics indicate potential for increased thermostability.

New biotechnology pii:S1871-6784(18)30258-9 [Epub ahead of print].

Metagenomics is a modern approach to discovery of new enzymes with novel properties. This article reports the structure of a new lipase, belonging to family I.1, obtained by means of metagenomics. Its structure presents a fold typical of α/β hydrolases, with the lid in closed conformation. The protein was previously shown to present high thermostability and to be stable in aqueous solutions of polar organic solvents at high concentrations [30% (V/V)]. Molecular dynamics studies showed that the protein maintains its structure well in organic solvents. They also suggested that its thermostability might be enhanced if it were mutated to present a disulfide bond similar to that typically found in lipase family I.2. These findings identify this lipase as a good candidate for further improvement through protein engineering.

RevDate: 2019-07-14

Singh NK, Wood JM, Mhatre SS, et al (2019)

Correction to: Metagenome to phenome approach enables isolation and genomics characterization of Kalamiella piersonii gen. nov., sp. nov. from the International Space Station.

In our original published manuscript entitled "Metagenome to phenome approach enables isolation and genomics characterization of Kalamiella piersonii gen. nov., sp. nov. from the International Space Station" (Singh et al. 2019), we found a taxonomic description format error: As per the Rule 27.

RevDate: 2019-07-14

Huang JM, Y Wang (2019)

Genomic differences within the phylum Marinimicrobia: From waters to sediments in the Mariana Trench.

Marine genomics pii:S1874-7787(19)30150-3 [Epub ahead of print].

Marinimicrobia are widespread from the marine surface to the hadal zone. Major clades of Marinimicrobia have evolved to different ecotypes along with energy gradients, but their genomes in deeper waters and sediments have rarely been studied. Here we obtained 11 Marinimicrobia draft genomes from the water column in the full-ocean depth and the hadal sediments in the Mariana Trench. All the predicted genomic capabilities of the metagenome-assembled genomes (MAGs) are indicative of heterotrophic lifestyle. The MAGs from the hadal depths are distinct from those from the mesopelagic and bathypelagic depths by enrichment of the genes involved in amino acids metabolism and mismatch repair. Compared with the MAGs from waters, those from the sediments were dramatically expanded by acquiring the genes responsible for chemotaxis, mobility and the two-component systems. Marinimicrobia were apparently differentiated in the environments with different depths, organic matters and electronic acceptors. Our results also posit a potential evolutionary relationship between the species inhabiting the waters and sediments, indicating the occurrence of allopatric speciation in Marinimicrobia.

RevDate: 2019-07-14

Kucharzyk KH, Rectanus HV, Bartling CM, et al (2019)

Use of omic tools to assess methyl tert-butyl ether (MTBE) degradation in groundwater.

Journal of hazardous materials pii:S0304-3894(19)30537-0 [Epub ahead of print].

This study employed innovative technologies to evaluate multiple lines of evidence for natural attenuation (NA) of methyl tertiary-butyl ether (MTBE) in groundwater at the 22 Area of Marine Corps Base (MCB) Camp Pendleton after decommissioning of a biobarrier system. For comparison, data from the 13 Area Gas Station where active treatment of MTBE is occurring was used to evaluate the effectiveness of omic techniques in assessing biodegradation. Overall, the 22 Area Gas Station appeared to be anoxic. MTBE was detected in large portion of the plume. In comparison, concentrations of MTBE at the 13 Area Gas Station were much higher (42,000 μg/L to 2800 μg/L); however, none of the oxygenates were detected. Metagenomic analysis of the indigenous groundwater microbial community revealed the presence of bacterial strains known to aerobically and anaerobically degrade MTBE at both sites. While proteomic analysis at the 22 Area Gas Station showed the presence of proteins of MTBE degrading microorganisms, the MTBE degradative proteins were only found at the 13 Area Gas Station. Taken together, these results provide evidence for previous NA of MTBE in the groundwater at 22 Area Gas Station and demonstrate the effectiveness of innovative-omic technologies to assist monitored NA assessments.

RevDate: 2019-07-19

Bengtsson-Palme J, Milakovic M, Švecová H, et al (2019)

Industrial wastewater treatment plant enriches antibiotic resistance genes and alters the structure of microbial communities.

Water research, 162:437-445 pii:S0043-1354(19)30595-0 [Epub ahead of print].

Antibiotic resistance is an emerging global health crisis, driven largely by overuse and misuse of antibiotics. However, there are examples in which the production of these antimicrobial agents has polluted the environment with active antibiotic residues, selecting for antibiotic resistant bacteria and the genes they carry. In this work, we have used shotgun metagenomics to investigate the taxonomic structure and resistance gene composition of sludge communities in a treatment plant in Croatia receiving wastewater from production of the macrolide antibiotic azithromycin. We found that the total abundance of antibiotic resistance genes was three times higher in sludge from the treatment plant receiving wastewater from pharmaceutical production than in municipal sludge from a sewage treatment plant in Zagreb. Surprisingly, macrolide resistance genes did not have higher abundances in the industrial sludge, but genes associated with mobile genetic elements such as integrons had. We conclude that at high concentrations of antibiotics, selection may favor taxonomic shifts towards intrinsically resistant species or strains harboring chromosomal resistance mutations rather than acquisition of mobile resistance determinants. Our results underscore the need for regulatory action also within Europe to avoid release of antibiotics into the environment.

RevDate: 2019-07-13

Sonthiphand P, Ruangroengkulrith S, Mhuantong W, et al (2019)

Metagenomic insights into microbial diversity in a groundwater basin impacted by a variety of anthropogenic activities.

Environmental science and pollution research international pii:10.1007/s11356-019-05905-5 [Epub ahead of print].

Microbial communities in groundwater are diverse and each may respond differently to environmental change. The goal of this study was to investigate the diversity, abundance, and dynamics of microbial communities in impacted groundwater and correlate them to the corresponding land use and groundwater geochemistry, using an Illumina MiSeq platform targeting the V3 and V4 regions of the 16S rRNA gene. The resulting MiSeq sequencing revealed the co-occurrence patterns of both abundant and rare microbial taxa within an impacted groundwater basin. Proteobacteria were the most common groundwater-associated bacterial phylum, mainly composed of the classes Gammaproteobacteria, Betaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria. The phyla detected at less abundances were the Firmicutes, Bacteroidetes, Planctomycetes, Actinobacteria, OD1, and Nitrospirae. The members of detected groundwater microorganisms involved in natural biogeochemical processes such as nitrification, anammox, methane oxidation, sulfate reduction, and arsenic transformation. Some of the detected microorganisms were able to perform anaerobic degradation of organic pollutants. The resulting PCA indicates that major land usage within the sampling area seemed to be significantly linked to the groundwater microbial distributions. The distinct microbial pattern was observed in the groundwater collected from a landfill area. This study suggests that the combinations of anthropogenic and natural effects possibly led to a unique pattern of microbial diversity across different locations at the impacted groundwater basin.

RevDate: 2019-07-13

Holt CC, Stone M, Bass D, et al (2019)

The first clawed lobster virus Homarus gammarus nudivirus (HgNV n. sp.) expands the diversity of the Nudiviridae.

Scientific reports, 9(1):10086 pii:10.1038/s41598-019-46008-y.

Viral diseases of crustaceans are increasingly recognised as challenges to shellfish farms and fisheries. Here we describe the first naturally-occurring virus reported in any clawed lobster species. Hypertrophied nuclei with emarginated chromatin, characteristic histopathological lesions of DNA virus infection, were observed within the hepatopancreatic epithelial cells of juvenile European lobsters (Homarus gammarus). Transmission electron microscopy revealed infection with a bacilliform virus containing a rod shaped nucleocapsid enveloped in an elliptical membrane. Assembly of PCR-free shotgun metagenomic sequencing produced a circular genome of 107,063 bp containing 97 open reading frames, the majority of which share sequence similarity with a virus infecting the black tiger shrimp: Penaeus monodon nudivirus (PmNV). Multiple phylogenetic analyses confirm the new virus to be a novel member of the Nudiviridae: Homarus gammarus nudivirus (HgNV). Evidence of occlusion body formation, characteristic of PmNV and its closest relatives, was not observed, questioning the horizontal transmission strategy of HgNV outside of the host. We discuss the potential impacts of HgNV on juvenile lobster growth and mortality and present HgNV-specific primers to serve as a diagnostic tool for monitoring the virus in wild and farmed lobster stocks.

RevDate: 2019-07-13

Gordon SP, Levy JJ, JP Vogel (2019)

PolyCRACKER, a robust method for the unsupervised partitioning of polyploid subgenomes by signatures of repetitive DNA evolution.

BMC genomics, 20(1):580 pii:10.1186/s12864-019-5828-5.

BACKGROUND: Our understanding of polyploid genomes is limited by our inability to definitively assign sequences to a specific subgenome without extensive prior knowledge like high resolution genetic maps or genome sequences of diploid progenitors. In theory, existing methods for assigning sequences to individual species from metagenome samples could be used to separate subgenomes in polyploid organisms, however, these methods rely on differences in coarse genome properties like GC content or sequences from related species. Thus, these approaches do not work for subgenomes where gross features are indistinguishable and related genomes are lacking. Here we describe a method that uses rapidly evolving repetitive DNA to circumvent these limitations.

RESULTS: By using short, repetitive, DNA sequences as species-specific signals we separated closely related genomes from test datasets and subgenomes from two polyploid plants, tobacco and wheat, without any prior knowledge.

CONCLUSION: This approach is ideal for separating the subgenomes of polyploid species with unsequenced or unknown progenitor genomes.

RevDate: 2019-07-12

Pjevac P, Dyksma S, Goldhammer T, et al (2019)

In situ abundance and carbon fixation activity of distinct anoxygenic phototrophs in the stratified seawater lake Rogoznica.

Environmental microbiology [Epub ahead of print].

Sulfide-driven anoxygenic photosynthesis is an ancient microbial metabolism that contributes significantly to inorganic carbon fixation in stratified, sulfidic water bodies. Methods commonly applied to quantify inorganic carbon fixation by anoxygenic phototrophs, however, cannot resolve the contributions of distinct microbial populations to the overall process. We implemented a straightforward workflow, consisting of radioisotope labeling and flow cytometric cell sorting based on the distinct autofluorescence of bacterial photo pigments, to discriminate and quantify contributions of co-occurring anoxygenic phototrophic populations to in situ inorganic carbon fixation in environmental samples. This allowed us to assign 89.3 ±7.6% of daytime inorganic carbon fixation by anoxygenic phototrophs in Lake Rogoznica (Croatia) to an abundant chemocline-dwelling population of green sulfur bacteria (dominated by Chlorobium phaeobacteroides), whereas the co-occurring purple sulfur bacteria (Halochromatium sp.) contributed only 1.8 ±1.4%. Furthermore, we obtained two metagenome assembled genomes of green sulfur bacteria and one of a purple sulfur bacterium which provides the first genomic insights into the genus Halochromatium, confirming its high metabolic flexibility and physiological potential for mixo- and heterotrophic growth. This article is protected by copyright. All rights reserved.

RevDate: 2019-07-12

Bartoszewicz JM, Seidel A, Rentzsch R, et al (2019)

DeePaC: Predicting pathogenic potential of novel DNA with reverse-complement neural networks.

Bioinformatics (Oxford, England) pii:5531656 [Epub ahead of print].

MOTIVATION: We expect novel pathogens to arise due to their fast-paced evolution, and new species to be discovered thanks to advances in DNA sequencing and metagenomics. Moreover, recent developments in synthetic biology raise concerns that some strains of bacteria could be modified for malicious purposes. Traditional approaches to open-view pathogen detection depend on databases of known organisms, which limits their performance on unknown, unrecognized, and unmapped sequences. In contrast, machine learning methods can infer pathogenic phenotypes from single NGS reads, even though the biological context is unavailable.

RESULTS: We present DeePaC, a Deep Learning Approach to Pathogenicity Classification. It includes a flexible framework allowing easy evaluation of neural architectures with reverse-complement parameter sharing. We show that convolutional neural networks and LSTMs outperform the state-of-the-art based on both sequence homology and machine learning. Combining a deep learning approach with integrating the predictions for both mates in a read pair results in cutting the error rate almost in half in comparison to the previous state-of-the-art.

AVAILABILITY: The code and the models are available at: https://gitlab.com/rki_bioinformatics/DeePaC.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

RevDate: 2019-07-12

Kandathil SM, Greener JG, DT Jones (2019)

Prediction of inter-residue contacts with DeepMetaPSICOV in CASP13.

Proteins [Epub ahead of print].

In this article, we describe our efforts in contact prediction in the CASP13 experiment. We employed a new deep learning-based contact prediction tool, DeepMetaPSICOV (or DMP for short), together with new methods and data sources for alignment generation. DMP evolved from MetaPSICOV and DeepCov and combines the input feature sets used by these methods as input to a deep, fully convolutional residual neural network. We also improved our method for multiple sequence alignment generation and included metagenomic sequences in the search. We discuss successes and failures of our approach and identify areas where further improvements may be possible. DMP is freely available at: https://github.com/psipred/DeepMetaPSICOV. This article is protected by copyright. All rights reserved.

RevDate: 2019-07-12

Michels N (2019)

Biological underpinnings from psychosocial stress towards appetite and obesity during youth: research implications towards metagenomics, epigenomics and metabolomics.

Nutrition research reviews pii:S0954422419000143 [Epub ahead of print].

Psychosocial stress, uncontrolled eating and obesity are three interrelated epidemiological phenomena already present during youth. This broad narrative conceptual review summarises main biological underpinnings of the stress-diet-obesity pathway and how new techniques can further knowledge. Cortisol seems the main biological factor from stress towards central adiposity; and diet, physical activity and sleep are the main behavioural pathways. Within stress-diet, the concepts of comfort food and emotional eating are highlighted, as cortisol affects reward pathways and appetite brain centres with a role for insulin, leptin, neuropeptide Y (NPY), endocannabinoids, orexin and gastrointestinal hormones. More recently researched biological underpinnings are microbiota, epigenetic modifications and metabolites. First, the gut microbiota reaches the stress-regulating and appetite-regulating brain centres via the gut-brain axis. Second, epigenetic analyses are recommended as diet, obesity, stress and gut microbiota can change gene expression which then affects appetite, energy homeostasis and stress reactivity. Finally, metabolomics would be a good technique to disentangle stress-diet-obesity interactions as multiple biological pathways are involved. Saliva might be an ideal biological matrix as it allows metagenomic (oral microbiota), epigenomic and metabolomic analyses. In conclusion, stress and diet/obesity research should be combined in interdisciplinary collaborations with implementation of several -omics analyses.

RevDate: 2019-07-12

Zhang Y, Zhang Y, Kuang Z, et al (2019)

Comparison of microbiomes and resistomes in two Karst groundwater sites in Chongqing, China.

Karst groundwater is an important water resource as it accounts for about 15% of the total landscape of the earth and supplies 20% of potable water worldwide. The antibiotics resistance is an emerging global concern, and antibiotics residual and increase of antibiotic resistance genes represent serious global concerns and emerging pollutants. There is no report on the antibiotic resistance genes in groundwater. To survey resistome and microbiome in Karst groundwater, two Karst water samples were chosen for metagenome and metatranscriptome study, namely the 37th spring (C) and Dongcao spring (R) in Beibei, Chongqing, China. The two sites differ significantly in sulfur content, geochemical parameters, community structure, antibiotic resistance genes and mechanisms, and these results may be influenced by anthropogenic activities. Combining with the Antibiotic Resistance Genes Database (ARDB), three types of resistance genes baca, sul2, sul1 are present in R and C, and ant3ia, ermc, tetpa are also present in R. The number of all resistance genes in R was more than C, and Proteobacteria, Bacteroidetes, Nitrospirae are the main sources of antibiotic resistance genes. In addition, a large number of genes related to antibiotic gene transmission and drug resistance were found in both samples. Karst groundwater is an important source of drinking water and a possible venue for the transmission of microbial antibiotic resistance genes. However, few studies addressed this issue in Karst groundwater, despite its widespread and great importance to global ecosystem. Karst groundwater is a reservoir for antibiotic resistant genes, and measures to control these resistant genes are urgently needed. This article is protected by copyright. All rights reserved.

RevDate: 2019-07-16

Dilthey AT, Jain C, Koren S, et al (2019)

Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps.

Nature communications, 10(1):3066 pii:10.1038/s41467-019-10934-2.

Metagenomic sequence classification should be fast, accurate and information-rich. Emerging long-read sequencing technologies promise to improve the balance between these factors but most existing methods were designed for short reads. MetaMaps is a new method, specifically developed for long reads, capable of mapping a long-read metagenome to a comprehensive RefSeq database with >12,000 genomes in <16 GB or RAM on a laptop computer. Integrating approximate mapping with probabilistic scoring and EM-based estimation of sample composition, MetaMaps achieves >94% accuracy for species-level read assignment and r2 > 0.97 for the estimation of sample composition on both simulated and real data when the sample genomes or close relatives are present in the classification database. To address novel species and genera, which are comparatively harder to predict, MetaMaps outputs mapping locations and qualities for all classified reads, enabling functional studies (e.g. gene presence/absence) and detection of incongruities between sample and reference genomes.

RevDate: 2019-07-15

Gehrig JL, Venkatesh S, Chang HW, et al (2019)

Effects of microbiota-directed foods in gnotobiotic animals and undernourished children.

Science (New York, N.Y.), 365(6449):.

To examine the contributions of impaired gut microbial community development to childhood undernutrition, we combined metabolomic and proteomic analyses of plasma samples with metagenomic analyses of fecal samples to characterize the biological state of Bangladeshi children with severe acute malnutrition (SAM) as they transitioned, after standard treatment, to moderate acute malnutrition (MAM) with persistent microbiota immaturity. Host and microbial effects of microbiota-directed complementary food (MDCF) prototypes targeting weaning-phase bacterial taxa underrepresented in SAM and MAM microbiota were characterized in gnotobiotic mice and gnotobiotic piglets colonized with age- and growth-discriminatory bacteria. A randomized, double-blind controlled feeding study identified a lead MDCF that changes the abundances of targeted bacteria and increases plasma biomarkers and mediators of growth, bone formation, neurodevelopment, and immune function in children with MAM.

RevDate: 2019-07-12

Shen N, Caixàs A, Ahlers M, et al (2019)

Longitudinal changes of microbiome composition and microbial metabolomics after surgical weight loss in individuals with obesity.

Surgery for obesity and related diseases : official journal of the American Society for Bariatric Surgery pii:S1550-7289(19)30264-3 [Epub ahead of print].

BACKGROUND: Some of the metabolic effects of bariatric surgery may be mediated by the gut microbiome.

OBJECTIVES: To study the effect of bariatric surgery on changes to gut microbiota composition and bacterial pathways, and their relation to metabolic parameters after bariatric surgery.

SETTINGS: University hospitals in the United States and Spain.

METHODS: Microbial diversity and composition by 16 S rRNA sequencing, putative bacterial pathways, and targeted circulating metabolites were studied in 26 individuals with severe obesity, with and without type 2 diabetes, before and at 3, 6, and 12 months after either gastric bypass or sleeve gastrectomy.

RESULTS: Bariatric surgery tended to increase alpha diversity, and significantly altered beta diversity, microbiota composition, and function up to 6 months after surgery, but these changes tend to regress to presurgery levels by 12 months. Twelve of 15 bacterial pathways enriched after surgery also regressed to presurgery levels at 12 months. Network analysis identified groups of bacteria significantly correlated with levels of circulating metabolites over time. There were no differences between study sites, surgery type, or diabetes status in terms of microbial diversity and composition at baseline and after surgery.

CONCLUSIONS: The association among changes in microbiome with decreased circulating biomarkers of inflammation, increased bile acids, and products of choline metabolism and other bacterial pathways suggest that the microbiome partially mediates improvement of metabolism during the first year after bariatric surgery.

RevDate: 2019-07-19

Quintela-Baluja M, Abouelnaga M, Romalde J, et al (2019)

Spatial ecology of a wastewater network defines the antibiotic resistance genes in downstream receiving waters.

Water research, 162:347-357 pii:S0043-1354(19)30597-4 [Epub ahead of print].

Wastewater treatment plants (WWTPs) are an effective barrier in the protection of human and environment health around the world, although WWTPs also are suggested to be selectors and-or reservoirs of antibiotic resistance genes (ARGs) before entering the environment. The dogma about WWTPs as "ARG selectors" presumes that biotreatment compartments (e.g., activated sludge; AS) are single densely populated ecosystems with elevated horizontal gene transfer. However, recent work has suggested WWTP biotreatment compartments may be different than previously believed relative to antibiotic resistance (AR) fate, and other process factors, such as bacterial separation and specific waste sources, may be key to ARGs released to the environment. Here we combined 16S rRNA metagenomic sequencing and high-throughput qPCR to characterise microbial communities and ARGs across a wastewater network in Spain that includes both community (i.e., non-clinical urban) and hospital sources. Contrary to expectations, ARGs found in downstream receiving waters were not dominated by AS biosolids (RAS), but more resembled raw wastewater sources. In fact, ARGs and microbial communities in liquid-phase WWTP effluents and RAS were significantly different (Bray-Curtis dissimilarity index = 0.66 ± 0.11), with a consequential fraction of influent ARGs and organisms passing directly through the WWTP with limited association with RAS. Instead, ARGs and organisms in the RAS may be more defined by biosolids separation and biophysical traits, such as flocculation, rather than ARG carriage. This explains why RAS has significantly lower ARG richness (47 ± 4 ARGs) than liquid-phase effluents (104 ± 5 ARGs), and downstream water column (135 ± 4 ARGs) and river sediments (120 ± 5 ARGs) (Tukey's test, p < 0.001). These data suggest RAS and liquid-phase WWTP effluents may reflect two parallel ecosystems with potentially limited ARG exchange. As such, ARG mitigation in WWTPs should more focus on removing bacterial hosts from the liquid phase, AR source reduction, and possibly disinfection to reduce ARG releases to the environment.

RevDate: 2019-07-11

PLOS ONE Staff (2019)

Correction: Scalable methods for analyzing and visualizing phylogenetic placement of metagenomic samples.

PloS one, 14(7):e0219925 pii:PONE-D-19-18998.

[This corrects the article DOI: 10.1371/journal.pone.0217050.].

RevDate: 2019-07-14

Erdogan IG, Mekuto L, Ntwampe SKO, et al (2019)

Metagenomic profiling dataset of bacterial communities of a drinking water supply system (DWSS) in the arid Namaqualand region, South Africa: Source (lower Orange River) to point-of-use (O'Kiep).

Data in brief, 25:104135 pii:104135.

The metagenomic data presented herein contains the bacterial community profile of a drinking water supply system (DWSS) supplying O'Kiep, Namaqualand, South Africa. Representative samples from the source (Orange River) to the point of use (O'Kiep), through a 150km DWSS used for drinking water distribution were analysed for bacterial content. PCR amplification of the 16S rRNA V1-V3 regions was undertaken using oligonucleotide primers 27F and 518R subsequent to DNA extraction. The PCR amplicons were processed using the illumina® reaction kits as per manufactures guidelines and sequenced using the illumina® MiSeq-2000, by means of MiSeq V3 kit. The data obtained was processed using a bioinformatics QIIME software with a compatible fast nucleic acid (fna) file. The raw sequences were deposited at the National Centre of Biotechnology (NCBI) and the Sequence Read Archive (SRA) database, obtaining accession numbers for each species identified.

RevDate: 2019-07-14

Zhou P, Li Z, Xu D, et al (2019)

Cepharanthine Hydrochloride Improves Cisplatin Chemotherapy and Enhances Immunity by Regulating Intestinal Microbes in Mice.

Frontiers in cellular and infection microbiology, 9:225.

Chemotherapy is one of the major treatment strategies for esophageal squamous cell carcinoma (ESCC). Unfortunately, most chemotherapeutic drugs have significant impacts on the intestinal microbes, resulting in side effects and reduced efficiency. Therefore, new strategies capable of overcoming these disadvantages of current chemotherapies are in urgent need. The natural product, Cepharanthine hydrochloride (CEH), is known for its anticancer and immunoregulatory properties. By sequencing the V4 region of 16S rDNA, we characterized the microbes of tumor-bearing mice treated with different chemotherapy strategies, including with CEH. We found that CEH improved the therapeutic effect of CDDP by manipulating the gut microbiota. Through metagenomic analyses of the microbes community, we identified a severe compositional and functional imbalance in the gut microbes community after CDDP treatment. However, CEH improved the effect of chemotherapy and ameliorated CDDP treatment-induced imbalance in the intestinal microbes. Mechanically, CEH activated TLR4 and MYD88 innate immune signaling, which is advantageous for the activation of the host's innate immunity to exert a balanced intestinal environment as well as to trigger a better chemotherapeutic response to esophageal cancer. In addition, TNFR death receptors were activated to induce apoptosis. In summary, our findings suggest that chemotherapy of CDDP combined with CEH increased the effect of chemotherapy and reduced the side effects on the microbes and intestinal mucosal immunity. We believe that these findings provide a theoretical basis for new clinical treatment strategies.

RevDate: 2019-07-14

Melkonian C, Gottstein W, Blasche S, et al (2019)

Finding Functional Differences Between Species in a Microbial Community: Case Studies in Wine Fermentation and Kefir Culture.

Frontiers in microbiology, 10:1347.

Microbial life usually takes place in a community where individuals interact, by competition for nutrients, cross-feeding, inhibition by end-products, but also by their spatial distribution. Lactic acid bacteria are prominent members of microbial communities responsible for food fermentations. Their niche in a community depends on their own properties as well as those of the other species. Here, we apply a computational approach, which uses only genomic and metagenomic information and functional annotation of genes, to find properties that distinguish a species from others in the community, as well as to follow individual species in a community. We analyzed isolated and sequenced strains from a kefir community, and metagenomes from wine fermentations. We demonstrate how the distinguishing properties of an organism lead to experimentally testable hypotheses concerning the niche and the interactions with other species. We observe, for example, that L. kefiranofaciens, a dominant organism in kefir, stands out among the Lactobacilli because it potentially has more amino acid auxotrophies. Using metagenomic analysis of industrial wine fermentations we investigate the role of an inoculated L. plantarum in malolactic fermentation. We observed that L. plantarum thrives better on white than on red wine fermentations and has the largest number of phosphotransferase system among the bacteria observed in the wine communities. Also, L. plantarum together with Pantoea, Erwinia, Asaia, Gluconobacter, and Komagataeibacter genera had the highest number of genes involved in biosynthesis of amino acids.

RevDate: 2019-07-11

Masoodi I, Alshanqeeti AS, Ahmad S, et al (2019)

Microbial dysbiosis in inflammatory bowel diseases: results of a metagenomic study in Saudi Arabia.

Minerva gastroenterologica e dietologica pii:S1121-421X.19.02576-5 [Epub ahead of print].

BACKGROUND: The intestinal Microbiota plays an essential role in the pathogenesis of Ulcerative colitis (UC)and Crohn's disease (CD).

METHODS: Metagenomic studies were used to study microbiota in the diagnosed cases of UC and CD at King Fahad Medical city Riyadh Saudi Arabia. Each segment of the colon was flushed with distilled water during colonoscopy, and the material was aspirated, immediately frozen for the study. The patients attending for screening colonoscopies were taken as age-matched healthy controls. The UC patients were followed clinically for any signs of exacerbation relapse, and CD patients were followed for any complications.

RESULTS: The metagenomic data on 46 (24 females) patients with Crohn's disease were analyzed along with a group of age and gender-matched controls. Their age ranged from 14 to 65 years, mean age 25.19±10.67 years. There were 50 UC patient (28 females) mean age of 34.42 ± 12.58, and their age ranged from 13-58 years. This study identified enrichment of 19 genera in the control group (Abiotrophia, Anaerofustis Butyrivibrio Campylobacter Catenibacterium Coprococcus Dorea Eubacterium Facklamia Klebsiella Lactococcus Oscillibacter Paenibacillus Parabacteroides Parasutterella Porphyromonas Prevotella Ruminococcus Treponema). There was a significant enrichment of 14 genera in our CD cohort (Beggiatoa Burkholderia Cyanothece Enterococcus Escherichia Fusobacterium Jonquetella Mitsuokella Parvimonas Peptostreptococcus Shigella Succinatimonas Thermoanaerobacter Verrucomicrobiales Vibrio) There was a significant enrichment of 7 genera in UC cohort (Beggiatoa Burkholderia Parascardovia Parvimonas Pseudoflavonifractor Thermoanaerobacter Verrucomicrobiales).

CONCLUSIONS: A significant dysbiosis was found in UC and CD patients compared to controls.

RevDate: 2019-07-11

Ji Y, Huotari T, Roslin T, et al (2019)

SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes.

Molecular ecology resources [Epub ahead of print].

The accurate quantification of eukaryotic species abundances from bulk samples remains a key challenge for community ecology and environmental biomonitoring. We resolve this challenge by combining shotgun sequencing, mapping to reference DNA barcodes or to mitogenomes, and three correction factors: (1) a percent-coverage threshold to filter out false positives, (2) an internal-standard DNA spike-in to correct for stochasticity during sequencing, and (3) technical replicates to correct for stochasticity across sequencing runs. The SPIKEPIPE pipeline achieves a strikingly high accuracy of intraspecific abundance estimates (in terms of DNA mass) from samples of known composition (mapping to barcodes R2 =0.93, mitogenomes R2 =0.95) and a high repeatability across environmental-sample replicates (barcodes R2 =0.94, mitogenomes R2 =0.93). As proof of concept, we sequence arthropod samples from the High Arctic, systematically collected over 17 years, detecting changes in species richness, species-specific abundances, and phenology. SPIKEPIPE provides cost-efficient and reliable quantification of eukaryotic communities. This article is protected by copyright. All rights reserved.

RevDate: 2019-07-19

Moeller AH, Gomes-Neto JC, Mantz S, et al (2019)

Experimental Evidence for Adaptation to Species-Specific Gut Microbiota in House Mice.

mSphere, 4(4): pii:4/4/e00387-19.

The gut microbial communities of mammals have codiversified with host species, and changes in the gut microbiota can have profound effects on host fitness. Therefore, the gut microbiota may drive adaptation in mammalian species, but this possibility is underexplored. Here, we show that the gut microbiota has codiversified with mice in the genus Mus over the past ∼6 million years, and we present experimental evidence that the gut microbiota has driven adaptive evolution of the house mouse, Mus musculusdomesticus Phylogenetic analyses of metagenome-assembled bacterial genomic sequences revealed that gut bacterial lineages have been retained within and diversified alongside Mus species over evolutionary time. Transplantation of gut microbiotas from various Mus species into germfree M. m. domesticus showed that foreign gut microbiotas slowed growth rate and upregulated macrophage inflammatory protein in hosts. These results suggest adaptation by M. m. domesticus to its gut microbiota since it diverged from other Mus species.IMPORTANCE The communities of bacteria that reside within mammalian guts are deeply integrated with their hosts, but the impact of this gut microbiota on mammalian evolution remains poorly understood. Experimental transplantation of the gut microbiota between mouse species revealed that foreign gut microbiotas lowered the host growth rate and upregulated the expression of an immunomodulating cytokine. In addition, foreign gut microbiotas increased host liver sizes and attenuated sex-specific differences in host muscle and fat content. These results suggest that the house mouse has adapted to its species-specific gut microbiota.

RevDate: 2019-07-15

Liu Y, Ajami NJ, El-Serag HB, et al (2019)

Dietary quality and the colonic mucosa-associated gut microbiome in humans.

The American journal of clinical nutrition pii:5530748 [Epub ahead of print].

BACKGROUND: Despite tremendous interest in modulating the microbiome to improve health, the association between diet and the colonic mucosa-associated gut microbiome in healthy individuals has not been examined.

OBJECTIVE: To investigate the associations between Healthy Eating Index (HEI)-2005 and the colonic mucosa-associated microbiota.

METHODS: In this cross-sectional observational study, we analyzed bacterial community composition and structure using 16S rRNA gene (V4 region) sequencing of 97 colonic mucosal biopsies obtained endoscopically from different colon segments of 34 polyp-free participants. Dietary consumption was ascertained using an FFQ. Differences in α- and β-diversity and taxonomic relative abundances between the higher and lower score of total HEI and its components were compared, followed by multivariable analyses.

RESULTS: The structure of the microbiota significantly differed by the scores for total HEI, total and whole fruits (HEI 1 and HEI 2), whole grains (HEI 6), milk products and soy beverages (HEI 7), and solid fat, alcohol, and added sugar (HEI 12). A lower score for total HEI and HEIs 2, 7, and 12 was associated with significantly lower richness. A lower score for total HEI was associated with significantly reduced relative abundance of Parabacteroides, Roseburia, and Subdoligranulum but higher Fusobacterium. A lower score for HEI 2 was associated with lower Roseburia but higher Bacteroides. A lower score for HEI 7 was associated with lower Faecalibacterium and Fusobacterium but higher Bacteroides. A lower score for HEI 12 was associated with lower Subdoligranulum but higher Escherichia and Fusobacterium (false discovery rate-adjusted P values <0.05). The findings were confirmed by multivariate analysis. Less abundant bacteria such as Alistipes, Odoribacter, Bilophila, and Tyzzerella were also associated with dietary quality.

CONCLUSIONS: A lower score for total HEI-2005 was significantly associated with reduced relative abundance of potentially beneficial bacteria but increased potentially harmful bacteria in the colonic mucosa of endoscopically normal individuals.

RevDate: 2019-07-16

Youens-Clark K, Bomhoff M, Ponsero AJ, et al (2019)

iMicrobe: Tools and data-dreaiven discovery platform for the microbiome sciences.

GigaScience, 8(7):.

BACKGROUND: Scientists have amassed a wealth of microbiome datasets, making it possible to study microbes in biotic and abiotic systems on a population or planetary scale; however, this potential has not been fully realized given that the tools, datasets, and computation are available in diverse repositories and locations. To address this challenge, we developed iMicrobe.us, a community-driven microbiome data marketplace and tool exchange for users to integrate their own data and tools with those from the broader community.

FINDINGS: The iMicrobe platform brings together analysis tools and microbiome datasets by leveraging National Science Foundation-supported cyberinfrastructure and computing resources from CyVerse, Agave, and XSEDE. The primary purpose of iMicrobe is to provide users with a freely available, web-based platform to (1) maintain and share project data, metadata, and analysis products, (2) search for related public datasets, and (3) use and publish bioinformatics tools that run on highly scalable computing resources. Analysis tools are implemented in containers that encapsulate complex software dependencies and run on freely available XSEDE resources via the Agave API, which can retrieve datasets from the CyVerse Data Store or any web-accessible location (e.g., FTP, HTTP).

CONCLUSIONS: iMicrobe promotes data integration, sharing, and community-driven tool development by making open source data and tools accessible to the research community in a web-based platform.

RevDate: 2019-07-10

Maritz JM, Ten Eyck TA, Elizabeth Alter S, et al (2019)

Patterns of protist diversity associated with raw sewage in New York City.

The ISME journal pii:10.1038/s41396-019-0467-z [Epub ahead of print].

Protists are ubiquitous components of terrestrial and aquatic environments, as well as animal and human microbiomes. Despite this, little is known about protists in urban environments. The ~7400-mile sewer system of New York City (NYC) collects human waste from ~8 million human inhabitants as well as from animals, street runoff, and groundwater, providing an ideal system to study these microbes. We used 18S rRNA amplicon sequencing and shotgun metagenomic sequencing to profile raw sewage microbial communities. Raw sewage samples were collected over a 12-month period from 14 treatment plants of the five NYC boroughs, and compared with samples from other environments including soil, stormwater, and sediment. Sewage contained a diverse protist community dominated by free-living clades, and communities were highly differentiated across environments. Seasonal differences in protist composition were observed; however, network analysis and functional profiling demonstrated that sewage communities were robust and functionally consistent. Protists typically associated with human and animal guts or feces were frequently detected. Abundance of these parasites varied significantly both spatially and temporally, suggesting that spikes could reflect trends in the source population. This underscores sewage as a valuable model system for monitoring patterns in urban microbes and provides a baseline protist metagenome of NYC.

RevDate: 2019-07-19

De Tender C, Mesuere B, Van der Jeugt F, et al (2019)

Peat substrate amended with chitin modulates the N-cycle, siderophore and chitinase responses in the lettuce rhizobiome.

Scientific reports, 9(1):9890 pii:10.1038/s41598-019-46106-x.

Chitin is a valuable peat substrate amendment by increasing lettuce growth and reducing the survival of the zoonotic pathogen Salmonella enterica on lettuce leaves. The production of chitin-catabolic enzymes (chitinases) play a crucial role and are mediated through the microbial community. A higher abundance of plant-growth promoting microorganisms and genera involved in N and chitin metabolism are present in a chitin-enriched substrate. In this study, we hypothesize that chitin addition to peat substrate stimulates the microbial chitinase production. The degradation of chitin leads to nutrient release and the production of small chitin oligomers that are related to plant growth promotion and activation of the plant's defense response. First a shotgun metagenomics approach was used to decipher the potential rhizosphere microbial functions then the nutritional content of the peat substrate was measured. Our results show that chitin addition increases chitin-catabolic enzymes, bacterial ammonium oxidizing and siderophore genes. Lettuce growth promotion can be explained by a cascade degradation of chitin to N-acetylglucosamine and eventually ammonium. The occurrence of increased ammonium oxidizing bacteria, Nitrosospira, and amoA genes results in an elevated concentration of plant-available nitrate. In addition, the increase in chitinase and siderophore genes may have stimulated the plant's systemic resistance.

RevDate: 2019-07-18

Wu L, Zeng T, Zinellu A, et al (2019)

A Cross-Sectional Study of Compositional and Functional Profiles of Gut Microbiota in Sardinian Centenarians.

mSystems, 4(4): pii:4/4/e00325-19.

Sardinia, Italy, has a high prevalence of residents who live more than 100 years. The reasons for longevity in this isolated region are currently unknown. Gut microbiota may hold a clue. To explore the role gut microbiota may play in healthy aging and longevity, we used metagenomic sequencing to determine the compositional and functional differences in gut microbiota associated with populations of different ages in Sardinia. Our data revealed that the gut microbiota of both young and elderly Sardinians shared similar taxonomic and functional profiles. A different pattern was found in centenarians. Within the centenarian group, the gut microbiota was correlated with the functional independence measurement of the host. Centenarians had a higher diversity of core microbiota species and microbial genes than those in the young and elderly. We found that the gut microbiota in Sardinian centenarians displayed a rearranged taxonomic pattern compared with those of the young and elderly, featured by depletion of Faecalibacterium prausnitzii and Eubacterium rectale and enriched for Methanobrevibacter smithii and Bifidobacterium adolescentis Moreover, functional analysis revealed that the microbiota in centenarians had high capacity for central metabolism, especially glycolysis and fermentation to short-chain fatty acids (SCFAs), although the gut microbiota in centenarians was low in genes encoding enzymes involved in degradation of carbohydrates, including fibers and galactose.IMPORTANCE The gut microbiota has been proposed as a promising determinant for human health. Centenarians as a model for extreme aging may help us understand the correlation of gut microbiota with healthy aging and longevity. Here we confirmed that centenarians had microbiota elements usually associated with benefits to health. Our finding of a high capacity of glycolysis and related SCFA production represented a healthy microbiome and environment that is regarded as beneficial for host gut epithelium. The low abundance of genes encoding components of pathways involved in carbohydrate degradation was also found in the gut microbiota of Sardinian centenarians and is often associated with poor gut health. Overall, our study here represents an expansion of previous research investigating the age-related changes in gut microbiota. Furthermore, our study provides a new prospective for potential targets for gut microbiota intervention directed at limiting gut inflammation and pathology and enhancing a healthy gut barrier.

RevDate: 2019-07-10

Wagatsuma K, Yamada S, Ao M, et al (2019)

Diversity of Gut Microbiota Affecting Serum Level of Undercarboxylated Osteocalcin in Patients with Crohn's Disease.

Nutrients, 11(7): pii:nu11071541.

Several reports have indicated a possible link between decreasing plasma levels of vitamin K and bone mineral density. It has been suggested that intestinal bacteria contribute to maintenance of vitamin K. Several factors are involved in the reduction of vitamin K in patients with Crohn's disease (CD). We aimed to assess the relationship between gut microbiota and alternative indicators of vitamin K deficiency in patients with CD. We collected the feces of 26 patients with clinically inactive CD. We extracted 16S rRNA from the intestinal bacteria in the feces and amplified it by polymerase chain reaction. The generated polymerase chain reaction product was analyzed using a 16S metagenomic approach by Illumina Miseq platform. Serum undercarboxylated osteocalcin concentration was used as an alternative indicator of vitamin K deficiency. There was a significant negative correlation between serum undercarboxylated osteocalcin and mean Chao1 index in cases of low activity. The diversity of the gut microbiota was significantly lower, and Ruminococcaceae and Lachnospiraceae were significantly decreased in the vitamin K-deficient group in comparison to the vitamin K-normal group. Taken together, these data suggested the significance of investigating the gut microbiota even in patients with clinically inactive CD for improving patients' vitamin K status.

RevDate: 2019-07-09

Matsumoto Y, Kinjo T, Motooka D, et al (2019)

Comprehensive subspecies identification of 175 nontuberculous mycobacteria species based on 7547 genomic profiles.

Emerging microbes & infections, 8(1):1043-1053.

The prevalence of nontuberculous mycobacteria (NTM) pulmonary diseases has been increasing worldwide. NTM consist of approximately 200 species and distinguishing between them at the subspecies level is critical to treatment. In this study, we sequenced 63 NTM genomes, 27 of which were newly determined, by hybrid assembly using sequencers from Illumina and Oxford Nanopore Technologies (ONT). This analysis expanded the available genomic data to 175 NTM species and redefined their subgenus classification. We also developed a novel multi-locus sequence typing (MLST) database based on 184 genes from 7547 assemblies and an identification software, mlstverse, which can also be used for detecting other bacteria given a suitable MLST database. This method showed the highest sensitivity and specificity amongst conventional methods and demonstrated the capacity for rapid detection of NTM, 10 min of sequencing of the ONT MinION being sufficient. Application of this methodology could improve disease epidemiology and increase the cure rates of NTM diseases.

RevDate: 2019-07-09

Suzuki N (2019)

Glycan diversity in the course of vertebrate evolution.

Glycobiology pii:5506440 [Epub ahead of print].

Vertebrates are estimated to have arisen over 500 million years ago in the Cambrian Period. Species that survived the Big Five extinction events at a global scale underwent repeated adaptive radiations along with habitat expansions from the sea to the land and sky. The development of the endoskeleton and neural tube enabled more complex body shapes. At the same time, vertebrates became suitable for the invasion and proliferation of foreign organisms. Adaptive immune systems were acquired for responses to a wide variety of pathogens, and more sophisticated systems developed during the evolution of mammals and birds. Vertebrate glycans consist of common core structures and various elongated structures, such as Neu5Gc, Galα1-3Gal, Galα1-4Gal, and Galβ1-4Gal epitopes, depending on the species. During species diversification, complex glycan structures were generated, maintained, or lost. Whole genome sequencing has revealed that vertebrates harbor numerous and even redundant glycosyltransferase genes. The production of various glycan structures is controlled at the genetic level in a species-specific manner. Because cell surface glycans are often targets of bacterial and viral infections, glycan structural diversity is presumed to be protective against infections. However, the maintenance of apparently redundant glycosyltransferase genes and investment in species-specific glycan structures, even in higher vertebrates with highly developed immune systems, are not well-explained. This fact suggests that glycans play important roles in unknown biological processes.

RevDate: 2019-07-18

Tschumi F, Schmutz S, Kufner V, et al (2019)

Meningitis and epididymitis caused by Toscana virus infection imported to Switzerland diagnosed by metagenomic sequencing: a case report.

BMC infectious diseases, 19(1):591 pii:10.1186/s12879-019-4231-9.

BACKGROUND: We report a rare case of Toscana virus infection imported into Switzerland in a 23-year old man who travelled to Imperia (Italy) 10 days before onset of symptoms. Symptoms included both meningitis and as well epididymitis. This is only the fourth case of Toscana virus reported in Switzerland.

CASE PRESENTATION: The patient presented with lymphocytic meningitis and scrotal pain due to epididymitis. Meningitis was initially treated with ceftriaxone. Herpes simplex, tick-borne encephalitis, enterovirus, measles, mumps, rubella and Treponema pallidum were excluded with specific polymerase chain reaction (PCR) or serology. In support of routine diagnostic PCR and serology assays, unbiased viral metagenomic sequencing was performed of cerebrospinal fluid and serum. Toscana virus infection was identified in cerebrospinal fluid and the full coding sequence could be obtained. Specific PCR in cerebrospinal fluid and blood and serology with Immunoglobulin (Ig) M and IgG against Toscana virus confirmed our diagnosis. Neurological symptoms recovered spontaneously after 5 days.

CONCLUSIONS: This case of Toscana virus infection highlights the benefits of unbiased metagenomic sequencing to support routine diagnostics in rare or unexpected viral infections. With increasing travel histories of patients, physicians should be aware of imported Toscana virus as the agent for viral meningitis and meningoencephalitis.

RevDate: 2019-07-09

Hjorth MF, Christensen L, Kjølbæk L, et al (2019)

Pretreatment Prevotella-to-Bacteroides ratio and markers of glucose metabolism as prognostic markers for dietary weight loss maintenance.

European journal of clinical nutrition pii:10.1038/s41430-019-0466-1 [Epub ahead of print].

BACKGROUND/OBJECTIVES: Pre-treatment gut microbial Prevotella-to-Bacteroides (P/B) ratio and markers of glucose metabolism (i.e., fasting glucose and insulin) have been suggested as biomarkers for optimal weight management. However, both biomarkers need further validation, and the interactions between them for optimal weight management are largely unknown. To investigate differences in weight loss maintenance between subjects with low and high P/B ratio and the potential interactions with markers of glucose metabolism and dietary fiber intake.

SUBJECTS/METHODS: Following an 8-week weight loss period using meal replacement products, subjects losing ≥ 8% of their initial body weight were randomized to one of three protein supplements or maltodextrin for a 24-week weight maintenance period. Habitual diet was consumed along with the supplements expected to constitute 10-15% of total energy. For this analysis we stratified the participants into low and high strata based on median values of pre-intervention P/B ratio, pre-weight loss Homeostatic model assessment of insulin resistance (HOMA-IR) (<2.33 or > 2.33), and dietary fiber intake during the intervention (< 28.5 or > 28.5 g/10 MJ).

RESULTS: Regardless of weight maintenance regimen, subjects with high P/B ratio (n = 63) regained 1.5 (95% CI 0.4, 2.7) kg body weight (P = 0.007) more than subjects with low P/B ratio (n = 63). The regain among subjects with high P/B ratio was particular evident if HOMA-IR was high and dietary fiber intake was low. Consequently, in the high P/B strata, subjects with high HOMA-IR and low fiber intake (n = 17) regained 5.3 (95% CI 3.3, 7.3) kg (P < 0.001) more body weight compared with participants with low HOMA-IR and high fiber intake (n = 16).

CONCLUSIONS: Subjects with high P/B ratio were more susceptible to regain body weight compared with subjects with low P/B ratio, especially when dietary fiber intake was low and glucose metabolism was impaired. These observations underline that both the P/B ratio and markers of glucose metabolism should be considered as important biomarkers within personalized nutrition for optimal weight management.

RevDate: 2019-07-09

Johnston ER, Hatt JK, He Z, et al (2019)

Responses of tundra soil microbial communities to half a decade of experimental warming at two critical depths.

Proceedings of the National Academy of Sciences of the United States of America pii:1901307116 [Epub ahead of print].

Northern-latitude tundra soils harbor substantial carbon (C) stocks that are highly susceptible to microbial degradation with rising global temperatures. Understanding the magnitude and direction (e.g., C release or sequestration) of the microbial responses to warming is necessary to accurately model climate change. In this study, Alaskan tundra soils were subjected to experimental in situ warming by ∼1.1 °C above ambient temperature, and the microbial communities were evaluated using metagenomics after 4.5 years, at 2 depths: 15 to 25 cm (active layer at outset of the experiment) and 45 to 55 cm (transition zone at the permafrost/active layer boundary at the outset of the experiment). In contrast to small or insignificant shifts after 1.5 years of warming, 4.5 years of warming resulted in significant changes to the abundances of functional traits and the corresponding taxa relative to control plots (no warming), and microbial shifts differed qualitatively between the two soil depths. At 15 to 25 cm, increased abundances of carbohydrate utilization genes were observed that correlated with (increased) measured ecosystem carbon respiration. At the 45- to 55-cm layer, increased methanogenesis potential was observed, which corresponded with a 3-fold increase in abundance of a single archaeal clade of the Methanosarcinales order, increased annual thaw duration (45.3 vs. 79.3 days), and increased CH4 emissions. Collectively, these data demonstrate that the microbial responses to warming in tundra soil are rapid and markedly different between the 2 critical soil layers evaluated, and identify potential biomarkers for the corresponding microbial processes that could be important in modeling.

RevDate: 2019-07-09

Lee YB, Byun EJ, AHS Kim (2019)

Potential Role of the Microbiome in Acne: A Comprehensive Review.

Journal of clinical medicine, 8(7): pii:jcm8070987.

Acne is a highly prevalent inflammatory skin condition involving sebaceous sties. Although it clearly develops from an interplay of multiple factors, the exact cause of acne remains elusive. It is increasingly believed that the interaction between skin microbes and host immunity plays an important role in this disease, with perturbed microbial composition and activity found in acne patients. Cutibacterium acnes (C. acnes; formerly called Propionibacterium acnes) is commonly found in sebum-rich areas and its over-proliferation has long been thought to contribute to the disease. However, information provided by advanced metagenomic sequencing has indicated that the cutaneous microbiota in acne patients and acne-free individuals differ at the virulent-specific lineage level. Acne also has close connections with the gastrointestinal tract, and many argue that the gut microbiota could be involved in the pathogenic process of acne. The emotions of stress (e.g., depression and anxiety), for instance, have been hypothesized to aggravate acne by altering the gut microbiota and increasing intestinal permeability, potentially contributing to skin inflammation. Over the years, an expanding body of research has highlighted the presence of a gut-brain-skin axis that connects gut microbes, oral probiotics, and diet, currently an area of intense scrutiny, to acne severity. This review concentrates on the skin and gut microbes in acne, the role that the gut-brain-skin axis plays in the immunobiology of acne, and newly emerging microbiome-based therapies that can be applied to treat acne.

RevDate: 2019-07-08

Aw W, S Fukuda (2019)

Protective effects of bifidobacteria against enteropathogens.

Microbial biotechnology [Epub ahead of print].

Recent major advances in metagenomics and metabolomics technologies have enabled us to collect more data on the gut microbiome and metabolome to evaluate its influence on host health. In this short opinion article, we have chosen to focus on summarizing the protective mechanisms of bifidobacteria, a highly regarded probiotic, and it's metabolite: acetate; against enteropathogens, specifically in the E. coli O157:H7 mice model. We advocate for using a novel approach metabologenomics, which is an integration of metagenomic and metabolomic information on a systems biology-wide approach to better understand this interplay between gut microbiome and host metabolism.

RevDate: 2019-07-16

Li Y, Gao Y, Zhang W, et al (2019)

Homogeneous selection dominates the microbial community assembly in the sediment of the Three Gorges Reservoir.

The Science of the total environment, 690:50-60 pii:S0048-9697(19)33127-4 [Epub ahead of print].

Deep-water reservoir sediment is a unique habitat sheltering indispensable microorganisms and facilitating their biogeochemical functions; however, the assembly processes of the microbial community therein remain elusive. This study focuses on the assembly processes in the Three Gorges Reservoir Area (TGRA). A total of 42 sediment samples were collected from the TGRA, both in the mainstream and the tributaries, and in different seasons. Metagenomic analyses of 16S rRNA using Exact Sequence Variants revealed the spatiotemporal distribution patterns of the microbial communities. Linear regressions between dissimilarity of microbial communities, geographic and environmental distance showed that environmental, rather than geographic factors, impacted the microbial community. However, the environmental differences explained little variations (14.14%) in community structure, implying the homogeneity of environmental conditions across the TGRA. From the quantification of ecological processes, homogeneous selection was shown to be a dominating factor (51.34%) in the assembly of the microbial communities. The co-occurrence network showed that keystone species were more important than prevalent abundant species in interspecies interactions. Overall, the assembly of microbial community in the deep-water reservoir sediment is mediated by both deterministic and stochastic processes, and homogeneous selection plays a leading role.

RevDate: 2019-07-08

Liang R, Davidova I, Hirano SI, et al (2019)

Community succession in an anaerobic long-chain paraffin-degrading consortium and impact on chemical and electrical microbially influenced iron corrosion.

FEMS microbiology ecology pii:5529450 [Epub ahead of print].

Community compositional changes and the corrosion of carbon steel in the presence of different electron donor and acceptor combinations was examined with a methanogenic consortium enriched for its ability to mineralize paraffins. Despite cultivation in the absence of sulfate, metagenomic analysis revealed the persistence of several sulfate-reducing bacterial taxa. Upon sulfate amendment, the consortium was able to couple C28H58 biodegradation with sulfate reduction. Comparative analysis suggested that Desulforhabdus and/or Desulfovibrio likely supplanted methanogens as syntrophic partners needed for C28H58 mineralization. Further enrichment in the absence of a paraffin revealed that the consortium could also utilize carbon steel as a source of electrons. The severity of both general and localized corrosion increased in the presence of sulfate, regardless of the electron donor utilized. With carbon steel as an electron donor, Desulfobulbus dominated in the consortium and electrons from iron accounted for ∼92% of that required for sulfate reduction. An isolated Desulfovibrio spp. was able to extract electrons from iron and accelerate corrosion. Thus, hydrogenotrophic partner micoorganisms required for syntrophic paraffin metabolism can be readily substituted depending on the availability of an external electron acceptor and a single paraffin-degrading consortium harbored microbes capable of both chemical (CMIC) and electrical (EMIC) microbial influenced iron corrosion.

RevDate: 2019-07-11

Klasek SA, Torres ME, Loher M, et al (2019)

Deep-Sourced Fluids From a Convergent Margin Host Distinct Subseafloor Microbial Communities That Change Upon Mud Flow Expulsion.

Frontiers in microbiology, 10:1436.

Submarine mud volcanoes (MVs) along continental margins emit mud breccia and globally significant amounts of hydrocarbon-rich fluids from the subsurface, and host distinct chemosynthetic communities of microbes and macrofauna. Venere MV lies at 1,600 m water depth in the Ionian Sea offshore Italy and is located in a forearc basin of the Calabrian accretionary prism. Porewaters of recently extruded mud breccia flowing from its west summit are considerably fresher than seawater (10 PSU), high in Li+ and B (up to 300 and 8,000 μM, respectively), and strongly depleted in K+ (<1 mM) at depths as shallow as 20 cm below seafloor. These properties document upward transport of fluids sourced from >3 km below seafloor. 16S rRNA gene and metagenomic sequencing were used to characterize microbial community composition and gene content within deep-sourced mud breccia flow deposits as they become exposed to seawater along a downslope transect of Venere MV. Summit samples showed consistency in microbial community composition. However, beta-diversity increased markedly in communities from downslope cores, which were dominated by methyl- and methanotrophic genera of Gammaproteobacteria. Methane, sulfate, and chloride concentrations were minor but significant contributors to variation in community composition. Metagenomic analyses revealed differences in relative abundances of predicted protein categories between Venere MV and other subsurface microbial communities, characterizing MVs as windows into distinct deep biosphere habitats.

RevDate: 2019-07-07

Chen H, Li C, Liu T, et al (2019)

A Metagenomic Study of Intestinal Microbial Diversity in Relation to Feeding Habits of Surface and Cave-Dwelling Sinocyclocheilus Species.

Microbial ecology pii:10.1007/s00248-019-01409-4 [Epub ahead of print].

Light is completely absent in cave habitats, causing a shortage or lack of autochthonous photosynthesis. Thus, understanding the mechanisms underlying the ability of organisms to adapt to the unique cave habitat is of great interest. We used high-throughput sequencing of the 16S ribosomal RNA gene of intestinal microorganisms from 11 Sinocyclocheilus (Cypriniformes: Cyprinidae) species, to explore the characteristics of intestinal microorganisms and the adaptive mechanisms of Sinocyclocheilus cavefish and surface fish. We found that the α-diversity and richness of the intestinal microbiome were much higher in cavefish than in surface fish. Principal coordinate analysis showed that cavefish and surface fish formed three clusters because of different dominant gut microorganisms which are generated by different habitats. Based on PICRUSt-predicted functions, harmful substance degradation pathways were much more common in cavefish intestinal microorganisms than in those from surface fish. The intestinal microbiota of surface fish group 1 had a higher capacity for carbohydrate metabolism, whereas protein and amino acid metabolism and digestive pathways were more abundant in microorganisms from the cavefish group and surface fish group 2. Combined analysis of the intestinal microbial composition and functional predictions further revealed the structures and functions of intestinal microbial communities in Sinocyclocheilus cave and surface species. Moreover, based on their habits and intestinal microbial composition and intestinal microbial functional predictions, we inferred that the three fish groups were all omnivorous; however, surface fish group 1 preferred feeding on plants, while surface fish group 2 and cavefish preferred meat. This study improves our understanding of mechanisms of adaptation in cave habitats and may contribute to the protection of these habitats from water pollution.

RevDate: 2019-07-19

Degli Esposti M, Lozano L, E Martínez-Romero (2019)

Current phylogeny of Rhodospirillaceae: A multi-approach study.

Molecular phylogenetics and evolution, 139:106546 pii:S1055-7903(18)30634-1 [Epub ahead of print].

Rhodospirillaceae represents a major family of the class alphaproteobacteria that includes an increasing number of functionally diverse taxa. The aim of this work is to evaluate the present phylogenetic diversity of the Rhodospirillaceae, which includes several metagenome-assembled genomes of uncultivated bacteria, as well as cultivated bacteria that were previously classified in different families. Various methodological approaches have been followed to discern the phylogenetic diversity of the taxa associated with the Rhodospirillaceae, which are grouped in three major sub-divisions and several other taxonomic entities that are currently confined to the genus rank. These genera include Tistrella, Elstera, Dongia and Ferrovibrio among cultivated organisms and alphaproteobacteria bacterium 41-28 among uncultivated bacteria. Overall, this study adds at least 11 genera and over 40 species to the current set of taxa belonging to the Rhodospirillaceae, a taxonomic term that clearly requires amendment. We propose to re-classify all taxa associated with the Rhodospirillaceae family under the new order, Diaforabacterales ord. nov. (from the Greek word for diversity, διάφορα). This study also uncovers the likely root of Rhodospirillaceae among recently reported metagenome-assembled genomes of uncultivated marine and groundwater bacteria.

RevDate: 2019-07-17

Velsko IM, Fellows Yates JA, Aron F, et al (2019)

Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage.

Microbiome, 7(1):102 pii:10.1186/s40168-019-0717-3.

BACKGROUND: Dental calculus, calcified oral plaque biofilm, contains microbial and host biomolecules that can be used to study historic microbiome communities and host responses. Dental calculus does not typically accumulate as much today as historically, and clinical oral microbiome research studies focus primarily on living dental plaque biofilm. However, plaque and calculus reflect different conditions of the oral biofilm, and the differences in microbial characteristics between the sample types have not yet been systematically explored. Here, we compare the microbial profiles of modern dental plaque, modern dental calculus, and historic dental calculus to establish expected differences between these substrates.

RESULTS: Metagenomic data was generated from modern and historic calculus samples, and dental plaque metagenomic data was downloaded from the Human Microbiome Project. Microbial composition and functional profile were assessed. Metaproteomic data was obtained from a subset of historic calculus samples. Comparisons between microbial, protein, and metabolomic profiles revealed distinct taxonomic and metabolic functional profiles between plaque, modern calculus, and historic calculus, but not between calculus collected from healthy teeth and periodontal disease-affected teeth. Species co-exclusion was related to biofilm environment. Proteomic profiling revealed that healthy tooth samples contain low levels of bacterial virulence proteins and a robust innate immune response. Correlations between proteomic and metabolomic profiles suggest co-preservation of bacterial lipid membranes and membrane-associated proteins.

CONCLUSIONS: Overall, we find that there are systematic microbial differences between plaque and calculus related to biofilm physiology, and recognizing these differences is important for accurate data interpretation in studies comparing dental plaque and calculus.

RevDate: 2019-07-17

Jia S, Wu J, Ye L, et al (2019)

Metagenomic assembly provides a deep insight into the antibiotic resistome alteration induced by drinking water chlorination and its correlations with bacterial host changes.

Journal of hazardous materials, 379:120841 pii:S0304-3894(19)30794-0 [Epub ahead of print].

Chlorination can contribute to the enrichment of specific antibiotic resistance genes (ARGs) in drinking water, but the underlying molecular ecological mechanisms remain unknown, which may hinder the assessment and control of the resulting health risks. In this study, metagenomic assembly and Resfams annotation were used to profile the co-occurrence patterns of ARGs, mobile genetic elements (MGEs) and their bacterial hosts, as well as the correlations of potential pathogens with the antibiotic resistome, in a full-scale drinking water treatment and transportation system. Seven ARG types involved in different resistance mechanisms occurred in drinking water and chlorination enhanced the total abundance of the ARGs (p < 0.05). The ARGs encoding resistance-nodulation-cell division and ATP-binding cassette antibiotic efflux pumps predominated in all the samples and were primarily responsible for the ARG accumulation. After chlorination, the ARGs were primarily carried by predominant Sphingomonas, Polaromonas, Hyphomicrobium, Acidovorax, Pseudomonas and Fluviicola. Further, enrichment of the bacterial hosts and MGEs greatly contributed to alteration of the antibiotic resistome. Pseudomonas alcaligenes, carrying multiple ARGs, was identified as a potential pathogen in the chlorinated drinking water. These findings provide novel insights into the host-ARG relationship and the mechanism underlying the resistome alteration during drinking water chlorination.

RevDate: 2019-07-06

Cait A, Cardenas E, Dimitriu P, et al (2019)

Reduced genetic potential for butyrate fermentation in the gut microbiome of infants who develop allergic sensitization.

The Journal of allergy and clinical immunology pii:S0091-6749(19)30891-7 [Epub ahead of print].

BACKGROUND: Allergic disease is the most frequent chronic health issue in children and has been linked to early-life gut microbiome dysbiosis. Many lines of evidence suggest that microbially derived short-chain fatty acids, and particularly butyrate, can promote immune tolerance.

OBJECTIVE: To determine if that bacterial butyrate production in the gut during early infancy is protective against the development of atopic disease in children.

METHODS: We used shotgun metagenomic analysis to determine whether dysbiosis in butyrate fermentation could be identified in human infants, prior to their developing allergic disease.

RESULTS: We found that the microbiome of infants that went on to develop allergic sensitization later in childhood lacked genes encoding key enzymes for carbohydrate breakdown and butyrate production.

CONCLUSION: Our findings support the importance of microbial carbohydrate metabolism during early infancy in protecting against development of allergies.

RevDate: 2019-07-06

Mitra S (2019)

Multiple Data Analyses and Statistical Approaches for Analyzing Data from Metagenomic Studies and Clinical Trials.

Methods in molecular biology (Clifton, N.J.), 1910:605-634.

Metagenomics, also known as environmental genomics, is the study of the genomic content of a sample of organisms (microbes) obtained from a common habitat. Metagenomics and other "omics" disciplines have captured the attention of researchers for several decades. The effect of microbes in our body is a relevant concern for health studies. There are plenty of studies using metagenomics which examine microorganisms that inhabit niches in the human body, sometimes causing disease, and are often correlated with multiple treatment conditions. No matter from which environment it comes, the analyses are often aimed at determining either the presence or absence of specific species of interest in a given metagenome or comparing the biological diversity and the functional activity of a wider range of microorganisms within their communities. The importance increases for comparison within different environments such as multiple patients with different conditions, multiple drugs, and multiple time points of same treatment or same patient. Thus, no matter how many hypotheses we have, we need a good understanding of genomics, bioinformatics, and statistics to work together to analyze and interpret these datasets in a meaningful way. This chapter provides an overview of different data analyses and statistical approaches (with example scenarios) to analyze metagenomics samples from different medical projects or clinical trials.

RevDate: 2019-07-06

Bağcı C, Beier S, Górska A, et al (2019)

Introduction to the Analysis of Environmental Sequences: Metagenomics with MEGAN.

Methods in molecular biology (Clifton, N.J.), 1910:591-604.

Metagenomics has become a part of the standard toolkit for scientists interested in studying microbes in the environment. Compared to 16S rDNA sequencing, which allows coarse taxonomic profiling of samples, shotgun metagenomic sequencing provides a more detailed analysis of the taxonomic and functional content of samples. Long read technologies, such as developed by Pacific Biosciences or Oxford Nanopore, produce much longer stretches of informative sequence, greatly simplifying the difficult and time-consuming process of metagenomic assembly. MEGAN6 provides a wide range of analysis and visualization methods for the analysis of short and long read metagenomic data. A simple and efficient analysis pipeline for metagenomic analysis consists of the DIAMOND alignment tool on short reads, or the LAST alignment tool on long reads, followed by MEGAN. This approach performs taxonomic and functional abundance analysis, supports comparative analysis of large-scale experiments, and allows one to involve experimental metadata in the analysis.

RevDate: 2019-07-06

Watson AK, Lannes R, Pathmanathan JS, et al (2019)

The Methodology Behind Network Thinking: Graphs to Analyze Microbial Complexity and Evolution.

Methods in molecular biology (Clifton, N.J.), 1910:271-308.

In the post genomic era, large and complex molecular datasets from genome and metagenome sequencing projects expand the limits of what is possible for bioinformatic analyses. Network-based methods are increasingly used to complement phylogenetic analysis in studies in molecular evolution, including comparative genomics, classification, and ecological studies. Using network methods, the vertical and horizontal relationships between all genes or genomes, whether they are from cellular chromosomes or mobile genetic elements, can be explored in a single expandable graph. In recent years, development of new methods for the construction and analysis of networks has helped to broaden the availability of these approaches from programmers to a diversity of users. This chapter introduces the different kinds of networks based on sequence similarity that are already available to tackle a wide range of biological questions, including sequence similarity networks, gene-sharing networks and bipartite graphs, and a guide for their construction and analyses.

RevDate: 2019-07-09

Visnovska T, Biggs PJ, Schmeier S, et al (2019)

Metagenomics and transcriptomics data from human colorectal cancer.

Scientific data, 6(1):116 pii:10.1038/s41597-019-0117-3.

Colorectal cancer is a heterogenous and mostly sporadic disease, the development of which is associated with microbial dysbiosis. Recent advances in subtype classification have successfully stratified the disease using molecular profiling. To understand potential relationships between molecular mechanisms differentiating the subtypes of colorectal cancer and composition of gut microbial community, we classified a set of 34 tumour samples into molecular subtypes using RNA-sequencing gene expression profiles and determined relative abundances of bacterial taxonomic groups. To identify bacterial community composition, 16S rRNA amplicon metabarcoding was used as well as whole genome metagenomics of the non-human part of RNA-sequencing data. The generated data expands the collection of the data sources related to the disease and connects molecular aspects of the cancer with environmental impact of microbial community.

RevDate: 2019-07-06

Shankar A, Sibley SD, Goldberg TL, et al (2019)

Molecular Analysis of the Complete Genome of a Simian Foamy Virus Infecting Hylobates pileatus (pileated gibbon) Reveals Ancient Co-Evolution with Lesser Apes.

Viruses, 11(7): pii:v11070605.

Foamy viruses (FVs) are complex retroviruses present in many mammals, including nonhuman primates, where they are called simian foamy viruses (SFVs). SFVs can zoonotically infect humans, but very few complete SFV genomes are available, hampering the design of diagnostic assays. Gibbons are lesser apes widespread across Southeast Asia that can be infected with SFV, but only two partial SFV sequences are currently available. We used a metagenomics approach with next-generation sequencing of nucleic acid extracted from the cell culture of a blood specimen from a lesser ape, the pileated gibbon (Hylobates pileatus), to obtain the complete SFVhpi_SAM106 genome. We used Bayesian analysis to co-infer phylogenetic relationships and divergence dates. SFVhpi_SAM106 is ancestral to other ape SFVs with a divergence date of ~20.6 million years ago, reflecting ancient co-evolution of the host and SFVhpi_SAM106. Analysis of the complete SFVhpi_SAM106 genome shows that it has the same genetic architecture as other SFVs but has the longest recorded genome (13,885-nt) due to a longer long terminal repeat region (2,071 bp). The complete sequence of the SFVhpi_SAM106 genome fills an important knowledge gap in SFV genetics and will facilitate future studies of FV infection, transmission, and evolutionary history.

RevDate: 2019-07-05

Lindsay MR, Colman DR, Amenabar MJ, et al (2019)

Probing the Geological Source and Biological Fate of Hydrogen in Yellowstone Hot Springs.

Environmental microbiology [Epub ahead of print].

Hydrogen (H2) is enriched in hot springs and can support microbial primary production. Using a series of geochemical proxies, a model to describe variable H2 concentrations in Yellowstone National Park (YNP) hot springs is presented. Interaction between water and crustal iron minerals yields H2 that partitions into the vapor phase during decompressional boiling of ascending hydrothermal fluids. Variable vapor input leads to differences in H2 concentration among springs. Analysis of 50 metagenomes from a variety of YNP springs reveals that genes encoding oxidative hydrogenases are enriched in communities inhabiting springs sourced with vapor-phase gas. Three springs in the Smokejumper (SJ) area of YNP that are sourced with vapor-phase gas and with the most H2 in YNP were examined to determine the fate of H2 . SJ3 had the most H2 , the most 16S rRNA gene templates, and the greatest abundance of culturable hydrogenotrophic and autotrophic cells of the three springs. Metagenomics and transcriptomics of SJ3 reveal a diverse community comprised of abundant populations expressing genes involved in H2 oxidation and carbon dioxide fixation. These observations suggest a link between geologic processes that generate and source H2 to hot springs and the distribution of organisms that use H2 to generate energy. This article is protected by copyright. All rights reserved.

RevDate: 2019-07-07

Borroni D, Romano V, Kaye SB, et al (2019)

Metagenomics in ophthalmology: current findings and future prospectives.

BMJ open ophthalmology, 4(1):e000248 pii:bmjophth-2018-000248.

Less than 1% of all microorganisms of the available environmental microbiota can be cultured with the currently available techniques. Metagenomics is a new methodology of high-throughput DNA sequencing, able to provide taxonomic and functional profiles of microbial communities without the necessity to culture microbes in the laboratory. Metagenomics opens to a 'hypothesis-free' approach, giving important details for future research and treatment of ocular diseases in ophthalmology, such as ocular infection and ocular surface diseases.

RevDate: 2019-07-07

Berini F, Casartelli M, Montali A, et al (2019)

Metagenome-Sourced Microbial Chitinases as Potential Insecticide Proteins.

Frontiers in microbiology, 10:1358.

Microbial chitinases are gaining interest as promising candidates for controlling plant pests. These enzymes can be used directly as biocontrol agents as well as in combination with chemical pesticides or other biopesticides, reducing their environmental impact and/or enhancing their efficacy. Chitinolytic enzymes can target two different structures in insects: the cuticle and the peritrophic matrix (PM). PM, formed by chitin fibrils connected to glycoproteins and proteoglycans, represents a physical barrier that plays an essential role in midgut physiology and insect digestion, and protects the absorptive midgut epithelium from food abrasion or pathogen infections. In this paper, we investigate how two recently discovered metagenome-sourced chitinases (Chi18H8 and 53D1) affect, in vitro and in vivo, the PM integrity of Bombyx mori, a model system among Lepidoptera. The two chitinases were produced in Escherichia coli or, alternatively, in the unconventional - but more environmentally acceptable - Streptomyces coelicolor. Although both the proteins dramatically altered the structure of B. mori PM in vitro, when administered orally only 53D1 caused adverse and marked effects on larval growth and development, inducing mortality and reducing pupal weight. These in vivo results demonstrate that 53D1 is a promising candidate as insecticide protein.

RevDate: 2019-07-07

Liu D, Sun H, H Ma (2019)

Deciphering Microbiome Related to Rusty Roots of Panax ginseng and Evaluation of Antagonists Against Pathogenic Ilyonectria.

Frontiers in microbiology, 10:1350.

Plant roots host diverse microbes that are closely associated with root fitness. Currently, the relationship between microbes and rusty roots of Panax ginseng remains unclear. Here, we described the root-associated microbiome in rusty and healthy ginseng by metagenomic sequencing of 16S rRNA and ITS regions. Being enriched in Diseased-roots (Dr) of ginseng and their rhizosphere soil, the fungus of Ilyonectria, was identified as the most probable cause of the disease after ITS analysis. Meanwhile, an increase of Mortierella was observed in Healthy-roots (Hr). Surprisingly, an enriched Fusarium was found in both Hr and their rhizosphere soil. Besides, in comparison with Hr, decreased relative abundance of Actinomycetales and increased relative abundance of Pseudomonadales was observed in Dr after 16S rRNA analysis. What's more, we isolated several microorganisms as antagonists that showed strong inhibiting effects on Ilyonectria in plate assays. In field trials, inoculation of Bacillus sp. S-11 displayed apparent suppression effect against Ilyonectria and shifted microbial communities in rhizosphere soil. Our research identified key microbiota involved in rusty roots of P. ginseng and offered potential biocontrol solutions to rusty disease.

RevDate: 2019-07-08

Rodionov DA, Arzamasov AA, Khoroshkin MS, et al (2019)

Micronutrient Requirements and Sharing Capabilities of the Human Gut Microbiome.

Frontiers in microbiology, 10:1316.

The human gut microbiome harbors a diverse array of metabolic pathways contributing to its development and homeostasis via a complex web of diet-dependent metabolic interactions within the microbial community and host. Genomics-based reconstruction and predictive modeling of these interactions would provide a framework for diagnostics and treatment of dysbiosis-related syndromes via rational selection of therapeutic prebiotics and dietary nutrients. Of particular interest are micronutrients, such as B-group vitamins, precursors of indispensable metabolic cofactors, that are produced de novo by some gut bacteria (prototrophs) but must be provided exogenously in the diet for many other bacterial species (auxotrophs) as well as for the mammalian host. Cross-feeding of B vitamins between prototrophic and auxotrophic species is expected to strongly contribute to the homeostasis of microbial communities in the distal gut given the efficient absorption of dietary vitamins in the upper gastrointestinal tract. To confidently estimate the balance of microbiome micronutrient biosynthetic capabilities and requirements using available genomic data, we have performed a subsystems-based reconstruction of biogenesis, salvage and uptake for eight B vitamins (B1, B2, B3, B5, B6, B7, B9, and B12) and queuosine (essential factor in tRNA modification) over a reference set of 2,228 bacterial genomes representing 690 cultured species of the human gastrointestinal microbiota. This allowed us to classify the studied organisms with respect to their pathway variants and infer their prototrophic vs. auxotrophic phenotypes. In addition to canonical vitamin pathways, several conserved partial pathways were identified pointing to alternative routes of syntrophic metabolism and expanding a microbial vitamin "menu" by several pathway intermediates (vitamers) such as thiazole, quinolinate, dethiobiotin, pantoate. A cross-species comparison was applied to assess the extent of conservation of vitamin phenotypes at distinct taxonomic levels (from strains to families). The obtained reference collection combined with 16S rRNA gene-based phylogenetic profiles was used to deduce phenotype profiles of the human gut microbiota across in two large cohorts. This analysis provided the first estimate of B-vitamin requirements, production and sharing capabilities in the human gut microbiome establishing predictive phenotype profiling as a new approach to classification of microbiome samples. Future expansion of our reference genomic collection of metabolic phenotypes will allow further improvement in coverage and accuracy of predictive phenotype profiling of the human microbiome.

RevDate: 2019-07-07

Laville E, Perrier J, Bejar N, et al (2019)

Investigating Host Microbiota Relationships Through Functional Metagenomics.

Frontiers in microbiology, 10:1286.

The human Intestinal mucus is formed by glycoproteins, the O- and N-linked glycans which constitute a crucial source of carbon for commensal gut bacteria, especially when deprived of dietary glycans of plant origin. In recent years, a dozen carbohydrate-active enzymes from cultivated mucin degraders have been characterized. But yet, considering the fact that uncultured species predominate in the human gut microbiota, these biochemical data are far from exhaustive. In this study, we used functional metagenomics to identify new metabolic pathways in uncultured bacteria involved in harvesting mucin glycans. First, we performed a high-throughput screening of a fosmid metagenomic library constructed from the ileum mucosa microbiota using chromogenic substrates. The screening resulted in the isolation of 124 clones producing activities crucial in the degradation of human O- and N-glycans, namely sialidases, β-D-N-acetyl-glucosaminidase, β-D-N-acetyl-galactosaminidase, and/or β-D-mannosidase. Thirteen of these clones were selected based on their diversified functional profiles and were further analyzed on a secondary screening. This step consisted of lectin binding assays to demonstrate the ability of the clones to degrade human intestinal mucus. In total, the structural modification of several mucin motifs, sialylated mucin ones in particular, was evidenced for nine clones. Sequencing their metagenomic loci highlighted complex catabolic pathways involving the complementary functions of glycan sensing, transport, hydrolysis, deacetylation, and deamination, which were sometimes associated with amino acid metabolism machinery. These loci are assigned to several Bacteroides and Feacalibacterium species highly prevalent and abundant in the gut microbiome and explain the metabolic flexibility of gut bacteria feeding both on dietary and human glycans.

RevDate: 2019-07-18

Zhao H, Chen J, Li X, et al (2019)

Compositional and functional features of the female premenopausal and postmenopausal gut microbiota.

FEBS letters [Epub ahead of print].

Endogenous estrogen deficiency accelerates many diseases in postmenopausal women, and gut microbes contribute to estrogen level modulation. However, the compositional alterations and influences of the gut microbiota in postmenopausal women remain uncertain. A metagenome-wide association study was performed to compare the gut microbiota of 24 premenopausal and 24 postmenopausal women. Firmicutes and Roseburia spp. are depleted, while Bacteroidetes and the toluene-producing genus Tolumonas are overrepresented in fecal samples from postmenopausal women. The pentose phosphate pathway is enriched in premenopausal women. Homocysteine synthesis-related processes are enriched in postmenopausal women. The gut microbiomes of premenopausal and postmenopausal women differ and produce different metabolites. The gut microbiome may be a therapeutic target to reduce risks and improve the quality of life in postmenopausal women.

RevDate: 2019-07-05

Kirby TO, Brown M, Ochoa-Repáraz J, et al (2019)

Microbiota Manipulation as a Metagenomic Therapeutic Approach for Rare Inherited Metabolic Disorders.

Clinical pharmacology and therapeutics [Epub ahead of print].

RevDate: 2019-07-05

Kerfahi D, Ogwu MC, Ariunzaya D, et al (2019)

Metal-Tolerant Fungal Communities Are Delineated by High Zinc, Lead, and Copper Concentrations in Metalliferous Gobi Desert Soils.

Microbial ecology pii:10.1007/s00248-019-01405-8 [Epub ahead of print].

The soil fungal ecology of the southern Gobi region of Mongolia has been little studied. We utilized the ITS1 region from soil DNA to study possible influences soil metal concentrations on soil fungal community variation. In the sample network, a distinctive fungal community was closely associated with high zinc (Zn), lead (Pb), and copper (Cu) concentrations. The pattern of occurrence suggests that high metal concentrations are natural and not a product of mining activities. The metal-associated fungal community differs little from the "normal" community in its major OTUs, and in terms of major fungal guilds and taxa, and its distinctiveness depends on a combination of many less common OTUs. The fungal community in the sites with high metal concentrations is no less diverse than that in areas with normal background levels. Overall, these findings raise interesting questions of the evolutionary origin and functional characteristics of this apparently "metal-tolerant" community, and of the associated soil biota in general. It is possible that rehabilitation of metal-contaminated mined soils from spoil heaps could benefit from the incorporation of fungi derived from these areas.

RevDate: 2019-07-05

Uritskiy G, Getsin S, Munn A, et al (2019)

Halophilic microbial community compositional shift after a rare rainfall in the Atacama Desert.

The ISME journal pii:10.1038/s41396-019-0468-y [Epub ahead of print].

Understanding the mechanisms underlying microbial resistance and resilience to perturbations is essential to predict the impact of climate change on Earth's ecosystems. However, the resilience and adaptation mechanisms of microbial communities to natural perturbations remain relatively unexplored, particularly in extreme environments. The response of an extremophile community inhabiting halite (salt rocks) in the Atacama Desert to a catastrophic rainfall provided the opportunity to characterize and de-convolute the temporal response of a highly specialized community to a major disturbance. With shotgun metagenomic sequencing, we investigated the halite microbiome taxonomic composition and functional potential over a 4-year longitudinal study, uncovering the dynamics of the initial response and of the recovery of the community after a rainfall event. The observed changes can be recapitulated by two general modes of community shifts-a rapid Type 1 shift and a more gradual Type 2 adjustment. In the initial response, the community entered an unstable intermediate state after stochastic niche re-colonization, resulting in broad predicted protein adaptations to increased water availability. In contrast, during recovery, the community returned to its former functional potential by a gradual shift in abundances of the newly acquired taxa. The general characterization and proposed quantitation of these two modes of community response could potentially be applied to other ecosystems, providing a theoretical framework for prediction of taxonomic and functional flux following environmental changes.

RevDate: 2019-07-05

Colombo RP, Benavidez ME, Fernandez Bidondo L, et al (2019)

Arbuscular mycorrhizal fungi in heavy metal highly polluted soil in the Riachuelo river basin.

Revista Argentina de microbiologia pii:S0325-7541(19)30053-7 [Epub ahead of print].

The Riachuelo river basin (RRB) is considered one of the most polluted environments in the world. Knowledge of arbuscular mycorrhizal fungi (AMF) adapted to this extremely polluted environment is important for the establishment of future soil restoration projects. This work aims to make a first list of AMF species present on the RRB. Soil and root samples were randomly taken in an area of approximately 1500m2, mycorrhization percentages were evaluated. AMF species were detected by molecular and morphological techniques. Sixteen AMF morphological species and 64 molecular species were reported in this work. Dominikia iranica, Funneliformis constrictum, Funneliformis mosseae, Rhizophagus intraradices, Rhizophagus irregularis and Septoglomus viscosum were detected by both techniques while Claroideoglomus sp. was only detected by pyrosequencing. The list of species reported in this work represents the first description of the RRB AMF community.

RevDate: 2019-07-17

Molinero N, Ruiz L, Milani C, et al (2019)

The human gallbladder microbiome is related to the physiological state and the biliary metabolic profile.

Microbiome, 7(1):100 pii:10.1186/s40168-019-0712-8.

BACKGROUND: The microbial populations of the human intestinal tract and their relationship to specific diseases have been extensively studied during the last decade. However, the characterization of the human bile microbiota as a whole has been hampered by difficulties in accessing biological samples and the lack of adequate methodologies to assess molecular studies. Although a few reports have described the biliary microbiota in some hepatobiliary diseases, the bile microbiota of healthy individuals has not been described. With this in mind, the goal of the present study was to generate fundamental knowledge on the composition and activity of the human bile microbiota, as well as establishing its potential relationship with human bile-related disorders.

RESULTS: Human bile samples from the gallbladder of individuals from a control group, without any record of hepatobiliary disorder, were obtained from liver donors during liver transplantation surgery. A bile DNA extraction method was optimized together with a quantitative PCR (qPCR) assay for determining the bacterial load. This allows the selection of samples to perform functional metagenomic analysis. Bile samples from the gallbladder of individuals suffering from lithiasis were collected during gallbladder resection and the microbial profiles assessed, using a 16S rRNA gene-based sequencing analysis, and compared with those of the control group. Additionally, the metabolic profile of the samples was analyzed by nuclear magnetic resonance (NMR). We detected, for the first time, bacterial communities in gallbladder samples of individuals without any hepatobiliary pathology. In the biliary microecosystem, the main bacterial phyla were represented by Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. Significant differences in the relative abundance of different taxa of both groups were found. Sequences belonging to the family Propionibacteriaceae were more abundant in bile samples from control subjects; meanwhile, in patients with cholelithiasis members of the families Bacteroidaceae, Prevotellaceae, Porphyromonadaceae, and Veillonellaceae were more frequently detected. Furthermore, the metabolomics analysis showed that the two study groups have different metabolic profiles.

CONCLUSIONS: Our results indicate that the gallbladder of human individuals, without diagnosed hepatobiliary pathology, harbors a microbial ecosystem that is described for the first time in this study. Its bacterial representatives and metabolites are different from those detected in people suffering from cholelithiasis. In this regard, since liver donors have been subjected to the specific conditions of the hospital's intensive care unit, including an antibiotic treatment, we must be cautious in stating that their bile samples contain a physiologically normal biliary microbiome. In any case, our results open up new possibilities to discover bacterial functions in a microbial ecosystem that has not previously been explored.

RevDate: 2019-07-04

Wang J, Qian T, Jiang J, et al (2019)

Gut microbial profile is altered in biliary atresia.

Journal of gastroenterology and hepatology [Epub ahead of print].

BACKGROUND AND AIM: Biliary atresia (BA) is a progressive fibro-inflammatory cholangiopathy with an unclear etiology. Various liver disorders are associated with an altered microbiome. However, gut microbiome in BA remains unknown. Here we performed a controlled study to investigate the gut microbiota in BA.

METHODS: A cross-sectional analysis was first conducted for 34 BA patients and 34 healthy controls. Then, we investigated the shift in gut microbiota 2 weeks post-Kasai procedure in 16 BA patients. Gut microbiome was initially analyzed using 16S ribosome RNA gene sequencing and further validated by metagenomic sequencing. Fecal bile acids were determined using ultra-high performance liquid chromatography.

RESULTS: Compared with healthy controls, BA showed lower diversity and significant structural segregation in the microbiome. At phylum level, Proteobacteria numbers increased, whereas those of Bacteroidetes decreased in BA. At genus level, several potential pathogens such as Streptococcus and Klebsiella thrived in BA; while numbers for Bifidobacterium and several butyrate-producing bacteria declined. The microbiome was also disturbed after Kasai procedure. Operational taxonomic units responding to BA showed significant correlation with liver function. Furthermore, the abundance ratio of Streptococcus/Bacteroides showed great promise in distinguishing BA from healthy controls. Intestinal bile acids were dramatically decreased in BA and Clostridium XIVa positively correlated with the ratio of primary/secondary bile acids.

CONCLUSIONS: Gut microbial dysbiosis, may be caused by decreased bile acids, was associated with liver function and had a good diagnostic potential for BA. Therefore, further exploration of gut microbiota may provide important insights into their potential diagnostic and therapeutic benefits.

RevDate: 2019-07-04

Huang Q, Lopez D, JD Evans (2019)

Shared and unique microbes between Small hive beetles (Aethina tumida) and their honey bee hosts.

MicrobiologyOpen [Epub ahead of print].

The small hive beetle (SHB) is an opportunistic parasite that feeds on bee larvae, honey, and pollen. While SHBs can also feed on fruit and other plant products, like its plant-feeding relatives, SHBs prefer to feed on hive resources and only reproduce inside bee colonies. As parasites, SHBs are inevitably exposed to bee-associated microbes, either directly from the bees or from the hive environment. These microbes have unknown impacts on beetles, nor is it known how extensively beetles transfer microbes among their bee hosts. To identify sets of beetle microbes and the transmission of microbes from bees to beetles, a metagenomic analysis was performed. We identified sets of herbivore-associated bacteria, as well as typical bee symbiotic bacteria for pollen digestion, in SHB larvae and adults. Deformed wing virus was highly abundant in beetles, which colonize SHBs as suggested by a controlled feeding trial. Our data suggest SHBs are vectors for pathogen transmission among bees and between colonies. The dispersal of host pathogens by social parasites via floral resources and the hive environment increases the threats of these parasites to honey bees.

RevDate: 2019-07-18

Chen H, Wang W, Wang S, et al (2019)

Near-Complete Genome Sequence of a Hepatitis A Subgenotype IB Virus Isolated from Frozen Raspberries.

Microbiology resource announcements, 8(27): pii:8/27/e00522-19.

Hepatitis A virus is one of the most common causes of foodborne viral illness. Here, we report the nearly complete genome sequence of a hepatitis A virus (subgenotype IB) isolated from frozen raspberries using RNA sequencing-based metagenomics.

RevDate: 2019-07-18

Xue Y, Jonassen I, Øvreås L, et al (2019)

Bacterial and Archaeal Metagenome-Assembled Genome Sequences from Svalbard Permafrost.

Microbiology resource announcements, 8(27): pii:8/27/e00516-19.

Permafrost contains one of the least known soil microbiomes, where microbial populations reside in an ice-locked environment. Here, 56 prokaryotic metagenome-assembled genome (MAG) sequences from 13 phyla are reported. These MAGs will provide information on metabolic pathways that could mediate biogeochemical cycles in Svalbard permafrost.

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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.

ESP Support

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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In reading the early works of classical genetics, one is drawn, almost inexorably, into ever more complex models, until molecular explanations begin to seem both necessary and natural. At that point, the tools for understanding genome research are at hand. Assisting readers reach this point was the original goal of The Electronic Scholarly Publishing Project.

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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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Early support from the DOE component of the Human Genome Project was critically important for getting the ESP project on a firm foundation. Since that funding ended (nearly 20 years ago), the project has been operated as a purely volunteer effort. Anyone wishing to assist in these efforts should send an email to Robbins.

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With the development of methods for adding typeset side notes to PDF files, the ESP project now plans to add annotated versions of some classical papers to its holdings. We also plan to add new reference and pedagogical material. We have already started providing regularly updated, comprehensive bibliographies to the ESP.ORG site.

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Papers in Classical Genetics

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Selected Bibliographies

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