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Bibliography on: Metagenomics

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Robert J. Robbins is a biologist, an educator, a science administrator, a publisher, an information technologist, and an IT leader and manager who specializes in advancing biomedical knowledge and supporting education through the application of information technology. More About:  RJR | OUR TEAM | OUR SERVICES | THIS WEBSITE

RJR: Recommended Bibliography 27 Sep 2020 at 01:30 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®)

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RevDate: 2020-09-25

Alejandre-Colomo C, Viver T, Urdiain M, et al (2020)

Taxonomic study of nine new Winogradskyella species occurring in the shallow waters of Helgoland Roads, North Sea. Proposal of Winogradskyella schleiferi sp. nov., Winogradskyella costae sp. nov., Winogradskyella helgolandensis sp. nov., Winogradskyella vidalii sp. nov., Winogradskyella forsetii sp. nov., Winogradskyella ludwigii sp. nov., Winogradskyella ursingii sp. nov., Winogradskyella wichelsiae sp. nov., and Candidatus "Winogradskyella atlantica" sp. nov.

Systematic and applied microbiology, 43(6):126128 pii:S0723-2020(20)30083-7 [Epub ahead of print].

Evaluation of bacterial succession with cultivation-dependent strategies during a spring phytoplankton bloom in the North Sea led to the isolation of 41 strains that affiliated with the genus Winogradskyella. Fifteen of the strains were selected for a taxonomic study after discarding clonal cultures. A thorough phylogenetic, genomic and phenotypic analysis of the isolates indicated that they represented eight new species that coexisted in North Sea waters. Molecular data revealed the existence of an as yet uncultivated novel species recurrently binned from the North Sea metagenomes. The metagenome-assembled genomes (MAGs) of this new Winogradskyella were used to classify it as a new Candidatus species. This study represented a new example of the use of the tandem approach of whole cell mass spectrometry linked to 16S rRNA gene sequencing in order to facilitate the discovery of new taxa by high-throughput cultivation, which increases the probability of finding more than a single isolate for new species. In addition, we demonstrated the reasons for classifying MAGs representing recurrently retrieved heterotrophic species that evade cultivation even after an important high-throughput effort. The taxonomic study resulted in the classification of eight new species and one new Candidatus species of the genus Winogradskyella for which we propose the names W. schleiferi sp. nov., W. costae sp. nov., W. helgolandensis sp. nov., W. vidalii sp. nov., W. forsetii sp. nov., W. ludwigii sp. nov., W. ursingii sp. nov., W. wichelsiae sp. nov., and Candidatus "W. atlantica" sp. nov.

RevDate: 2020-09-25

Łoniewski I, Misera A, Skonieczna-Żydecka K, et al (2020)

Major Depressive Disorder and gut microbiota - Association not causation. A scoping review.

Progress in neuro-psychopharmacology & biological psychiatry pii:S0278-5846(20)30427-9 [Epub ahead of print].

One very promising hypothesis of Major Depressive Disorder (MDD) pathogenesis is the gut-brain axis (GBA) dysfunction, which can lead to subclinical inflammation, hypothalamic-pituitary (HPA) axis dysregulation, and altered neural, metabolic and endocrine pathways. One of the most important parts of GBA is gut microbiota, which was shown to regulate different functions in the central nervous system (CNS). The purpose of this scoping review was to present the current state of research on the relationship between MDD and gut microbiota and extract causal relationships. Further, we presented the relationship between the use of probiotics and antidepressants, and the microbiota changes. We evaluated the data from 27 studies aimed to investigate microbial fingerprints associated with depression phenotype. We abstracted data from 16 to 11 observational and clinical studies, respectively; the latter was divided into trials evaluating the effects of psychiatric treatment (n = 3) and probiotic intervention (n = 9) on the microbiome composition and function. In total, the data of 1187 individuals from observational studies were assessed. In clinical studies, there were 490 individuals analysed. In probiotic studies, 220 and 218 patients with MDD received the intervention and non-active study comparator, respectively. It was concluded that in MDD, the microbiota is altered. Although the mechanism of this relationship is unknown, we hypothesise that the taxonomic changes observed in patients with MDD are associated with bacterial proinflammatory activity, reduced Schort Chain Fatty Acids (SCFAs) production, impaired intestinal barrier integrity and neurotransmitter production, impaired carbohydrates, tryptophane and glutamate metabolic pathways. However, only in few publications this effect was confirmed by metagenomic, metabolomic analysis, or by assessment of immunological parameters or intestinal permeability markers. Future research requires standardisation process starting from patient selection, material collection, DNA sequencing, and bioinformatic analysis. We did not observe whether antidepressive medications influence on gut microbiota, but the use of psychobiotics in patients with MDD has great prospects; however, this procedure requires also standardisation and thorough mechanistic research. The microbiota should be treated as an environmental element, which considers the aetiopathogenesis of the disease and provides new possibilities for monitoring and treating patients with MDD.

RevDate: 2020-09-25

Kazlauskas D, Krupovic M, Guglielmini J, et al (2020)

Diversity and evolution of B-family DNA polymerases.

Nucleic acids research pii:5911749 [Epub ahead of print].

B-family DNA polymerases (PolBs) represent the most common replicases. PolB enzymes that require RNA (or DNA) primed templates for DNA synthesis are found in all domains of life and many DNA viruses. Despite extensive research on PolBs, their origins and evolution remain enigmatic. Massive accumulation of new genomic and metagenomic data from diverse habitats as well as availability of new structural information prompted us to conduct a comprehensive analysis of the PolB sequences, structures, domain organizations, taxonomic distribution and co-occurrence in genomes. Based on phylogenetic analysis, we identified a new, widespread group of bacterial PolBs that are more closely related to the catalytically active N-terminal half of the eukaryotic PolEpsilon (PolEpsilonN) than to Escherichia coli Pol II. In Archaea, we characterized six new groups of PolBs. Two of them show close relationships with eukaryotic PolBs, the first one with PolEpsilonN, and the second one with PolAlpha, PolDelta and PolZeta. In addition, structure comparisons suggested common origin of the catalytically inactive C-terminal half of PolEpsilon (PolEpsilonC) and PolAlpha. Finally, in certain archaeal PolBs we discovered C-terminal Zn-binding domains closely related to those of PolAlpha and PolEpsilonC. Collectively, the obtained results allowed us to propose a scenario for the evolution of eukaryotic PolBs.

RevDate: 2020-09-25

Hu Y, Hu Y, Li Y, et al (2020)

Metagenomic insights into quorum sensing in membrane-aerated biofilm reactors for phenolic wastewater treatment.

Environmental technology [Epub ahead of print].

Quorum sensing (QS) is of crucial importance for the formation and performance of biofilms adhered to aerated membranes. In this study, the QS-related genes in membrane-aerated biofilm reactors (MABR) for phenolic wastewater treatment were investigated through high-throughput metagenomic sequencing. Results showed that numerous regulatory QS-related genes were associated with the production of signals including acyl-homoserine lactones (AHLs) and diguanylate monophosphate (c-di-GMP), indicating that the biofilms were potentially regulated by the AHL-mediated QS and c-di-GMP-mediated QS systems. Species and functional contribution analysis demonstrated that Pseudomonas, Achromobacter, Rhodococcus, Granulicoccus and Thauera were the key QS-related gene carriers. Redundancy analysis and Spearman correlation analysis showed that high influent phenolic loading gave rise to a high relative abundance of QS bacteria within the biofilm community. Thus, QS-related genes likely play an important role in strengthening biofilm resistance to phenolics, as well as the removal of phenolic contaminants.

RevDate: 2020-09-25

Omori M, Kato-Kogoe N, Sakaguchi S, et al (2020)

Comparative evaluation of microbial profiles of oral samples obtained at different collection time points and using different methods.

Clinical oral investigations pii:10.1007/s00784-020-03592-y [Epub ahead of print].

OBJECTIVES: Recently, the oral microbiome has been found to be associated with oral and general health status. Although various oral sample collection protocols are available, the potential differences between the results yielded by these protocols remain unclear. In this study, we aimed to determine the effects of different time points and methods of oral sample collection on the outcomes of microbiome analysis.

MATERIALS AND METHODS: Oral samples were collected from eight healthy individuals at four different time points: 2 h after eating, immediately after teeth brushing, immediately after waking up, and 2 h after eating on the subsequent day. Four methods of saliva collection were evaluated: spitting, gum chewing, cotton swab, and oral rinse. Oral microbiomes of these samples were compared by analyzing the bacterial 16S rRNA gene sequence data.

RESULTS: The oral microbial composition at the genus level was similar among all sample collection time points and methods. Alpha diversity was not significantly different among the groups, whereas beta diversity was different between the spitting and cotton swab methods. Compared with the between-subject variations, the weighted UniFrac distances between the groups were not minor.

CONCLUSIONS: Although the oral microbiome profiles obtained at different collection time points and using different methods were similar, some differences were detected.

CLINICAL RELEVANCE: The results of the present study suggest that although all the described protocols are useful, comparisons among microbiomes of samples collected by different methods are not appropriate. Researchers must be aware of the issues regarding the impact of saliva collection methods.

RevDate: 2020-09-25

Ouarabi L, Drider D, Taminiau B, et al (2020)

Vaginal Microbiota: Age Dynamic and Ethnic Particularities of Algerian Women.

Microbial ecology pii:10.1007/s00248-020-01606-6 [Epub ahead of print].

The composition of the vaginal microbiota is a key element for maintaining gynecological and reproductive health. With the aim of obtaining an accurate overview of the vaginal microbiota of Algerian women, in terms of their age and ethnic group, we conducted a 16S rRNA gene targeted metagenomic analysis of 100 vaginal samples taken from healthy childbearing and menopausal women. These data were used to establish the pattern of the vaginal microbiota during reproductive and postreproductive phases. Hormone levels were correlated to changes in microbial composition for menopausal women. The ethnic comparison revealed a particular microbiota profile for Algerian women, with a dominance of CST III and CST I. A rapid qPCR method developed by the authors was successfully used to identify the vaginal bacterial pattern for a customized gynecological management.

RevDate: 2020-09-25

Bhattacharya S, Roy C, Mandal S, et al (2020)

Aerobic microbial communities in the sediments of a marine oxygen minimum zone.

FEMS microbiology letters pii:5911577 [Epub ahead of print].

The ecology of aerobic microorganisms is never explored in marine oxygen minimum zone (OMZ) sediments. Here we reveal aerobic bacterial communities along ∼3 m sediment-horizons of the eastern Arabian Sea OMZ. Sulfide-containing sediment-cores retrieved from 530 mbsl (meters beneath the sea-level) and 580 mbsl were explored at 15-30 cm intervals, using metagenomics, pure-culture-isolation, genomics and metatranscriptomics. Genes for aerobic respiration, and oxidation of methane/ammonia/alcohols/thiosulfate/sulfite/organosulfur-compounds, were detected in the metagenomes from all 25 sediment-samples explored. Most probable numbers for aerobic chemolithoautotrophs and chemoorganoheterotrophs at individual sample-sites were up to 1.1 × 107 (g sediment)-1. The sediment-sample collected from 275 cmbsf (centimeters beneath the seafloor) of the 530-mbsl-core yielded many such obligately aerobic isolates belonging to Cereibacter, Guyparkeria, Halomonas, Methylophaga, Pseudomonas and Sulfitobacter which died upon anaerobic incubation, despite being provided all possible electron acceptors and fermentative substrates. High percentages of metatranscriptomic reads from the 275 cmbsf sediment-sample, and metagenomic reads from all 25 sediment-samples, matched the isolates' genomic sequences including those for aerobic metabolisms, genetic/environmental information processing and cell division, thereby illustrating the bacteria's in-situ activity, and ubiquity across the sediment-horizons, respectively. The findings hold critical implications for organic carbon sequestration/remineralization, and inorganic compounds oxidation, within the sediment realm of global marine OMZs.

RevDate: 2020-09-25

Trueba-Santiso A, Wasmund K, Soder-Walz JM, et al (2020)

Genome sequence, proteome profile and identification of a multi-protein reductive dehalogenase complex in Dehalogenimonas alkenigignens strain BRE15M.

Journal of proteome research [Epub ahead of print].

Bacteria of the genus Dehalogenimonas respire with vicinally halogenated alkanes via dihaloelimination. We aimed to describe involved proteins and their supermolecular organization. Metagenomic sequencing of a Dehalogenimonas-containing culture resulted in a 1.65 Mbp draft genome of Dehalogenimonas alkenigignens strain BRE15M. It contained 31 full-length reductive dehalogenase homologous genes (rdhA), but only eight had cognate rdhB genes coding for membrane-anchoring proteins. Shotgun proteomics of cells grown with 1,2-dichloropropane (1,2-DCP) as electron acceptor identified 1152 proteins representing more than 60% of the total proteome. Ten RdhA proteins were detected, including a DcpA ortholog, which was the strongest expressed RdhA. Blue native gel electrophoresis (BNE) demonstrated maximum activity was localized in a protein complex of 146-242 kDa. Protein mass spectrometry revealed the presence of DcpA, its membrane-anchoring protein DcpB, two hydrogen uptake hydrogenase subunits (HupL and HupS), an iron-sulfur protein (HupX), and subunits of a redox protein with a molybdopterin-binding motif (OmeA, OmeB) in the complex. BNE after protein solubilization with different detergent concentrations revealed no evidence for interaction between the putative respiratory electron input module (HupLS) and the OmeA/OmeB/HupX module. All detected RdhAs co-migrated with the organohalide respiration complex. Based on genomic and proteomic analysis, we propose quinone-independent respiration in Dehalogenimonas.

RevDate: 2020-09-25

Xu AA, Hoffman K, Gurwara S, et al (2020)

Oral Health and the Altered Colonic Mucosa-Associated Gut Microbiota.

Digestive diseases and sciences pii:10.1007/s10620-020-06612-9 [Epub ahead of print].

BACKGROUND: Systemic diseases have been associated with oral health and gut microbiota. We examined the association between oral health and the community composition and structure of the adherent colonic gut microbiota.

METHODS: We obtained 197 snap-frozen colonic biopsies from 62 colonoscopy-confirmed polyp-free individuals. Microbial DNA was sequenced for the 16S rRNA V4 region using the Illumina MiSeq, and the sequences were assigned to the operational taxonomic unit based on SILVA. We used a questionnaire to ascertain tooth loss, gum disease, and lifestyle factors. We compared biodiversity and relative abundance of bacterial taxa based on the amount of tooth loss and the presence of gum disease. The multivariable negative binomial regression model for panel data was used to estimate the association between the bacterial count and oral health. False discovery rate-adjusted P value (q value) < .05 indicated statistical significance.

RESULTS: More tooth loss and gum disease were associated with lower bacterial alpha diversity. The relative abundance of Faecalibacterium was lower (q values < .05) with more tooth loss. The association was significant after adjusting for age, ethnicity, obesity, smoking, alcohol use, hypertension, diabetes, and the colon segment. The relative abundance of Bacteroides was higher in those with gum disease.

CONCLUSIONS: Oral health was associated with alteration in the community composition and structure of the adherent gut bacteria in the colon. The reduced anti-inflammatory Faecalibacterium in participants with more tooth loss may indicate systemic inflammation. Future studies are warranted to confirm our findings and investigate the systemic role of Faecalibacterium.

RevDate: 2020-09-25

Smith AM, Tau NP, Kalule BJ, et al (2019)

Shiga toxin-producing Escherichia coli O26:H11 associated with a cluster of haemolytic uraemic syndrome cases in South Africa, 2017.

Access microbiology, 1(9):e000061 pii:000061.

Introduction: Shiga toxin-producing Escherichia coli (STEC) are foodborne pathogens that may cause diarrhoeal outbreaks and occasionally are associated with haemolytic-uraemic syndrome (HUS). We report on STEC O26:H11 associated with a cluster of four HUS cases in South Africa in 2017.

Methodology: All case-patients were female and aged 5 years and under. Standard microbiological tests were performed for culture and identification of STEC from specimens (human stool and food samples). Further analysis of genomic DNA extracted from bacterial cultures and specimens included PCR for specific virulence genes, whole-genome sequencing and shotgun metagenomic sequencing.

Results: For 2/4 cases, stool specimens revealed STEC O26:H11 containing eae, stx2a and stx2b virulence genes. All food samples were found to be negative for STEC. No epidemiological links could be established between the HUS cases. Dried meat products were the leading food item suspected to be the vehicle of transmission for these cases, as 3/4 case-patients reported they had eaten this. However, testing of dried meat products could not confirm this.

Conclusion: Since STEC infection does not always lead to severe symptoms, it is possible that many more cases were associated with this cluster and largely went unrecognized.

RevDate: 2020-09-25

Ponni Keerthana K, Radhesh Krishnan S, Ragunath Sengali S, et al (2019)

Microbiome digital signature of MCR genes - an in silico approach to study the diversity of methanogenic population in laboratory-developed and pilot-scale anaerobic digesters.

Access microbiology, 1(5):e000044 pii:000044.

The production of biogas by anaerobic digestion (AD) of organic/biological wastes has a firm place in sustainable energy production. A simple and cost-effective anaerobic jar at a laboratory scale is a prerequisite to study the microbial community involved in biomass conversion and releasing of methane gas. In this study, a simulation was carried out using a laboratory-modified anaerobic-jar-converted digester (AD1) with that of a commercial/pilot-scale anaerobic digester (AD2). Taxonomic profiling of biogas-producing communities by means of high-throughput methyl coenzyme-M reductase α-subunit (mcrA) gene amplicon sequencing provided high-resolution insights into bacterial and archaeal structures of AD assemblages and their linkages to fed substrates and process parameters. Commonly, the bacterial phyla Euryarchaeota , Chordata, Firmicutes and Proteobacteria appeared to dominate biogas communities in varying abundances depending on the apparent process conditions. Key micro-organisms identified from AD were Methanocorpusculum labreanum and Methanobacterium formicicum . Specific biogas production was found to be significantly correlating to Methanosarcinaceae . It can be implied from this study that the metagenomic sequencing data was able to dissect the microbial community structure in the digesters. The data gathered indicates that the anaerobic-jar system could throw light on the population dynamics of the methanogens at laboratory scale and its effectiveness at large-scale production of bio-methane. The genome sequence information of non-cultivable biogas community members, metagenome sequencing including assembly and binning strategies will be highly valuable in determining the efficacy of an anaerobic digester.

RevDate: 2020-09-25

Khandagale K, Krishna R, Roylawar P, et al (2020)

Omics approaches in Allium research: Progress and way ahead.

PeerJ, 8:e9824 pii:9824.

Background: The genus Allium (Family: Amaryllidaceae) is an economically important group of crops cultivated worldwide for their use as a vegetable and spices. Alliums are also well known for their nutraceutical properties. Among alliums, onion, garlic, leek, and chives cultivated worldwide. Despite their substantial economic and medicinal importance, the genome sequence of any of the Allium is not available, probably due to their large genome sizes. Recently evolved omics technologies are highly efficient and robust in elucidating molecular mechanisms of several complex life processes in plants. Omics technologies, such as genomics, transcriptomics, proteomics, metabolomics, metagenomics, etc. have the potential to open new avenues in research and improvement of allium crops where genome sequence information is limited. A significant amount of data has been generated using these technologies for various Allium species; it will help in understanding the key traits in Allium crops such as flowering, bulb development, flavonoid biosynthesis, male sterility and stress tolerance at molecular and metabolite level. This information will ultimately assist us in speeding up the breeding in Allium crops.

Method: In the present review, major omics approaches, and their progress, as well as potential applications in Allium crops, could be discussed in detail.

Results: Here, we have discussed the recent progress made in Allium research using omics technologies such as genomics, transcriptomics, micro RNAs, proteomics, metabolomics, and metagenomics. These omics interventions have been used in alliums for marker discovery, the study of the biotic and abiotic stress response, male sterility, organ development, flavonoid and bulb color, micro RNA discovery, and microbiome associated with Allium crops. Further, we also emphasized the integrated use of these omics platforms for a better understanding of the complex molecular mechanisms to speed up the breeding programs for better cultivars.

Conclusion: All the information and literature provided in the present review throws light on the progress and potential of omics platforms in the research of Allium crops. We also mentioned a few research areas in Allium crops that need to be explored using omics technologies to get more insight. Overall, alliums are an under-studied group of plants, and thus, there is tremendous scope and need for research in Allium species.

RevDate: 2020-09-25

Chen R, Wong HL, Kindler GS, et al (2020)

Discovery of an Abundance of Biosynthetic Gene Clusters in Shark Bay Microbial Mats.

Frontiers in microbiology, 11:1950.

Microbial mats are geobiological multilayered ecosystems that have significant evolutionary value in understanding the evolution of early life on Earth. Shark Bay, Australia has some of the best examples of modern microbial mats thriving under harsh conditions of high temperatures, salinity, desiccation, and ultraviolet (UV) radiation. Microorganisms living in extreme ecosystems are thought to potentially encode for secondary metabolites as a survival strategy. Many secondary metabolites are natural products encoded by a grouping of genes known as biosynthetic gene clusters (BGCs). Natural products have diverse chemical structures and functions which provide competitive advantages for microorganisms and can also have biotechnology applications. In the present study, the diversity of BGC were described in detail for the first time from Shark Bay microbial mats. A total of 1477 BGCs were detected in metagenomic data over a 20 mm mat depth horizon, with the surface layer possessing over 200 BGCs and containing the highest relative abundance of BGCs of all mat layers. Terpene and bacteriocin BGCs were highly represented and their natural products are proposed to have important roles in ecosystem function in these mat systems. Interestingly, potentially novel BGCs were detected from Heimdallarchaeota and Lokiarchaeota, two evolutionarily significant archaeal phyla not previously known to possess BGCs. This study provides new insights into how secondary metabolites from BGCs may enable diverse microbial mat communities to adapt to extreme environments.

RevDate: 2020-09-25

Papadimitriou K, Kline K, Renault P, et al (2020)

Editorial: Omics and Systems Approaches to Study the Biology and Applications of Lactic Acid Bacteria.

Frontiers in microbiology, 11:1786.

RevDate: 2020-09-25

Ferreira FC, Fonseca DM, Hamilton G, et al (2020)

Metagenomic analysis of human-biting cat fleas in urban northeastern United States of America reveals an emerging zoonotic pathogen.

Scientific reports, 10(1):15611 pii:10.1038/s41598-020-72956-x.

An infestation of cat fleas in a research center led to the detection of two genotypes of Ctenocephalides felis biting humans in New Jersey, USA. The rarer flea genotype had an 83% incidence of Rickettsia asembonensis, a recently described bacterium closely related to R. felis, a known human pathogen. A metagenomics analysis developed in under a week recovered the entire R. asembonensis genome at high coverage and matched it to identical or almost identical (> 99% similarity) strains reported worldwide. Our study exposes the potential of cat fleas as vectors of human pathogens in crowded northeastern U.S, cities and suburbs where free-ranging cats are abundant. Furthermore, it demonstrates the power of metagenomics to glean large amounts of comparative data regarding both emerging vectors and their pathogens.

RevDate: 2020-09-25

Babalola OO, Akinola SA, AS Ayangbenro (2020)

Shotgun Metagenomic Survey of Maize Soil Rhizobiome.

Microbiology resource announcements, 9(39): pii:9/39/e00860-20.

The plant soil rhizobiome induces critical functions in the plant proximal environment. Linkages between soil microbiota and primary functional attributes are underexplored. Here, we present the metagenomes of maize soil rhizosphere organisms with functional diversity associated with farms at two different municipalities in North West and Gauteng provinces of South Africa. We describe a plenteous and diverse microbial community.

RevDate: 2020-09-25

Xue Y, Lin L, Hu F, et al (2020)

Disruption of ruminal homeostasis by malnutrition involved in systemic ruminal microbiota-host interactions in a pregnant sheep model.

Microbiome, 8(1):138 pii:10.1186/s40168-020-00916-8.

BACKGROUND: Undernutrition is a prevalent and spontaneous condition in animal production which always affects microbiota-host interaction in gastrointestinal tract. However, how undernutrition affects crosstalk homeostasis is largely unknown. Here, we discover how undernutrition affects microbial profiles and subsequently how microbial metabolism affects the signal transduction and tissue renewal in ruminal epithelium, clarifying the detrimental effect of undernutrition on ruminal homeostasis in a pregnant sheep model.

RESULTS: Sixteen pregnant ewes (115 days of gestation) were randomly and equally assigned to the control (CON) and severe feed restriction (SFR) groups. Ewes on SFR treatment were restricted to a 30% level of ad libitum feed intake while the controls were fed normally. After 15 days, all ewes were slaughtered to collect ruminal digesta for 16S rRNA gene and metagenomic sequencing and ruminal epithelium for transcriptome sequencing. Results showed that SFR diminished the levels of ruminal volatile fatty acids and microbial proteins and repressed the length, width, and surface area of ruminal papillae. The 16S rRNA gene analysis indicated that SFR altered the relative abundance of ruminal bacterial community, showing decreased bacteria about saccharide degradation (Saccharofermentans and Ruminococcus) and propionate genesis (Succiniclasticum) but increased butyrate producers (Pseudobutyrivibrio and Papillibacter). Metagenome analysis displayed that genes related to amino acid metabolism, acetate genesis, and succinate-pathway propionate production were downregulated upon SFR, while genes involved in butyrate and methane genesis and acrylate-pathway propionate production were upregulated. Transcriptome and real-time PCR analysis of ruminal epithelium showed that downregulated collagen synthesis upon SFR lowered extracellular matrix-receptor interaction, inactivated JAK3-STAT2 signaling pathway, and inhibited DNA replication and cell cycle.

CONCLUSIONS: Generally, undernutrition altered rumen bacterial community and function profile to decrease ruminal energy retention, promoted epithelial glucose and fatty acid catabolism to elevate energy supply, and inhibited the proliferation of ruminal epithelial cells. These findings provide the first insight into the systemic microbiota-host interactions that are involved in disrupting the ruminal homeostasis under a malnutrition pattern. Video Abstract.

RevDate: 2020-09-25

Hewson I, Johnson MR, IR Tibbetts (2020)

An Unconventional Flavivirus and Other RNA Viruses in the Sea Cucumber (Holothuroidea; Echinodermata) Virome.

Viruses, 12(9): pii:v12091057.

Sea cucumbers (Holothuroidea; Echinodermata) are ecologically significant constituents of benthic marine habitats. We surveilled RNA viruses inhabiting eight species (representing four families) of holothurian collected from four geographically distinct locations by viral metagenomics, including a single specimen of Apostichopus californicus affected by a hitherto undocumented wasting disease. The RNA virome comprised genome fragments of both single-stranded positive sense and double stranded RNA viruses, including those assigned to the Picornavirales, Ghabrivirales, and Amarillovirales. We discovered an unconventional flavivirus genome fragment which was most similar to a shark virus. Ghabivirales-like genome fragments were most similar to fungal totiviruses in both genome architecture and homology and had likely infected mycobiome constituents. Picornavirales, which are commonly retrieved in host-associated viral metagenomes, were similar to invertebrate transcriptome-derived picorna-like viruses. The greatest number of viral genome fragments was recovered from the wasting A. californicus library compared to the asymptomatic A. californicus library. However, reads from the asymptomatic library recruited to nearly all recovered wasting genome fragments, suggesting that they were present but not well represented in the grossly normal specimen. These results expand the known host range of flaviviruses and suggest that fungi and their viruses may play a role in holothurian ecology.

RevDate: 2020-09-24
CmpDate: 2020-09-24

Debnath M, Banerjee M, M Berk (2020)

Genetic gateways to COVID-19 infection: Implications for risk, severity, and outcomes.

FASEB journal : official publication of the Federation of American Societies for Experimental Biology, 34(7):8787-8795.

The dynamics, such as transmission, spatial epidemiology, and clinical course of Coronavirus Disease-2019 (COVID-19) have emerged as the most intriguing features and remain incompletely understood. The genetic landscape of an individual in particular, and a population in general seems to play a pivotal role in shaping the above COVID-19 dynamics. Considering the implications of host genes in the entry and replication of SARS-CoV-2 and in mounting the host immune response, it appears that multiple genes might be crucially involved in the above processes. Herein, we propose three potentially important genetic gateways to COVID-19 infection; these could explain at least in part the discrepancies of its spread, severity, and mortality. The variations within Angiotensin-converting enzyme 2 (ACE2) gene might constitute the first genetic gateway, influencing the spatial transmission dynamics of COVID-19. The Human Leukocyte Antigen locus, a master regulator of immunity against infection seems to be crucial in influencing susceptibility and severity of COVID-19 and can be the second genetic gateway. The genes regulating Toll-like receptor and complement pathways and subsequently cytokine storm induced exaggerated inflammatory pathways seem to underlie the severity of COVID-19, and such genes might represent the third genetic gateway. Host-pathogen interaction is a complex event and some additional genes might also contribute to the dynamics of COVID-19. Overall, these three genetic gateways proposed here might be the critical host determinants governing the risk, severity, and outcome of COVID-19. Genetic variations within these gateways could be key in influencing geographical discrepancies of COVID-19.

RevDate: 2020-09-24

Dos Santos Bezerra R, Bitencourt HT, Covas DT, et al (2020)

Molecular evolution pattern of Merkel cell polyomavirus identified by viral metagenomics in plasma of high-risk blood donors from the Brazilian Amazon.

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases pii:S1567-1348(20)30394-4 [Epub ahead of print].

Merkel cell polyomavirus (MCPyV) is a common human skin pathogen, shows high seroprevalence and is considered the etiologic agent of Merkel cell carcinoma. However, studies which detect MCPyV DNA in blood products may reveal the importance of this virus for the transfusion medicine. In this study we analyzed by viral metagenomics 36 plasma samples obtained from blood donors positive for the common blood transmitted infections from the city of Macapá (Brazilian Amazon). The generated raw data was analyzed through a specific bioinformatics pipeline aimed at discovery of emerging viruses. The genomes of interest were analyzed phylogeographically and phylogenetically. MCPyV complete genome was recovered from one HBV-positive pool with high coverage (~ 223×) indicating suggesting acute viremia or reactivated infection. Interestingly, the performed phylogeographic position of the identified strain suggests its ancestry compared to MCPyV isolate from Colombian Amazon which hypothesizes that viral dissemination in the Amazon may have originated from Brazil. In conclusion, this study brings information for the genetic relationships of MCPyV isolated from blood donors from the Brazilian Amazon and demonstrates the possible phylogeographic behavior of our strain in relation to the other findings. We also demonstrated a strong evidence of viremic MCPyV phase in blood donations, however, more studies are necessary in order to understand the MCPyV impact on transfusion therapy.

RevDate: 2020-09-24

Charlys da Costa A, Moron AF, Forney LJ, et al (2020)

Identification of Bacteriophages in the Vagina of Pregnant Women: A Descriptive Study.

BJOG : an international journal of obstetrics and gynaecology [Epub ahead of print].

OBJECTIVE: Determine the presence and identity of extracellular bacteriophage (phage) families, genera and species in the vagina of pregnant women DESIGN: Descriptive, observational cohort study SETTING: São Paulo, Brazil POPULATION: Pregnant women at 21-24 weeks gestation METHODS: Vaginal samples from 107 women whose vaginal microbiome and pregnancy outcomes were previously determined were analyzed for phages by metagenomic sequencing, Main outcome measures Identification of phage families, genera and species RESULTS: Phages were detected in 96 (89.7%) of the samples. Six different phage families were identified: Siphoviridae in 69.2%, Myoviridae in 49.5%, Microviridae in 37.4%, Podoviridae in 20.6%, Herelleviridae in 10.3% and Inviridae in 1.9% of the women. Four different phage families were present in 14 women (13.1%), 3 families in 20 women (18.7%), 2 families in 31 women (29.1%) and 1 family in 31 women (29.1%). The most common phage species detected were Bacillus phages in 48 (43.6%), Escherichia phages in 45 (40.9%), Staphylococcus phages in 40 (36.4%), Gokushovirus in 33 (30.0%) and Lactobacillus phages in 29 (26.4%) women. In a preliminary exploratory analysis, there were no associations between a particular phage family, the number of phage families present in the vagina or any particular phage species and either gestational age at delivery or the bacterial community state type present in the vagina.

CONCLUSIONS: Multiple phages are present in the vagina of most mid-trimester pregnant women.

RevDate: 2020-09-24

Xu J, Y Yang (2020)

Implications of gut microbiome on coronary artery disease.

Cardiovascular diagnosis and therapy, 10(4):869-880.

Despite the enormous progress achieved in diagnosis and medical therapy of coronary artery disease (CAD) in the last decades, CAD continues to represent the leading cause of morbidity and mortality worldwide, leading to a massive health-care cost and social burden. Due to the dynamic and complex nature of CAD, the mechanisms underlying the progression of atherosclerotic plaque were largely unknown. With the development of metagenomics and bioinformatics, humans are gradually understanding the important role of the gut microbiome on their hosts. Trillions of microbes colonize in the human gut, they digest and absorb nutrients, as well as participate in a series of human functions and regulate the pathogenesis of diseases, including the cardiovascular disease (CVD) that has received much attention. Meanwhile, metabolomics studies have revealed associations between gut microbiota-derived metabolic bioactive signaling modules, including trimethylamine-N-oxide (TMAO), short-chain fatty acids (SCFAs), and bile acids (BAs), with the progression of CAD. Disturbance of the gut microbiome and microbial metabolites are important factors leading to CAD, which has become a novel target for CAD prevention and treatment. This review provides a brief overview of gut microbiome composition in CAD patients according to the recently reported studies, summarizes the underlying mechanisms, and highlights the prognostic value of the gut microbiome in CAD.

RevDate: 2020-09-24

Laue HE, Korrick SA, Baker ER, et al (2020)

Prospective associations of the infant gut microbiome and microbial function with social behaviors related to autism at age 3 years.

Scientific reports, 10(1):15515 pii:10.1038/s41598-020-72386-9.

The hypothesized link between gut bacteria and autism spectrum disorder (ASD) has been explored through animal models and human studies with microbiome assessment after ASD presentation. We aimed to prospectively characterize the association between the infant/toddler gut microbiome and ASD-related social behaviors at age 3 years. As part of an ongoing birth cohort gut bacterial diversity, structure, taxa, and function at 6 weeks (n = 166), 1 year (n = 158), 2 years (n = 129), and 3 years (n = 140) were quantified with 16S rRNA gene and shotgun metagenomic sequencing (n = 101 six weeks, n = 103 one year). ASD-related social behavior was assessed at age 3 years using Social Responsiveness Scale (SRS-2) T-scores. Covariate-adjusted linear and permutation-based models were implemented. Microbiome structure at 1 year was associated with SRS-2 total T-scores (p = 0.01). Several taxa at 1, 2, and 3 years were associated with SRS-2 performance, including many in the Lachnospiraceae family. Higher relative abundance of Adlercreutzia equolifaciens and Ruminococcus torques at 1 year related to poorer SRS-2 performance. Two functional pathways, L-ornithine and vitamin B6 biosynthesis, were associated with better social skills at 3 years. Our results support potential associations between early-childhood gut microbiome and social behaviors. Future mechanistic studies are warranted to pinpoint sensitive targets for intervention.

RevDate: 2020-09-24

Lavrinienko A, Tukalenko E, Mousseau TA, et al (2020)

Two hundred and fifty-four metagenome-assembled bacterial genomes from the bank vole gut microbiota.

Scientific data, 7(1):312 pii:10.1038/s41597-020-00656-2.

Vertebrate gut microbiota provide many essential services to their host. To better understand the diversity of such services provided by gut microbiota in wild rodents, we assembled metagenome shotgun sequence data from a small mammal, the bank vole Myodes glareolus (Rodentia, Cricetidae). We were able to identify 254 metagenome assembled genomes (MAGs) that were at least 50% (n = 133 MAGs), 80% (n = 77 MAGs) or 95% (n = 44 MAGs) complete. As typical for a rodent gut microbiota, these MAGs are dominated by taxa assigned to the phyla Bacteroidetes (n = 132 MAGs) and Firmicutes (n = 80), with some Spirochaetes (n = 15) and Proteobacteria (n = 11). Based on coverage over contigs, Bacteroidetes were estimated to be most abundant group, followed by Firmicutes, Spirochaetes and Proteobacteria. These draft bacterial genomes can be used freely to determine the likely functions of gut microbiota community composition in wild rodents.

RevDate: 2020-09-24

Hause BM, Nelson EA, J Christopher-Hennings (2020)

North American Big Brown Bats (Eptesicus fuscus) Harbor an Exogenous Deltaretrovirus.

mSphere, 5(5): pii:5/5/e00902-20.

Bats are the reservoir for a large number of zoonotic viruses, including members of Coronaviridae (severe acute respiratory syndrome coronavirus [SARS-CoV] and SARS-CoV-2), Paramyxoviridae (Hendra and Nipah viruses), Rhabdoviridae (rabies virus), and Filoviridae (Ebola virus) as exemplars. Many retroviruses, such as human immunodeficiency virus, are similarly zoonotic; however, only infectious exogenous gammaretroviruses have recently been identified in bats. Here, viral metagenomic sequencing of samples from bats submitted for rabies virus testing, largely due to human exposure, identified a novel, highly divergent exogenous Deltaretrovirus from a big brown bat (Eptesicus fuscus) in South Dakota. The virus sequence, corresponding to Eptesicus fuscus deltaretrovirus (EfDRV), comprised a nearly complete coding region comprised of canonical 5'-gag-pro-pol-env-3' genes with 37% to 51% identity to human T-lymphotropic virus (HTLV), an infectious retrovirus that causes T-cell lymphoma. A putative tax gene with 27% identity to HTLV was located downstream of the pol gene along with a gene harbored in an alternative reading frame which possessed a conserved domain for an Epstein-Barr virus nuclear antigen involved in gene transactivation, suggesting a regulatory function similar to that of the deltaretrovirus rex gene. A TaqMan reverse transcriptase PCR (RT-PCR) targeting the pol gene identified 4/60 (6.7%) bats as positive for EfDRV, which, combined with a search of the E. fuscus genome that failed to identify sequences with homology to EfDRV, suggests that EfDRV is an infectious exogenous virus. As all known members of Deltaretrovirus can cause malignancies and E. fuscus is widely distributed in the Americas, often with a colonial roosting behavior in human dwellings, further studies are needed to investigate potential zoonosis.IMPORTANCE Bats host a large numbers of viruses, many of which are zoonotic. In the United States, the big brown bat (Eptesicus fuscus) is widely distributed and lives in small colonies that roost in cavities, often in human dwellings, leading to frequent human interaction. Viral metagenomic sequencing of samples from an E. fuscus bat submitted for rabies testing identified the first exogenous bat Deltaretrovirus The E. fuscus deltaretrovirus (EfDRV) genome consists of the typical deltaretrovial 5'-gag-pro-pol-env-3' genes along with genes encoding two putative transcriptional transactivator proteins distantly related to the Tax protein of human T-cell lymphotrophic virus and nuclear antigen 3B of Epstein-Barr virus. Searches of the E. fuscus genome sequence failed to identify endogenous EfDRV. RT-PCR targeting the EfDRV pol gene identified 4/60 (6.7%) bats with positive results. Together, these results suggest that EfDRV is exogenous. As all members of Deltaretrovirus are associated with T- and B-cell malignancies or neurologic disease, further studies on possible zoonosis are warranted.

RevDate: 2020-09-24

Jackson EW, Wilhelm RC, Johnson MR, et al (2020)

Diversity of sea star-associated densoviruses and transcribed endogenized viral elements of densovirus origin.

Journal of virology pii:JVI.01594-20 [Epub ahead of print].

A viral etiology of Sea Star Wasting Syndrome (SSWS) was originally explored with virus-sized material challenge experiments, field surveys, and metagenomics leading to the conclusion that a densovirus is the predominant DNA virus associated with this syndrome, and, thus, the most promising viral candidate pathogen. Single-stranded DNA viruses are however highly diverse and pervasive among eukaryotic organisms which we hypothesize may confound the association between densoviruses and SSWS in sea stars. To test this hypothesis and assess the association of densoviruses to SSWS, we compiled past metagenomic data with new metagenomic-derived viral genomes from sea stars collected from Antarctica, California, Washington, and Alaska. We used 179 publicly available sea star transcriptomes to complement our approaches for densovirus discovery. Lastly, we focus the study to SSaDV, the first sea star densovirus discovered, by documenting its biogeography and putative tissue tropism. Transcriptomes contained mostly endogenized densovirus elements similar to the NS1 gene, while numerous complete and near-complete densoviral genomes were recovered from viral metagenomes. SSaDV was associated with nearly all tested species from southern California to Alaska, and in contrast to previous work, we show SSaDV is one genotype among a high diversity of densoviruses present in sea stars across the west coast of the United States and globally that are commonly associated with grossly normal (i.e. healthy or asymptomatic) animals. The diversity and ubiquity of these viruses in wild sea stars confounds the original hypothesis that one densovirus was the etiologic agent of SSWD.Importance:The primary interest in sea star densoviruses, specifically SSaDV, has been their association with Sea Star Wasting Syndrome (SSWS), a disease that has decimated sea star populations across the west coast of the United States since 2013. The association of SSaDV to SSWS was originally drawn from metagenomic analysis, which was further studied through field surveys using qPCR, concluding that that it was the most likely viral candidate in the metagenomic data based on its representation in symptomatic sea stars compared to asymptomatic specimens. We reexamined the original metagenomic data with additional genomic datasets and found that SSaDV was one of ten densoviruses present in the original dataset and was no more represented in symptomatic sea stars than in asymptomatic sea stars. Instead, SSaDV appears to be a widespread, generalist virus that exists among a large diversity of densoviruses present in sea star populations.

RevDate: 2020-09-24

Kim B, Cho EJ, Yoon JH, et al (2020)

Pathway-Based Integrative Analysis of Metabolome and Microbiome Data from Hepatocellular Carcinoma and Liver Cirrhosis Patients.

Cancers, 12(9): pii:cancers12092705.

Aberrations of the human microbiome are associated with diverse liver diseases, including hepatocellular carcinoma (HCC). Even if we can associate specific microbes with particular diseases, it is difficult to know mechanistically how the microbe contributes to the pathophysiology. Here, we sought to reveal the functional potential of the HCC-associated microbiome with the human metabolome which is known to play a role in connecting host phenotype to microbiome function. To utilize both microbiome and metabolomic data sets, we propose an innovative, pathway-based analysis, Hierarchical structural Component Model for pathway analysis of Microbiome and Metabolome (HisCoM-MnM), for integrating microbiome and metabolomic data. In particular, we used pathway information to integrate these two omics data sets, thus providing insight into biological interactions between different biological layers, with regard to the host's phenotype. The application of HisCoM-MnM to data sets from 103 and 97 patients with HCC and liver cirrhosis (LC), respectively, showed that this approach could identify HCC-related pathways related to cancer metabolic reprogramming, in addition to the significant metabolome and metagenome that make up those pathways.

RevDate: 2020-09-24

Guajardo-Leiva S, Chnaiderman J, Gaggero A, et al (2020)

Metagenomic Insights into the Sewage RNA Virosphere of a Large City.

Viruses, 12(9): pii:v12091050.

Sewage-associated viruses can cause several human and animal diseases, such as gastroenteritis, hepatitis, and respiratory infections. Therefore, their detection in wastewater can reflect current infections within the source population. To date, no viral study has been performed using the sewage of any large South American city. In this study, we used viral metagenomics to obtain a single sample snapshot of the RNA virosphere in the wastewater from Santiago de Chile, the seventh largest city in the Americas. Despite the overrepresentation of dsRNA viruses, our results show that Santiago's sewage RNA virosphere was composed mostly of unknown sequences (88%), while known viral sequences were dominated by viruses that infect bacteria (60%), invertebrates (37%) and humans (2.4%). Interestingly, we discovered three novel genogroups within the Picobirnaviridae family that can fill major gaps in this taxa's evolutionary history. We also demonstrated the dominance of emerging Rotavirus genotypes, such as G8 and G6, that have displaced other classical genotypes, which is consistent with recent clinical reports. This study supports the usefulness of sewage viral metagenomics for public health surveillance. Moreover, it demonstrates the need to monitor the viral component during the wastewater treatment and recycling process, where this virome can constitute a reservoir of human pathogens.

RevDate: 2020-09-24

Gomez-Llorente MA, Martínez-Cañavate A, Chueca N, et al (2020)

A Multi-Omics Approach Reveals New Signatures in Obese Allergic Asthmatic Children.

Biomedicines, 8(9): pii:biomedicines8090359.

Background: Asthma is a multifactorial condition where patients with identical clinical diagnoses do not have the same clinical history or respond to treatment. This clinical heterogeneity is reflected in the definition of two main endotypes. We aimed to explore the metabolic and microbiota signatures that characterize the clinical allergic asthma phenotype in obese children. Methods: We used a multi-omics approach combining clinical data, plasma and fecal inflammatory biomarkers, metagenomics, and metabolomics data in a cohort of allergic asthmatic children. Results: We observed that the obese allergic asthmatic phenotype was markedly associated with higher levels of leptin and lower relative proportions of plasma acetate and a member from the Clostridiales order. Moreover, allergic children with a worse asthma outcome showed higher levels of large unstained cells, fecal D lactate and D/L lactate ratio, and with a higher relative proportion of plasma creatinine and an unclassified family member from the RF39 order belonging to the Mollicutes class. Otherwise, children with persistent asthma presented lower levels of plasma citrate and dimethylsulfone. Conclusion: Our integrative approach shows the molecular heterogeneity of the allergic asthma phenotype while highlighting the use of omics technologies to examine the clinical phenotype at a more holistic level.

RevDate: 2020-09-16
CmpDate: 2020-09-16

Vancuren SJ, Dos Santos SJ, Hill JE, et al (2020)

Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling.

PloS one, 15(7):e0235682.

Amplification and sequencing of conserved genetic barcodes such as the cpn60 gene is a common approach to determining the taxonomic composition of microbiomes. Exact sequence variant calling has been proposed as an alternative to previously established methods for aggregation of sequence reads into operational taxonomic units (OTU). We investigated the utility of variant calling for cpn60 barcode sequences and determined the minimum sequence length required to provide species-level resolution. Sequence data from the 5´ region of the cpn60 barcode amplified from the human vaginal microbiome (n = 45), and a mock community were used to compare variant calling to de novo assembly of reads, and mapping to a reference sequence database in terms of number of OTU formed, and overall community composition. Variant calling resulted in microbiome profiles that were consistent in apparent composition to those generated with the other methods but with significant logistical advantages. Variant calling is rapid, achieves high resolution of taxa, and does not require reference sequence data. Our results further demonstrate that 150 bp from the 5´ end of the cpn60 barcode sequence is sufficient to provide species-level resolution of microbiota.

RevDate: 2020-09-23

Hoque MN, Istiaq A, Rahman MS, et al (2020)

Microbiome dynamics and genomic determinants of bovine mastitis.

Genomics pii:S0888-7543(20)31029-6 [Epub ahead of print].

The milk of lactating cows presents a complex ecosystem of interconnected microbial communities which can influence the pathophysiology of mastitis. We hypothesized possible dynamic shifts of microbiome composition and genomic features with different pathological conditions of mastitis (Clinical Mastitis; CM, Recurrent CM; RCM, Subclinical Mastitis; SCM). To evaluate this hypothesis, we employed whole metagenome sequencing (WMS) in 20 milk samples (CM, 5; RCM, 6; SCM, 4; H, 5) to unravel the microbiome dynamics, interrelation, and relevant metabolic functions. The WMS data mapped to 442 bacterial, 58 archaeal and 48 viral genomes with distinct variation in microbiome composition (CM > H > RCM > SCM). Furthermore, we identified a number of microbial genomic features, including 333, 304, 183 and 50 virulence factors-associated genes (VFGs) and 48, 31, 11 and 6 antibiotic resistance genes (ARGs) in CM, RCM, SCM, and H-microbiomes, respectively. We also detected different metabolic pathway and functional genes associated with mastitis pathogenesis. Therefore, profiling microbiome dynamics in different conditions of mastitis and associated microbial genomic features contributes to developing microbiome-based diagnostics and therapeutics for bovine mastitis.

RevDate: 2020-09-23

Xu R, Sun X, Lin H, et al (2020)

Microbial adaptation in vertical soil profiles contaminated by antimony smelting plant.

FEMS microbiology ecology pii:5910484 [Epub ahead of print].

Antimony mining has resulted in considerable pollution to the soil environment. Although studies on antinomy contamination have been conducted, its effects on vertical soil profiles and depth-resolved microbial communities remain unknown. Current study selected three vertical soil profiles (0-2 m) from the world's largest antimony mining area to characterize the depth-resolved soil microbiota and investigate the effects of mining contamination on microbial adaptation. Results demonstrated that contaminated soil profiles showed distinct depth-resolved effects when compared to uncontaminated soil profiles. As soil depth increased, the concentrations of antimony and arsenic gradually declined in the contaminated soil profiles. Acidobacteria, Chloroflexi, Proteobacteria, and Thaumarchaeota were the most variable phyla from surface to deep soil. The co-occurrence networks were loosely connected in surface soil, but obviously recovered and were well-connected in deep soil. The metagenomic results indicated that microbial metabolic potential also changed with soil depth. Genes encoding C metabolism pathways were negatively correlated with antimony and arsenic concentrations. Abundances of arsenic-related genes were enriched by severe contamination, but reduced with soil depth. Overall, soil depth-resolved characteristics are often many meters deep and such effects affected the indigenous microbial communities, as well as their metabolic potential due to different contaminants along vertical depths.

RevDate: 2020-09-23

Sun J, Li P, Liu Z, et al (2020)

A novel thermostable serine protease from a metagenomic library derived from marine sediments in the East China Sea.

Applied microbiology and biotechnology pii:10.1007/s00253-020-10879-3 [Epub ahead of print].

Thermal activity and stability are important characteristics for proteases applied in the detergent, pharmaceutical, food, and other green industries. With the intent to discover thermostable novel proteases, we constructed a fosmid metagenomic library from marine sediments in the East China Sea and isolated a clone endowed with high proteolytic activity from this library. Sequence analysis of the positive subclones allowed the identification of a coding region of 1254 bp related to protease activity. The unrooted phylogenetic tree and alignment results revealed that the sequence might be derived from Anaerolineaceae bacterium and encodes a new member of the peptidase S8A subfamily with the typical catalytic triad Asp119/His150/Ser325. The fusion protein, named pF1AL2, was expressed in Escherichia coli and showed a molecular weight of 35 kDa. pF1AL2 was active in the pH range of 5.0-11.0 with an optimal pH at 10.0 and had high stability under alkaline conditions, retaining more than 95% of its activity after 24 h at pH 11.0. The optimal temperature of pF1AL2 was 80 °C, and it retained nearly 80% of its activity after 6 h at 70 °C, showing great thermal activity and stability. In addition, the enzyme had great salt tolerance (the residual activity when kept in 3 M NaCl was 40%). Its thermal activity and stability, along with its halotolerance and pH-tolerance, indicate the high potential value of pF1AL2 in industrial applications. The exploitation of pF1AL2 could lay the foundation for the development and utilization of proteases with special features from marine resources by a metagenomic strategy. KEY POINTS: • A novel protease, pF1AL2, from marine sediments, was screened out by a metagenomic strategy. • The protease pF1AL2 analyzed in silico, cloned, and characterized. • pF1AL2 had an optimal temperature of 80 °C and retained nearly 80% of activity after 6 h at 70 °C. • pF1AL2 had great tolerance for high-temperature and acid, alkaline, and high salt environments.

RevDate: 2020-09-23

Asmerom B, Drobish I, Winckler B, et al (2020)

Detection of Neisseria gonorrhoeae from Joint Aspirate by Metagenomic Sequencing in Disseminated Gonococcal Infection.

Journal of the Pediatric Infectious Diseases Society pii:5910366 [Epub ahead of print].

Disseminated gonococcal infection (DGI) often manifests as gonococcal arthritis and may carry significant morbidity. However, diagnosis remains elusive due to limited sensitivity of available diagnostic tests. We used metagenomic next-generation sequencing to detect Neisseria gonorrhoeae from culture-negative joint aspirates of 2 patients with clinically diagnosed DGI.

RevDate: 2020-09-23

López-Pérez ME, Saldaña-Robles A, Zanor GA, et al (2020)

Microbiomes in agricultural and mining soils contaminated with arsenic in Guanajuato, Mexico.

Archives of microbiology pii:10.1007/s00203-020-01973-1 [Epub ahead of print].

In this report, physical and chemical properties, and total arsenic (As) concentrations were analyzed in agricultural (MASE) and mining soils (SMI) in the State of Guanajuato, México. Additionally, a metagenomic analysis of both types of soils was the bases for the identification and selection of bacteria and fungi resistant to As. The SMI soil showed higher concentration of As (39 mg kg-1) as compared to MASE soil (15 mg kg-1). The metagenome showed a total of 175,240 reads from both soils. MASE soil showed higher diversity of bacteria, while the SMI soil showed higher diversity of fungi. 16S rRNA analysis showed that the phylum Proteobacteria showed the highest proportion (39.6% in MASE and 36.4% in SMI) and Acidobacteria was the second most representative (24.2% in SMI and 11.6% in MASE). 18S rRNA analysis, showed that the phylum Glomeromycota was found only in the SMI soils (11.6%), while Ascomycota was the most abundant, followed by Basidiomycota, and Zygomycota, in both soils. Genera Bacillus and Penicillium were able to grow in As concentrations as high as 5 and 10 mM, reduced As (V) to As (III), and removed As at 9.8% and 12.1% rates, respectively. When aoxB, arsB, ACR3(1), ACR3(2,) and arrA genes were explored, only the arsB gene was identified in Bacillus sp., B. simplex, and B. megaterium. In general, SMI soils showed more microorganisms resistant to As than MASE soils. Bacteria and fungi selected in this work may show potential to be used as bioremediation agents in As contaminated soils.

RevDate: 2020-09-23

Zamkovaya T, Foster JS, de Crécy-Lagard V, et al (2020)

A network approach to elucidate and prioritize microbial dark matter in microbial communities.

The ISME journal pii:10.1038/s41396-020-00777-x [Epub ahead of print].

Microbes compose most of the biomass on the planet, yet the majority of taxa remain uncharacterized. These unknown microbes, often referred to as "microbial dark matter," represent a major challenge for biology. To understand the ecological contributions of these Unknown taxa, it is essential to first understand the relationship between unknown species, neighboring microbes, and their respective environment. Here, we establish a method to study the ecological significance of "microbial dark matter" by building microbial co-occurrence networks from publicly available 16S rRNA gene sequencing data of four extreme aquatic habitats. For each environment, we constructed networks including and excluding unknown organisms at multiple taxonomic levels and used network centrality measures to quantitatively compare networks. When the Unknown taxa were excluded from the networks, a significant reduction in degree and betweenness was observed for all environments. Strikingly, Unknown taxa occurred as top hubs in all environments, suggesting that "microbial dark matter" play necessary ecological roles within their respective communities. In addition, novel adaptation-related genes were detected after using 16S rRNA gene sequences from top-scoring hub taxa as probes to blast metagenome databases. This work demonstrates the broad applicability of network metrics to identify and prioritize key Unknown taxa and improve understanding of ecosystem structure across diverse habitats.

RevDate: 2020-09-23

Albaugh VL (2020)

Comment on: Fecal metagenomics and metabolomics reveal gut microbial changes after bariatric surgery.

RevDate: 2020-09-22

Wang XC, Wang H, Tan SD, et al (2020)

Viral metagenomics reveals diverse anelloviruses in bone marrow specimens from hematologic patients.

Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology, 132:104643 pii:S1386-6532(20)30385-1 [Epub ahead of print].

BACKGROUND: An infectious etiology has been proposed for many human cancers, but rarely have specific agents been identified. Viral metagenomic technique is useful for identification of viral pathogens potentially existing in bone marrow specimens from hematologic patients.

METHODS: A total of 24 patients were included in this study, including 14 female (58.3 %) and 10 male patients (41.7 %) with a mean age of 55.20 ± 18.02 years (16-89 years).Twenty-four bone marrow specimens were collected from 24 hematologic patients (diagnosed with hypoferric anemia, diffuse large B cell lymphoma, myelodysplastic syndrome, acute myelo-monocytic leukemia, acute myelocytic leukemia with maturation, multiple myeloma, lymphoma angioimmunoblastic T cell, acute myeloid leukemia-M1, polycythemia vera/hypoferric anemia, leukocythemia, or megaloblastic anemia). Viral nucleic acid from marrow samples of hematologic patients were subjected to viral metagenomic analysis. PCR method was used to investigate the prevalence of these new viruses in this cohort of hematologic patients. Phylogenetic tree was established to elucidate the relationship of anelloviruses found here and the previously define ones.

RESULTS: Anelloviridae family are the main group of viruses detected in all the 4 libraries. Forty-six different species of Anelloviruses belonging to genera Alphatorquevirus, Betatorquevirus and Gammatorquevirus and unclassified anellovirus were recovered. Fifteen novel strains with complete ORF1 coding sequence were acquired and phylogenetically analyzed, indicating 8 of the 15 strains are proposed novel species belonging to genus Gammatorquevirus. Nested-PCR were then performed for these15 novel anellovirus strains in the 24 individual bone marrow samples, which showed 13 of them were present in more than one bone marrow samples.

CONCLUSIONS: Diverse types of anellovirus were present in bone marrow samples of hematologic patients. Whether these novel anelloviruses have association with certain hematonosis needs further investigation.

RevDate: 2020-09-22

Crandall SG, Gold KM, Jiménez-Gasco MDM, et al (2020)

A multi-omics approach to solving problems in plant disease ecology.

PloS one, 15(9):e0237975 pii:PONE-D-20-20253.

The swift rise of omics-approaches allows for investigating microbial diversity and plant-microbe interactions across diverse ecological communities and spatio-temporal scales. The environment, however, is rapidly changing. The introduction of invasive species and the effects of climate change have particular impact on emerging plant diseases and managing current epidemics. It is critical, therefore, to take a holistic approach to understand how and why pathogenesis occurs in order to effectively manage for diseases given the synergies of changing environmental conditions. A multi-omics approach allows for a detailed picture of plant-microbial interactions and can ultimately allow us to build predictive models for how microbes and plants will respond to stress under environmental change. This article is designed as a primer for those interested in integrating -omic approaches into their plant disease research. We review -omics technologies salient to pathology including metabolomics, genomics, metagenomics, volatilomics, and spectranomics, and present cases where multi-omics have been successfully used for plant disease ecology. We then discuss additional limitations and pitfalls to be wary of prior to conducting an integrated research project as well as provide information about promising future directions.

RevDate: 2020-09-22

Sodhi KK, Kumar M, DK Singh (2020)

Assessing the bacterial diversity and functional profiles of the River Yamuna using Illumina MiSeq sequencing.

Archives of microbiology pii:10.1007/s00203-020-02045-0 [Epub ahead of print].

A small percentage of the total freshwater on Earth is represented by river water. Microbes have an essential role to play in the biogeochemical cycles, mineralization of organic water, along with xenobiotics degradation. Microbial dynamics are susceptible to environmental stressors which includes pollutants such as antibiotics, metals, and other degradants. River Yamuna is polluted extensively by domestic and industrial wastes. Xenobiotics, when released into the environment, can lead to water pollution. The present study evaluates the microbial diversity in Yamuna River (28°40'5.53'' N, 77°15'0.35'' E) along with the prediction of the metagenome function. In this context, the metagenomic DNA was extracted and sequencing was done on Illumina@MiSeq platform. The total number of OTUs picked was 41,994, out of which 74% were classified within the kingdom Bacteria. 35% of the OTUs were assigned to phylum Proteobacteria, followed by Bacteriodetes (22%), whereas 26% of OTUs were unassigned. PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) was used to predict metagenomic functions using 16S rDNA as a marker. Metagenomic reads were assigned to the Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous (COG), and Gene Ontology (GO). Functional characterization reveals the presence of methyl-accepting chemotaxis protein which is an important adaptation for the microbes in the environment. The enzymes can be mapped for the bioremediation of xenobiotics. Information obtained from the amplicon sequencing of River Yamuna, collaborated with "omic" studies, may help in the design of bioremediation strategies and can be used for environmental clean-up of pollutants.

RevDate: 2020-09-22

Williams E, Isles NS, Seemann T, et al (2020)

Case Report: Confirmation by Metagenomic Sequencing of Visceral Leishmaniasis in an Immunosuppressed Returned Traveler.

The American journal of tropical medicine and hygiene [Epub ahead of print].

There has been increased interest in using metagenomic next-generation sequencing as an unbiased approach for diagnosing infectious diseases. We describe a 61-year-old man on fingolimod therapy for multiple sclerosis with an extensive travel history who presented with 7 months of fevers, night sweats, and weight loss. Peripheral blood tests showed pancytopenia and abnormal acute phase reactants. A bone marrow aspirate showed the presence of numerous intracellular and extracellular amastigotes consistent with visceral leishmaniasis (VL). Metagenomic sequencing of the bone marrow aspirate confirmed Leishmania infantum, a species widely reported in the Mediterranean region. This correlated with acquisition of VL infection during the patient's most recent epidemiological exposure in southern Italy 12 months prior. This case demonstrates the potential application of metagenomic sequencing for identification and speciation of Leishmania in cases of VL; however, further assessment is required using other more readily obtained clinical samples such as blood.

RevDate: 2020-09-22

Tan SK, Granados AC, Bouquet J, et al (2020)

Metagenomic sequencing of stool samples in Bangladeshi infants: virome association with poliovirus shedding after oral poliovirus vaccination.

Scientific reports, 10(1):15392 pii:10.1038/s41598-020-71791-4.

The potential role of enteric viral infections and the developing infant virome in affecting immune responses to the oral poliovirus vaccine (OPV) is unknown. Here we performed viral metagenomic sequencing on 3 serially collected stool samples from 30 Bangladeshi infants following OPV vaccination and compared findings to stool samples from 16 age-matched infants in the United States (US). In 14 Bangladeshi infants, available post-vaccination serum samples were tested for polio-neutralizing antibodies. The abundance (p = 0.006) and richness (p = 0.013) of the eukaryotic virome increased with age and were higher than seen in age-matched US infants (p < 0.001). In contrast, phage diversity metrics remained stable and were similar to those in US infants. Non-poliovirus eukaryotic virus abundance (3.68 log10 vs. 2.25 log10, p = 0.002), particularly from potential viral pathogens (2.78log10 vs. 0.83log10, p = 0.002), and richness (p = 0.016) were inversely associated with poliovirus shedding. Following vaccination, 28.6% of 14 infants tested developed neutralizing antibodies to all three Sabin types and also exhibited higher rates of poliovirus shedding (p = 0.020). No vaccine-derived poliovirus variants were detected. These results reveal an inverse association between eukaryotic virome abundance and poliovirus shedding. Overall gut virome ecology and concurrent viral infections may impact oral vaccine responsiveness in Bangladeshi infants.

RevDate: 2020-09-22

Zhao Z, Cristian A, G Rosen (2020)

Keeping up with the genomes: efficient learning of our increasing knowledge of the tree of life.

BMC bioinformatics, 21(1):412 pii:10.1186/s12859-020-03744-7.

BACKGROUND: It is a computational challenge for current metagenomic classifiers to keep up with the pace of training data generated from genome sequencing projects, such as the exponentially-growing NCBI RefSeq bacterial genome database. When new reference sequences are added to training data, statically trained classifiers must be rerun on all data, resulting in a highly inefficient process. The rich literature of "incremental learning" addresses the need to update an existing classifier to accommodate new data without sacrificing much accuracy compared to retraining the classifier with all data.

RESULTS: We demonstrate how classification improves over time by incrementally training a classifier on progressive RefSeq snapshots and testing it on: (a) all known current genomes (as a ground truth set) and (b) a real experimental metagenomic gut sample. We demonstrate that as a classifier model's knowledge of genomes grows, classification accuracy increases. The proof-of-concept naïve Bayes implementation, when updated yearly, now runs in 1/4th of the non-incremental time with no accuracy loss.

CONCLUSIONS: It is evident that classification improves by having the most current knowledge at its disposal. Therefore, it is of utmost importance to make classifiers computationally tractable to keep up with the data deluge. The incremental learning classifier can be efficiently updated without the cost of reprocessing nor the access to the existing database and therefore save storage as well as computation resources.

RevDate: 2020-09-22

Feng L, Zhang A, Que J, et al (2020)

The metagenomic next-generation sequencing in diagnosing central nervous system angiostrongyliasis: a case report.

BMC infectious diseases, 20(1):691 pii:10.1186/s12879-020-05410-y.

BACKGROUNDS: The incidence of angiostrongyliasis is increasing in recent decades due to the expanding endemic areas all over the world. Clinicians face tremendous challenge of diagnosing angiostrongyliasis because of the lack of awareness of the disease and less effective definitive laboratory tests.

CASE PRESENTATION: A 27-year-old man initially manifested skin itching, emesis, myalgia and quadriparesis. With progressive weakness of four limbs and elevated protein in the cerebrospinal fluid (CSF), he was diagnosed as Guillain-Barré syndrome and treated with intravenous methylprednisolone and immunoglobulin. However, the patient deteriorated with hyperpyrexia, headache and then persistent coma. The routine tests for Angiostrongylus cantonensis (A. cantonensis) with both the CSF and the serum were all negative. In contrast, the metagenomic next-generation sequencing (mNGS) was applied with the serum sample and the CSF sample in the middle phase. The central nervous system (CNS) angiostrongyliasis was diagnosed by mNGS with the mid-phase CSF, but not the mid-phase serum. At the same time, the CSF analysis revealed eosinophils ratio up to 67%. The discovery of A. cantonensis was confirmed by PCR with CSF later. Unfortunately, the patient died of severe angiostrongyliasis. During his hospitalization, mNGS was carried out repeatedly after definitive diagnosis and targeted treatment. The DNA strictly map reads number of A. cantonensis detected by mNGS was positively correlated with the CSF opening pressure and clinical manifestations.

CONCLUSIONS: The case of A. cantonensis infection highlights the benefit of mNGS as a target-free identification in disclosing the rare CNS angiostrongyliasis in the unusual season, while solid evidence from routine clinical testing was absent. The appropriate sample of mNGS should be chosen according to the life cycle of A. cantonensis. Besides, given the fact that the DNA reads number of A. cantonensis fluctuated with CSF opening pressure and clinical manifestations, whether mNGS could be applied as a marker of effectiveness of treatment is worth further exploration.

RevDate: 2020-09-22

Rossi A, Treu L, Toppo S, et al (2020)

Evolutionary Study of the Crassphage Virus at Gene Level.

Viruses, 12(9): pii:v12091035.

crAss-like viruses are a putative family of bacteriophages recently discovered. The eponym of the clade, crAssphage, is an enteric bacteriophage estimated to be present in at least half of the human population and it constitutes up to 90% of the sequences in some human fecal viral metagenomic datasets. We focused on the evolutionary dynamics of the genes encoded on the crAssphage genome. By investigating the conservation of the genes, a consistent variation in the evolutionary rates across the different functional groups was found. Gene duplications in crAss-like genomes were detected. By exploring the differences among the functional categories of the genes, we confirmed that the genes encoding capsid proteins were the most ubiquitous, despite their overall low sequence conservation. It was possible to identify a core of proteins whose evolutionary trees strongly correlate with each other, suggesting their genetic interaction. This group includes the capsid proteins, which are thus established as extremely suitable for rebuilding the phylogenetic tree of this viral clade. A negative correlation between the ubiquity and the conservation of viral protein sequences was shown. Together, this study provides an in-depth picture of the evolution of different genes in crAss-like viruses.

RevDate: 2020-09-22

Zhang L, Luo J, Li X, et al (2020)

16S rRNA Sequencing and Metagenomics Study of Gut Microbiota: Implications of BDB on Type 2 Diabetes Mellitus.

Marine drugs, 18(9): pii:md18090469.

Gut microbiota has a critical role in metabolic diseases, including type 2 diabetes mellitus (T2DM). 3-bromo-4,5-bis(2,3-dibromo-4,5-dihydroxybenzyl)-1,2-benzenediol (BDB) is a natural bromophenol isolated from marine red alga Rhodomela confervoides. Our latest research showed that BDB could alleviate T2DM in diabetic BKS db mice. To find out whether BDB modulates the composition of the gut microbiota during T2DM treatment, 24 BKS db diabetic mice were randomly grouped to receive BDB (n = 6), metformin (n = 6), or the vehicle (n = 6) for 7 weeks in a blinded manner. Non-diabetic BKS mice (n = 6) were used as normal control. Diabetic mice treated with BDB or metformin demonstrated significant reductions in fasting blood glucose (FBG) levels compared with the vehicle-treated mice in the 7th week. Pyrosequencing of the V3-V4 regions of the 16S rRNA gene revealed the changes of gut microbiota in response to BDB treatment. The result demonstrated short-chain acid (SCFA) producing bacteria Lachnospiraceae and Bacteroides were found to be significantly more abundant in the BDB and metformin treated group than the vehicle-treatment diabetic group. Remarkably, at the genus levels, Akkermansia elevated significantly in the BDB-treatment group. Metagenomic results indicated that BDB may alleviate the metabolic disorder of diabetic mice by promoting propanoate metabolism and inhibiting starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism. In conclusion, our study suggests that the anti-diabetic effect of BDB is closely related to the modulating structure of gut microbiota and the improvement of functional metabolism genes of intestinal microorganisms.

RevDate: 2020-09-22

Ciezkowska M, Bajda T, Decewicz P, et al (2020)

Effect of Clinoptilolite and Halloysite Addition on Biogas Production and Microbial Community Structure during Anaerobic Digestion.

Materials (Basel, Switzerland), 13(18): pii:ma13184127.

The study presents a comparison of the influence of a clinoptilolite-rich rock-zeolite (commonly used for improving anaerobic digestion processes)-and a highly porous clay mineral, halloysite (mainly used for gas purification), on the biogas production process. Batch experiments showed that the addition of each mineral increased the efficiency of mesophilic anaerobic digestion of both sewage sludge and maize silage. However, halloysite generated 15% higher biogas production during maize silage transformation. Halloysite also contributed to a much higher reduction of chemical oxygen demand for both substrates (by ~8% for maize silage and ~14% for sewage sludge) and a higher reduction of volatile solids and total ammonia for maize silage (by ~8% and ~4%, respectively). Metagenomic analysis of the microbial community structure showed that the addition of both mineral sorbents influenced the presence of key members of archaea and bacteria occurring in a well-operated biogas reactor. The significant difference between zeolite and halloysite is that the latter promoted the immobilization of key methanogenic archaea Methanolinea (belong to Methanomicrobia class). Based on this result, we postulate that halloysite could be useful not only as a sorbent for (bio)gas treatment methodologies but also as an agent for improving biogas production.

RevDate: 2020-09-21

He R, Wang Q, Feiyang Z, et al (2020)

Application value of metagenomic sequencing in the management of fungal periprosthetic joint infection.

RevDate: 2020-09-21

Sun Y, Zuo T, Cheung CP, et al (2020)

Population-level configurations of gut mycobiome across six ethnicities in urban and rural China.

Gastroenterology pii:S0016-5085(20)35162-3 [Epub ahead of print].

BACKGROUND & AIMS: Beyond bacteria, the human gastrointestinal tract is host to a vast diversity of fungi, collectively known as the gut mycobiome. Little is known of the impact of geography, ethnicity and urbanization on the gut mycobiome at a large population level. We aim to delineate the variation of human gut mycobiome and its association with host factors, environmental factors and diets.

METHODS: Using shotgun metagenomic sequencing, we profiled and compared the fecal mycobiome of 942 healthy individuals across different geographic regions in China (Hong Kong and Yunnan), spanning six ethnicities, Han, Zang, Bai, Hani, Dai, and Miao (including both urban and rural residents to each ethnicity). In parallel to fecal sampling, we collected subject metadata (environmental exposure, bowel habits, anthropometrics and medication), diet and clinical blood measurement results (a total of 118 variables) and investigated their impact on the gut mycobiome variation in humans.

RESULTS: The human gut mycobiome was highly variable across populations. Urbanization-related factors had the strongest impact on gut mycobiome variation, followed by geography, dietary habit, and ethnicity. The Hong Kong population (highly urbanized) had a significantly lower fungal richness compared with Yunnan population. Saccharomyces cerevisiae was highly enriched in urban compared with rural populations, and showed significant inverse correlations with liver pathology-associated blood parameters, including aspartate transaminase (AST), alanine transaminase (ALT), gamma glutamyltransferase (GGT), and direct bilirubin. Candida dubliniensis, which was decreased in urban relative to rural populations, showed correlations with host metabolism-related parameters in blood, including a positive correlation with fasting high-density lipoprotein cholesterol (HDL-C) levels and a negative correlation with fasting glucose levels. The fungal-blood parameter correlations were highly geography- and ethnicity-specific. Food choices had differential influences on gut mycobiome and bacterial microbiome, where taxa from the same genus tended to be co-regulated by food and thereby co-bloom. Ethnicity-specific fungal signatures were associated with distinct habitual foods in each ethnic group.

CONCLUSIONS: Our data highlight for the first time that geography, urbanization, and ethnicity, and habitual diets play an important role in shaping the gut mycobiome composition. Gut fungal configurations in combination with population characteristics (such as residing region, ethnicity, diet, lifestyle) influence host metabolism and health.

RevDate: 2020-09-21

Mohamed I, Zakeer S, Azab M, et al (2020)

Changes in Vaginal Microbiome in Pregnant and Nonpregnant Women with Bacterial Vaginosis: Toward Microbiome Diagnostics?.

Omics : a journal of integrative biology [Epub ahead of print].

Bacterial vaginosis (BV) is highly common, adversely affecting the health of millions of women. New therapeutic targets and diagnostics are urgently needed for BV. Microbiome research offers new prospects in this context. We report here original findings on changes in the vaginal microbiome in pregnant and nonpregnant women with BV. Reproductive age women were recruited for this study after a clinical examination. The total sample (N = 33) included four study groups: (1) healthy nonpregnant women (n = 9), (2) nonpregnant women with symptomatic BV (n = 11), (3) healthy pregnant women without BV (n = 6), and (4) pregnant women with symptomatic BV (N = 7). The vaginal microbiota in healthy women was less diverse, with dominance of a single genus, Lactobacillus. Six major phyla appeared upon taxonomic analysis of the bacterial sequences: Firmicutes, Actinobacteria, Proteobacteria, Tenericutes, Bacteroidetes, and Fusobacteria. For instance, Firmicutes had a significantly higher abundance (98.3%) in the nonpregnant healthy group and 94.3% in pregnant healthy group, compared with nonpregnant (49.7%) and pregnant (67%) women with BV (p = 0.003). Moreover, women with BV had significant increases in representation of Actinobacteria, Fusobacteria, and Bacteroidetes (p = 0.0003, 0.004, and 0.01, respectively). Although the Lactobacillus genus was predominant in healthy women, Gardnerella, Atopobium, Sneathia, and Prevotella significantly increased in nonpregnant women with BV (p = 0.001, 0.014, 0.004, and 0.012, respectively). Dysbiosis of Lactobacillus in pregnant women with BV was accompanied by increased prevalence of the Streptococcus genus. These findings contribute new insights toward microbiome diagnostics and therapeutics innovation in BV.

RevDate: 2020-09-21

Compant S, Cambon MC, Vacher C, et al (2020)

The plant endosphere world - bacterial life within plants.

Environmental microbiology [Epub ahead of print].

The plant endosphere is colonized by complex microbial communities and microorganisms, which colonize the plant interior at least part of their lifetime and are termed endophytes. Their functions range from mutualism to pathogenicity. All plant organs and tissues are generally colonized by bacterial endophytes and their diversity and composition depend on the plant, the plant organ and its physiological conditions, the plant growth stage as well as on the environment. Plant-associated microorganisms, and in particular endophytes, have lately received high attention, because of the increasing awareness of the importance of host-associated microbiota for the functioning and performance of their host. Some endophyte functions are known from mostly lab assays, genome prediction and few metagenome analyses, however, we have limited understanding on in planta activities, particularly considering the diversity of micro-environments and the dynamics of conditions. In our review, we present recent findings on endosphere environments, their physiological conditions and endophyte colonization. Furthermore, we discuss microbial functions, the interaction between endophytes and plants as well as methodological limitations of endophyte research. We also provide an outlook on needs of future research to improve our understanding on the role of microbiota colonizing the endosphere on plant traits and ecosystem functioning. This article is protected by copyright. All rights reserved.

RevDate: 2020-09-21

Radwan O, ON Ruiz (2020)

Shotgun metagenomic data of microbiomes on plastic fabrics exposed to harsh tropical environments.

Data in brief, 32:106226 pii:S2352-3409(20)31120-3.

The development of more affordable high-throughput DNA sequencing technologies and powerful bioinformatics is making of shotgun metagenomics a common tool for effective characterization of microbiomes and robust functional genomics. A shotgun metagenomic approach was applied in the characterization of microbial communities associated with plasticized fabric materials exposed to a harsh tropical environment for 14 months. High-throughput sequencing of TruSeq paired-end libraries was conducted using a whole-genome shotgun (WGS) approach on an Illumina HiSeq2000 platform generating 100 bp reads. A multifaceted bioinformatics pipeline was developed and applied to conduct quality control and trimming of raw reads, microbial classification, assembly of multi-microbial genomes, binning of assembled contigs to individual genomes, and prediction of microbial genes and proteins. The bioinformatic analysis of the large 161 Gb sequence dataset generated 3,314,688 contigs and 120 microbial genomes. The raw metagenomic data and the detailed description of the bioinformatics pipeline applied in data analysis provide an important resource for the genomic characterization of microbial communities associated with biodegraded plastic fabric materials. The raw shotgun metagenomics sequence data of microbial communities on plastic fabric materials have been deposited in MG-RAST (https://www.mg-rast.org/) under accession numbers: mgm4794685.3-mgm4794690.3. The datasets and raw data presented here were associated with the main research work "Metagenomic characterization of microbial communities on plasticized fabric materials exposed to harsh tropical environments" (Radwan et al., 2020).

RevDate: 2020-09-21

Benavides A, Sanchez F, Alzate JF, et al (2020)

DATMA: Distributed AuTomatic Metagenomic Assembly and annotation framework.

PeerJ, 8:e9762 pii:9762.

Background: A prime objective in metagenomics is to classify DNA sequence fragments into taxonomic units. It usually requires several stages: read's quality control, de novo assembly, contig annotation, gene prediction, etc. These stages need very efficient programs because of the number of reads from the projects. Furthermore, the complexity of metagenomes requires efficient and automatic tools that orchestrate the different stages.

Method: DATMA is a pipeline for fast metagenomic analysis that orchestrates the following: sequencing quality control, 16S rRNA-identification, reads binning, de novo assembly and evaluation, gene prediction, and taxonomic annotation. Its distributed computing model can use multiple computing resources to reduce the analysis time.

Results: We used a controlled experiment to show DATMA functionality. Two pre-annotated metagenomes to compare its accuracy and speed against other metagenomic frameworks. Then, with DATMA we recovered a draft genome of a novel Anaerolineaceae from a biosolid metagenome.

Conclusions: DATMA is a bioinformatics tool that automatically analyzes complex metagenomes. It is faster than similar tools and, in some cases, it can extract genomes that the other tools do not. DATMA is freely available at https://github.com/andvides/DATMA.

RevDate: 2020-09-21

Tan KY, Dutta A, Tan TK, et al (2020)

Comprehensive genome analysis of a pangolin-associated Paraburkholderia fungorum provides new insights into its secretion systems and virulence.

PeerJ, 8:e9733 pii:9733.

Background: Paraburkholderia fungorum (P. fungorum) is a Gram-negative environmental species that has been commonly used as a beneficial microorganism in agriculture as an agent for biocontrol and bioremediation. Its use in agriculture is controversial as many people believe that it could harm human health; however, there is no clear evidence to support.

Methodology: The pangolin P. fungorum (pangolin Pf) genome has a genomic size of approximately 7.7 Mbps with N50 of 69,666 bps. Our study showed that pangolin Pf is a Paraburkholderia fungorum supported by evidence from the core genome SNP-based phylogenetic analysis and the ANI analysis. Functional analysis has shown that the presence of a considerably large number of genes related to stress response, virulence, disease, and defence. Interestingly, we identified different types of secretion systems in the genome of pangolin Pf, which are highly specialized and responsible for a bacterium's response to its environment and in physiological processes such as survival, adhesion, and adaptation. The pangolin Pf also shared some common virulence genes with the known pathogenic member of the Burkholderiales. These genes play important roles in adhesion, motility, and invasion.

Conclusion: This study may provide better insights into the functions, secretion systems and virulence of this pangolin-associated bacterial strain. The addition of this genome sequence is also important for future comparative analysis and functional work of P. fungorum.

RevDate: 2020-09-21

Huang Y, Zheng H, Tan K, et al (2020)

Circulating metabolomics profiling reveals novel pathways associated with cognitive decline in patients with hypertension.

Therapeutic advances in neurological disorders, 13:1756286420947973 pii:10.1177_1756286420947973.

Background: Hypertension is a significant risk factor for cardiovascular disease, and it is associated with dementia, including Alzheimer's disease (AD). Although it may be correlated with AD in terms of symptoms, the link between hypertension and AD pathological biomarkers, and the potential underlying mechanism of hypertension with cognitive decline, are still not well understood.

Methods: The Mini-Mental State Examination (MMSE) scores were used to evaluate cognitive function. Enzyme-linked immunosorbent assays were used to examine plasma amyloid-beta (Aβ)40, Aβ42, and tau concentration in hypertensive patients. Metabolomics and metagenomics were performed to identify the significantly changed circulating metabolites and microbiota between healthy individuals and hypertensive patients. Pearson's correlation was used to examine the association between cognitive indicators and differential metabolites.

Results: We found significantly decreased MMSE scores, elevated plasma Aβ40, and decreased Aβ42/Aβ40 ratio in hypertensive patients, which are critically associated with AD pathology. Based on metabolomics, we found that significantly altered metabolites in the plasma of hypertensive patients were enriched in the benzoate degradation and phenylpropanoid biosynthesis pathways, and they were also correlated with changes in MMSE scores and Aβ42/Aβ40 ratio. In addition, metabolomics signaling pathway analysis suggested that microbial metabolism was altered in hypertensive patients. We also identified altered blood microbiota in hypertensive patients compared with the controls.

Conclusions: Our study provides a novel metabolic and microbial mechanism, which may underlie the cognitive impairment in hypertensive patients.

RevDate: 2020-09-21

Finnigan JD, Young C, Cook DJ, et al (2020)

Cytochromes P450 (P450s): A review of the class system with a focus on prokaryotic P450s.

Advances in protein chemistry and structural biology, 122:289-320.

Cytochromes P450 (P450s) are a large superfamily of heme-containing monooxygenases. P450s are found in all Kingdoms of life and exhibit incredible diversity, both at sequence level and also on a biochemical basis. In the majority of cases, P450s can be assigned into one of ten classes based on their associated redox partners, domain architecture and cellular localization. Prokaryotic P450s now represent a large diverse collection of annotated/known enzymes, of which many have great potential biocatalytic potential. The self-sufficient P450 classes (Class VII/VIII) have been explored significantly over the past decade, with many annotated and biochemically characterized members. It is clear that the prokaryotic P450 world is expanding rapidly, as the number of published genomes and metagenome studies increases, and more P450 families are identified and annotated (CYP families).

RevDate: 2020-09-21

Zhang X, Das S, Dunbar S, et al (2020)

Molecular and non-molecular approaches to etiologic diagnosis of gastroenteritis.

Advances in clinical chemistry, 99:49-85.

Gastroenteritis is a major cause of mortality and morbidity globally and rapid identification of the causative pathogen is important for appropriate treatment and patient management, implementation of effective infection control measures, reducing hospital length of stay, and reducing overall medical costs. Although stool culture and microscopic examination of diarrheal stool has been the primary method for laboratory diagnosis, culture-independent proteomic and genomic tests are receiving increased attention. Antigen tests for stool pathogens are routinely implemented as rapid and simple analytics whereas molecular tests are now available in various formats from high complexity to waived point-of-care tests. In addition, metagenomic next-generation sequencing stands poised for use as a method for both diagnosis and routine characterization of the gut microbiome in the very near future. Analysis of host biomarkers as indicators of infection status and pathogenesis may also become important for prediction, diagnosis, and monitoring of gastrointestinal infection. Here we review current methods and emerging technologies for the etiologic diagnosis of gastroenteritis in the clinical laboratory. Benefits and limitations of these evolving methods are highlighted.

RevDate: 2020-09-21

Mayneris-Perxachs J, Arnoriaga-Rodríguez M, Luque-Córdoba D, et al (2020)

Gut microbiota steroid sexual dimorphism and its impact on gonadal steroids: influences of obesity and menopausal status.

Microbiome, 8(1):136 pii:10.1186/s40168-020-00913-x.

BACKGROUND: Gonadal steroid hormones have been suggested as the underlying mechanism responsible for the sexual dimorphism observed in metabolic diseases. Animal studies have also evidenced a causal role of the gut microbiome and metabolic health. However, the role of sexual dimorphism in the gut microbiota and the potential role of the microbiome in influencing sex steroid hormones and shaping sexually dimorphic susceptibility to disease have been largely overlooked. Although there is some evidence of sex-specific differences in the gut microbiota diversity, composition, and functionality, the results are inconsistent. Importantly, most of these studies have not taken into account the gonadal steroid status. Therefore, we investigated the gut microbiome composition and functionality in relation to sex, menopausal status, and circulating sex steroids.

RESULTS: No significant differences were found in alpha diversity indices among pre- and post-menopausal women and men, but beta diversity differed among groups. The gut microbiota from post-menopausal women was more similar to men than to pre-menopausal women. Metagenome functional analyses revealed no significant differences between post-menopausal women and men. Gonadal steroids were specifically associated with these differences. Hence, the gut microbiota of pre-menopausal women was more enriched in genes from the steroid biosynthesis and degradation pathways, with the former having the strongest fold change among all associated pathways. Microbial steroid pathways also had significant associations with the plasma levels of testosterone and progesterone. In addition, a specific microbiome signature was able to predict the circulating testosterone levels at baseline and after 1-year follow-up. In addition, this microbiome signature could be transmitted from humans to antibiotic-induced microbiome-depleted male mice, being able to predict donor's testosterone levels 4 weeks later, implying that the microbiota profile of the recipient mouse was influenced by the donor's gender. Finally, obesity eliminated most of the differences observed among non-obese pre-menopausal women, post-menopausal women, and men in the gut microbiota composition (Bray-Curtis and weighted unifrac beta diversity), functionality, and the gonadal steroid status.

CONCLUSIONS: The present findings evidence clear differences in the gut microbial composition and functionality between men and women, which is eliminated by both menopausal and obesity status. We also reveal a tight link between the gut microbiota composition and the circulating levels of gonadal steroids, particularly testosterone. Video Abstract.

RevDate: 2020-09-21

Negrey JD, Thompson ME, Langergraber KE, et al (2020)

Demography, life-history trade-offs, and the gastrointestinal virome of wild chimpanzees.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 375(1811):20190613.

In humans, senescence increases susceptibility to viral infection. However, comparative data on viral infection in free-living non-human primates-even in our closest living relatives, chimpanzees and bonobos (Pan troglodytes and P. paniscus)-are relatively scarce, thereby constraining an evolutionary understanding of age-related patterns of viral infection. We investigated a population of wild eastern chimpanzees (P. t. schweinfurthii), using metagenomics to characterize viromes (full viral communities) in the faeces of 42 sexually mature chimpanzees (22 males, 20 females) from the Kanyawara and Ngogo communities of Kibale National Park, Uganda. We identified 12 viruses from at least four viral families possessing genomes of both single-stranded RNA and single-stranded DNA. Faecal viromes of both sexes varied with chimpanzee age, but viral richness increased with age only in males. This effect was largely due to three viruses, salivirus, porprismacovirus and chimpanzee stool-associated RNA virus (chisavirus), which occurred most frequently in samples from older males. This finding is consistent with the hypothesis that selection on males for early-life reproduction compromises investment in somatic maintenance, which has delayed consequences for health later in life, in this case reflected in viral infection and/or shedding. Faecal viromes are therefore useful for studying processes related to the divergent reproductive strategies of males and females, ageing, and sex differences in longevity. This article is part of the theme issue 'Evolution of the primate ageing process'.

RevDate: 2020-09-18

Payne N, Kraberger S, Fontenele RS, et al (2020)

Novel Circoviruses Detected in Feces of Sonoran Felids.

Viruses, 12(9): pii:v12091027.

Sonoran felids are threatened by drought and habitat fragmentation. Vector range expansion and anthropogenic factors such as habitat encroachment and climate change are altering viral evolutionary dynamics and exposure. However, little is known about the diversity of viruses present in these populations. Small felid populations with lower genetic diversity are likely to be most threatened with extinction by emerging diseases, as with other selective pressures, due to having less adaptive potential. We used a metagenomic approach to identify novel circoviruses, which may have a negative impact on the population viability, from confirmed bobcat (Lynx rufus) and puma (Puma concolor) scats collected in Sonora, Mexico. Given some circoviruses are known to cause disease in their hosts, such as porcine and avian circoviruses, we took a non-invasive approach using scat to identify circoviruses in free-roaming bobcats and puma. Three circovirus genomes were determined, and, based on the current species demarcation, they represent two novel species. Phylogenetic analyses reveal that one circovirus species is more closely related to rodent associated circoviruses and the other to bat associated circoviruses, sharing highest genome-wide pairwise identity of approximately 70% and 63%, respectively. At this time, it is unknown whether these scat-derived circoviruses infect felids, their prey, or another organism that might have had contact with the scat in the environment. Further studies should be conducted to elucidate the host of these viruses and assess health impacts in felids.

RevDate: 2020-09-15

Vezza T, Abad-Jiménez Z, Marti-Cabrera M, et al (2020)

Microbiota-Mitochondria Inter-Talk: A Potential Therapeutic Strategy in Obesity and Type 2 Diabetes.

Antioxidants (Basel, Switzerland), 9(9): pii:antiox9090848.

The rising prevalence of obesity and type 2 diabetes (T2D) is a growing concern worldwide. New discoveries in the field of metagenomics and clinical research have revealed that the gut microbiota plays a key role in these metabolic disorders. The mechanisms regulating microbiota composition are multifactorial and include resistance to stress, presence of pathogens, diet, cultural habits and general health conditions. Recent evidence has shed light on the influence of microbiota quality and diversity on mitochondrial functions. Of note, the gut microbiota has been shown to regulate crucial transcription factors, coactivators, as well as enzymes implicated in mitochondrial biogenesis and metabolism. Moreover, microbiota metabolites seem to interfere with mitochondrial oxidative/nitrosative stress and autophagosome formation, thus regulating the activation of the inflammasome and the production of inflammatory cytokines, key players in chronic metabolic disorders. This review focuses on the association between intestinal microbiota and mitochondrial function and examines the mechanisms that may be the key to their use as potential therapeutic strategies in obesity and T2D management.

RevDate: 2020-09-17
CmpDate: 2020-09-17

Metwaly A, Dunkel A, Waldschmitt N, et al (2020)

Integrated microbiota and metabolite profiles link Crohn's disease to sulfur metabolism.

Nature communications, 11(1):4322.

Gut microbial and metabolite alterations have been linked to the pathogenesis of inflammatory bowel diseases. Here we perform a multi-omics microbiome and metabolite analysis of a longitudinal cohort of Crohn's disease patients undergoing autologous hematopoietic stem cell transplantation, and investigational therapy that induces drug free remission in a subset of patients. Via comparison of patients who responded and maintained remission, responded but experienced disease relapse and patients who did not respond to therapy, we identify shared functional signatures that correlate with disease activity despite the variability of gut microbiota profiles at taxonomic level. These signatures reflect the disease state when transferred to gnotobiotic mice. Taken together, the integration of microbiome and metabolite profiles from human cohort and mice improves the predictive modelling of disease outcome, and allows the identification of a network of bacteria-metabolite interactions involving sulfur metabolism as a key mechanism linked to disease activity in Crohn's disease.

RevDate: 2020-09-20

St James AR, Yavitt JB, Zinder SH, et al (2020)

Linking microbial Sphagnum degradation and acetate mineralization in acidic peat bogs: from global insights to a genome-centric case study.

The ISME journal pii:10.1038/s41396-020-00782-0 [Epub ahead of print].

Ombrotrophic bogs accumulate large stores of soil carbon that eventually decompose to carbon dioxide and methane. Carbon accumulates because Sphagnum mosses slow microbial carbon decomposition processes, leading to the production of labile intermediate compounds. Acetate is a major product of Sphagnum degradation, yet rates of hydrogenotrophic methanogenesis far exceed rates of aceticlastic methanogenesis, suggesting that alternative acetate mineralization processes exist. Two possible explanations are aerobic respiration and anaerobic respiration via humic acids as electron acceptors. While these processes have been widely observed, microbial community interactions linking Sphagnum degradation and acetate mineralization remain cryptic. In this work, we use ordination and network analysis of functional genes from 110 globally distributed peatland metagenomes to identify conserved metabolic pathways in Sphagnum bogs. We then use metagenome-assembled genomes (MAGs) from McLean Bog, a Sphagnum bog in New York State, as a local case study to reconstruct pathways of Sphagnum degradation and acetate mineralization. We describe metabolically flexible Acidobacteriota MAGs that contain all genes to completely degrade Sphagnum cell wall sugars under both aerobic and anaerobic conditions. Finally, we propose a hypothetical model of acetate oxidation driven by changes in peat redox potential that explain how bogs may circumvent aceticlastic methanogenesis through aerobic and humics-driven respiration.

RevDate: 2020-09-20

Chen J, Li Y, Li Z, et al (2020)

Metagenomic Next-generation Sequencing Identified Histoplasma Capsulatum in Lung and Epiglottis of a Chinese Patient: A Case Report.

Histoplasmosis is an endemic disease mainly occurring in North America and is rare in China. Confirmation of histoplasmosis is supposed to be based on a compatible clinical scenario and a positive culture or histopathology. However, there are still many cases that are misdiagnosed or missed, especially in individuals from non-endemic areas. In recent years, metagenomic next-generation sequencing (mNGS) has led to the accurate and timely diagnoses of some rare and complicated infectious diseases. We describe the case of a 27-year-old Chinese man who had chronic progressive pulmonary lesions without any symptoms for more than 1 year until the lesions reached the epiglottis and led to progressive pharyngeal pain. There were no positive results from bronchoalveolar lavage fluid (BALF) and epiglottis tissue cultures or from epiglottis and lung pathological examinations, but mNGS was able to identify Histoplasma capsulatum in the epiglottis tissues and BALF as the cause of the lesions. The patient was successfully treated with itraconazole.

RevDate: 2020-09-19

Hemmat-Jou MH, Safari-Sinegani AA, Che R, et al (2020)

Toxic trace element resistance genes and systems identified using the shotgun metagenomics approach in an Iranian mine soil.

Environmental science and pollution research international pii:10.1007/s11356-020-10824-x [Epub ahead of print].

This study aimed to identify the microbial communities, resistance genes, and resistance systems in an Iranian mine soil polluted with toxic trace elements (TTE). The polluted soil samples were collected from a mining area and compared against non-polluted (control) collected soils from the vicinity of the mine. The soil total DNA was extracted and sequenced, and bioinformatic analysis of the assembled metagenomes was conducted to identify soil microbial biodiversity, TTE resistance genes, and resistance systems. The results of the employed shotgun approach indicated that the relative abundance of Proteobacteria, Firmicutes, Bacteroidetes, and Deinococcus-Thermus was significantly higher in the TTE-polluted soils compared with those in the control soils, while the relative abundance of Actinobacteria and Acidobacteria was significantly lower in the polluted soils. The high concentration of TTE increased the ratio of archaea to bacteria and decreased the alpha diversity in the polluted soils compared with the control soils. Canonical correspondence analysis (CCA) demonstrated that heavy metal pollution was the major driving factor in shaping microbial communities compared with any other soil characteristics. In the identified heavy metal resistome (HV-resistome) of TTE-polluted soils, major functional pathways were carbohydrates metabolism, stress response, amino acid and derivative metabolism, clustering-based subsystems, iron acquisition and metabolism, cell wall synthesis and capsulation, and membrane transportation. Ten TTE resistance systems were identified in the HV-resistome of TTE-polluted soils, dominated by "P-type ATPases," "cation diffusion facilitators," and "heavy metal efflux-resistance nodulation cell division (HME-RND)." Most of the resistance genes (69%) involved in resistance systems are affiliated to cell wall, outer membrane, periplasm, and cytoplasmic membrane. The finding of this study provides insight into the microbial community in Iranian TTE-polluted soils and their resistance genes and systems.

RevDate: 2020-09-19

Ding X, Lan W, Wu J, et al (2020)

Microbiome and nitrate removal processes by microorganisms on the ancient Preah Vihear temple of Cambodia revealed by metagenomics and N-15 isotope analyses.

Applied microbiology and biotechnology pii:10.1007/s00253-020-10886-4 [Epub ahead of print].

Preah Vihear temple is one of the most significant representatives of the ancient Angkorian temples listed as United Nations Educational, Scientific and Cultural Organization (UNESCO) World Heritage Sites. The surfaces of this Angkor sandstone monument are covered with deteriorated materials, broadly called "sediments" here, resulting from a long time of weathering of the sandstone. The sediments might adversely affect the ancient sandstone substratum of this cultural heritage, and the potential risk from them is essential information for current strategies and on-going protection and management. The extracted DNA from the sediment samples of this temple was used for Illumina high-throughput sequencing analysis, resulting in approximately 12 Gb of metagenomic dataset. The results of this shotgun metagenomic analysis provided a thorough information of the phylogenetic groups presented in the microbiome of the sediment samples, indicating that potential metabolic activities, involving different geomicrobiological cycles, may occur in this microbiome. The phylogenetic result revealed that the majority of metagenomic reads were affiliated with Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes at the phylum level. The metabolic reconstruction results indicated that the important geomicrobiological cycling processes include carbon sequestration, and nitrogen and sulfur transformation as the potentially active ones in the sediments of the sampling sites. Specifically, the dissimilatory nitrate reduction to ammonium (DNRA) and the newly discovered complete ammonia oxidation (comammox) were retrieved from this metagenomic dataset. Furthermore, the genetic information on the presence of acid-producing processes by sulfur- and ammonia-oxidizing bacteria and archaea in this metagenomic dataset suggested that the microbial flora in these samples has the potential to participate in the degradation of sandstone cultural heritage by producing acids. N-15 isotope amendment and incubation analysis results confirmed the presence of active denitrification, but not anammox activity at this temple. These results are important for our knowledge on the microbial community composition and microbial biodeterioration processes affecting this sandstone cultural heritage and will aid in the protection and management of the ancient Preah Vihear temple.Key Points• Microbiota on Preah Viher temple was analyzed using NGS.• Nitrate-N transformation by DNRA, comammox, and denitrifcation was detected.• N-15 isotope analysis confirmed the active denitrifcation, but not Anammox.• Accumulation of nitrate is a result of less active removal by denitrification.

RevDate: 2020-09-19

Milani C, Alessandri G, Mancabelli L, et al (2020)

Deciphering the impact of diet and host physiology on the mammalian gut microbiome by multi-omics approaches.

Applied and environmental microbiology pii:AEM.01864-20 [Epub ahead of print].

In recent years various studies have demonstrated that the gut microbiota influences host metabolism. However, these studies were primarily focused on a single or a limited range of host species, thus preventing a full exploration of possible taxonomic and functional adaptations by gut microbiota members as a result of host-microbe co-evolution events. In the current study, the microbial taxonomic profiles of 250 fecal samples, corresponding to 77 host species that cover the mammalian branch of the tree of life, were reconstructed by 16S rRNA gene-based sequence analysis. Moreover, shotgun metagenomics was employed to investigate the metabolic potential of the fecal microbiomes of 24 mammals and subsequent statistical analyses were performed to assess the impact of host diet and corresponding physiology of the digestive system on gut microbiota composition and functionality. Functional data was confirmed and extended through metatranscriptome assessment of gut microbial populations of eight animals, thus providing insights into the transcriptional response of gut microbiota to specific dietary lifestyles. Therefore, the analyses performed in this study support the notion that the metabolic features of the mammalian gut microbiota have adopted to maximize energy extraction from the host's diet.ImportanceDiet and host physiology have been recognized as main factors affecting both taxonomic composition and functional features of the mammalian gut microbiota. However, very few studies have investigated the bacterial biodiversity of mammals involving large sample numbers that correspond to multiple mammalian species, thus resulting in an incomplete understanding of the functional aspects of their microbiome. Therefore, we investigated the bacterial taxonomic composition of 250 fecal samples belonging to 77 host species distributed along the tree of life in order to assess how diet and host physiology impacts on the intestinal microbial community by selecting specific microbial players. Conversely, the application of shotgun metagenomics and metatranscriptomics approaches to a group of selected fecal samples allowed us to shed light on both metabolic features and transcriptional responses of the intestinal bacterial community based on different diets.

RevDate: 2020-09-19

Liang Z, Shi J, Wang C, et al (2020)

Genome-centric metagenomic insights into the impact of alkaline/acid and thermal sludge pre-treatment on digestion sludge microbiome.

Applied and environmental microbiology pii:AEM.01920-20 [Epub ahead of print].

Pre-treatment of waste activated sludge (WAS) is an effective way to destabilize sludge floc structure and release organic matter for improving sludge digestion efficiency. Nonetheless, impacts of WAS pre-treatment on digestion sludge microbiomes, as well as mechanistic insights into how sludge pre-treatment improve digestion performance, remain elusive. In this study, genome-centric metagenomic approach was employed to investigate the digestion sludge microbiome in four sludge digesters with different feeding sludge: APAD, WAS pre-treated with 0.25 mol/L alkaline/acid; HS-APAD, WAS pre-treated with 0.8 mol/L alkaline/acid; Thermal-AD, thermal pre-treated WAS; Control-AD, fresh WAS. We retrieved 254 metagenomic-assembled genomes (MAGs) to identify the key functional populations involved in methanogenic digestion process. These MAGs span 28 phyla with 69 of them as yet-to-be-cultivated lineages, and 30 novel lineages were characterized with metabolic potential associated with hydrolysis and fermentation. Interestingly, functional populations involving carbohydrate digestion were enriched in APAD and HS-APAD, while lineages related to protein and lipid fermentation were enriched in Thermal-AD, corroborating different substrates released from alkaline/acid and thermal pre-treatments. Of the major functional populations (i.e., fermenters, syntrophic acetogens and methanogens), significant correlations between genome sizes and abundance of the fermenters were observed, particularly in the APAD and HS-APAD with improved digestion performance.IMPORTANCE Wastewater treatment generates large amounts of waste activated sludge (WAS), which mainly consist of recalcitrant microbial cells and particulate organic matter. Though WAS pre-treatment is an effective way to release sludge organic matter for subsequent digestion, information on detailed impacts of the sludge pre-treatment on digestion sludge microbiome remain scarce. Our study provides unprecedented genome-centric metagenomic insights into how WAS pre-treatments change the digestion sludge microbiomes, as well as their metabolic networks. Moreover, digestion sludge microbiome could be a unique source to explore microbial dark matter. These results may shed light on future optimization of methanogenic sludge digestion and resource recovery.

RevDate: 2020-09-19

Fonseca MJMD, Armstrong Z, Withers SG, et al (2020)

High-throughput generation of product profiles for arabinoxylan-active enzymes from metagenomes.

Applied and environmental microbiology pii:AEM.01505-20 [Epub ahead of print].

Metagenomics is an exciting alternative to seek for carbohydrate-active enzymes from a range of sources. Typically, metagenomics reveals dozens of putative catalysts that require functional characterization for further application in industrial processes. High-throughput screening methods compatible with adequate natural substrates are crucial for an accurate functional elucidation of substrate preferences. Based on DNA sequencer-aided fluorophore-assisted carbohydrate electrophoresis (DSA-FACE) analysis of enzymatic reaction products, we generated product profiles to consequently infer substrate cleavage positions, resulting in the generation of enzymatic degradation maps. Product profiles were produced in high-throughput for arabinoxylan (AX)-active enzymes belonging to the glycoside hydrolase families GH43 (subfamilies 2 (MG432), 7 (MG437) and 28 (MG4328)) and GH8 (MG8) starting from twelve (arabino)xylo-oligosaccharides. These enzymes were discovered through functional metagenomic studies of faeces from the North American beaver (Castor canadensis). This work shows how enzyme loading alters the product profiles produced by all enzymes studied and gives insight into AX degradation patterns revealing sequential substrate preferences of AX-active enzymes.Importance Arabinoxylan is mainly found in the hemicellulosic fractions of rice straw, corn cobs and rice husk. Converting arabinoxylan into (arabino)xylo-oligosaccharides as added value products that can be applied in food, feed, and cosmetics presents a sustainable and economic alternative for the biorefinery industries. An efficient and profitable AX degradation requires a set of enzymes with particular characteristics. Therefore, enzyme discovery and study of substrate preferences is of utmost importance. Beavers, as consumers of woody biomass are a promising source of a repertoire of enzymes able to deconstruct hemicelluloses into soluble oligosaccharides. High-throughput analysis of oligosaccharide profiles produced by these enzymes will assist in the selection of the most appropriate enzymes for the biorefinery.

RevDate: 2020-09-19

Białasek M, A Miłobędzka (2020)

Revealing antimicrobial resistance in stormwater with MinION.

Chemosphere, 258:127392.

Discharge of urban stormwater containing organic matter, heavy metals and sometime human feces, to the natural aquatic reservoirs without any treatment is not only an environmental problem. It can lead to prevalence of antibiotic resistant bacteria in stormwater systems and transmission of antibiotic resistance genes to the environment. We performed antibiotic resistome identification and virus detection in stormwater samples from Stockholm, using publicly available metagenomic sequencing MinION data. A MinION platform offers low-cost, precise environmental metagenomics analysis. 37 groups of antibiotic resistant bacteria (ARB), 11 resistance types with 26 resistance mechanisms - antibiotic resistance genes (ARGs) giving tolerance to the aminoglycoside, beta-lactams, fosmidomycin, MLS, multidrug and vancomycin were identified using ARGpore pipeline. The majority of the identified bacteria species were related to the natural environment such as soil and were not dangerous to human. Alarmingly, human pathogenic bacteria carrying resistance to antibiotics currently used against them (Bordetella resistant to macrolides and multidrug resistant Propionibacterium avidum) were also found in the samples. Most abundant viruses identified belonged to Caudovirales and Herpesvirales and they were not carrying ARGs. Unlike the virome, resistome and ARB were not unique for stormwater sampling points. This results underline the need for extensive monitoring of the microbial community structure in the urban stormwater systems to assess antimicrobial resistance spread.

RevDate: 2020-09-18

Søndertoft NB, Vogt JK, Arumugam M, et al (2020)

The intestinal microbiome is a co-determinant of the postprandial plasma glucose response.

PloS one, 15(9):e0238648 pii:PONE-D-20-08323.

Elevated postprandial plasma glucose is a risk factor for development of type 2 diabetes and cardiovascular disease. We hypothesized that the inter-individual postprandial plasma glucose response varies partly depending on the intestinal microbiome composition and function. We analyzed data from Danish adults (n = 106), who were self-reported healthy and attended the baseline visit of two previously reported randomized controlled cross-over trials within the Gut, Grain and Greens project. Plasma glucose concentrations at five time points were measured before and during three hours after a standardized breakfast. Based on these data, we devised machine learning algorithms integrating bio-clinical, as well as shotgun-sequencing-derived taxa and functional potentials of the intestinal microbiome to predict individual postprandial glucose excursions. In this post hoc study, we found microbial and clinical features, which predicted up to 48% of the inter-individual variance of postprandial plasma glucose responses (Pearson correlation coefficient of measured vs. predicted values, R = 0.69, 95% CI: 0.45 to 0.84, p<0.001). The features were age, fasting serum triglycerides, systolic blood pressure, BMI, fasting total serum cholesterol, abundance of Bifidobacterium genus, richness of metagenomics species and abundance of a metagenomic species annotated to Clostridiales at order level. A model based only on microbial features predicted up to 14% of the variance in postprandial plasma glucose excursions (R = 0.37, 95% CI: 0.02 to 0.64, p = 0.04). Adding fasting glycaemic measures to the model including microbial and bio-clinical features increased the predictive power to R = 0.78 (95% CI: 0.59 to 0.89, p<0.001), explaining more than 60% of the inter-individual variance of postprandial plasma glucose concentrations. The outcome of the study points to a potential role of the taxa and functional potentials of the intestinal microbiome. If validated in larger studies our findings may be included in future algorithms attempting to develop personalized nutrition, especially for prediction of individual blood glucose excursions in dys-glycaemic individuals.

RevDate: 2020-09-18

Park JM, Won SM, Kang CH, et al (2020)

Characterization of a novel carboxylesterase belonging to family VIII hydrolyzing β-lactam antibiotics from a compost metagenomic library.

International journal of biological macromolecules pii:S0141-8130(20)34430-5 [Epub ahead of print].

A novel esterase, EstCS3, was isolated from a metagenomic library constructed from a compost. The EstCS3, which consists of 409 amino acids with an anticipated molecular mass of 44 kDa, showed high amino acid sequence identities to predicted esterases, serine hydrolases and β-lactamases from uncultured and cultured bacteria. Phylogenetic analysis suggested that EstCS3 belongs to family VIII of lipolytic enzymes. EstCS3 had catalytic Ser78 residue in the consensus tetrapeptide motif SXXK, which is characteristic of family VIII esterases. Two conserved YXX and W(H or K)XG motifs in an oxyanion hole of family VIII esterases were also present in EstCS3. EstCS3 demonstrated the highest activity toward p-nitrophenyl butyrate (C4) and was stable up to 70 °C with optimal activity at 55 °C. EstCS3 had optimal activity at pH 8 and maintained its stability within pH range of 7-10. EstCS3 had over 70% activity in the presence of 20% (v/v) methanol and DMSO and hydrolyzed sterically hindered tertiary alcohol esters of t-butyl acetate and linalyl acetate. EstCS3 hydrolyzed ampicillin, cephalothin and cefepime. The properties of EstCS3, including moderate thermostability, stability against organic solvents and activity toward esters of tertiary alcohols, indicated that it has the potential to be used in industrial applications.

RevDate: 2020-09-18

Kumar V, Mahajan N, Khare P, et al (2020)

Role of TRPV1 in colonic mucin production and gut microbiota profile.

European journal of pharmacology pii:S0014-2999(20)30659-2 [Epub ahead of print].

This study focuses on exploring the role of sensory cation channel Transient Receptor Potential channel subfamily Vanilloid 1 (TRPV1) in gut health, specifically mucus production and microflora profile in gut. We employed resiniferatoxin (ultrapotent TRPV1 agonist) induced chemo-denervation model in rats and studied the effects of TRPV1 ablation on colonic mucus secretion patterns. Histological and transcriptional analysis showed substantial decrease in mucus production as well as in expression of genes involved in goblet cell differentiation, mucin production and glycosylation. 16S metagenome analysis revealed changes in abundance of various gut bacteria, including decrease in beneficial bacteria like Lactobacillus spp and Clostridia spp. Also, TRPV1 ablation significantly decreased the levels of short chain fatty acids, i.e. acetate and butyrate. The present study provides first evidence that systemic TRPV1 ablation leads to impairment in mucus production and causes dysbiosis in gut. Further, it suggests to address mucin production and gut microbiota related adverse effects during the development of TRPV1 antagonism/ablation-based therapeutic and preventive strategies.

RevDate: 2020-09-18

Alam MNU, UF Chowdhury (2020)

Short k-mer abundance profiles yield robust machine learning features and accurate classifiers for RNA viruses.

PloS one, 15(9):e0239381 pii:PONE-D-20-22563.

High-throughput sequencing technologies have greatly enabled the study of genomics, transcriptomics and metagenomics. Automated annotation and classification of the vast amounts of generated sequence data has become paramount for facilitating biological sciences. Genomes of viruses can be radically different from all life, both in terms of molecular structure and primary sequence. Alignment-based and profile-based searches are commonly employed for characterization of assembled viral contigs from high-throughput sequencing data. Recent attempts have highlighted the use of machine learning models for the task, but these models rely entirely on DNA genomes and owing to the intrinsic genomic complexity of viruses, RNA viruses have gone completely overlooked. Here, we present a novel short k-mer based sequence scoring method that generates robust sequence information for training machine learning classifiers. We trained 18 classifiers for the task of distinguishing viral RNA from human transcripts. We challenged our models with very stringent testing protocols across different species and evaluated performance against BLASTn, BLASTx and HMMER3 searches. For clean sequence data retrieved from curated databases, our models display near perfect accuracy, outperforming all similar attempts previously reported. On de novo assemblies of raw RNA-Seq data from cells subjected to Ebola virus, the area under the ROC curve varied from 0.6 to 0.86 depending on the software used for assembly. Our classifier was able to properly classify the majority of the false hits generated by BLAST and HMMER3 searches on the same data. The outstanding performance metrics of our model lays the groundwork for robust machine learning methods for the automated annotation of sequence data.

RevDate: 2020-09-18

Methe BA, Hiltbrand D, Roach J, et al (2020)

Functional gene categories differentiate maize leaf drought-related microbial epiphytic communities.

PloS one, 15(9):e0237493 pii:PONE-D-19-16307.

The phyllosphere epiphytic microbiome is composed of microorganisms that colonize the external aerial portions of plants. Relationships of plant responses to specific microorganisms-both pathogenic and beneficial-have been examined, but the phyllosphere microbiome functional and metabolic profile responses are not well described. Changing crop growth conditions, such as increased drought, can have profound impacts on crop productivity. Also, epiphytic microbial communities provide a new target for crop yield optimization. We compared Zea mays leaf microbiomes collected under drought and well-watered conditions by examining functional gene annotation patterns across three physically disparate locations each with and without drought treatment, through the application of short read metagenomic sequencing. Drought samples exhibited different functional sequence compositions at each of the three field sites. Maize phyllosphere functional profiles revealed a wide variety of metabolic and regulatory processes that differed in drought and normal water conditions and provide key baseline information for future selective breeding.

RevDate: 2020-09-18

Yan J, Wu X, Chen J, et al (2020)

Harnessing the strategy of metagenomics for exploring the intestinal microecology of sable (Martes zibellina), the national first-level protected animal.

AMB Express, 10(1):169 pii:10.1186/s13568-020-01103-6.

Sable (Martes zibellina), a member of family Mustelidae, order Carnivora, is primarily distributed in the cold northern zone of Eurasia. The purpose of this study was to explore the intestinal flora of the sable by metagenomic library-based techniques. Libraries were sequenced on an Illumina HiSeq 4000 instrument. The effective sequencing data of each sample was above 6000 M, and the ratio of clean reads to raw reads was over 98%. The total ORF length was approximately 603,031, equivalent to 347.36 Mbp. We investigated gene functions with the KEGG database and identified 7140 KEGG ortholog (KO) groups comprising 129,788 genes across all of the samples. We selected a subset of genes with the highest abundances to construct cluster heat maps. From the results of the KEGG metabolic pathway annotations, we acquired information on gene functions, as represented by the categories of metabolism, environmental information processing, genetic information processing, cellular processes and organismal systems. We then investigated gene function with the CAZy database and identified functional carbohydrate hydrolases corresponding to genes in the intestinal microorganisms of sable. This finding is consistent with the fact that the sable is adapted to cold environments and requires a large amount of energy to maintain its metabolic activity. We also investigated gene functions with the eggNOG database; the main functions of genes included gene duplication, recombination and repair, transport and metabolism of amino acids, and transport and metabolism of carbohydrates. In this study, we attempted to identify the complex structure of the microbial population of sable based on metagenomic sequencing methods, which use whole metagenomic data, and to map the obtained sequences to known genes or pathways in existing databases, such as CAZy, KEGG, and eggNOG. We then explored the genetic composition and functional diversity of the microbial community based on the mapped functional categories.

RevDate: 2020-09-18

Wang H, Chan MWM, Chan HH, et al (2020)

Longitudinal Changes in Skin Microbiome and Microbes Associated with Change in Skin Status in Patients with Psoriasis.

Acta dermato-venereologica [Epub ahead of print].

The aim of this study was to identify key microbes associated with change in skin status in patients with psoriasis over time. Longitudinal changes in the skin microbiome between patients with psoriasis and healthy family controls living in the same household were studied using whole genome metagenomic shotgun sequencing at 4 time-points. There were significant changes in abundance of the pathogen Campylobacter jejuni and its higher taxonomic levels when the skin status of patients with psoriasis changed. There were significant longitudinal variations in alpha and beta diversity of the skin microbiota in patients with psoriasis, but not in the control group. These results indicate a role for a balanced and dynamically stable skin microbiome in healthy skin, and will serve as the basis for future temporal studies of the skin microbiome and probiotic therapeutics.

RevDate: 2020-09-19

Chen P, Sun W, Y He (2020)

Comparison of metagenomic next-generation sequencing technology, culture and GeneXpert MTB/RIF assay in the diagnosis of tuberculosis.

Journal of thoracic disease, 12(8):4014-4024.

Background: With a high incidence rate and mortality rate, tuberculosis (TB) is a major public health concern worldwide. There is an urgent need to develop the rapid, reliable and affordable diagnostic test for the detection of Mycobacterium tuberculosis (Mtb). Metagenomic next-generation sequencing (mNGS) showed promising values in the rapid diagnosis of clinical TB, while studies on the application of mNGS in pulmonary and extrapulmonary TB remain scarce.

Methods: In this study, we collected the results of both mNGS and culture of 70 specimens from suspected TB patients at the Shanghai Pulmonary Hospital of Tongji University. Results of GeneXpert MTB/RIF assay (Xpert) were obtained from 19 patients. We also assessed the diagnostic performance, relationship and consistency between mNGS, traditional culture method, and Xpert.

Results: Overall, 36 of 70 suspected patients were finally diagnosed with TB. The sensitivity, specificity, positive predictive value, negative predictive value and the Youden index of mNGS in all clinical TB specimens were calculated as 66.7% (95% CI: 0.489-0.809), 97.1% (95% CI: 0.829-0.998), 96.0% (95% CI: 0.777-0.998), 73.3% (95% CI: 0.578-0.849), 63.8%, respectively. The sensitivity of mNGS was much superior to that of conventional culture method (66.7%, 95% CI: 0.489-0.809 vs. 36.1%, 95% CI: 0.213-0.538) and Xpert (76.9%, 95% CI: 0.460-0.938 vs. 61.5%, 95% CI: 0.323-0.849). In pulmonary TB cases, mNGS, culture, and Xpert all demonstrated better diagnostic capacity for TB when compared with extrapulmonary TB cases. Among all methods and sample classifications, the Youden index of parallel diagnostic test in pulmonary samples was outstanding (mNGS/culture 88.2%; mNGS/Xpert 100%). Furthermore, the correlation and concordance between mNGS and culture method in all types of specimens was statistically significant (both P<0.001).

Conclusions: With high sensitivity and specificity, mNGS showed remarkable diagnostic performance in various samples from suspected TB patients. Combining mNGS and culture or Xpert method had the potential for clinical application in TB.

RevDate: 2020-09-18

Wicaksono WA, Cernava T, Grube M, et al (2020)

Assembly of Bacterial Genomes from the Metagenomes of Three Lichen Species.

Microbiology resource announcements, 9(38): pii:9/38/e00622-20.

Bacteria have recently emerged as important constituents of lichen holobionts. Here, 29 bacterial metagenome-assembled genome (MAG) sequences were reconstructed from lichen metagenomes and taxonomically classified in four phyla. These results provide a pivotal resource for further exploration of the ecological roles played by bacterial symbionts in lichen holobionts.

RevDate: 2020-09-18

Cuevas JP, Moraga R, Sánchez-Alonzo K, et al (2020)

Characterization of the Bacterial Biofilm Communities Present in Reverse-Osmosis Water Systems for Haemodialysis.

Microorganisms, 8(9): pii:microorganisms8091418.

Biofilm in reverse osmosis (RO) membranes is a common problem in water treatment at haemodialysis facilities. Bacteria adhere and proliferate on RO membranes, forming biofilms, obstructing and damaging the membranes and allowing the transfer of bacteria and/or cellular components potentially harmful to the health of haemodialysis patients. Our aim was to characterize the bacterial community associated to biofilm of RO membranes and to identify potentially pathogenic bacteria present in the haemodialysis systems of two dialysis centres in Chile. The diversity of the bacterial communities present on RO membranes and potable and osmosed water samples was evaluated using Illumina sequencing. Additionally, bacteria from potable water, osmosed water and RO membrane samples were isolated, characterized and identified by Sanger's sequencing. The molecular analyses of metagenomics showed that the phyla having a greater relative abundance in both dialysis centres were Proteobacteria and Planctomycetes. Pseudomonas, Stenotrophomonas, Agrobacterium, Pigmentiphaga, Ralstonia, Arthrobacter, Bacteroides and Staphylococcus were bacterial genera isolated from the different samples obtained at both haemodialysis centres. Pseudomonas spp. was a bacterial genus with greater frequency in all samples. Pseudomonas and Staphylococcus showed higher levels of resistance to the antibiotics tested. Results demonstrated the presence of potentially pathogenic bacteria, showing resistance to antimicrobials on RO membranes and in osmosed water in both dialysis centres studied.

RevDate: 2020-09-17

Sulheim S, Kumelj T, van Dissel D, et al (2020)

Enzyme-Constrained Models and Omics Analysis of Streptomyces coelicolor Reveal Metabolic Changes that Enhance Heterologous Production.

iScience, 23(9):101525 pii:S2589-0042(20)30717-3 [Epub ahead of print].

Many biosynthetic gene clusters (BGCs) require heterologous expression to realize their genetic potential, including silent and metagenomic BGCs. Although the engineered Streptomyces coelicolor M1152 is a widely used host for heterologous expression of BGCs, a systemic understanding of how its genetic modifications affect the metabolism is lacking and limiting further development. We performed a comparative analysis of M1152 and its ancestor M145, connecting information from proteomics, transcriptomics, and cultivation data into a comprehensive picture of the metabolic differences between these strains. Instrumental to this comparison was the application of an improved consensus genome-scale metabolic model (GEM) of S. coelicolor. Although many metabolic patterns are retained in M1152, we find that this strain suffers from oxidative stress, possibly caused by increased oxidative metabolism. Furthermore, precursor availability is likely not limiting polyketide production, implying that other strategies could be beneficial for further development of S. coelicolor for heterologous production of novel compounds.

RevDate: 2020-09-17

Solé C, Guilly S, Da Silva K, et al (2020)

ALTERATIONS IN GUT MICROBIOME IN CIRRHOSIS AS ASSESSED BY QUANTITATIVE METAGENOMICS. RELATIONSHIP WITH ACUTE-ON-CHRONIC LIVER FAILURE AND PROGNOSIS.

Gastroenterology pii:S0016-5085(20)35150-7 [Epub ahead of print].

BACKGROUND & AIMS: Cirrhosis is associated with changes in gut microbiome composition. Although ACLF is the most severe clinical stage of cirrhosis, there is lack of information about gut microbiome alterations in ACLF using quantitative metagenomics. To investigate the gut microbiome in patients with cirrhosis encompassing the whole spectrum of disease: compensated, acutely decompensated without ACLF, and ACLF. A group of healthy subjects was used as controls.

METHODS: Stool samples were collected prospectively in 182 patients with cirrhosis. DNA library construction and sequencing was performed using the Ion Proton sequencer. Microbial genes were grouped into clusters, denoted as metagenomic species(MGS).

RESULTS: Cirrhosis was associated with a remarkable reduction in gene and MGS richness compared to healthy subjects. This loss of richness correlated with disease stages and was particularly marked in patients with ACLF and persisted after adjustment for antibiotic therapy. ACLF was associated with a significant increase of Enterococcus and Peptostreptococcus sp, and reduction of some autochthonous bacteria. Gut microbiome alterations correlated with MELD and Child-Pugh scores and organ failures and was associated with some complications, particularly hepatic encephalopathy and infections. Interestingly, gut microbiome predicted 3 month-survival with good stable predictors. Functional analysis showed that patients with cirrhosis had enriched pathways related to ethanol production, GABA metabolism, and endotoxin biosynthesis, among others.

CONCLUSIONS: Cirrhosis is characterized by marked alterations in gut microbiome that parallel disease stages with maximal changes in ACLF. Altered gut microbiome was associated with complications of cirrhosis and survival. Gut microbiome may contribute to disease progression and poor prognosis. These results should be confirmed in future studies.

RevDate: 2020-09-17

Yang S, Shan T, Xiao Y, et al (2020)

Digging metagenomic data of pangolins revealed SARS-CoV-2 related viruses and other significant viruses.

Journal of medical virology [Epub ahead of print].

Pangolin metagenomic data obtained from public databases were used to assemble partial or complete viral genomes showing genetic relationship to SARS-CoV-2, Sendai virus, flavivirus, picornavirus, parvovirus and genomovirus, respectively. Most of these virus genomes showed genomic recombination signals. Phylogeny based on the SARS-CoV-2-related virus sequences assembled in this study and those recently published indicated that pangolin SARS-CoV-2-related viruses were clustered into two sub-lineages according to geographic sampling sites. These findings suggest the need for further pangolin samples, from different countries, to be collected and analyzed for coronavirus in order to elucidate whether pangolins are intermittent hosts for SARS-CoV-2. This article is protected by copyright. All rights reserved.

RevDate: 2020-09-17

Liu S, Zhao W, Liu X, et al (2020)

Metagenomic analysis of the gut microbiome in atherosclerosis patients identify cross-cohort microbial signatures and potential therapeutic target.

FASEB journal : official publication of the Federation of American Societies for Experimental Biology [Epub ahead of print].

The gut microbiota is associated with cardiovascular diseases, including atherosclerosis. However, the composition, functional capacity, and metabolites of the gut microbiome about atherosclerosis have not been comprehensively studied. Here, we reanalyzed 25 metagenomic stool samples from Sweden and 385 metagenomic stool samples from China using HUMAnN2, PanPhlAn, and MelonnPan to obtain more sufficient information. We found that the samples from atherosclerotic patients in both cohorts were depleted in Bacteroides xylanisolvens, Odoribacter splanchnicus, Eubacterium eligens, Roseburia inulinivorans, and Roseburia intestinalis. At the functional level, healthy metagenomes were both enriched in pathways of starch degradation V, glycolysis III (from glucose), CDP-diacylglycerol biosynthesis, and folate transformations. R inulinivorans and R intestinalis are major contributors to starch degradation V, while E eligens greatly contribute to the pathway CDP-diacylglycerol biosynthesis, and B xylanisolvens and B uniformis contribute to folate transformations II. The 11 marker species selected from the Chinese cohort distinguish patients from controls with an area under the receiver operating characteristics curve (AUC) of 0.86. Strain-level microbial analysis revealed a geographically associated adaptation of the strains from E eligens, B uniformis, and E coli. Two gut microbial metabolites, nicotinic acid and hydrocinnamic acid, had significantly higher predicted abundance in the control samples compared to the patients in the Chinese cohort, and interestinglynicotinic acid is already an effective lipid-lowering drug to reducing cardiovascular risk. Our results indicate intestinal bacteria such as B xylanisolvens, E eligens, and R inulinivorans could be promising probiotics and potential therapeutic target for atherosclerosis.

RevDate: 2020-09-17

Belkova N, Klimenko E, Romanitsa A, et al (2020)

Metagenomic 16S rDNA amplicon datasets from adolescents with normal weight, obesity, and obesity with irritable bowel syndrome from Eastern Siberia, Russia.

Data in brief, 32:106141 pii:106141.

Childhood obesity and its consequences are a significant public health problem worldwide. Gut microbiota has a potential role in the development of. In the current datasets, we present 16S rDNA amplicon metasequencing of the gut microbiome of adolescents with normal weight, obesity, and obesity with irritable bowel syndrome (IBS) carried out using the Illumine platform. The datasets presented in this report are partly shown in the research article named "Composition and Structure of Gut Microbiome in Adolescents with Obesity and Different Breastfeeding Duration" [1]. The amplicon metasequencing data were deposited at NCBI SRA as BioProject PRJNA604466. A total of 22 phyla, 34 classes, and 231 genera were revealed. Three groups of adolescents had 196 core amplicon sequence variant (ASV), whereas 45, 24, and 1 ASV were unique for adolescents with normal body weight, obesity, and obesity with IBS, respectively. The metagenomic data were first obtained for adolescents from Eastern Siberian, Russia. They have the potential for predictive analysis, which is crucial for understanding microbial community dynamics and their role in the development of the intestinal microbiome. Considering the recent focus on gut microbiota, new datasets are needed to determine the association between gut microbes and the weight of adolescents from previously unexplored regions such as Siberia, Russia.

RevDate: 2020-09-17

Belkova N, Klimenko E, Vilson N, et al (2020)

Metagenome datasets from women with polycystic ovary syndrome from Irkutsk, Eastern Siberia, Russia.

Data in brief, 32:106137 pii:106137.

For the metagenomic characterization of potential taxonomic and functional diversity of microorganisms associated with polycystic ovary syndrome (PCOS) in women, we surveyed five women with PCOS and collected samples of feces, saliva, and serum. After quality processing, we have obtained from 915,594 to 3,880,379 reads; these 16,693 sequences had ribosomal RNA genes, 2,091,990 sequences contained predicted proteins with known functions, and 3,750,261 sequences had predicted proteins with unknown functions. Host DNA accounted for ca. 0.03% and less in datasets of fecal samples, from 1.41 to 24.94% in saliva samples; the remaining sequences were attributed to archaeal, bacterial, or viral DNA. In serum, from 38.18 to 75.77% were characterized as fragments of the human genome, but the remaining sequences were unidentified. Among microbes, a total of one archaeal and eight bacterial phyla were revealed. Viral DNA was detected in several fecal and one saliva sample and was classified as C2likevirus, Flavivirus, and Streptococcus bacteriophage. The metagenome sequence data were deposited at NCBI SRA as BioProject No. PRJNA625611.

RevDate: 2020-09-17

Long AM, Hou S, Ignacio-Espinoza JC, et al (2020)

Benchmarking microbial growth rate predictions from metagenomes.

The ISME journal pii:10.1038/s41396-020-00773-1 [Epub ahead of print].

Growth rates are central to understanding microbial interactions and community dynamics. Metagenomic growth estimators have been developed, specifically codon usage bias (CUB) for maximum growth rates and "peak-to-trough ratio" (PTR) for in situ rates. Both were originally tested with pure cultures, but natural populations are more heterogeneous, especially in individual cell histories pertinent to PTR. To test these methods, we compared predictors with observed growth rates of freshly collected marine prokaryotes in unamended seawater. We prefiltered and diluted samples to remove grazers and greatly reduce virus infection, so net growth approximated gross growth. We sampled over 44 h for abundances and metagenomes, generating 101 metagenome-assembled genomes (MAGs), including Actinobacteria, Verrucomicrobia, SAR406, MGII archaea, etc. We tracked each MAG population by cell-abundance-normalized read recruitment, finding growth rates of 0 to 5.99 per day, the first reported rates for several groups, and used these rates as benchmarks. PTR, calculated by three methods, rarely correlated to growth (r ~-0.26-0.08), except for rapidly growing γ-Proteobacteria (r ~0.63-0.92), while CUB correlated moderately well to observed maximum growth rates (r = 0.57). This suggests that current PTR approaches poorly predict actual growth of most marine bacterial populations, but maximum growth rates can be approximated from genomic characteristics.

RevDate: 2020-09-17

Yang J, Moon HE, Park HW, et al (2020)

Brain tumor diagnostic model and dietary effect based on extracellular vesicle microbiome data in serum.

Experimental & molecular medicine pii:10.1038/s12276-020-00501-x [Epub ahead of print].

The human microbiome has been recently associated with human health and disease. Brain tumors (BTs) are a particularly difficult condition to directly link to the microbiome, as microorganisms cannot generally cross the blood-brain barrier (BBB). However, some nanosized extracellular vesicles (EVs) released from microorganisms can cross the BBB and enter the brain. Therefore, we conducted metagenomic analysis of microbial EVs in both serum (152 BT patients and 198 healthy controls (HC)) and brain tissue (5 BT patients and 5 HC) samples based on the V3-V4 regions of 16S rDNA. We then developed diagnostic models through logistic regression and machine learning algorithms using serum EV metagenomic data to assess the ability of various dietary supplements to reduce BT risk in vivo. Models incorporating the stepwise method and the linear discriminant analysis effect size (LEfSe) method yielded 12 and 29 significant genera as potential biomarkers, respectively. Models using the selected biomarkers yielded areas under the curves (AUCs) >0.93, and the model using machine learning resulted in an AUC of 0.99. In addition, Dialister and [Eubacterium] rectale were significantly lower in both blood and tissue samples of BT patients than in those of HCs. In vivo tests showed that BT risk was decreased through the addition of sorghum, brown rice oil, and garlic but conversely increased by the addition of bellflower and pear. In conclusion, serum EV metagenomics shows promise as a rich data source for highly accurate detection of BT risk, and several foods have potential for mitigating BT risk.

RevDate: 2020-09-17

Rodino KG, Toledano M, Norgan AP, et al (2020)

Retrospective Review of Clinical Utility of Shotgun Metagenomic Sequencing Testing of Cerebrospinal Fluid at a U.S. Tertiary Care Medical Center.

Journal of clinical microbiology pii:JCM.01729-20 [Epub ahead of print].

Shotgun metagenomic sequencing can detect nucleic acids from bacteria, fungi, viruses, and/or parasites in clinical specimens; however, little data exist to guide its optimal application to clinical practice. We retrospectively reviewed results of shotgun metagenomic sequencing testing requested on cerebrospinal fluid submitted to a reference laboratory from December 2017 through December 2019. Of the 53 samples from Mayo Clinic patients, 47 were requested by neurologists, with infectious diseases consultation in 23 cases. The majority of patients presented with difficult to diagnose subacute or chronic conditions. Positive results were reported for 9 (17%) Mayo Clinic patient samples, with 6 interpreted as likely contamination. Potential pathogens reported included bunyavirus, human herpesvirus 7, and enterovirus D-68, ultimately impacting care in two cases. Twenty-seven additional samples were submitted from Mayo Clinic Laboratories reference clients, with positive results reported in 3 (11%): 2 potential pathogens (West Nile virus and Toxoplasma gondii), and Streptococcus species with other bacteria below the reporting threshold (considered to represent contamination). Of 68 negative results, 10 included comments on decreased sensitivity due to high DNA background (n=5), high RNA background (n=1), insufficient RNA read depth (n=3), or QC failure with external RNA control (n=1). The overall positive result rate was 15% (12/80), with 58% (7/12) of these interpreted as inconsistent with the patient's clinical presentation. Overall, potential pathogens were found in a low percentage of cases, and positive results were often of unclear clinical significance. Testing was commonly employed in cases of diagnostic uncertainty and when immunotherapy was being considered.

RevDate: 2020-09-17

Piantadosi A, S Kanjilal (2020)

Diagnostic approach for arboviral infections in the United States.

Journal of clinical microbiology pii:JCM.01926-19 [Epub ahead of print].

Domestic arthropod-borne viruses (arboviruses) are single stranded RNA viruses, the most common of which include the mosquito-borne West Nile virus, St. Louis Encephalitis virus, La Crosse virus, Jamestown Canyon virus, and Eastern Equine Encephalitis virus, as well as the tick-borne Powassan virus. Previously considered to be rare infections, they have been detected with increasing frequency over the past 2 decades. Here, we present an overview of the domestic arboviruses listed above and describe the modalities employed to diagnose infection. Global arboviruses including dengue virus, Zika virus, and chikungunya virus have also been increasingly detected in the United States within the last 5 years, but are not a focus of this minireview. Typical manifestations of arbovirus infection range from no symptoms, to meningitis or encephalitis, to death. Serologies are the standard means of diagnosis in the laboratory since most viruses have a limited period of replication, limiting the utility of molecular tests. Interpretation of serologies is confounded by antibody cross-reactivity with viruses belonging to the same serogroup and by long-lasting antibodies from prior infections. Next generation assays have improved performance by increasing antigen purity, selecting optimal epitopes and improving interpretive algorithms, but challenges remain. Due to cross-reactivity, a positive first-line serology test requires confirmation by either a plaque reduction neutralization test or detection of seroconversion or a four-fold rise in virus-specific IgM or IgG antibody titers from acute and convalescent sera. The use of molecular diagnostics such as reverse transcription polymerase chain reaction (RT-PCR) or unbiased metagenomic sequencing is limited to the minority of patients who present with ongoing viremia or CSF replication. With continued expansion of vector range, diagnosis of domestic arboviruses will become an increasingly important task for generalists and specialists alike.

RevDate: 2020-09-17

Wong HL, MacLeod FI, White RA, et al (2020)

Microbial dark matter filling the niche in hypersaline microbial mats.

Microbiome, 8(1):135 pii:10.1186/s40168-020-00910-0.

BACKGROUND: Shark Bay, Australia, harbours one of the most extensive and diverse systems of living microbial mats that are proposed to be analogs of some of the earliest ecosystems on Earth. These ecosystems have been shown to possess a substantial abundance of uncultivable microorganisms. These enigmatic microbes, jointly coined as 'microbial dark matter' (MDM), are hypothesised to play key roles in modern microbial mats.

RESULTS: We reconstructed 115 metagenome-assembled genomes (MAGs) affiliated to MDM, spanning 42 phyla. This study reports for the first time novel microorganisms (Zixibacterial order GN15) putatively taking part in dissimilatory sulfate reduction in surface hypersaline settings, as well as novel eukaryote signature proteins in the Asgard archaea. Despite possessing reduced-size genomes, the MDM MAGs are capable of fermenting and degrading organic carbon, suggesting a role in recycling organic carbon. Several forms of RuBisCo were identified, allowing putative CO2 incorporation into nucleotide salvaging pathways, which may act as an alternative carbon and phosphorus source. High capacity of hydrogen production was found among Shark Bay MDM. Putative schizorhodopsins were also identified in Parcubacteria, Asgard archaea, DPANN archaea, and Bathyarchaeota, allowing these members to potentially capture light energy. Diversity-generating retroelements were prominent in DPANN archaea that likely facilitate the adaptation to a dynamic, host-dependent lifestyle.

CONCLUSIONS: This is the first study to reconstruct and describe in detail metagenome-assembled genomes (MAGs) affiliated with microbial dark matter in hypersaline microbial mats. Our data suggests that these microbial groups are major players in these systems. In light of our findings, we propose H2, ribose and CO/CO2 as the main energy currencies of the MDM community in these mat systems. Video Abstract.

RevDate: 2020-09-17

Albrecht B, Bağcı C, DH Huson (2020)

MAIRA- real-time taxonomic and functional analysis of long reads on a laptop.

BMC bioinformatics, 21(Suppl 13):390 pii:10.1186/s12859-020-03684-2.

BACKGROUND: Advances in mobile sequencing devices and laptop performance make metagenomic sequencing and analysis in the field a technologically feasible prospect. However, metagenomic analysis pipelines are usually designed to run on servers and in the cloud.

RESULTS: MAIRA is a new standalone program for interactive taxonomic and functional analysis of long read metagenomic sequencing data on a laptop, without requiring external resources. The program performs fast, online, genus-level analysis, and on-demand, detailed taxonomic and functional analysis. It uses two levels of frame-shift-aware alignment of DNA reads against protein reference sequences, and then performs detailed analysis using a protein synteny graph.

CONCLUSIONS: We envision this software being used by researchers in the field, when access to servers or cloud facilities is difficult, or by individuals that do not routinely access such facilities, such as medical researchers, crop scientists, or teachers.

RevDate: 2020-09-17

Guerrini V, Louza FA, G Rosone (2020)

Metagenomic analysis through the extended Burrows-Wheeler transform.

BMC bioinformatics, 21(Suppl 8):299 pii:10.1186/s12859-020-03628-w.

BACKGROUND: The development of Next Generation Sequencing (NGS) has had a major impact on the study of genetic sequences. Among problems that researchers in the field have to face, one of the most challenging is the taxonomic classification of metagenomic reads, i.e., identifying the microorganisms that are present in a sample collected directly from the environment. The analysis of environmental samples (metagenomes) are particularly important to figure out the microbial composition of different ecosystems and it is used in a wide variety of fields: for instance, metagenomic studies in agriculture can help understanding the interactions between plants and microbes, or in ecology, they can provide valuable insights into the functions of environmental communities.

RESULTS: In this paper, we describe a new lightweight alignment-free and assembly-free framework for metagenomic classification that compares each unknown sequence in the sample to a collection of known genomes. We take advantage of the combinatorial properties of an extension of the Burrows-Wheeler transform, and we sequentially scan the required data structures, so that we can analyze unknown sequences of large collections using little internal memory. The tool LiME (Lightweight Metagenomics via eBWT) is available at https://github.com/veronicaguerrini/LiME .

CONCLUSIONS: In order to assess the reliability of our approach, we run several experiments on NGS data from two simulated metagenomes among those provided in benchmarking analysis and on a real metagenome from the Human Microbiome Project. The experiment results on the simulated data show that LiME is competitive with the widely used taxonomic classifiers. It achieves high levels of precision and specificity - e.g. 99.9% of the positive control reads are correctly assigned and the percentage of classified reads of the negative control is less than 0.01% - while keeping a high sensitivity. On the real metagenome, we show that LiME is able to deliver classification results comparable to that of MagicBlast. Overall, the experiments confirm the effectiveness of our method and its high accuracy even in negative control samples.

RevDate: 2020-09-17

Kim M, Cha IT, Lee KE, et al (2020)

Genomics Reveals the Metabolic Potential and Functions in the Redistribution of Dissolved Organic Matter in Marine Environments of the Genus Thalassotalea.

Microorganisms, 8(9): pii:microorganisms8091412.

Members of the bacterial genus Thalassotalea have been isolated recently from various marine environments, including marine invertebrates. A metagenomic study of the Deepwater Horizon oil plume has identified genes involved in aromatic hydrocarbon degradation in the Thalassotalea genome, shedding light on its potential role in the degradation of crude oils. However, the genomic traits of the genus are not well-characterized, despite the ability of the species to degrade complex natural compounds, such as agar, gelatin, chitin, or starch. Here, we obtained a complete genome of a new member of the genus, designated PS06, isolated from marine sediments containing dead marine benthic macroalgae. Unexpectedly, strain PS06 was unable to grow using most carbohydrates as sole carbon sources, which is consistent with the finding of few ABC transporters in the PS06 genome. A comparative analysis of 12 Thalassotalea genomes provided insights into their metabolic potential (e.g., microaerobic respiration and carbohydrate utilization) and evolutionary stability [including a low abundance of clustered regularly interspaced short palindromic repeats (CRISPR) loci and prophages]. The diversity and frequency of genes encoding extracellular enzymes for carbohydrate metabolism in the 12 genomes suggest that members of Thalassotalea contribute to nutrient cycling by the redistribution of dissolved organic matter in marine environments. Our study improves our understanding of the ecological and genomic properties of the genus Thalassotalea.

RevDate: 2020-09-15

Bose D, Saha P, Mondal A, et al (2020)

Obesity Worsens Gulf War Illness Symptom Persistence Pathology by Linking Altered Gut Microbiome Species to Long-Term Gastrointestinal, Hepatic, and Neuronal Inflammation in a Mouse Model.

Nutrients, 12(9): pii:nu12092764.

Persistence of Gulf War illness (GWI) pathology among deployed veterans is a clinical challenge even after almost three decades. Recent studies show a higher prevalence of obesity and metabolic disturbances among Gulf War veterans primarily due to the existence of post-traumatic stress disorder (PTSD), chronic fatigue, sedentary lifestyle, and consumption of a high-carbohydrate/high-fat diet. We test the hypothesis that obesity from a Western-style diet alters host gut microbial species and worsens gastrointestinal and neuroinflammatory symptom persistence. We used a 5 month Western diet feeding in mice that received prior Gulf War (GW) chemical exposure to mimic the home phase obese phenotype of the deployed GW veterans. The host microbial profile in the Western diet-fed GWI mice showed a significant decrease in butyrogenic and immune health-restoring bacteria. The altered microbiome was associated with increased levels of IL6 in the serum, Claudin-2, IL6, and IL1β in the distal intestine with concurrent inflammatory lesions in the liver and hyperinsulinemia. Microbial dysbiosis was also associated with frontal cortex levels of increased IL6 and IL1β, activated microglia, decreased levels of brain derived neurotrophic factor (BDNF), and higher accumulation of phosphorylated Tau, an indicator of neuroinflammation-led increased risk of cognitive deficiencies. Mechanistically, serum from Western diet-fed mice with GWI significantly increased microglial activation in transformed microglial cells, increased tyrosyl radicals, and secreted IL6. Collectively, the results suggest that an existing obese phenotype in GWI worsens persistent gastrointestinal and neuronal inflammation, which may contribute to poor outcomes in restoring cognitive function and resolving fatigue, leading to the deterioration of quality of life.

RevDate: 2020-09-16

Ganesan SM, Dabdoub SM, Nagaraja HN, et al (2020)

Adverse effects of electronic cigarettes on the disease-naive oral microbiome.

Science advances, 6(22): pii:6/22/eaaz0108.

Six percent of Americans, including 3 million high schoolers, use e-cigarettes, which contain potentially toxic substances, volatile organic compounds, and metals. We present the first human study on the effects of e-cigarette exposure in the oral cavity. By interrogating both immunoinflammatory responses and microbial functional dynamics, we discovered pathogen overrepresentation, higher virulence signatures, and a brisk proinflammatory signal in clinically healthy e-cigarette users, equivalent to patients with severe periodontitis. Using RNA sequencing and confocal and electron microscopy to validate these findings, we demonstrate that the carbon-rich glycol/glycerol vehicle is an important catalyst in transforming biofilm architecture within 24 hours of exposure. Last, a machine-learning classifier trained on the metagenomic signatures of e-cigarettes identified as e-cigarette users both those individuals who used e-cigarettes to quit smoking, and those who use both e-cigarettes and cigarettes. The present study questions the safety of e-cigarettes and the harm reduction narrative promoted by advertising campaigns.

RevDate: 2020-09-16

Zhao Z (2020)

Comparison of microbial communities and the antibiotic resistome between prawn mono- and poly-culture systems.

Ecotoxicology and environmental safety, 207:111310 pii:S0147-6513(20)31147-7 [Epub ahead of print].

Antibiotic resistance genes (ARGs) in mariculture sediments pose a potential risk to public health due to their ability to transfer from environmental bacteria to human pathogens. Long term, this may reduce pathogen susceptibility to antibiotics in medical settings. In recent years, the poly-culture of multiple species has become a popular mariculture approach in China, thanks to its environmental and economic benefits. However, differences in microbial communities and antibiotic resistome between mono- and poly-culture systems are still unclear. In this study, microbial community composition and profiles of entire (microbial DNA) and mobile (plasmid and phage) ARGs in prawn mono- and poly-culture systems were investigated using metagenomics. The abundance of several viruses and human pathogens were enhanced in prawn poly-culture ponds, when compared to monoculture systems. In contrast, sediments from poly-culture systems had a lower diversity and ARG abundance when compared to mono-culture approaches. These ARG variations were predominantly related to mobile genetic elements. Prawn mariculture activities exerted a unique selectivity for ARGs in plasmids, and this selectivity was not influenced by culture methods. The findings of this study have important implications for the selection of mariculture systems in preventing pollution with ARGs.

RevDate: 2020-09-16

Babiker A, Bradley H, Stittleburg V, et al (2020)

Metagenomic sequencing to detect respiratory viruses in persons under investigation for COVID-19.

medRxiv : the preprint server for health sciences.

We used metagenomic next-generation sequencing (mNGS) to assess the frequencies of alternative viral infections in SARS-CoV-2 RT-PCR negative persons under investigations (PUIs) (n=30) and viral co-infections in SARS-CoV-2 RT-PCR positive PUIs (n=45). mNGS identified both co-infections and alternative viral infections that were not detected by routine clinical workup.

RevDate: 2020-09-16

Lee JH, Choi JP, Yang J, et al (2020)

Metagenome analysis using serum extracellular vesicles identified distinct microbiota in asthmatics.

Scientific reports, 10(1):15125 pii:10.1038/s41598-020-72242-w.

Different patterns of bacterial communities have been reported in the airways and gastrointestinal tract of asthmatics when compared to healthy controls. However, the blood microbiome of asthmatics is yet to be investigated. Therefore, we aimed to determine whether a distinct serum microbiome is observed in asthmatics by metagenomic analysis of serum extracellular vesicles (EVs). We obtained serum from 190 adults with asthma and 260 healthy controls, from which EVs were isolated and analyzed. The bacterial composition of asthmatics was significantly different from that of healthy controls. Chao 1 index was significantly higher in the asthma group, while Shannon and Simpson indices were higher in the control group. At the phylum level, Bacteroidetes was more abundant in asthmatics, while Actinobacter, Verrucomicrobia, and Cyanobacteria were more abundant in healthy controls. At the genus level, 24 bacterial genera showed differences in relative abundance between asthmatics and controls, with linear discriminant analysis scores greater than 3. Further, in a diagnostic model based on these differences, a high predictive value with a sensitivity of 0.92 and a specificity of 0.93 was observed. In conclusion, we demonstrated distinct blood microbiome in asthma indicating the role of microbiome as a potential diagnostic marker of asthma.

RevDate: 2020-09-16

Chacón-Vargas K, Torres J, Giles-Gómez M, et al (2020)

Genomic profiling of bacterial and fungal communities and their predictive functionality during pulque fermentation by whole-genome shotgun sequencing.

Scientific reports, 10(1):15115 pii:10.1038/s41598-020-71864-4.

Pulque is a culturally important 4,000-year-old traditional Mexican fermented drink. Pulque is produced by adding fresh aguamiel (agave sap) to mature pulque, resulting in a mixture of microbial communities and chemical compositions. We performed shotgun metagenomic sequencing of five stages of pulque fermentation to characterize organismal and functional diversity. We identified 6 genera (Acinetobacter, Lactobacillus, Lactococcus, Leuconostoc, Saccharomyces and Zymomonas) and 10 species (Acinetobacter boissieri, Acinetobacter nectaris, Lactobacillus sanfranciscensis, Lactococcus lactis, Lactococcus piscium, Lactococcus plantarum, Leuconostoc citreum, Leuconostoc gelidum, Zymomonas mobilis and Saccharomyces cerevisiae) that were present ≥ 1% in at least one stage of pulque fermentation. The abundance of genera and species changed during fermentation and was associated with a decrease in sucrose and increases in ethanol and lactic acid, suggesting that resource competition shapes organismal diversity. We also predicted functional profiles, based on organismal gene content, for each fermentation stage and identified an abundance of genes associated with the biosynthesis of folate, an essential B-vitamin. Additionally, we investigated the evolutionary relationships of S. cerevisiae and Z. mobilis, two of the major microbial species found in pulque. For S. cerevisiae, we used a metagenomics assembly approach to identify S. cerevisiae scaffolds from pulque, and performed phylogenetic analysis of these sequences along with a collection of 158 S. cerevisiae strains. This analysis suggests that S. cerevisiae from pulque is most closely related to Asian strains isolated from sake and bioethanol. Lastly, we isolated and sequenced the whole-genomes of three strains of Z. mobilis from pulque and compared their relationship to seven previously sequenced isolates. Our results suggest pulque strains may represent a distinct lineage of Z. mobilis.

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RJR Experience and Expertise

Researcher

Robbins holds BS, MS, and PhD degrees in the life sciences. He served as a tenured faculty member in the Zoology and Biological Science departments at Michigan State University. He is currently exploring the intersection between genomics, microbial ecology, and biodiversity — an area that promises to transform our understanding of the biosphere.

Educator

Robbins has extensive experience in college-level education: At MSU he taught introductory biology, genetics, and population genetics. At JHU, he was an instructor for a special course on biological database design. At FHCRC, he team-taught a graduate-level course on the history of genetics. At Bellevue College he taught medical informatics.

Administrator

Robbins has been involved in science administration at both the federal and the institutional levels. At NSF he was a program officer for database activities in the life sciences, at DOE he was a program officer for information infrastructure in the human genome project. At the Fred Hutchinson Cancer Research Center, he served as a vice president for fifteen years.

Technologist

Robbins has been involved with information technology since writing his first Fortran program as a college student. At NSF he was the first program officer for database activities in the life sciences. At JHU he held an appointment in the CS department and served as director of the informatics core for the Genome Data Base. At the FHCRC he was VP for Information Technology.

Publisher

While still at Michigan State, Robbins started his first publishing venture, founding a small company that addressed the short-run publishing needs of instructors in very large undergraduate classes. For more than 20 years, Robbins has been operating The Electronic Scholarly Publishing Project, a web site dedicated to the digital publishing of critical works in science, especially classical genetics.

Speaker

Robbins is well-known for his speaking abilities and is often called upon to provide keynote or plenary addresses at international meetings. For example, in July, 2012, he gave a well-received keynote address at the Global Biodiversity Informatics Congress, sponsored by GBIF and held in Copenhagen. The slides from that talk can be seen HERE.

Facilitator

Robbins is a skilled meeting facilitator. He prefers a participatory approach, with part of the meeting involving dynamic breakout groups, created by the participants in real time: (1) individuals propose breakout groups; (2) everyone signs up for one (or more) groups; (3) the groups with the most interested parties then meet, with reports from each group presented and discussed in a subsequent plenary session.

Designer

Robbins has been engaged with photography and design since the 1960s, when he worked for a professional photography laboratory. He now prefers digital photography and tools for their precision and reproducibility. He designed his first web site more than 20 years ago and he personally designed and implemented this web site. He engages in graphic design as a hobby.

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Collection of publications by R J Robbins

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