@article {pmid31112880, year = {2019}, author = {Gopinath, D and Menon, RK and Banerjee, M and Su Yuxiong, R and Botelho, MG and Johnson, NW}, title = {Culture-independent studies on bacterial dysbiosis in oral and oropharyngeal squamous cell carcinoma: A systematic review.}, journal = {Critical reviews in oncology/hematology}, volume = {139}, number = {}, pages = {31-40}, doi = {10.1016/j.critrevonc.2019.04.018}, pmid = {31112880}, issn = {1879-0461}, abstract = {Imbalance within the resident bacterial community (dysbiosis), rather than the presence and activity of a single organism, has been proposed to be associated with, and to influence, the development and progression of various diseases; however, the existence and significance of dysbiosis in oral/oropharyngeal cancer is yet to be clearly established. A systematic search (conducted on 25/01/2018 and updated on 25/05/2018) was performed on three databases (Pubmed, Web of Science & Scopus) to identify studies employing culture-independent methods which investigated the bacterial community in oral/oropharyngeal cancer patients compared to control subjects. Of the 1546 texts screened, only fifteen publications met the pre-determined selection criteria. Data extracted from 731 cases and 809 controls overall, could not identify consistent enrichment of any particular taxon in oral/oropharyngeal cancers, although common taxa could be identified between studies. Six studies reported the enrichment of Fusobacteria in cancer at different taxonomic levels whereas four studies reported an increase in Parvimonas. Changes in microbial diversity remained inconclusive, with four studies showing a higher diversity in controls, three studies showing a higher diversity in tumors and three additional studies showing no difference between tumors and controls. Even though most studies identified a component of dysbiosis in oral/oropharyngeal cancer, methodological and analytical variations prevented a standardized summary, which highlights the necessity for studies of superior quality and magnitude employing standardized methodology and reporting. Indeed an holistic metagenomic approach is likely to be more meaningful, as is understanding of the overall metabolome, rather than a mere enumeration of the organisms present.}, }
@article {pmid31111267, year = {2019}, author = {Jadeja, NB and Purohit, HJ and Kapley, A}, title = {Decoding microbial community intelligence through metagenomics for efficient wastewater treatment.}, journal = {Functional & integrative genomics}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10142-019-00681-4}, pmid = {31111267}, issn = {1438-7948}, abstract = {Activated sludge, a microbial ecosystem at industrial wastewater treatment plants, is an active collection of diverse gene pool that creates the intelligence required for coexistence at the cost of pollutants. This study has analyzed one such ecosystem from a site treating wastewater pooled from over 200 different industries. The metagenomics approach used could predict the degradative pathways of more than 30 dominating molecules commonly found in wastewater. Results were extended to design a bioremediation strategy using 4-methylphenol, 2-chlorobenzoate, and 4-chlorobenzoate as target compounds. Catabolic potential required to degrade four aromatic families, namely benzoate family, PAH family, phenol family, and PCB family, was mapped. Results demonstrated a network of diverse genera, where a few phylotypes were seen to contain diverse catabolic capacities and were seen to be present in multiple networks. The study highlights the importance of looking more closely at the microbial community of activated sludge to harness its latent potential. Conventionally treated as a black box, the activated biomass does not perform at its full potential. Metagenomics allows a clearer insight into the complex pathways operating at the site and the detailed documentation of genes allows the activated biomass to be used as a bioresource.}, }
@article {pmid31110365, year = {2019}, author = {Low, SJ and Džunková, M and Chaumeil, PA and Parks, DH and Hugenholtz, P}, title = {Evaluation of a concatenated protein phylogeny for classification of tailed double-stranded DNA viruses belonging to the order Caudovirales.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41564-019-0448-z}, pmid = {31110365}, issn = {2058-5276}, abstract = {Viruses of bacteria and archaea are important players in global carbon cycling as well as drivers of host evolution, yet the taxonomic classification of viruses remains a challenge due to their genetic diversity and absence of universally conserved genes. Traditional classification approaches employ a combination of phenotypic and genetic information which is no longer scalable in the era of bulk viral genome recovery through metagenomics. Here, we evaluate a phylogenetic approach for the classification of tailed double-stranded DNA viruses from the order Caudovirales by inferring a phylogeny from the concatenation of 77 single-copy protein markers using a maximum-likelihood method. Our approach is largely consistent with the International Committee on Taxonomy of Viruses, with 72 and 89% congruence at the subfamily and genus levels, respectively. Discrepancies could be attributed to misclassifications and a small number of highly mosaic genera confounding the phylogenetic signal. We also show that confidently resolved nodes in the concatenated protein tree are highly reproducible across different software and models, and conclude that the approach can serve as a framework for a rank-normalized taxonomy of most tailed double-stranded DNA viruses.}, }
@article {pmid31110364, year = {2019}, author = {Diamond, S and Andeer, PF and Li, Z and Crits-Christoph, A and Burstein, D and Anantharaman, K and Lane, KR and Thomas, BC and Pan, C and Northen, TR and Banfield, JF}, title = {Mediterranean grassland soil C-N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41564-019-0449-y}, pmid = {31110364}, issn = {2058-5276}, abstract = {Soil microbial activity drives the carbon and nitrogen cycles and is an important determinant of atmospheric trace gas turnover, yet most soils are dominated by microorganisms with unknown metabolic capacities. Even Acidobacteria, among the most abundant bacteria in soil, remain poorly characterized, and functions across groups such as Verrucomicrobia, Gemmatimonadetes, Chloroflexi and Rokubacteria are understudied. Here, we have resolved 60 metagenomic and 20 proteomic data sets from a Mediterranean grassland soil ecosystem and recovered 793 near-complete microbial genomes from 18 phyla, representing around one-third of all microorganisms detected. Importantly, this enabled extensive genomics-based metabolic predictions for these communities. Acidobacteria from multiple previously unstudied classes have genomes that encode large enzyme complements for complex carbohydrate degradation. Alternatively, most microorganisms encode carbohydrate esterases that strip readily accessible methyl and acetyl groups from polymers like pectin and xylan, forming methanol and acetate, the availability of which could explain the high prevalence of C1 metabolism and acetate utilization in genomes. Microorganism abundances among samples collected at three soil depths and under natural and amended rainfall regimes indicate statistically higher associations of inorganic nitrogen metabolism and carbon degradation in deep and shallow soils, respectively. This partitioning decreased in samples under extended spring rainfall, indicating that long-term climate alteration can affect both carbon and nitrogen cycling. Overall, by leveraging natural and experimental gradients with genome-resolved metabolic profiles, we link microorganisms lacking prior genomic characterization to specific roles in complex carbon, C1, nitrate and ammonia transformations, and constrain factors that impact their distributions in soil.}, }
@article {pmid31109866, year = {2019}, author = {Chattopadhyay, I and Panda, M}, title = {Recent Trends of Saliva Omics Biomarkers for the Diagnosis and Treatment of Oral Cancer.}, journal = {Journal of oral biosciences}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.job.2019.03.002}, pmid = {31109866}, issn = {1880-3865}, abstract = {BACKGROUND: Recent advances in surgery, radiotherapy, and chemotherapy have no significant effect on oral cancer survival rates due to late diagnosis, poor tumor response to chemotherapy and radiotherapy, as well as a lack of effective biomarkers for early diagnosis.<br><br>HIGHLIGHTS: Therefore, an investigative study aimed at identifying genomics, proteomics, metagenomics, and, metabolomics derived biomarkers for early diagnosis may improve the survival rate of oral cancer patients. Identification and application of saliva-based ''omics'' biomarkers may overcome painful invasive procedures currently being used for the diagnosis of oral cancer. One single biomarker may not be able to differentiate between oral squamous cell carcinoma (OSCC) and controls. Thus, multiple sensitive and specific biomarkers may be needed for screening high-risk patients and following them up for early signs of OSCC occurrence. Validation of these biomarkers in large patient cohorts is, however, required before they can be used in clinical practice.<br><br>CONCLUSION: In this review, we summarize the potential of omics derived salivary biomarkers as diagnostic and prognostic tools in oral cancer detection and the future clinical benefits associated with these markers.}, }
@article {pmid31109865, year = {2019}, author = {Takahashi, Y and Park, J and Hosomi, K and Yamada, T and Kobayashi, A and Yamaguchi, Y and Iketani, S and Kunisawa, J and Mizuguchi, K and Nobuko, M and Ohshima, T}, title = {Analysis of oral microbiota in Japanese oral cancer patients using 16S rRNA sequencing.}, journal = {Journal of oral biosciences}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.job.2019.03.003}, pmid = {31109865}, issn = {1880-3865}, abstract = {OBJECTIVES: It is important to determine the cause of increasing oral cancer occurrence and mortality rates in Japan, because the mortality rate has recently decreased in other developed countries. The impact of microbiota in carcinogenesis, especially in the digestive tract has been reported. This study aimed to clarify the relationship between oral cancer and oral microbiota in Japanese patients.<br><br>METHODS: DNA was extracted from salivary samples of 60 oral cancer patients and 80 non-cancer individuals as controls. We performed metagenomic analysis using 16S rRNA amplicon sequencing. Statistical analysis in this study was performed using R (version 3.5.0).<br><br>RESULTS: Oral cancer patients showed higher α-diversity compared to the control group, and the β-diversity between the two groups differed significantly. Further, there was a significant difference in the abundance ratio of bacterial genera between the two groups. Peptostreptococcus, Fusobacterium, Alloprevotella, and Capnocytophaga were more abundant in the cancer group compared to the control, whereas Rothia and Haemophilus were less abundant (p < 0.01). A negative correlation in the microbiota composition was confirmed between the operational taxonomic units (OTU) of genus Rothia and T-stage progression using the TNM classification method. We performed logistic regression analysis to investigate the impact factor for the oral cancer group, and the result showed that Chao 1 index and sex are statistically significant variables.<br><br>CONCLUSIONS: In this study, we observed an increased bacterial diversity in oral cancer patients and found distribution changes for some bacteria.}, }
@article {pmid30449351, year = {2018}, author = {Amicucci, A and Barbieri, E and Sparvoli, V and Gioacchini, AM and Calcabrini, C and Palma, F and Stocchi, V and Zambonelli, A}, title = {Microbial and pigment profile of the reddish patch occurring within Tuber magnatum ascomata.}, journal = {Fungal biology}, volume = {122}, number = {12}, pages = {1134-1141}, doi = {10.1016/j.funbio.2018.07.007}, pmid = {30449351}, issn = {1878-6146}, mesh = {Ascomycota/*chemistry ; Bacteria/*classification/genetics/*isolation &amp; purification/metabolism ; Fruiting Bodies, Fungal/*chemistry ; Italy ; Metagenome ; Pigments, Biological/*analysis/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Tandem Mass Spectrometry ; }, abstract = {Tuber magnatum Pico, the delectable white truffle, is the most prized truffle species. In this study, we examined the reddish pigmentation that frequently occurs in T. magnatum ascomata for the presence of pigment-producing bacteria. The inner part of the reddish-pigmented region of three T. magnatum ascomata collected in North-Central Italy was analysed. This reddish part was used to establish a bacterial culture collection and to extract the total genomic DNA in order to obtain a library of 16S rRNA genes representative of the bacterial community. The molecular approach revealed limited microbial diversity within the reddish-pigmented regions compared to the wider range of bacterial species commonly found at the same maturation stage and season in T. magnatum ascomata. The pigmented regions showed a prevalence of specific bacterial species belonging to α-, β- and γ- Proteobacteria, Actinobacteria and Firmicutes. From the tandem mass spectrometry analysis of the extracted pigment, four compounds were identified: i) bixin, ii) β-carotene, iii) cis-1-glycosyl-apo-8'- lycopene and iv) the fucoxanthin. Carotenoid producing species such as Microbacterium and Chryseobacterium emerged as the most likely cause of the peculiar reddish pigment production. Indeed, our findings suggest that the peculiar reddish pigment might be produced by these bacterial species.}, }
@article {pmid29511332, year = {2018}, author = {}, title = {A different view of the environment.}, journal = {Nature nanotechnology}, volume = {13}, number = {3}, pages = {177}, doi = {10.1038/s41565-018-0106-2}, pmid = {29511332}, issn = {1748-3395}, mesh = {Animals ; Environment ; *Environmental Exposure/adverse effects ; Environmental Pollutants/chemistry/*metabolism/*toxicity ; Gold/chemistry/metabolism/toxicity ; Humans ; Metagenomics ; Nanoparticles/chemistry/metabolism/toxicity ; Nanostructures/chemistry/*toxicity ; Nanotechnology ; Waste Water/microbiology ; }, }
@article {pmid31108361, year = {2019}, author = {Regar, RK and Gaur, VK and Bajaj, A and Tambat, S and Manickam, N}, title = {Comparative microbiome analysis of two different long-term pesticide contaminated soils revealed the anthropogenic influence on functional potential of microbial communities.}, journal = {The Science of the total environment}, volume = {681}, number = {}, pages = {413-423}, doi = {10.1016/j.scitotenv.2019.05.090}, pmid = {31108361}, issn = {1879-1026}, abstract = {Microbial communities play a crucial role in bioremediation of pollutants in contaminated ecosystem. In addition to pure culture isolation and bacterial 16S rRNA based community studies, the focus has now shifted employing the omics technologies enormously for understanding the microbial diversity and functional potential of soil samples. Our previous report on two pesticide-contaminated sites revealed the diversity of both culturable and unculturable bacteria. In the present study, we have observed distinct taxonomic and functional communities in contaminated soil with respect to an uncontaminated soil as control by using shotgun metagenomic sequencing method. Our data demonstrated that Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, and Acidobacteria significantly dominated the microbial diversity with their cumulative abundance percentage in the range of 98.61, 87.38, and 80.52 for Hindustan Insecticides Limited (HIL), India Pesticides Limited (IPL), and control respectively. Functional gene analysis demonstrated the presence of large number of both substrate specific upper pathway and common lower pathway degradative genes. Relatively lower number of genes was found encoding the degradation of styrene, atrazine, bisphenol, dioxin, and naphthalene. When three bacteria were augumentated with rhamnolipid (20-100 μM) and Triton X-100 (84-417 μM) surfactants in HIL soil, an enhanced degradation to 76%, 70%, and 58% of HCH, Endosulfan, and DDT respectively was achieved. The overall data obtained from two heavily contaminated soil suggest the versatility of the microbial communities for the xenobiotic pollutant degradation which may help in exploiting their potential applications in bioremediation.}, }
@article {pmid31107955, year = {2019}, author = {Haston, JC and Rostad, CA and Jerris, RC and Milla, SS and McCracken, C and Pratt, C and Wiley, M and Prieto, K and Palacios, G and Shane, AL and McElroy, AK}, title = {Prospective Cohort Study of Next-Generation Sequencing as a Diagnostic Modality for Unexplained Encephalitis in Children.}, journal = {Journal of the Pediatric Infectious Diseases Society}, volume = {}, number = {}, pages = {}, doi = {10.1093/jpids/piz032}, pmid = {31107955}, issn = {2048-7207}, abstract = {BACKGROUND: Encephalitis is an inflammatory condition of the brain associated with long-term neurologic sequelae and even death in children. Although viruses are often implicated, an etiology is not identified in the majority of cases. Metagenomics-based next-generation sequencing (mNGS) is a high-throughput sequencing technique that can enhance the detection of novel or low-frequency pathogens.<br><br>METHODS: Hospitalized immunocompetent children aged 6 months to 18 years with encephalitis of unidentified etiology were eligible for enrollment. Demographic, historical, and clinical information was obtained, and residual blood and cerebrospinal fluid (CSF) samples were subjected to mNGS. Pathogens were identified by querying the sequence data against the NCBI GenBank database.<br><br>RESULTS: Twenty children were enrolled prospectively between 2013 and 2017. mNGS of CSF identified 7 nonhuman nucleic acid sequences of significant frequency in 6 patients, including that of Mycoplasma bovis, parvovirus B19, Neisseria meningitidis, and Balamuthia mandrillaris. mNGS also detected Cladophialophora species, tobacco mosaic virus, and human bocavirus, which were presumed to be contaminants or nonpathogenic organisms. One patient was found to have positive serology results for California encephalitis virus, but mNGS did not detect it. Patients for whom mNGS identified a diagnosis had a significantly higher CSF white blood cell count, a higher CSF protein concentration, and a lower CSF glucose level than patients for whom mNGS did not identify a diagnosis.<br><br>CONCLUSION: We describe here the results of a prospective cohort analysis to evaluate mNGS as a diagnostic tool for children with unexplained encephalitis. Although mNGS detected multiple nonpathogenic organisms, it also identified multiple pathogens successfully and was most useful in patients with a CSF abnormality.}, }
@article {pmid31107587, year = {2019}, author = {Poghosyan, L and Koch, H and Lavy, A and Frank, J and van Kessel, MAHJ and Jetten, MSM and Banfield, JF and Lücker, S}, title = {Metagenomic recovery of two distinct comammox Nitrospira from the terrestrial subsurface.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14691}, pmid = {31107587}, issn = {1462-2920}, abstract = {The recently discovered comammox process encompasses both nitrification steps, the aerobic oxidation of ammonia and nitrite, in a single organism. All known comammox bacteria are affiliated with Nitrospira sublineage II and can be grouped into two distinct clades, referred to as A and B, based on ammonia monooxygenase phylogeny. In this study, we report high-quality draft genomes of two novel comammox Nitrospira from the terrestrial subsurface, representing one clade A and one clade B comammox organism. The two metagenome-assembled genomes were compared to other representatives of Nitrospira sublineage II, including both canonical and comammox Nitrospira. Phylogenomic analyses confirmed the affiliation of the two novel Nitrospira with comammox clade A and B, respectively. Based on phylogenetic distance and pairwise average nucleotide identity values, both comammox Nitrospira were classified as novel species. Genomic comparison revealed high conservation of key metabolic features in sublineage II Nitrospira, including respiratory complexes I to V and the machineries for nitrite oxidation and carbon fixation via the reductive tricarboxylic acid cycle. In addition, the presence of the enzymatic repertoire for formate and hydrogen oxidation in the Rifle clade A and B comammox genomes, respectively, suggest a broader distribution of these metabolic features than previously anticipated. This article is protected by copyright. All rights reserved.}, }
@article {pmid31107251, year = {2019}, author = {Chong, PP and Atmar, RL}, title = {Norovirus in health care and implications for the immunocompromised host.}, journal = {Current opinion in infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1097/QCO.0000000000000557}, pmid = {31107251}, issn = {1473-6527}, abstract = {PURPOSE OF REVIEW: The majority of norovirus outbreaks in the United States occur in healthcare facilities. With the growing population of immunocompromised hosts who are in frequent contact with healthcare facilities, norovirus is not only a threat to hospitals and nursing homes but also to these individuals. This review summarizes the impact of norovirus infection on healthcare facilities and immunocompromised hosts.<br><br>RECENT FINDINGS: The natural history of norovirus infection in immunocompromised individuals remains poorly understood. Although host immune responses play a critical role in reducing duration of viral shedding and viral load in norovirus-infected individuals, why some immunocompromised patients spontaneously recover while others develop a chronic and protracted course of illness remains unclear. Norovirus outbreaks occur in healthcare facilities because the virus is highly contagious, resistant to disinfection and efficiently transmitted. The use of real-time metagenomic next-generation sequencing and phylogenetic analyses has provided valuable information on transmission patterns in complex hospital-associated norovirus outbreaks. The development of human intestinal enteroid cultures enables the determination of effectiveness of disinfectants against human noroviruses, circumventing the validity questions with surrogate virus models due to differences in susceptibility to inactivation and disinfectants.<br><br>SUMMARY: Metagenomics next-generation sequencing can enhance our understanding of norovirus transmission and lead to more timely mitigation strategies to curb norovirus outbreaks in healthcare facilities. With new in-vitro cultivation methods for human noroviruses, candidate vaccines and effective antivirals could be available in the near future.}, }
@article {pmid31107235, year = {2019}, author = {Fereidouni, S and Freimanis, GL and Orynbayev, M and Ribeca, P and Flannery, J and King, DP and Zuther, S and Beer, M and Höper, D and Kydyrmanov, A and Karamendin, K and Kock, R}, title = {Mass Die-Off of Saiga Antelopes, Kazakhstan, 2015.}, journal = {Emerging infectious diseases}, volume = {25}, number = {6}, pages = {1169-1176}, doi = {10.3201/eid2506.180990}, pmid = {31107235}, issn = {1080-6059}, abstract = {In 2015, a mass die-off of ≈200,000 saiga antelopes in central Kazakhstan was caused by hemorrhagic septicemia attributable to the bacterium Pasteurella multocida serotype B. Previous analyses have indicated that environmental triggers associated with weather conditions, specifically air moisture and temperature in the region of the saiga antelope calving during the 10-day period running up to the event, were critical to the proliferation of latent bacteria and were comparable to conditions accompanying historically similar die-offs in the same areas. We investigated whether additional viral or bacterial pathogens could be detected in samples from affected animals using 3 different high-throughput sequencing approaches. We did not identify pathogens associated with commensal bacterial opportunisms in blood, kidney, or lung samples and thus concluded that P. multocida serotype B was the primary cause of the disease.}, }
@article {pmid31105659, year = {2019}, author = {Fuertes, A and Pérez-Burillo, S and Apaolaza, I and Vallès, Y and Francino, MP and Rufián-Henares, JÁ and Planes, FJ}, title = {Adaptation of the Human Gut Microbiota Metabolic Network During the First Year After Birth.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {848}, doi = {10.3389/fmicb.2019.00848}, pmid = {31105659}, issn = {1664-302X}, abstract = {Predicting the metabolic behavior of the human gut microbiota in different contexts is one of the most promising areas of constraint-based modeling. Recently, we presented a supra-organismal approach to build context-specific metabolic networks of bacterial communities using functional and taxonomic assignments of meta-omics data. In this work, this algorithm is applied to elucidate the metabolic changes induced over the first year after birth in the gut microbiota of a cohort of Spanish infants. We used metagenomics data of fecal samples and nutritional data of 13 infants at five time points. The resulting networks for each time point were analyzed, finding significant alterations once solid food is introduced in the diet. Our work shows that solid food leads to a different pattern of output metabolites that can be potentially released from the gut microbiota to the host. Experimental validation is presented for ferulate, a neuroprotective metabolite involved in the gut-brain axis.}, }
@article {pmid30628657, year = {2019}, author = {Chen, L and Li, H and Li, J and Chen, Y and Yang, Y}, title = {Lactobacillus rhamnosus GG treatment improves intestinal permeability and modulates microbiota dysbiosis in an experimental model of sepsis.}, journal = {International journal of molecular medicine}, volume = {43}, number = {3}, pages = {1139-1148}, doi = {10.3892/ijmm.2019.4050}, pmid = {30628657}, issn = {1791-244X}, mesh = {Animals ; Apoptosis ; Biomarkers ; Cell Proliferation ; Colon/metabolism/microbiology/pathology ; Disease Models, Animal ; *Dysbiosis ; *Gastrointestinal Microbiome ; Lactobacillus rhamnosus/*physiology ; Male ; Metagenome ; Metagenomics/methods ; Mice ; Mortality ; Permeability ; Phylogeny ; Probiotics/*administration &amp; dosage ; RNA, Ribosomal, 16S/genetics ; Sepsis/diagnosis/*metabolism/*microbiology/therapy ; }, abstract = {Decrease of 'health‑benefiting' microbes and increase of pathogenic bacteria (a condition termed dysbiosis) in intensive care unit patients is considered to induce or aggravate sepsis (gut‑origin sepsis). Orally administered probiotics have been effective in the prevention of nosocomial infections. However, the mechanisms of probiotic‑induced anti‑infection and anti‑sepsis remain to be explored. In the present study, 4‑week‑old C57BL6 mice were orally administrated with Lactobacillus rhamnosus GG (LGG) or normal saline (control) 4 weeks prior to cecal ligation and puncture (CLP). A subset of the mice were sacrificed at 24 h post‑CLP, and the others were used for survival studies. Ileum tissues, blood and fecal samples were collected. The survival rate of septic mice pretreated with LGG was significantly improved compared with untreated mice. The levels of inflammatory cytokines were reduced in LGG‑pretreated septic mice. A decrease of colonic proliferation and epithelial tight junctions and an increase of colonic apoptosis were observed in control septic CLP+saline mice. LGG pretreatment reversed the colonic proliferation, apoptosis and expression of tight junction proteins to the levels of the sham group. LGG pretreatment improved the richness and diversity of intestinal microbiota in septic mice. The principal coordinates analysis clustering plots revealed a significant separate clustering in microbiota structure between three groups. Bacteria associated with energy consumption, including Bacteroidetes, with opportunistic infection, including Proteobacteria, Staphylococcaceae and Enterococcaceae, lipopolysaccharide producers, including Enterobacteriaceae, and facultative anaerobes, such as Bacteroidaceae and Erysipelotrichaceae, increased in septic mice. By contrast, bacteria associated with energy harvest, including Firmicutes, intestinal barrier function regulators, including Akkermansia, hepatic function regulators, including Coprococcus and Oscillospira, and obligate anaerobes, including Prevotellaceae, decreased in septic mice. With LGG pretreatment, the sepsis‑induced microbiota dysbiosis was reversed. The present results elucidated the potential mechanism of LGG treatment in sepsis, by improving intestinal permeability and modulating microbiota dysbiosis.}, }
@article {pmid30596703, year = {2018}, author = {Quinn, O and Gruber, MAM and Brown, RL and Baty, JW and Bulgarella, M and Lester, PJ}, title = {A metatranscriptomic analysis of diseased social wasps (Vespula vulgaris) for pathogens, with an experimental infection of larvae and nests.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0209589}, doi = {10.1371/journal.pone.0209589}, pmid = {30596703}, issn = {1932-6203}, mesh = {Animals ; Gene Expression Profiling/methods ; *Host-Pathogen Interactions ; Larva/microbiology ; *Metagenome ; *Metagenomics ; *Microbiota ; Phylogeny ; Wasps/*microbiology/ultrastructure ; }, abstract = {Social wasps are a major pest in many countries around the world. Pathogens may influence wasp populations and could provide an option for population management via biological control. We investigated the pathology of nests of apparently healthy common wasps, Vespula vulgaris, with nests apparently suffering disease. First, next-generation sequencing and metatranscriptomic analysis were used to examine pathogen presence. The transcriptome of healthy and diseased V. vulgaris showed 27 known microbial phylotypes. Four of these were observed in diseased larvae alone (Aspergillus fumigatus, Moellerella wisconsensis, Moku virus, and the microsporidian Vavraia culicis). Kashmir Bee Virus (KBV) was found to be present in both healthy and diseased larvae. Moellerella wisconsensis is a human pathogen that was potentially misidentified in our wasps by the MEGAN analysis: it is more likely to be the related bacteria Hafnia alvei that is known to infect social insects. The closest identification to the putative pathogen identified as Vavraia culicis was likely to be another microsporidian Nosema vulgaris. PCR and subsequent Sanger sequencing using published or our own designed primers, confirmed the identity of Moellerella sp. (which may be Hafnia alvei), Aspergillus sp., KBV, Moku virus and Nosema. Secondly, we used an infection study by homogenising diseased wasp larvae and feeding them to entire nests of larvae in the laboratory. Three nests transinfected with diseased larvae all died within 19 days. No pathogen that we monitored, however, had a significantly higher prevalence in diseased than in healthy larvae. RT-qPCR analysis indicated that pathogen infections were significantly correlated, such as between KBV and Aspergillus sp. Social wasps clearly suffer from an array of pathogens, which may lead to the collapse of nests and larval death.}, }
@article {pmid29808965, year = {2019}, author = {Grönroos, M and Parajuli, A and Laitinen, OH and Roslund, MI and Vari, HK and Hyöty, H and Puhakka, R and Sinkkonen, A}, title = {Short-term direct contact with soil and plant materials leads to an immediate increase in diversity of skin microbiota.}, journal = {MicrobiologyOpen}, volume = {8}, number = {3}, pages = {e00645}, doi = {10.1002/mbo3.645}, pmid = {29808965}, issn = {2045-8827}, mesh = {Bacteria/*classification/*genetics ; *Environmental Exposure ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; *Microbiota ; Plants ; Skin/*microbiology ; Soil ; }, abstract = {Immune-mediated diseases have increased during the last decades in urban environments. The hygiene hypothesis suggests that increased hygiene level and reduced contacts with natural biodiversity are related to the increase in immune-mediated diseases. We tested whether short-time contact with microbiologically diverse nature-based materials immediately change bacterial diversity on human skin. We tested direct skin contact, as two volunteers rubbed their hands with sixteen soil and plant based materials, and an exposure via fabric packets filled with moss material. Skin swabs were taken before and after both exposures. Next-generation sequencing showed that exposures increased, at least temporarily, the total diversity of skin microbiota and the diversity of Acidobacteria, Actinobacteria, Bacteroidetes, Proteobacteria and Alpha-, Beta- and Gammaproteobacteria suggesting that contact with nature-based materials modify skin microbiome and increase skin microbial diversity. Until now, approaches to cure or prevent immune system disorders using microbe-based treatments have been limited to use of a few microbial species. We propose that nature-based materials with high natural diversity, such as the materials tested here, might be more effective in modifying human skin microbiome, and eventually, in reducing immune system disorders. Future studies should investigate how long-term changes in skin microbiota are achieved and if the exposure induces beneficial changes in the immune system markers.}, }
@article {pmid28883460, year = {2017}, author = {Bridgewater, LC and Zhang, C and Wu, Y and Hu, W and Zhang, Q and Wang, J and Li, S and Zhao, L}, title = {Gender-based differences in host behavior and gut microbiota composition in response to high fat diet and stress in a mouse model.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {10776}, pmid = {28883460}, issn = {2045-2322}, mesh = {Animals ; *Behavior, Animal ; Computational Biology/methods ; *Diet, High-Fat ; Female ; *Gastrointestinal Microbiome ; Male ; Metagenome ; Metagenomics/methods ; Mice ; Sex Factors ; *Stress, Physiological ; }, abstract = {Obesity is associated with a high prevalence of mood disorders such as anxiety and depression. Both stress and high fat diet can alter the gut microbiota and contribute to obesity. To examine the interrelationships between obesity, stress, gut microbiota and mood disorders, obesity was induced in mice using a high fat diet, and the mice were subsequently stressed using a chronic unpredictable mild stress protocol. During the experiment, the composition of the gut microbiota was analyzed by 16 S rRNA gene high-throughput sequencing, and anxiety-like behaviors were measured. The results revealed distinct gender differences in the impacts of obesity and stress on anxiety-like behaviors, activity levels, and composition of the gut microbiota. Male mice were more vulnerable to the anxiogenic effects of the high fat diet, and obese male mice showed decreased locomotion activity in response to stress whereas obese female mice did not. In females, stress caused the gut microbiota of lean mice to more closely resemble that of obese mice. Taken together, these results suggest the importance of considering gender as a biological variable in studies on the role of gut microbiota in obesity-related mood disorders.}, }
@article {pmid31104215, year = {2019}, author = {Li, P and Wu, H and Jin, Y and Huang, X and Chen, Y and Yang, X and Wang, R and Zhang, W}, title = {Exploring the diversity and dynamic of bacterial community vertically distributed in Tongguling National Nature Reserve in Hainan Island, China.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, doi = {10.1007/s42770-019-00078-2}, pmid = {31104215}, issn = {1678-4405}, abstract = {National nature reserves are important for preserving ecological resources and constructing national ecological security barriers. Tongguling National Nature Reserve (TNNR) is known for its unique tropical island ecosystem and abundant biological resources. This study was conducted to characterize and compare its bacterial community diversity and composition in soils from 10, 20, and 30 cm in depth using high-throughput sequencing of 16S rDNA genes. We found that soils from 20 cm had the highest diversity and might serve as a &quot;middle bridge&quot; to the dynamic distribution between the 10- and 30-cm soil samples. The diversity pattern indicated that the main abundant groups varied distinctly and significantly among soils of different depths. Moreover, Chloroflexi was the most dynamic group in TNNR soils, together with another abundant but rarely reported group, Verrucomicrobia, which greatly enhanced the microbial diversity of TNNR soils. Overall, the results of this study emphasize the urgent need for greater understanding of bacterial community variations in response to human activities and climate change.}, }
@article {pmid31103724, year = {2019}, author = {Scherler, A and Ardissone, S and Moran-Gilad, J and Greub, G}, title = {ESCMID/ESGMD postgraduate technical workshop on diagnostic microbiology.}, journal = {Microbes and infection}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.micinf.2019.04.006}, pmid = {31103724}, issn = {1769-714X}, abstract = {The European Society of Clinical Microbiology and Infectious Diseases (ESCMID) workshop on diagnostic microbiology was held in Lausanne from 25th to 28th September 2018. A total of 87 participants from 31 countries participated to this postgraduate technical workshop. Over 4 days, the mornings were dedicated to talks, which covered many subjects including MALDI-TOF, molecular diagnosis, genomics and metagenomics as well as new innovative approaches. The afternoons were dedicated to 12 different practicals covering various aspects of microbiological diagnosis. This ESCMID meeting provided a unique opportunity to exchange knowledge and ideas on the recent tools developed in diagnostic laboratories. This meeting report summarises the key messages of this four-day workshop.}, }
@article {pmid31102963, year = {2019}, author = {Liu, S and Chen, Q and Zou, H and Yu, Y and Zhou, Z and Mao, J and Zhang, S}, title = {A metagenomic analysis of the relationship between microorganisms and flavor development in Shaoxing mechanized huangjiu fermentation mashes.}, journal = {International journal of food microbiology}, volume = {303}, number = {}, pages = {9-18}, doi = {10.1016/j.ijfoodmicro.2019.05.001}, pmid = {31102963}, issn = {1879-3460}, abstract = {Complex microbial metabolism is responsible for the unique flavor of Shaoxing mechanized huangjiu. However, the relationship between the microorganisms present during fermentation and the formation of specific flavor components is difficult to understand. In this study, gas chromatography-mass spectrometry and high-performance liquid chromatography were used to identify flavor components, and a metagenomic sequencing approach was used to characterize the taxonomic and functional attributes of the Shaoxing mechanized huangjiu fermentation microbiota. The metagenomic sequencing data were used to predict the relationship between microorganisms and flavor formation. The chromatographic analysis identified amino acids, alcohols, acids, phenols and esters as major flavor components, and six microbial genera (Saccharomyces, Aspergillus, Saccharopolyspora, Staphylococcus, Lactobacillus, and Lactococcus) were most closely related to the production of these flavor components. This study helps clarify the different metabolic roles of microorganisms in flavor formation during Shaoxing huangjiu fermentation.}, }
@article {pmid31102141, year = {2019}, author = {Sahoo, K and Sahoo, RK and Gaur, M and Subudhi, E}, title = {Cellulolytic thermophilic microorganisms in white biotechnology: a review.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, doi = {10.1007/s12223-019-00710-6}, pmid = {31102141}, issn = {1874-9356}, support = {YSS/2014/000413//Science and Engineering Research Board/ ; }, abstract = {Enzymes of microbial origin are of immense importance for organic material decomposition leading to bioremediation of organic waste, bioenergy generation, large-scale industrial bioprocesses, etc. The market demand for microbial cellulase enzyme is growing more rapidly which ultimately becomes the driving force towards research on this biocatalyst, widely used in various industrial activities. The use of novel cellulase genes obtained from various thermophiles through metagenomics and genetic engineering as well as following metabolic engineering pathways would be able to enhance the production of thermophilic cellulase at industrial scale. The present review is mainly focused on thermophilic cellulolytic bacteria, discoveries on cellulase gene, genetically modified cellulase, metabolic engineering, and their various industrial applications. A lot of lacunae are yet to overcome for thermophiles such as metagenome analysis, metabolic pathway modification study, search of heterologous hosts in gene expression system, and improved recombinant strain for better cellulase yield as well as value-added product formation.}, }
@article {pmid31102076, year = {2019}, author = {Wu, S and Nan, F and Jiang, J and Qiu, J and Zhang, Y and Qiao, B and Li, S and Xin, Z}, title = {Molecular cloning, expression and characterization of a novel feruloyl esterase from a soil metagenomic library with phthalate-degrading activity.}, journal = {Biotechnology letters}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10529-019-02693-3}, pmid = {31102076}, issn = {1573-6776}, support = {KYYJ201708//the Fundamental Research Funds for the Central Universities/ ; }, abstract = {OBJECTIVES: To discover novel feruloyl esterases (FAEs) by the function-driven screening procedure from soil metagenome.<br><br>RESULTS: A novel FAE gene bds4 was isolated from a soil metagenomic library and over-expressed in Escherichia coli. The recombinant enzyme BDS4 was purified to homogeneity with a predicted molecular weight of 38.8 kDa. BDS4 exhibited strong activity (57.05 U/mg) toward methyl ferulate under the optimum pH and temperature of 8.0 and 37°C. Based on its amino acid sequence and model substrates specificity, BDS4 was classified as a type-C FAE. The quantity of the releasing ferulic acid can be enhanced significantly in the presence of xylanase compared with BDS4 alone from de-starched wheat bran. In addition, BDS4 can also hydrolyze several phthalates such as diethyl phthalate, dimethyl phthalate and dibutyl phthalate.<br><br>CONCLUSION: The current investigation discovered a novel FAE with phthalate-degrading activity and highlighted the usefulness of metagenomic approaches as a powerful tool for discovery of novel FAEs.}, }
@article {pmid31101866, year = {2019}, author = {Cho, EJ and Leem, S and Kim, SA and Yang, J and Lee, YB and Kim, SS and Cheong, JY and Cho, SW and Kim, JW and Kim, SM and Yoon, JH and Park, T}, title = {Circulating Microbiota-Based Metagenomic Signature for Detection of Hepatocellular Carcinoma.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {7536}, doi = {10.1038/s41598-019-44012-w}, pmid = {31101866}, issn = {2045-2322}, support = {HI16C2037//Korea Health Industry Development Institute (KHIDI)/ ; NRF-2017R1D1A1B03034639//National Research Foundation of Korea (NRF)/ ; 04-2017-0640//Seoul National University Hospital (SNUH)/ ; }, abstract = {Circulating microbial dysbiosis is associated with chronic liver disease including nonalcoholic steatohepatitis and alcoholic liver disease. In this study, we evaluated whether disease-specific alterations of circulating microbiome are present in patients with cirrhosis and hepatocellular carcinoma (HCC), and their potential as diagnostic biomarkers for HCC. We performed cross-sectional metagenomic analyses of serum samples from 79 patients with HCC, 83 with cirrhosis, and 201 matching healthy controls, and validated the results in the same number of subjects. Serum bacterial DNA was analyzed using high-throughput pyrosequencing after amplification of the V3-V4 hypervariable regions of 16S rDNA. Blood microbial diversity was significantly reduced in HCC, compared with cirrhosis and control. There were significant differences in the relative abundances of several bacterial taxa that correlate with the presence of HCC, thus defining a specific blood microbiome-derived metagenomic signature of HCC. We identified 5 microbial gene markers-based model which distinguished HCC from controls with an area under the receiver-operating curve (AUC) of 0.879 and a balanced accuracy of 81.6%. In the validation, this model accurately distinguished HCC with an AUC of 0.875 and an accuracy of 79.8%. In conclusion, circulating microbiome-based signatures may be potential biomarkers for the detection HCC.}, }
@article {pmid31101811, year = {2019}, author = {Sande, CJ and Njunge, JM and Mwongeli Ngoi, J and Mutunga, MN and Chege, T and Gicheru, ET and Gardiner, EM and Gwela, A and Green, CA and Drysdale, SB and Berkley, JA and Nokes, J and Pollard, AJ}, title = {Airway response to respiratory syncytial virus has incidental antibacterial effects.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {2218}, doi = {10.1038/s41467-019-10222-z}, pmid = {31101811}, issn = {2041-1723}, support = {WT105882MA//Wellcome Trust (Wellcome)/ ; }, abstract = {RSV infection is typically associated with secondary bacterial infection. We hypothesise that the local airway immune response to RSV has incidental antibacterial effects. Using coordinated proteomics and metagenomics analysis we simultaneously analysed the microbiota and proteomes of the upper airway and determined direct antibacterial activity in airway secretions of RSV-infected children. Here, we report that the airway abundance of Streptococcus was higher in samples collected at the time of RSV infection compared with samples collected one month later. RSV infection is associated with neutrophil influx into the airway and degranulation and is marked by overexpression of proteins with known antibacterial activity including BPI, EPX, MPO and AZU1. Airway secretions of children infected with RSV, have significantly greater antibacterial activity compared to RSV-negative controls. This RSV-associated, neutrophil-mediated antibacterial response in the airway appears to act as a regulatory mechanism that modulates bacterial growth in the airways of RSV-infected children.}, }
@article {pmid31101528, year = {2019}, author = {Hagihara, M and Yamashita, R and Matsumoto, A and Mori, T and Inagaki, T and Nonogaki, T and Kuroki, Y and Higashi, S and Oka, K and Takahashi, M and Mikamo, H}, title = {The impact of probiotic Clostridium butyricum MIYAIRI 588 on murine gut metabolic alterations.}, journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jiac.2019.02.008}, pmid = {31101528}, issn = {1437-7780}, abstract = {INTRODUCTION: Clostridium butyricum MIYAIRI 588 (CBM 588) is a probiotic bacterium used in antidiarrheal medicine in Japan. A few studies analyzed the changes in gut microbiome in patients treated with antimicrobials based on metagenomics sequencing. However, the impact of CBM 588 on gut metabolic alterations has not been fully elucidated. This study was to reveal the impact of CBM 588 on gut metabolic alterations.<br><br>MATERIAL AND METHODS: In this in vivo study, mice were divided into four groups and CBM 588, clindamycin (CLDM), and normal saline (control) was orally administered (1. CLDM, 2. CBM 588, 3. CBM 588 + CLDM, 4. water) for 4 days. Fecal samples were collected to extract DNA for metagenomics analysis. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was used to obtain relative Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway abundance information derived from metagenomics data.<br><br>RESULTS: CLDM treatment resulted in a dramatic increase in Firmicutes phylum compared to non-CLDM-treated groups (control and CBM 588-treated group). Then, the CBM 588 + CLDM-treated group showed a trend similar in many metabolic pathways to the CLDM-treated group. On the other hand, the CBM 588 + CLDM-treated group showed higher relative abundance compared to the CLDM-treated group especially in starch and sucrose metabolism.<br><br>DISCUSSION: We concluded that CBM 588 caused a gut microbiome functional shift toward increased carbohydrate metabolism. These results support the hypothesis that CBM 588 treatment modulates gut microbiome under dysbiosis conditions due to antimicrobials.}, }
@article {pmid31100994, year = {2019}, author = {Zhang, YZ and Chen, YM and Wang, W and Qin, XC and Holmes, EC}, title = {Expanding the RNA Virosphere by Unbiased Metagenomics.}, journal = {Annual review of virology}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-virology-092818-015851}, pmid = {31100994}, issn = {2327-0578}, abstract = {Although viruses comprise the most abundant genetic material in the biosphere, to date only several thousand virus species have been formally defined. Such a limited perspective on virus diversity has in part arisen because viruses were traditionally considered only as etiologic agents of overt disease in humans or economically important species and were often difficult to identify using cell culture. This view has dramatically changed with the rise of metagenomics, which is transforming virus discovery and revealing a remarkable diversity of viruses sampled from diverse cellular organisms. These newly discovered viruses help fill major gaps in the evolutionary history of viruses, revealing a near continuum of diversity among genera, families, and even orders of RNA viruses. Herein, we review some of the recent advances in our understanding of the RNA virosphere that have stemmed from metagenomics, note future directions, and highlight some of the remaining challenges to this rapidly developing field. Expected final online publication date for the Annual Review of Virology Volume 6 is September 30, 2019. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.}, }
@article {pmid31100923, year = {2019}, author = {Di Pietro, M and Filardo, S and Romano, S and Sessa, R}, title = {Chlamydia trachomatis and Chlamydia pneumoniae Interaction with the Host: Latest Advances and Future Prospective.}, journal = {Microorganisms}, volume = {7}, number = {5}, pages = {}, doi = {10.3390/microorganisms7050140}, pmid = {31100923}, issn = {2076-2607}, abstract = {Research in Chlamydia trachomatis and Chlamydia pneumoniae has gained new traction due to recent advances in molecular biology, namely the widespread use of the metagenomic analysis and the development of a stable genomic transformation system, resulting in a better understanding of Chlamydia pathogenesis. C. trachomatis, the leading cause of bacterial sexually transmitted diseases, is responsible of cervicitis and urethritis, and C. pneumoniae, a widespread respiratory pathogen, has long been associated with several chronic inflammatory diseases with great impact on public health. The present review summarizes the current evidence regarding the complex interplay between C. trachomatis and host defense factors in the genital micro-environment as well as the key findings in chronic inflammatory diseases associated to C. pneumoniae.}, }
@article {pmid31100576, year = {2019}, author = {Tao, Y and Huang, X and Gao, D and Wang, X and Chen, C and Liang, H and van Loosdrecht, MCM}, title = {NanoSIMS reveals unusual enrichment of acetate and propionate by an anammox consortium dominated by Jettenia asiatica.}, journal = {Water research}, volume = {159}, number = {}, pages = {223-232}, doi = {10.1016/j.watres.2019.05.006}, pmid = {31100576}, issn = {1879-2448}, abstract = {Anaerobic ammonium-oxidizing (anammox) bacteria convert ammonium and nitrite into N2 in a chemolithoautotrophic way, meaning that they utilize CO2/HCO3 solely as their carbon sources. Such autotrophic behavior limits their competitiveness with heterotrophic microorganisms in both natural environments and engineered systems. Recently, environmental metagenomic results have indicated the capability of anammox bacteria to metabolize short-chain fatty acids, further confirmed by limited experimental evidence based on highly enriched cultures. However, clear evidence is difficult to get because of the limits of traditional methodologies which rely on the availability of a pure anammox culture. In this study, we identified and quantified the uptake of acetate and propionate, on a single-cell level, by an anammox consortium that was dominated by Candidatus Jettenia asiatica (relative abundance of 96%). The consortium, growing in granular form with an average relative abundance of anammox bacteria of 96.0%, was firstly incubated in a13C-labelled acetate or propionate medium; then microtome sections were scanned by a nanometer-scale secondary ion mass spectrometer (NanoSIMS). The NanoSIMS scannings revealed that the consortium enriched acetate and propionate at a >10 times higher efficiency than bicarbonate incorporation. Our results also suggest that acetate or propionate was likely not assimilated by J. asiatica directly, but firstly oxidized to CO2, which then served as carbon sources for the follow-up autotrophy in J. asiatica cells. Furthermore, more [15N]ammonium was enriched by the propionate-fed consortium than the acetate-fed consortium despite that exactly the same amount of 13C atoms were supplied. Our study strongly indicates an alternative lifestyle, namely organotrophy, in addition to chemolithoautotrophy of anammox bacteria, making it more versatile than often expected. It suggests that the niche of anammox bacteria in both natural and engineered ecosystems can be much broader than usual assumed. Recognising this is important for their role in wastewater treatment and the global nitrogen turn-over rates.}, }
@article {pmid31100040, year = {2019}, author = {Ramadan, M and Solyman, S and Yones, M and Abdallah, Y and Halaby, H and Hanora, A}, title = {Skin Microbiome Differences in Atopic Dermatitis and Healthy Controls in Egyptian Children and Adults, and Association with Serum Immunoglobulin E.}, journal = {Omics : a journal of integrative biology}, volume = {23}, number = {5}, pages = {247-260}, doi = {10.1089/omi.2019.0011}, pmid = {31100040}, issn = {1557-8100}, abstract = {Atopic dermatitis (AD) is a complex, multifactorial, chronic pruritic inflammatory skin disease. We report the first microbiome study and new insights on the relationship between skin microbiota variation and AD susceptibility in a population sample from Egypt. We characterized the skin microbiome in 75 patients with AD and 20 healthy controls using Illumina MiSeq sequencing of 16S rRNA gene. Overall, bacterial diversity of skin microbiome in patients with AD was less than those of the healthy subjects. Genus level analysis revealed significant abundance variations by age, disease severity, locality, or immune response. Among these genera, Streptococcus, Cutibacterium, and Corynebacterium appeared to be specific signatures for AD in children, adolescents, and adults, respectively, while Staphylococcus was noted as a potential biomarker candidate for AD. Additionally, functional potential of metagenomes shifted the overall metabolic pathways to participate in the exacerbation of disease. Total immunoglobulin E (IgE) levels were positively correlated with relative enrichment of certain Staphylococcus aureus subspecies. Finally, AD-related differences in skin bacterial diversity appeared to be in part linked to the serum IgE level. These new observations attest to the promise of microbiome science and metagenomic analysis in AD specifically, and clinical dermatology broadly.}, }
@article {pmid31098412, year = {2019}, author = {Sato, Y and Hori, T and Koike, H and Navarro, RR and Ogata, A and Habe, H}, title = {Transcriptome analysis of activated sludge microbiomes reveals an unexpected role of minority nitrifiers in carbon metabolism.}, journal = {Communications biology}, volume = {2}, number = {}, pages = {179}, doi = {10.1038/s42003-019-0418-2}, pmid = {31098412}, issn = {2399-3642}, abstract = {Although metagenomics researches have illuminated microbial diversity in numerous biospheres, understanding individual microbial functions is yet difficult due to the complexity of ecosystems. To address this issue, we applied a metagenome-independent, de novo assembly-based metatranscriptomics to a complex microbiome, activated sludge, which has been used for wastewater treatment for over a century. Even though two bioreactors were operated under the same conditions, their performances differed from each other with unknown causes. Metatranscriptome profiles in high- and low-performance reactors demonstrated that denitrifiers contributed to the anaerobic degradation of heavy oil; however, no marked difference in the gene expression was found. Instead, gene expression-based nitrification activities that fueled the denitrifiers by providing the respiratory substrate were notably high in the high-performance reactor only. Nitrifiers-small minorities with relative abundances of <0.25%-governed the heavy-oil degradation performances of the reactors, unveiling an unexpected linkage of carbon- and nitrogen-metabolisms of the complex microbiome.}, }
@article {pmid31098399, year = {2019}, author = {Armour, CR and Nayfach, S and Pollard, KS and Sharpton, TJ}, title = {A Metagenomic Meta-analysis Reveals Functional Signatures of Health and Disease in the Human Gut Microbiome.}, journal = {mSystems}, volume = {4}, number = {4}, pages = {}, doi = {10.1128/mSystems.00332-18}, pmid = {31098399}, issn = {2379-5077}, abstract = {While recent research indicates that human health is affected by the gut microbiome, the functional mechanisms that underlie host-microbiome interactions remain poorly resolved. Metagenomic clinical studies can address this problem by revealing specific microbial functions that stratify healthy and diseased individuals. To improve our understanding of the relationship between the gut microbiome and health, we conducted the first integrative functional analysis of nearly 2,000 publicly available fecal metagenomic samples obtained from eight clinical studies. We identified characteristics of the gut microbiome that associate generally with disease, including functional alpha-diversity, beta-diversity, and beta-dispersion. Using regression modeling, we identified specific microbial functions that robustly stratify diseased individuals from healthy controls. Many of these functions overlapped multiple diseases, suggesting a general role in host health, while others were specific to a single disease and may indicate disease-specific etiologies. Our results clarify potential microbiome-mediated mechanisms of disease and reveal features of the microbiome that may be useful for the development of microbiome-based diagnostics. IMPORTANCE The composition of the gut microbiome associates with a wide range of human diseases, but the mechanisms underpinning these associations are not well understood. To shift toward a mechanistic understanding, we integrated distinct metagenomic data sets to identify functions encoded in the gut microbiome that associate with multiple diseases, which may be important to human health. Additionally, we identified functions that associate with specific diseases, which may elucidate disease-specific etiologies. We demonstrated that the functions encoded in the microbiome can be used to classify disease status, but the inclusion of additional patient covariates may be necessary to obtain sufficient accuracy. Ultimately, this analysis advances our understanding of the gut microbiome functions that constitute a healthy microbiome and identifies potential targets for microbiome-based diagnostics and therapeutics.}, }
@article {pmid31097033, year = {2019}, author = {Lugli, GA and Milani, C and Duranti, S and Alessandri, G and Turroni, F and Mancabelli, L and Tatoni, D and Ossiprandi, MC and van Sinderen, D and Ventura, M}, title = {Isolation of novel gut bifidobacteria using a combination of metagenomic and cultivation approaches.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {96}, doi = {10.1186/s13059-019-1711-6}, pmid = {31097033}, issn = {1474-760X}, support = {15/JP-HDHL/3280//Science Foundation Ireland/Ireland ; SFI/12/RC/2273//Science Foundation Ireland/Ireland ; }, abstract = {Whole metagenome shotgun (WMGS) sequencing is a method that provides insights into the genomic composition and arrangement of complex microbial consortia. Here, we report how WMGS coupled with a cultivation approach allows the isolation of novel bifidobacteria from animal fecal samples. A combination of in silico analyses based on nucleotide and protein sequences facilitate the identification of genetic material belonging to putative novel species. Consequently, the prediction of metabolic properties by in silico analyses permits the identification of specific substrates that are then employed to isolate these species through a cultivation method.}, }
@article {pmid31097029, year = {2019}, author = {Altan, E and Kubiski, SV and Burchell, J and Bicknese, E and Deng, X and Delwart, E}, title = {The first reptilian circovirus identified infects gut and liver tissues of black-headed pythons.}, journal = {Veterinary research}, volume = {50}, number = {1}, pages = {35}, doi = {10.1186/s13567-019-0653-z}, pmid = {31097029}, issn = {1297-9716}, support = {5419.18//Vitalant Research Institute/ ; }, abstract = {Viral metagenomic analysis of the liver of a black headed python (Aspidites melanocephalus) euthanized for a proliferative spinal lesion of unknown etiology yielded the first characterized genome of a reptile-infecting circovirus (black-headed python circovirus or BhPyCV). BhPyCV-specific in situ hybridization (ISH) showed that viral nucleic acids were strongly expressed in the intestinal lining and mucosa and multifocally in the liver. To investigate the presence of this virus in other snakes and its possible pathogenicity, 17 snakes in the python family with spinal disease were screened with ISH yielding a second BhP positive in intestinal tissue, and a Boelen's python (Morelia boeleni) positive in the liver. BhPyCV specific PCR was used to screen available frozen tissues from 13 of these pythons, four additional deceased pythons with and without spinal disease, and fecal samples from 37 live snakes of multiple species with unknown disease status. PCR detected multiple positive tissues in both of the ISH positive BhP and in the feces of another two live BhP and two live annulated tree boas (Corallus annulatus). Preliminary analysis indicates this circovirus can infect BhPs where it was found in 4/5 BhPs tested (2/2 with spinal disease, 2/3 live with unknown status), Boelen's python (1/2 with spinal disease), and annulated tree boa (2/6 live with unknown status) but was not detected in other python species with the same spinal lesions. This circovirus' causal or contributory role in spinal disease remains speculative and not well supported by these initial data.}, }
@article {pmid31096909, year = {2019}, author = {Zhang, J and Lacroix, C and Wortmann, E and Ruscheweyh, HJ and Sunagawa, S and Sturla, SJ and Schwab, C}, title = {Gut microbial beta-glucuronidase and glycerol/diol dehydratase activity contribute to dietary heterocyclic amine biotransformation.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {99}, doi = {10.1186/s12866-019-1483-x}, pmid = {31096909}, issn = {1471-2180}, support = {ETH-41 16-1//ETHZ/ ; 201406320209//Chinese Government Scholarship/ ; }, abstract = {BACKGROUND: Consuming red and processed meat has been associated with an increased risk of colorectal cancer (CRC), which is partly attributed to exposure to carcinogens such as heterocyclic amines (HCA) formed during cooking and preservation processes. The interaction of gut microbes and HCA can result in altered bioactivities and it has been shown previously that human gut microbiota can transform mutagenic HCA to a glycerol conjugate with reduced mutagenic potential. However, the major form of HCA in the colon are glucuronides (HCA-G) and it is not known whether these metabolites, via stepwise microbial hydrolysis and acrolein conjugation, are viable precursors for glycerol conjugated metabolites. We hypothesized that such a process could be concurrently catalyzed by bacterial beta-glucuronidase (B-GUS) and glycerol/diol dehydratase (GDH) activity. We therefore investigated how the HCA-G PhIP-N2-β-D-glucuronide (PhIP-G), a representative liver metabolite of PhIP (2-Amino-1-methyl-6-phenylimidazo [4,5-b] pyridine), which is the most abundant carcinogenic HCA in well-cooked meat, is transformed by enzymatic activity of human gut microbial representatives of the phyla Firmicutes, Bacteroidetes, and Proteobacteria.<br><br>RESULTS: We employed a combination of growth and enzymatic assays, and a bioanalysis approach combined with metagenomics. B-GUS of Faecalibacterium prausnitzii converted PhIP-G to PhIP and GDH of Flavonifractor plautii, Blautia obeum, Eubacterium hallii, and Lactobacillus reuteri converted PhIP to PhIP-M1 in the presence of glycerol. In addition, B-GUS- and GDH-positive bacteria cooperatively converted PhIP-G to PhIP-M1. A screen of genes encoding B-GUS and GDH was performed for fecal microbiome data from healthy individuals (n = 103) and from CRC patients (n = 53), which revealed a decrease in abundance of taxa with confirmed GDH and HCA transformation activity in CRC patients.<br><br>CONCLUSIONS: This study for the first time demonstrates that gut microbes mediate the stepwise transformation of PhIP-G to PhIP-M1 via the intermediate production of PhIP. Findings from this study suggest that targeted manipulation with gut microbes bearing specific functions, or dietary glycerol supplementation might modify gut microbial activity to reduce HCA-induced CRC risk.}, }
@article {pmid31096848, year = {2019}, author = {Arruda, B and Piñeyro, P and Derscheid, R and Hause, B and Byers, E and Dion, K and Long, D and Sievers, C and Tangen, J and Williams, T and Schwartz, K}, title = {PCV3-associated disease in the United States swine herd.}, journal = {Emerging microbes &amp; infections}, volume = {8}, number = {1}, pages = {684-698}, doi = {10.1080/22221751.2019.1613176}, pmid = {31096848}, issn = {2222-1751}, abstract = {Porcine circovirus-associated disease encompasses multiple disease syndromes including porcine circovirus 2 systemic diseases, reproductive failure, and porcine dermatitis and nephropathy syndrome. Until recently, porcine circovirus 2 was the only species associated with the porcine circovirus-associated disease. In this report, diagnostic investigations of thirty-six field cases submitted from multiple production systems, numerous sites and varied geographic locations demonstrated porcine circovirus 3 within lesions by in situ hybridization including fetuses with myocarditis, weak-born neonatal piglets with encephalitis and myocarditis, from cases of porcine dermatitis and nephropathy syndrome, and in weaned pigs with systemic periarteritis. Porcine circovirus 3 was detected by PCR in numerous fetuses and perinatal piglets at high viral loads (trillions of genome copies per mL of tissue homogenate). Samples from all cases in this study were assayed and found negative for porcine circovirus 2 by PCR. Metagenomic sequencing was performed on a subset of reproductive cases, consisting of sixteen fetuses/fetal sample pools. PCV3 was identified in all pools and the only virus identified in fourteen pools. Based on these data, porcine circovirus 3 is considered a putative cause of reproductive failure, encephalitis and myocarditis in perinatal piglets, porcine dermatitis and nephropathy syndrome, and periarteritis in swine in the United States.}, }
@article {pmid30232678, year = {2019}, author = {Osman, JR and Regeard, C and Badel, C and Fernandes, G and DuBow, MS}, title = {Variation of bacterial biodiversity from saline soils and estuary sediments present near the Mediterranean Sea coast of Camargue (France).}, journal = {Antonie van Leeuwenhoek}, volume = {112}, number = {3}, pages = {351-365}, doi = {10.1007/s10482-018-1164-z}, pmid = {30232678}, issn = {1572-9699}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Estuaries ; France ; Geologic Sediments/*microbiology ; Mediterranean Sea ; Metagenomics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Salinity is an important environmental factor influencing microbial community composition. To better understand this influence, we determined the bacterial communities present in 17 different sites of brackish sediment (underwater) and soil (surface) samples from the Camargue region (Rhône river delta) in southern France during the fall of 2013 and 2014 using pyrosequencing of the V3-V4 regions of the 16S rRNA genes amplified by PCR. This region is known for abundant flora and fauna and, though saline, 30% of rice consumed in France is grown here. We found that bacterial abundance in 1 g of soil or sediment, calculated by qPCR, was higher in sediments than in surface soil samples. Members belonging to the Proteobacteria, Bacteroidetes, Chloroflexi and Firmicutes phyla dominated the bacterial communities of sediment samples, while members belonging to the Proteobacteria, Bacteroidetes, Gemmatimonadetes, Actinobacteria, Firmicutes and Acidobacteria phyla dominated the bacterial communities of the soil samples. The most abundant bacterial genera present in the saline sediments and soils from the Camargue belonged mostly to halophilic and sulphate reducing bacteria, suggesting that the Camargue may be a valuable system to investigate saline, yet agriculturally productive, sediment and soil microbial ecosystem.}, }
@article {pmid29878200, year = {2018}, author = {Lee, FJ and Miller, KI and McKinlay, JB and Newton, ILG}, title = {Differential carbohydrate utilization and organic acid production by honey bee symbionts.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {8}, pages = {}, doi = {10.1093/femsec/fiy113}, pmid = {29878200}, issn = {1574-6941}, mesh = {Acetates/metabolism ; Animals ; Bacteria/genetics/*metabolism ; Bees/*microbiology ; Carbohydrate Metabolism/*physiology ; Carbohydrates ; Fatty Acids, Volatile/biosynthesis/*metabolism ; Gastrointestinal Microbiome/genetics/*physiology ; Lactic Acid/metabolism ; Metagenome ; Symbiosis/physiology ; }, abstract = {The honey bee worker gut hosts a community of bacteria that comprises 8-10 core bacterial species, along with a set of more transient environmental microbes. Collectively, these microbes break down and ferment saccharides present in the host's diet, based on analyses of metagenomes, and metatranscriptomes from this environment. As part of this metabolism, the bacteria produce short-chain fatty acids that may serve as a food source for the host bee, stimulating biological processes that may contribute to host weight gain. To identify metabolic contributions of symbionts within the honey bee gut, we utilized a combination of molecular and biochemical approaches. We show significant variation in the metabolic capabilities of honey bee-associated taxa, highlighting the fact that honey bee gut microbiota members of the same clade are highly variable in their ability to use specific carbohydrates and produce organic acids. Finally, we confirm that the honey bee core microbes are active in vivo, expressing key enzymatic genes critical for utilizing plant-derived molecules and producing organic acids (i.e. acetate and lactate). These results suggest that core taxa may contribute significantly to weight gain in the honey bee, specifically through the production of organic acids.}, }
@article {pmid31095619, year = {2019}, author = {Motta, V and Luise, D and Bosi, P and Trevisi, P}, title = {Faecal microbiota shift during weaning transition in piglets and evaluation of AO blood types as shaping factor for the bacterial community profile.}, journal = {PloS one}, volume = {14}, number = {5}, pages = {e0217001}, doi = {10.1371/journal.pone.0217001}, pmid = {31095619}, issn = {1932-6203}, abstract = {The host-microbiota interplay is recognized as a key factor for the homeostatic maintenance in animals. In pigs, the weaning transition represents a drastic changes event leading to high risk of gut dysbiosis, which in most cases results in economic losses for swine industry. The blood type antigens expressed on mucosal surfaces can act as receptors for bacterial adhesion and the hypothesis of possible associations between blood groups and intestinal microbial profiles has been tested in human with contrasting results. Nevertheless, no studies testing the blood type as possible shaping factor for gut microbiota are available for pigs. The results of our previous study suggested the porcine AO blood types system as a possible factor influencing the microbiota composition. In the present study, the changes in fecal microbiota of 12 piglets were followed from 7 days after birth to 2 weeks post-weaning, testing the hypothesis that blood types may impact on its structure. No effects attributable to the difference in blood groups were detected, however, the sampling site (faeces) and the low statistical power might have masked the hypothesized impact. The data clearly showed the rearrangement of the bacterial ecosystem triggered by weaning transition; mainly consisting of a shift from a Bacteroidaceae-Enterobacteriaceae dominated community, to a Prevotellaceae-Ruminococcaceae dominated community. The functional analysis by metagenomic predictions suggested a role of the high levels of long-chain fatty acid in swine milk as energy source for Enterobacteriaceae (E. coli), in suckling piglets. This study provides a first insight for further investigations; indicating the need for larger sample size, preferably derived from intestinal mucosa, to test the potential effect of blood groups on gut microbiota profiles, and for analyses aimed at assessing the long-chain fatty acids degradation activity within the intestinal microbiota of suckling piglets, with particular attention to the role of E. coli.}, }
@article {pmid31095603, year = {2019}, author = {Khan, MAW and Stephens, WZ and Mohammed, AD and Round, JL and Kubinak, JL}, title = {Does MHC heterozygosity influence microbiota form and function?.}, journal = {PloS one}, volume = {14}, number = {5}, pages = {e0215946}, doi = {10.1371/journal.pone.0215946}, pmid = {31095603}, issn = {1932-6203}, abstract = {MHC molecules are essential for the adaptive immune response, and they are the most polymorphic genetic loci in vertebrates. Extreme genetic variation at these loci is paradoxical given their central importance to host health. Classic models of MHC gene evolution center on antagonistic host-pathogen interactions to promote gene diversification and allelic diversity in host populations. However, all multicellular organisms are persistently colonized by their microbiota that perform essential metabolic functions for their host and protect from infection. Here, we provide data to support the hypothesis that MHC heterozygote advantage (a main force of selection thought to drive MHC gene evolution), may operate by enhancing fitness advantages conferred by the host's microbiome. We utilized fecal 16S rRNA gene sequences and their predicted metagenome datasets collected from multiple MHC congenic homozygote and heterozygote mouse strains to describe the influence of MHC heterozygosity on microbiome form and function. We find that in contrast to homozygosity at MHC loci, MHC heterozygosity promotes functional diversification of the microbiome, enhances microbial network connectivity, and results in enrichment for a variety of microbial functions that are positively associated with host fitness. We demonstrate that taxonomic and functional diversity of the microbiome is positively correlated in MHC heterozygote but not homozygote animals, suggesting that heterozygote microbiomes are more functionally adaptive under similar environmental conditions than homozygote microbiomes. Our data complement previous observations on the role of MHC polymorphism in sculpting microbiota composition, but also provide functional insights into how MHC heterozygosity may enhance host health by modulating microbiome form and function. We also provide evidence to support that MHC heterozygosity limits functional redundancy among commensal microbes and may enhance the metabolic versatility of their microbiome. Results from our analyses yield multiple testable predictions regarding the role of MHC heterozygosity on the microbiome that will help guide future research in the area of MHC-microbiome interactions.}, }
@article {pmid31095297, year = {2019}, author = {Mhatre, SS and Kaufmann, S and Marshall, IPG and Obrochta, S and Andrèn, T and Jørgensen, BB and Lomstein, BAA}, title = {Microbial biomass turnover times and clues to cellular protein repair in energy-limited deep Baltic Sea sediments.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiz068}, pmid = {31095297}, issn = {1574-6941}, abstract = {The discovery of active microbial life deeply buried beneath the seafloor has opened important questions: how do microorganisms cope with extreme energy limitation, what is their metabolic activity, and how do they repair damages to essential biomolecules? We used a D:L-amino acid model to calculate microbial biomass turnover times. We used a metagenome and metatranscriptome analysis to investigate the distribution of the gene that encodes Protein-L-iso aspartate(D-aspartate) O-methyltransferase (PCMT), an enzyme which recognizes damaged L-isoapartyl and D-aspartyl residues in proteins and catalyzes their repair. Sediment was retrieved during the Integrated Ocean Drilling Program (IODP) Expedition 347 from Landsort Deep and the Little Belt in the Baltic Sea. The study covers the period from the Baltic Ice Lake ca. 13,000 years ago to the present. Our results provide new knowledge on microbial biomass turnover times and protein repair in relation to different regimes of organic matter input. For the first time, we show that the PCMT gene was widely distributed and expressed among phylogenetically diverse groups of microorganisms. Our findings suggest that microbial communities are capable of repairing D-amino acids within proteins using energy obtained from the degradation of a mixture of labile compounds in microbial necromass and more recalcitrant organic matter.}, }
@article {pmid31092601, year = {2019}, author = {Hu, H and da Costa, RR and Pilgaard, B and Schiøtt, M and Lange, L and Poulsen, M}, title = {Fungiculture in Termites Is Associated with a Mycolytic Gut Bacterial Community.}, journal = {mSphere}, volume = {4}, number = {3}, pages = {}, doi = {10.1128/mSphere.00165-19}, pmid = {31092601}, issn = {2379-5042}, abstract = {Termites forage on a range of substrates, and it has been suggested that diet shapes the composition and function of termite gut bacterial communities. Through comparative analyses of gut metagenomes in nine termite species with distinct diets, we characterize bacterial community compositions and use peptide-based functional annotation method to determine biomass-degrading enzymes and the bacterial taxa that encode them. We find that fungus-growing termite guts have relatively more fungal cell wall-degrading enzyme genes, while wood-feeding termite gut communities have relatively more plant cell wall-degrading enzyme genes. Interestingly, wood-feeding termite gut bacterial genes code for abundant chitinolytic enzymes, suggesting that fungal biomass within the decaying wood likely contributes to gut bacterial or termite host nutrition. Across diets, the dominant biomass-degrading enzymes are predominantly coded for by the most abundant bacterial taxa, suggesting tight links between diet and gut community composition, with the most marked difference being the communities coding for the mycolytic capacity of the fungus-growing termite gut.IMPORTANCE Understanding functional capacities of gut microbiomes is important to improve our understanding of symbiotic associations. Here, we use peptide-based functional annotation to show that the gut microbiomes of fungus-farming termites code for a wealth of enzymes that likely target the fungal diet the termites eat. Comparisons to other termites showed that fungus-growing termite guts have relatively more fungal cell wall-degrading enzyme genes, whereas wood-feeding termite gut communities have relatively more plant cell wall-degrading enzyme genes. Across termites with different diets, the dominant biomass-degrading enzymes are predominantly coded for by the most abundant bacterial taxa, suggesting tight links between diet and gut community compositions.}, }
@article {pmid31092577, year = {2019}, author = {Chen, Q and Godfrey, K and Liu, J and Mao, Q and Kuo, YW and Falk, BW}, title = {A nonstructural protein responsible for viral spread of a novel insect reovirus provides a safe channel for biparental virus transmission to progeny.}, journal = {Journal of virology}, volume = {}, number = {}, pages = {}, doi = {10.1128/JVI.00702-19}, pmid = {31092577}, issn = {1098-5514}, abstract = {Diaphorina citri reovirus (DcRV) was previously identified based on metagenomics surveys for virus discovery. Here, we demonstrated that DcRV induces persistent infections in its psyllid host, Diaphorina citri DcRV was efficiently vertically passed to offspring in a biparental manner. Transmission electron microscopic and immunological analysis showed that the DcRV-encoded nonstructural protein, P10, assembled into a virion-packaging tubular structure which is associated with the spread of DcRV throughout the bodies of D. citri P10 tubules containing virions were associated with oocytes of female and sperm of male D. citri, suggesting a role in the highly efficient biparental transmission of DcRV. Knocking down P10 by RNA interference for males reduced the percentage of DcRV-infected progeny, and for females reduced the viral accumulation in progeny. These results, for the first time, show that a nonstructural protein of a novel insect reovirus provides a safe and pivotal channel for virus spread and biparental transmission to progeny.IMPORTANCE The Asian citrus psyllid, Diaphorina citri Kuwayama, is an important pest in the worldwide citrus industry. It is the vector of Candidatus Liberibacter asiaticus (CLas), the bacterial pathogen of Huanglongbing (HLB), which is currently considered to be the most destructive disease of citrus worldwide. Diaphorina citri reovirus (DcRV) was previously identified based on metagenomics surveys for virus discovery. Here, we found that this novel and persistent insect reovirus took advantage of a viral-encoded nonstructural protein, P10, for efficient vertical transmission from parents to progeny. The P10 assembled into a virion-packaging tubular structure, and was associated with oocytes of female D. citri and sperm of males. Consistently, knockdown of P10 for either male or female D. citri inhibited DcRV transmission to offspring. This tubular strategy for viral spread and biparental transmission might serve as a target for controlling viral vertical transmission and population expansion.}, }
@article {pmid31092280, year = {2019}, author = {Heinken, A and Ravcheev, DA and Baldini, F and Heirendt, L and Fleming, RMT and Thiele, I}, title = {Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {75}, doi = {10.1186/s40168-019-0689-3}, pmid = {31092280}, issn = {2049-2618}, support = {FNR/A12/01//Fonds National de la Recherche Luxembourg (LU)/ ; FNR/O16/11402054//Fonds National de la Recherche Luxembourg/ ; 757922//H2020 European Research Council/ ; }, abstract = {BACKGROUND: The human gut microbiome performs important functions in human health and disease. A classic example for host-gut microbial co-metabolism is host biosynthesis of primary bile acids and their subsequent deconjugation and transformation by the gut microbiome. To understand these system-level host-microbe interactions, a mechanistic, multi-scale computational systems biology approach that integrates the different types of omic data is needed. Here, we use a systematic workflow to computationally model bile acid metabolism in gut microbes and microbial communities.<br><br>RESULTS: Therefore, we first performed a comparative genomic analysis of bile acid deconjugation and biotransformation pathways in 693 human gut microbial genomes and expanded 232 curated genome-scale microbial metabolic reconstructions with the corresponding reactions (available at https://vmh.life). We then predicted the bile acid biotransformation potential of each microbe and in combination with other microbes. We found that each microbe could produce maximally six of the 13 secondary bile acids in silico, while microbial pairs could produce up to 12 bile acids, suggesting bile acid biotransformation being a microbial community task. To investigate the metabolic potential of a given microbiome, publicly available metagenomics data from healthy Western individuals, as well as inflammatory bowel disease patients and healthy controls, were mapped onto the genomes of the reconstructed strains. We constructed for each individual a large-scale personalized microbial community model that takes into account strain-level abundances. Using flux balance analysis, we found considerable variation in the potential to deconjugate and transform primary bile acids between the gut microbiomes of healthy individuals. Moreover, the microbiomes of pediatric inflammatory bowel disease patients were significantly depleted in their bile acid production potential compared with that of controls. The contributions of each strain to overall bile acid production potential across individuals were found to be distinct between inflammatory bowel disease patients and controls. Finally, bottlenecks limiting secondary bile acid production potential were identified in each microbiome model.<br><br>CONCLUSIONS: This large-scale modeling approach provides a novel way of analyzing metagenomics data to accelerate our understanding of the metabolic interactions between the host and gut microbiomes in health and diseases states. Our models and tools are freely available to the scientific community.}, }
@article {pmid31089513, year = {2017}, author = {Cavallari, JF and Schertzer, JD}, title = {Intestinal Microbiota Contributes to Energy Balance, Metabolic Inflammation, and Insulin Resistance in Obesity.}, journal = {Journal of obesity &amp; metabolic syndrome}, volume = {26}, number = {3}, pages = {161-171}, doi = {10.7570/jomes.2017.26.3.161}, pmid = {31089513}, issn = {2508-7576}, abstract = {Obesity is associated with increased risk of developing metabolic diseases such as type 2 diabetes. The origins of obesity are multi-factorial, but ultimately rooted in increased host energy accumulation or retention. The gut microbiota has been implicated in control of host energy balance and nutrient extraction from dietary sources. The microbiota also impacts host immune status and dysbiosis-related inflammation can augment insulin resistance, independently of obesity. Advances in microbial metagenomic analyses and directly manipulating bacterial-host models of obesity have contributed to our understanding of the relationship between gut bacteria and metabolic disease. Foodborne, or drug-mediated perturbations to the gut microbiota can increase metabolic inflammation, insulin resistance, and dysglycemia. There is now some evidence that specific bacterial species can influence obesity and related metabolic defects such as insulin sensitivity. Components of bacteria are sufficient to impact obesity-related changes in metabolism. In fact, different microbial components derived from the bacterial cell wall can increase or decrease insulin resistance. Improving our understanding of the how components of the microbiota alter host metabolism is positioned to aid in the development of dietary interventions, avoiding triggers of dysbiosis, and generating novel therapeutic strategies to combat increasing rates of obesity and diabetes.}, }
@article {pmid31084612, year = {2019}, author = {Liekniņa, I and Kalniņš, G and Akopjana, I and Bogans, J and Šišovs, M and Jansons, J and Rūmnieks, J and Tārs, K}, title = {Production and characterization of novel ssRNA bacteriophage virus-like particles from metagenomic sequencing data.}, journal = {Journal of nanobiotechnology}, volume = {17}, number = {1}, pages = {61}, doi = {10.1186/s12951-019-0497-8}, pmid = {31084612}, issn = {1477-3155}, support = {1.1.1.1/16/A/104//European Research and Development Fund/ ; }, abstract = {BACKGROUND: Protein shells assembled from viral coat proteins are an attractive platform for development of new vaccines and other tools such as targeted bioimaging and drug delivery agents. Virus-like particles (VLPs) derived from the single-stranded RNA (ssRNA) bacteriophage coat proteins (CPs) have been important and successful contenders in the area due to their simplicity and robustness. However, only a few different VLP types are available that put certain limitations on continued developments and expanded adaptation of ssRNA phage VLP technology. Metagenomic studies have been a rich source for discovering novel viral sequences, and in recent years have unraveled numerous ssRNA phage genomes significantly different from those known before. Here, we describe the use of ssRNA CP sequences found in metagenomic data to experimentally produce and characterize novel VLPs.<br><br>RESULTS: Approximately 150 ssRNA phage CP sequences were sourced from metagenomic sequence data and grouped into 14 different clusters based on CP sequence similarity analysis. 110 CP-encoding sequences were obtained by gene synthesis and expressed in bacteria which in 80 cases resulted in VLP assembly. Production and purification of the VLPs was straightforward and compatible with established protocols, with the only exception that a considerable proportion of the CPs had to be produced at a lower temperature to ensure VLP assembly. The VLP morphology was similar to that of the previously studied phages, although a few deviations such as elongated or smaller particles were noted in certain cases. In addition, stabilizing inter-subunit disulfide bonds were detected in six VLPs and several possible candidate RNA structures in the phage genomes were identified that might bind to the coat protein and ensure specific RNA packaging.<br><br>CONCLUSIONS: Compared to the few types of ssRNA phage VLPs that were used before, several dozens of new particles representing ten distinct similarity groups are now available with a notable potential for biotechnological applications. It is believed that the novel VLPs described in this paper will provide the groundwork for future development of new vaccines and other applications based on ssRNA bacteriophage VLPs.}, }
@article {pmid29926341, year = {2019}, author = {Lladó Fernández, S and Větrovský, T and Baldrian, P}, title = {The concept of operational taxonomic units revisited: genomes of bacteria that are regarded as closely related are often highly dissimilar.}, journal = {Folia microbiologica}, volume = {64}, number = {1}, pages = {19-23}, doi = {10.1007/s12223-018-0627-y}, pmid = {29926341}, issn = {1874-9356}, support = {18-25706S//Czech Science Foundation/ ; LTT17022//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; }, mesh = {Bacteria/*classification/*genetics ; DNA, Bacterial/genetics ; Databases, Nucleic Acid ; Genes, Bacterial/genetics ; Genetic Variation ; Genome, Bacterial/*genetics ; Glycoside Hydrolases/genetics ; *Metagenomics ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The concept of operational taxonomic units (OTUs), which constructs &quot;mathematically&quot; defined taxa, is widely accepted and applied to describe bacterial communities using amplicon sequencing of 16S rRNA gene. OTUs are often used to infer functional traits since they are considered to fairly represent of community members. However, the link between molecular taxa, real taxa, and OTUs seems to be much more complicated. Strains of the same bacterial species (ideally belonging to the same OTU) typically only share some genes (the core genome), while other genes are strain-specific and unique. It is thus unclear to what extent are important functional traits homogeneous within an OTU and how correctly can functional traits be inferred for individual OTU members. Here, we have tested in silico the similarity of all genes and, more specifically, the set of genes encoding for glycoside hydrolases (GH) in bacterial genomes that belong to the same OTU. Genome similarity varied among OTUs, but as many as 5-78% of genes were not shared between the two bacterial genomes in the pair. The complement of GH families (the presence of gene families and the number of genes per family) differed in 95% of OTUs. In average, 43% of GH families either differed in gene counts or were present in one genome and absent in the other. These results show a serious limitation of the OTU-based approaches when used to infer the functional traits of bacterial communities and open the questions how to link environmental sequencing data and microbial functions.}, }
@article {pmid31091345, year = {2019}, author = {Riiser, ES and Haverkamp, THA and Varadharajan, S and Borgan, Ø and Jakobsen, KS and Jentoft, S and Star, B}, title = {Switching on the light: using metagenomic shotgun sequencing to characterize the intestinal microbiome of Atlantic cod.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14652}, pmid = {31091345}, issn = {1462-2920}, abstract = {Atlantic cod (Gadus morhua) is an ecologically important species with a wide-spread distribution in the North Atlantic Ocean, yet little is known about the diversity of its intestinal microbiome in its natural habitat. No geographical differentiation in this microbiome was observed based on 16S rRNA amplicon analyses, yet such finding may result from an inherent lack of power of this method to resolve fine-scaled biological complexity. Here, we use metagenomic shotgun sequencing to investigate the intestinal microbiome of 19 adult Atlantic cod individuals from two coastal populations in Norway - located 470 km apart. Resolving the species community to unprecedented resolution, we identify two abundant species, P. iliopiscarium and P. kishitanii, which comprise over 50% of the classified reads. Interestingly, the intestinal P. kishitanii strains have functionally intact lux genes, and its high abundance suggests that fish intestines form an important part of its ecological niche. These observations support a hypothesis that bioluminescence plays an ecological role in the marine food web. Despite our improved taxonomical resolution, we identify no geographical differences in bacterial community structure, indicating that the intestinal microbiome of these coastal cod is colonized by a limited number of closely related bacterial species with a broad geographical distribution. This article is protected by copyright. All rights reserved.}, }
@article {pmid31091277, year = {2019}, author = {Ribeiro, H and Martins, A and Gonçalves, M and Guedes, M and Tomasino, MP and Dias, N and Dias, A and Mucha, AP and Carvalho, MF and Almeida, CMR and Ramos, S and Almeida, JM and Silva, E and Magalhães, C}, title = {Development of an autonomous biosampler to capture in situ aquatic microbiomes.}, journal = {PloS one}, volume = {14}, number = {5}, pages = {e0216882}, doi = {10.1371/journal.pone.0216882}, pmid = {31091277}, issn = {1932-6203}, abstract = {The importance of planktonic microbial communities is well acknowledged, since they are fundamental for several natural processes of aquatic ecosystems. Microorganisms naturally control the flux of nutrients, and also degrade and recycle anthropogenic organic and inorganic contaminants. Nevertheless, climate change effects and/or the runoff of nutrients/pollutants can affect the equilibrium of natural microbial communities influencing the occurrence of microbial pathogens and/or microbial toxin producers, which can compromise ecosystem environmental status. Therefore, improved microbial plankton monitoring is essential to better understand how these communities respond to environmental shifts. The study of marine microbial communities typically involves highly cost and time-consuming sampling procedures, which can limit the frequency of sampling and data availability. In this context, we developed and validated an in situ autonomous biosampler (IS-ABS) able to collect/concentrate in situ planktonic communities of different size fractions (targeting prokaryotes and unicellular eukaryotes) for posterior genomic, metagenomic, and/or transcriptomic analysis at a home laboratory. The IS-ABS field prototype is a small size and compact system able to operate up to 150 m depth. Water is pumped by a micropump (TCS MG2000) through a hydraulic circuit that allows in situ filtration of environmental water in one or more Sterivex filters placed in a filter cartridge. The IS-ABS also includes an application to program sampling definitions, allowing pre-setting configuration of the sampling. The efficiency of the IS-ABS was tested against traditional laboratory filtration standardized protocols. Results showed a good performance in terms of DNA recovery, as well as prokaryotic (16S rDNA) and eukaryotic (18S rDNA) community diversity analysis, using either methodologies. The IS-ABS automates the process of collecting environmental DNA, and is suitable for integration in water observation systems, what will contribute to substantially increase biological surveillances. Also, the use of highly sensitive genomic approaches allows a further study of the diversity and functions of whole or specific microbial communities.}, }
@article {pmid31089679, year = {2019}, author = {Nicholls, SM and Quick, JC and Tang, S and Loman, NJ}, title = {Ultra-deep, long-read nanopore sequencing of mock microbial community standards.}, journal = {GigaScience}, volume = {8}, number = {5}, pages = {}, doi = {10.1093/gigascience/giz043}, pmid = {31089679}, issn = {2047-217X}, abstract = {BACKGROUND: Long sequencing reads are information-rich: aiding de novo assembly and reference mapping, and consequently have great potential for the study of microbial communities. However, the best approaches for analysis of long-read metagenomic data are unknown. Additionally, rigorous evaluation of bioinformatics tools is hindered by a lack of long-read data from validated samples with known composition.<br><br>FINDINGS: We sequenced 2 commercially available mock communities containing 10 microbial species (ZymoBIOMICS Microbial Community Standards) with Oxford Nanopore GridION and PromethION. Both communities and the 10 individual species isolates were also sequenced with Illumina technology. We generated 14 and 16 gigabase pairs from 2 GridION flowcells and 150 and 153 gigabase pairs from 2 PromethION flowcells for the evenly distributed and log-distributed communities, respectively. Read length N50 ranged between 5.3 and 5.4 kilobase pairs over the 4 sequencing runs. Basecalls and corresponding signal data are made available (4.2 TB in total). Alignment to Illumina-sequenced isolates demonstrated the expected microbial species at anticipated abundances, with the limit of detection for the lowest abundance species below 50 cells (GridION). De novo assembly of metagenomes recovered long contiguous sequences without the need for pre-processing techniques such as binning.<br><br>CONCLUSIONS: We present ultra-deep, long-read nanopore datasets from a well-defined mock community. These datasets will be useful for those developing bioinformatics methods for long-read metagenomics and for the validation and comparison of current laboratory and software pipelines.}, }
@article {pmid31088928, year = {2019}, author = {Schorn, MA and Jordan, PA and Podell, S and Blanton, JM and Agarwal, V and Biggs, JS and Allen, EE and Moore, BS}, title = {Comparative Genomics of Cyanobacterial Symbionts Reveals Distinct, Specialized Metabolism in Tropical Dysideidae Sponges.}, journal = {mBio}, volume = {10}, number = {3}, pages = {}, doi = {10.1128/mBio.00821-19}, pmid = {31088928}, issn = {2150-7511}, abstract = {Marine sponges are recognized as valuable sources of bioactive metabolites and renowned as petri dishes of the sea, providing specialized niches for many symbiotic microorganisms. Sponges of the family Dysideidae are well documented to be chemically talented, often containing high levels of polyhalogenated compounds, terpenoids, peptides, and other classes of bioactive small molecules. This group of tropical sponges hosts a high abundance of an uncultured filamentous cyanobacterium, Hormoscilla spongeliae Here, we report the comparative genomic analyses of two phylogenetically distinct Hormoscilla populations, which reveal shared deficiencies in essential pathways, hinting at possible reasons for their uncultivable status, as well as differing biosynthetic machinery for the production of specialized metabolites. One symbiont population contains clustered genes for expanded polybrominated diphenylether (PBDE) biosynthesis, while the other instead harbors a unique gene cluster for the biosynthesis of the dysinosin nonribosomal peptides. The hybrid sequencing and assembly approach utilized here allows, for the first time, a comprehensive look into the genomes of these elusive sponge symbionts.IMPORTANCE Natural products provide the inspiration for most clinical drugs. With the rise in antibiotic resistance, it is imperative to discover new sources of chemical diversity. Bacteria living in symbiosis with marine invertebrates have emerged as an untapped source of natural chemistry. While symbiotic bacteria are often recalcitrant to growth in the lab, advances in metagenomic sequencing and assembly now make it possible to access their genetic blueprint. A cell enrichment procedure, combined with a hybrid sequencing and assembly approach, enabled detailed genomic analysis of uncultivated cyanobacterial symbiont populations in two chemically rich tropical marine sponges. These population genomes reveal a wealth of secondary metabolism potential as well as possible reasons for historical difficulties in their cultivation.}, }
@article {pmid31087994, year = {2019}, author = {Yu, X and Sun, HW and Li, WW and Qi, GP and Ma, J and Cheng, YZ and Lü, XT}, title = {[Effect of Temperature on the Activity Kinetics of Nitrobacter].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {40}, number = {3}, pages = {1426-1430}, doi = {10.13227/j.hjkx.201808261}, pmid = {31087994}, issn = {0250-3301}, abstract = {A sequencing batch reactor (SBR) was operated in this study to investigate the effect of temperature on the kinetics of Nitrobacter activity among nitrite oxidizing bacteria. At the beginning of the experiment, the NO2--N concentration in the influent was changed to enrich Nitrobacter. Then, the sludge with enriched Nitrobacter was employed to determine the variation of the specific nitrite oxidation rate (SNiOR) during the nitrite oxidation process in batch tests. Metagenomics species annotation and abundance analysis showed that Nitrobacter accounted for 40.3% of the total bacterial population. The variation of SNiOR in the nitrite oxidation process was investigated under different NO2--N concentrations. The effect of temperature on the kinetics of Nitrobacter was investigated using the Monod model. Furthermore, the kinetics model of the effect of temperature on Nitrobacter activity was fitted for statistical analysis. The results showed that SNiOR reached its maximum at 30℃, which was 1.31 g·(g·d)-1. Statistical analysis showed that the Monod equation could describe the effect of substrate concentration on Nitrobacter activity under different temperature conditions. Calculating the temperature coefficient (θ) in different temperature intervals based on the Phelps equation, showed that when the system temperature is lower than 25℃ or higher than 30℃, the reaction rate is more sensitive to temperature changes.}, }
@article {pmid31087993, year = {2019}, author = {Liu, ZQ and Zhang, Y and Ma, XS and Zhang, BK and Cao, MJ and Chen, CM}, title = {[Nitrogen Removal Characteristics and Analysis of Microbial Community Structure in an IEM-UF Simultaneous Separation and Denitrification System].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {40}, number = {3}, pages = {1419-1425}, doi = {10.13227/j.hjkx.201808051}, pmid = {31087993}, issn = {0250-3301}, abstract = {A system that combines an ion exchange membrane and ultrafiltration membrane (IEM-UF) to form a simultaneous separation and denitrification system was proposed for domestic sewage with a low carbon/nitrogen ratio. The removal of nitrogen and COD in the system was studied under a three phase operating condition. The characteristics of the microbial community in each reactor were analyzed using metagenomics. The results show that, the average rate of ammonia nitrogen enrichment in the separator reached above 116.1% when the current intensity was 0.2 A. When the system was at C/N 2.80 and operating well, the average removal rates of COD and TN reached above 90% and 50%, respectively. The maximum removal rate of TN was above 65.4%. The results of metagenomics showed a genus of phylum Nitrospirae (Nitrospira) and a genus of phylum Proteobacteria (Nitrosomonas), with the proportions of 12.23% and 2.31%, respectively. In the denitrifying reactor, Dechloromonas, Thauera, and Azospira were detected in the proportions 4.57%, 1.76%, and 1.03%, respectively. These proportions were far larger than those of other bacteria in this reactor. Meanwhile, the presence of iron autotrophic denitrifying bacteria increased the denitrification efficiency of the system.}, }
@article {pmid31087742, year = {2019}, author = {Geiger, RA and Junghare, M and Mergelsberg, M and Ebenau-Jehle, C and Jesenofsky, VJ and Jehmlich, N and von Bergen, M and Schink, B and Boll, M}, title = {Enzymes involved in phthalate degradation in sulfate-reducing bacteria.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14681}, pmid = {31087742}, issn = {1462-2920}, abstract = {The complete degradation of the xenobiotic and environmentally harmful phthalate esters is initiated by hydrolysis to alcohols and o-phthalate (phthalate) by esterases. While further catabolism of phthalate has been studied in aerobic and denitrifying microorganisms, the degradation in obligately anaerobic bacteria has remained obscure. Here we demonstrate a previously overseen growth of the δ-proteobacterium Desulfosarcina cetonica with phthalate/sulfate as only carbon and energy sources. Differential proteome and CoA ester pool analyses together with in vitro enzyme assays identified the genes, enzymes and metabolites involved in phthalate uptake and degradation in D. cetonica. Phthalate is initially activated to the short-lived phthaloyl-CoA by an ATP-dependent phthalate CoA ligase (PCL) followed by decarboxylation to the central intermediate benzoyl-CoA by an UbiD-like phthaloyl-CoA decarboxylase (PCD) containing a prenylated flavin cofactor. Genome/metagenome analyses predicted phthalate degradation capacity also in the sulfate-reducing Desulfobacula toluolica, strain NaphS2, and other δ-proteobacteria. Our results suggest that phthalate degradation proceeds in all anaerobic bacteria via the labile phthaloyl-CoA that is captured and decarboxylated by highly abundant PCDs. In contrast, two alternative strategies have been established for the formation of phthaloyl-CoA, the possibly most unstable CoA ester in biology. This article is protected by copyright. All rights reserved.}, }
@article {pmid31087616, year = {2019}, author = {Martin-Cuadrado, AB and Senel, E and Martínez-García, M and Cifuentes, A and Santos, F and Almansa, C and Moreno-Paz, M and Blanco, Y and García-Villadangos, M and García Del Cura, MÁ and Sanz-Montero, ME and Rodríguez-Aranda, JP and Rosselló-Móra, R and Antón, J and Parro, V}, title = {Prokaryotic and viral community of the sulfate-rich crust from Peñahueca ephemeral lake, an astrobiology analogue.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14680}, pmid = {31087616}, issn = {1462-2920}, abstract = {Peñahueca is an athalassohaline hypersaline inland ephemeral lake originated under semiarid conditions in the central Iberian Peninsula (Spain). Its chemical composition makes it extreme for microbial life as well as a terrestrial analogue of other planetary environments. To investigate the persistence of microbial life associated with sulfate-rich crusts, we applied cultivation-independent methods (optical and electron microscopy, 16S rRNA gene profiling and metagenomics) to describe the prokaryotic community and its associated viruses. The diversity for Bacteria was very low and was vastly dominated by endospore formers related to Pontibacillus marinus of the Firmicutes phylum. The archaeal assemblage was more diverse and included taxa related to those normally found in hypersaline environments. Several &quot;metagenome assembled genomes&quot; were recovered, corresponding to new species of Pontibacillus, several species from the Halobacteria and one new member of the Nanohaloarchaeota. The viral assemblage, although composed of the morphotypes typical of high salt systems, showed little similarity to previously isolated/reconstructed halophages. Several putative prophages of Pontibacillus and haloarchaeal hosts were identified. Remarkably, the Peñahueca sulfate-rich metagenome contained CRISPR-associated proteins and repetitions which were over 10-fold higher than in most hypersaline systems analyzed so far. This article is protected by copyright. All rights reserved.}, }
@article {pmid31087436, year = {2019}, author = {Akiyama, K and Nishioka, K and Khan, KN and Tanaka, Y and Mori, T and Nakaya, T and Kitawaki, J}, title = {Molecular detection of microbial colonization in cervical mucus of women with and without endometriosis.}, journal = {American journal of reproductive immunology (New York, N.Y. : 1989)}, volume = {}, number = {}, pages = {e13147}, doi = {10.1111/aji.13147}, pmid = {31087436}, issn = {1600-0897}, abstract = {PROBLEM: Intrauterine microbial colonization and its association with the pathogenesis of endometriosis via an innate immune cascade have been reported. As a potential source of microbial transmission, information on microbial colonization in cervical mucus is unknown. We investigated pattern of microbiota in the cervical mucus collected from women with and without endometriosis using next-generation sequencing (NGS) technology.<br><br>METHOD OF STUDY: Cervical mucus samples were collected from women with (n = 30) and without (n = 39) endometriosis. The communities of microbiota in cervical mucus in the endometriosis group and the control group were examined by Gram staining and NGS targeting the V5-V6 region of 16S ribosomal RNA gene. Copy number of some target bacteria was detected by real-time PCR. Results We confirmed visual presence of bacteria in cervical mucus by Gram staining. NGS analysis showed that distribution of microbiota was similar in cervical mucus of women with and without endometriosis regardless of the phases of the menstrual cycle. In addition to predominant Lactobacilli spp. the populations of Corynebacterium, Enterobacteriaceae, Flavobacterium, Pseudomonas, and Streptococcus were increased in the endometriosis group. Of them, Enterobacteriaceae and Streptococcus were identified as the more significant candidates in the endometriosis group than in controls by real-time PCR (P < 0.05 for each). Conclusions Our NGS analysis of cervical mucus indicated that among a variable microbiota, two candidates (Enterobacteriaceae and Streptococcus) were more frequently detected in women with endometriosis. Further investigation is needed to elucidate a mechanistic link of these bacteria in the pathophysiology of endometriosis. This article is protected by copyright. All rights reserved.}, }
@article {pmid31086829, year = {2019}, author = {Burgsdorf, I and Handley, KM and Bar-Shalom, R and Erwin, PM and Steindler, L}, title = {Life at Home and on the Roam: Genomic Adaptions Reflect the Dual Lifestyle of an Intracellular, Facultative Symbiont.}, journal = {mSystems}, volume = {4}, number = {4}, pages = {}, doi = {10.1128/mSystems.00057-19}, pmid = {31086829}, issn = {2379-5077}, abstract = {&quot;Candidatus Synechococcus feldmannii&quot; is a facultative intracellular symbiont of the Atlanto-Mediterranean sponge Petrosia ficiformis. Genomic information of sponge-associated cyanobacteria derives thus far from the obligate and extracellular symbiont &quot;Candidatus Synechococcus spongiarum.&quot; Here we utilized a differential methylation-based approach for bacterial DNA enrichment combined with metagenomics to obtain the first draft genomes of &quot;Ca. Synechococcus feldmannii.&quot; By comparative genomics, we revealed that some genomic features (e.g., iron transport mediated by siderophores, eukaryotic-like proteins, and defense mechanisms, like CRISPR-Cas [clustered regularly interspaced short palindromic repeats-associated proteins]) are unique to both symbiont types and absent or rare in the genomes of taxonomically related free-living cyanobacteria. These genomic features likely enable life under the conditions found inside the sponge host. Interestingly, there are many genomic features that are shared by &quot;Ca. Synechococcus feldmannii&quot; and free-living cyanobacteria, while they are absent in the obligate symbiont &quot;Ca. Synechococcus spongiarum.&quot; These include genes related to cell surface structures, genetic regulation, and responses to environmental stress, as well as the composition of photosynthetic genes and DNA metabolism. We speculate that the presence of these genes confers on &quot;Ca. Synechococcus feldmannii&quot; its facultative nature (i.e., the ability to respond to a less stable environment when free-living). Our comparative analysis revealed that distinct genomic features depend on the nature of the symbiotic interaction: facultative and intracellular versus obligate and extracellular. IMPORTANCE Given the evolutionary position of sponges as one of the earliest phyla to depart from the metazoan stem lineage, studies on their distinct and exceptionally diverse microbial communities should yield a better understanding of the origin of animal-bacterium interactions. While genomes of several extracellular sponge symbionts have been published, the intracellular symbionts have, so far, been elusive. Here we compare the genomes of two unicellular cyanobacterial sponge symbionts that share an ancestor but followed different evolutionary paths-one became intracellular and the other extracellular. Counterintuitively, the intracellular cyanobacteria are facultative, while the extracellular ones are obligate. By sequencing the genomes of the intracellular cyanobacteria and comparing them to the genomes of the extracellular symbionts and related free-living cyanobacteria, we show how three different cyanobacterial lifestyles are reflected by adaptive genomic features.}, }
@article {pmid31086738, year = {2019}, author = {Warwick-Dugdale, J and Solonenko, N and Moore, K and Chittick, L and Gregory, AC and Allen, MJ and Sullivan, MB and Temperton, B}, title = {Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6800}, doi = {10.7717/peerj.6800}, pmid = {31086738}, issn = {2167-8359}, abstract = {Marine viruses impact global biogeochemical cycles via their influence on host community structure and function, yet our understanding of viral ecology is constrained by limitations in host culturing and a lack of reference genomes and 'universal' gene markers to facilitate community surveys. Short-read viral metagenomic studies have provided clues to viral function and first estimates of global viral gene abundance and distribution, but their assemblies are confounded by populations with high levels of strain evenness and nucleotide diversity (microdiversity), limiting assembly of some of the most abundant viruses on Earth. Such features also challenge assembly across genomic islands containing niche-defining genes that drive ecological speciation. These populations and features may be successfully captured by single-virus genomics and fosmid-based approaches, at least in abundant taxa, but at considerable cost and technical expertise. Here we established a low-cost, low-input, high throughput alternative sequencing and informatics workflow to improve viral metagenomic assemblies using short-read and long-read technology. The 'VirION' (Viral, long-read metagenomics via MinION sequencing) approach was first validated using mock communities where it was found to be as relatively quantitative as short-read methods and provided significant improvements in recovery of viral genomes. We then then applied VirION to the first metagenome from a natural viral community from the Western English Channel. In comparison to a short-read only approach, VirION: (i) increased number and completeness of assembled viral genomes; (ii) captured abundant, highly microdiverse virus populations, and (iii) captured more and longer genomic islands. Together, these findings suggest that VirION provides a high throughput and cost-effective alternative to fosmid and single-virus genomic approaches to more comprehensively explore viral communities in nature.}, }
@article {pmid31086312, year = {2019}, author = {Wu, L and Ning, D and Zhang, B and Li, Y and Zhang, P and Shan, X and Zhang, Q and Brown, M and Li, Z and Van Nostrand, JD and Ling, F and Xiao, N and Zhang, Y and Vierheilig, J and Wells, GF and Yang, Y and Deng, Y and Tu, Q and Wang, A and ,  and Zhang, T and He, Z and Keller, J and Nielsen, PH and Alvarez, PJJ and Criddle, CS and Wagner, M and Tiedje, JM and He, Q and Curtis, TP and Stahl, DA and Alvarez-Cohen, L and Rittmann, BE and Wen, X and Zhou, J}, title = {Global diversity and biogeography of bacterial communities in wastewater treatment plants.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41564-019-0426-5}, pmid = {31086312}, issn = {2058-5276}, abstract = {Microorganisms in wastewater treatment plants (WWTPs) are essential for water purification to protect public and environmental health. However, the diversity of microorganisms and the factors that control it are poorly understood. Using a systematic global-sampling effort, we analysed the 16S ribosomal RNA gene sequences from ~1,200 activated sludge samples taken from 269 WWTPs in 23 countries on 6 continents. Our analyses revealed that the global activated sludge bacterial communities contain ~1 billion bacterial phylotypes with a Poisson lognormal diversity distribution. Despite this high diversity, activated sludge has a small, global core bacterial community (n = 28 operational taxonomic units) that is strongly linked to activated sludge performance. Meta-analyses with global datasets associate the activated sludge microbiomes most closely to freshwater populations. In contrast to macroorganism diversity, activated sludge bacterial communities show no latitudinal gradient. Furthermore, their spatial turnover is scale-dependent and appears to be largely driven by stochastic processes (dispersal and drift), although deterministic factors (temperature and organic input) are also important. Our findings enhance our mechanistic understanding of the global diversity and biogeography of activated sludge bacterial communities within a theoretical ecology framework and have important implications for microbial ecology and wastewater treatment processes.}, }
@article {pmid31086216, year = {2019}, author = {Agamennone, V and Le, NG and van Straalen, NM and Brouwer, A and Roelofs, D}, title = {Antimicrobial activity and carbohydrate metabolism in the bacterial metagenome of the soil-living invertebrate Folsomia candida.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {7308}, doi = {10.1038/s41598-019-43828-w}, pmid = {31086216}, issn = {2045-2322}, abstract = {The microbiome associated with an animal's gut and other organs is considered an integral part of its ecological functions and adaptive capacity. To better understand how microbial communities influence activities and capacities of the host, we need more information on the functions that are encoded in a microbiome. Until now, the information about soil invertebrate microbiomes is mostly based on taxonomic characterization, achieved through culturing and amplicon sequencing. Using shotgun sequencing and various bioinformatics approaches we explored functions in the bacterial metagenome associated with the soil invertebrate Folsomia candida, an established model organism in soil ecology with a fully sequenced, high-quality genome assembly. Our metagenome analysis revealed a remarkable diversity of genes associated with antimicrobial activity and carbohydrate metabolism. The microbiome also contains several homologs to F. candida genes that were previously identified as candidates for horizontal gene transfer (HGT). We suggest that the carbohydrate- and antimicrobial-related functions encoded by Folsomia's metagenome play a role in the digestion of recalcitrant soil-born polysaccharides and the defense against pathogens, thereby significantly contributing to the adaptation of these animals to life in the soil. Furthermore, the transfer of genes from the microbiome may constitute an important source of new functions for the springtail.}, }
@article {pmid31086023, year = {2019}, author = {McLaughlin, J and Watterson, S and Layton, AM and Bjourson, AJ and Barnard, E and McDowell, A}, title = {Propionibacterium acnes and Acne Vulgaris: New Insights from the Integration of Population Genetic, Multi-Omic, Biochemical and Host-Microbe Studies.}, journal = {Microorganisms}, volume = {7}, number = {5}, pages = {}, doi = {10.3390/microorganisms7050128}, pmid = {31086023}, issn = {2076-2607}, support = {025/s/16//British Skin Foundation/ ; }, abstract = {The anaerobic bacterium Propionibacterium acnes is believed to play an important role in the pathophysiology of the common skin disease acne vulgaris. Over the last 10 years our understanding of the taxonomic and intraspecies diversity of this bacterium has increased tremendously, and with it the realisation that particular strains are associated with skin health while others appear related to disease. This extensive review will cover our current knowledge regarding the association of P. acnes phylogroups, clonal complexes and sequence types with acne vulgaris based on multilocus sequence typing of isolates, and direct ribotyping of the P. acnes strain population in skin microbiome samples based on 16S rDNA metagenomic data. We will also consider how multi-omic and biochemical studies have facilitated our understanding of P. acnes pathogenicity and interactions with the host, thus providing insights into why certain lineages appear to have a heightened capacity to contribute to acne vulgaris development, while others are positively associated with skin health. We conclude with a discussion of new therapeutic strategies that are currently under investigation for acne vulgaris, including vaccination, and consider the potential of these treatments to also perturb beneficial lineages of P. acnes on the skin.}, }
@article {pmid31085071, year = {2019}, author = {Jansson, JK and Hofmockel, KS}, title = {Corrigendum to &quot;The soil microbiome - from metagenomics to metaphenomics&quot; [Curr Opin Micrbiol 43 (June 2018) 162-168].}, journal = {Current opinion in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.mib.2019.04.004}, pmid = {31085071}, issn = {1879-0364}, }
@article {pmid31085022, year = {2019}, author = {Tsementzi, D and Rodriguez-R, LM and Ruiz-Perez, CA and Meziti, A and Hatt, JK and Konstantinidis, K}, title = {Ecogenomic characterization of widespread, closely-related SAR11 clades of the freshwater genus &quot;Candidatus Fonsibacter&quot; and proposal of Ca. Fonsibacter lacus sp. nov.}, journal = {Systematic and applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.syapm.2019.03.007}, pmid = {31085022}, issn = {1618-0984}, abstract = {The ubiquitous alpha-proteobacteria of the order &quot;Candidatus Pelagibacterales&quot; (SAR11) are highly abundant in aquatic environments, and among them, members of the monophyletic lineage LD12 (also known as SAR11 clade IIIb) are specifically found in lacustrine ecosystems. Clade IIIb bacteria are some of the most prominent members of freshwater environments, but little is known about their biology due to the lack of genome representatives. Only recently, the first non-marine isolate was cultured and described as &quot;Candidatus Fonsibacter ubiquis&quot;. Here, we expand the collection of freshwater IIIb representatives and describe a new IIIb species of the genus &quot;Ca. Fonsibacter&quot;. Specifically, we assembled a collection of 67 freshwater metagenomic datasets from the interconnected lakes of the Chattahoochee River basin (GA, USA) and obtained nearly complete metagenome-assembled genomes (MAGs) representing 5 distinct IIIb subclades, roughly equivalent to species based on genomic standards, including the previously described &quot;Ca. F. ubiquis&quot;. Genomic comparisons between members of the IIIb species revealed high similarity in gene content. However, when comparing their abundance profiles in the Chattahoochee basin and various aquatic environments, differences in temporal and spatial distributions among the distinct species were observed implying niche differentiation might be underlying the coexistence of the highly functionally similar representatives. The name Ca. Fonsibacter lacus sp. nov. is proposed for the most abundant and widespread species in the Chattahoochee River basin and various freshwater ecosystems.}, }
@article {pmid31081896, year = {2019}, author = {Rastelli, M and Cani, PD and Knauf, C}, title = {The gut microbiome influences host endocrine functions.}, journal = {Endocrine reviews}, volume = {}, number = {}, pages = {}, doi = {10.1210/er.2018-00280}, pmid = {31081896}, issn = {1945-7189}, abstract = {The gut microbiome is now considered as an organ contributing to the regulation of host metabolism. Since the finding of the existence of a relationship between the gut microbiome and specific diseases, numerous studies have also deciphered molecular mechanisms explaining how gut bacteria dialogue with host cells and eventually shape metabolism. Both metagenomic and metabolomic analyses have contributed to the discovery of bacterial-derived metabolites acting on host cells. In this review, we examine the molecular mechanisms by which bacterial metabolites are acting as paracrine or endocrine factors thereby regulating host metabolism. We highlight the impact of specific short chain fatty acids on the secretion of gut peptides (i.e., GLP-1, PYY) as well as other metabolites produced from different amino acids and regulating inflammation, glucose metabolism or energy homeostasis. We also discuss the role of gut microbes on the regulation of bioactive lipids that belong to the endocannabinoid system as well as specific neurotransmitters (e.g., GABA, serotonin, NO). Finally, we review the role of specific bacterial components (i.e., ClpB, Amuc_1100) also acting as endocrine factors and eventually controlling host metabolism. In conclusion, this review summarizes recent state-of-the art aiming at providing evidence that the gut microbiome influences host endocrine functions via several bacterial-derived metabolites.}, }
@article {pmid31081685, year = {2019}, author = {Thombre, RS and Shivakarthik, E and Sivaraman, B and Vaishampayan, PA and Seuylemezian, A and Meka, JK and Vijayan, S and Kulkarni, PP and Pataskar, T and Patil, BS}, title = {Survival of Extremotolerant Bacteria from the Mukundpura Meteorite Impact Crater.}, journal = {Astrobiology}, volume = {}, number = {}, pages = {}, doi = {10.1089/ast.2018.1928}, pmid = {31081685}, issn = {1557-8070}, abstract = {Carbonaceous meteorites provide clues with regard to prebiotic chemistry and the origin of life. Geological Survey of India recorded a carbonaceous chondrite meteorite fall in Mukundpura, India, on June 6, 2017. We conducted a study to investigate the microbial community that survived the meteorite impact. 16S rRNA metagenomic sequencing indicates the presence of Actinobacteria, Proteobacteria, and Acidobacteria in meteorite impact soil. Comparative phylogenetic analysis revealed an intriguing abundance of class Bacilli in the impact soil. Bacillus thermocopriae IR-1, a moderately thermotolerant organism, was isolated from a rock, impacted by the Mukundpura meteorite. We investigated the resilience of B. thermocopriae IR-1 to environmental stresses and impact shock in a Reddy shock tube. B. thermocopriae IR-1 survived (28.82% survival) the effect of shock waves at a peak shock pressure of 300 kPa, temperature 400 K, and Mach number of 1.47. This investigation presents the first report on the effect of impact shock on B. thermocopriae IR-1. The study is also the first report on studying the microbial diversity and isolation of bacteria from impact crater soil immediately after meteorite impact event.}, }
@article {pmid31081473, year = {2019}, author = {Suryawanshi, PR and Badapanda, C and Singh, KM and Rathore, A}, title = {Exploration of the rumen microbial diversity and carbohydrate active enzyme profile of black Bengal goat using metagenomic approach.}, journal = {Animal biotechnology}, volume = {}, number = {}, pages = {1-14}, doi = {10.1080/10495398.2019.1609489}, pmid = {31081473}, issn = {1532-2378}, abstract = {Black Bengal goats possess a rich source of rumen microbiota that helps them to adapt for the better utilization of plant biomaterial into energy and nutrients, a task largely performed by enzymes encoded by the rumen microbiota. Therefore the study was designed in order to explore the taxonomic profile of rumen microbial communities and potential biomass degradation enzymes present in the rumen of back Bengal goat using Illumina Nextseq-500 platform. A total of 83.18 million high-quality reads were generated and bioinformatics analysis was performed using various tools and subsequently, the predicted ORFs along with the rRNA containing contigs were then uploaded to MG-RAST to analyze taxonomic and functional profiling. The results highlighted that Bacteriodetes (41.38-59.74%) were the most abundant phyla followed by Firmicutes (30.59-39.96%), Proteobacteria (5.07-7.61%), Euryarcheaota (0.71-7.41%), Actinobacteria (2.05-2.75%). Genes that encode glycoside hydrolases (GHs) had the highest number of CAZymes, and accounted for (39.73-37.88%) of all CAZymes in goat rumen. The GT families were the second-most abundant in CAZymes (23.73-23.11%) and followed by Carbohydrate Binding module Domain (17.65-15.61%), Carbohydrate Esterase (12.90-11.95%). This study indicated that goat rumen had complex functional microorganisms produce numerous CAZymes, and that can be further effectively utilised for applied ruminant research and industry based applications.}, }
@article {pmid31080075, year = {2019}, author = {Macdonald, SS and Armstrong, Z and Morgan-Lang, C and Osowiecka, M and Robinson, K and Hallam, SJ and Withers, SG}, title = {Development and Application of a High-Throughput Functional Metagenomic Screen for Glycoside Phosphorylases.}, journal = {Cell chemical biology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chembiol.2019.03.017}, pmid = {31080075}, issn = {2451-9448}, abstract = {Glycoside phosphorylases (GPs) catalyze the reversible phosphorolysis of glycosidic bonds, releasing sugar 1-phosphates. To identify a greater range of these under-appreciated enzymes, we have developed a high-throughput functional screening method based on molybdenum blue formation. In a proof-of-principle screen focused on cellulose-degrading GPs we interrogated ∼23,000 large insert (fosmid) clones sourced from microbial communities inhabiting two separate environments and identified seven novel GPs from carbohydrate active enzyme family GH94 and one from GH149. Characterization identified cellobiose phosphorylases, cellodextrin phosphorylases, laminaribiose phosphorylases, and a β-1,3-glucan phosphorylase. To demonstrate the versatility of the screening method, varying substrate combinations were used to identify GP activity from families GH13, GH65, GH112, and GH130 in addition to GH94 and GH149. These pilot screen and substrate versatility results provide a screening paradigm platform for recovering diverse GPs from uncultivated microbial communities acting on different substrates with considerable potential to unravel previously unknown degradative pathways within microbiomes.}, }
@article {pmid30535578, year = {2019}, author = {Zhang, F and Zheng, W and Xue, Y and Yao, W}, title = {Suhuai suckling piglet hindgut microbiome-metabolome responses to different dietary copper levels.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {2}, pages = {853-868}, doi = {10.1007/s00253-018-9533-0}, pmid = {30535578}, issn = {1432-0614}, support = {JATS[2018]287//The earmarked fund for Jiangsu Agricultural Industry Technology System/ ; 31372321//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Animals, Newborn ; Blood Chemical Analysis ; Copper/*administration &amp; dosage ; Diet/*methods ; Feces/chemistry ; Gas Chromatography-Mass Spectrometry ; Gastrointestinal Microbiome/*drug effects ; High-Throughput Nucleotide Sequencing ; Metabolome/*drug effects ; Metabolomics ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Swine ; Trace Elements/*administration &amp; dosage ; }, abstract = {Unabsorbed copper accumulates in the hindgut of pigs that consume high levels of dietary copper, which enhances the coselection of antibiotic-resistant bacteria and is considered detrimental to the environment and to porcine health. In our study, a combination of 16S rRNA pyrosequencing and nontargeted metabolomics was used to investigate the microbiome-metabolome responses to dietary copper levels in the hindgut of suckling piglets. The results showed that the dietary copper level affected the abundance of several Clostridia genera and that the relative abundance of butyrate-producing bacteria, such as Coprococcus, Roseburia, and Acidaminococcus, was reduced in the 300 mg kg-1 (high) Cu group. Metabolomic analysis revealed that dietary copper levels affected protein and carbohydrate metabolites, protein biosynthesis, the urea cycle, galactose metabolism, gluconeogenesis, and amino acid metabolism (including the metabolism of arginine, proline, β-alanine, phenylalanine, tyrosine, and methionine). Furthermore, Pearson's correlation analysis showed that the abundance levels of Coprococcus (family Lachnospiraceae) and operational taxonomic unit (OTU) 18 (family Ruminococcaceae) were positively correlated with energy metabolism pathways (gluconeogenesis, glycolysis, and the pentose phosphate pathway). The abundance of Streptococcus was negatively correlated with amino acid metabolism pathways (protein biosynthesis, glycine, serine, threonine, methionine, phenylalanine, and tyrosine metabolism), and OTU583 and OTU1067 (family Rikenellaceae) were positively correlated with amino acid metabolism pathways. These results suggest that the copper levels consumed by LC (low-copper group) versus HC (high-copper group) animals alter the composition of the gut microbiota and modulate microbial metabolic pathways, which may further affect the health of suckling piglets.}, }
@article {pmid30474727, year = {2019}, author = {Meng, H and Zhou, Z and Wu, R and Wang, Y and Gu, JD}, title = {Diazotrophic microbial community and abundance in acidic subtropical natural and re-vegetated forest soils revealed by high-throughput sequencing of nifH gene.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {2}, pages = {995-1005}, doi = {10.1007/s00253-018-9466-7}, pmid = {30474727}, issn = {1432-0614}, support = {31470562//National Natural Science Foundation of China/ ; 701913//Hong Kong RGC GRF grant/ ; }, mesh = {Acids/analysis ; Archaea/*classification/enzymology/genetics/metabolism ; Bacteria/*classification/enzymology/genetics/metabolism ; Chemical Phenomena ; Forests ; *Genetic Variation ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Microbiota ; *Nitrogen Fixation ; Oxidoreductases/*genetics ; Seasons ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Biological nitrogen fixation (BNF) is an important natural biochemical process converting the inert dinitrogen gas (N2) in the atmosphere to ammonia (NH3) in the N cycle. In this study, the nifH gene was chosen to detect the diazotrophic microorganisms with high-throughput sequencing from five acidic forest soils, including three natural forests and two re-vegetated forests. Soil samples were taken in two seasons (summer and winter) at two depth layers (surface and lower depths). A dataset of 179,600 reads obtained from 20 samples were analyzed to provide the microbial community structure, diversity, abundance, and relationship with physiochemical parameters. Both archaea and bacteria were detected in these samples and diazotrophic bacteria were the dominant members contributing to the biological dinitrogen fixation in the acidic forest soils. Cyanobacteria, Firmicutes, Proteobacteria, Spirocheates, and Verrucomicrobia were observed, especially the Proteobacteria as the most abundant phylum. The core genera were Bradyrhizobium and Methylobacterium from α-Proteobacteia, and Desulfovibrio from δ-Proteobacteia in the phylum of Proteobacteia of these samples. The diversity indices and the gene abundances of all samples were higher in the surface layer than the lower layer. Diversity was apparently higher in re-vegetated forests than the natural forests. Significant positive correlation to the organic matter and nitrogen-related parameters was observed, but there was no significant seasonal variation on the community structure and diversity in these samples between the summer and winter. The application of high-throughput sequencing method provides a better understanding and more comprehensive information of diazotrophs in acidic forest soils than conventional and PCR-based ones.}, }
@article {pmid30377368, year = {2018}, author = {McDonald, D and Vázquez-Baeza, Y and Koslicki, D and McClelland, J and Reeve, N and Xu, Z and Gonzalez, A and Knight, R}, title = {Striped UniFrac: enabling microbiome analysis at unprecedented scale.}, journal = {Nature methods}, volume = {15}, number = {11}, pages = {847-848}, doi = {10.1038/s41592-018-0187-8}, pmid = {30377368}, issn = {1548-7105}, mesh = {*Algorithms ; Bacteria/*classification/*genetics ; Computational Biology/*methods ; Computer Simulation ; Humans ; *Metagenome ; *Microbiota ; Models, Statistical ; Phylogeny ; }, }
@article {pmid30275573, year = {2018}, author = {Gonzalez, A and Navas-Molina, JA and Kosciolek, T and McDonald, D and Vázquez-Baeza, Y and Ackermann, G and DeReus, J and Janssen, S and Swafford, AD and Orchanian, SB and Sanders, JG and Shorenstein, J and Holste, H and Petrus, S and Robbins-Pianka, A and Brislawn, CJ and Wang, M and Rideout, JR and Bolyen, E and Dillon, M and Caporaso, JG and Dorrestein, PC and Knight, R}, title = {Qiita: rapid, web-enabled microbiome meta-analysis.}, journal = {Nature methods}, volume = {15}, number = {10}, pages = {796-798}, pmid = {30275573}, issn = {1548-7105}, support = {R01 HG004872/HG/NHGRI NIH HHS/United States ; R01 HL140976/HL/NHLBI NIH HHS/United States ; R01 MD011389/MD/NIMHD NIH HHS/United States ; }, mesh = {Computational Biology/*methods ; Humans ; *Internet ; *Metagenomics ; *Microbiota ; *Software ; User-Computer Interface ; }, abstract = {Multi-omic insights into microbiome function and composition typically advance one study at a time. However, in order for relationships across studies to be fully understood, data must be aggregated into meta-analyses. This makes it possible to generate new hypotheses by finding features that are reproducible across biospecimens and data layers. Qiita dramatically accelerates such integration tasks in a web-based microbiome-comparison platform, which we demonstrate with Human Microbiome Project and Integrative Human Microbiome Project (iHMP) data.}, }
@article {pmid28883464, year = {2017}, author = {Pettersson, JH and Shi, M and Bohlin, J and Eldholm, V and Brynildsrud, OB and Paulsen, KM and Andreassen, Å and Holmes, EC}, title = {Characterizing the virome of Ixodes ricinus ticks from northern Europe.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {10870}, pmid = {28883464}, issn = {2045-2322}, mesh = {Animals ; Computational Biology/methods ; Disease Vectors ; Europe ; Evolution, Molecular ; Humans ; Ixodes/*virology ; *Metagenome ; *Metagenomics/methods ; Molecular Sequence Annotation ; Phylogeny ; Viruses/*classification/*genetics ; }, abstract = {RNA viruses are abundant infectious agents and present in all domains of life. Arthropods, including ticks, are well known as vectors of many viruses of concern for human and animal health. Despite their obvious importance, the extent and structure of viral diversity in ticks is still poorly understood, particularly in Europe. Using a bulk RNA-sequencing approach that captures the complete transcriptome, we analysed the virome of the most common tick in Europe - Ixodes ricinus. In total, RNA sequencing was performed on six libraries consisting of 33 I. ricinus nymphs and adults sampled in Norway. Despite the small number of animals surveyed, our virus identification pipeline revealed nine diverse and novel viral species, phylogenetically positioned within four different viral groups - bunyaviruses, luteoviruses, mononegavirales and partitiviruses - and sometimes characterized by extensive genetic diversity including a potentially novel genus of bunyaviruses. This work sheds new light on the virus diversity in I. ricinus, expands our knowledge of potential host/vector-associations and tick-transmitted viruses within several viral groups, and pushes the latitudinal limit where it is likely to find tick-associated viruses. Notably, our phylogenetic analysis revealed the presence of tick-specific virus clades that span multiple continents, highlighting the role of ticks as important virus reservoirs.}, }
@article {pmid31079214, year = {2019}, author = {Tamim, S and Matthijnssens, J and Heylen, E and Zeller, M and Van Ranst, M and Salman, M and Hasan, F}, title = {Evidence of zoonotic transmission of VP6 and NSP4 genes into human species A rotaviruses isolated in Pakistan in 2010.}, journal = {Archives of virology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00705-019-04271-4}, pmid = {31079214}, issn = {1432-8798}, abstract = {Introduction of animal group A rotavirus (RVA) gene segments into the human RVA population is a major factor shaping the genetic landscape of human RVA strains. The VP6 and NSP4 genes of 74 G/P-genotyped RVA isolates collected in Rawalpindi during 2010 were analyzed, revealing the presence of VP6 genotypes I1 (60.8%) and I2 (39.2%) and NSP4 genotypes E1 (60.8%), E2 (28.3%) and E-untypable (10.8%) among the circulating human RVA strains. The typical human RVA combinations I1E1 and I2E2 were found in 59.4% and 24.3% of the cases, respectively, whereas 5.4% of the RVA strains were reassortants, i.e., either I1E2 or I2E1. The phylogeny of the NSP4 gene showed that one G2P[4] and two G1P[6] RVA strains clustered with porcine E1 RVA strains or RVA strains that were considered to be (partially) of porcine origin. In addition, the NSP4 gene segment of the unusual human G6P[1] RVA strains clustered closely with bovine E2 RVA strains, further strengthening the hypothesis of an interspecies transmission event. The study further demonstrates the role of genomic re-assortment and the involvement of interspecies transmission in the evolution of human RVA strains. The VP6 and NSP4 nucleotide sequences analyzed in the study received the GenBank accession numbers KC846908- KC846971 and KC846972-KC847037, respectively.}, }
@article {pmid31078243, year = {2019}, author = {Koliani-Pace, JL and Siegel, CA}, title = {Prognosticating the Course of Inflammatory Bowel Disease.}, journal = {Gastrointestinal endoscopy clinics of North America}, volume = {29}, number = {3}, pages = {395-404}, doi = {10.1016/j.giec.2019.02.003}, pmid = {31078243}, issn = {1558-1950}, abstract = {Both Crohn's disease and ulcerative colitis are inflammatory bowel diseases (IBD) that can lead to progressive irreversible bowel damage. Selecting the most appropriate therapy for patients is a challenge because not all patients diagnosed with IBD have complications, and the amount of time to develop a complication is different for individuals. Models using patient characteristics, genetics, and immune responses help identify those patients who require early aggressive therapy with a goal to modify their disease course. Future research will help identify the role that the microbiome, metagenomics, metaproteomics, and microRNAs play in a patient prognosis.}, }
@article {pmid31077935, year = {2019}, author = {Trotter, AJ and Aydin, A and Strinden, MJ and O'Grady, J}, title = {Recent and emerging technologies for the rapid diagnosis of infection and antimicrobial resistance.}, journal = {Current opinion in microbiology}, volume = {51}, number = {}, pages = {39-45}, doi = {10.1016/j.mib.2019.03.001}, pmid = {31077935}, issn = {1879-0364}, abstract = {The rise in antimicrobial resistance (AMR) is predicted to cause 10 million deaths per year by 2050 unless steps are taken to prevent this looming crisis. Microbiological culture is the gold standard for the diagnosis of bacterial/fungal pathogens and antimicrobial resistance and takes 48 hours or longer. Hence, antibiotic prescriptions are rarely based on a definitive diagnosis and patients often receive inappropriate treatment. Rapid diagnostic tools are urgently required to guide appropriate antimicrobial therapy, thereby improving patient outcomes and slowing AMR development. We discuss new technologies for rapid infection diagnosis including: sample-in-answer-out PCR-based tests, BioFire FilmArray and Curetis Unyvero; rapid susceptibility tests, Accelerate Pheno and microfluidic tests; and sequencing-based approaches, focusing on targeted and clinical metagenomic nanopore sequencing.}, }
@article {pmid31076501, year = {2019}, author = {Toivonen, L and Hasegawa, K and Waris, M and Ajami, NJ and Petrosino, JF and Camargo, CA and Peltola, V}, title = {Early nasal microbiota and acute respiratory infections during the first years of life.}, journal = {Thorax}, volume = {}, number = {}, pages = {}, doi = {10.1136/thoraxjnl-2018-212629}, pmid = {31076501}, issn = {1468-3296}, abstract = {BACKGROUND: Emerging evidence shows that airway microbiota may modulate local immune responses, thereby contributing to the susceptibility and severity of acute respiratory infections (ARIs). However, there are little data on the longitudinal relationships between airway microbiota and susceptibility to ARIs in children.<br><br>OBJECTIVE: We aimed to investigate the association of early nasal microbiota and the subsequent risk of ARIs during the first years of life.<br><br>METHODS: In this prospective population-based birth-cohort study in Finland, we followed 839 healthy infants for ARIs from birth to age 24 months. Nasal microbiota was tested using 16S rRNA gene sequencing at age 2 months. We applied an unsupervised clustering approach to identify early nasal microbiota profiles, and examined the association of profiles with the rate of ARIs during age 2-24 months.<br><br>RESULTS: We identified five nasal microbiota profiles dominated by Moraxella, Streptococcus, Dolosigranulum, Staphylococcus and Corynebacteriaceae, respectively. Incidence rate of ARIs was highest in children with an early Moraxella-dominant profile and lowest in those with a Corynebacteriaceae-dominant profile (738 vs 552/100 children years; unadjusted incidence rate ratio (IRR), 1.34; 95% CI 1.16 to 1.54; p < 0.001). After adjusting for nine potential confounders, the Moraxella-dominant profile-ARI association persisted (adjusted IRR (aIRR), 1.19; 95% CI 1.04 to 1.37; p = 0.01). Similarly, the incidence rate of lower respiratory tract infections (a subset of all ARIs) was significantly higher in children with an early Moraxella-dominant profile (aIRR, 2.79; 95% CI 1.04 to 8.09; p = 0.04).<br><br>CONCLUSION: Moraxella-dominant nasal microbiota profile in early infancy was associated with an increased rate of ARIs during the first 2 years of life.}, }
@article {pmid31075586, year = {2019}, author = {Zhang, L and Zhang, Y and Gamal El-Din, M}, title = {Integrated mild ozonation with biofiltration can effectively enhance the removal of naphthenic acids from hydrocarbon-contaminated water.}, journal = {The Science of the total environment}, volume = {678}, number = {}, pages = {197-206}, doi = {10.1016/j.scitotenv.2019.04.302}, pmid = {31075586}, issn = {1879-1026}, abstract = {An innovative biofiltration-ozonation-biofiltration process was established and applied for the treatment of oil sands process water (OSPW). With an equivalent hydraulic retention time (HRT) of 8 h, the biofiltration pretreatment removed 24.4% of classical naphthenic acids (NAs) and 3.3% of oxidized NAs from raw OSPW with removal rate of 0.4 mg/L/h and 0.1 mg/L. Oxidized NAs showed higher resistance to the biofiltration process than classical NAs. The mild ozonation process (with utilized ozone dose of 30 mg/L) removed 84.8% of classical NAs and 11.5% of oxidized NAs from the biofiltrated OSPW with a degradation efficiency of 0.3 mg classical NAs/mg O3 and 0.1 mg oxidized NAs/mg O3. However, by using the same utilized ozone dose, the degradation of classical NAs and oxidized NAs from raw OSPW was 32.1% and 3.9% with ozonation efficiency of 0.1 mg classical NAs/mg O3 and 0.0 mg oxidized NAs/mg O3, respectively. Compared with the biofiltration pretreatment, the post biofiltration process (with HRT of 8 h) showed higher degradation effect on oxidized NAs with removal ratio of 22.9% and removal rate of 0.4 mg/L/h, but showed lower degradation effect on classical NAs with removal ratio of 6.7% and removal rate of 0.0 mg/L/h. After biofiltration-ozonation-biofiltration treatment, the microbial community structure in the biofilter was investigated by next generation sequencing. Proteobacteria and Rhodococcus were dominant bacterial phyla and genus in the biofilter, the abundance of which were 47.21% and 9.50% which were different from those in raw OSPW (62.88% and 0.72%). The change of microbial community structure could be resulted from the interaction between microbial community and the circulating OSPW. The ozonation integrated biodegradation process removed 89.3% and 34.0% of classical and oxidized NAs from OSPW which shows high potential to be applied by the oil and gas industry.}, }
@article {pmid31073898, year = {2019}, author = {Zhao, H and Yan, B and Mo, S and Nie, S and Li, Q and Ou, Q and Wu, B and Jiang, G and Tang, J and Li, N and Jiang, C}, title = {Carbohydrate metabolism genes dominant in a subtropical marine mangrove ecosystem revealed by metagenomics analysis.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {}, number = {}, pages = {}, doi = {10.1007/s12275-019-8679-5}, pmid = {31073898}, issn = {1976-3794}, abstract = {Mangrove sediment microorganisms play a vital role in the energy transformation and element cycling in marine wetland ecosystems. Using metagenomics analysis strategy, we compared the taxonomic structure and gene profile of the mangrove and non-mangrove sediment samples at the subtropical estuary in Beibu Gulf, South China Sea. Proteobacteria, Bacteroidetes, and Firmicutes were the most abundant bacterial phyla. Archaeal family Methanosarcinaceae and bacterial genera Vibrio and Dehalococcoides were significantly higher in the mangrove sediments than in the nonmangrove sediments. Functional analysis showed that &quot;Carbohydrate metabolism&quot; was the most abundant metabolic category. The feature of carbohydrate-active enzymes (CZs) was analyzed using the Carbohydrate-Active EnZymes Database. The significant differences of CZs between mangrove and non-mangrove sediments, were attributed to the amounts of polyphenol oxidase (EC 1.10.3.-), hexosyltransferase (EC 2.4.1.-), and β-N-acetylhexosaminidase (EC 3.2.1.52), which were higher in the mangrove sediment samples. Principal component analysis indicated that the microbial community and gene profile between mangrove and non-mangrove sediments were distinct. Redundancy analysis showed that total organic carbon is a significant factor that affects the microbial community and gene distribution. The results indicated that the mangrove ecosystem with massive amounts of organic carbon may promote the richness of carbohydrate metabolism genes and enhance the degradation and utilization of carbohydrates in the mangrove sediments.}, }
@article {pmid31073691, year = {2019}, author = {Bersanelli, M and Santoni, M and Ticinesi, A and Buti, S}, title = {The Urinary Microbiome and Anticancer Immunotherapy: The Potentially Hidden Role of Unculturable Microbes.}, journal = {Targeted oncology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11523-019-00643-7}, pmid = {31073691}, issn = {1776-260X}, abstract = {Several urinary disorders, including overactive bladder, urinary incontinence, and interstitial cystitis, are often characterized by negative urine cultures. The application of metagenomics (i.e., 16S rRNA microbial profiling or whole-genome shotgun sequencing) to urine samples has enabled the identification of previously undetected bacteria, contributing to the discovery and characterization of the urinary microbiome. The most frequent species isolated are Lactobacillus (15%), Corynebacterium (14.2%), Streptococcus (11.9%), Actinomyces (6.9%), and Staphylococcus (6.9%). Although several studies are emerging in this context, the role of urinary microbiota in the pathogenesis of infections and in tumor carcinogenesis remains unclear. Furthermore, data on the activity of gut microbiota in modulating sensitivity to immune checkpoint inhibitors in advanced cancer patients suggest that the influence of urinary microbiota on tumor response to anticancer therapy should also be investigated. Moreover, its possible relationship with tumor mutational burden, which is in turn correlated with response to immunotherapy, should be the focus of future studies. Of note, the effect of antibiotics on this complex scenario seems to deserve careful consideration.}, }
@article {pmid31071993, year = {2019}, author = {Ziko, L and Adel, M and Malash, MN and Siam, R}, title = {Insights into Red Sea Brine Pool Specialized Metabolism Gene Clusters Encoding Potential Metabolites for Biotechnological Applications and Extremophile Survival.}, journal = {Marine drugs}, volume = {17}, number = {5}, pages = {}, doi = {10.3390/md17050273}, pmid = {31071993}, issn = {1660-3397}, support = {NA//AUC Faculty Support Grant to RS/ ; }, abstract = {The recent rise in antibiotic and chemotherapeutic resistance necessitates the search for novel drugs. Potential therapeutics can be produced by specialized metabolism gene clusters (SMGCs). We mined for SMGCs in metagenomic samples from Atlantis II Deep, Discovery Deep and Kebrit Deep Red Sea brine pools. Shotgun sequence assembly and secondary metabolite analysis shell (antiSMASH) screening unraveled 2751 Red Sea brine SMGCs, pertaining to 28 classes. Predicted categorization of the SMGC products included those (1) commonly abundant in microbes (saccharides, fatty acids, aryl polyenes, acyl-homoserine lactones), (2) with antibacterial and/or anticancer effects (terpenes, ribosomal peptides, non-ribosomal peptides, polyketides, phosphonates) and (3) with miscellaneous roles conferring adaptation to the environment/special structure/unknown function (polyunsaturated fatty acids, ectoine, ladderane, others). Saccharide (80.49%) and putative (7.46%) SMGCs were the most abundant. Selected Red Sea brine pool sites had distinct SMGC profiles, e.g., for bacteriocins and ectoine. Top promising candidates, SMs with pharmaceutical applications, were addressed. Prolific SM-producing phyla (Proteobacteria, Actinobacteria, Cyanobacteria), were ubiquitously detected. Sites harboring the largest numbers of bacterial and archaeal phyla, had the most SMGCs. Our results suggest that the Red Sea brine niche constitutes a rich biological mine, with the predicted SMs aiding extremophile survival and adaptation.}, }
@article {pmid31071918, year = {2019}, author = {Dai, L and Zhang, G and Yu, Z and Ding, H and Xu, Y and Zhang, Z}, title = {Effect of Drought Stress and Developmental Stages on Microbial Community Structure and Diversity in Peanut Rhizosphere Soil.}, journal = {International journal of molecular sciences}, volume = {20}, number = {9}, pages = {}, doi = {10.3390/ijms20092265}, pmid = {31071918}, issn = {1422-0067}, support = {2018YFD0201007//National Key Research and Development Program of China/ ; SDAIT-04-06//Modern Agricultural Industry Technical System of Shandong Province/ ; }, abstract = {BACKGROUND: Peanut (Arachis hypogaea L.), an important oilseed and food legume, is widely cultivated in the semi-arid tropics. Drought is the major stress in this region which limits productivity. Microbial communities in the rhizosphere are of special importance to stress tolerance. However, relatively little is known about the relationship between drought and microbial communities in peanuts.<br><br>METHOD: In this study, deep sequencing of the V3-V4 region of the 16S rRNA gene was performed to characterize the microbial community structure of drought-treated and untreated peanuts.<br><br>RESULTS: Taxonomic analysis showed that Actinobacteria, Proteobacteria, Saccharibacteria, Chloroflexi, Acidobacteria and Cyanobacteria were the dominant phyla in the peanut rhizosphere. Comparisons of microbial community structure of peanuts revealed that the relative abundance of Actinobacteria and Acidobacteria dramatically increased in the seedling and podding stages in drought-treated soil, while that of Cyanobacteria and Gemmatimonadetes increased in the flowering stage in drought-treated rhizospheres. Metagenomic profiling indicated that sequences related to metabolism, signaling transduction, defense mechanism and basic vital activity were enriched in the drought-treated rhizosphere, which may have implications for plant survival and drought tolerance.<br><br>CONCLUSION: This microbial communities study will form the foundation for future improvement of drought tolerance of peanuts via modification of the soil microbes.}, }
@article {pmid31069047, year = {2017}, author = {Agafonov, A and Mattila, K and Tuan, CD and Tiede, L and Raknes, IA and Bongo, LA}, title = {META-pipe cloud setup and execution.}, journal = {F1000Research}, volume = {6}, number = {}, pages = {}, doi = {10.12688/f1000research.13204.1}, pmid = {31069047}, issn = {2046-1402}, abstract = {META-pipe is a complete service for the analysis of marine metagenomic data. It provides assembly of high-throughput sequence data, functional annotation of predicted genes, and taxonomic profiling. The functional annotation is computationally demanding and is therefore currently run on a high-performance computing cluster in Norway. However, additional compute resources are necessary to open the service to all ELIXIR users. We describe our approach for setting up and executing the functional analysis of META-pipe on additional academic and commercial clouds. Our goal is to provide a powerful analysis service that is easy to use and to maintain. Our design therefore uses a distributed architecture where we combine central servers with multiple distributed backends that execute the computationally intensive jobs. We believe our experiences developing and operating META-pipe provides a useful model for others that plan to provide a portal based data analysis service in ELIXIR and other organizations with geographically distributed compute and storage resources.}, }
@article {pmid31071295, year = {2019}, author = {Abbas, AA and Taylor, LJ and Dothard, MI and Leiby, JS and Fitzgerald, AS and Khatib, LA and Collman, RG and Bushman, FD}, title = {Redondoviridae, a Family of Small, Circular DNA Viruses of the Human Oro-Respiratory Tract Associated with Periodontitis and Critical Illness.}, journal = {Cell host &amp; microbe}, volume = {25}, number = {5}, pages = {719-729.e4}, doi = {10.1016/j.chom.2019.04.001}, pmid = {31071295}, issn = {1934-6069}, abstract = {The global virome is largely uncharacterized but is now being unveiled by metagenomic DNA sequencing. Exploring the human respiratory virome, in particular, can provide insights into oro-respiratory diseases. Here, we use metagenomics to identify a family of small circular DNA viruses-named Redondoviridae-associated with human diseases. We first identified two redondovirus genomes from bronchoalveolar lavage samples from human lung donors. We then queried thousands of metagenomic samples and recovered 17 additional complete redondovirus genomes. Detections were exclusively in human samples and mostly from respiratory tract and oro-pharyngeal sites, where Redondoviridae was the second most prevalent eukaryotic DNA virus family. Redondovirus sequences were associated with periodontal disease, and abundances decreased with treatment. Some critically ill patients in a medical intensive care unit were found to harbor high levels of redondoviruses in respiratory samples. These results suggest that redondoviruses colonize human oro-respiratory sites and can bloom in several human disorders.}, }
@article {pmid31071293, year = {2019}, author = {MacLeod, AS}, title = {Bad &quot;Staph&quot; in the Wound Environment of Diabetic Foot Ulcers.}, journal = {Cell host &amp; microbe}, volume = {25}, number = {5}, pages = {638-640}, doi = {10.1016/j.chom.2019.04.006}, pmid = {31071293}, issn = {1934-6069}, abstract = {Diabetic foot ulcers (DFUs) are a leading cause of high morbidity among diabetic patients. In this issue of Cell Host &amp; Microbe, Kalan et al. (2019) examine the microbial bio-burden of DFUs and reveal biofilm and virulence pathways in the microbial metagenome that are linked to clinical healing outcomes.}, }
@article {pmid31071291, year = {2019}, author = {Noell, K and Kolls, JK}, title = {Further Defining the Human Virome using NGS: Identification of Redondoviridae.}, journal = {Cell host &amp; microbe}, volume = {25}, number = {5}, pages = {634-635}, doi = {10.1016/j.chom.2019.04.010}, pmid = {31071291}, issn = {1934-6069}, abstract = {In this issue of Cell Host &amp; Microbe, Abbas et al. (2019) uncover a previously undefined family of single-stranded DNA viruses, Redondoviridae, in human ororespiratory sites. The presence of Redondoviridae associates with critical illness such as respiratory failure and periodontitis, illustrating the power of metagenomics to define the human virome.}, }
@article {pmid31069462, year = {2019}, author = {Mahapatra, GP and Raman, S and Nayak, S and Gouda, S and Das, G and Patra, JK}, title = {Metagenomics Approaches in Discovery and Development of New Bioactive Compounds from Marine Actinomycetes.}, journal = {Current microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00284-019-01698-5}, pmid = {31069462}, issn = {1432-0991}, abstract = {Marine actinomycetes are prolific sources of marine drug discovery system contributing for several bioactive compounds of biomedical prominence. Metagenomics, a culture-independent technique through its sequence- and function-based screening has led to the discovery and synthesis of numerous biologically significant compounds like polyketide synthase, Non-ribosomal peptide synthetase, antibiotics, and biocatalyst. While metagenomics offers different advantages over conventional sequencing techniques, they also have certain limitations including bias classification, non-availability of quality DNA samples, heterologous expression, and host selection. The assimilation of advanced amplification and screening methods such as φ29 DNA polymerase, Next-Generation Sequencing, Cosmids, and recent bioinformatics tools like automated genome mining, anti-SMASH have shown promising results to overcome these constrains. Consequently, functional genomics and bioinformatics along with synthetic biology will be crucial for the success of the metagenomic approach and indeed for exploring new possibilities among the microbial consortia for the future drug discovery process.}, }
@article {pmid31068916, year = {2019}, author = {Zhang, X and Payne, M and Lan, R}, title = {In silico Identification of Serovar-Specific Genes for Salmonella Serotyping.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {835}, doi = {10.3389/fmicb.2019.00835}, pmid = {31068916}, issn = {1664-302X}, abstract = {Salmonella enterica subspecies enterica is a highly diverse subspecies with more than 1500 serovars and the ability to distinguish serovars within this group is vital for surveillance. With the development of whole-genome sequencing technology, serovar prediction by traditional serotyping is being replaced by molecular serotyping. Existing in silico serovar prediction approaches utilize surface antigen encoding genes, core genome MLST and serovar-specific gene markers or DNA fragments for serotyping. However, these serovar-specific gene markers or DNA fragments only distinguished a small number of serovars. In this study, we compared 2258 Salmonella accessory genomes to identify 414 candidate serovar-specific or lineage-specific gene markers for 106 serovars which includes 24 polyphyletic serovars and the paraphyletic serovar Enteritidis. A combination of several lineage-specific gene markers can be used for the clear identification of the polyphyletic serovars and the paraphyletic serovar. We designed and evaluated an in silico serovar prediction approach by screening 1089 genomes representing 106 serovars against a set of 131 serovar-specific gene markers. The presence or absence of one or more serovar-specific gene markers was used to predict the serovar of an isolate from genomic data. We show that serovar-specific gene markers have comparable accuracy to other in silico serotyping methods with 84.8% of isolates assigned to the correct serovar with no false positives (FP) and false negatives (FN) and 10.5% of isolates assigned to a small subset of serovars containing the correct serovar with varied FP. Combined, 95.3% of genomes were correctly assigned to a serovar. This approach would be useful as diagnosis moves to culture-independent and metagenomic methods as well as providing a third alternative to confirm other genome-based analyses. The identification of a set of gene markers may also be useful in the development of more cost-effective molecular assays designed to detect specific gene markers of the all major serovars in a region. These assays would be useful in serotyping isolates where cultures are no longer obtained and traditional serotyping is therefore impossible.}, }
@article {pmid31068913, year = {2019}, author = {Ai, D and Pan, H and Li, X and Gao, Y and Liu, G and Xia, LC}, title = {Identifying Gut Microbiota Associated With Colorectal Cancer Using a Zero-Inflated Lognormal Model.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {826}, doi = {10.3389/fmicb.2019.00826}, pmid = {31068913}, issn = {1664-302X}, abstract = {Colorectal cancer (CRC) is the third most common cancer worldwide. Its incidence is still increasing, and the mortality rate is high. New therapeutic and prognostic strategies are urgently needed. It became increasingly recognized that the gut microbiota composition differs significantly between healthy people and CRC patients. Thus, identifying the difference between gut microbiota of the healthy people and CRC patients is fundamental to understand these microbes' functional roles in the development of CRC. We studied the microbial community structure of a CRC metagenomic dataset of 156 patients and healthy controls, and analyzed the diversity, differentially abundant bacteria, and co-occurrence networks. We applied a modified zero-inflated lognormal (ZIL) model for estimating the relative abundance. We found that the abundance of genera: Anaerostipes, Bilophila, Catenibacterium, Coprococcus, Desulfovibrio, Flavonifractor, Porphyromonas, Pseudoflavonifractor, and Weissella was significantly different between the healthy and CRC groups. We also found that bacteria such as Streptococcus, Parvimonas, Collinsella, and Citrobacter were uniquely co-occurring within the CRC patients. In addition, we found that the microbial diversity of healthy controls is significantly higher than that of the CRC patients, which indicated a significant negative correlation between gut microbiota diversity and the stage of CRC. Collectively, our results strengthened the view that individual microbes as well as the overall structure of gut microbiota were co-evolving with CRC.}, }
@article {pmid31068624, year = {2019}, author = {Catron, TR and Swank, A and Wehmas, LC and Phelps, D and Keely, SP and Brinkman, NE and McCord, J and Singh, R and Sobus, J and Wood, CE and Strynar, M and Wheaton, E and Tal, T}, title = {Microbiota alter metabolism and mediate neurodevelopmental toxicity of 17β-estradiol.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {7064}, doi = {10.1038/s41598-019-43346-9}, pmid = {31068624}, issn = {2045-2322}, abstract = {Estrogenic chemicals are widespread environmental contaminants associated with diverse health and ecological effects. During early vertebrate development, estrogen receptor signaling is critical for many different physiologic responses, including nervous system function. Recently, host-associated microbiota have been shown to influence neurodevelopment. Here, we hypothesized that microbiota may biotransform exogenous 17-βestradiol (E2) and modify E2 effects on swimming behavior. Colonized zebrafish were continuously exposed to non-teratogenic E2 concentrations from 1 to 10 days post-fertilization (dpf). Changes in microbial composition and predicted metagenomic function were evaluated. Locomotor activity was assessed in colonized and axenic (microbe-free) zebrafish exposed to E2 using a standard light/dark behavioral assay. Zebrafish tissue was collected for chemistry analyses. While E2 exposure did not alter microbial composition or putative function, colonized E2-exposed larvae showed reduced locomotor activity in the light, in contrast to axenic E2-exposed larvae, which exhibited normal behavior. Measured E2 concentrations were significantly higher in axenic relative to colonized zebrafish. Integrated peak area for putative sulfonated and glucuronidated E2 metabolites showed a similar trend. These data demonstrate that E2 locomotor effects in the light phase are dependent on the presence of microbiota and suggest that microbiota influence chemical E2 toxicokinetics. More broadly, this work supports the concept that microbial colonization status may influence chemical toxicity.}, }
@article {pmid31068435, year = {2019}, author = {Guron, GKP and Arango-Argoty, G and Zhang, L and Pruden, A and Ponder, MA}, title = {Effects of Dairy Manure-Based Amendments and Soil Texture on Lettuce- and Radish-Associated Microbiota and Resistomes.}, journal = {mSphere}, volume = {4}, number = {3}, pages = {}, doi = {10.1128/mSphere.00239-19}, pmid = {31068435}, issn = {2379-5042}, abstract = {Dairy cattle are routinely treated with antibiotics, and the resulting manure or composted manure is commonly used as a soil amendment for crop production, raising questions regarding the potential for antibiotic resistance to propagate from &quot;farm to fork.&quot; The objective of this study was to compare the microbiota and &quot;resistomes&quot; (i.e., carriage of antibiotic resistance genes [ARGs]) associated with lettuce leaf and radish taproot surfaces grown in different soils amended with dairy manure, compost, or chemical fertilizer only (control). Manure was collected from antibiotic-free dairy cattle (DC) or antibiotic-treated dairy cattle (DA), with a portion composted for parallel comparison. Amendments were applied to loamy sand or silty clay loam, and lettuce and radishes were cultivated to maturity in a greenhouse. Metagenomes were profiled via shotgun Illumina sequencing. Radishes carried a distinct ARG composition compared to that of lettuce, with greater relative abundance of total ARGs. Taxonomic species richness was also greater for radishes by 1.5-fold. The resistomes of lettuce grown with DC compost were distinct from those grown with DA compost, DC manure, or fertilizer only. Further, compost applied to loamy sand resulted in twofold-greater relative abundance of total ARGs on lettuce than when applied to silty clay loam. The resistomes of radishes grown with biological amendments were distinct from the corresponding fertilizer controls, but effects of composting or antibiotic use were not measureable. Cultivation in loamy sand resulted in higher species richness for both lettuce and radishes than when grown in silty clay loam by 2.2-fold and 1.2-fold, respectively, when amended with compost.IMPORTANCE A controlled, integrated, and replicated greenhouse study, along with comprehensive metagenomic analysis, revealed that multiple preharvest factors, including antibiotic use during manure collection, composting, biological soil amendment, and soil type, influence vegetable-borne resistomes. Here, radishes, a root vegetable, carried a greater load of ARGs and species richness than lettuce, a leafy vegetable. However, the lettuce resistome was more noticeably influenced by upstream antibiotic use and composting. Network analysis indicated that cooccurring ARGs and mobile genetic elements were almost exclusively associated with conditions receiving raw manure amendments, suggesting that composting could alleviate the mobility of manure-derived resistance traits. Effects of preharvest factors on associated microbiota and resistomes of vegetables eaten raw are worthy of further examination in terms of potential influence on human microbiomes and spread of antibiotic resistance. This research takes a step toward identifying on-farm management practices that can help mitigate the spread of agricultural sources of antibiotic resistance.}, }
@article {pmid31068191, year = {2019}, author = {Laiton-Donato, K and Alvarez, DA and Peláez-Carvajal, D and Mercado, M and Ajami, NJ and Bosch, I and Usme-Ciro, JA}, title = {Molecular characterization of dengue virus reveals regional diversification of serotype 2 in Colombia.}, journal = {Virology journal}, volume = {16}, number = {1}, pages = {62}, doi = {10.1186/s12985-019-1170-4}, pmid = {31068191}, issn = {1743-422X}, support = {210465740977//Colciencias/ ; }, abstract = {Dengue is hyperendemic in Colombia, where a cyclic behavior of serotype replacement leading to periodic epidemics has been observed for decades. This level of endemicity favors accumulation of dengue virus genetic diversity and could be linked to disease outcome. To assess the genetic diversity of dengue virus type 2 in Colombia, we sequenced the envelope gene of 24 virus isolates from acute cases of dengue or severe dengue fever during the period 2013-2016. The phylogenetic analysis revealed the circulation of the Asian-American genotype of dengue virus type 2 in Colombia during that period, the intra-genotype variability leading to divergence in two recently circulating lineages with differential geographic distribution, as well as the presence of nonsynonymous substitutions accompanying their emergence and diversification.}, }
@article {pmid31067837, year = {2019}, author = {Sarmiento, MRA and de Paula, TO and Borges, FM and Ferreira-Machado, AB and Resende, JA and Moreira, APB and Dutra Luquetti, SCP and Cesar, DE and da Silva, VL and Diniz, CG}, title = {Obesity, Xenobiotic Intake and Antimicrobial-Resistance Genes in the Human Gastrointestinal Tract: A Comparative Study of Eutrophic, Overweight and Obese Individuals.}, journal = {Genes}, volume = {10}, number = {5}, pages = {}, doi = {10.3390/genes10050349}, pmid = {31067837}, issn = {2073-4425}, abstract = {Although lifestyle and physiology in obese individuals are accepted to lead to changes in the intestinal microbiota, uncertainty remains about microbiota dysbiosis, and xenobiotics intake, as a source of selective pressure, independent of antimicrobial chemotherapy. The aim of this study was to compare the occurrence of antimicrobial resistance genetic markers (ARG) in faecal specimens of eutrophic, overweight and obese individuals, and their correlation with xenobiotic intake and gut bacteria density. Methods: This was a cross-sectional case-controlled study including 72 adult participants with no record of intestinal or systemic diseases, or recent use of antimicrobials, grouped as eutrophic, overweight, or obese. Anthropometric profile, eating habits and oral xenobiotics intake were recorded. Faecal metagenomic DNA was used to screen for ARG by PCR, and to measure bacterial groups by fluorescence in situ hybridization (FISH). Student's t and Wilcoxon tests were used to compare means and differences in ARG detection (95% confidence intervals). Correlation analyses (odds ratio) and relationships between bacteria density and ARG were determined. Results: Increase in abdominal circumference, waist circumference, hip, waist-hip ratio, BMI, carbohydrate, fibres, and total calorie intakes were different from eutrophic to obese participants. Habitual use of antihypertensive and anti-inflammatory drugs, antacids, and artificial sweeteners were associated mainly with obesity and overweight. Nutritional supplements were associated to the eutrophic group. ARG screening showed differences being more frequent among obese, and positive for 27 genetic markers related to β-lactams, tetracyclines, the macrolide lincosamide and streptogramin group, quinolones, sulfonamides, aminoglycosides, and efflux pump. Positive correlation between ARG and BMI, caloric intake, and intake of xenobiotics, was observed for obese individuals. Relationships among ARG detection and bacteria densities were also different. Conclusions: This study reinforces the hypothesis that obese individuals may harbour an altered gut microbiota, if compared to eutrophic. The overweight individuals display a transitional gut microbiota which seems to be between eutrophic and obese. Furthermore, the increased xenobiotic intake associated to obesity may play an important role in the antimicrobial resistance phenomenon.}, }
@article {pmid31067715, year = {2019}, author = {Ghai, V and Kim, TK and Etheridge, A and Nielsen, T and Hansen, T and Pedersen, O and Galas, D and Wang, K}, title = {Extracellular Vesicle Encapsulated MicroRNAs in Patients with Type 2 Diabetes Are Affected by Metformin Treatment.}, journal = {Journal of clinical medicine}, volume = {8}, number = {5}, pages = {}, doi = {10.3390/jcm8050617}, pmid = {31067715}, issn = {2077-0383}, support = {W81XWH-16-1-0301//U.S. Department of Defense/ ; HDTRA1-13-C-0055//Defense Threat Reduction Agency/ ; W911NF-17-2-0086//U.S. Department of Defense/ ; U01HL126496-02//National Institutes of Health/ ; R56HL133887//National Institutes of Health/ ; U01CA213330//National Institutes of Health/ ; R01DA040395//National Institutes of Health/ ; NNF18CC0034900//Novo Nordisk Fonden/ ; }, abstract = {Recently, microRNAs (miRNAs) in circulating extracellular vesicles (EVs), have emerged as a source of potential biomarkers for various pathophysiological conditions, including metabolic disorders such as diabetes. Type 2 diabetes mellitus (T2DM), is the most prevalent form of diabetes in the USA, with 30 million diagnosed patients. Identifying miRNA biomarkers that can be used to assess response to glucose lowering treatments would be useful. Using patient plasma samples from a subset of the Danish Metagenomics of the Human Intestinal Tract (MetaHIT) cohort, we characterized miRNAs from whole plasma, plasma-derived EVs, and EV-depleted plasma by small RNA-sequencing to identify T2DM associated miRNAs. We identified several miRNAs that exhibited concentration changes between controls and non-metformin treated T2DM patients and we validated a subset of these by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). The results showed that the concentrations of many T2DM-affected miRNAs in EV (but not in whole or EV-depleted plasma) decreased to levels close to those of healthy controls following metformin treatment. Among other potential uses of these differentially expressed miRNAs, some might be useful in assessing the response to metformin in T2DM patients.}, }
@article {pmid30208346, year = {2019}, author = {Zhou, X and Wang, M and Wen, C and Liu, D}, title = {Nitrogen release and its influence on anammox bacteria during the decay of Potamogeton crispus with different values of initial debris biomass.}, journal = {The Science of the total environment}, volume = {650}, number = {Pt 1}, pages = {604-615}, doi = {10.1016/j.scitotenv.2018.08.358}, pmid = {30208346}, issn = {1879-1026}, mesh = {Bacteria, Anaerobic/classification/*drug effects/genetics ; Biomass ; Ecosystem ; Environmental Monitoring ; *Fresh Water/chemistry/microbiology ; *Geologic Sediments/chemistry/microbiology ; Hydrogen-Ion Concentration ; Metagenome/genetics ; Nitrogen/analysis/*metabolism/*pharmacology ; Oxygen/analysis ; Phylogeny ; Potamogetonaceae/*metabolism ; RNA, Ribosomal, 16S/genetics ; Water Pollutants, Chemical/analysis/metabolism/pharmacology ; }, abstract = {Aquatic macrophytes play a significant role in the nutrient cycle of freshwater ecosystems. However, nutrients from plant debris release into both sediments and overlying water if not timely harvested. To date, minimal information is available regarding nutrient release and its subsequent influences on bacterial communities with decaying debris. In this study, Potamogeton crispus was used as a model plant. Debris biomass levels of 0 g (control, J-CK), 10 g dry weight (DW) (100 g DW/m2, J-10 g), 40 g DW (400 g DW/m2, J-40 g) and 80 g DW (800 g DW/m2, J-80 g) were used to simulate the different biomass densities of P. crispus in field. The physicochemical parameters of overlying water and sediment samples were analysed. The community composition of anammox bacteria in the sediment was also analysed using 16S rRNA genes as markers. The results showed that dissolved oxygen and pH dramatically decreased, whereas total nitrogen (TN) and NH4+-N concentrations increased in the overlying water in the initial stage of P. crispus decomposition. However, NO3--N concentration changes in the overlying water were more complicated. The concentrations of organic matter, TN and NH4+-N in the sediment all increased, but the rate of increase varied among the groups with different initial biomass levels, indicating that these physicochemical properties in sediment are significantly affected by debris biomass level and decay time. In addition, the order of anammox bacteria abundance was J-40 g > J-CK > J-80 g > J-10 g. Moreover, the community structure of anammox bacteria were simpler compared to that of J-CK as debris biomass level increased. The results demonstrate that P. crispus debris decomposition could affect the ecological distribution of anammox bacteria. Such influence clearly varies with varying amounts of P. crispus biomass debris. This information could be useful for the management of aquatic macrophytes in freshwater ecosystems.}, }
@article {pmid29702634, year = {2018}, author = {Eisenstein, M}, title = {Microbiology: making the best of PCR bias.}, journal = {Nature methods}, volume = {15}, number = {5}, pages = {317-320}, pmid = {29702634}, issn = {1548-7105}, mesh = {DNA, Bacterial/genetics ; *Metagenomics ; Microbiota/*genetics ; Polymerase Chain Reaction/*methods ; Selection Bias ; }, }
@article {pmid31066440, year = {2019}, author = {Klaassen, MAY and Imhann, F and Collij, V and Fu, J and Wijmenga, C and Zhernakova, A and Dijkstra, G and Festen, EAM and Gacesa, R and Vich Vila, A and Weersma, RK}, title = {Anti-inflammatory Gut Microbial Pathways Are Decreased During Crohn's Disease Exacerbations.}, journal = {Journal of Crohn's &amp; colitis}, volume = {}, number = {}, pages = {}, doi = {10.1093/ecco-jcc/jjz077}, pmid = {31066440}, issn = {1876-4479}, abstract = {BACKGROUND AND AIMS: Crohn's disease [CD] is a chronic inflammatory disorder of the gastrointestinal tract characterised by alternating periods of exacerbation and remission. We hypothesised that changes in the gut microbiome are associated with CD exacerbations, and therefore aimed to correlate multiple gut microbiome features to CD disease activity.<br><br>METHODS: Faecal microbiome data generated using whole-genome metagenomic shotgun sequencing of 196 CD patients were of obtained from the 1000IBD cohort [one sample per patient]. Patient disease activity status at time of sampling was determined by re-assessing clinical records 3 years after faecal sample production. Faecal samples were designated as taken 'in an exacerbation' or 'in remission'. Samples taken 'in remission' were further categorised as 'before the next exacerbation' or 'after the last exacerbation', based on the exacerbation closest in time to the faecal production date. CD activity was correlated with gut microbial composition and predicted functional pathways via logistic regressions using MaAsLin software.<br><br>RESULTS: In total, 105 bacterial pathways were decreased during CD exacerbation (false-discovery rate [FDR] <0.1) in comparison with the gut microbiome of patients both before and after an exacerbation. Most of these decreased pathways exert anti-inflammatory properties facilitating the biosynthesis and fermentation of various amino acids [tryptophan, methionine, and arginine], vitamins [riboflavin and thiamine], and short-chain fatty acids [SCFAs].<br><br>CONCLUSIONS: CD exacerbations are associated with a decrease in microbial genes involved in the biosynthesis of the anti-inflammatory mediators riboflavin, thiamine, and folate, and SCFAs, suggesting that increasing the intestinal abundances of these mediators might provide new treatment opportunities. These results were generated using bioinformatic analyses of cross-sectional data and need to be replicated using time-series and wet lab experiments.}, }
@article {pmid31066111, year = {2019}, author = {Prince, AL and Pace, RM and Dean, T and Takahashi, D and Kievit, P and Friedman, JE and Aagaard, KM}, title = {The development and ecology of the Japanese macaque gut microbiome from weaning to early adolescence in association with diet.}, journal = {American journal of primatology}, volume = {}, number = {}, pages = {e22980}, doi = {10.1002/ajp.22980}, pmid = {31066111}, issn = {1098-2345}, support = {//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; //National Institute of General Medical Sciences/ ; //National Institute of Diabetes and Digestive and Kidney Diseases/ ; R24 DK090964//NIH-NIDDK/ ; R01 DK089201//NIH-NIDDK/ ; R01 R01HD091731//NIH-NICHD/ ; NIGMS K12 GM084897//NIH-IRACDA Award/ ; F32 HD082969//NIH-NICHD NRSA Fellowship/ ; }, abstract = {Previously we have shown that the Japanese macaque gut microbiome differs not by obesity per se, but rather in association with high-fat diet (HFD) feeding. This held true for both pregnant dams, as well as their 1-year-old offspring, even when weaned onto a control diet. Here we aimed to examine the stability of the gut microbiome over time and in response to maternal and postweaning HFD feeding from 6 months of age, and at 1 and 3 years of age. In both cross-sectional and longitudinal specimens, we performed analysis of the V4 hypervariable region of the 16S rRNA gene on anus swabs collected from pregnant dams and their juveniles at age 6 months to 3 years (n = 55). Extracted microbial DNA was subjected to 16S-amplicon-based metagenomic sequencing on the Illumina MiSeq platform. We initially identified 272 unique bacterial genera, and multidimensional scaling revealed samples to cluster by age and diet exposures. Dirichlet multinomial mixture modeling of microbiota abundances enabled identification of two predominant enterotypes to which samples sorted, characterized primarily by Treponema abundance, or lack thereof. Approximating the time of initial weaning (6 months), the Japanese macaque offspring microbiome underwent a significant state type transition which stabilized from 1 to 3 years of age. However, we also found the low abundance Treponema enterotype to be strongly associated with HFD exposure, be it during gestation/lactation or in the postweaning interval. Examination of taxonomic co-occurrences revealed samples within the low Treponema cluster were relatively permissive (allowing for increased interactions between microbiota) whereas samples within the high Treponema cluster were relatively exclusionary (suggesting decreased interactions amongst microbiota). Taken together, these findings suggest that Treponemes are keystone species in the developing gut microbiome of the gut, and susceptible to HFD feeding in their relative abundance.}, }
@article {pmid31065734, year = {2019}, author = {Mikolajczyk, R and Roesner, LM}, title = {[General aspects regarding the skin microbiome].}, journal = {Der Hautarzt; Zeitschrift fur Dermatologie, Venerologie, und verwandte Gebiete}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00105-019-4412-x}, pmid = {31065734}, issn = {1432-1173}, abstract = {The human body is densely populated by trillions of microorganisms, which are collectively known as the human microbiota. On the outermost barrier, the skin, a plethora of different bacteria and fungi as well as viruses and mites reside. The skin of different body sites shows a high degree of heterogeneity, generating multiple ecological niches. For example, moisture, sebum and sweat promote the growth of different microorganisms. This diversity has hampered a global and objective analysis of the composition of the microbiota in the past. Today, approximately 10 years after the development of metagenome analysis by next generation high-throughput DNA sequencing, these techniques are now established and affordable in research fields. These techniques enable investigations on the microorganisms living in and on body surfaces and represent an important tool in diverse clinical questions. This review addresses new developments in the (physiological) composition of the skin microbiota and briefly summarizes the research techniques applied.}, }
@article {pmid31064831, year = {2019}, author = {Haran, JP and Bhattarai, SK and Foley, SE and Dutta, P and Ward, DV and Bucci, V and McCormick, BA}, title = {Alzheimer's Disease Microbiome Is Associated with Dysregulation of the Anti-Inflammatory P-Glycoprotein Pathway.}, journal = {mBio}, volume = {10}, number = {3}, pages = {}, doi = {10.1128/mBio.00632-19}, pmid = {31064831}, issn = {2150-7511}, abstract = {The microbiota-gut-brain axis is a bidirectional communication system that is poorly understood. Alzheimer's disease (AD), the most common cause of dementia, has long been associated with bacterial infections and inflammation-causing immunosenescence. Recent studies examining the intestinal microbiota of AD patients revealed that their microbiome differs from that of subjects without dementia. In this work, we prospectively enrolled 108 nursing home elders and followed each for up to 5 months, collecting longitudinal stool samples from which we performed metagenomic sequencing and in vitro T84 intestinal epithelial cell functional assays for P-glycoprotein (P-gp) expression, a critical mediator of intestinal homeostasis. Our analysis identified clinical parameters as well as numerous microbial taxa and functional genes that act as predictors of AD dementia in comparison to elders without dementia or with other dementia types. We further demonstrate that stool samples from elders with AD can induce lower P-gp expression levels in vitro those samples from elders without dementia or with other dementia types. We also paired functional studies with machine learning approaches to identify bacterial species differentiating the microbiome of AD elders from that of elders without dementia, which in turn are accurate predictors of the loss of dysregulation of the P-gp pathway. We observed that the microbiome of AD elders shows a lower proportion and prevalence of bacteria with the potential to synthesize butyrate, as well as higher abundances of taxa that are known to cause proinflammatory states. Therefore, a potential nexus between the intestinal microbiome and AD is the modulation of intestinal homeostasis by increases in inflammatory, and decreases in anti-inflammatory, microbial metabolism.IMPORTANCE Studies of the intestinal microbiome and AD have demonstrated associations with microbiome composition at the genus level among matched cohorts. We move this body of literature forward by more deeply investigating microbiome composition via metagenomics and by comparing AD patients against those without dementia and with other dementia types. We also exploit machine learning approaches that combine both metagenomic and clinical data. Finally, our functional studies using stool samples from elders demonstrate how the c microbiome of AD elders can affect intestinal health via dysregulation of the P-glycoprotein pathway. P-glycoprotein dysregulation contributes directly to inflammatory disorders of the intestine. Since AD has been long thought to be linked to chronic bacterial infections as a possible etiology, our findings therefore fill a gap in knowledge in the field of AD research by identifying a nexus between the microbiome, loss of intestinal homeostasis, and inflammation that may underlie this neurodegenerative disorder.}, }
@article {pmid31064768, year = {2019}, author = {Breitwieser, FP and Pertea, M and Zimin, A and Salzberg, SL}, title = {Human contamination in bacterial genomes has created thousands of spurious proteins.}, journal = {Genome research}, volume = {}, number = {}, pages = {}, doi = {10.1101/gr.245373.118}, pmid = {31064768}, issn = {1549-5469}, abstract = {Contaminant sequences that appear in published genomes can cause numerous problems for downstream analyses, particularly for evolutionary studies and metagenomics projects. Our large-scale scan of complete and draft bacterial and archaeal genomes in the NCBI RefSeq database reveals that 2250 genomes are contaminated by human sequence. The contaminant sequences derive primarily from high-copy human repeat regions, which themselves are not adequately represented in the current human reference genome, GRCh38. The absence of the sequences from the human assembly offers a likely explanation for their presence in bacterial assemblies. In some cases, the contaminating contigs have been erroneously annotated as containing protein-coding sequences, which over time have propagated to create spurious protein &quot;families&quot; across multiple prokaryotic and eukaryotic genomes. As a result, 3437 spurious protein entries are currently present in the widely-used nr and TrEMBL protein databases. We report here an extensive list of contaminant sequences in bacterial genome assemblies and the proteins associated with them. We found that nearly all contaminants occurred on small contigs in draft genomes, which suggests that filtering out small contigs from draft genome assemblies may mitigate the issue of contamination while still keeping nearly all of the genuine genomic sequences.}, }
@article {pmid31064055, year = {2019}, author = {Pineda-Quiroga, C and Borda-Molina, D and Chaves-Moreno, D and Ruiz, R and Atxaerandio, R and Camarinha-Silva, A and García-Rodríguez, A}, title = {Microbial and Functional Profile of the Ceca from Laying Hens Affected by Feeding Prebiotics, Probiotics, and Synbiotics.}, journal = {Microorganisms}, volume = {7}, number = {5}, pages = {}, doi = {10.3390/microorganisms7050123}, pmid = {31064055}, issn = {2076-2607}, support = {LIFE11/ENV/ES/000639//LIFE program of the European Union/ ; PRE/2013/1/1077//Department of Education, Language Policy and Culture, Scholarship, , Basque Government, Vitoria-Gasteiz, Spain/ ; }, abstract = {Diet has an essential influence in the establishment of the cecum microbial communities in poultry, so its supplementation with safe additives, such as probiotics, prebiotics, and synbiotics might improve animal health and performance. This study showed the ceca microbiome modulations of laying hens, after feeding with dry whey powder as prebiotics, Pediococcus acidilactici as probiotics, and the combination of both as synbiotics. A clear grouping of the samples induced per diet was observed (p < 0.05). Operational taxonomic units (OTUs) identified as Olsenella spp., and Lactobacilluscrispatus increased their abundance in prebiotic and synbiotic treatments. A core of the main functions was shared between all metagenomes (45.5%), although the genes encoding for the metabolism of butanoate, propanoate, inositol phosphate, and galactose were more abundant in the prebiotic diet. The results indicated that dietary induced-changes in microbial composition did not imply a disturbance in the principal biological roles, while the specific functions were affected.}, }
@article {pmid30789326, year = {2019}, author = {Duranti, S and Lugli, GA and Napoli, S and Anzalone, R and Milani, C and Mancabelli, L and Alessandri, G and Turroni, F and Ossiprandi, MC and van Sinderen, D and Ventura, M}, title = {Characterization of the phylogenetic diversity of five novel species belonging to the genus Bifidobacterium: Bifidobacterium castoris sp. nov., Bifidobacterium callimiconis sp. nov., Bifidobacterium goeldii sp. nov., Bifidobacterium samirii sp. nov. and Bifidobacterium dolichotidis sp. nov.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {69}, number = {5}, pages = {1288-1298}, doi = {10.1099/ijsem.0.003306}, pmid = {30789326}, issn = {1466-5034}, abstract = {Five Bifidobacterium strains, i.e. 2020BT, 2028BT, 2033BT, 2034BT and 2036BT, were isolated from European beaver (Castor fiber), Goeldi's marmoset (Callimicogoeldii), black-capped squirrel monkey (Saimiriboliviensissubsp. peruviensis) and Patagonian mara (Dolichotispatagonum). All of these isolates were shown to be Gram-positive, facultative anaerobic, d-fructose 6-phosphate phosphoketolase-positive, non-motile and non-sporulating. Phylogenetic analyses based on 16S rRNA gene sequences, multilocus sequences (including hsp60, rpoB, dnaJ, dnaG and clpC genes) and the core genome revealed that bifidobacterial strains 2020BT, 2028BT, 2033BT, 2034BT and 2036BT exhibit close phylogenetic relatedness to Bifidobacterium biavatii DSM 23969T, Bifidobacterium bifidum LMG 11041T, Bifidobacterium choerinum LMG 10510T, Bifidobacterium gallicum LMG 11596T, Bifidobacterium imperatoris LMG 30297T, Bifidobacterium italicum LMG 30187T and Bifidobacterium vansinderenii LMG 30126T, respectively. Further genotyping based on the genome sequence of the isolated strains combined with phenotypic analyses, clearly show that these strains are distinct from each of the type strains of the so far recognized Bifidobacterium species. Thus, Bifidobacterium castoris sp. nov. (2020BT=LMG 30937T=CCUG 72816T), Bifidobacterium callimiconis sp. nov. (2028BT=LMG 30938T=CCUG 72814T), Bifidobacterium samirii sp. nov. (2033BT=LMG 30940T=CCUG 72817T), Bifidobacterium goeldii sp. nov. (2034BT=LMG 30939T=CCUG 72815T) and Bifidobacterium dolichotidis sp. nov. (2036BT=LMG 30941T=CCUG 72818T) are proposed as novel Bifidobacterium species.}, }
@article {pmid30582999, year = {2019}, author = {Snowdon, RJ and Schiessl, S}, title = {Illuminating Crop Adaptation Using Population Genomics.}, journal = {Molecular plant}, volume = {12}, number = {1}, pages = {27-29}, doi = {10.1016/j.molp.2018.12.014}, pmid = {30582999}, issn = {1752-9867}, mesh = {Adaptation, Physiological/genetics ; Brassica rapa/*genetics ; Ecotype ; Genome ; Genomics ; Metagenomics ; }, }
@article {pmid31063007, year = {2019}, author = {Alkie, TN and Yitbarek, A and Hodgins, DC and Kulkarni, RR and Taha-Abdelaziz, K and Sharif, S}, title = {Development of innate immunity in chicken embryos and newly hatched chicks: A disease control perspective.}, journal = {Avian pathology : journal of the W.V.P.A}, volume = {}, number = {}, pages = {1-75}, doi = {10.1080/03079457.2019.1607966}, pmid = {31063007}, issn = {1465-3338}, abstract = {Newly hatched chickens are confronted by a wide array of pathogenic microbes when their adaptive immune defenses have limited capabilities to control these pathogens. In such circumstances and within this age group, innate responses provide a degree of protection. Moreover, as the adaptive immune system is relatively naïve to foreign antigens, synergy with innate defenses is critical. This review presents knowledge on the ontogeny of innate immunity in chicken pre-hatch and early post-hatch and provides insights into possible interventions to modulate innate responses early in the life of the bird. As in other vertebrate species, chicken innate immune system components, including cellular mediators, cytokine and chemokine repertoires and molecules involved in antigen detection, develop early in life. Comparison of innate immune systems in newly hatched chickens and mature birds has revealed differences, in magnitude and quality, but responses in younger chickens can be boosted using innate immune system modulators. Functional expression of pattern recognition receptors and several defense molecules by innate immune system cells of embryos and newly hatched chicks suggests that innate responses can be modulated at this stage of development to combat pathogens. Improved understanding of innate immune system ontogeny and functionality in chickens is critical for implementation of sound and safe interventions to provide long-term protection against pathogens. Technological approaches such as RNASeq and CRISPR/Cas9 for functional metagenomics and gene knockouts can be used in the future to explore and dissect the contributions of signaling pathways of innate immunity and to devise more efficacious disease control strategies.}, }
@article {pmid31062778, year = {2019}, author = {Liu, J and Hao, W and He, Z and Kwek, E and Zhao, Y and Zhu, H and Liang, N and Ma, KY and Lei, L and He, WS and Chen, ZY}, title = {Beneficial effects of tea water extracts on the body weight and gut microbiota in C57BL/6J mice fed with a high-fat diet.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/c8fo02051e}, pmid = {31062778}, issn = {2042-650X}, abstract = {Accumulative evidence has suggested that tea consumption has benefits in reducing body fat and alleviating metabolic syndrome. We hypothesize that benefits of tea consumption can be partially mediated by modulating intestinal microbiota via inhibiting the formation of lipopolysaccharides (LPS) and promoting the production of short chain fatty acids (SCFAs). C57BL/6J mice were fed a high fat diet with the addition of 1% water extracts of green tea, oolong tea and black tea. Results showed that the dietary supplementation of three tea water extracts equally improved the glucose tolerance and reduced a high fat diet-induced gain in weight, hepatic lipids, and white adipose tissue weights. This was accompanied by a significant reduction in plasma LPS and a significant increase in the production of SCFAs. The metagenomic analyses showed that the tea extracts changed the overall composition of gut microbiota and decreased the relative abundance of family Rikenellaceae and Desulfovibrionaceae. In addition, tea water extracts could also change the abundance of key operational taxonomic units (OTUs) including OTU473 (Alistipes), OTU229 (Rikenella), OTU179 (Ruminiclostridium) and OTU264 (Acetatifactor). In conclusion, three tea extracts could improve the glucose tolerance, induce the production of SCFAs and inhibit the production of endotoxin LPS, most likely mediated by modulating gut microbiota.}, }
@article {pmid31062682, year = {2019}, author = {Gruninger, RJ and Ribeiro, GO and Cameron, A and McAllister, TA}, title = {Invited review: Application of meta-omics to understand the dynamic nature of the rumen microbiome and how it responds to diet in ruminants.}, journal = {Animal : an international journal of animal bioscience}, volume = {}, number = {}, pages = {1-12}, doi = {10.1017/S1751731119000752}, pmid = {31062682}, issn = {1751-732X}, abstract = {Ruminants are unique among livestock due to their ability to efficiently convert plant cell wall carbohydrates into meat and milk. This ability is a result of the evolution of an essential symbiotic association with a complex microbial community in the rumen that includes vast numbers of bacteria, methanogenic archaea, anaerobic fungi and protozoa. These microbes produce a diverse array of enzymes that convert ingested feedstuffs into volatile fatty acids and microbial protein which are used by the animal for growth. Recent advances in high-throughput sequencing and bioinformatic analyses have helped to reveal how the composition of the rumen microbiome varies significantly during the development of the ruminant host, and with changes in diet. These sequencing efforts are also beginning to explain how shifts in the microbiome affect feed efficiency. In this review, we provide an overview of how meta-omics technologies have been applied to understanding the rumen microbiome, and the impact that diet has on the rumen microbial community.}, }
@article {pmid31061496, year = {2019}, author = {Gandy, KAO and Zhang, J and Nagarkatti, P and Nagarkatti, M}, title = {The role of gut microbiota in shaping the relapse-remitting and chronic-progressive forms of multiple sclerosis in mouse models.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {6923}, doi = {10.1038/s41598-019-43356-7}, pmid = {31061496}, issn = {2045-2322}, support = {F32AT008539//U.S. Department of Health &amp; Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; P01AT003961//U.S. Department of Health &amp; Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; R01AT006888//U.S. Department of Health &amp; Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; P01AT003961//U.S. Department of Health &amp; Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; R01MH094755//U.S. Department of Health &amp; Human Services | NIH | National Institute of Mental Health (NIMH)/ ; P20GM103641//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; P20GM103641//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01AI129788//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; R01AI123947//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; }, abstract = {Using a mouse model of multiple sclerosis (MS), experimental autoimmune encephalitis (EAE), we evaluated the role of gut microbiota in modulating chronic-progressive (CP) versus relapse-remitting (RR) forms of the disease. We hypothesized that clinical courses of EAE may be shaped by differential gut microbiota. Metagenomic sequencing of prokaryotic 16S rRNA present in feces from naïve mice and those exhibiting CP-EAE or RR-EAE revealed significantly diverse microbial populations. Microbiota composition was considerably different between naïve strains of mice, suggesting microbial components present in homeostatic conditions may prime mice for divergent courses of disease. Additionally, there were differentially abundant bacteria in CP and RR forms of EAE, indicating a potential role for gut microbiota in shaping tolerant or remittance-favoring, and pathogenic or pro-inflammatory-promoting conditions. Furthermore, immunization to induce EAE led to significant alterations in gut microbiota, some were shared between disease courses and others were course-specific, supporting a role for gut microbial composition in EAE pathogenesis. Moreover, using Linear Discriminant Analysis (LDA) coupled with effect size measurement (LEfSe) to analyze microbial content, biomarkers of each naïve and disease states were identified. Our findings demonstrate for the first time that gut microbiota may determine the susceptibility to CP or RR forms of EAE.}, }
@article {pmid31061483, year = {2019}, author = {Bin Jang, H and Bolduc, B and Zablocki, O and Kuhn, JH and Roux, S and Adriaenssens, EM and Brister, JR and Kropinski, AM and Krupovic, M and Lavigne, R and Turner, D and Sullivan, MB}, title = {Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41587-019-0100-8}, pmid = {31061483}, issn = {1546-1696}, abstract = {Microbiomes from every environment contain a myriad of uncultivated archaeal and bacterial viruses, but studying these viruses is hampered by the lack of a universal, scalable taxonomic framework. We present vConTACT v.2.0, a network-based application utilizing whole genome gene-sharing profiles for virus taxonomy that integrates distance-based hierarchical clustering and confidence scores for all taxonomic predictions. We report near-identical (96%) replication of existing genus-level viral taxonomy assignments from the International Committee on Taxonomy of Viruses for National Center for Biotechnology Information virus RefSeq. Application of vConTACT v.2.0 to 1,364 previously unclassified viruses deposited in virus RefSeq as reference genomes produced automatic, high-confidence genus assignments for 820 of the 1,364. We applied vConTACT v.2.0 to analyze 15,280 Global Ocean Virome genome fragments and were able to provide taxonomic assignments for 31% of these data, which shows that our algorithm is scalable to very large metagenomic datasets. Our taxonomy tool can be automated and applied to metagenomes from any environment for virus classification.}, }
@article {pmid31060321, year = {2019}, author = {Hufsky, F and Ibrahim, B and Modha, S and Clokie, MRJ and Deinhardt-Emmer, S and Dutilh, BE and Lycett, S and Simmonds, P and Thiel, V and Abroi, A and Adriaenssens, EM and Escalera-Zamudio, M and Kelly, JN and Lamkiewicz, K and Lu, L and Susat, J and Sicheritz, T and Robertson, DL and Marz, M}, title = {The Third Annual Meeting of the European Virus Bioinformatics Center.}, journal = {Viruses}, volume = {11}, number = {5}, pages = {}, doi = {10.3390/v11050420}, pmid = {31060321}, issn = {1999-4915}, abstract = {The Third Annual Meeting of the European Virus Bioinformatics Center (EVBC) took place in Glasgow, United Kingdom, 28-29 March 2019. Virus bioinformatics has become central to virology research, and advances in bioinformatics have led to improved approaches to investigate viral infections and outbreaks, being successfully used to detect, control, and treat infections of humans and animals. This active field of research has attracted approximately 110 experts in virology and bioinformatics/computational biology from Europe and other parts of the world to attend the two-day meeting in Glasgow to increase scientific exchange between laboratory- and computer-based researchers. The meeting was held at the McIntyre Building of the University of Glasgow; a perfect location, as it was originally built to be a place for &quot;rubbing your brains with those of other people&quot;, as Rector Stanley Baldwin described it. The goal of the meeting was to provide a meaningful and interactive scientific environment to promote discussion and collaboration and to inspire and suggest new research directions and questions. The meeting featured eight invited and twelve contributed talks, on the four main topics: (1) systems virology, (2) virus-host interactions and the virome, (3) virus classification and evolution and (4) epidemiology, surveillance and evolution. Further, the meeting featured 34 oral poster presentations, all of which focused on specific areas of virus bioinformatics. This report summarizes the main research findings and highlights presented at the meeting.}, }
@article {pmid31059918, year = {2019}, author = {Chen, C and Pankow, CA and Oh, M and Heath, LS and Zhang, L and Du, P and Xia, K and Pruden, A}, title = {Effect of antibiotic use and composting on antibiotic resistance gene abundance and resistome risks of soils receiving manure-derived amendments.}, journal = {Environment international}, volume = {128}, number = {}, pages = {233-243}, doi = {10.1016/j.envint.2019.04.043}, pmid = {31059918}, issn = {1873-6750}, abstract = {Manure-derived amendments are commonly applied to soil, raising questions about whether antibiotic use in livestock could influence the soil resistome (collective antibiotic resistance genes (ARGs)) and ultimately contribute to the spread of antibiotic resistance to humans during food production. Here, we examined the metagenomes of soils amended with raw or composted manure generated from dairy cows administered pirlimycin and cephapirin (antibiotic) or no antibiotics (control) relative to unamended soils. Initial amendment (Day 1) with manure or compost significantly increased the diversity (richness) of ARGs in soils (p < 0.01) and resulted in distinct abundances of individual ARG types. Notably, initial amendment with antibiotic-manure significantly increased the total ARG relative abundances (per 16S rRNA gene) in the soils (2.21 × unamended soils, p < 0.001). After incubating 120 days, to simulate a wait period before crop harvest, 282 ARGs reduced 4.33-fold (median) up to 307-fold while 210 ARGs increased 2.89-fold (median) up to 76-fold in the antibiotic-manure-amended soils, resulting in reduced total ARG relative abundances equivalent to those of the unamended soils. We further assembled the metagenomic data and calculated resistome risk scores, which was recently defined as a relative index comparing co-occurrence of sequences corresponding to ARGs, mobile genetic elements, and putative pathogens on the same scaffold. Initial amendment of manure significantly increased the soil resistome risk scores, especially when generated by cows administered antibiotics, while composting reduced the effects and resulted in soil resistomes more similar to the background. The risk scores of manure-amended soils reduced to levels comparable to the unamended soils after 120 days. Overall, this study provides an integrated, high-resolution examination of the effects of prior antibiotic use, composting, and a 120-day wait period on soil resistomes following manure-derived amendment, demonstrating that all three management practices have measurable effects and should be taken into consideration in the development of policy and practice for mitigating the spread of antibiotic resistance.}, }
@article {pmid31059795, year = {2019}, author = {Asplund, M and Kjartansdóttir, KR and Mollerup, S and Vinner, L and Fridholm, H and Herrera, JAR and Friis-Nielsen, J and Hansen, TA and Jensen, RH and Nielsen, IB and Richter, SR and Rey-Iglesia, A and Matey-Hernandez, ML and Alquezar-Planas, DE and Olsen, PVS and Sicheritz-Pontén, T and Willerslev, E and Lund, O and Brunak, S and Mourier, T and Nielsen, LP and Izarzugaza, JMG and Hansen, AJ}, title = {Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmi.2019.04.028}, pmid = {31059795}, issn = {1469-0691}, abstract = {OBJECTIVES: Sample preparation for High-throughput sequencing (HTS) includes treatment with various laboratory components, potentially carrying viral nucleic acids, the extent of which has not been thoroughly investigated. Our aim was to systematically examine a diverse repertoire of laboratory components used to prepare samples for HTS in order to identify contaminating viral sequences.<br><br>METHODS: A total of 322 samples of mainly human origin were analysed using eight protocols, applying a wide variety of laboratory components. Several samples (60% of human specimens) were processed by different protocols. In total 712 sequencing libraries were investigated for viral sequence contamination.<br><br>RESULTS: Among sequences showing similarity to viruses, 493 were significantly associated to the use of laboratory components. Each of these viral sequences showed sporadic appearance, only being identified in a subset of the samples treated with the linked laboratory component, and some were not identified in the non-template control (NTC) samples. Remarkably, more than 65% of all viral sequences identified were within viral clusters linked to the use of laboratory components.<br><br>CONCLUSIONS: We show that high prevalence of contaminating viral sequences can be expected in HTS-based virome data and provide an extensive list of novel contaminating viral sequences that can be used for evaluation of viral findings in future virome and metagenome studies. Moreover we show that detection can be problematic due to stochastic appearance and limited NTCs. Although the exact origin of these viral sequences requires further research, our results support laboratory component linked viral sequence contamination of both biological and synthetic origin.}, }
@article {pmid31059117, year = {2019}, author = {Jagodzinski, A and Zielinska, E and Laczmanski, L and Hirnle, L}, title = {The early years of life. Are they influenced by our microbiome?.}, journal = {Ginekologia polska}, volume = {90}, number = {4}, pages = {228-232}, doi = {10.5603/GP.2019.0041}, pmid = {31059117}, issn = {2543-6767}, abstract = {Human microbiome contains the genetic pool of bacteria and other microbes such as Achaea, fungi and viruses inhabiting the human body. It holds an immense potential to affect both physiological and pathological processes. The microbiome's composition can be defined in detail by analyzing ribosomal 16S rRNA and metagenomic tests. Recent increases in cesar- ean sections, the use of antibiotics during pregnancy, the increasing amount of prematurely born children and changes in infant nutrition have an impact on the microbiome forming process. A correlation between the bowel microbiome's com- position and the occurrence of certain diseases, especially inflammatory bowel diseases (IBD), asthma and type 1 diabetes has been demonstrated. The influence on the development of cognitive functions and behaviour has also been displayed. This correlation justifies attempts to restore the beneficial the composition of the microbiome through the use of probiotics, vaginal microflora transfer in case of cesarean section and encouraging breastfeeding. Development of multiple studies on the topic of the human microbiome and its impact on the human body is necessary in order to reach final conclusions. The aim of this article is to summarize recent findings regarding the development of the human microbiome from the first days of life and the influence of changes in its composition on human health.}, }
@article {pmid31058819, year = {2019}, author = {Elyamine, AM and Moussa, MG and Afzal, J and Rana, MS and Imran, M and Zhao, X and Hu, CX}, title = {Modified Rice Straw Enhanced Cadmium (II) Immobilization in Soil and Promoted the Degradation of Phenanthrene in Co-Contaminated Soil.}, journal = {International journal of molecular sciences}, volume = {20}, number = {9}, pages = {}, doi = {10.3390/ijms20092189}, pmid = {31058819}, issn = {1422-0067}, support = {No. 41271275//National Natural Science Foundation of China/ ; }, abstract = {Very limited information is available about heavy metal-polycyclic aromatic hydrocarbons (PAHs) depollution involving the modified natural material in soil. Using phenanthrene and cadmium (Cd) as model, this study investigated the effect(s) of modified rice straw by a NaOH solution and on PAHs, heavy metal availability, and their interactions. Treatment included chemical contaminant with/without modified/unmodified rice straw. Fourier Transform Infrared (FTIR) analysis revealed that certain functional groups including anionic matters groups, which can a complex with Cd2+, were exposed on the modified rice straw surfaces. Therefore, Cd concentration was significantly reduced by about 60%, 57%, 62.5 %, and, 64% in the root, shoot, CaCl2, diethylenetriaminepentaacetic acid (DTPA), and extractable Cd, respectively. Subsequently, the prediction of the functional profile of the soil metagenome using Clusters Orthologous Groups (COGs) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database revealed that the significantly changed individual COGs belonged to the carbohydrate metabolism, ion transports, and signaling (including cytochrome P450s) categories. This indicated that ion transports might be involved in Cd management, while carbohydrate metabolism, including bisphenol, benzoate, ethylbenzene degradation, and cytochrome P450s, were rather involved in phenanthrene metabolism. The exposed functional group might serve as an external substrate, and P450s might serve as a catalyst to activate and initiate phenanthrene metabolism process. These finding offer confirmation that modified straw could promote the reduction of heavy metal and the degradation of PAHs in soil.}, }
@article {pmid31057666, year = {2019}, author = {Jin, P and Gu, Y and Shi, X and Yang, W}, title = {Non-negligible greenhouse gases from urban sewer system.}, journal = {Biotechnology for biofuels}, volume = {12}, number = {}, pages = {100}, doi = {10.1186/s13068-019-1441-8}, pmid = {31057666}, issn = {1754-6834}, abstract = {Background: The urban sewer system is an important component of urban water infrastructure for sewage collection and transportation, and in-sewer transportation of sewage can cause multitudinous contaminant degradations which lead to formation of gaseous products. Although the greenhouse gases of methane and carbon dioxide have been confirmed to consist in the gaseous products, the mechanisms of greenhouse gas generation were unclear and the significances of greenhouse gases emission from sewers were generally underestimated.<br><br>Results: In this study, 3 years of monitoring was conducted to evaluate the greenhouse gases emission in 37-km-long urban sewer systems covering 13 km2. The results showed that the emission of carbon dioxide and methane was extensively existing in sewers, and especially, exhibited a characteristic of regional difference. In order to reveal the formation mechanism of carbon dioxide and methane in sewers, the metagenomic approach was utilized to analyze the annotated pathways and homologous bio-enzymes, and it indicated that fourteen pivotal annotated pathways were involved in the carbon dioxide and methane generation. According to the metagenomics and 3-year monitoring results, the total amounts of carbon dioxide and methane emission in sewers were calculated by the transformation venation of contaminants (such as methyl alcohol, methylamine and acetic acid along branch sewer, sub-main sewer and main sewer, respectively). The calculation results showed that the total greenhouse gas emissions in sewer were calculated to be 199 t/day in Xi'an, and if scaling up as population proportion, the greenhouse gas emission from sewer systems in China could be 30,685 t/day. Comparing with the greenhouse gas emissions from different metropolises (New York City, London and Tokyo) and industries (dairy farms, automobile production and steel enterprises), the amount of greenhouse gases produced by the urban sewer system is much higher.<br><br>Conclusions: This study revealed the transformation pathways of contaminants which promoted the generation of greenhouse gases in sewers. Based on this analysis, the greenhouse gas emissions along sewer systems were calculated. The results indicate that the greenhouse gas emission from sewer systems is non-negligible, and should be attracted sufficient attention.}, }
@article {pmid31057531, year = {2019}, author = {Lu, Z and Xu, Z and Shen, Z and Tian, Y and Shen, H}, title = {Dietary Energy Level Promotes Rumen Microbial Protein Synthesis by Improving the Energy Productivity of the Ruminal Microbiome.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {847}, doi = {10.3389/fmicb.2019.00847}, pmid = {31057531}, issn = {1664-302X}, abstract = {Improving the yield of rumen microbial protein (MCP) has significant importance in the promotion of animal performance and the reduction of protein feed waste. The amount of energy supplied to rumen microorganisms is an important factor affecting the amount of protein nitrogen incorporated into rumen MCP. Substrate-level phosphorylation (SLP) and electron transport phosphorylation (ETP) are two major mechanisms of energy generation within microbial cells. However, the way that energy and protein levels in the diet impact the energy productivity of the ruminal microbiome and, thereafter, rumen MCP yields is not known yet. In present study, we have investigated, by animal experiments and metagenome shotgun sequencing, the effects of energy-rich and protein-rich diets on rumen MCP yields, as well as SLP-coupled and ETP-coupled energy productivity of the ruminal microbiome. We have found that an energy-rich diet induces a significant increase in rumen MCP yield, whereas a protein-rich diet has no significant impacts on it. Based on 10 reconstructed pathways related to the energy metabolism of the ruminal microbiome, we have determined that the energy-rich diet induces significant increases in the total abundance of SLP enzymes coupled to the nicotinamide adenine dinucleotide (NADH) oxidation in the glucose fermentation and F-type ATPase of the electron transporter chain, whereas the protein-rich diet has no significant impact in the abundance of these enzymes. At the species level, the energy-rich diet induces significant increases in the total abundance of 15 ETP-related genera and 40 genera that have SLP-coupled fermentation pathways, whereas the protein-rich diet has no significant impact on the total abundance of these genera. Our results suggest that an increase in dietary energy levels promotes rumen energy productivity and MCP yield by improving levels of ETP and SLP coupled to glucose fermentation in the ruminal microbiome. But, an increase in dietary protein level has no such effects.}, }
@article {pmid31057513, year = {2019}, author = {Ponsero, AJ and Hurwitz, BL}, title = {The Promises and Pitfalls of Machine Learning for Detecting Viruses in Aquatic Metagenomes.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {806}, doi = {10.3389/fmicb.2019.00806}, pmid = {31057513}, issn = {1664-302X}, abstract = {Tools allowing for the identification of viral sequences in host-associated and environmental metagenomes allows for a better understanding of the genetics and ecology of viruses and their hosts. Recently, new approaches using machine learning methods to distinguish viral from bacterial signal using k-mer sequence signatures were published for identifying viral contigs in metagenomes. The promise of these content-based approaches is the ability to discover new viruses, with no or few known relatives. In this perspective paper, we examine the use of the content-based machine learning tool VirFinder for the identification of viral sequences in aquatic metagenomes and explore the possibility of using ecosystem-focused models targeted to marine metagenomes. We discuss the impact of the training set composition on the tool performance and the current limitation for the retrieval of low abundance viral sequences in metagenomes. We identify potential biases that could arise from machine learning approaches for viral hunting in real-world datasets and suggest possible avenues to overcome them.}, }
@article {pmid31057499, year = {2019}, author = {Burcham, ZM and Pechal, JL and Schmidt, CJ and Bose, JL and Rosch, JW and Benbow, ME and Jordan, HR}, title = {Bacterial Community Succession, Transmigration, and Differential Gene Transcription in a Controlled Vertebrate Decomposition Model.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {745}, doi = {10.3389/fmicb.2019.00745}, pmid = {31057499}, issn = {1664-302X}, abstract = {Decomposing remains are a nutrient-rich ecosystem undergoing constant change due to cell breakdown and abiotic fluxes, such as pH level and oxygen availability. These environmental fluxes affect bacterial communities who respond in a predictive manner associated with the time since organismal death, or the postmortem interval (PMI). Profiles of microbial taxonomic turnover and transmigration are currently being studied in decomposition ecology, and in the field of forensic microbiology as indicators of the PMI. We monitored bacterial community structural and functional changes taking place during decomposition of the intestines, bone marrow, lungs, and heart in a highly controlled murine model. We found that organs presumed to be sterile during life are colonized by Clostridium during later decomposition as the fluids from internal organs begin to emulsify within the body cavity. During colonization of previously sterile sites, gene transcripts for multiple metabolism pathways were highly abundant, while transcripts associated with stress response and dormancy increased as decomposition progressed. We found our model strengthens known bacterial taxonomic succession data after host death. This study is one of the first to provide data of expressed bacterial community genes, alongside transmigration and structural changes of microbial species during laboratory controlled vertebrate decomposition. This is an important dataset for studying the effects of the environment on bacterial communities in an effort to determine which bacterial species and which bacterial functional pathways, such as amino acid metabolism, provide key changes during stages of decomposition that relate to the PMI. Finding unique PMI species or functions can be useful for determining time since death in forensic investigations.}, }
@article {pmid31055095, year = {2019}, author = {Hassan, M and Essam, T and Mira, A and Megahed, S}, title = {Biomonitoring detoxification efficiency of an algal-bacterial microcosm system for treatment of coking wastewater: Harmonization between Chlorella vulgaris microalgae and wastewater microbiome.}, journal = {The Science of the total environment}, volume = {677}, number = {}, pages = {120-130}, doi = {10.1016/j.scitotenv.2019.04.304}, pmid = {31055095}, issn = {1879-1026}, abstract = {Nowadays, due to worldwide water shortage, water utilities are forced to re-evaluate treated wastewater. Consequently, wastewater treatment plants need to conduct biomonitoring. Coking wastewater (CWW) has toxic, mutative and carcinogenic components with threatening effect on the environment. CWW was selected as a model for complex highly toxic industrial wastewater that should be treated. CWW from Egypt was treated in a nine-liter photobioreactor using an algal-bacterial system. The photobioreactor was operated for 154 days changing different parameters (toxic load and light duration) for optimization. Optimized conditions achieved significant reduction (45%) in the operation cost. The algal-bacterial system was monitored using chemical assays (chemical oxygen demand and phenol analysis), bioassays (phytotoxicity, Artemia-toxicity, cytotoxicity, algal-bacterial ratio and settleability) and Illumina-MiSeq sequencing of 16S rRNA gene. The algal-bacterial system detoxified (in terms of phytotoxicity, cytotoxicity and Artemia-toxicity) CWW introduced as influent through all phases. A significant difference was recorded in the microbial diversity between influent and effluent samples. Four phyla dominated influent samples; Proteobacteria (77%), Firmicutes (11%), Bacteroidetes (5%) and Deferribacteres (3%) compared to only two in effluent samples; Proteobacteria (66%) and Bacteroidetes (26%). The significant relative-abundance of versatile aromatic degraders (Comamonadaceae and Pseudomonadaceae families) in influent samples conformed to the nature of CWW. Microbial community shifted and promoted the activity of catabolically versatile and xenobiotics degrading families (Chitinophagaceae and Xanthomonadaceae). Co-culture of microalgae had a positive effect on the biodegrading bacteria that was reflected by enhanced treatment efficiency, significant increase in relative abundance of bacterial genera with cyanide-decomposing potential and negative effect on waterborne pathogens.}, }
@article {pmid31055031, year = {2019}, author = {Seferovic, MD and Pace, RM and Caroll, M and Belfort, B and Major, AM and Chu, DM and Racusin, DA and Castro, ECC and Muldrew, KL and Versalovic, J and Aagaard, KM}, title = {Visualization of Microbes by 16S in situ Hybridization in Term and Preterm Placentae without Intraamniotic Infection.}, journal = {American journal of obstetrics and gynecology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajog.2019.04.036}, pmid = {31055031}, issn = {1097-6868}, abstract = {BACKGROUND: Numerous reports have documented bacteria in the placental membranes and basal plate decidua in the absence of immunopathology using histological techniques. Similarly, independent metagenomic characterizations have identified an altered taxonomical makeup in association with spontaneous preterm birth (PTB). Here we sought to corroborate these findings by localizing presumptive intact bacteria using molecular histology within the placental microanatomy.<br><br>OBJECTIVES: Here we examined for microbes in term and preterm gestations using a signal amplified 16S universal in situ hybridization (ISH) probe set for bacterial rRNA, alongside traditional histologic methods of Warthin-Starry and Gram stains, as well as clinical culture methodologies. We further sought to differentiate accompanying 16S gene sequencing taxonomic profiles from germ free (gnotobiotic) mouse and extraction and amplicon contamination controls.<br><br>STUDY DESIGN: Placentae were collected from a total of n=53 subjects, comprised of term, labored (n 4) and unlabored Cesarean deliveries (n 22) and preterm vaginal (n 18) and Cesarean deliveries (n 8); a placenta from a single subject with clinical and histologic evident choriomanionitis was employed as a 'positive' control (n 1). The preterm cohort included spontaneous PTB with (n 6) and without (n 10) preterm premature rupture of membranes (PPROM), as well as medically indicated PTBs (n 10). Placental microbes were visualized using an in situ hybridization probe set designed against highly conserved regions of the bacterial 16S ribosome, which produces an amplified stable signal using branched DNA probes. Extracted bacterial nucleic acid from these same samples were subjected to 16S rRNA metagenomic sequencing (Illumina, V4) for course taxonomical analysis, alongside environmental and kit contaminant controls. A subset of unlabored, Cesarean delivered term pregnancies were also assessed with clinical culture for readily cultivatable pathogenic microbes.<br><br>RESULTS: Molecular ISH of bacterial rRNA enabled visualization and localization of low-abundance microbes after systematic high power scanning. Despite the absence of clinical or histological chorioamnionitis in 52 of 53 subjects, instances of 16S rRNA signal were confidently observed in 13 of 16 sPTB placentas, which was not significantly different from term unlabored Cesarean specimens (18 of 22; p>0.05). 16S rRNA signal was largely localized to the villus parenchyma and/or syncytiotrophoblast, and less commonly the chorion and the maternal intervillous space. In all term and unlabored Cesarean deliveries, visualization of evident placental microbes by ISH occurred in the absence of clinical or histological detection using conventional clinical cultivation, H&amp;E, and Gram staining. In one subject, appreciable villous bacteria localized to an infarction, where 16S microbial detection was confirmed by Warthin-Starry stain. In all instances, parallel sample principle coordinate analysis using Bray-Cutis distances of 16S rRNA gene sequencing data demonstrated consistent taxonomical distinction from all negative or potential contamination controls (p=0.024, PERMANOVA). Classification from contaminant filtered data identified a distinct taxonomical makeup among term and preterm cohorts when compared to contaminant controls (FDR<0.05).<br><br>CONCLUSIONS: Presumptively intact placental microbes are visualized as low-abundance, low-biomass and sparse populations within the placenta regardless of gestational age and mode of delivery. Their taxonomic makeup is distinct from contamination controls. These findings further support several previously published findings, including our own, which have used metagenomics to characterize low-abundance and low-biomass microbial communities in the placenta.}, }
@article {pmid31055020, year = {2019}, author = {Xiao Joe, JT and Chiou, PP and Kuo, CY and Jia Lin, JH and Wu, JL and Lu, MW}, title = {The microbiota profile and transcriptome analysis of immune response during metamorphosis stages in orange spotted grouper (Epinephelus coioides).}, journal = {Fish &amp; shellfish immunology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.fsi.2019.03.063}, pmid = {31055020}, issn = {1095-9947}, abstract = {Metamorphosis is a transformation process in larval development associated with changes in morphological and physiological features, including the immune system. The gastrointestinal tract harbors a plethora of bacteria, which might affect the digestion and absorption of nutrients, immunity, and gut-brain crosstalk in the host. In this study, we have performed metagenomic and transcriptomic analyses on the intestines of grouper at the pre-, mid- and post-metamorphosis stages. The sequencing data of 16S rRNA gene showed drastic changes in the microbial communities at different developmental stages. The transcriptomic data revealed that the leukocyte transendothelial migration and the phagosome pathways might play important roles in mediating immunity in grouper at the three developmental stages. This information will increase our understanding of the metamorphosis process in grouper larvae, and shed light on the development of antimicrobial strategy during larval development.}, }
@article {pmid31054103, year = {2019}, author = {Han, Y and Jiang, X and Ling, Q and Wu, L and Wu, P and Tang, R and Xu, X and Yang, M and Zhang, L and Zhu, W and Wang, B and Li, L}, title = {Antibiotics-mediated intestinal microbiome perturbation aggravates tacrolimus-induced glucose disorders in mice.}, journal = {Frontiers of medicine}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11684-019-0686-8}, pmid = {31054103}, issn = {2095-0225}, abstract = {Both immunosuppressants and antibiotics (ABX) are indispensable for transplant patients. However, the former increases the risk of new-onset diabetes, whereas the latter impacts intestinal microbiota (IM). It is still unclear whether and how the interaction between immunosuppressants and ABX alters the IM and thus leads to glucose metabolism disorders. This study examined the alterations of glucose and lipid metabolism and IM in mice exposed to tacrolimus (TAC) with or without ABX. We found that ABX further aggravated TAC-induced glucose tolerance and increased insulin secretion. Combined treatment resulted in exacerbated lipid accumulation in the liver. TAC-altered microbial community was further amplified by ABX administration, as characterized by reductions in phylum Firmicutes, family Lachnospiraceae, and genus Coprococcus. Analyses based on the metagenomic profiles revealed that ABX augmented the effect of TAC on microbial metabolic function mostly related to lipid metabolism. The altered components of gut microbiome and predicted microbial functional profiles showed significant correlation with hepatic lipid accumulation and glucose disorders. In conclusion, ABX aggravated the effect of TAC on the microbiome and its metabolic capacities, which might contribute to hepatic lipid accumulation and glucose disorders. These findings suggest that the ABX-altered microbiome can amplify the diabetogenic effect of TAC and could be a novel therapeutic target for patients.}, }
@article {pmid31053982, year = {2019}, author = {Van Dexter, S and Oubre, C and Boopathy, R}, title = {Carbon ecology of termite gut and phenol degradation by a bacterium isolated from the gut of termite.}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10295-019-02183-5}, pmid = {31053982}, issn = {1476-5535}, abstract = {Metagenomics and transcriptomics have had some success analyzing community and functional ecology of the termite gut, but carbon utilization ecology and the effect of diet on the gut community are not well understood. This study was done to determine the effect of three hardwood tree types, oak (Quercus spp.), red maple (Acer rubrum), and tupelo (Nyssa aquatica) on the termite species, Reticulitermes flavipes in the family Rhinotermitidae. Termite abdomen homogenates were incubated on agar plates containing three common carbon sources in the termite gut, namely, acetate, cellobiose, and phenol under aerobic and anaerobic conditions. Bacterial growth was higher on cellobiose than any other carbon source. Higher bacterial growth on cellobiose was observed from termite colonies feeding on oak than on phenol from the other two wood types. The difference between aerobic and anaerobic conditions was not significant. A bacterium, Acinetobacter tandoii isolated and identified from our previous study was subjected to high concentrations of phenol as the sole carbon source and this bacterium was able to degrade phenol concentration up to 600 mg/L.}, }
@article {pmid31053918, year = {2019}, author = {Williams, W and Kunorozva, L and Klaiber, I and Henkel, M and Pfannstiel, J and Günther, J and Conrad, J and Van Zyl, LJ and Hausmann, R and Burger, A and Trindade, M}, title = {Correction to: Novel metagenome-derived ornithine lipids identified by functional screening for biosurfactants.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00253-019-09860-6}, pmid = {31053918}, issn = {1432-0614}, abstract = {The published online version contains mistake in the author list.}, }
@article {pmid31053813, year = {2019}, author = {}, title = {Metagenomics.}, journal = {Nature biotechnology}, volume = {37}, number = {5}, pages = {519}, doi = {10.1038/s41587-019-0118-y}, pmid = {31053813}, issn = {1546-1696}, }
@article {pmid31053581, year = {2019}, author = {Mandhania, MH and Paul, D and Suryavanshi, MV and Sharma, L and Chowdhury, S and Diwanay, SS and Diwanay, SS and Shouche, YS and Patole, MS}, title = {Diversity and Succession of Microbiota during Fermentation of Traditional Indian Food Idli.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.00368-19}, pmid = {31053581}, issn = {1098-5336}, abstract = {Idli, a naturally fermented Indian food, is prepared from mixture of rice and black gram (lentil). To understand its microbial community during fermentation, detailed analysis of the structural and functional dynamics of Idli microbiome was performed by culture-dependent and independent approaches. The bacterial diversity and microbial succession was assessed at different times of fermentation by 16S rRNA amplicon sequencing. Results highlighted that most microbiota belonged to phylum Firmicutes (70%) and Proteobacteria (22%). DGGE and qPCR analysis confirmed the diversity and succession involved therein. Culture dependent approach revealed that the microbial diversity was conserved across different geographical locations. The fermentation was primarily driven by lactic acid bacteria as they constitute 86% of the total bacterial population and genus Weissella emerged as the most important organism in the fermentation. The natural microbiota of the grains mainly drives the fermentation as surface sterilized grains did not show any fermentation. Growth kinetics of Idli microbiota and physico-chemical parameters corroborated correctly with the changes in microbial dynamics, acid production and leavening occurring during fermentation. Using metagenomic prediction tool, it was found that the major metabolic activities of these microbial fermenters augmented during the important phase of fermentation. Involvement of heterofermentative HMP pathway in batter leavening was substantiated by radiolabelled carbon dioxide generated from D-[1-14C]-glucose. Hydrolases degrading starch and phytins and production of B-vitamins was reported. Moreover, culturable isolates showing beneficial attributes such as acid and bile tolerance, hydrophobicity, antibiotic sensitivity and antimicrobial activity, suggest Idli to be a potential dietary supplement.IMPORTANCE: This is a comprehensive analysis of Idli fermentation employing modern molecular tools which provided valuable information about the bacterial diversity enabling its fermentation. The study has demonstrated the relationship between the bacterial population and its functional role in the process. The nature of Idli fermentation was found to be more complex as compared to other food fermentations due to the succession of bacterial population. Further studies using metatranscriptomics and metabolomics may enhance the understanding of this complex fermentation process. Moreover, the presence of microorganisms with beneficial properties, plausibly make Idli a suitable functional food.}, }
@article {pmid31053425, year = {2019}, author = {Keohane, DM and Woods, T and O'Connor, P and Underwood, S and Cronin, O and Whiston, R and O'Sullivan, O and Cotter, P and Shanahan, F and Molloy, MGM}, title = {Four men in a boat: Ultra-endurance exercise alters the gut microbiome.}, journal = {Journal of science and medicine in sport}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jsams.2019.04.004}, pmid = {31053425}, issn = {1878-1861}, abstract = {OBJECTIVES: Compositional and functional adaptions occur in the gut microbiome in response to habitual physical activity. The response of the gut microbiome to sustained, intense exercise in previously active individuals, however, is unknown. This study aimed to prospectively explore the gut microbiome response of four well-trained male athletes to prolonged, high intensity trans-oceanic rowing, describing changes in microbial diversity, abundance and metabolic capacity.<br><br>DESIGN: A prospective, repeated-measures, within-subject report.<br><br>METHODS: Serial stool samples were obtained from four male athletes for metagenomic whole-genome shotgun sequencing to record microbial community structure and relevant functional gene profiles before, during and after a continuous, unsupported 33-day, 5000 km transoceanic rowing race. Calorific intake and macronutrient composition were recorded by validated food frequency questionnaire and anthropometry was determined by body composition analysis and cardiorespiratory testing.<br><br>RESULTS: Microbial diversity increased throughout the ultra-endurance event. Variations in taxonomic composition included increased abundance of butyrate producing species and species associated with improved metabolic health, including improved insulin sensitivity. The functional potential of bacterial species involved in specific amino and fatty acid biosynthesis also increased. Many of the adaptions in microbial community structure and metaproteomics persisted at three months follow up.<br><br>CONCLUSIONS: These findings demonstrate that prolonged, intense exercise positively influences gut microbial diversity, increases the relative abundance of some bacterial species and up-regulates the metabolic potential of specific pathways expressing microbial gene products. These adaptions may play a compensatory role in controlling the physiological stress associated with sustained exertion as well as negating the deleterious consequences accompanying endurance exercise.}, }
@article {pmid31052348, year = {2019}, author = {Edridge, AWD and Deijs, M and van Zeggeren, IE and Kinsella, CM and Jebbink, MF and Bakker, M and van de Beek, D and Brouwer, MC and van der Hoek, L}, title = {Viral Metagenomics on Cerebrospinal Fluid.}, journal = {Genes}, volume = {10}, number = {5}, pages = {}, doi = {10.3390/genes10050332}, pmid = {31052348}, issn = {2073-4425}, support = {721367//Horizon 2020/ ; }, abstract = {Identifying the causative pathogen in central nervous system (CNS) infections is crucial for patient management and prognosis. Many viruses can cause CNS infections, yet screening for each individually is costly and time-consuming. Most metagenomic assays can theoretically detect all pathogens, but often fail to detect viruses because of their small genome and low viral load. Viral metagenomics overcomes this by enrichment of the viral genomic content in a sample. VIDISCA-NGS is one of the available workflows for viral metagenomics, which requires only a small input volume and allows multiplexing of multiple samples per run. The performance of VIDISCA-NGS was tested on 45 cerebrospinal fluid (CSF) samples from patients with suspected CNS infections in which a virus was identified and quantified by polymerase chain reaction. Eighteen were positive for an RNA virus, and 34 for a herpesvirus. VIDISCA-NGS detected all RNA viruses with a viral load >2 × 104 RNA copies/mL (n = 6) and 8 of 12 of the remaining low load samples. Only one herpesvirus was identified by VIDISCA-NGS, however, when withholding a DNase treatment, 11 of 18 samples with a herpesvirus load >104 DNA copies/mL were detected. Our results indicate that VIDISCA-NGS has the capacity to detect low load RNA viruses in CSF. Herpesvirus DNA in clinical samples is probably non-encapsidated and therefore difficult to detect by VIDISCA-NGS.}, }
@article {pmid31051396, year = {2019}, author = {Cabral, L and Noronha, MF and de Sousa, STP and Lacerda-Júnior, GV and Richter, L and Fostier, AH and Andreote, FD and Hess, M and Oliveira, VM}, title = {The metagenomic landscape of xenobiotics biodegradation in mangrove sediments.}, journal = {Ecotoxicology and environmental safety}, volume = {179}, number = {}, pages = {232-240}, doi = {10.1016/j.ecoenv.2019.04.044}, pmid = {31051396}, issn = {1090-2414}, abstract = {Metagenomics is a powerful approach to study microorganisms present in any given environment and their potential to maintain and improve ecosystem health without the need of cultivating these microorganisms in the laboratory. In this study, we combined a cultivation-independent metagenomics approach with functional assays to identify the detoxification potential of microbial genes evaluating their potential to contribute to xenobiotics resistance in oil-impacted mangrove sediments. A metagenomic fosmid library containing 12,960 clones from highly contaminated mangrove sediment was used in this study. For assessment of metal resistance, clones were grown in culture medium with increasing concentrations of mercury. The analyses metagenomic library sequences revealed the presence of genes related to heavy metals and antibiotics resistance in the oil-impacted mangrove microbiome. The taxonomic profiling of these sequences suggests that at the genus level, Geobacter was the most abundant genus in our dataset. A functional screening assessment of the metagenomic library successfully detected 24 potential heavy metal tolerant clones, six of which were capable of growing with increased concentrations of mercury. The genetic characterization of selected clones allowed the detection of genes related to detoxification processes, such as chromate transport protein ChrA, haloacid dehalogenase-like hydrolase, lipopolysaccharide transport system, and 3-oxoacyl-[acyl-carrier-protein] reductase. Clones were capable of growing in medium containing increased concentrations of metals and antibiotics, but none manifested strong mercury removal from culture medium characteristic of mercuric reductase activity. These results suggest that resistance to xenobiotic stress varies greatly and that additional studies to elucidate the potential of metal biotransformation need to be carried out with the goal of improving bioremediation application.}, }
@article {pmid31051349, year = {2019}, author = {Han, L and Zhang, H and Long, Z and Ge, Q and Mei, J and Yu, Y and Fang, H}, title = {Exploring microbial community structure and biological function in manured soil during ten repeated treatments with chlortetracycline and ciprofloxacin.}, journal = {Chemosphere}, volume = {228}, number = {}, pages = {469-477}, doi = {10.1016/j.chemosphere.2019.04.154}, pmid = {31051349}, issn = {1879-1298}, abstract = {The changes of enzyme activities, microbial community structure and function, and the diversity and resistance level of antibiotic-resistant bacteria (ARB) were studied in soil during ten repeated treatments with chlortetracycline (CTC) and/or ciprofloxacin (CIP) together with organic manure (OM) under laboratory conditions. The activities of neutral phosphatase (NPA) and catalase (CAT) displayed the suppression-recovery-stimulation trend in the OM&amp;CTC treatment but the stimulation trend in the OM&amp;CTC&amp;CIP treatment. The NPA was stimulated but the CAT was little affected in the OM&amp;CIP treatment. Soil microbial functional diversity displayed the suppression-recovery-stimulation trend in the OM&amp;CTC and OM&amp;CTC&amp;CIP treatments and the stimulation-suppression trend in the OM&amp;CIP treatment with the treatment frequency. Metagenomic analysis showed that the relative abundances of Actinobacteria and Firmicutes in the antibiotic treatment significantly increased by 0.5-235.6%, but that of Proteobacteria decreased by 0.2-27.3% compared to the control with the treatment frequency. Furthermore, the relative abundances of dominant bacterial genera including Streptomyces, Actinomadura, Mycobacterium, and Streptococcus in the antibiotic treatment significantly increased by 1.1-10433.3% compared to the control. Meanwhile, repeated antibiotic treatments induced a significant increase in the diversity and resistance level of ARB isolates, especially in the OM&amp;CTC treatment. It is concluded that repeated treatments with CTC and/or CIP can alter enzyme activities, microbial community structure and function, and increase the diversity and resistance level of ARB isolates.}, }
@article {pmid31051018, year = {2019}, author = {Blumenberg, M}, title = {Skinomics, transcriptional profiling approaches to molecular and structural biology of epidermis.}, journal = {Seminars in cutaneous medicine and surgery}, volume = {38}, number = {1}, pages = {E12-E18}, doi = {10.12788/j.sder.2019.004}, pmid = {31051018}, issn = {1558-0768}, abstract = {Skinomics is a field of bioinformatics applied specifically to skin biology and, by extension, to dermatology. Skinomics has been expanding into extensive genome-wide association studies, eg, of psoriasis, proteomics, lipidomics, metabolomics, metagenomics, and the studies of the microbiome. Here, the current state of the field of transcriptomics is reviewed, including the studies of the gene expression in human skin under several healthy and disease conditions. Specifically, transcriptional studies of epidermal differentiation, skin aging, effects of cytokines, inflammation with emphases on psoriasis and atopic dermatitis, and wound healing are reviewed. The transition from microarrays to NextGen sequencing is noted and potential future directions suggested.}, }
@article {pmid31050420, year = {2019}, author = {Mantilla-Calderon, D and Plewa, MJ and Michoud, G and Fodelianakis, S and Daffonchio, D and Hong, P}, title = {Water disinfection byproducts increase natural transformation rates of environmental DNA in Acinetobacter baylyi ADP1.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.9b00692}, pmid = {31050420}, issn = {1520-5851}, abstract = {The process of natural transformation allows for the stable uptake, integration and functional expression of extracellular DNA. This mechanism of horizontal gene transfer has been widely linked to the acquisition of antibiotic resistance and virulence factors. Here, we demonstrate that bromoacetic acid (BAA) - a regulated drinking water disinfection byproduct (DBP) - can stimulate natural transformation rates in the model organism Acinetobacter baylyi ADP1. We demonstrate that transformation stimulation in response to BAA is concentration-dependent and is linked to the ability of this compound to generate DNA damage via oxidative stress. In presence of BAA, transcription of recA was upregulated 20-40% compared to the non-treated controls, indicating that this component of the DNA damage response could be associated with the increase in transformation. Other genes associated with DNA-translocation across the cytoplasmic membrane (i.e. pilX, comA) did not exhibited increased transcription in presence of BAA, indicating that the enhancement of transformation is not associated with increased translocation rates of environmental DNA. Overall, these results lead us to speculate that elevated recA transcription levels could lead to increased integration rates of foreign DNA within the recipient cell during DNA repair. Lastly, we show that an artificial DBP cocktail simulating the environmental concentrations of five water DBP classes stimulates natural transformation by almost 2-fold. The results of this study suggest that mutagens like DBPs may play an important role in enhancing the fixation rates of extracellular DNA in the environmental metagenome.}, }
@article {pmid30992348, year = {2019}, author = {Holmes, EC and Duchêne, S}, title = {Can Sequence Phylogenies Safely Infer the Origin of the Global Virome?.}, journal = {mBio}, volume = {10}, number = {2}, pages = {}, doi = {10.1128/mBio.00289-19}, pmid = {30992348}, issn = {2150-7511}, mesh = {*Evolution, Molecular ; Metagenomics ; Phylogeny ; *RNA ; }, }
@article {pmid30814220, year = {2019}, author = {Berghuis, BA and Yu, FB and Schulz, F and Blainey, PC and Woyke, T and Quake, SR}, title = {Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {11}, pages = {5037-5044}, doi = {10.1073/pnas.1815631116}, pmid = {30814220}, issn = {1091-6490}, mesh = {Euryarchaeota/*classification/genetics/*metabolism ; Genes, Archaeal ; Hydrogen/*metabolism ; Metagenome ; Methane/*metabolism ; *Phylogeny ; }, abstract = {Methanogenic archaea are major contributors to the global carbon cycle and were long thought to belong exclusively to the euryarchaeal phylum. Discovery of the methanogenesis gene cluster methyl-coenzyme M reductase (Mcr) in the Bathyarchaeota, and thereafter the Verstraetearchaeota, led to a paradigm shift, pushing back the evolutionary origin of methanogenesis to predate that of the Euryarchaeota. The methylotrophic methanogenesis found in the non-Euryarchaota distinguished itself from the predominantly hydrogenotrophic methanogens found in euryarchaeal orders as the former do not couple methanogenesis to carbon fixation through the reductive acetyl-CoA [Wood-Ljungdahl pathway (WLP)], which was interpreted as evidence for independent evolution of the two methanogenesis pathways. Here, we report the discovery of a complete and divergent hydrogenotrophic methanogenesis pathway in a thermophilic order of the Verstraetearchaeota, which we have named Candidatus Methanohydrogenales, as well as the presence of the WLP in the crenarchaeal order Desulfurococcales. Our findings support the ancient origin of hydrogenotrophic methanogenesis, suggest that methylotrophic methanogenesis might be a later adaptation of specific orders, and provide insight into how the transition from hydrogenotrophic to methylotrophic methanogenesis might have occurred.}, }
@article {pmid29176696, year = {2017}, author = {}, title = {Overcoming hurdles in sharing microbiome data.}, journal = {Nature microbiology}, volume = {2}, number = {12}, pages = {1573}, doi = {10.1038/s41564-017-0077-3}, pmid = {29176696}, issn = {2058-5276}, mesh = {Computational Biology/*methods ; Information Dissemination/*methods ; Metagenomics/*methods ; *Microbiota ; }, }
@article {pmid28764816, year = {2018}, author = {Kosoy, M and McKee, C and Albayrak, L and Fofanov, Y}, title = {Genotyping of Bartonella bacteria and their animal hosts: current status and perspectives.}, journal = {Parasitology}, volume = {145}, number = {5}, pages = {543-562}, doi = {10.1017/S0031182017001263}, pmid = {28764816}, issn = {1469-8161}, mesh = {Animals ; Arthropods ; Bartonella/classification/*genetics ; Genetic Variation ; *Genotyping Techniques ; Mammals ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Whole Genome Sequencing ; }, abstract = {Growing evidence demonstrates that bacterial species diversity is substantial, and many of these species are pathogenic in some contexts or hosts. At the same time, laboratories and museums have collected valuable animal tissue and ectoparasite samples that may contain substantial novel information on bacterial prevalence and diversity. However, the identification of bacterial species is challenging, partly due to the difficulty in culturing many microbes and the reliance on molecular data. Although the genomics revolution will surely add to our knowledge of bacterial systematics, these approaches are not accessible to all researchers and rely predominantly on cultured isolates. Thus, there is a need for comprehensive molecular analyses capable of accurately genotyping bacteria from animal tissues or ectoparasites using common methods that will facilitate large-scale comparisons of species diversity and prevalence. To illustrate the challenges of genotyping bacteria, we focus on the genus Bartonella, vector-borne bacteria common in mammals. We highlight the value and limitations of commonly used techniques for genotyping bartonellae and make recommendations for researchers interested in studying the diversity of these bacteria in various samples. Our recommendations could be applicable to many bacterial taxa (with some modifications) and could lead to a more complete understanding of bacterial species diversity.}, }
@article {pmid28349932, year = {2017}, author = {Nunes-Alves, C}, title = {Microbial communities rock.}, journal = {Nature microbiology}, volume = {2}, number = {}, pages = {17041}, doi = {10.1038/nmicrobiol.2017.41}, pmid = {28349932}, issn = {2058-5276}, mesh = {Biotransformation ; *Environmental Microbiology ; Metabolic Networks and Pathways ; Metagenomics/methods/trends ; Microbiological Techniques/methods/trends ; Microbiology/trends ; *Microbiota ; Minerals/metabolism ; }, }
@article {pmid28120929, year = {2017}, author = {Soppa, J}, title = {Polyploidy and community structure.}, journal = {Nature microbiology}, volume = {2}, number = {}, pages = {16261}, doi = {10.1038/nmicrobiol.2016.261}, pmid = {28120929}, issn = {2058-5276}, mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics ; *Biota ; Eukaryota/classification/*genetics ; Metagenomics/methods ; *Polyploidy ; }, }
@article {pmid31049708, year = {2019}, author = {Dutta, A and Peoples, LM and Gupta, A and Bartlett, DH and Sar, P}, title = {Exploring the piezotolerant/piezophilic microbial community and genomic basis of piezotolerance within the deep subsurface Deccan traps.}, journal = {Extremophiles : life under extreme conditions}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00792-019-01094-8}, pmid = {31049708}, issn = {1433-4909}, support = {MoES/P.O.(Seismo)/1(181)/2013 dated April 7//Ministry of Earth Sciences, India/ ; 2014//Ministry of Earth Sciences, India/ ; IIT/SRIC/BT/ODM/2015-16/141//IIT Kharagpur SGBSI challenge grant 2015/ ; }, abstract = {The deep biosphere is often characterized by multiple extreme physical-chemical conditions, of which pressure is an important parameter that influences life but remains less studied. This geomicrobiology study was designed to understand the response of a subterranean microbial community of the Deccan traps to high-pressure conditions and to elucidate their genomic properties. Groundwater from a deep basaltic aquifer of the Deccan traps was used to ascertain the community response to 25 MPa and 50 MPa pressure following enrichment in high-salt and low-salt organic media. Quantitative PCR data indicated a decrease in bacterial and archaeal cell numbers with increasing pressure. 16S rRNA gene sequencing displayed substantial changes in the microbial community in which Acidovorax appeared to be the most dominant genus in the low-salt medium and Microbacteriaceae emerged as the major family in the high-salt medium under both pressure conditions. Genes present in metagenome-associated genomes which have previously been associated with piezotolerance include those related to nutrient uptake and extracytoplasmic stress (omp, rseC), protein folding and unfolding (dnaK, groEL and others), and DNA repair mechanisms (mutT, uvr and others). We hypothesize that these genes facilitate tolerance to high pressure by certain groups of microbes residing in subsurface Deccan traps.}, }
@article {pmid31049590, year = {2019}, author = {Butina, TV and Bukin, YS and Krasnopeev, AS and Belykh, OI and Tupikin, AE and Kabilov, MR and Sakirko, МV and Belikov, SI}, title = {Estimate of the diversity of viral and bacterial assemblage in the coastal water of Lake Baikal.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnz094}, pmid = {31049590}, issn = {1574-6968}, abstract = {In this study, we analysed the diversity and composition of double-stranded DNA viral and bacterial communities within the sample of surface coastal water of Southern Baikal through metagenomics and deep sequencing of the 16S ribosomal RNA gene, respectively. The 16S rRNA gene analysis has revealed 14 phyla and dominance of the 'Actinobacteria' (43.6%), 'Proteobacteria' (25.2%) and 'Bacteroidetes' (11.5%). The bacterial composition and structure were similar to those obtained previously in Lake Baikal littoral zone. Out of 1 030 169 processed virome reads, 37.4% of sequences (385 421) were identified as viral; 15.1% were identified as nonviral and related to the domains Eukarya, Bacteria and Archaea; and 47.5% had no matches in the databases. The identified virotypes belonged to different families and were predicted to infect a wide range of organisms, from bacteria to mammals. Six families (Myoviridae, Poxviridae, Mimiviridae, Siphoviridae, Phycodnaviridae, and Podoviridae) were dominant accounting for more than 90% of the identified sequences (48.3%, 17.4%, 8.3%, 6.8%, 5.8%, and 4.1%, respectively). In contrast to other freshwater systems, high percentage of the Poxviridae and Mimiviridae was recorded in the water sample of Lake Baikal.}, }
@article {pmid31048756, year = {2019}, author = {Schwank, K and Bornemann, TLV and Dombrowski, N and Spang, A and Banfield, JF and Probst, AJ}, title = {An archaeal symbiont-host association from the deep terrestrial subsurface.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0421-0}, pmid = {31048756}, issn = {1751-7370}, abstract = {DPANN archaea have reduced metabolic capacities and are diverse and abundant in deep aquifer ecosystems, yet little is known about their interactions with other microorganisms that reside there. Here, we provide evidence for an archaeal host-symbiont association from a deep aquifer system at the Colorado Plateau (Utah, USA). The symbiont, Candidatus Huberiarchaeum crystalense, and its host, Ca. Altiarchaeum hamiconexum, show a highly significant co-occurrence pattern over 65 metagenome samples collected over six years. The physical association of the two organisms was confirmed with genome-informed fluorescence in situ hybridization depicting small cocci of Ca. H. crystalense attached to Ca. A. hamiconexum cells. Based on genomic information, Ca. H. crystalense potentially scavenges vitamins, sugars, nucleotides, and reduced redox-equivalents from its host and thus has a similar metabolism as Nanoarchaeum equitans. These results provide insight into host-symbiont interactions among members of two uncultivated archaeal phyla that thrive in a deep subsurface aquifer.}, }
@article {pmid31048728, year = {2019}, author = {Lee, S and La, TM and Lee, HJ and Choi, IS and Song, CS and Park, SY and Lee, JB and Lee, SW}, title = {Characterization of microbial communities in the chicken oviduct and the origin of chicken embryo gut microbiota.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {6838}, doi = {10.1038/s41598-019-43280-w}, pmid = {31048728}, issn = {2045-2322}, support = {NRF-2016R1C1B2015343//National Research Foundation of Korea (NRF)/ ; NRF-2016R1C1B2015343//National Research Foundation of Korea (NRF)/ ; NRF-2016R1C1B2015343//National Research Foundation of Korea (NRF)/ ; NRF-2016R1C1B2015343//National Research Foundation of Korea (NRF)/ ; }, abstract = {The transferred microbiota from mother to baby constitutes the initial infant gastrointestinal microbiota and has an important influence on the development and health of infants in human. However, the reproductive tract microbiota of avian species and its inheritance have rarely been studied. We aimed to characterize the microbial community in the chicken reproductive tract and determine the origin of the chicken embryo gut microbiota. Microbiota in four different portions of chicken oviduct were determined using 16S rRNA metagenomic approach with the IonTorrent platform. Additionally, we analyzed the mother hen's magnum and cloaca, descendent egg, and embryo gut microbiota. The microbial composition and relative abundance of bacterial genera were stable throughout the entire chicken reproductive tract, without significant differences between the different parts of the oviduct. The chicken reproductive tract showed a relatively high abundance of Lactobacillus species. The number of bacterial species in the chicken reproductive tract significantly increased following sexual maturation. Core genera analysis detected 21 of common genera in the maternal magnum and cloaca, descendent egg shell, egg white, and embryo gut. Some elements of the maternal oviduct microbiota appear to be transferred to the embryo through the egg white and constitute most of the embryo gut bacterial population.}, }
@article {pmid31048319, year = {2019}, author = {Antipov, D and Raiko, M and Lapidus, A and Pevzner, PA}, title = {Plasmid detection and assembly in genomic and metagenomic datasets.}, journal = {Genome research}, volume = {}, number = {}, pages = {}, doi = {10.1101/gr.241299.118}, pmid = {31048319}, issn = {1549-5469}, abstract = {Although plasmids are important for bacterial survival and adaptation, plasmid detection and assembly from genomic, let alone metagenomic, samples remain challenging. The recently developed plasmidSPAdes assembler addressed some of these challenges in the case of isolate genomes but stopped short of detecting plasmids in metagenomic assemblies, an untapped source of yet to be discovered plasmids. We present the metaplasmidSPAdes tool for plasmid assembly in metagenomic datasets that reduced the false positive rate of plasmid detection as compared to the state-of-the-art approaches. We assembled plasmids in diverse datasets and have demonstrated that thousands of plasmids remained below the radar in already completed genomic and metagenomic studies. Our analysis revealed the extreme variability of plasmids and has led to the discovery of a high number of novel plasmids (including many plasmids carrying antibiotic-resistance genes) without significant similarities to currently known ones.}, }
@article {pmid31048075, year = {2019}, author = {Afolabi, KO and Iweriebor, BC and Okoh, AI and Obi, LC}, title = {Increasing diversity of swine parvoviruses and their epidemiology in African pigs.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.meegid.2019.04.029}, pmid = {31048075}, issn = {1567-7257}, abstract = {Detection of infectious viral agents has been on the increase globally with the advent and usage of more sensitive and selective novel molecular techniques in the epidemiological study of viral diseases of economic importance to the swine industry. The observation is not different for the pig-infecting member of the subfamily Parvovirinae in the family Parvoviridae as the application of novel molecular methods like metagenomics has brought about the detection of many other novel members of the group. Surprisingly, the list keeps increasing day by day with some of them possessing zoonotic potentials. In the last one decade, not less than ten novel swine-infecting viruses have been added to the subfamily, and ceaseless efforts have been in top gear to determine the occurrence and prevalence of the old and new swine parvoviruses in herds of pig-producing countries worldwide. The story, however, is on the contrary on the African continent as there is presently a dearth of information on surveillance initiatives of the viruses among swine herds of pig-producing countries in the region. Timely detection and characterization of the viral pathogens is highly imperative for the implementation of effective control and prevention of its spread. This review therefore presents a concise overview on the epidemiology of novel porcine parvoviruses globally and also provides up-to-date highlights on the reported cases of the viral agents in the African sub-region.}, }
@article {pmid31047827, year = {2019}, author = {Casati Pagani, S and Frigerio Malossa, S and Klaus, C and Hoffmann, D and Beretta, O and Bomio-Pacciorini, N and Lazzaro, M and Merlani, G and Ackermann, R and Beuret, C}, title = {First detection of TBE virus in ticks and sero-reactivity in goats in a non-endemic region in the southern part of Switzerland (Canton of Ticino).}, journal = {Ticks and tick-borne diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ttbdis.2019.04.006}, pmid = {31047827}, issn = {1877-9603}, abstract = {In Switzerland, tick-borne encephalitis (TBE) is a notifiable human disease with an average of 210 cases per year in the last 10 years (2008-2017). A national surveillance conducted in 2009 reported a prevalence of 0.46% for tick-borne encephalitis virus (TBEV) detected in ticks, which is in accordance with the prevalences found in Europe from 0.1%-5%. The Canton of Ticino in the southern part of Switzerland, geographically separated from the rest of the national territory by the Alps, is considered a non-endemic region, as no autochthonous clinical cases and no TBEV presence in ticks have ever been reported. In order to understand the epidemiological situation in Ticino, we conducted a large study investigating the TBEV presence in field-collected Ixodes ricinus ticks and in goat and human sera. Goats and sheep were considered as sentinel hosts showing persistence of antibodies also after 28 months in the absence of symptoms; this longevity supports the data validity to characterize an area with the TBEV status. The goat sera collection was composed of a total of 662 samples from 37 flocks. The total seroprevalence was 14.6%. 39 (40%) of the 97 SNT-positive samples showed an antibody titer ≥ 1:120 which indicates recent infection and consequently the probable presence of active foci among the pastures frequented by the goats belonging to 10 flocks. In total, 51 owners participated in the study and all were TBEV antibody-free. A total of 12'052 I. ricinus ticks (nymphs and adults) were collected and 1'371 pools were tested using quantitative real-time RT-PCR. Only one positive pool was reported with a prevalence of 0.35%. Metagenomic analysis revealed that the TBEV strain isolated from the ticks collected in Ticino is closely related to 2 strains coming from the Canton of Valais (99.1% and 98.7% identity, respectively), a neighbouring region of the Canton of Ticino. These two Cantons are close together but separated by high mountains (Alps) and we hypothesize that infected ticks were transported by wild animals from Valais into the Valle Maggia in Ticino where we found positive ticks. In conclusion, our data show for the first time the presence of TBEV in ticks and the related sero-reactivity in goats, confirming the presence of TBEV in the environment of the Canton of Ticino. Further surveillance studies will have to be conducted to follow the persistence of TBEV in this region.}, }
@article {pmid31046662, year = {2019}, author = {Metzler-Zebeli, BU and Newman, MA and Grüll, D and Zebeli, Q}, title = {Functional adaptations in the cecal and colonic metagenomes associated with the consumption of transglycosylated starch in a pig model.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {87}, doi = {10.1186/s12866-019-1462-2}, pmid = {31046662}, issn = {1471-2180}, support = {836447//Österreichische Forschungsförderungsgesellschaft/ ; }, abstract = {BACKGROUND: Both phylogeny and functional capabilities within the gut microbiota populations are of great importance for influencing host health. As a novel type of resistant starch, transglycosylated starch (TGS) modifies the microbial community and metabolite profiles along the porcine gut, but little is known about the related functional adaptations in key metabolic pathways and their taxonomic identity.<br><br>RESULTS: Metagenomic sequencing was used to characterize the functional alterations in the cecal and colonic microbiomes of growing pigs fed TGS or control starch (CON) diets for 10 days (n = 8/diet). Bacterial communities were clearly distinguishable at taxonomic and functional level based on the dietary starch, with effects being similar at both gut sites. Cecal and colonic samples from TGS-fed pigs were enriched in Prevotella, Bacteroides, Acidaminoccus and Veillonella, whereas Treponema, Ruminococcus, and Aeromonas declined at both gut sites compared to CON-fed pigs (log2 fold change > ±1; p < 0.001 (q < 0.05)). This was associated with increased enzymatic capacities for amino acid metabolism, galactose, fructose and mannose metabolism, pentose and glucuronate interconversions, citrate cycle and vitamin metabolism for samples from TGS-fed pigs. However, TGS-fed pigs comprised fewer reads for starch and sucrose metabolism and genetic information processing. Changes in key catabolic steps were found to be the result of changes in taxa associated with each type of starch. Functional analysis indicated steps in the breakdown of TGS by the action of α- and β-galactosidases, which mainly belonged to Bacteroides and Prevotella. Reads mapped to alpha-amylase were less frequent in TGS- compared to CON-fed pigs, with the major source of this gene pool being Bacillus, Aeromonas and Streptococcus. Due to the taxonomic shifts, gene abundances of potent stimulants of the mucosal innate immune response were altered by the starches. The cecal and colonic metagenomes of TGS-fed pigs comprised more reads annotated in lipopolysaccharides biosynthesis, whereas they became depleted of genes for flagellar assembly compared to CON-fed pigs.<br><br>CONCLUSIONS: Metagenomic sequencing revealed distinct cecal and colonic bacterial communities in CON- and TGS-fed pigs, with strong discrimination among samples by functional capacities related to the respective starch in each pig's diet.}, }
@article {pmid31043573, year = {2019}, author = {Williams, MR and Costa, SK and Zaramela, LS and Khalil, S and Todd, DA and Winter, HL and Sanford, JA and O'Neill, AM and Liggins, MC and Nakatsuji, T and Cech, NB and Cheung, AL and Zengler, K and Horswill, AR and Gallo, RL}, title = {Quorum sensing between bacterial species on the skin protects against epidermal injury in atopic dermatitis.}, journal = {Science translational medicine}, volume = {11}, number = {490}, pages = {}, doi = {10.1126/scitranslmed.aat8329}, pmid = {31043573}, issn = {1946-6242}, abstract = {Colonization of the skin by Staphylococcus aureus is associated with exacerbation of atopic dermatitis (AD), but any direct mechanism through which dysbiosis of the skin microbiome may influence the development of AD is unknown. Here, we show that proteases and phenol-soluble modulin α (PSMα) secreted by S. aureus lead to endogenous epidermal proteolysis and skin barrier damage that promoted inflammation in mice. We further show that clinical isolates of different coagulase-negative staphylococci (CoNS) species residing on normal skin produced autoinducing peptides that inhibited the S. aureus agr system, in turn decreasing PSMα expression. These autoinducing peptides from skin microbiome CoNS species potently suppressed PSMα expression in S. aureus isolates from subjects with AD without inhibiting S. aureus growth. Metagenomic analysis of the AD skin microbiome revealed that the increase in the relative abundance of S. aureus in patients with active AD correlated with a lower CoNS autoinducing peptides to S. aureus ratio, thus overcoming the peptides' capacity to inhibit the S. aureus agr system. Characterization of a S. hominis clinical isolate identified an autoinducing peptide (SYNVCGGYF) as a highly potent inhibitor of S. aureus agr activity, capable of preventing S. aureus-mediated epithelial damage and inflammation on murine skin. Together, these findings show how members of the normal human skin microbiome can contribute to epithelial barrier homeostasis by using quorum sensing to inhibit S. aureus toxin production.}, }
@article {pmid31043514, year = {2019}, author = {Escudeiro, P and Pothier, J and Dionisio, F and Nogueira, T}, title = {Antibiotic Resistance Gene Diversity and Virulence Gene Diversity Are Correlated in Human Gut and Environmental Microbiomes.}, journal = {mSphere}, volume = {4}, number = {3}, pages = {}, doi = {10.1128/mSphere.00135-19}, pmid = {31043514}, issn = {2379-5042}, abstract = {Human beings have used large amounts of antibiotics, not only in medical contexts but also, for example, as growth factors in agriculture and livestock, resulting in the contamination of the environment. Even when pathogenic bacteria are the targets of antibiotics, hundreds of nonpathogenic bacterial species are affected as well. Therefore, both pathogenic and nonpathogenic bacteria have gradually become resistant to antibiotics. We tested whether there is still cooccurrence of resistance and virulence determinants. We performed a comparative study of environmental and human gut metagenomes from different individuals and from distinct human populations across the world. We found a great diversity of antibiotic resistance determinants (AR diversity [ARd]) and virulence factors (VF diversity [VFd]) in metagenomes. Importantly there is a correlation between ARd and VFd, even after correcting for protein family richness. In the human gut, there are less ARd and VFd than in more diversified environments, and yet correlations between the ARd and VFd are stronger. They can vary from very high in Malawi, where antibiotic consumption is unattended, to nonexistent in the uncontacted Amerindian population. We conclude that there is cooccurrence of resistance and virulence determinants in human gut microbiomes, suggesting a possible coselective mechanism.IMPORTANCE Every year, thousands of tons of antibiotics are used, not only in human and animal health but also as growth promoters in livestock. Consequently, during the last 75 years, antibiotic-resistant bacterial strains have been selected in human and environmental microbial communities. This implies that, even when pathogenic bacteria are the targets of antibiotics, hundreds of nonpathogenic bacterial species are also affected. Here, we performed a comparative study of environmental and human gut microbial communities issuing from different individuals and from distinct human populations across the world. We found that antibiotic resistance and pathogenicity are correlated and speculate that, by selecting for resistant bacteria, we may be selecting for more virulent strains as a side effect of antimicrobial therapy.}, }
@article {pmid30850431, year = {2019}, author = {Schreiber, L and Fortin, N and Tremblay, J and Wasserscheid, J and Elias, M and Mason, J and Sanschagrin, S and Cobanli, S and King, T and Lee, K and Greer, CW}, title = {Potential for Microbially Mediated Natural Attenuation of Diluted Bitumen on the Coast of British Columbia (Canada).}, journal = {Applied and environmental microbiology}, volume = {85}, number = {10}, pages = {}, doi = {10.1128/AEM.00086-19}, pmid = {30850431}, issn = {1098-5336}, abstract = {Western Canada produces large amounts of bitumen, a heavy, highly weathered crude oil. Douglas Channel and Hecate Strait on the coast of British Columbia are two water bodies that may be impacted by a proposed pipeline and marine shipping route for diluted bitumen (dilbit). This study investigated the potential of microbial communities from these waters to mitigate the impacts of a potential dilbit spill. Microcosm experiments were set up with water samples representing different seasons, years, sampling stations, and dilbit blends. While the alkane fraction of the tested dilbit blends was almost completely degraded after 28 days, the majority of the polycyclic aromatic hydrocarbons (PAHs) remained. The addition of the dispersant Corexit 9500A most often had either no effect or an enhancing effect on dilbit degradation. Dilbit-degrading microbial communities were highly variable between seasons, years, and stations, with dilbit type having little impact on community trajectories. Potential oil-degrading genera showed a clear succession pattern and were for the most part recruited from the &quot;rare biosphere.&quot; At the community level, dispersant appeared to stimulate an accelerated enrichment of genera typically associated with hydrocarbon degradation, even in dilbit-free controls. This suggests that dispersant-induced growth of hydrocarbon degraders (and not only increased bioavailability of oil-associated hydrocarbons) contributes to the degradation-enhancing effect previously reported for Corexit 9500A.IMPORTANCE Western Canada hosts large petroleum deposits, which ultimately enter the market in the form of dilbit. Tanker-based shipping represents the primary means to transport dilbit to international markets. With anticipated increases in production to meet global energy needs, the risk of a dilbit spill is expected to increase. This study investigated the potential of microbial communities naturally present in the waters of a potential dilbit shipping lane to mitigate the effects of a spill. Here we show that microbial degradation of dilbit was mostly limited to n-alkanes, while the overall concentration of polycyclic aromatic hydrocarbons, which represent the most toxic fraction of dilbit, decreased only slightly within the time frame of our experiments. We further investigated the effect of the oil dispersant Corexit 9500A on microbial dilbit degradation. Our results highlight the fact that dispersant-associated growth stimulation, and not only increased bioavailability of hydrocarbons and inhibition of specific genera, contributes to the overall effect of dispersant addition.}, }
@article {pmid31040829, year = {2019}, author = {Peker, N and Garcia-Croes, S and Dijkhuizen, B and Wiersma, HH and van Zanten, E and Wisselink, G and Friedrich, AW and Kooistra-Smid, M and Sinha, B and Rossen, JWA and Couto, N}, title = {A Comparison of Three Different Bioinformatics Analyses of the 16S-23S rRNA Encoding Region for Bacterial Identification.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {620}, doi = {10.3389/fmicb.2019.00620}, pmid = {31040829}, issn = {1664-302X}, abstract = {Rapid and reliable identification of bacterial pathogens directly from patient samples is required for optimizing antimicrobial therapy. Although Sanger sequencing of the 16S ribosomal RNA (rRNA) gene is used as a molecular method, species identification and discrimination is not always achievable for bacteria as their 16S rRNA genes have sometimes high sequence homology. Recently, next generation sequencing (NGS) of the 16S-23S rRNA encoding region has been proposed for reliable identification of pathogens directly from patient samples. However, data analysis is laborious and time-consuming and a database for the complete 16S-23S rRNA encoding region is not available. Therefore, a better, faster, and stronger approach is needed for NGS data analysis of the 16S-23S rRNA encoding region. We compared speed and diagnostic accuracy of different data analysis approaches: de novo assembly followed by Basic Local Alignment Search Tool (BLAST), operational taxonomic unit (OTU) clustering, or mapping using an in-house developed 16S-23S rRNA encoding region database for the identification of bacterial species. De novo assembly followed by BLAST using the in-house database was superior to the other methods, resulting in the shortest turnaround time (2 h and 5 min), approximately 2 h less than OTU clustering and 4.5 h less than mapping, and a sensitivity of 80%. Mapping was the slowest and most laborious data analysis approach with a sensitivity of 60%, whereas OTU clustering was the least laborious approach with 70% sensitivity. Although the in-house database requires more sequence entries to improve the sensitivity, the combination of de novo assembly and BLAST currently appears to be the optimal approach for data analysis.}, }
@article {pmid31040301, year = {2019}, author = {Torres-Cortés, G and Garcia, BJ and Compant, S and Rezki, S and Jones, P and Préveaux, A and Briand, M and Roulet, A and Bouchez, O and Jacobson, D and Barret, M}, title = {Differences in resource use lead to coexistence of seed-transmitted microbial populations.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {6648}, doi = {10.1038/s41598-019-42865-9}, pmid = {31040301}, issn = {2045-2322}, abstract = {Seeds are involved in the vertical transmission of microorganisms in plants and act as reservoirs for the plant microbiome. They could serve as carriers of pathogens, making the study of microbial interactions on seeds important in the emergence of plant diseases. We studied the influence of biological disturbances caused by seed transmission of two phytopathogenic agents, Alternaria brassicicola Abra43 (Abra43) and Xanthomonas campestris pv. campestris 8004 (Xcc8004), on the structure and function of radish seed microbial assemblages, as well as the nutritional overlap between Xcc8004 and the seed microbiome, to find seed microbial residents capable of outcompeting this pathogen. According to taxonomic and functional inference performed on metagenomics reads, no shift in structure and function of the seed microbiome was observed following Abra43 and Xcc8004 transmission. This lack of impact derives from a limited overlap in nutritional resources between Xcc8004 and the major bacterial populations of radish seeds. However, two native seed-associated bacterial strains belonging to Stenotrophomonas rhizophila displayed a high overlap with Xcc8004 regarding the use of resources; they might therefore limit its transmission. The strategy we used may serve as a foundation for the selection of seed indigenous bacterial strains that could limit seed transmission of pathogens.}, }
@article {pmid31040238, year = {2019}, author = {Aouizerat, T and Gutman, I and Paz, Y and Maeir, AM and Gadot, Y and Gelman, D and Szitenberg, A and Drori, E and Pinkus, A and Schoemann, M and Kaplan, R and Ben-Gedalya, T and Coppenhagen-Glazer, S and Reich, E and Saragovi, A and Lipschits, O and Klutstein, M and Hazan, R}, title = {Isolation and Characterization of Live Yeast Cells from Ancient Vessels as a Tool in Bio-Archaeology.}, journal = {mBio}, volume = {10}, number = {2}, pages = {}, doi = {10.1128/mBio.00388-19}, pmid = {31040238}, issn = {2150-7511}, abstract = {Ancient fermented food has been studied based on recipes, residue analysis, and ancient-DNA techniques and reconstructed using modern domesticated yeast. Here, we present a novel approach based on our hypothesis that enriched yeast populations in fermented beverages could have become the dominant species in storage vessels and their descendants could be isolated and studied today. We developed a pipeline of yeast isolation from clay vessels and screened for yeast cells in beverage-related and non-beverage-related ancient vessels and sediments from several archaeological sites. We found that yeast cells could be successfully isolated specifically from clay containers of fermented beverages. The findings that genotypically the isolated yeasts are similar to those found in traditional African beverages and phenotypically they grow similar to modern beer-producing yeast strongly suggest that they are descendants of the original fermenting yeast. These results demonstrate that modern microorganisms can serve as a new tool in bio-archaeology research.IMPORTANCE So far, most of the study of ancient organisms has been based mainly on the analysis of ancient DNA. Here we show that it is possible to isolate and study microorganisms-yeast in this case-from ancient pottery vessels used for fermentation. We demonstrate that it is highly likely that these cells are descendants of the original yeast strains that participated in the fermentation process and were absorbed into the clay matrix of the pottery vessels. Moreover, we characterized the isolated yeast strains, their genomes, and the beer they produced. These results open new and exciting avenues in the study of domesticated microorganisms and contribute significantly to the fields of bio- and experimental archaeology that aim to reconstruct ancient artifacts and products.}, }
@article {pmid29194980, year = {2018}, author = {Tanner, K and Martí, JM and Belliure, J and Fernández-Méndez, M and Molina-Menor, E and Peretó, J and Porcar, M}, title = {Polar solar panels: Arctic and Antarctic microbiomes display similar taxonomic profiles.}, journal = {Environmental microbiology reports}, volume = {10}, number = {1}, pages = {75-79}, doi = {10.1111/1758-2229.12608}, pmid = {29194980}, issn = {1758-2229}, mesh = {Adaptation, Physiological ; Antarctic Regions ; Arctic Regions ; Bacteria/*classification/genetics/radiation effects ; Biodiversity ; Desiccation ; *Ecosystem ; Metagenomics ; *Microbiota ; *Solar Energy ; Ultraviolet Rays ; }, abstract = {Solar panels located on high (Arctic and Antarctic) latitudes combine the harshness of the climate with that of the solar exposure. We report here that these polar solar panels are inhabited by similar microbial communities in taxonomic terms, dominated by Hymenobacter spp., Sphingomonas spp. and Ascomycota. Our results suggest that solar panels, even on high latitudes, can shape a microbial ecosystem adapted to irradiation and desiccation.}, }
@article {pmid29070823, year = {2017}, author = {Solden, LM and Wrighton, KC}, title = {Finding life's missing pieces.}, journal = {Nature microbiology}, volume = {2}, number = {11}, pages = {1458-1459}, doi = {10.1038/s41564-017-0048-8}, pmid = {29070823}, issn = {2058-5276}, mesh = {*Metagenome ; Risk Factors ; }, }
@article {pmid28928474, year = {2018}, author = {Mehta, HH and Prater, AG and Shamoo, Y}, title = {Using experimental evolution to identify druggable targets that could inhibit the evolution of antimicrobial resistance.}, journal = {The Journal of antibiotics}, volume = {71}, number = {2}, pages = {279-286}, pmid = {28928474}, issn = {0021-8820}, support = {R01 AI080714/AI/NIAID NIH HHS/United States ; }, mesh = {Alleles ; Anti-Bacterial Agents/*chemical synthesis/*pharmacology ; Bacteria/*drug effects/*genetics ; Biofilms ; Bioreactors ; Colistin/pharmacology ; DNA, Bacterial/genetics ; Drug Discovery ; Drug Resistance, Bacterial/*drug effects/*genetics ; Drug Resistance, Multiple, Bacterial/drug effects ; *Evolution, Molecular ; Genome, Bacterial ; Metagenomics ; Microbial Sensitivity Tests ; Mutation ; Pseudomonas aeruginosa/drug effects ; }, abstract = {With multi-drug and pan-drug-resistant bacteria becoming increasingly common in hospitals, antibiotic resistance has threatened to return us to a pre-antibiotic era that would completely undermine modern medicine. There is an urgent need to develop new antibiotics and strategies to combat resistance that are substantially different from earlier drug discovery efforts. One such strategy that would complement current and future antibiotics would be a class of co-drugs that target the evolution of resistance and thereby extend the efficacy of specific classes of antibiotics. A critical step in the development of such strategies lies in understanding the critical evolutionary trajectories responsible for resistance and which proteins or biochemical pathways within those trajectories would be good candidates for co-drug discovery. We identify the most important steps in the evolution of resistance for a specific pathogen and antibiotic combination by evolving highly polymorphic populations of pathogens to resistance in a novel bioreactor that favors biofilm development. As the populations evolve to increasing drug concentrations, we use deep sequencing to elucidate the network of genetic changes responsible for resistance and subsequent in vitro biochemistry and often structure determination to determine how the adaptive mutations produce resistance. Importantly, the identification of the molecular steps, their frequency within the populations and their chronology within the evolutionary trajectory toward resistance is critical to assessing their relative importance. In this work, we discuss findings from the evolution of the ESKAPE pathogen, Pseudomonas aeruginosa to the drug of last resort, colistin to illustrate the power of this approach.}, }
@article {pmid31039443, year = {2019}, author = {Mintzer, V and Moran-Gilad, J and Simon-Tuval, T}, title = {Operational models and criteria for incorporating microbial whole genome sequencing in hospital microbiology - A systematic literature review.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmi.2019.04.019}, pmid = {31039443}, issn = {1469-0691}, abstract = {BACKGROUND: Microbial whole genome sequencing (WGS) has many advantages over standard microbiological methods. However, it is not yet widely implemented in routine hospital diagnostics due to notable challenges.<br><br>OBJECTIVES: to extract managerial, financial, and clinical criteria supporting the decision to implement WGS in routine diagnostic microbiology, across different operational models of implementation in the hospital setting.<br><br>DATA SOURCES: A systematic review of literature identified through PubMed and Web of Science.<br><br>STUDY ELIGIBILITY CRITERIA: English literature discussing the applications of microbial WGS without limitation on publication date.<br><br>METHODS: A narrative approach for categorization and synthesis of the sources identified was adopted.<br><br>RESULTS: A total of 98 sources were included. Four main alternative operational models for incorporating WGS in clinical microbiology laboratories were identified: full in-house sequencing and analysis, full outsourcing of sequencing and analysis and two hybrid models combining in-house/outsourcing of the sequencing and analysis components. Six main criteria (and multiple related sub-criteria) for WGS implementation emerged from our review and included: cost (e.g. the availability of resources for capital and operational investment); manpower (e.g. the ability to provide training programs or recruit trained personnel), laboratory infrastructure (e.g. the availability of supplies and consumables or sequencing platforms), bioinformatics requirements (e.g. the availability of valid analysis tools); computational infrastructure (e.g. the availability of storage space or data safety arrangements); and quality control (e.g. the existence of standardized procedures).<br><br>CONCLUSION: The decision to incorporate WGS in routine diagnostics involves multiple, sometimes competing, criteria and sub-criteria. Mapping these criteria systematically is an essential stage in developing policies for adoption of this technology, e.g. using a multicriteria decision tool. Future research that will prioritize criteria and sub-criteria that were identified in our review in the context of operational models will inform decision-making at clinical and managerial levels with respect to effective implementation of WGS for routine use. Beyond WGS, similar decision-making challenges are expected with respect to future integration of clinical metagenomics.}, }
@article {pmid31038936, year = {2019}, author = {Burte, L and Cravotta, C and Bethencourt, L and Farasin, J and Pédrot, M and Dufresne, A and Gerard, MF and Baranger, C and Le Borgne, T and Aquilina, L}, title = {Kinetic study on clogging of a geothermal pumping well triggered by mixing-induced biogeochemical reactions.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.9b00453}, pmid = {31038936}, issn = {1520-5851}, abstract = {The sustainability of ground-source geothermal systems can be severely impacted by microbially mediated clogging processes. Biofouling of water wells by hydrous ferric oxide is a widespread problem. Although the mechanisms and critical environmental factors associated with clogging development are widely recognized, effects of mixing processes within the wells and time scales for clogging processes are not well characterized. Here we report insights from a joint hydrological, geochemical and metagenomics characterization of a geothermal doublet in which hydrous ferric oxide and hydrous manganese oxide deposits had formed as a consequence of mixing shallow groundwater containing dissolved oxygen and nitrate with deeper, anoxic groundwater containing dissolved iron (FeII) and manganese (MnII). Metagenomics identify distinct bacteria consortia in the pumping well oxic and anoxic zones, including autotrophic iron-oxidizing bacteria. Batch mixing experiments and geochemical kinetics modeling of the associated reactions indicate that FeII and MnII oxidation are slow compared the residence time of water in the pumping well; however, adsorption of FeII and MnII by accumulated hydrous ferric oxide and hydrous manganese oxide in the well bore and pump riser provides &quot;infinite&quot; time for surface-catalyzed oxidation and a convenient source of energy for iron-oxidizing bacteria, which colonize the surfaces and also catalyze oxidation. Thus, rapid clogging is caused by mixing-induced redox reactions and is exacerbated by microbial activity on accumulated hydrous oxide surfaces.}, }
@article {pmid31036935, year = {2019}, author = {Lee, SM and Kim, N and Nam, RH and Park, JH and Choi, SI and Park, YT and Kim, YR and Seok, YJ and Shin, CM and Lee, DH}, title = {Gut microbiota and butyrate level changes associated with the long-term administration of proton pump inhibitors to old rats.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {6626}, doi = {10.1038/s41598-019-43112-x}, pmid = {31036935}, issn = {2045-2322}, support = {13-2016-002//Seoul National University Hospital (SNUH)/ ; 116017032HD030//Ministry of Agriculture, Food and Rural Affairs (MAFRA)/ ; Seoul National University Bundang Hospital//Ministry of Agriculture, Food and Rural Affairs (MAFRA)/ ; 116017032HD030//Ministry of Agriculture, Food and Rural Affairs (MAFRA)/ ; 116017032HD030//Ministry of Agriculture, Food and Rural Affairs (MAFRA)/ ; 116017032HD030//Ministry of Agriculture, Food and Rural Affairs (MAFRA)/ ; 116017032HD030//Ministry of Agriculture, Food and Rural Affairs (MAFRA)/ ; 116017032HD030//Ministry of Agriculture, Food and Rural Affairs (MAFRA)/ ; }, abstract = {The association between adverse effects of PPI and gut microbiota in old age has yet to be elucidated. We assessed changes in the gut microbiota and butyrate levels following the long-term administration of PPIs to old rats and investigated their associations. F344 aged male rats were fed a PPI-supplemented diet for 50 weeks. The ileal microbiota was analysed by metagenomic sequencing of the 16S rRNA, while the butyrate concentration was measured by high-performance liquid chromatography. We observed a significant decrease in microbial diversity following PPI administration in the 2-year-old rats but not in the 74-week-old rats. PPI treatment reduced both commensal bacteria and opportunistic pathogens, particularly in the 2-year-old rats. Enterotypes comprising the majority of the control samples were enriched in Lactobacillus, while other enterotypes in the PPI group were dominated by Turicibacter or Romboutsia. The PPI treatment reduced the butyrate concentrations in the intestines and colons of 74-week-old rats compared to the control group. The abundance of Lactobacillus significantly correlated with butyrate concentrations in 74-week-old rats. In conclusion, long-term administration of PPIs alters the gut microbiota and butyrate concentrations in rats, particularly in old age, which may be an underlying mechanism of PPI-induced adverse effects such as pseudomembranous colitis.}, }
@article {pmid31036930, year = {2019}, author = {Zhang, J and Liu, YX and Zhang, N and Hu, B and Jin, T and Xu, H and Qin, Y and Yan, P and Zhang, X and Guo, X and Hui, J and Cao, S and Wang, X and Wang, C and Wang, H and Qu, B and Fan, G and Yuan, L and Garrido-Oter, R and Chu, C and Bai, Y}, title = {NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41587-019-0104-4}, pmid = {31036930}, issn = {1546-1696}, abstract = {Nitrogen-use efficiency of indica varieties of rice is superior to that of japonica varieties. We apply 16S ribosomal RNA gene profiling to characterize root microbiota of 68 indica and 27 japonica varieties grown in the field. We find that indica and japonica recruit distinct root microbiota. Notably, indica-enriched bacterial taxa are more diverse, and contain more genera with nitrogen metabolism functions, than japonica-enriched taxa. Using genetic approaches, we provide evidence that NRT1.1B, a rice nitrate transporter and sensor, is associated with the recruitment of a large proportion of indica-enriched bacteria. Metagenomic sequencing reveals that the ammonification process is less abundant in the root microbiome of the nrt1.1b mutant. We isolated 1,079 pure bacterial isolates from indica and japonica roots and derived synthetic communities (SynComs). Inoculation of IR24, an indica variety, with an indica-enriched SynCom improved rice growth in organic nitrogen conditions compared with a japonica-enriched SynCom. The links between plant genotype and root microbiota membership established in this study will inform breeding strategies to improve nitrogen use in crops.}, }
@article {pmid31036834, year = {2019}, author = {Stahlschmidt, MC and Collin, TC and Fernandes, DM and Bar-Oz, G and Belfer-Cohen, A and Gao, Z and Jakeli, N and Matskevich, Z and Meshveliani, T and Pritchard, JK and McDermott, F and Pinhasi, R}, title = {Ancient Mammalian and Plant DNA from Late Quaternary Stalagmite Layers at Solkota Cave, Georgia.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {6628}, doi = {10.1038/s41598-019-43147-0}, pmid = {31036834}, issn = {2045-2322}, support = {GOIPD/775//Irish Research Council (An Chomhairle um Thaighde in &amp;#x00C9;irinn)/ ; }, abstract = {Metagenomic analysis is a highly promising technique in paleogenetic research that allows analysis of the complete genomic make-up of a sample. This technique has successfully been employed to archaeological sediments, but possible leaching of DNA through the sequence limits interpretation. We applied this technique to the analysis of ancient DNA (aDNA) from Late Quaternary stalagmites from two caves in Western Georgia, Melouri Cave and Solkota. Stalagmites form closed systems, limiting the effect of leaching, and can be securely dated with U-series. The analyses of the sequence data from the Melouri Cave stalagmite revealed potential contamination and low preservation of DNA. However, the two Solkota stalagmites preserved ancient DNA molecules of mammals (bear, roe deer, bats) and plants (chestnut, hazelnut, flax). The aDNA bearing layers from one of the two Solkota stalagmites were dated to between ~84 ka and ~56 ka BP by U-series. The second Solkota stalagmite contained excessive detrital clay obstructing U-series dating, but it also contained bear bones with a minimum age of ~50 BP uncalibrated years and ancient DNA molecules. The preservation of authentic ancient DNA molecules in Late Quaternary speleothems opens up a new paleogenetic archive for archaeological, paleontological and paleoenvironmental research.}, }
@article {pmid31036684, year = {2019}, author = {Mehta, HH and Prater, AG and Beabout, K and Elworth, RAL and Karavis, M and Gibbons, HS and Shamoo, Y}, title = {The essential role of hypermutation in rapid adaptation to antibiotic stress.}, journal = {Antimicrobial agents and chemotherapy}, volume = {}, number = {}, pages = {}, doi = {10.1128/AAC.00744-19}, pmid = {31036684}, issn = {1098-6596}, abstract = {A common outcome of antibiotic exposure in patients and in vitro is the evolution of a hypermutator phenotype that enables rapid adaptation by pathogens. While hypermutation is a robust mechanism for rapid adaptation, it requires trade-offs between the adaptive mutations and the more common &quot;hitchhiker&quot; mutations that accumulate from the increased mutation rate. Using quantitative experimental evolution, we examined the role of hypermutation in driving adaptation of Pseudomonas aeruginosa to colistin. Metagenomic deep sequencing revealed 2,657 mutations at ≥ 5% frequency in 1,197 genes and 761 mutations in 29 end point isolates. By combining genomic information, phylogenetic analyses, and statistical tests, we showed that evolutionary trajectories leading to resistance could be reliably discerned. In addition to known alleles such as pmrB, hypermutation allowed identification of additional adaptive alleles with epistatic relationships. Although hypermutation provided a short-term fitness benefit, it was detrimental to overall fitness. Alarmingly, a small fraction of the colistin adapted population remained colistin susceptible and escaped hypermutation. In a clinical population, such cells could play a role in re-establishing infection upon withdrawal of colistin. We present here a framework for evaluating the complex evolutionary trajectories of hypermutators that applies to both current and emerging pathogen populations.Importance Bacteria can increase mutation rates in response to stress as an evolutionary strategy to avoid extinction. However, the complex mutational landscape of hypermutators makes it difficult to distinguish truly adaptive mutations from hitchhikers that follow similar evolutionary trajectories. We provide a framework for evaluating the complex evolutionary trajectories of hypermutators that can be applied to both current and emerging pathogen populations. Using Pseudomonas aeruginosa evolving to colistin as a model system, we examine the essential role of hypermutation in the evolution of resistance. Additionally, our results highlight the presence of a subset of cells that survive and remain susceptible during colistin exposure which can serve as a reservoir for re-infection upon withdrawal of the drug in clinical infections. This study provides a broad understanding of hypermutation during adaptation and describes a series of analyses that will be useful in identifying adaptive mutations in well annotated and novel bacterial mutator populations.}, }
@article {pmid31036654, year = {2019}, author = {Saunders, JK and Fuchsman, CA and McKay, C and Rocap, G}, title = {Complete arsenic-based respiratory cycle in the marine microbial communities of pelagic oxygen-deficient zones.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {}, number = {}, pages = {}, doi = {10.1073/pnas.1818349116}, pmid = {31036654}, issn = {1091-6490}, abstract = {Microbial capacity to metabolize arsenic is ancient, arising in response to its pervasive presence in the environment, which was largely in the form of As(III) in the early anoxic ocean. Many biological arsenic transformations are aimed at mitigating toxicity; however, some microorganisms can respire compounds of this redox-sensitive element to reap energetic gains. In several modern anoxic marine systems concentrations of As(V) are higher relative to As(III) than what would be expected from the thermodynamic equilibrium, but the mechanism for this discrepancy has remained unknown. Here we present evidence of a complete respiratory arsenic cycle, consisting of dissimilatory As(V) reduction and chemoautotrophic As(III) oxidation, in the pelagic ocean. We identified the presence of genes encoding both subunits of the respiratory arsenite oxidase AioA and the dissimilatory arsenate reductase ArrA in the Eastern Tropical North Pacific (ETNP) oxygen-deficient zone (ODZ). The presence of the dissimilatory arsenate reductase gene arrA was enriched on large particles (>30 um), similar to the forward bacterial dsrA gene of sulfate-reducing bacteria, which is involved in the cryptic cycling of sulfur in ODZs. Arsenic respiratory genes were expressed in metatranscriptomic libraries from the ETNP and the Eastern Tropical South Pacific (ETSP) ODZ, indicating arsenotrophy is a metabolic pathway actively utilized in anoxic marine water columns. Together these results suggest arsenic-based metabolisms support organic matter production and impact nitrogen biogeochemical cycling in modern oceans. In early anoxic oceans, especially during periods of high marine arsenic concentrations, they may have played a much larger role.}, }
@article {pmid31035705, year = {2019}, author = {Igarashi, Y and Mori, D and Mitsuyama, S and Yoshitake, K and Ono, H and Watanabe, T and Taniuchi, Y and Sakami, T and Kuwata, A and Kobayashi, T and Ishino, Y and Watabe, S and Gojobori, T and Asakawa, S}, title = {A Preliminary Metagenome Analysis Based on a Combination of Protein Domains.}, journal = {Proteomes}, volume = {7}, number = {2}, pages = {}, doi = {10.3390/proteomes7020019}, pmid = {31035705}, issn = {2227-7382}, support = {no number//Core Research for Evolutional Science and Technology/ ; }, abstract = {Metagenomic data have mainly been addressed by showing the composition of organisms based on a small part of a well-examined genomic sequence, such as ribosomal RNA genes and mitochondrial DNAs. On the contrary, whole metagenomic data obtained by the shotgun sequence method have not often been fully analyzed through a homology search because the genomic data in databases for living organisms on earth are insufficient. In order to complement the results obtained through homology-search-based methods with shotgun metagenomes data, we focused on the composition of protein domains deduced from the sequences of genomes and metagenomes, and we utilized them in characterizing genomes and metagenomes, respectively. First, we compared the relationships based on similarities in the protein domain composition with the relationships based on sequence similarities. We searched for protein domains of 325 bacterial species produced using the Pfam database. Next, the correlation coefficients of protein domain compositions between every pair of bacteria were examined. Every pairwise genetic distance was also calculated from 16S rRNA or DNA gyrase subunit B. We compared the results of these methods and found a moderate correlation between them. Essentially, the same results were obtained when we used partial random 100 bp DNA sequences of the bacterial genomes, which simulated raw sequence data obtained from short-read next-generation sequences. Then, we applied the method for analyzing the actual environmental data obtained by shotgun sequencing. We found that the transition of the microbial phase occurred because the seasonal change in water temperature was shown by the method. These results showed the usability of the method in characterizing metagenomic data based on protein domain compositions.}, }
@article {pmid31035625, year = {2019}, author = {Fahsbender, E and Altan, E and Seguin, MA and Young, P and Estrada, M and Leutenegger, C and Delwart, E}, title = {Chapparvovirus DNA Found in 4% of Dogs with Diarrhea.}, journal = {Viruses}, volume = {11}, number = {5}, pages = {}, doi = {10.3390/v11050398}, pmid = {31035625}, issn = {1999-4915}, abstract = {Feces from dogs in an unexplained outbreak of diarrhea were analyzed by viral metagenomics revealing the genome of a novel parvovirus. The parvovirus was named cachavirus and was classified within the proposed Chapparvovirus genus. Using PCR, cachavirus DNA was detected in two of nine tested dogs from that outbreak. In order to begin to elucidate the clinical impact of this virus, 2,053 canine fecal samples were screened using real-time PCR. Stool samples from 203 healthy dogs were positive for cachavirus DNA at a rate of 1.47%, while 802 diarrhea samples collected in 2017 and 964 samples collected in 2018 were positive at rates of 4.0% and 4.66% frequencies, respectively (healthy versus 2017-2018 combined diarrhea p-value of 0.05). None of 83 bloody diarrhea samples tested positive. Viral loads were generally low with average real-time PCR Ct values of 36 in all three positive groups. The species tropism and pathogenicity of cachavirus, the first chapparvovirus reported in feces of a placental carnivore, remains to be fully determined.}, }
@article {pmid31035521, year = {2019}, author = {Agarbati, A and Canonico, L and Mancabelli, L and Milani, C and Ventura, M and Ciani, M and Comitini, F}, title = {The Influence of Fungicide Treatments on Mycobiota of Grapes and Its Evolution during Fermentation Evaluated by Metagenomic and Culture-Dependent Methods.}, journal = {Microorganisms}, volume = {7}, number = {5}, pages = {}, doi = {10.3390/microorganisms7050114}, pmid = {31035521}, issn = {2076-2607}, abstract = {The present study evaluated the impact of organic and conventional fungicide treatments compared with untreated samples (no fungicides were used) on the grape berry yeast community of the Montepulciano variety. The yeast dynamics during the spontaneous fermentation using culture-dependent and -independent methods was also evaluated. Results showed a reduction of yeast biodiversity by conventional treatments determining a negative influence on fermenting yeasts in favor of oxidative yeasts such as Aerobasidiumpullulans. Starmerellabacillaris was significantly more present in organic samples (detected by next generation sequencing (NGS)), while Hanseniaspopauvarum was significantly less present in untreated samples (detected by the culture-dependent method). The fermenting yeasts, developed during the spontaneous fermentation, were differently present depending on the fungicide treatments used. Culture-dependent and -independent methods exhibited the same most abundant yeast species during the spontaneous fermentation but a different relative abundance. Differently, the NGS method was able to detect a greater biodiversity (lower abundant species) in comparison with the culture-dependent method. In this regard, the methodologies used gave a different picture of yeast dynamics during the fermentation process. The results indicated that the fungal treatments can influence the yeast community of grapes leading must fermentation and the final composition of wine.}, }
@article {pmid31035394, year = {2019}, author = {Jaswal, R and Pathak, A and Iii, BE and Iii, RL and Seaman, JC and Stothard, P and Krivushin, K and Blom, J and Rupp, O and Chauhan, A}, title = {Metagenomics-Guided Survey, Isolation, and Characterization of Uranium Resistant Microbiota from the Savannah River Site, USA.}, journal = {Genes}, volume = {10}, number = {5}, pages = {}, doi = {10.3390/genes10050325}, pmid = {31035394}, issn = {2073-4425}, support = {DE-AC09-08SR22470//Savannah River National Laboratory/ ; }, abstract = {Despite the recent advancements in culturomics, isolation of the majority of environmental microbiota performing critical ecosystem services, such as bioremediation of contaminants, remains elusive. Towards this end, we conducted a metagenomics-guided comparative assessment of soil microbial diversity and functions present in uraniferous soils relative to those that grew in diffusion chambers (DC) or microbial traps (MT), followed by isolation of uranium (U) resistant microbiota. Shotgun metagenomic analysis performed on the soils used to establish the DC/MT chambers revealed Proteobacterial phyla and Burkholderia genus to be the most abundant among bacteria. The chamber-associated growth conditions further increased their abundances relative to the soils. Ascomycota was the most abundant fungal phylum in the chambers relative to the soils, with Penicillium as the most dominant genus. Metagenomics-based taxonomic findings completely mirrored the taxonomic composition of the retrieved isolates such that the U-resistant bacteria and fungi mainly belonged to Burkholderia and Penicillium species, thus confirming that the chambers facilitated proliferation and subsequent isolation of specific microbiota with environmentally relevant functions. Furthermore, shotgun metagenomic analysis also revealed that the gene classes for carbohydrate metabolism, virulence, and respiration predominated with functions related to stress response, membrane transport, and metabolism of aromatic compounds were also identified, albeit at lower levels. Of major note was the successful isolation of a potentially novel Penicillium species using the MT approach, as evidenced by whole genome sequence analysis and comparative genomic analysis, thus enhancing our overall understanding on the uranium cycling microbiota within the tested uraniferous soils.}, }
@article {pmid30482798, year = {2019}, author = {Katsumura, T and Oda, S and Mitani, H and Oota, H}, title = {Medaka Population Genome Structure and Demographic History Described via Genotyping-by-Sequencing.}, journal = {G3 (Bethesda, Md.)}, volume = {9}, number = {1}, pages = {217-228}, doi = {10.1534/g3.118.200779}, pmid = {30482798}, issn = {2160-1836}, mesh = {Animals ; DNA, Mitochondrial/genetics ; *Genetics, Population ; Genome/*genetics ; Genome-Wide Association Study ; Genotype ; Genotyping Techniques ; Metagenomics/methods ; Oryzias/*genetics ; Sequence Analysis, DNA ; }, abstract = {Medaka is a model organism in medicine, genetics, developmental biology and population genetics. Lab stocks composed of more than 100 local wild populations are available for research in these fields. Thus, medaka represents a potentially excellent bioresource for screening disease-risk- and adaptation-related genes in genome-wide association studies. Although the genetic population structure should be known before performing such an analysis, a comprehensive study on the genome-wide diversity of wild medaka populations has not been performed. Here, we performed genotyping-by-sequencing (GBS) for 81 and 12 medakas captured from a bioresource and the wild, respectively. Based on the GBS data, we evaluated the genetic population structure and estimated the demographic parameters using an approximate Bayesian computation (ABC) framework. The genome-wide data confirmed that there were substantial differences between local populations and supported our previously proposed hypothesis on medaka dispersal based on mitochondrial genome (mtDNA) data. A new finding was that a local group that was thought to be a hybrid between the northern and the southern Japanese groups was actually an origin of the northern Japanese group. Thus, this paper presents the first population-genomic study of medaka and reveals its population structure and history based on chromosomal genetic diversity.}, }
@article {pmid31035235, year = {2019}, author = {Lee, J and Koo, T and Yulisa, A and Hwang, S}, title = {Magnetite as an enhancer in methanogenic degradation of volatile fatty acids under ammonia-stressed condition.}, journal = {Journal of environmental management}, volume = {241}, number = {}, pages = {418-426}, doi = {10.1016/j.jenvman.2019.04.038}, pmid = {31035235}, issn = {1095-8630}, abstract = {Anaerobic batch tests with a 22 full-factorial design of ammonia (1.5, 6.5 g N/L) and magnetite concentrations (0, 20 mmol/L) were conducted separately for methanogenic degradation of acetate, propionate, and butyrate (volatile fatty acids (VFAs)) to 1) quantify the effect of magnetite as an enhancer in methanogenic degradation of each of the VFAs in conditions without ammonia stress (1.5 g N/L) and with ammonia stress (6.5 g N/L), and 2) identify methanogenic consortia that are related to such enhancement. Among the three VFAs, methanogenic degradation of propionate was the least feasible (57% lower specific methanogenic activity RCH4 and three times longer lag time λ than acetate degradation). At low ammonia concentration, only propionate showed improvement in RCH4 (46%) with supplementation of magnetite. In the ammonia-stressed condition without magnetite, RCH4 decreased by 38-58% and λ increased 2.2-8.8 times for all VFAs; magnetite supplementation significantly alleviated these effects. These results demonstrate that magnetite supplementation effectively increases methanogenic degradation of the VFAs even under ammonia-stressed conditions. 16S metagenomic sequencing revealed that distinctive methanogenic consortia were active in the different combinations of substrate, ammonia and magnetite. Alkaliphilus, Hyphomonadaceae SWB02 and Clostridia DTU014, Clostridia D8A-2, Christensenellaceae R-7 group and Rikenellaceae DMER64 were identified as potential syntrophic bacteria that can establish magnetite-mediated direct electron transfer with methanogens (Methanosaeta concilii, Methanosaeta harundinacea, Methanolinea tarda, Methanoculleus bourgensis and Methanosarcina spp.) during methanogenic degradation of VFAs. The results may be useful as a reference to develop effective strategies using magnetite supplementation to remediate anaerobic digestion processes that have been afflicted by VFA accumulation and ammonia inhibition.}, }
@article {pmid31034867, year = {2019}, author = {Tsiaoussis, J and Antoniou, MN and Koliarakis, I and Mesnage, R and Vardavas, CI and Izotov, BN and Psaroulaki, A and Tsatsakis, A}, title = {Effects of single and combined toxic exposures on the gut microbiome: current knowledge and future directions.}, journal = {Toxicology letters}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.toxlet.2019.04.014}, pmid = {31034867}, issn = {1879-3169}, abstract = {Human populations are chronically exposed to mixtures of toxic chemicals. Predicting the health effects of these mixtures require a large amount of information on the mode of action of their components. Xenobiotic metabolism by bacteria inhabiting the gastrointestinal tract has a major influence on human health. Our review aims to explore the literature for studies looking to characterize the different modes of action and outcomes of major chemical pollutants, and some components of cosmetics and food additives, on gut microbial communities in order to facilitate an estimation of their potential mixture effects. We identified good evidence that exposure to heavy metals, pesticides, nanoparticles, polycyclic aromatic hydrocarbons, dioxins, furans, polychlorinated biphenyls, and non-caloric artificial sweeteners affect the gut microbiome and which is associated with the development of metabolic, malignant, inflammatory, or immune diseases. Answering the question 'Who is there?' is not sufficient to define the mode of action of a toxicant in predictive modeling of mixture effects. Therefore, we recommend that new studies focus to simulate real-life exposure to diverse chemicals (toxicants, cosmetic/food additives), including as mixtures, and which combine metagenomics, metatranscriptomics and metabolomic analytical methods achieving in that way a comprehensive evaluation of effects on human health.}, }
@article {pmid31034054, year = {2019}, author = {Li, S and Chen, M and Chen, Y and Tong, J and Wang, L and Xu, Y and Hu, Z and Chen, H}, title = {Epibiotic bacterial community composition in red-tide dinoflagellate Akashiwo sanguinea culture under different growth conditions.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiz057}, pmid = {31034054}, issn = {1574-6941}, abstract = {The phycosphere of phytoplankton harbors a diversity of microbes that can potentially interact with host phytoplankton cell. In spite of increasing reports about the interactions between some model phytoplankton and bacteria, there are still lots of unknowns about interactions between dinoflagellate Akashiwo sanguinea and its phycosphere bacteria. Here we used both cultivation and metagenomic sequencing methods to investigate the microbial community composition in A. sanguinea batch cultures under different growth conditions. The microbial community dynamics under different growth stages and nutrient (nitrogen and iron) deplete scenarios were determined by Illumina MiSeq sequencing of 16S rRNA gene amplicons. Rhodobacteraceae, Alteromonadaceae and Flavobacteriaceae were the main bacterial families and varied significantly under different states of the host A. sanguinea. Selective fluorescence in situ hybridization (FISH) was also performed to label Rhodobacterale and Alteromonas clade bacteria to confirm their attachment with A. sanguinea cells under confocal laser scanning microscopy (CLSM). Plate streaking practice isolated 19 bacterial strains from A. sanguinea culture and identified through 16S rRNA analysis. Most culturable strains (11 out of 19) belonged to Rhodobacteraceae and consisted with the Illumina MiSeq sequencing data. The possible interaction pathway between these epibiotic bacteria and A. sanguinea in the phycosphere was also discussed.}, }
@article {pmid31032975, year = {2019}, author = {Budinska, E and Gojda, J and Heczkova, M and Bratova, M and Dankova, H and Wohl, P and Bastova, H and Lanska, V and Kostovcik, M and Dastych, M and Senkyrik, M and Krizova, J and Mraz, M and Hradecky, J and Hajslova, J and Lenicek, M and Podzimkova, K and Chalupsky, K and Sedlacek, R and Cahova, M}, title = {Microbiome and Metabolome Profiles Associated With Different Types of Short Bowel Syndrome: Implications for Treatment.}, journal = {JPEN. Journal of parenteral and enteral nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1002/jpen.1595}, pmid = {31032975}, issn = {1941-2444}, support = {15-28745A AZV CR//Ministry of Health of the Czech Republic/ ; 15-27863A AZV CR//Ministry of Health of the Czech Republic/ ; //MH CZ-DRO/ ; IN 00023001//Institute for Clinical and Experimental Medicine-IKEM/ ; }, abstract = {BACKGROUND: The gut microbiome and metabolome may significantly influence clinical outcomes in patients with short bowel syndrome (SBS). The study aimed to describe specific metagenomic/metabolomics profiles of different SBS types and to identify possible therapeutic targets.<br><br>METHODS: Fecal microbiome (FM), volatile organic compounds (VOCs), and bile acid (BA) spectrum were analyzed in parenteral nutrition (PN)-dependent SBS I, SBS II, and PN-independent (non-PN) SBS patients.<br><br>RESULTS: FM in SBS I, SBS II, and non-PN SBS shared characteristic features (depletion of beneficial anaerobes, high abundance of Lactobacilaceae and Enterobacteriaceae). SBS I patients were characterized by the abundance of oxygen-tolerant microrganisms and depletion of strict anaerobes. Non-PN SBS subjects showed markers of partial FM normalization. FM dysbiosis was translated into VOC and BA profiles characteristic for each SBS cohort. A typical signature of all SBS patients comprised high saturated aldehydes and medium-chain fatty acids and reduced short-chain fatty acid (SCFA) content. Particularly, SBS I and II exhibited low protein metabolism intermediate (indole, p-cresol) content despite the hypothetical presence of relevant metabolism pathways. Distinctive non-PN SBS marker was high phenol content. SBS patients' BA fecal spectrum was enriched by chenodeoxycholic and deoxycholic acids and depleted of lithocholic acid.<br><br>CONCLUSIONS: Environmental conditions in SBS gut significantly affect FM composition and metabolic activity. The common feature of diverse SBS subjects is the altered VOC/BA profile and the lack of important products of microbial metabolism. Strategies oriented on the microbiome/metabolome reconstitution and targeted delivery of key compounds may represent a promising therapeutic strategy in SBS patients.}, }
@article {pmid31031001, year = {2019}, author = {Gregory, AC and Zayed, AA and Conceição-Neto, N and Temperton, B and Bolduc, B and Alberti, A and Ardyna, M and Arkhipova, K and Carmichael, M and Cruaud, C and Dimier, C and Domínguez-Huerta, G and Ferland, J and Kandels, S and Liu, Y and Marec, C and Pesant, S and Picheral, M and Pisarev, S and Poulain, J and Tremblay, JÉ and Vik, D and ,  and Babin, M and Bowler, C and Culley, AI and de Vargas, C and Dutilh, BE and Iudicone, D and Karp-Boss, L and Roux, S and Sunagawa, S and Wincker, P and Sullivan, MB}, title = {Marine DNA Viral Macro- and Microdiversity from Pole to Pole.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2019.03.040}, pmid = {31031001}, issn = {1097-4172}, abstract = {Microbes drive most ecosystems and are modulated by viruses that impact their lifespan, gene flow, and metabolic outputs. However, ecosystem-level impacts of viral community diversity remain difficult to assess due to classification issues and few reference genomes. Here, we establish an ∼12-fold expanded global ocean DNA virome dataset of 195,728 viral populations, now including the Arctic Ocean, and validate that these populations form discrete genotypic clusters. Meta-community analyses revealed five ecological zones throughout the global ocean, including two distinct Arctic regions. Across the zones, local and global patterns and drivers in viral community diversity were established for both macrodiversity (inter-population diversity) and microdiversity (intra-population genetic variation). These patterns sometimes, but not always, paralleled those from macro-organisms and revealed temperate and tropical surface waters and the Arctic as biodiversity hotspots and mechanistic hypotheses to explain them. Such further understanding of ocean viruses is critical for broader inclusion in ecosystem models.}, }
@article {pmid31030919, year = {2019}, author = {Sun, HZ and Plastow, G and Guan, LL}, title = {Invited review: Advances and challenges in application of feedomics to improve dairy cow production and health.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2018-16126}, pmid = {31030919}, issn = {1525-3198}, abstract = {Dairy cattle science has evolved greatly over the past century, contributing significantly to the improvement in milk production achieved today. However, a new approach is needed to meet the increasing demand for milk production and address the increased concerns about animal health and welfare. It is now easy to collect and access large and complex data sets consisting of molecular, physiological, and metabolic data as well as animal-level data (such as behavior). This provides new opportunities to better understand the mechanisms regulating cow performance. The recently proposed concept of feedomics could help achieve this goal by increasing our understanding of interactions between the different components or levels and their impact on animal production. Feedomics is an emerging field that integrates a range of omics technologies (e.g., genomics, epigenomics, transcriptomics, proteomics, metabolomics, metagenomics, and metatranscriptomics) to provide these insights. In this way, we can identify the best strategies to improve overall animal productivity, product quality, welfare, and health. This approach can help research communities elucidate the complex interactions among nutrition, environment, management, animal genetics, metabolism, physiology, and the symbiotic microbiota. In this review, we summarize the outcomes of the most recent research on omics in dairy cows and highlight how an integrated feedomics approach could be applied in the future to improve dairy cow production and health. Specifically, we focus on 2 topics: (1) improving milk yield and milk quality, and (2) understanding metabolic physiology in transition dairy cows, which are 2 important challenges faced by the dairy industry worldwide.}, }
@article {pmid30728532, year = {2019}, author = {Stower, H}, title = {Sequencing for rapid response to Lassa fever.}, journal = {Nature medicine}, volume = {25}, number = {2}, pages = {197}, doi = {10.1038/s41591-019-0363-0}, pmid = {30728532}, issn = {1546-170X}, mesh = {Disease Outbreaks ; Humans ; Lassa Fever/*epidemiology ; Lassa virus ; Metagenomics ; Nigeria ; }, }
@article {pmid29988145, year = {2018}, author = {Delzenne, NM and Bindels, LB}, title = {Microbiome metabolomics reveals new drivers of human liver steatosis.}, journal = {Nature medicine}, volume = {24}, number = {7}, pages = {906-907}, doi = {10.1038/s41591-018-0126-3}, pmid = {29988145}, issn = {1546-170X}, mesh = {*Fatty Liver ; Female ; Humans ; Metabolomics ; Metagenomics ; *Microbiota ; Obesity ; }, }
@article {pmid29884828, year = {2018}, author = {Hao, L and McIlroy, SJ and Kirkegaard, RH and Karst, SM and Fernando, WEY and Aslan, H and Meyer, RL and Albertsen, M and Nielsen, PH and Dueholm, MS}, title = {Novel prosthecate bacteria from the candidate phylum Acetothermia.}, journal = {The ISME journal}, volume = {12}, number = {9}, pages = {2225-2237}, pmid = {29884828}, issn = {1751-7370}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification/metabolism ; DNA, Bacterial ; Fermentation ; Metagenome ; Phylogeny ; }, abstract = {Members of the candidate phylum Acetothermia are globally distributed and detected in various habitats. However, little is known about their physiology and ecological importance. In this study, an operational taxonomic unit belonging to Acetothermia was detected at high abundance in four full-scale anaerobic digesters by 16S rRNA gene amplicon sequencing. The first closed genome from this phylum was obtained by differential coverage binning of metagenomes and scaffolding with long nanopore reads. Genome annotation and metabolic reconstruction suggested an anaerobic chemoheterotrophic lifestyle in which the bacterium obtains energy and carbon via fermentation of peptides, amino acids, and simple sugars to acetate, formate, and hydrogen. The morphology was unusual and composed of a central rod-shaped cell with bipolar prosthecae as revealed by fluorescence in situ hybridization combined with confocal laser scanning microscopy, Raman microspectroscopy, and atomic force microscopy. We hypothesize that these prosthecae allow for increased nutrient uptake by greatly expanding the cell surface area, providing a competitive advantage under nutrient-limited conditions.}, }
@article {pmid31030156, year = {2019}, author = {Darlison, J and Mogren, L and Rosberg, AK and Grudén, M and Minet, A and Liné, C and Mieli, M and Bengtsson, T and Håkansson, Å and Uhlig, E and Becher, PG and Karlsson, M and Alsanius, BW}, title = {Leaf mineral content govern microbial community structure in the phyllosphere of spinach (Spinacia oleracea) and rocket (Diplotaxis tenuifolia).}, journal = {The Science of the total environment}, volume = {675}, number = {}, pages = {501-512}, doi = {10.1016/j.scitotenv.2019.04.254}, pmid = {31030156}, issn = {1879-1026}, abstract = {The plant microbiome is an important factor for plant health and productivity. While the impact of nitrogen (N) availability for plant growth and development is well established, its influence on the microbial phyllosphere community structure is unknown. We hypothesize that nitrogen impacts the growth and abundance of several microorganisms on the leaf surface. The bacterial and fungal communities of baby leaf spinach (Spinacia oleracea), and rocket (Diplotaxis tenuifolia) were investigated in a field trial for two years in a commercial setting. Nitrogen fertilizer was tested in four doses (basic nitrogen, basic + suboptimal, basic + commercial, basic + excess) with six replicates in each. Culture-independent (Illumina sequencing) and culture-dependent (viable count and identification of bacterial isolates) community studies were combined with monitoring of plant physiology and site weather conditions. This study found that alpha diversity of bacterial communities decreased in response to increasing nitrogen fertilizer dose, whereas viable counts showed no differences. Correspondingly, fungal communities of the spinach phyllosphere showed a decreasing pattern, whereas the decreasing diversity of fungal communities of rocket was not significant. Plant species and effects of annual variations on microbiome structure were observed for bacterial and fungal communities on both spinach and rocket. This study provides novel insights on the impact of nitrogen fertilizer regime on a nutrient scarce habitat, the phyllosphere.}, }
@article {pmid31028005, year = {2019}, author = {Zhao, S and Lieberman, TD and Poyet, M and Kauffman, KM and Gibbons, SM and Groussin, M and Xavier, RJ and Alm, EJ}, title = {Adaptive Evolution within Gut Microbiomes of Healthy People.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2019.03.007}, pmid = {31028005}, issn = {1934-6069}, abstract = {Natural selection shapes bacterial evolution in all environments. However, the extent to which commensal bacteria diversify and adapt within the human gut remains unclear. Here, we combine culture-based population genomics and metagenomics to investigate the within-microbiome evolution of Bacteroides fragilis. We find that intra-individual B. fragilis populations contain substantial de novo nucleotide and mobile element diversity, preserving years of within-person history. This history reveals multiple signatures of within-person adaptation, including parallel evolution in sixteen genes. Many of these genes are implicated in cell-envelope biosynthesis and polysaccharide utilization. Tracking evolutionary trajectories using near-daily metagenomic sampling, we find evidence for years-long coexistence in one subject despite adaptive dynamics. We used public metagenomes to investigate one adaptive mutation common in our cohort and found that it emerges frequently in Western, but not Chinese, microbiomes. Collectively, these results demonstrate that B. fragilis adapts within individual microbiomes, pointing to factors that promote long-term gut colonization.}, }
@article {pmid31027801, year = {2019}, author = {Pangallo, D and Kraková, L and Puškárová, A and Šoltys, K and Bučková, M and Koreňová, J and Budiš, J and Kuchta, T}, title = {Transcription activity of lactic acid bacterial proteolysis-related genes during cheese maturation.}, journal = {Food microbiology}, volume = {82}, number = {}, pages = {416-425}, doi = {10.1016/j.fm.2019.03.015}, pmid = {31027801}, issn = {1095-9998}, abstract = {The catabolism of milk protein in cheese is one way how the microorganisms influence the sensorial characteristics of the final product. In this investigation, we paid attention to four genes [prtP (cell-envelope proteinase gene), pepX (X-prolyl dipeptidyl aminopeptidase gene), pepN (aminopeptidase gene) and bcaT (branched chain aminotransferase gene)] responsible for the production of volatile aroma-active compounds from milk proteins by lactic acid bacteria (LAB). We studied the dynamics of these genes and their corresponding LAB host, during the maturation of a raw ewes' milk-based cheese, using metagenomics and metatranscriptomics approaches. The transcriptome-oriented experiments included the analysis of total RNA (at three stages of cheese maturation) and also the construction of specific cDNA sub-libraries of the abovementioned genes. The proteolytic transcriptome analysis was supported by following the transcription activity of 16S rRNA gene and by metagenomic investigation. The combination of the described methods permitted to screen the dynamics of targeted genes throughout the cheese production. Lactococci were the major players in the LAB group, but the analysis provided also information on the role and properties of members of the genus Lactobacillus, such as Lb. rhamnosus, Lb. helveticus, Lb. pentosus, Lb. curvatus, Lb. parabuchneri, Lb. plantarum, Lb. brevis, Lb. delbrueckii, Lb. paracasei, Lb. fermentum and Lb. heilongjiangensis, proteolysis-related genes of which were active during cheese ripening.}, }
@article {pmid31027761, year = {2019}, author = {Sala-Comorera, L and Blanch, AR and Casanovas-Massana, A and Monleón-Getino, A and García-Aljaro, C}, title = {Traceability of different brands of bottled mineral water during shelf life, using PCR-DGGE and next generation sequencing techniques.}, journal = {Food microbiology}, volume = {82}, number = {}, pages = {1-10}, doi = {10.1016/j.fm.2019.01.006}, pmid = {31027761}, issn = {1095-9998}, abstract = {Natural mineral waters contain indigenous bacteria characteristic of each spring source. Once bottled, these communities change over time until the water is consumed. Bottle material is believed to play a major role in the succession of these populations, but very few studies to date have evaluated the effect of this material on bacterial communities. In this study, we examined the microbial community structure of three natural mineral waters over 3 months after bottling in glass and polyethylene terephthalate (PET) bottles. To this end, we used culture-dependent (heterotrophic plate count) and culture-independent methods (16S rRNA massive gene sequencing, denaturing gradient gel electrophoresis (DGGE) and fluorescent microscopy with vital dyes). Total and viable cell counts increased by around 1-2 log10 units between 1 and 2 weeks after bottling and then remained constant over 3 months for all waters regardless of the bottle material. DGGE fingerprints and 16S rRNA massive sequencing analysis both indicated that different communities were established in the waters two weeks after bottling in the different bottle materials. In conclusion, no differences in total, viable and culturable bacteria counts were observed between mineral waters bottled with PET or glass during shelf life storage. Nevertheless, in spite of changes in the communities, each water brand and material presented a distinct microbial community structure clearly distinguishable from the others, which could be interesting for traceability purposes.}, }
@article {pmid31027515, year = {2019}, author = {Kim, J and Guk, JH and Mun, SH and An, JU and Song, H and Kim, J and Ryu, S and Jeon, B and Cho, S}, title = {Metagenomic analysis of isolation methods of a targeted microbe, Campylobacter jejuni, from chicken feces with high microbial contamination.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {67}, doi = {10.1186/s40168-019-0680-z}, pmid = {31027515}, issn = {2049-2618}, support = {NRF-2018R1A2B6002396//National Research Foundation of Korea/ ; 16162MFDS029//Ministry of Food and Drug Safety/ ; }, abstract = {BACKGROUND: Originating from poultry, particularly chickens, Campylobacter jejuni is the leading foodborne pathogen worldwide and a major cause of campylobacteriosis. Isolating C. jejuni is difficult due to its specific growth requirements, the presence of viable but non-culturable bacteria, and because it is often masked by competing flora. Currently, there is no optimized method for isolating C. jejuni from chicken feces. Here, we evaluated the method for isolating C. jejuni from chicken feces using culture-independent sequence-based metagenomics and culture-dependent tools. Further, we assessed changes in microbial communities during microbe isolation to determine how the process can be improved.<br><br>RESULTS: Fourteen different variations of C. jejuni isolation procedures were applied to all 35 chicken fecal samples. These variations included using different enrichment broths (without enrichment or enrichment in Bolton or Preston broth), different ratios of sample-to-enrichment broth (1:101, 1:102, and 1:103), and different selective agars (modified charcoal-cefoperazone-deoxycholate agar (mCCDA) or Preston agar). Enrichment during isolation of C. jejuni was evaluated on the basis of microbial diversity and taxonomic composition using metagenomics tools. The effect of selective media was evaluated using a combination of metagenomics and culture-dependent tools. Microbial diversity significantly decreased during the enrichment process, regardless of the type of enrichment broth, with the most significant decrease observed at a feces-to-broth ratio of 1:103. Particularly, in 103-Preston broth, the relative abundance of Campylobacter increased, while extended-spectrum beta-lactamase-producing Escherichia coli, which interfere with Campylobacter isolation, decreased. Metagenomics results were validated by quantitative PCR and culture-dependent analysis. Additionally, selective media affected the isolation results, although microbes with high relative abundance during enrichment were also frequently isolated using culture-dependent methods. Significantly more C. jejuni was isolated from mCCDA than from Preston agar enriched in 103 Preston broth.<br><br>CONCLUSIONS: Enrichment in Preston broth at a ratio of 1:103 followed by spreading onto mCCDA was the most effective method for isolating C. jejuni. This is the first study to apply metagenomics to evaluate a method for isolating a targeted microbe, C. jejuni, from chicken feces, a source with high microbial contamination. Thus, metagenomics can be applied to improve methods for isolating bacteria that are difficult to separate.}, }
@article {pmid31027194, year = {2019}, author = {Teigen, LM and Geng, Z and Sadowsky, MJ and Vaughn, BP and Hamilton, MJ and Khoruts, A}, title = {Dietary Factors in Sulfur Metabolism and Pathogenesis of Ulcerative Colitis.}, journal = {Nutrients}, volume = {11}, number = {4}, pages = {}, doi = {10.3390/nu11040931}, pmid = {31027194}, issn = {2072-6643}, support = {2017-2019//Allen Foundation/ ; 2017-2019//Healthy Foods, Healthy Lives Institute, University of Minnesota/ ; }, abstract = {The biogeography of inflammation in ulcerative colitis (UC) suggests a proximal to distal concentration gradient of a toxin. Hydrogen sulfide (H2S) has long been considered one such toxin candidate, and dietary sulfur along with the abundance of sulfate reducing bacteria (SRB) were considered the primary determinants of H2S production and clinical course of UC. The metabolic milieu in the lumen of the colon, however, is the result of a multitude of factors beyond dietary sulfur intake and SRB abundance. Here we present an updated formulation of the H2S toxin hypothesis for UC pathogenesis, which strives to incorporate the interdependency of diet composition and the metabolic activity of the entire colon microbial community. Specifically, we suggest that the increasing severity of inflammation along the proximal-to-distal axis in UC is due to the dilution of beneficial factors, concentration of toxic factors, and changing detoxification capacity of the host, all of which are intimately linked to the nutrient flow from the diet.}, }
@article {pmid31026705, year = {2019}, author = {Thamke, VR and Chaudhari, AU and Tapase, SR and Paul, D and Kodam, KM}, title = {In vitro toxicological evaluation of ionic liquids and development of effective bioremediation process for their removal.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {250}, number = {}, pages = {567-577}, doi = {10.1016/j.envpol.2019.04.043}, pmid = {31026705}, issn = {1873-6424}, abstract = {The present study deals with the cyto-genotoxicological impact of ionic liquids, 1-butyl-3-methylimidazolium bromide, trihexyl tetradecylphosphonium dicyanamide, 1-decyl-3-methylimidazolium tetrafluoroborate, benzyldimethyltetradecylammonium chloride, and 1-butyl-4-methylpyridinium chloride, on animal cells and their biodegradation. The long alkyl chain containing ionic liquids were found to be more toxic whereas benzene functional group in benzyldimethyltetradecylammonium chloride enhances its toxicity. Aerobic bacterial granules, a bacterial consortium, were developed that have promising ability to break down these organic pollutants. These aerobic bacterial granules have been applied for the biodegradation of ionic liquids. The biological oxygen demand (5 days) and chemical oxygen demand parameters confirmed that the biodegradation was solely due to aerobic bacterial granules which further decreased the time period needed for regular biodegradation by biological oxygen demand (28 days). The high resolution mass spectrometry analysis further approved that the degradation of ionic liquids was mainly via removal of the methyl group. Elevated N-demethylase enzyme activity supports the ionic liquids degradation which may be occurring through demethylation mechanism. The amplicon sequencing of aerobic bacterial granules gives insight into the involvement of the bacterial community in the biodegradation process.}, }
@article {pmid31026582, year = {2019}, author = {Li, J and Rettedal, EA and van der Helm, E and Ellabaan, M and Panagiotou, G and Sommer, MOA}, title = {Antibiotic Treatment Drives the Diversification of the Human Gut Resistome.}, journal = {Genomics, proteomics &amp; bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.gpb.2018.12.003}, pmid = {31026582}, issn = {2210-3244}, abstract = {Despite the documented antibiotic-induced disruption of the gut microbiota, the impact of antibiotic intake on strain-level dynamics, evolution of resistance genes, and factors influencing resistance dissemination potential remains poorly understood. To address this gap we analyzed public metagenomic datasets from 24 antibiotic treated subjects and controls, combined with an in-depth prospective functional study with two subjects investigating the bacterial community dynamics based on cultivation-dependent and independent methods. We observed that short-term antibiotic treatment shifted and diversified the resistome composition, increased the average copy number of antibiotic resistance genes, and altered the dominant strain genotypes in an individual-specific manner. More than 30% of the resistance genes underwent strong differentiation at the single nucleotide level during antibiotic treatment. We found that the increased potential for horizontal gene transfer, due to antibiotic administration, was ∼3-fold stronger in the differentiated resistance genes than the non-differentiated ones. This study highlights how antibiotic treatment has individualized impacts on the resistome and strain level composition, and drives the adaptive evolution of the gut microbiota.}, }
@article {pmid31026578, year = {2019}, author = {Li, J and Du, P and Yongxin Ye, A and Zhang, Y and Song, C and Zeng, H and Chen, C}, title = {Improving Assignment of Microbial Genetic Polymorphisms Assignments in Complex Samples by Bayesian Estimation.}, journal = {Genomics, proteomics &amp; bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.gpb.2018.12.005}, pmid = {31026578}, issn = {2210-3244}, abstract = {Identifying antimicrobial resistant (AMR) bacteria in metagenomics samples is essential for public health and food safety. Next-generation sequencing (NGS) technology has provided a powerful tool in identifying the genetic variation and constructing the correlations between genotype and phenotype in humans and other species. However, for complex bacterial samples, there lacks a powerful bioinformatic tool to identify genetic polymorphisms or copy number variations (CNVs) for given genes. Here we provide a Bayesian framework for genotype estimation for mixtures of multiple bacteria, named as Genetic Polymorphisms Assignments (GPA). Simulation results showed that GPA has reduced the false discovery rate (FDR) and mean absolute error (MAE) in CNV and single nucleotide variant (SNV) identification. This framework was validated by whole-genome sequencing and Pool-seq data from Klebsiella pneumoniae with multiple bacteria mixture models, and showed the high accuracy in the allele fraction detections of CNVs and SNVs in AMR genes between two populations. The quantitative study on the changes of AMR genes fraction between two samples showed a good consistency with the AMR pattern observed in the individual strains. Also, the framework together with the genome annotation and population comparison tools has been integrated into an application, which could provide a complete solution for AMR gene identification and quantification in unculturable clinical samples. The GPA package is available at https://github.com/IID-DTH/GPA-package.}, }
@article {pmid31026577, year = {2019}, author = {Jiang, X and Li, X and Yang, L and Liu, C and Wang, Q and Chi, W and Zhu, H}, title = {How Microbes Shape Their Communities? A Microbial Community Model Based on Functional Genes.}, journal = {Genomics, proteomics &amp; bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.gpb.2018.09.003}, pmid = {31026577}, issn = {2210-3244}, abstract = {Exploring the mechanisms of maintaining microbial community structure is important to understand biofilm development or microbiota dysbiosis. In this paper, we propose a functional gene-based composition prediction (FCP) model to predict the population structure composition within a microbial community. The model predicts the community composition well in both a low-complexity community as acid mine drainage (AMD) microbiota, and a complex community as human gut microbiota. Furthermore, we define community structure shaping (CSS) genes as functional genes crucial for shaping the microbial community. We have identified CSS genes in AMD and human gut microbiota samples with FCP model and find that CSS genes change with the conditions. Compared to essential genes for microbes, CSS genes are significantly enriched in the genes involved in mobile genetic elements, cell motility, and defense mechanisms, indicating that the functions of CSS genes are focused on communication and strategies in response to the environment factors. We further find that it is the minority, rather than the majority, which contributes to maintaining community structure. Compared to health control samples, we find that some functional genes associated with metabolism of amino acids, nucleotides, and lipopolysaccharide are more likely to be CSS genes in the disease group. CSS genes may help us to understand critical cellular processes and be useful in seeking addable gene circuitries to maintain artificial self-sustainable communities. Our study suggests that functional genes are important to the assembly of microbial communities.}, }
@article {pmid31025063, year = {2019}, author = {Negi, A and Sarethy, IP}, title = {Microbial Biodeterioration of Cultural Heritage: Events, Colonization, and Analyses.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01366-y}, pmid = {31025063}, issn = {1432-184X}, abstract = {Geochemical cycles result in the chemical, physical, and mineralogical modification of rocks, eventually leading to formation of soil. However, when the stones and rocks are a part of historic buildings and monuments, the effects are deleterious. In addition, microorganisms also colonize these monuments over a period of time, resulting in formation of biofilms; their metabolites lead to physical weakening and discoloration of stone eventually. This process, known as biodeterioration, leads to a significant loss of cultural heritage. For formulating effective conservation strategies to prevent biodeterioration and restore monuments, it is important to know which microorganisms are colonizing the substrate and the different energy sources they consume to sustain themselves. With this view in scope, this review focuses on studies that have attempted to understand the process of biodeterioration, the mechanisms by which they colonize and affect the monuments, the techniques used for assessment of biodeterioration, and conservation strategies that aim to preserve the original integrity of the monuments. This review also includes the &quot;omics&quot; technologies that have started playing a large role in elucidating the nature of microorganisms, and how they can play a role in hastening the formulation of effective conservation strategies.}, }
@article {pmid31024502, year = {2019}, author = {Zeineldin, MM and Megahed, A and Blair, B and Burton, B and Aldridge, B and Lowe, J}, title = {Negligible Impact of Perinatal Tulathromycin Metaphylaxis on the Developmental Dynamics of Fecal Microbiota and Their Accompanying Antimicrobial Resistome in Piglets.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {726}, doi = {10.3389/fmicb.2019.00726}, pmid = {31024502}, issn = {1664-302X}, abstract = {While the antimicrobial resistance profiles of cultured pathogens have been characterized in swine, the fluctuations in antimicrobial resistance genes (ARGs) associated with the developing gastrointestinal microbiota have not been elucidated. The objective of this study was to assess the impact of perinatal tulathromycin (TUL) metaphylaxis on the developmental dynamics of fecal microbiota and their accompanying antimicrobial resistome in pre-weaned piglets. Sixteen litters were given one of two treatments [control group (CONT; saline 1cc IM) and TUL group (TUL; 2.5 mg/kg IM)] directly after birth. Deep fecal swabs were collected at day 0 (prior to treatment), and again at days 5 and 20 post treatment. Shotgun metagenomic sequencing was performed on the extracted DNA, and the fecal microbiota structure and abundance of ARGs were assessed. Collectively, the swine fecal microbiota and their accompanying ARGs were diverse and established soon after birth. Across all samples, a total of 127 ARGs related to 19 different classes of antibiotics were identified. The majority of identified ARGs were observed in both experimental groups and at all-time points. The magnitude and extent of differences in microbial composition and abundance of ARGs between the TUL and CONT groups were statistically insignificant. However, both fecal microbiota composition and ARGs abundance were changed significantly between different sampling days. In combination, these results indicate that the perinatal TUL metaphylaxis has no measurable benefits or detriment impacts on fecal microbiota structure and abundance of ARGs in pre-weaned piglets.}, }
@article {pmid31024492, year = {2019}, author = {Luo, G and Li, B and Yang, C and Wang, Y and Bian, X and Li, W and Liu, F and Huo, G}, title = {Major Traditional Probiotics: Comparative Genomic Analyses and Roles in Gut Microbiome of Eight Cohorts.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {712}, doi = {10.3389/fmicb.2019.00712}, pmid = {31024492}, issn = {1664-302X}, abstract = {Modulating gut microbiota to promote host health is well recognized. Therefore, people consume dietary products containing traditional probiotics in wishing to improve their health, and they need more research-based advices on how to select products with suitable probiotic species. Probiotic designers are sometimes confused about how to design precision products for different consumers by taking advantages of different probiotic species' strengths. Additionally, large-scale analyses on traditional probiotic complementarity potentials and their roles in gut microbiome related to common diseases are not well understood. Here, we comprehensively analyzed 444 genomes of major traditional probiotic (sub) species (MTPS, n = 15) by combining one newly sequenced genome with all of the public NCBI-available MTPS-related genomes. The public human fecal metagenomic data (n = 1,815) of eight cohorts were used to evaluate the roles of MTPS, compared to other main gut bacteria, in disease association by examining the species enrichment direction in disease group or the control group. Our work provided a comprehensive genetic landscape and complementarity relations for MTPS and shed light on personalized probiotic supplements for consumers with different health status and the necessity that researchers and manufactures could explore novel probiotics as well as traditional ones.}, }
@article {pmid31024491, year = {2019}, author = {Dharmarha, V and Guron, G and Boyer, RR and Niemira, BA and Pruden, A and Strawn, LK and Ponder, MA}, title = {Gamma Irradiation Influences the Survival and Regrowth of Antibiotic-Resistant Bacteria and Antibiotic-Resistance Genes on Romaine Lettuce.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {710}, doi = {10.3389/fmicb.2019.00710}, pmid = {31024491}, issn = {1664-302X}, abstract = {Contamination of romaine lettuce with human pathogens, antibiotic-resistant bacteria (ARB), and antibiotic resistance genes (ARGs) occurs during production. Post-harvest interventions are emplaced to mitigate pathogens, but could also mitigate ARB and ARGs on vegetables. The objective of this research was to determine changes to lettuce phyllosphere microbiota, inoculated ARB, and the resistome (profile of ARGs) following washing with a sanitizer, gamma irradiation, and cold storage. To simulate potential sources of pre-harvest contamination, romaine lettuce leaves were inoculated with compost slurry containing antibiotic-resistant strains of pathogenic (Escherichia coli O157:H7) and representative of spoilage bacteria (Pseudomonas aeruginosa). Various combinations of washing with sodium hypochlorite (50 ppm free chlorine), packaging under modified atmosphere (98% nitrogen), irradiating (1.0 kGy) and storing at 4°C for 1 day versus 14 days were compared. Effects of post-harvest treatments on the resistome were profiled by shotgun metagenomic sequencing. Bacterial 16S rRNA gene amplicon sequencing was performed to determine changes to the phyllosphere microbiota. Survival and regrowth of inoculated ARB were evaluated by enumeration on selective media. Washing lettuce in water containing sanitizer was associated with reduced abundance of ARG classes that confer resistance to glycopeptides, β-lactams, phenicols, and sulfonamides (Wilcoxon, p < 0.05). Washing followed by irradiation resulted in a different resistome chiefly due to reductions in multidrug, triclosan, polymyxin, β-lactam, and quinolone ARG classes (Wilcoxon, p < 0.05). Irradiation followed by storage at 4°C for 14 days led to distinct changes to the β-diversity of the host bacteria of ARGs compared to 1 day after treatment (ANOSIM, R = 0.331; p = 0.003). Storage of washed and irradiated lettuce at 4°C for 14 days increased the relative abundance of Pseudomonadaceae and Carnobacteriaceae (Wilcoxon, p < 0.05), two groups whose presence correlated with detection of 10 ARG classes on the lettuce phyllosphere (p < 0.05). Irradiation resulted in a significant reduction (∼3.5 log CFU/g) of inoculated strains of E. coli O157:H7 and P. aeruginosa (ANOVA, p < 0.05). Results indicate that washing, irradiation and storage of modified atmosphere packaged lettuce at 4°C are effective strategies to reduce antibiotic-resistant E. coli O157:H7 and P. aeruginosa and relative abundance of various ARG classes.}, }
@article {pmid31024486, year = {2019}, author = {Sirén, K and Mak, SST and Melkonian, C and Carøe, C and Swiegers, JH and Molenaar, D and Fischer, U and Gilbert, MTP}, title = {Taxonomic and Functional Characterization of the Microbial Community During Spontaneous in vitro Fermentation of Riesling Must.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {697}, doi = {10.3389/fmicb.2019.00697}, pmid = {31024486}, issn = {1664-302X}, abstract = {Although there is an extensive tradition of research into the microbes that underlie the winemaking process, much remains to be learnt. We combined the high-throughput sequencing (HTS) tools of metabarcoding and metagenomics, to characterize how microbial communities of Riesling musts sampled at four different vineyards, and their subsequent spontaneously fermented derivatives, vary. We specifically explored community variation relating to three points: (i) how microbial communities vary by vineyard; (ii) how community biodiversity changes during alcoholic fermentation; and (iii) how microbial community varies between musts that successfully complete alcoholic fermentation and those that become 'stuck' in the process. Our metabarcoding data showed a general influence of microbial composition at the vineyard level. Two of the vineyards (4 and 5) had strikingly a change in the differential abundance of Metschnikowia. We therefore additionally performed shotgun metagenomic sequencing on a subset of the samples to provide preliminary insights into the potential relevance of this observation, and used the data to both investigate functional potential and reconstruct draft genomes (bins). At these two vineyards, we also observed an increase in non-Saccharomycetaceae fungal functions, and a decrease in bacterial functions during the early fermentation stage. The binning results yielded 11 coherent bins, with both vineyards sharing the yeast bins Hanseniaspora and Saccharomyces. Read recruitment and functional analysis of this data revealed that during fermentation, a high abundance of Metschnikowia might serve as a biocontrol agent against bacteria, via a putative iron depletion pathway, and this in turn could help Saccharomyces dominate the fermentation. During alcoholic fermentation, we observed a general decrease in biodiversity in both the metabarcoding and metagenomic data. Unexpected Micrococcus behavior was observed in vineyard 4 according to metagenomic analyses based on reference-based read mapping. Analysis of open reading frames using these data showed an increase of functions assigned to class Actinobacteria in the end of fermentation. Therefore, we hypothesize that bacteria might sit-and-wait until Saccharomyces activity slows down. Complementary approaches to annotation instead of relying a single database provide more coherent information true species. Lastly, our metabarcoding data enabled us to identify a relationship between stuck fermentations and Starmerella abundance. Given that robust chemical analysis indicated that although the stuck samples contained residual glucose, all fructose had been consumed, we hypothesize that this was because fructophilic Starmerella, rather than Saccharomyces, dominated these fermentations. Overall, our results showcase the different ways in which metagenomic analyses can improve our understanding of the wine alcoholic fermentation process.}, }
@article {pmid31024471, year = {2019}, author = {Lacerda-Júnior, GV and Noronha, MF and Cabral, L and Delforno, TP and de Sousa, STP and Fernandes-Júnior, PI and Melo, IS and Oliveira, VM}, title = {Land Use and Seasonal Effects on the Soil Microbiome of a Brazilian Dry Forest.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {648}, doi = {10.3389/fmicb.2019.00648}, pmid = {31024471}, issn = {1664-302X}, abstract = {Drylands occupy approximately 41% of the Earth's terrestrial surface. Climate change and land use practices are expected to affect biogeochemical cycling by the soil microbiome in these ecosystems. Understanding how soil microbial community might respond to these drivers is extremely important to mitigate the processes of land degradation and desertification. The Caatinga, an exclusively Brazilian biome composed of an extensive seasonal tropical dry forest, is exposed to variable spatiotemporal rainfall patterns as well as strong human-driven pressures. Herein, an integrated analysis of shotgun metagenomics approach coupled to meteorological data was employed to unravel the impact of seasonality and land use change on soil microbiome from preserved and agriculture-affected experimental fields in Caatinga drylands. Multivariate analysis suggested that microbial communities of preserved soils under seasonal changes were shaped primarily by water deficit, with a strong increase of Actinobacteria and Proteobacteria members in the dry and rainy seasons, respectively. In contrast, nutrient availability notably played a critical role in driving the microbial community in agriculture-affected soils. The strong enrichment of bacterial genera belonging to the poorly-known phylum Acidobacteria ('Candidatus Solibacter' and 'Candidatus Koribacter') in soils from dry season affected by ferti-irrigation practices presupposes a contrasting copiotrophic lifestyle and ecological role in mitigating the impact of chemical fertilization. Functional analyses identify overrepresented genes related to osmotic stress response (synthesis of osmoprotectant compounds, accumulation of potassium ions) and preferential carbon and nitrogen utilization when comparing the microbiome of preserved soils under seasonal changes, reflecting differences in the genetic potential for nutrient cycling and C acquisition in the environment. However, the prevalence of nitrosative stress and denitrification functions in irrigation/fertilization-affected soils of the dry season clearly suggest that nutrient input and disruption of natural water regime may impact biogeochemical cycles linked to the microbial processes, with potential impacts on the ecosystem functionality. These findings help to better understand how natural seasonality and agricultural management differentially affect soil microbial ecology from dry forests, providing support for the development of more sustainable land management in dryland ecosystems.}, }
@article {pmid31023794, year = {2019}, author = {Santos Júnior, CD and Toyama, D and de Oliveira, TCS and Pellon de Miranda, F and Henrique-Silva, F}, title = {Flood Season Microbiota from the Amazon Basin Lakes: Analysis with Metagenome Sequencing.}, journal = {Microbiology resource announcements}, volume = {8}, number = {17}, pages = {}, doi = {10.1128/MRA.00229-19}, pmid = {31023794}, issn = {2576-098X}, abstract = {Despite an apparent geographic separation of the Amazon water bodies, they are an interconnected system. During floods, the microbiota of rivers, lakes, and soil combines. This study used metagenomics sequencing to survey the microbiota of the Amazon Basin lakes during flood season, showing important patterns in microbial communities.}, }
@article {pmid31023629, year = {2019}, author = {Tokarz, R and Tagliafierro, T and Sameroff, S and Cucura, DM and Oleynik, A and Che, X and Jain, K and Lipkin, WI}, title = {Microbiome analysis of Ixodes scapularis ticks from New York and Connecticut.}, journal = {Ticks and tick-borne diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ttbdis.2019.04.011}, pmid = {31023629}, issn = {1877-9603}, abstract = {We employed high throughput sequencing to survey the microbiomes of Ixodes scapularis collected in New York and Connecticut. We examined 197 individual I. scapularis adults and pools from 132 adults and 197 nymphs. We detected Borrelia burgdorferi sensu stricto in 56.3% of individual ticks, Anaplasma phagocytophilum in 10.6%, Borrelia miyamotoi in 5%, Babesia microti in 7.6%, and Powassan virus in 3.6%. We did not detect Borrelia mayonii, Ehrlichia muris eauclairensis, Bartonella spp. or pathogenic Babesia species other than B. microti. The most abundant bacterium (65%), and only rickettsial species identified, was the endosymbiont Rickettsia buchneri. A filarial nematode was found in 13.7% of adult ticks. Fourteen viruses were detected including South Bay virus (22%) and blacklegged tick phlebovirus 1 and 2 (73%). This study provides insight into the microbial diversity of I. scapularis in New York State and Connecticut.}, }
@article {pmid31022923, year = {2019}, author = {Ribeiro da Cunha, B and Fonseca, LP and Calado, CRC}, title = {Antibiotic Discovery: Where Have We Come from, Where Do We Go?.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {8}, number = {2}, pages = {}, doi = {10.3390/antibiotics8020045}, pmid = {31022923}, issn = {2079-6382}, support = {IDI&amp;CA/IPL/2017/DrugsPlatf/ISEL//Instituto Politécnico de Lisboa/ ; }, abstract = {Given the increase in antibiotic-resistant bacteria, alongside the alarmingly low rate of newly approved antibiotics for clinical usage, we are on the verge of not having effective treatments for many common infectious diseases. Historically, antibiotic discovery has been crucial in outpacing resistance and success is closely related to systematic procedures-platforms-that have catalyzed the antibiotic golden age, namely the Waksman platform, followed by the platforms of semi-synthesis and fully synthetic antibiotics. Said platforms resulted in the major antibiotic classes: aminoglycosides, amphenicols, ansamycins, beta-lactams, lipopeptides, diaminopyrimidines, fosfomycins, imidazoles, macrolides, oxazolidinones, streptogramins, polymyxins, sulphonamides, glycopeptides, quinolones and tetracyclines. During the genomics era came the target-based platform, mostly considered a failure due to limitations in translating drugs to the clinic. Therefore, cell-based platforms were re-instituted, and are still of the utmost importance in the fight against infectious diseases. Although the antibiotic pipeline is still lackluster, especially of new classes and novel mechanisms of action, in the post-genomic era, there is an increasingly large set of information available on microbial metabolism. The translation of such knowledge into novel platforms will hopefully result in the discovery of new and better therapeutics, which can sway the war on infectious diseases back in our favor.}, }
@article {pmid30297749, year = {2018}, author = {Gutiérrez-Preciado, A and Saghaï, A and Moreira, D and Zivanovic, Y and Deschamps, P and López-García, P}, title = {Functional shifts in microbial mats recapitulate early Earth metabolic transitions.}, journal = {Nature ecology &amp; evolution}, volume = {2}, number = {11}, pages = {1700-1708}, pmid = {30297749}, issn = {2397-334X}, support = {322669//European Research Council/International ; }, mesh = {*Biofilms ; *Biological Evolution ; Cyanobacteria/genetics/*physiology ; Ecosystem ; Metagenome ; Oxygen/metabolism ; *Photosynthesis ; }, abstract = {Phototrophic microbial mats dominated terrestrial ecosystems for billions of years, largely causing, through cyanobacterial oxygenic photosynthesis, but also undergoing, the Great Oxidation Event approximately 2.5 billion years ago. Taking a space-for-time approach based on the universality of core metabolic pathways expressed at ecosystem level, we studied gene content and co-occurrence networks in high-diversity metagenomes from spatially close microbial mats along a steep redox gradient. The observed functional shifts suggest that anoxygenic photosynthesis was present but not predominant under early Precambrian conditions, being accompanied by other autotrophic processes. Our data also suggest that, in contrast to general assumptions, anoxygenic photosynthesis largely expanded in parallel with the subsequent evolution of oxygenic photosynthesis and aerobic respiration. Finally, our observations might represent space-for-time evidence that the Wood-Ljungdahl carbon fixation pathway dominated phototrophic mats in early ecosystems, whereas the Calvin cycle probably evolved from pre-existing variants before becoming the dominant contemporary form of carbon fixation.}, }
@article {pmid31022652, year = {2019}, author = {Sun, Y and Qiu, T and Gao, M and Shi, M and Zhang, H and Wang, X}, title = {Inorganic and organic fertilizers application enhanced antibiotic resistome in greenhouse soils growing vegetables.}, journal = {Ecotoxicology and environmental safety}, volume = {179}, number = {}, pages = {24-30}, doi = {10.1016/j.ecoenv.2019.04.039}, pmid = {31022652}, issn = {1090-2414}, abstract = {Antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in fertilizers pose risks to human health and their variation in soil after fertilization has been reported. However, some important questions, such as the origin of ARG and ARB observed in soil following fertilization, which are present in soil regardless of fertilizer type (i.e., core (shared) ARGs and ARB), and the contribution of various ARG subtypes to the soil antibiotic resistome, need to be addressed. In this study, the effects of a long-term (9-year) application of organic (manure) and inorganic (chemistry) fertilizers on ARGs in greenhouse soils growing vegetables were investigated using metagenomic sequencing. The results showed that both organic and inorganic fertilizers application increased the diversity and abundance of soil ARGs. The dominant ARG types in organic fertilizer (OF) were different from that in organic fertilizer treated soil (SO), inorganic fertilizer treated soil (SI) and no fertilizer control plots (SC). The difference of core ARGs abundance reflected the variation of ARG profiles among SC, SI and SO. The OF is likely a source of the elevated ARG subtypes in soil and almost all the soil core ARG subtypes can be detected in organic fertilizer. Fifteen ARG types were enriched in the soil with OF, and some ARG subtypes such as sul1, sul2, tetX and tetL might derived from OF while others including as vanR, tcmA, rosB, and mexF might be from indigenous microbes in soil. The nutrition factors were found to influence the ARG profiles in fertilized soil. In summary, this study revealed the possible reason for the soil total ARG numbers and their relative abundance increase after fertilization, which will facilitate the control of ARGs and ARB dissemination.}, }
@article {pmid31022528, year = {2019}, author = {Watts, MP and Spurr, LP and Lê Cao, KA and Wick, R and Banfield, JF and Moreau, JW}, title = {Genome-resolved metagenomics of an autotrophic thiocyanate-remediating microbial bioreactor consortium.}, journal = {Water research}, volume = {158}, number = {}, pages = {106-117}, doi = {10.1016/j.watres.2019.02.058}, pmid = {31022528}, issn = {1879-2448}, abstract = {Industrial thiocyanate (SCN-) waste streams from gold mining and coal coking have polluted environments worldwide. Modern SCN- bioremediation involves use of complex engineered heterotrophic microbiomes; little attention has been given to the ability of a simple environmental autotrophic microbiome to biodegrade SCN-. Here we present results from a bioreactor experiment inoculated with SCN- -loaded mine tailings, incubated autotrophically, and subjected to a range of environmentally relevant conditions. Genome-resolved metagenomics revealed that SCN- hydrolase-encoding, sulphur-oxidizing autotrophic bacteria mediated SCN- degradation. These microbes supported metabolically-dependent non-SCN--degrading sulphur-oxidizing autotrophs and non-sulphur oxidizing heterotrophs, and &quot;niche&quot; microbiomes developed spatially (planktonic versus sessile) and temporally (across changing environmental parameters). Bioreactor microbiome structures changed significantly with increasing temperature, shifting from Thiobacilli to a novel SCN- hydrolase-encoding gammaproteobacteria. Transformation of carbonyl sulphide (COS), a key intermediate in global biogeochemical sulphur cycling, was mediated by plasmid-hosted CS2 and COS hydrolase genes associated with Thiobacillus, revealing a potential for horizontal transfer of this function. Our work shows that simple native autotrophic microbiomes from mine tailings can be employed for SCN- bioremediation, thus improving the recycling of ore processing waters and reducing the hydrological footprint of mining.}, }
@article {pmid31021803, year = {2019}, author = {Wassan, JT and Wang, H and Browne, F and Zheng, H}, title = {Phy-PMRFI: Phylogeny-aware Prediction of Metagenomic Functions using Random Forest Feature Importance.}, journal = {IEEE transactions on nanobioscience}, volume = {}, number = {}, pages = {}, doi = {10.1109/TNB.2019.2912824}, pmid = {31021803}, issn = {1558-2639}, abstract = {High-throughput sequencing techniques have accelerated functional metagenomics studies through the generation of large volumes of &quot;omics&quot; data. The integration of these data using computational approaches is potentially useful for predicting metagenomic functions. Machine learning (ML) models can be trained using microbial features which are then used to classify microbial data into different functional classes. For example, ML analyses over the human microbiome data have been linked to the prediction of important biological states. For analysing omics data, integrating abundance count of taxonomical features with their biological relationships is important. These relationships can potentially be uncovered from the phylogenetic tree of microbial taxa. In this paper, we propose a novel integrative framework Phy-PMRFI. This framework is driven by the phylogeny-based modeling of omics data to predict metagenomic functions using important features selected by a Random Forest Importance (RFI) strategy. The proposed framework integrates the underlying phylogenetic tree information with abundance measures of microbial species (features) by creating a novel phylogeny and abundance aware matrix structure (PAAM). Phy-PMRFI progresses by ranking the microbial features using an RFI measure. This is then used as input for microbiome classification. The resultant feature set enhances the performance of state-of-art methods such as Support Vector Machines. Our proposed integrative framework also outperforms the state-of-the-art pipeline of Phylogenetic Isometric Log-Ratio Transform (PhILR) and MetaPhyl. Prediction accuracy of 90 % is obtained with Phy-PMRFI over human throat microbiome in comparison to other approaches of PhILR with 53% and MetaPhyl with 71% Accuracy.}, }
@article {pmid31021335, year = {2019}, author = {Zhang, Y and Ying, H and Xu, Y}, title = {Comparative genomics and metagenomics of the metallomes.}, journal = {Metallomics : integrated biometal science}, volume = {}, number = {}, pages = {}, doi = {10.1039/c9mt00023b}, pmid = {31021335}, issn = {1756-591X}, abstract = {Biological trace metals are needed by all living organisms in very small quantities. They play important roles in a variety of key cellular processes, resulting in a varying degree of dependence on metals for different organisms. While most effort has been placed on identifying metal metabolic pathways and characterizing metalloproteins and their functions, computational and systematical analyses of the metallomes (or metalloproteomes) have been limited. In the past several years, comparative genomics of the metallomes has arisen, which provides significant insights into the metabolism and function of metals as well as their evolution. This review focuses on recent progress in comparative genomic analysis of trace metals (such as copper, molybdenum, nickel, cobalt, selenium, iron and zinc) in both prokaryotes and eukaryotes. These studies reveal distinct and dynamic evolutionary patterns of the utilization of different metals and metalloproteins. We also discuss advances in comparative metagenomic analysis of metals in microbial communities in diverse environments such as the global marine ecosystem, which offer new clues to the relationship between metal utilization and different types of environmental factors. Overall, comparative genomic and metagenomic analyses of the metallomes provide a foundation for systematic understanding of metal utilization, function and related evolutionary trends in the three domains of life.}, }
@article {pmid31021333, year = {2019}, author = {Xu, H and Zhao, F and Hou, Q and Huang, W and Liu, Y and Zhang, H and Sun, Z}, title = {Metagenomic analysis revealed beneficial effects of probiotics in improving the composition and function of the gut microbiota in dogs with diarrhoea.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/c9fo00087a}, pmid = {31021333}, issn = {2042-650X}, abstract = {The aim of the present study was to evaluate the effects of probiotics on the composition and function of the gut microbiota in dogs with diarrhoea. Forty dogs with diarrhoea were randomly allocated to the treatment group or control group. Probiotics, containing Lactobacillus casei Zhang, Lactobacillus plantarum P-8, and Bifidobacterium animalis subsp. lactis V9, were only fed to 20 treated dogs for 60 days. The faecal samples of all dogs at day 0 and day 60 were analyzed using a metagenomic approach. The results showed a significantly higher microbial diversity and an obvious change in the structure of the gut microbiota in the treatment group. There was also an increase in the abundance of some beneficial bacteria in differently aged dogs, such as Lactobacillus johnsonii (P < 0.05), Lactobacillus reuteri (P < 0.01), Lactobacillus acidophilus (P < 0.05) and Butyricicoccus pullicaecorum (P < 0.05), and a reduction in the abundance of many opportunistic pathogenic bacteria such as Clostridium perfringens (P < 0.05) and Stenotrophomonas maltophilia (P < 0.05) with the supplementation of probiotics. Intriguingly, the correlated networks among some pathogenic bacteria decreased following the administration of probiotics. Additionally, metagenomic analysis revealed the upregulation of pathways involved in the metabolism of amino acids and biosynthesis of secondary metabolites, accompanied by the downregulation of pathways associated with virulence of pathogenic bacteria and cell signaling, suggesting that probiotics could improve the health of dogs with diarrhoea through regulation of the gut microbiota. Our research provides new information relevant to the treatment of diarrhoea in animals and humans.}, }
@article {pmid31020948, year = {2019}, author = {Tamukai, K and Sugiyama, J and Nagata, Y and Tsutomu, O and Katayama, Y and Mizutani, T and Kimura, M and Une, Y}, title = {Epidemic nodular facial myxomatous dermatitis in juvenile Cranwell's horned frogs Ceratophrys cranwelli.}, journal = {Diseases of aquatic organisms}, volume = {134}, number = {1}, pages = {57-64}, doi = {10.3354/dao03358}, pmid = {31020948}, issn = {0177-5103}, abstract = {In 2017, approximately 40 out of 100 captive Cranwell's horned frogs Ceratophrys cranwelli from several facilities in Japan exhibited protruding facial lesions. Histopathological examination was performed on 6 specimens with such lesions randomly selected from 2 facilities. Lesions consisted of scattered stellate to spindle-shaped cells without atypia in an abundant myxoid matrix and occasional lymphocytic infiltrates. Maxillary bone was resorbed. No etiological organisms were detected using light microscopy or metagenomic analysis of the lesions. Macroscopic and histological assessments indicate that the lesions are associated with nodular facial myxomatous dermatitis, which has never been reported in amphibians.}, }
@article {pmid31020042, year = {2019}, author = {Argüello, H and Estellé, J and Leonard, FC and Crispie, F and Cotter, PD and O'Sullivan, O and Lynch, H and Walia, K and Duffy, G and Lawlor, PG and Gardiner, GE}, title = {Influence of the Intestinal Microbiota on Colonization Resistance to Salmonella and the Shedding Pattern of Naturally Exposed Pigs.}, journal = {mSystems}, volume = {4}, number = {2}, pages = {}, doi = {10.1128/mSystems.00021-19}, pmid = {31020042}, issn = {2379-5077}, abstract = {Salmonella colonization and infection in production animals such as pigs are a cause for concern from a public health perspective. Variations in susceptibility to natural infection may be influenced by the intestinal microbiota. Using 16S rRNA compositional sequencing, we characterized the fecal microbiome of 15 weaned pigs naturally infected with Salmonella at 18, 33, and 45 days postweaning. Dissimilarities in microbiota composition were analyzed in relation to Salmonella infection status (infected, not infected), serological status, and shedding pattern (nonshedders, single-point shedders, intermittent-persistent shedders). Global microbiota composition was associated with the infection outcome based on serological analysis. Greater richness within the microbiota postweaning was linked to pigs being seronegative at the end of the study at 11 weeks of age. Members of the Clostridia, such as Blautia, Roseburia, and Anaerovibrio, were more abundant and part of the core microbiome in nonshedder pigs. Cellulolytic microbiota (Ruminococcus and Prevotella) were also more abundant in noninfected pigs during the weaning and growing stages. Microbial profiling also revealed that infected pigs had a higher abundance of Lactobacillus and Oscillospira, the latter also being part of the core microbiome of intermittent-persistent shedders. These findings suggest that a lack of microbiome maturation and greater proportions of microorganisms associated with suckling increase susceptibility to infection. In addition, the persistence of Salmonella shedding may be associated with an enrichment of pathobionts such as Anaerobiospirillum. Overall, these results suggest that there may be merit in manipulating certain taxa within the porcine intestinal microbial community to increase disease resistance against Salmonella in pigs. IMPORTANCESalmonella is a global threat for public health, and pork is one of the main sources of human salmonellosis. However, the complex epidemiology of the infection limits current control strategies aimed at reducing the prevalence of this infection in pigs. The present study analyzes for the first time the impact of the gut microbiota in Salmonella infection in pigs and its shedding pattern in naturally infected growing pigs. Microbiome (16S rRNA amplicon) analysis reveals that maturation of the gut microbiome could be a key consideration with respect to limiting the infection and shedding of Salmonella in pigs. Indeed, seronegative animals had higher richness of the gut microbiota early after weaning, and uninfected pigs had higher abundance of strict anaerobes from the class Clostridia, results which demonstrate that a fast transition from the suckling microbiota to a postweaning microbiota could be crucial with respect to protecting the animals.}, }
@article {pmid31020040, year = {2019}, author = {Zhang, J and Sun, Z and Jiang, S and Bai, X and Ma, C and Peng, Q and Chen, K and Chang, H and Fang, T and Zhang, H}, title = {Probiotic Bifidobacterium lactis V9 Regulates the Secretion of Sex Hormones in Polycystic Ovary Syndrome Patients through the Gut-Brain Axis.}, journal = {mSystems}, volume = {4}, number = {2}, pages = {}, doi = {10.1128/mSystems.00017-19}, pmid = {31020040}, issn = {2379-5077}, abstract = {Although a few studies have investigated the intestinal microbiota of women with polycystic ovary syndrome (PCOS), the functional and metabolic mechanisms of the microbes associated with PCOS, as well as potential microbial biomarkers, have not yet been identified. To address this gap, we designed a two-phase experiment in which we performed shotgun metagenomic sequencing and monitored the metabolic parameters, gut-brain mediators, and sex hormones of PCOS patients. In the first stage, we identified an imbalance in the intestinal microbiota of the PCOS patients, observing that Faecalibacterium, Bifidobacterium, and Blautia were significantly more abundant in the control group, whereas Parabacteroides and Clostridium were enriched in the PCOS group. In the second stage, we monitored the impact of the probiotic Bifidobacterium lactis V9 on the intestinal microbiome, gut-brain mediators, and sex hormones of 14 PCOS patients. Notably, we observed that the levels of luteinizing hormone (LH) and LH/follicle-stimulating hormone (LH/FSH) decreased significantly in 9 volunteers, whereas the levels of sex hormones and intestinal short-chain fatty acids (SCFAs) increased markedly. In contrast, the changes in the indices mentioned above were indistinct in the remaining 5 volunteers. The results of an analysis of the number of viable Bifidobacterium lactis V9 cells in the two groups were highly consistent with the clinical and SCFA results. Therefore, effective host gut colonization of the probiotic Bifidobacterium lactis V9 was crucial for its ability to function as a probiotic. Finally, we propose a potential mechanism describing how probiotics regulate the levels of sex hormones by manipulating the intestinal microbiome in PCOS patients. IMPORTANCE Polycystic ovary syndrome (PCOS) is a common metabolic disorder among women of reproductive age worldwide. Through a two-phase clinical experiment, we first revealed an imbalance in the intestinal microbiome of PCOS patients. By binning and annotating shotgun metagenomic sequences into metagenomic species (MGS), 61 MGSs were identified as potential PCOS-related microbial biomarkers. In the second stage, we monitored the impact of the probiotic Bifidobacterium lactis V9 on the intestinal microbiota, metabolic parameters, gut-brain mediators, and sex hormones of PCOS patients. Notably, we observed that the PCOS-related clinical indices and the intestinal microbiotas of the participating patients exhibited an inconsistent response to the intake of the B. lactis V9 probiotic. Therefore, effective host gut colonization of the probiotic was crucial for its ability to function as a probiotic. Finally, we propose a potential mechanism by which B. lactis V9 regulates the levels of sex hormones by manipulating the intestinal microbiome in PCOS patients.}, }
@article {pmid31015394, year = {2019}, author = {Seitz, KW and Dombrowski, N and Eme, L and Spang, A and Lombard, J and Sieber, JR and Teske, AP and Ettema, TJG and Baker, BJ}, title = {Asgard archaea capable of anaerobic hydrocarbon cycling.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1822}, doi = {10.1038/s41467-019-09364-x}, pmid = {31015394}, issn = {2041-1723}, abstract = {Large reservoirs of natural gas in the oceanic subsurface sustain complex communities of anaerobic microbes, including archaeal lineages with potential to mediate oxidation of hydrocarbons such as methane and butane. Here we describe a previously unknown archaeal phylum, Helarchaeota, belonging to the Asgard superphylum and with the potential for hydrocarbon oxidation. We reconstruct Helarchaeota genomes from metagenomic data derived from hydrothermal deep-sea sediments in the hydrocarbon-rich Guaymas Basin. The genomes encode methyl-CoM reductase-like enzymes that are similar to those found in butane-oxidizing archaea, as well as several enzymes potentially involved in alkyl-CoA oxidation and the Wood-Ljungdahl pathway. We suggest that members of the Helarchaeota have the potential to activate and subsequently anaerobically oxidize hydrothermally generated short-chain hydrocarbons.}, }
@article {pmid31015144, year = {2019}, author = {Corno, G and Yang, Y and Eckert, EM and Fontaneto, D and Fiorentino, A and Galafassi, S and Zhang, T and Di Cesare, A}, title = {Effluents of wastewater treatment plants promote the rapid stabilization of the antibiotic resistome in receiving freshwater bodies.}, journal = {Water research}, volume = {158}, number = {}, pages = {72-81}, doi = {10.1016/j.watres.2019.04.031}, pmid = {31015144}, issn = {1879-2448}, abstract = {Treated wastewater discharged into the environment acts as a disturbance of the natural microbial communities in terms of taxonomic composition and of functional gene pool, including antibiotic resistance genes. We tested whether stochastic and heterogeneous site-specific trajectories or generalities, potentially driven by deterministic processes, control the fate of allochthonous bacteria from anthropogenic sources and the persistence of their functional traits in freshwater. Finding generalities would allow the identification of wastewater treatments that could be effective in abating determinants of antibiotic resistance. We analysed the short-term response of native bacterial communities in waters exposed to the disturbance of wastewater at different dilutions, using a metagenomic approach that revealed both microbial community composition and the scope and abundance of the resistome that can pose indirect risks to human health. We found that the taxonomic composition of the communities after the disturbance was driven by case-specific stochastic processes, whereas the resistome had a deterministic trajectory, rapidly stabilising its functional traits with higher proportions of wastewater effluents, regardless of differences in taxonomic composition, richness of antibiotic resistance genes and of bacterial taxa, phenotypic features of the bacterial communities, and type of wastewater treatment. The observed deterministic proliferation of resistomes in freshwater bodies receiving wastewater effluents, suggests that this process may contribute to the global propagation of antibiotic resistance, and thus calls for new legislations promoting alternative tertiary treatments for the wastewater reuse, and targeting bacterial functional traits and not only bacterial abundances.}, }
@article {pmid31012058, year = {2019}, author = {Song, J and Jang, HJ and Joung, Y and Kang, I and Cho, JC}, title = {Sulfitobacter profundi sp. nov., isolated from deep seawater.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {}, number = {}, pages = {}, doi = {10.1007/s12275-019-9150-3}, pmid = {31012058}, issn = {1976-3794}, abstract = {A Gram-stain-negative, rod-shaped, obligately aerobic, chemoheterotrophic bacterium which is motile by means of a single polar flagellum, designated SAORIC-263T, was isolated from deep seawater of the Pacific Ocean. Phylogenetic analyses based on 16S rRNA gene sequences and genomebased phylogeny revealed that strain SAORIC-263T belonged to the genus Sulfitobacter and shared 96.1-99.9% 16S rRNA gene sequence similarities with Sulfitobacter species. Wholegenome sequencing of strain SAORIC-263T revealed a genome size of 3.9Mbp and DNA G+C content of 61.3 mol%. The SAORIC-263T genome shared an average nucleotide identity and digital DNA-DNA hybridization of 79.1-88.5% and 18.9-35.0%, respectively, with other Sulfitobacter genomes. The SAORIC-263T genome contained the genes related to benzoate degradation, which are frequently found in deep-sea metagenome. The strain contained summed feature 8 (C18:1ω7c), C18:1ω7c 11-methyl, and C16:0 as the predominant cellular fatty acids as well as ubiquinone-10 (Q-10) as the major respiratory quinone. The major polar lipids of the strain were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, and aminolipid. On the basis of taxonomic data obtained in this study, it is suggested that strain SAORIC-263T represents a novel species of the genus Sulfitobacter, for which the name Sulfitobacter profundi sp. nov. is proposed. The type strain is SAORIC-263T (= KACC 21183T = NBRC 113428T).}, }
@article {pmid31011775, year = {2019}, author = {Singh, NK and Wood, JM and Mhatre, SS and Venkateswaran, K}, title = {Metagenome to phenome approach enables isolation and genomics characterization of Kalamiella piersonii gen. nov., sp. nov. from the International Space Station.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00253-019-09813-z}, pmid = {31011775}, issn = {1432-0614}, support = {19-12829-26//2012 Space Biology NNH12ZTT001N/ ; }, abstract = {Several evolutionarily distinct, near full-length draft metagenome-resolved genomes (MRG), were assembled from sequences recovered from the International Space Station (ISS) environments. The retrieval of MRGs facilitated the exploration of a large collection of archived strains (~ 500 isolates) and assisted in isolating seven related strains. The whole genome sequences (WGS) of seven ISS strains exhibited 100% identity to the 4.85 × 106 bp of four MRGs. The &quot;metagenome to phenome&quot; approach led to the description of a novel bacterial genus from the ISS samples. The phylogenomics and traditional taxonomic approaches suggested that these seven ISS strains and four MRGs were not phylogenetically affiliated to any validly described genera of the family Erwiniaceae, but belong to a novel genus with the proposed name Kalamiella. Comparative genomic analyses of Kalamiella piersonii strains and MRGs showed genes associated with carbohydrate (348 genes), amino acid (384), RNA (59), and protein (214) metabolisms; membrane transport systems (108), pathways for biosynthesis of cofactors, vitamins, prosthetic groups, and pigments (179); as well as mechanisms for virulence, disease, and defense (50). Even though Kalamiella genome annotation and disc diffusion tests revealed multidrug resistance, the PathogenFinder algorithm predicted that K. piersonii strains are not human pathogens. This approach to isolating microbes allows for the characterization of functional pathways and their potential virulence properties that can directly affect human health. The isolation of novel strains from the ISS has broad applications in microbiology, not only because of concern for astronaut health but it might have a great potential for biotechnological relevance. The metagenome to phenome approach will help to improve our understanding of complex metabolic networks that control fundamental life processes under microgravity and in deep space.}, }
@article {pmid30128998, year = {2018}, author = {Santiago-Rodriguez, TM}, title = {Identification and Quantification of DNA Viral Populations in Human Urine Using Next-Generation Sequencing Approaches.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1838}, number = {}, pages = {191-200}, doi = {10.1007/978-1-4939-8682-8_14}, pmid = {30128998}, issn = {1940-6029}, mesh = {Bacteriophages/genetics ; Centrifugation, Density Gradient ; Computational Biology/methods ; *DNA, Viral ; *High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Metagenomics/methods ; Nucleic Acid Amplification Techniques ; Polymerase Chain Reaction ; Ultracentrifugation ; Urine/*virology ; Viral Load ; Virion/isolation &amp; purification ; Viruses/*genetics/isolation &amp; purification ; }, abstract = {The human urinary virome is comprised by diverse communities of both eukaryotic viruses and bacteriophages. Identification and quantification of human urinary viruses was limited to PCR-based and culture methods. Detection of viruses in human urine has long been associated with disease, but advances in next-generation sequencing have shown that it harbors robust viral communities. Human urinary viral communities are mainly comprised by bacteriophages and Human Papillomaviruses (HPVs) that remain to be characterized in association with health and diverse urinary disease states. In the present chapter, the methods to identify and quantify DNA viral populations in human urine using next-generation sequencing are described.}, }
@article {pmid30128992, year = {2018}, author = {Mayo-Muñoz, D}, title = {Viral Genome Isolation from Human Faeces for Succession Assessment of the Human Gut Virome.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1838}, number = {}, pages = {97-108}, doi = {10.1007/978-1-4939-8682-8_8}, pmid = {30128992}, issn = {1940-6029}, mesh = {Feces/*virology ; *Gastrointestinal Microbiome ; *Genome, Viral ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; *Metagenomics/methods ; Whole Genome Sequencing ; }, abstract = {Despite the important role of the microbiota in the human gastrointestinal tract (GIT) and its impact on life-long health, the successional process through which this microbial community develops during infancy is still poorly understood. Specially, little is known about how the amount and type of viruses present in the GIT, i.e., the virome, varies throughout this period and about the role this collection of viruses may play in the assembly of the GIT microbiota.The patterns of taxonomic change of the GIT viral community can be analyzed in a birth cohort of infants during the first year of life. The present chapter presents a detailed protocol for the isolation and extraction of viral nucleic acids from collected human faecal samples, whole genome amplification (WGA) using phi29 DNA polymerase and preparation for sequencing through high-throughput 454 pyrosequencing. The sequencing data can be posteriorly used for taxonomic classification in order to establish the composition of the virome present in each sample and to assess the process of viral dynamics through time.}, }
@article {pmid28852195, year = {2017}, author = {Ozkan, J and Nielsen, S and Diez-Vives, C and Coroneo, M and Thomas, T and Willcox, M}, title = {Temporal Stability and Composition of the Ocular Surface Microbiome.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {9880}, pmid = {28852195}, issn = {2045-2322}, mesh = {Adult ; Conjunctiva/*microbiology ; Eyelids/*microbiology ; Female ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; RNA, Ribosomal, 16S ; }, abstract = {To determine if there is a core ocular surface microbiome and whether there are microbial community changes over time, the conjunctiva of 45 healthy subjects were sampled at three time points over three months and processed using culture-dependent and -independent methods. Contaminant taxa were removed using a linear regression model using taxa abundances in negative controls as predictor of taxa abundances in subject samples. Both cultured cell counts and sequencing indicated low microbial biomass on the ocular surface. No cultured species was found in all subjects at all times or in all subjects at any one time. After removal of contaminant taxa identified in negative controls using a statistical model, the most commonly detected taxon was Corynebacterium (11.1%). No taxa were found in all subjects at all times or in all subjects in any one time, but there were 26 taxa present in at least one or more subjects at all times including Corynebacterium and Streptococcus. The ocular surface contains a low diversity of microorganisms. Using culture dependent and independent methods, the ocular surface does not appear to support a substantial core microbiome. However, consistently present taxa could be observed within individuals suggesting the possibility of individual-specific core microbiomes.}, }
@article {pmid28852143, year = {2017}, author = {Gribben, PE and Nielsen, S and Seymour, JR and Bradley, DJ and West, MN and Thomas, T}, title = {Microbial communities in marine sediments modify success of an invasive macrophyte.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {9845}, pmid = {28852143}, issn = {2045-2322}, mesh = {Australia ; Bacteria ; *Biodiversity ; Ecosystem ; Geologic Sediments/*microbiology ; *Introduced Species ; Metagenome ; Metagenomics/methods ; *Microbiota ; *Oceans and Seas ; *Plants ; }, abstract = {Invasive plants have extensive impacts on ecosystem function and biodiversity globally. Our inability to manage invasive species stems in part from a lack of understanding of the processes that control their successful establishment and spread. To date, studies have largely considered how above-ground processes control native/invasive plant interactions. Emerging research from terrestrial and wetland ecosystems demonstrates that below-ground processes under microbial control can determine the outcome of interactions between native and invasive plants. Whether sediment microbes modify the success of invasive macrophytes in marine ecosystems is untested, despite marine sediment microbes controlling many ecological processes (e.g. nutrient cycling) comparable to those in terrestrial ecosystems. We first show that sediment bacterial communities differ between the native seagrass Zostera capricorni and the invasive alga Caulerpa taxifolia and that those differences relate to functional changes in sulfur cycling between the macrophytes. Second, by experimentally manipulating the microbial communities we show that intact microbial communities in Z. capricorni sediments provide biotic resistance by reducing C. taxifolia fragment growth 119% compared to when they are inactive, and intact microbial communities in C. taxifolia sediments have positive feedbacks by increasing fragment growth 200%. Thus, similar to terrestrial ecosystems, microorganisms appear to indirectly control the success of invasive macrophytes in marine ecosystems.}, }
@article {pmid31009062, year = {2019}, author = {Zhang, J and Lin, W}, title = {Scalable estimation and regularization for the logistic normal multinomial model.}, journal = {Biometrics}, volume = {}, number = {}, pages = {}, doi = {10.1111/biom.13071}, pmid = {31009062}, issn = {1541-0420}, abstract = {Clustered multinomial data are prevalent in a variety of applications such as microbiome studies, where metagenomic sequencing data are summarized as multinomial counts for a large number of bacterial taxa per subject. Count normalization with ad hoc zero adjustment tends to result in poor estimates of abundances for taxa with zero or small counts. To account for heterogeneity and overdispersion in such data, we suggest using the logistic normal multinomial (LNM) model with an arbitrary correlation structure to simultaneously estimate the taxa compositions by borrowing information across subjects. We overcome the computational difficulties in high dimensions by developing a stochastic approximation EM algorithm with Hamiltonian Monte Carlo sampling for scalable parameter estimation in the LNM model. The ill-conditioning problem due to unstructured covariance is further mitigated by a covariance-regularized estimator with a condition number constraint. The advantages of the proposed methods are illustrated through simulations and an application to human gut microbiome data. This article is protected by copyright. All rights reserved.}, }
@article {pmid31006638, year = {2019}, author = {Kalan, LR and Meisel, JS and Loesche, MA and Horwinski, J and Soaita, I and Chen, X and Uberoi, A and Gardner, SE and Grice, EA}, title = {Strain- and Species-Level Variation in the Microbiome of Diabetic Wounds Is Associated with Clinical Outcomes and Therapeutic Efficacy.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2019.03.006}, pmid = {31006638}, issn = {1934-6069}, abstract = {Chronic wounds are a major complication of diabetes associated with high morbidity and health care expenditures. To investigate the role of colonizing microbiota in diabetic wound healing, clinical outcomes, and response to interventions, we conducted a longitudinal, prospective study of patients with neuropathic diabetic foot ulcers (DFU). Metagenomic shotgun sequencing revealed that strain-level variation of Staphylococcus aureus and genetic signatures of biofilm formation were associated with poor outcomes. Cultured wound isolates of S. aureus elicited differential phenotypes in mouse models that corresponded with patient outcomes, while wound &quot;bystanders&quot; such as Corynebacterium striatum and Alcaligenes faecalis, typically considered commensals or contaminants, also significantly impacted wound severity and healing. Antibiotic resistance genes were widespread, and debridement, rather than antibiotic treatment, significantly shifted the DFU microbiota in patients with more favorable outcomes. These findings suggest that the DFU microbiota may be a marker for clinical outcomes and response to therapeutic interventions.}, }
@article {pmid29795448, year = {2018}, author = {McClure, RS and Overall, CC and Hill, EA and Song, HS and Charania, M and Bernstein, HC and McDermott, JE and Beliaev, AS}, title = {Species-specific transcriptomic network inference of interspecies interactions.}, journal = {The ISME journal}, volume = {12}, number = {8}, pages = {2011-2023}, pmid = {29795448}, issn = {1751-7370}, mesh = {Algorithms ; Bacteria/*genetics/growth &amp; development ; Bacterial Physiological Phenomena ; Bacterial Proteins/genetics/metabolism ; Cyanobacteria/*genetics/growth &amp; development/physiology ; Gene Regulatory Networks ; Heterotrophic Processes ; Metagenome ; Microbiota ; Species Specificity ; Transcriptome ; }, abstract = {The advent of high-throughput 'omics approaches coupled with computational analyses to reconstruct individual genomes from metagenomes provides a basis for species-resolved functional studies. Here, a mutual information approach was applied to build a gene association network of a commensal consortium, in which a unicellular cyanobacterium Thermosynechococcus elongatus BP1 supported the heterotrophic growth of Meiothermus ruber strain A. Specifically, we used the context likelihood of relatedness (CLR) algorithm to generate a gene association network from 25 transcriptomic datasets representing distinct growth conditions. The resulting interspecies network revealed a number of linkages between genes in each species. While many of the linkages were supported by the existing knowledge of phototroph-heterotroph interactions and the metabolism of these two species several new interactions were inferred as well. These include linkages between amino acid synthesis and uptake genes, as well as carbohydrate and vitamin metabolism, terpenoid metabolism and cell adhesion genes. Further topological examination and functional analysis of specific gene associations suggested that the interactions are likely to center around the exchange of energetically costly metabolites between T. elongatus and M. ruber. Both the approach and conclusions derived from this work are widely applicable to microbial communities for identification of the interactions between species and characterization of community functioning as a whole.}, }
@article {pmid31006170, year = {2019}, author = {Coker, MO and Hoen, AG and Dade, E and Lundgren, S and Li, Z and Wong, AD and Zens, MS and Palys, TJ and Morrison, HG and Sogin, ML and Baker, ER and Karagas, MR and Madan, JC}, title = {Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study.}, journal = {BJOG : an international journal of obstetrics and gynaecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1471-0528.15799}, pmid = {31006170}, issn = {1471-0528}, abstract = {OBJECTIVE: To evaluate the potential impact of intrapartum antibiotics, and their specific classes, on the infant gut microbiota in the first year of life.<br><br>DESIGN: Prospective study of infants in the New Hampshire Birth Cohort Study (NHBCS).<br><br>SETTINGS: Rural New Hampshire, US.<br><br>POPULATION OR SAMPLE: 266 full-term infants from the NHBCS.<br><br>METHODS: Intrapartum antibiotic use during labor and delivery was abstracted from medical records. Fecal samples collected at 6 weeks and 1 year of age were characterized by 16S rRNA sequencing, and metagenomics analysis in a subset of samples.<br><br>EXPOSURES: Maternal exposure to antibiotics during labor and delivery.<br><br>MAIN OUTCOME MEASURE: Taxonomic and functional profiles of fecal samples.<br><br>RESULTS: Infant exposure to intrapartum antibiotics, particularly to two or more antibiotic classes, was independently associated with lower microbial diversity scores as well as a unique bacterial community at 6 weeks (GUnifrac, P=0.02). At 1 year, infants in the penicillin-only group had significantly lower alpha diversity scores than infants not exposed to intrapartum antibiotics. Within the first year of life, intrapartum exposure to penicillins was related to a significantly lower increase in several taxa including Bacteroides, use of cephalosporins was associated with a significantly lower rise over time in Bifidobacterium and infants in multi-class group experienced a significantly higher increase in Veillonella dispar.<br><br>CONCLUSIONS: Our findings suggest that intrapartum antibiotics alters the developmental trajectory of the infant gut microbiome, and specific antibiotic types may impact community composition, diversity, and keystone immune training taxa. This article is protected by copyright. All rights reserved.}, }
@article {pmid31005831, year = {2019}, author = {Samson, R and Shah, M and Yadav, R and Sarode, P and Rajput, V and Dastager, SG and Dharne, MS and Khairnar, K}, title = {Metagenomic insights to understand transient influence of Yamuna River on taxonomic and functional aspects of bacterial and archaeal communities of River Ganges.}, journal = {The Science of the total environment}, volume = {674}, number = {}, pages = {288-299}, doi = {10.1016/j.scitotenv.2019.04.166}, pmid = {31005831}, issn = {1879-1026}, abstract = {River confluences are interesting ecosystems to investigate for their microbial community structure and functional potentials. River Ganges is one of the most important and holy river of India with great mythological history and religious significance. The Yamuna River meets Ganges at the Prayagraj (formerly known as Allahabad), India to form a unique confluence. The influence of Yamuna River on taxonomic and functional aspects of microbiome at this confluence and its downstream, remains unexplored. To unveil this dearth, whole metagenome sequencing of the microbial (bacterial and archaeal) community from the sediment samples of December 2017 sampling expedition was executed using high throughput MinION technology. Results revealed differences in the relative abundance of bacterial and archaeal communities across the confluence. Grouped by the confluence, a higher abundance of Proteobacteria and lower abundance of Bacteroidetes and Firmicutes was observed for Yamuna River (G15Y) and at immediate downstream of confluence of Ganges (G15DS), as compared to the upstream, confluence, and farther downstream of confluence. A similar trend was observed for archaeal communities with a higher abundance of Euryarchaeota in G15Y and G15DS, indicating Yamuna River's influence. Functional gene(s) analysis revealed the influence of Yamuna River on xenobiotic degradation, resistance to toxic compounds, and antibiotic resistance interceded by the autochthonous microbes at the confluence and succeeding downstream locations. Overall, similar taxonomic and functional profiles of microbial communities before confluence (upstream of Ganges) and farther downstream of confluence, suggested a transient influence of Yamuna River. Our study is significant since it may be foundational basis to understand impact of Yamuna River and also rare event of mass bathing on the microbiome of River Ganges. Further investigation would be required to understand, the underlying cause behind the restoration of microbial profiles post-confluence farther zone, to unravel the rejuvenation aspects of this unique ecosystem.}, }
@article {pmid31005411, year = {2019}, author = {Hollister, EB and Oezguen, N and Chumpitazi, BP and Luna, RA and Weidler, EM and Rubio-Gonzales, M and Dahdouli, M and Cope, JL and Mistretta, TA and Raza, S and Metcalf, GA and Muzny, DM and Gibbs, RA and Petrosino, JF and Heitkemper, M and Savidge, TC and Shulman, RJ and Versalovic, J}, title = {Leveraging Human Microbiome Features to Diagnose and Stratify Children with Irritable Bowel Syndrome.}, journal = {The Journal of molecular diagnostics : JMD}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jmoldx.2019.01.006}, pmid = {31005411}, issn = {1943-7811}, abstract = {Accurate diagnosis and stratification of children with irritable bowel syndrome (IBS) remain challenging. Given the central role of recurrent abdominal pain in IBS, we evaluated the relationships of pediatric IBS and abdominal pain with intestinal microbes and fecal metabolites using a comprehensive clinical characterization and multiomics strategy. Using rigorous clinical phenotyping, we identified preadolescent children (aged 7 to 12 years) with Rome III IBS (n = 23) and healthy controls (n = 22) and characterized their fecal microbial communities using whole-genome shotgun metagenomics and global unbiased fecal metabolomic profiling. Correlation-based approaches and machine learning algorithms identified associations between microbes, metabolites, and abdominal pain. IBS cases differed from controls with respect to key bacterial taxa (eg, Flavonifractor plautii and Lachnospiraceae bacterium 7_1_58FAA), metagenomic functions (eg, carbohydrate metabolism and amino acid metabolism), and higher-order metabolites (eg, secondary bile acids, sterols, and steroid-like compounds). Significant associations between abdominal pain frequency and severity and intestinal microbial features were identified. A random forest classifier built on metagenomic and metabolic markers successfully distinguished IBS cases from controls (area under the curve, 0.93). Leveraging multiple lines of evidence, intestinal microbes, genes/pathways, and metabolites were associated with IBS, and these features were capable of distinguishing children with IBS from healthy children. These multi-omics features, and their links to childhood IBS coupled with nutritional interventions, may lead to new microbiome-guided diagnostic and therapeutic strategies.}, }
@article {pmid31004827, year = {2019}, author = {Sung, CM and Lin, YF and Chen, KF and Ke, HM and Huang, HY and Gong, YN and Tsai, WS and Lu, MJ and Cheng, HT and Lin, CY and Kuo, CJ and Tsai, IJ and Hsieh, SY}, title = {Predicting clinical outcomes of cirrhosis patients with hepatic encephalopathy from the fecal microbiome.}, journal = {Cellular and molecular gastroenterology and hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jcmgh.2019.04.008}, pmid = {31004827}, issn = {2352-345X}, abstract = {BACKGROUND &amp; AIMS: Gut dysbiosis plays a role in hepatic encephalopathy (HE), while its relationship at the acute episode of overt HE (AHE), the disease progression and clinical outcomes remains unclear. We aimed to identify AHE-specific microbiome and its association to patients' outcomes.<br><br>METHODS: We profiled fecal microbiome changes for a cohort of 62 patients with cirrhosis and AHE i) before treatment, ii) 2-3 days after medication and iii) 2-3 months after recovery, and three control cohorts i) healthy individuals, patients with ii) compensated or iii) decompensated cirrhosis.<br><br>RESULTS: Comparison of the microbiome shift from compensated, decompensated cirrhosis, AHE to recovery revealed the AHE-specific gut-dysbiosis. The gut microbiome diversity was decreased during AHE, further reduced after medication, and only partially reversed during the recovery. The relative abundance of Bacteroidetes phylum in the microbiome decreased, whereas that of Firmicute, Proteobacteria and Actinobacteria increased in patients during AHE compared to those with compensated cirrhosis. A total of 70 operational taxonomic units (OTUs) were significantly different between AHE and decompensated cirrhosis abundances. Of them, the abundance of Veillonella parvula increased the most during AHE via a metagenomics recovery of the genomes. Moreover, the relative abundances of three (Alistipes, Bacteroides, Phascolarctobacterium) and five OTUs (Clostridium-XI, Bacteroides, Bacteroides, Lactobacillus, Clostridium-sedis) at AHE were respectively associated with HE recurrence and overall survival during the subsequent one-year follow-up.<br><br>CONCLUSIONS: AHE-specific gut OTUs were identified that may be involved in HE development and able to predict clinical outcomes, providing new strategies for the prevention and treatment of HE recurrence in patients with cirrhosis.}, }
@article {pmid31004622, year = {2019}, author = {You, HS and Lee, SH and Ok, YJ and Kang, HG and Sung, HJ and Lee, JY and Kang, SS and Hyun, SH}, title = {Influence of swabbing solution and swab type on DNA recovery from rigid environmental surfaces.}, journal = {Journal of microbiological methods}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.mimet.2019.04.011}, pmid = {31004622}, issn = {1872-8359}, abstract = {Determination of the metagenome has become an important component of forensic identification, which requires efficient environmental sampling techniques. Therefore, in this study, we compared the efficiency of sample collection using swabbing with cotton swabs and three types of medical swabs (S7, S22, S24) along with three different solutions: phosphate-buffered saline (PBS), 1% Tween 20 + 1% glycerol in PBS (TG), and GS commercial solution (Noble Bio, Hwaseong, Republic of Korea). Combinations of the three solutions with the three types of swabs were tested at different volumes (cotton swab, S7: 0, 30, 50, 70 μL; S22, S24: 0, 70, 100, 130 μL). Escherichia coli and Staphylococcus aureus were selected as representative environmental microbial samples, and the number of colony-forming units (CFUs), DNA concentration, and DNA copy numbers were compared across groups. The sampling process had a clear effect on the efficiency of extraction, which allowed for determination of a more efficient sample sampling method. In particular, cotton swabs showed 2-10-fold greater CFUs of both species than the medical swabs, and resulted in significantly greater amounts of extracted DNA. TG was found to be the most efficient solution for bacterial DNA extraction, with higher CFUs and DNA obtained than with the other three solutions at all volumes tested. This study highlights the need for a standardized sampling method that can be applied to all environmental samples, especially for microbial quantification, and provides valuable reference data for the efficient collection of environmental samples for metagenomic analyses in microbial-based forensic assessments.}, }
@article {pmid31002069, year = {2019}, author = {Forth, LF and Scholes, SFE and Pesavento, PA and Jackson, K and Mackintosh, A and Carson, A and Howie, F and Schlottau, K and Wernike, K and Pohlmann, A and Höper, D and Beer, M}, title = {Novel Picornavirus in Lambs with Severe Encephalomyelitis.}, journal = {Emerging infectious diseases}, volume = {25}, number = {5}, pages = {963-967}, doi = {10.3201/eid2505.181573}, pmid = {31002069}, issn = {1080-6059}, abstract = {Using metagenomic analysis, we identified a novel picornavirus in young preweaned lambs with neurologic signs associated with severe nonsuppurative encephalitis and sensory ganglionitis in 2016 and 2017 in the United Kingdom. In situ hybridization demonstrated intralesional neuronotropism of this virus, which was also detected in archived samples of similarly affected lambs (1998-2014).}, }
@article {pmid31001490, year = {2019}, author = {Hu, Y and Feng, Y and Wu, J and Liu, F and Zhang, Z and Hao, Y and Liang, S and Li, B and Li, J and Lv, N and Xu, Y and Zhu, B and Sun, Z}, title = {The Gut Microbiome Signatures Discriminate Healthy From Pulmonary Tuberculosis Patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {90}, doi = {10.3389/fcimb.2019.00090}, pmid = {31001490}, issn = {2235-2988}, abstract = {Cross talk occurs between the human gut and the lung through a gut-lung axis involving the gut microbiota. However, the signatures of the human gut microbiota after active Mycobacterium tuberculosis infection have not been fully understood. Here, we investigated changes in the gut microbiota in tuberculosis (TB) patients by shotgun sequencing the gut microbiomes of 31 healthy controls and 46 patients. We observed a dramatic changes in gut microbiota in tuberculosis patients as reflected by significant decreases in species number and microbial diversity. The gut microbiota of TB patients were mostly featured by the striking decrease of short-chain fatty acids (SCFAs)-producingbacteria as well as associated metabolic pathways. A classification model based on the abundance of three species, Haemophilus parainfluenzae, Roseburia inulinivorans, and Roseburia hominis, performed well for discriminating between healthy and diseased patients. Additionally, the healthy and diseased states can be distinguished by SNPs in the species of B. vulgatus. We present a comprehensive profile of changes in the microbiota in clinical TB patients. Our findings will shed light on the design of future diagnoses and treatments for M. tuberculosis infections.}, }
@article {pmid31001212, year = {2019}, author = {Sessou, P and Keisam, S and Tuikhar, N and Gagara, M and Farougou, S and Jeyaram, K}, title = {High-Throughput Illumina MiSeq Amplicon Sequencing of Yeast Communities Associated With Indigenous Dairy Products From Republics of Benin and Niger.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {594}, doi = {10.3389/fmicb.2019.00594}, pmid = {31001212}, issn = {1664-302X}, abstract = {Traditional Wagashi cheese and fermented cow milk are among the most popular dairy products appreciated by people from Benin, Niger, and the neighboring region. These products are the main source of protein in the diet of the low-income population in the region. The fermented milk is prepared by spontaneous fermentation without back-slopping. Whereas, the leaf extract of Calotropis procera is used for curdling the milk to prepare the soft Wagashi cheese. The present study aims to provide in-depth analysis of yeast communities associated with these traditional milk products by high-throughput Illumina MiSeq amplicon sequencing of internal transcribed spacer (ITS) region of fungal rRNA genes. A total of 60 samples, 20 samples of fermented milk each from Benin and Niger, and 20 samples of Wagashi cheese from Benin were used for analysis. The metagenomic investigation revealed that Kluyveromyces marxianus, Saccharomyces cerevisiae, Candida parapsilosis, and Sagenomella keratitidis were the predominant yeast species present in the traditional milk products. Furthermore, we noticed a high presence of K. marxianus (61.1% relative abundance) in the Wagashi cheese and S. cerevisiae (28.4% relative abundance) in the fermented milk of Niger. The presence of potential pathogenic yeast C. parapsilosis and S. keratitidis in these African milk products calls for further investigation to assess their safety. The predominant yeast K. marxianus and S. cerevisiae, recognized with generally regarded as safe (GRAS) status, could be further selected as starter culture along with lactic acid bacteria for developing controlled fermentation processes with enhanced product quality and safety.}, }
@article {pmid31000700, year = {2019}, author = {Dong, X and Greening, C and Rattray, JE and Chakraborty, A and Chuvochina, M and Mayumi, D and Dolfing, J and Li, C and Brooks, JM and Bernard, BB and Groves, RA and Lewis, IA and Hubert, CRJ}, title = {Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1816}, doi = {10.1038/s41467-019-09747-0}, pmid = {31000700}, issn = {2041-1723}, abstract = {The lack of microbial genomes and isolates from the deep seabed means that very little is known about the ecology of this vast habitat. Here, we investigate energy and carbon acquisition strategies of microbial communities from three deep seabed petroleum seeps (3 km water depth) in the Eastern Gulf of Mexico. Shotgun metagenomic analysis reveals that each sediment harbors diverse communities of chemoheterotrophs and chemolithotrophs. We recovered 82 metagenome-assembled genomes affiliated with 21 different archaeal and bacterial phyla. Multiple genomes encode enzymes for anaerobic oxidation of aliphatic and aromatic compounds, including those of candidate phyla Aerophobetes, Aminicenantes, TA06 and Bathyarchaeota. Microbial interactions are predicted to be driven by acetate and molecular hydrogen. These findings are supported by sediment geochemistry, metabolomics, and thermodynamic modelling. Overall, we infer that deep-sea sediments experiencing thermogenic hydrocarbon inputs harbor phylogenetically and functionally diverse communities potentially sustained through anaerobic hydrocarbon, acetate and hydrogen metabolism.}, }
@article {pmid31000555, year = {2019}, author = {Retallack, H and Clubb, S and DeRisi, JL}, title = {Genome Sequence of a Divergent Avian Metapneumovirus from a Monk Parakeet (Myiopsitta monachus).}, journal = {Microbiology resource announcements}, volume = {8}, number = {16}, pages = {}, doi = {10.1128/MRA.00284-19}, pmid = {31000555}, issn = {2576-098X}, abstract = {Here, we report the coding-complete genome sequence of an avian metapneumovirus from a monk parakeet (Myiopsitta monachus), identified by metagenomic next-generation sequencing during an investigation into a disease outbreak in a captive parrot breeding facility. Based on divergence from known strains, this sequence represents a new subgroup of avian metapneumovirus.}, }
@article {pmid31000554, year = {2019}, author = {Šimić, I and Zorec, TM and Krešić, N and Poljak, M and Bedeković, T and Lojkić, I}, title = {Novel Circo-Like Virus Detected in a Croatian Bat Population.}, journal = {Microbiology resource announcements}, volume = {8}, number = {16}, pages = {}, doi = {10.1128/MRA.00280-19}, pmid = {31000554}, issn = {2576-098X}, abstract = {Viral metagenomics analysis of samples from bats has been carried out as part of bat rabies surveillance in Croatia. Here, we report the complete genome sequence of a novel circo-like virus isolated from a sample of Miniopterus schreibersii bat guano determined by Illumina next-generation sequencing.}, }
@article {pmid31000244, year = {2019}, author = {Rocchetti, G and Senizza, A and Gallo, A and Lucini, L and Giuberti, G and Patrone, V}, title = {In vitro large intestine fermentation of gluten-free rice cookies containing alfalfa seed (Medicago sativa L.) flour: A combined metagenomic/metabolomic approach.}, journal = {Food research international (Ottawa, Ont.)}, volume = {120}, number = {}, pages = {312-321}, doi = {10.1016/j.foodres.2019.03.003}, pmid = {31000244}, issn = {1873-7145}, abstract = {Alfalfa seed flour (ASF) at different inclusion levels (0% as control, 30% and 45% w/w) was used to prepare rice flour-based gluten-free (GF) cookies (CK). Samples underwent a simulated in vitro digestion and fermentation process. The comprehensive changes in the phenolic profiles were evaluated during 48 h of fermentation by means of untargeted UHPLC-QTOF mass spectrometry followed by multivariate statistics. Furthermore, the modifications in microbial profile and the production of short chain fatty acids (SCFA) were investigated. Cookies presenting 30% (30-CK) and 45% (45-CK) ASF possessed the greater total phenolic content when compared to the control, being 0.42 and 0.56 mg/g versus 0.15 mg/g, respectively. The orthogonal projection to latent structure discriminant analysis, applied to untargeted metabolomics-based data, showed a clear modulation of the profile in phenolic metabolites over time (from 8 up to 48 h of in vitro fermentation). In this regard, the in vitro fermentation of 30-CK and 45-CK resulted in the maximum increase in lignans and phenolic acids, whose bioaccessibility at 24 h of in vitro fermentation was 16.2% and 12.2%, respectively. In addition, the metagenomic sequencing approach allowed to identify in Clostridiaceae, Ruminococcaceae, Lachnospiraceae and Streptococcaceae the most represented bacterial populations during the in vitro fermentation. A greater total SCFA production (p < .05) was recorded overtime for all ASF-enriched cookies when compared to the control. Therefore, ASF proved to be an excellent alternative to common non-wheat cereal flours (such as pseudocereals or legumes) for improving possible health-promoting properties in GF cookie formulation.}, }
@article {pmid30999885, year = {2019}, author = {Fortune, B and Mhlongo, S and van Zyl, LJ and Huddy, R and Smart, M and Trindade, M}, title = {Characterisation of three novel α-L-arabinofuranosidases from a compost metagenome.}, journal = {BMC biotechnology}, volume = {19}, number = {1}, pages = {22}, doi = {10.1186/s12896-019-0510-1}, pmid = {30999885}, issn = {1472-6750}, support = {69116//National Research Foundation/ ; }, abstract = {BACKGROUND: The importance of the accessory enzymes such as α-L-arabinofuranosidases (AFases) in synergistic interactions within cellulolytic mixtures has introduced a paradigm shift in the search for hydrolytic enzymes. The aim of this study was to characterize novel AFase genes encoding enzymes with differing temperature optima and thermostabilities for use in hydrolytic cocktails.<br><br>RESULTS: Three fosmids, pFos-H4, E3 and D3 were selected from the cloned metagenome of high temperature compost, expressed in Escherichia coli and subsequently purified to homogeneity from cell lysate. All the AFases were clustered within the GH51 AFase family and shared a homo-hexameric structure. Both AFase-E3 and H4 showed optimal activity at 60 °C while AFase-D3 had unique properties as it showed optimal activity at 25 °C as well as the ability to maintain substantial activity at temperatures as high as 90 °C. However, AFase-E3 was the most thermostable amongst the three AFases showing full activity even at 70 °C. The maximum activity was observed at a pH profile between pH 4.0-6.0 for all three AFases with optimal activity for AFase H4, D3 and E3 at pH 5.0, 4.5 and 4.0, respectively. All the AFases showed KM range between 0.31 mM and 0.43 mM, Kcat range between 131 s- 1 and 219 s- 1 and the specific activity for AFase-H4, AFases-E3 and was 143, 228 and 175 U/mg, respectively. AFases-E3 and D3 displayed activities against pNP-β-L-arabinopyranoside and pNP-β-L-mannopyranoside respectively, and both hydrolysed pNP-β-D-glucopyranoside.<br><br>CONCLUSION: All three AFases displayed different biochemical characteristics despite all showing conserved overall structural similarity with typical domains of AFases belonging to GH51 family. The hydrolysis of cellobiose by a GH51 family AFase is demonstrated for the first time in this study.}, }
@article {pmid30997495, year = {2019}, author = {Hornung, BVH and Zwittink, RD and Kuijper, EJ}, title = {Issues and current standards of controls in microbiome research.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {5}, pages = {}, doi = {10.1093/femsec/fiz045}, pmid = {30997495}, issn = {1574-6941}, abstract = {Good scientific practice is important in all areas of science. In recent years this has gained more and more attention, especially considering the 'scientific reproducibility crisis'. While most researchers are aware of the issues with good scientific practice, not all of these issues are necessarily clear, and the details can be very complicated. For many years it has been accepted to perform and publish sequencing based microbiome studies without including proper controls. Although in recent years more scientists realize the necessity of implementing controls, this poses a problem due to the complexity of the field. Another concern is the inability to properly interpret the information gained from controls in microbiome studies. Here, we will discuss these issues and provide a comprehensive overview of problematic points regarding controls in microbiome research, and of the current standards in this area.}, }
@article {pmid30997302, year = {2019}, author = {Verma, S and Kumar, R and Meghwanshi, GK}, title = {Identification of new members of alkaliphilic lipases in archaea and metagenome database using reconstruction of ancestral sequences.}, journal = {3 Biotech}, volume = {9}, number = {5}, pages = {165}, doi = {10.1007/s13205-019-1693-9}, pmid = {30997302}, issn = {2190-572X}, abstract = {The application of bioinformatics in lipase research has the potential to discover robust members from different genomic/metagenomic databses. In this study, we explored the diversity and distribution of alkaliphilic lipases in archaea domain and metagenome data sets through phylogenetic survey. Reconstructed ancestral sequence of alkaphilic lipase was used to search the homologous alkaliphilic lipases among the archaea and metagenome public databases. Our investigation revealed a total 21 unique sequences of new alkaliphilic lipases in the archaeal and environmental metagenomic protein databases that shared significant sequence similarity to the bacterial alkaliphilic lipases. Most of the identified new members of alkaliphilic lipases belong to class Haloarchaea. The searched list of homologs also comprised of one characterized lipase from alkalohyperthermophilic Archaeoglobus fulgidus. All the newly identified alkaliphilic lipase members showed conserved pentapeptide [X-His-Ser-X-Gly] motif, a key feature of lipase family. Furthermore, detailed analysis of all these new sequences showed homology either with thermostable or alkalophilic lipases. The reconstructed ancestral sequence-based searches increased the sensitivity and efficacies to detect remotely homologous sequences. We hypothesize that this study can enrich our current knowledge on lipases in designing more potential thermo-alkaliphilic lipases for industrial applications.}, }
@article {pmid30997301, year = {2019}, author = {Haldar, S and Nazareth, SW}, title = {Diversity of fungi from mangrove sediments of Goa, India, obtained by metagenomic analysis using Illumina sequencing.}, journal = {3 Biotech}, volume = {9}, number = {5}, pages = {164}, doi = {10.1007/s13205-019-1698-4}, pmid = {30997301}, issn = {2190-572X}, abstract = {The fungal composition, abundance and diversity of the mangrove sediments from the Mandovi and Zuari estuaries, Goa, using paired-end Illumina sequencing, hitherto unexplored by a metagenomic approach, indicated that though the types of fungal phyla were similar between the two sediments, the abundance of the species was significantly different between them (p value < 0.005). Basidiomycota and Ascomycota were the two major phyla which were sub-divided into eighteen classes, families, orders, genera and species and one unassigned group in both the sediments. The top five classes observed were Agaricomycetes, Sordariomycetes, Saccharomycetes, Dothideomycetes and Eurotiomycetes from both the sediments. The diversity analysis based on the observed fungal species richness (Chao 1 for Mandovi were 614 and 714.7 while for Zuari were 665 and 771.2) revealed that Zuari sediment was taxonomically rich, indicating these to be potent candidates for bioremediation and a rich repository for biotechnologically important fungi. This is a first report on diversity of fungi from mangrove sediments of Goa using metagenomic studies.}, }
@article {pmid30997155, year = {2019}, author = {Mahar, JE and Hall, RN and Shi, M and Mourant, R and Huang, N and Strive, T and Holmes, EC}, title = {The discovery of three new hare lagoviruses reveals unexplored viral diversity in this genus.}, journal = {Virus evolution}, volume = {5}, number = {1}, pages = {vez005}, doi = {10.1093/ve/vez005}, pmid = {30997155}, issn = {2057-1577}, abstract = {Our knowledge of mammalian viruses has been strongly skewed toward those that cause disease in humans and animals. However, recent metagenomic studies indicate that most apparently healthy organisms carry viruses, and that these seemingly benign viruses may comprise the bulk of virus diversity. The bias toward studying viruses associated with overt disease is apparent in the lagoviruses (family Caliciviridae) that infect rabbits and hares: although most attention has been directed toward the highly pathogenic members of this genus-rabbit haemorrhagic disease virus and European brown hare syndrome virus-a number of benign lagoviruses have also been identified. To determine whether wild European brown hares in Australia might also carry undetected benign viruses, we used a meta-transcriptomics approach to explore the gut and liver RNA viromes of these invasive animals. This led to the discovery of three new lagoviruses. While one was only detected in a single hare, the other two viruses were detected in 20 per cent of all animals tested. All three viruses were most closely related to other hare lagoviruses, but were phylogenetically distinct from both known viruses and from each other, indicating that lagoviruses have circulated for longer than previously assumed. Their evolution was also characterised by complex recombination events. Mapping mutations onto the lagovirus phylogeny revealed no amino acid changes that were consistently associated with virulence phenotype. Overall, our study points to extensive unsampled diversity in this genus, such that additional metagenomic studies are needed to fill gaps in the lagovirus phylogeny and better understand the evolutionary history of this important group of mammalian viruses.}, }
@article {pmid30995949, year = {2019}, author = {Fessler, J and Matson, V and Gajewski, TF}, title = {Exploring the emerging role of the microbiome in cancer immunotherapy.}, journal = {Journal for immunotherapy of cancer}, volume = {7}, number = {1}, pages = {108}, doi = {10.1186/s40425-019-0574-4}, pmid = {30995949}, issn = {2051-1426}, support = {R35 CA210098//National Institutes of Health (US)/ ; T32 CA009594//National Cancer Institute/ ; Jules L. Plangere Jr. Family Foundation Professorship in Cancer Immunotherap//American Cancer Society (US)/ ; }, abstract = {The activity of the commensal microbiota significantly impacts human health and has been linked to the development of many diseases, including cancer. Gnotobiotic animal models have shown that the microbiota has many effects on host physiology, including on the development and regulation of immune responses. More recently, evidence has indicated that the microbiota can more specifically influence the outcome of cancer immunotherapy. Therapeutic interventions to optimize microbiota composition to improve immunotherapy outcomes have shown promise in mouse studies. Ongoing endeavors are translating these pre-clinical findings to early stage clinical testing. In this review we summarize 1) basic methodologies and considerations for studies of host-microbiota interactions; 2) experimental evidence towards a causal link between gut microbiota composition and immunotherapeutic efficacy; 3) possible mechanisms governing the microbiota-mediated impact on immunotherapy efficacy. Moving forward, there is need for a deeper understanding of the underlying biological mechanisms that link specific bacterial strains to host immunity. Integrating microbiome effects with other tumor and host factors regulating immunotherapy responsiveness versus resistance could facilitate optimization of therapeutic outcomes.}, }
@article {pmid30995938, year = {2019}, author = {Le Doujet, T and De Santi, C and Klemetsen, T and Hjerde, E and Willassen, NP and Haugen, P}, title = {Closely-related Photobacterium strains comprise the majority of bacteria in the gut of migrating Atlantic cod (Gadus morhua).}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {64}, doi = {10.1186/s40168-019-0681-y}, pmid = {30995938}, issn = {2049-2618}, abstract = {BACKGROUND: The population of Atlantic cod (Gadus morhua), also known as Northeast Arctic cod, migrating Atlantic cod, or simply &quot;skrei,&quot; lives mainly in the Barents Sea and Svalbard waters and migrates in annual cycles to the Norwegian coast in order to spawn eggs during late winter. It is the world's largest population of Atlantic cod, and the population is distinct from the Norwegian coastal cod (or &quot;fjord&quot; cod). Despite the biological, economic, and cultural importance of migrating Atlantic cod, current knowledge on the associated microbiota is very limited. Using shotgun metagenomics and metaproteomics approaches, we present here the gut microbiota, metagenome-assembled genomes (MAGs) of the most abundant bacterial species, DNA-based functional profile, and the metaproteome of Atlantic cod specimens caught at a spawning area in an open ocean outside of Tromsø, Norway.<br><br>RESULTS: Our analyses identified 268 bacterial families in DNA isolated from feces of 6 individual migrating Atlantic cod. The most abundant family was Vibrionaceae (52%; 83% if unclassified reads are excluded), with Photobacterium (genus) representing the vast majority. The recovery of metagenome-assembled genomes provided further details and suggests that several closely related Photobacterium strains from the Photobacterium phosphoreum clade are the most abundant. A genomic-based functional profiling showed that the most abundant functional subsystems are &quot;Carbohydrates&quot;; &quot;Amino Acids and Derivatives&quot;; &quot;Protein Metabolism&quot;; &quot;Cofactors, Vitamins, Prosthetic, Groups, and Pigments&quot;; and &quot;DNA Metabolism,&quot; which is in agreement with other studies of gut microbiomes of marine organisms. Finally, the MS-based metaproteomic dataset revealed that the functional category &quot;Protein Metabolism&quot; is highly overrepresented (3×) when compared to the genome-based functional profile, which shows that ribosomal proteins are rich in the bacterial cytosol.<br><br>CONCLUSION: We present here the first study of bacterial diversity of the gut of migrating Atlantic cod using shotgun sequencing and metagenome-assembled genomes (MAGs). The most abundant bacteria belong to the Photobacterium genus (Vibrionaceae family). We also constructed functional profiles of the gut microbiome. These may be used in future studies as a platform for mining of commercially interesting cold-active enzymes.}, }
@article {pmid30994912, year = {2019}, author = {Kucherov, G}, title = {Evolution of biosequence search algorithms: a brief survey.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btz272}, pmid = {30994912}, issn = {1367-4811}, abstract = {MOTIVATION: Although modern high-throughput biomolecular technologies produce various types of data, biosequence data remains at the core of bioinformatic analyses. However, computational techniques for dealing with this data evolved dramatically.<br><br>RESULTS: In this bird's-eye review, we overview the evolution of main algorithmic techniques for comparing and searching biological sequences. We highlight key algorithmic ideas emerged in response to several interconnected factors: shifts of biological analytical paradigm, advent of new sequencing technologies, and a substantial increase in size of the available data. We discuss the expansion of alignment-free techniques coming to replace alignment-based algorithms in large-scale analyses. We further emphasize recently emerged and growing applications of sketching methods which support comparison of massive datasets, such as metagenomics samples. Finally, we focus on the transition to population genomics and outline associated algorithmic challenges.}, }
@article {pmid30994668, year = {2019}, author = {Li, L and Guo, WL and Zhang, W and Xu, JX and Qian, M and Bai, WD and Zhang, YY and Rao, PF and Ni, L and Lv, XC}, title = {Grifola frondosa polysaccharides ameliorate lipid metabolic disorders and gut microbiota dysbiosis in high-fat diet fed rats.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/c9fo00075e}, pmid = {30994668}, issn = {2042-650X}, abstract = {The purpose of this study was to assess the potential effects of polysaccharides from edible mushroom Grifola frondosa (GFP) on lipid metabolic disorders and gut microbiota dysbiosis, and elucidate their possible regulatory mechanisms on lipid and cholesterol metabolism in high-fat diet (HFD)-exacerbated hyperlipidemic and hypercholesterolemic rats. Results showed that oral administration of GFP markedly alleviated dyslipidaemia through decreasing the serum levels of total triglycerides, total cholesterol, and free fatty acids, and significantly suppressing hepatic lipid accumulation and steatosis. Besides, the excretion of fecal bile acids was also promoted by oral administration of GFP. Metagenomic analysis revealed that GFP supplementation (400 mg kg-1 day-1) resulted in significant structure changes on gut microbiota in HFD-fed rats, in particular modulating the relative abundance of functionally relevant microbial phylotypes compared with the HFD group. Key microbial phylotypes responding to GFP intervention were identified to strongly correlate with the lipid metabolism disorder associated parameters using the correlation network based on Spearman's correlation coefficient. Serum and hepatic lipid profiles were found positively correlated with Clostridium-XVIII, Butyricicoccus and Turicibacter, but negatively correlated with Helicobater, Intestinimonas, Barnesiella, Parasutterella, Ruminococcus and Flavonifracter. Moreover, GFP treatment (400 mg kg-1 day-1) regulated the mRNA expression levels of the genes responsible for hepatic lipid and cholesterol metabolism. Oral supplementation of GFP markedly increased the mRNA expression of cholesterol 7α-hydroxylase (CYP7A1) and bile salt export pump (BSEP), suggesting an enhancement of bile acid (BA) synthesis and excretion from the liver. These findings illustrated that GFP could ameliorate lipid metabolic disorders through modulating specific gut microbial phylotypes and regulating hepatic lipid and cholesterol metabolism related genes, and therefore could be used as a potential functional food ingredient for the prevention or treatment of hyperlipidemia.}, }
@article {pmid30994187, year = {2019}, author = {Wang, T and Yang, C and Zhao, H}, title = {Prediction analysis for microbiome sequencing data.}, journal = {Biometrics}, volume = {}, number = {}, pages = {}, doi = {10.1111/biom.13061}, pmid = {30994187}, issn = {1541-0420}, support = {11601326//National Natural Science Foundation of China/ ; 2018YFC0910500//National Key R&amp;D Program of China/ ; 2017SHZDZX01//Shanghai Municipal Science and Technology Major Project/ ; //Neil Shen's SJTU Medical Research Fund/ ; 12316116//Hong Kong Research Grant Council/ ; 22302815//Hong Kong Research Grant Council/ ; 12301417//Hong Kong Research Grant Council/ ; 16307818//Hong Kong Research Grant Council/ ; IGN17SC02//Initiation Grant from University Grants Committee/ ; R9405//Hong Kong University of Science and Technology/ ; }, abstract = {One goal of human microbiome studies is to relate host traits with human microbiome compositions. The analysis of microbial community sequencing data presents great statistical challenges, especially when the samples have different library sizes and the data are overdispersed with many zeros. To address these challenges, we introduce a new statistical framework, called predictive analysis in metagenomics via inverse regression (PAMIR), to analyze microbiome sequencing data. Within this framework, an inverse regression model is developed for overdispersed microbiota counts given the trait, and then a prediction rule is constructed by taking advantage of the dimension-reduction structure in the model. An efficient Monte Carlo expectation-maximization algorithm is proposed for maximum likelihood estimation. The method is further generalized to accommodate other types of covariates. We demonstrate the advantages of PAMIR through simulations and two real data examples.}, }
@article {pmid30993331, year = {2019}, author = {Makarova, KS and Karamycheva, S and Shah, SA and Vestergaard, G and Garrett, RA and Koonin, EV}, title = {Predicted highly derived class 1 CRISPR-Cas system in Haloarchaea containing diverged Cas5 and Cas7 homologs but no CRISPR array.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnz079}, pmid = {30993331}, issn = {1574-6968}, abstract = {Screening of genomic and metagenomic databases for new variants of CRISPR-Cas systems increasingly results in the discovery of derived variants that do not seem to possess the interference capacity and are implicated in functions distinct from adaptive immunity. We describe an extremely derived putative class 1 CRISPR-Cas system that is present in many Halobacteria and consists of distant homologs of the Cas5 and Cas7 protein along with an uncharacterized conserved protein and various nucleases. We hypothesize that, although this system lacks typical CRISPR effectors or a CRISPR array, it functions as a RNA-dependent defense mechanism that, unlike other derived CRISPR-Cas, utilizes alternative nucleases to cleave invader genomes.}, }
@article {pmid30993316, year = {2019}, author = {Chen, S and Chen, Y and Sun, F and Waterman, MS and Zhang, X}, title = {A new statistic for efficient detection of repetitive sequences.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btz262}, pmid = {30993316}, issn = {1367-4811}, abstract = {MOTIVATION: Detecting sequences containing repetitive regions is a basic bioinformatics task with many applications. Several methods have been developed for various types of repeat detection tasks. An efficient generic method for detecting most types of repetitive sequences is still desirable. Inspired by the excellent properties and successful applications of the D2 family of statistics in comparative analyses of genomic sequences, we developed a new statistic D2R that can efficiently discriminate sequences with or without repetitive regions.<br><br>RESULTS: Using the statistic, we developed an algorithm of linear time and space complexity for detecting most types of repetitive sequences in multiple scenarios, including finding candidate CRISPR regions from bacterial genomic or metagenomics sequences. Simulation and real data experiments show that the method works well on both assembled sequences and unassembled short reads. The codes are available at https://github.com/XuegongLab/D2R_codes under GPL 3.0 license.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid30993253, year = {2019}, author = {Getz, TM and Hoffman, GS and Padmanabhan, R and Villa-Forte, A and Roselli, EE and Blackstone, E and Johnston, D and Pettersson, G and Soltesz, E and Svensson, LG and Calabrese, LH and Clifford, AH and Eng, C}, title = {Microbiomes of Inflammatory Thoracic Aortic Aneurysms Due to Giant Cell Arteritis and Clinically Isolated Aortitis Differ From Those of Non-Inflammatory Aneurysms.}, journal = {Pathogens &amp; immunity}, volume = {4}, number = {1}, pages = {105-123}, doi = {10.20411/pai.v4i1.269}, pmid = {30993253}, issn = {2469-2964}, abstract = {Objective: We sought to characterize microbiomes of thoracic aortas from patients with non-infectious aortitis due to giant cell arteritis (GCA) and clinically isolated aortitis (CIA) and to compare them to non-inflammatory aorta aneurysm controls. We also compared microbiomes from concurrently processed and separately reported temporal arteries (TA) and aortas.<br><br>Methods: From 220 prospectively enrolled patients undergoing surgery for thoracic aorta aneurysm, 49 were selected. Inflammatory and non-inflammatory cases were selected based on ability to match for age (+/-10 years), gender, and race. Biopsies were collected under aseptic conditions and snap-frozen. Taxonomic classification of bacterial sequences was performed to the genus level and relative abundances were calculated. Microbiome differential abundances were analyzed by principal coordinates analysis.<br><br>Results: Forty-nine patients with thoracic aortic aneurysms (12 CIA, 14 GCA, 23 non-inflammatory aneurysms) were enrolled. Alpha (P=0.018) and beta (P=0.024) diversity differed between specimens from aortitis cases and controls. There were no significant differences between CIA and GCA (P>0.7). The largest differential abundances between non-infectious aortitis and non-inflammatory control samples included Enterobacteriaceae, Phascolarctobacterium, Acinetobactor, Klebsiella, and Prevotella. Functional metagenomic predictions with PICRUSt revealed enrichment of oxidative phosphorylation and porphyrin metabolism pathways and downregulation of transcription factor pathways in aortitis compared to controls. Microbiomes of aortic samples differed significantly from temporal artery samples from a companion study, in both control and GCA groups (P=0.0002).<br><br>Conclusion: Thoracic aorta aneurysms, far from being sterile, contain unique microbiomes that differ from those found in temporal arteries. The aorta microbiomes are most similar between aneurysms that were associated with inflammation, GCA, and CIA, but differed from those associated with non-inflammatory etiologies. These findings are promising in that they indicate that microbes may play a role in the pathogenesis of aortitis-associated aneurysms or non-inflammatory aneurysms by promoting or protecting against inflammation. However, we cannot rule out that these changes are related to alterations in tissue substrate that favor secondary changes in microbial communities.}, }
@article {pmid30993039, year = {2019}, author = {Garretto, A and Hatzopoulos, T and Putonti, C}, title = {virMine: automated detection of viral sequences from complex metagenomic samples.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6695}, doi = {10.7717/peerj.6695}, pmid = {30993039}, issn = {2167-8359}, abstract = {Metagenomics has enabled sequencing of viral communities from a myriad of different environments. Viral metagenomic studies routinely uncover sequences with no recognizable homology to known coding regions or genomes. Nevertheless, complete viral genomes have been constructed directly from complex community metagenomes, often through tedious manual curation. To address this, we developed the software tool virMine to identify viral genomes from raw reads representative of viral or mixed (viral and bacterial) communities. virMine automates sequence read quality control, assembly, and annotation. Researchers can easily refine their search for a specific study system and/or feature(s) of interest. In contrast to other viral genome detection tools that often rely on the recognition of viral signature sequences, virMine is not restricted by the insufficient representation of viral diversity in public data repositories. Rather, viral genomes are identified through an iterative approach, first omitting non-viral sequences. Thus, both relatives of previously characterized viruses and novel species can be detected, including both eukaryotic viruses and bacteriophages. Here we present virMine and its analysis of synthetic communities as well as metagenomic data sets from three distinctly different environments: the gut microbiota, the urinary microbiota, and freshwater viromes. Several new viral genomes were identified and annotated, thus contributing to our understanding of viral genetic diversity in these three environments.}, }
@article {pmid30992716, year = {2019}, author = {Liu, H and Guo, M and Jiang, Y and Cao, Y and Qian, Q and He, X and Huang, K and Zhang, J and Xu, W}, title = {Diagnosing and tracing the pathogens of infantile infectious diarrhea by amplicon sequencing.}, journal = {Gut pathogens}, volume = {11}, number = {}, pages = {12}, doi = {10.1186/s13099-019-0292-y}, pmid = {30992716}, issn = {1757-4749}, abstract = {Background: Metagenomic methods have been widely applied to study the relationship between gut microbiota and human health. To test whether metagenomic amplicon sequencing could be an effective method to diagnose and trace the pathogens of infantile infectious diarrhea, the fecal samples of 20 diarrheic and 13 healthy infants were collected. After 16S rDNA amplicon sequencing, diversity analyses were carried out. The relationship between the pathogens of the gut microbiota and geography of patients was analyzed.<br><br>Results: The diversity of the gut microbiota in diarrheic infants was significantly lower than that of the gut microbiota in healthy ones and that, the composition of gut microbiota in the diarrheic group was significantly different than that of the gut microbiota in the healthy group. The results also indicated that in some of the patients, the amounts of Escherichia coli were significantly increased in the diarrheic infants, which was in agreement with the result of the qPCR analysis. Using a geographical map, we found some patterns between pathogen source and geographical location. This is helpful for an early warning of the disease.<br><br>Conclusions: The method of using high-throughput DNA sequencing and a comprehensive and deep data analysis can be a new strategy to detect and trace pathogens in infantile infectious diarrhea.Trial registration Diagnosing and tracing the pathogens of infantile infectious diarrhea by amplicon sequencing, ChiCTR-DDD-1701088, Registered 16 March 2017-Retrospectively registered, http://www.chictr.org.cn/showproj.aspx?proj=18477.}, }
@article {pmid30992508, year = {2019}, author = {Yang, Y and Zhang, S and Li, N and Chen, H and Jia, H and Song, X and Liu, G and Ni, C and Wang, Z and Shao, H and Zhang, S}, title = {Metagenomic insights into effects of wheat straw compost fertiliser application on microbial community composition and function in tobacco rhizosphere soil.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {6168}, doi = {10.1038/s41598-019-42667-z}, pmid = {30992508}, issn = {2045-2322}, abstract = {The application of fertilisers incorporated with plant residues improves nutrient availability in soils, which shifts the microbial community structure and favours plant growth. To understand the impact of wheat straw compost fertiliser on soil properties and microbial community structure, tobacco planting soils were treated with four different fertilisers using varied amounts of straw compost fertiliser and a no fertiliser control (CK). Results showed that different fertilisers affected available soil nutrient contents differently. Treatment of tobacco soil with application of combined chemical fertiliser/wheat straw compost led to improved soil chemical properties, and increased soil organic matter and available phosphorus and potassium content. Treatment with FT1 200 kg/mu straw was found to be superior in improving soil fertility. Metagenomic DNA sequencing revealed that different fertiliser treatments resulted in changes in the microbial community composition. In soil treated with FT2 300 kg/mu straw for 60 days, the predominant bacterial phyla were Proteobacteria, Actinobacteria, and Verrucomicrobia, whereas Cyanobacteria, Basidiomycota, and Chlorophyta were found in high abundance in soil samples treated with FT1 200 kg/mu straw for 30 days. Functional annotation of metagenomic sequences revealed that genes involved in metabolic pathways were among the most abundant type. PCoA analysis clearly separated the samples containing straw compost fertiliser and chemical fertiliser. A significant correlation between soil properties and the dominant phyla was identified.}, }
@article {pmid30992476, year = {2019}, author = {Couto, N and Schuele, L and Raangs, EC and Machado, MP and Mendes, CI and Jesus, TF and Chlebowicz, M and Rosema, S and Ramirez, M and Carriço, JA and Autenrieth, IB and Friedrich, AW and Peter, S and Rossen, JW}, title = {Author Correction: Critical steps in clinical shotgun metagenomics for the concomitant detection and typing of microbial pathogens.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {6406}, doi = {10.1038/s41598-019-42134-9}, pmid = {30992476}, issn = {2045-2322}, abstract = {A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.}, }
@article {pmid30992350, year = {2019}, author = {Cobián Güemes, AG and Lim, YW and Quinn, RA and Conrad, DJ and Benler, S and Maughan, H and Edwards, R and Brettin, T and Cantú, VA and Cuevas, D and Hamidi, R and Dorrestein, P and Rohwer, F}, title = {Cystic Fibrosis Rapid Response: Translating Multi-omics Data into Clinically Relevant Information.}, journal = {mBio}, volume = {10}, number = {2}, pages = {}, doi = {10.1128/mBio.00431-19}, pmid = {30992350}, issn = {2150-7511}, abstract = {Pulmonary exacerbations are the leading cause of death in cystic fibrosis (CF) patients. To track microbial dynamics during acute exacerbations, a CF rapid response (CFRR) strategy was developed. The CFRR relies on viromics, metagenomics, metatranscriptomics, and metabolomics data to rapidly monitor active members of the viral and microbial community during acute CF exacerbations. To highlight CFRR, a case study of a CF patient is presented, in which an abrupt decline in lung function characterized a fatal exacerbation. The microbial community in the patient's lungs was closely monitored through the multi-omics strategy, which led to the identification of pathogenic shigatoxigenic Escherichia coli (STEC) expressing Shiga toxin. This case study illustrates the potential for the CFRR to deconstruct complicated disease dynamics and provide clinicians with alternative treatments to improve the outcomes of pulmonary exacerbations and expand the life spans of individuals with CF.IMPORTANCE Proper management of polymicrobial infections in patients with cystic fibrosis (CF) has extended their life span. Information about the composition and dynamics of each patient's microbial community aids in the selection of appropriate treatment of pulmonary exacerbations. We propose the cystic fibrosis rapid response (CFRR) as a fast approach to determine viral and microbial community composition and activity during CF pulmonary exacerbations. The CFRR potential is illustrated with a case study in which a cystic fibrosis fatal exacerbation was characterized by the presence of shigatoxigenic Escherichia coli The incorporation of the CFRR within the CF clinic could increase the life span and quality of life of CF patients.}, }
@article {pmid30992304, year = {2019}, author = {Miller, S and Naccache, SN and Samayoa, E and Messacar, K and Arevalo, S and Federman, S and Stryke, D and Pham, E and Fung, B and Bolosky, WJ and Ingebrigtsen, D and Lorizio, W and Paff, SM and Leake, JA and Pesano, R and DeBiasi, R and Dominguez, S and Chiu, CY}, title = {Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid.}, journal = {Genome research}, volume = {}, number = {}, pages = {}, doi = {10.1101/gr.238170.118}, pmid = {30992304}, issn = {1549-5469}, abstract = {Metagenomic next-generation sequencing (mNGS) for pan-pathogen detection has been successfully tested in proof-of-concept case studies in patients with acute illness of unknown etiology but to date has been largely confined to research settings. Here, we developed and validated a clinical mNGS assay for diagnosis of infectious causes of meningitis and encephalitis from cerebrospinal fluid (CSF) in a licensed microbiology laboratory. A customized bioinformatics pipeline, SURPI+, was developed to rapidly analyze mNGS data, generate an automated summary of detected pathogens, and provide a graphical user interface for evaluating and interpreting results. We established quality metrics, threshold values, and limits of detection of 0.2-313 genomic copies or colony forming units per milliliter for each representative organism type. Gross hemolysis and excess host nucleic acid reduced assay sensitivity; however, spiked phages used as internal controls were reliable indicators of sensitivity loss. Diagnostic test accuracy was evaluated by blinded mNGS testing of 95 patient samples, revealing 73% sensitivity and 99% specificity compared to original clinical test results, and 81% positive percent agreement and 99% negative percent agreement after discrepancy analysis. Subsequent mNGS challenge testing of 20 positive CSF samples prospectively collected from a cohort of pediatric patients hospitalized with meningitis, encephalitis, and/or myelitis showed 92% sensitivity and 96% specificity relative to conventional microbiological testing of CSF in identifying the causative pathogen. These results demonstrate the analytic performance of a laboratory-validated mNGS assay for pan-pathogen detection, to be used clinically for diagnosis of neurological infections from CSF.}, }
@article {pmid30992161, year = {2019}, author = {Brussel, A and Brack, K and Muth, E and Zirwes, R and Cheval, J and Hebert, C and Charpin, JM and Marinaci, A and Flan, B and Ruppach, H and Beurdeley, P and Eloit, M}, title = {Use of a new RNA next generation sequencing approach for the specific detection of virus infection in cells.}, journal = {Biologicals : journal of the International Association of Biological Standardization}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.biologicals.2019.03.008}, pmid = {30992161}, issn = {1095-8320}, abstract = {The utilization of the current combination of in vitro, in vivo and PCR assays for the identification of adventitious viruses in production cells has a limited range of detection. While Next Generation Sequencing (NGS) has a broader breadth of detection, it is unable to differentiate sequences from replicating viruses versus background inert sequences. In order to improve NGS specificity, we have designed a new NGS approach which targets subsets of viral RNAs only synthesized during cell infection. In order to evaluate the performance of this approach for detecting low levels of adventitious viruses, we selected two difficult virus/cell systems. This included B95-8 cells persistently infected by Human herpesvirus 4 (HHV-4) and serially diluted into HHV-4 negative Ramos cells and Madin-Darby bovine kidney cells with an early infection produced via a low dose of Bovine viral diarrhea virus. We demonstrated that the sensitivity of our RNA NGS approach was equivalent to targeted PCR with an increased specificity for the detection of viral infection. We were also able to identify a previously undetected Murine Leukemia Virus contaminant in Ramos cells. Based on these results, we conclude that this new RNA NGS approach is suitable for conducting viral safety evaluations of cells.}, }
@article {pmid30992083, year = {2019}, author = {Arumugam, K and Bağcı, C and Bessarab, I and Beier, S and Buchfink, B and Górska, A and Qiu, G and Huson, DH and Williams, RBH}, title = {Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {61}, doi = {10.1186/s40168-019-0665-y}, pmid = {30992083}, issn = {2049-2618}, support = {0//National Research Foundation Singapore/ ; INST~37/935-1 FUGG//Deutsche Forschungsgemeinschaft/ ; HU 566/12-1//Deutsche Forschungsgemeinschaft/ ; }, abstract = {BACKGROUND: Short-read sequencing technologies have long been the work-horse of microbiome analysis. Continuing technological advances are making the application of long-read sequencing to metagenomic samples increasingly feasible.<br><br>RESULTS: We demonstrate that whole bacterial chromosomes can be obtained from an enriched community, by application of MinION sequencing to a sample from an EBPR bioreactor, producing 6 Gb of sequence that assembles into multiple closed bacterial chromosomes. We provide a simple pipeline for processing such data, which includes a new approach to correcting erroneous frame-shifts.<br><br>CONCLUSIONS: Advances in long-read sequencing technology and corresponding algorithms will allow the routine extraction of whole chromosomes from environmental samples, providing a more detailed picture of individual members of a microbiome.}, }
@article {pmid30992055, year = {2019}, author = {Zinter, MS and Mayday, MY and Ryckman, KK and Jelliffe-Pawlowski, LL and DeRisi, JL}, title = {Towards precision quantification of contamination in metagenomic sequencing experiments.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {62}, doi = {10.1186/s40168-019-0678-6}, pmid = {30992055}, issn = {2049-2618}, support = {K12HD000850//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; n/a//Chan Zuckerberg Biohub/ ; Preterm Birth Initiative (PTBi)//University of California, San Francisco/ ; Preterm Birth Initiative (PTBi)//University of California, San Francisco/ ; }, abstract = {Metagenomic next-generation sequencing (mNGS) experiments involving small amounts of nucleic acid input are highly susceptible to erroneous conclusions resulting from unintentional sequencing of occult contaminants, especially those derived from molecular biology reagents. Recent work suggests that, for any given microbe detected by mNGS, an inverse linear relationship between microbial sequencing reads and sample mass implicates that microbe as a contaminant. By associating sequencing read output with the mass of a spike-in control, we demonstrate that contaminant nucleic acid can be quantified in order to identify the mass contributions of each constituent. In an experiment using a high-resolution (n = 96) dilution series of HeLa RNA spanning 3-logs of RNA mass input, we identified a complex set of contaminants totaling 9.1 ± 2.0 attograms. Given the competition between contamination and the true microbiome in ultra-low biomass samples such as respiratory fluid, quantification of the contamination within a given batch of biological samples can be used to determine a minimum mass input below which sequencing results may be distorted. Rather than completely censoring contaminant taxa from downstream analyses, we propose here a statistical approach that allows separation of the true microbial components from the actual contribution due to contamination. We demonstrate this approach using a batch of n = 97 human serum samples and note that despite E. coli contamination throughout the dataset, we are able to identify a patient sample with significantly more E. coli than expected from contamination alone. Importantly, our method assumes no prior understanding of possible contaminants, does not rely on any prior collection of environmental or reagent-only sequencing samples, and does not censor potentially clinically relevant taxa, thus making it a generalized approach to any kind of metagenomic sequencing, for any purpose, clinical or otherwise.}, }
@article {pmid30991963, year = {2019}, author = {Foulex, A and Coen, M and Cherkaoui, A and Lazarevic, V and Gaïa, N and Leo, S and Girard, M and Mugnai, D and Schrenzel, J}, title = {Listeria monocytogenes infectious periaortitis: a case report from the infectious disease standpoint.}, journal = {BMC infectious diseases}, volume = {19}, number = {1}, pages = {326}, doi = {10.1186/s12879-019-3953-z}, pmid = {30991963}, issn = {1471-2334}, abstract = {BACKGROUND: Endograft infection is a rare but extremely dangerous complication of aortic repair (25-100% of mortality). We describe here the first case of Listeria monocytogenes abdominal periaortitis associated with a vascular graft. We also discuss the differential diagnosis of periaortitis and provide a literature review of L. monocytogenes infectious aortitis.<br><br>CASE PRESENTATION: Nine months after endovascular treatment of an abdominal aortic aneurysm (abdominal stent graft), a 76-year-old man was admitted for severe abdominal pain radiating to the back. Laboratory tests were normal apart from elevated C-reactive protein (CRP). Injected abdominal computed tomography (CT) showed infiltration of the fat tissues around the aortic endoprosthesis and aneurysmal sac expansion; positron emission tomography with 2-deoxy-2-[fluorine-18]fluoro- D-glucose integrated with computed tomography (18F-FDG PET/CT) showed a hypermetabolic mass in contact with the endoprosthesis. Blood cultures were negative. At surgical revision, an infra-renal peri-aortic abscess was evident; post-operative antibiotic therapy with ciprofloxacin and doxycycline was started. Cultures of intraoperative samples were positive for L. monocytogenes. Results were further confirmed by a broad-range polymerase chain reaction (PCR) and next-generation sequencing. Antibiotic treatment was switched to intravenous amoxicillin for 6 weeks. Evolution was uneventful with decrease of inflammatory parameters and regression of the abscess.<br><br>CONCLUSION: An etiologic bacterial diagnosis before starting antibiotic therapy is paramount; nevertheless, culture-independent methods may provide a microbiological diagnosis in those cases where antimicrobials are empirically used and when cultures remain negative.}, }
@article {pmid30991220, year = {2019}, author = {Zhang, S and He, Z and Meng, F}, title = {Floc-size effects of the pathogenic bacteria in a membrane bioreactor plant.}, journal = {Environment international}, volume = {127}, number = {}, pages = {645-652}, doi = {10.1016/j.envint.2019.04.002}, pmid = {30991220}, issn = {1873-6750}, abstract = {The size nature of sludge flocs could affect the occurrence and distribution of bacterial pathogens in wastewater treatment plants (WWTPs). In this study, the floc-size dependence of bacterial pathogens in the activated sludge of a WWTP was investigated using high-throughput metagenomic sequencing approaches. The results showed that a total of 423 pathogenic species belonging to 123 genera were identified in the three size-fractionated flocs. Also, we found that all the pathogens on the WHO's global priority pathogens list were detected in the size-fractionated flocs, with relative abundance of 0.4%, 0.3% and 0.3% for large-size, medium-size and small-size flocs, respectively, indicating the severe human and environmental health risks of activated sludge. Importantly, our results revealed that the pathogenic species showed a clear floc-size dependent distribution manner, leading to significant differences (P < 0.05) of pathogenic communities among the size-fractionated flocs. Additionally, by partitioning pathogens based on the occurrence and significant difference in abundances, we suggested the following distribution features: 1) large flocs-associated pathogens, such as Borrelia recurrentis, Actinobacillus ureae and Campylobacter gracilis; 2) medium flocs-associated pathogens, such as Mycobacterium szulgai and Ureaplasma urealyticum; and 3) small flocs-associated pathogens, such as Rickettsia akari, Staphylococcus anginosus and Helicobacter cinaedi. Overall, this study provides a comprehensive understanding of pathogens in activated sludge, which is expected to aid in assessment and management of pathogen risks.}, }
@article {pmid30989976, year = {2019}, author = {Chen, ST and Dai, J and Jiang, XP and Song, XW and Chen, CW and Chen, NF and Guo, LP and Han, BX}, title = {[Diversity and difference of endophytes in Dendrobium huoshanense with different growth years].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {44}, number = {6}, pages = {1145-1150}, doi = {10.19540/j.cnki.cjcmm.2019.0022}, pmid = {30989976}, issn = {1001-5302}, abstract = {In order to explore endophytes diversity and difference in Dendrobium huoshanense,in this paper,the metagenomics method was used to analyze the endophytic bacteria and fungi community of 5 groups include 30 samples in different growth years. The results indicate that 3 540 bacterial OTUs were identified from D. huoshanense,and there are 138 OTUs in 5 groups simultaneously;2 168 fungal OTUs were identified,and 143 OTUs exist in 5 groups simultaneously. The dominate endophytic bacteria community are Sphingomonas sp.,Acinetobacter sp.,Burkholderia sp.,Methylobacterium sp.,Enterococcus sp.,Bacillus sp.,the difference endophytic bacteria community are Oceanobacillusd sp.,Actinomycetospora sp.,Paenibacillus sp.. The dominate endophytic fungi community are Zasmidium sp.,Zymoseptoria sp.,Alternaria sp.,Cladosporium sp.,Fusarium sp.,the difference endophytic fungi community are Cyphellophore sp.,Fusarium sp.. The results of clustering revealed that both the endophytic bacteria and the endophytic fungi,ⅢY2 and ⅢY3 are complete clustered,and ⅡY1 and ⅢY1 are also cluster completely. These enriched the species and resources of endophytic bacteria and fungi in D. huoshanense,and provided a theoretical reference for the reasonable harvest of D. huoshanense.}, }
@article {pmid30989974, year = {2019}, author = {Yang, J and Dong, CB and Chen, WH and Liang, JD and Han, YF and Liang, ZQ}, title = {[Community composition and ecological functional structural analysis of endophytic fungi in bark of Eucommia ulmoides in different areas].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {44}, number = {6}, pages = {1126-1134}, doi = {10.19540/j.cnki.cjcmm.20181226.005}, pmid = {30989974}, issn = {1001-5302}, abstract = {Based on high-throughput sequencing and metagenomic technology,the community composition and ecological functions of endophytic fungi in the bark of Eucommia ulmoides from three producing areas,Fengxiang town in Zunyi county of Guizhou province,Lingyang town of Cili county of Hunan province and Mumen town of Wangcang county of Sichuan province,were analyzed. A total of110 865 effective sequences of endophytic fungi were obtained in the study. The corresponding fungal group of OTUs after clustering belonged to 3 phyla(Ascomycota,Basidiomycota,Zygomycota),10 classes,25 orders,41 families,57 genera and 74 species. Among them,the dominant genera of Sichuan Wangcang Bark of E. ulmoides(EWP) was an unclassified genus in the Nectriaceae of the Crimsonaceae,with a relative abundance of 54. 79%; The dominant species of Hunan Cili Bark of E. ulmoides(ECP) was the unclassified genus of Ascomycota,with a relative abundance of 39. 97% and the dominant species of Guizhou Zunyi bark(EZP) was Lophiostoma,and its relative abundance was 47. 07%. The analysis of α diversity indicated that the shannon diversity index of endophytic fungi from different places was as follows: ECP: 1. 340 2>EZP: 1. 380 4 > EWP: 1. 168 3. The simpson diversity index was: EWP(0. 427 3) >EZP(0. 332 5) > ECP(0. 313 6). FUNGuild software platform analysis displayed that endophytic fungi of E. ulmoides bark from three producing areas contained the following 14 functional groups: plant pathogen,animal pathogen and endophyte et al.,the number of functional groups in the 3 samples of E. ulmoides reached up 8 genera and exceeded one half of the total number. Correlation analysis of Canonical correspondence analysis(CCA) between endophytic fungal community diversity and four active compounds of E. ulmoides were analyzed,the results showed that the contents of pinoresinol diglucoside and chlorogenic acid,to a certain extend,had a positive correlation with an unclassified genus of Davidiellaceae,Mortierella,Chaetomium and Pestalotiopsis from the endophytic fungi in EWP sample.}, }
@article {pmid30989782, year = {2019}, author = {Guo, M and Hou, C and Bian, M and Shen, C and Zhang, S and Huo, D and Ma, Y}, title = {Characterization of microbial community profiles associated with quality of Chinese strong-aromatic liquor through metagenomics.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jam.14279}, pmid = {30989782}, issn = {1365-2672}, abstract = {AIMS: Microorganisms in fermentation-pits(FPs) play key roles for Chinese-strong-aromatic-liquor(CSAL) production. However, microbial community in the FPs is still poorly understood. Here, the aim of this study was to reveal the diversity and potential functions of microbiota in FPs.<br><br>METHODS AND RESULTS: Sequencing-by-synthesis-based metagenomic sequencing and annotation results revealed that the microbiota of FPs was primarily composed of Firmicutes(54.6%), Euryarchaeota(15.3%), Bacteroidetes(10.1%), Gammaproteobacteria(5.8%), Opisthokonta(5.7%), and Unclassified_Bacteria(2.3%). And 133 genera were identified as the dominant genera of this fermentative food. Lactobacillus, Sedimentibacter, Syntrophomonas, Methanoculleus, Methanobacterium, Bacillus, Clostridium, Galactomyces, Candida, Pichia, Penicillium and Aspergillus were defined as active populations for biosynthesizing the characteristic volatile compounds of CSAL. The study also revealed that the microbial community structures changed significantly with different cellar ages and over different geographical regions. (i)The presence of Bacteroidetes was the most distinctive feature that characterized the different FPs ages. (ii)Distinct contents of Gammaproteobacteria and Euryarchaeota were observed at different positions in the FPs. (iii)Euryarchaeota markedly contributed to the generation of the character of the liquors with distinct geographical associations.<br><br>CONCLUSIONS: The present study demonstrated that the changes of microbial communities determined the different quality characteristics of CSAL.<br><br>This research contributes to a deeper understanding of the FPs microbial composition and shows a new microbial resource for biotechnological applications. This article is protected by copyright. All rights reserved.}, }
@article {pmid30986551, year = {2019}, author = {Velasco, L and Arjona-Girona, I and Cretazzo, E and López-Herrera, C}, title = {Viromes in Xylariaceae fungi infecting avocado in Spain.}, journal = {Virology}, volume = {532}, number = {}, pages = {11-21}, doi = {10.1016/j.virol.2019.03.021}, pmid = {30986551}, issn = {1096-0341}, abstract = {Four isolates of Entoleuca sp., family Xylariaceae, Ascomycota, recovered from avocado rhizosphere in Spain were analyzed for mycoviruses presence. For that, the dsRNAs from the mycelia were extracted and subjected to metagenomics analysis that revealed the presence of eleven viruses putatively belonging to families Partitiviridae, Hypoviridae, Megabirnaviridae, and orders Tymovirales and Bunyavirales, in addition to one ourmia-like virus plus other two unclassified virus species. Moreover, a sequence with 98% nucleotide identity to plant endornavirus Phaseolus vulgaris alphaendornavirus 1 has been identified in the Entoleuca sp. isolates. Concerning the virome composition, the four isolates only differed in the presence of the bunyavirus and the ourmia-like virus, while all other viruses showed common patterns. Specific primers allowed the detection by RT-PCR of these viruses in a collection of Entoleuca sp. and Rosellinia necatrix isolates obtained from roots of avocado trees. Results indicate that intra- and interspecies horizontal virus transmission occur frequently in this pathosystem.}, }
@article {pmid30986455, year = {2019}, author = {Li, Z and Li, X and Liu, T and Chen, S and Liu, H and Wang, H and Li, K and Song, Y and Luo, X and Zhao, J and Zhang, T}, title = {The critical roles of exposed surface residues for the thermostability and halotolerance of a novel GH11 xylanase from the metagenomic library of a saline-alkaline soil.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ijbiomac.2019.04.090}, pmid = {30986455}, issn = {1879-0003}, abstract = {Thermostable and halotolerant GH11 xylanases are highly desirable in various industrial applications but they were rarely characterized. In this study, we firstly revealed the genetic diversity of GH11 xylanases from the metagenomic DNA of a saline-alkaline soil by constructing a gene fragment library. Twelve distinct xylanase fragment sequences were identified, which shared 62-96% identity to known GH11 xylanases. Among them, Xyn22 with the highest relative abundance was cloned and found to exhibit excellent halotolerance. Xyn22 retained 80 and 58% relative activity in the presence of 3 and 5 M NaCl, respectively, and had no loss of activity after incubation in 3 M NaCl at 37 °C for 1 h. Additionally, the acidic amino acid residues E137 and E139 on the protein's surface were revealed to cooperatively play important roles in its excellent halotolerance and halostabilty. Furthermore, the thermostability of Xyn22 was significantly improved without compromising halotolerance by introducing an aromatic interaction between Y48 and F53. In conclusion, this study not only provides a thermostable and halotolerant GH11 xylanase, but also reveals the key roles of surface-exposed amino acids in its thermostability and halotolerance, which could be used for further molecular modification of other xylanases and similar enzymes.}, }
@article {pmid30986208, year = {2019}, author = {Lambert, JS and Cook, MJ and Healy, JE and Murtagh, R and Avramovic, G and Lee, SH}, title = {Metagenomic 16S rRNA gene sequencing survey of Borrelia species in Irish samples of Ixodes ricinus ticks.}, journal = {PloS one}, volume = {14}, number = {4}, pages = {e0209881}, doi = {10.1371/journal.pone.0209881}, pmid = {30986208}, issn = {1932-6203}, abstract = {The spirochetal bacterium Borrelia miyamotoi is a human pathogen and has been identified in many countries throughout the world. This study reports for the first time the presence of Borrelia miyamotoi in Ireland, and confirms prior work with the detection of B. garinii and B. valaisiana infected ticks. Questing Ixodes ricinus nymph samples were taken at six localities within Ireland. DNA extraction followed by Sanger sequencing was used to identify the species and strains present in each tick. The overall rate of borrelial infection in the Irish tick population was 5%, with a range from 2% to 12% depending on the locations of tick collection. The most prevalent species detected was B. garinii (70%) followed by B. valaisiana (20%) and B. miyamotoi (10%). Knowledge of Borrelia species prevalence is important and will guide appropriate selection of antigens for serology test kit manufacture, help define the risk of infection, and allow medical authorities to formulate appropriate strategies and guidelines for diagnosis and treatment of Borrelia diseases.}, }
@article {pmid30985920, year = {2019}, author = {Langan, EA and Künstner, A and Miodovnik, M and Zillikens, D and Thaçi, D and Baines, JF and Ibrahim, SM and Solbach, W and Knobloch, JK}, title = {Combined culture and metagenomic analyses reveal significant shifts in the composition of the cutaneous microbiome in psoriasis.}, journal = {The British journal of dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1111/bjd.17989}, pmid = {30985920}, issn = {1365-2133}, abstract = {BACKGROUND: The treatment of psoriasis has been revolutionised by the development of biologic therapies. However, the pathogenesis of psoriasis, in particular the role of the cutaneous microbiome, remains incompletely understood. Moreover, skin microbiome studies have heavily relied on 16S rRNA sequencing data in the absence of bacterial culture.<br><br>OBJECTIVES: To characterise and compare the cutaneous microbiome in 20 healthy controls and 23 patients with psoriasis using metagenomic analyses and to determine changes in the microbiome during treatment.<br><br>METHODS: Swabs from lesional and non-lesional skin from psoriasis patients, and from site- and skin microenvironment matched controls, were analysed using both 16S rRNA sequencing and traditional culture combined with mass spectrometry (MALDI-TOF) in a prospective study.<br><br>RESULTS: Psoriasis was associated with an increased abundance of Firmicutes and a corresponding reduction in Actinobacteria, most marked in lesional skin, and at least partially reversed during systemic treatment. Shifts in bacterial community composition in lesional sites were reflected in similar changes in culturable bacteria, although changes in the microbiota over repeated swabbing were only detectable with sequencing. The composition of the microbial communities varied by skin site and microenvironment. Prevotella and Staphylococcus were significantly associated with lesional skin; Anaerococcus and Propionibacterium with non-lesional skin. There were no significant differences in the amount of bacteria cultured from the skin of healthy controls and psoriasis patients.<br><br>CONCLUSIONS: Shifts in the cutaneous microbiome in psoriasis, particularly during treatment, may shed new light on the pathogenesis of the disease and may be clinically exploited to predict treatment response. This article is protected by copyright. All rights reserved.}, }
@article {pmid30984155, year = {2019}, author = {Wang, L and Zhang, G and Xu, H and Xin, H and Zhang, Y}, title = {Metagenomic Analyses of Microbial and Carbohydrate-Active Enzymes in the Rumen of Holstein Cows Fed Different Forage-to-Concentrate Ratios.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {649}, doi = {10.3389/fmicb.2019.00649}, pmid = {30984155}, issn = {1664-302X}, abstract = {The objectives of this study were to investigate the effects of different forage-to-concentrate ratios and sampling times on the genetic diversity of carbohydrate-active enzymes (CAZymes) and the taxonomic profile of rumen microbial communities in dairy cows. Six ruminally cannulated Holstein cows were arbitrarily divided into groups fed high-forage (HF) or low-forage (LF) diets. The results showed that, for glycoside hydrolase (GH) families, there were greater differences based on dietary forage-to-concentrate ratio than sampling time. The HF treatment group at 4 h after feeding (AF4h) had the most microbial diversity. Genes that encode GHs had the highest number of CAZymes, and accounted for 57.33% and 56.48% of all CAZymes in the HF and LF treatments, respectively. The majority of GH family genes encode oligosaccharide-degrading enzymes, and GH2, GH3, and GH43 were synthesized by a variety of different genera. Notably, we found that GH3 was higher in HF than LF diet samples, and mainly produced by Prevotella, Bacteroides, and unclassified reads. Most predicted cellulase enzymes were encoded by GH5 (the BF0h group under HF treatment was highest) and GH95 (the BF0h group under LF treatment was highest), and were primarily derived from Bacteroides, Butyrivibrio, and Fibrobacter. Approximately 67.5% (GH28) and 65.5% (GH53) of the putative hemicellulases in LF and HF treatments, respectively. GH28 under LF treatment was more abundant than under HF treatment, and was mainly produced by Ruminococcus, Prevotella, and Bacteroides. This study revealed that HF-fed cows had increased microbial diversity of CAZyme producers, which encode enzymes that efficiently degrade plant cell wall polysaccharides in the cow rumen.}, }
@article {pmid30984151, year = {2019}, author = {Mindlin, S and Beletsky, A and Mardanov, A and Petrova, M}, title = {Adaptive dif Modules in Permafrost Strains of Acinetobacter lwoffii and Their Distribution and Abundance Among Present Day Acinetobacter Strains.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {632}, doi = {10.3389/fmicb.2019.00632}, pmid = {30984151}, issn = {1664-302X}, abstract = {The dif/Xer system of site-specific recombination allows resolution of chromosomal dimers during bacterial DNA replication. Recently, it was also shown to be involved in horizontal transfer of a few known Xer-dependent mobile elements. Here, we show that plasmids of various Acinetobacter species, including clinically important strains, often contain multiple pdif sites that are mainly located within their accessory regions. Chromosomes of Acinetobacter strains may also contain additional dif sites, and their similarity with plasmid pdif sites is higher than with the main chromosomal site dif1. We further identify putative mobile genetic elements containing pdif sites on both flanks of adaptive genes and analyze their distribution in Acinetobacter species. In total, we describe seven mobile elements containing genes with various adaptive functions from permafrost strains of A. lwoffii group. All of them are also spread in modern plasmids of different Acinetobacter species including A. baumannii. We could not detect pdif sites and corresponding mobile elements in closely related bacterial genera, including Psychrobacter and Moraxella. Thus, the widespread distribution of dif modules is a characteristic feature of Acinetobacter species and may contribute to their high adaptability both in the environment and in the clinic.}, }
@article {pmid30984144, year = {2019}, author = {Cui, J and Mai, G and Wang, Z and Liu, Q and Zhou, Y and Ma, Y and Liu, C}, title = {Metagenomic Insights Into a Cellulose-Rich Niche Reveal Microbial Cooperation in Cellulose Degradation.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {618}, doi = {10.3389/fmicb.2019.00618}, pmid = {30984144}, issn = {1664-302X}, abstract = {Background: Cellulose is the most abundant organic polymer mainly produced by plants in nature. It is insoluble and highly resistant to enzymatic hydrolysis. Cellulolytic microorganisms that are capable of producing a battery of related enzymes play an important role in recycling cellulose-rich plant biomass. Effective cellulose degradation by multiple synergic microorganisms has been observed within a defined microbial consortium in the lab culture. Metagenomic analysis may enable us to understand how microbes cooperate in cellulose degradation in a more complex microbial free-living ecosystem in nature.<br><br>Results: Here we investigated a typical cellulose-rich and alkaline niche where constituent microbes survive through inter-genera cooperation in cellulose utilization. The niche has been generated in an ancient paper-making plant, which has served as an isolated habitat for over 7 centuries. Combined amplicon-based sequencing of 16S rRNA genes and metagenomic sequencing, our analyses showed a microbial composition with 6 dominant genera including Cloacibacterium, Paludibacter, Exiguobacterium, Acetivibrio, Tolumonas, and Clostridium in this cellulose-rich niche; the composition is distinct from other cellulose-rich niches including a modern paper mill, bamboo soil, wild giant panda guts, and termite hindguts. In total, 11,676 genes of 96 glucoside hydrolase (GH) families, as well as 1,744 genes of carbohydrate transporters were identified, and modeling analysis of two representative genes suggested that these glucoside hydrolases likely evolved to adapt to alkaline environments. Further reconstruction of the microbial draft genomes by binning the assembled contigs predicted a mutualistic interaction between the dominant microbes regarding the cellulolytic process in the niche, with Paludibacter and Clostridium acting as helpers that produce endoglucanases, and Cloacibacterium, Exiguobacterium, Acetivibrio, and Tolumonas being beneficiaries that cross-feed on the cellodextrins by oligosaccharide uptake.<br><br>Conclusion: The analysis of the key genes involved in cellulose degradation and reconstruction of the microbial draft genomes by binning the assembled contigs predicted a mutualistic interaction based on public goods regarding the cellulolytic process in the niche, suggesting that in the studied microbial consortium, free-living bacteria likely survive on each other by acquisition and exchange of metabolites. Knowledge gained from this study will facilitate the design of complex microbial communities with a better performance in industrial bioprocesses.}, }
@article {pmid30983011, year = {2019}, author = {Ovadia, C and Perdones-Montero, A and Spagou, K and Smith, A and Sarafian, MH and Gomez Romero, M and Bellafante, E and Clarke, LC and Sadiq, F and Nikolova, V and Mitchell, A and Dixon, PH and Santa-Pinter, N and Wahlström, A and Abu-Hayyeh, S and Walters, J and Marschall, HU and Holmes, E and Marchesi, JR and Williamson, C}, title = {Enhanced microbial bile acid deconjugation and impaired ileal uptake in pregnancy repress intestinal regulation of bile acid synthesis.}, journal = {Hepatology (Baltimore, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1002/hep.30661}, pmid = {30983011}, issn = {1527-3350}, abstract = {Pregnancy is associated with progressive hypercholanemia, hypercholesterolemia and hypertriglyceridemia, which can result in metabolic disease in susceptible women. Gut signals modify hepatic homeostatic pathways, linking intestinal content to metabolic activity. We sought to identify whether enteric endocrine signals contribute to raised serum bile acids observed in human and murine pregnancies, by measuring fibroblast growth factor (FGF)19/15 protein and mRNA levels, and 7α-hydroxy-4-cholesten-3-one. Terminal ileal farnesoid X receptor(FXR)-mediated gene expression and apical sodium bile acid transporter (ASBT) protein concentration were measured by qPCR and western blotting. Shotgun whole genome sequencing and UPLC-MS were used to determine the cecal microbiome and metabonome. Targeted and untargeted pathway analyses were performed to predict the systemic effects of the altered metagenome and metabolite profiles. Dietary cholic acid supplementation was used to determine whether the observed alterations could be overcome by intestinal bile acids functioning as FXR agonists. Human and murine pregnancy were associated with reduced intestinal FXR signaling, with lower FGF19/15 and resultant increased hepatic bile acid synthesis. Terminal ileal ASBT protein was reduced in murine pregnancy. Cecal bile acid conjugation was reduced in pregnancy due to elevated bile salt hydrolase-producing Bacteroidetes. Cholic acid supplementation induced intestinal FXR signaling, which was not abrogated by pregnancy, with strikingly similar changes to the microbiota and metabonome as identified in pregnancy. CONCLUSION: the altered intestinal microbiota of pregnancy enhance bile acid deconjugation, reducing ileal bile acid uptake and lowering FXR induction in enterocytes. This exacerbates the effects mediated by reduced bile acid uptake transporters in pregnancy. Thus, in pregnant women and mice, there is reduced FGF19/15-mediated hepatic repression of hepatic bile acid synthesis, resulting in hypercholanemia. This article is protected by copyright. All rights reserved.}, }
@article {pmid30982088, year = {2019}, author = {Wang, H and Yang, S and Shan, T and Wang, X and Deng, X and Delwart, E and Zhang, W}, title = {A novel picornavirus in feces of a rainbow lorikeet (Trichoglossus moluccanus) shows a close relationship to members of the genus Avihepatovirus.}, journal = {Archives of virology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00705-019-04246-5}, pmid = {30982088}, issn = {1432-8798}, support = {2017YFC1200201//National Key Research and Development Programs of China/ ; BE2017693//Jiangsu Provincial Key Research and Development Projects/ ; 31872478//the National Natural Science Foundation/ ; }, abstract = {A novel picornavirus, named &quot;lorikeet picornavirus 1&quot; (LoPV-1), was detected in a fecal sample from rainbow lorikeets using viral metagenomic analysis, and its complete genome sequence was determined and analyzed. The genome of LoPV-1 is 7862 nt long, including a 617-nt 5' UTR, a type IV IRES 5'UTR with an '8-like' motif, a 7032-nt polyprotein ORF, and a 213-nt 3' UTR. Phylogenetic analysis and pairwise asequence comparisons based on the amino acid sequences of P1, P2, and P3 indicated that LoPV-1 showed the closest relationship to two picornaviruses that were isolated recently from red-crowned cranes and clustered together with members of the genus Avihepatovirus.}, }
@article {pmid30981803, year = {2019}, author = {Parida, S and Sharma, D}, title = {The power of small changes: Comprehensive analyses of microbial dysbiosis in breast cancer.}, journal = {Biochimica et biophysica acta. Reviews on cancer}, volume = {1871}, number = {2}, pages = {392-405}, doi = {10.1016/j.bbcan.2019.04.001}, pmid = {30981803}, issn = {1879-2561}, abstract = {Disparate occurrence of breast cancer remains an intriguing question since only a subset of women with known risk factors develop cancer. Recent studies suggest an active role of local and distant microbiota in breast cancer initiation, progression, and overall prognosis. A dysbiotic microbiota predisposes the body to develop cancer by inducing genetic instability, initiating DNA damage and proliferation of the damaged progeny, eliciting favorable immune response, metabolic dysregulation and altered response to therapy. In this review, we present our analyses of the existing datasets and discuss the local dysbiosis observed in breast cancer patients and different aspects of breast carcinogenesis that can be potentially influenced by local breast microbiota. Striking differences between microbial community compositions in breast of cancer patients compared to healthy individuals were noted. Differences in microbiome were also apparent between benign and malignant disease and between nipple aspirate fluid of healthy individuals and breast survivors. We also discuss the identification of distinct bacterial, fungal, viral as well as parasite signatures for breast cancer. These microbes are capable of producing numerous secondary metabolites that can act as signaling mediators effecting breast cancer progression. We review how microbes potentially alter response to therapy affecting drug metabolism, pharmacokinetics, anti-tumor effects and toxicity. In conclusion, breast harbors a community of microbes that can communicate with the host cells inducing downstream signaling pathways and modulating various aspects of breast cancer growth and metastatic progression and an improved understanding of microbial dysbiosis can potentially reduce breast cancer risk and improve outcomes of breast cancer patients. The human microbiome, now referred to as, the &quot;forgotten organ&quot; contains a metagenome that is 100-fold more diverse compared to the human genome, thereby, is critically associated with human health [1,2]. With the revelations of the human microbiome project and advent of deep sequencing techniques, a plethora of information has been acquired in recent years. Body sites like stomach, bladder and lungs, once thought to be sterile, are now known to harbor millions of indigenous microbial species. Approximately 80% of the healthy microbiome consists of Firmicutes and Bacteroidetes accompanied by Verrucomicrobia, Actinobacteria, Proteobacteria, Tenericutes and Cyanobacteria [2-7]. The role of microbiome in diabetes, obesity and even neurodegenerative diseases was greatly appreciated in the last decade [1,7-14] and now it has been established that microbiome significantly contributes to many organ specific cancers [1,15,16].}, }
@article {pmid30981666, year = {2019}, author = {Wang, JJ and Zhang, RQ and Zhai, QY and Liu, JC and Li, N and Liu, WX and Li, L and Shen, W}, title = {Metagenomic analysis of gut microbiota alteration in a mouse model exposed to mycotoxin deoxynivalenol.}, journal = {Toxicology and applied pharmacology}, volume = {372}, number = {}, pages = {47-56}, doi = {10.1016/j.taap.2019.04.009}, pmid = {30981666}, issn = {1096-0333}, abstract = {As one of the most prevalent contaminants in animal and human food, the deleterious effects of trichothecene mycotoxin deoxynivalenol (DON) warrant extensive investigation. Here, to assess the effects of DON exposure to the populations of gut microbiota, four-weeks-old mice were exposed to different doses (1.0 and 5.0 mg/kg) of DON every two days for 14 days. The contents of the cecum were then collected for DNA extraction and metagenomic shotgun sequencing, in order to detect alterations of the gut microbiota. We found that the average body weight and daily gain in the high dose DON treated group decreased. Metagenomic analysis demonstrated that the relative abundance of Firmicutes in the low and Bacteroidetes in the high dose groups increased compared to that in the untreated control group. Moreover, using gene calling and functional annotation, we found that large numbers of biosynthesis and degradation dependent populations were altered. As a result, metabolism pathways including sphingolipid, protein digestion/absorption, and lipoic acid pathways in the high dose DON exposed group dramatically fluctuated in comparison to the control and low dose groups. In addition, metagenomic binning identified ten microbiota genome drafts, with high levels of completeness, that further explain the DON-induced intestinal toxicity. Our findings suggested that DON exposure significantly impacted the microbiota community in the mouse, causing biosynthesis and degradation damage and metabolism pathway disorders.}, }
@article {pmid30981103, year = {2019}, author = {Roy, C and Bakshi, U and Rameez, MJ and Mandal, S and Haldar, PK and Pyne, P and Ghosh, W}, title = {Phylogenomics of an uncultivated, aerobic and thermophilic, photoheterotrophic member of Chlorobia sheds light into the evolution of the phylum Chlorobi.}, journal = {Computational biology and chemistry}, volume = {80}, number = {}, pages = {206-216}, doi = {10.1016/j.compbiolchem.2019.04.001}, pmid = {30981103}, issn = {1476-928X}, abstract = {All cultivated members of the phylum Chlorobi are classified under the two classes Chlorobia and Ignavibacteria. The recently-reported, uncultivated genome-species of Chlorobi have not suggested any alteration in the dichotomy of the two classes, but have hypothesized the existence of a distinct, aerobic and photoheterotrophic, order/family level lineage within Chlorobia, which otherwise was considered to be a monophyletic group of anaerobic sulfur-photolithoautotrophs. Here we report the discovery of a novel population genome bin (named Chlorobi-445) from the combined metagenomes of three spatially-contiguous but visually-distinct microbial mats growing along the 65-41 °C hydrothermal gradient of a boron-rich microbialite spring located in the Puga geothermal area of Eastern Ladakh, India. 1.3, 8.2 and 3.8% metagenomic reads from the mat communities located at 65 °C, 52 °C and 41 °C sample-sites respectively, were found to map-back to the 2,809,852 bp genome of Chlorobi-445. Phylogenomically, and therefore in terms of potential metabolic attributes, Chlorobi-445 showed close relationship with Ca. Thermochlorobacter aerophilum. Gene content suggested Chlorobi-445 to be an aerobic photoorganoheterotroph. Although this new lineage encodes all the proteins necessary for the biosynthesis of bacteriochlorophylls and the photosynthetic reaction centre, it is potentially devoid of genes concerned with lithotrophic sulfur oxidation and carbon-fixation. Individual Chlorobi phylogenies based on the sequence similarities of 16S rRNA genes, 22 ribosomal proteins, and 56 conserved marker-proteins that are encoded from single-copy genes, unanimously suggested that the class Chlorobia encompasses two major branches/clades. Whereas the Clade-I is a homogeneous cluster of culturable, anaerobic sulfur-/iron-oxidizing photolithoautotrophs, Clade-II harbors (i) Chloroherpeton species, and (ii) uncultivated aerobic photoheterotrophs such as Chlorobi-445, Chlorobium sp. GBChlB &amp;Ca. T. aerophilum, in its two sub-clades. Distribution of bioenergetic attributes over the different branches of Chlorobi, together with the aerobic chemoorganoheterotrophic nature of the deepest-branching genome-species NICIL-2, indicated that the early Chlorobi were aerobic chemoorganoheterotrophs, while anaerobicity, phototrophy, lithotrophy, and autotrophy were all potentially added in the course of evolution.}, }
@article {pmid30980894, year = {2019}, author = {Fraga, D and Stock, K and Aryal, M and Demoll, C and Fannin, L and Snidera, MJ}, title = {Bacterial arginine kinases have a highly skewed distribution within the proteobacteria.}, journal = {Comparative biochemistry and physiology. Part B, Biochemistry &amp; molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cbpb.2019.04.001}, pmid = {30980894}, issn = {1879-1107}, abstract = {Phosphagen kinases (PKs) are known to be distributed throughout the animal kingdom, but have recently been discovered in some protozoan and bacterial species. A recent search of the available bacterial genomes revealed 49 unique sequences that appear to code for an arginine kinase (AK). The distribution of sequences was highly skewed with thirty nine out the forty nine sequences being found in six Proteobacteria classes (α, β, δ, γ, ε, and ζ) which represented 46.6% of the 61,335 bacterial genomes available at JGI-IMG/M website. Moreover, twenty one of the unique and metagenome bAK sequences identified were from δ-Proteobacteria despite these representing only 0.88% of the total genomes available. Phylogenetic analyses revealed that the bacterial AK sequences were interpersed between basal species such as cnidarians, sponges and protozoa, displaying an unstable clustering that was dependent upon the parameters chosen for phylogenetic analysis. Three of these putative bacterial AK genes were cloned into the pET45 expression vector, expressed, and biochemically confirmed to be capable of phosphorylating arginine using ATP. Results of the kinetic analyses of the putative bAKs from Ahrensia, D. autotrophicum, and O. profundus show that the catalytic efficiencies with respect to arginine for each enzyme, measured at 104-105 M-1 s-1, fall within the range expected for competent arginine kinases.}, }
@article {pmid30980731, year = {2019}, author = {Tang, H and Xiao, X and Xu, Y and Li, C and Cheng, K and Pan, X and Li, W}, title = {Utilization of carbon sources in the rice rhizosphere and non-rhizosphere soils with different long-term fertilization management.}, journal = {Journal of basic microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1002/jobm.201800736}, pmid = {30980731}, issn = {1521-4028}, abstract = {Carbon (C) is playing an important role in the interaction between plant and rhizosphere microbial community, but there is still limited information about how C source utilization soil microbial structure responds to soil fertility changes under double-cropping rice (Oryza sativa L.) system in Southern of China paddy fields. Therefore, the effects of long-term (33 year) fertilizer regimes on the characteristics of C utilization in both the rhizosphere and non-rhizosphere soils under double-cropping rice fields in Southern of China were investigated by using metagenome sequencing technology. The experiment was begun in 1986, and including five fertilizer treatments: without fertilizer input (CK), chemical fertilizer alone (MF), rice straw residue and chemical fertilizer (RF), 30% organic matter and 70% chemical fertilizer (LOM), and 60% organic matter and 40% chemical fertilizer (HOM). The results showed that the relative abundance of Gemmatimonadetes and Planctomycetia in both the rhizosphere and non-rhizosphere soils were increased by application of rice straw residue and organic manure, whereas the relative abundance of Gammaproteobacteria and Nitrospira were promoted by application of inorganic fertilizers. The largest group of COG categories was &quot;Amino acid transport and metabolism&quot; with 16.46% unigenes, followed by &quot;General function prediction only&quot; (12.23%). Regarding the GO categories, biological process were the largest category (174 949, 46.40%), followed by cellular component (126 766, 33.62%) and molecular function (110 353, 29.26%). The PCoA analysis indicated that different parts of root zone were the most important factor affecting the variation of C source utilization bacteria community, and the different fertilizer treatments were the second important factor affecting the variation of C source utilization bacteria community. As a result, the application of fertilization practices had significantly effects on the abundance and community composition of C source utilization microbes in paddy soils. The results showed that the combined application of rice straw residue or organic manure with chemical fertilizer practices were significantly increases the C source utilization of soil microorganisms in double-cropping rice fields. This article is protected by copyright. All rights reserved.}, }
@article {pmid30980101, year = {2019}, author = {Ogwu, MC and Srinivasan, S and Dong, K and Ramasamy, D and Waldman, B and Adams, JM}, title = {Community Ecology of Deinococcus in Irradiated Soil.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01343-5}, pmid = {30980101}, issn = {1432-184X}, support = {2016E1D1A1B03930385//National Research Foundation Korea/ ; 2017R1D1A1B03035583//National Foundation foundation Korea/ ; }, abstract = {Deinococcus is a genus of soil bacteria known for radiation resistance. However, the effects of radiation exposure on its community structure are unknown. We exposed soil to three levels of gamma radiation, 0.1 kGy/h (low), 1 kGy/h (medium), and 3 kGy/h (high), once a week for 6 weeks and then extracted soil DNA for 16S rRNA amplicon sequencing. We found the following: (1) Increasing radiation dose produced a major increase in relative abundance of Deinococcus, reaching ~ 80% of reads at the highest doses. Differing abundances of the various Deinococcus species in relation to exposure levels indicate distinct &quot;radiation niches.&quot; At 3 kGy/h, a single OTU identified as D. ficus overwhelmingly dominated the mesocosms. (2) Corresponding published genome data show that the dominant species at 3 kGy/h, D. ficus, has a larger and more complex genome than other Deinococcus species with a greater proportion of genes related to DNA and nucleotide metabolism, cell wall, membrane, and envelope biogenesis as well as more cell cycle control, cell division, and chromosome partitioning-related genes. Deinococcus ficus also has a higher guanine-cytosine ratio than most other Deinococcus. These features may be linked to genome stability and may explain its greater abundance in this apparently competitive system, under high-radiation exposures. (3) Genomic analysis suggests that Deinococcus, including D. ficus, are capable of utilizing diverse carbon sources derived from both microbial cells killed by the radiation (including C5-C12-containing compounds, like arabinose, lactose, N-acetyl-D-glucosamine) and plant-derived organic matter in the soil (e.g., cellulose and hemicellulose). (4) Overall, based on its metagenome, even the most highly irradiated (3 kGy/h) soil possesses a wide range of the activities necessary for a functional soil system. Future studies may consider the resilience and sustainability of such soils in a high-radiation environment.}, }
@article {pmid30979963, year = {2019}, author = {Singer, GAC and Fahner, NA and Barnes, JG and McCarthy, A and Hajibabaei, M}, title = {Comprehensive biodiversity analysis via ultra-deep patterned flow cell technology: a case study of eDNA metabarcoding seawater.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {5991}, doi = {10.1038/s41598-019-42455-9}, pmid = {30979963}, issn = {2045-2322}, abstract = {The characterization of biodiversity is a crucial element of ecological investigations as well as environmental assessment and monitoring activities. Increasingly, amplicon-based environmental DNA metabarcoding (alternatively, marker gene metagenomics) is used for such studies given its ability to provide biodiversity data from various groups of organisms simply from analysis of bulk environmental samples such as water, soil or sediments. The Illumina MiSeq is currently the most popular tool for carrying out this work, but we set out to determine whether typical studies were reading enough DNA to detect rare organisms (i.e., those that may be of greatest interest such as endangered or invasive species) present in the environment. We collected sea water samples along two transects in Conception Bay, Newfoundland and analyzed them on the MiSeq with a sequencing depth of 100,000 reads per sample (exceeding the 60,000 per sample that is typical of similar studies). We then analyzed these same samples on Illumina's newest high-capacity platform, the NovaSeq, at a depth of 7 million reads per sample. Not surprisingly, the NovaSeq detected many more taxa than the MiSeq thanks to its much greater sequencing depth. However, contrary to our expectations this pattern was true even in depth-for-depth comparisons. In other words, the NovaSeq can detect more DNA sequence diversity within samples than the MiSeq, even at the exact same sequencing depth. Even when samples were reanalyzed on the MiSeq with a sequencing depth of 1 million reads each, the MiSeq's ability to detect new sequences plateaued while the NovaSeq continued to detect new sequence variants. These results have important biological implications. The NovaSeq found 40% more metazoan families in this environment than the MiSeq, including some of interest such as marine mammals and bony fish so the real-world implications of these findings are significant. These results are most likely associated to the advances incorporated in the NovaSeq, especially a patterned flow cell, which prevents similar sequences that are neighbours on the flow cell (common in metabarcoding studies) from being erroneously merged into single spots by the sequencing instrument. This study sets the stage for incorporating eDNA metabarcoding in comprehensive analysis of oceanic samples in a wide range of ecological and environmental investigations.}, }
@article {pmid30979882, year = {2019}, author = {Kelly, LW and Nelson, CE and Haas, AF and Naliboff, DS and Calhoun, S and Carlson, CA and Edwards, RA and Fox, MD and Hatay, M and Johnson, MD and Kelly, ELA and Lim, YW and Macherla, S and Quinlan, ZA and Silva, GGZ and Vermeij, MJA and Zgliczynski, B and Sandin, SA and Smith, JE and Rohwer, F}, title = {Diel population and functional synchrony of microbial communities on coral reefs.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1691}, doi = {10.1038/s41467-019-09419-z}, pmid = {30979882}, issn = {2041-1723}, abstract = {On coral reefs, microorganisms are essential for recycling nutrients to primary producers through the remineralization of benthic-derived organic matter. Diel investigations of reef processes are required to holistically understand the functional roles of microbial players in these ecosystems. Here we report a metagenomic analysis characterizing microbial communities in the water column overlying 16 remote forereef sites over a diel cycle. Our results show that microbial community composition is more dissimilar between day and night samples collected from the same site than between day or night samples collected across geographically distant reefs. Diel community differentiation is largely driven by the flux of Psychrobacter sp., which is two-orders of magnitude more abundant during the day. Nighttime communities are enriched with species of Roseobacter, Halomonas, and Alteromonas encoding a greater variety of pathways for carbohydrate catabolism, further illustrating temporal patterns of energetic provisioning between different marine microbes. Dynamic diel fluctuations of microbial populations could also support the efficient trophic transfer of energy posited in coral reef food webs.}, }
@article {pmid30979841, year = {2019}, author = {Dalcin Martins, P and Frank, J and Mitchell, H and Markillie, LM and Wilkins, MJ}, title = {Wetland sediments host diverse microbial taxa capable of cycling alcohols.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.00189-19}, pmid = {30979841}, issn = {1098-5336}, abstract = {Alcohols are commonly derived from the degradation of organic matter, and yet are rarely measured in environmental samples. Wetlands in the Prairie Pothole Region (PPR) support extremely high methane emissions and the highest sulfate reduction rates reported to date, likely contributing to a significant proportion of organic matter mineralization in this system. While ethanol and isopropanol concentrations up to 4-5 mM in PPR wetland pore fluids have been implicated in sustaining these high rates of microbial activity, the mechanisms that support alcohol cycling in this ecosystem are poorly understood. Here we leveraged metagenomic and transcriptomic tools to identify genes, pathways and microorganisms potentially accounting for alcohol cycling in PPR wetlands. Phylogenetic analyses revealed diverse alcohol dehydrogenases and putative substrates. Alcohol dehydrogenase and aldehyde dehydrogenase genes were encoded in 62 metagenome-assembled genomes (MAGs) affiliated to 16 phyla. The most frequently encoded pathway (in 30 MAGs) potentially accounting for alcohol production was a Pyrococcus furiosus-like fermentation which can involve pyruvate:ferredoxin oxidoreductase (PFOR). Transcripts for 93 out of 137 PFOR genes encoded in these MAGs were detected, as well as for 158 out of 243 alcohol dehydrogenase genes retrieved from these same MAGs. Mixed acid fermentation and heterofermentative lactate fermentation were also frequently encoded. Finally, we identified 19 novel putative isopropanol dehydrogenases in 15 MAGs affiliated to Proteobacteria, Acidobacteria, Chloroflexi, Planctomycetes, Ignavibacteriae, Thaumarchaeota, and the candidate divisions KSB1 and Rokubacteria. We conclude that diverse microorganisms may use uncommon and potentially novel pathways to produce ethanol and isopropanol in PPR wetland sediments.ImportanceUnderstanding patterns of organic matter degradation in wetlands is essential for identifying the substrates and mechanisms supporting greenhouse gas production and emissions from wetlands, the main natural source of methane to the atmosphere. Alcohols are common fermentation products but are poorly studied as key intermediates in organic matter degradation in wetlands. By investigating genes, pathways and microorganisms potentially accounting for the high concentrations of ethanol and isopropanol measured in Prairie Pothole wetland sediments, this work advanced our understanding of alcohol fermentations in wetlands linked to extremely high greenhouse gas emissions. Moreover, the novel alcohol dehydrogenases and microbial taxa potentially involved in alcohol metabolism may serve biotechnological efforts in bioengineering commercially valuable alcohol production, and in the discovery of novel isopropanol producers or isopropanol fermentation pathways.}, }
@article {pmid30978480, year = {2019}, author = {Reddy, B and Pandey, J and Dubey, SK}, title = {Assessment of environmental gene tags linked with carbohydrate metabolism and chemolithotrophy associated microbial community in River Ganga.}, journal = {Gene}, volume = {704}, number = {}, pages = {31-41}, doi = {10.1016/j.gene.2019.04.004}, pmid = {30978480}, issn = {1879-0038}, abstract = {The microbial community mediated biogeochemical cycles play important role in global C-cycle and display a sensitive response to environmental changes. Limited information is available on microbial composition and functional diversity controlling biogeochemical cycles in the riverine environment. The Ganga River water and sediment samples were studied for environmental gene tags with reference to carbohydrate metabolism, photoheterotrophy and chemolithotrophy using high throughput shotgun metagenomic sequencing and functional annotation. The diversity of environmental gene tags specific microbial community was annotated against reference sequence database using Kaiju taxonomic classifier. The metagenomic analyses revealed that the river harbored a broad range of carbohydrate and energy metabolism genes. The in-depth investigation of metagenomic data revealed that the enzymes associated with reverse TCA cycle, Calvin-Benson cycle enzyme RuBisCO, starch and sucrose metabolism genes were highly abundant. The enzymes associated with sulfur metabolism such as EC:2.7.7.4 (sulfate to ammonium per sulfate), EC:1.8.1.2, EC:1.8.7.1 (sulfite to H2S) were prevalent in both the class of samples. The principal component analysis of the functional profiles revealed that the water and sediment samples were clustered distinctly suggesting that both the sites had variable abundance of functional genes and associated microbiota. The taxonomic classification showed abundance of Proteobacteria, Actinobacteria and Bacteroidetes phyla. Also, the metagenomic study showed the presence of purple sulfur bacteria viz. Thiodictyon, Nitrosococcus and purple non-sulfur bacteria viz. Bradyrhozobium and Rhodobacter. The study demonstrates that the Ganga River microbiome has prevalence of functional genes involved in carbohydrate anabolism and catabolism, and CO2 fixation with great prospects in cellulose and sulfide degrading enzyme production and characterization.}, }
@article {pmid30977806, year = {2019}, author = {Wang, Z and Wang, Z and Lu, YY and Sun, F and Zhu, S}, title = {SolidBin: Improving Metagenome Binning with Semi-supervised Normalized Cut.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btz253}, pmid = {30977806}, issn = {1367-4811}, abstract = {MOTIVATION: Metagenomic contig binning is an important computational problem in metagenomic research, which aims to cluster contigs from the same genome into the same group. Unlike classical clustering problem, contig binning can utilize known relationships among some of the contigs or the taxonomic identity of some contigs. However, the current state-of-the-art contig binning methods do not make full use of the additional biological information except the coverage and sequence composition of the contigs.<br><br>RESULTS: We developed a novel contig binning method, SolidBin (Semi-supervised Spectral Normalized Cut for Binning), based on semi-supervised spectral clustering. Using sequence feature similarity and/or additional biological information, such as the reliable taxonomy assignments of some contigs, SolidBin constructs two types of prior information: must-link and cannot-link constraints. Must-link constraints mean that the pair of contigs should be clustered into the same group, while cannot-link constraints mean that the pair of contigs should be clustered in different groups. These constraints are then integrated into a classical spectral clustering approach, normalized cut (NCut), for improved contig binning. The performance of SolidBin is compared with five state-of-the-art genome binners, CONCOCT, COCACOLA, MaxBin, MetaBAT and BMC3C on five next-generation sequencing (NGS) benchmark datasets including simulated multi- and single-sample datasets and real multi-sample datasets. The experimental results show that, SolidBin has achieved the best performance in terms of F-score, ARI and NMI, especially while using the real datasets and the single sample dataset.<br><br>AVAILABILITY: https://github.com/sufforest/SolidBin.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid30975220, year = {2019}, author = {Chopyk, J and Kulkarni, P and Nasko, DJ and Bradshaw, R and Kniel, KE and Chiu, P and Sharma, M and Sapkota, AR}, title = {Zero-valent iron sand filtration reduces concentrations of virus-like particles and modifies virome community composition in reclaimed water used for agricultural irrigation.}, journal = {BMC research notes}, volume = {12}, number = {1}, pages = {223}, doi = {10.1186/s13104-019-4251-y}, pmid = {30975220}, issn = {1756-0500}, support = {2016-68007-25064//National Institute of Food and Agriculture/ ; DGE-1632976//National Science Foundation/ ; 8042-32420-006-00-D//Agricultural Research Service/ ; }, abstract = {OBJECTIVE: Zero-valent iron sand filtration can remove multiple contaminants, including some types of pathogenic bacteria, from contaminated water. However, its efficacy at removing complex viral populations, such as those found in reclaimed water used for agricultural irrigation, has not been fully evaluated. Therefore, this study utilized metagenomic sequencing and epifluorescent microscopy to enumerate and characterize viral populations found in reclaimed water and zero-valent iron-sand filtered reclaimed water sampled three times during a larger greenhouse study.<br><br>RESULTS: Zero-valent iron-sand filtered reclaimed water samples had significantly less virus-like particles than reclaimed water samples at all collection dates, with the reclaimed water averaging between 108 and 109 and the zero-valent iron-sand filtered reclaimed water averaging between 106 and 107 virus-like particles per mL. In addition, for both sample types, viral metagenomes (viromes) were dominated by bacteriophages of the order Caudovirales, largely Siphoviridae, and genes related to DNA metabolism. However, the proportion of sequences homologous to bacteria, as well as the abundance of genes possibly originating from a bacterial host, was higher in the viromes of zero-valent iron-sand filtered reclaimed water samples. Overall, zero-valent iron-sand filtered reclaimed water had a lower total concentration of virus-like particles and a different virome community composition compared to unfiltered reclaimed water.}, }
@article {pmid30975208, year = {2019}, author = {Liu, J and Zheng, Y and Lin, H and Wang, X and Li, M and Liu, Y and Yu, M and Zhao, M and Pedentchouk, N and Lea-Smith, DJ and Todd, JD and Magill, CR and Zhang, WJ and Zhou, S and Song, D and Zhong, H and Xin, Y and Yu, M and Tian, J and Zhang, XH}, title = {Proliferation of hydrocarbon-degrading microbes at the bottom of the Mariana Trench.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {47}, doi = {10.1186/s40168-019-0652-3}, pmid = {30975208}, issn = {2049-2618}, support = {91751202//National Natural Science Foundation of China (CN)/ ; 41730530//National Natural Science Foundation of China/ ; 41476112//National Natural Science Foundation of China/ ; 41506154//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: The Mariana Trench is the deepest known site in the Earth's oceans, reaching a depth of ~ 11,000 m at the Challenger Deep. Recent studies reveal that hadal waters harbor distinctive microbial planktonic communities. However, the genetic potential of microbial communities within the hadal zone is poorly understood.<br><br>RESULTS: Here, implementing both culture-dependent and culture-independent methods, we perform extensive analysis of microbial populations and their genetic potential at different depths in the Mariana Trench. Unexpectedly, we observed an abrupt increase in the abundance of hydrocarbon-degrading bacteria at depths > 10,400 m in the Challenger Deep. Indeed, the proportion of hydrocarbon-degrading bacteria at > 10,400 m is the highest observed in any natural environment on Earth. These bacteria were mainly Oleibacter, Thalassolituus, and Alcanivorax genera, all of which include species known to consume aliphatic hydrocarbons. This community shift towards hydrocarbon degraders was accompanied by increased abundance and transcription of genes involved in alkane degradation. Correspondingly, three Alcanivorax species that were isolated from 10,400 m water supplemented with hexadecane were able to efficiently degrade n-alkanes under conditions simulating the deep sea, as did a reference Oleibacter strain cultured at atmospheric pressure. Abundant n-alkanes were observed in sinking particles at 2000, 4000, and 6000 m (averaged 23.5 μg/gdw) and hadal surface sediments at depths of 10,908, 10,909, and 10,911 m (averaged 2.3 μg/gdw). The δ2H values of n-C16/18 alkanes that dominated surface sediments at near 11,000-m depths ranged from - 79 to - 93‰, suggesting that these sedimentary alkanes may have been derived from an unknown heterotrophic source.<br><br>CONCLUSIONS: These results reveal that hydrocarbon-degrading microorganisms are present in great abundance in the deepest seawater on Earth and shed a new light on potential biological processes in this extreme environment.}, }
@article {pmid30975205, year = {2019}, author = {Jin, M and Guo, X and Zhang, R and Qu, W and Gao, B and Zeng, R}, title = {Diversities and potential biogeochemical impacts of mangrove soil viruses.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {58}, doi = {10.1186/s40168-019-0675-9}, pmid = {30975205}, issn = {2049-2618}, support = {DY135-B-04//China Ocean Mineral Resources Research and Development Association/ ; 41606144//National Natural Science Foundation of China/ ; 2016J05098//Natural Science Foundation of Fujian Province/ ; 2015019//Scientific Research Foundation of Third Institute of Oceanography, SOA/ ; 201505026-2//Public Science and Technology Research Funds Projects of Ocean/ ; }, abstract = {BACKGROUND: Mangroves are ecologically and economically important forests of the tropics. As one of the most carbon-rich biomes, mangroves account for 11% of the total input of terrestrial carbon into oceans. Although viruses are considered to significantly influence local and global biogeochemical cycles, little information is available regarding the community structure, genetic diversity and ecological roles of viruses in mangrove ecosystems.<br><br>METHODS: Here, we utilised viral metagenomics sequencing and virome-specific bioinformatics tools to study viral communities in six mangrove soil samples collected from different mangrove habitats in Southern China.<br><br>RESULTS: Mangrove soil viruses were found to be largely uncharacterised. Phylogenetic analyses of the major viral groups demonstrated extensive diversity and previously unknown viral clades and suggested that global mangrove viral communities possibly comprise evolutionarily close genotypes. Comparative analysis of viral genotypes revealed that mangrove soil viromes are mainly affected by marine waters, with less influence coming from freshwaters. Notably, we identified abundant auxiliary carbohydrate-active enzyme (CAZyme) genes from mangrove viruses, most of which participate in biolysis of complex polysaccharides, which are abundant in mangrove soils and organism debris. Host prediction results showed that viral CAZyme genes are diverse and probably widespread in mangrove soil phages infecting diverse bacteria of different phyla.<br><br>CONCLUSIONS: Our results showed that mangrove viruses are diverse and probably directly manipulate carbon cycling by participating in biomass recycling of complex polysaccharides, providing the knowledge essential in revealing the ecological roles of viruses in mangrove ecosystems.}, }
@article {pmid30974826, year = {2019}, author = {Zhang, P and Jin, T and Kumar Sahu, S and Xu, J and Shi, Q and Liu, H and Wang, Y}, title = {The Distribution of Tryptophan-Dependent Indole-3-Acetic Acid Synthesis Pathways in Bacteria Unraveled by Large-Scale Genomic Analysis.}, journal = {Molecules (Basel, Switzerland)}, volume = {24}, number = {7}, pages = {}, doi = {10.3390/molecules24071411}, pmid = {30974826}, issn = {1420-3049}, abstract = {Bacterial indole-3-acetic acid (IAA), an effector molecule in microbial physiology, plays an important role in plant growth-promotion. Here, we comprehensively analyzed about 7282 prokaryotic genomes representing diverse bacterial phyla, combined with root-associated metagenomic data to unravel the distribution of tryptophan-dependent IAA synthesis pathways and to quantify the IAA synthesis-related genes in the plant root environments. We found that 82.2% of the analyzed bacterial genomes were potentially capable of synthesizing IAA from tryptophan (Trp) or intermediates. Interestingly, several phylogenetically diverse bacteria showed a preferential tendency to utilize different pathways and tryptamine and indole-3-pyruvate pathways are most prevalent in bacteria. About 45.3% of the studied genomes displayed multiple coexisting pathways, constituting complex IAA synthesis systems. Furthermore, root-associated metagenomic analyses revealed that rhizobacteria mainly synthesize IAA via indole-3-acetamide (IAM) and tryptamine (TMP) pathways and might possess stronger IAA synthesis abilities than bacteria colonizing other environments. The obtained results refurbished our understanding of bacterial IAA synthesis pathways and provided a faster and less labor-intensive alternative to physiological screening based on genome collections. The better understanding of IAA synthesis among bacterial communities could maximize the utilization of bacterial IAA to augment the crop growth and physiological function.}, }
@article {pmid30974798, year = {2019}, author = {Gantuya, B and El-Serag, HB and Matsumoto, T and Ajami, NJ and Oyuntsetseg, K and Azzaya, D and Uchida, T and Yamaoka, Y}, title = {Gastric Microbiota in Helicobacter pylori-Negative and -Positive Gastritis Among High Incidence of Gastric Cancer Area.}, journal = {Cancers}, volume = {11}, number = {4}, pages = {}, doi = {10.3390/cancers11040504}, pmid = {30974798}, issn = {2072-6694}, support = {15H02657, 16H06279, 16H05191 and 18KK0266//Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan/ ; DK62813//National Institutes of Health Grants/ ; RP150587//Cancer Prevention &amp; Research Institute of Texas grant/ ; NIDDK P30 DK 56338//Center for Gastrointestinal Development, Infection and Injury/ ; }, abstract = {Helicobacter pylori (H. pylori) related chronic gastritis is a well-known major etiological factor for gastric cancer development. However, H. pylori-negative gastritis (HpN) is not well described. We aimed to examine gastric mucosal microbiota in HpN compared to H. pylori-positive gastritis (HpP) and H. pylori-negative non-gastritis group (control). Here, we studied 11 subjects with HpN, 40 with HpP and 24 controls. We performed endoscopy with six gastric biopsies. Comparison groups were defined based on strict histological criteria for the disease and H. pylori diagnosis. We used 16S rRNA gene amplicon sequencing to profile the gastric microbiota according to comparison groups. These results demonstrate that the HpP group had significantly lower bacterial richness by the operational taxonomic unit (OTU) counts, and Shannon and Simpson indices as compared to HpN or controls. The linear discriminant analysis effect size analysis showed the enrichment of Firmicutes, Fusobacteria, Bacteroidetes and Actinobacteria at phylum level in the HpN group. In the age-adjusted multivariate analysis, Streptococcus sp. and Haemophilus parainfluenzae were at a significantly increased risk for HpN (odds ratio 18.9 and 12.3, respectively) based on abundance. Treponema sp. was uniquely found in HpN based on occurrence. In this paper, we conclude that Streptococcus sp., Haemophilus parainfluenzae and Treponema sp. are candidate pathogenic bacterial species for HpN. These results if confirmed may have important clinical implications.}, }
@article {pmid30973755, year = {2019}, author = {Liu, J and Li, H and Zhu, W and Mao, S}, title = {Dynamic changes in rumen fermentation and bacterial community following rumen fluid transplantation in a sheep model of rumen acidosis: implications for rumen health in ruminants.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {}, number = {}, pages = {fj201802456R}, doi = {10.1096/fj.201802456R}, pmid = {30973755}, issn = {1530-6860}, abstract = {Over the years, rumen fluid transplantation (RT) has been successfully applied to treat acute rumen acidosis in ruminants, but how it functions in the ruminal microbial homeostasis and host function remains largely unknown. Here, we investigated the dynamic changes of rumen fermentation and bacterial communities following RT and its beneficial effects on rumen epithelial morphology and function in a sheep model of rumen acidosis. The results showed that RT resulted in dynamic changes in rumen fermentation and increased the concentrations of total volatile fatty acid, acetate, propionate, and butyrate, but it decreased the levels of lactate and LPS in the rumen. Illumina MiSeq Sequencing data showed that RT facilitated rapid rebuilt of ruminal bacterial homeostasis (8 d in control vs. 2 d in RT) from a markedly dysbiotic acidosis state to a healthy level (similar with those of donors). At the genus level, RT increased the relative abundance of unclassified Bacteroidales, unclassified Prevotellaceae, unclassified Ruminococcaceae, and Acetitomaculum. Additionally, RT also accelerated recovery of the predicted metagenomic function of ruminal bacteria. Rumen papillae morphology results showed that RT alleviated the damage of rumen epithelia induced by acute rumen acidosis and increased the length of rumen papillae. Furthermore, real-time PCR results showed that RT modulated mRNA expression of genes related to cytokines and tight junctions in the rumen epithelia. In summary, these results reveal that RT accelerates recovery of rumen fermentation and bacterial homeostasis and modulates rumen epithelial morphology and function for sheep suffering from rumen acidosis.-Liu, J., Li, H., Zhu, W., Mao, S. Dynamic changes in rumen fermentation and bacterial community following rumen fluid transplantation in a sheep model of rumen acidosis: implications for rumen health in ruminants.}, }
@article {pmid30973601, year = {2018}, author = {Graells, T and Ishak, H and Larsson, M and Guy, L}, title = {The all-intracellular order Legionellales is unexpectedly diverse, globally distributed and lowly abundant.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {12}, pages = {}, doi = {10.1093/femsec/fiy185}, pmid = {30973601}, issn = {1574-6941}, abstract = {Legionellales is an order of the Gammaproteobacteria, only composed of host-adapted, intracellular bacteria, including the accidental human pathogens Legionella pneumophila and Coxiella burnetii. Although the diversity in terms of lifestyle is large across the order, only a few genera have been sequenced, owing to the difficulty to grow intracellular bacteria in pure culture. In particular, we know little about their global distribution and abundance. Here, we analyze 16/18S rDNA amplicons both from tens of thousands of published studies and from two separate sampling campaigns in and around ponds and in a silver mine. We demonstrate that the diversity of the order is much larger than previously thought, with over 450 uncultured genera. We show that Legionellales are found in about half of the samples from freshwater, soil and marine environments and quasi-ubiquitous in man-made environments. Their abundance is low, typically 0.1%, with few samples up to 1%. Most Legionellales OTUs are globally distributed, while many do not belong to a previously identified species. This study sheds a new light on the ubiquity and diversity of one major group of host-adapted bacteria. It also emphasizes the need to use metagenomics to better understand the role of host-adapted bacteria in all environments.}, }
@article {pmid30972461, year = {2019}, author = {Williams, W and Kunorozva, L and Klaiber, I and Henkel, M and Pfannstiel, J and Van Zyl, LJ and Hausmann, R and Burger, A and Trindade, M}, title = {Novel metagenome-derived ornithine lipids identified by functional screening for biosurfactants.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00253-019-09768-1}, pmid = {30972461}, issn = {1432-0614}, support = {UID 87326//South African National Research Foundation/ ; UWC 014-TSF//Technology Innovation Agency (ZA)/ ; 105876//South Africa- Germany Bilateral/ ; }, abstract = {Biosurfactants are amphiphilic molecules that interact with the surfaces of liquids leading to many useful applications. Most biosurfactants have been identified from cultured microbial sources, leaving a largely untapped resource of uncultured bacteria with potentially novel biosurfactant structures. To access the uncultured bacteria, a metagenomic library was constructed in Escherichia coli from environmental DNA within an E. coli, Pseudomonas putida and Streptomyces lividans shuttle vector. Phenotypic screening of the library in E. coli and P. putida by the paraffin spray assay identified a P. putida clone with biosurfactant activity. Sequence analysis and transposon mutagenesis confirmed that an ornithine acyl-ACP N-acyltransferase was responsible for the activity. Although the fosmid was not active in E. coli, overexpression of the olsB gene could be achieved under the control of the inducible T7 promoter, resulting in lyso-ornithine lipid production and biosurfactant activity in the culture supernatants. Screening for activity in more than one host increases the range of sequences that can be identified through metagenomic, since olsB would not have been identified if only E. coli had been used as a host. The potential of lyso-ornithine lipids as a biosurfactant has not been fully explored. Here, we present several biosurfactant parameters of lyso-ornithine lipid to assess its suitability for industrial application.}, }
@article {pmid30971183, year = {2019}, author = {Kurilshikov, A and van den Munckhof, IC and Chen, L and Bonder, MJ and Schraa, K and Rutten, J and Riksen, NP and de Graaf, J and Oosting, M and Sanna, S and Joosten, LA and van der Graaf, M and Brand, T and Koonen, DP and van Faassen, MJ and Slagboom, PE and Xavier, RJ and Kuipers, F and Hofker, M and Wijmenga, C and Netea, MG and Zhernakova, A and Fu, J}, title = {Gut Microbial Associations to Plasma Metabolites Linked to Cardiovascular Phenotypes and Risk: A Cross-Sectional Study.}, journal = {Circulation research}, volume = {}, number = {}, pages = {}, doi = {10.1161/CIRCRESAHA.118.314642}, pmid = {30971183}, issn = {1524-4571}, abstract = {RATIONALE: Altered gut microbial composition has been linked to cardiovascular diseases (CVD), but its functional links to host metabolism and immunity in relation to CVD development remain unclear.<br><br>OBJECTIVE: To systematically assess functional links between the microbiome and the plasma metabolome, cardiometabolic phenotypes and CVD risk and to identify diet-microbe-metabolism-immune interactions in well-documented cohorts.<br><br>METHODS AND RESULTS: We assessed metagenomics-based microbial associations between 231 plasma metabolites and microbial species and pathways in the population-based Lifelines-DEEP cohort (n=978) and a clinical obesity cohort (n=297). After correcting for age, gender and BMI, the gut microbiome could explain up to 11.1% and 16.4% of the variation in plasma metabolites in the population-based and obesity cohorts, respectively. Obese-specific microbial associations were found for lipid compositions in the VLDL, IDL and LDL lipoprotein subclasses. Bacterial L-methionine biosynthesis and a Ruminococcus species were associated to cardiovascular phenotypes in obese individuals, namely atherosclerosis and liver fat content, respectively. Integration of microbiome-diet-inflammation analysis in relation to metabolic risk score of CVD in the population cohort revealed 48 microbial pathways associated to CVD risk that were largely independent of diet and inflammation. Our data also showed that plasma levels rather than fecal levels of short chain fatty acids were relevant to inflammation and CVD risk.<br><br>CONCLUSIONS: This study presents the largest metagenome-based association study on plasma metabolism and microbiome relevance to diet, inflammation, CVD risk and cardiometabolic phenotypes in both population-based and clinical obesity cohorts. Our findings identified novel bacterial species and pathways that associated to specific lipoprotein subclasses and revealed functional links between the gut microbiome and host health that provide a basis for developing microbiome-targeted therapy for disease prevention and treatment.}, }
@article {pmid30969980, year = {2019}, author = {Mishra, N and Fagbo, SF and Alagaili, AN and Nitido, A and Williams, SH and Ng, J and Lee, B and Durosinlorun, A and Garcia, JA and Jain, K and Kapoor, V and Epstein, JH and Briese, T and Memish, ZA and Olival, KJ and Lipkin, WI}, title = {A viral metagenomic survey identifies known and novel mammalian viruses in bats from Saudi Arabia.}, journal = {PloS one}, volume = {14}, number = {4}, pages = {e0214227}, doi = {10.1371/journal.pone.0214227}, pmid = {30969980}, issn = {1932-6203}, abstract = {Bats are implicated as natural reservoirs for a wide range of zoonotic viruses including SARS and MERS coronaviruses, Ebola, Marburg, Nipah, Hendra, Rabies and other lyssaviruses. Accordingly, many One Health surveillance and viral discovery programs have focused on bats. In this report we present viral metagenomic data from bats collected in the Kingdom of Saudi Arabia [KSA]. Unbiased high throughput sequencing of fecal samples from 72 bat individuals comprising four species; lesser mouse-tailed bat (Rhinopoma hardwickii), Egyptian tomb bat (Taphozous perforatus), straw-colored fruit bat (Eidolon helvum), and Egyptian fruit bat (Rousettus aegyptiacus) revealed molecular evidence of a diverse set of viral families: Picornaviridae (hepatovirus, teschovirus, parechovirus), Reoviridae (rotavirus), Polyomaviridae (polyomavirus), Papillomaviridae (papillomavirus), Astroviridae (astrovirus), Caliciviridae (sapovirus), Coronaviridae (coronavirus), Adenoviridae (adenovirus), Paramyxoviridae (paramyxovirus), and unassigned mononegavirales (chuvirus). Additionally, we discovered a bastro-like virus (Middle East Hepe-Astrovirus), with a genomic organization similar to Hepeviridae. However, since it shared homology with Hepeviridae and Astroviridae at ORF1 and in ORF2, respectively, the newly discovered Hepe-Astrovirus may represent a phylogenetic bridge between Hepeviridae and Astroviridae.}, }
@article {pmid30969386, year = {2019}, author = {Johnson, G}, title = {High throughput DNA extraction of legume root nodules for rhizobial metagenomics.}, journal = {AMB Express}, volume = {9}, number = {1}, pages = {47}, doi = {10.1186/s13568-019-0771-z}, pmid = {30969386}, issn = {2191-0855}, abstract = {A novel combination of tissue homogenization, cell lysis, and DNA purification techniques was developed for isolating total DNA from whole legume root nodules on an automated robotic system. Silica dehydrated root nodules from soy bean, Glycine max cv. Tara, and mung bean, Vigna radiata cv. Crystal, were homogenized in 96-well plates and were enzymatically and chemically lysed before being loaded into the AutoGenprep 965 for automated phenol-chloroform based DNA isolation. The resulting DNAs were of relatively high concentration, low fragmentation, and free of phenolic and polysaccharide contaminants. In contrast to manual methods, this adaptation of the Autogen Prep automated DNA extraction instrument allows for 100's to 1000's of samples to be prepared in a fraction of the time and cost.}, }
@article {pmid30968165, year = {2019}, author = {Rossmassler, K and Snow, CD and Taggart, D and Brown, C and De Long, SK}, title = {Advancing biomarkers for anaerobic o-xylene biodegradation via metagenomic analysis of a methanogenic consortium.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00253-019-09762-7}, pmid = {30968165}, issn = {1432-0614}, support = {CBET 1438660//National Science Foundation/ ; }, abstract = {Quantifying functional biomarker genes and their transcripts provides critical lines of evidence for contaminant biodegradation; however, accurate quantification depends on qPCR primers that contain no, or minimal, mismatches with the target gene. Developing accurate assays has been particularly challenging for genes encoding fumarate-adding enzymes (FAE) due to the high level of genetic diversity in this gene family. In this study, metagenomics applied to a field-derived, o-xylene-degrading methanogenic consortium revealed genes encoding FAE that would not be accurately quantifiable by any previously available PCR assays. Sequencing indicated that a gene similar to the napthylmethylsuccinate synthase gene (nmsA) was most abundant, although benzylsuccinate synthase genes (bssA) also were present along with genes encoding alkylsuccinate synthase (assA). Upregulation of the nmsA-like gene was observed during o-xylene degradation. Protein homology modeling indicated that mutations in the active site, relative to a BssA that acts on toluene, increase binding site volume and accessibility, potentially to accommodate the relatively larger o-xylene. The new nmsA-like gene was also detected at substantial concentrations at field sites with a history of xylene contamination.}, }
@article {pmid30967123, year = {2019}, author = {Du, N and Chen, J and Sun, Y}, title = {Improving the sensitivity of long read overlap detection using grouped short k-mer matches.}, journal = {BMC genomics}, volume = {20}, number = {Suppl 2}, pages = {190}, doi = {10.1186/s12864-019-5475-x}, pmid = {30967123}, issn = {1471-2164}, abstract = {BACKGROUND: Single-molecule, real-time sequencing (SMRT) developed by Pacific BioSciences produces longer reads than second-generation sequencing technologies such as Illumina. The increased read length enables PacBio sequencing to close gaps in genome assembly, reveal structural variations, and characterize the intra-species variations. It also holds the promise to decipher the community structure in complex microbial communities because long reads help metagenomic assembly. One key step in genome assembly using long reads is to quickly identify reads forming overlaps. Because PacBio data has higher sequencing error rate and lower coverage than popular short read sequencing technologies (such as Illumina), efficient detection of true overlaps requires specially designed algorithms. In particular, there is still a need to improve the sensitivity of detecting small overlaps or overlaps with high error rates in both reads. Addressing this need will enable better assembly for metagenomic data produced by third-generation sequencing technologies.<br><br>RESULTS: In this work, we designed and implemented an overlap detection program named GroupK, for third-generation sequencing reads based on grouped k-mer hits. While using k-mer hits for detecting reads' overlaps has been adopted by several existing programs, our method uses a group of short k-mer hits satisfying statistically derived distance constraints to increase the sensitivity of small overlap detection. Grouped k-mer hit was originally designed for homology search. We are the first to apply group hit for long read overlap detection. The experimental results of applying our pipeline to both simulated and real third-generation sequencing data showed that GroupK enables more sensitive overlap detection, especially for datasets of low sequencing coverage.<br><br>CONCLUSIONS: GroupK is best used for detecting small overlaps for third-generation sequencing data. It provides a useful supplementary tool to existing ones for more sensitive and accurate overlap detection. The source code is freely available at https://github.com/Strideradu/GroupK .}, }
@article {pmid30967115, year = {2019}, author = {Guzmán-Sáenz, A and Haiminen, N and Basu, S and Parida, L}, title = {Signal enrichment with strain-level resolution in metagenomes using topological data analysis.}, journal = {BMC genomics}, volume = {20}, number = {Suppl 2}, pages = {194}, doi = {10.1186/s12864-019-5490-y}, pmid = {30967115}, issn = {1471-2164}, abstract = {BACKGROUND: A metagenome is a collection of genomes, usually in a micro-environment, and sequencing a metagenomic sample en masse is a powerful means for investigating the community of the constituent microorganisms. One of the challenges is in distinguishing between similar organisms due to rampant multiple possible assignments of sequencing reads, resulting in false positive identifications. We map the problem to a topological data analysis (TDA) framework that extracts information from the geometric structure of data. Here the structure is defined by multi-way relationships between the sequencing reads using a reference database.<br><br>RESULTS: Based primarily on the patterns of co-mapping of the reads to multiple organisms in the reference database, we use two models: one a subcomplex of a Barycentric subdivision complex and the other a Čech complex. The Barycentric subcomplex allows a natural mapping of the reads along with their coverage of organisms while the Čech complex takes simply the number of reads into account to map the problem to homology computation. Using simulated genome mixtures we show not just enrichment of signal but also microbe identification with strain-level resolution.<br><br>CONCLUSIONS: In particular, in the most refractory of cases where alternative algorithms that exploit unique reads (i.e., mapped to unique organisms) fail, we show that the TDA approach continues to show consistent performance. The Čech model that uses less information is equally effective, suggesting that even partial information when augmented with the appropriate structure is quite powerful.}, }
@article {pmid30967110, year = {2019}, author = {Hua, K and Zhang, X}, title = {Estimating the total genome length of a metagenomic sample using k-mers.}, journal = {BMC genomics}, volume = {20}, number = {Suppl 2}, pages = {183}, doi = {10.1186/s12864-019-5467-x}, pmid = {30967110}, issn = {1471-2164}, abstract = {BACKGROUND: Metagenomic sequencing is a powerful technology for studying the mixture of microbes or the microbiomes on human and in the environment. One basic task of analyzing metagenomic data is to identify the component genomes in the community. This task is challenging due to the complexity of microbiome composition, limited availability of known reference genomes, and usually insufficient sequencing coverage.<br><br>RESULTS: As an initial step toward understanding the complete composition of a metagenomic sample, we studied the problem of estimating the total length of all distinct component genomes in a metagenomic sample. We showed that this problem can be solved by estimating the total number of distinct k-mers in all the metagenomic sequencing data. We proposed a method for this estimation based on the sequencing coverage distribution of observed k-mers, and introduced a k-mer redundancy index (KRI) to fill in the gap between the count of distinct k-mers and the total genome length. We showed the effectiveness of the proposed method on a set of carefully designed simulation data corresponding to multiple situations of true metagenomic data. Results on real data indicate that the uncaptured genomic information can vary dramatically across metagenomic samples, with the potential to mislead downstream analyses.<br><br>CONCLUSIONS: We proposed the question of how long the total genome length of all different species in a microbial community is and introduced a method to answer it.}, }
@article {pmid30967109, year = {2019}, author = {Abe, K and Hirayama, M and Ohno, K and Shimamura, T}, title = {ENIGMA: an enterotype-like unigram mixture model for microbial association analysis.}, journal = {BMC genomics}, volume = {20}, number = {Suppl 2}, pages = {191}, doi = {10.1186/s12864-019-5476-9}, pmid = {30967109}, issn = {1471-2164}, abstract = {BACKGROUND: One of the major challenges in microbial studies is detecting associations between microbial communities and a specific disease. A specialized feature of microbiome count data is that intestinal bacterial communities form clusters called as &quot;enterotype&quot;, which are characterized by differences in specific bacterial taxa, making it difficult to analyze these data under health and disease conditions. Traditional probabilistic modeling cannot distinguish between the bacterial differences derived from enterotype and those related to a specific disease.<br><br>RESULTS: We propose a new probabilistic model, named as ENIGMA (Enterotype-like uNIGram mixture model for Microbial Association analysis), which can be used to address these problems. ENIGMA enabled simultaneous estimation of enterotype-like clusters characterized by the abundances of signature bacterial genera and the parameters of environmental effects associated with the disease.<br><br>CONCLUSION: In the simulation study, we evaluated the accuracy of parameter estimation. Furthermore, by analyzing the real-world data, we detected the bacteria related to Parkinson's disease. ENIGMA is implemented in R and is available from GitHub (https://github.com/abikoushi/enigma).}, }
@article {pmid30964891, year = {2019}, author = {Wee, WY and Dutta, A and Jayaraj, J and Choo, SW}, title = {Comparative genome sequencing and analyses of Mycobacterium cosmeticum reveal potential for biodesulfization of gasoline.}, journal = {PloS one}, volume = {14}, number = {4}, pages = {e0214663}, doi = {10.1371/journal.pone.0214663}, pmid = {30964891}, issn = {1932-6203}, abstract = {Mycobacterium cosmeticum is a nontuberculous Mycobacterium recovered from different water sources including household potable water and water collected at nail salon. Individual cases of this bacterium have been reported to be associated with gastrointestinal tract infections. Here we present the first whole-genome study and comparative analysis of two new clinically-derived Mycobacterium sp. UM_RHS (referred as UM_RHS after this) and Mycobacterium sp. UM_NYF (referred as UM_NYF after this) isolated from patients in Indonesia and Malaysia respectively to have a better understanding of the biological characteristic of these isolates. Both strains are likely Mycobacterium cosmeticum as supported by the evidence from molecular phylogenetic, comparative genomic and Average Nucleotide Identity (ANI) analyses. We found the presence of a considerably large number of putative virulence genes in the genomes of UM_RHS and UM_NYF. Interestingly, we also found a horizontally transferred genomic island carrying a putative dsz operon proposing that they may have potential to perform biodesulfization of dibenzothiophene (DBT) that may be effective in cost reduction and air pollution during fuel combustion. This comparative study may provide new insights into M. cosmeticum and serve as an important reference for future functional studies of this bacterial species.}, }
@article {pmid30964393, year = {2019}, author = {Navarro-Barrón, E and Hernández, C and Llera-Herrera, R and García-Gasca, A and Gómez-Gil, B}, title = {Overfeeding a High-Fat Diet Promotes Sex-Specific Alterations on the Gut Microbiota of the Zebrafish (Danio rerio).}, journal = {Zebrafish}, volume = {}, number = {}, pages = {}, doi = {10.1089/zeb.2018.1648}, pmid = {30964393}, issn = {1557-8542}, abstract = {Diet modulates the gut microbiota and is one of the main factors promoting obesity and overweight. In the present study, we investigated the effect of a high-fat diet (HFD) on the gut microbiota of the zebrafish (Danio rerio). Fish were separated into three groups and fed in different regimes: low fat, high fat, and high fat overfed; the experiments were performed on males and females separately. We analyzed more than 2.6 million sequences of variable region V3 of the 16S rRNA gene generated by the Illumina Miniseq platform, clustered to 97% similarity with vsearch and classified with the EzBioCloud database. The weight gain, condition factor (K), and body mass index were calculated as indicators of obesity. Multivariate analysis (PERMANOVA and ANOSIM) and diversity indices (Shannon and Dominance) revealed that overfeeding a HFD disturbs the gut microbiota differently in males and females suggesting that sex is a significant factor (p < 0.05) for the composition of the gut microbiota of zebrafish. The results also indicate that a HFD provided in a basal caloric regime does not promote obesity or alterations in the gut microbiota.}, }
@article {pmid30962514, year = {2019}, author = {Tan, S and Liu, J and Fang, Y and Hedlund, BP and Lian, ZH and Huang, LY and Li, JT and Huang, LN and Li, WJ and Jiang, HC and Dong, HL and Shu, WS}, title = {Insights into ecological role of a new deltaproteobacterial order Candidatus Acidulodesulfobacterales by metagenomics and metatranscriptomics.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0415-y}, pmid = {30962514}, issn = {1751-7370}, support = {U1501232//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31570506//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41603074//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31600077//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41773132//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41622106//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31570500//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41630103//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2016A030312003//Natural Science Foundation of Guangdong Province (Guangdong Natural Science Foundation)/ ; DEB-1557042//National Science Foundation (NSF)/ ; }, abstract = {Several abundant but yet uncultivated bacterial groups exist in extreme iron- and sulfur-rich environments, and the physiology, biodiversity, and ecological roles of these bacteria remain a mystery. Here we retrieved four metagenome-assembled genomes (MAGs) from an artificial acid mine drainage (AMD) system, and propose they belong to a new deltaproteobacterial order, Candidatus Acidulodesulfobacterales. The distribution pattern of Ca. Acidulodesulfobacterales in AMDs across Southeast China correlated strongly with ferrous iron. Reconstructed metabolic pathways and gene expression profiles showed that they were likely facultatively anaerobic autotrophs capable of nitrogen fixation. In addition to dissimilatory sulfate reduction, encoded by dsrAB, dsrD, dsrL, and dsrEFH genes, these microorganisms might also oxidize sulfide, depending on oxygen concentration and/or oxidation reduction potential. Several genes with homology to those involved in iron metabolism were also identified, suggesting their potential role in iron cycling. In addition, the expression of abundant resistance genes revealed the mechanisms of adaptation and response to the extreme environmental stresses endured by these organisms in the AMD environment. These findings shed light on the distribution, diversity, and potential ecological role of the new order Ca. Acidulodesulfobacterales in nature.}, }
@article {pmid30962259, year = {2019}, author = {Shrestha, S and Rasmussen, SH and Pottegård, A and Ängquist, LH and Jess, T and Allin, KH and Bjerregaard, LG and Baker, JL}, title = {Associations between adult height and type 2 diabetes mellitus: a systematic review and meta-analysis of observational studies.}, journal = {Journal of epidemiology and community health}, volume = {}, number = {}, pages = {}, doi = {10.1136/jech-2018-211567}, pmid = {30962259}, issn = {1470-2738}, abstract = {BACKGROUND: Although short adult height is generally associated with increased risks of type 2 diabetes mellitus (T2DM), there are large inconsistencies across studies. The aims of this study were to describe and quantify currently available evidence on the association between adult height and T2DM, to examine whether the reported associations differ by sex, and to examine the shapes of the height and T2DM associations.<br><br>METHODS: Relevant literature was identified using PubMed (1966-May 2018), EMBASE (1947-May 2018) and Google Scholar (May 2018). We identified cross-sectional and cohort studies with original publications on human subjects, which were included in a random-effects meta-analysis.<br><br>RESULTS: From 15 971 identified sources, 25 studies met the inclusion criteria for the systematic review (N=401 562 individuals). From these 25 studies, 16 (9 cross-sectional studies and 7 cohort studies) were included in the meta-analysis (n=261 496 individuals). The overall random-effects meta-analysis indicated an inverse association between adult height and T2DM (effect estimate=0.88, 95% CI 0.81 to 0.95). No sex differences in the associations between adult height and T2DM were found (effect estimate for men: 0.86, 95% CI 0.75 to 0.99; effect estimate for women: 0.90; 95% CI 0.80 to 1.01; p value for sex interaction=0.80). Due to lack of data, results on the shape of the association between height and T2DM were inconclusive.<br><br>CONCLUSIONS: Shorter height is associated with an increased risk of T2DM and the association does not significantly differ by sex. The currently available data are insufficient to support conclusions regarding the shape of the association between height and T2DM.<br><br>TRIAL REGISTRATION NUMBER: CRD42017062446.}, }
@article {pmid30962186, year = {2019}, author = {Shah, NB and Allegretti, AS and Nigwekar, SU and Kalim, S and Zhao, S and Lelouvier, B and Servant, F and Serena, G and Thadhani, RI and Raj, DS and Fasano, A}, title = {Blood Microbiome Profile in CKD : A Pilot Study.}, journal = {Clinical journal of the American Society of Nephrology : CJASN}, volume = {}, number = {}, pages = {}, doi = {10.2215/CJN.12161018}, pmid = {30962186}, issn = {1555-905X}, abstract = {BACKGROUND AND OBJECTIVES: The association between gut dysbiosis, high intestinal permeability, and endotoxemia-mediated inflammation is well established in CKD. However, changes in the circulating microbiome in patients with CKD have not been studied. In this pilot study, we compare the blood microbiome profile between patients with CKD and healthy controls using 16S ribosomal DNA sequencing.<br><br>Blood bacterial DNA was studied in buffy coat samples quantitatively by 16S PCR and qualitatively by 16S targeted metagenomic sequencing using a molecular pipeline specifically optimized for blood samples in a cross-sectional study comparing 20 nondiabetic patients with CKD and 20 healthy controls.<br><br>RESULTS: There were 22 operational taxonomic units significantly different between the two groups. 16S metagenomic sequencing revealed a significant reduction in α diversity (Chao1 index) in the CKD group compared with healthy controls (127±18 versus 145±31; P=0.04). Proteobacteria phylum, Gammaproteobacteria class, and Enterobacteriaceae and Pseudomonadaceae families were more abundant in the CKD group compared with healthy controls. Median 16S ribosomal DNA levels did not significantly differ between CKD and healthy groups (117 versus 122 copies/ng DNA; P=0.38). GFR correlated inversely with the proportion of Proteobacteria (r=-0.54; P≤0.01).<br><br>CONCLUSIONS: Our pilot study demonstrates qualitative differences in the circulating microbiome profile with lower α diversity and significant taxonomic variations in the blood microbiome in patients with CKD compared with healthy controls.}, }
@article {pmid30962101, year = {2019}, author = {Chen, YP and Liaw, LL and Kuo, JT and Wu, HT and Wang, GH and Chen, XQ and Tsai, CF and Young, CC}, title = {Evaluation of synthetic gene encoding α-galactosidase through metagenomic sequencing of paddy soil.}, journal = {Journal of bioscience and bioengineering}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jbiosc.2019.03.006}, pmid = {30962101}, issn = {1347-4421}, abstract = {Many genes of industrial relevance can be found in soil. In this study, metagenome sequencing of paddy soil was performed with 55.68 Gb sequences and 1,787,113 putative open reading frames (ORFs). The functional profiles and metabolic pathway of soil metagenomes were examined using Gene Ontology, Metagenomics RAST, and Kyoto Encyclopedia of Genes and Genomes. To verify the protein function and assembly of ORFs, a putative gene encoding α-galactosidase, namely GalR, which shares 65% identity with an unpublished glycoside hydrolase (GH) 27 family protein, was synthesized using its optimal codon for overexpression in Escherichia coli. GalR was successfully obtained and characterized. The optimal temperature and pH for GalR activity were 30°C and pH 9, respectively. Enzymatic activity indicated that GalR was alkaliphilic and different from acidophilic α-galactosidase in the GH 27 family. Furthermore, 50% of the relative activity of GalR can be attained for 1.7 and 0.7 h preincubation at 40°C and 50°C, respectively. Significant inhibition of GalR was observed in the presence of ethylenediaminetetraacetic acid (EDTA), MgCl2, sodium dodecyl sulfate (SDS), and H2O2; however, it was resistant to 0.1% methanol and ethanol and was slightly activated with NaCl and KCl. The specific activity of GalR was achieved at 11.6 and 0.59 μmol/min/mg of protein using p-nitrophenyl-α-d-galactopyranoside and raffinose as substrates, respectively. Consequently, the metagenomic sequencing-based strategy can provide information for mining novel genes.}, }
@article {pmid30962029, year = {2019}, author = {Brink, M and Rhode, C and Macey, BM and Christison, KW and Roodt-Wilding, R}, title = {Metagenomic assessment of body surface bacterial communities of the sea urchin, Tripneustes gratilla.}, journal = {Marine genomics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.margen.2019.03.010}, pmid = {30962029}, issn = {1876-7478}, abstract = {Sea urchins, including Tripneustes gratilla, are susceptible to a disease known as bald sea urchin disease, which has the potential to lead to economic losses in this emerging aquaculture industry in South Africa. This disease is characterized by lesions that form on sea urchin exoskeletal surfaces. This study aimed to characterize the body surface bacterial communities associated with T. gratilla, using a 16S rDNA gene metagenomics approach, to provide insight into the bacterial agents associated with this aquaculture species, as well as with this balding disease. Bacterial samples were collected from non-lesioned healthy animals obtained from natural locations along the eastern coast of South Africa, as well as from different cultured cohorts: non-lesioned healthy-, lesioned diseased- and non-lesioned stressed animals. A total of 1,067,515 individual bacterial operational taxonomic units (OTUs) were identified, belonging to 133 family-, 123 genus- and 113 species level OTU groups. Alpha diversity analyses, based on Chao1, Shannon and Simpson indices, showed that there were no statistically significant differences (ANOVA; P > 0.05) between the respective cohorts, as all cohorts displayed a high degree of bacterial diversity. Similarly, beta diversity analyses (Non-metric multidimensional scaling) showed a large degree of overlapping OTUs across the four cohorts. Within each cohort, various OTUs commonly associated with marine environments were found, predominantly belonging to the families Vibrionaceae, Saprospiraceae, Flavobacteriaceae and Sphingomonadaceae. Differential abundance analysis (DESeq2) revealed that OTUs that are differentially abundant across cohorts were likely not responsible for this balding disease, suggesting that complex bacterial agents, rather than a specific pathogenic agent, are likely causing this disease. Furthermore, the putative metabolic functions assigned to the bacterial communities showed that heterotrophic bacteria appear to be responsible for tissue lysis of degrading animal matter. The results from this study, obtained through univariate and multivariate-based approaches, contributes to future management strategies of this emerging aquaculture species by providing insight into the bacterial communities associated with both natural and cultured environments.}, }
@article {pmid30961537, year = {2019}, author = {Frickmann, H and Künne, C and Hagen, RM and Podbielski, A and Normann, J and Poppert, S and Looso, M and Kreikemeyer, B}, title = {Next-generation sequencing for hypothesis-free genomic detection of invasive tropical infections in poly-microbially contaminated, formalin-fixed, paraffin-embedded tissue samples - a proof-of-principle assessment.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {75}, doi = {10.1186/s12866-019-1448-0}, pmid = {30961537}, issn = {1471-2180}, support = {12K2-S-451315//German Ministry of Defense (MoD)/ ; EU-EFRE//European Funds for Regional Development/ ; }, abstract = {BACKGROUND: The potential of next-generation sequencing (NGS) for hypothesis-free pathogen diagnosis from (poly-)microbially contaminated, formalin-fixed, paraffin embedded tissue samples from patients with invasive fungal infections and amebiasis was investigated. Samples from patients with chromoblastomycosis (n = 3), coccidioidomycosis (n = 2), histoplasmosis (n = 4), histoplasmosis or cryptococcosis with poor histological discriminability (n = 1), mucormycosis (n = 2), mycetoma (n = 3), rhinosporidiosis (n = 2), and invasive Entamoeba histolytica infections (n = 6) were analyzed by NGS (each one Illumina v3 run per sample). To discriminate contamination from putative infections in NGS analysis, mean and standard deviation of the number of specific sequence fragments (paired reads) were determined and compared in all samples examined for the pathogens in question.<br><br>RESULTS: For matches between NGS results and histological diagnoses, a percentage of species-specific reads greater than the 4th standard deviation above the mean value of all 23 assessed sample materials was required. Potentially etiologically relevant pathogens could be identified by NGS in 5 out of 17 samples of patients with invasive mycoses and in 1 out of 6 samples of patients with amebiasis.<br><br>CONCLUSIONS: The use of NGS for hypothesis-free pathogen diagnosis from contamination-prone formalin-fixed, paraffin-embedded tissue requires further standardization.}, }
@article {pmid30961521, year = {2019}, author = {Dos Santos, HRM and Argolo, CS and Argôlo-Filho, RC and Loguercio, LL}, title = {A 16S rDNA PCR-based theoretical to actual delta approach on culturable mock communities revealed severe losses of diversity information.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {74}, doi = {10.1186/s12866-019-1446-2}, pmid = {30961521}, issn = {1471-2180}, abstract = {BACKGROUND: Subunits of ribosomal RNA genes (rDNAs) characterized by PCR-based protocols have been the proxy for studies in microbial taxonomy, phylogenetics, evolution and ecology. However, relevant factors have shown to interfere in the experimental outputs in a variety of systems. In this work, a 'theoretical' to 'actual' delta approach was applied to data on culturable mock bacterial communities (MBCs) to study the levels of losses in operational taxonomic units (OTUs) detectability. Computational and lab-bench strategies based on 16S rDNA amplification by 799F and U1492R primers were employed, using a fingerprinting method with highly improved detectability of fragments as a case-study tool. MBCs were of two major types: in silico MBCs, assembled with database-retrieved sequences, and in vitro MBCs, with AluI digestions of PCR data generated from culturable endophytes isolated from cacao trees.<br><br>RESULTS: Interfering factors for the 16 s rDNA amplifications, such as the type of template, direct and nested PCR, proportion of chloroplast DNA from a tropical plant source (Virola officinalis), and biased-amplification by the primers resulted in altered bacterial 16S rDNA amplification, both on MBCs and V. officinalis leaf-extracted DNA. For the theoretical data, the maximum number of fragments for in silico and in vitro cuts were not significantly different from each other. Primers' preferences for certain sequences were detected, depending on the MBCs' composition prior to PCR. The results indicated overall losses from 2.3 up to 8.2 times in the number of OTUs detected from actual AluI digestions of MBCs when compared to in silico and in vitro theoretical data.<br><br>CONCLUSIONS: Due to all those effects, the final amplification profile of the bacterial community assembled was remarkably simplified when compared to the expected number of detectable fragments known to be present in the MBC. From these findings, the scope of hypotheses generation and conclusions from experiments based on PCR amplifications of bacterial communities was discussed.}, }
@article {pmid30958827, year = {2019}, author = {Martí, JM}, title = {Recentrifuge: Robust comparative analysis and contamination removal for metagenomics.}, journal = {PLoS computational biology}, volume = {15}, number = {4}, pages = {e1006967}, doi = {10.1371/journal.pcbi.1006967}, pmid = {30958827}, issn = {1553-7358}, abstract = {Metagenomic sequencing is becoming widespread in biomedical and environmental research, and the pace is increasing even more thanks to nanopore sequencing. With a rising number of samples and data per sample, the challenge of efficiently comparing results within a specimen and between specimens arises. Reagents, laboratory, and host related contaminants complicate such analysis. Contamination is particularly critical in low microbial biomass body sites and environments, where it can comprise most of a sample if not all. Recentrifuge implements a robust method for the removal of negative-control and crossover taxa from the rest of samples. With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications. In addition to contamination-subtracted samples, Recentrifuge provides shared and exclusive taxa per sample, thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics. Regarding the first area, Recentrifuge's novel approach has already demonstrated its benefits showing that microbiomes of Arctic and Antarctic solar panels display similar taxonomic profiles. In the clinical field, to confirm Recentrifuge's ability to analyze complex metagenomes, we challenged it with data coming from a metagenomic investigation of RNA in plasma that suffered from critical contamination to the point of preventing any positive conclusion. Recentrifuge provided results that yielded new biological insight into the problem, supporting the growing evidence of a blood microbiota even in healthy individuals, mostly translocated from the gut, the oral cavity, and the genitourinary tract. We also developed a synthetic dataset carefully designed to rate the robust contamination removal algorithm, which demonstrated a significant improvement in specificity while retaining a high sensitivity even in the presence of cross-contaminants. Recentrifuge's official website is www.recentrifuge.org. The data and source code are anonymously and freely available on GitHub and PyPI. The computing code is licensed under the AGPLv3. The Recentrifuge Wiki is the most extensive and continually-updated source of documentation for Recentrifuge, covering installation, use cases, testing, and other useful topics.}, }
@article {pmid30957268, year = {2019}, author = {Tian, M and Chen, M and Bao, Y and Xu, C and Qin, Q and Zhang, W and He, Y and Shao, Q}, title = {Microbial contributions to bronchial asthma occurrence in children: A metagenomic study.}, journal = {Journal of cellular biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1002/jcb.28658}, pmid = {30957268}, issn = {1097-4644}, support = {81302552//National Natural Sciences Foundation of China/ ; NSFC 81302552//National Natural Sciences Foundation of China/ ; }, abstract = {Bronchial asthma, a common chronic respiratory disease in children, is traditionally regarded as a noninfectious disease. Current hypotheses, however, argue that asthma can be caused by microbial infection. We, therefore, hypothesize that a variety of microbes are more commonly found in the sputum of children with asthma, and these microbes may contribute to the occurrence and development of asthma. The present study proposes to use metagenomic approach to explore microbial diversity and to identify the microbial community characteristics of sputum from children with asthma. We found that microbial communities in the sputum of children differed significantly between asthmatics and controls. Kruskal-Wallis testing showed that 16 phyla, 104 genera, and 159 species were significantly downregulated, whereas two phyla including Platyhelminthes phylum and Chordata phylum, two genera including Spirometra genus and Homo sapiens, and the Spirometra erinaceieuropaei species were significantly upregulated in asthma patients compared with controls (P < 0.05). Among them, H. sapiens and S. erinaceieuropaei exhibited 2.3- and 2.0-fold overabundance in asthmatics vs controls, respectively. Meanwhile, metastats assay demonstrated that 31 phyla, 400 genera, and 813 species were significantly downregulated, whereas two phyla, 10 genera, and 16 species were significantly upregulated in asthma patients compared with controls (P < 0.05). Among them, Tetrahymena thermophila and Candidatus Zinderia insecticola exhibited 4.7-fold overabundance in asthmatics vs controls. Our study establishes a link between microbial infection and the mechanisms leading to asthma development, which will be useful for developing novel diagnostic biomarkers and aiding in the prevention and control of asthma.}, }
@article {pmid30956802, year = {2019}, author = {Keravec, M and Mounier, J and Guilloux, CA and Fangous, MS and Mondot, S and Vallet, S and Gouriou, S and Le Berre, R and Rault, G and Férec, C and Barbier, G and Lepage, P and Héry-Arnaud, G}, title = {Porphyromonas, a potential predictive biomarker of Pseudomonas aeruginosa pulmonary infection in cystic fibrosis.}, journal = {BMJ open respiratory research}, volume = {6}, number = {1}, pages = {e000374}, doi = {10.1136/bmjresp-2018-000374}, pmid = {30956802}, issn = {2052-4439}, abstract = {Introduction: Pseudomonas aeruginosa pulmonary infections are the primary cause of morbi-mortality in patients with cystic fibrosis (CF). In this cohort study, the objective was to identify candidate biomarkers of P. aeruginosa infection within the airway microbiota.<br><br>Methods: A 3-year prospective multicentre study (PYOMUCO study) was conducted in Western France and included patients initially P. aeruginosa free for at least 1 year. A 16S-targeted metagenomics approach was applied on iterative sputum samples of a first set of patients (n=33). The composition of airway microbiota was compared according to their P. aeruginosa status at the end of the follow-up (colonised vs non-colonised), and biomarkers associated with P. aeruginosa were screened. In a second step, the distribution of a candidate biomarker according to the two groups of patients was verified by qPCR on a second set of patients (n=52) coming from the same cohort and its load quantified throughout the follow-up.<br><br>Results: Porphyromonas (mainly P. catoniae) was found to be an enriched phylotype in patients uninfected by P. aeruginosa (p<0.001). This result was confirmed by quantitative PCR. Conversely, in patients who became P. aeruginosa-positive, P. catoniae significantly decreased before P. aeruginosa acquisition (p=0.014).<br><br>Discussion: Further studies on replication cohorts are needed to validate this potential predictive biomarker, which may be relevant for the follow-up in the early years of patients with CF. The identification of infection candidate biomarkers may offer new strategies for CF precision medicine.}, }
@article {pmid30955771, year = {2019}, author = {Cotta, SR and Cadete, LL and van Elsas, JD and Andreote, FD and Dias, ACF}, title = {Exploring bacterial functionality in mangrove sediments and its capability to overcome anthropogenic activity.}, journal = {Marine pollution bulletin}, volume = {141}, number = {}, pages = {586-594}, doi = {10.1016/j.marpolbul.2019.03.001}, pmid = {30955771}, issn = {1879-3363}, abstract = {Mangrove forests are highly productive yet vulnerable ecosystems that act as important carbon sinks (&quot;blue carbon&quot;). The objective of this work was to analyze the impact of anthropogenic activities on microbiome structure and functioning. The metagenomic analysis revealed that the taxonomic compositions were grossly similar across all mangrove microbiomes. Remarkably, these microbiomes, along the gradient of anthropogenic impact, showed fluctuations in the relative abundances of bacterial taxa predicted to be involved in sulfur cycling processes. Functions involved in sulfur metabolism, such as APS pathways (associated with sulfate reduction and sulfur oxidation processes) were prevalent across the microbiomes, being sox and dsrAB genes highly expressed on anthropogenically-impacted areas. Apparently, the oil-impacted microbiomes were more affected in taxonomic than in functional terms, as high functional redundancies were noted across them. The microbial gene diversity found was typical for a functional system, even following the previous disturbance.}, }
@article {pmid30955749, year = {2019}, author = {Fernandes, C and Kankonkar, H and Meena, RM and Menezes, G and Shenoy, BD and Khandeparker, R}, title = {Metagenomic analysis of tarball-associated bacteria from Goa, India.}, journal = {Marine pollution bulletin}, volume = {141}, number = {}, pages = {398-403}, doi = {10.1016/j.marpolbul.2019.02.040}, pmid = {30955749}, issn = {1879-3363}, abstract = {The beaches of Goa state in India are frequently polluted with tarballs, specifically during pre-monsoon and monsoon seasons. Tarballs contain hydrocarbons, including polycyclic aromatic hydrocarbons, which pose significant environmental risks. Microbes associated with tarballs reportedly possess capabilities to degrade toxic hydrocarbons present in tarballs. In this study, bacterial diversity associated with tarballs from Vagator and Morjim beaches of north Goa was analysed based on V3-V4 regions of 16S rRNA gene sequenced using Illumina Miseq Platform. The Proteobacterial members were dominant in both Vagator (≥85.5%) and Morjim (≥94.0%) samples. Many of the identified taxa have been previously reported as hydrocarbon degraders (e.g. Halomonas, Marinobacter) or possible human pathogens (e.g. Acinetobacter, Klebsiella, Rhodococcus, Staphylococcus, Vibrio). This is the first study reported on a metagenomic analysis of bacteria associated with tarballs from Goa.}, }
@article {pmid30954723, year = {2019}, author = {Yang, Y and Li, Z and Song, W and Du, L and Ye, C and Zhao, B and Liu, W and Deng, D and Pan, Y and Lin, H and Cao, X}, title = {Metagenomic insights into the abundance and composition of resistance genes in aquatic environments: Influence of stratification and geography.}, journal = {Environment international}, volume = {127}, number = {}, pages = {371-380}, doi = {10.1016/j.envint.2019.03.062}, pmid = {30954723}, issn = {1873-6750}, abstract = {A global survey was performed with 122 aquatic metagenomic DNA datasets (92 lake water and 30 seawater) obtained from the Sequence Read Archive (SRA). Antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) were derived from the dataset sequences via bioinformatic analysis. The relative abundances of ARGs and MRGs in lake samples were in the ranges ND (not detected)-1.34 × 100 and 1.22 × 10-3-1.98 × 10-1 copies per 16S rRNA, which were higher than those in seawater samples. Among ARGs, multidrug resistance genes and bacitracin resistance genes had high relative abundances in both lake and sea water samples. Multi-metal resistance genes, mercury resistance genes and copper resistance genes had the greatest relative abundance for MRGs. No significant difference was found between epilimnion and hypolimnion in abundance or the Shannon diversity index for ARGs and MRGs. Principal coordinates analysis and permutational multivariate analysis of variance (PERMANOVA) test showed that stratification and geography had significant influence on the composition of ARGs and MRGs in lakes (p < 0.05, PERMANOVA). Coastal seawater samples had significantly greater relative abundance and a higher Shannon index for both ARGs and MRGs than deep ocean and Antarctic seawater samples (p < 0.05, Kruskal-Wallis one-way ANOVA), suggesting that human activity may exert more selective pressure on ARGs and MRGs in coastal areas than those in deep ocean and Antarctic seawater.}, }
@article {pmid30953744, year = {2019}, author = {Lalitha, P and Seitzman, GD and Kotecha, R and Hinterwirth, A and Chen, C and Zhong, L and Cummings, S and Lebas, E and Sahoo, MK and Pinsky, BA and Lietman, TM and Doan, T}, title = {Unbiased Pathogen Detection and Host Gene Profiling for Conjunctivitis.}, journal = {Ophthalmology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ophtha.2019.03.039}, pmid = {30953744}, issn = {1549-4713}, support = {K08 EY026986/EY/NEI NIH HHS/United States ; }, abstract = {PURPOSE: The etiology of conjunctivitis is often misdiagnosed. An ideal diagnostic test would identify all possible infectious causes. In this study, we apply unbiased metagenomic RNA deep sequencing (MDS) to identify pathogens causing conjunctivitis.<br><br>DESIGN: Molecular study of prospectively collected conjunctival swabs from patients with presumed infectious conjunctivitis.<br><br>PARTICIPANTS: Patients with presumed acute infectious conjunctivitis.<br><br>METHODS: Conjunctival swabs were collected from patients presenting with acute conjunctivitis. Swabs were processed for MDS. Pathogens were identified using a rapid computational pipeline to analyze the non-host sequences obtained from MDS. Differential gene expression analysis was performed to evaluate for host transcriptome signatures for infectious types. Clinical samples were de-identified and laboratory personnel handling the samples and interpreting the data were masked.<br><br>MAIN OUTCOME MEASURES: Pathogens and differential transcripts identified by MDS.<br><br>RESULTS: MDS detected pathogens in 86% (12/14) of the patients tested. Swabs from 10 of 14 patients were positive for human adenovirus (HAdV) while swabs from 2 of 14 patients were positive for Vittaforma corneae (a parasitic fungal species of the microsporidia group). Samples positive for HAdV by RNA-seq were independently verified in a CLIA-certified laboratory. Directed pathogen-PCR confirmed the presence of V. corneae genome in the samples positive by RNA-seq. Local host transcriptome analysis identified 12 differentially expressed genes that provided distinct expression signatures for patients infected with HAdV compared to V. corneae.<br><br>CONCLUSIONS: MDS can reliably detect and quantify common and rare pathogens causing conjunctivitis, and identify strains. The unbiased nature of metagenomic RNA deep sequencing allowed an expanded scope of pathogen detection, including fungal species not commonly associated with acute conjunctivitis. In addition, the identification of infection type-specific local host transcriptome signatures may allow for pathogen detection even when the pathogen load is too low for direct identification.}, }
@article {pmid30953547, year = {2019}, author = {McIntyre, ABR and Ounit, R and Afshinnekoo, E and Prill, RJ and Hénaff, E and Alexander, N and Minot, SS and Danko, D and Foox, J and Ahsanuddin, S and Tighe, S and Hasan, NA and Subramanian, P and Moffat, K and Levy, S and Lonardi, S and Greenfield, N and Colwell, RR and Rosen, GL and Mason, CE}, title = {Correction to: Comprehensive benchmarking and ensemble approaches for metagenomic classifiers.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {72}, doi = {10.1186/s13059-019-1687-2}, pmid = {30953547}, issn = {1474-760X}, abstract = {Following publication of the original article [1], the authors would like to highlight the following two corrections.}, }
@article {pmid30953542, year = {2019}, author = {Raymond, F and Boissinot, M and Ouameur, AA and Déraspe, M and Plante, PL and Kpanou, SR and Bérubé, È and Huletsky, A and Roy, PH and Ouellette, M and Bergeron, MG and Corbeil, J}, title = {Culture-enriched human gut microbiomes reveal core and accessory resistance genes.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {56}, doi = {10.1186/s40168-019-0669-7}, pmid = {30953542}, issn = {2049-2618}, support = {Selectomics to monitor and predict the emergence of resistance to antibiotics//Québec Consortium for Drug Discovery/ ; Medical Genomics//Canada Research Chairs/ ; Antimicrobial Resistance//Canada Research Chairs/ ; RAC//Compute Canada/ ; }, abstract = {BACKGROUND: Low-abundance microorganisms of the gut microbiome are often referred to as a reservoir for antibiotic resistance genes. Unfortunately, these less-abundant bacteria can be overlooked by deep shotgun sequencing. In addition, it is a challenge to associate the presence of resistance genes with their risk of acquisition by pathogens. In this study, we used liquid culture enrichment of stools to assemble the genome of lower-abundance bacteria from fecal samples. We then investigated the gene content recovered from these culture-enriched and culture-independent metagenomes in relation with their taxonomic origin, specifically antibiotic resistance genes. We finally used a pangenome approach to associate resistance genes with the core or accessory genome of Enterobacteriaceae and inferred their propensity to horizontal gene transfer.<br><br>RESULTS: Using culture-enrichment approaches with stools allowed assembly of 187 bacterial species with an assembly size greater than 1 million nucleotides. Of these, 67 were found only in culture-enriched conditions, and 22 only in culture-independent microbiomes. These assembled metagenomes allowed the evaluation of the gene content of specific subcommunities of the gut microbiome. We observed that differentially distributed metabolic enzymes were associated with specific culture conditions and, for the most part, with specific taxa. Gene content differences between microbiomes, for example, antibiotic resistance, were for the most part not associated with metabolic enzymes, but with other functions. We used a pangenome approach to determine if the resistance genes found in Enterobacteriaceae, specifically E. cloacae or E. coli, were part of the core genome or of the accessory genome of this species. In our healthy volunteer cohort, we found that E. cloacae contigs harbored resistance genes that were part of the core genome of the species, while E. coli had a large accessory resistome proximal to mobile elements.<br><br>CONCLUSION: Liquid culture of stools contributed to an improved functional and comparative genomics study of less-abundant gut bacteria, specifically those associated with antibiotic resistance. Defining whether a gene is part of the core genome of a species helped in interpreting the genomes recovered from culture-independent or culture-enriched microbiomes.}, }
@article {pmid30953134, year = {2019}, author = {Grieco, MB and Lopes, FAC and Oliveira, LS and Tschoeke, DA and Popov, CC and Thompson, CC and Gonçalves, LC and Constantino, R and Martins, OB and Kruger, RH and de Souza, W and Thompson, FL}, title = {Metagenomic Analysis of the Whole Gut Microbiota in Brazilian Termitidae Termites Cornitermes cumulans, Cyrilliotermes strictinasus, Syntermes dirus, Nasutitermes jaraguae, Nasutitermes aquilinus, Grigiotermes bequaerti, and Orthognathotermes mirim.}, journal = {Current microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00284-019-01662-3}, pmid = {30953134}, issn = {1432-0991}, support = {563055/2010-3//Conselho Nacional de Desenvolvimento Científico e Tecnológico (BR)/ ; E-26/ 110.634/2014//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; }, abstract = {Although some previous studies have described the microbial diversity of termite in Brazil, the lack of studies about this subject is still evident. In the present study, we described by whole genome sequencing, the gut microbiota of seven species of termites (Termitidae) with different feeding habits from four Brazilian locations. For the litter species, the most abundant bacterial phylum was Firmicutes, where Cornitermes cumulans and Syntermes dirus (Syntermitinae) were identified. For the humus species, the most abundant bacterial phylum was Proteobacteria where three species were studied: Cyrilliotermes strictinasus (Syntermitinae), Grigiotermes bequaerti (Apicotermitinae), and Orthognathotermes mirim (Termitinae). For the wood termites, Firmicutes and Spirochaetes were the most abundant phyla, respectively, where two species were identified: Nasutitermes aquilinus and Nasutitermes jaraguae (Nasutitermitinae). The gut microbiota of all four examined subfamilies shared a conserved functional and carbohydrate-active enzyme profile and specialized in cellulose and chitin degradation. Taken together, these results provide insight into the partnerships between termite and microbes that permit the use of refractory energy sources.}, }
@article {pmid30953072, year = {2019}, author = {De Cesare, A and Faria do Valle, Ì and Sala, C and Sirri, F and Astolfi, A and Castellani, G and Manfreda, G}, title = {Effect of a low protein diet on chicken ceca microbiome and productive performances.}, journal = {Poultry science}, volume = {}, number = {}, pages = {}, doi = {10.3382/ps/pez132}, pmid = {30953072}, issn = {1525-3171}, abstract = {The aim of this study was to investigate the impact of supplementation of a low protein diet on ceca microbiome and productive performances of broiler chickens. A total of 1,170 one-day-old male chicks (Ross 308) were divided in 2 diet groups and reared in the same conditions up to 42 D. Birds belonging to the control group were fed a basal diet. Birds belonging to the low protein group the basal diet with a reduced level of crude protein (-7%). Cecum contents from randomly selected birds were collected at 14 and 42 D within each diet group, submitted to DNA extraction and then tested by shotgun metagenomic sequencing. Abundances of species belonging to Actinobacteria and Proteobacteria were mainly affected by the diet as well as interaction between diet and time, while species belonging to Firmicutes and Cyanobacteria changed mainly according to the age of the birds. At family level, Lactobacillaceae significantly decreased in the low protein group up to 14 D. However, at the end of the rearing period the same family was significantly higher in the low protein group. The most abundant functional genes, represented by cystine desulfurase, alpha-galactosidase, and serine hydroxymethyltransferase, displayed comparable abundances in both diet groups, although significative differences were identified for less abundant functional genes at both sampling times. Birds fed control and low protein diets showed similar productive performances. However, in the finisher phase, feed conversion rate was significantly better in chickens fed the low protein diet. Overall, this study showed that a reduced intake of crude protein in broilers increases the abundance of Lactobacillaceae in the ceca over time and this seems to be linked to a better feed conversion rate between 36 and 42 D. A reduced intake of crude protein in chicken production can help to improve exploitation of edible resources, while reducing the emission of nitrogen pollutants in the environment.}, }
@article {pmid30952995, year = {2019}, author = {Karthikeyan, S and Rodriguez-R, LM and Heritier-Robbins, P and Kim, M and Overholt, WA and Gaby, JC and Hatt, JK and Spain, JC and Rosselló-Móra, R and Huettel, M and Kostka, JE and Konstantinidis, KT}, title = {&quot;Candidatus Macondimonas diazotrophica&quot;, a novel gammaproteobacterial genus dominating crude-oil-contaminated coastal sediments.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0400-5}, pmid = {30952995}, issn = {1751-7370}, support = {231611-00//Gulf of Mexico Research Initiative (GoMRI)/ ; 231611-00//Gulf of Mexico Research Initiative (GoMRI)/ ; 231611-00//Gulf of Mexico Research Initiative (GoMRI)/ ; 231611-00//Gulf of Mexico Research Initiative (GoMRI)/ ; 231611-00//Gulf of Mexico Research Initiative (GoMRI)/ ; 231611-00//Gulf of Mexico Research Initiative (GoMRI)/ ; 231611-00//Gulf of Mexico Research Initiative (GoMRI)/ ; 231611-00//Gulf of Mexico Research Initiative (GoMRI)/ ; }, abstract = {Modeling crude-oil biodegradation in sediments remains a challenge due in part to the lack of appropriate model organisms. Here we report the metagenome-guided isolation of a novel organism that represents a phylogenetically narrow (>97% 16S rRNA gene identity) group of previously uncharacterized, crude-oil degraders. Analysis of available sequence data showed that these organisms are highly abundant in oiled sediments of coastal marine ecosystems across the world, often comprising ~30% of the total community, and virtually absent in pristine sediments or seawater. The isolate genome encodes functional nitrogen fixation and hydrocarbon degradation genes together with putative genes for biosurfactant production that apparently facilitate growth in the typically nitrogen-limited, oiled environment. Comparisons to available genomes revealed that this isolate represents a novel genus within the Gammaproteobacteria, for which we propose the provisional name &quot;Candidatus Macondimonas diazotrophica&quot; gen. nov., sp. nov. &quot;Ca. M. diazotrophica&quot; appears to play a key ecological role in the response to oil spills around the globe and could be a promising model organism for studying ecophysiological responses to oil spills.}, }
@article {pmid30952929, year = {2019}, author = {Li, Y and Zheng, L and Zhang, Y and Liu, H and Jing, H}, title = {Comparative metagenomics study reveals pollution induced changes of microbial genes in mangrove sediments.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {5739}, doi = {10.1038/s41598-019-42260-4}, pmid = {30952929}, issn = {2045-2322}, abstract = {Mangrove forests are widespread along the subtropical and tropical coasts. They provide a habitat for a wide variety of plants, animals and microorganisms, and act as a buffer zone between the ocean and land. Along with other coastal environments, mangrove ecosystems are under increasing pressure from human activities, such as excessive input of nutrients and toxic pollutants. Despite efforts to understand the diversity of microbes in mangrove sediments, their metabolic capability in pristine and contaminated mangrove sediments remains largely unknown. By using metagenomic approach, we investigated the metabolic capacity of microorganisms in contaminated (CMS) and pristine (PMS) mangrove sediments at subtropical and tropical coastal sites. When comparing the CMS with PMS, we found that the former had a reduced diazotroph abundance and nitrogen fixing capability, but an enhanced metabolism that is related to the generation of microbial greenhouse gases via increased methanogenesis and sulfate reduction. In addition, a high concentration of heavy metals (mainly Zn, Cd, and Pb) and abundance of metal/antibiotic resistance encoding genes were found in CMS. Together, these data provide evidence that contamination in mangrove sediment can markedly change microbial community and metabolism; however, no significant differences in gene distribution were found between the subtropical and tropical mangrove sediments. In summary, contamination in mangrove sediments might weaken the microbial metabolisms that enable the mangrove ecosystems to act as a buffer zone for terrestrial nutrients deposition, and induce bioremediation processes accompanied with an increase in greenhouse gas emission.}, }
@article {pmid30952693, year = {2019}, author = {Hay, ID and Lithgow, T}, title = {Filamentous phages: masters of a microbial sharing economy.}, journal = {EMBO reports}, volume = {}, number = {}, pages = {}, doi = {10.15252/embr.201847427}, pmid = {30952693}, issn = {1469-3178}, abstract = {Bacteriophage (&quot;bacteria eaters&quot;) or phage is the collective term for viruses that infect bacteria. While most phages are pathogens that kill their bacterial hosts, the filamentous phages of the sub-class Inoviridae live in cooperative relationships with their bacterial hosts, akin to the principal behaviours found in the modern-day sharing economy: peer-to-peer support, to offset any burden. Filamentous phages impose very little burden on bacteria and offset this by providing service to help build better biofilms, or provision of toxins and other factors that increase virulence, or modified behaviours that provide novel motile activity to their bacterial hosts. Past, present and future biotechnology applications have been built on this phage-host cooperativity, including DNA sequencing technology, tools for genetic engineering and molecular analysis of gene expression and protein production, and phage-display technologies for screening protein-ligand and protein-protein interactions. With the explosion of genome and metagenome sequencing surveys around the world, we are coming to realize that our knowledge of filamentous phage diversity remains at a tip-of-the-iceberg stage, promising that new biology and biotechnology are soon to come.}, }
@article {pmid30952661, year = {2019}, author = {Yu, J and Deem, LM and Crow, SE and Deenik, J and Penton, CR}, title = {Comparative Metagenomics Reveals Enhanced Nutrient Cycling Potential After Two Years of Biochar Amendment in a Tropical Oxisol.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02957-18}, pmid = {30952661}, issn = {1098-5336}, abstract = {The complex structural and functional responses of agricultural soil microbial communities to the addition of carbonaceous compounds such as biochar remains poorly understood. This severely limits the predictive ability for both the potential enhancement of soil fertility and greenhouse gas mitigation. In this study, we utilized shotgun metagenomics in order to decipher changes in the microbial community in soil microcosms after 14 days of incubation at 23°C, which contained soils from biochar-amended and control plots cultivated with napiergrass. Our analyses revealed that biochar-amended soil microbiomes exhibited a significant shift in both community composition and predicted metabolism. Key metabolic pathways related to carbon turnover, such as the utilization of plant-derived carbohydrates as well as denitrification were enriched under biochar amendment. These community shifts were in part associated with increased soil carbon, such as labile and aromatic carbon compounds, which was likely stimulated by the increased available nutrients associated with biochar amendment. These findings indicate that the soil microbiome response to the combination of biochar addition and to incubation conditions confers enhanced nutrient cycling, a small decrease in CO2 emissions, and potentially mitigates nitrous oxide emissions.Importance Incorporation of biochar into soil is a promising management strategy for sustainable agriculture owing to its potential to sequester carbon and improve soil fertility. Expanding the addition of biochar to large-scale agriculture hinges on its lasting beneficial effects on the microbial community. Yet, there exist a significant knowledge gap regarding the specific role that biochar plays in altering key biological soil processes that influence plant growth and carbon storage in soil. Previous studies that examined the soil microbiome under biochar amendment principally characterized only how the composition alters in response to biochar amendment. In the present study, we shed light on the functional alterations of the microbial community response two years after biochar amendment. Our results show that biochar increased the abundance of genes involved in denitrification and carbon turnover, and that biochar-amended soil microcosms had a reduction in cumulative CO2 production.}, }
@article {pmid30952342, year = {2019}, author = {Zhou, R and Zeng, S and Hou, D and Liu, J and Weng, S and He, J and Huang, Z}, title = {Occurrence of human pathogenic bacteria carrying antibiotic resistance genes revealed by metagenomic approach: A case study from an aquatic environment.}, journal = {Journal of environmental sciences (China)}, volume = {80}, number = {}, pages = {248-256}, doi = {10.1016/j.jes.2019.01.001}, pmid = {30952342}, issn = {1001-0742}, mesh = {Drug Resistance, Microbial/*genetics ; Environmental Monitoring/*methods ; Metagenome/*physiology ; *Water Microbiology ; Water Pollution/*analysis/*statistics &amp; numerical data ; }, abstract = {Antibiotic resistance genes (ARGs), human pathogenic bacteria (HPB), and HPB carrying ARGs are public issues that pose a high risk to aquatic environments and public health. Their diversity and abundance in water, intestine, and sediments of shrimp culture pond were investigated using metagenomic approach. A total of 19 classes of ARGs, 52 HPB species, and 7 species of HPB carrying ARGs were found. Additionally, 157, 104, and 86 subtypes of ARGs were detected in shrimp intestine, pond water, and sediment samples, respectively. In all the samples, multidrug resistance genes were the highest abundant class of ARGs. The dominant HPB was Enterococcus faecalis in shrimp intestine, Vibrio parahaemolyticus in sediments, and Mycobacterium yongonense in water, respectively. Moreover, E. faecalis (contig Intestine_364647) and Enterococcus faecium (contig Intestine_80272) carrying efrA, efrB and ANT(6)-Ia were found in shrimp intestine, Desulfosaricina cetonica (contig Sediment_825143) and Escherichia coli (contig Sediment_188430) carrying mexB and APH(3')-IIa were found in sediments, and Laribacter hongkongensis (contig Water_478168 and Water_369477), Shigella sonnei (contig Water_880246), and Acinetobacter baumannii (contig Water_525520) carrying sul1, sul2, ereA, qacH, OXA-21, and mphD were found in pond water. Mobile genetic elements (MGEs) analysis indicated that horizontal gene transfer (HGT) of integrons, insertion sequences, and plasmids existed in shrimp intestine, sediment, and water samples, and the abundance of integrons was higher than that of other two MGEs. The results suggested that HPB carrying ARGs potentially existed in aquatic environments, and that these contributed to the environment and public health risk evaluation.}, }
@article {pmid30950854, year = {2019}, author = {Houlihan, CF and Bharucha, T and Breuer, J}, title = {Advances in molecular diagnostic testing for central nervous system infections.}, journal = {Current opinion in infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1097/QCO.0000000000000548}, pmid = {30950854}, issn = {1473-6527}, abstract = {PURPOSE OF REVIEW: Central nervous system (CNS) infections present an ongoing diagnostic challenge for clinicians, with an aetiological agent remaining unidentified in the majority of cases even in high-income settings. This review summarizes developments in a range of diagnostic methods published in the past 18 months.<br><br>RECENT FINDINGS: Several commercial assays exist for the detection of viral, bacterial and fungal pathogens using single multiplex PCR. Multicentre validation of the Biofire FilmArray panel illustrated high sensitivity for bacterial and fungal pathogens, but poor results for Cryptococcus species detection. The development of microarray cards for bacterial CNS pathogens shows promise but requires further validation. Few developments have been made in proteomics and transcriptomics, contrasted with significant increase in the use of metagenomic (or unbiased) sequencing. Novel viruses causing CNS infection have been described using this technique but contamination, cost, expertise and turnaround time requirements remain restrictive. Finally, the development of Gene Xpert and Ultra has revolutionized tuberculosis meningitis diagnostics with newly released recommendations for their use from the WHO.<br><br>SUMMARY: Progress has been made in the clinical validation and international recommendation of PCR-based tests for CNS infections. Sequencing techniques present the most dynamic field, although significant ongoing challenges persist.}, }
@article {pmid30950294, year = {2019}, author = {Ding, W and Zhang, W and Wang, R and Sun, Y and Pei, B and Gao, Z and Qian, PY}, title = {Distribution, diversity and functional dissociation of the mac genes in marine biofilms.}, journal = {Biofouling}, volume = {}, number = {}, pages = {1-14}, doi = {10.1080/08927014.2019.1593384}, pmid = {30950294}, issn = {1029-2454}, abstract = {Bacteria produce metamorphosis-associated contractile (MAC) structures to induce larval metamorphosis in Hydroides elegans. The distribution and diversity of mac gene homologs in marine environments are largely unexplored. In the present study mac genes were examined in marine environments by analyzing 101 biofilm and 91 seawater metagenomes. There were more mac genes in biofilms than in seawater, and substratum type, location, or sampling time did not affect the mac genes in biofilms. The mac gene clusters were highly diverse and often incomplete while the three MAC components co-occurred with other genes of different functions. Genomic analysis of four Pseudoalteromonas and two Streptomyces strains revealed the mac genes transfers among different microbial taxa. It is proposed that mac genes are more specific to biofilms; gene transfer among different microbial taxa has led to highly diverse mac gene clusters; and in most cases, the three MAC components function individually rather than forming a complex.}, }
@article {pmid30950214, year = {2019}, author = {Borrel, V and Gannesen, AV and Barreau, M and Gaviard, C and Duclairoir-Poc, C and Hardouin, J and Konto-Ghiorghi, Y and Lefeuvre, L and Feuilloley, MGJ}, title = {Adaptation of acneic and non acneic strains of Cutibacterium acnes to sebum-like environment.}, journal = {MicrobiologyOpen}, volume = {}, number = {}, pages = {e841}, doi = {10.1002/mbo3.841}, pmid = {30950214}, issn = {2045-8827}, support = {//Campus France/ ; //Region Normandie/ ; //Evreux Porte de Normandie/ ; //European Union (FEDER)/ ; }, abstract = {Cutibacterium acnes, former Proprionibacterium acnes, is a heterogeneous species including acneic bacteria such as the RT4 strain, and commensal bacteria such as the RT6 strain. These strains have been characterized by metagenomic analysis but their physiology was not investigated until now. Bacteria were grown in different media, brain heart infusion medium (BHI), reinforced clostridial medium (RCM), and in sebum like medium (SLM) specifically designed to reproduce the lipid rich environment of the sebaceous gland. Whereas the RT4 acneic strain showed maximal growth in SLM and lower growth in RCM and BHI, the RT6 non acneic strain was growing preferentially in RCM and marginally in SLM. These differences were correlated with the lipophilic surface of the RT4 strain and to the more polar surface of the RT6 strain. Both strains also showed marked differences in biofilm formation activity which was maximal for the RT4 strain in BHI and for the RT6 strain in SLM. However, cytotoxicity of both strains on HaCaT keratinocytes remained identical and limited. The RT4 acneic strain showed higher inflammatory potential than the RT6 non acneic strain, but the growth medium was without significant influence. Both bacteria were also capable to stimulate β-defensine 2 secretion by keratinocytes but no influence of the bacterial growth conditions was observed. Comparative proteomics analysis was performed by nano LC-MS/MS and revealed that whereas the RT4 strain only expressed triacylglycerol lipase, the principal C. acnes virulence factor, when it was grown in SLM, the RT6 strain expressed another virulence factor, the CAMP factor, exclusively when it was grown in BHI and RCM. This study demonstrates the key influence of growth conditions on virulence expression by C. acnesand suggest that acneic and non acneic strains are related to different environmental niches.}, }
@article {pmid30949974, year = {2019}, author = {Zuckerman, NS and Indenbaum, V and Milo, R and Mendelson, E and Lustig, Y}, title = {JC virus identified in a patient with persistent and severe West Nile virus disease.}, journal = {Journal of neurovirology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s13365-019-00744-z}, pmid = {30949974}, issn = {1538-2443}, abstract = {West Nile virus is a notable cause of neuroinvasive disease, damage to the central nervous system, or even death. In this study, using metagenomics analysis and quantitative real-time PCR validation, we identified a JC virus infection in urine and cerebrospinal fluid samples of a West Nile virus patient with severe neurological symptoms and extended disease. JC virus is known to be involved in neurological complications, especially in immunocompromised individuals thus suggesting that the coinfection with JC virus is involved with the West Nile virus infection persistence and severe symptoms. JC virus was identified in urine samples from additional West Nile virus patients via quantitative real-time PCR, however, JC virus was not found in any cerebrospinal fluid samples of West Nile virus patients, suggesting that JC virus does not regularly infect the central nervous system of WNV patients. Overall, this study highlights the importance of identifying infection by opportunistic viruses in already-diagnosed patients and highlights the advantages of next-generation sequencing and metagenomics for viral diagnosis.}, }
@article {pmid30949677, year = {2019}, author = {Pillonel, T and Bertelli, C and Aeby, S and De-Barsy, M and Jacquier, N and Kebbi-Beghdadi, C and Mueller, L and Vouga, M and Greub, G}, title = {Sequencing the obligate intracellular Rhabdochlamydia helvetica within its tick host Ixodes ricinus to investigate their symbiotic relationship.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evz072}, pmid = {30949677}, issn = {1759-6653}, abstract = {The Rhabdochlamydiaceae family is one of the most widely distributed within the phylum Chlamydiae, but most of its members remain uncultivable. Rhabdochlamydia 16S rRNA was recently reported in more than 2% of 8534 pools of ticks from Switzerland. Shotgun metagenomics was performed on a pool of 5 female Ixodes ricinus ticks presenting a high concentration of chlamydial DNA, allowing the assembly of a high-quality draft genome. About 60% of sequence reads originated from a single bacterial population that was named 'Candidatus Rhabdochlamydia helvetica' whereas only few thousand reads mapped to the genome of 'Candidatus Midichloria mitochondrii', a symbiont normally observed in all I. ricinus females. The 1.8 Mbp genome of R. helvetica is smaller than other Chlamydia-related bacteria. Comparative analyses with other chlamydial genomes identified transposases of the PD-(D/E)XK nuclease family that are unique to this new genome. These transposases show evidence of inter-phylum horizontal gene transfers between multiple arthropod endosymbionts, including Cardinium spp. (Bacteroidetes) and diverse proteobacteria such as Wolbachia, Rickettsia spp. (Rickettsiales) and Caedimonas varicaedens (Holosporales). Bacterial symbionts were previously suggested to provide B-vitamins to hematophagous hosts. However, incomplete metabolic capacities including for B-vitamin biosynthesis, high bacterial density and limited prevalence suggest that R. helvetica is parasitic rather than symbiotic to its host. The identification of novel Rhabdochlamydia strains in different hosts and their sequencing will help understanding if members of this genus have become highly specialized parasites with reduced genomes, like the Chlamydiaceae, or if they could be pathogenic to humans using ticks as a transmission vector.}, }
@article {pmid30948795, year = {2019}, author = {D'Amico, F and Soverini, M and Zama, D and Consolandi, C and Severgnini, M and Prete, A and Pession, A and Barone, M and Turroni, S and Biagi, E and Brigidi, P and Masetti, R and Rampelli, S and Candela, M}, title = {Gut resistome plasticity in pediatric patients undergoing hematopoietic stem cell transplantation.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {5649}, doi = {10.1038/s41598-019-42222-w}, pmid = {30948795}, issn = {2045-2322}, abstract = {The gut microbiome of pediatric patients undergoing allo-hematopoietic stem cell transplantation (HSCT) has recently been considered as a potential reservoir of antimicrobial resistance, with important implications in terms of patient mortality rate. By means of shotgun metagenomics, here we explored the dynamics of the gut resistome - i.e. the pattern of antibiotic resistance genes provided by the gut microbiome - in eight pediatric patients undergoing HSCT, half of whom developed acute Graft-versus-Host Disease (aGvHD). According to our findings, the patients developing aGvHD are characterized by post-HSCT expansion of their gut resistome, involving the acquisition of new resistances, as well as the consolidation of those already present before HSCT. Interestingly, the aGvHD-associated bloom in resistome diversity is not limited to genes coding for resistance to the antibiotics administered along the therapeutic course, but rather involves a broad pattern of different resistance classes, including multidrug resistance, as well as resistance to macrolides, aminoglycosides, tetracyclines and beta-lactams. Our data stress the relevance of mapping the gut resistome in HSCT pediatric patients to define the most appropriate anti-infective treatment post HSCT.}, }
@article {pmid30948468, year = {2019}, author = {Rosales, SM and Vega Thurber, R}, title = {Draft Genome Sequence of Phocine Herpesvirus 1 Isolated from the Brain of a Harbor Seal.}, journal = {Microbiology resource announcements}, volume = {8}, number = {14}, pages = {}, doi = {10.1128/MRA.00210-19}, pmid = {30948468}, issn = {2576-098X}, abstract = {Phocine herpesvirus 1 (PhHV-1) is a viral pathogen with high prevalence, morbidity, and mortality in harbor seals. In this study, we used a metagenomic approach to assemble the PhHV-1 genome from the brain tissue of a harbor seal. Here, we present a 119-kb draft genome of PhHV-1 comprising 76 open reading frames.}, }
@article {pmid30947688, year = {2019}, author = {Sevigny, JL and Rothenheber, D and Diaz, KS and Zhang, Y and Agustsson, K and Bergeron, RD and Thomas, WK}, title = {Marker genes as predictors of shared genomic function.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {268}, doi = {10.1186/s12864-019-5641-1}, pmid = {30947688}, issn = {1471-2164}, support = {P20 GM103506/GM/NIGMS NIH HHS/United States ; 16-052: SA 16-18//Gulf of Mexico Research Initiative/ ; 5 P20 GM 10350605//National Institutes of Health: New Hampshire Idea Network of Biological Research Excellence/ ; }, abstract = {BACKGROUND: Although high-throughput marker gene studies provide valuable insight into the diversity and relative abundance of taxa in microbial communities, they do not provide direct measures of their functional capacity. Recently, scientists have shown a general desire to predict functional profiles of microbial communities based on phylogenetic identification inferred from marker genes, and recent tools have been developed to link the two. However, to date, no large-scale examination has quantified the correlation between the marker gene based taxonomic identity and protein coding gene conservation. Here we utilize 4872 representative prokaryotic genomes from NCBI to investigate the relationship between marker gene identity and shared protein coding gene content.<br><br>RESULTS: Even at 99-100% marker gene identity, genomes share on average less than 75% of their protein coding gene content. This occurs regardless of the marker gene(s) used: V4 region of the 16S rRNA, complete 16S rRNA, or single copy orthologs through a multi-locus sequence analysis. An important aspect related to this observation is the intra-organism variation of 16S copies from a single genome. Although the majority of 16S copies were found to have high sequence similarity (> 99%), several genomes contained copies that were highly diverged (< 97% identity).<br><br>CONCLUSIONS: This is the largest comparison between marker gene similarity and shared protein coding gene content to date. The study highlights the limitations of inferring a microbial community's functions based on marker gene phylogeny. The data presented expands upon the results of previous studies that examined one or few bacterial species and supports the hypothesis that 16S rRNA and other marker genes cannot be directly used to fully predict the functional potential of a bacterial community.}, }
@article {pmid30947033, year = {2019}, author = {Yuan, K and Yu, K and Yang, R and Zhang, Q and Yang, Y and Chen, E and Lin, L and Luan, T and Chen, W and Chen, B}, title = {Metagenomic characterization of antibiotic resistance genes in Antarctic soils.}, journal = {Ecotoxicology and environmental safety}, volume = {176}, number = {}, pages = {300-308}, doi = {10.1016/j.ecoenv.2019.03.099}, pmid = {30947033}, issn = {1090-2414}, abstract = {Antibiotic resistance genes (ARGs) are considered environmental pollutants. Comprehensive characterization of the ARGs in pristine environments is essential towards understanding the evolution of antibiotic resistance. Here, we analyzed ARGs in soil samples collected from relatively pristine Antarctica using metagenomic approaches. We identified 79 subtypes related to 12 antibiotic classes in Antarctic soils, in which ARGs related to multidrug and polypeptide were dominant. The characteristics of ARGs in Antarctic soils were significantly different from those in active sludge, chicken feces and swine feces, in terms of composition, abundance and potential transferability. ARG subtypes (e.g., bacA, ceoB, dfrE, mdtB, amrB, and acrB) were more abundant than others in Antarctic soils. Approximately 60% of the ARGs conferred antibiotic resistance via an efflux mechanism, and a low fraction of ARGs (∼16%) might be present on plasmids. Culturable bacterial consortiums isolated from Antarctic soils were consistently susceptible to most of the tested antibiotics frequently used in clinical therapies. The amrB and ceoB carried by culturable species did not express the resistance to aminoglycoside and fluoroquinolone at the levels of clinical concern. Our results suggest that the wide use of antibiotics may have contributed to developing higher antibiotic resistance and mobility.}, }
@article {pmid30946154, year = {2019}, author = {Sessa, L and Reddel, S and Manno, E and Quagliariello, A and Cotugno, N and Del Chierico, F and Amodio, D and Capponi, C and Leone, F and Bernardi, S and Rossi, P and Putignani, L and Palma, P}, title = {Distinct gut microbiota profile in antiretroviral therapy-treated perinatally HIV-infected patients associated with cardiac and inflammatory biomarkers.}, journal = {AIDS (London, England)}, volume = {33}, number = {6}, pages = {1001-1011}, doi = {10.1097/QAD.0000000000002131}, pmid = {30946154}, issn = {1473-5571}, abstract = {OBJECTIVE: Persistent inflammation and higher risk to develop cardiovascular diseases still represent a major complication for HIV-infected patients despite effective antiretroviral therapy (ART). We investigated the correlation between the gut microbiota profile, markers of inflammation, vascular endothelial activation (VEA) and microbial translocation (MT) in perinatally HIV-infected patients (PHIV) under ART.<br><br>DESIGN: Cross-sectional study including 61 ART-treated PHIV (age range 3-30 years old) and 71 age-matched healthy controls. Blood and stool sample were collected at the same time and analyzed for gut microbiota composition and plasma biomarkers.<br><br>METHODS: Gut microbiota composition was determined by 16S rRNA targeted-metagenomics. Soluble markers of MT, inflammation and VEA were quantified by ELISA or Luminex assay. Markers of immune activation were analyzed by flow cytometry on CD4 and CD8T cells.<br><br>RESULTS: We identified two distinct gut microbiota profiles (groups A and B) among PHIV. No different clinical parameters (age, sex, ethnicity, clinical class), dietary and sexual habits were found between the groups. The group A showed a relative dominance of Akkermansia muciniphila, whereas gut microbiota of group B was characterized by a higher biodiversity. The analysis of soluble markers revealed a significantly higher level of soluble E-selectine (P = 0.0296), intercellular adhesion molecule-1 (P = 0.0028), vascular adhesion molecule-1 (P = 0.0230), IL-6 (P = 0.0247) and soluble CD14 (P = 0.0142) in group A compared with group B.<br><br>CONCLUSION: Distinctive gut microbiota profiles are differently associated with inflammation, microbial translocation and VEA. Future studies are needed to understand the role of A. muciniphila and risk to develop cardiovascular diseases in PHIV.}, }
@article {pmid30945693, year = {2019}, author = {Siddavattam, D and Yakkala, H and Samantarrai, D}, title = {Lateral transfer of organophosphate degradation (opd) genes among soil bacteria: mode of transfer and contributions to organismal fitness.}, journal = {Journal of genetics}, volume = {98}, number = {1}, pages = {}, pmid = {30945693}, issn = {0973-7731}, abstract = {Genes encoding structurally independent phosphotriesterases (PTEs) are identified in soil bacteria. These pte genes, often identified on mobilizable and self-transmissible plasmids are organized as mobile genetic elements. Their dissemination through lateral gene transfer is evident due to the detection of identical organophosphate degradation genes among soil bacteria with little orno taxonomic relationship. Convergent evolution of PTEs provided selective advantages to the bacterial strain as they convert toxic phosphotriesters (PTs) into a source of phosphate. The residues of organophosphate (OP) compounds that accumulate in a soil are proposed to contribute to the evolution of PTEs through substrate-assisted gain-of-function. This review provides comprehensive information on lateral transfer of pte genes and critically examines proposed hypotheses on their evolution in the light of the short half-life of OPs in the environment. The review also proposes alternate factors that have possibly contributed to the evolution and lateral mobility of PTEs by taking into account their biology and analyses of pte genes in genomic and metagenomic databases.}, }
@article {pmid30945175, year = {2019}, author = {Linden, A and Gilliaux, G and Paternostre, J and Benzarti, E and Rivas, JF and Desmecht, D and Garigliany, M}, title = {A novel parvovirus, Roe deer copiparvovirus, identified in Ixodes ricinus ticks.}, journal = {Virus genes}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11262-019-01661-3}, pmid = {30945175}, issn = {1572-994X}, support = {NA//Public Service of Wallonia/ ; Research Council in Life Sciences//Universite de Liege/ ; }, abstract = {The family Parvoviridae contains diverse viruses that are capable of infecting a wide range of hosts. In this study, metagenomic sequencing of Ixodes ricinus ticks harvested in 2016 on red deer (Cervus elaphus) and European roe deer (Capreolus capreolus) in Belgium detected a new 6296-bp parvoviral genome. Phylogenetic and sequence analyses showed the new virus belongs to a new species within the Copiparvovirus genus. PCR screening of 4 pools of 10 serum samples from both deer species identified the new copiparvovirus DNA only in roe deer sera. Together, these results are the first evidence of a copiparvovirus in a deer species. Besides its potential pathogenicity to roe deers, the detection of this new virus in ticks raises questions about the possible transmission of parvoviruses by ticks. This report further increases the current knowledge on the evolution and diversity of copiparvoviruses.}, }
@article {pmid30944967, year = {2019}, author = {Dixon, M and Stefil, M and McDonald, M and Bjerklund-Johansen, TE and Naber, K and Wagenlehner, F and Mouraviev, V}, title = {Metagenomics in diagnosis and improved targeted treatment of UTI.}, journal = {World journal of urology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00345-019-02731-9}, pmid = {30944967}, issn = {1433-8726}, abstract = {INTRODUCTION: The genomic revolution has transformed our understanding of urinary tract infection. There has been a paradigm shift from the dogmatic statement that urine is sterile in healthy people, as we are becoming forever more familiar with the knowledge that bacterial communities exist within the urinary tracts of healthy people. Metagenomics can investigate the broad populations of microbial communities, analysing all the DNA present within a sample, providing comprehensive data regarding the state of the microenvironment of a patient's urinary tract. This permits medical practitioners to more accurately target organisms that may be responsible for disease-a form of 'precision medicine'.<br><br>METHODS AND RESULTS: This paper is derived from an extensive review and analysis of the available literature on the topic of metagenomic sequencing in urological science, using the PubMed search engine. The search yielded a total of 406 results, and manual selection of appropriate papers was subsequently performed. Only one randomised clinical trial comparing metagenomic sequencing to standard culture and sensitivity in the arena of urinary tract infection was found.<br><br>CONCLUSION: Out of this process, this paper explores the limitations of traditional methods of culture and sensitivity and delves into the recent studies involving new high-throughput genomic technologies in urological basic and clinical research, demonstrating the advances made in the urinary microbiome in its entire spectrum of pathogens and the first attempts of clinical implementation in several areas of urology. Finally, this paper discusses the challenges that must be overcome for such technology to become widely used in clinical practice.}, }
@article {pmid30944872, year = {2019}, author = {Camejo, PY and Oyserman, BO and McMahon, KD and Noguera, DR}, title = {Integrated Omic Analyses Provide Evidence that a &quot;Candidatus Accumulibacter phosphatis&quot; Strain Performs Denitrification under Microaerobic Conditions.}, journal = {mSystems}, volume = {4}, number = {1}, pages = {}, doi = {10.1128/mSystems.00193-18}, pmid = {30944872}, issn = {2379-5077}, abstract = {The ability of &quot;Candidatus Accumulibacter phosphatis&quot; to grow and remove phosphorus from wastewater under cycling anaerobic and aerobic conditions has also been investigated as a metabolism that could lead to simultaneous removal of nitrogen and phosphorus by a single organism. However, although phosphorus removal under cyclic anaerobic and anoxic conditions has been demonstrated, clarifying the role of &quot;Ca. Accumulibacter phosphatis&quot; in this process has been challenging, since (i) experimental research describes contradictory findings, (ii) none of the published &quot;Ca. Accumulibacter phosphatis&quot; genomes show the existence of a complete respiratory pathway for denitrification, and (iii) some genomes lacking a complete respiratory pathway have genes for assimilatory nitrate reduction. In this study, we used an integrated omics analysis to elucidate the physiology of a &quot;Ca. Accumulibacter phosphatis&quot; strain enriched in a reactor operated under cyclic anaerobic and microaerobic conditions. The reactor's performance suggested the ability of the enriched &quot;Ca. Accumulibacter phosphatis&quot; strain (clade IC) to simultaneously use oxygen and nitrate as electron acceptors under microaerobic conditions. A draft genome of this organism was assembled from metagenomic reads (&quot;Ca. Accumulibacter phosphatis&quot; UW-LDO-IC) and used as a reference to examine transcript abundance throughout one reactor cycle. The genome of UW-LDO-IC revealed the presence of a full pathway for respiratory denitrification. The observed transcript abundance patterns showed evidence of coregulation of the denitrifying genes along with a cbb3 cytochrome, which has been characterized as having high affinity for oxygen. Furthermore, we identified an FNR-like binding motif upstream of the coregulated genes, suggesting transcription-level regulation of both denitrifying and respiratory pathways in UW-LDO-IC. Taking the results together, the omics analysis provides strong evidence that &quot;Ca. Accumulibacter phosphatis&quot; UW-LDO-IC uses oxygen and nitrate simultaneously as electron acceptors under microaerobic conditions. IMPORTANCE &quot;Candidatus Accumulibacter phosphatis&quot; is widely found in full-scale wastewater treatment plants, where it has been identified as the key organism for biological removal of phosphorus. Since aeration can account for 50% of the energy use during wastewater treatment, microaerobic conditions for wastewater treatment have emerged as a cost-effective alternative to conventional biological nutrient removal processes. Our report provides strong genomics-based evidence not only that &quot;Ca. Accumulibacter phosphatis&quot; is the main organism contributing to phosphorus removal under microaerobic conditions but also that this organism simultaneously respires nitrate and oxygen in this environment, consequently removing nitrogen and phosphorus from the wastewater. Such activity could be harnessed in innovative designs for cost-effective and energy-efficient optimization of wastewater treatment systems.}, }
@article {pmid30944520, year = {2019}, author = {Paley, EL}, title = {Diet-Related Metabolic Perturbations of Gut Microbial Shikimate Pathway-Tryptamine-tRNA Aminoacylation-Protein Synthesis in Human Health and Disease.}, journal = {International journal of tryptophan research : IJTR}, volume = {12}, number = {}, pages = {1178646919834550}, doi = {10.1177/1178646919834550}, pmid = {30944520}, issn = {1178-6469}, abstract = {Human gut bacterial Na(+)-transporting NADH:ubiquinone reductase (NQR) sequence is associated with Alzheimer disease (AD). Here, Alzheimer disease-associated sequence (ADAS) is further characterized in cultured spore-forming Clostridium sp. Tryptophan and NQR substrate ubiquinone have common precursor chorismate in microbial shikimate pathway. Tryptophan-derived tryptamine presents in human diet and gut microbiome. Tryptamine inhibits tryptophanyl-tRNA synthetase (TrpRS) with consequent neurodegeneration in cell and animal models. Tryptophanyl-tRNA synthetase inhibition causes protein biosynthesis impairment similar to that revealed in AD. Tryptamine-induced TrpRS gene-dose reduction is associated with TrpRS protein deficiency and cell death. In animals, tryptamine treatment results in toxicity, weight gain, and prediabetes-related hypoglycemia. Sequence analysis of gut microbiome database reveals 89% to 100% ADAS nucleotide identity in American Indian (Cheyenne and Arapaho [C&amp;A]) Oklahomans, of which ~93% being overweight or obese and 50% self-reporting type 2 diabetes (T2D). Alzheimer disease-associated sequence occurs in 10.8% of C&amp;A vs 1.3% of healthy American population. This observation is of considerable interest because T2D links to AD and obesity. Alzheimer disease-associated sequence prevails in gut microbiome of colorectal cancer, which linked to AD. Metabolomics revealed that tryptamine, chorismate precursor quinate, and chorismate product 4-hydroxybenzoate (ubiquinone precursor) are significantly higher, while tryptophan-containing dipeptides are lower due to tRNA aminoacylation deficiency in C&amp;A compared with non-native Oklahoman who showed no ADAS. Thus, gut microbial tryptamine overproduction correlates with ADAS occurrence. Antibiotic and diet additives induce ADAS and tryptamine. Mitogenic/cytotoxic tryptamine cause microbial and human cell death, gut dysbiosis, and consequent disruption of host-microbe homeostasis. Present analysis of 1246 participants from 17 human gut metagenomics studies revealed ADAS in cell death diseases.}, }
@article {pmid30944212, year = {2019}, author = {Vlok, M and Lang, AS and Suttle, CA}, title = {Marine RNA Virus Quasispecies Are Distributed throughout the Oceans.}, journal = {mSphere}, volume = {4}, number = {2}, pages = {}, doi = {10.1128/mSphereDirect.00157-19}, pmid = {30944212}, issn = {2379-5042}, abstract = {RNA viruses, particularly genetically diverse members of the Picornavirales, are widespread and abundant in the ocean. Gene surveys suggest that there are spatial and temporal patterns in the composition of RNA virus assemblages, but data on their diversity and genetic variability in different oceanographic settings are limited. Here, we show that specific RNA virus genomes have widespread geographic distributions and that the dominant genotypes are under purifying selection. Genomes from three previously unknown picorna-like viruses (BC-1, -2, and -3) assembled from a coastal site in British Columbia, Canada, as well as marine RNA viruses JP-A, JP-B, and Heterosigma akashiwo RNA virus exhibited different biogeographical patterns. Thus, biotic factors such as host specificity and viral life cycle, and not just abiotic processes such as dispersal, affect marine RNA virus distribution. Sequence differences relative to reference genomes imply that virus quasispecies are under purifying selection, with synonymous single-nucleotide variations dominating in genomes from geographically distinct regions resulting in conservation of amino acid sequences. Conversely, sequences from coastal South Africa that mapped to marine RNA virus JP-A exhibited more nonsynonymous mutations, probably representing amino acid changes that accumulated over a longer separation. This biogeographical analysis of marine RNA viruses demonstrates that purifying selection is occurring across oceanographic provinces. These data add to the spectrum of known marine RNA virus genomes, show the importance of dispersal and purifying selection for these viruses, and indicate that closely related RNA viruses are pathogens of eukaryotic microbes across oceans.IMPORTANCE Very little is known about aquatic RNA virus populations and genome evolution. This is the first study that analyzes marine environmental RNA viral assemblages in an evolutionary and broad geographical context. This study contributes the largest marine RNA virus metagenomic data set to date, substantially increasing the sequencing space for RNA viruses and also providing a baseline for comparisons of marine RNA virus diversity. The new viruses discovered in this study are representative of the most abundant family of marine RNA viruses, the Marnaviridae, and expand our view of the diversity of this important group. Overall, our data and analyses provide a foundation for interpreting marine RNA virus diversity and evolution.}, }
@article {pmid30943009, year = {2019}, author = {Amarelle, V and Sanches-Medeiros, A and Silva-Rocha, R and Guazzaroni, ME}, title = {Expanding the Toolbox of Broad Host-Range Transcriptional Terminators for Proteobacteria through Metagenomics.}, journal = {ACS synthetic biology}, volume = {8}, number = {4}, pages = {647-654}, doi = {10.1021/acssynbio.8b00507}, pmid = {30943009}, issn = {2161-5063}, abstract = {As the field of synthetic biology moves toward the utilization of novel bacterial chassis, there is a growing need for biological parts with enhanced performance in a wide number of hosts. Is not unusual that biological parts (such as promoters and terminators), initially characterized in the model bacterium Escherichia coli, do not perform well when implemented in alternative hosts, such as Pseudomonas, therefore limiting the construction of synthetic circuits in industrially relevant bacteria, for instance Pseudomonas putida. In order to address this limitation, we present here the mining of transcriptional terminators through functional metagenomics to identify novel parts with broad host-range activity. Using a GFP-based terminator trap strategy and a broad host-range plasmid, we identified 20 clones with potential terminator activity in P. putida. Further characterization allowed the identification of 4 unique sequences ranging from 58 to 181 bp long that efficiently terminate transcription in P. putida, E. coli, Burkholderia phymatum, and two Pseudomonas strains isolated from Antarctica. Therefore, this work presents a new set of biological parts useful for the engineering of synthetic circuits in Proteobacteria.}, }
@article {pmid30942867, year = {2019}, author = {Brown, SM and Chen, H and Hao, Y and Laungani, BP and Ali, TA and Dong, C and Lijeron, C and Kim, B and Wultsch, C and Pei, Z and Krampis, K}, title = {MGS-Fast: Metagenomic shotgun data fast annotation using microbial gene catalogs.}, journal = {GigaScience}, volume = {8}, number = {4}, pages = {}, doi = {10.1093/gigascience/giz020}, pmid = {30942867}, issn = {2047-217X}, abstract = {BACKGROUND: Current methods used for annotating metagenomics shotgun sequencing (MGS) data rely on a computationally intensive and low-stringency approach of mapping each read to a generic database of proteins or reference microbial genomes.<br><br>RESULTS: We developed MGS-Fast, an analysis approach for shotgun whole-genome metagenomic data utilizing Bowtie2 DNA-DNA alignment of reads that is an alternative to using the integrated catalog of reference genes database of well-annotated genes compiled from human microbiome data. This method is rapid and provides high-stringency matches (>90% DNA sequence identity) of the metagenomics reads to genes with annotated functions. We demonstrate the use of this method with data from a study of liver disease and synthetic reads, and Human Microbiome Project shotgun data, to detect differentially abundant Kyoto Encyclopedia of Genes and Genomes gene functions in these experiments. This rapid annotation method is freely available as a Galaxy workflow within a Docker image.<br><br>CONCLUSIONS: MGS-Fast can confidently transfer functional annotations from gene databases to metagenomic reads, with speed and accuracy.}, }
@article {pmid30942859, year = {2019}, author = {Paul, VJ and Freeman, CJ and Agarwal, V}, title = {Chemical ecology of marine sponges: new opportunities through &quot;-omics&quot;.}, journal = {Integrative and comparative biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/icb/icz014}, pmid = {30942859}, issn = {1557-7023}, abstract = {The chemical ecology and chemical defenses of sponges have been investigated for decades; consequently, sponges are among the best understood marine organisms in terms of their chemical ecology, from the level of molecules to ecosystems. Thousands of natural products have been isolated and characterized from sponges, and although relatively few of these compounds have been studied for their ecological functions, some are known to serve as chemical defenses against predators, microorganisms, fouling organisms and other competitors. Sponges are hosts to an exceptional diversity of microorganisms, with almost 40 microbial phyla found in these associations to date. Microbial community composition and abundance is highly variable across host taxa, with a continuum from diverse assemblages of many microbial taxa to those that are dominated by a single microbial group. Microbial communities expand the nutritional repertoire of their hosts by providing access to inorganic and dissolved sources of nutrients. Not only does this continuum of microorganism-sponge associations lead to divergent nutritional characteristics in sponges, these associated microorganisms and symbionts have long been suspected, and are now known, to biosynthesize some of the natural products found in sponges. Modern &quot;omics&quot; tools provide ways to study these sponge-microbe associations that would have been difficult even a decade ago. Metabolomics facilitate comparisons of sponge compounds produced within and among taxa, and metagenomics and metatranscriptomics provide tools to understand the biology of host-microbe associations and the biosynthesis of ecologically relevant natural products. These combinations of ecological, microbiological, metabolomic and genomics tools and techniques provide unprecedented opportunities to advance sponge biology and chemical ecology across many marine ecosystems.}, }
@article {pmid30941274, year = {2019}, author = {García-Jiménez, B and Wilkinson, MD}, title = {Robust and automatic definition of microbiome states.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6657}, doi = {10.7717/peerj.6657}, pmid = {30941274}, issn = {2167-8359}, abstract = {Analysis of microbiome dynamics would allow elucidation of patterns within microbial community evolution under a variety of biologically or economically important circumstances; however, this is currently hampered in part by the lack of rigorous, formal, yet generally-applicable approaches to discerning distinct configurations of complex microbial populations. Clustering approaches to define microbiome &quot;community state-types&quot; at a population-scale are widely used, though not yet standardized. Similarly, distinct variations within a state-type are well documented, but there is no rigorous approach to discriminating these more subtle variations in community structure. Finally, intra-individual variations with even fewer differences will likely be found in, for example, longitudinal data, and will correlate with important features such as sickness versus health. We propose an automated, generic, objective, domain-independent, and internally-validating procedure to define statistically distinct microbiome states within datasets containing any degree of phylotypic diversity. Robustness of state identification is objectively established by a combination of diverse techniques for stable cluster verification. To demonstrate the efficacy of our approach in detecting discreet states even in datasets containing highly similar bacterial communities, and to demonstrate the broad applicability of our method, we reuse eight distinct longitudinal microbiome datasets from a variety of ecological niches and species. We also demonstrate our algorithm's flexibility by providing it distinct taxa subsets as clustering input, demonstrating that it operates on filtered or unfiltered data, and at a range of different taxonomic levels. The final output is a set of robustly defined states which can then be used as general biomarkers for a wide variety of downstream purposes such as association with disease, monitoring response to intervention, or identifying optimally performant populations.}, }
@article {pmid30941204, year = {2019}, author = {Tedeschi, A and Popovich, PG}, title = {The Application of Omics Technologies to Study Axon Regeneration and CNS Repair.}, journal = {F1000Research}, volume = {8}, number = {}, pages = {}, doi = {10.12688/f1000research.17084.1}, pmid = {30941204}, issn = {2046-1402}, abstract = {Traumatic brain and spinal cord injuries cause permanent disability. Although progress has been made in understanding the cellular and molecular mechanisms underlying the pathophysiological changes that affect both structure and function after injury to the brain or spinal cord, there are currently no cures for either condition. This may change with the development and application of multi-layer omics, new sophisticated bioinformatics tools, and cutting-edge imaging techniques. Already, these technical advances, when combined, are revealing an unprecedented number of novel cellular and molecular targets that could be manipulated alone or in combination to repair the injured central nervous system with precision. In this review, we highlight recent advances in applying these new technologies to the study of axon regeneration and rebuilding of injured neural circuitry. We then discuss the challenges ahead to translate results produced by these technologies into clinical application to help improve the lives of individuals who have a brain or spinal cord injury.}, }
@article {pmid30940882, year = {2019}, author = {Naginyte, M and Do, T and Meade, J and Devine, DA and Marsh, PD}, title = {Enrichment of periodontal pathogens from the biofilms of healthy adults.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {5491}, doi = {10.1038/s41598-019-41882-y}, pmid = {30940882}, issn = {2045-2322}, abstract = {Periodontitis is associated with shifts in the balance of the subgingival microbiome. Many species that predominate in disease have not been isolated from healthy sites, raising questions as to the origin of these putative pathogens. The study aim was to determine whether periodontal pathogens could be enriched from pooled saliva, plaque and tongue samples from dentally-healthy adult volunteers using growth media that simulate nutritional aspects of the inflamed subgingival environment. The microbiome was characterised before and after enrichment using established metagenomic approaches, and the data analysed bioinformatically to identify major functional changes. After three weeks, there was a shift from an inoculum in which Streptococcus, Haemophilus, Neisseria, Veillonella and Prevotella species predominated to biofilms comprising an increased abundance of taxa implicated in periodontitis, including Porphyromonas gingivalis, Fretibacterium fastidiosum, Filifactor alocis, Tannerella forsythia, and several Peptostreptococcus and Treponema spp., with concomitant decreases in health-associated species. Sixty-four species were present after enrichment that were undetectable in the inoculum, including Jonquetella anthropi, Desulfovibrio desulfuricans and Dialister invisus. These studies support the Ecological Plaque Hypothesis, providing evidence that putative periodontopathogens are present in health at low levels, but changes to the subgingival nutritional environment increase their competitiveness and drive deleterious changes to biofilm composition.}, }
@article {pmid30939077, year = {2019}, author = {Altan, E and Kubiski, SV and Boros, Á and Reuter, G and Sadeghi, M and Deng, X and Creighton, EK and Crim, MJ and Delwart, E}, title = {A Highly Divergent Picornavirus Infecting the Gut Epithelia of Zebrafish (Danio rerio) in Research Institutions Worldwide.}, journal = {Zebrafish}, volume = {}, number = {}, pages = {}, doi = {10.1089/zeb.2018.1710}, pmid = {30939077}, issn = {1557-8542}, abstract = {Zebrafish have been extensively used as a model system for research in vertebrate development and pathogen-host interactions. We describe the complete genome of a novel picornavirus identified during a viral metagenomics analysis of zebrafish gut tissue. The closest relatives of this virus showed identity of <20% in their P1 capsids and <36% in their RdRp qualifying zebrafish picornavirus-1 (ZfPV-1) as member of a novel genus with a proposed name of Cyprivirus. Reverse transcription (RT)-PCR testing of zebrafish from North America, Europe, and Asia showed ZfPV-1 to be globally distributed, being detected in 23 of 41 (56%) institutions tested. In situ hybridization of whole zebrafish showed viral RNA was restricted to a subset of enterocytes and cells in the subjacent lamina propria of the intestine and the intestinal mucosa. This naturally occurring and apparently asymptomatic infection (in wild-type zebrafish lineage AB) provides a natural infection system to study picornavirus-host interactions in an advanced vertebrate model organism. Whether ZfPV-1 infection affects any immunological, developmental, or other biological processes in wild-type or mutant zebrafish lineages remains to be determined.}, }
@article {pmid30938752, year = {2019}, author = {Koedooder, R and Mackens, S and Budding, A and Fares, D and Blockeel, C and Laven, J and Schoenmakers, S}, title = {Identification and evaluation of the microbiome in the female and male reproductive tracts.}, journal = {Human reproduction update}, volume = {25}, number = {3}, pages = {298-325}, doi = {10.1093/humupd/dmy048}, pmid = {30938752}, issn = {1460-2369}, abstract = {BACKGROUND: The existence of an extensive microbiome in and on the human body has increasingly dominated the scientific literature during the last decade. A shift from culture-dependent to culture-independent identification of microbes has occurred since the emergence of next-generation sequencing (NGS) techniques, whole genome shotgun and metagenomic sequencing. These sequencing analyses have revealed the presence of a rich diversity of microbes in most exposed surfaces of the human body, such as throughout the reproductive tract. The results of microbiota analyses are influenced by the technical specifications of the applied methods of analyses. Therefore, it is difficult to correctly compare and interpret the results of different studies of the same anatomical niche.<br><br>OBJECTIVES AND RATIONALE: The aim of this narrative review is to provide an overview of the currently used techniques and the reported microbiota compositions in the different anatomical parts of the female and male reproductive tracts since the introduction of NGS in 2005. This is crucial to understand and determine the interactions and roles of the different microbes necessary for successful reproduction.<br><br>SEARCH METHODS: A search in Embase, Medline Ovid, Web of science, Cochrane and Google scholar was conducted. The search was limited to English language and studies published between January 2005 and April 2018. Included articles needed to be original microbiome research related to the reproductive tracts.<br><br>OUTCOMES: The review provides an extensive up-to-date overview of current microbiome research in the field of human reproductive medicine. The possibility of drawing general conclusions is limited due to diversity in the execution of analytical steps in microbiome research, such as local protocols, sampling methods, primers used, sequencing techniques and bioinformatic pipelines, making it difficult to compare and interpret results of the available studies. Although some microbiota are associated with reproductive success and a good pregnancy outcome, it is still unknown whether a causal link exists. More research is needed to further explore the possible clinical implications and therapeutic interventions.<br><br>WIDER IMPLICATIONS: For the field of reproductive medicine, determination of what is a favourable reproductive tract microbiome will provide insight into the mechanisms of both unsuccessful and successful human reproduction. To increase pregnancy chances with live birth and to reduce reproduction-related health costs, future research could focus on postponing treatment or conception in case of the presence of unfavourable microbiota and on the development of therapeutic interventions, such as microbial therapeutics and lifestyle adaptations.}, }
@article {pmid30937887, year = {2019}, author = {Sharma, A and Buschmann, MM and Gilbert, JA}, title = {Pharmacomicrobiomics: The holy grail to variability in drug response?.}, journal = {Clinical pharmacology and therapeutics}, volume = {}, number = {}, pages = {}, doi = {10.1002/cpt.1437}, pmid = {30937887}, issn = {1532-6535}, abstract = {The human body, with 3.0×1013 cells and more than 3.8×1013 microorganisms, has nearly a one-to-one ratio of resident microbes to human cells. Initiatives like the Human Microbiome Project, American Gut, and Flemish Gut have identified associations between microbial taxa and human health. The study of interactions between microbiome and pharmaceutical agents i.e. pharamacomicrobiomics has revealed an instrumental role of the microbiome in modulating drug response that alters the therapeutic outcomes. In this review, we present our current comprehension of the relationship of the microbiome, host biology, and pharmaceutical agents such as cardiovascular drugs, analgesics and chemotherapeutic-agents to human disease and treatment outcomes. We also discuss the significance of studying diet-gene-drug interactions and further address the key challenges associated with pharamacomicrobiomics. Finally, we examine proposed models employing systems biology for the application of pharmacomicrobiomics and other omics data, and provide approaches to elucidate microbiome-drug interactions to improve future translation to personalized medicine. This article is protected by copyright. All rights reserved.}, }
@article {pmid30937653, year = {2019}, author = {Parvathi, A and Jasna, V and Aswathy, VK and Nathan, VK and Aparna, S and Balachandran, KK}, title = {Microbial diversity in a coastal environment with co-existing upwelling and mud-banks along the south west coast of India.}, journal = {Molecular biology reports}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11033-019-04766-y}, pmid = {30937653}, issn = {1573-4978}, support = {OLP1709//National Institute of Oceanography, India/ ; }, abstract = {Upwelling and mud banks are two prominent oceanographic features in the coastal waters along the south west coast of India during the southwest monsoon (MON) season. The present study investigates the microbial diversity in the coastal environments of Alappuzha, India, where upwelling and mud banks co-exist. Water samples were collected from three stations, M1, M2, and M3, on a weekly basis to estimate the physico-chemical parameters and microbial abundance (MA). Presence of cold waters (< 26 °C) with high nitrate (6-8 µM) and low dissolved oxygen (5 µM) in the sub surface waters during monsoon (M) confirmed the presence of upwelling at all the three stations. Simultaneously, presence of unusually calm waters was seen at M2 alone during M indicating the formation of mud banks. The microbial diversity was determined from three stations, with distinct oceanographic conditions (M1: coastal reference station with only upwelling, M2: mud banks + upwelling, and M3: offshore reference station with only upwelling). The water samples were collected during two seasons, pre-monsoon (April) and M (July) and analysed using 16S rRNA-based Illumina high-throughput metagenomic sequencing. Proteobacteria was the most dominant phyla, followed by Bacteroidetes, Firmicutes, Cyanobacteria, Actinobacteria, and Verrucomicrobia in order, with variations in their relative abundance spatially and seasonally. Though the MA increased during M at all the stations, the relative abundance of most of the bacterial phyla except Proteobacteria decreased during M season. Interestingly, most of the sequences at M2 during mud banks were unclassified at the class level indicating the presence of unique microbial populations in this station. Prediction of metabolic activity revealed ammonia oxidation, nitrite reduction, sulphate reduction, xylan degradation, dehalogenation, chitin degradation, etc. as important functions. The metabolic activity throws light on the role of microbes in this environment thereby providing a system-scale perspective of microbial community interactions.}, }
@article {pmid30937543, year = {2019}, author = {Aguilar-Durán, L and Figueiredo, R and Seminago, R and Roig, FJ and Llorens, C and Valmaseda-Castellón, E}, title = {A metagenomic study of patients with alveolar osteitis after tooth extraction. A preliminary case-control study.}, journal = {Clinical oral investigations}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00784-019-02855-7}, pmid = {30937543}, issn = {1436-3771}, abstract = {OBJECTIVE: To identify the microbiome in sockets with alveolar osteitis and compare it with a control group using metagenomic techniques.<br><br>MATERIALS AND METHODS: A case-control study was conducted in subjects that had undergone a tooth extraction. Microbiological samples were taken from the sockets of 10 patients with dry socket after tooth extraction (AO group) and 10 patients in whom exodontia resulted in no postoperative complications (control group). Bacterial DNA was isolated, and the 16S rRNA gene was amplified and sequenced. Multiplexed tag-encoded sequencing of DNA from the samples was performed, and the reads were processed by Metagenomic Rapid Annotation.<br><br>RESULTS: A total of 151 different species were found: 55 bacteria were only found in the AO group, 51 were specific to the control group, and 45 were common to both groups. The most frequently found genera in both groups were Prevotella. Prevotella nanceiensis, Actinomyces odontolyticus, Treponema maltophilum, Veillonella dispar, Tannerella forsythia, and Leuconostoc mesenteroides were found in several patients with alveolar osteitis, with an abundance greater than 0.5%, and were absent in all the control group samples.<br><br>CONCLUSIONS: Patients who develop alveolar osteitis after dental extractions might have a different microbiota from that of patients without postoperative complications. Since this is a preliminary report, further research is needed to assess whether bacteria play an important role in the etiology of dry socket.<br><br>CLINICAL RELEVANCE: This study seems to indicate that bacteria may play an important role in the alveolar osteitis etiology. Thus, new prevention and treatment strategies should be considered.}, }
@article {pmid30936548, year = {2019}, author = {Thomas, AM and Manghi, P and Asnicar, F and Pasolli, E and Armanini, F and Zolfo, M and Beghini, F and Manara, S and Karcher, N and Pozzi, C and Gandini, S and Serrano, D and Tarallo, S and Francavilla, A and Gallo, G and Trompetto, M and Ferrero, G and Mizutani, S and Shiroma, H and Shiba, S and Shibata, T and Yachida, S and Yamada, T and Wirbel, J and Schrotz-King, P and Ulrich, CM and Brenner, H and Arumugam, M and Bork, P and Zeller, G and Cordero, F and Dias-Neto, E and Setubal, JC and Tett, A and Pardini, B and Rescigno, M and Waldron, L and Naccarati, A and Segata, N}, title = {Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation.}, journal = {Nature medicine}, volume = {25}, number = {4}, pages = {667-678}, doi = {10.1038/s41591-019-0405-7}, pmid = {30936548}, issn = {1546-170X}, abstract = {Several studies have investigated links between the gut microbiome and colorectal cancer (CRC), but questions remain about the replicability of biomarkers across cohorts and populations. We performed a meta-analysis of five publicly available datasets and two new cohorts and validated the findings on two additional cohorts, considering in total 969 fecal metagenomes. Unlike microbiome shifts associated with gastrointestinal syndromes, the gut microbiome in CRC showed reproducibly higher richness than controls (P < 0.01), partially due to expansions of species typically derived from the oral cavity. Meta-analysis of the microbiome functional potential identified gluconeogenesis and the putrefaction and fermentation pathways as being associated with CRC, whereas the stachyose and starch degradation pathways were associated with controls. Predictive microbiome signatures for CRC trained on multiple datasets showed consistently high accuracy in datasets not considered for model training and independent validation cohorts (average area under the curve, 0.84). Pooled analysis of raw metagenomes showed that the choline trimethylamine-lyase gene was overabundant in CRC (P = 0.001), identifying a relationship between microbiome choline metabolism and CRC. The combined analysis of heterogeneous CRC cohorts thus identified reproducible microbiome biomarkers and accurate disease-predictive models that can form the basis for clinical prognostic tests and hypothesis-driven mechanistic studies.}, }
@article {pmid30936547, year = {2019}, author = {Wirbel, J and Pyl, PT and Kartal, E and Zych, K and Kashani, A and Milanese, A and Fleck, JS and Voigt, AY and Palleja, A and Ponnudurai, R and Sunagawa, S and Coelho, LP and Schrotz-King, P and Vogtmann, E and Habermann, N and Niméus, E and Thomas, AM and Manghi, P and Gandini, S and Serrano, D and Mizutani, S and Shiroma, H and Shiba, S and Shibata, T and Yachida, S and Yamada, T and Waldron, L and Naccarati, A and Segata, N and Sinha, R and Ulrich, CM and Brenner, H and Arumugam, M and Bork, P and Zeller, G}, title = {Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer.}, journal = {Nature medicine}, volume = {25}, number = {4}, pages = {679-689}, doi = {10.1038/s41591-019-0406-6}, pmid = {30936547}, issn = {1546-170X}, abstract = {Association studies have linked microbiome alterations with many human diseases. However, they have not always reported consistent results, thereby necessitating cross-study comparisons. Here, a meta-analysis of eight geographically and technically diverse fecal shotgun metagenomic studies of colorectal cancer (CRC, n = 768), which was controlled for several confounders, identified a core set of 29 species significantly enriched in CRC metagenomes (false discovery rate (FDR) < 1 × 10-5). CRC signatures derived from single studies maintained their accuracy in other studies. By training on multiple studies, we improved detection accuracy and disease specificity for CRC. Functional analysis of CRC metagenomes revealed enriched protein and mucin catabolism genes and depleted carbohydrate degradation genes. Moreover, we inferred elevated production of secondary bile acids from CRC metagenomes, suggesting a metabolic link between cancer-associated gut microbes and a fat- and meat-rich diet. Through extensive validations, this meta-analysis firmly establishes globally generalizable, predictive taxonomic and functional microbiome CRC signatures as a basis for future diagnostics.}, }
@article {pmid30936376, year = {2019}, author = {Quach, HT and Robbins, CJ and Balko, JM and Chiu, CY and Miller, S and Wilson, MR and Nelson, GE and Johnson, DB}, title = {Severe Epididymo-Orchitis and Encephalitis Complicating Anti-PD-1 Therapy.}, journal = {The oncologist}, volume = {}, number = {}, pages = {}, doi = {10.1634/theoncologist.2018-0722}, pmid = {30936376}, issn = {1549-490X}, abstract = {BACKGROUND: Immune checkpoint inhibitors such as pembrolizumab and nivolumab have emerged as active treatment options for patients with many cancers, including metastatic melanoma, but can also cause symptomatic or life-threatening immune-related adverse events, including encephalitis. Epididymitis and orchitis are rare complications of these therapies.<br><br>CASE PRESENTATION: We describe herein a patient with metastatic melanoma who developed epididymo-orchitis followed by encephalitis while receiving pembrolizumab. The patient developed testicular pain and fever after his third dose of pembrolizumab; ultrasound evaluation demonstrated bilateral epididymo-orchitis. He then developed headaches, fever, and altered mental status over the next week and was admitted to the hospital. Lumbar puncture revealed inflammatory changes consistent with meningoencephalitis; he did not improve with broad-spectrum antibiotics, and an extensive workup for infectious etiologies, including cerebrospinal fluid testing using a clinical metagenomic next-generation sequencing assay, was negative. He received high-dose steroids for suspected autoimmune encephalitis, and both his orchitis and meningoencephalitis improved rapidly after one dose. He fully recovered after a 5-week taper of oral steroids.<br><br>DISCUSSION: Here, we report a case of epididymo-orchitis complicating immune checkpoint inhibitor therapy. This patient subsequently developed severe encephalitis but rapidly improved with steroids. Clinicians should be aware of rare complications of these agents.<br><br>KEY POINTS: Epididymo-orchitis is a rare and potentially life-threatening complication of anti-programmed death protein 1 (anti-PD-1) therapy.For patients on anti-PD-1 therapy who develop either epididymo-orchitis or epididymitis without clear infectious cause, immune-related adverse events should be considered in the differential diagnosis.If severe, epididymo-orchitis related to anti-PD-1 therapy may be treated with high-dose corticosteroids.}, }
@article {pmid30935879, year = {2019}, author = {Wang, Y and Hu, Y and Cao, J and Bi, Y and Lv, N and Liu, F and Liang, S and Shi, Y and Jiao, X and Gao, GF and Zhu, B}, title = {Antibiotic resistance gene reservoir in live poultry markets.}, journal = {The Journal of infection}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jinf.2019.03.012}, pmid = {30935879}, issn = {1532-2742}, abstract = {OBJECTIVES: The heavy use of antibiotics in farm animals contributes to the enrichment and spread of antibiotic resistance genes (ARGs) in &quot;one-health&quot; settings. Numerous ARGs have been identified in livestock-associated environments but not in Chinese live poultry markets (LPMs).<br><br>METHODS: We collected 753 poultry fecal samples from LPMs of 18 provinces and municipalities in China and sequenced the metagenomes of 130 samples. Bioinformatic tools were used to construct the gene catalog and analyze the ARG content. PCR amplification and Sanger sequencing were used to survey the distribution of mcr-1 gene in all 753 fecal samples.<br><br>RESULTS: We found that a low number of genes but a high percentage of gene functions were shared among the poultry, human and pig gut gene catalogs. The poultry gut possessed 539 ARGs which were classified into 235 types. Both the ARG number and abundance were significantly higher in poultry than that in either pigs or humans. Fourteen ARG types were found present in all 130 samples, and tetracycline resistance (TcR) genes were the most abundant ARGs in both animals and humans. Moreover, 59.63% LPM samples harbored the colistin resistance gene mcr-1, and other mcr gene variants were also found.<br><br>CONCLUSIONS: We demonstrated that the Chinese LPMs is a repository for ARGs, posing a high risk for ARG dissemination from food animals to humans under such a trade system, which has not been addressed before.}, }
@article {pmid30935870, year = {2019}, author = {Jabłońska, J and Tawfik, DS}, title = {The number and type of oxygen-utilizing enzymes indicates aerobic vs. anaerobic phenotype.}, journal = {Free radical biology &amp; medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.freeradbiomed.2019.03.031}, pmid = {30935870}, issn = {1873-4596}, abstract = {Oxygen is a major metabolic driving force that enabled the expansion of metabolic networks including new metabolites and new enzymes. It had a dramatic impact on the primary electron transport chain where it serves as terminal electron acceptor, but oxygen is also used by many enzymes as electron acceptor for a variety of reactions. The organismal oxygen phenotype, aerobic vs. anaerobic, should be manifested in its O2-utilizing enzymes. Traditionally, enzymes involved in primary oxygen metabolism such as cytochrome c, and reactive oxygen species (ROS)-neutralizing enzymes (e.g. catalase), were used as identifiers of oxygen phenotype. However, these enzymes are often found in strict anaerobes. We aimed to identify the O2-utilizing enzymes that may distinguish between aerobes and anaerobes. To this end, we annotated the O2-utilizing enzymes across the prokaryotic tree of life. We recovered over 700 enzymes and mapped their presence/absence in 272 representative genomes. As seen before, enzymes mediating primary oxygen metabolism, and ROS neutralizing enzymes, could be found in both aerobes and anaerobes. However, there exists a subset of enzymes, primarily oxidases that catabolyze various substrates, including amino acids and xenobiotics, that are preferentially enriched in aerobes. Overall it appears that the total number of oxygen-utilizing enzymes, and the presence of enzymes involved in 'peripheral', secondary oxygen metabolism, can reliably distinguish aerobes from anaerobes based solely on genome sequences. These criteria can also indicate the oxygen phenotype in metagenomic samples.}, }
@article {pmid30935838, year = {2019}, author = {Lin, BY and Lin, WD and Huang, CK and Hsin, MC and Lin, WY and Pryor, AD}, title = {Changes of gut microbiota between different weight reduction programs.}, journal = {Surgery for obesity and related diseases : official journal of the American Society for Bariatric Surgery}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.soard.2019.01.026}, pmid = {30935838}, issn = {1878-7533}, abstract = {BACKGROUND: Gut microbiota may induce obesity, diabetes, and metabolic syndrome. Different weight reduction programs may induce different changes in gut microbiota.<br><br>OBJECTIVES: To assess the changes in gut microbiota between obese adults who participated in 2 different weight reduction programs, the dietary counseling (DC) group and sleeve gastrectomy (SG) group, for 3 months.<br><br>SETTING: A University Hospital.<br><br>METHODS: Ten obese participants from each group were matched according to sex, age, and body mass index. Gut microbiota compositions were determined by metagenomics using next-generation sequencing before and after treatment. Anthropometric indices, metabolic factors, and gut microbiota were compared between and within groups.<br><br>RESULTS: After 3 months of treatment, compared with subjects in DC group, subjects in SG group experienced a greater reduction in body weight, body mass index, body fat, waist and hip circumference, diastolic blood pressure, hemoglobin, insulin, insulin resistance, glutamate pyruvate transaminase, blood urine nitrogen, and glycated hemoglobin (HbA1C). A total of 8, 17, and 46 species experienced significant abundance changes in DC, in SG, and between the 2 groups, respectively. Diversity of the gut flora increased in SG and between the 2 groups after treatment. The weight change over the course of the weight loss program was further adjusted and only 4 species, including Peptoniphilus lacrimalis 315 B, Selenomonas 4 sp., Prevotella 2 sp., and Pseudobutyrivibrio sp., were found to be significantly different between the 2 weight loss programs. These 4 species may be the different gut microbiota change between internal and surgical weight reduction programs.<br><br>CONCLUSIONS: There are significant differences not only in anthropometric indices and metabolic factors but also in gut microbiota change between the 2 programs.}, }
@article {pmid30935502, year = {2019}, author = {Veldhuis, A and Mars, J and Stegeman, A and van Schaik, G}, title = {Changing surveillance objectives during the different phases of an emerging vector-borne disease outbreak: The Schmallenberg virus example.}, journal = {Preventive veterinary medicine}, volume = {166}, number = {}, pages = {21-27}, doi = {10.1016/j.prevetmed.2019.03.008}, pmid = {30935502}, issn = {1873-1716}, mesh = {Animals ; Bunyaviridae Infections/epidemiology/prevention &amp; control/*veterinary/virology ; Cattle ; Cattle Diseases/*epidemiology/prevention &amp; control/virology ; Communicable Disease Control/*methods ; Disease Outbreaks/prevention &amp; control/*veterinary ; Female ; Netherlands/epidemiology ; Orthobunyavirus/physiology ; Population Surveillance/methods ; Sentinel Surveillance/*veterinary ; }, abstract = {In the late summer of 2011, a sudden rise in incidence of fever, drop in milk production and diarrhoea was observed in dairy cows in the eastern region of the Netherlands and in north-western Germany. In the autumn of 2011, a novel orthobunyavirus was identified by metagenomic analyses in samples from acutely diseased cows on a farm near the German city of Schmallenberg, and was thereafter named Schmallenberg virus (SBV). Due to the novelty of the virus, there was an immediate need for knowledge regarding the epidemiological characteristics of SBV-infections to inform surveillance and control strategies. A rapid assessment of the spread and impact of an emerging disease supports decision-makers on allocation of resources. This paper reviews the disease mitigation activities during and after the SBV epidemic in the Netherlands, to illustrate the phases in surveillance when a new (vector-borne) pathogen emerges in a country or region. Immediate and short-term disease mitigation activities that were initiated after SBV was identified are discussed in detail, as well as ways to enhance future surveillance (e.g. by syndromic surveillance) and preparedness for similar disease outbreaks. By doing so, lessons learnt from the SBV epidemic will also improve surveillance for other emerging diseases in cattle.}, }
@article {pmid30935423, year = {2019}, author = {Prussin, AJ and Torres, PJ and Shimashita, J and Head, SR and Bibby, KJ and Kelley, ST and Marr, LC}, title = {Seasonal dynamics of DNA and RNA viral bioaerosol communities in a daycare center.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {53}, doi = {10.1186/s40168-019-0672-z}, pmid = {30935423}, issn = {2049-2618}, support = {1-DP2-A1112243//National Institutes of Health/ ; Postdoctoral Fellowship//Alfred P. Sloan Foundation (US)/ ; CBET-1438103//National Science Foundation/ ; ECCS-1542100//National Science Foundation/ ; }, abstract = {BACKGROUND: Viruses play an important role in ecosystems, including the built environment (BE). While numerous studies have characterized bacterial and fungal microbiomes in the BE, few have focused on the viral microbiome (virome). Longitudinal microbiome studies provide insight into the stability and dynamics of microbial communities; however, few such studies exist for the microbiome of the BE, and most have focused on bacteria. Here, we present a longitudinal, metagenomic-based analysis of the airborne DNA and RNA virome of a children's daycare center. Specifically, we investigate how the airborne virome varies as a function of season and human occupancy, and we identify possible sources of the viruses and their hosts, mainly humans, animals, plants, and insects.<br><br>RESULTS: Season strongly influenced the airborne viral community composition, and a single sample collected when the daycare center was unoccupied suggested that occupancy also influenced the community. The pattern of influence differed between DNA and RNA viromes. Human-associated viruses were much more diverse and dominant in the winter, while the summertime virome contained a high relative proportion and diversity of plant-associated viruses.<br><br>CONCLUSIONS: This airborne microbiome in this building exhibited seasonality in its viral community but not its bacterial community. Human occupancy influenced both types of communities. By adding new data about the viral microbiome to complement burgeoning information about the bacterial and fungal microbiomes, this study contributes to a more complete understanding of the airborne microbiome.}, }
@article {pmid30935407, year = {2019}, author = {Berglund, F and Österlund, T and Boulund, F and Marathe, NP and Larsson, DGJ and Kristiansson, E}, title = {Identification and reconstruction of novel antibiotic resistance genes from metagenomes.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {52}, doi = {10.1186/s40168-019-0670-1}, pmid = {30935407}, issn = {2049-2618}, abstract = {BACKGROUND: Environmental and commensal bacteria maintain a diverse and largely unknown collection of antibiotic resistance genes (ARGs) that, over time, may be mobilized and transferred to pathogens. Metagenomics enables cultivation-independent characterization of bacterial communities but the resulting data is noisy and highly fragmented, severely hampering the identification of previously undescribed ARGs. We have therefore developed fARGene, a method for identification and reconstruction of ARGs directly from shotgun metagenomic data.<br><br>RESULTS: fARGene uses optimized gene models and can therefore with high accuracy identify previously uncharacterized resistance genes, even if their sequence similarity to known ARGs is low. By performing the analysis directly on the metagenomic fragments, fARGene also circumvents the need for a high-quality assembly. To demonstrate the applicability of fARGene, we reconstructed β-lactamases from five billion metagenomic reads, resulting in 221 ARGs, of which 58 were previously not reported. Based on 38 ARGs reconstructed by fARGene, experimental verification showed that 81% provided a resistance phenotype in Escherichia coli. Compared to other methods for detecting ARGs in metagenomic data, fARGene has superior sensitivity and the ability to reconstruct previously unknown genes directly from the sequence reads.<br><br>CONCLUSIONS: We conclude that fARGene provides an efficient and reliable way to explore the unknown resistome in bacterial communities. The method is applicable to any type of ARGs and is freely available via GitHub under the MIT license.}, }
@article {pmid30934749, year = {2019}, author = {Hamner, S and Brown, BL and Hasan, NA and Franklin, MJ and Doyle, J and Eggers, MJ and Colwell, RR and Ford, TE}, title = {Metagenomic Profiling of Microbial Pathogens in the Little Bighorn River, Montana.}, journal = {International journal of environmental research and public health}, volume = {16}, number = {7}, pages = {}, doi = {10.3390/ijerph16071097}, pmid = {30934749}, issn = {1660-4601}, support = {n/a//United for Health Innovation/ ; }, abstract = {The Little Bighorn River is the primary source of water for water treatment plants serving the local Crow Agency population, and has special significance in the spiritual and ceremonial life of the Crow tribe. Unfortunately, the watershed suffers from impaired water quality, with high counts of fecal coliform bacteria routinely measured during run-off events. A metagenomic analysis was carried out to identify potential pathogens in the river water. The Oxford Nanopore MinION platform was used to sequence DNA in near real time to identify both uncultured and a coliform-enriched culture of microbes collected from a popular summer swimming area of the Little Bighorn River. Sequences were analyzed using CosmosID bioinformatics and, in agreement with previous studies, enterohemorrhagic and enteropathogenic Escherichia coli and other E. coli pathotypes were identified. Noteworthy was detection and identification of enteroaggregative E. coli O104:H4 and Vibrio cholerae serotype O1 El Tor, however, cholera toxin genes were not identified. Other pathogenic microbes, as well as virulence genes and antimicrobial resistance markers, were also identified and characterized by metagenomic analyses. It is concluded that metagenomics provides a useful and potentially routine tool for identifying in an in-depth manner microbial contamination of waterways and, thereby, protecting public health.}, }
@article {pmid30933772, year = {2019}, author = {Muñoz-García, A and Mestanza, O and Isaza, JP and Figueroa-Galvis, I and Vanegas, J}, title = {Influence of salinity on the degradation of xenobiotic compounds in rhizospheric mangrove soil.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {249}, number = {}, pages = {750-757}, doi = {10.1016/j.envpol.2019.03.056}, pmid = {30933772}, issn = {1873-6424}, abstract = {Mangroves are highly productive tropical ecosystems influenced by seasonal and daily salinity changes, often exposed to sewage contamination, oil spills and heavy metals, among others. There is limited knowledge of the influence of salinity on the ability of microorganisms to degrade xenobiotic compounds. The aim of this study were to determine the salinity influence on the degradation of xenobiotic compounds in a semi-arid mangrove in La Guajira-Colombia and establish the more abundant genes and degradation pathways. In this study, rhizospheric soil of Avicennia germinans was collected in three points with contrasting salinity (4H, 2 M and 3 L). Total DNA extraction was performed and shotgun sequenced using the Illumina HiSeq technology. We annotated 507,343 reads associated with 21 pathways and detected 193 genes associated with the degradation of xenobiotics using orthologous genes from the KEGG Orthology (KO) database, of which 16 pathways and 113 genes were influenced by salinity. The highest abundances were found in high salinity. The degradation of benzoate showed the highest abundance, followed by the metabolism of the drugs and the degradation of chloroalkane and chloroalkene. The majority of genes were associated with phase I degradation of xenobiotics. The most abundant genes were acetyl-CoA C-acetyltransferase (atoB), catalase-peroxidase (katG) and GMP synthase (glutamine-hydrolysing) (guaA). In conclusion, the metagenomic analysis detected all the degradation pathways of xenobiotics of KEGG and 59% of the genes associated with these pathways were influenced by salinity.}, }
@article {pmid30932733, year = {2019}, author = {Xiao, H and Li, C and Al Rwahnih, M and Dolja, V and Meng, B}, title = {Metagenomic Analysis of Riesling Grapevine Reveals a Complex Virome Including Two New and Divergent Variants of Grapevine leafroll-associated virus 3.}, journal = {Plant disease}, volume = {}, number = {}, pages = {PDIS09181503RE}, doi = {10.1094/PDIS-09-18-1503-RE}, pmid = {30932733}, issn = {0191-2917}, abstract = {The virome of a major white wine grape of cultivar Riesling showing decline and leafroll disease symptoms was analyzed through high-throughput sequencing (HTS) using total RNAs as templates and the Illumina HiSeq 2500 platform. Analysis of HTS data revealed the presence of five viruses and three viroids in the infected vine. These viruses are Grapevine leafroll-associated virus 1 (GLRaV-1) and GLRaV-3 (genus Ampelovirus, family Closteroviridae) and three viruses of the family Betaflexiviridae (namely, Grapevine virus A [GVA], Grapevine virus B, and Grapevine rupestris stem pitting-associated virus [GRSPaV]). We also show that multiple distinct strains of three viruses (GLRaV-3, GVA, and GRSPaV) were present in this diseased grapevine. The complete genomes of two novel and highly divergent isolates of GLRaV-3 were determined using the draft genomes derived from HTS data and two independent rapid amplification of cDNA ends (RACE) strategies to obtain sequences at both the 5' and the 3' termini of the viral genomes. Questionable genome regions of both isolates were also verified through cloning of reverse transcription polymerase chain reaction products and Sanger sequencing. These two isolates are vastly divergent from all other isolates of GLRaV-3 whose genome sequences are available in GenBank. Isolate ON8415A has up to 76% nucleotide sequence identities to other isolates representing existing variant groups. We also revealed high degrees of variation in both length and sequence in the terminal untranslated regions (UTRs) of GLRaV-3 variants. The 5'-UTR of most GLRaV-3 isolates whose complete genomes have been sequenced contain tandem repeats of 65 nucleotides, a highly unusual feature rarely observed in (+)single-stranded RNA viruses. Mechanisms for the biogenesis of these tandem repeats and their function in virus replication and pathogenesis require investigation. Findings of this research add to the genetic diversity, evolutionary biology, and diagnostics of GLRaV-3 that afflicts the global grape wine industry.}, }
@article {pmid30930686, year = {2019}, author = {Leipold, L and Dobrijevic, D and Jeffries, JWE and Bawn, M and Moody, TS and Ward, JM and Hailes, HC}, title = {The identification and use of robust transaminases from a domestic drain metagenome.}, journal = {Green chemistry : an international journal and green chemistry resource : GC}, volume = {21}, number = {1}, pages = {75-86}, doi = {10.1039/c8gc02986e}, pmid = {30930686}, issn = {1463-9262}, abstract = {Transaminases remain one of the most promising biocatalysts for use in chiral amine synthesis, however their industrial implementation has been hampered by their general instability towards, for example, high amine donor concentrations and organic solvent content. Herein we describe the identification, cloning and screening of 29 novel transaminases from a household drain metagenome. The most promising enzymes were fully characterised and the effects of pH, temperature, amine donor concentration and co-solvent determined. Several enzymes demonstrated good substrate tolerance as well as an unprecedented robustness for a wild-type transaminase. One enzyme in particular readily accepted IPA as an amine donor giving the same conversion with 2-50 equivalents, as well as being tolerant to a number of co-solvents, and operational in up to 50% DMSO - a characteristic as yet unobserved in a wild-type transaminase. This work highlights the value of using metagenomics for biocatalyst discovery from niche environments, and here has led to the identification of one of the most robust native transaminases described to date, with respect to IPA and DMSO tolerance.}, }
@article {pmid30929665, year = {2019}, author = {Caesar, R}, title = {Pharmacologic and Nonpharmacologic Therapies for the Gut Microbiota in Type 2 Diabetes.}, journal = {Canadian journal of diabetes}, volume = {43}, number = {3}, pages = {224-231}, doi = {10.1016/j.jcjd.2019.01.007}, pmid = {30929665}, issn = {2352-3840}, abstract = {The gut microbiota is an important regulator of host metabolism. Metagenome analyses have demonstrated that the gut microbiota differs between patients with type 2 diabetes and healthy subjects, and several studies have shown that impaired glucose metabolism is associated with decreased levels of butyrate-producing bacteria. Gut microbiota-produced metabolites, such as short-chain fatty acids, amino acid derivatives and secondary bile acids, participate in metabolic and immunologic processes and, hence, pose putative links between the gut microbiota and glucose homeostasis. Strategies to prevent and treat type 2 diabetes through manipulation of the gut microbiota are being developed. These include replacement of the gut microbiota by fecal transplantation, consumption of fibres to promote the function and growth of beneficial bacteria and treatment with probiotic bacterial strains. Furthermore, it has been shown that many drugs, including drugs used for treatment of diabetes, have major impacts on gut microbiota and, thereby, potentially on glucose metabolism. In particular, the commonly used drug metformin has been shown to influence the functional capacity of the gut microbiota, and recent evidence indicates that this may contribute to the antidiabetes effect of metformin.}, }
@article {pmid30929407, year = {2019}, author = {Calle, ML}, title = {Statistical Analysis of Metagenomics Data.}, journal = {Genomics &amp; informatics}, volume = {17}, number = {1}, pages = {e6}, doi = {10.5808/GI.2019.17.1.e6}, pmid = {30929407}, issn = {1598-866X}, support = {//Ministerio de Economía y Competitividad/ ; }, abstract = {Understanding the role of the microbiome in human health and how it can be modulated is becoming increasingly relevant for preventive medicine and for the medical management of chronic diseases. The development of high-throughput sequencing technologies has boosted microbiome research through the study of microbial genomes and allowing a more precise quantification of microbiome abundances and function. Microbiome data analysis is challenging because it involves high-dimensional structured multivariate sparse data and because of its compositional nature. In this review we outline some of the procedures that are most commonly used for microbiome analysis and that are implemented in R packages. We place particular emphasis on the compositional structure of microbiome data. We describe the principles of compositional data analysis and distinguish between standard methods and those that fit into compositional data analysis.}, }
@article {pmid30928850, year = {2019}, author = {Chen, H and Jing, L and Yao, Z and Meng, F and Teng, Y}, title = {Prevalence, source and risk of antibiotic resistance genes in the sediments of Lake Tai (China) deciphered by metagenomic assembly: A comparison with other global lakes.}, journal = {Environment international}, volume = {127}, number = {}, pages = {267-275}, doi = {10.1016/j.envint.2019.03.048}, pmid = {30928850}, issn = {1873-6750}, abstract = {Lakes are one of the natural reservoirs of antibiotic resistance genes (ARGs) in environments. Long retention times in lakes potentially allow ARGs to persist and may create increased opportunities for the emergence of resistant pathogens. In this study, we investigated the prevalence, source and dissemination risk of ARGs in the sediments of a typical urban lake, Lake Tai (China) which has been a drastic example of water pollution with eutrophication in the world due to its proliferated cyanobacterial blooms. High-throughput profilings of ARGs in the sediments of Lake Tai were characterized with metagenomic assembly, and were compared with those in other global lakes from Australia, Canada, Indonesia, Rwanda and the United States of America. The hosts of ARGs in the sediments of Lake Tai were explored based on the taxonomic annotation of ARG-carrying contigs and network analysis, and a novel recently-discovered crAssphage was employed for source tracking of resistance bacteria. Meanwhile, the potential resistome risk was identified by projecting the co-occurrence of acquired ARGs, mobile genetic elements (MGEs) and human bacterial pathogens into a three-dimensional exposure space. Results showed 321 ARG subtypes belonging to 21 ARG types were detected in the sediments of Lake Tai, dominated by multidrug, macrolide-lincosamide-streptogramin, bacitracin, quinolone, mupirocin and trimethoprim resistance genes. Relatively, the ARG levels in the sediments of Lake Tai were significantly higher than those in other global lakes. Source tracking showed the coverages of detected crAssphage in the sediments of Lake Tai were positively correlated with the total ARG coverage, suggesting the contribution of human fecal contamination to the prevalence of ARGs in this lake. It should be noted that the co-occurrence ratio of ARGs, MGEs and human pathogens in the sediments of Lake Tai was higher than that in other global lakes, likely indicating a higher risk for the resistance dissemination in the China's third largest freshwater lake.}, }
@article {pmid30928715, year = {2019}, author = {Li, Y and Yu, T and Kang, D and Shan, X and Zheng, P and Hu, Z and Ding, A and Wang, R and Zhang, M}, title = {Sources of anammox granular sludge and their sustainability in treating low-strength wastewater.}, journal = {Chemosphere}, volume = {226}, number = {}, pages = {229-237}, doi = {10.1016/j.chemosphere.2019.03.049}, pmid = {30928715}, issn = {1879-1298}, abstract = {Anaerobic ammonium oxidation (anammox) has been widely applied in the treatment of high-strength nitrogen wastewaters. However, few engineering practices were reported to treat low-strength nitrogen wastewaters. In this study, three types of anammox granular sludge (GS) were separately collected from the expanded granular sludge bed (EGSB) reactors treating nitrogen wastewaters at high (H-), moderate (M-) and low (L-) nitrogen loading rates (NLRs), and employed for the treatment of low-strength nitrogen wastewater in sequencing batch advanced nitrogen removal (ANR) systems. The ANR system with M-GS (namely M-ANR system) was most useful. At the initial biomass concentration of 2.43 g-VSS·L-1, cycle length of 8 h and influent total nitrogen (TN) concentration of less than 15 mg·L-1, the performance data were as follows: effluent TN of less than 1 mg·L-1, TN removal efficiency of more than 92.8%, the nitrogen removal rate (NRR) of 0.039 kg-N·m-3·d-1. The efficient performance lasted as long as 46 cycles, indicating the sustainability of the M-ANR system. The advanced microscopic analysis and metagenomic analysis were applied to reveal the successful but non-permanent treatment by the M-ANR system. The long-time lag between biomass decay and sludge activity decay provided a window period for the good performance of M-ANR system. However, the weak support of oligotrophic habitat for anaerobic ammonium oxidizing bacteria community was doomed to the degradation of anammox GS, resulting in gradual loss of their activities. A periodic addition of fresh M-GS or a periodic rejuvenation cultivation in the eutrophic habitat is necessary to achieve a permanent performance.}, }
@article {pmid30928605, year = {2019}, author = {Kraberger, S and Cook, CN and Schmidlin, K and Fontenele, RS and Bautista, J and Smith, B and Varsani, A}, title = {Diverse single-stranded DNA viruses associated with honey bees (Apis mellifera).}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {71}, number = {}, pages = {179-188}, doi = {10.1016/j.meegid.2019.03.024}, pmid = {30928605}, issn = {1567-7257}, abstract = {Honey bees (Apis mellifera) research has increased in light of their progressive global decline over the last decade and the important role they play in pollination. One expanding area of honey bee research is analysis of their microbial community including viruses. Several RNA viruses have been characterized but little is known about DNA viruses associated with bees. Here, using a metagenomics based approach, we reveal the presence of a broad range of novel single-stranded DNA viruses from the hemolymph and brain of nurse and forager (worker divisions of labour) bees belonging to two honey bees subspecies, Italian (Apis mellifera linguistica) and New World Carniolan (Apis mellifera carnica). Genomes of 100 diverse viruses were identified, designated into three groupings; genomoviruses (family Genomoviridae) (n = 4), unclassified replication associated protein encoding single-stranded DNA viruses (n = 28), and microviruses (family Microviridae; subfamily Gokushovirinae) (n = 70). Amongst the viruses identified, it appears that nurses harbour a higher diversity of these viruses comparative to the foragers. Between subspecies, the most striking outcome was the extremely high number of diverse microviruses identified in the Italian bees comparative to the New World Carniolan, likely indicating an association to the diversity of the bacterial community associated with these subspecies.}, }
@article {pmid30927724, year = {2019}, author = {Dandare, SU and Young, JM and Kelleher, BP and Allen, CCR}, title = {The distribution of novel bacterial laccases in alpine paleosols is directly related to soil stratigraphy.}, journal = {The Science of the total environment}, volume = {671}, number = {}, pages = {19-27}, doi = {10.1016/j.scitotenv.2019.03.250}, pmid = {30927724}, issn = {1879-1026}, abstract = {Bacterial laccases are now known to be abundant in soil and to function outside of the cell facilitating the bacterial degradation of lignin. In this study we wanted to test the hypotheses that: i) Such enzymes can be identified readily in stratified paleosols using metagenomics approaches, ii) The distribution of these genes as potential 'public good' proteins in soil is a function of the soil environment, iii) Such laccase genes can be readily retrieved and expressed in E. coli cloning systems to demonstrate that de novo assembly processes can be used to obtain similar metagenome-derived enzyme activities. To test these hypotheses, in silico gene-targeted assembly was employed to identify genes encoding novel type B two-domain bacterial laccases from alpine soil metagenomes sequenced on an Illumina MiSeq sequencer. The genes obtained from different strata were heterologously cloned, expressed and the gene products were shown to be active against two classical laccase substrates. The use of a metagenome-driven pipeline to obtain such active biocatalysts has demonstrated the potential for gene mining to be applied systematically for the discovery of such enzymes. These data ultimately further demonstrate the application of soil pedology methods to environmental enzyme discovery. As an interdisciplinary effort, we can now establish that paleosols can serve as a useful source of novel biocatalytic enzymes for various applications. We also, for the first time, link soil stratigraphy to enzyme profiling for widespread functional gene activity in paleosols.}, }
@article {pmid30927646, year = {2019}, author = {Rong, H and Xie, XH and Zhao, J and Lai, WT and Wang, MB and Xu, D and Liu, YH and Guo, YY and Xu, SX and Deng, WF and Yang, QF and Xiao, L and Zhang, YL and He, FS and Wang, S and Liu, TB}, title = {Similarly in depression, nuances of gut microbiota: Evidences from a shotgun metagenomics sequencing study on major depressive disorder versus bipolar disorder with current major depressive episode patients.}, journal = {Journal of psychiatric research}, volume = {113}, number = {}, pages = {90-99}, doi = {10.1016/j.jpsychires.2019.03.017}, pmid = {30927646}, issn = {1879-1379}, abstract = {BACKGROUND: To probe the differences of gut microbiota among major depressive disorder (MDD), bipolar disorder with current major depressive episode (BPD) and health participants.<br><br>METHODS: Thirty one MDD patients, thirty BPD patients, and thirty healthy controls (HCs) were recruited. All the faecal samples were analyzed by shotgun metagenomics sequencing. Except for routine analyses of alpha diversity, we specially designed a new indicator, the Gm coefficient, to evaluate the inequality of relative abundances of microbiota for each participant.<br><br>RESULTS: The Gm coefficients are significant decreased in both MDD and BPD groups. The relative abundances of increased phyla Firmicutes and Actinobacteria and decreased Bacteroidetes were significantly in the MDD and BPD groups. At genus level, four of top five enriched genera (Bacteroides, Clostridium, Bifidobacterium, Oscillibacter and Streptococcus) were found increased significantly in the MDD and BPD groups compared with HCs. The genera Escherichia and Klebsiella showed significant changes in abundances only between the BPD and HC groups. At the species level, compared with BPD patients, MDD patients had a higher abundance of Prevotellaceae including Prevotella denticola F0289, Prevotella intermedia 17, Prevotella ruminicola, and Prevotella intermedia. Furthermore, the abundance of Fusobacteriaceae, Escherichia blattae DSM 4481 and Klebsiella oxytoca were significantly increased, whereas the Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 was significantly reduced in BPD group compared with MDD group.<br><br>CONCLUSIONS: Our study suggested that gut microbiota may be involved in the pathogenesis of both MDD and BPD patients, and the nuances of bacteria may have the potentiality of being the biomarkers of MDD and BPD.}, }
@article {pmid30927638, year = {2019}, author = {Wei, Z and Yu, S and Huang, Z and Xiao, X and Tang, M and Li, B and Zhang, X}, title = {Simultaneous removal of elemental mercury and NO by mercury induced thermophilic community in membrane biofilm reactor.}, journal = {Ecotoxicology and environmental safety}, volume = {176}, number = {}, pages = {170-177}, doi = {10.1016/j.ecoenv.2019.03.082}, pmid = {30927638}, issn = {1090-2414}, abstract = {Thermophilic membrane biofilm reactor (TMBR) for elemental mercury (Hg0) and NO removal in simulated flue gas was investigated at oxygen content of 6% and 60 °C. The performance, the microbial community structures, gene function and the mechanism for Hg0 and NO removal in the TMBR were evaluated. TMBR achieved effective simultaneous Hg0 and NO removal in 210 days of operation, Hg0 and NO removal efficiency were up to 88.9% and 85.3%, respectively. Mercury induced thermophilic community had been formed significantly. Comamonas, Pseudomonas, Desulfomicrobium, Burkholderia and Halomonas were thermophilic mercury resistant bacteria. Brucella, Paracoccus, Tepidiphilus, Proteobacteria, Pseudomonas and Symbiobacterium were nitrifying/denitrifying genera, and had functional genes of mercury and nitrogen metabolism, as shown by16S rDNA and metagenomic sequencing. The biofilm in TMBR was characterized by XPS, HPLC. XPS and HPLC spectra indicate the formation of a mercuric species (Hg2+) from mercury oxidation. TMBR used oxygen as electron acceptor, NO and Hg0 as electron donor in nitrification; O2, NO and NO3- could be used as electron acceptor and Hg0 as electron donor in denitrification.}, }
@article {pmid30927421, year = {2019}, author = {Ding, GC and Bai, M and Han, H and Li, H and Ding, X and Yang, H and Xu, T and Li, J}, title = {Microbial taxonomic, nitrogen cycling and phosphorus recycling community composition during long-term organic greenhouse farming.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {5}, pages = {}, doi = {10.1093/femsec/fiz042}, pmid = {30927421}, issn = {1574-6941}, abstract = {Understanding the interplay between the farming system and soil microbiomes could aid the design of a sustainable and efficient farming system. A comparative greenhouse experiment consisting of organic (ORG), integrated (INT) and conventional (CON) farming systems was established in northern China in 2002. The effects of 12 years of organic farming on soil microbiomes were explored by metagenomic and 16S rRNA gene amplicon sequencing analyses. Long-term ORG shifted the community composition of dominant phyla, especially Acidobacteria, increased the relative abundance of Ignavibacteria and Acidobacteria Gp6 and decreased the relative abundance of Nitrosomonas, Bacillus and Paenibacillus. Metagenomic analysis further revealed that relative abundance of ammonia oxidizing microorganisms (Bacteria and Archaea) and anaerobic ammonium oxidation bacteria decreased during ORG. Conversely, the relative abundance of bacteria-carrying periplasmic nitrate reductases (napA) was slightly higher for ORG. Long-term organic farming also caused significant alterations to the community composition of functional groups associated with ammonia oxidation, denitrification and phosphorus recycling. In summary, this study provides key insights into the composition of soil microbiomes and long-term organic farming under greenhouse conditions.}, }
@article {pmid30927379, year = {2019}, author = {Tremblay, J and Fortin, N and Elias, M and Wasserscheid, J and King, TL and Lee, K and Greer, CW}, title = {Metagenomic and metatranscriptomic responses of natural oil degrading bacteria in the presence of dispersants.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14609}, pmid = {30927379}, issn = {1462-2920}, abstract = {Oil biodegradation has been extensively studied in the wake of the Deepwater Horizon spill, but the application of dispersant to oil spills in marine environments remains controversial. Here we report metagenomic (MG) and metatranscriptomic (MT) data mining from microcosm experiments investigating the oil degrading potential of Canadian west and east coasts in order to estimate the gene abundance and activity of oil degrading bacteria in the presence of dispersant. We found that the addition of dispersant to crude oil mainly favors the abundance of Thalassolituus in the summer and Oleispira in the winter, two key natural oil degrading bacteria. We found a high abundance of genes related not only to n-alkane and aromatics degradation, but also associated with transporters, two-component systems, bacterial motility, secretion systems and bacterial chemotaxis. This article is protected by copyright. All rights reserved.}, }
@article {pmid30927185, year = {2019}, author = {Zhang, Y and Shan, TL and Li, F and Yu, T and Chen, X and Deng, XT and Delwart, E and Feng, XP}, title = {A novel phage from periodontal pockets associated with chronic periodontitis.}, journal = {Virus genes}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11262-019-01658-y}, pmid = {30927185}, issn = {1572-994X}, support = {81800967//National Natural Science Foundation of China/ ; 81470737//National Natural Science Foundation of China/ ; }, abstract = {Bacteriophages often constitute the majority of periodontal viral communities, but phages that infect oral bacteria remain uncharacterized. Here, we present the genetic analysis of the genome of a novel siphovirus, named Siphoviridae_29632, which was isolated from a patient with periodontitis using a viral metagenomics-based approach. Among 43 predicted open reading frames (ORFs) in the genome, the viral genes encoding structural proteins were distinct from the counterparts of other viruses, although a distant homology is shared among viral morphogenesis proteins. A total of 28 predicted coding sequences had significant homology to other known phage ORF sequences. In addition, the prevalence of Siphoviridae_29632 in a cohort of patients with chronic periodontitis was 41.67%, which was significantly higher than that in the healthy group (4.55%, P < 0.001), suggesting that this virus as well as its hosts may contribute to the ecological environment favored for chronic periodontitis.}, }
@article {pmid30926543, year = {2019}, author = {Jun, C and Huan, H and Wei, F and Duozhi, S and Chen, L and Yang, S and GuoFeng, G and Hao, W and Qian, Z and LiQing, W and HongLong, W and Long, H and Luyao, C and Jin, Z and Shela, L and FeiYan, W and Zhou, Z}, title = {Detection of pathogens from resected heart valves of patients with infective endocarditis by next-generation sequencing.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ijid.2019.03.007}, pmid = {30926543}, issn = {1878-3511}, abstract = {OBJECTIVES: Identification of the underlying pathogens of infective endocarditis (IE) is critical for precision therapy.<br><br>METHODS: We evaluated a metagenomic method with next-generation sequencing (NGS) for the direct detection of pathogens from the resected valves of 44 IE patients and seven rejected IE patients according to the modified Duke criteria.<br><br>RESULTS: NGS displayed sensitivity, specificity, positive predictive values and negative predictive values of 97.6%, 85.7%, 97.6%, and 85.7% compared with 46.2%, 100%, 100%, and 12.5% for blood culture and 17.1%, 100%, 100%, and 17.1% for valve culture and 51.4%, 100%, 100%, and 26.1% for valve Gram staining, respectively.<br><br>CONCLUSIONS: NGS technique had superior sensitivity and shorter turnaround time compared with culture-based methods for identifying causative pathogens of IE. The NGS technology should be considered an essential supplement to culture-based methods, particularly for unculturable or difficult-to-culture microorganisms.}, }
@article {pmid30924428, year = {2019}, author = {Precup, G and Vodnar, DC}, title = {Gut Prevotella as a possible biomarker of diet and its eubiotic versus dysbiotic roles-A comprehensive literature review.}, journal = {The British journal of nutrition}, volume = {}, number = {}, pages = {1-24}, doi = {10.1017/S0007114519000680}, pmid = {30924428}, issn = {1475-2662}, abstract = {Gut microbiota has a profound impact on human health. Emerging data shows that dietary patterns are associated with different communities of bacterial species within the gut. Prevotella species have been correlated with plant rich diets, abundant in carbohydrates and fibres. Dysbiosis within the gut ecosystem has been associated with the development of non-communicable diseases such as obesity, metabolic syndrome, inflammatory bowel disease, irritable bowel syndrome, colorectal cancer, type 1 diabetes, allergies and other diseases. The purpose of this comprehensive literature review was to evaluate the available data on the impact of diet on Prevotella genus, as a dietary fibre fermenter in the gut, as well as its implications as a potential biomarker for homeostasis or disease state, through its metabolite signature. Studies were identified by conducting PubMed, Web of Science Core Collection and Google Scholar electronic searches. We found 85 publications reporting the impact of dietary patterns on gut microbial communities including Prevotella or Prevotella/Bacteroides ratio in particular. Moreover, the role of Prevotella species on health status was also evaluated. Prevotella possess a high genetic diversity, representing one of the important groups found in the oral cavity and large intestine of man. The gut commensal Prevotella bacteria contribute to polysaccharide breakdown, being dominant colonizers of agrarian societies. However, studies also suggested a potential role of Prevotella species as intestinal pathobionts. Further metagenomic studies are needed in order to reveal health- or disease-modulating properties of Prevotella species. in the gut.}, }
@article {pmid30924222, year = {2019}, author = {Zou, D and Li, Y and Kao, SJ and Liu, H and Li, M}, title = {Genomic adaptation to eutrophication of ammonia-oxidizing archaea in the Pearl River estuary.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14613}, pmid = {30924222}, issn = {1462-2920}, support = {JCYJ20170818091727570//Science and Technology Innovation Committee of Shenzhen/ ; 91851105，31622002//National Natural Science Foundation of China/ ; //State Key Laboratory of Marine Pollution/ ; //Research Grants Council of the Hong Kong Special Administrative Region/ ; }, abstract = {Ammonia-oxidizing archaea (AOA) are ubiquitous in natural ecosystems, and they are responsible for a significant fraction of ammonia oxidation globally. Since the first AOA isolate was established a decade ago, molecular surveys of their environmental distribution [based primarily on amplicon sequencing of the amoA, which codes for the alpha subunit of ammonia monooxygenase (AMO)], show that their habitats are believed to range from marine to terrestrial environments. However, the mechanisms of adaptation underpinning to their habitat expansion remain poorly understood. Here, we report that AOA accounts for almost all of the ammonia oxidizers in the shelf water adjacent to the Pearl River estuary (PRE), with the Nitrosopumilus maritimus SCM1-like (SCM1-like) being the main amoA genotype. Using a metagenomic approach, seven high-quality AOA genomes were reconstructed from the PRE. Phylogenetic analysis indicated that four of these genomes with high completeness were closely affiliated with the Nitrosomatrinus catalina strain SPOT01, which was originally isolated off the coast of California. Genomic comparison revealed that the PRE AOA genomes encoded genes functioning in amino acid synthesis, xenobiotic biodegradation metabolism and transportation of inorganic phosphate and heavy metals. This illustrates the different adaptations of AOA in one of the largest estuaries in China, which is strongly influenced by anthropogenic input. Overall, this study provides additional genomic information about estuarine AOA and highlights the importance of their contribution to nitrification in eutrophic coastal environments.}, }
@article {pmid30923648, year = {2019}, author = {Xia, Y and Zhu, Y and Li, Q and Lu, J}, title = {Human gut resistome can be country-specific.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6389}, doi = {10.7717/peerj.6389}, pmid = {30923648}, issn = {2167-8359}, abstract = {The emergence and spread of antibiotic resistance have become emerging threats to human health. The human gut is a large reservoir for antibiotic resistance genes. The gut resistome may be influenced by many factors, but the consumption of antibiotics at both individual and country level should be one of the most significant factors. Previous studies have suggested that the gut resistome of different populations may vary, but lack quantitative characterization supported with relatively large datasets. In this study, we filled the gap by analyzing a large gut resistome dataset of 1,267 human gut samples of America, China, Denmark, and Spain. We built a stacking machine-learning model to determine whether the gut resistome can act as the sole feature to identify the nationality of an individual reliably. It turned out that the machine learning method could successfully identify American, Chinese, Danish, and Spanish populations with F1 score of 0.964, 0.987, 0.971, and 0.986, respectively. Our finding does highlight the significant differences in the composition of the gut resistome among different nationalities. Our study should be valuable for policy-makers to look into the influences of country-specific factors of the human gut resistome.}, }
@article {pmid30922090, year = {2019}, author = {Zana, B and Geiger, L and Kepner, A and Földes, F and Urbán, P and Herczeg, R and Kemenesi, G and Jakab, F}, title = {First molecular detection of Apis mellifera filamentous virus in honey bees (Apis mellifera) in Hungary.}, journal = {Acta veterinaria Hungarica}, volume = {67}, number = {1}, pages = {151-157}, doi = {10.1556/004.2019.017}, pmid = {30922090}, issn = {0236-6290}, abstract = {Western honey bees (Apis mellifera) are important pollinators in the ecosystem and also play a crucial economic role in the honey industry. During the last decades, a continuous decay was registered in honey bee populations worldwide, including Hungary. In our study, we used metagenomic approaches and conventional PCR screening on healthy and winter mortality affected colonies from multiple sites in Hungary. The major goal was to discover presumed bee pathogens with viral metagenomic experiments and gain prevalence and distribution data by targeted PCR screening. We examined 664 honey bee samples that had been collected during winter mortality from three seemingly healthy colonies and from one colony infested heavily by the parasitic mite Varroa destructor in 2016 and 2017. The subsequent PCR screening of honey bee samples revealed the abundant presence of Apis mellifera filamentous virus (AmFV) for the first time in Central Europe. Based on phylogeny reconstruction, the newly-detected virus was found to be most closely related to a Chinese AmFV strain. More sequence data from multiple countries would be needed for studying the detailed phylogeographical patterns and worldwide spreading process of AmFV. Here we report the prevalent presence of this virus in Hungarian honey bee colonies.}, }
@article {pmid30922086, year = {2019}, author = {Amoroso, MG and Cerutti, F and D'Alessio, N and Lucibelli, MG and Cerrone, A and Acutis, PL and Galiero, G and Fusco, G and Peletto, S}, title = {First identification of porcine parvovirus 3 in a wild boar in Italy by viral metagenomics - Short communication.}, journal = {Acta veterinaria Hungarica}, volume = {67}, number = {1}, pages = {135-139}, doi = {10.1556/004.2019.015}, pmid = {30922086}, issn = {0236-6290}, abstract = {Metagenomic analysis revealed the presence of porcine parvovirus 3 (PPV3) in the pool of the internal organs of a wild boar found dead in Southern Italy. Phylogenetic analysis based on the complete coding sequences showed that the newly detected virus is most closely related to those found also in wild boars in Romania during 2010-2011. Even though the death could not be associated with this virus, PPV3 could have contributed to lowering the host's immunological defences.}, }
@article {pmid30920634, year = {2019}, author = {De Grandi, R and Bottagisio, M and Di Girolamo, S and Bidossi, A and De Vecchi, E and Drago, L}, title = {Modulation of opportunistic species Corynebacterium diphtheriae, Haemophilus parainfluenzae, Moraxella catarrhalis, Prevotella denticola, Prevotella melaninogenica, Rothia dentocariosa, Staphylococcus aureus and Streptococcus pseudopneumoniae by intranasal administration of Streptococcus salivarius 24SMBc and Streptococcus oralis 89a combination in healthy subjects.}, journal = {European review for medical and pharmacological sciences}, volume = {23}, number = {1 Suppl}, pages = {60-66}, doi = {10.26355/eurrev_201903_17351}, pmid = {30920634}, issn = {2284-0729}, abstract = {OBJECTIVE: Probiotics S. salivarius 24SMBc and S. oralis 89a comprised in the nasal spray Rinogermina are known to exert inhibition of harmful pathogens and ameliorate the outcome of patients with chronic upper airways infections. In this study, for the first time, the effect of this formulation on the modulation of the microflora of healthy subjects was evaluated, with particular interest on pathobionts and pathogens present.<br><br>PATIENTS AND METHODS: Metagenomic identification and quantification of bacterial abundances in healthy subjects were carried out by means of Ion Torrent Personal Machine. In particular, nasal swabs were sampled one, two and four weeks after seven days of treatment with Rinogermina.<br><br>RESULTS: The modulation of the abundance of pathobionts and pathogenic species (i.e., Corynebacterium diphtheriae, Haemophilus parainfluenzae, Moraxella catarrhalis, Prevotella denticola, Prevotella melaninogenica, Rothia dentocariosa, Staphylococcus aureus and Streptococcus pseudopneumoniae) was characterized and a significant temporary decrease in their presence was identified.<br><br>CONCLUSIONS: The beneficial effects of S. salivarius 24SMBc and S. oralis 89a nasal intake was assessed but seemed to be restricted in specific temporal windows. Thus it would be interesting to evaluate also this positive impact of longer administration of this probiotic formulation.}, }
@article {pmid30920125, year = {2019}, author = {Mizuno, CM and Prajapati, B and Lucas-Staat, S and Sime-Ngando, T and Forterre, P and Bamford, DH and Prangishvili, D and Krupovic, M and Oksanen, HM}, title = {Novel haloarchaeal viruses from Lake Retba infecting Haloferax and Halorubrum species.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14604}, pmid = {30920125}, issn = {1462-2920}, support = {//Academy of Finland (project Instruct-FI)/ ; #ANR-17-CE15-0005-01//Agence Nationale pour la Recherche/ ; ALTF 1562-2015//European Molecular Biology Organization/ ; 340440//European Research Council (ERC)/ ; GA-2013-609409//Marie Curie Actions program from the European Commission/ ; LTFCOFUND2013//Marie Curie Actions program from the European Commission/ ; }, abstract = {The diversity of archaeal viruses is severely undersampled compared with that of viruses infecting bacteria and eukaryotes, limiting our understanding on their evolution and environmental impacts. Here, we describe the isolation and characterization of four new viruses infecting halophilic archaea from the saline Lake Retba, located close to Dakar on the coast of Senegal. Three of the viruses, HRPV10, HRPV11 and HRPV12, have enveloped pleomorphic virions and should belong to the family Pleolipoviridae, whereas the forth virus, HFTV1, has an icosahedral capsid and a long non-contractile tail, typical of bacterial and archaeal members of the order Caudovirales. Comparative genomic and phylogenomic analyses place HRPV10, HRPV11 and HRPV12 into the genus Betapleolipovirus, whereas HFTV1 appears to be most closely related to the unclassified Halorubrum virus HRTV-4. Differently from HRTV-4, HFTV1 encodes host-derived minichromosome maintenance helicase and PCNA homologues, which are likely to orchestrate its genome replication. HFTV1, the first archaeal virus isolated on a Haloferax strain, could also infect Halorubrum sp., albeit with an eightfold lower efficiency, whereas pleolipoviruses nearly exclusively infected autochthonous Halorubrum strains. Mapping of the metagenomic sequences from this environment to the genomes of isolated haloarchaeal viruses showed that these known viruses are underrepresented in the available viromes.}, }
@article {pmid30918994, year = {2019}, author = {Klima, CL and Holman, DB and Ralston, BJ and Stanford, K and Zaheer, R and Alexander, TW and McAllister, TA}, title = {Lower Respiratory Tract Microbiome and Resistome of Bovine Respiratory Disease Mortalities.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01361-3}, pmid = {30918994}, issn = {1432-184X}, support = {2015R025R//Alberta Livestock and Meat Agency/ ; 001//Growing Forward II/ ; 001//Genomics Research Initiative/ ; }, abstract = {Bovine respiratory disease (BRD) continues to be a serious health problem in beef cattle production. A multifactorial condition, BRD encompasses several types of pneumonia that are associated with multiple viral and bacterial agents. Comprehensive identification of microbes associated with BRD fatalities could enhance our understanding of the range of pathogens that contribute to the disease and identify new therapeutic targets. This study used metagenomic analysis to describe the lower respiratory tract microbiome and resistome of 15 feedlot cattle BRD and 3 non-BRD mortalities along with any affiliated integrative and conjugative elements (ICEs). Known bacterial pathogens associated with BRD, including Histophilus somni, Mannheimia haemolytica, and Mycoplasma bovis, were relatively abundant (> 5%) in most, but not all samples. Other relatively abundant genera (> 1%) included Acinetobacter, Bacillus, Bacteroides, Clostridium, Enterococcus, and Pseudomonas. Antimicrobial resistance genes (ARGs) comprised up to 0.5% of sequences and many of these genes were associated with ICEs previously described within the Pasteurellaceae family. A total of 20 putative ICEs were detected among 16 samples. These results document the wide diversity of microorganisms in the lower respiratory tract of cattle that have succumbed to BRD. The data also strongly suggest that antimicrobial-resistant Pasteurellaceae strains are prevalent in BRD cases in Alberta and that the resistance observed is associated with ICEs. The presence of ICEs harboring a wide array of ARGs holds significant consequence for the effectiveness of drug therapies for the control of BRD in beef cattle.}, }
@article {pmid30918501, year = {2019}, author = {Verce, M and De Vuyst, L and Weckx, S}, title = {Shotgun Metagenomics of a Water Kefir Fermentation Ecosystem Reveals a Novel Oenococcus Species.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {479}, doi = {10.3389/fmicb.2019.00479}, pmid = {30918501}, issn = {1664-302X}, abstract = {Water kefir is a fruity, sour, slightly alcoholic and carbonated beverage, which is made by fermentation of an aqueous sucrose solution in the presence of dried figs and water kefir grains. These polysaccharide grains contain lactic acid bacteria (LAB), yeasts, and sometimes bifidobacteria and/or acetic acid bacteria, which consume sucrose to produce exopolysaccharides, lactic acid, acetic acid, ethanol, and carbon dioxide. Shotgun metagenomic sequencing was used to examine the microbial species diversity present at two time points during water kefir fermentation in detail, both in the water kefir liquor and on the water kefir grains, hence representing four samples. Lactobacillus harbinensis, Lactobacillus hilgardii, Lactobacillus nagelii, Lactobacillus paracasei, and a Lactobacillus species similar to Lactobacillus hordei/mali were present in the water kefir examined, along with Bifidobacterium aquikefiri and two yeast species, namely Saccharomyces cerevisiae and Dekkera bruxellensis. In addition, evidence for a novel Oenococcus species related to Oenococcus oeni and Oenococcus kitaharae was found. Its genome was derived from the metagenome and made available under the name of Candidatus Oenococcus aquikefiri. Through functional analysis of the four metagenomic data sets, it was possible to link the production of lactic acid, acetic acid, ethanol, and carbon dioxide to subgroups of the microbial species found. In particular, the production of mannitol from fructose was linked to L. hilgardii, Candidatus O. aquikefiri, and B. aquikefiri, whereas glycerol production was associated with S. cerevisiae. Also, there were indications of cross-feeding, for instance in the case of amino acid supply. Few bacterial species could synthesize a limited number of cofactors, making them reliant on the figs or S. cerevisiae. The LAB species in turn were found to be capable of contributing to water kefir grain growth, as dextransucrase-encoding genes were attributed to L. hilgardii, L. hordei/mali, and Candidatus O. aquikefiri.}, }
@article {pmid30918369, year = {2019}, author = {Chiu, CY and Miller, SA}, title = {Clinical metagenomics.}, journal = {Nature reviews. Genetics}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41576-019-0113-7}, pmid = {30918369}, issn = {1471-0064}, abstract = {Clinical metagenomic next-generation sequencing (mNGS), the comprehensive analysis of microbial and host genetic material (DNA and RNA) in samples from patients, is rapidly moving from research to clinical laboratories. This emerging approach is changing how physicians diagnose and treat infectious disease, with applications spanning a wide range of areas, including antimicrobial resistance, the microbiome, human host gene expression (transcriptomics) and oncology. Here, we focus on the challenges of implementing mNGS in the clinical laboratory and address potential solutions for maximizing its impact on patient care and public health.}, }
@article {pmid30918057, year = {2019}, author = {Thomas, M and Wongkuna, S and Ghimire, S and Kumar, R and Antony, L and Doerner, KC and Singery, A and Nelson, E and Woyengo, T and Chankhamhaengdecha, S and Janvilisri, T and Scaria, J}, title = {Gut Microbial Dynamics during Conventionalization of Germfree Chicken.}, journal = {mSphere}, volume = {4}, number = {2}, pages = {}, doi = {10.1128/mSphere.00035-19}, pmid = {30918057}, issn = {2379-5042}, abstract = {A gnotobiotic Gallus gallus (chicken) model was developed to study the dynamics of intestinal microflora from hatching to 18 days of age employing metagenomics. Intestinal samples were collected from a local population of feral chickens and administered orally to germfree 3-day-old chicks. Animals were euthanized on days 9 and 18 postinoculation, and intestinal samples were collected and subjected to metagenomic analysis. On day 18, the five most prevalent phyla were Bacteroidetes (43.03 ± 3.19%), Firmicutes (38.51 ± 2.67%), Actinobacteria (6.77 ± 0.7%), Proteobacteria (6.38 ± 0.7%), and Spirochaetes (2.71 ± 0.55%). Principal-coordinate analysis showed that the day 18 variables clustered more closely than the day 9 variables, suggesting that the microbial communities had changed temporally. The Morista-Horn index values ranged from 0.7 to 1, indicating that the communities in the inoculum and in the day 9 and day 18 samples were more similar than dissimilar. The predicted functional profiles of the microbiomes of the inoculum and the day 9 and day 18 samples were also similar (values of 0.98 to 1). These results indicate that the gnotobiotic chicks stably maintained the phylogenetic diversity and predicted metabolic functionality of the inoculum community.IMPORTANCE The domestic chicken is the cornerstone of animal agriculture worldwide, with a flock population exceeding 40 billion birds/year. It serves as an economically valuable source of protein globally. The microbiome of poultry has important effects on chicken growth, feed conversion, immune status, and pathogen resistance. The aim of our research was to develop a gnotobiotic chicken model appropriate for the study chicken gut microbiota function. Our experimental model shows that young germfree chicks are able to colonize diverse sets of gut bacteria. Therefore, besides the use of this model to study mechanisms of gut microbiota interactions in the chicken gut, it could be also used for applied aspects such as determining the safety and efficacy of new probiotic strains derived from chicken gut microbiota.}, }
@article {pmid30916575, year = {2019}, author = {Khandelwal, P and Andersen, H and Romick-Rosendale, L and Taggart, CB and Watanabe, M and Lane, A and Dandoy, CE and Lake, KE and Litts, BA and Morrow, AL and Lee, ML and Haslam, DB and Davies, SM}, title = {A Pilot Study of Human Milk to Reduce Intestinal Inflammation After Bone Marrow Transplant.}, journal = {Breastfeeding medicine : the official journal of the Academy of Breastfeeding Medicine}, volume = {14}, number = {3}, pages = {193-202}, doi = {10.1089/bfm.2018.0199}, pmid = {30916575}, issn = {1556-8342}, abstract = {OBJECTIVE: Human milk administration in the early peritransplant period would lower intestinal inflammation after bone marrow transplant (BMT).<br><br>MATERIALS AND METHODS: Children 0-5 years undergoing BMT received either a ready-to-feed human milk preparation designed for these children (Prolacta Bioscience, Duarte, CA) or standard formula. Babies breastfeeding at the time of BMT were also enrolled on the human milk arm. Human milk was administered from day -3 until day +14 after BMT. Metagenomic shotgun sequencing and metabolomics of stool, plasma cytokines, and regenerating islet-derived 3α (REG3α) levels were measured at enrollment and day +14. Human leukocyte antigen-DR isotype (HLA-DR), CD38, and CD69 expression on T cells were evaluated at day +21.<br><br>RESULTS: Forty-six children were enrolled, 32 received human milk (donor milk n = 23, breastfeeding babies n = 9), and 14 were controls who received standard feeds supervised by a BMT dietician. Twenty-four patients received at least 60% of goal human milk and were evaluable. Plasma interleukin (IL)-8 (p = 0.04), IL-10 (p = 0.02), and REG3α (p = 0.03) were decreased in the human milk cohort. Peripheral blood CD69+ CD8+ T cells were higher in controls (p = 0.01). Species abundance of Adenovirus (p = 0.00034), Escherichia coli (p = 0.0017), Cryptosporidium parvum (p = 0.0006), Dialister invisus (p = 0.01), and Pseudomonas aeruginosa (p = 0.05) from stool was higher in controls. Stool alanine, tyrosine, methionine, and the ratio of fecal alanine to choline and phosphocholine were higher in controls (p < 0.05). No difference was observed in stool propionate and butyrate levels as measures of short-chain fatty acids between the two cohorts.<br><br>CONCLUSIONS: Administration of human milk resulted in decreased markers of intestinal inflammation and could be a valuable adjunct for patients after BMT.}, }
@article {pmid30915691, year = {2019}, author = {Akyol, Ç and Ozbayram, EG and Demirel, B and Onay, TT and Ince, O and Ince, B}, title = {Linking nano-ZnO contamination to microbial community profiling in sanitary landfill simulations.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11356-019-04906-8}, pmid = {30915691}, issn = {1614-7499}, support = {112Y322//TUBITAK/ ; 13081//Boğaziçi University Research Fund Project/ ; }, abstract = {Nanomaterials (NMs) commercially used for various activities mostly end up in landfills. Reduced biogas productions reported in landfill reactors create a need for more comprehensive research on these greatly-diverse microbial pools. In order to evaluate the impact of one of the most widely-used NMs, namely nano-zinc oxide (nano-ZnO), simulated bioreactor and conventional landfills were operated using real municipal solid waste (MSW) for 300 days with addition nano-ZnO. Leachate samples were taken at different phases and analyzed by 16S rRNA gene amplicon sequencing. The bacterial communities were distinctly characterized by Cloacamonaceae (phylum WWE1), Rhodocyclaceae (phylum Proteobacteria), Porphyromonadaceae (phylum Bacteroidetes), and Synergistaceae (phylum Synergistetes). The bacterial community in the bioreactors shifted at the end of the operation and was dominated by Rhodocyclaceae. There was not a major change in the bacterial community in the conventional reactors. The methanogenic archaeal diversity highly differed between the bioreactors and conventional reactors. The dominance of Methanomicrobiaceae was observed in the bioreactors during the peak methane-production period; however, their prominence shifted to WSA2 in the nano-ZnO-added bioreactor and to Methanocorpusculaceae in the control bioreactor towards the end. Methanocorpusculaceae was the most abundant family in both conventional control and nano-ZnO-containing reactors.}, }
@article {pmid30915664, year = {2019}, author = {da Costa, AC and Leal, E and Gill, D and Milagres, FAP and Komninakis, SV and Brustulin, R and Teles, MDAR and Lobato, MCABS and das Chagas, RT and Abrão, MFNDS and Soares, CVDA and Deng, X and Delwart, E and Sabino, EC and Luchs, A}, title = {Discovery of Cucumis melo endornavirus by deep sequencing of human stool samples in Brazil.}, journal = {Virus genes}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11262-019-01648-0}, pmid = {30915664}, issn = {1572-994X}, support = {2015/12944-9//Fundação de Amparo a Pesquisa do Estado de São Paulo/ ; 2017/00021-9//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2016/01735-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 400354/2016-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico (BR)/ ; }, abstract = {The nearly complete genome sequences of two Cucumis melo endornavirus (CmEV) strains were obtained using deep sequencing while investigating fecal samples for the presence of gastroenteritis viruses. The Brazilian CmEV BRA/TO-23 (aa positions 116-5027) and BRA/TO-74 (aa positions 26-5057) strains were nearly identical to the reference CmEV CL-01 (USA) and SJ1 (South Korea) strains, showing 97% and 98% of nucleotide and amino acid identity, respectively. Endornaviruses are not known to be associated with human disease and their presence may simply reflect recent dietary consumption. Metagenomic analyses offered an opportunity to identify for the first time in Brazil a newly described endornavirus species.}, }
@article {pmid30915459, year = {2019}, author = {Pankoke, H and Maus, I and Loh, G and Hüser, A and Seifert, J and Tilker, A and Hark, S and Sczyrba, A and Pelzer, S and Kleinbölting, J}, title = {F5Evaluation of commercially available DNA extraction kits for the analysis of the broiler chicken cecal microbiota.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnz033}, pmid = {30915459}, issn = {1574-6968}, abstract = {16S amplicon sequencing is a state of the art technology to analyze bacterial communities via microbiome profiling. Choosing an appropriate DNA extraction protocol is crucial for characterizing the microbial community and can be challenging, especially when preliminary knowledge about the sample matrix is scarce. The aim of the present study was to evaluate seven commercial DNA extraction kits suitable for 16S rRNA gene amplicon sequencing of the bacterial community of the chicken cecum, taking into account different criteria such as high technical reproducibility, high bacterial diversity and easy handling. The DNA extraction kits differed strongly with respect to extractable DNA quantity, DNA quality, technical reproducibility and bacterial diversity determined after 16S rRNA gene amplicon sequencing and subsequent bioinformatic and biostatistical data processing. While some of the DNA extraction protocols under-represented specific bacterial community members, the removal of PCR inhibitors supported technical reproducibility and subsequently enhanced the recovered bacterial diversity from the chicken cecum community. In conclusion, the removal of PCR inhibitors from the sample matrix seemed to be one of the main drivers for a consistent representation of the bacterial community even of low abundant taxa in chicken cecum samples.}, }
@article {pmid30915455, year = {2019}, author = {Taft, DH and Salinero, LK and Vongbhavit, K and Kalanetra, KM and Masarweh, C and Yu, A and Underwood, MA and Mills, DA}, title = {Bacterial colonization and antimicrobial resistance genes in neonatal enteral feeding tubes.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {4}, pages = {}, doi = {10.1093/femsec/fiz039}, pmid = {30915455}, issn = {1574-6941}, support = {F32 HD093185/HD/NICHD NIH HHS/United States ; R01 AT008759/AT/NCCIH NIH HHS/United States ; S10 RR027303/RR/NCRR NIH HHS/United States ; S10 RR029668/RR/NCRR NIH HHS/United States ; }, abstract = {Enteral feeding is a key component of care in neonatal intensive care units (NICUs); however, feeding tubes harbor microbes. These microbes have the potential to cause disease, yet their source remains controversial and clinical recommendations to reduce feeding tube colonization are lacking. This study aims to improve our understanding of the bacteria in neonatal feeding tubes and to evaluate factors that may affect these bacteria. 16S rRNA gene sequencing was used to characterize the bacteria present in pharyngeal, esophageal, and gastric portions of feeding tubes, residual fluid of the tubes, and infant stool using samples from 47 infants. Similar distributions of taxa were observed in all samples, although beta diversity differed by sample type. Feeding tube samples had lower alpha diversity than stool samples, and alpha diversity increased with gestational age, day of life, and tube dwell time. In a subset of samples from 6 infants analyzed by whole metagenome sequencing, there was greater overlap in transferable antimicrobial resistance genes between tube and fecal samples in breast milk fed infants than in formula fed infants. These findings develop our understanding of neonatal feeding tube colonization, laying a foundation for research into methods for minimizing NICU patients' exposure to antimicrobial resistant microbes.}, }
@article {pmid30915051, year = {2019}, author = {Payler, SJ and Biddle, JF and Sherwood Lollar, B and Fox-Powell, MG and Edwards, T and Ngwenya, BT and Paling, SM and Cockell, CS}, title = {An Ionic Limit to Life in the Deep Subsurface.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {426}, doi = {10.3389/fmicb.2019.00426}, pmid = {30915051}, issn = {1664-302X}, abstract = {The physical and chemical factors that can limit or prevent microbial growth in the deep subsurface are not well defined. Brines from an evaporite sequence were sampled in the Boulby Mine, United Kingdom between 800 and 1300 m depth. Ionic, hydrogen and oxygen isotopic composition were used to identify two brine sources, an aquifer situated in strata overlying the mine, and another ambiguous source distinct from the regional groundwater. The ability of the brines to support microbial replication was tested with culturing experiments using a diversity of inocula. The examined brines were found to be permissive for growth, except one. Testing this brine's physicochemical properties showed it to have low water activity and to be chaotropic, which we attribute to the high concentration of magnesium and chloride ions. Metagenomic sequencing of the brines that supported growth showed their microbial communities to be similar to each other and comparable to those found in other hypersaline environments. These data show that solutions high in dissolved ions can shape the microbial diversity of the continental deep subsurface biosphere. Furthermore, under certain circumstances, complex brines can establish a hard limit to microbial replication in the deep biosphere, highlighting the potential for subsurface uninhabitable aqueous environments at depths far shallower than a geothermally-defined limit to life.}, }
@article {pmid30915047, year = {2019}, author = {Hara, S and Morikawa, T and Wasai, S and Kasahara, Y and Koshiba, T and Yamazaki, K and Fujiwara, T and Tokunaga, T and Minamisawa, K}, title = {Identification of Nitrogen-Fixing Bradyrhizobium Associated With Roots of Field-Grown Sorghum by Metagenome and Proteome Analyses.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {407}, doi = {10.3389/fmicb.2019.00407}, pmid = {30915047}, issn = {1664-302X}, abstract = {Sorghum (Sorghum bicolor) is cultivated worldwide for food, bioethanol, and fodder production. Although nitrogen fixation in sorghum has been studied since the 1970s, N2-fixing bacteria have not been widely examined in field-grown sorghum plants because the identification of functional diazotrophs depends on the culture method used. The aim of this study was to identify functional N2-fixing bacteria associated with field-grown sorghum by using &quot;omics&quot; approaches. Four lines of sorghum (KM1, KM2, KM4, and KM5) were grown in a field in Fukushima, Japan. The nitrogen-fixing activities of the roots, leaves, and stems were evaluated by acetylene reduction and 15N2-feeding assays. The highest nitrogen-fixing activities were detected in the roots of lines KM1 and KM2 at the late growth stage. Bacterial cells extracted from KM1 and KM2 roots were analyzed by metagenome, proteome, and isolation approaches and their DNA was isolated and sequenced. Nitrogenase structural gene sequences in the metagenome sequences were retrieved using two nitrogenase databases. Most sequences were assigned to nifHDK of Bradyrhizobium species, including non-nodulating Bradyrhizobium sp. S23321 and photosynthetic B. oligotrophicum S58T. Amplicon sequence and metagenome analysis revealed a relatively higher abundance (2.9-3.6%) of Bradyrhizobium in the roots. Proteome analysis indicated that three NifHDK proteins of Bradyrhizobium species were consistently detected across sample replicates. By using oligotrophic media, we purified eight bradyrhizobial isolates. Among them, two bradyrhizobial isolates possessed 16S rRNA and nif genes similar to those in S23321 and S58T which were predicted as functional diazotrophs by omics approaches. Both free-living cells of the isolates expressed N2-fixing activity in a semi-solid medium according to an acetylene reduction assay. These results suggest that major functional N2-fixing bacteria in sorghum roots are unique bradyrhizobia that resemble photosynthetic B. oligotrophicum S58T and non-nodulating Bradyrhizobium sp. S23321. Based on our findings, we discuss the N2-fixing activity level of sorghum plants, phylogenetic and genomic comparison with diazotrophic bacteria in other crops, and Bradyrhizobium diversity in N2 fixation and nodulation.}, }
@article {pmid30914777, year = {2019}, author = {Auladell, A and Sánchez, P and Sánchez, O and Gasol, JM and Ferrera, I}, title = {Long-term seasonal and interannual variability of marine aerobic anoxygenic photoheterotrophic bacteria.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0401-4}, pmid = {30914777}, issn = {1751-7370}, abstract = {We studied the long-term temporal dynamics of the aerobic anoxygenic phototrophic (AAP) bacteria, a relevant functional group in the coastal marine microbial food web, using high-throughput sequencing of the pufM gene coupled with multivariate, time series and co-occurrence analyses at the Blanes Bay Microbial Observatory (NW Mediterranean). Additionally, using metagenomics, we tested whether the used primers captured accurately the seasonality of the most relevant AAP groups. Phylogroup K (Gammaproteobacteria) was the greatest contributor to community structure over all seasons, with phylogroups E and G (Alphaproteobacteria) being prevalent in spring. Diversity indices showed a clear seasonal trend, with maximum values in winter, which was inverse to that of AAP abundance. Multivariate analyses revealed sample clustering by season, with a relevant proportion of the variance explained by day length, temperature, salinity, phototrophic nanoflagellate abundance, chlorophyll a, and silicate concentration. Time series analysis showed robust rhythmic patterns of co-occurrence, but distinct seasonal behaviors within the same phylogroup, and even within different amplicon sequence variants (ASVs) conforming the same operational taxonomic unit (OTU). Altogether, our results picture the AAP assemblage as highly seasonal and recurrent but containing ecotypes showing distinctive temporal niche partitioning, rather than being a cohesive functional group.}, }
@article {pmid30914698, year = {2019}, author = {Durai, DA and Schulz, MH}, title = {Improving in-silico normalization using read weights.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {5133}, doi = {10.1038/s41598-019-41502-9}, pmid = {30914698}, issn = {2045-2322}, abstract = {Specialized de novo assemblers for diverse datatypes have been developed and are in widespread use for the analyses of single-cell genomics, metagenomics and RNA-seq data. However, assembly of large sequencing datasets produced by modern technologies is challenging and computationally intensive. In-silico read normalization has been suggested as a computational strategy to reduce redundancy in read datasets, which leads to significant speedups and memory savings of assembly pipelines. Previously, we presented a set multi-cover optimization based approach, ORNA, where reads are reduced without losing important k-mer connectivity information, as used in assembly graphs. Here we propose extensions to ORNA, named ORNA-Q and ORNA-K, which consider a weighted set multi-cover optimization formulation for the in-silico read normalization problem. These novel formulations make use of the base quality scores obtained from sequencers (ORNA-Q) or k-mer abundances of reads (ORNA-K) to improve normalization further. We devise efficient heuristic algorithms for solving both formulations. In applications to human RNA-seq data, ORNA-Q and ORNA-K are shown to assemble more or equally many full length transcripts compared to other normalization methods at similar or higher read reduction values. The algorithm is implemented under the latest version of ORNA (v2.0, https://github.com/SchulzLab/ORNA).}, }
@article {pmid30914068, year = {2019}, author = {Wang, W and Hu, H and Zijlstra, RT and Zheng, J and Gänzle, MG}, title = {Metagenomic reconstructions of gut microbial metabolism in weanling pigs.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {48}, doi = {10.1186/s40168-019-0662-1}, pmid = {30914068}, issn = {2049-2618}, abstract = {BACKGROUND: The piglets' transition from milk to solid feed induces a succession of bacterial communities, enhancing the hosts' ability to harvest energy from dietary carbohydrates. To reconstruct microbial carbohydrate metabolism in weanling pigs, this study combined 16S rRNA gene sequencing (n = 191) and shotgun metagenomics (n = 72).<br><br>RESULTS: Time and wheat content in feed explained most of the variation of the microbiota as assessed by 16S rRNA gene sequencing in weanling pigs. De novo metagenomic binning reconstructed 360 high-quality genomes that represented 11 prokaryotic and 1 archaeal phylum. Analysis of carbohydrate metabolism in these genomes revealed that starch fermentation is carried out by a consortium of Firmicutes expressing extracellular α-(1 → 4)-glucan branching enzyme (GH13) and Bacteroidetes expressing periplasmic neopullulanase (GH13) and α-glucosidase (GH97). Fructans were degraded by extracellular GH32 enzymes from Bacteriodetes and Lactobacillus. Lactose fermentation by β-galactosidases (GH2 and GH42) was identified in Firmicutes. In conclusion, the assembly of 360 high-quality genomes as the first metagenomic reference for swine intestinal microbiota allowed identification of key microbial contributors to degradation of starch, fructans, and lactose.<br><br>CONCLUSIONS: Microbial consortia that are responsible for degradation of these glycans differ substantially from the microbial consortia that degrade the same glycans in humans. Our study thus enables improvement of feeding models with higher feed efficiency and better pathogen control for weanling pigs.}, }
@article {pmid30913359, year = {2019}, author = {Chao, L and Jongkees, SAK}, title = {High Throughput Approaches in Carbohydrate-Active Enzymology: Glycosidase and Glycosyl Transferase Inhibitors, Evolution, and Discovery.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {}, number = {}, pages = {}, doi = {10.1002/anie.201900055}, pmid = {30913359}, issn = {1521-3773}, abstract = {Carbohydrates are attached and removed in living systems through the action of carbohydrate-active enzymes such as glycosyl transferases and glycoside hydrolases. The molecules resulting from these enzymes have many important roles in organisms, such as cellular communication, structural support, and energy metabolism. In general, each carbohydrate transformation requires a separate catalyst, and so these enzyme families are extremely diverse. To make this diversity manageable, high throughput approaches look at many enzymes at once. Similarly, high throughput approaches can be a powerful way of finding inhibitors that can be used to tune the reactivity of these enzymes, either in an industrial, a laboratory, or a medicinal setting. We provide here an overview of how these enzymes and inhibitors can be sought using techniques such as high-throughput natural product and combinatorial library screening, phage and mRNA display of (glyco)peptides, fluorescence-activated cell sorting, and metagenomics.}, }
@article {pmid30913025, year = {2019}, author = {Tauzin, AS and Bruel, L and Laville, E and Nicoletti, C and Navarro, D and Henrissat, B and Perrier, J and Potocki-Veronese, G and Giardina, T and Lafond, M}, title = {Sucrose 6F-phosphate phosphorylase: a novel insight in the human gut microbiome.}, journal = {Microbial genomics}, volume = {}, number = {}, pages = {}, doi = {10.1099/mgen.0.000253}, pmid = {30913025}, issn = {2057-5858}, abstract = {The human gut microbiome plays an essential role in maintaining human health including in degradation of dietary fibres and carbohydrates further used as nutrients by both the host and the gut bacteria. Previously, we identified a polysaccharide utilization loci (PUL) involved in sucrose and raffinose family oligosaccharide (RFO) metabolism from one of the most common Firmicutes present in individuals, Ruminococcus gnavus E1. One of the enzymes encoded by this PUL was annotated as a putative sucrose phosphate phosphorylase (RgSPP). In the present study, we have in-depth characterized the heterologously expressed RgSPP as sucrose 6F-phosphate phosphorylase (SPP), expanding our knowledge of the glycoside hydrolase GH13_18 subfamily. Specifically, the enzymatic characterization showed a selective activity on sucrose 6F-phosphate (S6FP) acting both in phosphorolysis releasing alpha-d-glucose-1-phosphate (G1P) and alpha-d-fructose-6-phosphate (F6P), and in reverse phosphorolysis from G1P and F6P to S6FP. Interestingly, such a SPP activity had never been observed in gut bacteria before. In addition, a phylogenetic and synteny analysis showed a clustering and a strictly conserved PUL organization specific to gut bacteria. However, a wide prevalence and abundance study with a human metagenomic library showed a correlation between SPP activity and the geographical origin of the individuals and, thus, most likely linked to diet. Rgspp gene overexpression has been observed in mice fed with a high-fat diet suggesting, as observed for humans, that intestine lipid and carbohydrate microbial metabolisms are intertwined. Finally, based on the genomic environment analysis, in vitro and in vivo studies, results provide new insights into the gut microbiota catabolism of sucrose, RFOs and S6FP.}, }
@article {pmid30912350, year = {2019}, author = {Yue, X and Chen, P and Zhu, Y and Zeng, Y and Liu, H and Liu, H and Wang, M and Sun, Y}, title = {[Heterologous expression and characterization of Aspergillus oryzae acidic protease in Pichia pastoris].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {35}, number = {3}, pages = {415-424}, doi = {10.13345/j.cjb.180321}, pmid = {30912350}, issn = {1000-3061}, abstract = {Acid protease, an important aspartic protease, has been widely used in food, pharmaceutical and tanning industries. To promote the research and application of acid protease, an acid protease gene (pepA) from Aspergillus oryzae was obtained from fermented soy based on metagenome sequencing, and then cloned and transformed into Pichia pastoris GS115 for heterologous expression. The characteristic of recombinant PepA was also investigated. The activity of acid protease in the culture supernatant of P. pastoris was 50.62 U/mL. The molecular mass of PepA was about 50 kDa, and almost no other proteins in the supernatant were observed, as shown by SDS-PAGE. The optimum pH and temperature of PepA were determined as pH 4.5 and 50 ℃. Mn²⁺ and Cu²⁺ enhanced the activity of PepA, whereas Fe³⁺, Fe²⁺ and Ca² had inhibitory effects on its activity. The above findings can provide guidance for heterologous expression and industrial application of acid protease from Aspergillus oryzae.}, }
@article {pmid30910513, year = {2019}, author = {López-Mondéjar, R and Algora, C and Baldrian, P}, title = {Lignocellulolytic systems of soil bacteria: A vast and diverse toolbox for biotechnological conversion processes.}, journal = {Biotechnology advances}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.biotechadv.2019.03.013}, pmid = {30910513}, issn = {1873-1899}, abstract = {Lignocellulose from plant biomass represents an abundant and renewable source for the production of environmentally friendly chemicals and biofuels. However, its recalcitrant nature entails the use of complex biochemical reactions that are still challenging. Since the degradation of lignocellulose is the current bottleneck of the conversion processes, the search for novel enzymes and microbial strains for degrading plant biomass is of high importance. Currently, bacteria are in the spotlight as promising candidates for novel conversion strategies due to their wide functional diversity and versatility. Here, we review the lines of evidence that show the high potential of bacterial strains from soil for biomass conversion ranging from strain characterization to metagenome and metatranscriptome analysis. Substantial and diverse fractions of soil bacteria are able to decompose the major lignocellulose components. To do that, bacteria evolved structurally variable and often highly complex lignocellulolytic systems composed of enzymes as well as proteins involved in efficient substrate binding. Both as individual components or in combination, bacterial enzymes, and accessory proteins appear to be promising tools in the biotechnological valorization of lignocellulose.}, }
@article {pmid30910274, year = {2019}, author = {Leynaert, B and Le Moual, N and Neukirch, C and Siroux, V and Varraso, R}, title = {[Environmental risk factors for asthma developement].}, journal = {Presse medicale (Paris, France : 1983)}, volume = {48}, number = {3 Pt 1}, pages = {262-273}, doi = {10.1016/j.lpm.2019.02.022}, pmid = {30910274}, issn = {2213-0276}, abstract = {The prevalence of asthma has increased rapidly since the early 1970s, and only changes in exposure to environmental factors; which go together with changes in lifestyle, are likely to explain such a rapid increase. Exposure to allergens is a risk factor for allergic sensitization, and allergic sensitization is a risk factor for allergic asthma. However, apart from indoor mold exposure as a risk factor for childhood asthma, there is insufficient evidence to conclude that the associations between allergen exposure and asthma development are causal. A new challenge for research is to analyze the huge amount of data derived from the metagenomic characterization of the environmental and human microbiome, to understand the role of interactions between viruses, bacteria and allergens in the development of asthma. It is recognized that prenatal and postnatal exposure to air pollution and maternal smoking increase the risk of developing asthma in children. In adults, the data are scarce and the results remain controversial as regards these exposures and asthma incidence. Further research is needed to appraise the effect of exposure to phenols, phthalates and perfluorinated compounds, which are widespread in the environment and may be associated with asthma, especially in children. Frequent use of chemicals for home cleaning especially in the form of sprays - which is a common practice at the population level - is a risk factor for the development of adult asthma. The domestic use of cleaning products might also be a risk factor for asthma in children exposed at home. The chemicals involved in these relationships are still to be identified. Occupational asthma is a major phenotype of adult asthma. A significant part of these asthma cases might relate to occupational exposure to cleaning products. While there is evidence of associations between diet during pregnancy or during childhood and the risk of developing asthma in children, the data in adults are insufficient. Beyond genetic factors, body composition is influenced by dietary choices and physical activity. Further research is needed to clarify the complex interplay between these nutritional factors and asthma development. The new challenge for research is to decipher the role of all the environmental factors to which the individual is exposed since conception (&quot;exposome&quot;) in the development of asthma, using a holistic approach.}, }
@article {pmid30909631, year = {2019}, author = {de Souza, WM and Fumagalli, MJ and Sabino-Santos, G and Motta Maia, FG and Modha, S and Teixeira Nunes, MR and Murcia, PR and Moraes Figueiredo, LT}, title = {A Novel Hepacivirus in Wild Rodents from South America.}, journal = {Viruses}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/v11030297}, pmid = {30909631}, issn = {1999-4915}, support = {13/14929-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 12/24150-9//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 15/05778-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 17/13981-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 16/01414-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 08/06411-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 11/06810-9//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 11/22663-6//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 16/02568-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; MC_UU_120/14/9//Medical Research Council of the United Kingdom/ ; }, abstract = {The Hepacivirus genus comprises single-stranded positive-sense RNA viruses within the family Flaviviridae. Several hepaciviruses have been identified in different mammals, including multiple rodent species in Africa, Asia, Europe, and North America. To date, no rodent hepacivirus has been identified in the South American continent. Here, we describe an unknown hepacivirus discovered during a metagenomic screen in Akodon montensis, Calomys tener, Oligoryzomys nigripes, Necromys lasiurus, and Mus musculus from São Paulo State, Brazil. Molecular detection of this novel hepacivirus by RT-PCR showed a frequency of 11.11% (2/18) in Oligoryzomys nigripes. This is the first identification of hepavivirus in sigmondonine rodents and in rodents from South America. In sum, our results expand the host range, viral diversity, and geographical distribution of the Hepacivirus genus.}, }
@article {pmid30906284, year = {2019}, author = {Cycoń, M and Mrozik, A and Piotrowska-Seget, Z}, title = {Antibiotics in the Soil Environment-Degradation and Their Impact on Microbial Activity and Diversity.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {338}, doi = {10.3389/fmicb.2019.00338}, pmid = {30906284}, issn = {1664-302X}, abstract = {Antibiotics play a key role in the management of infectious diseases in humans, animals, livestock, and aquacultures all over the world. The release of increasing amount of antibiotics into waters and soils creates a potential threat to all microorganisms in these environments. This review addresses issues related to the fate and degradation of antibiotics in soils and the impact of antibiotics on the structural, genetic and functional diversity of microbial communities. Due to the emergence of bacterial resistance to antibiotics, which is considered a worldwide public health problem, the abundance and diversity of antibiotic resistance genes (ARGs) in soils are also discussed. When antibiotic residues enter the soil, the main processes determining their persistence are sorption to organic particles and degradation/transformation. The wide range of DT50 values for antibiotic residues in soils shows that the processes governing persistence depend on a number of different factors, e.g., physico-chemical properties of the residue, characteristics of the soil, and climatic factors (temperature, rainfall, and humidity). The results presented in this review show that antibiotics affect soil microorganisms by changing their enzyme activity and ability to metabolize different carbon sources, as well as by altering the overall microbial biomass and the relative abundance of different groups (i.e., Gram-negative bacteria, Gram-positive bacteria, and fungi) in microbial communities. Studies using methods based on analyses of nucleic acids prove that antibiotics alter the biodiversity of microbial communities and the presence of many types of ARGs in soil are affected by agricultural and human activities. It is worth emphasizing that studies on ARGs in soil have resulted in the discovery of new genes and enzymes responsible for bacterial resistance to antibiotics. However, many ambiguous results indicate that precise estimation of the impact of antibiotics on the activity and diversity of soil microbial communities is a great challenge.}, }
@article {pmid30905871, year = {2019}, author = {Folch-Mallol, JL and Zárate, A and Sánchez-Reyes, A and López-Lara, IM}, title = {Expression, purification, and characterization of a metagenomic thioesterase from activated sludge involved in the degradation of acylCoA-derivatives.}, journal = {Protein expression and purification}, volume = {159}, number = {}, pages = {49-52}, doi = {10.1016/j.pep.2019.03.008}, pmid = {30905871}, issn = {1096-0279}, abstract = {Metagenomic libraries are a novel and powerful approach to seek for pathways involved in xenobiotic degradation, since this technique abolishes the need for cultivating microorganisms that otherwise would be overlooked if they cannot grow on standard laboratory media and conditions. In this paper, we describe the expression, purification and characterization of a novel metagenomic thioesterase which was described to be involved in phenylacetic acid degradation (A. Sánchez-Reyes, R. Batista-García, G. Valdés-García E. Ortiz, L. Perezgasga, A. Zárate-Romero, N. Pastor, J. L. Folch-Mallol, A Family 13 thioesterase isolated from an activated sludge metagenome: insights into aromatic compounds metabolism, Proteins 85 (2017) 1222-1237). According to similarity and phylogenetic analyses, the enzyme seems to belong to an Actinobacterium. Nevertheless, after a process of denaturation and refolding, the protein expressed in E. coli was obtained in an active form. New data concerning the substrate preferences for this enzyme are presented which suggest that this thioesterase could be involved in breaking the ester bond in the CoA-linear acyl derivatives of the phenylacetic acetic pathway.}, }
@article {pmid30904192, year = {2019}, author = {Dubois, H and van Loo, G and Wullaert, A}, title = {Nucleic Acid Induced Interferon and Inflammasome Responses in Regulating Host Defense to Gastrointestinal Viruses.}, journal = {International review of cell and molecular biology}, volume = {345}, number = {}, pages = {137-171}, doi = {10.1016/bs.ircmb.2018.08.003}, pmid = {30904192}, issn = {1937-6448}, abstract = {The gut bacterial and fungal communities residing in the gastrointestinal tract have undisputed far-reaching effects in regulating host health. In the meantime, however, metagenomic sequencing efforts are revealing enteric viruses as the most abundant dimension of the intestinal gut ecosystem, and the first gut virome-wide association studies showed that inflammatory bowel disease as well as type 1 diabetes could be linked to the presence or absence of particular viral inhabitants in the intestine. In line with the genetic component of these human diseases, mouse model studies demonstrated how beneficial functions of a resident virus can switch to detrimental inflammatory effects in a genetically predisposed host. Such viral-induced intestinal immune disturbances are also recapitulated by several gastrointestinal infectious viruses such as rotavirus and human norovirus. This wide range of viral effects on intestinal immunity emphasizes the need for understanding the innate immune responses to gastrointestinal viruses. Numerous nucleic acid sensors such as DexD/H helicases and AIM2 serve as cytosolic viral guardians to induce antiviral interferon and/or pro-inflammatory inflammasome responses. In both cases, pioneering examples are emerging in which RNA helicases cooperate with particular Nod-like receptors to trigger these cellular responses to enteric viruses. Here we summarize the reported beneficial versus detrimental effects of enteric viruses in the intestinal immune system, and we zoom in on the mechanisms through which sensing of nucleic acids from these enteric viruses trigger interferon and inflammasome responses.}, }
@article {pmid30904077, year = {2019}, author = {Grogan, MD and Bartow-McKenney, C and Flowers, L and Knight, SAB and Uberoi, A and Grice, EA}, title = {Research Techniques Made Simple: Profiling the Skin Microbiota.}, journal = {The Journal of investigative dermatology}, volume = {139}, number = {4}, pages = {747-752.e1}, doi = {10.1016/j.jid.2019.01.024}, pmid = {30904077}, issn = {1523-1747}, abstract = {Skin is colonized by microbial communities (microbiota) that participate in immune homeostasis, development and maintenance of barrier function, and protection from pathogens. The past decade has been marked by an increased interest in the skin microbiota and its role in cutaneous health and disease, in part due to advances in next-generation sequencing platforms that enable high-throughput, culture-independent detection of bacteria, fungi, and viruses. Various approaches, including bacterial 16S ribosomal RNA gene sequencing and metagenomic shotgun sequencing, have been applied to profile microbial communities colonizing healthy skin and diseased skin including atopic dermatitis, psoriasis, and acne, among others. Here, we provide an overview of culture-dependent and -independent approaches to profiling the skin microbiota and the types of questions that may be answered by each approach. We additionally highlight important study design considerations, selection of controls, interpretation of results, and limitations and challenges.}, }
@article {pmid30903144, year = {2019}, author = {Lannes, R and Olsson-Francis, K and Lopez, P and Bapteste, E}, title = {Carbon Fixation by Marine Ultrasmall Prokaryotes.}, journal = {Genome biology and evolution}, volume = {11}, number = {4}, pages = {1166-1177}, doi = {10.1093/gbe/evz050}, pmid = {30903144}, issn = {1759-6653}, abstract = {Autotrophic carbon fixation is a crucial process for sustaining life on Earth. To date, six pathways, the Calvin-Benson-Bassham cycle, the reductive tricarboxylic acid cycle, the 3-hydroxypropionate bi-cycle, the Wood-Ljungdahl pathway, the dicarboxylate/4-hydroxybutyrate cycle, and the 4-hydroxybutyrate cycle, have been described. Nano-organisms such as members of the Candidate Phyla Radiation (CPR) bacterial superphylum and the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohalorchaeota (DPANN) archaeal superphylum could deeply impact carbon cycling and carbon fixation in ways that are still to be determined. CPR and DPANN are ubiquitous in the environment but understudied; their gene contents are not exhaustively described; and their metabolisms are not yet fully understood. Here, the completeness of each of the above pathways was quantified and tested for the presence of all key enzymes in nano-organisms from across the World Ocean. The novel marine ultrasmall prokaryotes were demonstrated to collectively harbor the genes required for carbon fixation, in particular the &quot;energetically efficient&quot; dicarboxylate/4-hydroxybutyrate pathway and the 4-hydroxybutyrate pathway. This contrasted with the known carbon metabolic pathways associated with CPR members in aquifers, where they are described as degraders (Castelle CJ, et al. 2015. Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling. Curr Biol. 25(6):690-701; Castelle CJ, et al. 2018. Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations. Nat Rev Microbiol. 16(10):629-645; Anantharaman K, et al. 2016. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat Commun. 7:13219.). Our findings suggest that nano-organisms have a broader contribution to carbon fixation and cycling than currently assumed. Furthermore, CPR and DPANN superphyla are possibly not the only nanosized prokaryotes; therefore, the discovery of new autotrophic marine nano-organisms by future single cell genomics is anticipated.}, }
@article {pmid30902854, year = {2019}, author = {Youssef, NH and Farag, IF and Hahn, CR and Jarett, J and Becraft, E and Eloe-Fadrosh, E and Lightfoot, J and Bourgeois, A and Cole, T and Ferrante, S and Truelock, M and Marsh, W and Jamaleddine, M and Ricketts, S and Simpson, R and McFadden, A and Hoff, W and Ravin, NV and Sievert, S and Stepanauskas, R and Woyke, T and Elshahed, M}, title = {Genomic characterization of candidate division LCP-89 reveals an atypical cell wall structure, microcompartment production, and dual respiratory and fermentative capacities.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.00110-19}, pmid = {30902854}, issn = {1098-5336}, abstract = {Recent experimental and bioinformatic advances enable the recovery of genomes belonging to yet-uncultured microbial lineages directly from environmental samples. Here, we report on the recovery and characterization of single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) representing candidate phylum LCP-89, previously defined based on 16S rRNA gene sequences. Analysis of LCP-89 genomes recovered from Zodletone spring, an anoxic spring in Oklahoma, predicts slow-growing, rod-shaped organisms. LCP-89 genomes encode genes for cell wall lipopolysaccharide (LPS) production but lack the entire machinery for peptidoglycan biosynthesis, suggesting an atypical cell wall structure. Genomes, however, encode for S-layer homology domain-containing proteins, as well as for the biosynthesis of CMP-legionaminate, inferring the possession of an S-layer glycoprotein. A near complete chemotaxis machinery coupled to the absence of flagellar synthesis and assembly genes argue for the utilization of alternative types of motility. A strict anaerobic lifestyle is predicted, with dual respiratory (nitrite ammonification) and fermentative capacities. Predicted substrates include a wide range of sugars, sugar alcohols, and few amino acids. The capability of rhamnose metabolism is confirmed by the identification of bacterial microcompartment genes to sequester the generated toxic intermediates. Comparative genomic analysis identified differences in oxygen sensitivities, respiratory capabilities, substrate utilization preferences, and fermentation end products between LCP-89 genomes, and those belonging to its four sister phyla (Calditrichota, SM32-31, AABM5-125-24, and KSB1) within the broader FCB superphylum. Our results provide a detailed characterization of members of the candidate division LCP-89, and highlight the importance of reconciling 16S rRNA-based and genome-based phylogenies.Importance. Our understanding of the metabolic capacities, physiological preferences, and ecological roles of yet-uncultured microbial phyla is rapidly expanding. Two distinct approaches are currently being utilized for characterizing microbial communities in nature: amplicon-based 16S rRNA gene surveys for community characterization, and metagenomics/single cell genomics for detailed metabolic reconstruction. The occurrence of multiple, yet-uncultured bacterial phyla has been documented using 16S rRNA surveys, and obtaining genome representatives of these yet-uncultured lineages is critical to our understanding of the role of yet-uncultured organisms in nature. This study provides a genomics-based analysis highlighting the structural features and metabolic capacities of a yet-uncultured bacterial phylum (LCP-89) previously identified in 16S rRNA surveys for which no prior genomes have been described. Our analysis identifies several interesting structural features for members of this phylum e.g. lack of peptidoglycan biosynthetic machinery and ability to form bacterial microcompartments. Predicted metabolic capabilities include degradation of a wide range of sugars, anaerobic respiratory capacity, as well as fermentative capacities. In addition to the detailed structural and metabolic analysis provided for candidate division LCP-89, this effort represents an additional step towards a unified scheme for microbial taxonomy by reconciling 16S rRNA gene-based and genomics-based taxonomic outlines.}, }
@article {pmid30902785, year = {2019}, author = {Kumar, R and Mishra, A and Jha, B}, title = {Bacterial community structure and functional diversity in subsurface seawater from the western coastal ecosystem of the Arabian Sea, India.}, journal = {Gene}, volume = {701}, number = {}, pages = {55-64}, doi = {10.1016/j.gene.2019.02.099}, pmid = {30902785}, issn = {1879-0038}, abstract = {The present study revealed the spatial variability of bacteria in relation to physicochemical variations at four different locations (Diu - DIU, Veraval - VER, Porbandar - POR and Okha - OKH) along the Gujarat coast (Arabian Sea, India). The natural habitat was analyzed for temperature, salinity, pH, total dissolved solids, total organic content, total inorganic content, biological oxygen demand, conductivity and total dissolved oxygen. The lowest salinity and conductivity were observed at the VER site, whereas the highest salinity and conductivity were measured with OKH samples. In contrast, the pH was slightly alkaline at all of the sites. The VER site contained the maximum total dissolved solids (TDS), total carbon (TC), total organic carbon (TOC), and total inorganic carbon (TIC), while OKH showed the maximum dissolve oxygen (DO), biological oxygen demand (BOD), pH, temperature, conductivity, and salinity. The physicochemical characteristics showed that the Gujarat coast is alkaline and has a nutrient heterogeneous nature. Average well color development (AWCD) values, calculated using Biolog EcoPlates, showed that the microbial community from VER contained the highest metabolic activities and could metabolize all 31 substrates, followed by DIU > OKH > POR samples. In contrast, the abundance of the bacterial community, determined by qRT-PCR, was maximum in VER samples, followed by OKH > POR > DIU samples. The Shannon and Simpson indices showed that DIU, POR and OKH seawater clone libraries were more diverse. Furthermore, Chao estimator revealed the high diversity of POR and DIU clone libraries. Interestingly, DIU and OKH did not share any common operational taxonomic units (OTUs), and overall, the maximum bacterial diversity was observed with the POR seawater sample. Moreover, these observations were supported by statistical analysis, such as canonical correspondence analysis (CCA) and principal component analysis (PCA). The molecular phylogeny revealed the dominance of Proteobacteria followed by Firmicutes. Within the Proteobacteria phylum, most of the sequences were affiliated with the Gammaproteobacteria class. In total, about 726 OTUs were observed from all four sites which covers 59.79% DIU, 87.5% VER, 50% POR and 98.83% OKH of samples. This study is the first report to describe physicochemical attributes and the bacterial diversity of the coastal area of Gujarat. The study will provide useful insights about bacterial diversity, distribution, and abundance, as well as their relationships with the habitat.}, }
@article {pmid30902113, year = {2019}, author = {Clarke, EL and Taylor, LJ and Zhao, C and Connell, A and Lee, JJ and Fett, B and Bushman, FD and Bittinger, K}, title = {Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {46}, doi = {10.1186/s40168-019-0658-x}, pmid = {30902113}, issn = {2049-2618}, support = {T32 AI007324/AI/NIAID NIH HHS/United States ; R01 HL113252/HL/NHLBI NIH HHS/United States ; U01HL112712//National Heart, Lung, and Blood Institute/ ; R01HL113252//National Heart, Lung, and Blood Institute/ ; P30 AI045008/AI/NIAID NIH HHS/United States ; R61 HL137063/HL/NHLBI NIH HHS/United States ; 4100068710//Pennsylvania Department of Health/ ; U01 HL112712/HL/NHLBI NIH HHS/United States ; P30AI045008//National Institute of Allergy and Infectious Diseases/ ; }, abstract = {BACKGROUND: Analysis of mixed microbial communities using metagenomic sequencing experiments requires multiple preprocessing and analytical steps to interpret the microbial and genetic composition of samples. Analytical steps include quality control, adapter trimming, host decontamination, metagenomic classification, read assembly, and alignment to reference genomes.<br><br>RESULTS: We present a modular and user-extensible pipeline called Sunbeam that performs these steps in a consistent and reproducible fashion. It can be installed in a single step, does not require administrative access to the host computer system, and can work with most cluster computing frameworks. We also introduce Komplexity, a software tool to eliminate potentially problematic, low-complexity nucleotide sequences from metagenomic data. A unique component of the Sunbeam pipeline is an easy-to-use extension framework that enables users to add custom processing or analysis steps directly to the workflow. The pipeline and its extension framework are well documented, in routine use, and regularly updated.<br><br>CONCLUSIONS: Sunbeam provides a foundation to build more in-depth analyses and to enable comparisons in metagenomic sequencing experiments by removing problematic, low-complexity reads and standardizing post-processing and analytical steps. Sunbeam is written in Python using the Snakemake workflow management software and is freely available at github.com/sunbeam-labs/sunbeam under the GPLv3.}, }
@article {pmid30901843, year = {2019}, author = {Cortes, L and Wopereis, H and Tartiere, A and Piquenot, J and Gouw, JW and Tims, S and Knol, J and Chelsky, D}, title = {Metaproteomic and 16S rRNA Gene Sequencing Analysis of the Infant Fecal Microbiome.}, journal = {International journal of molecular sciences}, volume = {20}, number = {6}, pages = {}, doi = {10.3390/ijms20061430}, pmid = {30901843}, issn = {1422-0067}, abstract = {A metaproteomic analysis was conducted on the fecal microbiome of eight infants to characterize global protein and pathway expression. Although mass spectrometry-based proteomics is now a routine tool, analysis of the microbiome presents specific technical challenges, including the complexity and dynamic range of member taxa, the need for well-annotated metagenomic databases, and high inter-protein sequence redundancy and similarity. In this study, an approach was developed for assessment of biological phenotype and metabolic status, as a functional complement to DNA sequence analysis. Fecal samples were prepared and analysed by tandem mass spectrometry and a homology-based meta-clustering strategy was used to combine peptides from multiple species into representative proteins. In total, 15,250 unique peptides were sequenced and assigned to 2154 metaclusters, which were then assigned to pathways and functional groups. Differences were noted in several pathways, consistent with the dominant genera observed in different subjects. Although this study was not powered to draw conclusions from the comparisons, the results obtained demonstrate the applicability of this approach and provide the methods needed for performing semi-quantitative comparisons of human fecal microbiome composition, physiology and metabolism, as well as a more detailed assessment of microbial composition in comparison to 16S rRNA gene sequencing.}, }
@article {pmid30901643, year = {2019}, author = {Appolinario, LR and Tschoeke, D and Paixão, RVS and Venas, T and Calegario, G and Leomil, L and Silva, BS and Thompson, CC and Thompson, FL}, title = {Metagenomics sheds light on the metabolic repertoire of oil-biodegrading microbes of the South Atlantic Ocean.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {249}, number = {}, pages = {295-304}, doi = {10.1016/j.envpol.2019.03.007}, pmid = {30901643}, issn = {1873-6424}, abstract = {Unplanned oil spills during offshore oil production are a serious problem for the industry and the marine environment. Here we assess the biodegradation potential of marine microorganisms from three water depths in the Campos Basin (South Atlantic Ocean): (i) 5 m (surface), (ii) ∼80 m (chlorophyll maximum layer), and (iii) ∼1200 m (near the bottom). After incubating seawater samples with or without crude oil for 52 days, we used metagenomics and classic microbiology techniques to analyze microbial abundance and diversity, and measured physical-chemical parameters to better understand biodegradation processes. We observed increased microbial abundance and concomitant decreases in dissolved oxygen and hydrocarbon concentrations, indicating oil biodegradation in the three water depths treatments within approximately 27 days. An increase in metagenomic sequences of oil-degrading archaea, fungi, and bacteria (Alcanivorax, Alteromonas, Colwellia, Marinobacter, and Pseudomonas) accompanied by a significant increase in metagenomic sequences involved in the degradation of aromatic compounds indicate that crude oil promotes the growth of microorganisms with oil degradation potential. The abundance of genes involved in biodegrading benzene, toluene, ethylbenzene, xylene, alkanes, and poly-aromatic hydrocarbons peaked approximately 3 days after oil addition. All 12 novel metagenome-assembled genomes contained genes involved in hydrocarbon degradation, indicating the oil-degrading potential of planktonic microbes in the Campos Basin.}, }
@article {pmid30899254, year = {2019}, author = {Willms, IM and Kamran, A and Aßmann, NF and Krone, D and Bolz, SH and Fiedler, F and Nacke, H}, title = {Discovery of Novel Antibiotic Resistance Determinants in Forest and Grassland Soil Metagenomes.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {460}, doi = {10.3389/fmicb.2019.00460}, pmid = {30899254}, issn = {1664-302X}, abstract = {Soil represents a significant reservoir of antibiotic resistance genes (ARGs), which can potentially spread across distinct ecosystems and be acquired by pathogens threatening human as well as animal health. Currently, information on the identity and diversity of these genes, enabling anticipation of possible future resistance development in clinical environments and the livestock sector, is lacking. In this study, we applied functional metagenomics to discover novel sulfonamide as well as tetracycline resistance genes in soils derived from forest and grassland. Screening of soil metagenomic libraries revealed a total of eight so far unknown ARGs. The recovered genes originate from phylogenetically diverse soil bacteria (e.g., Actinobacteria, Chloroflexi, or Proteobacteria) and encode proteins with a minimum identity of 46% to other antibiotic resistance determinants. In particular forest soil ecosystems have so far been neglected in studies focusing on antibiotic resistance. Here, we detected for the first time non-mobile dihydropteroate synthase (DHPS) genes conferring resistance to sulfonamides in forest soil with no history of exposure to these synthetic drugs. In total, three sulfonamide resistant DHPSs, differing in taxonomic origin, were discovered in beech or pine forest soil. This indicates that sulfonamide resistance naturally occurs in forest-resident soil bacterial communities. Besides forest soil-derived sulfonamide resistance proteins, we also identified a DHPS affiliated to Chloroflexi in grassland soil. This enzyme and the other recovered DHPSs confer reduced susceptibility toward sulfamethazine, which is widely used in food animal production. With respect to tetracycline resistance, four efflux proteins affiliated to the major facilitator superfamily (MFS) were identified. Noteworthy, one of these proteins also conferred reduced susceptibility toward lincomycin.}, }
@article {pmid30899180, year = {2019}, author = {Hashem, A and Kumar, A and Al-Dbass, AM and Alqarawi, AA and Al-Arjani, AF and Singh, G and Farooq, M and Abd Allah, EF}, title = {Arbuscular mycorrhizal fungi and biochar improves drought tolerance in chickpea.}, journal = {Saudi journal of biological sciences}, volume = {26}, number = {3}, pages = {614-624}, doi = {10.1016/j.sjbs.2018.11.005}, pmid = {30899180}, issn = {1319-562X}, abstract = {Arbuscular mycorrhizal fungi (AMF) inoculation and biochar amendment has been reported to improve growth of several crop plants however their role in stress amelioration individually as well as in combination has not been worked out. This experiment was conducted to evaluate the application of AMF and biochar on the performance of chickpea under drought stress. The treatments included the individual as well as combined treatment of AMF and biochar to drought stressed and normal chickpea plants. Plants inoculation improved growth in terms of shoot and root length, leaf area and number of branches which was observed to show a steep decline due to drought stress. Drought declined the AMF colonization potential though biochar amendment ameliorated the negative effects of drought significantly by improving the spore population, number of mycelium, vesicle and arbuscules and the percentage of colonization as well. Increased chlorophyll synthesis in biochar and AMF treated plants was obvious, which lead to significant enhancement in the net photosynthetic efficiency. Drought stress also declined the relative water content (RWC) and membrane stability index (MSI), while treatment of biochar and AMF either individually or in combination mitigated the deleterious effects to considerable extent and caused a significant enhancement in RWC and MSI under normal conditions. Amendments with biochar and AMF inoculation increased the nitrogen fixation attributes including the number and weight of nodules, leghemoglobin content and activity of nitrate reductase enzyme leading to greater uptake and assimilation of nitrogen in them when compared to drought stressed plants. Drought stressed chickpea plants exhibited considerable reduction in uptake of nitrogen and phosphorous which was ameliorated by biochar and AMF treatments. It could be suggested that increase in growth and physiological attributes in chickpea due to biochar amendments and AMF inoculation under drought stress were plausibly due to their involvement in nitrogen and phosphorous uptake, chlorophyll synthesis and photosynthesis.}, }
@article {pmid30899033, year = {2019}, author = {Reddel, S and Del Chierico, F and Quagliariello, A and Giancristoforo, S and Vernocchi, P and Russo, A and Fiocchi, A and Rossi, P and Putignani, L and El Hachem, M}, title = {Gut microbiota profile in children affected by atopic dermatitis and evaluation of intestinal persistence of a probiotic mixture.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {4996}, doi = {10.1038/s41598-019-41149-6}, pmid = {30899033}, issn = {2045-2322}, support = {201502P003534//Ministero della Salute (Ministry of Health, Italy)/ ; 201602P00370//Ministero della Salute (Ministry of Health, Italy)/ ; 201503X003570//Ministero della Salute (Ministry of Health, Italy)/ ; }, abstract = {Atopic dermatitis (AD) has been hypothesised to be associated with gut microbiota (GM) composition. We performed a comparative study of the GM profile of 19 AD children and 18 healthy individuals aimed at identifying bacterial biomarkers associated with the disease. The effect of probiotic intake (Bifidobacterium breve plus Lactobacillus salivarius) on the modulation of GM and the probiotic persistence in the GM were also evaluated. Faecal samples were analysed by real-time PCR and 16S rRNA targeted metagenomics. Although the probiotics, chosen for this study, did not shape the entire GM profile, we observed the ability of these species to pass through the gastrointestinal tract and to persist (only B. breve) in the GM. Moreover, the GM of patients compared to CTRLs showed a dysbiotic status characterised by an increase of Faecalibacterium, Oscillospira, Bacteroides, Parabacteroides and Sutterella and a reduction of short-chain fatty acid (SCFA)-producing bacteria (i.e., Bifidobacterium, Blautia, Coprococcus, Eubacterium and Propionibacterium). Taken togheter these results show an alteration in AD microbiota composition with the depletion or absence of some species, opening the way to future probiotic intervention studies.}, }
@article {pmid30898140, year = {2019}, author = {Che, Y and Xia, Y and Liu, L and Li, AD and Yang, Y and Zhang, T}, title = {Mobile antibiotic resistome in wastewater treatment plants revealed by Nanopore metagenomic sequencing.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {44}, doi = {10.1186/s40168-019-0663-0}, pmid = {30898140}, issn = {2049-2618}, abstract = {BACKGROUND: Wastewater treatment plants (WWTPs) are recognized as hotspots for horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). Despite our understanding of the composition and distribution of ARGs in WWTPs, the genetic location, host, and fate of ARGs remain largely unknown.<br><br>RESULTS: In this study, we combined Oxford Nanopore and Illumina metagenomics sequencing to comprehensively uncover the resistome context of influent, activated sludge, and effluent of three WWTPs and simultaneously track the hosts of the ARGs. The results showed that most of the ARGs detected in all compartments of the WWTPs were carried by plasmids. Transposons and integrons also showed higher prevalence on plasmids than on the ARG-carrying chromosome. Notably, integrative and conjugative elements (ICEs) carrying five types of ARGs were detected, and they may play an important role in facilitating the transfer of ARGs, particularly for tetracycline and macrolide-lincosamide-streptogramin (MLS). A broad spectrum of ARGs carried by plasmids (29 subtypes) and ICEs (4 subtypes) was persistent across the WWTPs. Host tracking showed a variety of antibiotic-resistant bacteria in the effluent, suggesting the high potential for their dissemination into receiving environments. Importantly, phenotype-genotype analysis confirmed the significant role of conjugative plasmids in facilitating the survival and persistence of multidrug-resistant bacteria in the WWTPs. At last, the consistency in the quantitative results for major ARGs types revealed by Nanopore and Illumina sequencing platforms demonstrated the feasibility of Nanopore sequencing for resistome quantification.<br><br>CONCLUSION: Overall, these findings substantially expand our current knowledge of resistome in WWTPs, and help establish a baseline analysis framework to study ARGs in the environment.}, }
@article {pmid30895843, year = {2019}, author = {Hadjadj, L and Baron, SA and Diene, SM and Rolain, JM}, title = {How to discover new antibiotic resistance genes?.}, journal = {Expert review of molecular diagnostics}, volume = {}, number = {}, pages = {1-14}, doi = {10.1080/14737159.2019.1592678}, pmid = {30895843}, issn = {1744-8352}, abstract = {INTRODUCTION: Antibiotic resistance (AR) is a worldwide concern and the description of AR have been discovered mainly because of their implications in human medicine. Since the recent burden of whole-genome sequencing of microorganisms, the number of new AR genes (ARGs) have dramatically increased over the last decade. Areas covered: In this review, we will describe the different methods that could be used to characterize new ARGs using classic or innovative methods. First, we will focus on the biochemical methods, then we will develop on molecular methods, next-generation sequencing and bioinformatics approaches. The use of various methods, including cloning, mutagenesis, transposon mutagenesis, functional genomics, whole genome sequencing, metagenomic and functional metagenomics will be reviewed here, outlining the advantages and drawbacks of each method. Bioinformatics softwares used for resistome analysis and protein modeling will be also described. Expert opinion: Biological experiments and bioinformatics analysis are complementary. Nowadays, the ARGs described only account for the tip of the iceberg of all existing resistance mechanisms. The multiplication of the ecosystems studied allows us to find a large reservoir of AR mechanisms. Furthermore, the adaptation ability of bacteria facing new antibiotics promises a constant discovery of new AR mechanisms.}, }
@article {pmid30895406, year = {2019}, author = {Nguyen, VD and Nguyen, TT and Pham, TT and Packianather, M and Le, CH}, title = {Molecular screening and genetic diversity analysis of anticancer Azurin-encoding and Azurin-like genes in human gut microbiome deduced through cultivation-dependent and cultivation-independent studies.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10123-019-00070-8}, pmid = {30895406}, issn = {1618-1905}, support = {106-YS.04-2014.40//National Foundation for Science and Technology Development/ ; }, abstract = {Azurin, a bacteriocin produced by a human gut bacterium Pseudomonas aeruginosa, can reveal selectively cytotoxic and induce apoptosis in cancer cells. After overcoming two phase I trials, a functional region of Azurin called p28 has been approved as a drug for the treatment of brain tumor glioma by FDA. The present study aims to improve a screening procedure and assess genetic diversity of Azurin genes in P. aeruginosa and Azurin-like genes in the gut microbiome of a specific population in Vietnam and global populations. Firstly, both cultivation-dependent and cultivation-independent techniques based on genomic and metagenomic DNAs extracted from fecal samples of the healthy specific population were performed and optimized to detect Azurin genes. Secondly, the Azurin gene sequences were analyzed and compared with global populations by using bioinformatics tools. Finally, the screening procedure improved from the first step was applied for screening Azurin-like genes, followed by the protein synthesis and NCI in vitro screening for anticancer activity. As a result, this study has successfully optimized the annealing temperatures to amplify DNAs for screening Azurin genes and applying to Azurin-like genes from human gut microbiota. The novelty of this study is the first of its kind to classify Azurin genes into five different genotypes at a global scale and confirm the potential anticancer activity of three Azurin-like synthetic proteins (Cnazu1, Dlazu11, and Ruazu12). The results contribute to the procedure development applied for screening anticancer proteins from human microbiome and a comprehensive understanding of their therapeutic response at a genetic level.}, }
@article {pmid30894435, year = {2019}, author = {Majta, J and Odrzywolek, K and Milanovic, B and Hubar, V and Wrobel, S and Strycharz-Angrecka, E and Wojciechowski, S and Milanowska, K}, title = {Identification of Differentiating Metabolic Pathways between Infant Gut Microbiome Populations Reveals Depletion of Function-Level Adaptation to Human Milk in the Finnish Population.}, journal = {mSphere}, volume = {4}, number = {2}, pages = {}, doi = {10.1128/mSphereDirect.00152-19}, pmid = {30894435}, issn = {2379-5042}, abstract = {A variety of autoimmune and allergy events are becoming increasingly common, especially in Western countries. Some pieces of research link such conditions with the composition of microbiota during infancy. In this period, the predominant form of nutrition for gut microbiota is oligosaccharides from human milk (HMO). A number of gut-colonizing strains, such as Bifidobacterium and Bacteroides, are able to utilize HMO, but only some Bifidobacterium strains have evolved to digest the specific composition of human oligosaccharides. Differences in the proportions of the two genera that are able to utilize HMO have already been associated with the frequency of allergies and autoimmune diseases in the Finnish and the Russian populations. Our results show that differences in terms of the taxonomic annotation do not explain the reason for the differences in the Bifidobacterium/Bacteroides ratio between the Finnish and the Russian populations. In this paper, we present the results of function-level analysis. Unlike the typical workflow for gene abundance analysis, BiomeScout technology explains the differences in the Bifidobacterium/Bacteroides ratio. Our research shows the differences in the abundances of the two enzymes that are crucial for the utilization of short type 1 oligosaccharides.IMPORTANCE Knowing the limitations of taxonomy-based research, there is an emerging need for the development of higher-resolution techniques. The significance of this research is demonstrated by the novel method used for the analysis of function-level metagenomes. BiomeScout-the presented technology-utilizes proprietary algorithms for the detection of differences between functionalities present in metagenomic samples.}, }
@article {pmid30894139, year = {2019}, author = {Szafrańska, AK and Junker, V and Steglich, M and Nübel, U}, title = {Rapid cell division of Staphylococcus aureus during colonization of the human nose.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {229}, doi = {10.1186/s12864-019-5604-6}, pmid = {30894139}, issn = {1471-2164}, support = {643476//Horizon 2020 Framework Programme/ ; }, abstract = {BACKGROUND: Staphylococcus aureus is an important opportunistic pathogen and a commensal bacterium, thriving in the nasal cavities of 20% of the human population. Little is known about the dynamics of asymptomatic colonization and the occasional transition to infectious disease.<br><br>RESULTS: In this study, we inferred that S. aureus cells replicate every one to three hours on average while colonizing the human nose, based on two independent lines of genomic evidence. First, we collected nasal swab samples from human subjects, extracted and sequenced metagenomic DNA, and analyzed the distribution of sequencing coverage along the staphylococcal chromosome. Calibration of this data by comparison to a laboratory culture enabled measuring S. aureus cell division rates in nasal samples. Second, we applied mutation accumulation experiments paired with genome sequencing to measure spontaneous mutation rates at a genome scale. Relating these mutation rates to annual evolutionary rates confirmed that nasal S. aureus continuously pass several thousand cell divisions per year when averaged over large, globally distributed populations and over many years, corresponding to generation times of less than two hours.<br><br>CONCLUSIONS: The cell division rates we determined were higher than the fastest documented rates during fulminant disease progression (in a mouse model of systemic infection) and much higher than those previously measured in expectorated sputum from cystic fibrosis patients. This paper supplies absolute in-vivo generation times for an important bacterial commensal, indicating that colonization of the human upper respiratory tract is characterized by a highly dynamic equilibrium between bacterial growth and removal.}, }
@article {pmid30894059, year = {2019}, author = {Bjørkhaug, ST and Aanes, H and Neupane, SP and Bramness, JG and Malvik, S and Henriksen, C and Skar, V and Medhus, AW and Valeur, J}, title = {Characterization of gut microbiota composition and functions in patients with chronic alcohol overconsumption.}, journal = {Gut microbes}, volume = {}, number = {}, pages = {1-13}, doi = {10.1080/19490976.2019.1580097}, pmid = {30894059}, issn = {1949-0984}, abstract = {Excessive alcohol intake can alter the gut microbiota, which may underlie the pathophysiology of alcohol-related diseases. We examined gut microbiota composition and functions in patients with alcohol overconsumption for >10 years, compared to a control group of patients with a history of no or low alcohol intake. Faecal microbiota composition was assessed by 16S rRNA sequencing. Gut microbiota functions were evaluated by quantification of short-chain fatty acids (SCFAs) and predictive metagenome profiling (PICRUSt). Twenty-four patients, mean age 64.8 years (19 males), with alcohol overconsumption, and 18 control patients, mean age 58.2 years (14 males) were included. The two groups were comparable regarding basic clinical variables. Nutritional assessment revealed lower total score on the screening tool Mini Nutritional Assessment, lower muscle mass as assessed by handgrip strength, and lower plasma vitamin C levels in the alcohol overconsumption group. Bacteria from phylum Proteobacteria were found in higher relative abundance, while bacteria from genus Faecalibacterium were found in lower relative abundance in the group of alcohol overconsumers. The group also had higher levels of the genera Sutterella, Holdemania and Clostridium, and lower concentration and percentage of butyric acid. When applying PICRUSt to predict the metagenomic composition, we found that genes related to invasion of epithelial cells were more common in the group of alcohol overconsumers. We conclude that gut microbiota composition and functions in patients with alcohol overconsumption differ from patients with low consumption of alcohol, and seem to be skewed into a putative pro-inflammatory direction.}, }
@article {pmid30893890, year = {2019}, author = {Tatsika, S and Karamanoli, K and Karayanni, H and Genitsaris, S}, title = {Metagenomic Characterization of Bacterial Communities on Ready-to-Eat Vegetables and Effects of Household Washing on their Diversity and Composition.}, journal = {Pathogens (Basel, Switzerland)}, volume = {8}, number = {1}, pages = {}, doi = {10.3390/pathogens8010037}, pmid = {30893890}, issn = {2076-0817}, abstract = {Ready-to-eat (RTE) leafy salad vegetables are considered foods that can be consumed immediately at the point of sale without further treatment. The aim of the study was to investigate the bacterial community composition of RTE salads at the point of consumption and the changes in bacterial diversity and composition associated with different household washing treatments. The bacterial microbiomes of rocket and spinach leaves were examined by means of 16S rRNA gene high-throughput sequencing. Overall, 886 Operational Taxonomic Units (OTUs) were detected in the salads' leaves. Proteobacteria was the most diverse high-level taxonomic group followed by Bacteroidetes and Firmicutes. Although they were processed at the same production facilities, rocket showed different bacterial community composition than spinach salads, mainly attributed to the different contributions of Proteobacteria and Bacteroidetes to the total OTU number. The tested household decontamination treatments proved inefficient in changing the bacterial community composition in both RTE salads. Furthermore, storage duration of the salads at refrigeration temperatures affected the microbiome, by decreasing the bacterial richness and promoting the dominance of psychrotropic bacteria. Finally, both salads were found to be a reservoir of opportunistic human pathogens, while washing methods usually applied at home proved to be inefficient in their removal.}, }
@article {pmid30891366, year = {2019}, author = {Wainaina, JM and Ateka, E and Makori, T and Kehoe, MA and Boykin, LM}, title = {A metagenomic study of DNA viruses from samples of local varieties of common bean in Kenya.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6465}, doi = {10.7717/peerj.6465}, pmid = {30891366}, issn = {2167-8359}, abstract = {Common bean (Phaseolus vulgaris L.) is the primary source of protein and nutrients in the majority of households in sub-Saharan Africa. However, pests and viral diseases are key drivers in the reduction of bean production. To date, the majority of viruses reported in beans have been RNA viruses. In this study, we carried out a viral metagenomic analysis on virus symptomatic bean plants. Our virus detection pipeline identified three viral fragments of the double-stranded DNA virus Pelargonium vein banding virus (PVBV) (family, Caulimoviridae, genus Badnavirus). This is the first report of the dsDNA virus and specifically PVBV in legumes to our knowledge. In addition two previously reported +ssRNA viruses the bean common mosaic necrosis virus (BCMNVA) (Potyviridae) and aphid lethal paralysis virus (ALPV) (Dicistroviridae) were identified. Bayesian phylogenetic analysis of the Badnavirus (PVBV) using amino acid sequences of the RT/RNA-dependent DNA polymerase region showed the Kenyan sequence (SRF019_MK014483) was closely matched with two Badnavirus viruses: Dracaena mottle virus (DrMV) (YP_610965) and Lucky bamboo bacilliform virus (ABR01170). Phylogenetic analysis of BCMNVA was based on amino acid sequences of the Nib region. The BCMNVA phylogenetic tree resolved two clades identified as clade (I and II). Sequence from this study SRF35_MK014482, clustered within clade I with other Kenyan sequences. Conversely, Bayesian phylogenetic analysis of ALPV was based on nucleotide sequences of the hypothetical protein gene 1 and 2. Three main clades were resolved and identified as clades I-III. The Kenyan sequence from this study (SRF35_MK014481) clustered within clade II, and nested within a sub-clade; comprising of sequences from China and an earlier ALPV sequences from Kenya isolated from maize (MF458892). Our findings support the use of viral metagenomics to reveal the nascent viruses, their viral diversity and evolutionary history of these viruses. The detection of ALPV and PVBV indicate that these viruses have likely been underreported due to the unavailability of diagnostic tools.}, }
@article {pmid30891034, year = {2019}, author = {Bello-Gil, D and Audebert, C and Olivera-Ardid, S and Pérez-Cruz, M and Even, G and Khasbiullina, N and Gantois, N and Shilova, N and Merlin, S and Costa, C and Bovin, N and Mañez, R}, title = {The Formation of Glycan-Specific Natural Antibodies Repertoire in GalT-KO Mice Is Determined by Gut Microbiota.}, journal = {Frontiers in immunology}, volume = {10}, number = {}, pages = {342}, doi = {10.3389/fimmu.2019.00342}, pmid = {30891034}, issn = {1664-3224}, abstract = {Gut commensal bacteria are known to have a significant role in regulating the innate and adaptive immune homeostasis. Alterations in the intestinal microbial composition have been associated with several disease states, including autoimmune and inflammatory conditions. However, it is not entirely clear how commensal gut microbiota modulate and contribute to the systemic immunity, and whether circulating elements of the host immune system could regulate the microbiome. Thus, we have studied the diversity and abundance of specific taxons in the gut microbiota of inbred GalT-KO mice during 7 months of animal life by metagenetic high-throughput sequencing (16S rRNA gene, variable regions V3-V5). The repertoire of glycan-specific natural antibodies, obtained by printed glycan array technology, was then associated with the microbial diversity for each animal by metagenome-wide association studies (MWAS). Our data show that the orders clostridiales (most abundant), bacteriodales, lactobacillales, and deferribacterales may be associated with the development of the final repertoire of natural anti-glycan antibodies in GalT-KO mice. The main changes in microbiota diversity (month-2 and month-3) were related to important changes in levels and repertoire of natural anti-glycan antibodies in these mice. Additionally, significant positive and negative associations were found between the gut microbiota and the pattern of specific anti-glycan antibodies. Regarding individual features, the gut microbiota and the corresponding repertoire of natural anti-glycan antibodies showed differences among the examined animals. We also found redundancy in different taxa associated with the development of specific anti-glycan antibodies. Differences in microbial diversity did not, therefore, necessarily influence the overall functional output of the gut microbiome of GalT-KO mice. In summary, the repertoire of natural anti-carbohydrate antibodies may be partially determined by the continuous antigenic stimulation produced by the gut bacterial population of each GalT-KO mouse. Small differences in gut microbiota diversity could determine different repertoire and levels of natural anti-glycan antibodies and consequently might induce different immune responses to pathogens or other potential threats.}, }
@article {pmid30890906, year = {2019}, author = {Hewel, C and Kaiser, J and Wierczeiko, A and Linke, J and Reinhardt, C and Endres, K and Gerber, S}, title = {Common miRNA Patterns of Alzheimer's Disease and Parkinson's Disease and Their Putative Impact on Commensal Gut Microbiota.}, journal = {Frontiers in neuroscience}, volume = {13}, number = {}, pages = {113}, doi = {10.3389/fnins.2019.00113}, pmid = {30890906}, issn = {1662-4548}, abstract = {With the rise of Next-Generation-Sequencing (NGS) methods, Micro-RNAs (miRNAs) have achieved an important position in the research landscape and have been found to present valuable diagnostic tools in various diseases such as multiple sclerosis or lung cancer. There is also emerging evidence that miRNAs play an important role in the pathogenesis of neurodegenerative diseases such as Alzheimer's disease (AD) or Parkinson's disease (PD). Apparently, these diseases come along with changes in miRNA expression patterns which led to attempts from researchers to use these small RNA species from several body fluids for a better diagnosis and in order to observe disease progression. Additionally, it became evident that microbial commensals might play an important role for pathology development and were shown to have a significantly different composition in patients suffering from neurodegeneration compared with healthy controls. As it could recently be shown that secreted miRNAs are able to enter microbial organisms, it is conceivable that the host's miRNA might affect the gut microbial ecosystem. As such, miRNAs may inherit a central role in shaping the &quot;diseased microbiome&quot; and thereby mutually act on the characteristics of these neurodegenerative diseases. We have therefore (1) compiled a list of miRNAs known to be associated with AD and/or PD, (2) performed an in silico target screen for binding sites of these miRNA on human gut metagenome sequences and (3) evaluated the hit list for interesting matches potentially relevant to the etiology of AD and or PD. The examination of protein identifiers connected to bacterial secretion system, lipopolysaccharide biosynthesis and biofilm formation revealed an overlap of 37 bacterial proteins that were targeted by human miRNAs. The identified links of miRNAs to the biological processes of bacteria connected to AD and PD have yet to be validated via in vivo experiments. However, our results show a promising new approach for understanding aspects of these neurodegenerative diseases in light of the regulation of the microbiome.}, }
@article {pmid30890181, year = {2019}, author = {Zheng, T and Li, J and Ni, Y and Kang, K and Misiakou, MA and Imamovic, L and Chow, BKC and Rode, AA and Bytzer, P and Sommer, M and Panagiotou, G}, title = {Mining, analyzing, and integrating viral signals from metagenomic data.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {42}, doi = {10.1186/s40168-019-0657-y}, pmid = {30890181}, issn = {2049-2618}, abstract = {BACKGROUND: Viruses are important components of microbial communities modulating community structure and function; however, only a couple of tools are currently available for phage identification and analysis from metagenomic sequencing data. Here we employed the random forest algorithm to develop VirMiner, a web-based phage contig prediction tool especially sensitive for high-abundances phage contigs, trained and validated by paired metagenomic and phagenomic sequencing data from the human gut flora.<br><br>RESULTS: VirMiner achieved 41.06% ± 17.51% sensitivity and 81.91% ± 4.04% specificity in the prediction of phage contigs. In particular, for the high-abundance phage contigs, VirMiner outperformed other tools (VirFinder and VirSorter) with much higher sensitivity (65.23% ± 16.94%) than VirFinder (34.63% ± 17.96%) and VirSorter (18.75% ± 15.23%) at almost the same specificity. Moreover, VirMiner provides the most comprehensive phage analysis pipeline which is comprised of metagenomic raw reads processing, functional annotation, phage contig identification, and phage-host relationship prediction (CRISPR-spacer recognition) and supports two-group comparison when the input (metagenomic sequence data) includes different conditions (e.g., case and control). Application of VirMiner to an independent cohort of human gut metagenomes obtained from individuals treated with antibiotics revealed that 122 KEGG orthology and 118 Pfam groups had significantly differential abundance in the pre-treatment samples compared to samples at the end of antibiotic administration, including clustered regularly interspaced short palindromic repeats (CRISPR), multidrug resistance, and protein transport. The VirMiner webserver is available at http://sbb.hku.hk/VirMiner/ .<br><br>CONCLUSIONS: We developed a comprehensive tool for phage prediction and analysis for metagenomic samples. Compared to VirSorter and VirFinder-the most widely used tools-VirMiner is able to capture more high-abundance phage contigs which could play key roles in infecting bacteria and modulating microbial community dynamics.<br><br>TRIAL REGISTRATION: The European Union Clinical Trials Register, EudraCT Number: 2013-003378-28 . Registered on 9 April 2014.}, }
@article {pmid30889229, year = {2019}, author = {Portillo, A and Palomar, AM and de Toro, M and Santibáñez, S and Santibáñez, P and Oteo, JA}, title = {Exploring the bacteriome in anthropophilic ticks: To investigate the vectors for diagnosis.}, journal = {PloS one}, volume = {14}, number = {3}, pages = {e0213384}, doi = {10.1371/journal.pone.0213384}, pmid = {30889229}, issn = {1932-6203}, abstract = {OBJECTIVE: The aim of this study was to characterize the bacterial microbiome of hard ticks with affinity to bite humans in La Rioja (North of Spain).<br><br>METHODS: A total of 88 adult ticks (22 Rhipicephalus sanguineus sensu lato, 27 Haemaphysalis punctata, 30 Dermacentor marginatus and 9 Ixodes ricinus) and 120 I. ricinus nymphs (CRETAV collection, La Rioja, Spain), representing the main anthropophilic species in our environment, were subjected to a metagenomic analysis of the V3-V4 region of the 16S rRNA gene using an Illumina MiSeq platform. Data obtained with Greengenes database were refined with BLAST. Four groups of samples were defined, according to the four tick species.<br><br>RESULTS: Proteobacteria was the predominant phylum observed in all groups. Gammaproteobacteria was the most abundant class, followed by Alphaproteobacteria for R. sanguineus, H. punctata and D. marginatus but the relative abundance of reads for these classes was reversed for I. ricinus. This tick species showed more than 46% reads corresponding to 'not assigned' OTUs (Greengenes), and >97% of them corresponded to 'Candidatus Midichloriaceae' using BLAST. Within Rickettsiales, 'Candidatus Midichloria', Rickettsia, Ehrlichia, 'Candidatus Neoehrlichia' and Wolbachia were detected. I. ricinus was the most alpha-diverse species. Regarding beta-diversity, I. ricinus and H. punctata samples grouped according to their tick species but microbial communities of some R. sanguineus and D. marginatus specimens clustered together.<br><br>CONCLUSIONS: The metagenomics approach seems useful to discover the spectrum of tick-related bacteria. More studies are needed to identify and differentiate bacterial species, and to improve the knowledge of tick-borne diseases in Spain.}, }
@article {pmid30887877, year = {2019}, author = {Polzin, J and Arevalo, P and Nussbaumer, T and Polz, MF and Bright, M}, title = {Polyclonal symbiont populations in hydrothermal vent tubeworms and the environment.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1896}, pages = {20181281}, doi = {10.1098/rspb.2018.1281}, pmid = {30887877}, issn = {1471-2954}, abstract = {Horizontally transmitted symbioses usually house multiple and variable symbiont genotypes that are acquired from a much more diverse environmental pool via partner choice mechanisms. However, in the deep-sea hydrothermal vent tubeworm Riftia pachyptila (Vestimentifera, Siboglinidae), it has been suggested that the Candidatus Endoriftia persephone symbiont is monoclonal. Here, we show with high-coverage metagenomics that adult R. pachyptila house a polyclonal symbiont population consisting of one dominant and several low-frequency variants. This dominance of one genotype is confirmed by multilocus gene sequencing of amplified housekeeping genes in a broad range of host individuals where three out of four loci (atpA, uvrD and recA) revealed no genomic differences, while one locus (gyrB) was more diverse in adults than in juveniles. We also analysed a metagenome of free-living Endoriftia and found that the free-living population showed greater sequence variability than the host-associated population. Most juveniles and adults shared a specific dominant genotype, while other genotypes can dominate in few individuals. We suggest that although generally permissive, partner choice is selective enough to restrict uptake of some genotypes present in the environment.}, }
@article {pmid30887686, year = {2019}, author = {Weyrich, LS and Farrer, AG and Eisenhofer, R and Arriola, LA and Young, J and Selway, CA and Handsley-Davis, M and Adler, C and Breen, J and Cooper, A}, title = {Laboratory contamination over time during low-biomass sample analysis.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13011}, pmid = {30887686}, issn = {1755-0998}, abstract = {Bacteria are not only ubiquitous on earth but can also be incredibly diverse within clean laboratories and reagents. The presence of both living and dead bacteria in laboratory environments and reagents is especially problematic when examining samples with low endogenous content (e.g. skin swabs, tissue biopsies, ice, water, degraded forensic samples, or ancient material), where contaminants can outnumber endogenous microorganisms within samples. The contribution of contaminants within high-throughput studies remains poorly understood because of the relatively low number of contaminant surveys. Here, we examined 144 negative control samples (extraction blank and no-template amplification controls) collected in both typical molecular laboratories and an ultraclean ancient DNA laboratory over five years to characterize long-term contaminant diversity. We additionally compared the contaminant content within a homemade silica-based extraction method, commonly used to analyse low-endogenous samples, with a widely used commercial DNA extraction kit. The contaminant taxonomic profile of the ultraclean ancient DNA laboratory was unique compared to the modern molecular biology laboratories, and changed over time according to researchers, month, and season. The commercial kit contained higher microbial diversity and several human-associated taxa in comparison to the homemade silica extraction protocol. We recommend a minimum of two strategies to reduce the impacts of laboratory contaminants within low-biomass metagenomic studies: 1) extraction blank controls should be included and sequenced with every batch of extractions and 2) the contributions of laboratory contamination should be assessed and reported in each high-throughput metagenomic study. This article is protected by copyright. All rights reserved.}, }
@article {pmid30886779, year = {2019}, author = {Eisenhofer, R and Weyrich, LS}, title = {Assessing alignment-based taxonomic classification of ancient microbial DNA.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6594}, doi = {10.7717/peerj.6594}, pmid = {30886779}, issn = {2167-8359}, abstract = {The field of palaeomicrobiology-the study of ancient microorganisms-is rapidly growing due to recent methodological and technological advancements. It is now possible to obtain vast quantities of DNA data from ancient specimens in a high-throughput manner and use this information to investigate the dynamics and evolution of past microbial communities. However, we still know very little about how the characteristics of ancient DNA influence our ability to accurately assign microbial taxonomies (i.e. identify species) within ancient metagenomic samples. Here, we use both simulated and published metagenomic data sets to investigate how ancient DNA characteristics affect alignment-based taxonomic classification. We find that nucleotide-to-nucleotide, rather than nucleotide-to-protein, alignments are preferable when assigning taxonomies to short DNA fragment lengths routinely identified within ancient specimens (<60 bp). We determine that deamination (a form of ancient DNA damage) and random sequence substitutions corresponding to ∼100,000 years of genomic divergence minimally impact alignment-based classification. We also test four different reference databases and find that database choice can significantly bias the results of alignment-based taxonomic classification in ancient metagenomic studies. Finally, we perform a reanalysis of previously published ancient dental calculus data, increasing the number of microbial DNA sequences assigned taxonomically by an average of 64.2-fold and identifying microbial species previously unidentified in the original study. Overall, this study enhances our understanding of how ancient DNA characteristics influence alignment-based taxonomic classification of ancient microorganisms and provides recommendations for future palaeomicrobiological studies.}, }
@article {pmid30886772, year = {2019}, author = {Jiang, H and Zhang, X and Li, L and Ma, J and He, N and Liu, H and Han, R and Li, H and Wu, Z and Chen, J}, title = {Identification of Austwickia chelonae as cause of cutaneous granuloma in endangered crocodile lizards using metataxonomics.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6574}, doi = {10.7717/peerj.6574}, pmid = {30886772}, issn = {2167-8359}, abstract = {The crocodile lizard (Shinisaurus crocodilurus Ahl, 1930) is an endangered reptile species, and in recent years many have died from diseases, especially the rescued and breeding individuals. However, pathogens underlying these diseases are unclear. In this study, we report our effort in rapidly identifying and isolating the pathogen that causes high mortality in crocodile lizards from Guangdong Luokeng Shinisaurus crocodilurus National Nature Reserve. The typical symptom is cutaneous granuloma in the infected crocodile lizards. Metagenomic next-generation sequencing (mNGS) is a comprehensive approach for sequence-based identification of pathogenic microbes. In this study, 16S rDNA based mNGS was used for rapid identification of pathogens, and microscopy and microbe isolation were used to confirm the results. Austwickia chelonae was identified to be the dominant pathogen in the granuloma using 16S rDNA based mNGS. Chinese skinks were used as an animal model to verify the pathogenicity of A. chelonae to fulfill Koch's postulates. As expected, subcutaneous inoculation of A. chelonae induced granulomas in the healthy Chinese skinks and the A. chelonae was re-isolated from the induced granulomas. Therefore, A. chelonae was the primary pathogen that caused this high mortality disease, cutaneous granuloma, in crocodile lizards from Guangdong Luokeng Shinisaurus crocodilurus National Nature Reserve. Antibiotics analysis demonstrated that A. chelonae was sensitive to cephalothin, minocycline and ampicillin, but not to kanamycin, gentamicin, streptomycin and clarithromycin, suggesting a possible treatment for the infected crocodile lizards. However, surgical resection of the nodules as early as possible was recommended. This study is the first report of pathogenic analysis in crocodile lizards and provides a reference for disease control and conservations of the endangered crocodile lizards and other reptiles. In addition, this study indicated that mNGS of lesions could be used to detect the pathogens in animals with benefits in speed and convenient.}, }
@article {pmid30886359, year = {2019}, author = {Lee, KS and Palatinszky, M and Pereira, FC and Nguyen, J and Fernandez, VI and Mueller, AJ and Menolascina, F and Daims, H and Berry, D and Wagner, M and Stocker, R}, title = {An automated Raman-based platform for the sorting of live cells by functional properties.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41564-019-0394-9}, pmid = {30886359}, issn = {2058-5276}, abstract = {Stable-isotope probing is widely used to study the function of microbial taxa in their natural environment, but sorting of isotopically labelled microbial cells from complex samples for subsequent genomic analysis or cultivation is still in its early infancy. Here, we introduce an optofluidic platform for automated sorting of stable-isotope-probing-labelled microbial cells, combining microfluidics, optical tweezing and Raman microspectroscopy, which yields live cells suitable for subsequent single-cell genomics, mini-metagenomics or cultivation. We describe the design and optimization of this Raman-activated cell-sorting approach, illustrate its operation with four model bacteria (two intestinal, one soil and one marine) and demonstrate its high sorting accuracy (98.3 ± 1.7%), throughput (200-500 cells h-1; 3.3-8.3 cells min-1) and compatibility with cultivation. Application of this sorting approach for the metagenomic characterization of bacteria involved in mucin degradation in the mouse colon revealed a diverse consortium of bacteria, including several members of the underexplored family Muribaculaceae, highlighting both the complexity of this niche and the potential of Raman-activated cell sorting for identifying key players in targeted processes.}, }
@article {pmid30885807, year = {2019}, author = {Murray, AK and Zhang, L and Snape, J and Gaze, WH}, title = {Comparing the selective and co-selective effects of different antimicrobials in bacterial communities.}, journal = {International journal of antimicrobial agents}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ijantimicag.2019.03.001}, pmid = {30885807}, issn = {1872-7913}, abstract = {Bacterial communities are exposed to a cocktail of antimicrobial agents, including antibiotics, heavy metals and biocidal antimicrobials such as quaternary ammonium compounds (QACs). The extent to which these compounds may select or co-select for antimicrobial resistance (AMR) is not fully understood. In this study, human-associated, wastewater-derived bacterial communities were exposed to either benzalkonium chloride (BAC), ciprofloxacin or trimethoprim at sub-point-of-use concentrations for one week to determine selective and co-selective potential. Metagenome analyses were performed to determine effects on bacterial community structure and prevalence of antibiotic resistance genes (ARGs) and metal or biocide resistance genes (MBRGS). Ciprofloxacin had the greatest co-selective potential, significantly enriching for resistance mechanisms to multiple antibiotic classes. Conversely, BAC exposure significantly reduced relative abundance of ARGs and MBRGS, including the well characterised qac efflux genes. However, BAC exposure significantly impacted bacterial community structure. Therefore BAC, and potentially other QACs, did not play as significant a role in co-selection for AMR as antibiotics such as ciprofloxacin at sub-point-of-use concentrations in this study. This approach can be used to identify priority compounds for further study, to better understand evolution of AMR in bacterial communities exposed to sub-point-of-use concentrations of antimicrobials.}, }
@article {pmid30885780, year = {2019}, author = {Zuo, X and Deguchi, Y and Xu, W and Liu, Y and Li, HS and Wei, D and Tian, R and Chen, W and Xu, M and Yang, Y and Gao, S and Jaoude, JC and Liu, F and Chrieki, SP and Moussalli, MJ and Gagea, M and Sebastian, MM and Zheng, X and Tan, D and Broaddus, R and Wang, J and Ajami, NJ and Swennes, AG and Watowich, SS and Shureiqi, I}, title = {PPARD and Interferon gamma Promote Transformation of Gastric Progenitor Cells and Tumorigenesis in Mice.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2019.03.018}, pmid = {30885780}, issn = {1528-0012}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; R01 CA142969/CA/NCI NIH HHS/United States ; R01 CA195686/CA/NCI NIH HHS/United States ; R01 CA206539/CA/NCI NIH HHS/United States ; }, abstract = {BACKGROUND &amp; AIMS: The peroxisome proliferator activated receptor delta (PPARD) regulates cell metabolism, proliferation, and inflammation and has been associated with gastric and other cancers. Villin-positive epithelial cells are a small population of quiescent gastric progenitor cells. We expressed PPARD from a villin promoter to investigate the role of these cells and PPARD in development of gastric cancer.<br><br>METHODS: We analyzed gastric tissues from mice that express the Ppard (PPARD1 and PPARD2 mice) from a villin promoter, and mice that did not carry this transgene (controls), by histology and immunohistochemistry. We performed cell lineage tracing experiments and analyzed the microbiomes, chemokine and cytokine production, and immune cells and transcriptomes of stomachs of these mice. We also performed immunohistochemical analysis of PPARD levels in in 2 sets of human gastric tissue microarrays.<br><br>RESULTS: Thirty-eight percent of PPARD mice developed spontaneous, invasive gastric adenocarcinomas, with severe chronic inflammation. Levels of PPARD were increased in human gastric cancer tissues, compared with non-tumor tissues, and associated with gastric cancer stage and grade. We found an inverse correlation between level of PPARD in tumor tissue and patients survival time. Gastric microbiomes from PPARD and control mice did not differ significantly. Lineage-tracing experiments identified villin-expressing gastric progenitor cells (VGPCs) as the origin of gastric tumors in PPARD mice. In these mice, PPARD upregulated CCL20 and CXCL1, which increased infiltration of the gastric mucosa by immune cells. Immune cell production of inflammatory cytokines promoted chronic gastric inflammation and expansion and transformation of VGPCs, leading to tumorigenesis. We identified a positive-feedback loop between PPARD and interferon gamma signaling that sustained gastric inflammation to induce VGPC transformation and gastric carcinogenesis.<br><br>CONCLUSIONS: We found PPARD overexpression in VPGCs to result in inflammation, dysplasia, and tumor formation. PPARD and VGPCs might be therapeutic targets for stomach cancer.}, }
@article {pmid30885720, year = {2019}, author = {LaPierre, N and Ju, CJ and Zhou, G and Wang, W}, title = {MetaPheno: A critical evaluation of deep learning and machine learning in metagenome-based disease prediction.}, journal = {Methods (San Diego, Calif.)}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ymeth.2019.03.003}, pmid = {30885720}, issn = {1095-9130}, support = {R01 GM115833/GM/NIGMS NIH HHS/United States ; }, abstract = {The human microbiome plays a number of critical roles, impacting almost every aspect of human health and well-being. Conditions in the microbiome have been linked to a number of significant diseases. Additionally, revolutions in sequencing technology have led to a rapid increase in publicly-available sequencing data. Consequently, there have been growing efforts to predict disease status from metagenomic sequencing data, with a proliferation of new approaches in the last few years. Some of these efforts have explored utilizing a powerful form of machine learning called deep learning, which has been applied successfully in several biological domains. Here, we review some of these methods and the algorithms that they are based on, with a particular focus on deep learning methods. We also perform a deeper analysis of Type 2 Diabetes and obesity datasets that have eluded improved results, using a variety of machine learning and feature extraction methods. We conclude by offering perspectives on study design considerations that may impact results and future directions the field can take to improve results and offer more valuable conclusions. The scripts and extracted features for the analyses conducted in this paper are available via GitHub:https://github.com/nlapier2/metapheno.}, }
@article {pmid30885689, year = {2019}, author = {Hildonen, M and Kodama, M and Puetz, LC and Gilbert, MTP and Limborg, MT}, title = {A comparison of storage methods for gut microbiome studies in teleosts: Insights from rainbow trout (Oncorhynchus mykiss).}, journal = {Journal of microbiological methods}, volume = {160}, number = {}, pages = {42-48}, doi = {10.1016/j.mimet.2019.03.010}, pmid = {30885689}, issn = {1872-8359}, abstract = {Immediate freezing is perhaps the most preferred method used for preserving gut microbial samples, but research on sample preservation has been principally based around samples from mammalian species, and little is known about the advantages or disadvantages relating to different storage methods for fish guts. Fish gut samples may pose additional challenges due to the different chemical and enzymatic profile, as well as the higher water content, which might affect the yield and purity of DNA recovered. To explore this, we took gut content and mucosal scrape samples from 10 rainbow trout (Oncorhynchus mykiss), and tested whether different preservation methods have any effect on the ability to construct high quality genomic libraries for shotgun and 16S rRNA gene sequencing. Four different storage methods were compared for the gut content samples (immediate freezing on dry ice, 96% ethanol, RNAlater and DNA/RNA shield), while two different methods were compared for mucosal scrape samples (96% ethanol and RNAlater). The samples were thereafter stored at -80 °C. Our findings concluded that 96% ethanol outperforms the other storage methods when considering DNA quantity, quality, cost and labor. Ethanol works consistently well for both gut content and mucosal scrape samples, and enables construction of DNA sequencing libraries of sufficient quantity and with a fragment length distribution suitable for shotgun sequencing. Two main conclusions from our study are i) sample storage optimisation is an important part of establishing a microbiome research program in a new species or sample type system, and ii) 96% ethanol is the preferred method for storing rainbow trout gut content and mucosal scrape samples.}, }
@article {pmid30885626, year = {2019}, author = {Oberbach, A and Friedrich, M and Lehmann, S and Schlichting, N and Kullnick, Y and Gräber, S and Buschmann, T and Hagl, C and Bagaev, E and ,  and ,  and , }, title = {Bacterial infiltration in structural heart valve disease.}, journal = {The Journal of thoracic and cardiovascular surgery}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jtcvs.2019.02.019}, pmid = {30885626}, issn = {1097-685X}, abstract = {OBJECTIVES: The pathology of structural valvular heart disease (sVHD) ranges from basic diseases of rheumatologic origin to chronic degenerative remodeling processes after acute bacterial infections. Molecular genetic methods allow detection of the complete microbial spectrum in heart valve tissues independent of microbiological cultivation. In particular, whole-metagenome analysis is a sensitive and highly specific analytical method that allows a deeper insight into the pathogenicity of the diseases. In the present study we assessed the pathogen spectrum in heart valve tissue from 25 sVHD patients using molecular and microbiological methods.<br><br>METHODS: Twenty-five sVHD patients were selected randomly from an observational cohort study (March 2016 to January 2017). The explanted native heart valves were examined using microbiological methods and immunohistological structural analysis. In addition, the bacterial metagenome of the heart valve tissue was determined using next-generation sequencing.<br><br>RESULTS: The use of sonication as a pretreatment of valve tissue from 4 sVHD patients permitted successful detection of Clostridium difficile, Enterococcus faecalis, Staphylococcus saccharolyticus, and Staphylococcus haemolyticus using microbial cultivation. Histological staining revealed intramural localization. Metagenome analysis identified a higher rate of bacterial infiltration in 52% of cases. The pathogen spectrum included both gram-positive and gram-negative bacteria.<br><br>CONCLUSIONS: Microbiological and molecular biological studies are necessary to detect the spectrum of bacteria in a calcified heart valve. Metagenome analysis is a valid method to gain new insight into the polymicrobial pathophysiology of sVHD. Our results suggest that an undetected proportion of sVHD might be triggered by chronic inflammation or influenced by secondary bacterial infiltration.}, }
@article {pmid30885397, year = {2019}, author = {Ashokan, A and Papanicolas, LE and Leong, LEX and Theodossi, M and Daniel, S and Wesselingh, SL and Rogers, GB and Gordon, DL}, title = {Case report: Identification of intra-laboratory blood culture contamination with Staphylococcus aureus by whole genome sequencing.}, journal = {Diagnostic microbiology and infectious disease}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.diagmicrobio.2019.02.016}, pmid = {30885397}, issn = {1879-0070}, abstract = {Staphylococcus aureus in blood cultures is rarely considered a contaminant. We report a case of intra-laboratory contamination between blood culture bottles which was confirmed by whole genome sequencing, highlighting the importance of molecular analysis in the clinical laboratory setting.}, }
@article {pmid30885294, year = {2019}, author = {Prodan, A and Levin, E and Nieuwdorp, M}, title = {Does disease start in the mouth, the gut or both?.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, doi = {10.7554/eLife.45931}, pmid = {30885294}, issn = {2050-084X}, abstract = {Oral bacteria colonize the gut more frequently than previously thought.}, }
@article {pmid30885224, year = {2019}, author = {Liu, P and Qiu, Y and Xing, C and Zhou, JH and Yang, WH and Wang, Q and Li, JY and Han, X and Zhang, YZ and Ge, XY}, title = {Detection and genome characterization of two novel papillomaviruses and a novel polyomavirus in tree shrew (Tupaia belangeri chinensis) in China.}, journal = {Virology journal}, volume = {16}, number = {1}, pages = {35}, doi = {10.1186/s12985-019-1141-9}, pmid = {30885224}, issn = {1743-422X}, abstract = {BACKGROUND: Papillomaviruses (PVs) and polyomaviruses (PyVs) infect diverse vertebrates including human and cause a broad spectrum of outcomes from asymptomatic infection to severe disease. There has been no PV and only one PyV detected in tree shrews, though the genomic properties of tree shrews are highly similar to those of the primates.<br><br>METHODS: Swab and organ samples of tree shrews collected in the Yunnan Province of China, were tested by viral metagenomic analysis and random PCR to detect the presence of PVs and PyVs. By PCR amplification using specific primers, cloning, sequencing and assembling, genomes of two PVs and one PyV were identified in the samples.<br><br>RESULTS: Two novel PVs and a novel PyV, named tree shrew papillomavirus 1 and 2 (TbelPV1 and TbelPV2) and polyomavirus 1 (TbelPyV1) were characterized in the Chinese tree shrew (Tupaia belangeri chinensis). The genomes of TbelPV1, TbelPV2, and TbelPyV1 are 7410 bp, 7526 bp, and 4982 bp in size, respectively. The TbelPV1 genome contains 7 putative open-reading frames (ORFs) coding for viral proteins E1, E2, E4, E6, E7, L1, and L2; the TbelPV2 genome contains 6 ORFs coding for viral proteins E1, E2, E6, E7, L1, and L2; and the TbelPyV1 genome codes for the typical small and large T antigens of PyV, as well as the VP1, VP2, and VP3 capsid proteins. Genomic comparison and phylogenetic analysis indicated that TbelPV1 and TbelPV2 represented 2 novel PV genera of Papillomaviridae, and TbelPyV1 represented a new species of genus Alphapolyomavirus. Our epidemiologic study indicated that TbelPV1 and TbelPV2 were both detected in oral swabs, while TbelPyV1 was detected in oral swabs and spleens.<br><br>CONCLUSION: Two novel PVs (TbelPV1 and TbelPV2) and a novel PyV (TbelPyV) were discovered in tree shrews and their genomes were characterized. TbelPV1, TbelPV2, and TbelPyV1 have the highest similarity to Human papillomavirus type 63, Ursus maritimus papillomavirus 1, and Human polyomavirus 9, respectively. TbelPV1 and TbelPV2 only showed oral tropism, while TbelPyV1 showed oral and spleen tropism.}, }
@article {pmid30885206, year = {2019}, author = {Ziko, L and Saqr, AA and Ouf, A and Gimpel, M and Aziz, RK and Neubauer, P and Siam, R}, title = {Antibacterial and anticancer activities of orphan biosynthetic gene clusters from Atlantis II Red Sea brine pool.}, journal = {Microbial cell factories}, volume = {18}, number = {1}, pages = {56}, doi = {10.1186/s12934-019-1103-3}, pmid = {30885206}, issn = {1475-2859}, abstract = {BACKGROUND: Cancer and infectious diseases are problematic because of continuous emergence of drug resistance. One way to address this enormous global health threat is bioprospecting the unlikeliest environments, such as extreme marine niches, which have tremendous biodiversity that is barely explored. One such environment is the Red Sea brine pool, Atlantis II Deep (ATII). Here, we functionally screened a fosmid library of metagenomic DNA isolated from the ATII lower convective layer (LCL) for antibacterial and anticancer activities.<br><br>RESULTS: Selected clones, 14-7E and 10-2G, displayed antibacterial effects on the marine strain Bacillus sp. Cc6. Moreover, whole cell lysates from 14-7E and 10-2G exhibited decreased cell viability against MCF-7 (39.1% ± 6.6, 42% ± 8.1 at 50% v/v) and U2OS cells (35.7% ± 1.9, 79.9% ± 5.9 at 50% v/v), respectively. By sequencing the insert DNA from 14-7E and 10-2G, we identified two putative orphan biosynthetic gene clusters. Both clusters harbored putative ATP-binding cassette (ABC) transporter permeases and S-adenosylmethionine-related genes. Interestingly, the biosynthetic gene cluster identified on 14-7E is of archaeal origin and harbors a putative transcription factor. Several identified genes may be responsible for the observed antibacterial and anticancer activities. The 14-7E biosynthetic gene cluster may be encoding enzymes producing a specialized metabolite (effect of detected genes involved in C-C bond formation and glycosylation). The bioactivity may also be due to predicted subtilases encoded by this cluster. The 10-2G cluster harbored putative glycosyltransferase and non-ribosomal peptide synthase genes; thus the observed activity of this clone could be caused by a bioactive peptide.<br><br>CONCLUSIONS: The ATII LCL prokaryotic metagenome hosts putative orphan biosynthetic gene clusters that confer antibiotic and anticancer effects. Further biochemical studies should characterize the detected bioactive components, and the potential use of 14-7E metabolite for antibiosis and 10-2G metabolite as a selective anti-breast cancer drug.}, }
@article {pmid30884876, year = {2019}, author = {Pu, G and Zeng, D and Mo, L and Liao, J and Chen, X}, title = {Artificial Light at Night Alleviates the Negative Effect of Pb on Freshwater Ecosystems.}, journal = {International journal of molecular sciences}, volume = {20}, number = {6}, pages = {}, doi = {10.3390/ijms20061343}, pmid = {30884876}, issn = {1422-0067}, abstract = {Artificial light at night (ALAN) is an increasing phenomenon worldwide that can cause a series of biological and ecological effects, yet little is known about its potential interaction with other stressors in aquatic ecosystems. Here, we tested whether the impact of lead (Pb) on litter decomposition was altered by ALAN exposure using an indoor microcosm experiment. The results showed that ALAN exposure alone significantly increased leaf litter decomposition, decreased the lignin content of leaf litter, and altered fungal community composition and structure. The decomposition rate was 51% higher in Pb with ALAN exposure treatments than in Pb without ALAN treatments, resulting in increased microbial biomass, β-glucosidase (β-G) activity, and the enhanced correlation between β-G and litter decomposition rate. These results indicate that the negative effect of Pb on leaf litter decomposition in aquatic ecosystems may be alleviated by ALAN. In addition, ALAN exposure also alters the correlation among fungi associated with leaf litter decomposition. In summary, this study expands our understanding of Pb toxicity on litter decomposition in freshwater ecosystems and highlights the importance of considering ALAN when assessing environmental metal pollutions.}, }
@article {pmid30882592, year = {2019}, author = {Ikawa, T and Watanabe, Y and Okuzaki, D and Goto, N and Okamura, N and Yamanishi, K and Higashino, T and Yamanishi, H and Okamura, H and Higashino, H}, title = {A new approach to identifying hypertension-associated genes in the mesenteric artery of spontaneously hypertensive rats and stroke-prone spontaneously hypertensive rats.}, journal = {Journal of hypertension}, volume = {}, number = {}, pages = {}, doi = {10.1097/HJH.0000000000002083}, pmid = {30882592}, issn = {1473-5598}, abstract = {OBJECTIVE: Hypertension is one of the most prevalent diseases in humans who live a modern lifestyle. Alongside more effective care, clarification of the genetic background of hypertension is urgently required. Gene expression in mesenteric resistance arteries of spontaneously hypertensive rats (SHR), stroke-prone SHR (SHRSP) and two types of renal hypertensive Wistar Kyoto rats (WKY), two kidneys and one clip renal hypertensive rat (2K1C) and one kidney and one clip renal hypertensive rat (1K1C), was compared using DNA microarrays.<br><br>METHODS: We used a simultaneous equation and comparative selection method to identify genes associated with hypertension using the Reactome analysis tool and GenBank database.<br><br>RESULTS: The expression of 298 genes was altered between SHR and WKY (44 upregulated and 254 downregulated), while the expression of 290 genes was altered between SHRSP and WKY (83 upregulated and 207 downregulated). For SHRSP versus SHR, the expression of 60 genes was altered (36 upregulated and 24 downregulated). Several genes expressed in SHR and SHRSP were also expressed in the renovascular hypertensive 2K1C and 1K1C rats, indicative of the existence of hyper-renin and/or hypervolemic pathophysiological changes in SHR and SHRSP.<br><br>CONCLUSION: The overexpression of Kcnq1, Crlf1, Alb and Xirp1 and the inhibition of Galr2, Kcnh1, Ache, Chrm2 and Slc5a7 expression may indicate that a relationship exists between these genes and the cause and/or worsening of hypertension in SHR and SHRSP.This is an open access article distributed under the terms of the Creative Commons Attribution-Non Commercial-No Derivatives License 4.0 (CCBY-NC-ND), where it is permissible to download and share the work provided it is properly cited. The work cannot be changed in any way or used commercially without permission from the journal. http://creativecommons.org/licenses/by-nc-nd/4.0.}, }
@article {pmid30881924, year = {2019}, author = {Tribble, GD and Angelov, N and Weltman, R and Wang, BY and Eswaran, SV and Gay, IC and Parthasarathy, K and Dao, DV and Richardson, KN and Ismail, NM and Sharina, IG and Hyde, ER and Ajami, NJ and Petrosino, JF and Bryan, NS}, title = {Frequency of Tongue Cleaning Impacts the Human Tongue Microbiome Composition and Enterosalivary Circulation of Nitrate.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {39}, doi = {10.3389/fcimb.2019.00039}, pmid = {30881924}, issn = {2235-2988}, abstract = {The oral microbiome has the potential to provide an important symbiotic function in human blood pressure physiology by contributing to the generation of nitric oxide (NO), an essential cardiovascular signaling molecule. NO is produced by the human body via conversion of arginine to NO by endogenous nitric oxide synthase (eNOS) but eNOS activity varies by subject. Oral microbial communities are proposed to supplement host NO production by reducing dietary nitrate to nitrite via bacterial nitrate reductases. Unreduced dietary nitrate is delivered to the oral cavity in saliva, a physiological process termed the enterosalivary circulation of nitrate. Previous studies demonstrated that disruption of enterosalivary circulation via use of oral antiseptics resulted in increases in systolic blood pressure. These previous studies did not include detailed information on the oral health of enrolled subjects. Using 16S rRNA gene sequencing and analysis, we determined whether introduction of chlorhexidine antiseptic mouthwash for 1 week was associated with changes in tongue bacterial communities and resting systolic blood pressure in healthy normotensive individuals with documented oral hygiene behaviors and free of oral disease. Tongue cleaning frequency was a predictor of chlorhexidine-induced changes in systolic blood pressure and tongue microbiome composition. Twice-daily chlorhexidine usage was associated with a significant increase in systolic blood pressure after 1 week of use and recovery from use resulted in an enrichment in nitrate-reducing bacteria on the tongue. Individuals with relatively high levels of bacterial nitrite reductases had lower resting systolic blood pressure. These results further support the concept of a symbiotic oral microbiome contributing to human health via the enterosalivary nitrate-nitrite-NO pathway. These data suggest that management of the tongue microbiome by regular cleaning together with adequate dietary intake of nitrate provide an opportunity for the improvement of resting systolic blood pressure.}, }
@article {pmid30878035, year = {2019}, author = {Rowe, WP and Carrieri, AP and Alcon-Giner, C and Caim, S and Shaw, A and Sim, K and Kroll, JS and Hall, LJ and Pyzer-Knapp, EO and Winn, MD}, title = {Streaming histogram sketching for rapid microbiome analytics.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {40}, doi = {10.1186/s40168-019-0653-2}, pmid = {30878035}, issn = {2049-2618}, support = {BB/M011216/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; //Wellcome Trust/United Kingdom ; 100/974/C/13/Z//Wellcome Trust/United Kingdom ; BB/R012490/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004529/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {BACKGROUND: The growth in publically available microbiome data in recent years has yielded an invaluable resource for genomic research, allowing for the design of new studies, augmentation of novel datasets and reanalysis of published works. This vast amount of microbiome data, as well as the widespread proliferation of microbiome research and the looming era of clinical metagenomics, means there is an urgent need to develop analytics that can process huge amounts of data in a short amount of time. To address this need, we propose a new method for tyrhe compact representation of microbiome sequencing data using similarity-preserving sketches of streaming k-mer spectra. These sketches allow for dissimilarity estimation, rapid microbiome catalogue searching and classification of microbiome samples in near real time.<br><br>RESULTS: We apply streaming histogram sketching to microbiome samples as a form of dimensionality reduction, creating a compressed 'histosketch' that can efficiently represent microbiome k-mer spectra. Using public microbiome datasets, we show that histosketches can be clustered by sample type using the pairwise Jaccard similarity estimation, consequently allowing for rapid microbiome similarity searches via a locality sensitive hashing indexing scheme. Furthermore, we use a 'real life' example to show that histosketches can train machine learning classifiers to accurately label microbiome samples. Specifically, using a collection of 108 novel microbiome samples from a cohort of premature neonates, we trained and tested a random forest classifier that could accurately predict whether the neonate had received antibiotic treatment (97% accuracy, 96% precision) and could subsequently be used to classify microbiome data streams in less than 3 s.<br><br>CONCLUSIONS: Our method offers a new approach to rapidly process microbiome data streams, allowing samples to be rapidly clustered, indexed and classified. We also provide our implementation, Histosketching Using Little K-mers (HULK), which can histosketch a typical 2 GB microbiome in 50 s on a standard laptop using four cores, with the sketch occupying 3000 bytes of disk space. (https://github.com/will-rowe/hulk).}, }
@article {pmid30877015, year = {2019}, author = {Gómez-Acata, ES and Centeno, CM and Falcón, LI}, title = {Methods for extracting 'omes from microbialites.}, journal = {Journal of microbiological methods}, volume = {160}, number = {}, pages = {1-10}, doi = {10.1016/j.mimet.2019.02.014}, pmid = {30877015}, issn = {1872-8359}, abstract = {Microbialites are organo-sedimentary structures formed by complex microbial communities that interact with abiotic factors to form carbonate rich fabrics. Extraction of DNA or total RNA from microbialites can be difficult because of the high carbonate mineral concentration and exopolymeric substances. The methods employed until now include substances such as cetyltrimethylammonium bromide, sodium dodecyl sulfate, xanthogenate, lysozyme and proteinase K, as well as mechanical disruption. Additionally, several commercial kits have been used to improve DNA and total RNA extraction. This minireview presents different methods applied for DNA and RNA extraction from microbialites and discusses their advantages and disadvantages. Moreover, extraction of all 'omes (DNA, RNA, Protein, Lipids, polar metabolites) using multiomic extraction methods (MPlex), as well as the state of art for extraction of viruses from microbialites, are also discussed.}, }
@article {pmid30875864, year = {2019}, author = {Uritskiy, G and DiRuggiero, J}, title = {Applying Genome-Resolved Metagenomics to Deconvolute the Halophilic Microbiome.}, journal = {Genes}, volume = {10}, number = {3}, pages = {}, doi = {10.3390/genes10030220}, pmid = {30875864}, issn = {2073-4425}, support = {NNX15AP18G//National Aeronautics and Space Administration/ ; DEB1556574//National Science Foundation/ ; }, abstract = {In the past decades, the study of microbial life through shotgun metagenomic sequencing has rapidly expanded our understanding of environmental, synthetic, and clinical microbial communities. Here, we review how shotgun metagenomics has affected the field of halophilic microbial ecology, including functional potential reconstruction, virus⁻host interactions, pathway selection, strain dispersal, and novel genome discoveries. However, there still remain pitfalls and limitations from conventional metagenomic analysis being applied to halophilic microbial communities. Deconvolution of halophilic metagenomes has been difficult due to the high G + C content of these microbiomes and their high intraspecific diversity, which has made both metagenomic assembly and binning a challenge. Halophiles are also underrepresented in public genome databases, which in turn slows progress. With this in mind, this review proposes experimental and analytical strategies to overcome the challenges specific to the halophilic microbiome, from experimental designs to data acquisition and the computational analysis of metagenomic sequences. Finally, we speculate about the potential applications of other next-generation sequencing technologies in halophilic communities. RNA sequencing, long-read technologies, and chromosome conformation assays, not initially intended for microbiomes, are becoming available in the study of microbial communities. Together with recent analytical advancements, these new methods and technologies have the potential to rapidly advance the field of halophile research.}, }
@article {pmid30875404, year = {2019}, author = {Kumar, S and Suyal, DC and Yadav, A and Shouche, Y and Goel, R}, title = {Microbial diversity and soil physiochemical characteristic of higher altitude.}, journal = {PloS one}, volume = {14}, number = {3}, pages = {e0213844}, doi = {10.1371/journal.pone.0213844}, pmid = {30875404}, issn = {1932-6203}, abstract = {Altitude is the major factor affecting both biodiversity and soil physiochemical properties of soil ecosystems. In order to understand the effect of altitude on soil physiochemical properties and bacterial diversity across the Himalayan cold desert, high altitude Gangotri soil ecosystem was studied and compared with the moderate altitude Kandakhal soil. Soil physiochemical analysis showed that altitude was positively correlated with soil pH, organic matter and total nitrogen content. However soil mineral nutrients and soil phosphorus were negatively correlated to the altitude. RT-PCR based analysis revealed the decreased bacterial and diazotrophic abundance at high altitude. Metagenomic study showed that Proteobacteria, Acidobacteria and Actinobacteria were dominant bacteria phyla at high altitude soil while Bacteroidetes and Fermicutes were found dominant at low altitude. High ratio of Gram-negative to Gram positive bacteria at Gangotri suggests the selective proliferation of Gram negative bacteria at high altitude with decrease in Gram positive bacteria. Moreover, Alphaproteobacteria was found more abundant at high altitude while the opposite was true for Betaproteobacteria. Abundance of Cytophaga, Flavobacterium and Bacteroides (CFB) were also found comparatively high at high altitude. Presence of many taxonomically unclassified sequences in Gangotri soil indicates the presence of novel bacterial diversity at high altitude. Further, isolation of bacteria through indigenously designed diffusion chamber revealed the existence of bacteria which has been documented in unculturable study of WIH (Western Indian Himalaya) but never been cultivated from WIH. Nevertheless, diverse functional free-living psychrotrophic diazotrophs were isolated only from the high altitude Gangotri soil. Molecular characterization revealed them as Arthrobacter humicola, Brevibacillus invocatus, Pseudomonas mandelii and Pseudomonas helmanticensis. Thus, this study documented the bacterial and psychrophilic diazotrophic diversity at high altitude and is an effort for exploration of low temperature bacteria in agricultural productivity with the target for sustainable hill agriculture.}, }
@article {pmid30875247, year = {2019}, author = {Taylor, SL and Leong, LEX and Mobegi, FM and Choo, JM and Wesselingh, S and Yang, IA and Upham, JW and Reynolds, PN and Hodge, S and James, AL and Jenkins, C and Peters, MJ and Baraket, M and Marks, GB and Gibson, PG and Rogers, GB and Simpson, JL}, title = {Long-Term Azithromycin Reduces Haemophilus influenzae and Increases Antibiotic Resistance in Severe Asthma.}, journal = {American journal of respiratory and critical care medicine}, volume = {}, number = {}, pages = {}, doi = {10.1164/rccm.201809-1739OC}, pmid = {30875247}, issn = {1535-4970}, abstract = {Rationale The macrolide antibiotic, azithromycin, reduces exacerbations in adults with persistent symptomatic asthma. However, owing to the pleotropic properties of macrolides, unintended bacteriological consequences such as augmented pathogen colonization or dissemination of antibiotic-resistant organisms can occur, calling into question the long-term safety of azithromycin maintenance therapy. Objectives To assess the effects of azithromycin on the airway microbiota, pathogen abundance, and carriage of antibiotic-resistance genes. Methods 16S rRNA sequencing and quantitative PCR (qPCR) were performed to assess the effect of azithromycin on sputum microbiology from participants of the AMAZES trial: a 48-week, double-blind, placebo-controlled trial of thrice-weekly 500mg oral azithromycin in adults with persistent uncontrolled asthma. Pooled-template shotgun metagenomic sequencing, qPCR, and isolate whole genome sequencing were performed to assess antibiotic resistance. Measurements and Main Results Paired sputum was available from 61 patients (n=34 placebo, n=27 azithromycin). Azithromycin did not affect bacterial load (p=0.37) but did significantly decrease Faith's bacterial diversity (p=0.026) and Haemophilus influenzae load (p<0.001). Azithromycin did not significantly affect levels of Streptococcus pneumoniae, Staphylococcus aureus, Pseudomonas aeruginosa or Moraxella catarrhalis. Of the 89 antibiotic resistance genes detected, macrolide resistance genes (erm(B), erm(F), msr(E), mef(A), and mel) and tetracycline resistance genes (tet(M) and tet(W)) were increased significantly. Conclusions In patients with persistent uncontrolled asthma, addition of azithromycin reduced airway H. influenzae load, with no changes to total or pathogenic bacterial loads. Macrolide resistance increased, reflecting previous studies. These results highlight the need for studies assessing the efficacy of non-antibiotic macrolides as long-term therapy for patients with persistent uncontrolled asthma.}, }
@article {pmid30875042, year = {2019}, author = {Epp, LS and Zimmermann, HH and Stoof-Leichsenring, KR}, title = {Sampling and Extraction of Ancient DNA from Sediments.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {31-44}, doi = {10.1007/978-1-4939-9176-1_5}, pmid = {30875042}, issn = {1940-6029}, abstract = {Environmental DNA preserved in sediments is rapidly gaining importance as a tool in paleoecology. Sampling procedures for sedimentary ancient DNA (sedaDNA) have to be well planned to ensure clean subsampling of the inside of sediment cores and avoid introducing contamination. Additionally, ancient DNA extraction protocols may need to be optimized for the recovery of DNA from sediments, which may contain inhibitors. Here we describe procedures for subsampling both nonfrozen and frozen sediment cores, and we describe an efficient method for ancient DNA extraction from such samples.}, }
@article {pmid30875036, year = {2019}, author = {Al-Masaudi, S and El Kaoutari, A and Drula, E and Redwan, EM and Lombard, V and Henrissat, B}, title = {A metagenomics investigation of carbohydrate-active enzymes along the goat and camel intestinal tract.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10123-019-00068-2}, pmid = {30875036}, issn = {1618-1905}, support = {67/130/35-HiCi//Deanship of Scientific Research, King Abdulaziz University, Jeddah/ ; }, abstract = {Studies of the digestive microbiota of ruminant animals most often focus on the bacterial diversity in the rumen or the feces of the animals, but little is known about the diversity and functions of their distal intestine. Here, the bacterial microbiota of the distal intestinal tract of two goats and two camels was investigated by metagenomics techniques. The bacterial taxonomic diversity and carbohydrate-active enzyme profile were estimated for samples taken from the small intestine, the large intestine, and the rectum of each animal. The bacterial diversity and abundance in the small intestine were lower than in the rectal and large intestinal samples. Analysis of the carbohydrate-active enzyme profiles at each site revealed a comparatively low abundance of enzymes targeting xylan and cellulose in all animals examined, similar to what has been reported earlier for sheep and therefore suggesting that plant cell wall digestion probably takes place elsewhere, such as in the rumen.}, }
@article {pmid30873724, year = {2019}, author = {Zhang, M and Hill, JE and Fernando, C and Alexander, TW and Timsit, E and van der Meer, F and Huang, Y}, title = {Respiratory viruses identified in western Canadian beef cattle by metagenomic sequencing and their association with bovine respiratory disease.}, journal = {Transboundary and emerging diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/tbed.13172}, pmid = {30873724}, issn = {1865-1682}, support = {//China Scholarship Council/ ; 20160092//Saskatchewan Cattleman Association/ ; //Alberta Livestock and Meat Agency Ltd., and Genome Alberta/ ; }, abstract = {Bovine respiratory disease (BRD) causes considerable economic losses in North America. The pathogenesis involves interactions between bacteria, viruses, environment and management factors. Primary viral infection can increase the risk of secondary fatal bacterial infection. The objective of this study was to use metagenomic sequencing to characterize the respiratory viromes of paired nasal swabs and tracheal washes from western Canadian feedlot cattle, with or without BRD. A total of 116 cattle (116 nasal swabs and 116 tracheal washes) were analysed. The presence of influenza D virus (IDV), bovine rhinitis A virus (BRAV), bovine rhinitis B virus (BRBV), bovine coronavirus (BCV) and bovine respiratory syncytial virus (BRSV) was associated with BRD. Agreement between identification of viruses in nasal swabs and tracheal washes was generally weak, indicating that sampling location may affect detection of infection. This study reported several viruses for the first time in Canada and provides a basis for further studies investigating candidate viruses important to the prevention of BRD.}, }
@article {pmid30872807, year = {2019}, author = {Thomas, F and Corre, E and Cébron, A}, title = {Stable isotope probing and metagenomics highlight the effect of plants on uncultured phenanthrene-degrading bacterial consortium in polluted soil.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0394-z}, pmid = {30872807}, issn = {1751-7370}, support = {ANR-13-JSV7-0007_01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-13-JSV7-0007_01//Agence Nationale de la Recherche (French National Research Agency)/ ; }, abstract = {Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous soil pollutants. The discovery that plants can stimulate microbial degradation of PAHs has promoted research on rhizoremediation strategies. We combined DNA-SIP with metagenomics to assess the influence of plants on the identity and metabolic functions of active PAH-degrading bacteria in contaminated soil, using phenanthrene (PHE) as a model hydrocarbon. 13C-PHE dissipation was 2.5-fold lower in ryegrass-planted conditions than in bare soil. Metabarcoding of 16S rDNA revealed significantly enriched OTUs in 13C-SIP incubations compared to 12C-controls, namely 130 OTUs from bare soil and 73 OTUs from planted soil. Active PHE-degraders were taxonomically diverse (Proteobacteria, Actinobacteria and Firmicutes), with Sphingomonas and Sphingobium dominating in bare and planted soil, respectively. Plant root exudates favored the development of PHE-degraders having specific functional traits at the genome level. Indeed, metagenomes of 13C-enriched DNA fractions contained more genes involved in aromatic compound metabolism in bare soil, whereas carbohydrate catabolism genes were more abundant in planted soil. Functional gene annotation allowed reconstruction of complete pathways with several routes for PHE catabolism. Sphingomonadales were the major taxa performing the first steps of PHE degradation in both conditions, suggesting their critical role to initiate in situ PAH remediation. Active PHE-degraders act in a consortium, whereby complete PHE mineralization is achieved through the combined activity of taxonomically diverse co-occurring bacteria performing successive metabolic steps. Our study reveals hitherto underestimated functional interactions for full microbial detoxification in contaminated soils.}, }
@article {pmid30872803, year = {2019}, author = {Fones, EM and Colman, DR and Kraus, EA and Nothaft, DB and Poudel, S and Rempfert, KR and Spear, JR and Templeton, AS and Boyd, ES}, title = {Physiological adaptations to serpentinization in the Samail Ophiolite, Oman.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0391-2}, pmid = {30872803}, issn = {1751-7370}, abstract = {Hydration of ultramafic rock during the geologic process of serpentinization can generate reduced substrates that microorganisms may use to fuel their carbon and energy metabolisms. However, serpentinizing environments also place multiple constraints on microbial life by generating highly reduced hyperalkaline waters that are limited in dissolved inorganic carbon. To better understand how microbial life persists under these conditions, we performed geochemical measurements on waters from a serpentinizing environment and subjected planktonic microbial cells to metagenomic and physiological analyses. Metabolic potential inferred from metagenomes correlated with fluid type, and genes involved in anaerobic metabolisms were enriched in hyperalkaline waters. The abundance of planktonic cells and their rates of utilization of select single-carbon compounds were lower in hyperalkaline waters than alkaline waters. However, the ratios of substrate assimilation to dissimilation were higher in hyperalkaline waters than alkaline waters, which may represent adaptation to minimize energetic and physiologic stress imposed by highly reducing, carbon-limited conditions. Consistent with this hypothesis, estimated genome sizes and average oxidation states of carbon in inferred proteomes were lower in hyperalkaline waters than in alkaline waters. These data suggest that microorganisms inhabiting serpentinized waters exhibit a unique suite of physiological adaptations that allow for their persistence under these polyextremophilic conditions.}, }
@article {pmid30871469, year = {2019}, author = {Perz, AI and Giles, CB and Brown, CA and Porter, H and Roopnarinesingh, X and Wren, JD}, title = {MNEMONIC: MetageNomic Experiment Mining to create an OTU Network of Inhabitant Correlations.}, journal = {BMC bioinformatics}, volume = {20}, number = {Suppl 2}, pages = {96}, doi = {10.1186/s12859-019-2623-x}, pmid = {30871469}, issn = {1471-2105}, support = {P20 GM103636/GM/NIGMS NIH HHS/United States ; P30 AG050911/AG/NIA NIH HHS/United States ; }, abstract = {BACKGROUND: The number of publicly available metagenomic experiments in various environments has been rapidly growing, empowering the potential to identify similar shifts in species abundance between different experiments. This could be a potentially powerful way to interpret new experiments, by identifying common themes and causes behind changes in species abundance.<br><br>RESULTS: We propose a novel framework for comparing microbial shifts between conditions. Using data from one of the largest human metagenome projects to date, the American Gut Project (AGP), we obtain differential abundance vectors for microbes using experimental condition information provided with the AGP metadata, such as patient age, dietary habits, or health status. We show it can be used to identify similar and opposing shifts in microbial species, and infer putative interactions between microbes. Our results show that groups of shifts with similar effects on microbiome can be identified and that similar dietary interventions display similar microbial abundance shifts.<br><br>CONCLUSIONS: Without comparison to prior data, it is difficult for experimentalists to know if their observed changes in species abundance have been observed by others, both in their conditions and in others they would never consider comparable. Yet, this can be a very important contextual factor in interpreting the significance of a shift. We've proposed and tested an algorithmic solution to this problem, which also allows for comparing the metagenomic signature shifts between conditions in the existing body of data.}, }
@article {pmid30871459, year = {2019}, author = {Thrash, A and Arick, M and Barbato, RA and Jones, RM and Douglas, TA and Esdale, J and Perkins, EJ and Garcia-Reyero, N}, title = {Keanu: a novel visualization tool to explore biodiversity in metagenomes.}, journal = {BMC bioinformatics}, volume = {20}, number = {Suppl 2}, pages = {103}, doi = {10.1186/s12859-019-2629-4}, pmid = {30871459}, issn = {1471-2105}, abstract = {BACKGROUND: One of the main challenges when analyzing complex metagenomics data is the fact that large amounts of information need to be presented in a comprehensive and easy-to-navigate way. In the process of analyzing FASTQ sequencing data, visualizing which organisms are present in the data can be useful, especially with metagenomics data or data suspected to be contaminated. Here, we describe the development and application of a command-line tool, Keanu, for visualizing and exploring sample content in metagenomics data. We developed Keanu as an interactive tool to make viewing complex data easier.<br><br>RESULTS: Keanu, a tool for exploring sequence content, helps a user to understand the presence and abundance of organisms in a sample by analyzing alignments against a database that contains taxonomy data and displaying them in an interactive web page. The content of a sample can be presented either as a collapsible tree, with node size indicating abundance, or as a bilevel partition graph, with arc size indicating abundance. Here, we illustrate how Keanu works by exploring shotgun metagenomics data from a sample collected from a bluff that contained paleosols and a krotovina in an alpine site in Ft. Greely, Alaska.<br><br>CONCLUSIONS: Keanu provides a simple means by which researchers can explore and visualize species present in sequence data generated from complex communities and environments. Keanu is written in Python and is freely available at https://github.com/IGBB/keanu .}, }
@article {pmid30871224, year = {2019}, author = {Gurwara, S and Ajami, NJ and Jang, A and Hessel, FC and Chen, L and Plew, S and Wang, Z and Graham, DY and Hair, C and White, DL and Kramer, J and Kourkoumpetis, T and Hoffman, K and Cole, R and Hou, J and Husain, N and Jarbrink-Sehgal, M and Hernaez, R and Kanwal, F and Ketwaroo, G and Shah, R and Velez, M and Natarajan, Y and El-Serag, HB and Petrosino, JF and Jiao, L}, title = {Dietary Nutrients Involved in One-Carbon Metabolism and Colonic Mucosa-Associated Gut Microbiome in Individuals with an Endoscopically Normal Colon.}, journal = {Nutrients}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/nu11030613}, pmid = {30871224}, issn = {2072-6643}, support = {RP#140767//Cancer Prevention and Research Institute of Texas/ ; 1000//Gillson Longenbaugh Foundation/ ; 0000//Golfers Against Cancer/ ; }, abstract = {One carbon (1C) metabolism nutrients influence epigenetic regulation and they are supplied by diet and synthesized by gut microbiota. We examined the association between dietary consumption of methyl donors (methionine, betaine and choline) and B vitamins (folate, B2, B6, and B12) and the community composition and structure of the colonic mucosa-associated gut microbiota determined by 16S rRNA gene sequencing in 97 colonic biopsies of 35 men. We used the food frequency questionnaire to assess daily consumption of nutrients, and the UPARSE and SILVA databases for operational taxonomic unit classification. The difference in bacterial diversity and taxonomic relative abundance were compared between low versus high consumption of these nutrients. False discover rate (FDR) adjusted p value < 0.05 indicated statistical significance. The bacterial richness and composition differed significantly by the consumption of folate and B vitamins (p < 0.001). Compared with higher consumption, a lower consumption of these nutrients was associated with a lower abundance of Akkermansia (folate), Roseburia (vitamin B2), and Faecalibacterium (vitamins B2, B6, and B12) but a higher abundance of Erysipelatoclostridium (vitamin B2) (FDR p values < 0.05). The community composition and structure of the colonic bacteria differed significantly by dietary consumption of folate and B vitamins.}, }
@article {pmid30871085, year = {2019}, author = {Lin, JH and Wu, ZY and Gong, L and Wong, CH and Chao, WC and Yen, CM and Wang, CP and Wei, CL and Huang, YT and Liu, PY}, title = {Complex Microbiome in Brain Abscess Revealed by Whole-Genome Culture-Independent and Culture-Based Sequencing.}, journal = {Journal of clinical medicine}, volume = {8}, number = {3}, pages = {}, doi = {10.3390/jcm8030351}, pmid = {30871085}, issn = {2077-0383}, support = {TCVGH-1083901B//Taichung Veterans General Hospital/ ; }, abstract = {Brain abscess is a severe infectious disease with high mortality and mobility. Although culture-based techniques have been widely used for the investigation of microbial composition of brain abscess, these approaches are inherent biased. Recent studies using 16S ribosomal sequencing approaches revealed high complexity of the bacterial community involved in brain abscess but fail to detect fungal and viral composition. In the study, both culture-independent nanopore metagenomic sequencing and culture-based whole-genome sequencing using both the Illumina and the Nanopore platforms were conducted to investigate the microbial composition and genomic characterization in brain abscess. Culture-independent metagenomic sequencing revealed not only a larger taxonomic diversity of bacteria but also the presence of fungi and virus communities. The culture-based whole-genome sequencing identified a novel species in Prevotella and reconstructs a Streptococcus constellatus with a high GC-skew genome. Antibiotic-resistance genes CfxA and ErmF associated with resistance to penicillin and clindamycin were also identified in culture-based and culture-free sequencing. This study implies current understanding of brain abscess need to consider the broader diversity of microorganisms.}, }
@article {pmid30868805, year = {2019}, author = {Liu, ZX and Xu, J and Sun, W and Shi, YH and Chen, SL}, title = {[Application of DNA metabarcoding in species identification of Chinese herbal medicines].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {44}, number = {1}, pages = {1-8}, doi = {10.19540/j.cnki.cjcmm.2019.0001}, pmid = {30868805}, issn = {1001-5302}, abstract = {DNA metabarcoding,one rapid and robust method using specific standard DNA fragments,has been widely used for rapid species identification of a bulk sample through high-throughput sequencing technologies.While it has been widely used in the studies of metagenomics,animal and plant biodiversity,it has gradually come to be used as a profitable method in species identification of mixed Chinese herbal medicines.In this paper,we mainly summarize the current studies of the application of DNA metabarcoding in species identification of mixed Chinese herbal medicines.Moreover,high-throughput sequencing technologies adopted in those studies,such as Sanger,the next-generation,and third-generation sequencing technologies,are discussed.It is conducted to provide a theoretical guidance for the application of DNA metabarcoding in species identification of mixed Chinese herbal medicines and in more other biodiversity studies.}, }
@article {pmid30867546, year = {2019}, author = {Smith, AR and Kieft, B and Mueller, R and Fisk, MR and Mason, OU and Popa, R and Colwell, FS}, title = {Carbon fixation and energy metabolisms of a subseafloor olivine biofilm.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0385-0}, pmid = {30867546}, issn = {1751-7370}, abstract = {Earth's largest aquifer ecosystem resides in igneous oceanic crust, where chemosynthesis and water-rock reactions provide the carbon and energy that support an active deep biosphere. The Calvin Cycle is the predominant carbon fixation pathway in cool, oxic, crust; however, the energy and carbon metabolisms in the deep thermal basaltic aquifer are poorly understood. Anaerobic carbon fixation pathways such as the Wood-Ljungdahl pathway, which uses hydrogen (H2) and CO2, may be common in thermal aquifers since water-rock reactions can produce H2 in hydrothermal environments and bicarbonate is abundant in seawater. To test this, we reconstructed the metabolisms of eleven bacterial and archaeal metagenome-assembled genomes from an olivine biofilm obtained from a Juan de Fuca Ridge basaltic aquifer. We found that the dominant carbon fixation pathway was the Wood-Ljungdahl pathway, which was present in seven of the eight bacterial genomes. Anaerobic respiration appears to be driven by sulfate reduction, and one bacterial genome contained a complete nitrogen fixation pathway. This study reveals the potential pathways for carbon and energy flux in the deep anoxic thermal aquifer ecosystem, and suggests that ancient H2-based chemolithoautotrophy, which once dominated Earth's early biosphere, may thus remain one of the dominant metabolisms in the suboceanic aquifer today.}, }
@article {pmid30867542, year = {2019}, author = {Amato, P and Besaury, L and Joly, M and Penaud, B and Deguillaume, L and Delort, AM}, title = {Metatranscriptomic exploration of microbial functioning in clouds.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {4383}, doi = {10.1038/s41598-019-41032-4}, pmid = {30867542}, issn = {2045-2322}, support = {ANR-15-CE01-0002//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-DFG-14-CE35-005-02//Agence Nationale de la Recherche (French National Research Agency)/ ; }, abstract = {Clouds constitute the uppermost layer of the biosphere. They host diverse communities whose functioning remains obscure, although biological activity potentially participates to atmospheric chemical and physical processes. In order to gain information on the metabolic functioning of microbial communities in clouds, we conducted coordinated metagenomics/metatranscriptomics profiling of cloud water microbial communities. Samples were collected from a high altitude atmospheric station in France and examined for biological content after untargeted amplification of nucleic acids. Living microorganisms, essentially bacteria, maintained transcriptional and translational activities and expressed many known complementary physiological responses intended to fight oxidants, osmotic variations and cold. These included activities of oxidant detoxification and regulation, synthesis of osmoprotectants/cryoprotectants, modifications of membranes, iron uptake. Consistently these energy-demanding processes were fueled by central metabolic routes involved in oxidative stress response and redox homeostasis management, such as pentose phosphate and glyoxylate pathways. Elevated binding and transmembrane ion transports demonstrated important interactions between cells and their cloud droplet chemical environments. In addition, polysaccharides, potentially beneficial for survival like exopolysaccharides, biosurfactants and adhesins, were synthesized. Our results support a biological influence on cloud physical and chemical processes, acting notably on the oxidant capacity, iron speciation and availability, amino-acids distribution and carbon and nitrogen fates.}, }
@article {pmid30867497, year = {2019}, author = {Tu, P and Gao, B and Chi, L and Lai, Y and Bian, X and Ru, H and Lu, K}, title = {Subchronic low-dose 2,4-D exposure changed plasma acylcarnitine levels and induced gut microbiome perturbations in mice.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {4363}, doi = {10.1038/s41598-019-40776-3}, pmid = {30867497}, issn = {2045-2322}, support = {R01ES024950//U.S. Department of Health &amp; Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; R01ES024950//U.S. Department of Health &amp; Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; R01ES024950//U.S. Department of Health &amp; Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; R01ES024950//U.S. Department of Health &amp; Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; R01ES024950//U.S. Department of Health &amp; Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; R01ES024950//U.S. Department of Health &amp; Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; R01ES024950//U.S. Department of Health &amp; Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; }, abstract = {The gut microbiota critically confers various health benefits, whereas environmental chemicals can affect its constitution and functionality thereby increasing disease risk. In the present study, we aim to evaluate the toxic effects of a wildly-used herbicide 2,4-D (2,4-dichlorophenoxyacetic acid) on the gut microbiome and host using an occupationally relevant dose. A mouse model was used combined with metagenomic sequencing and metabolomic profiling to examine the alterations induced by subchronic low-dose 2,4-D exposure in fecal and plasma samples. The metagenomics results revealed a distinct gut microbial community with profound changes in diverse microbial pathways including urea degradation, amino acid and carbohydrate metabolism in 2,4-D-treated mice. Moreover, the metabolomics results revealed that the metabolic profiles in treatment group were differentiated from control group in both fecal and plasma samples. Toxic effects on the host of 2,4-D at an occupationally relevant dose were observed indicated by decreased acylcarnitine levels in plasma. These findings indicated that 2,4-D can cause toxicity and substantially impact the gut microbiome in mice at occupationally relevant doses, inferring that the relationship between environmental contaminants and microbiota is largely underestimated calling for more comprehensive consideration of the toxicity of occupational exposures.}, }
@article {pmid30867308, year = {2019}, author = {Chong, R and Shi, M and Grueber, CE and Holmes, EC and Hogg, CJ and Belov, K and Barrs, VR}, title = {Fecal viral diversity of captive and wild Tasmanian devils characterized using virion-enriched metagenomics and meta-transcriptomics.}, journal = {Journal of virology}, volume = {}, number = {}, pages = {}, doi = {10.1128/JVI.00205-19}, pmid = {30867308}, issn = {1098-5514}, abstract = {The Tasmanian devil is an endangered carnivorous marsupial threatened by devil facial tumour disease (DFTD). While research on DFTD has been extensive, little is known about viruses in devils, and whether any are of potential conservation relevance for this endangered species. Using both metagenomics based on virion enrichment and sequence-independent amplification (virion-enriched metagenomics) and meta-transcriptomics based on bulk RNA sequencing, we characterized and compared the fecal viromes of captive and wild devils. A total of 54 fecal samples collected from 2 captive and 4 wild populations were processed for virome characterization using both approaches. In total, 24 novel marsupial-related viruses, comprising a sapelovirus, astroviruses, rotaviruses, picobirnaviruses, parvoviruses, papillomaviruses, polyomaviruses and a gammaherpesvirus were identified, as well as known mammalian pathogens such as rabbit haemorrhagic disease virus 2. Captive devils showed significantly lower viral diversity than wild devils. Comparison of the two virus discovery approaches revealed substantial differences in the number and types of viruses detected, with meta-transcriptomics better suited for RNA viruses and virion-enriched metagenomics largely identifying more DNA viruses. Thus, the viral communities revealed by virion-enriched metagenomics and meta-transcriptomics were not interchangeable and neither approach was able to detect all viruses present. An integrated approach using both virion-enriched metagenomics and meta-transcriptomics constitutes a powerful tool for obtaining a complete overview of both the taxonomic and functional profiles of viral communities within a sample.Importance: The Tasmanian devil is an iconic Australian marsupial that has suffered an 80% population decline due to a contagious cancer, devil facial tumour disease, along with other threats. Until now, viral discovery in this species has been confined to one gammaherpesvirus (DaHV-2), for which captivity was identified as a significant risk factor. Our discovery of 24 novel marsupial-associated RNA and DNA viruses, and that viral diversity is lower in captive than wild devils, has greatly expanded our knowledge of gut-associated viruses in devils and provides important baseline information that will contribute to the conservation and captive management of this endangered species. Our results also revealed that a combination of virion-enriched metagenomics and meta-transcriptomics may be a more comprehensive approach for virome characterization than either method alone. Our results thus provide a springboard for continuous improvements in the way we study complex viral communities.}, }
@article {pmid30866812, year = {2019}, author = {Das, P and Babaei, P and Nielsen, J}, title = {Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {208}, doi = {10.1186/s12864-019-5591-7}, pmid = {30866812}, issn = {1471-2164}, support = {HEALTH-F4-2012-305312//METACARDIS/ ; }, abstract = {BACKGROUND: Human gut microbial communities have been known to produce vitamins, which are subsequently absorbed by the host in the large intestine. However, the relationship between species with vitamin pathway associated functional features or their gene abundance in different states of health and disease is lacking. Here, we analyzed shotgun fecal metagenomes of individuals from four different countries for genes that are involved in vitamin biosynthetic pathways and transport mechanisms and corresponding species' abundance.<br><br>RESULTS: We found that the prevalence of these genes were found to be distributed across the dominant phyla of gut species. The number of positive correlations were high between species harboring genes related to vitamin biosynthetic pathways and transporter mechanisms than that with either alone. Although, the range of total gene abundances remained constant across healthy populations at the global level, species composition and their presence for metabolic pathway related genes determine the abundance and functional genetic content of vitamin metabolism. Based on metatranscriptomics data, the equation between abundance of vitamin-biosynthetic enzymes and vitamin-dependent enzymes suggests that the production and utilization potential of these enzymes seems way more complex usage allocations than just mere direct linear associations.<br><br>CONCLUSIONS: Our findings provide a rationale to examine and disentangle the interrelationship between B-vitamin dosage (dietary or microbe-mediated) on gut microbial members and the host, in the gut microbiota of individuals with under- or overnutrition.}, }
@article {pmid30866778, year = {2019}, author = {Li, J and Cui, L and Deng, X and Yu, X and Zhang, Z and Yang, Z and Delwart, E and Zhang, W and Hua, X}, title = {Canine bufavirus in faeces and plasma of dogs with diarrhoea, China.}, journal = {Emerging microbes &amp; infections}, volume = {8}, number = {1}, pages = {245-247}, doi = {10.1080/22221751.2018.1563457}, pmid = {30866778}, issn = {2222-1751}, }
@article {pmid30866714, year = {2019}, author = {Park, H and Laffin, MR and Jovel, J and Millan, B and Hyun, JE and Hotte, N and Kao, D and Madsen, KL}, title = {The success of fecal microbial transplantation in Clostridium difficile infection correlates with bacteriophage relative abundance in the donor: a retrospective cohort study.}, journal = {Gut microbes}, volume = {}, number = {}, pages = {1-12}, doi = {10.1080/19490976.2019.1586037}, pmid = {30866714}, issn = {1949-0984}, abstract = {BACKGROUND: Fecal microbial transplantation (FMT) is used in the treatment of relapsing Clostridium difficile infection (rCDI). Failure rate for FMT is as high as 10% but the mechanisms contributing to a failed FMT are not understood. We utilized metagenomic data to identify the role of bacteria and bacteriophages on FMT success.<br><br>RESULTS: Subjects with rCDI (n = 19) received FMT from volunteer donors (n = 7) via colonoscopy. Twelve patients fully recovered after a single FMT, while seven patients required a subsequent FMT. DNA was extracted from patient and donor stool samples for shotgun metagenomic analysis. Metagenomics libraries were analyzed focusing on bacterial taxonomy and bacteriophage sequences. Gammaproteobacteria were dominant in rCDI patients prior to FMT largely due to elevated levels of Klebsiella and Escherichia. A successful FMT led to increased levels of Clostridia and Bacteroidia and a reduction in Gammaproteobacteria. In contrast, a failed FMT led to no significant changes in bacterial composition. Bacteriophages were classified during whole metagenomic analysis of each sample and were markedly different between rCDI patients, donors, and a healthy control cohort (n = 96). Bacteriophage sequence reads were increased in CDI patients compared with donors and healthy controls. Successful FMT donors had higher bacteriophage α-diversity and lower relative abundance compared to the donors of a failed initial FMT.<br><br>CONCLUSIONS: In this retrospective analysis, FMTs with increased bacteriophage α-diversity were more likely to successfully treat rCDI. In addition, the relative number of bacteriophage reads was lower in donations leading to a successful FMT. These results suggest that bacteriophage abundance may have some role in determining the relative success of FMT.}, }
@article {pmid30866521, year = {2019}, author = {François, S and Mutuel, D and Duncan, AB and Rodrigues, LR and Danzelle, C and Lefevre, S and Santos, I and Frayssinet, M and Fernandez, E and Filloux, D and Roumagnac, P and Froissart, R and Ogliastro, M}, title = {A New Prevalent Densovirus Discovered in Acari. Insight from Metagenomics in Viral Communities Associated with Two-Spotted Mite (Tetranychus urticae) Populations.}, journal = {Viruses}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/v11030233}, pmid = {30866521}, issn = {1999-4915}, abstract = {Viral metagenomics and high throughput sequence mining have revealed unexpected diversity, and the potential presence, of parvoviruses in animals from all phyla. Among arthropods, this diversity highlights the poor knowledge that we have regarding the evolutionary history of densoviruses. The aim of this study was to explore densovirus diversity in a small arthropod pest belonging to Acari, the two-spotted spider mite Tetranychus urticae, while using viral metagenomics based on virus-enrichment. Here, we present the viromes obtained from T. urticae laboratory populations made of contigs that are attributed to nine new potential viral species, including the complete sequence of a novel densovirus. The genome of this densovirus has an ambisens genomic organization and an unusually compact size with particularly small non-structural proteins and a predicted major capsid protein that lacks the typical PLA2 motif that is common to all ambidensoviruses described so far. In addition, we showed that this new densovirus had a wide prevalence across populations of mite species tested and a genomic diversity that likely correlates with the host phylogeny. In particular, we observed a low densovirus genomic diversity between the laboratory and natural populations, which suggests that virus within-species evolution is probably slower than initially thought. Lastly, we showed that this novel densovirus can be inoculated to the host plant following feeding by infected mites, and circulate through the plant vascular system. These findings offer new insights into densovirus prevalence, evolution, and ecology.}, }
@article {pmid30866512, year = {2019}, author = {Amor Stander, E and Williams, W and Rautenbach, F and Le Roes-Hill, M and Mgwatyu, Y and Marnewick, J and Hesse, U}, title = {Visualization of Aspalathin in Rooibos (Aspalathus linearis) Plant and Herbal Tea Extracts Using Thin-Layer Chromatography.}, journal = {Molecules (Basel, Switzerland)}, volume = {24}, number = {5}, pages = {}, doi = {10.3390/molecules24050938}, pmid = {30866512}, issn = {1420-3049}, support = {CSUR150714125961//National Research Foundation/ ; }, abstract = {Aspalathin, the main polyphenol of rooibos (Aspalathus linearis), is associated with diverse health promoting properties of the tea. During fermentation, aspalathin is oxidized and concentrations are significantly reduced. Standardized methods for quality control of rooibos products do not investigate aspalathin, since current techniques of aspalathin detection require expensive equipment and expertise. Here, we describe a simple and fast thin-layer chromatography (TLC) method that can reproducibly visualize aspalathin in rooibos herbal tea and plant extracts at a limit of detection (LOD) equal to 178.7 ng and a limit of quantification (LOQ) equal to 541.6 ng. Aspalathin is a rare compound, so far only found in A. linearis and its (rare) sister species A. pendula. Therefore, aspalathin could serve as a marker compound for authentication and quality control of rooibos products, and the described TLC method represents a cost-effective approach for high-throughput screening of plant and herbal tea extracts.}, }
@article {pmid30864784, year = {2019}, author = {Zhang, W and Gu, J and Li, Y and Lin, L and Wang, P and Wang, C and Qian, B and Wang, H and Niu, L and Wang, L and Zhang, H and Gao, Y and Zhu, M and Fang, S}, title = {New Insights into Sediment Transport in Interconnected River-Lake Systems Through Tracing Microorganisms.}, journal = {Environmental science &amp; technology}, volume = {53}, number = {8}, pages = {4099-4108}, doi = {10.1021/acs.est.8b07334}, pmid = {30864784}, issn = {1520-5851}, abstract = {A growing awareness of the wider environmental significance of diffuse sediment pollution in interconnected river-lake systems has generated the need for reliable provenance information. Owing to their insufficient ability to distinguish between multiple sources, common sediment source apportionment methods would rarely be a practical solution. On the basis of the inseparable relationships between sediment and adsorbed microorganisms, community-based microbial source tracking may be a novel method of identifying dominant sediment sources in the era of high-throughput sequencing. Dongting Lake was selected as a study area as it receives considerable sediment import from its inflowing rivers during the flood season. This study was conducted to characterize the bacterial community composition of sediment samples from the inflow-river estuaries and quantify their sediment microbe contributions to the central lake. Metagenomic analysis revealed that the community compositions of source sediment samples were significantly different, allowing specific sources to be identified with the machine learning classification program SourceTracker. A modified analysis using SourceTracker found that the major contributors to three major lake districts were the Songzi, Zishui, and Xinqiang Rivers. The impacts of hydrodynamic conditions on source apportionment were further verified and suggested the practicability of this method to offer a systematic and comprehensive understanding of sediment sources, pathways, and transport dynamics. Finally, a novel framework for sediment source-tracking was established to develop effective sediment management and control strategies in river-lake systems.}, }
@article {pmid30864326, year = {2019}, author = {Han, W and Ye, Y}, title = {A repository of microbial marker genes related to human health and diseases for host phenotype prediction using microbiome data.}, journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing}, volume = {24}, number = {}, pages = {236-247}, pmid = {30864326}, issn = {2335-6936}, support = {R01 AI108888/AI/NIAID NIH HHS/United States ; R01 AI143254/AI/NIAID NIH HHS/United States ; }, abstract = {The microbiome research is going through an evolutionary transition from focusing on the characterization of reference microbiomes associated with different environments/hosts to the translational applications, including using microbiome for disease diagnosis, improving the effcacy of cancer treatments, and prevention of diseases (e.g., using probiotics). Microbial markers have been identified from microbiome data derived from cohorts of patients with different diseases, treatment responsiveness, etc, and often predictors based on these markers were built for predicting host phenotype given a microbiome dataset (e.g., to predict if a person has type 2 diabetes given his or her microbiome data). Unfortunately, these microbial markers and predictors are often not published so are not reusable by others. In this paper, we report the curation of a repository of microbial marker genes and predictors built from these markers for microbiome-based prediction of host phenotype, and a computational pipeline called Mi2P (from Microbiome to Phenotype) for using the repository. As an initial effort, we focus on microbial marker genes related to two diseases, type 2 diabetes and liver cirrhosis, and immunotherapy efficacy for two types of cancer, non-small-cell lung cancer (NSCLC) and renal cell carcinoma (RCC). We characterized the marker genes from metagenomic data using our recently developed subtractive assembly approach. We showed that predictors built from these microbial marker genes can provide fast and reasonably accurate prediction of host phenotype given microbiome data. As understanding and making use of microbiome data (our second genome) is becoming vital as we move forward in this age of precision health and precision medicine, we believe that such a repository will be useful for enabling translational applications of microbiome data.}, }
@article {pmid30864226, year = {2019}, author = {Zhang, Y and Zhao, R and Shi, D and Sun, S and Ren, H and Zhao, H and Wu, W and Jin, L and Sheng, J and Shi, Y}, title = {Characterization of the circulating microbiome in acute-on-chronic liver failure associated with hepatitis B.}, journal = {Liver international : official journal of the International Association for the Study of the Liver}, volume = {}, number = {}, pages = {}, doi = {10.1111/liv.14097}, pmid = {30864226}, issn = {1478-3231}, support = {81670567//National Natural Science Foundation of China/ ; 81671949//National Natural Science Foundation of China/ ; 81870425//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Patients with hepatitis B-related acute-on-chronic liver failure (HB-ACLF) may have an increased circulating microbial burden. This study aimed to assess circulating microbial load and composition and to explore the association between the circulating microbiome and both systemic inflammation (SI) and clinical outcome in HB-ACLF.<br><br>METHODS: Plasma from 50 HB-ACLF patients, 23 healthy controls and 25 patients with compensated liver cirrhosis (C-LC) was analysed for chemokines/cytokines and bacterial DNA and further analysed by 16S rDNApyrosequencing. Linear discriminant analysis effect size (LEfSe) and inferred metagenomics analyses were performed.<br><br>RESULTS: The circulating bacterial DNA was significantly increased in HB-ACLF patients compared to that in the control groups. The overall microbial diversity was significantly decreased in HB-ACLF patients. HB-ACLF patients were enriched with Moraxellaceae, Sulfurovum, Comamonas and Burkholderiaceae but were depleted in Actinobacteria, Deinococcus-Thermus, Alphaproteobacteria, Xanthomonadaceae and Enterobacteriaceae compared to controls. Network analysis revealed a direct positive correlation between Burkholderiaceae and chemokine IP-10 in HB-ACLF patients. The relative abundance of Prevotellaceae independently predicted 28-day mortality. Inferred functional metagenomics predicted an enrichment of bacteria with genes related to methane, alanine, aspartate, glutamate, pyrimidine, purine and energy metabolism.<br><br>CONCLUSIONS: HB-ACLF patients display increased circulating microbial burden, altered microbiome composition and a shift in microbiome functionality. The alteration in circulating microbiota is associated with SI and clinical outcome in HB-ACLF.}, }
@article {pmid30863724, year = {2019}, author = {Iyer, LR and Verma, AK and Paul, J and Bhattacharya, A}, title = {Phagocytosis of Gut Bacteria by Entamoeba histolytica.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {34}, doi = {10.3389/fcimb.2019.00034}, pmid = {30863724}, issn = {2235-2988}, abstract = {The protist parasite Entamoeba histolytica causes amoebiasis, a major public health problem in developing countries. Only a small fraction of patients infected with the parasite display invasive disease involving colon or extra intestinal tissues such as liver. E. histolytica exists as two distinct forms, cysts, the infective form, and trophozoites, that are responsible for disease pathology. The latter multiply in the large intestine occasionally causing disease. The large intestine in humans is populated by a number of different bacterial communities and amoebic cells grow in their midst using some as food material. Several studies have shown relationship between bacteria and E. histolytica growth and virulence. However, an understanding of this relationship in human gut environment is not clear. We have investigated the possibility that there may be specific interaction of amoeba with different bacteria present in the gut environment by using a metagenomic pipe line. This was done by incubating bacteria isolated from human fecal material with E. histolytica and then identifying the bacterial population isolated from amoebic cells using a rRNA based metagenomic approach. Our results show that the parasite prefers a few bacterial species. One of these species is Lactobacillus ruminus which has never shown to be associated with E. histolytica.}, }
@article {pmid30863691, year = {2019}, author = {Gupta, V and Singh, I and Kumar, P and Rasool, S and Verma, V}, title = {A hydrolase with esterase activity expressed from a fosmid gene bank prepared from DNA of a North West Himalayan glacier frozen soil sample.}, journal = {3 Biotech}, volume = {9}, number = {3}, pages = {107}, doi = {10.1007/s13205-019-1621-z}, pmid = {30863691}, issn = {2190-572X}, abstract = {Screening of 20,000 clones of a fosmid gene bank, constructed from DNA extracted from North West Himalaya (NWH) glacier soil sample, using functional approach identified 10 esterase/lipase-producing clones. Of these, a clone designated pFG43 with an insert size of 45 kb which produced the highest concentration of enzyme (467.43 U/mg) was sequenced. Clone pFG43 contained 61 open reading frames (ORF) and of these an ORF of 1155 bp designated ME-003, was found to be closely related to a hydrolase from Acidobacteria sps (77% sequence identity and E value = 1e-164) and subsequently identified as a putative cocaine esterase. ORF ME-003 was amplified and sub-cloned using a TA vector system into E. coli (DH5α). The purified recombinant enzyme with a molecular weight of 43 kDa had optimal activity at 40 °C, pH 6 and the highest activity with shorter chain fatty acids than with higher chain length fatty acids. There is insignificant effect of inhibitors on the enzyme activity of ME-003, except PMSF which completely inhibited its activity. ME-003 activity was also inhibited in the presence of copper oxide but remained stable in presence of other metal ions. The enzyme activity was also inhibited in the presence of organic solvents; however, in the presence of 10% isopropanol, 12% of enzymatic activity was retained. Among various detergents, SDS completely inhibited enzymatic activity. The recombinant enzyme also shows enantio-specific activity against the racemic drug intermediates/precursors and exhibited 90% ee against racemic 1-phenyl ethanol and fluoxetine.}, }
@article {pmid30863681, year = {2019}, author = {Klimina, KM and Kasianov, AS and Poluektova, EU and Emelyanov, KV and Voroshilova, VN and Zakharevich, NV and Kudryavtseva, AV and Makeev, VJ and Danilenko, VN}, title = {Employing toxin-antitoxin genome markers for identification of Bifidobacterium and Lactobacillus strains in human metagenomes.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6554}, doi = {10.7717/peerj.6554}, pmid = {30863681}, issn = {2167-8359}, abstract = {Recent research has indicated that in addition to the unique genotype each individual may also have a unique microbiota composition. Difference in microbiota composition may emerge from both its species and strain constituents. It is important to know the precise composition especially for the gut microbiota (GM), since it can contribute to the health assessment, personalized treatment, and disease prevention for individuals and groups (cohorts). The existing methods for species and strain composition in microbiota are not always precise and usually not so easy to use. Probiotic bacteria of the genus Bifidobacterium and Lactobacillus make an essential component of human GM. Previously we have shown that in certain Bifidobacterium and Lactobacillus species the RelBE and MazEF superfamily of toxin-antitoxin (TA) systems may be used as functional biomarkers to differentiate these groups of bacteria at the species and strain levels. We have composed a database of TA genes of these superfamily specific for all lactobacilli and bifidobacteria species with complete genome sequence and confirmed that in all Lactobacillus and Bifidobacterium species TA gene composition is species and strain specific. To analyze composition of species and strains of two bacteria genera, Bifidobacterium and Lactobacillus, in human GM we developed TAGMA (toxin antitoxin genes for metagenomes analyses) software based on polymorphism in TA genes. TAGMA was tested on gut metagenomic samples. The results of our analysis have shown that TAGMA can be used to characterize species and strains of Lactobacillus and Bifidobacterium in metagenomes.}, }
@article {pmid30863388, year = {2019}, author = {Yang, W and Wang, L and Hu, Q and Pei, F and Mugambi, MA}, title = {Identification of Bacterial Composition in Freeze-Dried Agaricus bisporus During Storage and the Resultant Odor Deterioration.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {349}, doi = {10.3389/fmicb.2019.00349}, pmid = {30863388}, issn = {1664-302X}, abstract = {Moisture absorption and bacterial growth are critical factors for quality deterioration of freeze-dried Agaricus bisporus. In order to explore the bacterial composition and the resultant odor changes in freeze-dried A. bisporus during storage under three typical conditions (RT: 25°C, 55% RH; HT: 37°C, 85% RH; AT: ambient temperature), bacterial diversity and communities were analyzed using metagenomics. Moreover, volatile compounds were determined using SPME-GC-MS. The results demonstrated that the bacterial composition in freeze-dried A. bisporus was dominated by Pseudomonas, followed by Rhizobium and Pedobacter. In addition, Mucilaginibacter, Flavobacterium, and Thermus were a few other genera more dominant in HT samples, Chryseobacterium was the other genera more dominant in AT samples, while, Sphingobacterium and Chryseobacterium were a few other genera more dominant in RT samples. Furthermore, the increase of benzaldehyde content in HT samples may have been induced by the growth of Pseudomonads and the esters production in RT and AT samples might have been induced by Chryseobacterium. This study provided comprehensive information on exogenous bacterial composition and the resultant odor in freeze-dried A. bisporus. These results may be a theoretical basis for quality control and quick quality detection based on volatiles of freeze-dried A. bisporus.}, }
@article {pmid30863381, year = {2019}, author = {Takhampunya, R and Korkusol, A and Pongpichit, C and Yodin, K and Rungrojn, A and Chanarat, N and Promsathaporn, S and Monkanna, T and Thaloengsok, S and Tippayachai, B and Kumfao, N and Richards, AL and Davidson, SA}, title = {Metagenomic Approach to Characterizing Disease Epidemiology in a Disease-Endemic Environment in Northern Thailand.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {319}, doi = {10.3389/fmicb.2019.00319}, pmid = {30863381}, issn = {1664-302X}, abstract = {In this study, we used a metagenomic approach to analyze bacterial communities from diverse populations (humans, animals, and vectors) to investigate the role of these microorganisms as causative agents of disease in human and animal populations. Wild rodents and ectoparasites were collected from 2014 to 2018 in Nan province, Thailand where scrub typhus is highly endemic. Samples from undifferentiated febrile illness (UFI) patients were obtained from a local hospital. A total of 200 UFI patient samples were obtained and 309 rodents and 420 pools of ectoparasites were collected from rodents (n = 285) and domestic animals (n = 135). The bacterial 16S rRNA gene was amplified and sequenced with the Illumina. Real-time PCR and Sanger sequencing were used to confirm the next-generation sequencing (NGS) results and to characterize pathogen species. Several pathogens were detected by NGS in all populations studied and the most common pathogens identified included Bartonella spp., Rickettsia spp., Leptospira spp., and Orientia tsutsugamushi. Interestingly, Anaplasma spp. was detected in patient, rodent and tick populations, although they were not previously known to cause human disease from this region. Candidatus Neoehrlichia, Neorickettsia spp., Borrelia spp., and Ehrlichia spp. were detected in rodents and their associated ectoparasites. The same O. tsutsugamushi genotypes were shared among UFI patients, rodents, and chiggers in a single district indicating that the chiggers found on rodents were also likely responsible for transmitting to people. Serological testing using immunofluorescence assays in UFI samples showed high prevalence (IgM/IgG) of Rickettsia and Orientia pathogens, most notably among samples collected during September-November. Additionally, a higher number of seropositive samples belonged to patients in the working age population (20-60 years old). The results presented in this study demonstrate that the increased risk of human infection or exposure to chiggers and their associated pathogen (O. tsutsugamushi) resulted in part from two important factors; working age group and seasons for rice cultivation and harvesting. Evidence of pathogen exposure was shown to occur as there was seropositivity (IgG) in UFI patients for bartonellosis as well as for anaplasmosis. Using a metagenomic approach, this study demonstrated the circulation and transmission of several pathogens in the environment, some of which are known causative agents of illness in human populations.}, }
@article {pmid30863380, year = {2019}, author = {Advani, J and Verma, R and Chatterjee, O and Pachouri, PK and Upadhyay, P and Singh, R and Yadav, J and Naaz, F and Ravikumar, R and Buggi, S and Suar, M and Gupta, UD and Pandey, A and Chauhan, DS and Tripathy, SP and Gowda, H and Prasad, TSK}, title = {Whole Genome Sequencing of Mycobacterium tuberculosis Clinical Isolates From India Reveals Genetic Heterogeneity and Region-Specific Variations That Might Affect Drug Susceptibility.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {309}, doi = {10.3389/fmicb.2019.00309}, pmid = {30863380}, issn = {1664-302X}, abstract = {Whole genome sequencing (WGS) of Mycobacterium tuberculosis has been constructive in understanding its evolution, genetic diversity and the mechanisms involved in drug resistance. A large number of sequencing efforts from across the globe have revealed genetic diversity among clinical isolates and the genetic determinants for their resistance to anti-tubercular drugs. Considering the high TB burden in India, the availability of WGS studies is limited. Here we present, WGS results of 200 clinical isolates of M. tuberculosis from North India which are categorized as sensitive to first-line drugs, mono-resistant, multi-drug resistant and pre-extensively drug resistant isolates. WGS revealed that 20% of the isolates were co-infected with M. tuberculosis and non-tuberculous mycobacteria species. We identified 12,802 novel genetic variations in M. tuberculosis isolates including 343 novel SNVs in 38 genes which are known to be associated with drug resistance and are not currently used in the diagnostic kits for detection of drug resistant TB. We also identified M. tuberculosis lineage 3 to be predominant in the northern region of India. Additionally, several novel SNVs, which may potentially confer drug resistance were found to be enriched in the drug resistant isolates sampled. This study highlights the significance of employing WGS in diagnosis and for monitoring further development of MDR-TB strains.}, }
@article {pmid30863369, year = {2019}, author = {Allemann, A and Kraemer, JG and Korten, I and Ramsey, K and Casaulta, C and ,  and Wüthrich, D and Ramette, A and Endimiani, A and Latzin, P and Hilty, M}, title = {Nasal Resistome Development in Infants With Cystic Fibrosis in the First Year of Life.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {212}, doi = {10.3389/fmicb.2019.00212}, pmid = {30863369}, issn = {1664-302X}, abstract = {Polymicrobial infections of the respiratory tract due to antibiotic resistant bacteria are a great concern in patients with cystic fibrosis (CF). We therefore aimed at establishing a functional metagenomic method to analyze the nasal resistome in infants with CF within the first year of life. We included samples from patients before antibiotic treatment, which allowed obtaining information regarding natural status of the resistome. In total, we analyzed 130 nasal swabs from 26 infants with CF and screened for β-lactams (ampicillin, amoxicillin-clavulanic acid, and cefuroxime) and other classes of antibiotic resistances (tetracycline, chloramphenicol and trimethoprim-sulfamethoxazole). For 69 swabs (53% of total), we found at least one non-susceptible phenotype. Analyses of the inserts recovered from non-susceptible clones by nanopore MinION sequencing revealed a large reservoir of resistance genes including mobile elements within the antibiotic naïve samples. Comparing the data of the resistome with the microbiota composition showed that the bacterial phyla and operational taxonomic units (OTUs) of the microbiota rather than the antibiotic treatment were associated with the majority of non-susceptible phenotypes in the resistome. Future studies will reveal if characterization of the resistome can help in clinical decision-making in patients with CF.}, }
@article {pmid30862830, year = {2019}, author = {Sieradzki, ET and Ignacio-Espinoza, JC and Needham, DM and Fichot, EB and Fuhrman, JA}, title = {Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporal picoplankton metatranscriptomes.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1169}, doi = {10.1038/s41467-019-09106-z}, pmid = {30862830}, issn = {2041-1723}, mesh = {Bacteriophages/*genetics/metabolism ; Cyanobacteria/*physiology/virology ; Genome, Viral/genetics ; Host Microbial Interactions/physiology ; Metagenome/genetics ; Microbiota/*physiology ; Photosynthesis/*physiology ; Photosystem II Protein Complex/metabolism ; Phylogeny ; Phytoplankton/*physiology/virology ; Seawater/microbiology/virology ; Sequence Analysis, DNA ; }, abstract = {Viruses provide top-down control on microbial communities, yet their direct study in natural environments was hindered by culture limitations. The advance of bioinformatics enables cultivation-independent study of viruses. Many studies assemble new viral genomes and study viral diversity using marker genes from free viruses. Here we use cellular metatranscriptomics to study active community-wide viral infections. Recruitment to viral contigs allows tracking infection dynamics over time and space. Our assemblies represent viral populations, but appear biased towards low diversity viral taxa. Tracking relatives of published T4-like cyanophages and pelagiphages reveals high genomic continuity. We determine potential hosts by matching dynamics of infection with abundance of particular microbial taxa. Finally, we quantify the relative contribution of cyanobacteria and viruses to photosystem-II psbA (reaction center) expression in our study sites. We show sometimes >50% of all cyanobacterial+viral psbA expression is of viral origin, highlighting the contribution of viruses to photosynthesis and oxygen production.}, }
@article {pmid30861447, year = {2019}, author = {Xu, R and Yang, ZH and Zheng, Y and Wang, QP and Bai, Y and Liu, JB and Zhang, YR and Xiong, WP and Lu, Y and Fan, CZ}, title = {Metagenomic analysis reveals the effects of long-term antibiotic pressure on sludge anaerobic digestion and antimicrobial resistance risk.}, journal = {Bioresource technology}, volume = {282}, number = {}, pages = {179-188}, doi = {10.1016/j.biortech.2019.02.120}, pmid = {30861447}, issn = {1873-2976}, abstract = {Continuous stirred-tank digesters with tetracyclines and sulfonamides were operated to investigate the impacts of antibiotic pressure on sludge anaerobic digestion. The versatile methanogen Methanosarcinales and strictly hydrogenotrophic methanogen Methanobacteriales increased and decreased by 21.1% and 10.9% under antibiotic pressure, respectively. KEGG analysis revealed that hydrogenotrophic and acetoclastic methanogenesis pathways were all affected. The decrease in abundance of function genes involved in lipid metabolism, carbohydrate metabolism, and fatty acid degradation, would lead to a reduction in methane production by 25%. Network analysis indicated positive associations among tetracycline residuals, abundance of resistance genes (ARGs), and specific member of potential hosts. Over 1000 ARG subtypes were widely detected in sludge, including macrolide (28%), tetracycline (24%), fluoroquinolone (20%), and peptide (20%) resistance genes. AD process exposed to long-term antibiotic would increase the diversity and abundance of ARG, enhance the association of ARG with specific microbes, and select bacteria able to perform chemotaxis mechanism.}, }
@article {pmid30860877, year = {2019}, author = {Larsen, IS and Fritzen, AM and Carl, CS and Agerholm, M and Damgaard, MTF and Holm, JB and Marette, A and Nordkild, P and Kiens, B and Kristiansen, K and Wehkamp, J and Jensen, BAH}, title = {Human Paneth cell α-defensin 5 treatment reverses dyslipidemia and improves glucoregulatory capacity in diet-induced obese mice.}, journal = {American journal of physiology. Endocrinology and metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1152/ajpendo.00019.2019}, pmid = {30860877}, issn = {1522-1555}, abstract = {OBJECTIVE: Overnutrition is the principal cause of insulin resistance (IR) and dyslipidemia, which drive non-alcoholic fatty liver disease (NAFLD). Overnutrition is further linked to disrupted bowel function, microbiota alterations and change-of-function in gut-lining cell populations including Paneth cells of the small intestine. Paneth cells regulate microbial diversity through expression of antimicrobial peptides, particularly human alpha-defensin-5 (HD-5), and have shown repressed secretory capacity in human obesity.<br><br>METHODS: Mice were fed a 60%HFD for 13 weeks and subsequently treated with physiologically relevant amounts of HD-5 (0,001%) or vehicle for 10 weeks. The glucoregulatory capacity was determined by glucose tolerance tests and measurements of corresponding insulin concentrations both before and during intervention. Gut microbiome composition was examined by 16S rRNA gene amplicon sequencing. Fresh fecal samples were collected immediately before and after intervention. Small intestine samples were harvested at necropsy. Plasma and liver lipid and protein profiles were determined by biochemical analyses.<br><br>RESULTS: HD-5 treated mice exhibited improved glucoregulatory capacity along with an ameliorated plasma- and liver lipid profile. This was accompanied by specific decrease in jejunal inflammation and gut microbiota alterations including increased Bifidobacterium abundances, whichcorrelated inversely with metabolic dysfunctions.<br><br>CONCLUSION: This study provides proof-of-concept for the use of human defensins to improve host metabolism by mitigating the triad cluster of dyslipidemia, IR and NAFLD.}, }
@article {pmid30860572, year = {2019}, author = {Wang, Z and Wang, Y and Fuhrman, JA and Sun, F and Zhu, S}, title = {Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences.}, journal = {Briefings in bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1093/bib/bbz025}, pmid = {30860572}, issn = {1477-4054}, abstract = {In metagenomic studies of microbial communities, the short reads come from mixtures of genomes. Read assembly is usually an essential first step for the follow-up studies in metagenomic research. Understanding the power and limitations of various read assembly programs in practice is important for researchers to choose which programs to use in their investigations. Many studies evaluating different assembly programs used either simulated metagenomes or real metagenomes with unknown genome compositions. However, the simulated datasets may not reflect the real complexities of metagenomic samples and the estimated assembly accuracy could be misleading due to the unknown genomes in real metagenomes. Therefore, hybrid strategies are required to evaluate the various read assemblers for metagenomic studies. In this paper, we benchmark the metagenomic read assemblers by mixing reads from real metagenomic datasets with reads from known genomes and evaluating the integrity, contiguity and accuracy of the assembly using the reads from the known genomes. We selected four advanced metagenome assemblers, MEGAHIT, MetaSPAdes, IDBA-UD and Faucet, for evaluation. We showed the strengths and weaknesses of these assemblers in terms of integrity, contiguity and accuracy for different variables, including the genetic difference of the real genomes with the genome sequences in the real metagenomic datasets and the sequencing depth of the simulated datasets. Overall, MetaSPAdes performs best in terms of integrity and continuity at the species-level, followed by MEGAHIT. Faucet performs best in terms of accuracy at the cost of worst integrity and continuity, especially at low sequencing depth. MEGAHIT has the highest genome fractions at the strain-level and MetaSPAdes has the overall best performance at the strain-level. MEGAHIT is the most efficient in our experiments. Availability: The source code is available at https://github.com/ziyewang/MetaAssemblyEval.}, }
@article {pmid30858836, year = {2019}, author = {Watanabe, T and Kojima, H and Umezawa, K and Hori, C and Takasuka, TE and Kato, Y and Fukui, M}, title = {Genomes of Neutrophilic Sulfur-Oxidizing Chemolithoautotrophs Representing 9 Proteobacterial Species From 8 Genera.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {316}, doi = {10.3389/fmicb.2019.00316}, pmid = {30858836}, issn = {1664-302X}, abstract = {Even in the current era of metagenomics, the interpretation of nucleotide sequence data is primarily dependent on knowledge obtained from a limited number of microbes isolated in pure culture. Thus, it is of fundamental importance to expand the variety of strains available in pure culture, to make reliable connections between physiological characteristics and genomic information. In this study, two sulfur oxidizers that potentially represent two novel species were isolated and characterized. They were subjected to whole-genome sequencing together with 7 neutrophilic and chemolithoautotrophic sulfur-oxidizing bacteria. The genes for sulfur oxidation in the obtained genomes were identified and compared with those of isolated sulfur oxidizers in the classes Betaproteobacteria and Gammaproteobacteria. Although the combinations of these genes in the respective genomes are diverse, typical combinations corresponding to three types of core sulfur oxidation pathways were identified. Each pathway involves one of three specific sets of proteins, SoxCD, DsrABEFHCMKJOP, and HdrCBAHypHdrCB. All three core pathways contain the SoxXYZAB proteins, and a cytoplasmic sulfite oxidase encoded by soeABC is a conserved component in the core pathways lacking SoxCD. Phylogenetically close organisms share same core sulfur oxidation pathway, but a notable exception was observed in the family 'Sulfuricellaceae'. In this family, some strains have either core pathway involving DsrABEFHCMKJOP or HdrCBAHypHdrCB, while others have both pathways. A proteomics analysis showed that proteins constituting the core pathways were produced at high levels. While hypothesized function of HdrCBAHypHdrCB is similar to that of Dsr system, both sets of proteins were detected with high relative abundances in the proteome of a strain possessing genes for these proteins. In addition to the genes for sulfur oxidation, those for arsenic metabolism were searched for in the sequenced genomes. As a result, two strains belonging to the families Thiobacillaceae and Sterolibacteriaceae were observed to harbor genes encoding ArxAB, a type of arsenite oxidase that has been identified in a limited number of bacteria. These findings were made with the newly obtained genomes, including those from 6 genera from which no genome sequence of an isolated organism was previously available. These genomes will serve as valuable references to interpret nucleotide sequences.}, }
@article {pmid30858573, year = {2019}, author = {Kessler, AJ and Chen, YJ and Waite, DW and Hutchinson, T and Koh, S and Popa, ME and Beardall, J and Hugenholtz, P and Cook, PLM and Greening, C}, title = {Bacterial fermentation and respiration processes are uncoupled in anoxic permeable sediments.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41564-019-0391-z}, pmid = {30858573}, issn = {2058-5276}, abstract = {Permeable (sandy) sediments cover half of the continental margin and are major regulators of oceanic carbon cycling. The microbial communities within these highly dynamic sediments frequently shift between oxic and anoxic states, and hence are less stratified than those in cohesive (muddy) sediments. A major question is, therefore, how these communities maintain metabolism during oxic-anoxic transitions. Here, we show that molecular hydrogen (H2) accumulates in silicate sand sediments due to decoupling of bacterial fermentation and respiration processes following anoxia. In situ measurements show that H2 is 250-fold supersaturated in the water column overlying these sediments and has an isotopic composition consistent with fermentative production. Genome-resolved shotgun metagenomic profiling suggests that the sands harbour diverse and specialized microbial communities with a high abundance of [NiFe]-hydrogenase genes. Hydrogenase profiles predict that H2 is primarily produced by facultatively fermentative bacteria, including the dominant gammaproteobacterial family Woeseiaceae, and can be consumed by aerobic respiratory bacteria. Flow-through reactor and slurry experiments consistently demonstrate that H2 is rapidly produced by fermentation following anoxia, immediately consumed by aerobic respiration following reaeration and consumed by sulfate reduction only during prolonged anoxia. Hydrogenotrophic sulfur, nitrate and nitrite reducers were also detected, although contrary to previous hypotheses there was limited capacity for microalgal fermentation. In combination, these experiments confirm that fermentation dominates anoxic carbon mineralization in these permeable sediments and, in contrast to the case in cohesive sediments, is largely uncoupled from anaerobic respiration. Frequent changes in oxygen availability in these sediments may have selected for metabolically flexible bacteria while excluding strict anaerobes.}, }
@article {pmid30858509, year = {2019}, author = {Ghanbari, M and Klose, V and Crispie, F and Cotter, PD}, title = {The dynamics of the antibiotic resistome in the feces of freshly weaned pigs following therapeutic administration of oxytetracycline.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {4062}, doi = {10.1038/s41598-019-40496-8}, pmid = {30858509}, issn = {2045-2322}, support = {853863 &amp; 859603//&amp;#x00D6;sterreichische Forschungsf&amp;#x00F6;rderungsgesellschaft (Austrian Research Promotion Agency)/ ; 853863 &amp; 859603//&amp;#x00D6;sterreichische Forschungsf&amp;#x00F6;rderungsgesellschaft (Austrian Research Promotion Agency)/ ; 853863 &amp; 859603//&amp;#x00D6;sterreichische Forschungsf&amp;#x00F6;rderungsgesellschaft (Austrian Research Promotion Agency)/ ; 853863 &amp; 859603//&amp;#x00D6;sterreichische Forschungsf&amp;#x00F6;rderungsgesellschaft (Austrian Research Promotion Agency)/ ; }, abstract = {In this study, shotgun metagenomics was employed to monitor the effect of oxytetracycline, administered at a therapeutic dose, on the dynamics of the microbiota and resistome in the feces of weaned pigs. Sixteen weaning pigs were assigned to one of two treatments including standard starter diet for 21 days or antibiotic-supplemented diet (10 g oxytetracycline/100 kg body weight/day) for 7 days, followed by 14 days of standard starter diet. Feces were collected from the pigs on days 0, 8, and 21 for microbiota and resistome profiling. Pigs receiving oxytetracycline exhibited a significantly greater richness (ANOVA, P = 0.034) and diversity (ANOVA, P = 0.048) of antibiotic resistance genes (ARGs) than the control pigs. Antibiotic administration significantly enriched the abundances of 41 ARGs, mainly from the tetracycline, betalactam and multidrug resistance classes. Compositional shifts in the bacterial communities were observed following 7 days of antibiotic adminstration, with the medicated pigs showing an increase in Escherichia (Proteobacteria) and Prevotella (Bacteroidetes) populations compared with the nonmedicated pigs. This might be explained by the potential of these taxa to carry ARGs that may be transferred to other susceptible bacteria in the densely populated gut environment. These findings will help in the optimization of therapeutic schemes involving antibiotic usage in swine production.}, }
@article {pmid30858464, year = {2019}, author = {Yang, P and Tan, GA and Aslam, M and Kim, J and Lee, PH}, title = {Metatranscriptomic evidence for classical and RuBisCO-mediated CO2 reduction to methane facilitated by direct interspecies electron transfer in a methanogenic system.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {4116}, doi = {10.1038/s41598-019-40830-0}, pmid = {30858464}, issn = {2045-2322}, support = {PF13-12713//Research Grants Council, University Grants Committee (RGC, UGC)/ ; 15273316//Research Grants Council, University Grants Committee (RGC, UGC)/ ; C7044-14G//Research Grants Council, University Grants Committee (RGC, UGC)/ ; 2017RA1A2B4007804//National Research Foundation of Korea (NRF)/ ; }, abstract = {In a staged anaerobic fluidized-bed ceramic membrane bioreactor, metagenomic and metatranscriptomic analyses were performed to decipher the microbial interactions on the granular activated carbon. Metagenome bins, representing the predominating microbes in the bioreactor: syntrophic propionate-oxidizing bacteria (SPOB), acetoclastic Methanothrix concilii, and exoelectrogenic Geobacter lovleyi, were successfully recovered for the reconstruction and analysis of metabolic pathways involved in the transformation of fatty acids to methane. In particular, SPOB degraded propionate into acetate, which was further converted into methane and CO2 by M. concilii via the acetoclastic methanogenesis. Concurrently, G. lovleyi oxidized acetate into CO2, releasing electrons into the extracellular environment. By accepting these electrons through direct interspecies electron transfer (DIET), M. concilii was capable of performing CO2 reduction for further methane formation. Most notably, an alternative RuBisCO-mediated CO2 reduction (the reductive hexulose-phosphate (RHP) pathway) is transcriptionally-active in M. concilii. This RHP pathway enables M. concilii dominance and energy gain by carbon fixation and methanogenesis, respectively via a methyl-H4MPT intermediate, constituting the third methanogenesis route. The complete acetate reduction (2 mole methane formation/1 mole acetate consumption), coupling of acetoclastic methanogenesis and two CO2 reduction pathways, are thermodynamically favorable even under very low substrate condition (down to to 10-5 M level). Such tight interactions via both mediated and direct interspecies electron transfer (MIET and DIET), induced by the conductive GAC promote the overall efficiency of bioenergy processes.}, }
@article {pmid30857856, year = {2019}, author = {Castelán-Sánchez, HG and Lopéz-Rosas, I and García-Suastegui, WA and Peralta, R and Dobson, ADW and Batista-García, RA and Dávila-Ramos, S}, title = {Extremophile deep-sea viral communities from hydrothermal vents: Structural and functional analysis.}, journal = {Marine genomics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.margen.2019.03.001}, pmid = {30857856}, issn = {1876-7478}, abstract = {Ten publicly available metagenomic data sets from hydrothermal vents were analyzed to determine the taxonomic structure of the viral communities present, as well as their potential metabolic functions. The type of natural selection on two auxiliary metabolic genes was also analyzed. The structure of the virome in the hydrothermal vents was quite different in comparison with the viruses present in sediments, with specific populations being present in greater abundance in the plume samples when compared with the sediment samples. ssDNA genomes such as Circoviridae and Microviridae were predominantly present in the sediment samples, with Caudovirales which are dsDNA being present in the vent samples. Genes potentially encoding enzymes that participate in carbon, nitrogen and sulfur metabolic pathways were found in greater abundance, than those involved in the oxygen cycle, in the hydrothermal vents. Functional profiling of the viromes, resulted in the discovery of genes encoding proteins involved in bacteriophage capsids, DNA synthesis, nucleotide synthesis, DNA repair, as well as viral auxiliary metabolic genes such as cytitidyltransferase and ribonucleotide reductase. These auxiliary metabolic genes participate in the synthesis of phospholipids and nucleotides respectively and are likely to contribute to enhancing the fitness of their bacterial hosts within the hydrothermal vent communities. Finally, evolutionary analysis suggested that these auxiliary metabolic genes are highly conserved and evolve under purifying selection, and are thus maintained in their genome.}, }
@article {pmid30856245, year = {2019}, author = {Omori, WP and Pinheiro, DG and Kishi, LT and Fernandes, CC and Fernandes, GC and Gomes-Pepe, ES and Pavani, CD and Lemos, EGM and Souza, JAM}, title = {Draft genome of Thermomonospora sp. CIT 1 (Thermomonosporaceae) and in silico evidence of its functional role in filter cake biomass deconstruction.}, journal = {Genetics and molecular biology}, volume = {42}, number = {1}, pages = {145-150}, doi = {10.1590/1678-4685-GMB-2017-0376}, pmid = {30856245}, issn = {1415-4757}, abstract = {The filter cake from sugar cane processing is rich in organic matter and nutrients, which favors the proliferation of microorganisms with potential to deconstruct plant biomass. From the metagenomic data of this material, we assembled a draft genome that was phylogenetically related to Thermomonospora curvata DSM 43183, which shows the functional and ecological importance of this bacterium in the filter cake. Thermomonospora is a gram-positive bacterium that produces cellulases in compost, and it can survive temperatures of 60 ºC. We identified a complete set of biomass depolymerizing enzymes in the draft genome of Thermomonospora sp. CIT 1, such as α-amylase, catalase-peroxidases, β-mannanase, and arabinanase, demonstrating the potential of this bacterium to deconstruct the components of starch, lignin, and hemicellulose. In addition, the draft genome of Thermomonospora sp. CIT 1 contains 18 genes that do not share identity with five other species of Thermomonospora, suggesting that this bacterium has different genetic characteristics than those present in genomes reported so far for this genus. These findings add a new dimension to the current understanding of the functional profile of this microorganism that inhabits agro-industrial waste, which may boost new gene discoveries and be of importance for application in the production of bioethanol.}, }
@article {pmid30856229, year = {2019}, author = {Salgado-Flores, A and Tveit, AT and Wright, AD and Pope, PB and Sundset, MA}, title = {Characterization of the cecum microbiome from wild and captive rock ptarmigans indigenous to Arctic Norway.}, journal = {PloS one}, volume = {14}, number = {3}, pages = {e0213503}, doi = {10.1371/journal.pone.0213503}, pmid = {30856229}, issn = {1932-6203}, abstract = {Rock ptarmigans (Lagopus muta) are gallinaceous birds inhabiting arctic and sub-arctic environments. Their diet varies by season, including plants or plant parts of high nutritional value, but also toxic plant secondary metabolites (PSMs). Little is known about the microbes driving organic matter decomposition in the cecum of ptarmigans, especially the last steps leading to methanogenesis. The cecum microbiome in wild rock ptarmigans from Arctic Norway was characterized to unveil their functional potential for PSM detoxification, methanogenesis and polysaccharides degradation. Cecal samples were collected from wild ptarmigans from Svalbard (L. m. hyperborea) and northern Norway (L. m. muta) during autumn/winter (Sept-Dec). Samples from captive Svalbard ptarmigans fed commercial pelleted feed were included to investigate the effect of diet on microbial composition and function. Abundances of methanogens and bacteria were determined by qRT-PCR, while microbial community composition and functional potential were studied using 16S rRNA gene sequencing and shotgun metagenomics. Abundances of bacteria and methanogenic Archaea were higher in wild ptarmigans compared to captive birds. The ceca of wild ptarmigans housed bacterial groups involved in PSM-degradation, and genes mediating the conversion of phenol compounds to pyruvate. Methanomassiliicoccaceae was the major archaeal family in wild ptarmigans, carrying the genes for methanogenesis from methanol. It might be related to increased methanol production from pectin degradation in wild birds due to a diet consisting of primarily fresh pectin-rich plants. Both wild and captive ptarmigans possessed a broad suite of genes for the depolymerization of hemicellulose and non-cellulosic polysaccharides (e.g. starch). In conclusion, there were no physiological and phenotypical dissimilarities in the microbiota found in the cecum of wild ptarmigans on mainland Norway and Svalbard. While substantial differences in the functional potential for PSM degradation and methanogenesis in wild and captive birds seem to be a direct consequence of their dissimilar diets.}, }
@article {pmid30853940, year = {2019}, author = {Jaiswal, S and Singh, DK and Shukla, P}, title = {Gene Editing and Systems Biology Tools for Pesticide Bioremediation: A Review.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {87}, doi = {10.3389/fmicb.2019.00087}, pmid = {30853940}, issn = {1664-302X}, abstract = {Bioremediation is the degradation potential of microorganisms to dissimilate the complex chemical compounds from the surrounding environment. The genetics and biochemistry of biodegradation processes in datasets opened the way of systems biology. Systemic biology aid the study of interacting parts involved in the system. The significant keys of system biology are biodegradation network, computational biology, and omics approaches. Biodegradation network consists of all the databases and datasets which aid in assisting the degradation and deterioration potential of microorganisms for bioremediation processes. This review deciphers the bio-degradation network, i.e., the databases and datasets (UM-BBD, PAN, PTID, etc.) aiding in assisting the degradation and deterioration potential of microorganisms for bioremediation processes, computational biology and multi omics approaches like metagenomics, genomics, transcriptomics, proteomics, and metabolomics for the efficient functional gene mining and their validation for bioremediation experiments. Besides, the present review also describes the gene editing tools like CRISPR Cas, TALEN, and ZFNs which can possibly make design microbe with functional gene of interest for degradation of particular recalcitrant for improved bioremediation.}, }
@article {pmid30853704, year = {2019}, author = {Watahiki, S and Kimura, N and Yamazoe, A and Miura, T and Sekiguchi, Y and Noda, N and Matsukura, S and Kasai, D and Takahata, Y and Nojiri, H and Fukuda, M}, title = {Ecological impact assessment of a bioaugmentation site on remediation of chlorinated ethylenes by multi-omics analysis.}, journal = {The Journal of general and applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.2323/jgam.2018.10.003}, pmid = {30853704}, issn = {1349-8037}, abstract = {Bioremediation may affect the ecological system around bioremediation sites. However, little is known about how microbial community structures change over time after the initial injection of degraders. In this study, we have assessed the ecological impact of bioaugmentation using metagenomic and metatranscriptomic approaches to remove trichlorinated ethylene/cis-dichloroethylene (TCE/cDCE) by Rhodococcus jostii strain RHA1 as an aerobic chemical compound degrader. Metagenomic analysis showed that the number of organisms belonging to the genus Rhodococcus, including strain RHA1, increased from 0.1% to 76.6% of the total microbial community on day 0 at the injection site. Subsequently, the populations of strain RHA1 and other TCE/cDCE-degrading bacteria gradually decreased over time, whereas the populations of the anaerobic dechlorinators Geobacter and Dehalococcoides increased at later stages. Metatranscriptomic analysis revealed a high expression of aromatic compound-degrading genes (bphA1-A4) in strain RHA1 after RHA1 injection. From these results, we concluded that the key dechlorinators of TCE/cDCE were mainly aerobic bacteria, such as RHA1, until day 1, after which the key dechlorinators changed to anaerobic bacteria, such as Geobacter and Dehalococcocides, after day 6 at the injection well. Based on the α-diversity, the richness levels of the microbial community were increased after injection of strain RHA1, and the microbial community composition had not been restored to that of the original composition during the 19 days after treatment. These results provide insights into the assessment of the ecological impact and bioaugmentation process of RHA1 at bioremediation sites.}, }
@article {pmid30853065, year = {2019}, author = {Accetto, T and Avguštin, G}, title = {The diverse and extensive plant polysaccharide degradative apparatuses of the rumen and hindgut Prevotella species: A factor in their ubiquity?.}, journal = {Systematic and applied microbiology}, volume = {42}, number = {2}, pages = {107-116}, doi = {10.1016/j.syapm.2018.10.001}, pmid = {30853065}, issn = {1618-0984}, mesh = {Animals ; *Carbohydrate Metabolism ; Cattle/microbiology ; Metagenome ; Phylogeny ; Plants/*chemistry ; Polysaccharides/*metabolism ; Prevotella/*metabolism ; Rumen/*metabolism/microbiology ; Sequence Analysis, DNA ; Sheep/microbiology ; Swine/microbiology ; }, abstract = {Although the Prevotella are commonly observed in high shares in the mammalian hindgut and rumen studies using NGS approach, the knowledge on their actual role, though postulated to lie in soluble fibre degradation, is scarce. Here we analyse in total 23, more than threefold of hitherto known rumen and hindgut Prevotella species and show that rumen/hindgut Prevotella generally possess extensive repertoires of polysaccharide utilization loci (PULs) and carbohydrate active enzymes targeting various plant polysaccharides. These PUL repertoires separate analysed Prevotella into generalists and specialists yet a finer diversity among generalists is evident too, both in range of substrates targeted and in PUL combinations targeting the same broad substrate classes. Upon evaluation of the shares of species analysed in this study in rumen metagenomes we found firstly, that they contributed significantly to total Prevotella abundance though much of rumen Prevotella diversity may still be unknown. Secondly, the hindgut Prevotella species originally isolated in pigs and humans occasionally dominated among the Prevotella with surprisingly high metagenome read shares and were consistently found in rumen metagenome samples from sites as apart as New Zealand and Scotland. This may indicate frequent passage between different hosts and relatively low barriers to their successful establishment in rumen versus the hindgut.}, }
@article {pmid30853028, year = {2019}, author = {Yason, JA and Liang, YR and Png, CW and Zhang, Y and Tan, KSW}, title = {Interactions between a pathogenic Blastocystis subtype and gut microbiota: in vitro and in vivo studies.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {30}, doi = {10.1186/s40168-019-0644-3}, pmid = {30853028}, issn = {2049-2618}, abstract = {BACKGROUND: Blastocystis is a common gut eukaryote detected in humans and animals. It has been associated with gastrointestinal disease in the past although recent metagenomic studies also suggest that it is a member of normal microbiota. This study investigates interactions between pathogenic human isolates belonging to Blastocystis subtype 7 (ST7) and bacterial representatives of the gut microbiota.<br><br>RESULTS: Generally, Blastocystis ST7 exerts a positive effect on the viability of representative gut bacteria except on Bifidobacterium longum. Gene expression analysis and flow cytometry indicate that the bacterium may be undergoing oxidative stress in the presence of Blastocystis. In vitro assays demonstrate that Blastocystis-induced host responses are able to decrease Bifidobacterium counts. Mice infected with Blastocystis also reveal a decrease in beneficial bacteria Bifidobacterium and Lactobacillus.<br><br>CONCLUSIONS: This study shows that particular isolates of Blastocystis ST7 cause changes in microbiota populations and potentially lead to an imbalance of the gut microbiota. This study suggests that certain isolates of Blastocystis exert their pathogenic effects through disruption of the gut microbiota and provides a counterpoint to the increasing reports indicating the commensal nature of this ubiquitous parasite.}, }
@article {pmid30852315, year = {2019}, author = {Gao, H and Mao, Y and Zhao, X and Liu, WT and Zhang, T and Wells, G}, title = {Genome-centric metagenomics resolves microbial diversity and prevalent truncated denitrification pathways in a denitrifying PAO-enriched bioprocess.}, journal = {Water research}, volume = {155}, number = {}, pages = {275-287}, doi = {10.1016/j.watres.2019.02.020}, pmid = {30852315}, issn = {1879-2448}, abstract = {Denitrification is the stepwise microbial reduction of nitrate or nitrite (NO2-) to nitrogen gas via the obligate intermediates nitric oxide (NO) and nitrous oxide (N2O). Substantial N2O accumulation has been reported in denitrifying enhanced biological phosphorus removal (EBPR) bioreactors enriched in denitrifying polyphosphate accumulating organisms (DPAOs), but little is known about underlying mechanisms for N2O generation, prevalence of complete versus truncated denitrification pathways, or the impact of NO2- feed on DPAO-enriched consortia. To address this knowledge gap, we employed genome-resolved metagenomics to investigate nitrogen transformation potential in a NO2- fed denitrifying EBPR bioreactor enriched in Candidatus Accumulibacter and prone to N2O accumulation. Our analysis yielded 41 near-complete metagenome-assembled genomes (MAGs), including two co-occurring Accumulibacter strains affiliated with clades IA and IC (the first published genome from this clade) and 39 non-PAO flanking bacterial genomes. The dominant Accumulibacter clade IA encoded genes for complete denitrification, while the lower abundance Accumulibacter clade IC harbored all denitrification genes except for a canonical respiratory NO reductase. Analysis of the 39 non-PAO MAGs revealed a high prevalence of taxa harboring an incomplete denitrification pathway. Of the 27 MAGs harboring capacity for at least one step in the denitrification pathway, 10 were putative N2O producers lacking N2O reductase, 16 were putative N2O reducers that lacked at least one upstream denitrification gene, and only one harbored a complete denitrification pathway. We also documented increasing abundance over the course of reactor operation of putative N2O producers. Our results suggest that the unusually high levels of N2O production observed in this Accumulibacter-enriched consortium are linked in part to the selection for non-PAO flanking microorganisms with truncated denitrification pathways.}, }
@article {pmid30852309, year = {2019}, author = {Garau, G and Porceddu, A and Sanna, M and Silvetti, M and Castaldi, P}, title = {Municipal solid wastes as a resource for environmental recovery: Impact of water treatment residuals and compost on the microbial and biochemical features of As and trace metal-polluted soils.}, journal = {Ecotoxicology and environmental safety}, volume = {174}, number = {}, pages = {445-454}, doi = {10.1016/j.ecoenv.2019.03.007}, pmid = {30852309}, issn = {1090-2414}, abstract = {In this study we evaluated the microbiological and biochemical impact of iron-based water treatment residuals (Fe-WTRs) and municipal solid waste compost (MSWC), alone and combined, on three different soils co-contaminated with arsenic (As) and trace-metals (TM), i.e. Pb, Cu and Zn. Overall, all the amendments considered significantly increased the abundance of culturable heterotrophic bacteria, with MSWC showing the greatest impact across all soils (up to a 24% increase). In most of treated soils this was accompanied by a significant reduction of both the (culturable) fungal/bacterial ratio, and the proportion of culturable As(V)- and As(III)-resistant bacteria with respect to total bacterial population. The catabolic potential and versatility of the resident microbial communities (assessed by community level physiological profile) was highly soil-dependent and substantial increases of both parameters were observed in the amended soils with the higher total As concentration (from approx. 749 to 22,600 mg kg-1). Moreover, both carbon source utilisation profile and 16S rRNA soil metagenome sequencing indicated a significant impact of MSWC and Fe-WTRs on the structure and diversity of soil microbial communities, with Proteobacteria, Actinobacteria and Firmicutes being the most affected taxa. The assessment of selected soil enzyme activities (dehydrogenase, urease and β-glucosidase) indicated an increase of metabolic functioning especially in soils treated with MSWC (e.g. dehydrogenase activity increased up to 19.5-fold in the most contaminated soil treated with MSWC). Finally, the microbial and biochemical features of treated (and untreated) contaminated soils (i.e. total bacterial counts, catabolic potential and versatility and soil enzyme activities) were highly correlated with the concentrations of labile As and TM in these latter soils and supported a clear role of the tested amendments (especially MSWC) as As- and TM-immobilising agents.}, }
@article {pmid30851141, year = {2019}, author = {Nadeau, SA and Roco, CA and Debenport, SJ and Anderson, TR and Hofmeister, KL and Walter, MT and Shapleigh, JP}, title = {Metagenomic analysis reveals distinct patterns of denitrification gene abundance across soil moisture, nitrate gradients.}, journal = {Environmental microbiology}, volume = {21}, number = {4}, pages = {1255-1266}, doi = {10.1111/1462-2920.14587}, pmid = {30851141}, issn = {1462-2920}, support = {DGE-1650441//Division of Graduate Education/ ; 2014-67019-21636//National Institute of Food and Agriculture/ ; NYC-123425//National Institute of Food and Agriculture/ ; Grant No. 1069193//National Science Foundation/ ; DGE-1650441//National Science Foundation/ ; //Department of Agriculture/ ; //Cornell University/ ; 2014-67019-21636//United States Department of Agriculture/ ; NYC-123425//National Institute of Food and Agriculture/ ; }, abstract = {This study coupled a landscape-scale metagenomic survey of denitrification gene abundance in soils with in situ denitrification measurements to show how environmental factors shape distinct denitrification communities that exhibit varying denitrification activity. Across a hydrologic gradient, the distribution of total denitrification genes (nap/nar + nirK/nirS + cNor/qNor + nosZ) inferred from metagenomic read abundance exhibited no consistent patterns. However, when genes were considered independently, nirS, cNor and nosZ read abundance was positively associated with areas of higher soil moisture, higher nitrate and higher annual denitrification rates, whereas nirK and qNor read abundance was negatively associated with these factors. These results suggest that environmental conditions, in particular soil moisture and nitrate, select for distinct denitrification communities that are characterized by differential abundance of genes encoding apparently functionally redundant proteins. In contrast, taxonomic analysis did not identify notable variability in denitrifying community composition across sites. While the capacity to denitrify was ubiquitous across sites, denitrification genes with higher energetic costs, such as nirS and cNor, appear to confer a selective advantage in microbial communities experiencing more frequent soil saturation and greater nitrate inputs. This study suggests metagenomics can help identify denitrification hotspots that could be protected or enhanced to treat non-point source nitrogen pollution.}, }
@article {pmid30851123, year = {2019}, author = {Slavov, SN and Rodrigues, ES and Sauvage, V and Caro, V and Diefenbach, CF and Zimmermann, AM and Covas, DT and Laperche, S and Kashima, S}, title = {Parvovirus B19 seroprevalence, viral load, and genotype characterization in volunteer blood donors from southern Brazil.}, journal = {Journal of medical virology}, volume = {}, number = {}, pages = {}, doi = {10.1002/jmv.25453}, pmid = {30851123}, issn = {1096-9071}, support = {2009/16623-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; INCTC-FAPESP-2014/50947-7//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2017/23205-8//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; CTC-2013/081352//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; INCTC-465539/2014-9//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 455503/2014-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 245/2016//Financiadora de Estudos e Projetos/ ; }, abstract = {Usually transmitted via respiratory droplets, parvovirus B19 (B19V) can also be acquired by blood transfusion especially because of viral persistence, resistance to blood treatment procedures, and high viral load during the early infection phase. This is particularly problematic in immunocompromised or anemic patients where the infection can have a severe outcome. As B19V DNA was detected in blood donations from South Brazil during a viral metagenomic survey performed by Next-Generation Sequencing, the objective of this retrospective study was to evaluate the seroprevalence, B19V DNA presence and circulating genotypes in a Hospital Blood Transfusion Service in Santa Maria city in South Brazil (Rio Grande do Sul state). Among 480 volunteer blood donors, 53.9% (n = 258 of 479) were anti-B19V IgG-positive, and 9 (1.9%) plasma samples presented B19V DNA. In almost all cases (n = 7 of 9, 77.8%), B19V DNA load was accompanied by the presence of anti-B19V IgG suggesting a persistent infection. The sequencing of the strains demonstrated that all belong to genotype 1 which is the most prevalent worldwide. The analysis of the recipient information of the positive for B19V DNA units revealed no related posttransfusion adverse effects. Our results demonstrate for the first time, B19V seroprevalence, viral load, and genotypes among blood donors from South Brazil and give a light for the circulation and impact of this B19V in this part of the country.}, }
@article {pmid30851083, year = {2019}, author = {Calderon, D and Peña, L and Suarez, A and Villamil, C and Ramirez-Rojas, A and Anzola, JM and García-Betancur, JC and Cepeda, ML and Uribe, D and Del Portillo, P and Mongui, A}, title = {Recovery and functional validation of hidden soil enzymes in metagenomic libraries.}, journal = {MicrobiologyOpen}, volume = {8}, number = {4}, pages = {e00572}, doi = {10.1002/mbo3.572}, pmid = {30851083}, issn = {2045-8827}, abstract = {The vast microbial diversity on the planet represents an invaluable source for identifying novel activities with potential industrial and therapeutic application. In this regard, metagenomics has emerged as a group of strategies that have significantly facilitated the analysis of DNA from multiple environments and has expanded the limits of known microbial diversity. However, the functional characterization of enzymes, metabolites, and products encoded by diverse microbial genomes is limited by the inefficient heterologous expression of foreign genes. We have implemented a pipeline that combines NGS and Sanger sequencing as a way to identify fosmids within metagenomic libraries. This strategy facilitated the identification of putative proteins, subcloning of targeted genes and preliminary characterization of selected proteins. Overall, the in silico approach followed by the experimental validation allowed us to efficiently recover the activity of previously hidden enzymes derived from agricultural soil samples. Therefore, the methodology workflow described herein can be applied to recover activities encoded by environmental DNA from multiple sources.}, }
@article {pmid30850636, year = {2019}, author = {Hendriksen, RS and Munk, P and Njage, P and van Bunnik, B and McNally, L and Lukjancenko, O and Röder, T and Nieuwenhuijse, D and Pedersen, SK and Kjeldgaard, J and Kaas, RS and Clausen, PTLC and Vogt, JK and Leekitcharoenphon, P and van de Schans, MGM and Zuidema, T and de Roda Husman, AM and Rasmussen, S and Petersen, B and ,  and Amid, C and Cochrane, G and Sicheritz-Ponten, T and Schmitt, H and Alvarez, JRM and Aidara-Kane, A and Pamp, SJ and Lund, O and Hald, T and Woolhouse, M and Koopmans, MP and Vigre, H and Petersen, TN and Aarestrup, FM}, title = {Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1124}, doi = {10.1038/s41467-019-08853-3}, pmid = {30850636}, issn = {2041-1723}, mesh = {Africa ; Asia ; Bacteria/classification/*drug effects/genetics/isolation &amp; purification ; Drug Resistance, Multiple, Bacterial/*genetics ; Epidemiological Monitoring ; Europe ; *Genes, Bacterial ; Humans ; *Metagenome ; Metagenomics/methods ; Microbial Consortia/drug effects/genetics ; North America ; Oceania ; Population Health ; Sewage/*microbiology ; Socioeconomic Factors ; South America ; }, abstract = {Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use metagenomic analysis of untreated sewage to characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data and bacterial taxonomy only explains a minor part of the AMR variation that we observe. We find no evidence for cross-selection between antimicrobial classes, or for effect of air travel between sites. However, AMR gene abundance strongly correlates with socio-economic, health and environmental factors, which we use to predict AMR gene abundances in all countries in the world. Our findings suggest that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR. We propose metagenomic analysis of sewage as an ethically acceptable and economically feasible approach for continuous global surveillance and prediction of AMR.}, }
@article {pmid30850433, year = {2019}, author = {Graham, EB and Yang, F and Bell, S and Hofmockel, KS}, title = {High Genetic Potential for Proteolytic Decomposition in Northern Peatland Ecosystems.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02851-18}, pmid = {30850433}, issn = {1098-5336}, abstract = {Nitrogen (N) is a scarce nutrient commonly limiting primary productivity. Microbial decomposition of complex carbon (C) into small organic molecules (e.g., free amino acids) has been suggested to supplement biologically-fixed N in northern peatlands. We evaluated the microbial (fungal, bacterial, and archaeal) genetic potential for organic N depolymerization in peatlands at Marcell Experimental Forest (MEF) in northern Minnesota. We used guided gene assembly to examine the abundance and diversity of protease genes; and further compared to those of N-fixing (nifH) genes in shotgun metagenomic data collected across depths and in two distinct peatland environments (bogs and fens). Microbial proteases greatly outnumbered nifH genes with the most abundant genes (archaeal M1 and bacterial trypsin (S01)) each containing more sequences than all sequences attributed to nifH Bacterial protease gene assemblies were diverse and abundant across depth profiles, indicating a role for bacteria in releasing free amino acids from peptides through depolymerization of older organic material and contrasting the paradigm of fungal dominance in depolymerization in forest soils. Although protease gene assemblies for fungi were much less abundant overall than for bacteria, fungi were prevalent in surface samples and therefore may be vital in degrading large soil polymers from fresh plant inputs during early stage of depolymerization. In total, we demonstrate that depolymerization enzymes from a diverse suite of microorganisms, including understudied bacterial and archaeal lineages, are prevalent within northern peatlands and likely to influence C and N cycling.Importance Nitrogen (N) is a common limitation on primary productivity, and its source remains unresolved in northern peatlands that are vulnerable to environmental change. Decomposition of complex organic matter into free amino acids has been proposed as an important N source, but the genetic potential of microorganisms mediating this process has not been examined. Such information can elucidate possible responses of northern peatlands to environmental change. We show high genetic potential for microbial production of free amino acids across a range of microbial guilds in northern peatlands. In particular, the abundance and diversity of bacterial genes encoding proteolytic activity suggests a predominant role for bacteria in regulating productivity and contrasts a paradigm of fungal dominance of organic N decomposition. Our results expand our current understanding of coupled carbon and nitrogen cycles in north peatlands and indicate that understudied bacterial and archaeal lineages may be central in this ecosystem's response to environmental change.}, }
@article {pmid30847760, year = {2019}, author = {Valles, SM and Rivers, AR}, title = {Nine new RNA viruses associated with the fire ant Solenopsis invicta from its native range.}, journal = {Virus genes}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11262-019-01652-4}, pmid = {30847760}, issn = {1572-994X}, abstract = {The red imported fire ant (Solenopsis invicta) escaped its natural enemies when it was introduced into North America in the 1930s from South America. US efforts have focused on discovery of natural enemies, like viruses, to provide sustainable control of the ant. Nine new virus genomes were sequenced from the invasive fire ant Solenopsis invicta using metagenomic RNA sequencing. The virus genomes were verified by Sanger sequencing and random amplification of cDNA ends reactions. In addition to the nine new virus genomes, the previously described Solenopsis viruses were also detected, including Solenopsis invicta virus 1 (SINV-1), SINV-2, SINV-3, SINV-4, SINV-5, and Solenopsis invicta densovirus. The virus sequences came from S. invicta workers, larvae, pupae, and dead workers taken from midden piles collected from across the ant's native range in Formosa, Argentina. One of the new virus genomes (Solenopsis invicta virus 6) was also detected in populations of North American S. invicta. Phylogenetic analysis of the RNA dependent RNA polymerase, the entire nonstructural polyprotein, and genome characteristics were used to tentatively taxonomically place these new virus genome sequences; these include four new species of Dicistroviridae, one Polycipiviridae, one Iflaviridae, one Totiviridae, and two genome sequences that were too taxonomically divergent to be placed with certainty. The S. invicta virome is the best characterized from any ant species and includes 13 positive-sense, single-stranded RNA viruses (Solenopsis invicta virus 1 to Solenopsis invicta virus 13), one double-stranded RNA virus (Solenopsis midden virus), and one double-stranded DNA virus (Solenopsis invicta densovirus). These new additions to the S. invicta virome offer potentially new classical biological control agents for S. invicta.}, }
@article {pmid30847068, year = {2019}, author = {Dietrich, M and Markotter, W}, title = {Studying the microbiota of bats: Accuracy of direct and indirect samplings.}, journal = {Ecology and evolution}, volume = {9}, number = {4}, pages = {1730-1735}, doi = {10.1002/ece3.4842}, pmid = {30847068}, issn = {2045-7758}, abstract = {Given the recurrent bat-associated disease outbreaks in humans and recent advances in metagenomics sequencing, the microbiota of bats is increasingly being studied. However, obtaining biological samples directly from wild individuals may represent a challenge, and thus, indirect passive sampling (without capturing bats) is sometimes used as an alternative. Currently, it is not known whether the bacterial community assessed using this approach provides an accurate representation of the bat microbiota. This study was designed to compare the use of direct sampling (based on bat capture and handling) and indirect sampling (collection of bat's excretions under bat colonies) in assessing bacterial communities in bats. Using high-throughput 16S rRNA sequencing of urine and feces samples from Rousettus aegyptiacus, a cave-dwelling fruit bat species, we found evidence of niche specialization among different excreta samples, independent of the sampling approach. However, sampling approach influenced both the alpha- and beta-diversity of urinary and fecal microbiotas. In particular, increased alpha-diversity and more overlapping composition between urine and feces samples was seen when direct sampling was used, suggesting that cross-contamination may occur when collecting samples directly from bats in hand. In contrast, results from indirect sampling in the cave may be biased by environmental contamination. Our methodological comparison suggested some influence of the sampling approach on the bat-associated microbiota, but both approaches were able to capture differences among excreta samples. Assessment of these techniques opens an avenue to use more indirect sampling, in order to explore microbial community dynamics in bats.}, }
@article {pmid30846976, year = {2019}, author = {Kuntal, BK and Gadgil, C and Mande, SS}, title = {Web-gLV: A Web Based Platform for Lotka-Volterra Based Modeling and Simulation of Microbial Populations.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {288}, doi = {10.3389/fmicb.2019.00288}, pmid = {30846976}, issn = {1664-302X}, abstract = {The affordability of high throughput DNA sequencing has allowed us to explore the dynamics of microbial populations in various ecosystems. Mathematical modeling and simulation of such microbiome time series data can help in getting better understanding of bacterial communities. In this paper, we present Web-gLV-a GUI based interactive platform for generalized Lotka-Volterra (gLV) based modeling and simulation of microbial populations. The tool can be used to generate the mathematical models with automatic estimation of parameters and use them to predict future trajectories using numerical simulations. We also demonstrate the utility of our tool on few publicly available datasets. The case studies demonstrate the ease with which the current tool can be used by biologists to model bacterial populations and simulate their dynamics to get biological insights. We expect Web-gLV to be a valuable contribution in the field of ecological modeling and metagenomic systems biology.}, }
@article {pmid30846762, year = {2019}, author = {Cárcel-Márquez, J and Flores, A and Martín-Cabello, G and Santero, E and Camacho, EM}, title = {Development of an inducible lytic system for functional metagenomic screening.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {3887}, doi = {10.1038/s41598-019-40470-4}, pmid = {30846762}, issn = {2045-2322}, support = {SAF2017-85785-R//Ministerio de Educaci&amp;#x00F3;n, Cultura y Deporte (Ministry of Education, Culture and Sports, Spain)/ ; SAF2017-85785-R//Ministerio de Educaci&amp;#x00F3;n, Cultura y Deporte (Ministry of Education, Culture and Sports, Spain)/ ; SAF2017-85785-R//Ministerio de Educaci&amp;#x00F3;n, Cultura y Deporte (Ministry of Education, Culture and Sports, Spain)/ ; }, abstract = {Functional metagenomic is a powerful tool that allows the discovery of new enzymes with biotechnological potential. During functional screenings of enzymes, the ability of the substrate to enter the surrogate host or the ability of this bacterium to export heterologous extracellular enzymes may hamper the technique. Here we have used an inducible autolysis system that lyses bacteria thus releasing its content in both, liquid and solid cultures, in response to anhydrotetracycline. The lytic cluster is tightly regulated to prevent impaired bacterial growth in absence of the inducer and produced very efficient though not complete bacterial lysis upon induction, which allowed the recovery of live bacteria. The system can be used in combination with specialised fosmids and E. coli strains that maximize transcription of metagenomic DNA. Our results show that colony-lysis on plates allows detection of an endogenous intracellular amylase activity naturally present in E. coli and clearly increased detection of clones coding for cellulase activities in a metagenomic screening, while allowing recovery of survivor positive clones from the lysed colonies in all cases. Therefore, this tool represents an important step towards the effective access to the extraordinary potential of the uncultivated bacteria genetic resources.}, }
@article {pmid30844814, year = {2019}, author = {Yun, Y and Kim, HN and Chang, Y and Lee, Y and Ryu, S and Shin, H and Kim, WS and Kim, HL and Nam, JH}, title = {Characterization of the Blood Microbiota in Korean Females with Rosacea.}, journal = {Dermatology (Basel, Switzerland)}, volume = {}, number = {}, pages = {1-5}, doi = {10.1159/000496968}, pmid = {30844814}, issn = {1421-9832}, }
@article {pmid30844545, year = {2019}, author = {Haleyur, N and Shahsavari, E and Jain, SS and Koshlaf, E and Ravindran, VB and Morrison, PD and Osborn, AM and Ball, AS}, title = {Influence of bioaugmentation and biostimulation on PAH degradation in aged contaminated soils: Response and dynamics of the bacterial community.}, journal = {Journal of environmental management}, volume = {238}, number = {}, pages = {49-58}, doi = {10.1016/j.jenvman.2019.02.115}, pmid = {30844545}, issn = {1095-8630}, abstract = {Polycyclic aromatic hydrocarbons (PAHs) represent a group of hazardous compounds that are ubiquitous and persistent. The main aim of this study was to investigate the degradation of PAHs in chronically contaminated, aged and weathered soils obtained from a former gas plant of Australia. Biostimulation and bioaugmentation using individual isolates (Rhodococcus sp. (NH2), Achromobacter sp. (NH13), Oerskovia paurometabola (NH11), Pantoea sp. (NH15), Sejongia sp. (NH20), Microbacterium maritypicum (NH30) and Arthrobacter equi (NH21)) and a consortium of these isolates were tested during mesocosm studies. A significant reduction (99%) in PAH concentration was observed in all the treatments. In terms of the abundance of PAH-degrading genes and microbial community structure during PAH degradation, qPCR results revealed that Gram-positive bacteria were dominant over other bacterial communities in all the treatments. 16S sequencing results revealed that the inoculated organisms did not establish themselves during the treatment. However, substantial bacterial community changes during the treatments were observed, suggesting that the natural community exhibited sufficient resilience and diversity to enable an active, but changing degrading community at all stages of the degradation process. Consequently, biostimulation is proposed as the best strategy to remediate PAHs in aged, weathered and chronically contaminated soils.}, }
@article {pmid30844413, year = {2019}, author = {Amrane, S and Lagier, JC and Raoult, D}, title = {Failure of metagenomics in detecting emerging pathogens, the Clostridium difficile paradigm.}, journal = {The Journal of infection}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jinf.2019.02.014}, pmid = {30844413}, issn = {1532-2742}, }
@article {pmid30844070, year = {2019}, author = {Fritz, B and Stavnsbjerg, C and Markvart, M and Damgaard, PB and Nielsen, SH and Bjørndal, L and Qvortrup, K and Bjarnsholt, T}, title = {Shotgun sequencing of clinical biofilm following scanning electron microscopy identifies bacterial community composition.}, journal = {Pathogens and disease}, volume = {77}, number = {1}, pages = {}, doi = {10.1093/femspd/ftz013}, pmid = {30844070}, issn = {2049-632X}, abstract = {Bacterial biofilm infections often involve aggregates of bacteria heterogeneously distributed throughout a tissue or on a surface (such as an implanted medical device). Identification of a biofilm infection requires direct visualization via microscopy, followed by characterization of the microbial community by culturing or sequencing-based approaches. A sample, therefore, must be divided prior to analysis, often leading to inconsistent results. We demonstrate a combined approach, using scanning electron microscopy and next-generation shotgun sequencing, to visually identify a biofilm and characterize the microbial community, without dividing the sample. A clinical sample recovered from a patient following a dental root-filling procedure was prepared and visualized by scanning electron microscopy. DNA was then extracted from the sample several years later and analyzed by shotgun sequencing. The method was subsequently validated on in vitro cultures of Pseudomonas aeruginosa biofilm. Between 19 and 21 different genera and species were identified in the clinical sample with an estimated relative abundance greater than 1% by two different estimation approaches. Only eight genera identified were not associated with endodontic infections. This provides a proof-of-concept for a dual, microscopy and sequencing-based approach to identify and characterize bacterial biofilms, which could also easily be implemented in other scientific fields.}, }
@article {pmid30843322, year = {2019}, author = {More, KD and Giosan, L and Grice, K and Coolen, MJL}, title = {Holocene paleodepositional changes reflected in the sedimentary microbiome of the Black Sea.}, journal = {Geobiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/gbi.12338}, pmid = {30843322}, issn = {1472-4669}, support = {EAR 0952146//National Science Foundation/ ; OCE 0602423//National Science Foundation/ ; OCE 0825020//National Science Foundation/ ; //Woods Hole Oceanographic Institution/ ; }, abstract = {Subsurface microbial communities are generally thought to be structured through in situ environmental conditions such as the availability of electron acceptors and donors and porosity, but recent studies suggest that the vertical distribution of a subset of subseafloor microbial taxa, which were present at the time of deposition, were selected by the paleodepositional environment. However, additional highly resolved temporal records of subsurface microbiomes and paired paleoenvironmental reconstructions are needed to justify this claim. Here, we performed a highly resolved shotgun metagenomics survey to study the taxonomic and functional diversity of the subsurface microbiome in Holocene sediments underlying the permanently stratified and anoxic Black Sea. Obligate aerobic bacteria made the largest contribution to the observed shifts in microbial communities associated with known Holocene climate stages and transitions. This suggests that the aerobic fraction of the subseafloor microbiome was seeded from the water column and did not undergo post-depositional selection. In contrast, obligate and facultative anaerobic bacteria showed the most significant response to the establishment of modern-day environmental conditions 5.2 ka ago that led to a major shift in planktonic communities and in the type of sequestered organic matter available for microbial degradation. No significant shift in the subseafloor microbiome was observed as a result of environmental changes that occurred shortly after the marine reconnection, 9 ka ago. This supports the general view that the marine reconnection was a gradual process. We conclude that a high-resolution analysis of downcore changes in the subseafloor microbiome can provide detailed insights into paleoenvironmental conditions and biogeochemical processes that occurred at the time of deposition.}, }
@article {pmid30842565, year = {2019}, author = {Stewart, LC and Algar, CK and Fortunato, CS and Larson, BI and Vallino, JJ and Huber, JA and Butterfield, DA and Holden, JF}, title = {Fluid geochemistry, local hydrology, and metabolic activity define methanogen community size and composition in deep-sea hydrothermal vents.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0382-3}, pmid = {30842565}, issn = {1751-7370}, support = {GBMF 3297//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; GBMF 3297//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; GBMF 3297//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; GBMF 3297//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; NNX11AP78H//National Aeronautics and Space Administration (NASA)/ ; NNX11AP78H//National Aeronautics and Space Administration (NASA)/ ; OCE-1547004//NSF | GEO | Division of Ocean Sciences (OCE)/ ; OCE-0939564//NSF | GEO | Division of Ocean Sciences (OCE)/ ; OCE-1546695//NSF | GEO | Division of Ocean Sciences (OCE)/ ; GEO-1451356//NSF | GEO | Division of Earth Sciences (EAR)/ ; GEO-1238212//NSF | GEO | Division of Earth Sciences (EAR)/ ; NA15OAR4320063//United States Department of Commerce | National Oceanic and Atmospheric Administration (NOAA)/ ; }, abstract = {The size and biogeochemical impact of the subseafloor biosphere in oceanic crust remain largely unknown due to sampling limitations. We used reactive transport modeling to estimate the size of the subseafloor methanogen population, volume of crust occupied, fluid residence time, and nature of the subsurface mixing zone for two low-temperature hydrothermal vents at Axial Seamount. Monod CH4 production kinetics based on chemostat H2 availability and batch-culture Arrhenius growth kinetics for the hyperthermophile Methanocaldococcus jannaschii and thermophile Methanothermococcus thermolithotrophicus were used to develop and parameterize a reactive transport model, which was constrained by field measurements of H2, CH4, and metagenome methanogen concentration estimates in 20-40 °C hydrothermal fluids. Model results showed that hyperthermophilic methanogens dominate in systems where a narrow flow path geometry is maintained, while thermophilic methanogens dominate in systems where the flow geometry expands. At Axial Seamount, the residence time of fluid below the surface was 29-33 h. Only 1011 methanogenic cells occupying 1.8-18 m3 of ocean crust per m2 of vent seafloor area were needed to produce the observed CH4 anomalies. We show that variations in local geology at diffuse vents can create fluid flow paths that are stable over space and time, harboring persistent and distinct microbial communities.}, }
@article {pmid30842490, year = {2019}, author = {Chatterjee, A and Sicheritz-Pontén, T and Yadav, R and Kondabagil, K}, title = {Genomic and metagenomic signatures of giant viruses are ubiquitous in water samples from sewage, inland lake, waste water treatment plant, and municipal water supply in Mumbai, India.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {3690}, doi = {10.1038/s41598-019-40171-y}, pmid = {30842490}, issn = {2045-2322}, abstract = {We report the detection of genomic signatures of giant viruses (GVs) in the metagenomes of three environment samples from Mumbai, India, namely, a pre-filter of a household water purifier, a sludge sample from wastewater treatment plant (WWTP), and a drying bed sample of the same WWTP. The de novo assembled contigs of each sample yielded 700 to 2000 maximum unique matches with the GV genomic database. In all three samples, the maximum number of reads aligned to Pandoraviridae, followed by Phycodnaviridae, Mimiviridae, Iridoviridae, and other Megaviruses. We also isolated GVs from every environmental sample (n = 20) we tested using co-culture of the sample with Acanthomoeba castellanii. From this, four randomly selected GVs were subjected to the genomic characterization that showed remarkable cladistic homology with the three GV families viz., Mimivirirdae (Mimivirus Bombay [MVB]), Megaviruses (Powai lake megavirus [PLMV] and Bandra megavius [BAV]), and Marseilleviridae (Kurlavirus [KV]). All 4 isolates exhibited remarkable genomic identity with respective GV families. Functionally, the genomes were indistinguishable from other previously reported GVs, encoding nearly all COGs across extant family members. Further, the uncanny genomic homogeneity exhibited by individual GV families across distant geographies indicate their yet to be ascertained ecological significance.}, }
@article {pmid30842211, year = {2019}, author = {Zuo, T and Lu, XJ and Zhang, Y and Cheung, CP and Lam, S and Zhang, F and Tang, W and Ching, JYL and Zhao, R and Chan, PKS and Sung, JJY and Yu, J and Chan, FKL and Cao, Q and Sheng, JQ and Ng, SC}, title = {Gut mucosal virome alterations in ulcerative colitis.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2018-318131}, pmid = {30842211}, issn = {1468-3288}, abstract = {OBJECTIVE: The pathogenesis of UC relates to gut microbiota dysbiosis. We postulate that alterations in the viral community populating the intestinal mucosa play an important role in UC pathogenesis. This study aims to characterise the mucosal virome and their functions in health and UC.<br><br>DESIGN: Deep metagenomics sequencing of virus-like particle preparations and bacterial 16S rRNA sequencing were performed on the rectal mucosa of 167 subjects from three different geographical regions in China (UC=91; healthy controls=76). Virome and bacteriome alterations in UC mucosa were assessed and correlated with patient metadata. We applied partition around medoids clustering algorithm and classified mucosa viral communities into two clusters, referred to as mucosal virome metacommunities 1 and 2.<br><br>RESULTS: In UC, there was an expansion of mucosa viruses, particularly Caudovirales bacteriophages, and a decrease in mucosa Caudovirales diversity, richness and evenness compared with healthy controls. Altered mucosal virome correlated with intestinal inflammation. Interindividual dissimilarity between mucosal viromes was higher in UC than controls. Escherichia phage and Enterobacteria phage were more abundant in the mucosa of UC than controls. Compared with metacommunity 1, metacommunity 2 was predominated by UC subjects and displayed a significant loss of various viral species. Patients with UC showed substantial abrogation of diverse viral functions, whereas multiple viral functions, particularly functions of bacteriophages associated with host bacteria fitness and pathogenicity, were markedly enriched in UC mucosa. Intensive transkingdom correlations between mucosa viruses and bacteria were significantly depleted in UC.<br><br>CONCLUSION: We demonstrated for the first time that UC is characterised by substantial alterations of the mucosa virobiota with functional distortion. Enrichment of Caudovirales bacteriophages, increased phage/bacteria virulence functions and loss of viral-bacterial correlations in the UC mucosa highlight that mucosal virome may play an important role in UC pathogenesis.}, }
@article {pmid30841606, year = {2019}, author = {Kwon, M and Seo, SS and Kim, MK and Lee, DO and Lim, MC}, title = {Compositional and Functional Differences between Microbiota and Cervical Carcinogenesis as Identified by Shotgun Metagenomic Sequencing.}, journal = {Cancers}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/cancers11030309}, pmid = {30841606}, issn = {2072-6694}, support = {1610210//National Cancer Center/Republic of Korea ; }, abstract = {Recent studies have reported the potential role of microbiomes in cervical disease. However, little is known about the microbiome composition and function in cervical carcinogenesis. We aimed to identify the compositional and functional alterations of cervical microbiomes in cases of cervical carcinogenesis of Korean women using shotgun metagenomic sequencing. In this study, using shotgun sequencing, we sequenced the cervical metagenomes of cervical intraneoplasia 2/3 (n = 17), cervical cancer (n = 12), and normal controls (n = 18) to identify the microbial abundances and enriched metabolic functions in cervical metagenomes. At the genus level, the microbiota of cervical cancer were differentially enriched with genera Alkaliphilus, Pseudothermotoga, and Wolbachia. Cervical intraepithelial neoplasia (CIN) 2/3 were enriched with Lactobacillus, Staphylococcus, and Candidatus Endolissoclinum. The normal group was enriched with Pseudoalteromonas and Psychrobacter. Further characterization of the functionalities of the metagenomes may suggest that six Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologies (KOs) that are involved in 10 pathways are associated with an increased risk of CIN2/3 and cervical cancer. Specifically, cervical metagenomes were enriched in the course of peptidoglycan synthesis and depleted by dioxin degradation and 4-oxalocrotonate tautomerase. The Cluster of Orthologous Groups (COG) category 'Defense mechanisms' was depleted in cervical cancer patients. Our findings based on shotgun metagenomic sequencing suggest that cervical microbiome community compositions and their metagenomics profiles differed between cervical lesions and normal subjects. Future studies should have larger sample sizes and/or aggregate their results to have sufficient power to detect reproducible and significant associations.}, }
@article {pmid30841520, year = {2019}, author = {Sanborn, MA and Klein, TA and Kim, HC and Fung, CK and Figueroa, KL and Yang, Y and Asafo-Adjei, EA and Jarman, RG and Hang, J}, title = {Metagenomic Analysis Reveals Three Novel and Prevalent Mosquito Viruses from a Single Pool of Aedes vexans nipponii Collected in the Republic of Korea.}, journal = {Viruses}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/v11030222}, pmid = {30841520}, issn = {1999-4915}, support = {P0082_18_WR_02//Global Emerging Infections Surveillance and Response System (GEIS), Division of the Armed Forces Health Surveillance Center/ ; }, abstract = {Arboviruses continue to be a significant global health concern. The unbiased metagenomic analyses of mosquito-borne and mosquito-specific viruses are useful to understand viral diversity and for the surveillance of pathogens of medical and veterinary importance. Metagenomic analysis was conducted on 6368 mosquitoes (736 pools), covering 16 species from 18 locations throughout the Republic of Korea (ROK) in 2016. In this report, we describe three viruses detected in a single pool of Aedes vexans nipponii collected at Yongsan U.S. Army Garrison, located in a densely populated district of Seoul, the ROK. The three novel viruses, designated as Yongsan bunyavirus 1 (YBV1), Yongsan picorna-like virus 3 (YPLV3) and Yongsan sobemo-like virus 1 (YSLV1), share sequence and structural characteristics with members belonging to the family Bunyaviridae, order Picornavirales, and family Solemoviridae, with shared RNA-dependent RNA polymerase (RdRp) amino acid identities of 40%, 42% and 86%, respectively. The real-time reverse transcription and polymerase chain reaction (RT-PCR) of 3493 Aedes vexans nipponii (257 pools) showed a high prevalence of YBV1 and YSLV1 viruses, which were present in 65% and 62% of tested pools, respectively. This study highlighted the utility of a metagenomic sequencing approach for arbovirus discovery and for a better understanding of the virome of potential medically relevant vectors.}, }
@article {pmid30841491, year = {2019}, author = {Seifert, J and Muth, T}, title = {Editorial for Special Issue: Metaproteomics.}, journal = {Proteomes}, volume = {7}, number = {1}, pages = {}, doi = {10.3390/proteomes7010009}, pmid = {30841491}, issn = {2227-7382}, abstract = {As the proteome-level counterpart of metagenomics, metaproteomics extends conventional single-organism proteomics and allows researchers to characterize the entire protein complement of complex microbiomes on a large scale [...].}, }
@article {pmid30841395, year = {2019}, author = {Cordeiro, MC and Garcia, GD and Rocha, AM and Tschoeke, DA and Campeão, ME and Appolinario, LR and Soares, AC and Leomil, L and Froes, A and Bahiense, L and Rezende, CE and de Almeida, MG and Rangel, TP and De Oliveira, BCV and de Almeida, DQR and Thompson, MC and Thompson, CC and Thompson, FL}, title = {Insights on the freshwater microbiomes metabolic changes associated with the world's largest mining disaster.}, journal = {The Science of the total environment}, volume = {654}, number = {}, pages = {1209-1217}, doi = {10.1016/j.scitotenv.2018.11.112}, pmid = {30841395}, issn = {1879-1026}, mesh = {*Chemical Hazard Release ; Disasters ; *Environmental Monitoring ; Fresh Water/*microbiology ; Microbiota ; Mining ; *Water Microbiology ; Water Pollutants, Chemical/*analysis ; }, abstract = {To evaluate the impacts of the Fundão tailings dam failure (Minas Gerais, Brazil) on water quality of the Doce River, we analyzed metagenomics and physicochemical parameters during the month of the disaster and again 6 and 10 months after the disaster. To compare dam conditions before and after the failure, we performed a meta-analysis of physicochemical data from a public database. Immediately after the failure, suspended particulate matter (SPM) in the Doce River was 225-1877 mg L-1. Turbidity and dissolved aluminum and iron concentrations were extremely high, whereas dissolved oxygen was below Brazilian legislation norm (<5 mg L-1) in several locations. Six months later, physicochemical values were below thresholds set by Brazilian guidelines (e.g., SPM = 8-166 mg L-1). Short-term impacts on microbial communities included an increase in Actinobacteria and Bacteroidetes and gene sequences related to microbial virulence, motility, respiration, membrane transport, iron and nitrogen metabolism, suggesting changes in microbial metabolic profiles. The 11 recovered partial genomes from metagenomes (MAGs) had genes related to Fe cycle and metal resistance.}, }
@article {pmid30838598, year = {2019}, author = {Divaris, K and Shungin, D and Rodríguez-Cortés, A and Basta, PV and Roach, J and Cho, H and Wu, D and Ferreira Zandoná, AG and Ginnis, J and Ramamoorthy, S and Kinchen, JM and Kwintkiewicz, J and Butz, N and Ribeiro, AA and Azcarate-Peril, MA}, title = {The Supragingival Biofilm in Early Childhood Caries: Clinical and Laboratory Protocols and Bioinformatics Pipelines Supporting Metagenomics, Metatranscriptomics, and Metabolomics Studies of the Oral Microbiome.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1922}, number = {}, pages = {525-548}, doi = {10.1007/978-1-4939-9012-2_40}, pmid = {30838598}, issn = {1940-6029}, support = {U01 DE025046/DE/NIDCR NIH HHS/United States ; }, abstract = {Early childhood caries (ECC) is a biofilm-mediated disease. Social, environmental, and behavioral determinants as well as innate susceptibility are major influences on its incidence; however, from a pathogenetic standpoint, the disease is defined and driven by oral dysbiosis. In other words, the disease occurs when the natural equilibrium between the host and its oral microbiome shifts toward states that promote demineralization at the biofilm-tooth surface interface. Thus, a comprehensive understanding of dental caries as a disease requires the characterization of both the composition and the function or metabolic activity of the supragingival biofilm according to well-defined clinical statuses. However, taxonomic and functional information of the supragingival biofilm is rarely available in clinical cohorts, and its collection presents unique challenges among very young children. This paper presents a protocol and pipelines available for the conduct of supragingival biofilm microbiome studies among children in the primary dentition, that has been designed in the context of a large-scale population-based genetic epidemiologic study of ECC. The protocol is being developed for the collection of two supragingival biofilm samples from the maxillary primary dentition, enabling downstream taxonomic (e.g., metagenomics) and functional (e.g., transcriptomics and metabolomics) analyses. The protocol is being implemented in the assembly of a pediatric precision medicine cohort comprising over 6000 participants to date, contributing social, environmental, behavioral, clinical, and biological data informing ECC and other oral health outcomes.}, }
@article {pmid30838416, year = {2019}, author = {Miller, IJ and Rees, ER and Ross, J and Miller, I and Baxa, J and Lopera, J and Kerby, RL and Rey, FE and Kwan, JC}, title = {Autometa: automated extraction of microbial genomes from individual shotgun metagenomes.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkz148}, pmid = {30838416}, issn = {1362-4962}, abstract = {Shotgun metagenomics is a powerful, high-resolution technique enabling the study of microbial communities in situ. However, species-level resolution is only achieved after a process of 'binning' where contigs predicted to originate from the same genome are clustered. Such culture-independent sequencing frequently unearths novel microbes, and so various methods have been devised for reference-free binning. As novel microbiomes of increasing complexity are explored, sometimes associated with non-model hosts, robust automated binning methods are required. Existing methods struggle with eukaryotic contamination and cannot handle highly complex single metagenomes. We therefore developed an automated binning pipeline, termed 'Autometa', to address these issues. This command-line application integrates sequence homology, nucleotide composition, coverage and the presence of single-copy marker genes to separate microbial genomes from non-model host genomes and other eukaryotic contaminants, before deconvoluting individual genomes from single metagenomes. The method is able to effectively separate over 1000 genomes from a metagenome, allowing the study of previously intractably complex environments at the level of single species. Autometa is freely available at https://bitbucket.org/jason_c_kwan/autometa and as a docker image at https://hub.docker.com/r/jasonkwan/autometa under the GNU Affero General Public License 3 (AGPL 3).}, }
@article {pmid30838178, year = {2019}, author = {Nearing, JT and Connors, J and Whitehouse, S and Van Limbergen, J and Macdonald, T and Kulkarni, K and Langille, MGI}, title = {Infectious Complications Are Associated With Alterations in the Gut Microbiome in Pediatric Patients With Acute Lymphoblastic Leukemia.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {28}, doi = {10.3389/fcimb.2019.00028}, pmid = {30838178}, issn = {2235-2988}, abstract = {Acute lymphoblastic leukemia is the most common pediatric cancer. Fortunately, survival rates exceed 90%, however, infectious complications remain a significant issue that can cause reductions in the quality of life and prognosis of patients. Recently, numerous studies have linked shifts in the gut microbiome composition to infection events in various hematological malignances including acute lymphoblastic leukemia (ALL). These studies have been limited to observing broad taxonomic changes using 16S rRNA gene profiling, while missing possible differences within microbial functions encoded by individual species. In this study we present the first combined 16S rRNA gene and metagenomic shotgun sequencing study on the gut microbiome of an independent pediatric ALL cohort during treatment. In this study we found distinctive differences in alpha diversity and beta diversity in samples from patients with infectious complications in the first 6 months of therapy. We were also able to find specific species and functional pathways that were significantly different in relative abundance between samples that came from patients with infectious complications. Finally, machine learning models based on patient metadata and bacterial species were able to classify samples with high accuracy (84.09%), with bacterial species being the most important classifying features. This study strengthens our understanding of the association between infection and pediatric acute lymphoblastic leukemia treatment and warrants further investigation in the future.}, }
@article {pmid30837951, year = {2019}, author = {Covasa, M and Stephens, RW and Toderean, R and Cobuz, C}, title = {Intestinal Sensing by Gut Microbiota: Targeting Gut Peptides.}, journal = {Frontiers in endocrinology}, volume = {10}, number = {}, pages = {82}, doi = {10.3389/fendo.2019.00082}, pmid = {30837951}, issn = {1664-2392}, abstract = {There are more than 2 billion overweight and obese individuals worldwide, surpassing for the first time, the number of people affected by undernutrition. Obesity and its comorbidities inflict a heavy burden on the global economies and have become a serious threat to individuals' wellbeing with no immediate cure available. The causes of obesity are manifold, involving several factors including physiological, metabolic, neural, psychosocial, economic, genetics and the environment, among others. Recent advances in genome sequencing and metagenomic profiling have added another dimension to this complexity by implicating the gut microbiota as an important player in energy regulation and the development of obesity. As such, accumulating evidence demonstrate the impact of the gut microbiota on body weight, adiposity, glucose, lipid metabolism, and metabolic syndrome. This also includes the role of microbiota as a modulatory signal either directly or through its bioactive metabolites on intestinal lumen by releasing chemosensing factors known to have a major role in controlling food intake and regulating body weight. The importance of gut signaling by microbiota signaling is further highlighted by the presence of taste and nutrient receptors on the intestinal epithelium activated by the microbial degradation products as well as their role in release of peptides hormones controlling appetite and energy homeostasis. This review present evidence on how gut microbiota interacts with intestinal chemosensing and modulates the release and activity of gut peptides, particularly GLP-1 and PYY.}, }
@article {pmid30837511, year = {2019}, author = {Gałan, W and Bąk, M and Jakubowska, M}, title = {Host Taxon Predictor - A Tool for Predicting Taxon of the Host of a Newly Discovered Virus.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {3436}, doi = {10.1038/s41598-019-39847-2}, pmid = {30837511}, issn = {2045-2322}, abstract = {Recent advances in metagenomics provided a valuable alternative to culture-based approaches for better sampling viral diversity. However, some of newly identified viruses lack sequence similarity to any of previously sequenced ones, and cannot be easily assigned to their hosts. Here we present a bioinformatic approach to this problem. We developed classifiers capable of distinguishing eukaryotic viruses from the phages achieving almost 95% prediction accuracy. The classifiers are wrapped in Host Taxon Predictor (HTP) software written in Python which is freely available at https://github.com/wojciech-galan/viruses_classifier . HTP's performance was later demonstrated on a collection of newly identified viral genomes and genome fragments. In summary, HTP is a culture- and alignment-free approach for distinction between phages and eukaryotic viruses. We have also shown that it is possible to further extend our method to go up the evolutionary tree and predict whether a virus can infect narrower taxa.}, }
@article {pmid30837458, year = {2019}, author = {Reveillaud, J and Bordenstein, SR and Cruaud, C and Shaiber, A and Esen, ÖC and Weill, M and Makoundou, P and Lolans, K and Watson, AR and Rakotoarivony, I and Bordenstein, SR and Eren, AM}, title = {The Wolbachia mobilome in Culex pipiens includes a putative plasmid.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1051}, doi = {10.1038/s41467-019-08973-w}, pmid = {30837458}, issn = {2041-1723}, support = {R01 AI132581/AI/NIAID NIH HHS/United States ; R21 AI133522/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteriophages/genetics ; Culex/*microbiology ; Female ; France ; Genome, Bacterial/*genetics ; Host Microbial Interactions/genetics ; Metagenome/*genetics ; Metagenomics/methods ; Mosquito Vectors/microbiology ; Ovary/microbiology ; Plasmids/*genetics ; Sequence Analysis, DNA ; Symbiosis/genetics ; Wolbachia/*genetics/virology ; }, abstract = {Wolbachia is a genus of obligate intracellular bacteria found in nematodes and arthropods worldwide, including insect vectors that transmit dengue, West Nile, and Zika viruses. Wolbachia's unique ability to alter host reproductive behavior through its temperate bacteriophage WO has enabled the development of new vector control strategies. However, our understanding of Wolbachia's mobilome beyond its bacteriophages is incomplete. Here, we reconstruct near-complete Wolbachia genomes from individual ovary metagenomes of four wild Culex pipiens mosquitoes captured in France. In addition to viral genes missing from the Wolbachia reference genome, we identify a putative plasmid (pWCP), consisting of a 9.23-kbp circular element with 14 genes. We validate its presence in additional Culex pipiens mosquitoes using PCR, long-read sequencing, and screening of existing metagenomes. The discovery of this previously unrecognized extrachromosomal element opens additional possibilities for genetic manipulation of Wolbachia.}, }
@article {pmid30837341, year = {2019}, author = {Nasko, DJ and Ferrell, BD and Moore, RM and Bhavsar, JD and Polson, SW and Wommack, KE}, title = {CRISPR Spacers Indicate Preferential Matching of Specific Virioplankton Genes.}, journal = {mBio}, volume = {10}, number = {2}, pages = {}, doi = {10.1128/mBio.02651-18}, pmid = {30837341}, issn = {2150-7511}, support = {P20 GM103446/GM/NIGMS NIH HHS/United States ; R21 AI109555/AI/NIAID NIH HHS/United States ; }, abstract = {Viral infection exerts selection pressure on marine microbes, as virus-induced cell lysis causes 20 to 50% of cell mortality, resulting in fluxes of biomass into oceanic dissolved organic matter. Archaeal and bacterial populations can defend against viral infection using the clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) system, which relies on specific matching between a spacer sequence and a viral gene. If a CRISPR spacer match to any gene within a viral genome is equally effective in preventing lysis, no viral genes should be preferentially matched by CRISPR spacers. However, if there are differences in effectiveness, certain viral genes may demonstrate a greater frequency of CRISPR spacer matches. Indeed, homology search analyses of bacterioplankton CRISPR spacer sequences against virioplankton sequences revealed preferential matching of replication proteins, nucleic acid binding proteins, and viral structural proteins. Positive selection pressure for effective viral defense is one parsimonious explanation for these observations. CRISPR spacers from virioplankton metagenomes preferentially matched methyltransferase and phage integrase genes within virioplankton sequences. These virioplankton CRISPR spacers may assist infected host cells in defending against competing phage. Analyses also revealed that half of the spacer-matched viral genes were unknown, some genes matched several spacers, and some spacers matched multiple genes, a many-to-many relationship. Thus, CRISPR spacer matching may be an evolutionary algorithm, agnostically identifying those genes under stringent selection pressure for sustaining viral infection and lysis. Investigating this subset of viral genes could reveal those genetic mechanisms essential to virus-host interactions and provide new technologies for optimizing CRISPR defense in beneficial microbes.IMPORTANCE The CRISPR-Cas system is one means by which bacterial and archaeal populations defend against viral infection which causes 20 to 50% of cell mortality in the ocean. We tested the hypothesis that certain viral genes are preferentially targeted for the initial attack of the CRISPR-Cas system on a viral genome. Using CASC, a pipeline for CRISPR spacer discovery, and metagenome data from oceanic microbes and viruses, we found a clear subset of viral genes with high match frequencies to CRISPR spacers. Moreover, we observed a many-to-many relationship of spacers and viral genes. These high-match viral genes were involved in nucleotide metabolism, DNA methylation, and viral structure. It is possible that CRISPR spacer matching is an evolutionary algorithm pointing to those viral genes most important to sustaining infection and lysis. Studying these genes may advance the understanding of virus-host interactions in nature and provide new technologies for leveraging CRISPR-Cas systems in beneficial microbes.}, }
@article {pmid30837339, year = {2019}, author = {Bäckström, D and Yutin, N and Jørgensen, SL and Dharamshi, J and Homa, F and Zaremba-Niedwiedzka, K and Spang, A and Wolf, YI and Koonin, EV and Ettema, TJG}, title = {Virus Genomes from Deep Sea Sediments Expand the Ocean Megavirome and