@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.
METHODS: We used a simultaneous equation and comparative selection method to identify genes associated with hypertension using the Reactome analysis tool and GenBank database.
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.
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 = {100/974/C/13/Z//Wellcome Trust/United Kingdom ; BB/M011216/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012490/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; None//Winnicott Foundation/ ; }, 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.
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.
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 = {}, number = {}, pages = {}, 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}, 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 analyzed. 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. This article is protected by copyright. All rights reserved.}, }
@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}, 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.
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.
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.
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.
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 {pmid30609875, year = {2019}, author = {Waseem, H and Jameel, S and Ali, J and Saleem Ur Rehman, H and Tauseef, I and Farooq, U and Jamal, A and Ali, MI}, title = {Contributions and Challenges of High Throughput qPCR for Determining Antimicrobial Resistance in the Environment: A Critical Review.}, journal = {Molecules (Basel, Switzerland)}, volume = {24}, number = {1}, pages = {}, doi = {10.3390/molecules24010163}, pmid = {30609875}, issn = {1420-3049}, mesh = {Anti-Infective Agents/*pharmacology ; Computational Biology/methods ; Data Analysis ; *Drug Resistance, Microbial ; *Environmental Microbiology ; Gastrointestinal Microbiome ; Genes, Bacterial ; *High-Throughput Screening Assays ; Humans ; Metagenome ; Metagenomics/methods ; Quality Control ; *Real-Time Polymerase Chain Reaction ; }, abstract = {Expansion in whole genome sequencing and subsequent increase in antibiotic resistance targets have paved the way of high throughput qPCR (HT-qPCR) for analyzing hundreds of antimicrobial resistance genes (ARGs) in a single run. A meta-analysis of 51 selected studies is performed to evaluate ARGs abundance trends over the last 7 years. WaferGenTM SmartChip is found to be the most widely used HT-qPCR platform among others for evaluating ARGs. Up till now around 1000 environmental samples (excluding biological replicates) from different parts of the world have been analyzed on HT-qPCR. Calculated detection frequency and normalized ARGs abundance (ARGs/16S rRNA gene) reported in gut microbiome studies have shown a trend of low ARGs as compared to other environmental matrices. Disparities in the HT-qPCR data analysis which are causing difficulties to researchers in precise interpretation of results have been highlighted and a possible way forward for resolving them is also suggested. The potential of other amplification technologies and point of care or field deployable devices for analyzing ARGs have also been discussed in the review. Our review has focused on updated information regarding the role, current status and future perspectives of HT-qPCR in the field of antimicrobial resistance.}, }
@article {pmid29611114, year = {2018}, author = {Wang, J and Chen, L and Zhao, N and Xu, X and Xu, Y and Zhu, B}, title = {Of genes and microbes: solving the intricacies in host genomes.}, journal = {Protein & cell}, volume = {9}, number = {5}, pages = {446-461}, pmid = {29611114}, issn = {1674-8018}, mesh = {Animals ; Biomedical Research ; *Genes ; *Genetic Variation ; *Genome ; Host-Pathogen Interactions/*genetics ; Humans ; Metagenomics ; *Microbiota ; }, abstract = {Microbiome research is a quickly developing field in biomedical research, and we have witnessed its potential in understanding the physiology, metabolism and immunology, its critical role in understanding the health and disease of the host, and its vast capacity in disease prediction, intervention and treatment. However, many of the fundamental questions still need to be addressed, including the shaping forces of microbial diversity between individuals and across time. Microbiome research falls into the classical nature vs. nurture scenario, such that host genetics shape part of the microbiome, while environmental influences change the original course of microbiome development. In this review, we focus on the nature, i.e., the genetic part of the equation, and summarize the recent efforts in understanding which parts of the genome, especially the human and mouse genome, play important roles in determining the composition and functions of microbial communities, primarily in the gut but also on the skin. We aim to present an overview of different approaches in studying the intricate relationships between host genetic variations and microbes, its underlying philosophy and methodology, and we aim to highlight a few key discoveries along this exploration, as well as current pitfalls. More evidence and results will surely appear in upcoming studies, and the accumulating knowledge will lead to a deeper understanding of what we could finally term a "hologenome", that is, the organized, closely interacting genome of the host and the microbiome.}, }
@article {pmid28827532, year = {2017}, author = {Jiang, J and Song, Z and Yang, X and Mao, Z and Nie, X and Guo, H and Peng, X}, title = {Microbial community analysis of apple rhizosphere around Bohai Gulf.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {8918}, pmid = {28827532}, issn = {2045-2322}, mesh = {Biodiversity ; Environment ; Malus/*microbiology ; Metagenome ; Metagenomics ; *Microbiota ; Plant Roots/microbiology ; *Rhizosphere ; *Soil Microbiology ; }, abstract = {Bohai Gulf is the main area for apple tree cultivation in China. Consecutive replanting significantly affects the yield and quality of apple trees in this area. Microecological imbalance in apple trees' rhizospheres caused by variation in the soil microbial community is considered the primary cause of apple replant disease (ARD). This study analysed the microbial communities of the rhizospheres of perennial apple trees (PAT) and apple tree saplings under replanting (ATS) around Bohai Gulf using high-throughput sequencing. The results revealed increased populations of typical pathogenic fungi Verticillium and bacteria Xanthomonadaceae, and decreased populations of beneficial bacterial populations Pseudomonas and Bacillus with replanting, suggesting that competition between pathogens and beneficial microbes varies according to the ratio of pathogens to beneficial microbes in rhizosphere soil under the replanting system. Meanwhile, replanting was accompanied by an increase in the antagonistic bacteria Arthrobacter and fungus Chaetomium, suggesting that increased numbers of pathogens can lead to more instances of antagonism. Redundancy analysis (RDA) revealed site position and the main soil properties (pH, organic matter, available N, available K, available P, and moisture) affected the microbial community composition. It found clear differences in soil microbial communities and demonstrated a better understanding of the causes for ARD.}, }
@article {pmid28821872, year = {2017}, author = {Nakagawa, S and Saito, H and Tame, A and Hirai, M and Yamaguchi, H and Sunata, T and Aida, M and Muto, H and Sawayama, S and Takaki, Y}, title = {Microbiota in the coelomic fluid of two common coastal starfish species and characterization of an abundant Helicobacter-related taxon.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {8764}, pmid = {28821872}, issn = {2045-2322}, mesh = {Animals ; *Biodiversity ; Fish Diseases/microbiology ; Helicobacter/*classification/*genetics ; Metagenome ; Metagenomics/methods ; *Microbiota ; Phylogeography ; RNA, Ribosomal, 16S/genetics ; Starfish/*microbiology ; }, abstract = {Marine invertebrates associate with diverse microorganisms. Microorganisms even inhabit coelomic fluid (CF), namely, the fluid filling the main body cavity of echinoderms. The CF microbiota potentially impacts host health and disease. Here, we analysed the CF microbiota in two common coastal starfish species, Patiria pectinifera and Asterias amurensis. Although microbial community structures were highly variable among individual starfish, those of P. pectinifera were compositionally similar to those in the surrounding seawater. By contrast, many A. amurensis individuals harboured unique microbes in the CF, which was dominated by the unclassified Thiotrichales or previously unknown Helicobacter-related taxon. In some individuals, the Helicobacter-related taxon was the most abundant genus-level taxon, accounting for up to 97.3% of reads obtained from the CF microbial community. Fluorescence in situ hybridization using a Helicobacter-related-taxon-specific probe suggested that probe-reactive cells in A. amurensis were spiral-shaped, morphologically similar to known Helicobacter species. Electron microscopy revealed that the spiral cells had a prosthecate-like polar appendage that has never been reported in Helicobacter species. Although culture of Helicobacter-related taxon was unsuccessful, this is the first report of the dominance of a Helicobacter-related taxon in invertebrates and non-digestive organs, reshaping our knowledge of the phylogeography of Helicobacter-related taxa.}, }
@article {pmid28821814, year = {2017}, author = {Fang, D and Shi, D and Lv, L and Gu, S and Wu, W and Chen, Y and Guo, J and Li, A and Hu, X and Guo, F and Ye, J and Li, Y and Li, L}, title = {Bifidobacterium pseudocatenulatum LI09 and Bifidobacterium catenulatum LI10 attenuate D-galactosamine-induced liver injury by modifying the gut microbiota.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {8770}, pmid = {28821814}, issn = {2045-2322}, mesh = {Animals ; Bifidobacterium/*physiology ; Bifidobacterium pseudocatenulatum/*physiology ; Cytokines/blood/metabolism ; Galactosamine/*adverse effects ; Gastrointestinal Microbiome/*drug effects ; Inflammation Mediators/blood/metabolism ; Intestinal Mucosa/drug effects/metabolism/pathology ; Liver Diseases/*etiology/metabolism/pathology ; Male ; Metagenome ; Metagenomics ; Models, Biological ; Rats ; }, abstract = {The gut microbiota is altered in liver diseases, and several probiotics have been shown to reduce the degree of liver damage. We hypothesized that oral administration of specific Bifidobacterium strains isolated from healthy guts could attenuate liver injury. Five strains were tested in this study. Acute liver injury was induced by D-galactosamine after pretreating Sprague-Dawley rats with the Bifidobacterium strains, and liver function, liver and ileum histology, plasma cytokines, bacterial translocation and the gut microbiome were assessed. Two strains, Bifidobacterium pseudocatenulatum LI09 and Bifidobacterium catenulatum LI10, conferred liver protection, as well as alleviated the increase in plasma M-CSF, MIP-1α and MCP-1 and bacterial translocation. They also ameliorated ileal mucosal injury and gut flora dysbiosis, especially the enrichment of the opportunistic pathogen Parasutterella and the depletion of the SCFA-producing bacteria Anaerostipes, Coprococcus and Clostridium XI. Negative correlations were found between MIP-1α / MCP-1 and Odoribacter (LI09 group) and MIP-1α / M-CSF and Flavonifractor (LI10 group). Our results indicate that the liver protection effects might be mediated through gut microbiota modification, which thus affect the host immune profile. The desirable characteristics of these two strains may enable them to serve as potential probiotics for the prevention or adjuvant treatment of liver injury.}, }
@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 & Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; R01ES024950//U.S. Department of Health & Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; R01ES024950//U.S. Department of Health & Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; R01ES024950//U.S. Department of Health & Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; R01ES024950//U.S. Department of Health & Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; R01ES024950//U.S. Department of Health & Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; R01ES024950//U.S. Department of Health & 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.
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.
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 & 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.
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.
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 {pmid30594064, year = {2019}, author = {Procopio, N and Ghignone, S and Williams, A and Chamberlain, A and Mello, A and Buckley, M}, title = {Metabarcoding to investigate changes in soil microbial communities within forensic burial contexts.}, journal = {Forensic science international. Genetics}, volume = {39}, number = {}, pages = {73-85}, doi = {10.1016/j.fsigen.2018.12.002}, pmid = {30594064}, issn = {1878-0326}, mesh = {Animals ; Burial ; DNA Barcoding, Taxonomic/*methods ; Forensic Sciences ; Metagenomics/methods ; Microbiota/*genetics ; Models, Animal ; Polymerase Chain Reaction ; *Postmortem Changes ; RNA, Ribosomal, 16S ; *Soil Microbiology ; Swine ; }, abstract = {The estimation of the time elapsed since death (post-mortem interval, or PMI) is one of the key themes that forensic scientists have to address frequently. However, the estimation of PMI still suffers from poor accuracy and biases especially when decomposition stages are prolonged, so further improvements in methods for PMI estimation are desirable. Soil microbial communities associated with decomposing bodies have been shown to be good candidates for the estimation of the PMI of exposed bodies. Nevertheless, further research is required to better understand the bacterial succession associated with decomposition of buried carcasses in order to test its reliability and applicability for the estimation of PMI and to better understand the dynamics involved with decomposition within this particular scenario. Therefore we explored the succession of soil microbial communities associated with four decomposing pig carcasses (from one to six months PMI) using a metabarcoding approach. The sequencing of the bacterial 16S rRNA variable region 4 (V4) revealed trends linking particular microbial taxa with specific PMIs, and notably an increase in Proteobacteria, Firmicutes and Bacteroidetes at specific PMIs as well as a decrease in Acidobacteria. Our results, in accordance with previous studies conducted on exposed bodies of different mammalian species (including humans), also showed a general reduction of the taxonomic richness from two months PMI onwards, as well as an incomplete re-establishment of the starting soil microbial conditions after six months PMI. We also found specific mammal-derived taxa, such as Bacteroides spp., being still present in the soil after six months PMI. As such, this study serves as a baseline for additional research to allow the characterisation of biomarkers associated with specific PMIs. Due to the similarity between the results presented here and those reported in other types of decomposition studies we believe that the metabarcoding approach has considerable potential in the estimation of the PMI, particularly to clarify cases involving heavily skeletonised bodies or for the investigation of clandestine graves in which the carcass has been moved from its original place of deposition.}, }
@article {pmid30496170, year = {2018}, author = {Shoko, R and Manasa, J and Maphosa, M and Mbanga, J and Mudziwapasi, R and Nembaware, V and Sanyika, WT and Tinago, T and Chikwambi, Z and Mawere, C and Matimba, A and Mugumbate, G and Mufandaedza, J and Mulder, N and Patterton, H}, title = {Strategies and opportunities for promoting bioinformatics in Zimbabwe.}, journal = {PLoS computational biology}, volume = {14}, number = {11}, pages = {e1006480}, doi = {10.1371/journal.pcbi.1006480}, pmid = {30496170}, issn = {1553-7358}, mesh = {*Computational Biology ; Food Supply ; Health Status Indicators ; Humans ; Interprofessional Relations ; Metagenomics ; Zimbabwe/epidemiology ; }, }
@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 & technology}, volume = {}, number = {}, pages = {}, 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. Based on 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. 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 {pmid30864339, year = {2019}, author = {Gürsoy, G and Harmanci, A and Tang, H and Ayday, E and Brenner, SE}, title = {When Biology Gets Personal: Hidden Challenges of Privacy and Ethics in Biological Big Data.}, journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing}, volume = {24}, number = {}, pages = {386-390}, pmid = {30864339}, issn = {2335-6936}, abstract = {High-throughput technologies for biological data acquisition are advancing at an increasing pace. Most prominently, the decreasing cost of DNA sequencing has led to an exponential growth of sequence information, including individual human genomes. This session of the 2019 Pacific Symposium on Biocomputing presents the distinctive privacy and ethical challenges related to the generation, storage, processing, study, and sharing of individuals' biological data generated by multitude of technologies including but not limited to genomics, proteomics, metagenomics, bioimaging, biosensors, and personal health trackers. The mission is to bring together computational biologists, experimental biologists, computer scientists, ethicists, and policy and lawmakers to share ideas, discuss the challenges related to biological data and privacy.}, }
@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}, 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}, 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 and clinical outcome in HB-ACLF.
METHODS: Plasma from 50 HB-ACLF patients, 23 healthy controls (HCs) and 25 patients with compensated liver cirrhosis (C-LC) was analyzed for chemokines/cytokines and bacterial DNA and further analysed by 16S rDNApyrosequencing. Linear discriminant analysis effect size (LEfSe) and inferred metagenomics analyses were performed.
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. Networkanalysis 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.
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 systemic inflammation (SI) and clinical outcome in HB-ACLF. This article is protected by copyright. All rights reserved.}, }
@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 {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.
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.
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.
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 & 859603//Österreichische Forschungsförderungsgesellschaft (Austrian Research Promotion Agency)/ ; 853863 & 859603//Österreichische Forschungsförderungsgesellschaft (Austrian Research Promotion Agency)/ ; 853863 & 859603//Österreichische Forschungsförderungsgesellschaft (Austrian Research Promotion Agency)/ ; 853863 & 859603//Österreichische Forschungsförderungsgesellschaft (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 {pmid29961769, year = {2019}, author = {Bylstra, Y and Kuan, JL and Lim, WK and Bhalshankar, JD and Teo, JX and Davila, S and Teh, BT and Rozen, S and Tan, EC and Liew, WKM and Yeo, KK and Tan, P and , and Saw, SM and Cheng, CY and Cook, S and Foo, R and Jamuar, SS}, title = {Population genomics in South East Asia captures unexpectedly high carrier frequency for treatable inherited disorders.}, journal = {Genetics in medicine : official journal of the American College of Medical Genetics}, volume = {21}, number = {1}, pages = {207-212}, doi = {10.1038/s41436-018-0008-6}, pmid = {29961769}, issn = {1530-0366}, mesh = {Asia ; Ethnic Groups ; Exome/*genetics ; Gene Frequency ; *Genetic Carrier Screening ; Genetic Diseases, Inborn/classification/epidemiology/*genetics/pathology ; *Genetic Predisposition to Disease ; Genetic Variation ; Genetics, Population ; Humans ; Male ; Metagenomics ; Mutation/genetics ; Precision Medicine ; }, abstract = {PURPOSE: Genomic studies have demonstrated the necessity of ethnicity-specific population data to ascertain variant pathogenicity for disease diagnosis and treatment. This study examined the carrier prevalence of treatable inherited disorders (TIDs), where early diagnosis of at-risk offspring can significantly improve clinical outcomes.
METHODS: Existing exome/ genome sequencing data of 831 Singaporeans were aggregated and examined for disease causing variants in 104 genes associated with 80 TIDs.
RESULTS: Among the 831 Singaporean participants, genomic variant filtering and analysis identified 1 in 18 individuals (6%) to be carriers amongst one of 13 TIDs. Citrin deficiency and Wilson disease had the highest carrier frequency of 1 in 41, and 1 in 103 individuals, respectively. The pathogenic variants associated with citrin deficiency were 24 times more prevalent in our local cohorts when compared to Western cohorts.
CONCLUSION: This study demonstrates the value of a population specific genomic database to determine true disease prevalence and has enabled the discovery of carrier frequencies of treatable genetic conditions specific to South East Asian populations, which are currently underestimated in existing data sources. This study framework can be adapted to other population groups and expanded to multiple genetic conditions to inform health policies directing precision medicine.}, }
@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 = {}, number = {}, pages = {}, 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}, 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}, support = {R-571-000-037-114//Ministry of Education (SG)/ ; }, 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.
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.
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 {pmid30479272, year = {2018}, author = {Glover, AG and Wiklund, H and Chen, C and Dahlgren, TG}, title = {Managing a sustainable deep-sea 'blue economy' requires knowledge of what actually lives there.}, journal = {eLife}, volume = {7}, number = {}, pages = {}, pmid = {30479272}, issn = {2050-084X}, mesh = {*Biodiversity ; Conservation of Energy Resources/*methods ; *Ecosystem ; Metagenomics/*methods ; *Oceans and Seas ; }, abstract = {Ensuring that the wealth of resources contained in our oceans are managed and developed in a sustainable manner is a priority for the emerging 'blue economy'. However, modern ecosystem-based management approaches do not translate well to regions where we know almost nothing about the individual species found in the ecosystem. Here, we propose a new taxon-focused approach to deep-sea conservation that includes regulatory oversight to set targets for the delivery of taxonomic data. For example, a five-year plan to deliver taxonomic and genomic knowledge on a thousand species in regions of the ocean earmarked for industrial activity is an achievable target. High-throughput, integrative taxonomy can, therefore, provide the data that is needed to monitor various ecosystem services (such as the natural history, connectivity, value and function of species) and to help break the regulatory deadlock of high-seas conservation.}, }
@article {pmid28819272, year = {2017}, author = {Concheri, G and Stevanato, P and Zaccone, C and Shotyk, W and D'Orazio, V and Miano, T and Piffanelli, P and Rizzi, V and Ferrandi, C and Squartini, A}, title = {Rapid peat accumulation favours the occurrence of both fen and bog microbial communities within a Mediterranean, free-floating peat island.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {8511}, pmid = {28819272}, issn = {2045-2322}, mesh = {Bacteria/*classification/genetics ; DNA, Bacterial/chemistry/genetics/isolation & purification ; DNA, Fungal/chemistry/genetics/isolation & purification ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Fungi/*classification/genetics ; *Islands ; Italy ; Metagenomics ; *Microbiota ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; *Soil Microbiology ; Wetlands ; }, abstract = {The unique environment of a 4m-thick, free-floating peat island within the Posta Fibreno lake (Central Italy) was analyzed using DNA-based techniques to assess bacterial and fungal community members identity and abundance. Two depths were sampled at 41 and 279 cm from the surface, the former corresponding to an emerged portion of Sphagnum residues accumulated less than 30 yrs ago, and the latter mainly consisting of silty peat belonging to the deeply submerged part of the island, dating back to 1520-1660 AD. The corresponding communities were very diverse, each of them dominated by a different member of the Delta-proteobacteria class for prokaryotes. Among Eukaryotes, Ascomycota prevailed in the shallow layer while Basidiomycota were abundant in the deep sample. The identity of taxa partitioning between acidic surface layer and neutral core is very reminiscent of the differences reported between bogs and fens respectively, supporting the view of Posta Fibreno as a relic transitional floating mire. Moreover, some microbial taxa show an unusual concurrent species convergence between this sub-Mediterranean site and far Nordic or circumpolar environments. This study represents the first report describing the biotic assemblages of such a peculiar environment, and provides some insights into the possible mechanisms of its evolution.}, }
@article {pmid28819242, year = {2017}, author = {Lim, Y and Totsika, M and Morrison, M and Punyadeera, C}, title = {The saliva microbiome profiles are minimally affected by collection method or DNA extraction protocols.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {8523}, pmid = {28819242}, issn = {2045-2322}, mesh = {Adult ; Bacteria/classification/genetics ; Cluster Analysis ; DNA, Bacterial/analysis/genetics/*isolation & purification ; DNA, Ribosomal/chemistry/genetics ; Healthy Volunteers ; Humans ; Metagenomics/*methods ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Saliva/*microbiology ; Sequence Analysis, DNA ; Specimen Handling/*methods ; Young Adult ; beta-Globins/analysis/genetics ; }, abstract = {Saliva has attracted attention as a diagnostic fluid due to the association of oral microbiota with systemic diseases. However, the lack of standardised methods for saliva collection has led to the slow uptake of saliva in microbiome research. The aim of this study was to systematically evaluate the potential effects on salivary microbiome profiles using different methods of saliva collection, storage and gDNA extraction. Three types of saliva fractions were collected from healthy individuals with or without the gDNA stabilising buffer. Subsequently, three types of gDNA extraction methods were evaluated to determine the gDNA extraction efficiencies from saliva samples. The purity of total bacterial gDNA was evaluated using the ratio of human β-globin to bacterial 16S rRNA PCR while 16S rRNA gene amplicon sequencing was carried out to identify the bacterial profiles present in these samples. The quantity and quality of extracted gDNA were similar among all three gDNA extraction methods and there were no statistically significant differences in the bacterial profiles among different saliva fractions at the genus-level of taxonomic classification. In conclusion, saliva sampling, processing and gDNA preparation do not have major influence on microbiome profiles.}, }
@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 = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14587}, pmid = {30851141}, issn = {1462-2920}, 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, while 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, like 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 nonpoint source nitrogen pollution. This article is protected by copyright. All rights reserved.}, }
@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}, abstract = {Usually transmitted via respiratory droplets, parvovirus B19 (B19V) can also be acquired by blood transfusion especially because of viral persistency, 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 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=258/479) were anti-B19V IgG positive, and 9 (1.9%) plasma samples presented B19V DNA. In almost all cases (n=7/9, 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 post-transfusion 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. This article is protected by copyright. All rights reserved.}, }
@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 = {}, number = {}, pages = {e00572}, doi = {10.1002/mbo3.572}, pmid = {30851083}, issn = {2045-8827}, support = {415-2007//Cenicafé/ ; 2,943//Fundación para la Promoción de la Investigación y la Tecnología -FPIT, Banco de la República/ ; 0142-2013//Colombian Agency to support science and technology COLCIENCIAS/ ; 032-2017//Colombian Agency to support science and technology COLCIENCIAS/ ; }, 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}, 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 Educación, Cultura y Deporte (Ministry of Education, Culture and Sports, Spain)/ ; SAF2017-85785-R//Ministerio de Educación, Cultura y Deporte (Ministry of Education, Culture and Sports, Spain)/ ; SAF2017-85785-R//Ministerio de Educación, 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 {pmid29878111, year = {2018}, author = {Kocarnik, JM and Richard, M and Graff, M and Haessler, J and Bien, S and Carlson, C and Carty, CL and Reiner, AP and Avery, CL and Ballantyne, CM and LaCroix, AZ and Assimes, TL and Barbalic, M and Pankratz, N and Tang, W and Tao, R and Chen, D and Talavera, GA and Daviglus, ML and Chirinos-Medina, DA and Pereira, R and Nishimura, K and Bužková, P and Best, LG and Ambite, JL and Cheng, I and Crawford, DC and Hindorff, LA and Fornage, M and Heiss, G and North, KE and Haiman, CA and Peters, U and Le Marchand, L and Kooperberg, C}, title = {Discovery, fine-mapping, and conditional analyses of genetic variants associated with C-reactive protein in multiethnic populations using the Metabochip in the Population Architecture using Genomics and Epidemiology (PAGE) study.}, journal = {Human molecular genetics}, volume = {27}, number = {16}, pages = {2940-2953}, pmid = {29878111}, issn = {1460-2083}, support = {HHSN268201100012C/HL/NHLBI NIH HHS/United States ; U01 HG007417/HG/NHGRI NIH HHS/United States ; HHSN268201100001I/HL/NHLBI NIH HHS/United States ; HHSN268201100009I/HL/NHLBI NIH HHS/United States ; HHSN268201300026C/HL/NHLBI NIH HHS/United States ; U01 HG007419/HG/NHGRI NIH HHS/United States ; U01 HL041642/HL/NHLBI NIH HHS/United States ; U01 HL041654/HL/NHLBI NIH HHS/United States ; HHSN268201100010C/HL/NHLBI NIH HHS/United States ; HHSN268201100008C/HL/NHLBI NIH HHS/United States ; U01 HL080295/HL/NHLBI NIH HHS/United States ; U01 HG004790/HG/NHGRI NIH HHS/United States ; HHSN268201100005G/HL/NHLBI NIH HHS/United States ; HHSN268201100004I/HL/NHLBI NIH HHS/United States ; HHSN268201100008I/HL/NHLBI NIH HHS/United States ; U01 HG004802/HG/NHGRI NIH HHS/United States ; U01 HG007416/HG/NHGRI NIH HHS/United States ; U01 HL130114/HL/NHLBI NIH HHS/United States ; HHSN268201100007C/HL/NHLBI NIH HHS/United States ; HHSN268200800007C/HL/NHLBI NIH HHS/United States ; HHSN268201100046C/HL/NHLBI NIH HHS/United States ; HHSN268201100011I/HL/NHLBI NIH HHS/United States ; HHSN268201100011C/HL/NHLBI NIH HHS/United States ; N01HC65236/HL/NHLBI NIH HHS/United States ; HHSN268201100003C/WH/WHI NIH HHS/United States ; U01 HG007376/HG/NHGRI NIH HHS/United States ; N01HC65235/HL/NHLBI NIH HHS/United States ; HHSN268201300025C/HL/NHLBI NIH HHS/United States ; N01HC55222/HL/NHLBI NIH HHS/United States ; U01 HL041652/HL/NHLBI NIH HHS/United States ; N01HC85086/HL/NHLBI NIH HHS/United States ; N01HC65234/HL/NHLBI NIH HHS/United States ; HHSN268201300027C/HL/NHLBI NIH HHS/United States ; HHSN268201100006C/HL/NHLBI NIH HHS/United States ; N01HC65233/HL/NHLBI NIH HHS/United States ; HHSN268201200036C/HL/NHLBI NIH HHS/United States ; HHSN268200900041C/HL/NHLBI NIH HHS/United States ; HHSN268201300028C/HL/NHLBI NIH HHS/United States ; N01HC65237/HL/NHLBI NIH HHS/United States ; U01 HG004803/HG/NHGRI NIH HHS/United States ; HHSN268201100005I/HL/NHLBI NIH HHS/United States ; HHSN271201100004C/AG/NIA NIH HHS/United States ; P01 CA033619/CA/NCI NIH HHS/United States ; HHSN268201100002C/WH/WHI NIH HHS/United States ; N01HC85082/HL/NHLBI NIH HHS/United States ; KL2 TR002317/TR/NCATS NIH HHS/United States ; HHSN268201100009C/HL/NHLBI NIH HHS/United States ; U01 CA098758/CA/NCI NIH HHS/United States ; N01HC85083/HL/NHLBI NIH HHS/United States ; HHSN268201100005C/HL/NHLBI NIH HHS/United States ; U01 HL065521/HL/NHLBI NIH HHS/United States ; HHSN268201100007I/HL/NHLBI NIH HHS/United States ; HHSN268201100002I/HL/NHLBI NIH HHS/United States ; KL2 TR000421/TR/NCATS NIH HHS/United States ; N01HC85079/HL/NHLBI NIH HHS/United States ; HHSN268201300029C/HL/NHLBI NIH HHS/United States ; R01 AG023629/AG/NIA NIH HHS/United States ; U01 CA136792/CA/NCI NIH HHS/United States ; R01 HL109301/HL/NHLBI NIH HHS/United States ; N01HC85080/HL/NHLBI NIH HHS/United States ; U01 HG007397/HG/NHGRI NIH HHS/United States ; R37 CA054281/CA/NCI NIH HHS/United States ; HHSN268201100001C/WH/WHI NIH HHS/United States ; U01 HL065520/HL/NHLBI NIH HHS/United States ; HHSN268201100004C/WH/WHI NIH HHS/United States ; N01HC85081/HL/NHLBI NIH HHS/United States ; U01 HG004801/HG/NHGRI NIH HHS/United States ; /RA/ARRA NIH HHS/United States ; }, mesh = {C-Reactive Protein/*genetics ; Enoyl-CoA Hydratase/genetics ; European Continental Ancestry Group/genetics ; Female ; *Genome-Wide Association Study ; Glycoproteins/genetics ; Group VI Phospholipases A2/genetics ; Humans ; Linkage Disequilibrium ; Male ; *Metagenomics ; Molecular Epidemiology/*methods ; Polymorphism, Single Nucleotide ; }, abstract = {C-reactive protein (CRP) is a circulating biomarker indicative of systemic inflammation. We aimed to evaluate genetic associations with CRP levels among non-European-ancestry populations through discovery, fine-mapping and conditional analyses. A total of 30 503 non-European-ancestry participants from 6 studies participating in the Population Architecture using Genomics and Epidemiology study had serum high-sensitivity CRP measurements and ∼200 000 single nucleotide polymorphisms (SNPs) genotyped on the Metabochip. We evaluated the association between each SNP and log-transformed CRP levels using multivariate linear regression, with additive genetic models adjusted for age, sex, the first four principal components of genetic ancestry, and study-specific factors. Differential linkage disequilibrium patterns between race/ethnicity groups were used to fine-map regions associated with CRP levels. Conditional analyses evaluated for multiple independent signals within genetic regions. One hundred and sixty-three unique variants in 12 loci in overall or race/ethnicity-stratified Metabochip-wide scans reached a Bonferroni-corrected P-value <2.5E-7. Three loci have no (HACL1, OLFML2B) or only limited (PLA2G6) previous associations with CRP levels. Six loci had different top hits in race/ethnicity-specific versus overall analyses. Fine-mapping refined the signal in six loci, particularly in HNF1A. Conditional analyses provided evidence for secondary signals in LEPR, IL1RN and HNF1A, and for multiple independent signals in CRP and APOE. We identified novel variants and loci associated with CRP levels, generalized known CRP associations to a multiethnic study population, refined association signals at several loci and found evidence for multiple independent signals at several well-known loci. This study demonstrates the benefit of conducting inclusive genetic association studies in large multiethnic populations.}, }
@article {pmid28025179, year = {2018}, author = {Finotello, F and Mastrorilli, E and Di Camillo, B}, title = {Measuring the diversity of the human microbiota with targeted next-generation sequencing.}, journal = {Briefings in bioinformatics}, volume = {19}, number = {4}, pages = {679-692}, doi = {10.1093/bib/bbw119}, pmid = {28025179}, issn = {1477-4054}, mesh = {Bacteria/*classification/*genetics/isolation & purification ; Computational Biology/*methods ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenome ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {The human microbiota is a complex ecological community of commensal, symbiotic and pathogenic microorganisms harboured by the human body. Next-generation sequencing (NGS) technologies, in particular targeted amplicon sequencing of the 16S ribosomal RNA gene (16S-seq), are enabling the identification and quantification of human-resident microorganisms at unprecedented resolution, providing novel insights into the role of the microbiota in health and disease. Once microbial abundances are quantified through NGS data analysis, diversity indices provide valuable mathematical tools to describe the ecological complexity of a single sample or to detect species differences between samples. However, diversity is not a determined physical quantity for which a consensus definition and unit of measure have been established, and several diversity indices are currently available. Furthermore, they were originally developed for macroecology and their robustness to the possible bias introduced by sequencing has not been characterized so far. To assist the reader with the selection and interpretation of diversity measures, we review a panel of broadly used indices, describing their mathematical formulations, purposes and properties, and characterize their behaviour and criticalities in dependence of the data features using simulated data as ground truth. In addition, we make available an R package, DiversitySeq, which implements in a unified framework the full panel of diversity indices and a simulator of 16S-seq data, and thus represents a valuable resource for the analysis of diversity from NGS count data and for the benchmarking of computational methods for 16S-seq.}, }
@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 = {}, number = {}, 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.
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.
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.
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}, 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 {pmid28811619, year = {2017}, author = {Chen, ZT and Lü, L and Lu, MX and Du, YZ}, title = {Comparative mitogenomic analysis of Aposthonia borneensis and Aposthonia japonica (Embioptera: Oligotomidae) reveals divergent evolution of webspinners.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {8279}, pmid = {28811619}, issn = {2045-2322}, mesh = {Animals ; Base Composition ; *Evolution, Molecular ; Gene Rearrangement ; *Genetic Variation ; Genome Size ; *Genome, Insect ; Genome, Mitochondrial ; *Metagenome ; *Metagenomics/methods ; Neoptera/*classification/*genetics ; Open Reading Frames ; Phylogeny ; }, abstract = {In this study, we report the complete mitochondrial genome (mitogenome, mtDNA) of Aposthonia borneensis and compare it with another sequenced webspinner, Aposthonia japonica. The A. borneensis mitogenome is smaller than A. japonica, but the size of each gene and the A + T content of protein-coding genes (PCGs) are almost identical in the two mitogenomes. Among the PCGs, atp6 shows the highest evolutionary rate and cox1 the lowest. The mtDNA map in A. borneensis is similar to Drosophila yakuba, but distinctly different from A. japonica, which has extensive rearrangement. Phylogenetic analyses dated the divergence time of the two webspinners at ca. 103 Ma. We speculate that the most recent common ancestor (MRCA) of A. borneensis and A. japonica was divided into several geographic groups during the Pangea breakup. Geographic isolation between the Japanese islands and the continental southeastern Asia resulted in the divergent evolution of A. borneensis and A. japonica, thus generating mtDNA structural variations between the two species. Based on the phylogenetic analyses and specific distributional features, the genus Aposthonia was supported as non-monophyly, and we speculate that both highly rearranged and relatively conserved mitogenomes exist in other webspinners.}, }
@article {pmid28811583, year = {2017}, author = {Chen, CH and Lin, YL and Chen, KH and Chen, WP and Chen, ZF and Kuo, HY and Hung, HF and Tang, CY and Liou, ML}, title = {Bacterial diversity among four healthcare-associated institutes in Taiwan.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {8230}, pmid = {28811583}, issn = {2045-2322}, mesh = {Bacteria/*classification/*genetics ; *Biodiversity ; Cross Infection/epidemiology/microbiology ; *Environmental Microbiology ; *Health Facilities ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/methods ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Taiwan/epidemiology ; }, abstract = {Indoor microbial communities have important implications for human health, especially in health-care institutes (HCIs). The factors that determine the diversity and composition of microbiomes in a built environment remain unclear. Herein, we used 16S rRNA amplicon sequencing to investigate the relationships between building attributes and surface bacterial communities among four HCIs located in three buildings. We examined the surface bacterial communities and environmental parameters in the buildings supplied with different ventilation types and compared the results using a Dirichlet multinomial mixture (DMM)-based approach. A total of 203 samples from the four HCIs were analyzed. Four bacterial communities were grouped using the DMM-based approach, which were highly similar to those in the 4 HCIs. The α-diversity and β-diversity in the naturally ventilated building were different from the conditioner-ventilated building. The bacterial source composition varied across each building. Nine genera were found as the core microbiota shared by all the areas, of which Acinetobacter, Enterobacter, Pseudomonas, and Staphylococcus are regarded as healthcare-associated pathogens (HAPs). The observed relationship between environmental parameters such as core microbiota and surface bacterial diversity suggests that we might manage indoor environments by creating new sanitation protocols, adjusting the ventilation design, and further understanding the transmission routes of HAPs.}, }
@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}, 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 {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}, 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 Support Independent Origins of Viral Gigantism.}, journal = {mBio}, volume = {10}, number = {2}, pages = {}, doi = {10.1128/mBio.02497-18}, pmid = {30837339}, issn = {2150-7511}, abstract = {The nucleocytoplasmic large DNA viruses (NCLDV) of eukaryotes (proposed order, "Megavirales") include the families Poxviridae, Asfarviridae, Iridoviridae, Ascoviridae, Phycodnaviridae, Marseilleviridae, and Mimiviridae, as well as still unclassified pithoviruses, pandoraviruses, molliviruses, and faustoviruses. Several of these virus groups include giant viruses, with genome and particle sizes exceeding those of many bacterial and archaeal cells. We explored the diversity of the NCLDV in deep sea sediments from the Loki's Castle hydrothermal vent area. Using metagenomics, we reconstructed 23 high-quality genomic bins of novel NCLDV, 15 of which are related to pithoviruses, 5 to marseilleviruses, 1 to iridoviruses, and 2 to klosneuviruses. Some of the identified pithovirus-like and marseillevirus-like genomes belong to deep branches in the phylogenetic tree of core NCLDV genes, substantially expanding the diversity and phylogenetic depth of the respective groups. The discovered viruses, including putative giant members of the family Marseilleviridae, have a broad range of apparent genome sizes, in agreement with the multiple, independent origins of gigantism in different branches of the NCLDV. Phylogenomic analysis reaffirms the monophyly of the pithovirus-iridovirus-marseillevirus branch of the NCLDV. Similarly to other giant viruses, the pithovirus-like viruses from Loki's Castle encode translation systems components. Phylogenetic analysis of these genes indicates a greater bacterial contribution than had been detected previously. Genome comparison suggests extensive gene exchange between members of the pithovirus-like viruses and Mimiviridae Further exploration of the genomic diversity of Megavirales in additional sediment samples is expected to yield new insights into the evolution of giant viruses and the composition of the ocean megavirome.IMPORTANCE Genomics and evolution of giant viruses are two of the most vigorously developing areas of virus research. Lately, metagenomics has become the main source of new virus genomes. Here we describe a metagenomic analysis of the genomes of large and giant viruses from deep sea sediments. The assembled new virus genomes substantially expand the known diversity of the nucleocytoplasmic large DNA viruses of eukaryotes. The results support the concept of independent evolution of giant viruses from smaller ancestors in different virus branches.}, }
@article {pmid30486439, year = {2018}, author = {Yi, X and Yuan, J and Zhu, Y and Yi, X and Zhao, Q and Fang, K and Cao, L}, title = {Comparison of the Abundance and Community Structure of N-Cycling Bacteria in Paddy Rhizosphere Soil under Different Rice Cultivation Patterns.}, journal = {International journal of molecular sciences}, volume = {19}, number = {12}, pages = {}, doi = {10.3390/ijms19123772}, pmid = {30486439}, issn = {1422-0067}, mesh = {Bacteria/*classification/genetics/metabolism ; *Biodiversity ; Enzymes/genetics/metabolism ; Metagenome ; Metagenomics/methods ; Nitrogen ; Oryza/*microbiology ; Phylogeny ; *Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Eco-agricultural systems aim to reduce the use of chemical fertilizers in order to improve sustainable production and maintain a healthy ecosystem. The aim of this study was to explore the effects of rice-frog farming on the bacterial community and N-cycling microbes in paddy rhizosphere soil. This experiment involved three rice cultivation patterns: Conventionally cultivated rice (CR), green rice-frog farming (GR), and organic rice-frog farming (OR). The rice yield, paddy soil enzyme activities, physicochemical variables and bacterial and N-cycling bacterial abundances were quantitatively analyzed. Rice-frog cultivations significantly increased soil protease, nitrate and reductase activity. Additionally, the nirS gene copy number and the relative abundance of denitrifying bacteria also increased, however urease activity and the relative abundance of nitrifying bacteria significantly decreased. The bacterial community richness and diversity of OR soil was significantly higher than that of the GR or CR soil. Nitrogen use efficiency (NUE) of GR was highest. The N-cycling bacterial community was positively correlated with the total carbon (TC), total nitrogren (TN) and carbon to nitrogen (C:N) ratio. The present work strengthens our current understanding of the soil bacterial community structure and its functions under rice-frog farming. The present work also provides certain theoretical support for the selection of rational rice cultivation patterns.}, }
@article {pmid30486338, year = {2018}, author = {Amedei, A and Boem, F}, title = {I've Gut A Feeling: Microbiota Impacting the Conceptual and Experimental Perspectives of Personalized Medicine.}, journal = {International journal of molecular sciences}, volume = {19}, number = {12}, pages = {}, doi = {10.3390/ijms19123756}, pmid = {30486338}, issn = {1422-0067}, support = {FAS SALUTE 2014//Regione Toscana/ ; P2016.0808//Ente Cassa di Risparmio di Firenze/ ; }, mesh = {Animals ; Biodiversity ; Biological Therapy ; Disease Susceptibility ; Fecal Microbiota Transplantation ; Feces/microbiology ; *Gastrointestinal Microbiome ; Genomics/methods ; Humans ; Metagenomics/methods ; Microbiota ; Organ Specificity ; *Precision Medicine/methods ; Research ; Symbiosis ; }, abstract = {In recent years, the human microbiota has gained increasing relevance both in research and clinical fields. Increasing studies seem to suggest the centrality of the microbiota and its composition both in the development and maintenance of what we call "health" and in generating and/or favoring (those cases in which the microbiota's complex relational architecture is dysregulated) the onset of pathological conditions. The complex relationships between the microbiota and human beings, which invest core notions of biomedicine such as "health" and "individual," do concern not only problems of an empirical nature but seem to require the need to adopt new concepts and new perspectives in order to be properly analysed and utilized, especially for their therapeutic implementation. In this contribution we report and discuss some of the theoretical proposals and innovations (from the ecological component to the notion of polygenomic organism) aimed at producing this change of perspective. In conclusion, we summarily analyze what impact and what new challenges these new approaches might have on personalized/person centred/precision medicine.}, }
@article {pmid30252901, year = {2018}, author = {Poirier, S and Rué, O and Peguilhan, R and Coeuret, G and Zagorec, M and Champomier-Vergès, MC and Loux, V and Chaillou, S}, title = {Deciphering intra-species bacterial diversity of meat and seafood spoilage microbiota using gyrB amplicon sequencing: A comparative analysis with 16S rDNA V3-V4 amplicon sequencing.}, journal = {PloS one}, volume = {13}, number = {9}, pages = {e0204629}, pmid = {30252901}, issn = {1932-6203}, mesh = {Animals ; Bacteria/classification/*genetics/isolation & purification ; DNA Gyrase/*genetics ; DNA Topoisomerase IV/genetics ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Food Microbiology/*methods ; Genes, Bacterial ; Genetic Markers ; Genetic Variation ; High-Throughput Nucleotide Sequencing ; Humans ; Meat/*microbiology ; Metagenome ; Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seafood/*microbiology ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Meat and seafood spoilage ecosystems harbor extensive bacterial genomic diversity that is mainly found within a small number of species but within a large number of strains with different spoilage metabolic potential. To decipher the intraspecies diversity of such microbiota, traditional metagenetic analysis using the 16S rRNA gene is inadequate. We therefore assessed the potential benefit of an alternative genetic marker, gyrB, which encodes the subunit B of DNA gyrase, a type II DNA topoisomerase. A comparison between 16S rDNA-based (V3-V4) amplicon sequencing and gyrB-based amplicon sequencing was carried out in five types of meat and seafood products, with five mock communities serving as quality controls. Our results revealed that bacterial richness in these mock communities and food samples was estimated with higher accuracy using gyrB than using16S rDNA. However, for Firmicutes species, 35% of putative gyrB reads were actually identified as sequences of a gyrB paralog, parE, which encodes subunit B of topoisomerase IV; we therefore constructed a reference database of published sequences of both gyrB and pare for use in all subsequent analyses. Despite this co-amplification, the deviation between relative sequencing quantification and absolute qPCR quantification was comparable to that observed for 16S rDNA for all the tested species. This confirms that gyrB can be used successfully alongside 16S rDNA to determine the species composition (richness and evenness) of food microbiota. The major benefit of gyrB sequencing is its potential for improving taxonomic assignment and for further investigating OTU richness at the subspecies level, thus allowing more accurate discrimination of samples. Indeed, 80% of the reads of the 16S rDNA dataset were represented by thirteen 16S rDNA-based OTUs that could not be assigned at the species-level. Instead, these same clades corresponded to 44 gyrB-based OTUs, which differentiated various lineages down to the subspecies level. The increased ability of gyrB-based analyses to track and trace phylogenetically different groups of strains will generate improved resolution and more reliable results for studies of the strains implicated in food processes.}, }
@article {pmid30836173, year = {2019}, author = {Ruppé, E and Schrenzel, J}, title = {Messages from the third International Conference on Clinical Metagenomics (ICCMg3).}, journal = {Microbes and infection}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.micinf.2019.02.004}, pmid = {30836173}, issn = {1769-714X}, abstract = {Clinical metagenomics (CMg), referring to as the application of metagenomic sequencing of clinical samples in order to recover clinically-relevant information, has been rapidly evolving these last years. Following this trend, we held the third International Conference on Clinical Metagenomics (ICCMg3) in Geneva in October 2018. During the two days of the conference, several aspects of CMg were addressed, which we propose to summarize in the present manuscript. During this ICCMg3, we kept on following the progresses achieved worldwide on clinical metagenomics, but also this year in clinical genomics. Besides, the use of metagenomics in cancer diagnostic and management was addressed. Some new challenges have also been raised such as the way to report clinical (meta)genomics output to clinicians and the pivotal place of ethics in this expandng field.}, }
@article {pmid30834996, year = {2019}, author = {Boers, SA and Jansen, R and Hays, JP}, title = {Understanding and overcoming the pitfalls and biases of next-generation sequencing (NGS) methods for use in the routine clinical microbiological diagnostic laboratory.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10096-019-03520-3}, pmid = {30834996}, issn = {1435-4373}, support = {602860//FP7 Health/ ; }, abstract = {Recent advancements in next-generation sequencing (NGS) have provided the foundation for modern studies into the composition of microbial communities. The use of these NGS methods allows for the detection and identification of ('difficult-to-culture') microorganisms using a culture-independent strategy. In the field of routine clinical diagnostics however, the application of NGS is currently limited to microbial strain typing for epidemiological purposes only, even though the implementation of NGS for microbial community analysis may yield clinically important information. This lack of NGS implementation is due to many different factors, including issues relating to NGS method standardization and result reproducibility. In this review article, the authors provide a general introduction to the most widely used NGS methods currently available (i.e., targeted amplicon sequencing and shotgun metagenomics) and the strengths and weaknesses of each method is discussed. The focus of the publication then shifts toward 16S rRNA gene NGS methods, which are currently the most cost-effective and widely used NGS methods for research purposes, and are therefore more likely to be successfully implemented into routine clinical diagnostics in the short term. In this respect, the experimental pitfalls and biases created at each step of the 16S rRNA gene NGS workflow are explained, as well as their potential solutions. Finally, a novel diagnostic microbiota profiling platform ('MYcrobiota') is introduced, which was developed by the authors by taking into consideration the pitfalls, biases, and solutions explained in this article. The development of the MYcrobiota, and future NGS methodologies, will help pave the way toward the successful implementation of NGS methodologies into routine clinical diagnostics.}, }
@article {pmid30834332, year = {2019}, author = {Dunivin, TK and Choi, J and Howe, A and Shade, A}, title = {RefSoil+: a Reference Database for Genes and Traits of Soil Plasmids.}, journal = {mSystems}, volume = {4}, number = {1}, pages = {}, doi = {10.1128/mSystems.00349-18}, pmid = {30834332}, issn = {2379-5077}, abstract = {Plasmids harbor transferable genes that contribute to the functional repertoire of microbial communities, yet their contributions to metagenomes are often overlooked. Environmental plasmids have the potential to spread antibiotic resistance to clinical microbial strains. In soils, high microbiome diversity and high variability in plasmid characteristics present a challenge for studying plasmids. To improve the understanding of soil plasmids, we present RefSoil+, a database containing plasmid sequences from 922 soil microorganisms. Soil plasmids were larger than other described plasmids, which is a trait associated with plasmid mobility. There was a weak relationship between chromosome size and plasmid size and no relationship between chromosome size and plasmid number, suggesting that these genomic traits are independent in soil. We used RefSoil+ to inform the distributions of antibiotic resistance genes among soil microorganisms compared to those among nonsoil microorganisms. Soil-associated plasmids, but not chromosomes, had fewer antibiotic resistance genes than other microorganisms. These data suggest that soils may offer limited opportunity for plasmid-mediated transfer of described antibiotic resistance genes. RefSoil+ can serve as a reference for the diversity, composition, and host associations of plasmid-borne functional genes in soil, a utility that will be enhanced as the database expands. Our study improves the understanding of soil plasmids and provides a resource for assessing the dynamics of the genes that they carry, especially genes conferring antibiotic resistances. IMPORTANCE Soil-associated plasmids have the potential to transfer antibiotic resistance genes from environmental to clinical microbial strains, which is a public health concern. A specific resource is needed to aggregate the knowledge of soil plasmid characteristics so that the content, host associations, and dynamics of antibiotic resistance genes can be assessed and then tracked between the environment and the clinic. Here, we present RefSoil+, a database of soil-associated plasmids. RefSoil+ presents a contemporary snapshot of antibiotic resistance genes in soil that can serve as a reference as novel plasmids and transferred antibiotic resistances are discovered. Our study broadens our understanding of plasmids in soil and provides a community resource of important plasmid-associated genes, including antibiotic resistance genes.}, }
@article {pmid30834326, year = {2019}, author = {Vigneron, A and Alsop, EB and Cruaud, P and Philibert, G and King, B and Baksmaty, L and Lavallee, D and Lomans, BP and Eloe-Fadrosh, E and Kyrpides, NC and Head, IM and Tsesmetzis, N}, title = {Contrasting Pathways for Anaerobic Methane Oxidation in Gulf of Mexico Cold Seep Sediments.}, journal = {mSystems}, volume = {4}, number = {1}, pages = {}, doi = {10.1128/mSystems.00091-18}, pmid = {30834326}, issn = {2379-5077}, abstract = {Gulf of Mexico sediments harbor numerous hydrocarbon seeps associated with high sedimentation rates and thermal maturation of organic matter. These ecosystems host abundant and diverse microbial communities that directly or indirectly metabolize components of the emitted fluid. To investigate microbial function and activities in these ecosystems, metabolic potential (metagenomic) and gene expression (metatranscriptomic) analyses of two cold seep areas of the Gulf of Mexico were carried out. Seeps emitting biogenic methane harbored microbial communities dominated by archaeal anaerobic methane oxidizers of phylogenetic group 1 (ANME-1), whereas seeps producing fluids containing a complex mixture of thermogenic hydrocarbons were dominated by ANME-2 lineages. Metatranscriptome measurements in both communities indicated high levels of expression of genes for methane metabolism despite their distinct microbial communities and hydrocarbon composition. In contrast, the transcription level of sulfur cycle genes was quite different. In the thermogenic seep community, high levels of transcripts indicative of syntrophic anaerobic oxidation of methane (AOM) coupled to sulfate reduction were detected. This syntrophic partnership between the dominant ANME-2 and sulfate reducers potentially involves direct electron transfer through multiheme cytochromes. In the biogenic methane seep, genes from an ANME-1 lineage that are potentially involved in polysulfide reduction were highly expressed, suggesting a novel bacterium-independent anaerobic methane oxidation pathway coupled to polysulfide reduction. The observed divergence in AOM activities provides a new model for bacterium-independent AOM and emphasizes the variation that exists in AOM pathways between different ANME lineages. IMPORTANCE Cold seep sediments are complex and widespread marine ecosystems emitting large amounts of methane, a potent greenhouse gas, and other hydrocarbons. Within these sediments, microbial communities play crucial roles in production and degradation of hydrocarbons, modulating oil and gas emissions to seawater. Despite this ecological importance, our understanding of microbial functions and methane oxidation pathways in cold seep ecosystems is poor. Based on gene expression profiling of environmental seep sediment samples, the present work showed that (i) the composition of the emitted fluids shapes the microbial community in general and the anaerobic methanotroph community specifically and (ii) AOM by ANME-2 in this seep may be coupled to sulfate reduction by Deltaproteobacteria by electron transfer through multiheme cytochromes, whereas AOM by ANME-1 lineages in this seep may involve a different, bacterium-independent pathway, coupling methane oxidation to elemental sulfur/polysulfide reduction.}, }
@article {pmid30834068, year = {2019}, author = {Bhushan, B and Yadav, AP and Singh, SB and Ganju, L}, title = {Diversity and functional analysis of salivary microflora of Indian Antarctic expeditionaries.}, journal = {Journal of oral microbiology}, volume = {11}, number = {1}, pages = {1581513}, doi = {10.1080/20002297.2019.1581513}, pmid = {30834068}, issn = {2000-2297}, abstract = {Introduction: The human oral microbiota continues to change phenotype by many factors (environment, diet, genetics, stress, etc.), throughout life with a major impact on human physiology, psychology, metabolism and immune system. Amongst one such factor with unique and extreme environmental conditions is Antarctica. The sea voyage to Antarctica has many risks than at station for expedition members. In this study, we investigated the influence of Antarctic sea voyage and stay at the Indian Antarctic station Maitri, on the health of Indian expedition members by using a metagenomic approach to explore oral biodiversity. Methods: Saliva samples were collected from 12 expedition members, at 3 different time points viz. before the start of the ship voyage, after the completion of the voyage and at the end of the stay at Antarctica. Samples were analyzed for whole genome and 16S rRNA sequencing. Result: The oral microbial diversity of the expedition members was significantly changed, during the days of sailing and after the stay at Antarctica. The oral microbiota comprised mainly of the phyla Firmicutes (46%, 29% & 36%); Proteobacteria (40%, 48%, & 44%), Bacteroidetes (10%, 22%, &14%), Fusobacterium and Actinobacteria (5%-1%) and Unclassified (17%, 25% & 23%), at three time points, respectively. Further, the differential analysis of microbes across all the phyla revealed 89, 157 and 157 OTUs genera. The altered microbiota indicated changes in amino acid, lipid and carbohydrate metabolism. Conclusion: Study suggests that understanding the compositional and functional differences in the oral microbiota of Antarctic expedition members, can lay the foundation to relate these differences to their health status. It will further demonstrate the need for providing improved management during ship voyage and stay in Antarctica.}, }
@article {pmid30833934, year = {2019}, author = {Ng, C and Tan, B and Jiang, XT and Gu, X and Chen, H and Schmitz, BW and Haller, L and Charles, FR and Zhang, T and Gin, K}, title = {Metagenomic and Resistome Analysis of a Full-Scale Municipal Wastewater Treatment Plant in Singapore Containing Membrane Bioreactors.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {172}, doi = {10.3389/fmicb.2019.00172}, pmid = {30833934}, issn = {1664-302X}, abstract = {Reclaimed water provides a water supply alternative to address problems of scarcity in urbanized cities with high living densities and limited natural water resources. In this study, wastewater metagenomes from 6 stages of a wastewater treatment plant (WWTP) integrating conventional and membrane bioreactor (MBR) treatment were evaluated for diversity of antibiotic resistance genes (ARGs) and bacteria, and relative abundance of class 1 integron integrases (intl1). ARGs confering resistance to 12 classes of antibiotics (ARG types) persisted through the treatment stages, which included genes that confer resistance to aminoglycoside [aadA, aph(6)-I, aph(3')-I, aac(6')-I, aac(6')-II, ant(2″)-I], beta-lactams [class A, class C, class D beta-lactamases (blaOXA)], chloramphenicol (acetyltransferase, exporters, floR, cmIA), fosmidomycin (rosAB), macrolide-lincosamide-streptogramin (macAB, ereA, ermFB), multidrug resistance (subunits of transporters), polymyxin (arnA), quinolone (qnrS), rifamycin (arr), sulfonamide (sul1, sul2), and tetracycline (tetM, tetG, tetE, tet36, tet39, tetR, tet43, tetQ, tetX). Although the ARG subtypes in sludge and MBR effluents reduced in diversity relative to the influent, clinically relevant beta lactamases (i.e., blaKPC, blaOXA) were detected, casting light on other potential point sources of ARG dissemination within the wastewater treatment process. To gain a deeper insight into the types of bacteria that may survive the MBR removal process, genome bins were recovered from metagenomic data of MBR effluents. A total of 101 close to complete draft genomes were assembled and annotated to reveal a variety of bacteria bearing metal resistance genes and ARGs in the MBR effluent. Three bins in particular were affiliated to Mycobacterium smegmatis, Acinetobacter Iwoffii, and Flavobacterium psychrophila, and carried aquired ARGs aac(2')-Ib, blaOXA-278, and tet36 respectively. In terms of indicator organisms, cumulative log removal values (LRV) of Escherichia coli, Enterococci, and P. aeruginosa from influent to conventional treated effluent was lower (0-2.4), compared to MBR effluent (5.3-7.4). We conclude that MBR is an effective treatment method for reducing fecal indicators and ARGs; however, incomplete removal of P. aeruginosa in MBR treated effluents (<8 MPN/100 mL) and the presence of ARGs and intl1 underscores the need to establish if further treatment should be applied prior to reuse.}, }
@article {pmid30833730, year = {2019}, author = {McKay, LJ and Dlakić, M and Fields, MW and Delmont, TO and Eren, AM and Jay, ZJ and Klingelsmith, KB and Rusch, DB and Inskeep, WP}, title = {Co-occurring genomic capacity for anaerobic methane and dissimilatory sulfur metabolisms discovered in the Korarchaeota.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41564-019-0362-4}, pmid = {30833730}, issn = {2058-5276}, abstract = {Phylogenetic and geological evidence supports the hypothesis that life on Earth originated in thermal environments and conserved energy through methanogenesis or sulfur reduction. Here we describe two populations of the deeply rooted archaeal phylum Korarchaeota, which were retrieved from the metagenome of a circumneutral, suboxic hot spring that contains high levels of sulfate, sulfide, methane, hydrogen and carbon dioxide. One population is closely related to 'Candidatus Korarchaeum cryptofilum OPF8', while the more abundant korarchaeote, 'Candidatus Methanodesulfokores washburnensis', contains genes that are necessary for anaerobic methane and dissimilatory sulfur metabolisms. Phylogenetic and ancestral reconstruction analyses suggest that methane metabolism originated in the Korarchaeota, whereas genes for dissimilatory sulfite reduction were horizontally transferred to the Korarchaeota from the Firmicutes. Interactions among enzymes involved in both metabolisms could facilitate exergonic, sulfite-dependent, anaerobic oxidation of methane to methanol; alternatively, 'Ca. M. washburnensis' could conduct methanogenesis and sulfur reduction independently. Metabolic reconstruction suggests that 'Ca. M. washburnensis' is a mixotroph, capable of amino acid uptake, assimilation of methane-derived carbon and/or CO2 fixation by archaeal type III-b RuBisCO for scavenging ribose carbon. Our findings link anaerobic methane metabolism and dissimilatory sulfur reduction within a single deeply rooted archaeal population and have implications for the evolution of these traits throughout the Archaea.}, }
@article {pmid30833729, year = {2019}, author = {Borrel, G and Adam, PS and McKay, LJ and Chen, LX and Sierra-García, IN and Sieber, CMK and Letourneur, Q and Ghozlane, A and Andersen, GL and Li, WJ and Hallam, SJ and Muyzer, G and de Oliveira, VM and Inskeep, WP and Banfield, JF and Gribaldo, S}, title = {Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41564-019-0363-3}, pmid = {30833729}, issn = {2058-5276}, abstract = {Methanogenesis is an ancient metabolism of key ecological relevance, with direct impact on the evolution of Earth's climate. Recent results suggest that the diversity of methane metabolisms and their derivations have probably been vastly underestimated. Here, by probing thousands of publicly available metagenomes for homologues of methyl-coenzyme M reductase complex (MCR), we have obtained ten metagenome-assembled genomes (MAGs) belonging to potential methanogenic, anaerobic methanotrophic and short-chain alkane-oxidizing archaea. Five of these MAGs represent under-sampled (Verstraetearchaeota, Methanonatronarchaeia, ANME-1 and GoM-Arc1) or previously genomically undescribed (ANME-2c) archaeal lineages. The remaining five MAGs correspond to lineages that are only distantly related to previously known methanogens and span the entire archaeal phylogeny. Comprehensive comparative annotation substantially expands the metabolic diversity and energy conservation systems of MCR-bearing archaea. It also suggests the potential existence of a yet uncharacterized type of methanogenesis linked to short-chain alkane/fatty acid oxidation in a previously undescribed class of archaea ('Candidatus Methanoliparia'). We redefine a common core of marker genes specific to methanogenic, anaerobic methanotrophic and short-chain alkane-oxidizing archaea, and propose a possible scenario for the evolutionary and functional transitions that led to the emergence of such metabolic diversity.}, }
@article {pmid30833728, year = {2019}, author = {Wang, Y and Wegener, G and Hou, J and Wang, F and Xiao, X}, title = {Expanding anaerobic alkane metabolism in the domain of Archaea.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41564-019-0364-2}, pmid = {30833728}, issn = {2058-5276}, abstract = {Methanogenesis and anaerobic methane oxidation through methyl-coenzyme M reductase (MCR) as a key enzyme have been suggested to be basal pathways of archaea1. How widespread MCR-based alkane metabolism is among archaea, where it occurs and how it evolved remain elusive. Here, we performed a global survey of MCR-encoding genomes based on metagenomic data from various environments. Eleven high-quality mcr-containing metagenomic-assembled genomes were obtained belonging to the Archaeoglobi in the Euryarchaeota, Hadesarchaeota and different TACK superphylum archaea, including the Nezhaarchaeota, Korarchaeota and Verstraetearchaeota. Archaeoglobi WYZ-LMO1 and WYZ-LMO3 and Korarchaeota WYZ-LMO9 encode both the (reverse) methanogenesis and the dissimilatory sulfate reduction pathway, suggesting that they have the genomic potential to couple both pathways in individual organisms. The Hadesarchaeota WYZ-LMO4-6 and Archaeoglobi JdFR-42 encode highly divergent MCRs, enzymes that may enable them to thrive on non-methane alkanes. The occurrence of mcr genes in different archaeal phyla indicates that MCR-based alkane metabolism is common in the domain of Archaea.}, }
@article {pmid30833676, year = {2019}, author = {Pearson-Leary, J and Zhao, C and Bittinger, K and Eacret, D and Luz, S and Vigderman, AS and Dayanim, G and Bhatnagar, S}, title = {The gut microbiome regulates the increases in depressive-type behaviors and in inflammatory processes in the ventral hippocampus of stress vulnerable rats.}, journal = {Molecular psychiatry}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41380-019-0380-x}, pmid = {30833676}, issn = {1476-5578}, support = {W911NF1010093//United States Department of Defense | Defense Advanced Research Projects Agency (DARPA)/ ; }, abstract = {Chronic exposure to stress is associated with increased incidence of depression, generalized anxiety, and PTSD. However, stress induces vulnerability to such disorders only in a sub-population of individuals, as others remain resilient. Inflammation has emerged as a putative mechanism for promoting stress vulnerability. Using a rodent model of social defeat, we have previously shown that rats with short-defeat latencies (SL/vulnerable rats) show increased anxiety- and depression-like behaviors, and these behaviors are mediated by inflammation in the ventral hippocampus. The other half of socially defeated rats show long-latencies to defeat (LL/resilient) and are similar to controls. Because gut microbiota are important activators of inflammatory substances, we assessed the role of the gut microbiome in mediating vulnerability to repeated social defeat stress. We analyzed the fecal microbiome of control, SL/vulnerable, and LL/resilient rats using shotgun metagenome sequencing and observed increased expression of immune-modulating microbiota, such as Clostridia, in SL/vulnerable rats. We then tested the importance of gut microbiota to the SL/vulnerable phenotype. In otherwise naive rats treated with microbiota from SL/vulnerable rats, there was higher microglial density and IL-1β expression in the vHPC, and higher depression-like behaviors relative to rats that received microbiota from LL/resilient rats, non-stressed control rats, or vehicle-treated rats. However, anxiety-like behavior during social interaction was not altered by transplant of the microbiome of SL/vulnerable rats into non-stressed rats. Taken together, the results suggest the gut microbiome contributes to the depression-like behavior and inflammatory processes in the vHPC of stress vulnerable individuals.}, }
@article {pmid30833550, year = {2019}, author = {Milanese, A and Mende, DR and Paoli, L and Salazar, G and Ruscheweyh, HJ and Cuenca, M and Hingamp, P and Alves, R and Costea, PI and Coelho, LP and Schmidt, TSB and Almeida, A and Mitchell, AL and Finn, RD and Huerta-Cepas, J and Bork, P and Zeller, G and Sunagawa, S}, title = {Microbial abundance, activity and population genomic profiling with mOTUs2.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1014}, doi = {10.1038/s41467-019-08844-4}, pmid = {30833550}, issn = {2041-1723}, abstract = {Metagenomic sequencing has greatly improved our ability to profile the composition of environmental and host-associated microbial communities. However, the dependency of most methods on reference genomes, which are currently unavailable for a substantial fraction of microbial species, introduces estimation biases. We present an updated and functionally extended tool based on universal (i.e., reference-independent), phylogenetic marker gene (MG)-based operational taxonomic units (mOTUs) enabling the profiling of >7700 microbial species. As more than 30% of them could not previously be quantified at this taxonomic resolution, relative abundance estimates based on mOTUs are more accurate compared to other methods. As a new feature, we show that mOTUs, which are based on essential housekeeping genes, are demonstrably well-suited for quantification of basal transcriptional activity of community members. Furthermore, single nucleotide variation profiles estimated using mOTUs reflect those from whole genomes, which allows for comparing microbial strain populations (e.g., across different human body sites).}, }
@article {pmid30832984, year = {2019}, author = {Theis, KR and Romero, R and Winters, AD and Greenberg, JM and Gomez-Lopez, N and Alhousseini, A and Bieda, J and Maymon, E and Pacora, P and Fettweis, JM and Buck, GA and Jefferson, KK and Strauss, JF and Erez, O and Hassan, SS}, title = {Does the human placenta delivered at term have a microbiota? Results of cultivation, quantitative real-time PCR, 16S rRNA gene sequencing, and metagenomics.}, journal = {American journal of obstetrics and gynecology}, volume = {220}, number = {3}, pages = {267.e1-267.e39}, doi = {10.1016/j.ajog.2018.10.018}, pmid = {30832984}, issn = {1097-6868}, abstract = {BACKGROUND: The human placenta has been traditionally viewed as sterile, and microbial invasion of this organ has been associated with adverse pregnancy outcomes. Yet, recent studies that utilized sequencing techniques reported that the human placenta at term contains a unique microbiota. These conclusions are largely based on the results derived from the sequencing of placental samples. However, such an approach carries the risk of capturing background-contaminating DNA (from DNA extraction kits, polymerase chain reaction reagents, and laboratory environments) when low microbial biomass samples are studied.
OBJECTIVE: To determine whether the human placenta delivered at term in patients without labor who undergo cesarean delivery harbors a resident microbiota ("the assemblage of microorganisms present in a defined niche or environment").
STUDY DESIGN: This cross-sectional study included placentas from 29 women who had a cesarean delivery without labor at term. The study also included technical controls to account for potential background-contaminating DNA, inclusive in DNA extraction kits, polymerase chain reaction reagents, and laboratory environments. Bacterial profiles of placental tissues and background technical controls were characterized and compared with the use of bacterial culture, quantitative real-time polymerase chain reaction, 16S ribosomal RNA gene sequencing, and metagenomic surveys.
RESULTS: (1) Twenty-eight of 29 placental tissues had a negative culture for microorganisms. The microorganisms retrieved by culture from the remaining sample were likely contaminants because corresponding 16S ribosomal RNA genes were not detected in the same sample. (2) Quantitative real-time polymerase chain reaction did not indicate greater abundances of bacterial 16S ribosomal RNA genes in placental tissues than in technical controls. Therefore, there was no evidence of the presence of microorganisms above background contamination from reagents in the placentas. (3) 16S ribosomal RNA gene sequencing did not reveal consistent differences in the composition or structure of bacterial profiles between placental samples and background technical controls. (4) Most of the bacterial sequences obtained from metagenomic surveys of placental tissues were from cyanobacteria, aquatic bacteria, or plant pathogens, which are microbes unlikely to populate the human placenta. Coprobacillus, which constituted 30.5% of the bacterial sequences obtained through metagenomic sequencing of placental samples, was not identified in any of the 16S ribosomal RNA gene surveys of these samples. These observations cast doubt as to whether this organism is really present in the placenta of patients at term not in labor.
CONCLUSION: With the use of multiple modes of microbiologic inquiry, a resident microbiota could not be identified in human placentas delivered at term from women without labor. A consistently significant difference in the abundance and/or presence of a microbiota between placental tissue and background technical controls could not be found. All cultures of placental tissue, except 1, did not yield bacteria. Incorporating technical controls for potential sources of background-contaminating DNA for studies of low microbial biomass samples, such as the placenta, is necessary to derive reliable conclusions.}, }
@article {pmid30832740, year = {2019}, author = {Song, W and Wemheuer, B and Zhang, S and Steensen, K and Thomas, T}, title = {MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {36}, doi = {10.1186/s40168-019-0649-y}, pmid = {30832740}, issn = {2049-2618}, support = {201508200019//China Scholarship Council/ ; 201708200017//China Scholarship Council/ ; }, abstract = {BACKGROUND: Metagenomic datasets provide an opportunity to study horizontal gene transfer (HGT) on the level of a microbial community. However, current HGT detection methods cannot be applied to community-level datasets or require reference genomes. Here, we present MetaCHIP, a pipeline for reference-independent HGT identification at the community level.
RESULTS: Assessment of MetaCHIP's performance on simulated datasets revealed that it can predict HGTs with various degrees of genetic divergence from metagenomic datasets. The results also indicated that the detection of very recent gene transfers (i.e. those with low levels of genetic divergence) from metagenomics datasets is largely affected by the read assembly step. Comparison of MetaCHIP with a previous analysis on soil bacteria showed a high level of consistency for the prediction of recent HGTs and revealed a large number of additional non-recent gene transfers, which can provide new biological and ecological insight. Assessment of MetaCHIP's performance on real metagenomic datasets confirmed the role of HGT in the spread of genes related to antibiotic resistance in the human gut microbiome. Further testing also showed that functions related to energy production and conversion as well as carbohydrate transport and metabolism are frequently transferred among free-living microorganisms.
CONCLUSION: MetaCHIP provides an opportunity to study HGTs among members of a microbial community and therefore has several applications in the field of microbial ecology and evolution. MetaCHIP is implemented in Python and freely available at https://github.com/songweizhi/MetaCHIP .}, }
@article {pmid30832730, year = {2019}, author = {Meyer, F and Bremges, A and Belmann, P and Janssen, S and McHardy, AC and Koslicki, D}, title = {Assessing taxonomic metagenome profilers with OPAL.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {51}, doi = {10.1186/s13059-019-1646-y}, pmid = {30832730}, issn = {1474-760X}, abstract = {The explosive growth in taxonomic metagenome profiling methods over the past years has created a need for systematic comparisons using relevant performance criteria. The Open-community Profiling Assessment tooL (OPAL) implements commonly used performance metrics, including those of the first challenge of the initiative for the Critical Assessment of Metagenome Interpretation (CAMI), together with convenient visualizations. In addition, we perform in-depth performance comparisons with seven profilers on datasets of CAMI and the Human Microbiome Project. OPAL is freely available at https://github.com/CAMI-challenge/OPAL .}, }
@article {pmid30832616, year = {2019}, author = {Kazlauskas, A and Darinskas, A and Meškys, R and Tamašauskas, A and Urbonavičius, J}, title = {Isocytosine deaminase Vcz as a novel tool for the prodrug cancer therapy.}, journal = {BMC cancer}, volume = {19}, number = {1}, pages = {197}, doi = {10.1186/s12885-019-5409-7}, pmid = {30832616}, issn = {1471-2407}, support = {SEN-07/2015//Lietuvos Mokslo Taryba/ ; }, abstract = {BACKGROUND: The cytosine deaminase (CD)/5-fluorocytosine (5-FC) system is among the best explored enzyme/prodrug systems in the field of the suicide gene therapy. Recently, by the screening of the environmental metagenomic libraries we identified a novel isocytosine deaminase (ICD), termed Vcz, which is able of specifically converting a prodrug 5-fluoroisocytosine (5-FIC) into toxic drug 5-fluorouracil (5-FU). The aim of this study is to test the applicability of the ICD Vcz / 5-FIC pair as a potential suicide gene therapy tool.
METHODS: Vcz-expressing human glioblastoma U87 and epithelial colorectal adenocarcinoma Caco-2 cells were treated with 5-FIC, and the Vcz-mediated cytotoxicity was evaluated by performing an MTT assay. In order to examine anti-tumor effects of the Vcz/5-FIC system in vivo, murine bone marrow-derived mesenchymal stem cells (MSC) were transduced with the Vcz-coding lentivirus and co-injected with 5-FIC or control reagents into subcutaneous GL261 tumors evoked in C57/BL6 mice.
RESULTS: 5-FIC alone showed no significant toxic effects on U87 and Caco-2 cells at 100 μM concentration, whereas the number of cells of both cell lines that express Vcz cytosine deaminase gene decreased by approximately 60% in the presence of 5-FIC. The cytotoxic effects on cells were also induced by media collected from Vcz-expressing cells pre-treated with 5-FIC. The co-injection of the Vcz-transduced mesenchymal stem cells and 5-FIC have been shown to augment tumor necrosis and increase longevity of tumorized mice by 50% in comparison with control group animals.
CONCLUSIONS: We have confirmed that the novel ICD Vcz together with the non-toxic prodrug 5-FIC has a potential of being a new enzyme/prodrug system for suicide gene therapy.}, }
@article {pmid30832576, year = {2019}, author = {Stewart, CJ and Fatemizadeh, R and Parsons, P and Lamb, CA and Shady, DA and Petrosino, JF and Hair, AB}, title = {Using formalin fixed paraffin embedded tissue to characterize the preterm gut microbiota in necrotising enterocolitis and spontaneous isolated perforation using marginal and diseased tissue.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {52}, doi = {10.1186/s12866-019-1426-6}, pmid = {30832576}, issn = {1471-2180}, abstract = {BACKGROUND: Necrotising enterocolitis (NEC) is a common cause of death in preterm infants and is closely linked to the gut microbiota. Spontaneous intestinal perforation (SIP) also occurs in preterm neonates, but results in lower mortality and less adverse neonatal outcomes than NEC. Existing studies are largely limited to non-invasive stool samples, which may not be reflective of the anatomical site of disease. Therefore, we analysed historical formalin-fixed paraffin-embedded (FFPE) tissue from NEC and SIP preterm infants. A total of 13 NEC and 16 SIP infants were included. Extracted DNA from FFPE tissue blocks underwent 16S rRNA gene sequencing. For a subset of infants, diseased tissue and marginal healthy tissue from the same infant were compared.
RESULTS: Xylene provided a cost and time effective means of deparaffinization. Tissue from the site of disease was highly comparable to adjacent healthier tissue. Comparing only diseased tissue from all infants showed significantly lower Shannon diversity in NEC (P = 0.026). The overall bacterial communities were also significantly different in NEC samples compared to SIP (P = 0.038), and large variability within NEC infants was observed. While no single OTU or genus was significantly associated with NEC or SIP, at the phylum level Proteobacteria (P = 0.045) and Bacteroidetes (P = 0.024) were significantly higher in NEC and SIP infants, respectively.
CONCLUSIONS: Existing banks of intestinal FFPE blocks provide a robust and specific sample for profiling the microbiota at the site of disease. We showed preterm infants with NEC have lower diversity and different bacterial communities when compared to SIP controls.}, }
@article {pmid30831513, year = {2019}, author = {Ariaeenejad, S and Maleki, M and Hosseini, E and Kavousi, K and Moosavi-Movahedi, AA and Salekdeh, GH}, title = {Mining of camel rumen metagenome to identify novel alkali-thermostable xylanase capable of enhancing the recalcitrant lignocellulosic biomass conversion.}, journal = {Bioresource technology}, volume = {281}, number = {}, pages = {343-350}, doi = {10.1016/j.biortech.2019.02.059}, pmid = {30831513}, issn = {1873-2976}, abstract = {The aim of this study was to isolate and characterize novel alkali-thermostable xylanase genes from the mixed genome DNA of camel rumen metagenome. In this study, a five-stage computational screening procedure was utilized to find the primary candidate enzyme with superior properties from the camel rumen metagenome. This enzyme was subjected to cloning, purification, and structural and functional characterization. It showed high thermal stability, high activity in a broad range of pH (6-11) and temperature (30-90 °C) and effectivity in recalcitrant lignocellulosic biomass degradation. Our results demonstrated the power of in silico analysis to discover novel alkali-thermostable xylanases, effective for the bioconversion of lignocellulosic biomass.}, }
@article {pmid30830220, year = {2019}, author = {Helber, SB and Steinert, G and Wu, YC and Rohde, S and Hentschel, U and Muhando, CA and Schupp, PJ}, title = {Sponges from Zanzibar host diverse prokaryotic communities with potential for natural product synthesis.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiz026}, pmid = {30830220}, issn = {1574-6941}, abstract = {Sponges are one of the most dominant organisms in marine ecosystems. One reason for their success is their association with microorganisms that are besides the host itself responsible for the chemical defence. Sponge abundances have been increasing on coral reefs in the Western Indian Ocean (WIO) and are predicted to increase further with rising anthropogenic impacts on coral reefs. However, there is a paucity of information on chemical ecology of sponges from the WIO and their prokaryotic community composition. We used a combination of Illumina sequencing and a predictive metagenomic analysis to (1) assess the prokaryotic community composition of sponges from Zanzibar, (2) predict the presence of KEGG metabolic pathways responsible for bioactive compound production and (3) relate their presence to the degree of observed chemical defence in their respective sponge host. We found that sponges from Zanzibar host diverse prokaryotic communities that are host species-specific. Sponge-species and respective specimens that showed strong chemical defences in previous studies were also predicted to be highly enriched in various pathways responsible for secondary metabolite production. Hence, the combined sequencing and predictive metagenomic approach proved to be a useful indicator for the metabolic potential of sponge holobionts.}, }
@article {pmid30828378, year = {2019}, author = {Wang, L and Ding, J and Yang, Z and Chen, H and Yao, R and Dai, Q and Ding, Y and Zhu, L}, title = {Père David's deer gut microbiome changes across captive and translocated populations: Implications for conservation.}, journal = {Evolutionary applications}, volume = {12}, number = {3}, pages = {622-635}, doi = {10.1111/eva.12743}, pmid = {30828378}, issn = {1752-4571}, abstract = {The gut microbial composition and function are shaped by different factors (e.g., host diet and phylogeny). Gut microbes play an important role in host nutrition and development. The gut microbiome may be used to evaluate the host potential environmental adaptation. In this study, we focused on the coevolution of the gut microbiome of captive and translocated Père David's deer populations (Elaphurus davidianus; Chinese: Père David's deer). To address this, we used several different macro- and micro-ecological approaches (landscape ecology, nutritional methods, microscopy, isotopic analysis, and metagenomics). In this long-term study (2011-2014), we observed some dissimilarities in gut microbiome community and function between the captive and wild/translocated Dafeng Père David's deer populations. These differences might link microbiome composition with deer diet within a given season. The proportion of genes coding for putative enzymes (endoglucanase, beta-glucosidase, and cellulose 1,4-beta-cellobiosidase) involved in cellulose digestion in the gut microbiome of the captive populations was higher than that of the translocated population, possibly because of the high proportion of cellulose, hemicellulose, and lignin in the plants most consumed by the captive populations. However, the two enzymes (natA and natB) involved in sodium transport system were enriched in the gut microbiome in translocated population, possibly because of their high salt diet (e.g., Spartina alterniflora). Thus, our results suggested that Père David's deer gut microorganisms potentially coevolved with host diet, and reflected the local adaptation of translocated population in the new environment (e.g., new dietary plants: Spartina alterniflora). A current problem for Père David's deer conservation is the saturation of captive populations. Given that the putative evolutionary adaptation of Père David's deer gut microbiome and its possible applications in conservation, the large area of wetlands along the Yellow Sea dominated by S. alterniflora might be the major translocation region in the future.}, }
@article {pmid30828325, year = {2019}, author = {Lambrechts, S and Willems, A and Tahon, G}, title = {Uncovering the Uncultivated Majority in Antarctic Soils: Toward a Synergistic Approach.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {242}, doi = {10.3389/fmicb.2019.00242}, pmid = {30828325}, issn = {1664-302X}, abstract = {Although Antarctica was once believed to be a sterile environment, it is now clear that the microbial communities inhabiting the Antarctic continent are surprisingly diverse. Until the beginning of the new millennium, little was known about the most abundant inhabitants of the continent: prokaryotes. From then on, however, the rising use of deep sequencing techniques has led to a better understanding of the Antarctic prokaryote diversity and provided insights in the composition of prokaryotic communities in different Antarctic environments. Although these cultivation-independent approaches can produce millions of sequences, linking these data to organisms is hindered by several problems. The largest difficulty is the lack of biological information on large parts of the microbial tree of life, arising from the fact that most microbial diversity on Earth has never been characterized in laboratory cultures. These unknown prokaryotes, also known as microbial dark matter, have been dominantly detected in all major environments on our planet. Laboratory cultures provide access to the complete genome and the means to experimentally verify genomic predictions and metabolic functions and to provide evidence of horizontal gene transfer. Without such well-documented reference data, microbial dark matter will remain a major blind spot in deep sequencing studies. Here, we review our current understanding of prokaryotic communities in Antarctic ice-free soils based on cultivation-dependent and cultivation-independent approaches. We discuss advantages and disadvantages of both approaches and how these strategies may be combined synergistically to strengthen each other and allow a more profound understanding of prokaryotic life on the frozen continent.}, }
@article {pmid30826702, year = {2019}, author = {Yadav, A and Raj, A and Purchase, D and Ferreira, LFR and Saratale, GD and Bharagava, RN}, title = {Phytotoxicity, cytotoxicity and genotoxicity evaluation of organic and inorganic pollutants rich tannery wastewater from a Common Effluent Treatment Plant (CETP) in Unnao district, India using Vigna radiata and Allium cepa.}, journal = {Chemosphere}, volume = {224}, number = {}, pages = {324-332}, doi = {10.1016/j.chemosphere.2019.02.124}, pmid = {30826702}, issn = {1879-1298}, abstract = {The leather industry is a major source of environmental pollution in India. The wastewater generated by leather industries contains very high pollution parameters due to the presence of a complex mixture of organic and inorganic pollutants even after the treatment at a Common Effluent Treatment Plant (CETP) and disturbs the ecological flora and fauna. The nature, characteristics and toxicity of CETP treated wastewater is yet to be fully elucidated. Thus, this study aims to characterize and evaluate the toxicity of CETP treated tannery wastewater collected from the Unnao district of Uttar Pradesh, India. In addition to measuring the physico-chemical parameters, the residual organic pollutants was identified by GC-MS analysis and phytotoxicity, cytotoxicity and genotoxicity of the treated wastewater was evaluated using Vigna radiata L. and Allium cepa L. Results showed that the treated wastewater contained very high pollution parameters (TDS 3850 mg/L, BOD 680 mg/L, COD-1300 mg/L). GC-MS analysis revealed the presence of various types of residual organic pollutants including benzoic acid, 3-[4,-(T-butyl) Phenyl] furan-2-5-dione, benzeneacetamide, resorcinol, dibutyl phthalate, and benzene-1,2,4-triol. Further, toxicological studies showed the phytotoxic nature of the wastewater as it inhibited seed germination in V. radiata L. and root growth of A. cepa. Genotoxicity was evidenced in the root tip cell of A. cepa where chromosomal aberrations (stickiness, chromosome loss, C-mitosis, and vagrant chromosome) and nuclear abnormalities like micronucleated and binucleated cells were observed. Thus, results suggested that it is not safe to discharge these wastewater into the environment.}, }
@article {pmid30826613, year = {2019}, author = {Zeng, J and Pan, Y and Yang, J and Hou, M and Zeng, Z and Xiong, W}, title = {Metagenomic insights into the distribution of antibiotic resistome between the gut-associated environments and the pristine environments.}, journal = {Environment international}, volume = {126}, number = {}, pages = {346-354}, doi = {10.1016/j.envint.2019.02.052}, pmid = {30826613}, issn = {1873-6750}, abstract = {Antibiotic resistance genes (ARGs) in the environment are promoted by anthropogenic activities, which cause potential risks to human health. However, large-scale quantitative data on antibiotic resistome from the pristine and anthropogenic environments remains largely unexplored. Here, we used metagenome-wide analysis to investigate the share and divergence in ARG profiles and their potential bacterial hosts between the pristine and gut-associated environments. We found that the abundance of total ARGs in gut-associated environments was significantly higher than the pristine environments (P < 0.001). The mcr-1 and tetX, the genes resistant to the last resort antibiotics (colistin and tigecycline, respectively), were in high abundance (4.57 copies/Gb and 3.39 copies/Gb, respectively) in gut-associated environments, suggesting the ARG pollution caused by anthropogenic antibiotics. Metagenomic assembly-based host-tracking analysis identified Escherichia, Bacteroides, and Clostridium as the predominant bacterial hosts of ARGs in gut-associated environments, while Alteromonas, Vibrio, and Proteobacteria as the predominant bacterial hosts of ARGs in pristine environments. We first described the broad diversity of ARG hosts in different environments using metagenome-wide analysis. Our results revealed the heterogeneous distribution of ARGs and their hosts among different microbial niches in gut-associated environments and the pristine environments.}, }
@article {pmid30826606, year = {2019}, author = {Bai, Y and Ruan, X and Xie, X and Yan, Z}, title = {Antibiotic resistome profile based on metagenomics in raw surface drinking water source and the influence of environmental factor: A case study in Huaihe River Basin, China.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {248}, number = {}, pages = {438-447}, doi = {10.1016/j.envpol.2019.02.057}, pmid = {30826606}, issn = {1873-6424}, abstract = {The contamination with antibiotic resistance genes (ARGs) in raw drinking water source may pose a direct threat to human health. In this study, metagenomics sequencing and analysis were applied to investigate the ARG pattern in 12 drinking water sources in upper and middle reach of Huaihe River Basin, China. Based on the redundant analysis and multi-linear regression model, location, specific microbial taxa, number of livestock and health facilities significantly influenced the ARG profile in drinking water sources. Besides the cluster effect of ARG in samples from plain and bedrock mountain areas, the samples from fracture aquifer areas also showed a distinctive biogeographic pattern with that from porous aquifer areas. Putative ARGs host Opitutus and Flavobacterium were the enriched biomarkers in plain and fracture aquifer area respectively, which mainly carried bacitracin, multidrug, beta-lactam and tetracycline ARGs. This result illuminated that both natural background and anthropogenic activities in the watershed influenced the ARG profile in natural freshwater system significantly. The low MGEs abundance and absence of pathogen revealed a low ARG dissemination risk in sampled drinking water sources, while Polynucleobacter was an abundant ARGs host and was significantly related to the ARG profile, which indicated that specific bacteria was responsible for ARGs propagation and accumulation in surface freshwater system. Further researches are needed to assess human exposure to raw drinking water source and the potential risk, as well as the species interaction in microbial community and its impact on ARG propagation under oligotrophic condition.}, }
@article {pmid30825371, year = {2019}, author = {Koohi-Moghadam, M and Borad, M and Tran, N and Swanson, K and Boardman, L and Sun, H and Wang, J}, title = {MetaMarker: a de novo pipeline for discovering novel metagenomic biomarkers.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btz123}, pmid = {30825371}, issn = {1367-4811}, abstract = {SUMMARY: We present MetaMarker, a pipeline for discovering metagenomic biomarkers from WMS samples. Different from existing methods, MetaMarker is based on a de novo approach that does not require mapping raw reads to a reference database. We applied MetaMarker on WMS of colorectal cancer (CRC) stool samples from France to discover CRC specific metagenomic biomarkers. We showed robustness of the discovered biomarkers by validating in independent samples from Hong Kong, Austria, Germany and Denmark. We further demonstrated these biomarkers could be used to build a machine learning classifier for colorectal cancer prediction.
MetaMarker is freely available at https://bitbucket.org/mkoohim/metamarker under GPLv3 license.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid30824917, year = {2019}, author = {Kitson, E and Suttle, CA}, title = {VHost-Classifier: Virus-Host Classification using natural language processing.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btz151}, pmid = {30824917}, issn = {1367-4811}, abstract = {MOTIVATION: When analysing viral metagenomic sequences, it is often desired to filter the results of a BLAST analysis by the host species of the virus. VHost-Classifier automates this procedure using a natural language processing algorithm written in Python 3, which takes a list of taxonomic identifiers (taxids) returned from a BLAST query using viral sequences as input. The taxid output is binned by the evolutionary lineage of their host, based on string matching the words in their English names. If VHost-Classifier cannot identify a host, it attempts to bin the sequences by the environment from which the sample originated. VHost-Classifier predicts the evolutionary lineage of the host from the virus name and does not rely on referencing taxids against a database; therefore, it is not constrained by the size of a database and can host classify newly characterized viruses.
RESULTS: Benchmarked on a test dataset of 1000 randomly selected viral taxids on the NCBI taxonomy database, VHost-Classifier assigned, with 100% accuracy, a host to the rank of Class for >93% of viruses, and to the rank of Family for >37% of viruses.
AVAILABILITY: For more information about VHost-Classifier as well as implementation instructions, visit https://github.com/Kzra/VHost-Classifier.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid30824791, year = {2019}, author = {McGaughey, KD and Yilmaz-Swenson, T and Elsayed, NM and Cruz, DA and Rodriguiz, RM and Kritzer, MD and Peterchev, AV and Roach, J and Wetsel, WC and Williamson, DE}, title = {Relative abundance of Akkermansia spp. and other bacterial phylotypes correlates with anxiety- and depressive-like behavior following social defeat in mice.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {3281}, doi = {10.1038/s41598-019-40140-5}, pmid = {30824791}, issn = {2045-2322}, support = {R01 MH091083/MH/NIMH NIH HHS/United States ; R01MH091083//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; }, abstract = {As discussion of stress and stress-related disorders rapidly extends beyond the brain, gut microbiota have emerged as a promising contributor to individual differences in the risk of illness, disease course, and treatment response. Here, we employed chronic mild social defeat stress and 16S rRNA gene metagenomic sequencing to investigate the role of microbial composition in mediating anxiety- and depressive-like behavior. In socially defeated animals, we found significant reductions in the overall diversity and relative abundances of numerous bacterial genera, including Akkermansia spp., that positively correlated with behavioral metrics of both anxiety and depression. Functional analyses predicted a reduced frequency of signaling molecule pathways, including G-protein-coupled receptors, in defeated animals. Collectively, our data suggest that shifts in microbial composition may play a role in the pathogenesis of anxiety and depression.}, }
@article {pmid30824633, year = {2019}, author = {Solomon, IH and Docken, WP and Padera, RF}, title = {Giant cell arteritis is not associated with varicella zoster virus in temporal artery biopsies or ascending aortic resections.}, journal = {The Journal of rheumatology}, volume = {}, number = {}, pages = {}, doi = {10.3899/jrheum.180912}, pmid = {30824633}, issn = {0315-162X}, abstract = {OBJECTIVE: A variety of infectious agents, including varicella zoster virus (VZV), have been hypothesized to play a role in the pathogenesis of giant cell arteritis (GCA). The detectability of the virus in patients with GCA has been controversial. To further investigate an association between GCA and VZV infection, ten years of GCA cases were evaluated for VZV by immunohistochemistry (IHC).
METHODS: All temporal artery biopsies and ascending aortic resections positive for GCA from 2007-2017 at Brigham and Women's Hospital were immunostained using a VZV antibody cocktail (SG1-1, SG1-SG4, NCP-1, and IE-62) (Cell Marque, Rocklin, CA).
RESULTS: Forty-one temporal artery biopsies and 47 ascending aortic resections positive for GCA were identified, all of which were found to be negative for VZV by IHC. Twelve temporal artery biopsies in this cohort were previously analyzed by unbiased metagenomics sequencing and were negative for VZV DNA.
CONCLUSION: These results argue against a clinically relevant association between VZV infection and GCA, and support neither routine testing for VZV nor treatment with antiviral drugs.}, }
@article {pmid30824335, year = {2019}, author = {Davies, NK and O'Sullivan, JM and Plank, LD and Murphy, R}, title = {Altered gut microbiome after bariatric surgery and its association with metabolic benefits: A systematic review.}, journal = {Surgery for obesity and related diseases : official journal of the American Society for Bariatric Surgery}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.soard.2019.01.033}, pmid = {30824335}, issn = {1878-7533}, abstract = {Bariatric surgery is currently the recommended therapy for significant weight reduction and remission of type 2 diabetes. Different types of bariatric surgery result in dramatic changes to gut bacteria but the contribution of such changes to the metabolic benefits achieved is still unclear. This systematic review of 14 clinical studies, incorporating 222 participants (146 patients with Roux-en-Y gastric bypass, 25 with sleeve gastrectomy, 30 with biliointestinal bypass, 7 with vertical banded gastroplasty, and 14 with an adjustable gastric band) reveals generally increased microbial diversity and gene richness after surgery. Major species-level changes include a decrease in the relative abundance of Faecalibacterium prausnitzii and increase in Escherichia coli. Decreases in the relative abundance of Firmicutes after sleeve gastrectomy and increases in Bacteroidetes and Proteobacteria after Roux-en-Y gastric bypass were seen. Microbial changes after surgery are discussed in the context of potential confounding effects of baseline diet, medications, and type 2 diabetes, with recommendations to consider these factors in future studies, to identify potentially causal associations with observed metabolic benefits.}, }
@article {pmid30822726, year = {2019}, author = {Fang, H and Huang, K and Yu, J and Ding, C and Wang, Z and Zhao, C and Yuan, H and Wang, Z and Wang, S and Hu, J and Cui, Y}, title = {Metagenomic analysis of bacterial communities and antibiotic resistance genes in the Eriocheir sinensis freshwater aquaculture environment.}, journal = {Chemosphere}, volume = {224}, number = {}, pages = {202-211}, doi = {10.1016/j.chemosphere.2019.02.068}, pmid = {30822726}, issn = {1879-1298}, abstract = {Aquaculture has attracted significant attention as an environmental gateway to the development of antibiotic resistance. The industry of Chinese mitten crab Eriocheir sinensis contributes significantly to the freshwater aquaculture industry in China. However, the situation of antibiotic resistance in the E. sinensis aquaculture environment is not known. In this study, high-throughput sequencing based metagenomic approaches were used to comprehensively investigate the structure of bacterial communities, the abundance and diversity of antibiotic resistance genes (ARGs), as well as mobile genetic elements (MGEs) in three E. sinensis aquaculture ponds in Jiangsu Province, China. The dominant phyla were Proteobacteria, Actinobacteria, and Bacteroidetes in water samples and Proteobacteria, Chloroflexi, Verrucomicrobia, and Bacteroidetes in sediment samples. Bacitracin and multidrug were predominant ARG types in water and sediment samples, respectively. There was a significant correlation between MGEs and ARGs. In particular, plasmids were the most abundant MGEs and strongly correlated with ARGs. This is the first study of antibiotic resistome that uses metagenomic approaches in the E. sinensis aquaculture environment. The results indicate that the opportunistic pathogens may acquire ARGs via horizontal gene transfer, intensifying the potential risk to human health.}, }
@article {pmid30819245, year = {2019}, author = {Fresia, P and Antelo, V and Salazar, C and Giménez, M and D'Alessandro, B and Afshinnekoo, E and Mason, C and Gonnet, GH and Iraola, G}, title = {Urban metagenomics uncover antibiotic resistance reservoirs in coastal beach and sewage waters.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {35}, doi = {10.1186/s40168-019-0648-z}, pmid = {30819245}, issn = {2049-2618}, support = {OPR_X_2016_1_1006944//Agencia Nacional de Investigación e Innovación/ ; }, abstract = {BACKGROUND: Microbial communities present in environmental waters constitute a reservoir for antibiotic-resistant pathogens that impact human health. For this reason, a diverse variety of water environments are being analyzed using metagenomics to uncover public health threats. However, the composition of these communities along the coastal environment of a whole city, where sewage and beach waters are mixed, is poorly understood.
RESULTS: We shotgun-sequenced 20 coastal areas from the city of Montevideo (capital of Uruguay) including beach and sewage water samples to characterize bacterial communities and their virulence and antibiotic resistance repertories. As expected, we found that sewage and beach environments present significantly different bacterial communities. This baseline allowed us to detect a higher prevalence and a more diverse repertory of virulence and antibiotic-resistant genes in sewage samples. Many of these genes come from well-known enterobacteria and represent carbapenemases and extended-spectrum betalactamases reported in hospital infections in Montevideo. Additionally, we were able to genotype the presence of both globally disseminated pathogenic clones and emerging antibiotic-resistant bacteria in sewage waters.
CONCLUSIONS: Our study represents the first in using metagenomics to jointly analyze beaches and the sewage system from an entire city, allowing us to characterize antibiotic-resistant pathogens circulating in urban waters. The data generated in this initial study represent a baseline metagenomic exploration to guide future longitudinal (time-wise) studies, whose systematic implementation will provide useful epidemiological information to improve public health surveillance.}, }
@article {pmid30817265, year = {2019}, author = {Touyz, RM and Camargo, LL}, title = {Microglia, the Missing Link in the Brain-Gut-Hypertension Axis.}, journal = {Circulation research}, volume = {124}, number = {5}, pages = {671-673}, doi = {10.1161/CIRCRESAHA.119.314718}, pmid = {30817265}, issn = {1524-4571}, }
@article {pmid30816928, year = {2019}, author = {Shi, L and Meng, X and Tseng, E and Mascagni, M and Wang, Z}, title = {SpaRC: scalable sequence clustering using Apache Spark.}, journal = {Bioinformatics (Oxford, England)}, volume = {35}, number = {5}, pages = {760-768}, doi = {10.1093/bioinformatics/bty733}, pmid = {30816928}, issn = {1367-4811}, abstract = {MOTIVATION: Whole genome shotgun based next-generation transcriptomics and metagenomics studies often generate 100-1000 GB sequence data derived from tens of thousands of different genes or microbial species. Assembly of these data sets requires tradeoffs between scalability and accuracy. Current assembly methods optimized for scalability often sacrifice accuracy and vice versa. An ideal solution would both scale and produce optimal accuracy for individual genes or genomes.
RESULTS: Here we describe an Apache Spark-based scalable sequence clustering application, SparkReadClust (SpaRC), that partitions reads based on their molecule of origin to enable downstream assembly optimization. SpaRC produces high clustering performance on transcriptomes and metagenomes from both short and long read sequencing technologies. It achieves near-linear scalability with input data size and number of compute nodes. SpaRC can run on both cloud computing and HPC environments without modification while delivering similar performance. Our results demonstrate that SpaRC provides a scalable solution for clustering billions of reads from next-generation sequencing experiments, and Apache Spark represents a cost-effective solution with rapid development/deployment cycles for similar large-scale sequence data analysis problems.
https://bitbucket.org/berkeleylab/jgi-sparc.}, }
@article {pmid30816927, year = {2019}, author = {Dai, Z and Wong, SH and Yu, J and Wei, Y}, title = {Batch effects correction for microbiome data with Dirichlet-multinomial regression.}, journal = {Bioinformatics (Oxford, England)}, volume = {35}, number = {5}, pages = {807-814}, doi = {10.1093/bioinformatics/bty729}, pmid = {30816927}, issn = {1367-4811}, abstract = {MOTIVATION: Metagenomic sequencing techniques enable quantitative analyses of the microbiome. However, combining the microbial data from these experiments is challenging due to the variations between experiments. The existing methods for correcting batch effects do not consider the interactions between variables-microbial taxa in microbial studies-and the overdispersion of the microbiome data. Therefore, they are not applicable to microbiome data.
RESULTS: We develop a new method, Bayesian Dirichlet-multinomial regression meta-analysis (BDMMA), to simultaneously model the batch effects and detect the microbial taxa associated with phenotypes. BDMMA automatically models the dependence among microbial taxa and is robust to the high dimensionality of the microbiome and their association sparsity. Simulation studies and real data analysis show that BDMMA can successfully adjust batch effects and substantially reduce false discoveries in microbial meta-analyses.
An R package" BDMMA" for Windows and Linux is available at https://github.com/DAIZHENWEI/BDMMA/BDMMA, and a version for MacOS is provided at https://github.com/DAIZHENWEI/BDMMA/BDMMA_MacOS.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid30816674, year = {2019}, author = {Philley, JV and Kannan, A and Olusola, P and McGaha, P and Singh, KP and Samten, B and Griffith, DE and Dasgupta, S}, title = {Microbiome Diversity in Sputum of Nontuberculous Mycobacteria Infected Women with a History of Breast Cancer.}, journal = {Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology}, volume = {52}, number = {2}, pages = {263-279}, doi = {10.33594/000000020}, pmid = {30816674}, issn = {1421-9778}, support = {Startup Fund//The University of Texas Health Science Center at Tyler/International ; }, abstract = {BACKGROUND/AIMS: The nontuberculous mycobacterial lung disease (NTM), caused by Mycobacterium avium complex (MAC) is an increasing health problem in the USA and worldwide. The NTM disease is prevalent in Caucasian women with a current diagnosis or history of breast cancer (BCa), posing a significant challenge towards treatment. We hypothesize that NTM affected women with considerable therapeutic resistance may harbor pathogenic microbes other than nontuberculous mycobacterium, aiding in disease progression and therapeutic resistance.
METHODS: We assessed microbiome diversity in sputa from healthy women, women with nontuberculous mycobacterial lung disease (NTM) and women with both nontuberculous mycobacterial lung disease and breast cancer (NTM-BCa). First, we collected sputa and isolated DNA from sputa of these healthy women and women with NTM and NTM-BCa. We also isolated DNA from sera derived extracellular vesicles from women with NTM-BCa. To identify diverse pathogenic microbes in various groups of subjects, we then performed 16S rDNA sequencing. Data analysis was performed utilizing the analytical pipelines at the Center for Metagenomic and Microbiome Research (CMMR), Baylor College of Medicine.
RESULTS: A large community of resident microbes, including bacteria, virus, Archeas and Fungi live in the human body are being increasingly recognized as the key components of human health and disease. We identified a diverse microbiome community in the sputa and the extracellular vesicles dominated by Streptococcus, Haemophillus, Veillonella, Neisseria, Prevotella, Fusobacterium, Bacteroides, Allistipes, Faecalibacterium and Staphylococcus in women with nontuberculous mycobacterial lung disease as well as women with both nontuberculous mycobacterial lung disease and breast cancer. Some of these genera, including Fusobacterium, Bacteroides, and Allistipes have estrobolome activity and associated with breast and other neoplasms.
CONCLUSION: This work confirms the presence of a distinct pathogenic microbiome other than nontuberculous mycobacteria in the sputa and the circulating extracellular vesicles of these patients. This information could be useful for better therapeutic design to treat the NTM patients.}, }
@article {pmid30816592, year = {2019}, author = {Subramaniyan, V and Gurumurthy, K}, title = {Diversity of probiotic adhesion genes in the gastrointestinal tract of goats.}, journal = {Journal of cellular biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1002/jcb.28508}, pmid = {30816592}, issn = {1097-4644}, abstract = {Gastrointestinal (GI) microflora is an important system in the host, as it has both pathogenic and probiotic bacteria. Most of the studies were focused on the human gut microflora and the available information on the intestinal microflora of goats was limited. This urged the need to inspect the impacts of the goat's gut microflora. Metagenomic investigation of probiotic bacteria in the GI tract of goat is one of the challenging streams because of the less available data of the uncultivable bacteria. In our report, comparative analysis of metagenomic and enrichment samples of goat intestinal content was done and this approach will be helpful in analyzing the identification of uncultivable and cultivable probiotic bacteria. This study mainly focused on three key probiotic adhesion genes, such as EF-Tu, mapA, and mub. The GI of four different goats were investigated for these genes. The data from this study showed that there is a wide diversity of these genes among goat intestinal samples.}, }
@article {pmid30816276, year = {2019}, author = {Kasanke, CP and Collins, RE and Leigh, MB}, title = {Identification and Characterization of a Dominant Sulfolane-Degrading Rhodoferax sp. via Stable Isotope Probing Combined with Metagenomics.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {3121}, doi = {10.1038/s41598-019-40000-2}, pmid = {30816276}, issn = {2045-2322}, support = {P20GM103395//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; P20GM103395//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, abstract = {Sulfolane is an industrial solvent and emerging organic contaminant affecting groundwater around the world, but little is known about microbes capable of biodegrading sulfolane or the pathways involved. We combined DNA-based stable isotope probing (SIP) with genome-resolved metagenomics to identify microorganisms associated with sulfolane biodegradation in a contaminated subarctic aquifer. In addition to 16S rRNA gene amplicon sequencing, we performed shotgun metagenomics on the 13C-labeled DNA to obtain functional and taxonomic information about the active sulfolane-degrading community. We identified the primary sulfolane degrader, comprising ~85% of the labeled community in the amplicon sequencing dataset, as closely related to Rhodoferax ferrireducens strain T118. We obtained a 99.8%-complete metagenome-assembled genome for this strain, allowing us to identify putative pathways of sulfolane biodegradation. Although the 4S dibenzothiophene desulfurization pathway has been proposed as an analog for sulfolane biodegradation, we found only a subset of the required genes, suggesting a novel pathway specific to sulfolane. DszA, the enzyme likely responsible for opening the sulfolane ring structure, was encoded on both the chromosome and a plasmid. This study demonstrates the power of integrating DNA-SIP with metagenomics to characterize emerging organic contaminant degraders without culture bias and expands the known taxonomic distribution of sulfolane biodegradation.}, }
@article {pmid30816235, year = {2019}, author = {Wilkins, LGE and Ettinger, CL and Jospin, G and Eisen, JA}, title = {Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {3059}, doi = {10.1038/s41598-019-39576-6}, pmid = {30816235}, issn = {2045-2322}, support = {P2LAP3_164915//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; }, abstract = {Culture-independent methods have contributed substantially to our understanding of global microbial diversity. Recently developed algorithms to construct whole genomes from environmental samples have further refined, corrected and revolutionized understanding of the tree of life. Here, we assembled draft metagenome-assembled genomes (MAGs) from environmental DNA extracted from two hot springs within an active volcanic ecosystem on the Kamchatka peninsula, Russia. This hydrothermal system has been intensively studied previously with regard to geochemistry, chemoautotrophy, microbial isolation, and microbial diversity. We assembled genomes of bacteria and archaea using DNA that had previously been characterized via 16S rRNA gene clone libraries. We recovered 36 MAGs, 29 of medium to high quality, and inferred their placement in a phylogenetic tree consisting of 3,240 publicly available microbial genomes. We highlight MAGs that were taxonomically assigned to groups previously underrepresented in available genome data. This includes several archaea (Korarchaeota, Bathyarchaeota and Aciduliprofundum) and one potentially new species within the bacterial genus Sulfurihydrogenibium. Putative functions in both pools were compared and are discussed in the context of their diverging geochemistry. This study adds comprehensive information about phylogenetic diversity and functional potential within two hot springs in the caldera of Kamchatka.}, }
@article {pmid30815668, year = {2019}, author = {Ayling, M and Clark, MD and Leggett, RM}, title = {New approaches for metagenome assembly with short reads.}, journal = {Briefings in bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1093/bib/bbz020}, pmid = {30815668}, issn = {1477-4054}, abstract = {In recent years, the use of longer range read data combined with advances in assembly algorithms has stimulated big improvements in the contiguity and quality of genome assemblies. However, these advances have not directly transferred to metagenomic data sets, as assumptions made by the single genome assembly algorithms do not apply when assembling multiple genomes at varying levels of abundance. The development of dedicated assemblers for metagenomic data was a relatively late innovation and for many years, researchers had to make do using tools designed for single genomes. This has changed in the last few years and we have seen the emergence of a new type of tool built using different principles. In this review, we describe the challenges inherent in metagenomic assemblies and compare the different approaches taken by these novel assembly tools.}, }
@article {pmid30815250, year = {2018}, author = {Cuscó, A and Catozzi, C and Viñes, J and Sanchez, A and Francino, O}, title = {Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and whole rrn operon.}, journal = {F1000Research}, volume = {7}, number = {}, pages = {1755}, doi = {10.12688/f1000research.16817.1}, pmid = {30815250}, issn = {2046-1402}, abstract = {Background: Profiling the microbiome of low-biomass samples is challenging for metagenomics since these samples often contain DNA from other sources, such as the host or the environment. The usual approach is sequencing specific hypervariable regions of the 16S rRNA gene, which fails to assign taxonomy to genus and species level. Here, we aim to assess long-amplicon PCR-based approaches for assigning taxonomy at the genus and species level. We use Nanopore sequencing with two different markers: full-length 16S rRNA (~1,500 bp) and the whole rrn operon (16S rRNA-ITS-23S rRNA; 4,500 bp). Methods: We sequenced a clinical isolate of Staphylococcus pseudintermedius, two mock communities (HM-783D, Bei Resources; D6306, ZymoBIOMICS™) and two pools of low-biomass samples (dog skin from either the chin or dorsal back), using the MinION™ sequencer 1D PCR barcoding kit. Sequences were pre-processed, and data were analyzed using the WIMP workflow on EPI2ME or Minimap2 software with rrn database. Results: The full-length 16S rRNA and the rrn operon were used to retrieve the microbiota composition at the genus and species level from the bacterial isolate, mock communities and complex skin samples. For the Staphylococcus pseudintermedius isolate, when using EPI2ME, the amplicons were assigned to the correct bacterial species in ~98% of the cases with the rrn operon marker, and in ~68% of the cases with the 16S rRNA gene. In both skin microbiota samples, we detected many species with an environmental origin. In chin, we found different Pseudomonas species in high abundance, whereas in dorsal skin there were more taxa with lower abundances. Conclusions: Both full-length 16S rRNA and the rrn operon retrieved the microbiota composition of simple and complex microbial communities, even from the low-biomass samples such as dog skin. For an increased resolution at the species level, using the rrn operon would be the best choice.}, }
@article {pmid30814921, year = {2019}, author = {Xie, J and Liu, Y and Chen, B and Zhang, G and Ou, S and Luo, J and Peng, X}, title = {Ganoderma lucidum polysaccharide improves rat DSS-induced colitis by altering cecal microbiota and gene expression of colonic epithelial cells.}, journal = {Food & nutrition research}, volume = {63}, number = {}, pages = {}, doi = {10.29219/fnr.v63.1559}, pmid = {30814921}, issn = {1654-661X}, abstract = {Background: The effects of β-glucan on colitis mice are contradictory in previous reports. As a result, it is still unclear whether there is an anti-colitis effect in Ganoderma lucidum polysaccharide (GLP), which is mainly composed of β-glucan. Moreover, the association between GLP function and gut microbiota remains to be elucidated.
Objective: This study aimed to investigate whether GLP consumption improved rat dextran sodium sulfate (DSS)-induced colitis by regulating gut microbiota and altering colonic epithelial expression.
Design: The disease activity index (DAI) scores and the cecal short chain fatty acid (SCFA) levels of DSS-induced colitis rats fed with a GLP diet (Group GLP, n = 6) and a control diet (Group Con, n = 6) were investigated and analyzed. Moreover, the profiles of gut microbiota and colonic epithelial expression were analyzed using metagenomics and transcriptomics.
Results: GLP consumption significantly lowered animal DAI scores by producing more SCFAs by increasing SCFA-producing bacteria such as Ruminococcus_1 and reducing pathogens such as Escherichia-Shigella in both the small intestine and cecum of rat. Moreover, GLP consumption regulated 11 genes, including six upregulated (Ccl5, Cd3e, Cd8a, Il21r, Lck, and Trbv) and five downregulated (Ccl3, Gro, Il11, Mhc2, and Ptgs) genes enriched in six inflammation-related Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, resulting in enhancement of immunity and reduction of inflammatory response and colonic cancer risk.
Conclusions: GLP consumption alleviated DSS-induced colitis and may have potential for ulcerative colitis relief.}, }
@article {pmid30814504, year = {2019}, author = {Mahnert, A and Moissl-Eichinger, C and Zojer, M and Bogumil, D and Mizrahi, I and Rattei, T and Martinez, JL and Berg, G}, title = {Man-made microbial resistances in built environments.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {968}, doi = {10.1038/s41467-019-08864-0}, pmid = {30814504}, issn = {2041-1723}, abstract = {Antimicrobial resistance is a serious threat to global public health, but little is known about the effects of microbial control on the microbiota and its associated resistome. Here we compare the microbiota present on surfaces of clinical settings with other built environments. Using state-of-the-art metagenomics approaches and genome and plasmid reconstruction, we show that increased confinement and cleaning is associated with a loss of microbial diversity and a shift from Gram-positive bacteria, such as Actinobacteria and Firmicutes, to Gram-negative such as Proteobacteria. Moreover, the microbiome of highly maintained built environments has a different resistome when compared to other built environments, as well as a higher diversity in resistance genes. Our results highlight that the loss of microbial diversity correlates with an increase in resistance, and the need for implementing strategies to restore bacterial diversity in certain built environments.}, }
@article {pmid30813540, year = {2019}, author = {Lam, KL and Ko, KC and Li, X and Ke, X and Cheng, WY and Chen, T and You, L and Kwan, HS and Cheung, PC}, title = {In Vitro Infant Faecal Fermentation of Low Viscosity Barley β-Glucan and Its Acid Hydrolyzed Derivatives: Evaluation of Their Potential as Novel Prebiotics.}, journal = {Molecules (Basel, Switzerland)}, volume = {24}, number = {5}, pages = {}, doi = {10.3390/molecules24050828}, pmid = {30813540}, issn = {1420-3049}, support = {14114115//Research Grants Council, University Grants Committee/ ; }, abstract = {Barley contains high level of β-1,3-1,4-glucans (BBGs) which can be fermented by microbes and are a potential prebiotic. In the present study, native BBG with low viscosity and a MW of 319 kDa was depolymerized by acid hydrolysis to produce a series of four structurally characterized fragments with MWs ranging from 6⁻104 kDa. In vitro fermentation of these BBG samples by infant faecal microbiome was evaluated using a validated deep-well plate protocol as parallel miniature bioreactors. Microbial taxa were identified using 16S amplicon sequencing after 40 h of anaerobic fermentation. Bioinformatics analysis including diversity indexes, predicted metagenomic KEGG functions and predicted phenotypes were performed on the sequenced data. Short chain fatty acids and dissolved ammonia were quantified and the SCFAs/NH₃ ratio was used to evaluate the eubiosis/dysbiosis potential. Correlation analysis showed that most of the parameters investigated showed a parabolic function instead of a monotonous function with the BBG samples having different MWs. Among the five BBGs, it was concluded that BBG with an intermediate MW of 28 kDa is the most promising candidate to be developed as a novel prebiotic.}, }
@article {pmid30810995, year = {2019}, author = {Wiscovitch-Russo, R and Narganes-Stordes, Y and Cano, RJ and Toranzos, GA}, title = {Origin of the New World Plasmodium vivax: Facts and New Approaches.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10123-018-00053-1}, pmid = {30810995}, issn = {1139-6709}, support = {5R25GM061151-17//National Institutes of Health/ ; }, abstract = {Malaria is one of the most important human diseases throughout tropical and sub-tropical regions of the world. Global distribution and ample host range have contributed to the genetic diversity of the etiological agent, Plasmodium. Phylogeographical analyses demonstrated that Plasmodium falciparum and Plasmodium vivax follow an Out of Africa (OOA) expansion, having a higher genetic diversity in African populations and a low genetic diversity in South American populations. Modeling the evolutionary rate of conserved genes for both P. falciparum and P. vivax determined the approximate arrival of human malaria in South America. Bayesian computational methods suggest that P. falciparum originated in Africa and arrived in South America through multiple independent introductions by the transatlantic African slave trade; however, in South America, P. vivax could have been introduced through an alternate migratory route. Alignments of P. vivax mitogenomes have revealed low genetic variation between the South American and Southeast Asian populations suggesting introduction through either pre-Columbian human migration or post-colonization events. To confirm the findings of these phylogeographical analyses, molecular methods were used to diagnose malaria infection in archeological remains of pre-Columbian ethnic groups. Immunohistochemistry tests were used and identified P. vivax but not P. falciparum in histologically prepared tissues from pre-Columbian Peruvian mummies, whereas shotgun metagenomics sequencing of DNA isolated from pre-Columbian Caribbean coprolites revealed Plasmodium-homologous reads; current evidence suggests that only P. vivax might have been present in pre-Columbian South America.}, }
@article {pmid30810441, year = {2019}, author = {Dostal Webster, A and Staley, C and Hamilton, MJ and Huang, M and Fryxell, K and Erickson, R and Kabage, AJ and Sadowsky, MJ and Khoruts, A}, title = {Influence of short-term changes in dietary sulfur on the relative abundances of intestinal sulfate-reducing bacteria.}, journal = {Gut microbes}, volume = {}, number = {}, pages = {1-11}, doi = {10.1080/19490976.2018.1559682}, pmid = {30810441}, issn = {1949-0984}, abstract = {High-protein diets may be linked to gut inflammation due to increased production of hydrogen sulfide (H2S), a potential toxin, as an end product of microbial fermentation in the colon by sulfidogenic sulfate-reducing bacteria (SRB). We hypothesized that dietary content of sulfur-containing amino acids (SAA) leads to variation in the relative abundances of intestinal SRB, which include Desulfovibrio and Bilophila taxa. To test this hypothesis we performed a pilot crossover study in four healthy volunteers, who consumed two interventional diets for 10-14 days, containing high or low SAA content. The total energy intake was similar between the two dietary extremes. Microbial communities were characterized by 16S rRNA gene amplicon and shotgun next-generation DNA sequencing. While the relative abundance of Desulfovibrio differed among participants (ANOVA P= 0.001), we could not detect a change with dietary treatments. Similarly, no differences in Bilophila abundance were observed among individuals or dietary arms. Inter-personal differences in microbial community composition and functional gene categories differed between subjects and these differences were maintained over the course of the study. These observations are consistent with re-analysis of two previously published dietary intervention studies. Finally, we found that inter-personal differences in the taxonomic composition of fecal microbiota, including the relative abundances of SRB, were maintained over time in 19 healthy individuals in our stool donor program. These results suggest that the use of dietary interventions alone may be insufficient for rapid therapeutic targeting of SRB. Nevertheless, these pilot data provide a foundation to inform future, statistically powered, studies.}, }
@article {pmid30809711, year = {2019}, author = {Lu, M and Dukunde, A and Daniel, R}, title = {Biochemical profiles of two thermostable and organic solvent-tolerant esterases derived from a compost metagenome.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00253-019-09695-1}, pmid = {30809711}, issn = {1432-0614}, abstract = {Owing to the functional versatility and potential applications in industry, interest in lipolytic enzymes tolerant to organic solvents is increasing. In this study, functional screening of a compost soil metagenome resulted in identification of two lipolytic genes, est1 and est2, encoding 270 and 389 amino acids, respectively. The two genes were heterologously expressed and characterized. Est1 and Est2 are thermostable enzymes with optimal enzyme activities at 80 and 70 °C, respectively. A second-order rotatable design, which allows establishing the relationship between multiple variables with the obtained responses, was used to explore the combined effects of temperature and pH on esterase stability. The response curve indicated that Est1, and particularly Est2, retained high stability within a broad range of temperature and pH values. Furthermore, the effects of organic solvents on Est1 and Est2 activities and stabilities were assessed. Notably, Est2 activity was significantly enhanced (two- to tenfold) in the presence of ethanol, methanol, isopropanol, and 1-propanol over a concentration range between 6 and 30% (v/v). For the short-term stability (2 h of incubation), Est2 exhibited high tolerance against 60% (v/v) of ethanol, methanol, isopropanol, DMSO, and acetone, while Est1 activity resisted these solvents only at lower concentrations (below 30%, v/v). Est2 also displayed high stability towards some water-immiscible organic solvents, such as ethyl acetate, diethyl ether, and toluene. With respect to long-term stability, Est2 retained most of its activity after 26 days of incubation in the presence of 30% (v/v) ethanol, methanol, isopropanol, DMSO, or acetone. All of these features indicate that Est1 and Est2 possess application potential.}, }
@article {pmid30809472, year = {2019}, author = {Ge, C and Wei, C and Yang, BX and Cheng, J and Huang, YS}, title = {Conjunctival microbiome changes associated with fungal keratitis: metagenomic analysis.}, journal = {International journal of ophthalmology}, volume = {12}, number = {2}, pages = {194-200}, doi = {10.18240/ijo.2019.02.02}, pmid = {30809472}, issn = {2222-3959}, abstract = {AIM: To investigate the ocular surface microbiome profile of patients with fungal keratitis (FK) through bacterial 16S rDNA sequencing.
METHODS: The swab samples were collected from 8 patients with FK (Group 1 from the corneal ulcer, Group 2 from the conjunctival sac of the infected eyes, and Group 3 from the conjunctival sac of the fellow eyes) and 10 healthy eyes (Group 4 from the conjunctival sac). Bacterial 16S rDNA V4-V5 region sequencing was performed to characterize the bacterial communities on the ocular surfaces of the patients with FK.
RESULTS: Our metagenomic data showed that 97% of the sequence reads were categorized into 245 distinct bacterial genera, with 67.75±7.79 genera detected in Group 1, 73.80±13.44 in Group 2, 74.57±14.14 in Group 3, and 89.60±27.49 in Group 4. Compared with the healthy eyes (Group 4), both infected (Groups 1 and 2) and fellow eyes (Group 3) of the patients with FK showed reduced bacterial diversity and altered ocular surface microbiota compositions, with lower abundance of Corynebacterium and Staphylococcus and higher abundances of Pseudomonas, Achromobacter, Caulobacter and Psychrobacter.
CONCLUSION: Our report depicts the altered ocular surface bacterial community structures both in the affected and fellow eyes of patients with FK. These changes may contribute to the pathogenesis of FK or the increased risk for FK.}, }
@article {pmid30809304, year = {2019}, author = {Sun, L and Ma, L and Zhang, H and Cao, Y and Wang, C and Hou, N and Huang, N and von Deneen, KM and Zhao, C and Shi, Y and Pan, Y and Wang, M and Ji, G and Nie, Y}, title = {Fto Deficiency Reduces Anxiety- and Depression-Like Behaviors in Mice via Alterations in Gut Microbiota.}, journal = {Theranostics}, volume = {9}, number = {3}, pages = {721-733}, doi = {10.7150/thno.31562}, pmid = {30809304}, issn = {1838-7640}, abstract = {Depression and obesity have high concurrence within individuals, which may be explained by sharing the same risk factors, including disruption of the intestinal microbiota. However, evidence that delineated the causal connections is extremely scarce. Methods: Mice lacking fat mass- and obesity-associated gene (Fto) were generated. Fto-deficient and wild-type control mice were subjected to novel conditions with or without chronic unpredictable mild stress (CUMS) for 6 weeks. Some mice were treated with antibiotics via their drinking water for 6 weeks in order to deplete their microbiota. Behavioral tests were performed to evaluate anxiety- and depression-like behaviors. 16S rRNA amplicon and metagenomic sequencing were employed to analyse fecal microbiota. Plasma levels of inflammatory cytokines and lipopolysaccharides (LPS) were also compared. Results: Deletion of Fto led to lower body weight and decreased anxiety- and depression-like behaviors, Fto+/- mice were also less susceptible to stress stimulation, highlighting the essential role of Fto in pathogenesis of depression. With regard to gut microbiota, Fto deficiency mice harbored specific bacterial signature of suppressing inflammation, characterized with higher abundance of Lactobacillus, lower Porphyromonadaceae and Helicobacter. Critically, behavioral alterations of Fto+/- mice are mediated by shift in gut microbiota, as such changes can be partially attenuated using antibiotics. Exposure to CUMS increased serum IL-6 level while Fto deficiency reduced its level, which may be explained by a lower LPS concentration. Conclusion: Together, our findings uncover the roles of Fto on depression and provide insights into microbiota-related biological mechanisms underlying the association between obesity and depression.}, }
@article {pmid30809252, year = {2019}, author = {Hirata, A}, title = {Recent Insights Into the Structure, Function, and Evolution of the RNA-Splicing Endonucleases.}, journal = {Frontiers in genetics}, volume = {10}, number = {}, pages = {103}, doi = {10.3389/fgene.2019.00103}, pmid = {30809252}, issn = {1664-8021}, abstract = {RNA-splicing endonuclease (EndA) cleaves out introns from archaeal and eukaryotic precursor (pre)-tRNA and is essential for tRNA maturation. In archaeal EndA, the molecular mechanisms underlying complex assembly, substrate recognition, and catalysis have been well understood. Recently, certain studies have reported novel findings including the identification of new subunit types in archaeal EndA structures, providing insights into the mechanism underlying broad substrate specificity. Further, metagenomics analyses have enabled the acquisition of numerous DNA sequences of EndAs and intron-containing pre-tRNAs from various species, providing information regarding the co-evolution of substrate specificity of archaeal EndAs and tRNA genetic diversity, and the evolutionary pathway of archaeal and eukaryotic EndAs. Although the complex structure of the heterothermic form of eukaryotic EndAs is unknown, previous reports regarding their functions indicated that mutations in human EndA cause neurological disorders including pontocerebellar hypoplasia and progressive microcephaly, and yeast EndA significantly cleaves mitochondria-localized mRNA encoding cytochrome b mRNA processing 1 (Cpb1) for mRNA maturation. This mini-review summarizes the aforementioned results, discusses their implications, and offers my personal opinion regarding future directions for the analysis of the structure and function of EndAs.}, }
@article {pmid30809205, year = {2019}, author = {Marco, DE and Abram, F}, title = {Editorial: Using Genomics, Metagenomics and Other "Omics" to Assess Valuable Microbial Ecosystem Services and Novel Biotechnological Applications.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {151}, doi = {10.3389/fmicb.2019.00151}, pmid = {30809205}, issn = {1664-302X}, }
@article {pmid30809011, year = {2019}, author = {Bouma-Gregson, K and Olm, MR and Probst, AJ and Anantharaman, K and Power, ME and Banfield, JF}, title = {Impacts of microbial assemblage and environmental conditions on the distribution of anatoxin-a producing cyanobacteria within a river network.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0374-3}, pmid = {30809011}, issn = {1751-7370}, support = {91767101-0//U.S. Environmental Protection Agency (US Environmental Protection Agency)/ ; EAR-1331940//National Science Foundation (NSF)/ ; DFG PR 1603/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, abstract = {Blooms of planktonic cyanobacteria have long been of concern in lakes, but more recently, harmful impacts of riverine benthic cyanobacterial mats been recognized. As yet, we know little about how various benthic cyanobacteria are distributed in river networks, or how environmental conditions or other associated microbes in their consortia affect their biosynthetic capacities. We performed metagenomic sequencing for 22 Oscillatoriales-dominated (Cyanobacteria) microbial mats collected across the Eel River network in Northern California and investigated factors associated with anatoxin-a producing cyanobacteria. All microbial communities were dominated by one or two cyanobacterial species, so the key mat metabolisms involve oxygenic photosynthesis and carbon oxidation. Only a few metabolisms fueled the growth of the mat communities, with little evidence for anaerobic metabolic pathways. We genomically defined four cyanobacterial species, all which shared <96% average nucleotide identity with reference Oscillatoriales genomes and are potentially novel species in the genus Microcoleus. One of the Microcoleus species contained the anatoxin-a biosynthesis genes, and we describe the first anatoxin-a gene cluster from the Microcoleus clade within Oscillatoriales. Occurrence of these four Microcoleus species in the watershed was correlated with total dissolved nitrogen and phosphorus concentrations, and the species that contains the anatoxin-a gene cluster was found in sites with higher nitrogen concentrations. Microbial assemblages in mat samples with the anatoxin-a gene cluster consistently had a lower abundance of Burkholderiales (Betaproteobacteria) species than did mats without the anatoxin-producing genes. The associations of water nutrient concentrations and certain co-occurring microbes with anatoxin-a producing Microcoleus motivate further exploration for their roles as potential controls on the distributions of toxigenic benthic cyanobacteria in river networks.}, }
@article {pmid30809010, year = {2019}, author = {Jones, DS and Walker, GM and Johnson, NW and Mitchell, CPJ and Coleman Wasik, JK and Bailey, JV}, title = {Molecular evidence for novel mercury methylating microorganisms in sulfate-impacted lakes.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0376-1}, pmid = {30809010}, issn = {1751-7370}, abstract = {Methylmercury (MeHg) is a bioaccumulative neurotoxin that is produced by certain anaerobic microorganisms, but the abundance and importance of different methylating populations in the environment is not well understood. We combined mercury geochemistry, hgcA gene cloning, rRNA methods, and metagenomics to compare microbial communities associated with MeHg production in two sulfate-impacted lakes on Minnesota's Mesabi Iron Range. The two lakes represent regional endmembers among sulfate-impacted sites in terms of their dissolved sulfide concentrations and MeHg production potential. rRNA amplicon sequencing indicates that sediments and anoxic bottom waters from both lakes contained diverse communities with multiple clades of sulfate reducing Deltaproteobacteria and Clostridia. In hgcA gene clone libraries, however, hgcA sequences were from taxa associated with methanogenesis and iron reduction in addition to sulfate reduction, and the most abundant clones were from unknown groups. We therefore applied metagenomics to identify the unknown populations in the lakes with the capability to methylate mercury, and reconstructed 27 genomic bins with hgcA. Some of the most abundant potential methylating populations were from phyla that are not typically associated with MeHg production, including a relative of the Aminicenantes (formerly candidate phylum OP8) and members of the Kiritimatiellaeota (PVC superphylum) and Spirochaetes that, together, were more than 50% of the potential methylators in some samples. These populations do not have genes for sulfate reduction, and likely degrade organic compounds by fermentation or other anaerobic processes. Our results indicate that previously unrecognized populations with hgcAB are abundant and may be important for MeHg production in some freshwater ecosystems.}, }
@article {pmid30808753, year = {2019}, author = {Ramírez-Flandes, S and González, B and Ulloa, O}, title = {Redox traits characterize the organization of global microbial communities.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {9}, pages = {3630-3635}, doi = {10.1073/pnas.1817554116}, pmid = {30808753}, issn = {1091-6490}, abstract = {The structure of biological communities is conventionally described as profiles of taxonomic units, whose ecological functions are assumed to be known or, at least, predictable. In environmental microbiology, however, the functions of a majority of microorganisms are unknown and expected to be highly dynamic and collectively redundant, obscuring the link between taxonomic structure and ecosystem functioning. Although genetic trait-based approaches at the community level might overcome this problem, no obvious choice of gene categories can be identified as appropriate descriptive units in a general ecological context. We used 247 microbial metagenomes from 18 biomes to determine which set of genes better characterizes the differences among biomes on the global scale. We show that profiles of oxidoreductase genes support the highest biome differentiation compared with profiles of other categories of enzymes, general protein-coding genes, transporter genes, and taxonomic gene markers. Based on oxidoreductases' description of microbial communities, the role of energetics in differentiation and particular ecosystem function of different biomes become readily apparent. We also show that taxonomic diversity is decoupled from functional diversity, e.g., grasslands and rhizospheres were the most diverse biomes in oxidoreductases but not in taxonomy. Considering that microbes underpin biogeochemical processes and nutrient recycling through oxidoreductases, this functional diversity should be relevant for a better understanding of the stability and conservation of biomes. Consequently, this approach might help to quantify the impact of environmental stressors on microbial ecosystems in the context of the global-scale biome crisis that our planet currently faces.}, }
@article {pmid30808411, year = {2019}, author = {, }, title = {A review of 10 years of human microbiome research activities at the US National Institutes of Health, Fiscal Years 2007-2016.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {31}, doi = {10.1186/s40168-019-0620-y}, pmid = {30808411}, issn = {2049-2618}, abstract = {The National Institutes of Health (NIH) is the primary federal government agency for biomedical research in the USA. NIH provides extensive support for human microbiome research with 21 of 27 NIH Institutes and Centers (ICs) currently funding this area through their extramural research programs. This analysis of the NIH extramural portfolio in human microbiome research briefly reviews the early history of this field at NIH, summarizes the program objectives and the resources developed in the recently completed 10-year (fiscal years 2007-2016) $215 M Human Microbiome Project (HMP) program, evaluates the scope and range of the $728 M NIH investment in extramural human microbiome research activities outside of the HMP over fiscal years 2012-2016, and highlights some specific areas of research which emerged from this investment. This analysis closes with a few comments on the technical needs and knowledge gaps which remain for this field to be able to advance over the next decade and for the outcomes of this research to be able to progress to microbiome-based interventions for treating disease and supporting health.}, }
@article {pmid30808380, year = {2019}, author = {DeMaere, MZ and Darling, AE}, title = {bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {46}, doi = {10.1186/s13059-019-1643-1}, pmid = {30808380}, issn = {1474-760X}, abstract = {Most microbes cannot be easily cultured, and metagenomics provides a means to study them. Current techniques aim to resolve individual genomes from metagenomes, so-called metagenome-assembled genomes (MAGs). Leading approaches depend upon time series or transect studies, the efficacy of which is a function of community complexity, target abundance, and sequencing depth. We describe an unsupervised method that exploits the hierarchical nature of Hi-C interaction rates to resolve MAGs using a single time point. We validate the method and directly compare against a recently announced proprietary service, ProxiMeta. bin3C is an open-source pipeline and makes use of the Infomap clustering algorithm (https://github.com/cerebis/bin3C).}, }
@article {pmid30808306, year = {2019}, author = {Paskey, AC and Frey, KG and Schroth, G and Gross, S and Hamilton, T and Bishop-Lilly, KA}, title = {Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {155}, doi = {10.1186/s12864-019-5543-2}, pmid = {30808306}, issn = {1471-2164}, support = {N/A//US. Navy, Office of Naval Research, In-House Laboratory Independent Research (ILIR) Program/ ; }, abstract = {BACKGROUND: Sequencing-based detection and characterization of viruses in complex samples can suffer from lack of sensitivity due to a variety of factors including, but not limited to, low titer, small genome size, and contribution of host or environmental nucleic acids. Hybridization-based target enrichment is one potential method for increasing the sensitivity of viral detection via high-throughput sequencing.
RESULTS: This study expands upon two previously developed panels of virus enrichment probes (for filoviruses and for respiratory viruses) to include other viruses of biodefense and/or biosurveillance concern to the U.S. Department of Defense and various international public health agencies. The newly expanded and combined panel is tested using carefully constructed synthetic metagenomic samples that contain clinically relevant amounts of viral genetic material. Target enrichment results in a dramatic increase in sensitivity for virus detection as compared to shotgun sequencing, yielding full, deeply covered viral genomes from materials with Ct values suggesting that amplicon sequencing would be likely to fail. Increased pooling to improve cost- and time-effectiveness does not negatively affect the ability to obtain full-length viral genomes, even in the case of co-infections, although as expected, it does decrease depth of coverage.
CONCLUSIONS: Hybridization-based target enrichment is an effective solution to obtain full-length viral genomes for samples from which virus detection would fail via unbiased, shotgun sequencing or even via amplicon sequencing. As the development and testing of probe sets for viral target enrichment expands and continues, the application of this technique, in conjunction with deeper pooling strategies, could make high-throughput sequencing more economical for routine use in biosurveillance, biodefense and outbreak investigations.}, }
@article {pmid30807598, year = {2019}, author = {Chen, L and Gu, W and Liu, C and Wang, W and Li, N and Chen, Y and Lu, C and Sun, X and Han, Y and Kuang, D and Tong, P and Dai, J}, title = {Characteristics of the tree shrew gut virome.}, journal = {PloS one}, volume = {14}, number = {2}, pages = {e0212774}, doi = {10.1371/journal.pone.0212774}, pmid = {30807598}, issn = {1932-6203}, abstract = {The tree shrew (Tupaia belangeri) has been proposed as an alternative laboratory animal to primates in biomedical research in recent years. However, characteristics of the tree shrew gut virome remain unclear. In this study, the metagenomic analysis method was used to identify the features of gut virome from fecal samples of this animal. Results showed that 5.80% of sequence reads in the libraries exhibited significant similarity to sequences deposited in the viral reference database (NCBI non-redundant nucleotide databases, viral protein databases and ACLAME database), and these reads were further classified into three major orders: Caudovirales (58.0%), Picornavirales (16.0%), and Herpesvirales (6.0%). Siphoviridae (46.0%), Myoviridae (45.0%), and Podoviridae (8.0%) comprised most Caudovirales. Picornaviridae (99.9%) and Herpesviridae (99.0%) were the primary families of Picornavirales and Herpesvirales, respectively. According to the host types and nucleic acid classifications, all of the related viruses in this study were divided into bacterial phage (61.83%), animal-specific virus (34.50%), plant-specific virus (0.09%), insect-specific virus (0.08%) and other viruses (3.50%). The dsDNA virus accounted for 51.13% of the total, followed by ssRNA (33.51%) and ssDNA virus (15.36%). This study provides an initial understanding of the community structure of the gut virome of tree shrew and a baseline for future tree shrew virus investigation.}, }
@article {pmid30806942, year = {2019}, author = {Li, X and Guo, J and Hu, Y and Yang, Y and Jiang, J and Nan, F and Wu, S and Xin, Z}, title = {Author Correction: Identification of a Novel Feruloyl Esterase by Functional Screening of a Soil Metagenomic Library.}, journal = {Applied biochemistry and biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s12010-019-02978-3}, pmid = {30806942}, issn = {1559-0291}, abstract = {The original version of this article unfortunately contained a mistake in the image and caption of Fig. 6. The corrected version of the image and caption is shown here.}, }
@article {pmid30806802, year = {2019}, author = {Saxena, G and Purchase, D and Mulla, SI and Saratale, GD and Bharagava, RN}, title = {Phytoremediation of Heavy Metal-Contaminated Sites: Eco-environmental Concerns, Field Studies, Sustainability Issues, and Future Prospects.}, journal = {Reviews of environmental contamination and toxicology}, volume = {}, number = {}, pages = {}, doi = {10.1007/398_2019_24}, pmid = {30806802}, issn = {0179-5953}, abstract = {Environmental contamination due to heavy metals (HMs) is of serious ecotoxicological concern worldwide because of their increasing use at industries. Due to non-biodegradable and persistent nature, HMs cause serious soil/water pollution and severe health hazards in living beings upon exposure. HMs can be genotoxic, carcinogenic, mutagenic, and teratogenic in nature even at low concentration. They may also act as endocrine disruptors and induce developmental as well as neurological disorders, and thus, their removal from our natural environment is crucial for the rehabilitation of contaminated sites. To cope with HM pollution, phytoremediation has emerged as a low-cost and eco-sustainable solution to conventional physicochemical cleanup methods that require high capital investment and labor alter soil properties and disturb soil microflora. Phytoremediation is a green technology wherein plants and associated microbes are used to remediate HM-contaminated sites to safeguard the environment and protect public health. Hence, in view of the above, the present paper aims to examine the feasibility of phytoremediation as a sustainable remediation technology for the management of metal-contaminated sites. Therefore, this paper provides an in-depth review on both the conventional and novel phytoremediation approaches; evaluates their efficacy to remove toxic metals from our natural environment; explores current scientific progresses, field experiences, and sustainability issues; and revises world over trends in phytoremediation research for its wider recognition and public acceptance as a sustainable remediation technology for the management of contaminated sites in the twenty-first century.}, }
@article {pmid30806063, year = {2019}, author = {Yu, G and Yuan, H and Luo, Z and Liu, Y and Liu, X and Gao, Y and Gong, M and Zou, Z}, title = {[Establishment of a plant phosphorus utilization and weed control system based on phosphite and its dehydrogenase].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {35}, number = {2}, pages = {327-336}, doi = {10.13345/j.cjb.180158}, pmid = {30806063}, issn = {1000-3061}, abstract = {Nowadays, available phosphorus (P) deficiency in soil and weed resistance to herbicides have emerged as two severe limiting factors for sustainable agriculture. Therefore, it is of urgent needs to improve plant absorption/utilization ability of the soil P, seek phosphate (Pi)-alternative P fertilizers, and develop new forms of weed control systems. Phosphite (Phi), as a P resource of relatively high amount only less than Pi in Earth, can be converted to utilizable Pi uniquely in some bacterial species by oxidization via its specific dehydrogenase (PTDH), but inhibits plant growth and development. This implies that Phi might rather become a suitable P fertilizer for plants if introducing a PTDH detoxifier from bacteria. Herein, we created the transgenic tobaccos harboring a Pseudomonas PTDH gene (PsPtx) amplified from the soil metagenome previously. RT-PCR showed that the exotic PsPtx gene could express similarly in root, stem and leaf tissues of all transgenic lines. PsPtx transgenic tobaccos could utilize Phi by oxidization as the sole Pi supply, and also outperformed wild-type tobacco with a remarkably dominant growth under Phi stress conditions. Moreover, the PsPtx gene was preliminarily evaluated with a notable quality as a potential candidate of the selection marker in plant genetic transformation. Conclusively, PsPtx and its encoded phosphite dehydrogenase might be applicable for developing a dual system of plant phosphorus utilization and weed control using Phi as P fertilizer and herbicide, and provide an effectual solution to some obstacles in the current crop transgenic studies.}, }
@article {pmid30806022, year = {2019}, author = {Chen, F and Knutson, TP and Braun, E and Jiang, Y and Rossow, S and Marthaler, DG}, title = {Semi-quantitative duplex RT-PCR reveals the low occurrence of Porcine Pegivirus and Atypical Porcine Pestivirus in diagnostic samples from the United States.}, journal = {Transboundary and emerging diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/tbed.13154}, pmid = {30806022}, issn = {1865-1682}, abstract = {Porcine Pegivirus (PPgV) and Atypical Porcine Pestivirus (APPV) are two recently identified porcine viruses. In this study, the identification of two viruses by metagenomic sequencing, and a duplex semi-quantitative RT-PCR was developed to detect these pathogens simultaneously. The PPgV strain Minnesota-1/2016 had a 95.5-96.3% nucleotide identity and clustered with the recently identified US PPgV strains, which is a distant clade from the German PPgV strains. The APPV strain Minnesota-1/2016 shared an 87.3-92.0% nucleotide identity with the other global APPV strains identity but only shared an 82.8-83.0% nucleotide identity with clade II consisting of strain identified in China. Detection of both PPgV and APPV was 9.0% of the diagnostic cases. Co-infection of PPgV and APPV was identified in 7.5% of the diagnostic cases. The occurrence and genetic characterization of PPgV and APPV further enhance our knowledge regarding these new pathogens in the United States. This article is protected by copyright. All rights reserved.}, }
@article {pmid30805695, year = {2019}, author = {Strain, CR and Collins, KC and Naughton, V and McSorley, EM and Stanton, C and Smyth, TJ and Soler-Vila, A and Rea, MC and Ross, PR and Cherry, P and Allsopp, PJ}, title = {Effects of a polysaccharide-rich extract derived from Irish-sourced Laminaria digitata on the composition and metabolic activity of the human gut microbiota using an in vitro colonic model.}, journal = {European journal of nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00394-019-01909-6}, pmid = {30805695}, issn = {1436-6215}, support = {MFFRI/07/01//Sea Change Strategy, Department of Agriculture, Food and the Marine (IE)/ ; }, abstract = {BACKGROUND: Brown seaweeds are known to be a rich source of fiber with the presence of several non-digestible polysaccharides including laminarin, fucoidan and alginate. These individual polysaccharides have previously been shown to favorably alter the gut microbiota composition and activity albeit the effect of the collective brown seaweed fiber component on the microbiota remains to be determined.
METHODS: This study investigated the effect of a crude polysaccharide-rich extract obtained from Laminaria digitata (CE) and a depolymerized CE extract (DE) on the gut microbiota composition and metabolism using an in vitro fecal batch culture model though metagenomic compositional analysis using 16S rRNA FLX amplicon pyrosequencing and short-chain fatty acid (SCFA) analysis using GC-FID.
RESULTS: Selective culture analysis showed no significant changes in cultured lactobacilli or bifidobacteria between the CE or DE and the cellulose-negative control at any time point measured (0, 5, 10, 24, 36, 48 h). Following metagenomic analysis, the CE and DE significantly altered the relative abundance of several families including Lachnospiraceae and genera including Streptococcus, Ruminococcus and Parabacteroides of human fecal bacterial populations in comparison to cellulose after 24 h. The concentrations of acetic acid, propionic acid, butyric acid and total SCFA were significantly higher for both the CE and DE compared to cellulose after 10, 24, 36 and 48 h fermentation (p < 0.05). Furthermore, the acetate:propionate ratio was significantly reduced (p < 0.05) for both CD and DE following 24, 36 and 48 h fermentation.
CONCLUSION: The microbiota-associated metabolic and compositional changes noted provide initial indication of putative beneficial health benefits of L. digitata in vitro; however, research is needed to clarify if L. digitata-derived fiber can favorably alter the gut microbiota and confer health benefits in vivo.}, }
@article {pmid30804923, year = {2018}, author = {Ma, Z and Li, L}, title = {Semen Microbiome Biogeography: An Analysis Based on a Chinese Population Study.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3333}, doi = {10.3389/fmicb.2018.03333}, pmid = {30804923}, issn = {1664-302X}, abstract = {Investigating inter-subject heterogeneity (or spatial distribution) of human semen microbiome diversity is of important significance. Theoretically, the spatial distribution of biodiversity constitutes the core of microbiome biogeography. Practically, the inter-subject heterogeneity is crucial for understanding the normal (healthy) flora of semen microbiotas as well as their possible changes associated with abnormal fertility. In this article, we analyze the scaling (changes) of semen microbiome diversity across individuals with DAR (diversity-area relationship) analysis, a recent extension to classic SAR (species-area relationship) law in biogeography and ecology. Specifically, the unit of "area" is individual subject, and the microbial diversity in seminal fluid of an individual (area) is assessed via metagenomic DNA sequencing technique and measured in the Hill numbers. The DAR models were then fitted to the accrued diversity across different number of individuals (area size). We further tested the difference in DAR parameters among the healthy, subnormal, and abnormal microbiome samples in terms of their fertility status based on a cross-sectional study of a Chinese cohort. Given that no statistically significant differences in the DAR parameters were detected among the three groups, we built unified DAR models for semen microbiome by combining the healthy, subnormal, and abnormal groups. The model parameters were used to (i) estimate the microbiome diversity scaling in a population (cohort), and construct the so-termed DAR profile; (ii) predict/construct the maximal accrual diversity (MAD) profile in a population; (iii) estimate the pair-wise diversity overlap (PDO) between two individuals and construct the PDO profile; (iv) assess the ratio of individual diversity to population (RIP) accrual diversity. The last item (RIP) is a new concept we propose in this study, which is essentially a ratio of local diversity to regional or global diversity (LRD/LGD), applicable to general biodiversity investigation beyond human microbiome.}, }
@article {pmid30804916, year = {2019}, author = {Gatica, J and Jurkevitch, E and Cytryn, E}, title = {Comparative Metagenomics and Network Analyses Provide Novel Insights Into the Scope and Distribution of β-Lactamase Homologs in the Environment.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {146}, doi = {10.3389/fmicb.2019.00146}, pmid = {30804916}, issn = {1664-302X}, abstract = {The β-lactams are the largest group of clinically applied antibiotics, and resistance to these is primarily associated with β-lactamases. There is increasing understanding that these enzymes are ubiquitous in natural environments and henceforth, elucidating the global diversity, distribution, and mobility of β-lactamase-encoding genes is crucial for holistically understanding resistance to these antibiotics. In this study, we screened 232 shotgun metagenomes from ten different environments against a custom-designed β-lactamase database, and subsequently analyzed β-lactamase homologs with a suite of bioinformatic platforms including cluster and network analyses. Three interrelated β-lactamase clusters encompassed all of the human and bovine feces metagenomes, while β-lactamases from soil, freshwater, glacier, marine, and wastewater grouped within a separate "environmental" cluster that displayed high levels of inter-network connectivity. Interestingly, almost no connectivity occurred between the "feces" and "environmental" clusters. We attributed this in part to the divergence in microbial community composition (dominance of Bacteroidetes and Firmicutes vs. Proteobacteria, respectively). The β-lactamase diversity in the "environmental" cluster was significantly higher than in human and bovine feces microbiomes. Several class A, B, C, and D β-lactamase homologs (blaCTX-M, blaKPC, blaGES) were ubiquitous in the "environmental" cluster, whereas bovine and human feces metagenomes were dominated by class A (primarily cfxA) β-lactamases. Collectively, this study highlights the ubiquitous presence and broad diversity of β-lactamase gene precursors in non-clinical environments. Furthermore, it suggests that horizontal transfer of β-lactamases to human-associated bacteria may be more plausible from animals than from terrestrial and aquatic microbes, seemingly due to phylogenetic similarities.}, }
@article {pmid30804909, year = {2019}, author = {Dick, JM and Yu, M and Tan, J and Lu, A}, title = {Changes in Carbon Oxidation State of Metagenomes Along Geochemical Redox Gradients.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {120}, doi = {10.3389/fmicb.2019.00120}, pmid = {30804909}, issn = {1664-302X}, abstract = {There is widespread interest in how geochemistry affects the genomic makeup of microbial communities, but the possible impacts of oxidation-reduction (redox) conditions on the chemical composition of biomacromolecules remain largely unexplored. Here we document systematic changes in the carbon oxidation state, a metric derived from the chemical formulas of biomacromolecular sequences, using published metagenomic and metatranscriptomic datasets from 18 studies representing different marine and terrestrial environments. We find that the carbon oxidation states of DNA, as well as proteins inferred from coding sequences, follow geochemical redox gradients associated with mixing and cooling of hot spring fluids in Yellowstone National Park (USA) and submarine hydrothermal fluids. Thermodynamic calculations provide independent predictions for the environmental shaping of the gene and protein composition of microbial communities in these systems. On the other hand, the carbon oxidation state of DNA is negatively correlated with oxygen concentration in marine oxygen minimum zones. In this case, a thermodynamic model is not viable, but the low carbon oxidation state of DNA near the ocean surface reflects a low GC content, which can be attributed to genome reduction in organisms adapted to low-nutrient conditions. We also present evidence for a depth-dependent increase of oxidation state at the species level, which might be associated with alteration of DNA through horizontal gene transfer and/or selective degradation of relatively reduced (AT-rich) extracellular DNA by heterotrophic bacteria. Sediments exhibit even more complex behavior, where carbon oxidation state minimizes near the sulfate-methane transition zone and rises again at depth; markedly higher oxidation states are also associated with older freshwater-dominated sediments in the Baltic Sea that are enriched in iron oxides and have low organic carbon. This geobiochemical study of carbon oxidation state reveals a new aspect of environmental information in metagenomic sequences, and provides a reference frame for future studies that may use ancient DNA sequences as a paleoredox indicator.}, }
@article {pmid30804903, year = {2019}, author = {Connelly, S and Fanelli, B and Hasan, NA and Colwell, RR and Kaleko, M}, title = {Oral Metallo-Beta-Lactamase Protects the Gut Microbiome From Carbapenem-Mediated Damage and Reduces Propagation of Antibiotic Resistance in Pigs.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {101}, doi = {10.3389/fmicb.2019.00101}, pmid = {30804903}, issn = {1664-302X}, abstract = {Antibiotics can damage the gut microbiome, leading to serious adventitious infections and emergence of antibiotic resistant pathogens. Antibiotic inactivation in the GI tract represents a strategy to protect colonic microbiota integrity and reduce antibiotic resistance. Clinical utility of this approach was established when SYN-004 (ribaxamase), an orally-administered beta-lactamase, was demonstrated to degrade ceftriaxone in the GI tract and preserve the gut microbiome. Ribaxamase degrades penicillins and cephalosporin beta-lactams, but not carbapenems. To expand this prophylactic approach to include all classes of beta-lactam antibiotics, a novel carbapenemase, formulated for oral administration, SYN-006, was evaluated in a porcine model of antibiotic-mediated gut dysbiosis. Pigs (20 kg, n = 16) were treated with the carbapenem, ertapenem (ERT), (IV, 30 mg/kg, SID) for 4 days and a cohort (n = 8) also received SYN-006 (PO, 50 mg, QID), beginning the day before antibiotic administration. ERT serum levels were not statistically different in ERT and ERT + SYN-006 groups, indicating that SYN-006 did not alter systemic antibiotic levels. Microbiomes were evaluated using whole genome shotgun metagenomics analyses of fecal DNA collected prior to and after antibiotic treatment. ERT caused significant changes to the gut microbiome that were mitigated in the presence of SYN-006. In addition, SYN-006 attenuated emergence of antibiotic resistance, including encoded beta-lactamases and genes conferring resistance to a broad range of antibiotics such as aminoglycosides and macrolides. SYN-006 has the potential to become the first therapy designed to protect the gut microbiome from all classes of beta-lactam antibiotics and reduce emergence of carbapenem-resistant pathogens.}, }
@article {pmid30804813, year = {2018}, author = {Dao, MC and Sokolovska, N and Brazeilles, R and Affeldt, S and Pelloux, V and Prifti, E and Chilloux, J and Verger, EO and Kayser, BD and Aron-Wisnewsky, J and Ichou, F and Pujos-Guillot, E and Hoyles, L and Juste, C and Doré, J and Dumas, ME and Rizkalla, SW and Holmes, BA and Zucker, JD and Clément, K and , }, title = {A Data Integration Multi-Omics Approach to Study Calorie Restriction-Induced Changes in Insulin Sensitivity.}, journal = {Frontiers in physiology}, volume = {9}, number = {}, pages = {1958}, doi = {10.3389/fphys.2018.01958}, pmid = {30804813}, issn = {1664-042X}, abstract = {Background: The mechanisms responsible for calorie restriction (CR)-induced improvement in insulin sensitivity (IS) have not been fully elucidated. Greater insight can be achieved through deep biological phenotyping of subjects undergoing CR, and integration of big data. Materials and Methods: An integrative approach was applied to investigate associations between change in IS and factors from host, microbiota, and lifestyle after a 6-week CR period in 27 overweight or obese adults (ClinicalTrials.gov: NCT01314690). Partial least squares regression was used to determine associations of change (week 6 - baseline) between IS markers and lifestyle factors (diet and physical activity), subcutaneous adipose tissue (sAT) gene expression, metabolomics of serum, urine and feces, and gut microbiota composition. ScaleNet, a network learning approach based on spectral consensus strategy (SCS, developed by us) was used for reconstruction of biological networks. Results: A spectrum of variables from lifestyle factors (10 nutrients), gut microbiota (10 metagenomics species), and host multi-omics (metabolic features: 84 from serum, 73 from urine, and 131 from feces; and 257 sAT gene probes) most associated with IS were identified. Biological network reconstruction using SCS, highlighted links between changes in IS, serum branched chain amino acids, sAT genes involved in endoplasmic reticulum stress and ubiquitination, and gut metagenomic species (MGS). Linear regression analysis to model how changes of select variables over the CR period contribute to changes in IS, showed greatest contributions from gut MGS and fiber intake. Conclusion: This work has enhanced previous knowledge on links between host glucose homeostasis, lifestyle factors and the gut microbiota, and has identified potential biomarkers that may be used in future studies to predict and improve individual response to weight-loss interventions. Furthermore, this is the first study showing integration of the wide range of data presented herein, identifying 115 variables of interest with respect to IS from the initial input, consisting of 9,986 variables. Clinical Trial Registration: clinicaltrials.gov (NCT01314690).}, }
@article {pmid30802772, year = {2019}, author = {Liu, P and Hou, J and Zou, Y and Stephenson, SL and Huo, X and Hu, X and Li, Y}, title = {Developmental features and associated symbiont bacterial diversity in essential life cycle stages of Heterostelium colligatum.}, journal = {European journal of protistology}, volume = {68}, number = {}, pages = {99-107}, doi = {10.1016/j.ejop.2019.02.003}, pmid = {30802772}, issn = {1618-0429}, abstract = {Dictyostelium discoideum is a specialized amoebozoan protist that can feed on, carry and disperse bacteria. However, the symbiont bacterial diversity in other species of dictyostelids and the diversity associated with essential life cycle stages are still unknown until now. Here, another species of dictyostelids, Heterostelium colligatum, a new record for tropical China, was isolated from the soil collected in Xishuangbanna Tropical Botanical Garden, Yunnan Province, China. We describe the complete life cycle of this species and illustrate details of spore-to-spore development. The symbiont bacterial diversity and relative abundance associated with life cycle stages of H. colligatum, including the aggregation, pseudoplasmodium, and sorocarp stages, were investigated by high throughput metagenomic techniques. H. colligatum appears to be capable of carrying different types of bacteria during its life history in addition to those used as a food resource. The dominant groups of those three stages in its life cycle were the Proteobacteria, Actinobacteria and Firmicutes. The relative abundance of the dominant phyla and shared OTUs were different for the aggregation, pseudoplasmodium, and sorocarp stages. A comparison of the symbiont bacterial assemblages associated with D. discoideum and H. colligatum indicated that different dictyostelid species carried different species of symbiont associated bacteria.}, }
@article {pmid30802355, year = {2019}, author = {Kang, H and Park, B and Bolo, NR and Pathiraja, D and Park, S and Cha, M and Choi, IG and Chang, IS}, title = {Gene-centric metagenome analysis reveals gene clusters for carbon monoxide conversion and validates isolation of a clostridial acetogen for C2 chemical production.}, journal = {Biotechnology journal}, volume = {}, number = {}, pages = {e1800471}, doi = {10.1002/biot.201800471}, pmid = {30802355}, issn = {1860-7314}, abstract = {Synthetic gas (syngas) fermentation is largely dependent on acetogens that occur in various anaerobic environmental samples including soil, sediment, and feces. Here we report the metagenomic isolation of acetogens for C2 chemical production from syngas. Screening acetogens for C2 chemical production typically involves detecting the presence of the Wood-Ljungdahl Pathway (WLP) for carbon monoxide (CO) conversion. We collected samples from river-bed sediments potentially having conditions suitable for CO-converting anaerobes, and enriched the samples under CO selection pressure. Changes in the microbial community during the experimental procedure were investigated using both amplicon and shotgun metagenome sequencing. Combined next-generation sequencing techniques enabled in-situ tracking of the major acetogenic bacterial group and led to the discovery of a 16 kb of gene cluster for WLP. We isolated an acetogenic clostridial strain from the enrichment culture (strain H21-9) from the enrichment culture. Whole genome sequencing of H21-9 confirmed the presence of the gene cluster for CO conversion found in the gene-centric metagenome analysis. The functional activity of H21-9 was confirmed by its high level of production of C2 chemicals from CO (77.4 mM acetate and 2.5 mM of ethanol). Our approach of incorporating experimental enrichment with metagenomic analysis can facilitate the discovery of novel strains from environmental habitats by tracking target strains during the screening process, combined with validation of their functional activity. This article is protected by copyright. All rights reserved.}, }
@article {pmid30802245, year = {2019}, author = {Gaithuma, AK and Yamagishi, J and Martinelli, A and Hayashida, K and Kawai, N and Marsela, M and Sugimoto, C}, title = {A single test approach for accurate and sensitive detection and taxonomic characterization of Trypanosomes by comprehensive analysis of internal transcribed spacer 1 amplicons.}, journal = {PLoS neglected tropical diseases}, volume = {13}, number = {2}, pages = {e0006842}, doi = {10.1371/journal.pntd.0006842}, pmid = {30802245}, issn = {1935-2735}, abstract = {To improve our knowledge on the epidemiological status of African trypanosomiasis, better tools are required to monitor Trypanosome genotypes circulating in both mammalian hosts and tsetse fly vectors. This is important in determining the diversity of Trypanosomes and understanding how environmental factors and control efforts affect Trypanosome evolution. We present a single test approach for molecular detection of different Trypanosome species and subspecies using newly designed primers to amplify the Internal Transcribed Spacer 1 region of ribosomal RNA genes, coupled to Illumina sequencing of the amplicons. The protocol is based on Illumina's widely used 16s bacterial metagenomic analysis procedure that makes use of multiplex PCR and dual indexing. Results from analysis of wild tsetse flies collected from Zambia and Zimbabwe show that conventional methods for Trypanosome species detection based on band size comparisons on gels is not always able to accurately distinguish between T. vivax and T. godfreyi. Additionally, this approach shows increased sensitivity in the detection of Trypanosomes at species level with the exception of the Trypanozoon subgenus. We identified subspecies of T. congolense, T. simiae, T. vivax, and T. godfreyi without the need for additional tests. Results show T. congolense Kilifi subspecies is more closely related to T. simiae than to other T. congolense subspecies. This agrees with previous studies using satellite DNA and 18s RNA analysis. While current classification does not list any subspecies for T. godfreyi, we observed two distinct clusters for these species. Interestingly, sequences matching T. congolense Tsavo (now classified as T. simiae Tsavo) clusters distinctly from other T. simiae Tsavo sequences suggesting the Nannomonas group is more divergent than currently thought thus the need for better classification criteria. This method presents a simple but comprehensive way of identification of Trypanosome species and subspecies-specific using one PCR assay for molecular epidemiology of trypanosomes.}, }
@article {pmid30802241, year = {2019}, author = {Sodré, V and Araujo, JN and Gonçalves, TA and Vilela, N and Braz, ASK and Franco, TT and de Oliveira Neto, M and Damasio, ARL and Garcia, W and Squina, FM}, title = {An alkaline active feruloyl-CoA synthetase from soil metagenome as a potential key enzyme for lignin valorization strategies.}, journal = {PloS one}, volume = {14}, number = {2}, pages = {e0212629}, doi = {10.1371/journal.pone.0212629}, pmid = {30802241}, issn = {1932-6203}, abstract = {Ferulic acid (FA), a low-molecular weight aromatic compound derived from lignin, represents a high-value molecule, used for applications in the cosmetic and pharmaceutical industries. FA can be further enzymatically converted in other commercially interesting molecules, such as vanillin and bioplastics. In several organisms, these transformations often start with a common step of FA activation via CoA-thioesterification, catalyzed by feruloyl-CoA synthetases (Fcs). In this context, these enzymes are of biotechnological interest for conversion of lignin-derived FA into high value chemicals. In this study, we describe the first structural characterization of a prokaryotic Fcs, named FCS1, isolated from a lignin-degrading microbial consortium. The FCS1 optimum pH and temperature were 9 and 37°C, respectively, with Km of 0.12 mM and Vmax of 36.82 U/mg. The circular dichroism spectra indicated a notable secondary structure stability at alkaline pH values and high temperatures. This secondary structure stability corroborates the activity data, which remains high until pH 9. The Small Angle X-Ray Scattering analyses resulted on the tertiary/quaternary structure and the low-resolution envelope in solution of FCS1, which was modeled as a homodimer using the hyperthermophilic nucleoside diphosphate-forming acetyl-CoA synthetase from Candidatus Korachaeum cryptofilum. This study contributes to the field of research by establishing the first biophysical and structural characterization for Fcs, and our data may be used for comparison against novel enzymes of this class that to be studied in the future.}, }
@article {pmid30801645, year = {2019}, author = {Gaisin, VA and Burganskaya, EI and Grouzdev, DS and Ashikhmin, AA and Kostrikina, NA and Bryantseva, IA and Koziaeva, VV and Gorlenko, VM}, title = {'Candidatus Viridilinea mediisalina', a novel phototrophic Chloroflexi bacterium from a Siberian soda lake.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnz043}, pmid = {30801645}, issn = {1574-6968}, abstract = {In this article, we present the description of a novel mesophilic phototrophic Chloroflexi bacterium, 'Candidatus Viridilinea mediisalina' Kir15-3F. We have isolated an anaerobic, highly-enriched culture of this bacterium from the Kiran soda lake (Siberia) and optimized its cultivation. Metagenomic sequencing revealed that 'Ca. Viridilinea mediisalina' Kir15-3F is a bacteriochlorophyll-containing Chloroflexi bacterium in the enrichment culture. Fluorescent in situ hybridisation demonstrated a link between the phenotype described here and the 'Ca. Viridilinea mediisalina' Kir15-3F genome. Spectrophotometry and high-performance liquid chromatography (HPLC) analyses showed the presence of bacteriochlorophylls d, c and a, as well as lycopene, γ-carotene and β-carotene. Transmission electron microscopy showed chlorosomes, gas vesicles, polyhydroxyalkanoate-like and polyphosphate-like granules. Our results illustrated that 'Ca. Viridilinea mediisalina' Kir15-3F is an alkaliphilic, salt-tolerant, obligately mesophilic, anaerobic, phototrophic bacterium. The genome sequences lack genes of the Calvin cycle and a sulphide:quinone reductase gene for sulphide oxidation. Owing to the lack of an axenic culture and based on the genomic and phenotypic data, we have presented the description of the bacterium in the Candidatus category.}, }
@article {pmid30801062, year = {2019}, author = {Sazinas, P and Michniewski, S and Rihtman, B and Redgwell, T and Grigonyte, A and Brett, A and Guck, B and Smith, R and Hooton, SP and Hobman, JL and Millard, AD}, title = {Metagenomics of the Viral Community in Three Cattle Slurry Samples.}, journal = {Microbiology resource announcements}, volume = {8}, number = {7}, pages = {}, doi = {10.1128/MRA.01442-18}, pmid = {30801062}, issn = {2576-098X}, abstract = {The diversity of viruses in slurries from dairy farming remains largely uncharacterized. Here we report viral diversity found in cattle slurry from a dairy farm in the East Midlands in the United Kingdom. The same slurry tank was sampled in three consecutive years, and the viral fraction was isolated and sequenced.}, }
@article {pmid30801026, year = {2019}, author = {Mills, RH and Vázquez-Baeza, Y and Zhu, Q and Jiang, L and Gaffney, J and Humphrey, G and Smarr, L and Knight, R and Gonzalez, DJ}, title = {Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease.}, journal = {mSystems}, volume = {4}, number = {1}, pages = {}, doi = {10.1128/mSystems.00337-18}, pmid = {30801026}, issn = {2379-5077}, abstract = {Although genetic approaches are the standard in microbiome analysis, proteome-level information is largely absent. This discrepancy warrants a better understanding of the relationship between gene copy number and protein abundance, as this is crucial information for inferring protein-level changes from metagenomic data. As it remains unknown how metaproteomic systems evolve during dynamic disease states, we leveraged a 4.5-year fecal time series using samples from a single patient with colonic Crohn's disease. Utilizing multiplexed quantitative proteomics and shotgun metagenomic sequencing of eight time points in technical triplicate, we quantified over 29,000 protein groups and 110,000 genes and compared them to five protein biomarkers of disease activity. Broad-scale observations were consistent between data types, including overall clustering by principal-coordinate analysis and fluctuations in Gene Ontology terms related to Crohn's disease. Through linear regression, we determined genes and proteins fluctuating in conjunction with inflammatory metrics. We discovered conserved taxonomic differences relevant to Crohn's disease, including a negative association of Faecalibacterium and a positive association of Escherichia with calprotectin. Despite concordant associations of genera, the specific genes correlated with these metrics were drastically different between metagenomic and metaproteomic data sets. This resulted in the generation of unique functional interpretations dependent on the data type, with metaproteome evidence for previously investigated mechanisms of dysbiosis. An example of one such mechanism was a connection between urease enzymes, amino acid metabolism, and the local inflammation state within the patient. This proof-of-concept approach prompts further investigation of the metaproteome and its relationship with the metagenome in biologically complex systems such as the microbiome. IMPORTANCE A majority of current microbiome research relies heavily on DNA analysis. However, as the field moves toward understanding the microbial functions related to healthy and disease states, it is critical to evaluate how changes in DNA relate to changes in proteins, which are functional units of the genome. This study tracked the abundance of genes and proteins as they fluctuated during various inflammatory states in a 4.5-year study of a patient with colonic Crohn's disease. Our results indicate that despite a low level of correlation, taxonomic associations were consistent in the two data types. While there was overlap of the data types, several associations were uniquely discovered by analyzing the metaproteome component. This case study provides unique and important insights into the fundamental relationship between the genes and proteins of a single individual's fecal microbiome associated with clinical consequences.}, }
@article {pmid30801021, year = {2019}, author = {Martino, C and Morton, JT and Marotz, CA and Thompson, LR and Tripathi, A and Knight, R and Zengler, K}, title = {A Novel Sparse Compositional Technique Reveals Microbial Perturbations.}, journal = {mSystems}, volume = {4}, number = {1}, pages = {}, doi = {10.1128/mSystems.00016-19}, pmid = {30801021}, issn = {2379-5077}, support = {R21 AR071731/AR/NIAMS NIH HHS/United States ; }, abstract = {The central aims of many host or environmental microbiome studies are to elucidate factors associated with microbial community compositions and to relate microbial features to outcomes. However, these aims are often complicated by difficulties stemming from high-dimensionality, non-normality, sparsity, and the compositional nature of microbiome data sets. A key tool in microbiome analysis is beta diversity, defined by the distances between microbial samples. Many different distance metrics have been proposed, all with varying discriminatory power on data with differing characteristics. Here, we propose a compositional beta diversity metric rooted in a centered log-ratio transformation and matrix completion called robust Aitchison PCA. We demonstrate the benefits of compositional transformations upstream of beta diversity calculations through simulations. Additionally, we demonstrate improved effect size, classification accuracy, and robustness to sequencing depth over the current methods on several decreased sample subsets of real microbiome data sets. Finally, we highlight the ability of this new beta diversity metric to retain the feature loadings linked to sample ordinations revealing salient intercommunity niche feature importance. IMPORTANCE By accounting for the sparse compositional nature of microbiome data sets, robust Aitchison PCA can yield high discriminatory power and salient feature ranking between microbial niches. The software to perform this analysis is available under an open-source license and can be obtained at https://github.com/biocore/DEICODE; additionally, a QIIME 2 plugin is provided to perform this analysis at https://library.qiime2.org/plugins/deicode/.}, }
@article {pmid30800603, year = {2019}, author = {Zainith, S and Purchase, D and Saratale, GD and Ferreira, LFR and Bilal, M and Bharagava, RN}, title = {Isolation and characterization of lignin-degrading bacterium Bacillus aryabhattai from pulp and paper mill wastewater and evaluation of its lignin-degrading potential.}, journal = {3 Biotech}, volume = {9}, number = {3}, pages = {92}, doi = {10.1007/s13205-019-1631-x}, pmid = {30800603}, issn = {2190-572X}, abstract = {This study reports the degradation and decolourization capability of a manganese peroxidase enzyme producing bacterium isolated from pulp and paper mill wastewater. The isolate was identified as Bacillus aryabhattai based on biochemical analysis and 16S rRNA gene sequencing. The strain was designated MG966493. This bacterium was able to reduce 67% and 54% colour and lignin, respectively, from the pulp and paper mill wastewater after 144 h of treatment at 32 °C, pH 7.6 and 120 rpm. Further, FT-IR analysis showed that during the lignin degradation process a number of metabolites were produced comprising different functional groups such as carbonyl (C=C), carboxyl (-COOH), alkene (C=C), amines (-NH2), sulphonic (-SO3) and nitro (-NO2). In addition, the SEM analysis showed that the bacterial cells exposed to pulp and paper mill wastewater have rough surfaces with reduced size as compared to the unexposed cells with smooth surfaces. This study concluded that the isolated bacterium B. aryabhattai has significant potential for the bioremediation of pulp and paper mill wastewater and thus, can be applied for their treatment at an industrial scale.}, }
@article {pmid30800169, year = {2019}, author = {Seo, SH and Park, SE and Kim, EJ and Youn, D and Lee, YM and Lee, SY and Bok, SH and Park, DH and Seo, CS and Byun, SH and Jun, KY and Kim, DS and Na, CS and Son, HS}, title = {GC/MS-Based Metabolomics Approach to Evaluate the Effect of Jackyakgamcho-Tang on Acute Colitis.}, journal = {Evidence-based complementary and alternative medicine : eCAM}, volume = {2019}, number = {}, pages = {4572764}, doi = {10.1155/2019/4572764}, pmid = {30800169}, issn = {1741-427X}, abstract = {The objective of this study was to examine the effects of Jackyakgamcho-tang (JGT) on acute colitis. GC/MS-based metabolomics and NGS-based metagenomics were applied to investigate the alteration of metabolites and microbiota in an acute colitis model. The severity of acute colitis symptoms was alleviated by JGT treatment. Induction of colitis and JGT treatment changed compositions of gut microbiota and inflammatory cytokine levels (TNF-α and IL-6). They also substantially change metabolites (i.e., lactic acid, linoleic acid, monostearin, and palmitoylglycerol). In addition, some clear correlations were observed among metabolites, cytokine, and microbiota. This study highlights the applicability of metabolomics and metagenomics study for evaluating anti-inflammatory effects of a new functional herbal medicine as a therapeutic agent for acute colitis.}, }
@article {pmid30800107, year = {2019}, author = {Wang, H and Yan, Y and Yi, X and Duan, Y and Wang, J and Li, S and Luo, L and Huang, T and Inglis, B and Li, X and Ji, W and Tan, T and Si, W}, title = {Histopathological Features and Composition of Gut Microbiota in Rhesus Monkey of Alcoholic Liver Disease.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {165}, doi = {10.3389/fmicb.2019.00165}, pmid = {30800107}, issn = {1664-302X}, abstract = {Alcohol-induced chronic liver disease (ALD) is becoming the most common liver disease in the world. However, there are no effective, universally accepted therapies for ALD. The etiology of ALD remains blurry so far. Historical evidence has demonstrated a link between the liver and gut microbiota. But it is difficult to distinguish the effect of gut microbiota changes caused by alcohol consumption in humans since the microbiota change detected in humans is complicated by diet and environmental factors. Due to the genetic, physiological, metabolic, and behavioral similarities to humans, the rhesus monkey provides excellent translational validity in preclinical studies, and the diet and environmental conditions can be controlled well in rhesus monkey. In our study, we explored the relationship between ALD and the gut microbiome in the rhesus monkeys with alcoholic liver steatosis. Our results showed that there was a change of the bacterial community structure in monkeys with ALD. Differences of the relative abundances of gut microbiota at phylum, order, family, genus, and species levels were observed between control monkeys and monkeys with ALD, and different pathways enriched in the monkeys with ALD were identified by metagenomic function analysis. Firmicutes, Proteobacteria, Verrucomicrobia tended to increase whereas Bacteroidetes and Actinobacteria decreased in the fecal microbiota of ALD group compared to the control group. Lactobacillales and Lactobacillus significantly decreased in ALD monkeys compared with normal monkeys, Streptococcus was lower in the ALD group compared with the control group. The non-human primate model of ALD will be useful for exploration of the microbiome markers as diagnosis and potentially prognosis for ALD. The ALD model will benefit the development of new therapeutic procedures for treating ALD and provide safety and efficacy evaluation for clinical application.}, }
@article {pmid30800106, year = {2019}, author = {Bodkhe, R and Shetty, SA and Dhotre, DP and Verma, AK and Bhatia, K and Mishra, A and Kaur, G and Pande, P and Bangarusamy, DK and Santosh, BP and Perumal, RC and Ahuja, V and Shouche, YS and Makharia, GK}, title = {Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {164}, doi = {10.3389/fmicb.2019.00164}, pmid = {30800106}, issn = {1664-302X}, abstract = {Recent studies on celiac disease (CeD) have reported alterations in the gut microbiome. Whether this alteration in the microbial community is the cause or effect of the disease is not well understood, especially in adult onset of disease. The first-degree relatives (FDRs) of CeD patients may provide an opportunity to study gut microbiome in pre-disease state as FDRs are genetically susceptible to CeD. By using 16S rRNA gene sequencing, we observed that ecosystem level diversity measures were not significantly different between the disease condition (CeD), pre-disease (FDR) and control subjects. However, differences were observed at the level of amplicon sequence variant (ASV), suggesting alterations in specific ASVs between pre-disease and diseased condition. Duodenal biopsies showed higher differences in ASVs compared to fecal samples indicating larger disruption of the microbiota at the disease site. The duodenal microbiota of FDR was characterized by significant abundance of ASVs belonging to Parvimonas, Granulicatella, Gemella, Bifidobacterium, Anaerostipes, and Actinomyces genera. The duodenal microbiota of CeD was characterized by higher abundance of ASVs from genera Megasphaera and Helicobacter compared to the FDR microbiota. The CeD and FDR fecal microbiota had reduced abundance of ASVs classified as Akkermansia and Dorea when compared to control group microbiota. In addition, predicted functional metagenome showed reduced ability of gluten degradation by CeD fecal microbiota in comparison to FDRs and controls. The findings of the present study demonstrate differences in ASVs and predicts reduced ability of CeD fecal microbiota to degrade gluten compared to the FDR fecal microbiota. Further research is required to investigate the strain level and active functional profiles of FDR and CeD microbiota to better understand the role of gut microbiome in pathophysiology of CeD.}, }
@article {pmid30799264, year = {2019}, author = {De Filippis, F and Pasolli, E and Tett, A and Tarallo, S and Naccarati, A and De Angelis, M and Neviani, E and Cocolin, L and Gobbetti, M and Segata, N and Ercolini, D}, title = {Distinct Genetic and Functional Traits of Human Intestinal Prevotella copri Strains Are Associated with Different Habitual Diets.}, journal = {Cell host & microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2019.01.004}, pmid = {30799264}, issn = {1934-6069}, abstract = {The role of intestinal Prevotella species in human health is controversial, with both positive and negative associations. Strain-level diversity may contribute to discrepancies in genus and species associations with health and disease. We dissected the gut metagenomes of Italians with varying dietary habits, investigating the presence of distinct Prevotella copri strains. Fiber-rich diets were linked to P. copri types with enhanced potential for carbohydrate catabolism. P. copri strains associated with an omnivore diet had a higher prevalence of the leuB gene-involved in branched-chain amino acid biosynthesis-a risk factor for glucose intolerance and type 2 diabetes. These P. copri pangenomes were compared to existing cohorts, providing evidence of distinct gene repertoires characterizing different P. copri populations, with drug metabolism and complex carbohydrate degradation significantly associated with Western and non-Western individuals, respectively. Strain-level P. copri diversity in gut microbiomes is affected by diet and should be considered when examining host-microbe associations.}, }
@article {pmid30798243, year = {2019}, author = {Wang, S and Chen, C and Zhao, S and He, J}, title = {Microbial synergistic interactions for reductive dechlorination of polychlorinated biphenyls.}, journal = {The Science of the total environment}, volume = {666}, number = {}, pages = {368-376}, doi = {10.1016/j.scitotenv.2019.02.283}, pmid = {30798243}, issn = {1879-1026}, abstract = {Dehalococcoides usually work closely with other beneficial microorganisms for removal of halogenated organic compounds at contaminated sites. Traditional microbial cultivation is necessary but not enough to gain insights into key microbial populations and their interactions in complex communities. In this study, we cultivated and characterized two D. mccartyi strains (CG3 and SG1), and further revealed interspecies synergistic interactions in PCB-dechlorinating microbial communities via metagenomic analysis. Strain CG3 and SG1 originated from distinct geographic sites employ reductive dehalogenase CG3-RD11 (PcbA1-like) and SG1-RD28 (PcbA4/5-like), respectively, to catalyze chlorine-removal from PCBs. In their parent mixed cultures CG-3 and SG-1, as well as in previously enriched PCB-dechlorinating cultures CG-1, CG-4 and CG-5, Methanosarcina and Desulfovibrio were found as major non-dechlorinating populations which may play roles in mediating acetate- and H2-sources for D. mccartyi. They together form a stable microbial community for interspecies carbon- and electron-transfers to facilitate organohalide respiration of D. mccartyi, being confirmed in a synthetic microbial community consisting of the Dehalococcoides, Methanosarcina and Desulfovibrio. The results provide insights into which and how other microorganisms support D. mccartyi to dechlorinate PCBs, and suggest that Methanosarcina may play a larger role in PCB-dechlorinating communities than currently appreciated.}, }
@article {pmid30798235, year = {2019}, author = {Sun, H and Narihiro, T and Ma, X and Zhang, XX and Ren, H and Ye, L}, title = {Diverse aromatic-degrading bacteria present in a highly enriched autotrophic nitrifying sludge.}, journal = {The Science of the total environment}, volume = {666}, number = {}, pages = {245-251}, doi = {10.1016/j.scitotenv.2019.02.172}, pmid = {30798235}, issn = {1879-1026}, abstract = {Biotransformation of refractory organics by ammonia-oxidizing microorganisms in nitrifying sludge have been widely reported, while the contribution of heterotrophic bacteria in nitrifying sludge in the biotransformation and degradation process might be overlooked. Here, we provide metagenomic and metatranscriptomic evidences showing that heterotrophic bacteria in a highly enriched autotrophic nitrifying sludge could significantly contribute to the aromatic biotransformation and biodegradation. Diverse genes encoding enzymes for aromatic degradation were observed in an enriched autotrophic nitrifying sludge. These genes are involved in the degradation of at least 15 complex aromatics. Genome binning results showed that these genes were mainly carried by species in Bacteroidetes (Flavobacteriaceae and Sphingobacteriales), Alphaproteobacteria (Rhodobacter) and Betaproteobacteria (Bordetella, Acidovorax, Ramlibacter and Pusillimonas). According to the metatranscriptomic analysis, the overall expression of the potential aromatic-degrading genes was significantly upregulated, and almost all genes involved in phenol degradation were over expressed after the nitrifying sludge was exposed to phenol. Overall, our results suggest that certain heterotrophs in nitrifying sludge are involved aromatic biotransformation and biodegradation and advance our knowledge of the underlying properties and metabolic mechanisms of the nitrifying sludge.}, }
@article {pmid30796503, year = {2019}, author = {Lebre, PH and Cowan, DA}, title = {Genomics of Alkaliphiles.}, journal = {Advances in biochemical engineering/biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/10_2018_83}, pmid = {30796503}, issn = {0724-6145}, abstract = {Alkalinicity presents a challenge for life due to a "reversed" proton gradient that is unfavourable to many bioenergetic processes across the membranes of microorganisms. Despite this, many bacteria, archaea, and eukaryotes, collectively termed alkaliphiles, are adapted to life in alkaline ecosystems and are of great scientific and biotechnological interest due to their niche specialization and ability to produce highly stable enzymes. Advances in next-generation sequencing technologies have propelled not only the genomic characterization of many alkaliphilic microorganisms that have been isolated from nature alkaline sources but also our understanding of the functional relationships between different taxa in microbial communities living in these ecosystems. In this review, we discuss the genetics and molecular biology of alkaliphiles from an "omics" point of view, focusing on how metagenomics and transcriptomics have contributed to our understanding of these extremophiles. Graphical Abstract.}, }
@article {pmid30794590, year = {2019}, author = {Saito, K and Koido, S and Odamaki, T and Kajihara, M and Kato, K and Horiuchi, S and Adachi, S and Arakawa, H and Yoshida, S and Akasu, T and Ito, Z and Uchiyama, K and Saruta, M and Xiao, JZ and Sato, N and Ohkusa, T}, title = {Metagenomic analyses of the gut microbiota associated with colorectal adenoma.}, journal = {PloS one}, volume = {14}, number = {2}, pages = {e0212406}, doi = {10.1371/journal.pone.0212406}, pmid = {30794590}, issn = {1932-6203}, abstract = {Recent studies have suggested an association between certain members of the Fusobacterium genus, especially F. nucleatum, and the progression of advanced colorectal carcinoma (CRC). We assessed such an association of the gut microbiota in Japanese patients with colorectal adenoma (CRA) or intramucosal CRC using colonoscopy aspirates. We analyzed samples from 81 Japanese patients, including 47 CRA and 24 intramucosal CRC patients, and 10 healthy subjects. Metagenomic analysis of the V3-V4 region of the 16S ribosomal RNA gene was performed. The linear discriminant analysis (LDA) effect size (LEfSe) method was used to examine microbial dysbiosis, revealing significant differences in bacterial abundances between the healthy controls and CRA or intramucosal CRC patients. In particular, F. varium was statistically more abundant in patients with CRA and intramucosal CRC than in healthy subjects. Here, we present the metagenomic profile of CRA and intramucosal CRC and demonstrate that F. varium is at least partially involved in the pathogenesis of CRA and intramucosal CRC.}, }
@article {pmid30794288, year = {2019}, author = {Banerjee, S and Alwine, JC and Wei, Z and Tian, T and Shih, N and Sperling, C and Guzzo, T and Feldman, MD and Robertson, ES}, title = {Microbiome signatures in prostate cancer.}, journal = {Carcinogenesis}, volume = {}, number = {}, pages = {}, doi = {10.1093/carcin/bgz008}, pmid = {30794288}, issn = {1460-2180}, abstract = {We have established a microbiome signature for prostate cancer using an array-based metagenomic and capture-sequencing approach. A diverse microbiome signature (viral, bacterial, fungal and parasitic) was observed in the prostate cancer samples compared with benign prostate hyperplasia controls. Hierarchical clustering analysis identified three distinct prostate cancer-specific microbiome signatures. The three signatures correlated with different grades, stages and scores of the cancer. Thus, microbiome signature analysis potentially provides clinical diagnosis and outcome predictions. The array data were validated by PCR and targeted next-generation sequencing (NGS). Specific NGS data suggested that certain viral genomic sequences were inserted into the host somatic chromosomes of the prostate cancer samples. A randomly selected group of these was validated by direct PCR and sequencing. In addition, PCR validation of Helicobacter showed that Helicobacter cagA sequences integrated within specific chromosomes of prostate tumor cells. The viral and Helicobacter integrations are predicted to affect the expression of several cellular genes associated with oncogenic processes.}, }
@article {pmid30793504, year = {2019}, author = {Kwon, YM and Patra, AK and Chiura, HX and Kim, SJ}, title = {Production of extracellular vesicles with light-induced proton pump activity by proteorhodopsin-containing marine bacteria.}, journal = {MicrobiologyOpen}, volume = {}, number = {}, pages = {e808}, doi = {10.1002/mbo3.808}, pmid = {30793504}, issn = {2045-8827}, support = {2019M00700//MABIK/ ; }, abstract = {The production and release of extracellular vesicles (EVs) is a common process occurring in various types of bacteria. However, little is known regarding the functions of EVs derived from marine bacteria. We observed that during cell growth, Sediminicola sp. YIK13, a proteorhodopsin (PR)-containing marine flavobacterium, produces EVs (S13EVs). Transmission electron microscopy showed that Sediminicola sp. YIK13 released two spherical vesicle types, with mono- and/or bi-layered membranes, in the culture. Interestingly, the S13EVs have an orange pigment, indicating the presence of putative carotenoid and PR pigments ascribed to the parental cells. The S13EVs demonstrated the same PR-derived absorption peak spectrum and light-induced proton pump activity as the parental cells. Western blot (immunoblot) analysis of the S13EVs revealed the presence of PR. We confirmed the 16S rRNA gene, pro gene, and genes required for chromophore retinal synthesis, namely blh and crtI, in the DNA packaged into these vesicles. In addition, by metagenomic sequencing, we found microbial rhodopsin-related genes in vesicles derived from natural aquatic environments. Our results suggest that EVs as well potentially pursue horizontal gene transfer of diverse microbial rhodopsin genes in marine ecosystems.}, }
@article {pmid30790413, year = {2019}, author = {Wang, Y and Feng, X and Natarajan, VP and Xiao, X and Wang, F}, title = {Diverse anaerobic methane- and multi-carbon alkane-metabolizing archaea coexist and show activity in Guaymas Basin hydrothermal sediment.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14568}, pmid = {30790413}, issn = {1462-2920}, abstract = {Anaerobic oxidation of methane greatly contributes to global carbon cycling, yet the anaerobic oxidation of non-methane alkanes by archaea was only recently detected in lab enrichments. The distribution and activity of these archaea in natural environments are not yet reported and understood. Here, a combination of metagenomic and metatranscriptomic approaches was utilized to understand the ecological roles and metabolic potentials of methyl-coenzyme M reductase (MCR)-based alkane oxidizing (MAO) archaea in Guaymas Basin sediments. Diverse MAO archaea, including multi-carbon alkane oxidizer Ca. Syntrophoarchaeum spp., anaerobic methane oxidizing archaea ANME-1 and ANME-2c as well as sulfate-reducing bacteria HotSeep-1 and Seep-SRB2 that potentially involved in MAO processes, coexisted and showed activity in Guaymas Basin sediments. High-quality genomic bins of Ca. Syntrophoarchaeum spp., ANME-1 and ANME-2c were retrieved. They all contain and expressed mcr genes and genes in Wood-Ljungdahl pathway for the complete oxidation from alkane to CO2 in local environment, while Ca. Syntrophoarchaeum spp. also possess beta-oxidation genes for multi-carbon alkane degradation. A global survey of potential multi-carbon alkane metabolism archaea shows that they are usually present in organic rich environments but are not limit to hydrothermal or marine ecosystems. Our study provided new insights into ecological and metabolic potentials of MAO archaea in natural environments. This article is protected by copyright. All rights reserved.}, }
@article {pmid30788781, year = {2019}, author = {Ke, J and Yoshikuni, Y}, title = {Pathway and Gene Discovery from Natural Hosts and Organisms.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1927}, number = {}, pages = {1-9}, doi = {10.1007/978-1-4939-9142-6_1}, pmid = {30788781}, issn = {1940-6029}, abstract = {Information in public sequence databases on the genomes and metagenomes of microbes and plants has grown rapidly. In conjunction with technological developments in computational identification of biosynthetic gene clusters, molecular biology, synthetic biology, and analytical tools, this has revealed genes for enzymes with optimal and targeted function, as well as a rich pool of uncharacterized metabolic pathways. This chapter discusses different approaches to discovery of genes and metabolic pathways in microbes and plants in nature, such as genomic mining, transcriptome analysis, and metabolite profiling.}, }
@article {pmid30788772, year = {2019}, author = {Federici, M}, title = {Gut microbiome and microbial metabolites: a new system affecting metabolic disorders.}, journal = {Journal of endocrinological investigation}, volume = {}, number = {}, pages = {}, doi = {10.1007/s40618-019-01022-9}, pmid = {30788772}, issn = {1720-8386}, abstract = {INTRODUCTION: The gut microbiome is emerging as an important player in the field of metabolic disorders.
MATERIALS AND METHODS: Currently, several studies are ongoing to determine whether the effect of gut microbiome on obesity, type 2 diabetes, non-alcoholic fatty liver disease, and other metabolic diseases is determined by singular species or rather by a functional role of bacterial metabolism at higher taxonomical level. Deciphering if a single or more species are responsible for metabolic traits or rather microbial metabolic pathways are responsible for effects on host metabolism may help to identify appropriate dietary interventions to support microbial functions according to the prevalent host disease. Furthermore, the combination of metagenomics and metabolomics-based signature might be applied in the future to improve the risk prediction in healthy subjects.
CONCLUSION: In this review, I will summarize the current findings regarding the role of gut microbiome and metabolites in metabolic disorders to argue whether the current achievements may be translated into clinical practice.}, }
@article {pmid30787921, year = {2019}, author = {Zhou, J and Xiong, X and Yin, J and Zou, L and Wang, K and Shao, Y and Yin, Y}, title = {Dietary Lysozyme Alters Sow's Gut Microbiota, Serum Immunity and Milk Metabolite Profile.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {177}, doi = {10.3389/fmicb.2019.00177}, pmid = {30787921}, issn = {1664-302X}, abstract = {The aim of current study was to determine variations in sow's gut microbiota, serum immunity, and milk metabolite profile mediated by lysozyme supplementation. Twenty-four pregnant sows were assigned to a control group without supplementation and two treatments with 0.5 kg/t and 1.0 kg/t lysozyme provided in formula feed for 21 days (n = 8 per treatment). Microbiota analysis and metagenomic predictions were based on 16s RNA high-throughput sequencing. Milk metabolome was assessed by untargeted liquid chromatography tandem mass spectrometry. Serum biochemical indicators and immunoglobulins were also determined. Gut microbial diversity of sows receiving 1.0 kg/t lysozyme treatment was significantly reduced after the trial. Spirochaetes, Euryarchaeota, and Actinobacteria significantly increased while Firmicutes showed a remarkable reduction in 1.0 kg/t group compared with control. Lysozyme addition rebuilt sow's gut microbiota to beneficial composition identified by reduced richness of Escherichia coli and increased abundance of Lactobacillus amylovorus. Accordingly, microbial metabolic functions including pyrimidine metabolism, purine metabolism, and amino acid related enzymes were significantly up-regulated in 1.0 kg/t group. Microbial metabolic phenotypes like the richness of Gram-positive bacteria and oxidative stress tolerance were also significantly reduced by lysozyme treatment. Serum alanine transaminase (ALT) activity and IgA levels were significantly down-regulated in the 1.0 kg/t group compared with control, but IgM levels showed a significantly increase in 1.0 kg/t group. Milk metabolites such as L-glutamine, creatine, and L-arginine showed significantly dose-dependent changes after treatment. Overall, lysozyme supplementation could effectively improve the composition, metabolic functions, and phenotypes of sow's gut microbiota and it also benefit sows with better serum immunity and milk composition. This research could provide theoretical support for further application of lysozyme in promoting animal gut health and prevent pathogenic infections in livestock production.}, }
@article {pmid30787417, year = {2019}, author = {Eibach, D and Hogan, B and Sarpong, N and Winter, D and Struck, NS and Adu-Sarkodie, Y and Owusu-Dabo, E and Schmidt-Chanasit, J and May, J and Cadar, D}, title = {Viral metagenomics revealed novel betatorquevirus species in pediatric inpatients with encephalitis/meningoencephalitis from Ghana.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {2360}, doi = {10.1038/s41598-019-38975-z}, pmid = {30787417}, issn = {2045-2322}, abstract = {The cause of acute encephalitis/meningoencephalitis in pediatric patients remains often unexplained despite extensive investigations for large panel of pathogens. To explore a possible viral implication, we investigated the virome of cerebrospinal fluid specimens of 70 febrile pediatric inpatients with clinical compatible encephalitis/meningoencephalitis. Using viral metagenomics, we detected and genetically characterized three novel human Torque teno mini virus (TTMV) species (TTMV-G1-3). Phylogenetically, TTMV-G1-3 clustered in three novel monophyletic lineages within genus Betatorquevirus of the Anelloviridae family. TTMV-G1-3 were highly prevalent in diseased children, but absent in the healthy cohort which may indicate an association of TTMV species with febrile illness. With 2/3 detected malaria co-infection, it remains unclear if these novel anellovirus species are causative agents or increase disease severity by interaction with malaria parasites. The presence of the viruses 28 days after initiating antimalarial and/or antibiotic treatment suggests a still active viral infection likely as effect of parasitic and/or bacterial co-infection that may have initiated a modulated immune system environment for viral replication or a defective virus clearance. This study increases the current knowledge on the genetic diversity of TTMV and strengthens that human anelloviruses can be considered as biomarkers for strong perturbations of the immune system in certain pathological conditions.}, }
@article {pmid30787410, year = {2019}, author = {Shaw, LM and Blanchard, A and Chen, Q and An, X and Davies, P and Tötemeyer, S and Zhu, YG and Stekel, DJ}, title = {DirtyGenes: testing for significant changes in gene or bacterial population compositions from a small number of samples.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {2373}, doi = {10.1038/s41598-019-38873-4}, pmid = {30787410}, issn = {2045-2322}, support = {EP/P510993/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; EP/M027333/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; EP/M027333/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; EP/M027333/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; EP/M027333/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; 21210008//National Natural Science Foundation of China (National Science Foundation of China)/ ; 21210008//National Natural Science Foundation of China (National Science Foundation of China)/ ; 21210008//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {High throughput genomics technologies are applied widely to microbiomes in humans, animals, soil and water, to detect changes in bacterial communities or the genes they carry, between different environments or treatments. We describe a method to test the statistical significance of differences in bacterial population or gene composition, applicable to metagenomic or quantitative polymerase chain reaction data. Our method goes beyond previous published work in being universally most powerful, thus better able to detect statistically significant differences, and through being more reliable for smaller sample sizes. It can also be used for experimental design, to estimate how many samples to use in future experiments, again with the advantage of being universally most powerful. We present three example analyses in the area of antimicrobial resistance. The first is to published data on bacterial communities and antimicrobial resistance genes (ARGs) in the environment; we show that there are significant changes in both ARG and community composition. The second is to new data on seasonality in bacterial communities and ARGs in hooves from four sheep. While the observed differences are not significant, we show that a minimum group size of eight sheep would provide sufficient power to observe significance of similar changes in further experiments. The third is to published data on bacterial communities surrounding rice crops. This is a much larger data set and is used to verify the new method. Our method has broad uses for statistical testing and experimental design in research on changing microbiomes, including studies on antimicrobial resistance.}, }
@article {pmid30787169, year = {2019}, author = {Leung, DYM and Calatroni, A and Zaramela, LS and LeBeau, PK and Dyjack, N and Brar, K and David, G and Johnson, K and Leung, S and Ramirez-Gama, M and Liang, B and Rios, C and Montgomery, MT and Richers, BN and Hall, CF and Norquest, KA and Jung, J and Bronova, I and Kreimer, S and Conover Talbot, C and Crumrine, D and Cole, RN and Elias, P and Zengler, K and Seibold, MA and Berdyshev, E and Goleva, E}, title = {The nonlesional skin surface distinguishes atopic dermatitis with food allergy as a unique endotype.}, journal = {Science translational medicine}, volume = {11}, number = {480}, pages = {}, doi = {10.1126/scitranslmed.aav2685}, pmid = {30787169}, issn = {1946-6242}, support = {R01 HL128439/HL/NHLBI NIH HHS/United States ; R01 MD010443/MD/NIMHD NIH HHS/United States ; }, abstract = {Skin barrier dysfunction has been reported in both atopic dermatitis (AD) and food allergy (FA). However, only one-third of patients with AD have FA. The purpose of this study was to use a minimally invasive skin tape strip sampling method and a multiomics approach to determine whether children with AD and FA (AD FA+) have stratum corneum (SC) abnormalities that distinguish them from AD without FA (AD FA-) and nonatopic (NA) controls. Transepidermal water loss was found to be increased in AD FA+. Filaggrin and the proportion of ω-hydroxy fatty acid sphingosine ceramide content in nonlesional skin of children with AD FA+ were substantially lower than in AD FA- and NA skin. These abnormalities correlated with morphologic changes in epidermal lamellar bilayer architecture responsible for barrier homeostasis. Shotgun metagenomic studies revealed that the nonlesional skin of AD FA+ had increased abundance of Staphylococcus aureus compared to NA. Increased expression of keratins 5, 14, and 16 indicative of hyperproliferative keratinocytes was observed in the SC of AD FA+. The skin transcriptome of AD FA+ had increased gene expression for dendritic cells and type 2 immune pathways. A network analysis revealed keratins 5, 14, and 16 were positively correlated with AD FA+, whereas filaggrin breakdown products were negatively correlated with AD FA+. These data suggest that the most superficial compartment of nonlesional skin in AD FA+ has unique properties associated with an immature skin barrier and type 2 immune activation.}, }
@article {pmid30785912, year = {2019}, author = {Qiu, Y and Wang, S and Huang, B and Zhong, H and Pan, Z and Zhuang, Q and Peng, C and Hou, G and Wang, K}, title = {Viral infection detection using metagenomics technology in six poultry farms of eastern China.}, journal = {PloS one}, volume = {14}, number = {2}, pages = {e0211553}, doi = {10.1371/journal.pone.0211553}, pmid = {30785912}, issn = {1932-6203}, abstract = {With rapidly increasing animal pathogen surveillance requirements, new technologies are needed for a comprehensive understanding of the roles of pathogens in the occurrence and development of animal diseases. We applied metagenomic technology to avian virus surveillance to study the main viruses infecting six poultry farms in two provinces in eastern China. Cloacal/throat double swabs were collected from 60 birds at each farm according to a random sampling method. The results showed that the method could simultaneously detect major viruses infecting farms, including avian influenza virus, infectious bronchitis virus, Newcastle disease virus, rotavirus G, duck hepatitis B virus, and avian leukemia virus subgroup J in several farms. The test results were consistent with the results from traditional polymerase chain reaction (PCR) or reverse transcription-PCR analyses. Five H9N2 and one H3N8 avian influenza viruses were detected at the farms and were identified as low pathogenic avian influenza viruses according to HA cleavage sites analysis. One detected Newcastle disease virus was classified as Class II genotype I and avirulent type according to F0 cleavage sites analysis. Three avian infectious bronchitis viruses were identified as 4/91, CK/CH/LSC/99I and TC07-2 genotypes by phylogenetic analysis of S1 genes. The viral infection surveillance method using metagenomics technology enables the monitoring of multiple viral infections, which allows the detection of main infectious viruses.}, }
@article {pmid30785347, year = {2019}, author = {Menegaux, R and Vert, JP}, title = {Continuous Embeddings of DNA Sequencing Reads and Application to Metagenomics.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {}, number = {}, pages = {}, doi = {10.1089/cmb.2018.0174}, pmid = {30785347}, issn = {1557-8666}, abstract = {We propose a new model for fast classification of DNA sequences output by next-generation sequencing machines. The model, which we call fastDNA, embeds DNA sequences in a vector space by learning continuous low-dimensional representations of the k-mers it contains. We show on metagenomics benchmarks that it outperforms the state-of-the-art methods in terms of accuracy and scalability.}, }
@article {pmid30784601, year = {2019}, author = {Nelson, MT and Pope, CE and Marsh, RL and Wolter, DJ and Weiss, EJ and Hager, KR and Vo, AT and Brittnacher, MJ and Radey, MC and Hayden, HS and Eng, A and Miller, SI and Borenstein, E and Hoffman, LR}, title = {Human and Extracellular DNA Depletion for Metagenomic Analysis of Complex Clinical Infection Samples Yields Optimized Viable Microbiome Profiles.}, journal = {Cell reports}, volume = {26}, number = {8}, pages = {2227-2240.e5}, doi = {10.1016/j.celrep.2019.01.091}, pmid = {30784601}, issn = {2211-1247}, abstract = {Metagenomic sequencing is a promising approach for identifying and characterizing organisms and their functional characteristics in complex, polymicrobial infections, such as airway infections in people with cystic fibrosis. These analyses are often hampered, however, by overwhelming quantities of human DNA, yielding only a small proportion of microbial reads for analysis. In addition, many abundant microbes in respiratory samples can produce large quantities of extracellular bacterial DNA originating either from biofilms or dead cells. We describe a method for simultaneously depleting DNA from intact human cells and extracellular DNA (human and bacterial) in sputum, using selective lysis of eukaryotic cells and endonuclease digestion. We show that this method increases microbial sequencing depth and, consequently, both the number of taxa detected and coverage of individual genes such as those involved in antibiotic resistance. This finding underscores the substantial impact of DNA from sources other than live bacteria in microbiological analyses of complex, chronic infection specimens.}, }
@article {pmid30783771, year = {2019}, author = {Ling, Y and Zhang, X and Qi, G and Yang, S and Jingjiao, L and Shen, Q and Wang, X and Cui, L and Hua, X and Deng, X and Delwart, E and Zhang, W}, title = {Viral metagenomics reveals significant viruses in the genital tract of apparently healthy dairy cows.}, journal = {Archives of virology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00705-019-04158-4}, pmid = {30783771}, issn = {1432-8798}, support = {2017YFC1200201//National Key Research and Development Programs of China/ ; BE2017693//Jiangsu Provincial Key Research and Development Projects/ ; 81741062//National Natural Science Foundation of China/ ; }, abstract = {The virome in genital tract secretion samples collected from 80 dairy cattle in Shanghai, China, was characterized. Viruses detected included members of the families Papillomaviridae, Polyomaviridae, Hepeviridae, Parvoviridae, Astroviridae, Picornaviridae, and Picobirnaviridae. A member of a new species within the genus Dyoxipapillomavirus and six circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) viral genomes were fully sequenced and phylogenetically analyzed. The prevalence of bovine polyomaviruses 1 and 2 was measured by PCR to be 10% (8/80) and 6.25% (5/80), respectively. PCR screening also indicated that the novel papillomavirus ujs-21015 and bovine herpesvirus 6 were present in three and two out of the 80 samples, respectively.}, }
@article {pmid30783213, year = {2019}, author = {Coskun, ÖK and Özen, V and Wankel, SD and Orsi, WD}, title = {Quantifying population-specific growth in benthic bacterial communities under low oxygen using H218O.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0373-4}, pmid = {30783213}, issn = {1751-7370}, support = {OR 417/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, abstract = {The benthos in estuarine environments often experiences periods of regularly occurring hypoxic and anoxic conditions, dramatically impacting biogeochemical cycles. How oxygen depletion affects the growth of specific uncultivated microbial populations within these diverse benthic communities, however, remains poorly understood. Here, we applied H218O quantitative stable isotope probing (qSIP) in order to quantify the growth of diverse, uncultured bacterial populations in response to low oxygen concentrations in estuarine sediments. Over the course of 7- and 28-day incubations with redox conditions spanning from hypoxia to euxinia (sulfidic), 18O labeling of bacterial populations exhibited different patterns consistent with micro-aerophilic, anaerobic, facultative anaerobic, and aerotolerant anaerobic growth. 18O-labeled populations displaying anaerobic growth had a significantly non-random phylogenetic distribution, exhibited by numerous clades currently lacking cultured representatives within the Planctomycetes, Actinobacteria, Latescibacteria, Verrucomicrobia, and Acidobacteria. Genes encoding the beta-subunit of the dissimilatory sulfate reductase (dsrB) became 18O labeled only during euxinic conditions. Sequencing of these 18O-labeled dsrB genes showed that Acidobacteria were the dominant group of growing sulfate-reducing bacteria, highlighting their importance for sulfur cycling in estuarine sediments. Our findings provide the first experimental constraints on the redox conditions underlying increased growth in several groups of "microbial dark matter", validating hypotheses put forth by earlier metagenomic studies.}, }
@article {pmid30782660, year = {2019}, author = {López-Pérez, M and Jayakumar, JM and Haro-Moreno, JM and Zaragoza-Solas, A and Reddi, G and Rodriguez-Valera, F and Shapiro, OH and Alam, M and Almagro-Moreno, S}, title = {Evolutionary Model of Cluster Divergence of the Emergent Marine Pathogen Vibrio vulnificus: From Genotype to Ecotype.}, journal = {mBio}, volume = {10}, number = {1}, pages = {}, doi = {10.1128/mBio.02852-18}, pmid = {30782660}, issn = {2150-7511}, abstract = {Vibrio vulnificus, an opportunistic pathogen, is the causative agent of a life-threatening septicemia and a rising problem for aquaculture worldwide. The genetic factors that differentiate its clinical and environmental strains remain enigmatic. Furthermore, clinical strains have emerged from every clade of V. vulnificus In this work, we investigated the underlying genomic properties and population dynamics of the V. vulnificus species from an evolutionary and ecological point of view. Genome comparisons and bioinformatic analyses of 113 V. vulnificus isolates indicate that the population of V. vulnificus is made up of four different clusters. We found evidence that recombination and gene flow between the two largest clusters (cluster 1 [C1] and C2) have drastically decreased to the point where they are diverging independently. Pangenome and phenotypic analyses showed two markedly different lifestyles for these two clusters, indicating commensal (C2) and bloomer (C1) ecotypes, with differences in carbohydrate utilization, defense systems, and chemotaxis, among other characteristics. Nonetheless, we identified frequent intra- and interspecies exchange of mobile genetic elements (e.g., antibiotic resistance plasmids, novel "chromids," or two different and concurrent type VI secretion systems) that provide high levels of genetic diversity in the population. Surprisingly, we identified strains from both clusters in the mucosa of aquaculture species, indicating that manmade niches are bringing strains from the two clusters together. We propose an evolutionary model of V. vulnificus that could be broadly applicable to other pathogenic vibrios and facultative bacterial pathogens to pursue strategies to prevent their infections and emergence.IMPORTANCEVibrio vulnificus is an emergent marine pathogen and is the cause of a deadly septicemia. However, the genetic factors that differentiate its clinical and environmental strains and its several biotypes remain mostly enigmatic. In this work, we investigated the underlying genomic properties and population dynamics of the V. vulnificus species to elucidate the traits that make these strains emerge as a human pathogen. The acquisition of different ecological determinants could have allowed the development of highly divergent clusters with different lifestyles within the same environment. However, we identified strains from both clusters in the mucosa of aquaculture species, indicating that manmade niches are bringing strains from the two clusters together, posing a potential risk of recombination and of emergence of novel variants. We propose a new evolutionary model that provides a perspective that could be broadly applicable to other pathogenic vibrios and facultative bacterial pathogens to pursue strategies to prevent their infections.}, }
@article {pmid30782566, year = {2019}, author = {Bennouna, A and Gil, P and El Rhaffouli, H and Exbrayat, A and Loire, E and Balenghien, T and Chlyeh, G and Gutierrez, S and Fihri, OF}, title = {Identification of Eilat virus and prevalence of infection among Culex pipiens L. populations, Morocco, 2016.}, journal = {Virology}, volume = {530}, number = {}, pages = {85-88}, doi = {10.1016/j.virol.2019.02.007}, pmid = {30782566}, issn = {1096-0341}, abstract = {Eilat virus (EILV) is described as one of the few alphaviruses restricted to insects. We report the record of a nearly-complete sequence of an alphavirus genome showing 95% identity with EILV during a metagenomic analysis performed on 1488 unblood-fed females and 1076 larvae of the mosquito Culex pipiens captured in Rabat (Morocco). Genetic distance and phylogenetic analyses placed the EILV-Morocco as a variant of EILV. The observed infection rates in both larvae and adults suggested an active circulation of the virus in Rabat and its maintenance in the environment either through vertical transmission or through horizontal infection of larvae in breeding sites. This is the first report of EILV out of Israel and in Culex pipiens populations.}, }
@article {pmid30782206, year = {2019}, author = {Lagkouvardos, I and Lesker, TR and Hitch, TCA and Gálvez, EJC and Smit, N and Neuhaus, K and Wang, J and Baines, JF and Abt, B and Stecher, B and Overmann, J and Strowig, T and Clavel, T}, title = {Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {28}, doi = {10.1186/s40168-019-0637-2}, pmid = {30782206}, issn = {2049-2618}, support = {CL481/2-1//German Research Foundation/ ; STR1343/1-2//Deutsche Forschungsgemeinschaft/ ; BA2863/5-1//Deutsche Forschungsgemeinschaft/ ; }, abstract = {BACKGROUND: Bacteria within family S24-7 (phylum Bacteroidetes) are dominant in the mouse gut microbiota and detected in the intestine of other animals. Because they had not been cultured until recently and the family classification is still ambiguous, interaction with their host was difficult to study and confusion still exists regarding sequence data annotation.
METHODS: We investigated family S24-7 by combining data from large-scale 16S rRNA gene analysis and from functional and taxonomic studies of metagenomic and cultured species.
RESULTS: A total of 685 species was inferred by full-length 16S rRNA gene sequence clustering. While many species could not be assigned ecological habitats (93,045 samples analyzed), the mouse was the most commonly identified host (average of 20% relative abundance and nine co-occurring species). Shotgun metagenomics allowed reconstruction of 59 molecular species, of which 34 were representative of the 16S rRNA gene-derived species clusters. In addition, cultivation efforts allowed isolating five strains representing three species, including two novel taxa. Genome analysis revealed that S24-7 spp. are functionally distinct from neighboring families and versatile with respect to complex carbohydrate degradation.
CONCLUSIONS: We provide novel data on the diversity, ecology, and description of bacterial family S24-7, for which the name Muribaculaceae is proposed.}, }
@article {pmid30779273, year = {2019}, author = {Chekanov, K and Kublanovskaya, A and Lobakova, E}, title = {Eukaryotic Sequences in the 16SrRNA Metagenomic Dataset of Algal-bacterial Consortia of the White Sea Coastal Zone.}, journal = {The Journal of eukaryotic microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jeu.12722}, pmid = {30779273}, issn = {1550-7408}, abstract = {The libraries of bacterial 16SrRNA gene fragment from algal-bacterial consortia of the White Sea coastal zone are analyzed. Up to 3% of the reads have revealed to correspond to eukaryotic rRNA. They related to following main eukaryotic clades: Discoba, Stramenopiles, Ciliata, Amoebozoa, and Nucletmycea. Amoebae, especially Vermamoeba, were present in all samples. In one sample, heterolobose amoeba Paravahlkampfia was detected. These microorganisms are parasites of microalgae, which can induce significant damage to industrial cultures. However, the data on their physiology and distribution are scarce. This study provides new evidence about the diversity of herbivorous eukaryotic microorganisms in natural algal-containing consortia. This article is protected by copyright. All rights reserved.}, }
@article {pmid30778224, year = {2019}, author = {Sanna, S and van Zuydam, NR and Mahajan, A and Kurilshikov, A and Vich Vila, A and Võsa, U and Mujagic, Z and Masclee, AAM and Jonkers, DMAE and Oosting, M and Joosten, LAB and Netea, MG and Franke, L and Zhernakova, A and Fu, J and Wijmenga, C and McCarthy, MI}, title = {Causal relationships among the gut microbiome, short-chain fatty acids and metabolic diseases.}, journal = {Nature genetics}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41588-019-0350-x}, pmid = {30778224}, issn = {1546-1718}, support = {U01 DK105535/DK/NIDDK NIH HHS/United States ; }, abstract = {Microbiome-wide association studies on large population cohorts have highlighted associations between the gut microbiome and complex traits, including type 2 diabetes (T2D) and obesity1. However, the causal relationships remain largely unresolved. We leveraged information from 952 normoglycemic individuals for whom genome-wide genotyping, gut metagenomic sequence and fecal short-chain fatty acid (SCFA) levels were available2, then combined this information with genome-wide-association summary statistics for 17 metabolic and anthropometric traits. Using bidirectional Mendelian randomization (MR) analyses to assess causality3, we found that the host-genetic-driven increase in gut production of the SCFA butyrate was associated with improved insulin response after an oral glucose-tolerance test (P = 9.8 × 10-5), whereas abnormalities in the production or absorption of another SCFA, propionate, were causally related to an increased risk of T2D (P = 0.004). These data provide evidence of a causal effect of the gut microbiome on metabolic traits and support the use of MR as a means to elucidate causal relationships from microbiome-wide association findings.}, }
@article {pmid30778155, year = {2019}, author = {Ata, B and Yildiz, S and Turkgeldi, E and Brocal, VP and Dinleyici, EC and Moya, A and Urman, B}, title = {The Endobiota Study: Comparison of Vaginal, Cervical and Gut Microbiota Between Women with Stage 3/4 Endometriosis and Healthy Controls.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {2204}, doi = {10.1038/s41598-019-39700-6}, pmid = {30778155}, issn = {2045-2322}, abstract = {Dysbiosis in the genital tract or gut microbiome can be associated with endometriosis. We sampled vaginal, cervical and gut microbiota from 14 women with histology proven stage 3/4 endometriosis and 14 healthy controls. The V3 and V4 regions of the 16S rRNA gene were amplified following the 16S Metagenomic Sequencing Library Preparation. Despite overall similar vaginal, cervical and intestinal microbiota composition between stage 3/4 endometriosis group and controls, we observed differences at genus level. The complete absence of Atopobium in the vaginal and cervical microbiota of the stage 3/4 endometriosis group was noteworthy. In the cervical microbiota, Gardnerella, Streptococcus, Escherichia, Shigella, and Ureoplasma, all of which contain potentially pathogenic species, were increased in stage 3/4 endometriosis. More women in the stage 3/4 endometriosis group had Shigella/Escherichia dominant stool microbiome. Further studies can clarify whether the association is causal, and whether dysbiosis leads to endometriosis or endometriosis leads to dysbiosis.}, }
@article {pmid30777801, year = {2019}, author = {Bonants, P and Griekspoor, Y and Houwers, I and Krijger, M and van der Zouwen, P and van der Lee, TAJ and van der Wolf, J}, title = {Development and Evaluation of a Triplex TaqMan Assay and Next-Generation Sequence Analysis for Improved Detection of Xylella in Plant Material.}, journal = {Plant disease}, volume = {}, number = {}, pages = {PDIS08181433RE}, doi = {10.1094/PDIS-08-18-1433-RE}, pmid = {30777801}, issn = {0191-2917}, abstract = {Xylella fastidiosa is a heterogenous gram-negative bacterial plant pathogen with a wide host range covering over 300 plant species. Since 2013, in Europe, the presence of the pathogen is increasing in a part of the Mediterranean area, but it causes in particular severe disease problems in olive orchards in the Southern part of Italy. Various subspecies of the pathogen were also diagnosed in natural outbreaks and intercepted ornamental plants in Europe, among them Olea europaea, Coffea arabica, and Nerium oleander. The host range of the pathogen can vary, depending on the subspecies and even the strain. The availability of fast and reliable diagnostic tools is indispensable in management strategies to control diseases caused by X. fastidiosa. To improve the reliability of the TaqMan assay, currently widely used in surveys, a triplex TaqMan assay was developed in which two specific and sensitive TaqMan assays, previously designed for X. fastidiosa, were combined with an internal control. The triplex assay exhibited the same diagnostic sensitivity as the simplex assays. In addition, the usefulness of a metagenomic approach using next-generation sequencing (NGS) was demonstrated, in which total DNA extracted from plant material was sequenced. DNA extracts from plant material free of X. fastidiosa, from artificially inoculated hosts plants or from naturally infected plants sampled in France, Spain, and Italy, or intercepted in Austria and the Netherlands, were analyzed for the presence of X. fastidiosa using the metagenomic approach. In all samples, even in samples with a low infection level, but not in the pathogen-free samples, DNA reads were detected specific for X. fastidiosa. In most cases, the pathogen could be identified to the subspecies level, and for one sample even the whole genome could be assembled and the sequence type could be determined. All results of NGS-analyzed samples were confirmed with the triplex TaqMan polymerase chain reaction and loop-mediated isothermal amplification.}, }
@article {pmid30777011, year = {2019}, author = {Feng, Y and Ramnarine, VR and Bell, R and Volik, S and Davicioni, E and Hayes, VM and Ren, S and Collins, CC}, title = {Metagenomic and metatranscriptomic analysis of human prostate microbiota from patients with prostate cancer.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {146}, doi = {10.1186/s12864-019-5457-z}, pmid = {30777011}, issn = {1471-2164}, support = {CSC201606325044//China Scholarship Council/ ; 201012TFF//Terry Fox Foundation/ ; T2013-01//Prostate Cancer Canada/ ; 81472397//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Prostate cancer (PCa) is the most common malignant neoplasm among men in many countries. Since most precancerous and cancerous tissues show signs of inflammation, chronic bacterial prostatitis has been hypothesized to be a possible etiology. However, establishing a causal relationship between microbial inflammation and PCa requires a comprehensive analysis of the prostate microbiome. The aim of this study was to characterize the microbiome in prostate tissue of PCa patients and investigate its association with tumour clinical characteristics as well as host expression profiles.
RESULTS: The metagenome and metatranscriptome of tumour and the adjacent benign tissues were assessed in 65 Chinese radical prostatectomy specimens. Escherichia, Propionibacterium, Acinetobacter and Pseudomonas were abundant in both metagenome and metatranscriptome, thus constituting the core of the prostate microbiome. The biodiversity of the microbiomes could not be differentiated between the matched tumour/benign specimens or between the tumour specimens of low and high Gleason Scores. The expression profile of ten Pseudomonas genes was strongly correlated with that of eight host small RNA genes; three of the RNA genes may negatively associate with metastasis. Few viruses could be identified from the prostate microbiomes.
CONCLUSIONS: This is the first study of the human prostate microbiome employing an integrated metagenomics and metatranscriptomics approach. In this Chinese cohort, both metagenome and metatranscriptome analyses showed a non-sterile microenvironment in the prostate of PCa patients, but we did not find links between the microbiome and local progression of PCa. However, the correlated expression of Pseudomonas genes and human small RNA genes may provide tantalizing preliminary evidence that Pseudomonas infection may impede metastasis.}, }
@article {pmid30775338, year = {2018}, author = {Hussein, EI and Jacob, JH and Shakhatreh, MAK and Al-Razaq, MAA and Juhmani, AF and Cornelison, CT}, title = {Detection of antibiotic-producing Actinobacteria in the sediment and water of Ma'in thermal springs (Jordan).}, journal = {Germs}, volume = {8}, number = {4}, pages = {191-198}, doi = {10.18683/germs.2018.1146}, pmid = {30775338}, issn = {2248-2997}, abstract = {Introduction: Detection of new Actinobacteria is significant to discover new antibiotics because development of new antibiotics is connected to the characterization of novel bacterial taxa. This study has focused on the identification and isolation of antibiotic-producing Actinobacteria from the sediment and the water of Ma'in thermal springs (48-59°C) situated in the center area of Jordan.
Methods: Samples of sediment and water were transferred to glucose yeast malt agar medium and Actinobacteria were cultivated, isolated and identified according to scanning electron microscopy and 16S rRNA gene analysis. Antibacterial activities of the isolates were then tested against different test bacteria by agar well diffusion method.
Results: Three different species of Actinobacteria were isolated (M1-1, M2-2, M3-2) from sediment samples. Based on 16S rRNA gene analysis, isolate M1-1 was found to have only 90% identity percentage with Nocardiopsis sp., however, isolates M2-2 and M3-2 were found to be closely related Streptomyces sp. (97%) and Nocardioides luteus (99%), respectively. The antibacterial activity showed that strain M1-1 is active against P. aeruginosa ATCC 2785 (inhibition zone, 9 mm). Strain M2-2 was found to be active against S. aureus ATCC 29213 (12 mm), B. cereus ATCC 11778 (11 mm), and E. coli ATCC 25922 (9 mm). In respect to strain M3-2, it was found to be active against S. aureus ATCC 29213 (14 mm) and B. cereus ATCC 11778 (9 mm). There were no actinobacterial isolates obtained from water samples despite their significant diversity revealed by our previous metagenomic analysis, which showed the presence of 13 different species dominated by Arthrobacter (an Actinobacterium belonging to family Actinomycetales).
Conclusion: There were 17 different Actinobacteria that could be detected in Ma'in thermal springs (13 unculturable species and 3 culturable species). The culturable Actinobacteria were found to have some antimicrobial activity. Further chemical analysis of the bioactive compounds is recommended.}, }
@article {pmid30774969, year = {2019}, author = {Santillan, E and Seshan, H and Constancias, F and Drautz-Moses, DI and Wuertz, S}, title = {Frequency of disturbance alters diversity, function, and underlying assembly mechanisms of complex bacterial communities.}, journal = {NPJ biofilms and microbiomes}, volume = {5}, number = {}, pages = {8}, doi = {10.1038/s41522-019-0079-4}, pmid = {30774969}, issn = {2055-5008}, abstract = {Disturbance is known to affect the ecosystem structure, but predicting its outcomes remains elusive. Similarly, community diversity is believed to relate to ecosystem functions, yet the underlying mechanisms are poorly understood. Here, we tested the effect of disturbance on the structure, assembly, and ecosystem function of complex microbial communities within an engineered system. We carried out a microcosm experiment where activated sludge bioreactors operated in daily cycles were subjected to eight different frequency levels of augmentation with a toxic pollutant, from never (undisturbed) to every day (press-disturbed), for 35 days. Microbial communities were assessed by combining distance-based methods, general linear multivariate models, α-diversity indices, and null model analyses on metagenomics and 16S rRNA gene amplicon data. A stronger temporal decrease in α-diversity at the extreme, undisturbed and press-disturbed, ends of the disturbance range led to a hump-backed pattern, with the highest diversity found at intermediate levels of disturbance. Undisturbed and press-disturbed levels displayed the highest community and functional similarity across replicates, suggesting deterministic processes were dominating. The opposite was observed amongst intermediately disturbed levels, indicating stronger stochastic assembly mechanisms. Trade-offs were observed in the ecosystem function between organic carbon removal and both nitrification and biomass productivity, as well as between diversity and these functions. Hence, not every ecosystem function was favoured by higher community diversity. Our results show that the assessment of changes in diversity, along with the underlying stochastic-deterministic assembly processes, is essential to understanding the impact of disturbance in complex microbial communities.}, }
@article {pmid30774267, year = {2019}, author = {Sarangi, AN and Goel, A and Aggarwal, R}, title = {Methods for Studying Gut Microbiota: A Primer for Physicians.}, journal = {Journal of clinical and experimental hepatology}, volume = {9}, number = {1}, pages = {62-73}, doi = {10.1016/j.jceh.2018.04.016}, pmid = {30774267}, issn = {0973-6883}, abstract = {Human gastrointestinal tract contains a large variety of microbes, in particular bacteria. Studies in recent years have strongly suggested a role for these microbes, collectively referred to as gut microbiota, in the maintenance of homeostasis during health. In addition, alterations in gut microbiota have been reported in several diseases, including those related to the gastrointestinal tract and several systemic conditions, and are believed to play a pathogenetic role in at least some of these. Given the close association between the human gut and liver, the association with gut microbiota appears to be particularly strong for a wide variety of liver diseases. This piece, aimed primarily at physicians, reviews in brief the methods used to study gut microbiota, with particular emphasis on those that use sequences of bacterial 16S rRNA gene or its components.}, }
@article {pmid30774010, year = {2019}, author = {Umiker, B and Lee, HH and Cope, J and Ajami, NJ and Laine, JP and Fregeau, C and Ferguson, H and Alves, SE and Sciammetta, N and Kleinschek, M and Salmon, M}, title = {The NLRP3 inflammasome mediates DSS-induced intestinal inflammation in Nod2 knockout mice.}, journal = {Innate immunity}, volume = {25}, number = {2}, pages = {132-143}, doi = {10.1177/1753425919826367}, pmid = {30774010}, issn = {1753-4267}, abstract = {Crohn's disease (CD) is a chronic disorder of the gastrointestinal tract characterized by inflammation and intestinal epithelial injury. Loss of function mutations in the intracellular bacterial sensor NOD2 are major risk factors for the development of CD. In the absence of robust bacterial recognition by NOD2 an inflammatory cascade is initiated through alternative PRRs leading to CD. In the present study, MCC950, a specific small molecule inhibitor of NLR pyrin domain-containing protein 3 (NLRP3), abrogated dextran sodium sulfate (DSS)-induced intestinal inflammation in Nod2-/- mice. NLRP3 inflammasome formation was observed at a higher rate in NOD2-deficient small intestinal lamina propria cells after insult by DSS. NLRP3 complex formation led to an increase in IL-1β secretion in both the small intestine and colon of Nod2ko mice. This increase in IL-1β secretion in the intestine was attenuated by MCC950 leading to decreased disease severity in Nod2ko mice. Our work suggests that NLRP3 inflammasome activation may be a key driver of intestinal inflammation in the absence of functional NOD2. NLRP3 pathway inhibition can prevent intestinal inflammation in the absence of robust NOD2 signaling.}, }
@article {pmid30773302, year = {2018}, author = {Sasaki, H and Kawamura, K and Kawamura, T and Odamaki, T and Katsumata, N and Xiao, JZ and Suzuki, N and Tanaka, M}, title = {Distinctive subpopulations of the intestinal microbiota are present in women with unexplained chronic anovulation.}, journal = {Reproductive biomedicine online}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.rbmo.2018.12.026}, pmid = {30773302}, issn = {1472-6491}, abstract = {RESEARCH QUESTION: Do gut microbiota associate with the ovulatory cycle in women showing normogonadotrophic anovulation? In humans, the gut microbiota affects diverse physiological functions and dysbiosis (microbial imbalance) may lead to pathological syndromes. However, there is comparatively little information on the relevance of gut microbiota to reproductive functions in women. Here, a group of women with idiopathic chronic anovulation were examined, who do not exhibit any apparent endocrinological disorder, as they are suitable for investigating the relationship between intestinal bacteria and ovulatory disorders.
DESIGN: A prospective observational cohort study was performed on two groups of women who did not exhibit apparent endocrinological disorders but showed either irregular menstrual cycles (IMC group) or normal menstrual cycles (controls). The bacterial composition of faeces from rectal swabs from the women was analysed using next-generation sequencing based on bacterial 16SrRNA genes.
RESULTS: A metagenomic analysis indicated that the two groups of women had significant differences in 28 bacterial taxa in their faeces. Prevotella-enriched microbiomes were more abundant in the IMC group, whereas Clostridiales, Ruminococcus and Lachnospiraceae (butyrate-producing bacteria) were present at lower levels in the IMC group.
CONCLUSIONS: Distinctive subpopulations of intestinal microbiota were identified in women with unexplained chronic anovulation. The results indicate that gut microbiota could be associated with ovarian functions.}, }
@article {pmid30773139, year = {2019}, author = {Sáenz, JS and Marques, TV and Barone, RSC and Cyrino, JEP and Kublik, S and Nesme, J and Schloter, M and Rath, S and Vestergaard, G}, title = {Oral administration of antibiotics increased the potential mobility of bacterial resistance genes in the gut of the fish Piaractus mesopotamicus.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {24}, doi = {10.1186/s40168-019-0632-7}, pmid = {30773139}, issn = {2049-2618}, support = {#2013/09543-7//The São Paulo Research Foundation/ ; }, abstract = {BACKGROUND: Aquaculture is on the rise worldwide, and the use of antibiotics is fostering higher production intensity. However, recent findings suggest that the use of antibiotics comes at the price of increased antibiotic resistance. Yet, the effect of the oral administration of antibiotics on the mobility of microbial resistance genes in the fish gut is not well understood. In the present study, Piaractus mesopotamicus was used as a model to evaluate the effect of the antimicrobial florfenicol on the diversity of the gut microbiome as well as antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) using a metagenomic approach.
RESULTS: The total relative abundance of ARGs and MGEs significantly increased during the antibiotic exposure. Additionally, phage integrases, transposases, and transposons flanking ARGs accumulated in the gut microbiome of P. mesopotamicus because of the antibiotic exposure. MGEs co-occurring with ARGs showed a significant positive correlation with the total ARGs found. Furthermore, shifts in the gut microbiome towards well-known putative pathogens such as Salmonella, Plesiomonas, and Citrobacter were observed following florfenicol treatment. Mainly Plesiomonas and Citrobacter harbored genes that code for multidrug and phenicol efflux pumps. Moreover, several genes related to RNA processing and modification, cell motility, SOS response, and extracellular structure were enriched due to the antibiotic application. The observed effects were visible during the complete application phase and disappeared at the post-exposure phase.
CONCLUSIONS: Our findings suggest that the oral administration of antibiotics increases the potential for MGE-mediated exchange of ARGs in the gut of fish and could contribute to the enrichment and dispersion of ARGs in aquaculture systems. Importantly, this increase in the potential for ARGs exchange could be an effect of changes in community structure and/or ARG mobilization.}, }
@article {pmid30772567, year = {2019}, author = {Casero, MC and Velázquez, D and Medina-Cobo, M and Quesada, A and Cirés, S}, title = {Unmasking the identity of toxigenic cyanobacteria driving a multi-toxin bloom by high-throughput sequencing of cyanotoxins genes and 16S rRNA metabarcoding.}, journal = {The Science of the total environment}, volume = {665}, number = {}, pages = {367-378}, doi = {10.1016/j.scitotenv.2019.02.083}, pmid = {30772567}, issn = {1879-1026}, abstract = {Cyanobacterial harmful algal blooms (CyanoHABs) are complex communities that include coexisting toxic and non-toxic strains only distinguishable by genetic methods. This study shows a water-management oriented use of next generation sequencing (NGS) to specifically pinpoint toxigenic cyanobacteria within a bloom simultaneously containing three of the most widespread cyanotoxins (the hepatotoxins microcystins, MCs; and the neurotoxins anatoxin-a, ATX, and saxitoxins, STXs). The 2013 summer bloom in Rosarito reservoir (Spain) comprised 33 cyanobacterial OTUs based on 16S rRNA metabarcoding, 7 of which accounted for as much as 96.6% of the community. Cyanotoxins and their respective biosynthesis genes were concurrently present throughout the entire bloom event including: MCs and mcyE gene; ATX and anaF gene; and STXs and sxtI gene. NGS applied to amplicons of cyanotoxin-biosynthesis genes unveiled 6 toxigenic OTUs, comprising 3 involved in MCs production (Planktothrix agardhii and 2 Microcystis spp.), 2 in ATX production (Cuspidothrix issatschenkoi and Phormidium/Tychonema spp.) and 1 in STXs production (Aphanizomenon gracile). These toxigenic taxa were also present in 16S rRNA OTUs list and their relative abundance was positively correlated with the respective toxin concentrations. Our results point at MC-producing P. agardhii and ATX-producing C. issatschenkoi as the main contributors to the moderate toxin concentrations observed, and suggest that their distribution in Southern Europe is broader than previously thought. Our findings also stress the need for monitoring low-abundance cyanobacteria (<1% relative abundance) in cyanotoxicity studies, and provide novel data on the presence of picocyanobacteria and potentially ATX-producing benthic taxa (e.g., Phormidium) in deep thermally-stratified water bodies. This study showcases a straightforward use of amplicon metagenomics of cyanotoxin biosynthesis genes in a multi-toxin bloom thus illustrating the broad applicability of NGS for water management in risk-oriented monitoring of CyanoHABs.}, }
@article {pmid30772134, year = {2019}, author = {Bjerregaard, LG and Adelborg, K and Baker, JL}, title = {Change in body mass index from childhood onwards and risk of adult cardiovascular disease.}, journal = {Trends in cardiovascular medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tcm.2019.01.011}, pmid = {30772134}, issn = {1873-2615}, abstract = {Childhood obesity adversely affects the structure and function of the cardiovascular system, but the relationship between excessive weight gain during childhood and adult cardiovascular disease (CVD) is not fully understood. This review summarizes evidence for associations of change in body mass index (BMI) from childhood onwards with CVD outcomes. We found that excessive gain in BMI from childhood onwards was consistently associated with the presence of CVD risk factors, with increased risks of coronary heart disease, and there were suggestions of associations with stroke, atrial fibrillation and heart failure, but a lack of evidence precludes firm conclusions. These results indicate that the risk of CVD can be traced back to child ages and highlights the importance of primordial prevention of CVD by preventing excessive weight gain in childhood.}, }
@article {pmid30771735, year = {2019}, author = {Petersen, C and Wankhade, UD and Bharat, D and Wong, K and Mueller, JE and Chintapalli, SV and Piccolo, BD and Jalili, T and Jia, Z and Symons, JD and Shankar, K and Anandh Babu, PV}, title = {Dietary supplementation with strawberry induces marked changes in the composition and functional potential of the gut microbiome in diabetic mice.}, journal = {The Journal of nutritional biochemistry}, volume = {66}, number = {}, pages = {63-69}, doi = {10.1016/j.jnutbio.2019.01.004}, pmid = {30771735}, issn = {1873-4847}, abstract = {Gut microbiota contributes to the biological activities of berry anthocyanins by transforming them into bioactive metabolites, and anthocyanins support the growth of specific bacteria, indicating a two-way relationship between anthocyanins and microbiota. In the present study, we tested the hypothesis that strawberry supplementation alters gut microbial ecology in diabetic db/db mice. Control (db/+) and diabetic (db/db) mice (7 weeks old) consumed standard diet or diet supplemented with 2.35% freeze-dried strawberry (db/db+SB) for 10 weeks. Colon contents were used to isolate bacterial DNA. V4 variable region of 16S rRNA gene was amplified. Data analyses were performed using standardized pipelines (QIIME 1.9 and R packages). Differences in predictive metagenomics function were identified by PICRUSt. Principal coordinate analyses confirmed that the microbial composition was significantly influenced by both host genotype and strawberry consumption. Further, α-diversity indices and β-diversity were different at the phylum and genus levels, and genus and operational taxonomical units levels, respectively (P<.05). At the phylum level, strawberry supplementation decreased the abundance of Verrucomicrobia in db/db+SB vs. db/db mice (P<.05). At the genus level, db/db mice exhibited a decrease in the abundance of Bifidobacterium, and strawberry supplementation increased Bifidobacterium in db/db+SB vs. db/db mice (P<.05). PICRUSt revealed significant differences in 45 predicted metabolic functions among the 3 groups. Our study provides evidence for marked changes in the composition and functional potential of the gut microbiome with strawberry supplementation in diabetic mice. Importantly, strawberry supplementation increased the abundance of beneficial bacteria Bifidobacterium which play a pivotal role in the metabolism of anthocyanins.}, }
@article {pmid30771442, year = {2019}, author = {Lee, CM and Kim, SY and Yoon, SH and Kim, JB and Yeo, YS and Sim, JS and Hahn, BS and Kim, DG}, title = {Characterization of a novel antibacterial N-acyl amino acid synthase from soil metagenome.}, journal = {Journal of biotechnology}, volume = {294}, number = {}, pages = {19-25}, doi = {10.1016/j.jbiotec.2019.01.017}, pmid = {30771442}, issn = {1873-4863}, abstract = {In an effort to isolate novel natural antibiotics, we searched for antibacterial long-chain N-acyl amino acid synthase (NAS) genes from 70,000 soil metagenome clones by Bacillus subtilis-overlaying screening. In an antibacterial cosmid clone, YS92B, a single gene nasYPL was responsible for the production of the Nas. nasYPL was 903 bp long, and the deduced amino acid sequence showed the highest 71% identity with a hypothetical protein from Massilia niastensis. Phylogenetic analysis demonstrated that NasYPL belongs to Group 1 Nas. Heterologous expression of the same nasYPL gene in Escherichia coli and two Pseudomonas strains (P. putida and P. koreensis) conferred antibacterial activities against Listeria monocytogenes, Staphylococcus epidermidis, and Bacillus subtilis. Mass spectral analysis of the antibacterial fractions identified 7 peaks corresponding to long-chain N-acyl tyrosine, 5 peaks to N-acyl phenylalanine, and 3 peaks to N-acyl leucine (or isoleucine) derivatives linked with 7 fatty acids, indicating enzymatic products derived by NasYPL. Therefore, NasYPL expression by host-specific manner may provide applicable antibacterial characteristics to biotechnologically important Pseudomonas strains.}, }
@article {pmid30770850, year = {2019}, author = {Kouchaki, S and Tapinos, A and Robertson, DL}, title = {A signal processing method for alignment-free metagenomic binning: multi-resolution genomic binary patterns.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {2159}, doi = {10.1038/s41598-018-38197-9}, pmid = {30770850}, issn = {2045-2322}, support = {634650//EC | Horizon 2020 (Horizon 2020 - Research and Innovation Framework Programme)/ ; 634650//EC | Horizon 2020 (Horizon 2020 - Research and Innovation Framework Programme)/ ; BB/M001121/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; 555 (MC_UU_1201412)//RCUK | Medical Research Council (MRC)/ ; }, abstract = {Algorithms in bioinformatics use textual representations of genetic information, sequences of the characters A, T, G and C represented computationally as strings or sub-strings. Signal and related image processing methods offer a rich source of alternative descriptors as they are designed to work in the presence of noisy data without the need for exact matching. Here we introduce a method, multi-resolution local binary patterns (MLBP) adapted from image processing to extract local 'texture' changes from nucleotide sequence data. We apply this feature space to the alignment-free binning of metagenomic data. The effectiveness of MLBP is demonstrated using both simulated and real human gut microbial communities. Sequence reads or contigs can be represented as vectors and their 'texture' compared efficiently using machine learning algorithms to perform dimensionality reduction to capture eigengenome information and perform clustering (here using randomized singular value decomposition and BH-tSNE). The intuition behind our method is the MLBP feature vectors permit sequence comparisons without the need for explicit pairwise matching. We demonstrate this approach outperforms existing methods based on k-mer frequencies. The signal processing method, MLBP, thus offers a viable alternative feature space to textual representations of sequence data. The source code for our Multi-resolution Genomic Binary Patterns method can be found at https://github.com/skouchaki/MrGBP .}, }
@article {pmid30770768, year = {2019}, author = {Olm, MR and West, PT and Brooks, B and Firek, BA and Baker, R and Morowitz, MJ and Banfield, JF}, title = {Genome-resolved metagenomics of eukaryotic populations during early colonization of premature infants and in hospital rooms.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {26}, doi = {10.1186/s40168-019-0638-1}, pmid = {30770768}, issn = {2049-2618}, support = {R01 AI092531/AI/NIAID NIH HHS/United States ; S10 OD018174/OD/NIH HHS/United States ; RAI092531A//National Institutes of Health (US)/ ; APSF-2012-10-05//Alfred P. Sloan Foundation (US)/ ; }, abstract = {BACKGROUND: Fungal infections are a significant cause of mortality and morbidity in hospitalized preterm infants, yet little is known about eukaryotic colonization of infants and of the neonatal intensive care unit as a possible source of colonizing strains. This is partly because microbiome studies often utilize bacterial 16S rRNA marker gene sequencing, a technique that is blind to eukaryotic organisms. Knowledge gaps exist regarding the phylogeny and microdiversity of eukaryotes that colonize hospitalized infants, as well as potential reservoirs of eukaryotes in the hospital room built environment.
RESULTS: Genome-resolved analysis of 1174 time-series fecal metagenomes from 161 premature infants revealed fungal colonization of 10 infants. Relative abundance levels reached as high as 97% and were significantly higher in the first weeks of life (p = 0.004). When fungal colonization occurred, multiple species were present more often than expected by random chance (p = 0.008). Twenty-four metagenomic samples were analyzed from hospital rooms of six different infants. Compared to floor and surface samples, hospital sinks hosted diverse and highly variable communities containing genomically novel species, including from Diptera (fly) and Rhabditida (worm) for which genomes were assembled. With the exception of Diptera and two other organisms, zygosity of the newly assembled diploid eukaryote genomes was low. Interestingly, Malassezia and Candida species were present in both room and infant gut samples.
CONCLUSIONS: Increased levels of fungal co-colonization may reflect synergistic interactions or differences in infant susceptibility to fungal colonization. Discovery of eukaryotic organisms that have not been sequenced previously highlights the benefit of genome-resolved analyses, and low zygosity of assembled genomes could reflect inbreeding or strong selection imposed by room conditions.}, }
@article {pmid30769104, year = {2019}, author = {Conrads, G and Abdelbary, MMH}, title = {Challenges of next-generation sequencing targeting anaerobes.}, journal = {Anaerobe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.anaerobe.2019.02.006}, pmid = {30769104}, issn = {1095-8274}, abstract = {Next-generation sequencing allows for investigating the composition of microbiomes that are associated with infection (clinical microbiology) or dysbiosis (microbial ecology). The most commonly applied short-read sequencing technologies are Illumina MiSeq/HiSeq and Ion Torrent PGM, however, other platforms that generate long-reads are under way and optimized. A pre-condition for representative results is an appropriate method for contamination-free collection, homogenization, storage of specimens and a subsequent efficient DNA extraction protocol. As some of the anaerobes such as Clostridia or anaerobe Archaea are robust while others of the same environment, such as spirochetes, possess a very thin cell wall, a chemico-mechanical lysing strategy is recommended but with some precautions to avoid DNA-sheering and overheating. For amplicon sequencing, the Silva-TestPrime online tool helps to find the optimal 16S directed primers for individual studies. For metagenome profiling, the classifier tool has to be selected with helpful decision trees available but a combination based on different strategies seems to be indispensable. Further development of both hard- and software is needed before microbiome results become free of a substantial technology-dependent bias.}, }
@article {pmid30768760, year = {2019}, author = {St John, E and Flores, GE and Meneghin, J and Reysenbach, AL}, title = {Deep-sea hydrothermal vent metagenome-assembled genomes provide insight into the phylum Nanoarchaeota.}, journal = {Environmental microbiology reports}, volume = {}, number = {}, pages = {}, doi = {10.1111/1758-2229.12740}, pmid = {30768760}, issn = {1758-2229}, abstract = {Ectosymbiotic Nanoarchaeota live on the surface of diverse archaeal hosts. Despite being broadly distributed in global geothermal systems, only three Nanoarchaeota have been successfully co-cultivated with their hosts, and until now no nanoarchaeotal cultures or genomes have been described from deep-sea hydrothermal vents. We recovered three nanoarchaeotal metagenome-assembled genomes (MAGs) from deep-sea hydrothermal vent sites at the Eastern Lau Spreading Center (M10-121), Guaymas Basin (Gua-46) and the Mid-Cayman Rise (MC-1). Based on average amino acid identity analysis, M10-121 is a novel species in the candidate genus Nanoclepta, while the other two MAGs represent novel genera in the Nanoarchaeota. Like previously sequenced Nanoarchaeota, each MAG encodes at least one split protein-coding gene. The MAGs also contain a mosaic of key nanoarchaeotal features, including CRISPR repeat regions and marker genes for gluconeogenesis and archaeal flagella. MC-1 also encodes the pentose bisphosphate pathway, which may allow the nanoarchaeote to bypass several steps in glycolysis and produce ATP. This article is protected by copyright. All rights reserved.}, }
@article {pmid30768641, year = {2019}, author = {Agga, GE and Cook, KL and Netthisinghe, AMP and Gilfillen, RA and Woosley, PB and Sistani, KR}, title = {Persistence of antibiotic resistance genes in beef cattle backgrounding environment over two years after cessation of operation.}, journal = {PloS one}, volume = {14}, number = {2}, pages = {e0212510}, doi = {10.1371/journal.pone.0212510}, pmid = {30768641}, issn = {1932-6203}, abstract = {Confined animal feeding operations can facilitate the spread of genes associated with antibiotic resistance. It is not known how cattle removal from beef cattle backgrounding operation affects the persistence of antibiotic resistance genes (ARGs) in the environment. We investigated the effect of cessation of beef cattle backgrounding operation on the persistence and distribution of ARGs in the beef cattle backgrounding environment. The study was conducted at a pasture-feedlot type beef cattle backgrounding operation which consisted of feeding and grazing areas that were separated by a fence with an access gate. Backgrounding occurred for seven years before cattle were removed from the facility. Soil samples (n = 78) from 26 georeferenced locations were collected at the baseline before cattle were removed, and then one year and two years after cattle were removed. Metagenomic DNA was extracted from the soil samples and total bacterial population (16S rRNA), total Enterococcus species and class 1 integrons (intI1), and erythromycin (ermB and ermF), sulfonamide (sul1 and sul2) and tetracycline (tetO, tetW and tetQ) resistance genes were quantified. Concentrations of total bacteria, Enterococcus spp., class 1 integrons, and ARGs were higher in the feeding area and its immediate vicinity (around the fence and the gate) followed by a gradient decline along the grazing area. Although the concentrations of total bacteria, Enterococcus spp., class 1 integrons and ARGs in the feeding area significantly decreased two years after cattle removal, their concentrations were still higher than that observed in the grazing area. Higher concentrations over two years in the feeding area when compared to the grazing area suggest a lasting effect of confined beef cattle production system on the persistence of bacteria and ARGs in the soil.}, }
@article {pmid30767012, year = {2019}, author = {Heller, RC and Chung, S and Crissy, K and Dumas, K and Schuster, D and Schoenfeld, TW}, title = {Engineering of a thermostable viral polymerase using metagenome-derived diversity for highly sensitive and specific RT-PCR.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkz104}, pmid = {30767012}, issn = {1362-4962}, abstract = {Reverse transcription is an essential initial step in the analysis of RNA for most PCR-based amplification and detection methods. Despite advancements in these technologies, efficient conversion of RNAs that form stable secondary structures and double-stranded RNA targets remains challenging as retroviral-derived reverse transcriptases are often not sufficiently thermostable to catalyze synthesis at temperatures high enough to completely relax these structures. Here we describe the engineering and improvement of a thermostable viral family A polymerase with inherent reverse transcriptase activity for use in RT-PCR. Using the 3173 PyroPhage polymerase, previously identified from hot spring metagenomic sampling, and additional thermostable orthologs as a source of natural diversity, we used gene shuffling for library generation and screened for novel variants that retain high thermostability and display elevated reverse transcriptase activity. We then created a fusion enzyme between a high-performing variant polymerase and the 5'→3' nuclease domain of Taq DNA polymerase that provided compatibility with probe-based detection chemistries and enabled highly sensitive detection of structured RNA targets. This technology enables a flexible single-enzyme RT-PCR system that has several advantages compared with standard heat-labile reverse transcription methods.}, }
@article {pmid30765765, year = {2019}, author = {Singhal, M and Turturice, BA and Manzella, CR and Ranjan, R and Metwally, AA and Theorell, J and Huang, Y and Alrefai, WA and Dudeja, PK and Finn, PW and Perkins, DL and Gill, RK}, title = {Serotonin Transporter Deficiency is Associated with Dysbiosis and Changes in Metabolic Function of the Mouse Intestinal Microbiome.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {2138}, doi = {10.1038/s41598-019-38489-8}, pmid = {30765765}, issn = {2045-2322}, support = {R01 DK109709//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; R01 DK071596/DK/NIDDK NIH HHS/United States ; R01 DK109709/DK/NIDDK NIH HHS/United States ; BX 002011//U.S. Department of Veterans Affairs (Department of Veterans Affairs)/ ; R01 DK92441//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; R01 DK054016/DK/NIDDK NIH HHS/United States ; R01 DK098170/DK/NIDDK NIH HHS/United States ; R01 DK092441/DK/NIDDK NIH HHS/United States ; F30 DK113703/DK/NIDDK NIH HHS/United States ; I01 BX000152/BX/BLRD VA/United States ; BX 000152//U.S. Department of Veterans Affairs (Department of Veterans Affairs)/ ; I01 BX002011/BX/BLRD VA/United States ; R01 HL138628/HL/NHLBI NIH HHS/United States ; F30 DK113703//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; R01 DK71596//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; R01 DK81858//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; R01 DK098170//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; R01 DK081858/DK/NIDDK NIH HHS/United States ; R01 DK54016//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; }, abstract = {Serotonin transporter (SERT) plays a critical role in regulating extracellular availability of serotonin (5-HT) in the gut and brain. Mice with deletion of SERT develop metabolic syndrome as they age. Changes in the gut microbiota are being increasingly implicated in Metabolic Syndrome and Diabetes. To investigate the relationship between the gut microbiome and SERT, this study assessed the fecal and cecal microbiome profile of 11 to 12 week-old SERT+/+ and SERT-/- mice. Microbial DNA was isolated, processed for metagenomics shotgun sequencing, and taxonomic and functional profiles were assessed. 34 differentially abundant bacterial species were identified between SERT+/+ and SERT-/-. SERT-/- mice displayed higher abundances of Bacilli species including genera Lactobacillus, Streptococcus, Enterococcus, and Listeria. Furthermore, SERT-/- mice exhibited significantly lower abundances of Bifidobacterium species and Akkermansia muciniphilia. Bacterial community structure was altered in SERT-/- mice. Differential abundance of bacteria was correlated with changes in host gene expression. Bifidobacterium and Bacilli species exhibited significant associations with host genes involved in lipid metabolism pathways. Our results show that SERT deletion is associated with dysbiosis similar to that observed in obesity. This study contributes to the understanding as to how changes in gut microbiota are associated with metabolic phenotype seen in SERT deficiency.}, }
@article {pmid30765709, year = {2019}, author = {Mizuno, CM and Guyomar, C and Roux, S and Lavigne, R and Rodriguez-Valera, F and Sullivan, MB and Gillet, R and Forterre, P and Krupovic, M}, title = {Numerous cultivated and uncultivated viruses encode ribosomal proteins.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {752}, doi = {10.1038/s41467-019-08672-6}, pmid = {30765709}, issn = {2041-1723}, abstract = {Viruses modulate ecosystems by directly altering host metabolisms through auxiliary metabolic genes. However, viral genomes are not known to encode the core components of translation machinery, such as ribosomal proteins (RPs). Here, using reference genomes and global-scale viral metagenomic datasets, we identify 14 different RPs across viral genomes arising from cultivated viral isolates and metagenome-assembled viruses. Viruses tend to encode dynamic RPs, easily exchangeable between ribosomes, suggesting these proteins can replace cellular versions in host ribosomes. Functional assays confirm that the two most common virus-encoded RPs, bS21 and bL12, are incorporated into 70S ribosomes when expressed in Escherichia coli. Ecological distribution of virus-encoded RPs suggests some level of ecosystem adaptations as aquatic viruses and viruses of animal-associated bacteria are enriched for different subsets of RPs. Finally, RP genes are under purifying selection and thus likely retained an important function after being horizontally transferred into virus genomes.}, }
@article {pmid30764497, year = {2019}, author = {Plaza-Díaz, J and Gómez-Fernández, A and Chueca, N and Torre-Aguilar, MJ and Gil, Á and Perez-Navero, JL and Flores-Rojas, K and Martín-Borreguero, P and Solis-Urra, P and Ruiz-Ojeda, FJ and Garcia, F and Gil-Campos, M}, title = {Autism Spectrum Disorder (ASD) with and without Mental Regression is Associated with Changes in the Fecal Microbiota.}, journal = {Nutrients}, volume = {11}, number = {2}, pages = {}, doi = {10.3390/nu11020337}, pmid = {30764497}, issn = {2072-6643}, support = {404 Research Grant INVEST from the Spanish Society of Pediatrics and Red de Salud Materno Infantil (RED SAMID)//FUNDACIÓ AGRUPACIÓ Àmbit de la Infància/ ; }, abstract = {New microbiome sequencing technologies provide novel information about the potential interactions among intestinal microorganisms and the host in some neuropathologies as autism spectrum disorders (ASD). The microbiota⁻gut⁻brain axis is an emerging aspect in the generation of autistic behaviors; evidence from animal models suggests that intestinal microbial shifts may produce changes fitting the clinical picture of autism. The aim of the present study was to evaluate the fecal metagenomic profiles in children with ASD and compare them with healthy participants. This comparison allows us to ascertain how mental regression (an important variable in ASD) could influence the intestinal microbiota profile. For this reason, a subclassification in children with ASD by mental regression (AMR) and no mental regression (ANMR) phenotype was performed. The present report was a descriptive observational study. Forty-eight children aged 2⁻6 years with ASD were included: 30 with ANMR and 18 with AMR. In addition, a control group of 57 normally developing children was selected and matched to the ASD group by sex and age. Fecal samples were analyzed with a metagenomic approach using a next-generation sequencing platform. Several differences between children with ASD, compared with the healthy group, were detected. Namely, Actinobacteria and Proteobacteria at phylum level, as well as, Actinobacteria, Bacilli, Erysipelotrichi, and Gammaproteobacteria at class level were found at higher proportions in children with ASD. Additionally, Proteobacteria levels showed to be augmented exclusively in AMR children. Preliminary results, using a principal component analysis, showed differential patterns in children with ASD, ANMR and AMR, compared to healthy group, both for intestinal microbiota and food patterns. In this study, we report, higher levels of Actinobacteria, Proteobacteria and Bacilli, aside from Erysipelotrichi, and Gammaproteobacteria in children with ASD compared to healthy group. Furthermore, AMR children exhibited higher levels of Proteobacteria. Further analysis using these preliminary results and mixing metagenomic and other "omic" technologies are needed in larger cohorts of children with ASD to confirm these intestinal microbiota changes.}, }
@article {pmid30763538, year = {2019}, author = {Gogokhia, L and Buhrke, K and Bell, R and Hoffman, B and Brown, DG and Hanke-Gogokhia, C and Ajami, NJ and Wong, MC and Ghazaryan, A and Valentine, JF and Porter, N and Martens, E and O'Connell, R and Jacob, V and Scherl, E and Crawford, C and Stephens, WZ and Casjens, SR and Longman, RS and Round, JL}, title = {Expansion of Bacteriophages Is Linked to Aggravated Intestinal Inflammation and Colitis.}, journal = {Cell host & microbe}, volume = {25}, number = {2}, pages = {285-299.e8}, doi = {10.1016/j.chom.2019.01.008}, pmid = {30763538}, issn = {1934-6069}, abstract = {Bacteriophages are the most abundant members of the microbiota and have the potential to shape gut bacterial communities. Changes to bacteriophage composition are associated with disease, but how phages impact mammalian health remains unclear. We noted an induction of host immunity when experimentally treating bacterially driven cancer, leading us to test whether bacteriophages alter immune responses. Treating germ-free mice with bacteriophages leads to immune cell expansion in the gut. Lactobacillus, Escherichia, and Bacteroides bacteriophages and phage DNA stimulated IFN-γ via the nucleotide-sensing receptor TLR9. The resultant immune responses were both phage and bacteria specific. Additionally, increasing bacteriophage levels exacerbated colitis via TLR9 and IFN-γ. Similarly, ulcerative colitis (UC) patients responsive to fecal microbiota transplantation (FMT) have reduced phages compared to non-responders, and mucosal IFN-γ positively correlates with bacteriophage levels. Bacteriophages from active UC patients induced more IFN-γ compared to healthy individuals. Collectively, these results indicate that bacteriophages can alter mucosal immunity to impact mammalian health.}, }
@article {pmid30761723, year = {2019}, author = {Nowinski, B and Motard-Côté, J and Landa, M and Preston, CM and Scholin, CA and Birch, JM and Kiene, RP and Moran, MA}, title = {Microdiversity and Temporal Dynamics of Marine Bacterial Dimethylsulfoniopropionate Genes.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14560}, pmid = {30761723}, issn = {1462-2920}, abstract = {Dimethylsulfoniopropionate (DMSP) is an abundant organic sulfur metabolite produced by many phytoplankton species and degraded by bacteria via two distinct pathways with climate-relevant implications. We assessed the diversity and abundance of bacteria possessing these pathways in the context of phytoplankton community composition over a three-week time period spanning September - October, 2014 in Monterey Bay, CA. The dmdA gene from the DMSP demethylation pathway dominated the DMSP gene pool and was harbored mostly by members of the alphaproteobacterial SAR11 clade and secondarily by the Roseobacter group, particularly during the second half of the study. Novel members of the DMSP-degrading community emerged from dmdA sequences recovered from metagenome assemblies and single-cell sequencing, including largely uncharacterized Gammaproteobacteria and Alphaproteobacteria taxa. In the DMSP cleavage pathway, the SAR11 gene dddK was the most abundant early in the study, but was supplanted by dddP over time. SAR11 members, especially those harboring genes for both DMSP degradation pathways, had a strong positive relationship with the abundance of dinoflagellates, and DMSP-degrading Gammaproteobacteria co-occurred with haptophytes. This in situ study of the drivers of DMSP fate in a coastal ecosystem demonstrates for the first time correlations between specific groups of bacterial DMSP degraders and phytoplankton taxa. This article is protected by copyright. All rights reserved.}, }
@article {pmid30761333, year = {2018}, author = {Kachiprath, B and Puthumana, J and Gopi, J and Solomon, S and Krishnan, KP and Philip, R}, title = {Amplicon sequencing based profiling of bacterial diversity from Krossfjorden, Arctic.}, journal = {Data in brief}, volume = {21}, number = {}, pages = {2522-2525}, doi = {10.1016/j.dib.2018.11.101}, pmid = {30761333}, issn = {2352-3409}, abstract = {In this study, Illumina Miseq sequencing of 16S rRNA gene amplicon was performed on sediments collected from Krossfjorden, Arctic for analyzing the bacterial community structure. Metagenome contained 15,936 sequences with 5,809,491 bp size and 53% G+C content. Metagenome sequence information are now available at NCBI under the Sequence Read Archive (SRA) database with accession no. SRP159159. Taxonomic hits distribution from MG-RAST analysis revealed the dominance of Alpha- and Gamma-subdivisions of Proteobacteria (88.89%) along with Bacteriodetes (8.89%) and Firmicutes (2.22%). Predominant species were Alteromonadales bacterium TW-7 (24%), Pseudoalteromonas haloplanktis (20%) and Pseudoalteromonas spp. SM9913 (18%). MG-RAST assisted analysis also detected the presence of a variety of marine taxa like Bacteriodes, Pseudovibrio, Marinobacter, Idiomarina, Teredinibacter, etc. which take part in key ecological functions and biogeochemical activities of Arctic fjord ecosystems.}, }
@article {pmid30761142, year = {2019}, author = {Kim, M and Gu, B and Madison, MC and Song, HW and Norwood, K and Hill, AA and Wu, WJ and Corry, D and Kheradmand, F and Diehl, GE}, title = {Cigarette Smoke Induces Intestinal Inflammation via a Th17 Cell-Neutrophil Axis.}, journal = {Frontiers in immunology}, volume = {10}, number = {}, pages = {75}, doi = {10.3389/fimmu.2019.00075}, pmid = {30761142}, issn = {1664-3224}, abstract = {Epidemiological evidence finds cigarette smoking is a common risk factor for a number of diseases, not only in the lung but also in other tissues, such as the gastrointestinal tract. While it is well-documented that smoking directly drives lung inflammatory disease, how it promotes disease in peripheral tissues is incompletely understood. In this study, we utilized a mouse model of short-term smoke exposure and found increased Th17 cells and neutrophilia in the lung as well as in the circulation. Following intestinal inflammatory challenge, smoke exposed mice showed increased pathology which corresponds to enhanced intestinal Th17 cells, ILC3 and neutrophils within intestinal tissue. Using cellular depletion and genetic deficiencies, we define a cellular loop by which IL-17A and downstream neutrophils drive cigarette smoke-enhanced intestinal inflammation. Collectively, cigarette smoke induced local lung Th17 responses lead to increased systemic susceptibility to inflammatory insult through enhanced circulating neutrophils. These data demonstrate a cellular pathway by which inflammatory challenge in the lung can sensitize the intestine to enhanced pathological innate and adaptive immune responses.}, }
@article {pmid30761108, year = {2019}, author = {Ulloa, R and Moya-Beltrán, A and Rojas-Villalobos, C and Nuñez, H and Chiacchiarini, P and Donati, E and Giaveno, A and Quatrini, R}, title = {Domestication of Local Microbial Consortia for Efficient Recovery of Gold Through Top-Down Selection in Airlift Bioreactors.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {60}, doi = {10.3389/fmicb.2019.00060}, pmid = {30761108}, issn = {1664-302X}, abstract = {Extreme acidophiles play central roles in the geochemical cycling of diverse elements in low pH environments. This has been harnessed in biotechnologies such as biomining, where microorganisms facilitate the recovery of economically important metals such as gold. By generating both extreme acidity and a chemical oxidant (ferric iron) many species of prokaryotes that thrive in low pH environments not only catalyze mineral dissolution but also trigger both community and individual level adaptive changes. These changes vary in extent and direction depending on the ore mineralogy, water availability and local climate. The use of indigenous versus introduced microbial consortia in biomining practices is still a matter of debate. Yet, indigenous microbial consortia colonizing sulfidic ores that have been domesticated, i.e., selected for their ability to survive under specific polyextreme conditions, are claimed to outperform un-adapted foreign consortia. Despite this, little is known on the domestication of acidic microbial communities and the changes elicited in their members. In this study, high resolution targeted metagenomic techniques were used to analyze the changes occurring in the community structure of local microbial consortia acclimated to growing under extreme acidic conditions and adapted to endure the conditions imposed by the target mineral during biooxidation of a gold concentrate in an airlift reactor over a period of 2 years. The results indicated that operative conditions evolving through biooxidation of the mineral concentrate exerted strong selective pressures that, early on, purge biodiversity in favor of a few Acidithiobacillus spp. over other iron oxidizing acidophiles. Metagenomic analysis of the domesticated consortium present at the end of the adaptation experiment enabled reconstruction of the RVS1-MAG, a novel representative of Acidithiobacillus ferrooxidans from the Andacollo gold mineral district. Comparative genomic analysis performed with this genome draft revealed a net enrichment of gene functions related to heavy metal transport and stress management that are likely to play a significant role in adaptation and survival to adverse conditions experienced by these acidophiles during growth in presence of gold concentrates.}, }
@article {pmid30761104, year = {2019}, author = {Quan, J and Cai, G and Yang, M and Zeng, Z and Ding, R and Wang, X and Zhuang, Z and Zhou, S and Li, S and Yang, H and Li, Z and Zheng, E and Huang, W and Yang, J and Wu, Z}, title = {Exploring the Fecal Microbial Composition and Metagenomic Functional Capacities Associated With Feed Efficiency in Commercial DLY Pigs.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {52}, doi = {10.3389/fmicb.2019.00052}, pmid = {30761104}, issn = {1664-302X}, abstract = {Gut microbiota has indispensable roles in nutrient digestion and energy harvesting, especially in processing the indigestible components of dietary polysaccharides. Searching for the microbial taxa and functional capacity of the gut microbiome associated with feed efficiency (FE) can provide important knowledge to increase profitability and sustainability of the swine industry. In the current study, we performed a comparative analysis of the fecal microbiota in 50 commercial Duroc × (Landrace × Yorkshire) (DLY) pigs with polarizing FE using 16S rRNA gene sequencing and shotgun metagenomic sequencing. There was a different microbial community structure in the fecal microbiota of pigs with different FE. Random forest analysis identified 24 operational taxonomic units (OTUs) as potential biomarkers to improve swine FE. Multiple comparison analysis detected 8 OTUs with a significant difference or tendency toward a difference between high- and low-FE pigs (P < 0.01, q < 0.1). The high-FE pigs had a greater abundance of OTUs that were from the Lachnospiraceae and Prevotellaceae families and the Escherichia-Shigella and Streptococcus genera than low-FE pigs. A sub-species Streptococcus gallolyticus subsp. gallolyticus could be an important candidate for improving FE. The functional capacity analysis found 18 KEGG pathways and CAZy EC activities that were different between high- and low-FE pigs. The fecal microbiota in high FE pigs have greater functional capacity to degrade dietary cellulose, polysaccharides, and protein and may have a greater abundance of microbes that can promote intestinal health. These results provided insights for improving porcine FE through modulating the gut microbiome.}, }
@article {pmid30759800, year = {2019}, author = {Tremblay, ÉD and Kimoto, T and Bérubé, JA and Bilodeau, GJ}, title = {High-Throughput Sequencing to Investigate Phytopathogenic Fungal Propagules Caught in Baited Insect Traps.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {5}, number = {1}, pages = {}, doi = {10.3390/jof5010015}, pmid = {30759800}, issn = {2309-608X}, support = {OLF-P-1304, GRDI, QIS and CFIA OFL-P-1411, Genome Canada, and Genome BC (LSARP2112), CFIA-RPS and CFIA-TD and GRDI-CFIA mandated//Canadian Food Inspection Agency/ ; }, abstract = {Studying the means of dispersal of plant pathogens is crucial to better understand the dynamic interactions involved in plant infections. On one hand, entomologists rely mostly on both traditional molecular methods and morphological characteristics, to identify pests. On the other hand, high-throughput sequencing (HTS) is becoming the go-to avenue for scientists studying phytopathogens. These organisms sometimes infect plants, together with insects. Considering the growing number of exotic insect introductions in Canada, forest pest-management efforts would benefit from the development of a high-throughput strategy to investigate the phytopathogenic fungal and oomycete species interacting with wood-boring insects. We recycled formerly discarded preservative fluids from the Canadian Food Inspection Agency annual survey using insect traps and analysed more than one hundred samples originating from across Canada. Using the Ion Torrent Personal Genome Machine (PGM) HTS technology and fusion primers, we performed metabarcoding to screen unwanted fungi and oomycetes species, including Phytophthora spp. Community profiling was conducted on the four different wood-boring, insect-attracting semiochemicals; although the preservative (contained ethanol) also attracted other insects. Phytopathogenic fungi (e.g., Leptographium spp. and Merialaricis in the pine sawyer semiochemical) and oomycetes (mainly Peronospora spp. and Pythium aff. hypogynum in the General Longhorn semiochemical), solely associated with one of the four types of semiochemicals, were detected. This project demonstrated that the insect traps' semiochemical microbiome represents a new and powerful matrix for screening phytopathogens. Compared to traditional diagnostic techniques, the fluids allowed for a faster and higher throughput assessment of the biodiversity contained within. Additionally, minimal modifications to this approach would allow it to be used in other phytopathology fields.}, }
@article {pmid30759613, year = {2019}, author = {Wang, X and Li, X and Yu, L and Huang, L and Xiu, J and Lin, W and Zhang, Y}, title = {Characterizing the microbiome in petroleum reservoir flooded by different water sources.}, journal = {The Science of the total environment}, volume = {653}, number = {}, pages = {872-885}, doi = {10.1016/j.scitotenv.2018.10.410}, pmid = {30759613}, issn = {1879-1026}, abstract = {Petroleum reservoir is an unusual subsurface biosphere, where indigenous microbes lived and evolved for million years. However, continual water injection changed the situation by introduction of new electron acceptors, donors and exogenous microbes. In this study, 16S-rRNA gene sequencing, comparative metagenomics and genomic bins reconstruction were employed to investigate the microbial community and metabolic potential in three typical water-flooded blocks of the Shen84 oil reservoir in Liaohe oil field, China. The results showed significant difference of microbial community compositions and metabolic characteristics existed between the injected water and the produced water/oil mixtures; however, there was considerable uniformity between the produced samples in different blocks. Microbial communities in the produced fluids were dominated by exogenous facultative microbes such as Pseudomonas and Thauera members from Proteobacteria phylum. Metabolic potentials for O2-dependent hydrocarbon degradation, dissimilarly nitrate reduction, and thiosulfate‑sulfur oxidation were much more abundant, whereas genes involved in dissimilatory sulfate reduction, anaerobic hydrocarbon degradation and methanogenesis were less abundant in the oil reservoir. Statistical analysis indicated the water composition had an obvious influence on microbial community composition and metabolic potential. The water-flooding process accompanied with introduction of nitrate or nitrite, and dissolved oxygen promoted the alteration of microbiome in oil reservoir from slow-growing anaerobic indigenous microbes (such as Thermotoga, Clostridia, and Syntrophobacter) to fast-growing opportunists as Beta- and Gama- Proteobacteria. The findings of this study shed light on the microbial ecology change in water flooded petroleum reservoir.}, }
@article {pmid30759585, year = {2019}, author = {Chen, H and Bai, X and Jing, L and Chen, R and Teng, Y}, title = {Characterization of antibiotic resistance genes in the sediments of an urban river revealed by comparative metagenomics analysis.}, journal = {The Science of the total environment}, volume = {653}, number = {}, pages = {1513-1521}, doi = {10.1016/j.scitotenv.2018.11.052}, pmid = {30759585}, issn = {1879-1026}, abstract = {The over-use of antibiotics causes growing concerns about human health risks induced by increasing rates of antimicrobial resistance. Riverine systems are considered generally as a natural reservoir of antibiotic resistance genes (ARGs). In this study, several methods including high-throughput sequencing-based metagenomics approach, statistical analysis and network analysis were applied jointly to characterize the wide-spectrum profile of ARGs in the sediments of an urban river in Beijing. Furthermore, contribution of human activities for the presence of ARGs was identified through comparative studies on the metagenomic profiling of ARGs between the river sediments and pristine niches (remote Antarctic soils and deep sea sediments). In total, 442 ARG subtypes belonging to 22 ARG types were detected in the human-impacted river sediments with an abundance range of 1.1 × 10-1-8.1 × 10-1 copy of ARG per copy of 16S-rRNA gene. The most abundant and diverse ARGs were commonly associated with antibiotics that have been extensively used in that area, likely indicating the spread of ARGs in river environments because of the selective pressure resulting from antibiotic use. As a whole, anthropogenic activities were the dominant contributor of major ARG types, for example, occupying 100% for sulfonamide-ARGs, 97% for beta-lactam-ARGs, 94% for aminoglycoside-ARGs and 64% for tetracycline-ARGs. This study provides insights into the role of human activities in accelerating the dissemination and proliferation of ARGs in urban river environment and draws attention to controlling the use and discharge of antibiotics for protection of public health.}, }
@article {pmid30758305, year = {2019}, author = {Farhat, M and Alkharsah, KR and Alkhamis, FI and Bukharie, HA}, title = {Metagenomic study on the composition of culturable and non-culturable bacteria in tap water and biofilms at intensive care units.}, journal = {Journal of water and health}, volume = {17}, number = {1}, pages = {72-83}, doi = {10.2166/wh.2018.213}, pmid = {30758305}, issn = {1477-8920}, abstract = {Bacterial community diversity of bulk water and corresponding biofilms of four intensive care units' (ICUs) drinking water systems were studied and compared using 16S rRNA gene amplicons and next generation sequencing. Proteobacteria, mainly Alphaproteobacteria and Betaproteobacteria were dominant in the bulk water and biofilms. Principal component analysis showed different bacterial communities characterizing each of the bulk water and the biofilms in three of the studied ICUs. Taxonomic classification and comparison of different genera between samples highlighted the dominance of Aquabacterium (80%) and Novosphingobium (72%) in bulk water while biofilms harbored different bacteria affiliated to Pelomonas (97%) and Caulobacter (96%), Porphyrobacter (78%) and Staphylococcus (74%). Staphylococcus aureus was the only possible pathogen found with low percentage (2.32%) in three of the ICUs' biofilm and only in one of the ICU's bulk water. This study sheds light on the prevalence of unculturable bacterial flora in the biofilm ignored by the microbiological standard methods. This study was performed on tap and bulk water from ICUs; however, it indicates the need for further studies to investigate the function and activity of the microbial diversity in order to assess the real risk presented by this water microflora on patients' health.}, }
@article {pmid30755848, year = {2019}, author = {Huang, Z and Zhang, C and Li, W and Fang, X and Wang, Q and Xing, L and Li, Y and Nie, X and Yang, B and Zhang, W}, title = {Metagenomic next-generation sequencing contribution in identifying prosthetic joint infection due to Parvimonas micra: a case report.}, journal = {Journal of bone and joint infection}, volume = {4}, number = {1}, pages = {50-55}, doi = {10.7150/jbji.30615}, pmid = {30755848}, issn = {2206-3552}, abstract = {Identifying fastidious pathogens in patients with prosthetic joint infection (PJI) by culture is challenging. Metagenomic next-generation sequencing (mNGS) is a novel culture-independent approach that is associated with a higher likelihood for identifying pathogens. We present a case where mNGS was implemented to identify Parvimonas micra, a rarely reported and difficult-to-culture PJI pathogen.}, }
@article {pmid30755506, year = {2019}, author = {Hausmann, B and Pelikan, C and Rattei, T and Loy, A and Pester, M}, title = {Long-Term Transcriptional Activity at Zero Growth of a Cosmopolitan Rare Biosphere Member.}, journal = {mBio}, volume = {10}, number = {1}, pages = {}, doi = {10.1128/mBio.02189-18}, pmid = {30755506}, issn = {2150-7511}, abstract = {Microbial diversity in the environment is mainly concealed within the rare biosphere (all species with <0.1% relative abundance). While dormancy explains a low-abundance state very well, the mechanisms leading to rare but active microorganisms remain elusive. We used environmental systems biology to genomically and transcriptionally characterize "Candidatus Desulfosporosinus infrequens," a low-abundance sulfate-reducing microorganism cosmopolitan to freshwater wetlands, where it contributes to cryptic sulfur cycling. We obtained its near-complete genome by metagenomics of acidic peat soil. In addition, we analyzed anoxic peat soil incubated under in situ-like conditions for 50 days by Desulfosporosinus-targeted qPCR and metatranscriptomics. The Desulfosporosinus population stayed at a constant low abundance under all incubation conditions, averaging 1.2 × 106 16S rRNA gene copies per cm³ soil. In contrast, transcriptional activity of "Ca. Desulfosporosinus infrequens" increased at day 36 by 56- to 188-fold when minor amendments of acetate, propionate, lactate, or butyrate were provided with sulfate, compared to the no-substrate-control. Overall transcriptional activity was driven by expression of genes encoding ribosomal proteins, energy metabolism, and stress response but not by expression of genes encoding cell growth-associated processes. Since our results did not support growth of these highly active microorganisms in terms of biomass increase or cell division, they had to invest their sole energy for maintenance, most likely counterbalancing acidic pH conditions. This finding explains how a rare biosphere member can contribute to a biogeochemically relevant process while remaining in a zero-growth state over a period of 50 days.IMPORTANCE The microbial rare biosphere represents the largest pool of biodiversity on Earth and constitutes, in sum of all its members, a considerable part of a habitat's biomass. Dormancy or starvation is typically used to explain the persistence of low-abundance microorganisms in the environment. We show that a low-abundance microorganism can be highly transcriptionally active while remaining in a zero-growth state for at least 7 weeks. Our results provide evidence that this zero growth at a high cellular activity state is driven by maintenance requirements. We show that this is true for a microbial keystone species, in particular a cosmopolitan but permanently low-abundance sulfate-reducing microorganism in wetlands that is involved in counterbalancing greenhouse gas emissions. In summary, our results provide an important step forward in understanding time-resolved activities of rare biosphere members relevant for ecosystem functions.}, }
@article {pmid30755154, year = {2019}, author = {Cronin, O and Barton, W and Moran, C and Sheehan, D and Whiston, R and Nugent, H and McCarthy, Y and Molloy, CB and O'Sullivan, O and Cotter, PD and Molloy, MG and Shanahan, F}, title = {Moderate-intensity aerobic and resistance exercise is safe and favorably influences body composition in patients with quiescent Inflammatory Bowel Disease: a randomized controlled cross-over trial.}, journal = {BMC gastroenterology}, volume = {19}, number = {1}, pages = {29}, doi = {10.1186/s12876-019-0952-x}, pmid = {30755154}, issn = {1471-230X}, support = {N/a//Irish Centre for Arthritis Research and Education/ ; SFI/12/RC/2273//Science Foundation Ireland/Ireland ; 11/PI/1137//Science Foundation Ireland/Ireland ; 13/SIRG/2160//Science Foundation Ireland/Ireland ; 13/SIRG/2160//Science Foundation Ireland/Ireland ; }, mesh = {Adult ; Affect ; *Body Composition ; Body Mass Index ; Cross-Over Studies ; Cytokines/blood ; *Exercise ; Female ; Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/*complications/immunology/microbiology/psychology ; Male ; Overweight/*complications/*therapy ; Prospective Studies ; Quality of Life ; *Resistance Training/adverse effects ; Young Adult ; }, abstract = {BACKGROUND: Overweight and metabolic problems now add to the burden of illness in patients with Inflammatory Bowel Disease. We aimed to determine if a program of aerobic and resistance exercise could safely achieve body composition changes in patients with Inflammatory Bowel Disease.
METHODS: A randomized, cross-over trial of eight weeks combined aerobic and resistance training on body composition assessed by Dual Energy X-ray Absorptiometry was performed. Patients in clinical remission and physically inactive with a mean age of 25 ± 6.5 years and Body Mass Index of 28.9 ± 3.8 were recruited from a dedicated Inflammatory Bowel Disease clinic. Serum cytokines were quantified, and microbiota assessed using metagenomic sequencing.
RESULTS: Improved physical fitness was demonstrated in the exercise group by increases in median estimated VO2max (Baseline: 43.41mls/kg/min; post-intervention: 46.01mls/kg/min; p = 0.03). Improvement in body composition was achieved by the intervention group (n = 13) with a median decrease of 2.1% body fat compared with a non-exercising group (n = 7) (0.1% increase; p = 0.022). Lean tissue mass increased by a median of 1.59 kg and fat mass decreased by a median of 1.52 kg in the exercising group. No patients experienced a deterioration in disease activity scores during the exercise intervention. No clinically significant alterations in the α- and β-diversity of gut microbiota and associated metabolic pathways were evident.
CONCLUSIONS: Moderate-intensity combined aerobic and resistance training is safe in physically unfit patients with quiescent Inflammatory Bowel Disease and can quickly achieve favourable body compositional changes without adverse effects.
TRIAL REGISTRATION: The study was registered at ClinicalTrials.gov; Trial number: NCT02463916 .}, }
@article {pmid30748086, year = {2019}, author = {Piel, J and Cahn, J}, title = {Opening up the Single-Cell Toolbox for Microbial Natural Products Research.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {}, number = {}, pages = {}, doi = {10.1002/anie.201900532}, pmid = {30748086}, issn = {1521-3773}, abstract = {The diverse microbes that produce natural products represent an important source of novel therapeutics, drug leads, and scientific tools. However, the vast majority have not been grown in axenic culture and are members of complex communities. While meta-'omic methods such as metagenomics, -transcriptomics, and -proteomics reveal collective molecular features of "microbial dark matter", the study of individual microbiome members can be challenging. To address these limits, a number of techniques with single-bacterial resolution have been developed in the last decade-and-a-half. While several of these were embraced by microbial ecologists, there has been less use by researchers interested in mining microbes for natural products. In this review, we discuss the available and emerging techniques for targeted single-cell analysis with a particular focus on applications to the discovery and study of natural products.}, }
@article {pmid30747914, year = {2019}, author = {Gastauer, M and Vera, MPO and de Souza, KP and Pires, ES and Alves, R and Caldeira, CF and Ramos, SJ and Oliveira, G}, title = {A metagenomic survey of soil microbial communities along a rehabilitation chronosequence after iron ore mining.}, journal = {Scientific data}, volume = {6}, number = {}, pages = {190008}, doi = {10.1038/sdata.2019.8}, pmid = {30747914}, issn = {2052-4463}, abstract = {Microorganisms are useful environmental indicators, able to deliver essential insights to processes regarding mine land rehabilitation. To compare microbial communities from a chronosequence of mine land rehabilitation to pre-disturbance levels from references sites covered by native vegetation, we sampled non-rehabilitated, rehabilitating and reference study sites from the Urucum Massif, Southwestern Brazil. From each study site, three composed soil samples were collected for chemical, physical, and metagenomics analysis. We used a paired-end library sequencing technology (NextSeq 500 Illumina); the reads were assembled using MEGAHIT. Coding DNA sequences (CDS) were identified using Kaiju in combination with non-redundant NCBI BLAST reference sequences containing archaea, bacteria, and viruses. Additionally, a functional classification was performed by EMG v2.3.2. Here, we provide the raw data and assembly (reads and contigs), followed by initial functional and taxonomic analysis, as a base-line for further studies of this kind. Further investigation is needed to fully understand the mechanisms of environmental rehabilitation in tropical regions, inspiring further researchers to explore this collection for hypothesis testing.}, }
@article {pmid30746561, year = {2019}, author = {Liu, C and Li, M and Redda, ET and Mei, J and Zhang, J and Elena, SF and Wu, B and Jiang, X}, title = {Complete nucleotide sequence of a novel mycovirus from Trichoderma harzianum in China.}, journal = {Archives of virology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00705-019-04145-9}, pmid = {30746561}, issn = {1432-8798}, support = {2017YFD0201100-2017YFD0201102//Research and demonstration of a new high efficiency biocide/ ; 2018YFD0201200-2018YFD0201202//Research and demonstration of technology integration on reducing chemical fertilizer and pesticide application in open field vegetables/ ; SQ2018YFD080026//Demonstration of comprehensive prevention and control technology of non-point source pollution in main vegetable producing areas of Huang Huai Hai/ ; BFU2015-65037-P//Spain's Agencia Estatal de Investigación - FEDER grant BFU2015-65037-P/ ; }, abstract = {A new mycovirus was identified in Trichoderma harzianum strain 137 isolated in Xinjiang province, China. The whole genome sequence of the mycovirus was determined by metagenomic sequencing, RT-PCR, and RACE cloning. The mycovirus contained two genomic segments. The first segment was 2088 bp long and contained a single ORF (ORF1) encoding the RNA-dependent RNA polymerase (RdRP) (72.26 kDa). The second segment was 1634 bp long and also contained a single ORF (ORF2) encoding a hypothetical protein of 37.472 kDa. We named this novel mycovirus "Trichoderma harzianum bipartite mycovirus 1" (ThBMV1). Phylogenetic analysis showed that ThBMV1 clusters with other unclassified dsRNA mycoviruses.}, }
@article {pmid30746494, year = {2019}, author = {Tecon, R and Mitri, S and Ciccarese, D and Or, D and van der Meer, JR and Johnson, DR}, title = {Bridging the Holistic-Reductionist Divide in Microbial Ecology.}, journal = {mSystems}, volume = {4}, number = {1}, pages = {}, doi = {10.1128/mSystems.00265-18}, pmid = {30746494}, issn = {2379-5077}, abstract = {Microbial communities are inherently complex systems. To address this complexity, microbial ecologists are developing new, more elaborate laboratory models at an ever-increasing pace. These model microbial communities and habitats have opened up the exploration of new territories that lie between the simplicity and controllability of "synthetic" systems and the convolution and complexity of natural environments. Here, we discuss this classic methodological divide, we propose a conceptual perspective that integrates new research developments, and we sketch a 3-point possible roadmap to cross the divide between controllability and complexity in microbial ecology.}, }
@article {pmid30745586, year = {2019}, author = {Almeida, A and Mitchell, AL and Boland, M and Forster, SC and Gloor, GB and Tarkowska, A and Lawley, TD and Finn, RD}, title = {A new genomic blueprint of the human gut microbiota.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41586-019-0965-1}, pmid = {30745586}, issn = {1476-4687}, abstract = {The composition of the human gut microbiota is linked to health and disease, but knowledge of individual microbial species is needed to decipher their biological roles. Despite extensive culturing and sequencing efforts, the complete bacterial repertoire of the human gut microbiota remains undefined. Here we identify 1,952 uncultured candidate bacterial species by reconstructing 92,143 metagenome-assembled genomes from 11,850 human gut microbiomes. These uncultured genomes substantially expand the known species repertoire of the collective human gut microbiota, with a 281% increase in phylogenetic diversity. Although the newly identified species are less prevalent in well-studied populations compared to reference isolate genomes, they improve classification of understudied African and South American samples by more than 200%. These candidate species encode hundreds of newly identified biosynthetic gene clusters and possess a distinctive functional capacity that might explain their elusive nature. Our work expands the known diversity of uncultured gut bacteria, which provides unprecedented resolution for taxonomic and functional characterization of the intestinal microbiota.}, }
@article {pmid30744870, year = {2019}, author = {Lin, S and Han, Y and Jiangyuan, C and Luo, Y and Xu, W and Luo, H and Pang, G}, title = {Revealing the biodiversity and the response of pathogen to a combined use of procymidone and thiamethoxam in tomatoes.}, journal = {Food chemistry}, volume = {284}, number = {}, pages = {73-79}, doi = {10.1016/j.foodchem.2019.01.094}, pmid = {30744870}, issn = {1873-7072}, abstract = {The dissipation kinetics of a combined use of procymidone and thiamethoxam, and their impact on the biodiversity and pathogen on surface of tomatoes were studied. The half-lives of procymidone and thiamethoxam, used either on their own or in combination with each other, were 2.94 or 3.26 days and 2.41 or 2.67 days, respectively. The residues dropped below the maximum residue limit (MRL) after 7 or 10 days (MRL 2 mg·kg-1 for procymidone), and 10 or 14 days (MRL 0.2 mg·kg-1 for thiamethoxam), respectively. The phylum Bacteroidetes, Cyanobacteria, and Proteobacteria, were dominantly present in all studied samples. The genus Escherichia-Shigella was found and exposed to the dissipation of procymidone (r = -0.9209 for procymidone on its own, and r = -0.8611 for procymidone in combination with thiamethoxam). These results will contribute to establish adequate monitoring of pesticides residues and their incorporation in surface ecology and pathogen management strategies in tomatoes.}, }
@article {pmid30744159, year = {2019}, author = {Ribeiro, GO and Monteiro, FJC and Rego, MODS and Ribeiro, ESD and Castro, DF and Caseiro, MM and Souza Marinho, RDS and Komninakis, SV and Witkin, SS and Deng, X and Delwart, E and Sabino, EC and da Costa, AC and Leal, É}, title = {Detection of RNA-Dependent RNA Polymerase of Hubei Reo-Like Virus 7 by Next-Generation Sequencing in Aedes aegypti and Culex quinquefasciatus Mosquitoes from Brazil.}, journal = {Viruses}, volume = {11}, number = {2}, pages = {}, doi = {10.3390/v11020147}, pmid = {30744159}, issn = {1999-4915}, support = {2016/01735-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 400354/2016-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {Advancements in next-generation sequencing and bioinformatics have expanded our knowledge of the diversity of viruses (pathogens and non-pathogens) harbored by mosquitoes. Hubei reo-like virus 7 (HRLV 7) was recently detected by the virome analysis of fecal samples from migratory birds in Australia. We now report the detection of RNA-dependent RNA polymerase sequences of HRLV 7 in pools of Aedes aegypti and Culex quinquefasciatus mosquitoes species from the Brazilian Amazon forest. Phylogenetic inferences indicated that all HRLV 7 strains fall within the same independent clade. In addition, HRLV 7 shared a close ancestral lineage with the Dinovernavirus genus of the Reoviridae family. Our findings indicate that HRLV 7 is present in two species of mosquitoes.}, }
@article {pmid30743828, year = {2018}, author = {Lai, CY and Dong, QY and Zhao, HP}, title = {Oxygen exposure deprives antimonate-reducing capability of a methane fed biofilm.}, journal = {The Science of the total environment}, volume = {644}, number = {}, pages = {1152-1159}, doi = {10.1016/j.scitotenv.2018.07.047}, pmid = {30743828}, issn = {1879-1026}, mesh = {Antimony/*metabolism ; Biofilms ; Bioreactors/*microbiology ; Methane/*metabolism ; Oxygen/metabolism ; Waste Disposal, Fluid/methods ; }, abstract = {This work is aiming at achieving antimonate (Sb(V)) bio-reduction in a methane (CH4) based membrane biofilm reactor (MBfR), and elucidating the effect of oxygen (O2) on the performance of the biofilm. Scanning electron microscope (SEM), energy dispersive X-ray (EDS) and X-ray photoelectron spectroscopy (XPS) confirm Sb2O3 precipitates were the main product formed from Sb(V) reduction in the CH4-fed biofilm. Illumina sequencing shows Thermomonas may be responsible for Sb(V) reduction. Moreover, we found 8 mg/L of O2 in the influent irreversibly inhibited Sb(V) reduction. Metagenomic prediction by Reconstruction of Unobserved State (PICRUSt) shows that the biofilm lacked efficient defense system to the oxidative stress, leading to the great suppress of key biological metabolisms such as TCA cycle, glycolysis and DNA replication, as well as potential Sb(V) reductases, by O2. However, methanotrophs Methylomonas and Methylosinus were enriched in the biofilm with O2 intrusion, in accordance with the enhanced abundance of genes encoding aerobic CH4 oxidation. These insights evoke the theoretical guidance of microbial remediation using CH4 as the electron donor towards Sb(V) contamination, and will give us a strong reference with regard to wastewater disposal.}, }
@article {pmid30743822, year = {2018}, author = {Liu, T and Cui, C and He, J and Tang, J}, title = {Insights into the succession of the bacterial microbiota during biodrying of storage sludge mixed with beer lees: Studies on its biodiversity, structure, associations, and functionality.}, journal = {The Science of the total environment}, volume = {644}, number = {}, pages = {1088-1100}, doi = {10.1016/j.scitotenv.2018.06.298}, pmid = {30743822}, issn = {1879-1026}, mesh = {Beer ; *Biodiversity ; *Microbiota ; Phylogeny ; Waste Disposal, Fluid/*methods ; }, abstract = {Biodrying was first used for post-treatment of storage sludge mixed with beer lees. In this study, dynamic changes in dissolved organic matter (DOM), bacterial community structure, bacterial associations as well as metabolic functions were investigated using Excitation-Emission Matrix (EEM) spectra, high-throughput sequencing, network and correlation matrix analyses, and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Furthermore, a hypothetical model was proposed to better understand the biodrying process. The results showed that desired performance was obtained and DOM variations revealed that biodrying can increase biostability of the matrix. The bacterial communities differed among different stages of the biodrying. At the phylum level, the dominant phyla were Proteobacteria and Bacteroidetes in the mesophilic and cooling phases, whereas Firmicutes became the most dominant phylum in the thermophilic phase. At the genus level, the dominant bacteria in the mesophilic and cooling phases were not obvious, while Ureibacillus and Bacillus were the dominant genera in the thermophilic phase. Network and correlation matrix analyses were useful tools for insights into the bacterial interactions. PICRUSt metagenome inference indicated that metabolism, genetic information processing, and environmental information processing were the primary metabolic pathways. These results allowed us to advance a hypothetical model explaining how succession in bacterial associations regulates the dynamics of a biodrying system.}, }
@article {pmid30742684, year = {2019}, author = {You, SH and Lim, HD and Cheong, DE and Kim, ES and Kim, GJ}, title = {Rapid and sensitive detection of NADPH via mBFP-mediated enhancement of its fluorescence.}, journal = {PloS one}, volume = {14}, number = {2}, pages = {e0212061}, doi = {10.1371/journal.pone.0212061}, pmid = {30742684}, issn = {1932-6203}, abstract = {The reduced form of nicotinamide adenine dinucleotide phosphate (NADPH) functions as a reducing agent involved in many biosynthetic and antioxidant reactions in cells. Therefore, a lots of detection or assaying method of this cofactor are developed and used broadly in various research and application fields. These detection or assay tools, however, have often some problems, such as the low sensitivity, susceptibility to environmental interference and time-consuming pretreatment steps, remaining hurdle to successful quantification of NADPH or its derivatives accurately and immediately. Herein, we present a rapid (assay time < 30 s) and sensitive (detection limit < 2 pmol) detection method of NADPH using metagenome-derived blue fluorescent protein (mBFP), a protein capable of significantly enhancing NADPH fluorescence upon binding to this cofactor. Our method takes advantage of the high specificity of mBFP to NADPH and the immediate fluorescence enhancement upon the addition of mBFP to a solution of interest containing NADPH. We can apply this detection scheme to directly quantitative assessment of NADP(H)-dependent enzyme activities in-vitro, and further accessed to quantitative assay of other nicotine amide cofactors, such as NAD+ and NADH, by coupling assay using NAD(H) kinase. Thus, our method enabled us to quantitatively assess the activity of nicotinamide cofactor-associated enzymes in both bacterial and human cell lysates.}, }
@article {pmid30742071, year = {2019}, author = {Blauwkamp, TA and Thair, S and Rosen, MJ and Blair, L and Lindner, MS and Vilfan, ID and Kawli, T and Christians, FC and Venkatasubrahmanyam, S and Wall, GD and Cheung, A and Rogers, ZN and Meshulam-Simon, G and Huijse, L and Balakrishnan, S and Quinn, JV and Hollemon, D and Hong, DK and Vaughn, ML and Kertesz, M and Bercovici, S and Wilber, JC and Yang, S}, title = {Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41564-018-0349-6}, pmid = {30742071}, issn = {2058-5276}, abstract = {Thousands of pathogens are known to infect humans, but only a fraction are readily identifiable using current diagnostic methods. Microbial cell-free DNA sequencing offers the potential to non-invasively identify a wide range of infections throughout the body, but the challenges of clinical-grade metagenomic testing must be addressed. Here we describe the analytical and clinical validation of a next-generation sequencing test that identifies and quantifies microbial cell-free DNA in plasma from 1,250 clinically relevant bacteria, DNA viruses, fungi and eukaryotic parasites. Test accuracy, precision, bias and robustness to a number of metagenomics-specific challenges were determined using a panel of 13 microorganisms that model key determinants of performance in 358 contrived plasma samples, as well as 2,625 infections simulated in silico and 580 clinical study samples. The test showed 93.7% agreement with blood culture in a cohort of 350 patients with a sepsis alert and identified an independently adjudicated cause of the sepsis alert more often than all of the microbiological testing combined (169 aetiological determinations versus 132). Among the 166 samples adjudicated to have no sepsis aetiology identified by any of the tested methods, sequencing identified microbial cell-free DNA in 62, likely derived from commensal organisms and incidental findings unrelated to the sepsis alert. Analysis of the first 2,000 patient samples tested in the CLIA laboratory showed that more than 85% of results were delivered the day after sample receipt, with 53.7% of reports identifying one or more microorganisms.}, }
@article {pmid30741334, year = {2019}, author = {Suleiman, M and Klippel, B and Busch, P and Schäfers, C and Moccand, C and Bel-Rhlid, R and Palzer, S and Antranikian, G}, title = {Enrichment of anaerobic heterotrophic thermophiles from four Azorean hot springs revealed different community composition and genera abundances using recalcitrant substrates.}, journal = {Extremophiles : life under extreme conditions}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00792-019-01079-7}, pmid = {30741334}, issn = {1433-4909}, abstract = {DGGE analysis combined with a metagenomic approach was used to get insights into heterotrophic anoxic enrichment cultures of four hot springs of Vale das Furnas, Portugal, using the recalcitrant substrate spent coffee ground (SCG). Parallel enrichment cultures were performed using the major components of spent coffee ground, namely arabinogalactan, galactomannan, cellulose, and proteins. DGGE revealed that heterotrophic thermophilic bacteria are highly abundant in the hydrothermal springs and significant differences in community composition depending on the substrate were observed. DNA, isolated from enrichment cultures of different locations that were grown on the same substrate were pooled, and the respective metagenomes were analyzed. Results indicated that cultures grown on recalcitrant substrate SCG consists of a totally different thermophilic community, dominated by Dictyoglomus. Enrichments with galactomannan and arabinogalactan were dominated by Thermodesulfovibrio, while cultures with casein and cellulose were dominated by Thermus. This study indicates the high potential of thermophilic bacteria degrading recalcitrant substrate such as SCG and furthermore how the accessibility to complex polymers shapes the bacterial community.}, }
@article {pmid30740092, year = {2019}, author = {Grządziel, J and Gałązka, A}, title = {Fungal Biodiversity of the Most Common Types of Polish Soil in a Long-Term Microplot Experiment.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {6}, doi = {10.3389/fmicb.2019.00006}, pmid = {30740092}, issn = {1664-302X}, abstract = {The aim of the study was to investigate fungal genetic diversity in eight different types of soil in a long-term microplot experiment founded in 1881 in Puławy, Poland. The experiment consists of eight plots (14 m2), each 1 m deep with concrete walls, filled with profiles of different soils. The soils represent the most common Polish soil types (Cambic Leptosol, Fluvic Cambisol, Gleyic Chernozem, Cambisol and Haplic Cambisol, two Brunic Arenosols and Haplic Luvisol). Each soil was characterized by different pH (from 4.0 to 7.5) and organic carbon content (4.5-21.3 g kg-1). The soil structure was not destroyed by compaction because the soils had always been cultivated by hand. The same plant species were always grown in all plots at the same time and the soils received the same fertilization. Moreover, the soils were always under the same weather conditions. Ascomycota was the most abundant phylum in all samples, ranging from 70 to 90% of total fungi. Some genera (Mortierella, Solicoccozyma, and Mycosphaerella) were found to be adapted to a wide range of pH. Acidic soils were dominated by Talaromyces, Cladophialophora, Devriesia, and Saitozyma, while good quality soils primarily consisted of Plectosphaerella, Tetracladium, and Mortierella. The study confirmed previous reports that pH has a decisive influence on soil fungal diversity, but also indicated the strong impact of soil type itself. These studies have launched a new cycle of research in these historical soil profiles.}, }
@article {pmid30739073, year = {2019}, author = {Zhu, J and Liu, R and Cao, N and Yu, J and Liu, X and Yu, Z}, title = {Mycobacterial metabolic characteristics in a water meter biofilm revealed by metagenomics and metatranscriptomics.}, journal = {Water research}, volume = {153}, number = {}, pages = {315-323}, doi = {10.1016/j.watres.2019.01.032}, pmid = {30739073}, issn = {1879-2448}, abstract = {Mycobacteria represent one of the most persistent bacterial populations in drinking water distribution system (DWDS) biofilm communities; however, mycobacterial in situ metabolic profiles are largely unknown. In this study, the metabolic characteristics of mycobacteria in a household water meter biofilm were unveiled using a coupled metagenomic/metatranscriptomic approach. The water meter biofilm appeared to express nitrogenase genes (nifDKH) and a full complement of genes coding for several carbon-fixation pathways, especially the Calvin cycle, suggesting the CO2 sequestration and dinitrogen fixation potential of the biofilm. These findings indicate that it may be difficult to prevent the formation of DWDS biofilms simply by controlling the availability of organic carbon or nitrogen. The composite genome of mycobacteria (CG-M) was reconstructed based on the obtained omics data. CG-M shared similar genome phylogeny and virulence-factor profiles with Mycobacterium avium complex, suggesting that population CG-M might represent a member of mycobacteria with pathogenicity. According to the gene expression patterns, population CG-M showed the metabolic potential to assimilate CO2 via the Calvin cycle and/or anaplerotic reactions, and even to grow autotrophically with CO as the sole carbon and energy source. This suggests that organic carbon may not be a limiting factor for mycobacterial growth in DWDSs. Moreover, our results suggest that mycobacterial aromatic degradation is primarily achieved through the catechol meta-cleavage pathway, and biofilm mycobacteria could prefer phosphate as the phosphorus source.}, }
@article {pmid30738947, year = {2019}, author = {Blanco-Míguez, A and Blanco, G and Gutierrez-Jácome, A and Fdez-Riverola, F and Sánchez, B and Lourenço, A}, title = {Computational prediction of the bioactivity potential of proteomes based on expert knowledge.}, journal = {Journal of biomedical informatics}, volume = {}, number = {}, pages = {103121}, doi = {10.1016/j.jbi.2019.103121}, pmid = {30738947}, issn = {1532-0480}, abstract = {Advances in the field of genome sequencing have enabled a comprehensive analysis and annotation of the dynamics of the protein inventory of cells. This has been proven particularly rewarding for microbial cells, for which the majority of proteins are already accessible to analysis through automatic metagenome annotation. The large-scale in silico screening of proteomes and metaproteomes is key to uncover bioactivities of translational, clinical and biotechnological interest, and to help assign functions to certain proteins, such as those predicted as hypothetical. This work introduces a new method for the prediction of the bioactivity potential of proteomes/metaproteomes, supporting the discovery of functionally relevant proteins based on prior knowledge. This methodology complements functional annotation enrichment methods by allowing the assignment of functions to proteins annotated as hypothetical/putative/uncharacterised, as well as and enabling the detection of specific bioactivities and the recovery of proteins from defined taxa. This work shows how the new method can be applied to screen proteome and metaproteome sets to obtain predictions of clinical or biotechnological interest based on reference datasets. Notably, with this methodology, the large information files obtained after DNA sequencing or protein identification experiments can be associated for translational purposes that, in cases such as antibiotic-resistance pathogens or foodborne diseases, may represent changes in how these important and global health burdens are approached in the clinical practice. Finally, the Sequence-based Expert-driven pRoteome bioactivity Prediction EnvironmENT, a public Web service implemented in Scala functional programming style, is introduced as means to ensure broad access to the method as well as to discuss main implementation issues, such as modularity, extensibility and interoperability.}, }
@article {pmid30737865, year = {2019}, author = {Berde, MS and Jolis, D}, title = {Solubilization of Organics Due to Thermal Hydrolysis Pretreatment and the Shift in Microbial Population in Anaerobic Digestion.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {}, number = {}, pages = {}, doi = {10.1002/wer.1086}, pmid = {30737865}, issn = {1061-4303}, abstract = {A study was conducted to analyze the effect of solubilization due to thermal hydrolysis pretreatment on the microbial population responsible for anaerobic digestion at mesophilic temperature. Metagenomic and microbial population analysis was done on digesters receiving sludge with and without thermal hydrolysis pretreatment. The digester receiving thermal hydrolysis pretreatment was stable at lower detention times and showed a shift in microbial population with predominance of methane-producing population in comparison to conventional digesters receiving no thermal hydrolysis pretreatment. Among methanogens, Methanosarcina showed dominance in the thermal hydrolysis pretreatment digester. Digesters with no thermal hydrolysis pretreatment had a mixed culture of acid-producing bacteria and methane-producing archaea, with almost equal proportion of methane-producing Methanobacterium and Methanosarcina. Kinetic parameters showed high growth and substrate utilization rates in digester receiving thermal hydrolysis pretreatment. This article is protected by copyright. All rights reserved.}, }
@article {pmid30737379, year = {2019}, author = {Colman, DR and Lindsay, MR and Boyd, ES}, title = {Mixing of meteoric and geothermal fluids supports hyperdiverse chemosynthetic hydrothermal communities.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {681}, doi = {10.1038/s41467-019-08499-1}, pmid = {30737379}, issn = {2041-1723}, abstract = {Little is known of how mixing of meteoric and geothermal fluids supports biodiversity in non-photosynthetic ecosystems. Here, we use metagenomic sequencing to investigate a chemosynthetic microbial community in a hot spring (SJ3) of Yellowstone National Park that exhibits geochemistry consistent with mixing of a reduced volcanic gas-influenced end member with an oxidized near-surface meteoric end member. SJ3 hosts an exceptionally diverse community with representatives from ~50% of known higher-order archaeal and bacterial lineages, including several divergent deep-branching lineages. A comparison of functional potential with other available chemosynthetic community metagenomes reveals similarly high diversity and functional potentials (i.e., incorporation of electron donors supplied by volcanic gases) in springs sourced by mixed fluids. Further, numerous closely related SJ3 populations harbor differentiated metabolisms that may function to minimize niche overlap, further increasing endemic diversity. We suggest that dynamic mixing of waters generated by subsurface and near-surface geological processes may play a key role in the generation and maintenance of chemosynthetic biodiversity in hydrothermal and other similar environments.}, }
@article {pmid30737349, year = {2019}, author = {Tuttle, RN and Demko, AM and Patin, N and Kapono, CA and Donia, MS and Dorrestein, P and Jensen, PR}, title = {The Detection of Natural Products and Their Producers in Ocean Sediments.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02830-18}, pmid = {30737349}, issn = {1098-5336}, abstract = {Thousands of natural products have been identified from cultured microorganisms yet evidence of their production in the environment has proven elusive. Technological advances in mass spectrometry combined with public databases now make it possible to address this disparity by detecting compounds directly from environmental samples. Here we used adsorbent resins, tandem mass spectrometry, and next generation sequencing to assess the metabolome of marine sediments and its relationship to bacterial community structure. We identified natural products previously reported from cultured bacteria, providing evidence they are produced in situ, and compounds of anthropogenic origin, suggesting this approach can be used as an indicator of environmental impact. The bacterial metabolite staurosporine was quantified and shown to reach physiologically relevant concentrations, indicating it may influence sediment community structure. Staurosporine concentrations were correlated with the relative abundance of the staurosporine producing bacterial genus Salinispora and production confirmed in strains cultured from the same location, providing a link between compound and candidate producer. Metagenomic analyses revealed numerous biosynthetic gene clusters related to indolocarbazole biosynthesis, providing evidence for non-canonical sources of staurosporine and a path forward to assess the relationships between natural products and the organisms that produce them. Untargeted environmental metabolomics circumvents the need for laboratory cultivation and represents a promising approach to understanding the functional roles of natural products in shaping microbial community structure in marine sediments.ImportanceNatural products are readily isolated from cultured bacteria and exploited for useful purposes including drug discovery. However, these compounds are rarely detected in the environments from which the bacteria are obtained thus limiting our understanding of their ecological significance. Here we used environmental metabolomics to assess chemical diversity directly in marine sediments. We identified numerous metabolites and, in one case, isolated strains of bacteria capable of producing one of the compounds detected. Coupling environmental metabolomics with community and metagenomic analyses provides opportunities to link compounds and producers and begin to assess the complex interactions mediated by specialized metabolites in marine sediments.}, }
@article {pmid30737174, year = {2019}, author = {Uribe, RV and van der Helm, E and Misiakou, MA and Lee, SW and Kol, S and Sommer, MOA}, title = {Discovery and Characterization of Cas9 Inhibitors Disseminated across Seven Bacterial Phyla.}, journal = {Cell host & microbe}, volume = {25}, number = {2}, pages = {233-241.e5}, doi = {10.1016/j.chom.2019.01.003}, pmid = {30737174}, issn = {1934-6069}, abstract = {CRISPR-Cas systems in bacteria and archaea provide immunity against bacteriophages and plasmids. To overcome CRISPR immunity, phages have acquired anti-CRISPR genes that reduce CRISPR-Cas activity. Using a synthetic genetic circuit, we developed a high-throughput approach to discover anti-CRISPR genes from metagenomic libraries based on their functional activity rather than sequence homology or genetic context. We identified 11 DNA fragments from soil, animal, and human metagenomes that circumvent Streptococcus pyogenes Cas9 activity in our selection strain. Further in vivo and in vitro characterization of a subset of these hits validated the activity of four anti-CRISPRs. Notably, homologs of some of these anti-CRISPRs were detected in seven different phyla, namely Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Cyanobacteria, Spirochaetes, and Balneolaeota, and have high sequence identity suggesting recent horizontal gene transfer. Thus, anti-CRISPRs against type II-A CRISPR-Cas systems are widely distributed across bacterial phyla, suggesting a more complex ecological role than previously appreciated.}, }
@article {pmid30736849, year = {2019}, author = {Fritz, A and Hofmann, P and Majda, S and Dahms, E and Dröge, J and Fiedler, J and Lesker, TR and Belmann, P and DeMaere, MZ and Darling, AE and Sczyrba, A and Bremges, A and McHardy, AC}, title = {CAMISIM: simulating metagenomes and microbial communities.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {17}, doi = {10.1186/s40168-019-0633-6}, pmid = {30736849}, issn = {2049-2618}, abstract = {BACKGROUND: Shotgun metagenome data sets of microbial communities are highly diverse, not only due to the natural variation of the underlying biological systems, but also due to differences in laboratory protocols, replicate numbers, and sequencing technologies. Accordingly, to effectively assess the performance of metagenomic analysis software, a wide range of benchmark data sets are required.
RESULTS: We describe the CAMISIM microbial community and metagenome simulator. The software can model different microbial abundance profiles, multi-sample time series, and differential abundance studies, includes real and simulated strain-level diversity, and generates second- and third-generation sequencing data from taxonomic profiles or de novo. Gold standards are created for sequence assembly, genome binning, taxonomic binning, and taxonomic profiling. CAMSIM generated the benchmark data sets of the first CAMI challenge. For two simulated multi-sample data sets of the human and mouse gut microbiomes, we observed high functional congruence to the real data. As further applications, we investigated the effect of varying evolutionary genome divergence, sequencing depth, and read error profiles on two popular metagenome assemblers, MEGAHIT, and metaSPAdes, on several thousand small data sets generated with CAMISIM.
CONCLUSIONS: CAMISIM can simulate a wide variety of microbial communities and metagenome data sets together with standards of truth for method evaluation. All data sets and the software are freely available at https://github.com/CAMI-challenge/CAMISIM.}, }
@article {pmid30735978, year = {2019}, author = {Liu, K and Han, J and Li, S and Liu, L and Lin, W and Luo, J}, title = {Insight into the diversity of antibiotic resistance genes in the intestinal bacteria of shrimp Penaeus vannamei by culture-dependent and independent approaches.}, journal = {Ecotoxicology and environmental safety}, volume = {172}, number = {}, pages = {451-459}, doi = {10.1016/j.ecoenv.2019.01.109}, pmid = {30735978}, issn = {1090-2414}, abstract = {Antibiotic resistance genes (ARGs) that distributed in antibiotic resistant bacteria (ARBs) are widespread in aquaculture and have great threats to the aquatic organism as well as to human. However, our understanding about the risk of ARGs to the health of aquatic organism is still limited. In the present study, we got a deep insight into the diversity of ARGs in the intestinal bacteria of shrimp by culture-dependent and independent approaches. Results of the PCR-based detection and culture-dependent analysis indicated that the tetracycline, sulfadiazine, quinolone and erythromycin resistance genes were prevalent in the commercial shrimps that bought from aquatic markets or supermarket. The culture-independent plasmid metagenomic analysis identified 62 different ARGs, which were classified into 21 types, with abundances ranging from 13 to 1418 ppm. The analysis suggested that most of the ARGs come from the plasmids originating from Vibrio (accounted for 2.8-51%) and Aeromonas (accounted for 16-55%), and the Vibrio group was concluded to be the main bacterial pathogen that probably resulted in the shrimp disease. Accordingly, the plasmid metagenomic that focuses on the mobile genetic elements has great potential on the identification of ARGs in complex environments.}, }
@article {pmid30735616, year = {2019}, author = {Wu, C and Shang, Z and Lemetre, C and Ternei, MA and Brady, SF}, title = {Cadasides, Calcium-Dependent Acidic Lipopeptides from the Soil Metagenome That Are Active against Multidrug-Resistant Bacteria.}, journal = {Journal of the American Chemical Society}, volume = {}, number = {}, pages = {}, doi = {10.1021/jacs.8b12087}, pmid = {30735616}, issn = {1520-5126}, support = {R35 GM122559/GM/NIGMS NIH HHS/United States ; U01 GM110714/GM/NIGMS NIH HHS/United States ; U19 AI109713/AI/NIAID NIH HHS/United States ; }, abstract = {The growing threat of antibiotic resistance necessitates the discovery of antibiotics that are active against resistant pathogens. Calcium-dependent antibiotics are a small family of structurally diverse acidic lipopeptides assembled by nonribosomal peptide synthetases (NRPSs) that are known to display various modes of action against antibiotic-resistant pathogens. Here we use NRPS adenylation (AD) domain sequencing to guide the identification, recovery, and cloning of the cde biosynthetic gene cluster from a soil metagenome. Heterologous expression of the cde biosynthetic gene cluster led to the production of cadasides A (1) and B (2), a subfamily of acidic lipopeptides that is distinct from previously characterized calcium-dependent antibiotics in terms of both overall structure and acidic residue rich peptide core. The cadasides inhibit the growth of multidrug-resistant Gram-positive pathogens by disrupting cell wall biosynthesis in the presence of high concentrations of calcium. Interestingly, sequencing of AD domains from diverse soils revealed that sequences predicted to arise from cadaside-like gene clusters are predominantly found in soils containing high levels of calcium carbonate.}, }
@article {pmid30735254, year = {2019}, author = {Shah, A and Morrison, M and Burger, D and Martin, N and Rich, J and Jones, M and Koloski, N and Walker, MM and Talley, NJ and Holtmann, GJ}, title = {Systematic review with meta-analysis: the prevalence of small intestinal bacterial overgrowth in inflammatory bowel disease.}, journal = {Alimentary pharmacology & therapeutics}, volume = {49}, number = {6}, pages = {624-635}, doi = {10.1111/apt.15133}, pmid = {30735254}, issn = {1365-2036}, abstract = {BACKGROUND: Current data on small intestinal bacterial overgrowth (SIBO) in patients with inflammatory bowel diseases (IBD) are controversial.
AIM: To conduct a systematic review and meta-analysis to determine the prevalence of SIBO in patients with ulcerative colitis (UC) and Crohn's disease (CD).
METHODS: Electronic databases were searched up to May 2018 for studies reporting prevalence of SIBO in IBD patients. The prevalence rate of SIBO among IBD patients and the odds ratio (OR) and 95% CI of SIBO in IBD patients compared with controls were calculated.
RESULTS: The final dataset included 11 studies (1175 adult patients with IBD and 407 controls), all utilising breath test for diagnosis of SIBO. The proportion of SIBO in IBD patients was 22.3% (95% CI 19.92-24.68). The OR for SIBO in IBD patients was 9.51 (95% CI 3.39-26.68) compared to non-IBD controls, and high in both CD (OR = 10.86; 95% CI 2.76-42.69) and UC (OR = 7.96; 95% CI 1.66-38.35). In patients with CD, subgroup analysis showed the presence of fibrostenosing disease (OR = 7.47; 95% CI 2.51-22.20) and prior bowel surgery (OR = 2.38; 95% CI 1.65-3.44), especially resection of the ileocecal valve, increased the odds of SIBO. Individual studies suggest that combined small and large bowel disease but not disease activity may be associated with SIBO.
CONCLUSIONS: Overall, there is a substantial increase in the prevalence of SIBO in IBD patients compared to controls. Prior surgery and the presence of fibrostenosing disease are risk factors for SIBO in IBD.}, }
@article {pmid30734843, year = {2019}, author = {Phetcharat, T and Dawkrajai, P and Chitov, T and Mhuantong, W and Champreda, V and Bovonsombut, S}, title = {Biosurfactant-Producing Capability and Prediction of Functional Genes Potentially Beneficial to Microbial Enhanced Oil Recovery in Indigenous Bacterial Communities of an Onshore Oil Reservoir.}, journal = {Current microbiology}, volume = {76}, number = {3}, pages = {382-391}, doi = {10.1007/s00284-019-01641-8}, pmid = {30734843}, issn = {1432-0991}, abstract = {Microbial enhanced oil recovery (MEOR) is a bio-based technology with economic and environmental benefits. The success of MEOR depends greatly on the types and characteristics of indigenous microbes. The aim of this study was to evaluate the feasibility of applying MEOR at Mae Soon Reservoir, an onshore oil reservoir experiencing a decline in its production rate. We investigated the capability of the reservoir's bacteria to produce biosurfactants, and evaluated the potentials of uncultured indigenous bacteria to support MEOR by means of prediction of MEOR-related functional genes, based on a set of metagenomic 16s rRNA gene data. The biosurfactant-producing bacteria isolated from the oil-bearing sandstones from the reservoir belonged to one species: Bacillus licheniformis, with one having the ability to decrease surface tension from 72 to 32 mN/m. Gene sequences responsible for biosurfactant (licA3), lipase (lipP1) and catechol 2,3-dioxygenase (C23O) were detected in these isolates. The latter two, and other genes encoding MEOR-related functional proteins such as enoyl-CoA hydratase and alkane 1-monooxygenase, were predicted in the bacterial communities residing the reservoir's sandstones. Exposure of these sandstones to nutrients, consisting of KNO3 and NaH2PO4, resulted in an increase in the proportions of some predicted functional genes. These results indicated the potentials of MEOR application at Mae Soon site. Using the approaches demonstrated in this study would also assist evaluation of the feasibility of applying MEOR in oil reservoirs, which may be enhanced by an appropriate nutrient treatment.}, }
@article {pmid30733714, year = {2018}, author = {Tamames, J and Puente-Sánchez, F}, title = {SqueezeMeta, A Highly Portable, Fully Automatic Metagenomic Analysis Pipeline.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3349}, doi = {10.3389/fmicb.2018.03349}, pmid = {30733714}, issn = {1664-302X}, abstract = {The improvement of sequencing technologies has facilitated generalization of metagenomic sequencing, which has become a standard procedure for analyzing the structure and functionality of microbiomes. Bioinformatic analysis of sequencing results poses a challenge because it involves many different complex steps. SqueezeMeta is a fully automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support that enables co-assembly of related metagenomes and retrieval of individual genomes via binning procedures. SqueezeMeta features several unique characteristics: co-assembly procedure or co-assembly of unlimited number of metagenomes via merging of individual assembled metagenomes, both with read mapping for estimation of the abundances of genes in each metagenome. It also includes binning and bin checking for retrieving individual genomes. Internal checks for the assembly and binning steps provide information about the consistency of contigs and bins. Moreover, results are stored in a MySQL database, where they can be easily exported and shared, and can be inspected anywhere using a flexible web interface that allows simple creation of complex queries. We illustrate the potential of SqueezeMeta by analyzing 32 gut metagenomes in a fully automatic way, enabling retrieval of several million genes and several hundreds of genomic bins. One of the motivations in the development of SqueezeMeta was producing a software capable of running in small desktop computers and thus amenable to all users and settings. We were also able to co-assemble two of these metagenomes and complete the full analysis in less than one day using a simple laptop computer. This reveals the capacity of SqueezeMeta to run without high-performance computing infrastructure and in absence of any network connectivity. It is therefore adequate for in situ, real time analysis of metagenomes produced by nanopore sequencing. SqueezeMeta can be downloaded from https://github.com/jtamames/SqueezeMeta.}, }
@article {pmid30733546, year = {2019}, author = {Wally, N and Schneider, M and Thannesberger, J and Kastner, MT and Bakonyi, T and Indik, S and Rattei, T and Bedarf, J and Hildebrand, F and Law, J and Jovel, J and Steininger, C}, title = {Plasmid DNA contaminant in molecular reagents.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {1652}, doi = {10.1038/s41598-019-38733-1}, pmid = {30733546}, issn = {2045-2322}, support = {P28102-B30//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; P25353-B21//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; P28102-B30//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; }, abstract = {Background noise in metagenomic studies is often of high importance and its removal requires extensive post-analytic, bioinformatics filtering. This is relevant as significant signals may be lost due to a low signal-to-noise ratio. The presence of plasmid residues, that are frequently present in reagents as contaminants, has not been investigated so far, but may pose a substantial bias. Here we show that plasmid sequences from different sources are omnipresent in molecular biology reagents. Using a metagenomic approach, we identified the presence of the (pol) of equine infectious anemia virus in human samples and traced it back to the expression plasmid used for generation of a commercial reverse transcriptase. We found fragments of multiple other expression plasmids in human samples as well as commercial polymerase preparations. Plasmid contamination sources included production chain of molecular biology reagents as well as contamination of reagents from environment or human handling of samples and reagents. Retrospective analyses of published metagenomic studies revealed an inaccurate signal-to-noise differentiation. Hence, the plasmid sequences that seem to be omnipresent in molecular biology reagents may misguide conclusions derived from genomic/metagenomics datasets and thus also clinical interpretations. Critical appraisal of metagenomic data sets for the possibility of plasmid background noise is required to identify reliable and significant signals.}, }
@article {pmid30733472, year = {2019}, author = {Zhang, W and Li, J and Lu, S and Han, N and Miao, J and Zhang, T and Qiang, Y and Kong, Y and Wang, H and Gao, T and Liu, Y and Li, X and Peng, X and Chen, X and Zhao, X and Che, J and Zhang, L and Chen, X and Zhang, Q and Hu, M and Li, Q and Kan, B}, title = {Gut microbiota community characteristics and disease-related microorganism pattern in a population of healthy Chinese people.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {1594}, doi = {10.1038/s41598-018-36318-y}, pmid = {30733472}, issn = {2045-2322}, support = {81301402//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81700016//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {China's population accounts for about 1/5th of the world's total population. Owing to differences in environment, race, living habits, and other factors, the structure of the intestinal flora of Chinese individuals is expected to have unique features; however, this has not been thoroughly examined. Here, we collected faecal samples from healthy adults living in three cities of China and investigated their gut microbiome using metagenomics and bioinformatics technology. We found that 11 core bacterial genera were present in all of the Chinese faecal samples; moreover, several patient characteristics (age, region, body mass index, physical exercise, smoking habits, and alcoholic drink, and yogurt consumption) were found to have different effects on the gut microbiome of healthy Chinese people. We also examined the distribution patterns of disease-related microorganisms (DRMs), revealing which DRMs can potentially be used as markers for assessment of health risk. We also developed a program called "Guthealthy" for evaluating the health status associated with the microbiome and DRM pattern in the faecal samples. The microbiota data obtained in this study will provide a basis for a healthy gut microbiome composition in the Chinese population.}, }
@article {pmid30729265, year = {2019}, author = {Bernard, C and Escalas, A and Villeriot, N and Agogué, H and Hugoni, M and Duval, C and Carré, C and Got, P and Sarazin, G and Jézéquel, D and Leboulanger, C and Grossi, V and Ader, M and Troussellier, M}, title = {Very Low Phytoplankton Diversity in a Tropical Saline-Alkaline Lake, with Co-dominance of Arthrospira fusiformis (Cyanobacteria) and Picocystis salinarum (Chlorophyta).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01332-8}, pmid = {30729265}, issn = {1432-184X}, support = {ANR-13-BS06-0001//Agence Nationale de la Recherche/ ; }, abstract = {Lake Dziani Dzaha (Mayotte Island, Indian Ocean) is a tropical thalassohaline lake which geochemical and biological conditions make it a unique aquatic ecosystem considered as a modern analogue of Precambrian environments. In the present study, we focused on the diversity of phytoplanktonic communities, which produce very high and stable biomass (mean2014-2015 = 652 ± 179 μg chlorophyll a L-1). As predicted by classical community ecology paradigms, and as observed in similar environments, a single species is expected to dominate the phytoplanktonic communities. To test this hypothesis, we sampled water column in the deepest part of the lake (18 m) during rainy and dry seasons for two consecutive years. Phytoplanktonic communities were characterized using a combination of metagenomic, microscopy-based and flow cytometry approaches, and we used statistical modeling to identify the environmental factors determining the abundance of dominant organisms. As hypothesized, the overall diversity of the phytoplanktonic communities was very low (15 OTUs), but we observed a co-dominance of two, and not only one, OTUs, viz., Arthrospira fusiformis (Cyanobacteria) and Picocystis salinarum (Chlorophyta). We observed a decrease in the abundance of these co-dominant taxa along the depth profile and identified the adverse environmental factors driving this decline. The functional traits measured on isolated strains of these two taxa (i.e., size, pigment composition, and concentration) are then compared and discussed to explain their capacity to cope with the extreme environmental conditions encountered in the aphotic, anoxic, and sulfidic layers of the water column of Lake Dziani Dzaha.}, }
@article {pmid30729070, year = {2019}, author = {Salam, LB and Ishaq, A}, title = {Biostimulation potentials of corn steep liquor in enhanced hydrocarbon degradation in chronically polluted soil.}, journal = {3 Biotech}, volume = {9}, number = {2}, pages = {46}, doi = {10.1007/s13205-019-1580-4}, pmid = {30729070}, issn = {2190-572X}, abstract = {The effects of corn steep liquor (CSL) on hydrocarbon degradation and microbial community structure and function was evaluated in field-moist soil microcosms. Chronically polluted soil treated with CSL (AB4) and an untreated control (3S) was compared over a period of 6 weeks. Gas chromatographic fingerprints of residual hydrocarbons revealed removal of 95.95% and 94.60% aliphatic and aromatic hydrocarbon fractions in AB4 system with complete disappearance of nC1-nC8, nC10, nC15, nC20-nC23 aliphatics and aromatics such as naphthalene, acenaphthylene, fluorene, phenanthrene, pyrene, benzo(a)anthracene, and indeno(123-cd)pyrene in 42 days. In 3S system, there is removal of 61.27% and 66.58% aliphatic and aromatic fractions with complete disappearance of nC2 and nC21 aliphatics and naphthalene, acenaphthylene, fluorene, phenanthrene, pyrene, and benzo(a)anthracene aromatics in 42 days. Illumina shotgun sequencing of the DNA extracted from the two systems showed the preponderance of Actinobacteria (31.46%) and Proteobacteria (38.95%) phyla in 3S and AB4 with the dominance of Verticillium (22.88%) and Microbacterium (8.16%) in 3S, and Laceyella (24.23%), Methylosinus (8.93%) and Pedobacter (7.73%) in AB4. Functional characterization of the metagenomic reads revealed diverse metabolic potentials and adaptive traits of the microbial communities in the two systems to various environmental stressors. It also revealed the exclusive detection of catabolic enzymes in AB4 system belonging to the aldehyde dehydrogenase superfamily. The results obtained in this study showed that CSL is a potential resource for bioremediation of hydrocarbon-polluted soils.}, }
@article {pmid30728468, year = {2019}, author = {Carr, SA and Jungbluth, SP and Eloe-Fadrosh, EA and Stepanauskas, R and Woyke, T and Rappé, MS and Orcutt, BN}, title = {Carboxydotrophy potential of uncultivated Hydrothermarchaeota from the subseafloor crustal biosphere.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0352-9}, pmid = {30728468}, issn = {1751-7370}, support = {OCE-0726887//National Science Foundation (NSF)/ ; OCE-1031808//National Science Foundation (NSF)/ ; OCE-1233226//National Science Foundation (NSF)/ ; OCE-0939564//National Science Foundation (NSF)/ ; OCE-1233226//National Science Foundation (NSF)/ ; OCE-1260723//National Science Foundation (NSF)/ ; MCB-0604014//National Science Foundation (NSF)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; }, abstract = {The exploration of Earth's terrestrial subsurface biosphere has led to the discovery of several new archaeal lineages of evolutionary significance. Similarly, the deep subseafloor crustal biosphere also harbors many unique, uncultured archaeal taxa, including those belonging to Candidatus Hydrothermarchaeota, formerly known as Marine Benthic Group-E. Recently, Hydrothermarchaeota was identified as an abundant lineage of Juan de Fuca Ridge flank crustal fluids, suggesting its adaptation to this extreme environment. Through the investigation of single-cell and metagenome-assembled genomes, we provide insight into the lineage's evolutionary history and metabolic potential. Phylogenomic analysis reveals the Hydrothermarchaeota to be an early-branching archaeal phylum, branching between the superphylum DPANN, Euryarchaeota, and Asgard lineages. Hydrothermarchaeota genomes suggest a potential for dissimilative and assimilative carbon monoxide oxidation (carboxydotrophy), as well as sulfate and nitrate reduction. There is also a prevalence of chemotaxis and motility genes, indicating adaptive strategies for this nutrient-limited fluid-rock environment. These findings provide the first genomic interpretations of the Hydrothermarchaeota phylum and highlight the anoxic, hot, deep marine crustal biosphere as an important habitat for understanding the evolution of early life.}, }
@article {pmid30728279, year = {2019}, author = {Props, R and Monsieurs, P and Vandamme, P and Leys, N and Denef, VJ and Boon, N}, title = {Gene Expansion and Positive Selection as Bacterial Adaptations to Oligotrophic Conditions.}, journal = {mSphere}, volume = {4}, number = {1}, pages = {}, doi = {10.1128/mSphereDirect.00011-19}, pmid = {30728279}, issn = {2379-5042}, abstract = {We examined the genomic adaptations of prevalent bacterial taxa in a highly nutrient- and ion-depleted freshwater environment located in the secondary cooling water system of a nuclear research reactor. Using genome-centric metagenomics, we found that none of the prevalent bacterial taxa were related to typical freshwater bacterial lineages. We also did not identify strong signatures of genome streamlining, which has been shown to be one of the ecoevolutionary forces shaping the genome characteristics of bacterial taxa in nutrient-depleted environments. Instead, focusing on the dominant taxon, a novel Ramlibacter sp. which we propose to name Ramlibacter aquaticus, we detected extensive positive selection on genes involved in phosphorus and carbon scavenging pathways. These genes were involved in the high-affinity phosphate uptake and storage into polyphosphate granules, metabolism of nitrogen-rich organic matter, and carbon/energy storage into polyhydroxyalkanoate. In parallel, comparative genomics revealed a high number of paralogs and an accessory genome significantly enriched in environmental sensing pathways (i.e., chemotaxis and motility), suggesting extensive gene expansions in R. aquaticus The type strain of R. aquaticus (LMG 30558T) displayed optimal growth kinetics and productivity at low nutrient concentrations, as well as substantial cell size plasticity. Our findings with R. aquaticus LMG 30558T demonstrate that positive selection and gene expansions may represent successful adaptive strategies to oligotrophic environments that preserve high growth rates and cellular productivity.IMPORTANCE By combining a genome-centric metagenomic approach with a culture-based approach, we investigated the genomic adaptations of prevalent populations in an engineered oligotrophic freshwater system. We found evidence for widespread positive selection on genes involved in phosphorus and carbon scavenging pathways and for gene expansions in motility and environmental sensing to be important genomic adaptations of the abundant taxon in this system. In addition, microscopic and flow cytometric analysis of the first freshwater representative of this population (Ramlibacter aquaticus LMG 30558T) demonstrated phenotypic plasticity, possibly due to the metabolic versatility granted by its larger genome, to be a strategy to cope with nutrient limitation. Our study clearly demonstrates the need for the use of a broad set of genomic tools combined with culture-based physiological characterization assays to investigate and validate genomic adaptations.}, }
@article {pmid30728080, year = {2019}, author = {Yu, K and Yi, S and Li, B and Guo, F and Peng, X and Wang, Z and Wu, Y and Alvarez-Cohen, L and Zhang, T}, title = {An integrated meta-omics approach reveals substrates involved in synergistic interactions in a bisphenol A (BPA)-degrading microbial community.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {16}, doi = {10.1186/s40168-019-0634-5}, pmid = {30728080}, issn = {2049-2618}, support = {NSFC21277113//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Understanding microbial interactions in engineering bioprocesses is important to enhance and optimize performance outcomes and requires dissection of the multi-layer complexities of microbial communities. However, unraveling microbial interactions as well as substrates involved in complex microbial communities is a challenging task. Here, we demonstrate an integrated approach of metagenomics, metatranscriptomics, and targeted metabolite analysis to identify the substrates involved in interspecies interactions from a potential cross-feeding model community-bisphenol A (BPA)-biodegrading community, aiming to establish an identification method of microbial interactions in engineering or environmental bioprocesses.
RESULTS: The community-level BPA-metabolic pathway was constructed using integrated metagenomics and targeted metabolite analyses. The dynamics of active functions and metabolism of major community members were identified using metagenomic and metatranscriptomic analyses in concert. Correlating the community BPA biodegradation performance to the individual bacterial activities enabled the discovery of substrates involved in a synergistic interaction of cross-feeding between BPA-degrading Sphingonomas species and intermediate users, Pseudomonas sp. and Pusillimonas sp. This proposed synergistic interaction was confirmed by the co-culture of a Sphingonomas sp. and Pseudomonas sp. isolates, which demonstrated enhanced BPA biodegradation compared to the isolate of Sphingonomas sp. alone.
CONCLUSION: The three types of integrated meta-omics analyses effectively revealed the metabolic capability at both community-wide and individual bacterial levels. The correlation between these two levels revealed the hidden connection between apparent overall community performance and the contributions of individual community members and their interactions in a BPA-degrading microbial community. In addition, we demonstrated that using integrated multi-omics in conjunction with culture-based confirmation approach is effective to elucidate the microbial interactions affecting the performance outcome. We foresee this approach would contribute the future application and operation of environmental bioprocesses on a knowledge-based control.}, }
@article {pmid30728065, year = {2019}, author = {Johnson, ME and Franks, JM and Cai, G and Mehta, BK and Wood, TA and Archambault, K and Pioli, PA and Simms, RW and Orzechowski, N and Arron, S and Whitfield, ML}, title = {Microbiome dysbiosis is associated with disease duration and increased inflammatory gene expression in systemic sclerosis skin.}, journal = {Arthritis research & therapy}, volume = {21}, number = {1}, pages = {49}, doi = {10.1186/s13075-019-1816-z}, pmid = {30728065}, issn = {1478-6362}, support = {T32 LM012204/LM/NLM NIH HHS/United States ; W81XWH-14-1-0224//U.S. Department of Defense/ ; }, abstract = {BACKGROUND: Infectious agents have long been postulated to be disease triggers for systemic sclerosis (SSc), but a definitive link has not been found. Metagenomic analyses of high-throughput data allows for the unbiased identification of potential microbiome pathogens in skin biopsies of SSc patients and allows insight into the relationship with host gene expression.
METHODS: We examined skin biopsies from a diverse cohort of 23 SSc patients (including lesional forearm and non-lesional back samples) by RNA-seq. Metagenomic filtering and annotation was performed using the Integrated Metagenomic Sequencing Analysis (IMSA). Associations between microbiome composition and gene expression were analyzed using single-sample gene set enrichment analysis (ssGSEA).
RESULTS: We find the skin of SSc patients exhibits substantial changes in microbial composition relative to controls, characterized by sharp decreases in lipophilic taxa, such as Propionibacterium, combined with increases in a wide range of gram-negative taxa, including Burkholderia, Citrobacter, and Vibrio.
CONCLUSIONS: Microbiome dysbiosis is associated with disease duration and increased inflammatory gene expression. These data provide a comprehensive portrait of the SSc skin microbiome and its association with local gene expression, which mirrors the molecular changes in lesional skin.}, }
@article {pmid30726303, year = {2019}, author = {Lokmer, A and Cian, A and Froment, A and Gantois, N and Viscogliosi, E and Chabé, M and Ségurel, L}, title = {Use of shotgun metagenomics for the identification of protozoa in the gut microbiota of healthy individuals from worldwide populations with various industrialization levels.}, journal = {PloS one}, volume = {14}, number = {2}, pages = {e0211139}, doi = {10.1371/journal.pone.0211139}, pmid = {30726303}, issn = {1932-6203}, abstract = {Protozoa have long been considered undesirable residents of the human gut, but recent findings suggest that some of them may positively affect the gut ecosystem. To better understand the role and ecological dynamics of these commensal and potentially beneficial protozoan symbionts, we need efficient methods to detect them, as well as accurate estimates of their prevalence across human populations. Metagenomics provides such an opportunity, allowing simultaneous detection of multiple symbionts in a single analytical procedure. In this study, we collected fecal samples of 68 individuals from three Cameroonian populations with different subsistence modes and compared metagenomics-based and targeted methods of detection for two common protozoan genera: Blastocystis and Entamoeba. In addition, we analyzed our data along with publicly available fecal metagenomes from various worldwide populations to explore the prevalence and association patterns of ten protozoan genera. Regarding the detection method, microscopy was much less sensitive than metagenomics for Entamoeba, whereas qPCR was at least as sensitive as metagenomics for Blastocystis sp. However, metagenomics was more likely to detect co-colonizations by multiple subtypes. Out of the ten examined genera in 127 individuals from Cameroon, Tanzania, Peru, Italy or USA, only three (Blastocystis, Entamoeba and Enteromonas) had an overall prevalence exceeding 10%. All three genera were more common in less industrialized populations and their prevalence differed between continents and subsistence modes, albeit not in a straightforward manner. The majority (72.5%) of colonized individuals carried at least two protozoan species, indicating that mixed-species colonizations are common. In addition, we detected only positive and no negative association patterns between different protozoa. Despite the pitfalls of the metagenomic approach, ranging from the availability of good-quality sequencing data to the lack of standard analytical procedures, we demonstrated its utility in simultaneous detection of multiple protozoan genera, and especially its ability to efficiently detect mixed-species colonizations. Our study corroborates and expands prevalence results previously obtained for Blastocystis sp. and provides novel data for Entamoeba spp. and several other protozoan genera. Furthermore, it indicates that multiple protozoa are common residents of the healthy human gut worldwide.}, }
@article {pmid30725462, year = {2019}, author = {Morales, E and Chen, J and Greathouse, KL}, title = {Compositional Analysis of the Human Microbiome in Cancer Research.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1928}, number = {}, pages = {299-335}, doi = {10.1007/978-1-4939-9027-6_16}, pmid = {30725462}, issn = {1940-6029}, abstract = {Gut microbial composition has shown to be associated with obesity, diabetes mellitus, inflammatory bowel disease, colitis, autoimmune disorders, and cancer, among other diseases. Microbiome research has significantly evolved through the years and continues to advance as we develop new and better strategies to more accurately measure its composition and function. Careful selection of study design, inclusion and exclusion criteria of participants, and methodology are paramount to accurately analyze microbial structure. Here we present the most up-to-date available information on methods for gut microbial collection and analysis.}, }
@article {pmid30724441, year = {2019}, author = {Ghaly, TM and Geoghegan, JL and Alroy, J and Gillings, MR}, title = {High diversity and rapid spatial turnover of integron gene cassettes in soil.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14551}, pmid = {30724441}, issn = {1462-2920}, support = {DP130103839//Australian Research Council/ ; }, abstract = {Integrons are genetic elements that promote rapid adaptation in bacteria by capturing exogenous, mobile gene cassettes. Recently, a subset of gene cassettes has facilitated the global spread of antibiotic resistance. However, outside clinical settings, very little is known about their diversity and spatial ecology. To address this question, we sequenced integron gene cassettes from soils sampled across Australia and Antarctica. We recovered 44 970 open reading frames that encoded 27 215 unique proteins, representing an order of magnitude more cassettes than previous sequencing efforts. We found that cassettes have extremely high local richness, significantly greater than previously predicted, with estimates ranging from 4000 to 18 000 unique cassettes per 0.3 g of soil. We show that cassettes have a heterogeneous distribution across space, and that they exhibit rapid turnover with distance. Similarity between samples drops to between 0.1% and 10% at distances of as little as 100 m. Together, these data provide key insights into the ecology and size of the gene cassette metagenome.}, }
@article {pmid30724439, year = {2019}, author = {Ramos-Barbero, MD and Martínez, JM and Almansa, C and Rodríguez, N and Villamor, J and Gomariz, M and Escudero, C and Rubin, SD and Antón, J and Martínez-García, M and Amils, R}, title = {Prokaryotic and viral community structure in the singular chaotropic salt lake Salar de Uyuni.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14549}, pmid = {30724439}, issn = {1462-2920}, support = {CGL2015-66242-R//MINECO/ ; CLG2015_66686-C3-3//MINECO/ ; //European Regional Development Fund (FEDER)/ ; }, abstract = {Salar de Uyuni (SdU) is the largest hypersaline salt flat and the highest lithium reservoir on Earth. In addition to extreme temperatures and high UV irradiance, SdU has high concentrations of chaotropic salts which can be important factors in controlling microbial diversity. Here, for the first time we characterize the viral diversity of this hypersaline environment during the two seasons, as well as the physicochemical characteristics and the prokaryotic communities of the analysed samples. Most of the selected samples showed a peculiar physicochemical composition and prokaryotic diversity, mostly different from each other even for samples from locations in close proximity or the same season. In contrast to most hypersaline systems Bacteria frequently outnumbered Archaea. Furthermore, an outstanding percentage of members of Salinibacter sp., likely a species different from the cosmopolitan Salinibacter ruber, was obtained in most of the samples. Viral communities displayed the morphologies normally found in hypersaline environments. Two seasonal samples were chosen for a detailed metagenomic analysis of the viral assemblage. Both viral communities shared common sequences but were dominated by sample-specific viruses, mirroring the differences also observed in physicochemical and prokaryotic community composition. These metaviromes were distinct from those detected in other hypersaline systems analysed to date.}, }
@article {pmid30724437, year = {2019}, author = {Ma, Y and Zilles, JL and Kent, AD}, title = {An evaluation of primers for detecting denitrifiers via their functional genes.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14555}, pmid = {30724437}, issn = {1462-2920}, abstract = {Microbial populations provide nitrogen cycling ecosystem services at the nexus of agriculture, environmental quality, and climate change. Denitrification, in particular, impacts socio-environmental systems in both positive and negative ways, through reduction of aquatic and atmospheric nitrogen pollution, but also reduction of soil fertility and production of greenhouse gases. However, denitrification rates are quite variable in time and space, and therefore difficult to model. Microbial ecology is working to improve the predictive ecology of denitrifiers by quantifying and describing the diversity of microbial functional groups. However, metagenomic sequencing has revealed previously undescribed diversity within these functional groups, and highlighted a need to reevaluate coverage of existing DNA primers for denitrification functional genes. We provide here a comprehensive in silico evaluation of primer sets that target diagnostic genes in the denitrification pathway. This analysis makes use of current DNA sequence data available for each functional gene. It contributes a comparative analysis of the strengths and limitations of each primer set for describing denitrifier functional groups. This analysis identifies genes for which development of new tools is needed, and aids in interpretation of existing datasets, both of which will facilitate application of molecular methods to further develop the predictive ecology of denitrifiers. This article is protected by copyright. All rights reserved.}, }
@article {pmid30723610, year = {2019}, author = {Greenfield, P and Tran-Dinh, N and Midgley, D}, title = {Kelpie: generating full-length 'amplicons' from whole-metagenome datasets.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e6174}, doi = {10.7717/peerj.6174}, pmid = {30723610}, issn = {2167-8359}, abstract = {Introduction: Whole-metagenome sequencing can be a rich source of information about the structure and function of entire metagenomic communities, but getting accurate and reliable results from these datasets can be challenging. Analysis of these datasets is founded on the mapping of sequencing reads onto known genomic regions from known organisms, but short reads will often map equally well to multiple regions, and to multiple reference organisms. Assembling metagenomic datasets prior to mapping can generate much longer and more precisely mappable sequences but the presence of closely related organisms and highly conserved regions makes metagenomic assembly challenging, and some regions of particular interest can assemble poorly. One solution to these problems is to use specialised tools, such as Kelpie, that can accurately extract and assemble full-length sequences for defined genomic regions from whole-metagenome datasets.
Methods: Kelpie is a kMer-based tool that generates full-length amplicon-like sequences from whole-metagenome datasets. It takes a pair of primer sequences and a set of metagenomic reads, and uses a combination of kMer filtering, error correction and assembly techniques to construct sets of full-length inter-primer sequences.
Results: The effectiveness of Kelpie is demonstrated here through the extraction and assembly of full-length ribosomal marker gene regions, as this allows comparisons with conventional amplicon sequencing and published metagenomic benchmarks. The results show that the Kelpie-generated sequences and community profiles closely match those produced by amplicon sequencing, down to low abundance levels, and running Kelpie on the synthetic CAMI metagenomic benchmarking datasets shows similar high levels of both precision and recall.
Conclusions: Kelpie can be thought of as being somewhat like an in-silico PCR tool, taking a primer pair and producing the resulting 'amplicons' from a whole-metagenome dataset. Marker regions from the 16S rRNA gene were used here as an example because this allowed the overall accuracy of Kelpie to be evaluated through comparisons with other datasets, approaches and benchmarks. Kelpie is not limited to this application though, and can be used to extract and assemble any genomic region present in a whole metagenome dataset, as long as it is bound by a pairs of highly conserved primer sequences.}, }
@article {pmid30720420, year = {2019}, author = {Salter, SJ and Scott, P and Page, AJ and Tracey, A and de Goffau, MC and Cormie, C and Ochoa-Montaño, B and Ling, CL and Tangmanakit, J and Turner, P and Parkhill, J}, title = {'Candidatus Ornithobacterium hominis': insights gained from draft genomes obtained from nasopharyngeal swabs.}, journal = {Microbial genomics}, volume = {5}, number = {2}, pages = {}, doi = {10.1099/mgen.0.000247}, pmid = {30720420}, issn = {2057-5858}, abstract = {'Candidatus Ornithobacterium hominis' represents a new member of the Flavobacteriaceae detected in 16S rRNA gene surveys of people from South-East Asia, Africa and Australia. It frequently colonizes the infant nasopharynx at high proportional abundance, and we demonstrate its presence in 42 % of nasopharyngeal swabs from 12-month-old children in the Maela refugee camp in Thailand. The species, a Gram-negative bacillus, has not yet been cultured, but the cells can be identified in mixed samples by fluorescent hybridization. Here, we report seven genomes assembled from metagenomic data, two to improved draft standard. The genomes are approximately 1.9 Mb, sharing 62 % average amino acid identity with the only other member of the genus, the bird pathogen Ornithobacterium rhinotracheale. The draft genomes encode multiple antibiotic-resistance genes, competition factors, Flavobacterium johnsoniae-like gliding motility genes and a homologue of the Pasteurella multocida mitogenic toxin. Intra- and inter-host genome comparison suggests that colonization with this bacterium is both persistent and strain exclusive.}, }
@article {pmid30719705, year = {2019}, author = {Cheng, L and Chen, Y and Zhang, X and Zheng, X and Cao, J and Wu, Z and Qin, W and Cheng, K}, title = {A metagenomic analysis of the modulatory effect of Cyclocarya paliurus flavonoids on the intestinal microbiome in a high fat diet-induced obesity mouse model.}, journal = {Journal of the science of food and agriculture}, volume = {}, number = {}, pages = {}, doi = {10.1002/jsfa.9622}, pmid = {30719705}, issn = {1097-0010}, abstract = {BACKGROUND: Due to low bioavailability, the majority of Cyclocarya paliurus flavonoids (CPF) remain in the large intestine where they may accumulate to exert a modulatory effect on the intestinal micro-ecology. Therefore, in this study, the modulatory effect of CPF on intestinal microbiota was investigated.
RESULTS: CPF dramatically ameliorated the obesity-induced gut dysbiosis. A significant decrease (P < 0.05) was observed in the ratio of Firmicutes/Bacteroidetes after CPF treatment for 8 weeks. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of biosynthesis of amino acids, two-component system and ATP-binding cassette (ABC) transporters enriched the most differentially expressed genes after CPF intervention.
CONCLUSION: This study indicated CPF might have prebiotic-like activity and could be used as a functional food component with potential therapeutic utility to prevent obesity-related metabolic disorders by manipulating the gut flora and affecting certain metabolic pathways, contributing to the improvement of human health. This article is protected by copyright. All rights reserved.}, }
@article {pmid30719076, year = {2019}, author = {Segal, JP and Mullish, BH and Quraishi, MN and Acharjee, A and Williams, HRT and Iqbal, T and Hart, AL and Marchesi, JR}, title = {The application of omics techniques to understand the role of the gut microbiota in inflammatory bowel disease.}, journal = {Therapeutic advances in gastroenterology}, volume = {12}, number = {}, pages = {1756284818822250}, doi = {10.1177/1756284818822250}, pmid = {30719076}, issn = {1756-283X}, abstract = {The aetiopathogenesis of inflammatory bowel diseases (IBD) involves the complex interaction between a patient's genetic predisposition, environment, gut microbiota and immune system. Currently, however, it is not known if the distinctive perturbations of the gut microbiota that appear to accompany both Crohn's disease and ulcerative colitis are the cause of, or the result of, the intestinal inflammation that characterizes IBD. With the utilization of novel systems biology technologies, we can now begin to understand not only details about compositional changes in the gut microbiota in IBD, but increasingly also the alterations in microbiota function that accompany these. Technologies such as metagenomics, metataxomics, metatranscriptomics, metaproteomics and metabonomics are therefore allowing us a deeper understanding of the role of the microbiota in IBD. Furthermore, the integration of these systems biology technologies through advancing computational and statistical techniques are beginning to understand the microbiome interactions that both contribute to health and diseased states in IBD. This review aims to explore how such systems biology technologies are advancing our understanding of the gut microbiota, and their potential role in delineating the aetiology, development and clinical care of IBD.}, }
@article {pmid30718896, year = {2019}, author = {Shin, B and Kim, M and Zengler, K and Chin, KJ and Overholt, WA and Gieg, LM and Konstantinidis, KT and Kostka, JE}, title = {Anaerobic degradation of hexadecane and phenanthrene coupled to sulfate reduction by enriched consortia from northern Gulf of Mexico seafloor sediment.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {1239}, doi = {10.1038/s41598-018-36567-x}, pmid = {30718896}, issn = {2045-2322}, abstract = {To advance understanding of the fate of hydrocarbons released from the Deepwater Horizon oil spill and deposited in marine sediments, this study characterized the microbial populations capable of anaerobic hydrocarbon degradation coupled with sulfate reduction in non-seep sediments of the northern Gulf of Mexico. Anaerobic, sediment-free enrichment cultures were obtained with either hexadecane or phenanthrene as sole carbon source and sulfate as a terminal electron acceptor. Phylogenetic analysis revealed that enriched microbial populations differed by hydrocarbon substrate, with abundant SSU rRNA gene amplicon sequences from hexadecane cultures showing high sequence identity (up to 98%) to Desulfatibacillum alkenivorans (family Desulfobacteraceae), while phenanthrene-enriched populations were most closely related to Desulfatiglans spp. (up to 95% sequence identity; family Desulfarculaceae). Assuming complete oxidation to CO2, observed stoichiometric ratios closely resembled the theoretical ratios of 12.25:1 for hexadecane and 8.25:1 for phenanthrene degradation coupled to sulfate reduction. Phenanthrene carboxylic acid was detected in the phenanthrene-degrading enrichment cultures, providing evidence to indicate carboxylation as an activation mechanism for phenanthrene degradation. Metagenome-assembled genomes (MAGs) revealed that phenanthrene degradation is likely mediated by novel genera or families of sulfate-reducing bacteria along with their fermentative syntrophic partners, and candidate genes linked to the degradation of aromatic hydrocarbons were detected for future study.}, }
@article {pmid30718881, year = {2019}, author = {Metsky, HC and Siddle, KJ and Gladden-Young, A and Qu, J and Yang, DK and Brehio, P and Goldfarb, A and Piantadosi, A and Wohl, S and Carter, A and Lin, AE and Barnes, KG and Tully, DC and Corleis, B and Hennigan, S and Barbosa-Lima, G and Vieira, YR and Paul, LM and Tan, AL and Garcia, KF and Parham, LA and Odia, I and Eromon, P and Folarin, OA and Goba, A and , and Simon-Lorière, E and Hensley, L and Balmaseda, A and Harris, E and Kwon, DS and Allen, TM and Runstadler, JA and Smole, S and Bozza, FA and Souza, TML and Isern, S and Michael, SF and Lorenzana, I and Gehrke, L and Bosch, I and Ebel, G and Grant, DS and Happi, CT and Park, DJ and Gnirke, A and Sabeti, PC and Matranga, CB}, title = {Capturing sequence diversity in metagenomes with comprehensive and scalable probe design.}, journal = {Nature biotechnology}, volume = {37}, number = {2}, pages = {160-168}, doi = {10.1038/s41587-018-0006-x}, pmid = {30718881}, issn = {1546-1696}, support = {R01 AI099210/AI/NIAID NIH HHS/United States ; }, abstract = {Metagenomic sequencing has the potential to transform microbial detection and characterization, but new tools are needed to improve its sensitivity. Here we present CATCH, a computational method to enhance nucleic acid capture for enrichment of diverse microbial taxa. CATCH designs optimal probe sets, with a specified number of oligonucleotides, that achieve full coverage of, and scale well with, known sequence diversity. We focus on applying CATCH to capture viral genomes in complex metagenomic samples. We design, synthesize, and validate multiple probe sets, including one that targets the whole genomes of the 356 viral species known to infect humans. Capture with these probe sets enriches unique viral content on average 18-fold, allowing us to assemble genomes that could not be recovered without enrichment, and accurately preserves within-sample diversity. We also use these probe sets to recover genomes from the 2018 Lassa fever outbreak in Nigeria and to improve detection of uncharacterized viral infections in human and mosquito samples. The results demonstrate that CATCH enables more sensitive and cost-effective metagenomic sequencing.}, }
@article {pmid30718869, year = {2019}, author = {Forster, SC and Kumar, N and Anonye, BO and Almeida, A and Viciani, E and Stares, MD and Dunn, M and Mkandawire, TT and Zhu, A and Shao, Y and Pike, LJ and Louie, T and Browne, HP and Mitchell, AL and Neville, BA and Finn, RD and Lawley, TD}, title = {A human gut bacterial genome and culture collection for improved metagenomic analyses.}, journal = {Nature biotechnology}, volume = {37}, number = {2}, pages = {186-192}, doi = {10.1038/s41587-018-0009-7}, pmid = {30718869}, issn = {1546-1696}, abstract = {Understanding gut microbiome functions requires cultivated bacteria for experimental validation and reference bacterial genome sequences to interpret metagenome datasets and guide functional analyses. We present the Human Gastrointestinal Bacteria Culture Collection (HBC), a comprehensive set of 737 whole-genome-sequenced bacterial isolates, representing 273 species (105 novel species) from 31 families found in the human gastrointestinal microbiota. The HBC increases the number of bacterial genomes derived from human gastrointestinal microbiota by 37%. The resulting global Human Gastrointestinal Bacteria Genome Collection (HGG) classifies 83% of genera by abundance across 13,490 shotgun-sequenced metagenomic samples, improves taxonomic classification by 61% compared to the Human Microbiome Project (HMP) genome collection and achieves subspecies-level classification for almost 50% of sequences. The improved resource of gastrointestinal bacterial reference sequences circumvents dependence on de novo assembly of metagenomes and enables accurate and cost-effective shotgun metagenomic analyses of human gastrointestinal microbiota.}, }
@article {pmid30718868, year = {2019}, author = {Zou, Y and Xue, W and Luo, G and Deng, Z and Qin, P and Guo, R and Sun, H and Xia, Y and Liang, S and Dai, Y and Wan, D and Jiang, R and Su, L and Feng, Q and Jie, Z and Guo, T and Xia, Z and Liu, C and Yu, J and Lin, Y and Tang, S and Huo, G and Xu, X and Hou, Y and Liu, X and Wang, J and Yang, H and Kristiansen, K and Li, J and Jia, H and Xiao, L}, title = {1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses.}, journal = {Nature biotechnology}, volume = {37}, number = {2}, pages = {179-185}, doi = {10.1038/s41587-018-0008-8}, pmid = {30718868}, issn = {1546-1696}, abstract = {Reference genomes are essential for metagenomic analyses and functional characterization of the human gut microbiota. We present the Culturable Genome Reference (CGR), a collection of 1,520 nonredundant, high-quality draft genomes generated from >6,000 bacteria cultivated from fecal samples of healthy humans. Of the 1,520 genomes, which were chosen to cover all major bacterial phyla and genera in the human gut, 264 are not represented in existing reference genome catalogs. We show that this increase in the number of reference bacterial genomes improves the rate of mapping metagenomic sequencing reads from 50% to >70%, enabling higher-resolution descriptions of the human gut microbiome. We use the CGR genomes to annotate functions of 338 bacterial species, showing the utility of this resource for functional studies. We also carry out a pan-genome analysis of 38 important human gut species, which reveals the diversity and specificity of functional enrichment between their core and dispensable genomes.}, }
@article {pmid30718848, year = {2019}, author = {Valles-Colomer, M and Falony, G and Darzi, Y and Tigchelaar, EF and Wang, J and Tito, RY and Schiweck, C and Kurilshikov, A and Joossens, M and Wijmenga, C and Claes, S and Van Oudenhove, L and Zhernakova, A and Vieira-Silva, S and Raes, J}, title = {The neuroactive potential of the human gut microbiota in quality of life and depression.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41564-018-0337-x}, pmid = {30718848}, issn = {2058-5276}, abstract = {The relationship between gut microbial metabolism and mental health is one of the most intriguing and controversial topics in microbiome research. Bidirectional microbiota-gut-brain communication has mostly been explored in animal models, with human research lagging behind. Large-scale metagenomics studies could facilitate the translational process, but their interpretation is hampered by a lack of dedicated reference databases and tools to study the microbial neuroactive potential. Surveying a large microbiome population cohort (Flemish Gut Flora Project, n = 1,054) with validation in independent data sets (ntotal = 1,070), we studied how microbiome features correlate with host quality of life and depression. Butyrate-producing Faecalibacterium and Coprococcus bacteria were consistently associated with higher quality of life indicators. Together with Dialister, Coprococcus spp. were also depleted in depression, even after correcting for the confounding effects of antidepressants. Using a module-based analytical framework, we assembled a catalogue of neuroactive potential of sequenced gut prokaryotes. Gut-brain module analysis of faecal metagenomes identified the microbial synthesis potential of the dopamine metabolite 3,4-dihydroxyphenylacetic acid as correlating positively with mental quality of life and indicated a potential role of microbial γ-aminobutyric acid production in depression. Our results provide population-scale evidence for microbiome links to mental health, while emphasizing confounder importance.}, }
@article {pmid30718806, year = {2019}, author = {Bischoff, V and Bunk, B and Meier-Kolthoff, JP and Spröer, C and Poehlein, A and Dogs, M and Nguyen, M and Petersen, J and Daniel, R and Overmann, J and Göker, M and Simon, M and Brinkhoff, T and Moraru, C}, title = {Cobaviruses - a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0362-7}, pmid = {30718806}, issn = {1751-7370}, support = {AWI-HE440//Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research (Alfred-Wegener- Institute, Helmholtz Centre for Polar and Marine Research)/ ; TRR51//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, abstract = {Bacteriophages are widely considered to influence bacterial communities, however most phages are still unknown or not studied well enough to understand their ecological roles. We have isolated two phages infecting Lentibacter sp. SH36, affiliated with the marine Roseobacter group, and retrieved similar phage genomes from publicly available metagenomics databases. Phylogenetic analysis placed the new phages within the Cobavirus group, in the here newly proposed genus Siovirus and subfamily Riovirinae of the Podoviridae. Gene composition and presence of direct terminal repeats in cultivated cobaviruses point toward a genome replication and packaging strategy similar to the T7 phage. Investigation of the genomes suggests that viral lysis of the cell proceeds via the canonical holin-endolysin pathway. Cobaviral hosts include members of the genera Lentibacter, Sulfitobacter and Celeribacter of the Roseobacter group within the family Rhodobacteraceae (Alphaproteobacteria). Screening more than 5,000 marine metagenomes, we found cobaviruses worldwide from temperate to tropical waters, in the euphotic zone, mainly in bays and estuaries, but also in the open ocean. The presence of cobaviruses in protist metagenomes as well as the phylogenetic neighborhood of cobaviruses in glutaredoxin and ribonucleotide reductase trees suggest that cobaviruses could infect bacteria associated with phototrophic or grazing protists. With this study, we expand the understanding of the phylogeny, classification, genomic organization, biogeography and ecology of this phage group infecting marine Rhodobacteraceae.}, }
@article {pmid30718727, year = {2019}, author = {Neethu, CS and Saravanakumar, C and Purvaja, R and Robin, RS and Ramesh, R}, title = {Oil-Spill Triggered Shift in Indigenous Microbial Structure and Functional Dynamics in Different Marine Environmental Matrices.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {1354}, doi = {10.1038/s41598-018-37903-x}, pmid = {30718727}, issn = {2045-2322}, abstract = {Microbial degradation has long been recognized as the key rescue mechanism in shaping the oil polluted marine environments and the role of indigenous populations or their functional genomics have never been explored from Indian marine environments, post an oil spill event. In the current study, high throughput metagenomic analysis, PLFA profiling and mass spectrophotometric analysis was performed in combination with metabolomics to capture signature variations among the microbial communities in sediment, water and laboratory enrichments. Contrary to the previous reports, the bloom of Pseudomonadales (specifically genus Acinetobacter) in oiled sediment and Methylococcales in oiled water outnumbered the relative abundance of Alcanivorax in response to hydrocarbon contamination. Overall enhancement of xenobiotic degradation was suggested by metabolomic analysis in sediment and water post the spill event and varying quantitative assemblage of enzymes were found to be involved in hydrocarbon utilization. Laboratory enrichments revealed the competitive advantage of sediment communities over the water communities although unique taxa belonging to the later were also found to be enriched under in vitro conditions. Simultaneous analysis of sediment and water in the study provided explicit evidences on existence of differential microbial community dynamics, offering insight into possibilities of formulating nature identical solutions for hydrocarbon pollution.}, }
@article {pmid30718047, year = {2019}, author = {Zegarra-Ruiz, DF and Diehl, GE}, title = {Skin IL-17-Producing T Cells Support Repair 2!.}, journal = {Trends in immunology}, volume = {40}, number = {3}, pages = {177-179}, doi = {10.1016/j.it.2019.01.004}, pmid = {30718047}, issn = {1471-4981}, abstract = {In a recent study, Harrison et al. (Science 2019;363;eaat6280) report that RORγt-expressing skin commensal-specific T cells rapidly respond to tissue wounding by producing type 2 T helper cell (Th2) cytokines in mice. The cells constitutively coexpress GATA-3 and type 2 cytokine mRNAs that are translated after injury. These T cells act as sentinels, linking T cell receptor (TCR) recognition of commensals, tissue damage, and wound repair.}, }
@article {pmid30717674, year = {2019}, author = {Lei, Z and Zhang, K and Li, C and Jiao, T and Wu, J and Wei, Y and Tian, K and Li, C and Tang, D and Davis, DI and Casper, DP and Jiang, H and Wang, X and Wang, J}, title = {Ruminal metagenomic analyses of goat data reveals potential functional microbiota by supplementation with essential oil-cobalt complexes.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {30}, doi = {10.1186/s12866-019-1400-3}, pmid = {30717674}, issn = {1471-2180}, support = {No. 201503134, 201303059//Agro-scientific Research in the Public Interest/ ; No. CARS-39-18//China Agriculture Research System/ ; No. 17ZD2NC020//the major science and technology projects of Gansu Province/ ; No. 2012-2-159//Lanzhou Science & Technology Bureau/ ; }, abstract = {BACKGROUND: Essential Oils (EO) are complex mixtures of plant secondary metabolites that have been proposed as promising feed additives for mitigating methane and ammonia emissions. We have previously demonstrated that Essential Oil-Cobalt (EOC) supplementation resulted in increased average daily gain and improved phenotypes (cashmere fiber traits, carcass weight, and meat quality) when cashmere goats received supplementation at approximately 2 mg/kg of body weight. However, the ruminal microbiological effects of EO remain poorly understood with regard to the extent to which ruminal populations can adapt to EO presence as feed ingredients. The effects of varying levels of EO require additional study.
RESULTS: In this study, we conducted metagenomic analyses using ruminal fluid samples from three groups (addition of 0, 52, and 91 mg) to evaluate the influence of dietary EOC supplementation on goat rumen bacterial community dynamics. EOC addition resulted in changes of ruminal fermentation types and the EOC dose strongly impacted the stability of ruminal microbiota. The Bacteroides sp. and Succinivibrio sp. type bacterial community was positively associated with improved volatile fatty acid production when the diet was supplemented with EOC.
CONCLUSIONS: A clear pattern was found that reflected rapid fermentative improvement in the rumen, subsequent to butyrate metabolism and EOC based feed additives may affect rumen microbes to further improve feed conversion. This observation indicates that EOC can be safely used to enhance animal productivity and to reduce ammonia and waste gas emissions, thus positively impacting the environment.}, }
@article {pmid30717665, year = {2019}, author = {Jayasundara, D and Herath, D and Senanayake, D and Saeed, I and Yang, CY and Sun, Y and Chang, BC and Tang, SL and Halgamuge, SK}, title = {ENVirT: inference of ecological characteristics of viruses from metagenomic data.}, journal = {BMC bioinformatics}, volume = {19}, number = {Suppl 13}, pages = {377}, doi = {10.1186/s12859-018-2398-5}, pmid = {30717665}, issn = {1471-2105}, support = {LP140100670//Australian Research Council/ ; DP150103512//Australian Research Council/ ; }, mesh = {*Algorithms ; Computer Simulation ; *Ecological and Environmental Phenomena ; Fermented Foods ; Gastrointestinal Microbiome ; Genome, Viral ; Humans ; Lakes/virology ; *Metagenomics ; Time Factors ; Viruses/genetics ; }, abstract = {BACKGROUND: Estimating the parameters that describe the ecology of viruses,particularly those that are novel, can be made possible using metagenomic approaches. However, the best-performing existing methods require databases to first estimate an average genome length of a viral community before being able to estimate other parameters, such as viral richness. Although this approach has been widely used, it can adversely skew results since the majority of viruses are yet to be catalogued in databases.
RESULTS: In this paper, we present ENVirT, a method for estimating the richness of novel viral mixtures, and for the first time we also show that it is possible to simultaneously estimate the average genome length without a priori information. This is shown to be a significant improvement over database-dependent methods, since we can now robustly analyze samples that may include novel viral types under-represented in current databases. We demonstrate that the viral richness estimates produced by ENVirT are several orders of magnitude higher in accuracy than the estimates produced by existing methods named PHACCS and CatchAll when benchmarked against simulated data. We repeated the analysis of 20 metavirome samples using ENVirT, which produced results in close agreement with complementary in virto analyses.
CONCLUSIONS: These insights were previously not captured by existing computational methods. As such, ENVirT is shown to be an essential tool for enhancing our understanding of novel viral populations.}, }
@article {pmid30717284, year = {2019}, author = {Ai, D and Pan, H and Han, R and Li, X and Liu, G and Xia, LC}, title = {Using Decision Tree Aggregation with Random Forest Model to Identify Gut Microbes Associated with Colorectal Cancer.}, journal = {Genes}, volume = {10}, number = {2}, pages = {}, doi = {10.3390/genes10020112}, pmid = {30717284}, issn = {2073-4425}, support = {61873027,61370131//National Natural Science Foundation of China/ ; HG006137-07//Foundation for the National Institutes of Health/ ; 132922-PF-18-184-01-TBG//Intermountain Healthcare/ ; }, abstract = {The imbalance of human gut microbiota has been associated with colorectal cancer. In recent years, metagenomics research has provided a large amount of scientific data enabling us to study the dedicated roles of gut microbes in the onset and progression of cancer. We removed unrelated and redundant features during feature selection by mutual information. We then trained a random forest classifier on a large metagenomics dataset of colorectal cancer patients and healthy people assembled from published reports and extracted and analysed the information from the learned decision trees. We identified key microbial species associated with colorectal cancers. These microbes included Porphyromonasasaccharolytica, Peptostreptococcusstomatis, Fusobacterium,Parvimonas sp., Streptococcusvestibularis and Flavonifractorplautii. We obtained the optimal splitting abundance thresholds for these species to distinguish between healthy and colorectal cancer samples. This extracted consensus decision tree may be applied to the diagnosis of colorectal cancers.}, }
@article {pmid30716065, year = {2019}, author = {Louca, S and Mazel, F and Doebeli, M and Parfrey, LW}, title = {A census-based estimate of Earth's bacterial and archaeal diversity.}, journal = {PLoS biology}, volume = {17}, number = {2}, pages = {e3000106}, doi = {10.1371/journal.pbio.3000106}, pmid = {30716065}, issn = {1545-7885}, abstract = {The global diversity of Bacteria and Archaea, the most ancient and most widespread forms of life on Earth, is a subject of intense controversy. This controversy stems largely from the fact that existing estimates are entirely based on theoretical models or extrapolations from small and biased data sets. Here, in an attempt to census the bulk of Earth's bacterial and archaeal ("prokaryotic") clades and to estimate their overall global richness, we analyzed over 1.7 billion 16S ribosomal RNA amplicon sequences in the V4 hypervariable region obtained from 492 studies worldwide, covering a multitude of environments and using multiple alternative primers. From this data set, we recovered 739,880 prokaryotic operational taxonomic units (OTUs, 16S-V4 gene clusters at 97% similarity), a commonly used measure of microbial richness. Using several statistical approaches, we estimate that there exist globally about 0.8-1.6 million prokaryotic OTUs, of which we recovered somewhere between 47%-96%, representing >99.98% of prokaryotic cells. Consistent with this conclusion, our data set independently "recaptured" 91%-93% of 16S sequences from multiple previous global surveys, including PCR-independent metagenomic surveys. The distribution of relative OTU abundances is consistent with a log-normal model commonly observed in larger organisms; the total number of OTUs predicted by this model is also consistent with our global richness estimates. By combining our estimates with the ratio of full-length versus partial-length (V4) sequence diversity in the SILVA sequence database, we further estimate that there exist about 2.2-4.3 million full-length OTUs worldwide. When restricting our analysis to the Americas, while controlling for the number of studies, we obtain similar richness estimates as for the global data set, suggesting that most OTUs are globally distributed. Qualitatively similar results are also obtained for other 16S similarity thresholds (90%, 95%, and 99%). Our estimates constrain the extent of a poorly quantified rare microbial biosphere and refute recent predictions that there exist trillions of prokaryotic OTUs.}, }
@article {pmid30715617, year = {2019}, author = {Zhao, H and Gao, H and Ji, K and Yan, B and Li, Q and Mo, S and Zheng, M and Ou, Q and Wu, B and Li, N and Jiang, C}, title = {Isolation and biochemical characterization of a metagenome-derived 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase gene from subtropical marine mangrove wetland sediments.}, journal = {AMB Express}, volume = {9}, number = {1}, pages = {19}, doi = {10.1186/s13568-019-0742-4}, pmid = {30715617}, issn = {2191-0855}, support = {31760437//National Natural Science Foundation of China/ ; 2017FY100704//Science and Technology Basic Resources Investigation Program of China/ ; 2017JJB130020//Natural Science Foundation of Guangxi Zhuang Autonomous Region of China/ ; GKLMC-201702//Open Research Fund Program of Guangxi Key Lab of Mangrove Conservation and Utilization/ ; 2016Q07//Basic Scientific Fund for National Public Research Institutes of China/ ; }, abstract = {3-Deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHPS) is a key rate-limiting enzyme in aromatic amino acid anabolism. A new Iβ-type DAHPS gene (aro1A) was identified in a metagenomic library from subtropical marine mangrove sediment. The gene encoded a polypeptide composed of 272 amino acids and had a maximum similarity of 52.4% to a known DAHPS at the amino acid level. Multiple sequence alignment, homologous modeling, and molecular docking showed that Aro1A had the typical (β/α)8 barrel-shaped catalytic structural domain of DAHPS. The motifs and amino acid residues involved in the combination of substrates and metal ligand were highly conservative with the known DAHPS. The putative DAHPS gene was subcloned into a pET-30a(+) vector and was overexpressed in Escherichia coli Rosetta (DE3) cells. The recombinant protein was purified to homogeneity. The maximum activity for the recombinant Aro1A protein occurred at pH 8.0 and 40 °C. Ba2+ and Ca2+ stimulated the activity of Aro1A protein. The enzyme showed high affinity and catalytic efficiency (K mPEP = 19.58 μM, V maxPEP = 29.02 μM min-1, and k catPEP /K mPEP = 0.88 s-1 μM-1) under optimal reaction conditions. The enzymatic property of Aro1A indicates its potential in aromatic amino acid industrial production.}, }
@article {pmid30715365, year = {2019}, author = {Goss-Souza, D and Mendes, LW and Borges, CD and Rodrigues, JLM and Tsai, SM}, title = {Amazon forest-to-agriculture conversion alters rhizosphere microbiome composition while functions are kept.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiz009}, pmid = {30715365}, issn = {1574-6941}, abstract = {The conversion of native forest to agriculture is the main cause of microbial biodiversity loss in Amazon soils. In order to better understand this effect, we used metagenomics to investigate microbial patterns and functions in bulk soil and rhizosphere of soybean, in a long-term forest-to-agriculture conversion. Long-term forest-to-agriculture led to microbial homogenization and loss of diversity in both bulk soil and rhizosphere, mainly driven by decreasing aluminum concentration and increased cations saturation in soil, due liming and fertilization in long-term no-till cropping. Data revealed that long-term no-till culminated with decrease in Acidobacteria, Actinobacteria and Proteobacteria abundances. However, α- and β-Proteobacteria abundances were higher in rhizosphere than in bulk soil, regardless time after forest-to-agriculture conversion. Changes in functional potential occurred predominantly in bulk soil, with decreases in functions related to potassium metabolism and virulence, disease and defense while functions related to nucleic acids metabolism increased. Functions in soybean rhizosphere remained stable, except for those related to potassium metabolism, which decreased after 20-year no-till cropping. Together, our results show that soybean root system selects microbial taxa via trade-offs, to keep functional resilience in the rhizosphere microbiome along time.}, }
@article {pmid30715242, year = {2019}, author = {Wang, J and Li, Y and He, X and Ma, J and Hong, W and Hu, F and Zhao, L and Li, Q and Zhang, J and Zhang, C and Zhang, F}, title = {Gemykibivirus genome in lower respiratory tract of elderly woman with unexplained acute respiratory distress syndrome.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {}, number = {}, pages = {}, doi = {10.1093/cid/ciz072}, pmid = {30715242}, issn = {1537-6591}, abstract = {We identified, for the first time, the presence of small circular single stranded Gemykibivirus (GkV) genome from the respiratory tract of an elderly woman with severe acute respiratory distress syndrome using metagenomics analysis. Our results suggest that further studies on whether GkVs infect humans and cause respiratory disease are needed.}, }
@article {pmid30713820, year = {2019}, author = {Chua, EG and Chong, JY and Lamichhane, B and Webberley, KM and Marshall, BJ and Wise, MJ and Tay, CY}, title = {Gastric Helicobacter pylori infection perturbs human oral microbiota.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6336}, doi = {10.7717/peerj.6336}, pmid = {30713820}, issn = {2167-8359}, abstract = {Background: We investigated the effects of gastric Helicobacter pylori infection on the daytime and overnight human oral microbiota.
Methods: Twenty four volunteers were recruited. Ten tested positive for H. pylori infection by the Carbon-14 Urea Breath Test, and the rest were negative. Two oral swabs were collected: one immediately after waking up in the morning and before brushing teeth, and another in the evening before teeth-brushing. DNA extract acquired from each swab was subjected to Illumina sequencing of 16S rRNA gene amplicons. The microbial abundance and composition were analysed in relation to H. pylori infection status.
Results: Helicobacter pylori-positive individuals had significant changes in the alpha and beta diversities in the daytime samples in comparison to those who were H. pylori negative. To identify which taxa could be significantly affected within the cohorts in the daytime, we employed the LEfSe method. When compared against UBT-negative samples, significantly higher abundances were detected in both Pseudomonas and Roseomonas, while Fusobacterium, Solobacterium, Haemophilus and Streptococcus were significantly decreased in the UBT-positive samples.
Discussion: Our data demonstrated that H. pylori infection affects the human daytime oral microbiota. The hitherto undocumented changes of several bacterial genera due to H. pylori infection require more studies to examine their potential health effects on affected individuals.}, }
@article {pmid30705748, year = {2018}, author = {Huynh, T and Xu, S}, title = {Gene Annotation Easy Viewer (GAEV): Integrating KEGG's Gene Function Annotations and Associated Molecular Pathways.}, journal = {F1000Research}, volume = {7}, number = {}, pages = {416}, doi = {10.12688/f1000research.14012.2}, pmid = {30705748}, issn = {2046-1402}, abstract = {We developed a Gene Annotation Easy Viewer (GAEV) that integrates the gene annotation data from the KEGG (Kyoto Encyclopedia of Genes and Genomes) Automatic Annotation Server. GAEV generates an easy-to-read table that summarizes the query gene name, the KO (KEGG Orthology) number, name of gene orthologs, functional definition of the ortholog, and the functional pathways that query gene has been mapped to. Via links to KEGG pathway maps, users can directly examine the interaction between gene products involved in the same molecular pathway. We provide a usage example by annotating the newly published freshwater microcrustacean Daphnia pulex genome. This gene-centered view of gene function and pathways will greatly facilitate the genome annotation of non-model species and metagenomics data. GAEV runs on a Windows or Linux system equipped with Python 3 and provides easy accessibility to users with no prior Unix command line experience.}, }
@article {pmid30712189, year = {2019}, author = {Brito, EMS and Romero-Núñez, VM and Caretta, CA and Bertin, P and Valerdi-Negreros, JC and Guyoneaud, R and Goñi-Urriza, M}, title = {The bacterial diversity on steam vents from Paricutín and Sapichu volcanoes.}, journal = {Extremophiles : life under extreme conditions}, volume = {23}, number = {2}, pages = {249-263}, doi = {10.1007/s00792-019-01078-8}, pmid = {30712189}, issn = {1433-4909}, support = {0627/15//Convocatoria de Apoyo a la Investigacion de la UG (DAIP)/ ; ANR-CONACyT-188775//Biometal Project/ ; }, abstract = {Vapor steam vents are prevailing structures on geothermal sites in which local geochemical conditions allow the development of extremophilic microorganisms. We describe the structure of the prokaryotic community able to grow on the walls and rocks of such microecosystems in two terrestrial Mexican volcanoes: Paricutín (PI and PII samples) and its satellite Sapichu (S sample). The investigated samples showed similar diversity indices, with few dominant OTUs (abundance > 1%): 21, 16 and 23, respectively for PI, PII and S. However, each steam vent showed a particular community profile: PI was dominated by photosynthetic bacteria (Cyanobacteria and Chloroflexia class), PII by Actinobacteria and Proteobacteria, and S by Ktedonobacteria class, Acidobacteria and Cyanobacteria phyla. Concerning the predicted metabolic potential, we found a dominance of cellular pathways, especially the ones for energy generation with metabolisms for sulfur respiration, nitrogen fixation, methanogenesis, carbon fixation, photosynthesis, and metals, among others. We suggest a different maturity stage for the three studied fumaroles, from the youngest (PI) to the oldest (S and PII), also influenced by the temperature and other geochemical parameters. Furthermore, four anaerobic strains were isolated, belonging to Clostridia class (Clostridium sphenoides, C. swellfunanium and Anaerocolumna cellulosilytica) and to Bacilli class (Paenibacillus azoreducens).}, }
@article {pmid30711887, year = {2019}, author = {Lugli, GA and Mangifesta, M and Mancabelli, L and Milani, C and Turroni, F and Viappiani, A and van Sinderen, D and Ventura, M}, title = {Compositional assessment of bacterial communities in probiotic supplements by means of metagenomic techniques.}, journal = {International journal of food microbiology}, volume = {294}, number = {}, pages = {1-9}, doi = {10.1016/j.ijfoodmicro.2019.01.011}, pmid = {30711887}, issn = {1879-3460}, abstract = {Health promoting or probiotic bacteria are commonly incorporated into a variety of functional foods and drug formulations, due to their purported ability to confer benefit to host health. Despite the extensive commercial exploitation of probiotic formulations there are still major knowledge gaps regarding the precise molecular mechanism of action and corresponding genetic/genomic properties of probiotic bacteria. In the current study, we describe a metagenomic approach which allows determination of the composition of probiotic supplements through next-generation sequencing analyses based on rRNA-associated sequences to assess bacterial composition of the product combined with a shotgun metagenomics approach directed to decode the genome sequences of the probiotic strains for each product assayed. The here developed approach has been tested for 10 probiotic supplements, revealing inconsistencies between the identified probiotic strains and the declared strains as indicated by the producers. Furthermore, the decoded bacterial genome sequence of Bifidobacterium animalis subsp. lactis BB-12 from a 1995 frozen dried stock revealed genetic evidence for genome evolution and stability of this microorganism when compared with the re-constructed genome of the identical strain from a probiotic supplement of 2017.}, }
@article {pmid30710817, year = {2019}, author = {Pore, SD and Engineer, A and Dagar, SS and Dhakephalkar, PK}, title = {Meta-omics based analyses of microbiome involved in biomethanation of rice straw in a thermophilic anaerobic bioreactor under optimized conditions.}, journal = {Bioresource technology}, volume = {279}, number = {}, pages = {25-33}, doi = {10.1016/j.biortech.2019.01.099}, pmid = {30710817}, issn = {1873-2976}, abstract = {Biomethanation of rice straw was performed at 55 °C without thermochemical pretreatment using cattle dung supplemented with Methanothermobacter thermautotrophicus strains. Methane yield of 323 ml g-1 VS obtained under optimized conditions such as particle size (1 mm), carbon to nitrogen ratio (15:1), substrate to inoculum ratio (1:1), organic loading rate (7.5% w/v) and hydraulic retention time (20 days), was one of the highest ever reported from rice straw. Metagenome analysis revealed several putative novel taxa among resident microbes. The genomes of Clostridium, Hungateiclostridium, Alkaliphilus, Anaerocolumna, Olsenella, Paenibacillus, Pseudoclostridium, Tepidanaerobacter and Turicibacter were recovered as metagenome assisted genomes. Clostridium spp. and M. thermautotrophicus were the dominant hydrolytic and methanogenic microbes, respectively. Syntrophic acetate oxidation coupled to hydrogenotrophic methanogenesis was found to be the major pathway for methane production. Efficient thermophilic biomethanation of rice straw without thermochemical pretreatment using cattle dung supplemented with M. thermautotrophicus is reported for the first time.}, }
@article {pmid30710781, year = {2019}, author = {Sun, FL and Fan, LL and Wang, YS and Huang, LY}, title = {Metagenomic analysis of the inhibitory effect of chromium on microbial communities and removal efficiency in A2O sludge.}, journal = {Journal of hazardous materials}, volume = {368}, number = {}, pages = {523-529}, doi = {10.1016/j.jhazmat.2019.01.076}, pmid = {30710781}, issn = {1873-3336}, abstract = {This is the first study exploring the effects of persistent Cr(VI) treatment on microbial communities and function as well as the process efficiency of an A2O system. The inhibitory effect was clearly higher at a high Cr(VI) concentration than a low Cr(VI) concentration, and different Cr(VI) concentrations had distinct effects on the microbial communities as well as on the performance efficiency of the system. Functional annotation analysis indicated that Cr(VI) stress inhibited most of the metabolic pathway and functional genes of the microbial communities, especially those involved in the denitrification pathway. Network analysis was used to investigate the co-occurrence patterns between denitrification genes and microbial taxa; the results indicated that microorganisms with functional genes had high diversity and were adversely affected by Cr(VI) exposure. This study is the first to establish a relationship between Cr(VI) stress and microbial communities and function as well as to determine the underlying mechanisms and roles of Cr(VI) in A2O sludge.}, }
@article {pmid30709420, year = {2019}, author = {Shi, W and Li, M and Wei, G and Tian, R and Li, C and Wang, B and Lin, R and Shi, C and Chi, X and Zhou, B and Gao, Z}, title = {The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {14}, doi = {10.1186/s40168-019-0629-2}, pmid = {30709420}, issn = {2049-2618}, support = {41306150//National Natural Science Foundation Project of China/ ; 201708370022//China Scholarship Council/ ; 2017YFD0201100 and 2017YFD0800200//National Key R&D Program of China/ ; SDAIT-16-01//Potato Innovation Program for Chief Expert of Shandong Province/ ; }, abstract = {BACKGROUND: Soil microorganisms can mediate the occurrence of plant diseases. Potato common scab (CS) is a refractory disease caused by pathogenic Streptomyces that occurs worldwide, but little is known about the interactions between CS and the soil microbiome. In this study, four soil-root system compartments (geocaulosphere soil (GS), rhizosphere soil (RS), root-zone soil (ZS), and furrow soil (FS)) were analyzed for potato plants with naturally high (H) and low (L) scab severity levels. We aimed to determine the composition and putative function of the soil microbiome associated with potato CS.
RESULTS: The copy numbers of the scab phytotoxin biosynthetic gene txtAB and the bacterial 16S rRNA gene as well as the diversity and composition of each of the four soil-root system compartments were examined; GS was the only compartment that exhibited significant differences between the H and L groups. Compared to the H group, the L group exhibited a lower txtAB gene copy number, lower bacterial 16S copy number, higher diversity, higher co-occurrence network complexity, and higher community function similarity within the GS microbiome. The community composition and function of the GS samples were further revealed by shotgun metagenomic sequencing. Variovorax, Stenotrophomonas, and Agrobacterium were the most abundant genera that were significantly and positively correlated with the scab severity level, estimated absolute abundance (EAA) of pathogenic Streptomyces, and txtAB gene copy number. In contrast, Geobacillus, Curtobacterium, and unclassified Geodermatophilaceae were significantly negatively correlated with these three parameters. Compared to the function profiles in the L group, several genes involved in "ABC transporters," the "bacterial secretion system," "quorum sensing (QS)," "nitrogen metabolism," and some metabolism by cytochrome P450 were enriched in the H group. In contrast, some antibiotic biosynthesis pathways were enriched in the L group. Based on the differences in community composition and function, a simple model was proposed to explain the putative relationships between the soil microbiome and CS occurrence.
CONCLUSIONS: The GS microbiome was closely associated with CS severity in the soil-root system, and the occurrence of CS was accompanied by changes in community composition and function. The differential functions provide new clues to elucidate the mechanism underlying the interaction between CS occurrence and the soil microbiome, and varying community compositions provide novel insights into CS occurrence.}, }
@article {pmid30709355, year = {2019}, author = {Warwick-Dugdale, J and Buchholz, HH and Allen, MJ and Temperton, B}, title = {Host-hijacking and planktonic piracy: how phages command the microbial high seas.}, journal = {Virology journal}, volume = {16}, number = {1}, pages = {15}, doi = {10.1186/s12985-019-1120-1}, pmid = {30709355}, issn = {1743-422X}, support = {NE/L002434/1//Natural Environment Research Council (GB) Great Western Four+ (GW4+) Doctoral Training Partnership PhD/ ; NE/R010935/1//Natural Environment Research Council/ ; NE/P008534/1//Natural Environment Research Council/ ; BIOS-SCOPE//Simons Foundation (US)/ ; }, abstract = {Microbial communities living in the oceans are major drivers of global biogeochemical cycles. With nutrients limited across vast swathes of the ocean, marine microbes eke out a living under constant assault from predatory viruses. Viral concentrations exceed those of their bacterial prey by an order of magnitude in surface water, making these obligate parasites the most abundant biological entities in the ocean. Like the pirates of the 17th and 18th centuries that hounded ships plying major trade and exploration routes, viruses have evolved mechanisms to hijack microbial cells and repurpose their cargo and indeed the vessels themselves to maximise viral propagation. Phenotypic reconfiguration of the host is often achieved through Auxiliary Metabolic Genes - genes originally derived from host genomes but maintained and adapted in viral genomes to redirect energy and substrates towards viral synthesis. In this review, we critically evaluate the literature describing the mechanisms used by bacteriophages to reconfigure host metabolism and to plunder intracellular resources to optimise viral production. We also highlight the mechanisms used when, in challenging environments, a 'batten down the hatches' strategy supersedes that of 'plunder and pillage'. Here, the infecting virus increases host fitness through phenotypic augmentation in order to ride out the metaphorical storm, with a concomitant impact on host substrate uptake and metabolism, and ultimately, their interactions with their wider microbial community. Thus, the traditional view of the virus-host relationship as predator and prey does not fully characterise the variety or significance of the interactions observed. Recent advances in viral metagenomics have provided a tantalising glimpse of novel mechanisms of viral metabolic reprogramming in global oceans. Incorporation of these new findings into global biogeochemical models requires experimental evidence from model systems and major improvements in our ability to accurately predict protein function from sequence data.}, }
@article {pmid30709012, year = {2019}, author = {Dang, Z and McLenachan, PA and Lockhart, PJ and Waipara, N and Er, O and Reynolds, C and Blanchon, D}, title = {Metagenome Profiling Identifies Potential Biocontrol Agents for Selaginella kraussiana in New Zealand.}, journal = {Genes}, volume = {10}, number = {2}, pages = {}, doi = {10.3390/genes10020106}, pmid = {30709012}, issn = {2073-4425}, abstract = {Metagenomics can be used to identify potential biocontrol agents for invasive species and was used here to identify candidate species for biocontrol of an invasive club moss in New Zealand. Profiles were obtained for Selaginella kraussiana collected from nine geographically disjunct locations in Northern New Zealand. These profiles were distinct from those obtained for the exotic club moss Selaginella moellendorffii and the native club mosses Lycopodium deuterodensum and Lycopodium volubile also collected in Northern New Zealand. Fungi and bacteria implicated elsewhere in causing plant disease were identified on plants of Selaginella that exhibited signs of necrosis. Most notably, high densities of sequence reads from Xanthomonas translucens and Pseudomonas syringae were associated with some populations of Selaginella but not Lycopodium. Since these bacteria are already in use as biocontrol agents elsewhere, further investigation into their potential as biocontrol of Selaginella in New Zealand is suggested.}, }
@article {pmid30708164, year = {2019}, author = {Tian, Z and Chi, Y and Yu, B and Yang, M and Zhang, Y}, title = {Thermophilic anaerobic digestion reduces ARGs in excess sludge even under high oxytetracycline concentrations.}, journal = {Chemosphere}, volume = {222}, number = {}, pages = {305-313}, doi = {10.1016/j.chemosphere.2019.01.139}, pmid = {30708164}, issn = {1879-1298}, abstract = {The feasibility of thermophilic anaerobic digestion (AD) for the attenuation of antibiotic resistance genes (ARGs) in biomass wastes under high antibiotic concentrations remains unclear. In this study, a thermophilic completely stirred digester (55 °C) was fed with municipal excess sludge spiked with increasing concentrations of oxytetracycline (OTC) (0-1000 mg/L) over a period of 280 days. Results showed that thermophilic AD could maintain stable methane production (338.40 ± 26.26 mL/d/gVS) even at an OTC dose of 1000 mg/L with the sludge phase OTC concentration reaching around 24,000 mg/kg. More important, the abundance of resistome detected by high-throughput quantitative PCR in the substrate was reduced (p < 0.01) by 55.54%-86.27% by thermophilic AD over the whole period. Partial canonical correspondence and network analyses showed that the reduction of ARGs was achieved mainly through two ways: eliminating the original hosts of ARGs in the substrate (from 41.74% ± 2.60% in the substrate to 12.08% ± 1.02% in digested sludge), and blocking the horizontal proliferation of ARGs in the digested sludge by reducing the abundance of mobile genetic elements and restricting their horizontal exchange within a small number of thermophilic genera. This study showed that thermophilic AD is feasible for the attenuation of ARGs in biomass even containing high level of OTC.}, }
@article {pmid30706916, year = {2019}, author = {Li, Y and Han, H and Yin, J and He, X and Tang, Z and Li, T and Yao, K and Yin, Y}, title = {d- and l-Aspartate regulates growth performance, inflammation and intestinal microbial community in young pigs.}, journal = {Food & function}, volume = {10}, number = {2}, pages = {1028-1037}, doi = {10.1039/c8fo01410h}, pmid = {30706916}, issn = {2042-650X}, abstract = {d-aspartate (d-Asp), an endogenous amino acid, occurs widely in animals and humans with d-enantiomers and plays an important role in the endocrine and nervous systems. However, very few studies are available on growth performance, microbial community, and the intestinal immune and inflammatory status in response to d- and l-aspartate (l-Asp). Thus, in this study, we mainly investigated the effects of dietary 1% d- and l-Asp on growth performance, inflammation, and microbial community in young pigs. Twenty-eight young pigs were randomly divided into four groups (n = 7): a control group, in which piglets were fed a basal diet, and other three groups, in which piglets received 1% d-Asp, 1% l-Asp, and 1% dl-aspartate (dl-Asp) for 35 days. The results showed that dietary 1% d-Asp significantly inhibited average daily feed intake and average daily weight gain. Gut microbes were tested and the results showed that l-Asp enhanced bacterial diversity (Shannon and Simpson). At the phylum level, l-Asp enhanced intestinal Actinobacteria and Bacteroidetes abundance but decreased Firmicutes abundance. In contrast, dl-Asp decreased intestinal Actinobacteria and Bacteroidetes abundance and increased Firmicutes abundance. At the genus level, d-Asp enhanced Clostridium sensu stricto 1 and Intestinibacter abundance. Metagenomic predictions by PICRUSt suggested that the altered microbiota were mainly involved in membrane transport, carbohydrate metabolism, amino acid metabolism, replication and repair, translation, and nucleotide metabolism. In addition, dl-Asp markedly increased the activities of serum alanine aminotransferase, aspartate transaminase and alkaline phosphatase. Also, dietary d- and dl-Asp down-regulated TLR 4, NOD1, and MyD88 in the jejunum to mediate the inflammatory response. Collectively, these results indicated that dietary d-Asp and l-Asp affect the growth performance and inflammation in piglets, which might be associated with gut microbiota.}, }
@article {pmid30704903, year = {2019}, author = {Qian, W and Ma, B and Li, X and Zhang, Q and Peng, Y}, title = {Long-term effect of pH on denitrification: High pH benefits achieving partial-denitrification.}, journal = {Bioresource technology}, volume = {278}, number = {}, pages = {444-449}, doi = {10.1016/j.biortech.2019.01.105}, pmid = {30704903}, issn = {1873-2976}, abstract = {Partial-denitrification (nitrate to nitrite) can supply nitrite for anammox which can reduce organic matter consumption in wastewater treatment plants (WWTPs). In order to achieve stable partial-denitrification, the effect of pH on denitrification were investigated for 420 days in three reactors with influent pH of 5.0, 7.0 and 9.0. The results indicate that the nitrite accumulation rate (NAR) increased with pH, with average effluent NARs being 21%, 38% and 57% in the above reactors, respectively. The sludge cultivated at a high pH of 9.0 was resistant to pH shock, with a high NAR being maintained at 83% when it was exposed to a low pH of 5.0. Metagenomic analysis showed that the higher NAR at pH 9.0 was correlated with an enrichment of Thauera, which harbored more nitrate reductase (8098 hits) than nitrite reductase (2950 hits). Based on these findings, a novel process was proposed for achieving partial-denitrification/anammox in mainstream WWTPs.}, }
@article {pmid30704595, year = {2019}, author = {Kamimura, BA and De Filippis, F and Sant'Ana, AS and Ercolini, D}, title = {Large-scale mapping of microbial diversity in artisanal Brazilian cheeses.}, journal = {Food microbiology}, volume = {80}, number = {}, pages = {40-49}, doi = {10.1016/j.fm.2018.12.014}, pmid = {30704595}, issn = {1095-9998}, abstract = {Brazilian artisanal cheeses are characterized by the use of raw milk and in some cases, natural starter cultures, known as "pingo", as well as following simple and traditional manufacturing technology. In this study, a large-scale screening of the microbial ecology of 11 different types of artisanal cheeses produced in five geographical areas of Brazil was performed. Besides, the specific origin-related microbial signatures were identified. Clear geography- and technology-based differences in the microbiota were observed. Lactic acid bacteria dominated in all cheeses although Enterobacteriaceae and Staphylococcus also occurred in North, Northeast and Central cheeses. Differences in the lactic acid bacteria patterns were also highlighted: Streptococcus, Leuconostoc, Lactococcus and Lactobacillus were differently combined in terms of relative abundance according to product type and region of production. This study provides a comprehensive, unprecedented microbiological mapping of Brazilian cheeses, highlighting the impact of geographical origin and mode of production on microbial diversity. The results obtained will help to plan an evaluation of microbial contamination sources that will need to be studied for the improvement of cheese quality and safety.}, }
@article {pmid30701765, year = {2018}, author = {Parfenov, AI and Knyazev, OV and Kagramanova, AV and Fadeeva, NA}, title = {Personalized medicine in the treatment of inflammatory bowel diseases.}, journal = {Terapevticheskii arkhiv}, volume = {90}, number = {2}, pages = {4-11}, doi = {10.26442/terarkh20189024-11}, pmid = {30701765}, issn = {0040-3660}, abstract = {Personalized medicine (personalized medicine, individualized medicine) represents the totality of methods of prevention of a pathological condition, diagnosis and treatment in the event of its occurrence, based on individual patient characteristics. Such individual characteristics include genetic, epigenetic, and transcript, proteome, metabolomic and metagenomic markers, as well as a set of variable phenotypic traits - both of the patient's body and its separate tissues or cells. For example, treatment of inflammatory bowel diseases (IBD) can most clearly show the importance of applying personalized approaches. Currently in the treatment of patients with IBD paid great attention to genetic studies, monitoring of the concentration of the biological drugs and the level of antibodies to them, the role of microbiota as a predictor of effectiveness of therapy of IBD. Used clinical, laboratory, instru- mental methods, as well as new biomarkers to assess the forecasting efficiency of conservative therapy in IBD patient. In the future treatment of patients with IBD will include a number of personalized data in order to better predict outcomes of the disease in each patient and more ac- curately select the appropriate treatment regimen.}, }
@article {pmid30701707, year = {2019}, author = {Jerde, CL and Wilson, EA and Dressler, TL}, title = {Measuring global fish species richness with eDNA metabarcoding.}, journal = {Molecular ecology resources}, volume = {19}, number = {1}, pages = {19-22}, doi = {10.1111/1755-0998.12929}, pmid = {30701707}, issn = {1755-0998}, support = {AID-OAA-A-16-00057//United States Agency for International Development/ ; }, mesh = {Animals ; *Biodiversity ; Computational Biology ; DNA/chemistry/genetics/isolation & purification ; DNA Barcoding, Taxonomic/*methods ; Fishes/*classification/*genetics ; French Guiana ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; Water/chemistry ; }, abstract = {Despite mounting threats to global freshwater and marine biodiversity, including climate change, habitat alteration, overharvesting and pollution, we struggle to know which species are present below the water's surface that are suffering from these stressors. However, the idea that a water sample containing environmental DNA (eDNA) can be screened using high-throughput sequencing and bioinformatics to reveal the identity of aquatic species is a revolutionary advance for studying the patterns of species extirpation, invasive species establishment and the dynamics of species richness. To date, many of the critical tests of fisheries diversity using this metabarcoding approach have been conducted in lower diversity systems (<40 fish species), but in this issue of Molecular Ecology Resources, Cilleros et al. (2018) described their eDNA application in the species-rich French Guiana fishery (>200 fish species) and showed the greater potential and some limitations of using eDNA in species-rich environments.}, }
@article {pmid30701587, year = {2019}, author = {Kumar, K and Dhoke, GV and Sharma, AK and Jaiswal, SK and Sharma, VK}, title = {Mechanistic elucidation of amphetamine metabolism by tyramine oxidase from human gut microbiota using molecular dynamics simulations.}, journal = {Journal of cellular biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1002/jcb.28396}, pmid = {30701587}, issn = {1097-4644}, abstract = {The human gut harbors diverse bacterial species in the gut, which play an important role in the metabolism of food and host health. Recent studies have also revealed their role in altering the pharmacological properties and efficacy of oral drugs through promiscuous metabolism. However, the atomistic details of the enzyme-drug interactions of gut bacterial enzymes which can potentially carry out the metabolism of drug molecules are still scarce. A well-known example is the FDA drug amphetamine (a central nervous system stimulant), which has been predicted to undergo promiscuous metabolism by gut bacteria. Therefore, to understand the atomistic details and energy landscape of the gut microbial enzyme-mediated metabolism of this drug, molecular dynamics studies were performed. It was observed that amphetamine binds to tyramine oxidase from the Escherichia coli strain present in the human gut microbiota at the binding site harboring polar and nonpolar amino acids. The stability analysis of amphetamine at the binding site showed that the binding is stable and the free energy for the binding of amphetamine was found to be ~ -51.71 kJ/mol. The insights provided by this study on promiscuous metabolism of amphetamine by a gut enzyme will be very useful to improve the efficacy of the drug.}, }
@article {pmid30701229, year = {2019}, author = {Zhang, X and Li, W and Zhou, C}, title = {Near-Complete Genome Sequence of a Human Pegivirus Variant Isolated from a Hepatitis E Virus-Infected Patient.}, journal = {Microbiology resource announcements}, volume = {8}, number = {4}, pages = {}, doi = {10.1128/MRA.01151-18}, pmid = {30701229}, issn = {2576-098X}, abstract = {Using viral metagenomics, we analyzed the virome of a blood sample from a hepatitis E patient. We identified viral sequences showing significant similarity to human pegivirus (HPgV), anellovirus, and hepatitis E virus. The near-complete genome of a genotype 3 HPgV strain was acquired and characterized.}, }
@article {pmid30701194, year = {2019}, author = {Wang, M and Wan, J and Rong, H and He, F and Wang, H and Zhou, J and Cai, C and Wang, Y and Xu, R and Yin, Z and Zhou, W}, title = {Alterations in Gut Glutamate Metabolism Associated with Changes in Gut Microbiota Composition in Children with Autism Spectrum Disorder.}, journal = {mSystems}, volume = {4}, number = {1}, pages = {}, doi = {10.1128/mSystems.00321-18}, pmid = {30701194}, issn = {2379-5077}, abstract = {Changes in the gut microenvironment may influence the pathogenesis of autism spectrum disorders (ASD). Here, we investigated the composition of the gut microbiota and metabolites in children with ASD. Ninety-two children with ASD and 42 age-matched children exhibiting typical development (TD) were enrolled in the two-stage study. In the discovery stage, shotgun metagenomic sequencing and liquid chromatography-mass spectrometry (LC-MS) were performed simultaneously on fecal samples obtained from 43 children in the ASD group and 31 children in the TD group. Systematic bioinformatic analyses were performed to identify gut metabolites associated with altered gut microbiota composition. At the validation stage, differential metabolites were tested using LC-MS with an additional 49 and 11 children in the ASD and TD groups, respectively. Altered glutamate metabolites were found in the ASD group, along with a decline in 2-keto-glutaramic acid and an abundance of microbiota associated with glutamate metabolism. These changes in glutamate metabolism were correlated with lower levels of the highly abundant bacteria Bacteroides vulgatus and higher levels of the potentially harmful Eggerthella lenta and Clostridium botulinum. Lower gut cortisol levels have also been identified in the ASD group and associated with changes in gut microbiota glutamate metabolism. Finally, gut 2-keto-glutaramic acid was validated as a potential biomarker for ASD. The significant changes in the gut microenvironment in children with ASD may provide new insight into the cause of ASD and aid in the search for diagnostic and therapeutic approaches. IMPORTANCE Multiple lines of evidence suggest that the gut microbiota may play an important role in the pathogenesis of ASD, but the specific mechanism is still unclear. Through a comprehensive gut metagenomic and metabolome study of children with ASD, alterations in gut metabolite composition were found in children with ASD, and these alterations were linked to changes in gut microbiota composition. This may give us a deeper understanding of the role of gut microbiota in the pathogenesis of ASD.}, }
@article {pmid30701191, year = {2019}, author = {Leviatan, S and Segal, E}, title = {A Significant Expansion of Our Understanding of the Composition of the Human Microbiome.}, journal = {mSystems}, volume = {4}, number = {1}, pages = {}, doi = {10.1128/mSystems.00010-19}, pmid = {30701191}, issn = {2379-5077}, abstract = {Shotgun sequencing of samples taken from the human microbiome often reveals only partial mapping of the sequenced metagenomic reads to existing reference genomes. Such partial mappability indicates that many genomes are missing in our reference genome set. This is particularly true for non-Western populations and for samples that do not originate from the gut. Pasolli et al. (E. Pasolli, F. Asnicar, S. Manara, M. Zolfo, et al., Cell, 2019, https://doi.org/10.1016/j.cell.2019.01.001) perform a grand effort to expand the reference set, and to better classify its members, revealing a wider pangenome of existing species as well as identifying new species of previously unknown taxonomic branches.}, }
@article {pmid30701137, year = {2019}, author = {Pyysalo, MJ and Mishra, PP and Sundström, K and Lehtimäki, T and Karhunen, PJ and Pessi, T}, title = {Increased tooth brushing frequency is associated with reduced gingival pocket bacterial diversity in patients with intracranial aneurysms.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6316}, doi = {10.7717/peerj.6316}, pmid = {30701137}, issn = {2167-8359}, abstract = {Objectives: The objective of this study was to investigate the association of tooth brushing frequency and bacterial communities of gingival crevicular fluid in patients subjected to preoperative dental examination prior to operative treatment for unruptured intracranial aneurysms.
Methods: Gingival crevicular fluid samples were taken from their deepest gingival pocket from a series of hospitalized neurosurgical patients undergoing preoperative dental screening (n = 60). The patients were asked whether they brushed their teeth two times a day, once a day, or less than every day. Total bacterial DNA was isolated and the V3-V4 region of the 16S rRNA gene was amplificated. Sequencing was performed with Illumina's 16S metagenomic sequencing library preparation protocol and data were analyzed with QIIME (1.9.1) and R statistical software (3.3.2).
Results: Bacterial diversity (Chao1 index) in the crevicular fluid reduced along with reported tooth brushing frequency (p = 0.0002; R2 = 34%; p (adjusted with age and sex) = 0.09; R2 = 11%) showing that patients who reported brushing their teeth twice a day had the lowest bacterial diversity. According to the differential abundant analysis between the tooth brushing groups, tooth brushing associated with two phyla of fusobacteria [p = 0.0001; p = 0.0007], and one bacteroidetes (p = 0.004) by reducing their amounts.
Conclusions: Tooth brushing may reduce the gingival bacterial diversity and the abundance of periodontal bacteria maintaining oral health and preventing periodontitis, and thus it is highly recommended for neurosurgical patients.}, }
@article {pmid30701077, year = {2019}, author = {Lindefeldt, M and Eng, A and Darban, H and Bjerkner, A and Zetterström, CK and Allander, T and Andersson, B and Borenstein, E and Dahlin, M and Prast-Nielsen, S}, title = {The ketogenic diet influences taxonomic and functional composition of the gut microbiota in children with severe epilepsy.}, journal = {NPJ biofilms and microbiomes}, volume = {5}, number = {}, pages = {5}, doi = {10.1038/s41522-018-0073-2}, pmid = {30701077}, issn = {2055-5008}, abstract = {The gut microbiota has been linked to various neurological disorders via the gut-brain axis. Diet influences the composition of the gut microbiota. The ketogenic diet (KD) is a high-fat, adequate-protein, low-carbohydrate diet established for treatment of therapy-resistant epilepsy in children. Its efficacy in reducing seizures has been confirmed, but the mechanisms remain elusive. The diet has also shown positive effects in a wide range of other diseases, including Alzheimer's, depression, autism, cancer, and type 2 diabetes. We collected fecal samples from 12 children with therapy-resistant epilepsy before starting KD and after 3 months on the diet. Parents did not start KD and served as diet controls. Applying shotgun metagenomic DNA sequencing, both taxonomic and functional profiles were established. Here we report that alpha diversity is not changed significantly during the diet, but differences in both taxonomic and functional composition are detected. Relative abundance of bifidobacteria as well as E. rectale and Dialister is significantly diminished during the intervention. An increase in relative abundance of E. coli is observed on KD. Functional analysis revealed changes in 29 SEED subsystems including the reduction of seven pathways involved in carbohydrate metabolism. Decomposition of these shifts indicates that bifidobacteria and Escherichia are important contributors to the observed functional shifts. As relative abundance of health-promoting, fiber-consuming bacteria becomes less abundant during KD, we raise concern about the effects of the diet on the gut microbiota and overall health. Further studies need to investigate whether these changes are necessary for the therapeutic effect of KD.}, }
@article {pmid30700057, year = {2019}, author = {Castillo Villamizar, GA and Nacke, H and Griese, L and Tabernero, L and Funkner, K and Daniel, R}, title = {Characteristics of the First Protein Tyrosine Phosphatase with Phytase Activity from a Soil Metagenome.}, journal = {Genes}, volume = {10}, number = {2}, pages = {}, doi = {10.3390/genes10020101}, pmid = {30700057}, issn = {2073-4425}, abstract = {Protein tyrosine phosphatases (PTPs) fulfil multiple key regulatory functions. Within the group of PTPs, the atypical lipid phosphatases (ALPs) are known for their role as virulence factors associated with human pathogens. Another group of PTPs, which is capable of using inositol-hexakisphosphate (InsP₆) as substrate, are known as phytases. Phytases play major roles in the environmental phosphorus cycle, biotechnology, and pathogenesis. So far, all functionally characterized PTPs, including ALPs and PTP-phytases, have been derived exclusively from isolated microorganisms. In this study, screening of a soil-derived metagenomic library resulted in identification of a gene (pho16B), encoding a PTP, which shares structural characteristics with the ALPs. In addition, the characterization of the gene product (Pho16B) revealed the capability of the protein to use InsP₆ as substrate, and the potential of soil as a source of phytases with so far unknown characteristics. Thus, Pho16B represents the first functional environmentally derived PTP-phytase. The enzyme has a molecular mass of 38 kDa. The enzyme is promiscuous, showing highest activity and affinity toward naphthyl phosphate (Km 0.966 mM). Pho16B contains the HCXXGKDR[TA]G submotif of PTP-ALPs, and it is structurally related to PtpB of Mycobacterium tuberculosis. This study demonstrates the presence and functionality of an environmental gene codifying a PTP-phytase homologous to enzymes closely associated to bacterial pathogenicity.}, }
@article {pmid30699048, year = {2019}, author = {Zylberberg, M}, title = {Next-Generation Ecological Immunology.}, journal = {Physiological and biochemical zoology : PBZ}, volume = {92}, number = {2}, pages = {177-188}, doi = {10.1086/702440}, pmid = {30699048}, issn = {1537-5293}, mesh = {Animals ; Ecology/*methods ; *High-Throughput Nucleotide Sequencing ; Immunologic Techniques/*methods ; Invertebrates/genetics/immunology ; Vertebrates/genetics/immunology ; }, abstract = {The application of next-generation sequencing (NGS) to the study of whole genomes and transcriptomes is becoming commonplace in molecular biology and molecular medicine. Over the past decade, these technologies have become more accessible to the broader biological community as the cost of NGS has decreased significantly and the availability of ready-to-use library preparation kits and user-friendly bioinformatic tools has increased. Indeed, these technologies are starting to be deployed in the study of ecological systems and immune function and have already yielded new discoveries and insights. However, despite the power of these techniques, they remain underutilized by the ecological immunology (ecoimmunology) community. This is unfortunate because there are several key challenges faced by ecological immunologists that these technologies are particularly well suited to address: (1) to measure immune function in biologically meaningful ways, (2) to describe the complex relationship between immunology and other aspects of physiology in an ecological context, and (3) to relate ecoimmunology to disease ecology. Each of these three challenges confronting the ecoimmunology community is critical to understanding ecoimmunology, and each has been stymied by a lack of sufficient data to effectively tackle the questions at hand. Deploying NGS methods to tackle these challenges promises to revolutionize the field of ecoimmunology by facilitating the unbiased, broad-scale, and efficient discovery of novel immune genes and mechanisms; the quantification of variation in immune systems; the characterization of relevant physiological pathways; and the description of microbial communities.}, }
@article {pmid30698687, year = {2019}, author = {Dhakan, DB and Maji, A and Sharma, AK and Saxena, R and Pulikkan, J and Grace, T and Gomez, A and Scaria, J and Amato, KR and Sharma, VK}, title = {The unique composition of Indian gut microbiome, gene catalogue, and associated fecal metabolome deciphered using multi-omics approaches.}, journal = {GigaScience}, volume = {8}, number = {3}, pages = {}, doi = {10.1093/gigascience/giz004}, pmid = {30698687}, issn = {2047-217X}, abstract = {BACKGROUND: Metagenomic studies carried out in the past decade have led to an enhanced understanding of the gut microbiome in human health; however, the Indian gut microbiome has not been well explored. We analyzed the gut microbiome of 110 healthy individuals from two distinct locations (North-Central and Southern) in India using multi-omics approaches, including 16S rRNA gene amplicon sequencing, whole-genome shotgun metagenomic sequencing, and metabolomic profiling of fecal and serum samples.
RESULTS: The gene catalogue established in this study emphasizes the uniqueness of the Indian gut microbiome in comparison to other populations. The gut microbiome of the cohort from North-Central India, which was primarily consuming a plant-based diet, was found to be associated with Prevotella and also showed an enrichment of branched chain amino acid (BCAA) and lipopolysaccharide biosynthesis pathways. In contrast, the gut microbiome of the cohort from Southern India, which was consuming an omnivorous diet, showed associations with Bacteroides, Ruminococcus, and Faecalibacterium and had an enrichment of short chain fatty acid biosynthesis pathway and BCAA transporters. This corroborated well with the metabolomics results, which showed higher concentration of BCAAs in the serum metabolome of the North-Central cohort and an association with Prevotella. In contrast, the concentration of BCAAs was found to be higher in the fecal metabolome of the Southern-India cohort and showed a positive correlation with the higher abundance of BCAA transporters.
CONCLUSIONS: The study reveals the unique composition of the Indian gut microbiome, establishes the Indian gut microbial gene catalogue, and compares it with the gut microbiome of other populations. The functional associations revealed using metagenomic and metabolomic approaches provide novel insights on the gut-microbe-metabolic axis, which will be useful for future epidemiological and translational researches.}, }
@article {pmid30698645, year = {2019}, author = {Linard, B and Swenson, K and Pardi, F}, title = {Rapid alignment-free phylogenetic identification of metagenomic sequences.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btz068}, pmid = {30698645}, issn = {1367-4811}, abstract = {Motivation: Taxonomic classification is at the core of environmental DNA analysis. When a phylogenetic tree can be built as a prior hypothesis to such classification, phylogenetic placement (PP) provides the most informative type of classification because each query sequence is assigned to its putative origin in the tree. This is useful whenever precision is sought (e.g. in diagnostics). However, likelihood-based PP algorithms struggle to scale with the ever-increasing throughput of DNA sequencing.
Results: We have developed RAPPAS (Rapid Alignment-free Phylogenetic Placement via Ancestral Sequences) which uses an alignment-free approach, removing the hurdle of query sequence alignment as a preliminary step to PP. Our approach relies on the precomputation of a database of k-mers that may be present with non-negligible probability in relatives of the reference sequences. The placement is performed by inspecting the stored phylogenetic origins of the k-mers in the query, and their probabilities. The database can be reused for the analysis of several different metagenomes. Experiments show that the first implementation of RAPPAS is already faster than competing likelihood-based PP algorithms, while keeping similar accuracy for short reads. RAPPAS scales PP for the era of routine metagenomic diagnostics.
Availability: Program and sources freely available for download at https://github.com/blinard-BIOINFO/RAPPAS.
Supplementary information: Supplementary data are available at Bioinformatics online.}, }
@article {pmid30697958, year = {2019}, author = {Dharnidharka, VR and Ruzinova, MB and Chen, CC and Parameswaran, P and O'Gorman, H and Goss, CW and Gu, H and Storch, GA and Wylie, K}, title = {Metagenomic analysis of DNA viruses from posttransplant lymphoproliferative disorders.}, journal = {Cancer medicine}, volume = {}, number = {}, pages = {}, doi = {10.1002/cam4.1985}, pmid = {30697958}, issn = {2045-7634}, support = {MC-II-2014-394//Children's Discovery Institute/ ; }, abstract = {Posttransplant lymphoproliferative disorders (PTLDs), 50%-80% of which are strongly associated with Epstein-Barr virus (EBV), carry a high morbidity and mortality. Most clinical/epidemiological/tumor characteristics do not consistently associate with worse patient survival, so our aim was to identify if other viral genomic characteristics associated better with survival. We extracted DNA from stored paraffin-embedded PTLD tissues at our center, identified viral sequences by metagenomic shotgun sequencing (MSS), and analyzed the data in relation to clinical outcomes. Our study population comprised 69 PTLD tissue samples collected between 1991 and 2015 from 60 subjects. Nucleotide sequences from at least one virus were detected by MSS in 86% (59/69) of the tissues (EBV in 61%, anelloviruses 52%, gammapapillomaviruses 14%, CMV 7%, and HSV in 3%). No viruses were present in higher proportion in EBV-negative PTLD (compared to EBV-positive PTLD). In univariable analysis, death within 5 years of PTLD diagnosis was associated with anellovirus (P = 0.037) and gammapapillomavirus (P = 0.036) detection by MSS, higher tissue qPCR levels of the predominant human anellovirus species torque teno virus (TTV; P = 0.016), T cell type PTLD, liver, brain or bone marrow location. In multivariable analyses, T cell PTLD (P = 0.006) and TTV PCR level (P = 0.012) remained significant. In EBV-positive PTLD, EBNA-LP, EBNA1 and EBNA3C had significantly higher levels of nonsynonymous gene variants compared to the other EBV genes. Multiple viruses are detectable in PTLD tissues by MSS. Anellovirus positivity, not EBV positivity,was associated with worse patient survival in our series. Confirmation and extension of this work in larger multicenter studies is desirable.}, }
@article {pmid30696918, year = {2019}, author = {Song, HK and Shi, Y and Yang, T and Chu, H and He, JS and Kim, H and Jablonski, P and Adams, JM}, title = {Environmental filtering of bacterial functional diversity along an aridity gradient.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {866}, doi = {10.1038/s41598-018-37565-9}, pmid = {30696918}, issn = {2045-2322}, support = {0409-20160032//National Research Foundation of Korea (NRF)/ ; 0409-20160032//National Research Foundation of Korea (NRF)/ ; 2014CB954002//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; }, abstract = {Studying how metagenome composition and diversity varies along environmental gradients may improve understanding of the general principles of community and ecosystem structuring. We studied soil bacterial metagenomes along a precipitation gradient on the eastern Tibetan Plateau, varying between 500 mm and 60 mm mean annual precipitation (MAP). We found that lower MAP was strongly associated with reduced functional diversity of bacterial genes. It appears that extreme environmental conditions associated with aridity constrain the diversity of functional strategies present in soil biota - analogous to broad scale patterns found in plant functional diversity along environmental gradients. In terms of specific functions, more extreme arid conditions were also associated with increased relative abundance of genes related to dormancy and osmoprotectants. Decreased relative abundance of genes related to antibiotic resistance and virulence in more arid conditions suggests reduced intensity of biotic interaction under extreme physiological conditions. These trends parallel those seen in earlier, more preliminary comparisons of metagenomes across biomes.}, }
@article {pmid30696861, year = {2019}, author = {Okazaki, F and Zang, L and Nakayama, H and Chen, Z and Gao, ZJ and Chiba, H and Hui, SP and Aoki, T and Nishimura, N and Shimada, Y}, title = {Microbiome Alteration in Type 2 Diabetes Mellitus Model of Zebrafish.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {867}, doi = {10.1038/s41598-018-37242-x}, pmid = {30696861}, issn = {2045-2322}, support = {VP29117938605//MEXT | Japan Science and Technology Agency (JST)/ ; }, abstract = {Understanding the gut microbiota in metabolic disorders, including type 2 diabetes mellitus (T2DM), is now gaining importance due to its potential role in disease risk and progression. We previously established a zebrafish model of T2DM, which shows glucose intolerance with insulin resistance and responds to anti-diabetic drugs. In this study, we analysed the gut microbiota of T2DM zebrafish by deep sequencing the 16S rRNA V3-V4 hypervariable regions, and imputed a functional profile using predictive metagenomic tools. While control and T2DM zebrafish were fed with the same kind of feed, the gut microbiota in T2DM group was less diverse than that of the control. Predictive metagenomics profiling using PICRUSt revealed functional alternation of the KEGG pathways in T2DM zebrafish. Several amino acid metabolism pathways (arginine, proline, and phenylalanine) were downregulated in the T2DM group, similar to what has been previously reported in humans. In summary, we profiled the gut microbiome in T2DM zebrafish, which revealed functional similarities in gut bacterial environments between these zebrafish and T2DM affected humans. T2DM zebrafish can become an alternative model organism to study host-bacterial interactions in human obesity and related diseases.}, }
@article {pmid30696742, year = {2019}, author = {Castillo Villamizar, GA and Nacke, H and Boehning, M and Herz, K and Daniel, R}, title = {Functional Metagenomics Reveals an Overlooked Diversity and Novel Features of Soil-Derived Bacterial Phosphatases and Phytases.}, journal = {mBio}, volume = {10}, number = {1}, pages = {}, doi = {10.1128/mBio.01966-18}, pmid = {30696742}, issn = {2150-7511}, abstract = {Phosphatases, including phytases, play a major role in cell metabolism, phosphorus cycle, biotechnology, and pathogenic processes. Nevertheless, their discovery by functional metagenomics is challenging. Here, soil metagenomic libraries were successfully screened for genes encoding phosphatase activity. In this context, we report the largest number and diversity of phosphatase genes derived from functional metagenome analysis. Two of the detected gene products carry domains which have never been associated with phosphatase activity before. One of these domains, the SNARE-associated domain DedA, harbors a so-far-overlooked motif present in numerous bacterial SNARE-associated proteins. Our analysis revealed a previously unreported phytase activity of the alkaline phosphatase and sulfatase superfamily (cl23718) and of purple acid phosphatases from nonvegetal origin. This suggests that the classical concept comprising four classes of phytases should be modified and indicates high performance of our screening method for retrieving novel types of phosphatases/phytases hidden in metagenomes of complex environments.IMPORTANCE Phosphorus (P) is a key element involved in numerous cellular processes and essential to meet global food demand. Phosphatases play a major role in cell metabolism and contribute to control the release of P from phosphorylated organic compounds, including phytate. Apart from the relationship with pathogenesis and the enormous economic relevance, phosphatases/phytases are also important for reduction of phosphorus pollution. Almost all known functional phosphatases/phytases are derived from cultured individual microorganisms. We demonstrate here for the first time the potential of functional metagenomics to exploit the phosphatase/phytase pools hidden in environmental soil samples. The recovered diversity of phosphatases/phytases comprises new types and proteins exhibiting largely unknown characteristics, demonstrating the potential of the screening method for retrieving novel target enzymes. The insights gained into the unknown diversity of genes involved in the P cycle highlight the power of function-based metagenomic screening strategies to study Earth's phosphatase pools.}, }
@article {pmid30696492, year = {2019}, author = {Cernava, T and Erlacher, A and Soh, J and Sensen, CW and Grube, M and Berg, G}, title = {Enterobacteriaceae dominate the core microbiome and contribute to the resistome of arugula (Eruca sativa Mill.).}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {13}, doi = {10.1186/s40168-019-0624-7}, pmid = {30696492}, issn = {2049-2618}, support = {A3-11.P-33/2011-6//European Regional Development Fund/ ; }, abstract = {BACKGROUND: Arugula is a traditional medicinal plant and popular leafy green today. It is mainly consumed raw in the Western cuisine and known to contain various bioactive secondary metabolites. However, arugula has been also associated with high-profile outbreaks causing severe food-borne human diseases. A multiphasic approach integrating data from metagenomics, amplicon sequencing, and arugula-derived bacterial cultures was employed to understand the specificity of the indigenous microbiome and resistome of the edible plant parts.
RESULTS: Our results indicate that arugula is colonized by a diverse, plant habitat-specific microbiota. The indigenous phyllosphere bacterial community was shown to be dominated by Enterobacteriaceae, which are well-equipped with various antibiotic resistances. Unexpectedly, the prevalence of specific resistance mechanisms targeting therapeutic antibiotics (fluoroquinolone, chloramphenicol, phenicol, macrolide, aminocoumarin) was only surpassed by efflux pump assignments.
CONCLUSIONS: Enterobacteria, being core microbiome members of arugula, have a substantial implication in the overall resistome. Detailed insights into the natural occurrence of antibiotic resistances in arugula-associated microorganisms showed that the plant is a hotspot for distinctive defense mechanisms. The specific functioning of microorganisms in this unusual ecosystem provides a unique model to study antibiotic resistances in an ecological context.}, }
@article {pmid30695998, year = {2019}, author = {Sen, P and Orešič, M}, title = {Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An Overview.}, journal = {Metabolites}, volume = {9}, number = {2}, pages = {}, doi = {10.3390/metabo9020022}, pmid = {30695998}, issn = {2218-1989}, support = {Decision No. 250114, to M.O.//Academy of Finland (Centre of Excellence in Molecular Systems Immunology and Physiology Research 2012-2017)/ ; 2-SRA-2014-159-Q-R to M.O.//Juvenile Diabetes Research Foundation (JDRF)/ ; }, abstract = {There is growing interest in the metabolic interplay between the gut microbiome and host metabolism. Taxonomic and functional profiling of the gut microbiome by next-generation sequencing (NGS) has unveiled substantial richness and diversity. However, the mechanisms underlying interactions between diet, gut microbiome and host metabolism are still poorly understood. Genome-scale metabolic modeling (GSMM) is an emerging approach that has been increasingly applied to infer diet⁻microbiome, microbe⁻microbe and host⁻microbe interactions under physiological conditions. GSMM can, for example, be applied to estimate the metabolic capabilities of microbes in the gut. Here, we discuss how meta-omics datasets such as shotgun metagenomics, can be processed and integrated to develop large-scale, condition-specific, personalized microbiota models in healthy and disease states. Furthermore, we summarize various tools and resources available for metagenomic data processing and GSMM, highlighting the experimental approaches needed to validate the model predictions.}, }
@article {pmid30694507, year = {2019}, author = {Delafont, V and Perrin, Y and Bouchon, D and Moulin, L and Héchard, Y}, title = {Targeted Metagenomics of Microbial Diversity in Free-Living Amoebae and Water Samples.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1921}, number = {}, pages = {421-428}, doi = {10.1007/978-1-4939-9048-1_26}, pmid = {30694507}, issn = {1940-6029}, abstract = {The presence of Legionella spp. in natural and man-made water systems is a great public health concern and heavily depends on the presence of free-living amoebae. Taking advantage of the development and affordability of next-generation sequencing technology, we present here a method to characterize the whole bacterial community directly from water samples, as well as from isolated free-living amoebae.}, }
@article {pmid30693008, year = {2018}, author = {Agnolucci, M and Avio, L and Pepe, A and Turrini, A and Cristani, C and Bonini, P and Cirino, V and Colosimo, F and Ruzzi, M and Giovannetti, M}, title = {Bacteria Associated With a Commercial Mycorrhizal Inoculum: Community Composition and Multifunctional Activity as Assessed by Illumina Sequencing and Culture-Dependent Tools.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {1956}, doi = {10.3389/fpls.2018.01956}, pmid = {30693008}, issn = {1664-462X}, abstract = {The implementation of sustainable agriculture encompasses practices enhancing the activity of beneficial soil microorganisms, able to modulate biogeochemical soil cycles and to affect soil fertility. Among them, arbuscular mycorrhizal fungi (AMF) establish symbioses with the roots of most food crops and play a key role in nutrient uptake and plant protection from biotic and abiotic stresses. Such beneficial services, encompassing improved crop performances, and soil resources availability, are the outcome of the synergistic action of AMF and the vast communities of mycorrhizospheric bacteria living strictly associated with their mycelium and spores, most of which showing plant growth promoting (PGP) activities, such as the ability to solubilize phosphate and produce siderophores and indole acetic acid (IAA). One of the strategies devised to exploit AMF benefits is represented by the inoculation of selected isolates, either as single species or in a mixture. Here, for the first time, the microbiota associated with a commercial AMF inoculum was identified and characterized, using a polyphasic approach, i.e., a combination of culture-dependent analyses and metagenomic sequencing. Overall, 276 bacterial genera were identified by Illumina high-throughput sequencing, belonging to 165 families, 107 orders, and 23 phyla, mostly represented by Proteobacteria and Bacteroidetes. The commercial inoculum harbored a rich culturable heterotrophic bacterial community, whose populations ranged from 2.5 to 6.1 × 106 CFU/mL. The isolation of functional groups allowed the selection of 36 bacterial strains showing PGP activities. Among them, 14 strains showed strong IAA and/or siderophores production and were affiliated with Actinomycetales (Microbacterium trichotecenolyticum, Streptomyces deccanensis/scabiei), Bacillales (Bacillus litoralis, Bacillus megaterium), Enterobacteriales (Enterobacter), Rhizobiales (Rhizobium radiobacter). This work demonstrates for the first time that an AMF inoculum, obtained following industrial production processes, is home of a large and diverse community of bacteria with important functional PGP traits, possibly acting in synergy with AMF and providing additional services and benefits. Such bacteria, available in pure culture, could be utilized, individually and/or in multispecies consortia with AMF, as biofertilizers and bioenhancers in sustainable agroecosystems, aimed at minimizing the use of chemical fertilizers and pesticides, promoting primary production, and maintaining soil health and fertility.}, }
@article {pmid30692979, year = {2018}, author = {Nagpal, S and Haque, MM and Singh, R and Mande, SS}, title = {iVikodak-A Platform and Standard Workflow for Inferring, Analyzing, Comparing, and Visualizing the Functional Potential of Microbial Communities.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3336}, doi = {10.3389/fmicb.2018.03336}, pmid = {30692979}, issn = {1664-302X}, abstract = {Background: The objectives of any metagenomic study typically include identification of resident microbes and their relative proportions (taxonomic analysis), profiling functional diversity (functional analysis), and comparing the identified microbes and functions with available metadata (comparative metagenomics). Given the advantage of cost-effectiveness and convenient data-size, amplicon-based sequencing has remained the technology of choice for exploring phylogenetic diversity of an environment. A recent school of thought, employing the existing genome annotation information for inferring functional capacity of an identified microbiome community, has given a promising alternative to Whole Genome Shotgun sequencing for functional analysis. Although a handful of tools are currently available for function inference, their scope, functionality and utility has essentially remained limited. Need for a comprehensive framework that expands upon the existing scope and enables a standardized workflow for function inference, analysis, and visualization, is therefore felt. Methods: We present iVikodak, a multi-modular web-platform that hosts a logically inter-connected repertoire of functional inference and analysis tools, coupled with a comprehensive visualization interface. iVikodak is equipped with microbial co-inhabitance pattern driven published algorithms along with multiple updated databases of various curated microbe-function maps. It also features an advanced task management and result sharing system through introduction of personalized and portable dashboards. Results: In addition to inferring functions from 16S rRNA gene data, iVikodak enables (a) an in-depth analysis of specific functions of interest (b) identification of microbes contributing to various functions (c) microbial interaction patterns through function-driven correlation networks, and (d) simultaneous functional comparison between multiple microbial communities. We have bench-marked iVikodak through multiple case studies and comparisons with existing state of art. We also introduce the concept of a public repository which provides a first of its kind community-driven framework for scientific data analytics, collaboration and sharing in this area of microbiome research. Conclusion: Developed using modern design and task management practices, iVikodak provides a multi-modular, yet inter-operable, one-stop framework, that intends to simplify the entire approach toward inferred function analysis. It is anticipated to serve as a significant value addition to the existing space of functional metagenomics. iVikodak web-server may be freely accessed at https://web.rniapps.net/iVikodak/.}, }
@article {pmid30691652, year = {2019}, author = {Nayeemul Bari, SM and Hatoum-Aslan, A}, title = {CRISPR-Cas10 assisted editing of virulent staphylococcal phages.}, journal = {Methods in enzymology}, volume = {616}, number = {}, pages = {385-409}, doi = {10.1016/bs.mie.2018.10.023}, pmid = {30691652}, issn = {1557-7988}, abstract = {Phages are the most abundant entities in the biosphere and profoundly impact the bacterial populations within and around us. They attach to a specific host, inject their DNA, hijack the host's cellular processes, and replicate exponentially while destroying the host. Historically, phages have been exploited as powerful antimicrobials, and phage-derived proteins have constituted the basis for numerous biotechnological applications. Only in recent years have metagenomic studies revealed that phage genomes harbor a rich reservoir of genetic diversity, which might afford further therapeutic and/or biotechnological value. Nevertheless, functions for the majority of phage genes remain unknown, and due to their swift and destructive replication cycle, many phages are intractable by current genetic engineering techniques. Whether to advance the basic understanding of phage biology or to tap into their potential applications, efficient methods for phage genetic engineering are needed. Recent reports have shown that CRISPR-Cas systems, a class of prokaryotic immune systems that protect against phage infection, can be harnessed to engineer diverse phages. In this chapter, we describe methods to genetically manipulate virulent phages using CRISPR-Cas10, a Type III-A CRISPR-Cas system native to Staphylococcus epidermidis. A method for engineering phages that infect a CRISPR-less Staphylococcus aureus host is also described. Both approaches have proved successful in isolating desired phage mutants with 100% efficiency, demonstrating that CRISPR-Cas10 constitutes a powerful tool for phage genetic engineering. The relatively widespread presence of Type III CRISPR-Cas systems in bacteria and archaea imply that similar strategies may be used to manipulate the genomes of diverse prokaryotic viruses.}, }
@article {pmid30691532, year = {2019}, author = {Korzhenkov, AA and Toshchakov, SV and Bargiela, R and Gibbard, H and Ferrer, M and Teplyuk, AV and Jones, DL and Kublanov, IV and Golyshin, PN and Golyshina, OV}, title = {Archaea dominate the microbial community in an ecosystem with low-to-moderate temperature and extreme acidity.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {11}, doi = {10.1186/s40168-019-0623-8}, pmid = {30691532}, issn = {2049-2618}, abstract = {BACKGROUND: The current view suggests that in low-temperature acidic environments, archaea are significantly less abundant than bacteria. Thus, this study of the microbiome of Parys Mountain (Anglesey, UK) sheds light on the generality of this current assumption. Parys Mountain is a historically important copper mine and its acid mine drainage (AMD) water streams are characterised by constant moderate temperatures (8-18 °C), extremely low pH (1.7) and high concentrations of soluble iron and other metal cations.
RESULTS: Metagenomic and SSU rRNA amplicon sequencing of DNA from Parys Mountain revealed a significant proportion of archaea affiliated with Euryarchaeota, which accounted for ca. 67% of the community. Within this phylum, potentially new clades of Thermoplasmata were overrepresented (58%), with the most predominant group being "E-plasma", alongside low-abundant Cuniculiplasmataceae, 'Ca. Micrarchaeota' and 'Terrestrial Miscellaneous Euryarchaeal Group' (TMEG) archaea, which were phylogenetically close to Methanomassilicoccales and clustered with counterparts from acidic/moderately acidic settings. In the sediment, archaea and Thermoplasmata contributed the highest numbers in V3-V4 amplicon reads, in contrast with the water body community, where Proteobacteria, Nitrospirae, Acidobacteria and Actinobacteria outnumbered archaea. Cultivation efforts revealed the abundance of archaeal sequences closely related to Cuniculiplasma divulgatum in an enrichment culture established from the filterable fraction of the water sample. Enrichment cultures with unfiltered samples showed the presence of Ferrimicrobium acidiphilum, C. divulgatum, 'Ca. Mancarchaeum acidiphilum Mia14', 'Ca. Micrarchaeota'-related and diverse minor (< 2%) bacterial metagenomic reads.
CONCLUSION: Contrary to expectation, our study showed a high abundance of archaea in this extremely acidic mine-impacted environment. Further, archaeal populations were dominated by one particular group, suggesting that they are functionally important. The prevalence of archaea over bacteria in these microbiomes and their spatial distribution patterns represents a novel and important advance in our understanding of acidophile ecology. We also demonstrated a procedure for the specific enrichment of cell wall-deficient members of the archaeal component of this community, although the large fraction of archaeal taxa remained unculturable. Lastly, we identified a separate clustering of globally occurring acidophilic members of TMEG that collectively belong to a distinct order within Thermoplasmata with yet unclear functional roles in the ecosystem.}, }
@article {pmid30691529, year = {2019}, author = {Sutton, TDS and Clooney, AG and Ryan, FJ and Ross, RP and Hill, C}, title = {Choice of assembly software has a critical impact on virome characterisation.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {12}, doi = {10.1186/s40168-019-0626-5}, pmid = {30691529}, issn = {2049-2618}, support = {SFI/12/RC/2273//Science Foundation Ireland/Ireland ; SFI/14/SP APC/B3032//European Regional Development Fund ()/ ; N/A//Janssen Biotech/ ; }, abstract = {BACKGROUND: The viral component of microbial communities plays a vital role in driving bacterial diversity, facilitating nutrient turnover and shaping community composition. Despite their importance, the vast majority of viral sequences are poorly annotated and share little or no homology to reference databases. As a result, investigation of the viral metagenome (virome) relies heavily on de novo assembly of short sequencing reads to recover compositional and functional information. Metagenomic assembly is particularly challenging for virome data, often resulting in fragmented assemblies and poor recovery of viral community members. Despite the essential role of assembly in virome analysis and difficulties posed by these data, current assembly comparisons have been limited to subsections of virome studies or bacterial datasets.
DESIGN: This study presents the most comprehensive virome assembly comparison to date, featuring 16 metagenomic assembly approaches which have featured in human virome studies. Assemblers were assessed using four independent virome datasets, namely, simulated reads, two mock communities, viromes spiked with a known phage and human gut viromes.
RESULTS: Assembly performance varied significantly across all test datasets, with SPAdes (meta) performing consistently well. Performance of MIRA and VICUNA varied, highlighting the importance of using a range of datasets when comparing assembly programs. It was also found that while some assemblers addressed the challenges of virome data better than others, all assemblers had limitations. Low read coverage and genomic repeats resulted in assemblies with poor genome recovery, high degrees of fragmentation and low-accuracy contigs across all assemblers. These limitations must be considered when setting thresholds for downstream analysis and when drawing conclusions from virome data.}, }
@article {pmid30689834, year = {2019}, author = {Zheng, Q and Lu, J and Wang, Y and Jiao, N}, title = {Genomic reconstructions and potential metabolic strategies of generalist and specialist heterotrophic bacteria associated with an estuary Synechococcus culture.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {3}, pages = {}, doi = {10.1093/femsec/fiz017}, pmid = {30689834}, issn = {1574-6941}, abstract = {Interactions between photoautotrophs and heterotrophs are central to marine microbial ecosystems. Synechococcus are dominant marine phototrophs, and they are frequently associated with heterotrophic bacteria. These co-cultures provide a useful research system to investigate photoautotroph-heterotroph interactions in marine systems. Bacteria within the Roseobacter clade and Flavobacteria are two of the main bacterial lineages that exhibit intimate associations with Synechococcus populations. We conducted metagenomic analyses of a Synechococcus culture, followed by genomic binning of metagenomic contigs, and recovered five nearly complete genomes, including members of the Roseobacter clade (i.e. Marivita sp. XM-24) and Flavobacteria (i.e. Fluviicola sp. XM-24). Marivita sp. XM-24 is an ecological generalist of the Roseobacter clade and displays diverse metabolic capacities for the acquisition of nutrients and energy sources. Specifically, the genome contained numerous gene complements involved in the uptake and metabolism of nitrogen- and phosphorus-containing inorganic and organic compounds, in addition to the potential for aerobic anoxygenic photosynthesis, oxidation of carbon monoxide, inorganic sulfur oxidation, DMSP demethylation and PHA metabolism. The genome of the Flavobacteria representative, Fluviicola sp. XM-24, contained numerous peptidases, glycoside hydrolases, adhesion-related proteins and genes involved in gliding motility. Fluviicola sp. XM-24 likely specialize in the degradation of high molecular weight compound exudates from Synechococcus cells, including polysaccharides and polypeptides via attachment to particles, surfaces or cells. The distinct metabolic strategies identified within several heterotrophic bacteria that are associated with Syneochococcus cells provide insights into their lifestyles and nutrient utilization patterns, in addition to their interactions with photoautotrophs. Biological interactions, including mutualism, competition and antagonism, shape the microbial community structure of marine environments and are critical for understanding biogeochemical cycling in the ocean. These results provide valuable insights into the nature of interactions between dominant marine photoautotrophs and associated bacterial heterotrophs.}, }
@article {pmid30689669, year = {2019}, author = {Weiland-Bräuer, N and Malek, I and Schmitz, RA}, title = {Metagenomic quorum quenching enzymes affect biofilm formation of Candida albicans and Staphylococcus epidermidis.}, journal = {PloS one}, volume = {14}, number = {1}, pages = {e0211366}, doi = {10.1371/journal.pone.0211366}, pmid = {30689669}, issn = {1932-6203}, abstract = {Biofilm formation in the clinical environment is of increasing concern since a significant part of human infections is associated, and caused by biofilm establishment of (opportunistic) pathogens, for instance Candida albicans and Staphylococcus epidermidis. The rapidly increasing number of antibiotic-resistant biofilms urgently requires the development of novel and effective strategies to prevent biofilm formation ideally targeting a wide range of infectious microorganisms. Both, synthesis of extracellular polymeric substances and quorum sensing are crucial for biofilm formation, and thus potential attractive targets to combat undesirable biofilms.We evaluated the ability of numerous recently identified metagenome-derived bacterial quorum quenching (QQ) proteins to inhibit biofilm formation of C. albicans and S. epidermidis. Here, proteins QQ-5 and QQ-7 interfered with the morphogenesis of C. albicans by inhibiting the yeast-to-hyphae transition, ultimately leading to impaired biofilm formation. Moreover, QQ5 and QQ-7 inhibited biofilm formation of S. epidermidis; in case of QQ7 most likely due to induced expression of the icaR gene encoding the repressor for polysaccharide intercellular adhesin (PIA) synthesis, the main determinant for staphylococcal biofilm formation. Our results indicate that QQ-5 and QQ-7 are attractive potential anti-biofilm agents in the prevention and treatment of C. albicans and S. epidermidis mono-species biofilms, and potentially promising anti-biofilm drugs in also combating multi-species infections.}, }
@article {pmid30689286, year = {2019}, author = {Berg, JS and Pjevac, P and Sommer, T and Buckner, CRT and Philippi, M and Hach, PF and Liebeke, M and Holtappels, M and Danza, F and Tonolla, M and Sengupta, A and Schubert, CJ and Milucka, J and Kuypers, MMM}, title = {Dark aerobic sulfide oxidation by anoxygenic phototrophs in anoxic waters.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14543}, pmid = {30689286}, issn = {1462-2920}, support = {//Deutsche Forschungsgemeinschaft/ ; Cross Disciplinary Fellowship, LT000993/2014-C//Human Frontier Science Program/ ; //International Max Planck Research School of Marine Microbiology/ ; //Max Planck Society/ ; }, abstract = {Anoxygenic phototrophic sulfide oxidation by green and purple sulfur bacteria (PSB) plays a key role in sulfide removal from anoxic shallow sediments and stratified waters. Although some PSB can also oxidize sulfide with nitrate and oxygen, little is known about the prevalence of this chemolithotrophic lifestyle in the environment. In this study, we investigated the role of these phototrophs in light-independent sulfide removal in the chemocline of Lake Cadagno. Our temporally resolved, high-resolution chemical profiles indicated that dark sulfide oxidation was coupled to high oxygen consumption rates of ~9 μM O2 ·h-1 . Single-cell analyses of lake water incubated with 13 CO2 in the dark revealed that Chromatium okenii was to a large extent responsible for aerobic sulfide oxidation and it accounted for up to 40% of total dark carbon fixation. The genome of Chr. okenii reconstructed from the Lake Cadagno metagenome confirms its capacity for microaerophilic growth and provides further insights into its metabolic capabilities. Moreover, our genomic and single-cell data indicated that other PSB grow microaerobically in these apparently anoxic waters. Altogether, our observations suggest that aerobic respiration may not only play an underappreciated role in anoxic environments but also that organisms typically considered strict anaerobes may be involved.}, }
@article {pmid30687779, year = {2019}, author = {Jia, Y and Leung, MHY and Tong, X and Wilkins, D and Lee, PKH}, title = {Rare Taxa Exhibit Disproportionate Cell-Level Metabolic Activity in Enriched Anaerobic Digestion Microbial Communities.}, journal = {mSystems}, volume = {4}, number = {1}, pages = {}, doi = {10.1128/mSystems.00208-18}, pmid = {30687779}, issn = {2379-5077}, abstract = {Microbial communities are composed of populations with vastly different abundances and levels of metabolic and replicative activity, ranging from actively metabolizing and dividing to dormant or nonviable. The 16S rRNA/rDNA ratio is an emerging tool for evaluating cell-level metabolic activity independent of abundance. In this study, we used five long-term enriched model anaerobic digestion (AD) communities to investigate community composition, diversity, structure, and in particular activity based on the rRNA/rDNA ratio. We cross-validated the 16S amplicon-based results using two alternative operational taxonomic unit (OTU) formation methods (conventional 97% sequence similarity and 100% sequence similar zero-radius OTUs by UNOISE3) and compared these to metagenome-derived population genomes and metatranscriptomes. Significant positive correlations were observed between microbial total activity and abundance with both the amplicon- and omic-based methods. All three methods revealed disproportionately high transcription/abundance ratios for some rare taxa but lower ratios for most abundant taxa for all the communities, which was further corroborated by the high replication rate (iRep) of most low-abundance population genomes. IMPORTANCE Variation in microbial activity levels is increasingly being recognized as both an important dimension in community function and a complicating factor in sequencing-based survey methods. This study extends previous reports that rare taxa may contribute disproportionately to community activity in some natural environments, showing that this may also hold in artificially maintained model communities with well-described inputs, outputs, and biochemical functions. These results demonstrate that assessment of activity levels using the rRNA/rDNA ratio is robust across taxonomic unit formation methods and is independently corroborated by omics methods. The results also provide insight into the comparative advantages and disadvantages of different taxonomic unit formation methods in amplicon sequencing studies, showing that UNOISE3 provides comparable microbial diversity, structure, and activity information as the 97% sequence similarity method but potentially loses some phylogenetic diversity and creates more "phantom taxa" (which are present in the RNA pool but not the corresponding DNA pool).}, }
@article {pmid30687284, year = {2018}, author = {Shates, TM and Sun, P and Malmstrom, CM and Dominguez, C and Mauck, KE}, title = {Addressing Research Needs in the Field of Plant Virus Ecology by Defining Knowledge Gaps and Developing Wild Dicot Study Systems.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3305}, doi = {10.3389/fmicb.2018.03305}, pmid = {30687284}, issn = {1664-302X}, abstract = {Viruses are ubiquitous within all habitats that support cellular life and represent the most important emerging infectious diseases of plants. Despite this, it is only recently that we have begun to describe the ecological roles of plant viruses in unmanaged systems and the influence of ecosystem properties on virus evolution. We now know that wild plants frequently harbor infections by diverse virus species, but much remains to be learned about how viruses influence host traits and how hosts influence virus evolution and vector interactions. To identify knowledge gaps and suggest avenues for alleviating research deficits, we performed a quantitative synthesis of a representative sample of virus ecology literature, developed criteria for expanding the suite of pathosystems serving as models, and applied these criteria through a case study. We found significant gaps in the types of ecological systems studied, which merit more attention. In particular, there is a strong need for a greater diversity of logistically tractable, wild dicot perennial study systems suitable for experimental manipulations of infection status. Based on criteria developed from our quantitative synthesis, we evaluated three California native dicot perennials typically found in Mediterranean-climate plant communities as candidate models: Cucurbita foetidissima (buffalo gourd), Cucurbita palmata (coyote gourd), and Datura wrightii (sacred thorn-apple). We used Illumina sequencing and network analyses to characterize viromes and viral links among species, using samples taken from multiple individuals at two different reserves. We also compared our Illumina workflow with targeted RT-PCR detection assays of varying costs. To make this process accessible to ecologists looking to incorporate virology into existing studies, we describe our approach in detail and discuss advantages and challenges of different protocols. We also provide a bioinformatics workflow based on open-access tools with graphical user interfaces. Our study provides evidence that dicot perennials in xeric habitats support multiple, asymptomatic infections by viruses known to be pathogenic in related crop hosts. Quantifying the impacts of these interactions on plant performance and virus epidemiology in our logistically tractable host systems will provide fundamental information about plant virus ecology outside of crop environments.}, }
@article {pmid30687279, year = {2018}, author = {Shi, LD and Chen, YS and Du, JJ and Hu, YQ and Shapleigh, JP and Zhao, HP}, title = {Metagenomic Evidence for a Methylocystis Species Capable of Bioremediation of Diverse Heavy Metals.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3297}, doi = {10.3389/fmicb.2018.03297}, pmid = {30687279}, issn = {1664-302X}, abstract = {Heavy metal pollution has become an increasingly serious problem worldwide. Co-contamination with toxic mercury (Hg) and arsenic (As) presents a particularly difficult bioremediation trouble. By oxidizing the greenhouse gas methane, methanotrophs have been demonstrated to have high denitrification activity in eutrophic waters, indicating their possible potential for use in bioremediation of Hg(II) and As(V) in polluted water. Using metagenomics, a novel Methylocystis species (HL18), which was one of the most prevalent bacteria (9.9% of the relative abundance) in a CH4-based bio-reactor, is described here. The metagenomic-assembled genome (MAG) HL18 had gene products whose average amino acid identity against other known Methylocystis species varied from 69 to 85%, higher than the genus threshold but lower than the species boundary. Genomic analysis indicated that HL18 possessed all the genes necessary for the reduction of Hg(II) and As(V). Phylogenetic investigation of mercuric reductase (MerA) found that the HL18 protein was most closely affiliated with proteins from two Hg(II)-reducing bacteria, Bradyrhizobium sp. strain CCH5-F6 and Paracoccus halophilus. The genomic organization and phylogeny of the genes in the As(V)-reducing operon (arsRCCB) had significant identity with those from a As(V)-reducing bacterium belonging to the Rhodopseudomonas genus, indicating their reduction capability of As(V). Further analysis found that at least eight genera of methanotrophs possess both Hg(II) and As(V) reductases, illustrating the generally overlooked metabolic potential of methanotrophs. These results suggest that methanotrophs have greater bioremediation potential in heavy metal contaminated water than has been appreciated and could play an important role in the mitigation of heavy metal toxicity of contaminated wastewater.}, }
@article {pmid30687241, year = {2018}, author = {Thiel, V and Garcia Costas, AM and Fortney, NW and Martinez, JN and Tank, M and Roden, EE and Boyd, ES and Ward, DM and Hanada, S and Bryant, DA}, title = {"Candidatus Thermonerobacter thiotrophicus," A Non-phototrophic Member of the Bacteroidetes/Chlorobi With Dissimilatory Sulfur Metabolism in Hot Spring Mat Communities.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3159}, doi = {10.3389/fmicb.2018.03159}, pmid = {30687241}, issn = {1664-302X}, abstract = {In this study we present evidence for a novel, thermophilic bacterium with dissimilatory sulfur metabolism, tentatively named "Candidatus Thermonerobacter thiotrophicus," which is affiliated with the Bacteroides/Ignavibacteria/Chlorobi and which we predict to be a sulfate reducer. Dissimilatory sulfate reduction (DSR) is an important and ancient metabolic process for energy conservation with global importance for geochemical sulfur and carbon cycling. Characterized sulfate-reducing microorganisms (SRM) are found in a limited number of bacterial and archaeal phyla. However, based on highly diverse environmental dsrAB sequences, a variety of uncultivated and unidentified SRM must exist. The recent development of high-throughput sequencing methods allows the phylogenetic identification of some of these uncultured SRM. In this study, we identified a novel putative SRM inhabiting hot spring microbial mats that is a member of the OPB56 clade ("Ca. Kapabacteria") within the Bacteroidetes/Chlorobi superphylum. Partial genomes for this new organism were retrieved from metagenomes from three different hot springs in Yellowstone National Park, United States, and Japan. Supporting the prediction of a sulfate-reducing metabolism for this organism during period of anoxia, diel metatranscriptomic analyses indicate highest relative transcript levels in situ for all DSR-related genes at night. The presence of terminal oxidases, which are transcribed during the day, further suggests that these organisms might also perform aerobic respiration. The relative phylogenetic proximity to the sulfur-oxidizing, chlorophototrophic Chlorobi further raises new questions about the evolution of dissimilatory sulfur metabolism.}, }
@article {pmid30685659, year = {2019}, author = {Tan, Z and Yu, H and Xu, L and Zhao, Z and Zhang, P and Qu, Y and He, B and Tu, C}, title = {Virome profiling of rodents in Xinjiang Uygur Autonomous Region, China: Isolation and characterization of a new strain of Wenzhou virus.}, journal = {Virology}, volume = {529}, number = {}, pages = {122-134}, doi = {10.1016/j.virol.2019.01.010}, pmid = {30685659}, issn = {1096-0341}, abstract = {Rodents, as the most diverse and widest distributed mammals, are a natural reservoir of many zoonotic viruses. However, little is known about the viral diversity harbored by rodents in China. Here we performed viral metagenomic analyses of 314 wild rodents covering 7 species, sampled in North-western China. We also conducted a systematic virological characterization of a new Wenzhou virus (WENV) isolate, QARn1, from a brown rat (Rattus norvegicus). Full genomic and phylogenetic analyses showed that QARn1 is a previously unidentified strain of Wenzhou mammarenavirus and forms a new branch within the Asian clade. Experimental infection of Sprague-Dawley rats with QARn1 did not present overt pathology, but specific humoral immune responses developed and mild hemorrhage and immunocyte infiltration of the lungs and thymus were observed. These observations have expanded the geographic distribution of WENV to Central Asia, and further confirm that brown rats are natural hosts of Wenzhou virus.}, }
@article {pmid30685331, year = {2019}, author = {Pienkowska, K and Wiehlmann, L and Tümmler, B}, title = {Metagenome - Inferred bacterial replication rates in cystic fibrosis airways.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jcf.2019.01.003}, pmid = {30685331}, issn = {1873-5010}, abstract = {Bacterial replication rates were determined from metagenome sequencing of nasal lavage, throat swabs and induced sputa collected from healthy subjects and individuals with COPD or cystic fibrosis. More than 90% of peak-to-trough coverage ratios of major clones were above 1.4 indicating that the most abundant bacterial species in the microbial communities were replicating in the airways including common inhabitants such as Prevotella and Streptococcus species as well as the cystic fibrosis pathogens Staphylococcus aureus and Pseudomonas aeruginosa. The populations of P. aeruginosa and S. aureus were replicating their pool of chromosomes more slowly than the populations of the common inhabitants of a healthy airway microbial flora. The assessment of growth dynamics in microbial metagenomes could become a decision-making tool for the diagnosis and management of bacterial infections in cystic fibrosis.}, }
@article {pmid30684744, year = {2019}, author = {Wang, G and Xu, N and Yang, L and Zheng, F and Sai, L and Zhou, J and Yang, S}, title = {Community acquired Stenotrophomonas maltophilia discitis: Diagnosis aided by shotgun metagenomic sequencing.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {81}, number = {}, pages = {1-3}, doi = {10.1016/j.ijid.2019.01.032}, pmid = {30684744}, issn = {1878-3511}, abstract = {We report a rare case of culture negative L4-L5 discitis and epidural abscess in an immunocompetent child who had dry cupping therapy performed to treat low back strain. The causative pathogen was identified as Stenotrophomonas maltophilia by shotgun metagenomic sequencing of spinal cord aspirate after more than one month of unsuccessful empirical treatment with 6 different antibiotics. The patient was successfully treated with Sulfamethoxazole-trimethoprim and minocycline. Cupping therapy is a very popular medical procedure widely used in China, but the potential risk for severe infections such as discitis and epidural abscess described in this case should be recognized.}, }
@article {pmid30683956, year = {2019}, author = {Mahato, NK and Sharma, A and Singh, Y and Lal, R}, title = {Comparative metagenomic analyses of a high-altitude Himalayan geothermal spring revealed temperature-constrained habitat-specific microbial community and metabolic dynamics.}, journal = {Archives of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00203-018-01616-6}, pmid = {30683956}, issn = {1432-072X}, support = {BT/PR15118/BCE/8/1141/2015//Department of Biotechnology, Ministry of Science and Technology/ ; }, abstract = {Metagenomic surveys across microbial mat (~ 55 °C) samples of high-altitude (1760 m above sea level) Himalayan geothermal springs have revealed specialized community enriched with niche-specific functions. In this study, we have performed metagenomic sequence-based analyses to get insights into taxonomic composition and functional potential of hyperthermophiles in water (~ 95 °C) and sediment samples (78-98 °C). Community analyses revealed predominance of thermophilic bacterial and archeal genera dwelling in water in contrast to microbial mats (55 °C), namely Methylophilus, Methyloversatilis, Emticicia, Caulobacter, Thermus, Enhydrobacter and Pyrobaculum. Sediment samples having surface temperature (~ 78 °C) were colonized by Pyrobaculum and Chloroflexus while genus Massilia was found to be inhabited in high-temperature sediments (~ 98 °C). Functional analyses of metagenomic sequences revealed genetic enrichment of genes such as type IV secretion system, flagellar assembly and two-component system in contrast to mats. Furthermore, inter-sample comparison of enriched microbial diversity among water, sediment and microbial mats revealed habitat-specific clustering of the samples within same environment highlighting the role of temperature dynamics in modulating community structure across different habitats in same niche. However, function-based analysis demonstrated site-specific clustering among sediment, microbial mat and water samples. Furthermore, a novel thermophilic genotype of the genus Emticicia (designated as strain MM) was reconstructed from metagenome data. This is a correlative study between three major habitats present in geothermal spring environment, i.e., water, sediment and microbial mats revealing greater phylogenetic and functional dispersion emphasizing changing habitat-specific dynamics with temperature.}, }
@article {pmid30683920, year = {2019}, author = {Vacheron, J and Péchy-Tarr, M and Brochet, S and Heiman, CM and Stojiljkovic, M and Maurhofer, M and Keel, C}, title = {T6SS contributes to gut microbiome invasion and killing of an herbivorous pest insect by plant-beneficial Pseudomonas protegens.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0353-8}, pmid = {30683920}, issn = {1751-7370}, support = {31003A-159520//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 31003A-159520//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 31003A-159520//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 31003A-159520//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 31003A-159520//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; }, abstract = {Pseudomonas protegens are multi-talented plant-colonizing bacteria that suppress plant pathogens and stimulate plant defenses. In addition, they are capable of invading and killing agriculturally important plant pest insects that makes them promising candidates for biocontrol applications. Here we assessed the role of type VI secretion system (T6SS) components of type strain CHA0 during interaction with larvae of the cabbage pest Pieris brassicae. We show that the T6SS core apparatus and two VgrG modules, encompassing the respective T6SS spikes (VgrG1a and VgrG1b) and associated effectors (RhsA and Ghh1), contribute significantly to insect pathogenicity of P. protegens in oral infection assays but not when bacteria are injected directly into the hemolymph. Monitoring of the colonization levels of P. protegens in the gut, hemolymph, and excrements of the insect larvae revealed that the invader relies on T6SS and VgrG1a module function to promote hemocoel invasion. A 16S metagenomic analysis demonstrated that T6SS-supported invasion by P. protegens induces significant changes in the insect gut microbiome affecting notably Enterobacteriaceae, a dominant group of the commensal gut bacteria. Our study supports the concept that pathogens deploy T6SS-based strategies to disrupt the commensal microbiota in order to promote host colonization and pathogenesis.}, }
@article {pmid30683856, year = {2019}, author = {Ellegaard, KM and Engel, P}, title = {Genomic diversity landscape of the honey bee gut microbiota.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {446}, doi = {10.1038/s41467-019-08303-0}, pmid = {30683856}, issn = {2041-1723}, mesh = {Age Factors ; Animals ; Bees/*microbiology ; Bifidobacterium/classification/*genetics/isolation & purification ; *Biological Variation, Individual ; DNA, Bacterial/genetics ; Firmicutes/classification/*genetics/isolation & purification ; Gammaproteobacteria/classification/*genetics/isolation & purification ; Gastrointestinal Microbiome/*genetics ; Genetic Variation ; Metagenomics ; Microbial Consortia/genetics ; Phylogeny ; Symbiosis/physiology ; }, abstract = {The structure and distribution of genomic diversity in natural microbial communities is largely unexplored. Here, we used shotgun metagenomics to assess the diversity of the honey bee gut microbiota, a community consisting of few bacterial phylotypes. Our results show that most phylotypes are composed of sequence-discrete populations, which co-exist in individual bees and show age-specific abundance profiles. In contrast, strains present within these sequence-discrete populations were found to segregate into individual bees. Consequently, despite a conserved phylotype composition, each honey bee harbors a distinct community at the functional level. While ecological differentiation seems to facilitate coexistence at higher taxonomic levels, our findings suggest that, at the level of strains, priority effects during community assembly result in individualized profiles, despite the social lifestyle of the host. Our study underscores the need to move beyond phylotype-level characterizations to understand the function of this community, and illustrates its potential for strain-level analysis.}, }
@article {pmid30683748, year = {2019}, author = {Burkert, A and Douglas, TA and Waldrop, MP and Mackelprang, R}, title = {Changes in the Active, Dead, and Dormant Microbial Community Structure Across a Pleistocene Permafrost Chronosequence.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02646-18}, pmid = {30683748}, issn = {1098-5336}, abstract = {Permafrost hosts a community of microorganisms that survive and reproduce for millennia despite extreme environmental conditions such as water stress, subzero temperatures, high salinity, and low nutrient availability. Many studies focused on permafrost microbial community composition use DNA-based methods such as metagenomic and 16S rRNA gene sequencing. However, these methods do not distinguish between active, dead, and dormant cells. This is of particular concern in ancient permafrost where constant subzero temperatures preserve DNA from dead organisms and dormancy may be a common survival strategy. To circumvent this we applied: (i) live/dead differential staining coupled with microscopy, (ii) endospore enrichment, and (iii) selective depletion of DNA from dead cells to permafrost microbial communities across a Pleistocene permafrost chronosequence (19 thousand years (K), 27K, and 33K). Cell counts and analysis of 16S rRNA gene amplicons from live, dead, and dormant cells revealed how communities differ between these pools, how they are influenced by soil physicochemical properties, and whether they change over geologic time. We found evidence that cells capable of forming endospores are not necessarily dormant and that members of class Bacilli were more likely to form endospores in response to long-term stressors associated with permafrost environmental conditions than members of Clostridia, which were more likely to persist as vegetative cells in our older samples. We also found that removing exogenous 'relic' DNA preserved within permafrost did not significantly alter microbial community composition. These results link the live, dead, and dormant microbial communities to physicochemical characteristics and provides insights into the survival of microbial communities in ancient permafrost.IMPORTANCE Permafrost soils store more than half earth's soil carbon despite covering ∼15% of the land area (Tarnocai C et al. 2009. Global Biogeochemical Cycles 23:2. doi: 10.1029/2008GB003327). This permafrost carbon is rapidly degraded following thaw (Schuur EAG et al. 2015. Nature. 520:171-179.). Understanding microbial communities in permafrost will contribute to the knowledge base necessary to understand the rates and forms of permafrost C and N cycling post thaw. Permafrost is also an analog for frozen extraterrestrial environments and evidence of viable organisms in ancient permafrost is of interest to those searching for potential life on distant worlds. If we can identify strategies microbial communities utilize to survive permafrost, it may yield insights into how life (if it exists) survives in frozen environments outside of Earth. Our work is significant because it contributes to an understanding of how microbial life adapts and survives in the extreme environmental conditions in permafrost terrains.}, }
@article {pmid30680888, year = {2019}, author = {Kraiselburd, I and Brüls, T and Heilmann, G and Kaschani, F and Kaiser, M and Meckenstock, RU}, title = {Metabolic reconstruction of the genome of candidate Desulfatiglans TRIP_1 and identification of key candidate enzymes for anaerobic phenanthrene degradation.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14527}, pmid = {30680888}, issn = {1462-2920}, support = {//University of Duisburg-Essen/ ; //Horizon 2020 research and innovation program/ ; 705321//Marie Sklodowska-Curie/ ; 666952//ERC advanced grant EcOILogy/ ; }, abstract = {Polycyclic aromatic hydrocarbons (PAHs) are widely distributed pollutants. As oxygen is rapidly depleted in water-saturated PAH-contaminated sites, anaerobic microorganisms are crucial for their consumption. Here, we report the metabolic pathway for anaerobic degradation of phenanthrene by a sulfate-reducing enrichment culture (TRIP) obtained from a natural asphalt lake. The dominant organism of this culture belongs to the Desulfobacteraceae family of Deltaproteobacteria and genome-resolved metagenomics led to the reconstruction of its genome along with a handful of genomes from lower abundance bacteria. Proteogenomic analyses confirmed metabolic capabilities for dissimilatory sulfate reduction and indicated the presence of the Embden-Meyerhof-Parnas pathway, a complete tricarboxylic acid cycle as well as a complete Wood-Ljungdahl pathway. Genes encoding enzymes putatively involved in the degradation of phenanthrene were identified. This includes two gene clusters encoding a multisubunit carboxylase complex likely involved in the activation of phenanthrene, as well as genes encoding reductases potentially involved in subsequent ring dearomatization and reduction steps. The predicted metabolic pathways were corroborated by transcriptome and proteome analyses, and provide the first insights into the metabolic pathway responsible for the anaerobic degradation of three-ringed PAHs.}, }
@article {pmid30680877, year = {2019}, author = {Alessandri, G and Milani, C and Mancabelli, L and Mangifesta, M and Lugli, GA and Viappiani, A and Duranti, S and Turroni, F and Ossiprandi, MC and van Sinderen, D and Ventura, M}, title = {Metagenomic dissection of the canine gut microbiota: insights into taxonomic, metabolic and nutritional features.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14540}, pmid = {30680877}, issn = {1462-2920}, abstract = {Domestication of dogs from wolves is the oldest known example of ongoing animal selection, responsible for generating more than 300 dog breeds worldwide. In order to investigate the taxonomic and functional evolution of the canine gut microbiota, a multi-omics approach was applied to six wild wolves and 169 dog fecal samples, the latter encompassing 51 breeds, which fully covers currently known canine genetic biodiversity. Specifically, 16S rRNA gene and bifidobacterial Internally Transcribed Spacer (ITS) profiling were employed to reconstruct and then compare the canine core gut microbiota to those of wolves and humans, revealing that artificial selection and subsequent cohabitation of dogs with their owners influenced the microbial population of canine gut through loss and acquisition of specific bacterial taxa. Moreover, comparative analysis of the intestinal bacterial population of dogs fed on Bones and Raw Food (BARF) or commercial food (CF) diet, coupled with shotgun metagenomics, highlighted that both bacterial composition and metabolic repertoire of the canine gut microbiota have evolved to adapt to high-protein or high-carbohydrates intake. Altogether, these data indicate that artificial selection and domestication not only affected the canine genome, but also shaped extensively the bacterial population harbored by the canine gut. This article is protected by copyright. All rights reserved.}, }
@article {pmid30680826, year = {2019}, author = {Docherty, KM and Gutknecht, JLM}, title = {Soil microbial restoration strategies for promoting climate-ready prairie ecosystems.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {}, number = {}, pages = {e01858}, doi = {10.1002/eap.1858}, pmid = {30680826}, issn = {1051-0761}, abstract = {Tractable practices for soil microbial restoration in tallgrass prairies reclaimed from agriculture are a critical gap in traditional ecological restoration. Long-term fertilization and tilling permanently alter soil bacterial and fungal communities, requiring microbe-targeted restoration methods to improve belowground ecosystem services and carbon storage in newly restored prairies. These techniques are particularly important when restoring for climate-ready ecosystems, adapted to altered temperature regimes. To approach these issues, we conducted a multi-factorial greenhouse experiment to test the effects of plant species richness, soil amendment and elevated temperature on soil microbial diversity, growth, and function. Treatments consisted of three seedlings of one plant species (Andropogon gerardii) or one seedling each of three plant species (A. gerardii, Echinacea pallida, Coreopsis lanceolata). Soil amendments included cellulose addition, inoculation with a microbial community collected from an undisturbed remnant prairie, and a control. We assessed microbial communities using extracellular enzyme assays, Illumina sequencing of the bacterial 16S rRNA gene, predicted bacterial metabolic pathways from sequence data and phospholipid fatty acid analysis (PLFA), which includes both bacterial and fungal lipid abundances. Our results indicate that addition of cellulose selects for slow-growing bacterial taxa (Verrucomicrobia) and fungi at ambient temperature. However, at elevated temperature, selection for slow-growing bacterial taxa is enhanced, while selection for fungi is lost, indicating temperature sensitivity among fungi. Cellulose addition was a more effective means of altering soil community composition than addition of microbial communities harvested from a remnant prairie. Soil water content was typically higher in the A. gerardii treatment alone, regardless of temperature, but at ambient temperature only, predicted metagenomics pathways for bacterial carbon metabolism were more abundant with A. gerardii. In summary, these results from a mesocosm test case indicate that adding cellulose to newly restored soil and increasing the abundance of C4 grasses, such as A. gerardii, can select for microbial communities adapted for slow growth and carbon storage. Further testing is required to determine if these approaches yield the same results in a field-level experiment.}, }
@article {pmid30680143, year = {2019}, author = {Rytkönen, S and Vesterinen, EJ and Westerduin, C and Leviäkangas, T and Vatka, E and Mutanen, M and Välimäki, P and Hukkanen, M and Suokas, M and Orell, M}, title = {From feces to data: A metabarcoding method for analyzing consumed and available prey in a bird-insect food web.}, journal = {Ecology and evolution}, volume = {9}, number = {1}, pages = {631-639}, doi = {10.1002/ece3.4787}, pmid = {30680143}, issn = {2045-7758}, abstract = {Diets play a key role in understanding trophic interactions. Knowing the actual structure of food webs contributes greatly to our understanding of biodiversity and ecosystem functioning. The research of prey preferences of different predators requires knowledge not only of the prey consumed, but also of what is available. In this study, we applied DNA metabarcoding to analyze the diet of 4 bird species (willow tits Poecile montanus, Siberian tits Poecile cinctus, great tits Parus major and blue tits Cyanistes caeruleus) by using the feces of nestlings. The availability of their assumed prey (Lepidoptera) was determined from feces of larvae (frass) collected from the main foraging habitat, birch (Betula spp.) canopy. We identified 53 prey species from the nestling feces, of which 11 (21%) were also detected from the frass samples (eight lepidopterans). Approximately 80% of identified prey species in the nestling feces represented lepidopterans, which is in line with the earlier studies on the parids' diet. A subsequent laboratory experiment showed a threshold for fecal sample size and the barcoding success, suggesting that the smallest frass samples do not contain enough larval DNA to be detected by high-throughput sequencing. To summarize, we apply metabarcoding for the first time in a combined approach to identify available prey (through frass) and consumed prey (via nestling feces), expanding the scope and precision for future dietary studies on insectivorous birds.}, }
@article {pmid30679061, year = {2019}, author = {Chadha, BS and Kaur, B and Basotra, N and Tsang, A and Pandey, A}, title = {Thermostable xylanases from thermophilic fungi and bacteria: Current perspective.}, journal = {Bioresource technology}, volume = {277}, number = {}, pages = {195-203}, doi = {10.1016/j.biortech.2019.01.044}, pmid = {30679061}, issn = {1873-2976}, abstract = {Thermostable xylanases from thermophilic fungi and bacteria have a wide commercial acceptability in feed, food, paper and pulp and bioconversion of lignocellulosics with an estimated annual market of USD 500 Million. The genome wide analysis of thermophilic fungi clearly shows the presence of elaborate genetic information coding for multiple xylanases primarily coding for GH10, GH11 in addition to GH7 and GH30 xylanases. The transcriptomics and proteome profiling has given insight into the differential expression of these xylanases in some of the thermophilic fungi. Bioprospecting has resulted in identification of novel thermophilic xylanases that have been endorsed by the industrial houses for heterologous over- expression and formulations. The future use of xylanases is expected to increase exponentially for their role in biorefineries. The discovery of new and improvement of existing xylanases using molecular tools such as directed evolution is expected to be the mainstay to meet increasing demand of thermostable xylanases.}, }
@article {pmid30678352, year = {2019}, author = {Yang, Q and Gao, C and Jiang, Y and Wang, M and Zhou, X and Shao, H and Gong, Z and McMinn, A}, title = {Metagenomic Characterization of the Viral Community of the South Scotia Ridge.}, journal = {Viruses}, volume = {11}, number = {2}, pages = {}, doi = {10.3390/v11020095}, pmid = {30678352}, issn = {1999-4915}, support = {41676178//National Natural Science Foundation of China/ ; 41076088//National Natural Science Foundation of China/ ; 31500339//National Natural Science Foundation of China/ ; 2016ASKJ14//Scientific and Technological Innovation Project Financially Supported by Qingdao National Laboratory for Marine Science and Technology/ ; 2017YFA0603200//National Key Research and Development Program of China/ ; }, abstract = {Viruses are the most abundant biological entities in aquatic ecosystems and harbor an enormous amount of genetic diversity. Whereas their influence on marine ecosystems is widely acknowledged, current information about their diversity remains limited. We conducted a viral metagenomic analysis of water samples collected during the austral summer of 2016 from the South Scotia Ridge (SSR), near the Antarctic Peninsula. The taxonomic composition and diversity of the viral communities were investigated, and a functional assessment of the sequences was performed. Phylotypic analysis showed that most viruses belonged to the order Caudovirales, especially the family Podoviridae (41.92⁻48.7%), which is similar to the situation in the Pacific Ocean. Functional analysis revealed a relatively high frequency of phage-associated and metabolism genes. Phylogenetic analyses of phage TerL and Capsid_NCLDV (nucleocytoplasmic large DNA viruses) marker genes indicated that many sequences associated with Caudovirales and NCLDV were novel and distinct from known phage genomes. High Phaeocystis globosa virus virophage (Pgvv) signatures were found and complete and partial Pgvv-like were obtained, which influence host⁻virus interactions. Our study expands existing knowledge of viral communities and their diversities from the Antarctic region and provides basic data for further exploring polar microbiomes.}, }
@article {pmid30678330, year = {2019}, author = {Levin, S and Sela, N and Erez, T and Nestel, D and Pettis, J and Neumann, P and Chejanovsky, N}, title = {New Viruses from the Ectoparasite Mite Varroa destructor Infesting Apis mellifera and Apis cerana.}, journal = {Viruses}, volume = {11}, number = {2}, pages = {}, doi = {10.3390/v11020094}, pmid = {30678330}, issn = {1999-4915}, support = {MO-TAU-11-M32-035//United States Agency for International Development/ ; 131-1857//Chief Scientist Ministry of Agriculture of Israel/ ; }, abstract = {Varroa destructor is an ectoparasitic mite of Asian or Eastern honeybees Apis cerana(A. cerana) which has become a serious threat to European subspecies of Western honeybees Apis mellifera (A. mellifera) within the last century. V.destructor and its vectored honeybee viruses became serious threats for colony survival. This is a short period for pathogen- and host-populations to adapt. To look for possible variation in the composition of viral populations we performed RNA metagenomic analysis of the Western honeybee subspecies A. m. ligustica, A. m.syriaca, A. m. intermissa, and A. cerana and their respective V. destructor mites. The analysis revealed two novel viruses: Varroa orthomyxovirus-1 (VOV-1) in A. mellifera and V. destructor and a Hubei like-virga virus-14 homolog in V. destructor. VOV-1 was more prevalent in V. destructor than in A. mellifera and we found evidence for viral replication in both hosts. Interestingly, we found differences in viral loads of A. cerana and their V. destructor, A. m. intermissa, and its V. destructor showed partial similarity, while A. m.ligustica and A. m.syriaca and their varroa where very similar. Deformed wing virus exhibited 82.20%, 99.20%, 97.90%, and 0.76% of total viral reads in A. m. ligustica, A. m. syriaca, A. m. intermissa, and A. cerana, respectively. This is the first report of a complete segmented-single-stranded negative-sense RNA virus genome in honeybees and V. destructor mites.}, }
@article {pmid30678005, year = {2019}, author = {Huang, ZS and Wei, ZS and Xiao, XL and Tang, MR and Li, BL and Zhang, X}, title = {Simultaneous mercury oxidation and NO reduction in a membrane biofilm reactor.}, journal = {The Science of the total environment}, volume = {658}, number = {}, pages = {1465-1474}, doi = {10.1016/j.scitotenv.2018.12.105}, pmid = {30678005}, issn = {1879-1026}, mesh = {Bacteria/classification/genetics ; *Bacterial Physiological Phenomena ; *Biofilms ; Bioreactors/*microbiology ; DNA, Bacterial/analysis ; Denitrification ; Membranes, Artificial ; Mercury/*metabolism ; Metagenome ; Nitric Oxide/*metabolism ; Oxidation-Reduction ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, DNA ; }, abstract = {This work demonstrates bacterial oxidation of mercury (Hg0) coupled to nitric oxide (NO) reduction in a denitrifying membrane biofilm reactor (MBfR). In 93 days' operation, Hg0 and NO removal efficiency attained 90.7% and 74.1%, respectively. Thauera, Pseudomonas, Paracoccus and Pannonibacter played dual roles as Hg0 oxidizers and denitrifiers simultaneously. Denitrifying bacteria and the potential mercury resistant bacteria dominated the bacterial community. Denitrification-related genes (norB, norC, norD, norE, norQ and norV) and enzymatic Hg0 oxidation-related genes (katG, katE) were responsible for bacterial oxidation of Hg0 and NO reduction, as shown by metagenomic sequencing. XPS, HPLC-ICP-MS and SEM-EDS indicated the formation of a stable mercuric species (Hg2+) reasulting from Hg0 oxidation in the biofilm. Bacterial oxidation of Hg0 was coupled to NO reduction in which Hg0 served as the initial electron donor while NO served as the terminal electron acceptor and thereby redox between Hg0 and NO was formed. MBfR was capable of both Hg0 bio-oxidation and denitrifying NO reduction. This research opens up new possibilities for application of MBfR to simultaneous flue gas demercuration and denitration.}, }
@article {pmid30677208, year = {2019}, author = {Pasin, F and Menzel, W and Daròs, JA}, title = {Harnessed viruses in the age of metagenomics and synthetic biology: an update on infectious clone assembly and biotechnologies of plant viruses.}, journal = {Plant biotechnology journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/pbi.13084}, pmid = {30677208}, issn = {1467-7652}, support = {BIO2017-83184-R//Ministerio de Ciencia, Innovación y Universidades (Spain)/ ; }, abstract = {Recent metagenomic studies have provided an unprecedented wealth of data, which are revolutionizing our understanding of virus diversity. A redrawn landscape highlights viruses as active players in the phytobiome, and surveys have uncovered their positive roles in environmental stress tolerance of plants. Viral infectious clones are key tools for functional characterization of known and newly identified viruses. Knowledge of viruses and their components has been instrumental for the development of modern plant molecular biology and biotechnology. In this review, we provide extensive guidelines built on current synthetic biology advances that streamline infectious clone assembly, thus lessening a major technical constraint of plant virology. The focus is on generation of infectious clones in binary T-DNA vectors, which are delivered efficiently to plants by Agrobacterium. We then summarize recent applications of plant viruses and explore emerging trends in microbiology, bacterial and human virology that, once translated to plant virology, could lead to the development of virus-based gene therapies for ad hoc engineering of plant traits. The systematic characterization of plant virus roles in the phytobiome and next-generation virus-based tools will be indispensable landmarks in the synthetic biology roadmap to better crops.}, }
@article {pmid30677104, year = {2019}, author = {Cameron, A and Barbieri, R and Read, R and Church, D and Adator, EH and Zaheer, R and McAllister, TA}, title = {Functional screening for triclosan resistance in a wastewater metagenome and isolates of Escherichia coli and Enterococcus spp. from a large Canadian healthcare region.}, journal = {PloS one}, volume = {14}, number = {1}, pages = {e0211144}, doi = {10.1371/journal.pone.0211144}, pmid = {30677104}, issn = {1932-6203}, abstract = {The biocide triclosan is in many consumer products and is a frequent contaminant of wastewater (WW) such that there is concern that triclosan promotes resistance to important antibiotics. This study identified functional mechanisms of triclosan resistance (TCSR) in WW metagenomes, and assessed the frequency of TCSR in WW-derived and clinical isolates of Escherichia coli and Enterococcus spp. Metagenomic DNA extracted from WW was used to profile the microbiome and construct large-insert cosmid libraries, which were screened for TCSR. Resistant cosmids were sequenced and the TCSR determinant identified by transposon mutagenesis. Wastewater Enterococcus spp. (N = 94) and E. coli (N = 99) and clinical Enterococcus spp. (N = 146) and vancomycin-resistant E. faecium (VRE; N = 149) were collected and tested for resistance to triclosan and a comprehensive drug panel. Functional metagenomic screening revealed diverse FabV homologs as major WW TCSR determinants. Resistant clones harboured sequences likely originating from Aeromonas spp., a common WW microbe. The triclosan MIC90s for E. coli, E. faecalis, and E. faecium isolates were 0.125, 32, and 32 mg/L, respectively. For E. coli, there was no correlation between the triclosan MIC and any drug tested. Negative correlations were detected between the triclosan MIC and levofloxacin resistance for E. faecalis, and between triclosan and vancomycin, teicoplanin, and ampicillin resistance for E. faecium. Thus, FabV homologs were the major contributor to the WW triclosan resistome and high-level TCSR was not observed in WW or clinical isolates. Elevated triclosan MICs were not positively correlated with antimicrobial resistance to any drug tested.}, }
@article {pmid30674646, year = {2019}, author = {Yinda, CK and Vanhulle, E and Conceição-Neto, N and Beller, L and Deboutte, W and Shi, C and Ghogomu, SM and Maes, P and Van Ranst, M and Matthijnssens, J}, title = {Gut Virome Analysis of Cameroonians Reveals High Diversity of Enteric Viruses, Including Potential Interspecies Transmitted Viruses.}, journal = {mSphere}, volume = {4}, number = {1}, pages = {}, doi = {10.1128/mSphere.00585-18}, pmid = {30674646}, issn = {2379-5042}, abstract = {Diarrhea remains one of the most common causes of deaths in children. A limited number of studies have investigated the prevalence of enteric pathogens in Cameroon, and as in many other African countries, the cause of many diarrheal episodes remains unexplained. A proportion of these unknown cases of diarrhea are likely caused by yet-unidentified viral agents, some of which could be the result of (recent) interspecies transmission from animal reservoirs, like bats. Using viral metagenomics, we screened fecal samples of 221 humans (almost all with gastroenteritis symptoms) between 0 and 89 years of age with different degrees of bat contact. We identified viruses belonging to families that are known to cause gastroenteritis such as Adenoviridae, Astroviridae, Caliciviridae, Picornaviridae, and Reoviridae Interestingly, a mammalian orthoreovirus, picobirnaviruses, a smacovirus, and a pecovirus were also found. Although there was no evidence of interspecies transmission of the most common human gastroenteritis-related viruses (Astroviridae, Caliciviridae, and Reoviridae), the phylogenies of the identified orthoreovirus, picobirnavirus, and smacovirus indicate a genetic relatedness of these viruses identified in stools of humans and those of bats and/or other animals. These findings points out the possibility of interspecies transmission or simply a shared host of these viruses (bacterial, fungal, parasitic, …) present in both animals (bats) and humans. Further screening of bat viruses in humans or vice versa will elucidate the epidemiological potential threats of animal viruses to human health. Furthermore, this study showed a huge diversity of highly divergent novel phages, thereby expanding the existing phageome considerably.IMPORTANCE Despite the availability of diagnostic tools for different enteric viral pathogens, a large fraction of human cases of gastroenteritis remains unexplained. This could be due to pathogens not tested for or novel divergent viruses of potential animal origin. Fecal virome analyses of Cameroonians showed a very diverse group of viruses, some of which are genetically related to those identified in animals. This is the first attempt to describe the gut virome of humans from Cameroon. Therefore, the data represent a baseline for future studies on enteric viral pathogens in this area and contribute to our knowledge of the world's virome. The studies also highlight the fact that more viruses may be associated with diarrhea than the typical known ones. Hence, it provides meaningful epidemiological information on diarrhea-related viruses in this area.}, }
@article {pmid30674352, year = {2019}, author = {Pedron, R and Esposito, A and Bianconi, I and Pasolli, E and Tett, A and Asnicar, F and Cristofolini, M and Segata, N and Jousson, O}, title = {Genomic and metagenomic insights into the microbial community of a thermal spring.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {8}, doi = {10.1186/s40168-019-0625-6}, pmid = {30674352}, issn = {2049-2618}, support = {2731/16//Fondazione Cassa Di Risparmio Di Trento E Rovereto/ ; }, abstract = {BACKGROUND: Water springs provide important ecosystem services including drinking water supply, recreation, and balneotherapy, but their microbial communities remain largely unknown. In this study, we characterized the spring water microbiome of Comano Terme (Italy) at four sampling points of the thermal spa, including natural (spring and well) and human-built (storage tank, bathtubs) environments. We integrated large-scale culturing and metagenomic approaches, with the aim of comprehensively determining the spring water taxonomic composition and functional potential.
RESULTS: The groundwater feeding the spring hosted the most atypical microbiome, including many taxa known to be recalcitrant to cultivation. The core microbiome included the orders Sphingomonadales, Rhizobiales, and Caulobacterales, and the families Bradyrhizobiaceae and Moraxellaceae. A comparative genomic analysis of 72 isolates and 30 metagenome-assembled genomes (MAGs) revealed that most isolates and MAGs belonged to new species or higher taxonomic ranks widely distributed in the microbial tree of life. Average nucleotide identity (ANI) values calculated for each isolated or assembled genome showed that 10 genomes belonged to known bacterial species (> 95% ANI), 36 genomes (including 1 MAG) had ANI values ranging 85-92.5% and could be assigned as undescribed species belonging to known genera, while the remaining 55 genomes had lower ANI values (< 85%). A number of functional features were significantly over- or underrepresented in genomes derived from the four sampling sites. Functional specialization was found between sites, with for example methanogenesis being unique to groundwater whereas methanotrophy was found in all samples.
CONCLUSIONS: Current knowledge on aquatic microbiomes is essentially based on surface or human-associated environments. We started uncovering the spring water microbiome, highlighting an unexpected diversity that should be further investigated. This study confirms that groundwater environments host highly adapted, stable microbial communities composed of many unknown taxa, even among the culturable fraction.}, }
@article {pmid30673701, year = {2019}, author = {Garud, NR and Good, BH and Hallatschek, O and Pollard, KS}, title = {Evolutionary dynamics of bacteria in the gut microbiome within and across hosts.}, journal = {PLoS biology}, volume = {17}, number = {1}, pages = {e3000102}, doi = {10.1371/journal.pbio.3000102}, pmid = {30673701}, issn = {1545-7885}, abstract = {Gut microbiota are shaped by a combination of ecological and evolutionary forces. While the ecological dynamics have been extensively studied, much less is known about how species of gut bacteria evolve over time. Here, we introduce a model-based framework for quantifying evolutionary dynamics within and across hosts using a panel of metagenomic samples. We use this approach to study evolution in approximately 40 prevalent species in the human gut. Although the patterns of between-host diversity are consistent with quasi-sexual evolution and purifying selection on long timescales, we identify new genealogical signatures that challenge standard population genetic models of these processes. Within hosts, we find that genetic differences that accumulate over 6-month timescales are only rarely attributable to replacement by distantly related strains. Instead, the resident strains more commonly acquire a smaller number of putative evolutionary changes, in which nucleotide variants or gene gains or losses rapidly sweep to high frequency. By comparing these mutations with the typical between-host differences, we find evidence that some sweeps may be seeded by recombination, in addition to new mutations. However, comparisons of adult twins suggest that replacement eventually overwhelms evolution over multi-decade timescales, hinting at fundamental limits to the extent of local adaptation. Together, our results suggest that gut bacteria can evolve on human-relevant timescales, and they highlight the connections between these short-term evolutionary dynamics and longer-term evolution across hosts.}, }
@article {pmid30673580, year = {2018}, author = {Al Rwahnih, M and Alabi, OJ and Westrick, NM and Golino, D}, title = {Prunus geminivirus A: A Novel Grablovirus Infecting Prunus spp.}, journal = {Plant disease}, volume = {102}, number = {7}, pages = {1246-1253}, doi = {10.1094/PDIS-09-17-1486-RE}, pmid = {30673580}, issn = {0191-2917}, mesh = {Base Sequence ; Geminiviridae/classification/genetics/*physiology ; Genome, Viral/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Nucleotide Motifs/genetics ; Phylogeny ; Plant Diseases/*virology ; Prunus/*virology ; Prunus armeniaca/virology ; Prunus avium/virology ; Prunus domestica/virology ; Species Specificity ; }, abstract = {Increased use of metagenomics for routine virus diagnosis has led to the characterization of several genus level geminiviruses from tree fruit long thought to exclusively host RNA viruses. In this study, the identification and molecular characterization of a novel geminivirus is reported for the first time in Prunus spp. The virus, provisionally named Prunus geminivirus A (PrGVA), was identified by Illumina sequencing from an asymptomatic plum tree. PrGVA was subsequently confirmed by rolling cycle amplification, cloning, and Sanger sequencing of its complete genome (3,174 to 3,176 nucleotides) from an additional 18 (9 apricot and 9 plum) field isolates. Apart from the nonanucleotide motif TAATATT↓AC present in its virion strand origin of replication, other conserved motifs of PrGVA support its geminiviral origin. PrGVA shared highest complete genome (73 to 74%), coat protein amino acid (83 to 85%) and rep-associated amino acid (74%) identities with Grapevine red blotch virus (GRBV). PrGVA was graft but not mechanically transmissible. Quantitative polymerase chain reaction screening of Prunus spp. in the National Clonal Germplasm Repository collection using newly designed primers and probes revealed 69.4% (apricot), 55.8% (plum), and 8.3% (cherry) incidences of PrGVA. PrGVA is proposed as a novel member of the genus Grablovirus based on its close genome and phylogenetic relationship with GRBV.}, }
@article {pmid30673217, year = {2019}, author = {Zhang, H and Chang, F and Shi, P and Ye, L and Zhou, Q and Pan, Y and Li, A}, title = {Antibiotic Resistome Alteration by Different Disinfection Strategies in a Full-Scale Drinking Water Treatment Plant Deciphered by Metagenomic Assembly.}, journal = {Environmental science & technology}, volume = {53}, number = {4}, pages = {2141-2150}, doi = {10.1021/acs.est.8b05907}, pmid = {30673217}, issn = {1520-5851}, abstract = {Disinfection regimes are considered the most solid strategy to reduce microbial risks in drinking water, but their roles in shaping the antibiotic resistome are poorly understood. This study revealed the alteration of antibiotic resistance genes (ARGs) profiles, their co-occurrence with mobile genetic elements (MGEs), and potential hosts during drinking water disinfection based on metagenomic assembly. We found the ozone/chlorine (O3/Cl2) coupled disinfection significantly increased the relative abundance of ARGs and MGE-carrying antibiotic resistance contigs (ARCs) through the enrichment of ARGs within the resistance-nodulation-cell division and ATP-binding cassette antibiotic efflux families that are primarily carried by Pseudomonas, Acinetobacter, Mycobacterium, and Methylocystis, whereas the antimicrobial resin/chlorine coupled disinfection posed unremarkable changes to the ARG and MGE abundances. Moreover, the co-occurrence patterns of antibiotic efflux and beta-lactam ARGs and MGEs were widely identified, and ARCs carrying the recR and mexH genes were detected in all the samples, with the highest abundance of 2.25 × 10-2 copies per cell after O3/Cl2 disinfection. Sequence-independent binning analysis successfully retrieved two draft ARG-carrying genomes of Acidovorax sp. MR-S7 and Hydrogenophaga sp. IBVHS2, further revealing the host-ARG relationship during O3/Cl2 disinfection. Overall, this study provides novel insights into the antibiotic resistome alteration during drinking water disinfection.}, }
@article {pmid30671359, year = {2019}, author = {Nurul, ANA and Muhammad, DD and Okomoda, VT and Nur, AAB}, title = {16S rRNA-Based metagenomic analysis of microbial communities associated with wild Labroides dimidiatus from Karah Island, Terengganu, Malaysia.}, journal = {Biotechnology reports (Amsterdam, Netherlands)}, volume = {21}, number = {}, pages = {e00303}, doi = {10.1016/j.btre.2019.e00303}, pmid = {30671359}, issn = {2215-017X}, abstract = {This study was designed to evaluate the bacterial composition of the Labroides dimidiatus and its surrounding water. Fish and carriage water samples were obtained from corals of the Karah Island in Terengganu Malaysia. DNA was extracted and the bacteria communities on the skin mucus and stomach as well as water sample were classified (to family level) using the 16S rRNA-based metagenomics analysis. 1,426,740 amplicon sequence reads corresponding to 508 total operational taxonomic units were obtained from the three metagenomics libraries in this study. The Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria and Fusobacteria were the most dominant bacterial phyla in all samples. A total of 36 different classes and 132 families were identified, many of which had shared presence in all samples while others were exclusive to different sample. Thirty-three of these were identified as pathogenic zoonotic bacterial. The results obtained indicate a strong influence of host environment on the composition of its microbiota. Knowing the composition of the microbiota is the first step toward exploring proper management of this ornamental fish in captivity.}, }
@article {pmid30671194, year = {2019}, author = {Al-Hebshi, NN and Baraniya, D and Chen, T and Hill, J and Puri, S and Tellez, M and Hasan, NA and Colwell, RR and Ismail, A}, title = {Metagenome sequencing-based strain-level and functional characterization of supragingival microbiome associated with dental caries in children.}, journal = {Journal of oral microbiology}, volume = {11}, number = {1}, pages = {1557986}, doi = {10.1080/20002297.2018.1557986}, pmid = {30671194}, issn = {2000-2297}, abstract = {Studies of the microbiome associated with dental caries have largely relied on 16S rRNA sequence analysis, which is associated with PCR biases, low taxonomic resolution, and inability to accurately study functions. Here, we employed whole metagenome shotgun sequencing, coupled with high-resolution analysis algorithm, to analyze supragingival microbiomes from 30 children with or without dental caries. A total of 726 bacterial strains belonging to 406 species, in addition to 34 bacteriophages were identified. A core bacteriome was identified at the species and strain levels. Species of Prevotella, Veillonella, as yet unnamed Actinomyces, and Atopobium showed strongest association with caries; Streptococcus sp. AS14 and Leptotrichia sp. Oral taxon 225, among others, were overabundant in caries-free. For several species, the association was strain-specific. Furthermore, for some species, e.g. Streptococcus mitis and Streptococcus sanguinis, sister strains showed differential associations. Noteworthy, associations were also identified for phages: Streptococcus phage M102 with caries and Haemophilus phage HP1 with caries-free. Functionally, potentially relevant features were identified including urate, vitamin K2, and polyamine biosynthesis in association with caries; and three deiminases and lactate dehydrogenase with health. The results demonstrate new associations between the microbiome and dental caries at the strain and functional levels that need further investigation.}, }
@article {pmid30671046, year = {2018}, author = {Zhang, C and Thakkar, PV and Powell, SE and Sharma, P and Vennelaganti, S and Betel, D and Shah, MA}, title = {A Comparison of Homogenization vs. Enzymatic Lysis for Microbiome Profiling in Clinical Endoscopic Biopsy Tissue Samples.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3246}, doi = {10.3389/fmicb.2018.03246}, pmid = {30671046}, issn = {1664-302X}, abstract = {Identification of the human microbiome has proven to be of utmost importance with the emerging role of bacteria in various physiological and pathological processes. High throughput sequencing strategies have evolved to assess the composition of the microbiome. To identify possible bias that may exist in the processing of tissue for whole genome sequencing (WGS), it is important to evaluate the extraction method on the overall microbial content and composition. Here we compare two different methods of extraction, homogenization vs. enzymatic lysis, on gastric, esophageal and colorectal biopsies and survey the microbial content and composition using WGS and quantitative PCR (qPCR). We examined total bacterial content using universal 16S rDNA qPCR as well as the abundance of three phyla (Actinobacter, Firmicutes, Bacteroidetes) and one genus (Fusobacterium). We found minimal differences between the two extraction methods in the overall community structure. Furthermore, based on our qPCR analysis, neither method demonstrated preferential extraction of any particular clade of bacteria, nor significantly altered the detection of Gram-positive or Gram-negative organisms. However, although the overall microbial composition remained very similar and the most prevalent bacteria could be detected effectively using either method, the precise community structure and microbial abundances between the two methods were different, primarily due to variations in detection of low abundance genus. We also demonstrate that the homogenization extraction method provides higher microbial DNA content and higher read counts from human tissue biopsy samples of the gastrointestinal tract.}, }
@article {pmid30670612, year = {2019}, author = {Bowers, JR and Valentine, M and Harrison, V and Fofanov, VY and Gillece, J and Delisle, J and Patton, B and Schupp, J and Sheridan, K and Lemmer, D and Ostdiek, S and Bains, HK and Heim, J and Sylvester, T and Prasai, S and Kretschmer, M and Fowle, N and Komatsu, K and Brady, S and Robinson, S and Fitzpatrick, K and Ostovar, GA and Alsop, E and Hutchins, E and Jensen, K and Keim, P and Engelthaler, DM}, title = {Genomic Analyses of Acute Flaccid Myelitis Cases among a Cluster in Arizona Provide Further Evidence of Enterovirus D68 Role.}, journal = {mBio}, volume = {10}, number = {1}, pages = {}, doi = {10.1128/mBio.02262-18}, pmid = {30670612}, issn = {2150-7511}, abstract = {Enteroviruses are a common cause of respiratory and gastrointestinal illness, and multiple subtypes, including poliovirus, can cause neurologic disease. In recent years, enterovirus D68 (EV-D68) has been associated with serious neurologic illnesses, including acute flaccid myelitis (AFM), frequently preceded by respiratory disease. A cluster of 11 suspect cases of pediatric AFM was identified in September 2016 in Phoenix, AZ. To determine if these cases were associated with EV-D68, we performed multiple genomic analyses of nasopharyngeal (NP) swabs and cerebrospinal fluid (CSF) material from the patients, including real-time PCR and amplicon sequencing targeting the EV-D68 VP1 gene and unbiased microbiome and metagenomic sequencing. Four of the 11 patients were classified as confirmed cases of AFM, and an additional case was classified as probable AFM. Real-time PCR and amplicon sequencing detected EV-D68 virus RNA in the three AFM patients from which NP swabs were collected, as well as in a fourth patient diagnosed with acute disseminated encephalomyelitis, a disease that commonly follows bacterial or viral infections, including enterovirus. No other obvious etiological causes for AFM were identified by 16S or RNA and DNA metagenomic sequencing in these cases, strengthening the likelihood that EV-D68 is an etiological factor. Herpes simplex viral DNA was detected in the CSF of the fourth case of AFM and in one additional suspect case from the cluster. Multiple genomic techniques, such as those described here, can be used to diagnose patients with suspected EV-D68 respiratory illness, to aid in AFM diagnosis, and for future EV-D68 surveillance and epidemiology.IMPORTANCE Enteroviruses frequently result in respiratory and gastrointestinal illness; however, multiple subtypes, including poliovirus, can cause severe neurologic disease. Recent biennial increases (i.e., 2014, 2016, and 2018) in cases of non-polio acute flaccid paralysis have led to speculations that other enteroviruses, specifically enterovirus D68 (EV-D68), are emerging to fill the niche that was left from poliovirus eradication. A cluster of 11 suspect cases of pediatric acute flaccid myelitis (AFM) was identified in 2016 in Phoenix, AZ. Multiple genomic analyses identified the presence of EV-D68 in the majority of clinical AFM cases. Beyond limited detection of herpesvirus, no other likely etiologies were found in the cluster. These findings strengthen the likelihood that EV-D68 is a cause of AFM and show that the rapid molecular assays developed for this study are useful for investigations of AFM and EV-D68.}, }
@article {pmid30670143, year = {2019}, author = {Bal, A and Sabatier, M and Wirth, T and Coste-Burel, M and Lazrek, M and Stefic, K and Brengel-Pesce, K and Morfin, F and Lina, B and Schuffenecker, I and Josset, L}, title = {Emergence of enterovirus D68 clade D1, France, August to November 2018.}, journal = {Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin}, volume = {24}, number = {3}, pages = {}, doi = {10.2807/1560-7917.ES.2019.24.3.1800699}, pmid = {30670143}, issn = {1560-7917}, abstract = {We report a seasonal increase of enterovirus D68 (EV-D68) cases in France, with 54 cases detected between 19 August and 14 November 2018. Molecular typing revealed that 20 of 32 of the isolates belonged to clade D1, only sporadically detected before in France. Median age of D1-cases was 42 years, 10 developed severe respiratory signs and one had neurological complications. The 2018-D1 viruses showed a genetic divergence of 3.34 % with D1 viruses identified previously.}, }
@article {pmid30669548, year = {2019}, author = {Chávez-Carbajal, A and Nirmalkar, K and Pérez-Lizaur, A and Hernández-Quiroz, F and Ramírez-Del-Alto, S and García-Mena, J and Hernández-Guerrero, C}, title = {Gut Microbiota and Predicted Metabolic Pathways in a Sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome.}, journal = {International journal of molecular sciences}, volume = {20}, number = {2}, pages = {}, doi = {10.3390/ijms20020438}, pmid = {30669548}, issn = {1422-0067}, support = {11a Convocatoria Para Proyectos de Investigación Básica.//Universidad Iberoamericana Ciudad de México/ ; CONACyT-163235 INFR-2011-01//Consejo Nacional de Ciencia y Tecnología/ ; FONSEC SS/IMSS/ISSSTE-CONACYT-233361.//Consejo Nacional de Ciencia y Tecnología/ ; }, abstract = {Obesity is an excessive fat accumulation that could lead to complications like metabolic syndrome. There are reports on gut microbiota and metabolic syndrome in relation to dietary, host genetics, and other environmental factors; however, it is necessary to explore the role of the gut microbiota metabolic pathways in populations like Mexicans, where the prevalence of obesity and metabolic syndrome is high. This study identify alterations of the gut microbiota in a sample of healthy Mexican women (CO), women with obesity (OB), and women with obesity plus metabolic syndrome (OMS). We studied 67 women, characterizing their anthropometric and biochemical parameters along with their gut bacterial diversity by high-throughput DNA sequencing. Our results indicate that in OB or OMS women, Firmicutes was the most abundant bacterial phylum. We observed significant changes in abundances of bacteria belonging to the Ruminococcaceae, Lachnospiraceae, and Erysipelotrichaceae families and significant enrichment of gut bacteria from 16 different taxa that might explain the observed metabolic alterations between the groups. Finally, the predicted functional metagenome of the gut microbiota found in each category shows differences in metabolic pathways related to lipid metabolism. We demonstrate that Mexican women have a particular bacterial gut microbiota characteristic of each phenotype. There are bacteria that potentially explain the observed metabolic differences between the groups, and gut bacteria in OMS and OB conditions carry more genes of metabolic pathways implicated in lipid metabolism.}, }
@article {pmid30669085, year = {2019}, author = {Liu, JL and Yao, J and Wang, F and Min, N and Gu, JH and Li, ZF and Sunahara, G and Duran, R and Solevic-Knudsen, T and Hudson-Edwards, KA and Alakangas, L}, title = {Bacterial diversity in typical abandoned multi-contaminated nonferrous metal(loid) tailings during natural attenuation.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {247}, number = {}, pages = {98-107}, doi = {10.1016/j.envpol.2018.12.045}, pmid = {30669085}, issn = {1873-6424}, abstract = {Abandoned nonferrous metal(loid) tailings sites are anthropogenic, and represent unique and extreme ecological niches for microbial communities. Tailings contain elevated and toxic content of metal(loid)s that had negative effects on local human health and regional ecosystems. Microbial communities in these typical tailings undergoing natural attenuation are often very poorly examined. The diversity and inferred functions of bacterial communities were examined at seven nonferrous metal(loid) tailings sites in Guangxi (China), which were abandoned between 3 and 31 years ago. The acidity of the tailings sites rose over 31 years of site inactivity. Desulfurivibrio, which were always coupled with sulfur/sulfide oxidation to dissimilate the reduction of nitrate/nitrite, were specific in tailings with 3 years abandonment. However, genus beneficial to plant growth (Rhizobium), and iron/sulfur-oxidizing bacteria and metal(loid)-related genera (Acidiferrobacter and Acidithiobacillus) were specific within tailings abandoned for 23 years or more. The increased abundance of acid-generating iron/sulfur-oxidizing and metal(loid)-related bacteria and specific bacterial communities during the natural attenuation could provide new insights for understanding microbial ecosystem functioning in mine tailings. OTUs related to Sulfuriferula, Bacillus, Sulfurifustis, Gaiella, and Thiobacillus genera were the main contributors differentiating the bacterial communities between the different tailing sites. Multiple correlation analyses between bacterial communities and geochemical parameters indicated that pH, TOC, TN, As, Pb, and Cu were the main drivers influencing the bacterial community structures. PICRUSt functional exploration revealed that the main functions were related to DNA repair and recombination, important functions for bacterial adaptation to cope with the multi-contamination of tailings. Such information provides new insights to guide future metagenomic studies for the identification of key functions beyond metal-transformation/resistance. As well, our results offers novel outlooks for the management of bacterial communities during natural attenuation of multi-contaminated nonferrous metal(loid) tailings sites.}, }
@article {pmid30669041, year = {2019}, author = {Ma, L and Li, B and Zhang, T}, title = {New insights into antibiotic resistome in drinking water and management perspectives: A metagenomic based study of small-sized microbes.}, journal = {Water research}, volume = {152}, number = {}, pages = {191-201}, doi = {10.1016/j.watres.2018.12.069}, pmid = {30669041}, issn = {1879-2448}, abstract = {The proliferation of antibiotic resistance genes (ARGs) in drinking water and their potential horizontal transfer to pathogenic microbes may cause failure of antibiotics. However, antimicrobial resistome monitoring in drinking water is not currently routine. The bacterial hosts of ARGs, especially small-sized microbes in drinking water, may not be effectively removed by membrane filtration disinfection and thus pose threats to human health. In the present study, using metagenomic based approach, we investigated antibiotic resistome of small-sized microbes (0.2-0.45 μm) in 20 household drinking water samples from 12 cities in Mainland China, Hong Kong and Singapore. A total of 265 ARG subtypes belonging to 17 ARG types were detected at abundances ranging from 4.0 × 10-2 to 1.0 × 100 copies/cell. Multidrug, bacitracin and aminoglycoside resistance genes are dominant, and 43 ARG subtypes were specifically carried by small-size microbes. Metagenomic assembly strategy revealed fragments of three opportunistic pathogen, i.e. Pseudomonas alcaligenes, Pseudomonas aeruginosa and Mycobacterium gordonae, carried mexW, aph(3')-I and aac(2')-I, respectively. Drinking water samples were classified into three groups based on the presence of ARG, pathogen and ARG-carrying pathogen. These new insights into the antibiotic resistome of small microbes in drinking water over a broad scale indicate the need for more comprehensive ARGs monitoring and surveillance of drinking water supplies. These findings, together with the perspectives and strategies proposed in this study, could support initiatives to improve drinking water safety.}, }
@article {pmid30669029, year = {2019}, author = {Zeng, D and Yin, Q and Du, Q and Wu, G}, title = {System performance and microbial community in ethanol-fed anaerobic reactors acclimated with different organic carbon to sulfate ratios.}, journal = {Bioresource technology}, volume = {278}, number = {}, pages = {34-42}, doi = {10.1016/j.biortech.2019.01.047}, pmid = {30669029}, issn = {1873-2976}, abstract = {Sulfate influences the organics removal and methanogenic performance during anaerobic wastewater treatment. System performance, microbial community and metabolic pathways in ethanol-fed anaerobic reactors were investigated under different COD/SO42- ratios (2, 1 and 0.67) and control without sulfate addition. The sulfate removal percentages declined (99%, 60% and 49%) with decreasing COD/SO42- ratios, and methanogenesis was completely inhibited. Acetate accumulated to 903-734 mg/L, though propionate was constantly lower than 30 mg/L. Without sulfate, acetate and propionate did not accumulate, despite the extended time for propionate degradation. Incomplete oxidizing sulfate reducing bacteria (Desulfobulbus and Desulfomicrobium) and hydrolysis-acidification genera (Treponema and Bacteroidales) predominated but could not degrade acetate. Desulfobulbus was the key genus for propionate degradation through the pyruvate & propanoate metabolism pathway. Pseudomonas and Desulfobulbus, possessing genes encoding Type IV pili and cytochrome c6 OmcF, respectively, potentially participated in the direct interspecies electron transfer in sulfate-rich conditions.}, }
@article {pmid30668611, year = {2019}, author = {Xu, L and Wu, J and Li, Q and Wei, Y and Tan, Z and Cai, J and Guo, H and Yang, L and Huang, X and Chen, J and Zhang, F and He, B and Tu, C}, title = {Seroprevalence, cross antigenicity and circulation sphere of bat-borne hantaviruses revealed by serological and antigenic analyses.}, journal = {PLoS pathogens}, volume = {15}, number = {1}, pages = {e1007545}, doi = {10.1371/journal.ppat.1007545}, pmid = {30668611}, issn = {1553-7374}, abstract = {Bats are newly identified reservoirs of hantaviruses (HVs) among which very divergent HVs have been discovered in recent years. However, their significance for public health remains unclear since their seroprevalence as well as antigenic relationship with human-infecting HVs have not been investigated. In the present study archived tissues of 1,419 bats of 22 species from 6 families collected in 5 south and southwest provinces in China were screened by pan-HV RT-PCR following viral metagenomic analysis. As a result nine HVs have been identified in two bat species in two provinces and phylogenetically classified into two species, Laibin virus (LAIV, ICTV approved species, 1 strain) and Xuan son virus (XSV, proposed species, 8 strains). Additionally, 709 serum samples of these bats were also analyzed by ELISA to investigate the seroprevalence and cross-reactivity between different HVs using expressed recombinant nucleocapsid proteins (rNPs) of LAIV, XSV and Seoul virus (SEOV). The cross-reactivity of some bat sera were further confirmed by western blot (WB) using three rNPs followed by fluorescent antibody virus neutralization test (FAVNT) against live SEOV. Results showed that the total HV seropositive rate of bat sera was 18.5% (131/709) with many cross reacting with two or all three rNPs and several able to neutralize SEOV. WB analysis using the three rNPs and their specific hyperimmune sera demonstrated cross-reactivity between XSV/SEOV and LAIV/XSV, but not LAIV/SEOV, indicating that XSV is antigenically closer to human-infecting HVs. In addition a study of the distribution of the viruses identified an area covering the region between Chinese Guangxi and North Vietnam, in which XSV and LAIV circulate within different bat colonies with a high seroprevalence. A circulation sphere of bat-borne HVs has therefore been proposed.}, }
@article {pmid30667580, year = {2019}, author = {Chen, T and Liu, AB and Sun, S and Ajami, NJ and Ross, MC and Wang, H and Zhang, L and Reuhl, K and Kobayashi, K and Onishi, JC and Zhao, L and Yang, CS}, title = {Green Tea Polyphenols Modify the Gut Microbiome in db/db Mice as Co-Abundance Groups Correlating with the Blood Glucose Lowering Effect.}, journal = {Molecular nutrition & food research}, volume = {}, number = {}, pages = {e1801064}, doi = {10.1002/mnfr.201801064}, pmid = {30667580}, issn = {1613-4133}, support = {CA133024//National Institutes of Health/ ; ES005022//National Institutes of Health/ ; ES023512//National Institutes of Health/ ; }, abstract = {SCOPE: The effects of green tea polyphenols, Polyphenon E (PPE), and black tea polyphenols, theaflavins (TFs), on gut microbiota and development of diabetes in db/db mice are investigated and compared.
METHODS AND RESULTS: Supplementation of PPE (0.1%) in the diet of female db/db mice for 7 weeks decreases fasting blood glucose levels and mesenteric fat while increasing the serum level of insulin, possibly through protection against β-cell damage. However, TFs are less or not effective. Microbiome analysis through 16S rRNA gene sequencing shows that PPE and TFs treatments significantly alter the bacterial community structure in the cecum and colon, but not in the ileum. The key bacterial phylotypes responding to the treatments are then clustered into 11 co-abundance groups (CAGs). CAGs 6 and 7, significantly increased by PPE but not by TFs, are negatively associated with blood glucose levels. The operational taxonomic units in these CAGs are from two different phyla, Firmicutes and Bacteroidetes. CAG 10, decreased by PPE and TFs, is positively associated with blood glucose levels.
CONCLUSION: Gut microbiota respond to tea polyphenol treatments as CAGs instead of taxa. Some of the CAGs associated with the blood glucose lowering effect are enriched by PPE, but not TFs.}, }
@article {pmid30666828, year = {2019}, author = {Časaitė, V and Sadauskas, M and Vaitekūnas, J and Gasparavičiūtė, R and Meškienė, R and Skikaitė, I and Sakalauskas, M and Jakubovska, J and Tauraitė, D and Meškys, R}, title = {Engineering of a chromogenic enzyme screening system based on an auxiliary indole-3-carboxylic acid monooxygenase.}, journal = {MicrobiologyOpen}, volume = {}, number = {}, pages = {e795}, doi = {10.1002/mbo3.795}, pmid = {30666828}, issn = {2045-8827}, support = {634486//European Union's Horizon 2020 research and innovation/ ; }, abstract = {Here, we present a proof-of-principle for a new high-throughput functional screening of metagenomic libraries for the selection of enzymes with different activities, predetermined by the substrate being used. By this approach, a total of 21 enzyme-coding genes were selected, including members of xanthine dehydrogenase, aldehyde dehydrogenase (ALDH), and amidohydrolase families. The screening system is based on a pro-chromogenic substrate, which is transformed by the target enzyme to indole-3-carboxylic acid. The later compound is converted to indoxyl by a newly identified indole-3-carboxylate monooxygenase (Icm). Due to the spontaneous oxidation of indoxyl to indigo, the target enzyme-producing colonies turn blue. Two types of pro-chromogenic substrates have been tested. Indole-3-carboxaldehydes and the amides of indole-3-carboxylic acid have been applied as substrates for screening of the ALDHs and amidohydrolases, respectively. Both plate assays described here are rapid, convenient, easy to perform, and adaptable for the screening of a large number of samples both in Escherichia coli and Rhodococcus sp. In addition, the fine-tuning of the pro-chromogenic substrate allows screening enzymes with the desired substrate specificity.}, }
@article {pmid30666248, year = {2018}, author = {Malla, MA and Dubey, A and Kumar, A and Yadav, S and Hashem, A and Abd Allah, EF}, title = {Exploring the Human Microbiome: The Potential Future Role of Next-Generation Sequencing in Disease Diagnosis and Treatment.}, journal = {Frontiers in immunology}, volume = {9}, number = {}, pages = {2868}, doi = {10.3389/fimmu.2018.02868}, pmid = {30666248}, issn = {1664-3224}, abstract = {The interaction between the human microbiome and immune system has an effect on several human metabolic functions and impacts our well-being. Additionally, the interaction between humans and microbes can also play a key role in determining the wellness or disease status of the human body. Dysbiosis is related to a plethora of diseases, including skin, inflammatory, metabolic, and neurological disorders. A better understanding of the host-microbe interaction is essential for determining the diagnosis and appropriate treatment of these ailments. The significance of the microbiome on host health has led to the emergence of new therapeutic approaches focused on the prescribed manipulation of the host microbiome, either by removing harmful taxa or reinstating missing beneficial taxa and the functional roles they perform. Culturing large numbers of microbial taxa in the laboratory is problematic at best, if not impossible. Consequently, this makes it very difficult to comprehensively catalog the individual members comprising a specific microbiome, as well as understanding how microbial communities function and influence host-pathogen interactions. Recent advances in sequencing technologies and computational tools have allowed an increasing number of metagenomic studies to be performed. These studies have provided key insights into the human microbiome and a host of other microbial communities in other environments. In the present review, the role of the microbiome as a therapeutic agent and its significance in human health and disease is discussed. Advances in high-throughput sequencing technologies for surveying host-microbe interactions are also discussed. Additionally, the correlation between the composition of the microbiome and infectious diseases as described in previously reported studies is covered as well. Lastly, recent advances in state-of-the-art bioinformatics software, workflows, and applications for analysing metagenomic data are summarized.}, }
@article {pmid30666247, year = {2018}, author = {Richert-Pöggeler, KR and Franzke, K and Hipp, K and Kleespies, RG}, title = {Electron Microscopy Methods for Virus Diagnosis and High Resolution Analysis of Viruses.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3255}, doi = {10.3389/fmicb.2018.03255}, pmid = {30666247}, issn = {1664-302X}, abstract = {The term "virosphere" describes both the space where viruses are found and the space they influence, and can extend to their impact on the environment, highlighting the complexity of the interactions involved. Studying the biology of viruses and the etiology of virus disease is crucial to the prevention of viral disease, efficient and reliable virus diagnosis, and virus control. Electron microscopy (EM) is an essential tool in the detection and analysis of virus replication. New EM methods and ongoing technical improvements offer a broad spectrum of applications, allowing in-depth investigation of viral impact on not only the host but also the environment. Indeed, using the most up-to-date electron cryomicroscopy methods, such investigations are now close to atomic resolution. In combination with bioinformatics, the transition from 2D imaging to 3D remodeling allows structural and functional analyses that extend and augment our knowledge of the astonishing diversity in virus structure and lifestyle. In combination with confocal laser scanning microscopy, EM enables live imaging of cells and tissues with high-resolution analysis. Here, we describe the pivotal role played by EM in the study of viruses, from structural analysis to the biological relevance of the viral metagenome (virome).}, }
@article {pmid30665461, year = {2019}, author = {Hansen, MEB and Rubel, MA and Bailey, AG and Ranciaro, A and Thompson, SR and Campbell, MC and Beggs, W and Dave, JR and Mokone, GG and Mpoloka, SW and Nyambo, T and Abnet, C and Chanock, SJ and Bushman, FD and Tishkoff, SA}, title = {Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {16}, doi = {10.1186/s13059-018-1616-9}, pmid = {30665461}, issn = {1474-760X}, support = {5T32AI007532-18/NH/NIH HHS/United States ; DP1 ES022577-04/NH/NIH HHS/United States ; 1R01DK104339-01/NH/NIH HHS/United States ; 1R01GM113657-01/NH/NIH HHS/United States ; T32ES019851-02/NH/NIH HHS/United States ; }, abstract = {BACKGROUND: Gut microbiota from individuals in rural, non-industrialized societies differ from those in individuals from industrialized societies. Here, we use 16S rRNA sequencing to survey the gut bacteria of seven non-industrialized populations from Tanzania and Botswana. These include populations practicing traditional hunter-gatherer, pastoralist, and agropastoralist subsistence lifestyles and a comparative urban cohort from the greater Philadelphia region.
RESULTS: We find that bacterial diversity per individual and within-population phylogenetic dissimilarity differs between Botswanan and Tanzanian populations, with Tanzania generally having higher diversity per individual and lower dissimilarity between individuals. Among subsistence groups, the gut bacteria of hunter-gatherers are phylogenetically distinct from both agropastoralists and pastoralists, but that of agropastoralists and pastoralists were not significantly different from each other. Nearly half of the Bantu-speaking agropastoralists from Botswana have gut bacteria that are very similar to the Philadelphian cohort. Based on imputed metagenomic content, US samples have a relative enrichment of genes found in pathways for degradation of several common industrial pollutants. Within two African populations, we find evidence that bacterial composition correlates with the genetic relatedness between individuals.
CONCLUSIONS: Across the cohort, similarity in bacterial presence/absence compositions between people increases with both geographic proximity and genetic relatedness, while abundance weighted bacterial composition varies more significantly with geographic proximity than with genetic relatedness.}, }
@article {pmid30665024, year = {2019}, author = {Kitamoto, M and Tokuda, G and Watanabe, H and Arioka, M}, title = {Characterization of CBM36-containing GH11 endoxylanase NtSymX11 from the hindgut metagenome of higher termite Nasutitermes takasagoensis displaying prominent catalytic activity.}, journal = {Carbohydrate research}, volume = {474}, number = {}, pages = {1-7}, doi = {10.1016/j.carres.2019.01.003}, pmid = {30665024}, issn = {1873-426X}, abstract = {Symbionts in the gut of termites are expected to be large sources of enzymes involved in lignocellulose degradation, but their biotechnological potential has not been fully explored. In this study, we expressed, purified, and biochemically characterized a glycoside hydrolase family 11 xylanase, NtSymX11, from a symbiotic bacterium of the higher termite, Nasutitermes takasagoensis. NtSymX11 is a multimodular enzyme consisting of a catalytic domain and two tandem carbohydrate-binding modules (CBM36). The pH and temperature optima of NtSymX11 were pH 6.0 and 40 °C, respectively. By comparing the properties of full-length and truncated variants of NtSymX11, it was shown that CBM36 decreases the enzyme stability at acidic pH and high temperature. The main products from xylohexaose and various xylan substrates were X1-X3 xylooligosaccharides. Analysis of kinetic parameters indicated that NtSymX11 displays an outstanding catalytic performance when compared to other reported xylanases, and CBM36 enhances the activity by increasing the affinity to the substrate. Addition of Ca2+ boosted the activity of full-length enzyme, but not the truncated variant lacking the CBM, against the insoluble substrate, suggesting that CBM36 plays a role in the Ca2+-dependent increase of catalytic efficiency.}, }
@article {pmid30664775, year = {2019}, author = {Lin, M and Kussell, E}, title = {Inferring bacterial recombination rates from large-scale sequencing datasets.}, journal = {Nature methods}, volume = {16}, number = {2}, pages = {199-204}, doi = {10.1038/s41592-018-0293-7}, pmid = {30664775}, issn = {1548-7105}, abstract = {We present a robust, computationally efficient method (https://github.com/kussell-lab/mcorr) for inferring the parameters of homologous recombination in bacteria, which can be applied in diverse datasets, from whole-genome sequencing to metagenomic shotgun sequencing data. Using correlation profiles of synonymous substitutions, we determine recombination rates and diversity levels of the shared gene pool that has contributed to a given sample. We validated the recombination parameters using data from laboratory experiments. We determined the recombination parameters for a wide range of bacterial species, and inferred the distribution of shared gene pools for global Helicobacter pylori isolates. Using metagenomics data of the infant gut microbiome, we measured the recombination parameters of multidrug-resistant Escherichia coli ST131. Lastly, we analyzed ancient samples of bacterial DNA from the Copper Age 'Iceman' mummy and from 14th century victims of the Black Death, obtaining measurements of bacterial recombination rates and gene pool diversity of earlier eras.}, }
@article {pmid30664014, year = {2019}, author = {Joris, BR and Gloor, GB}, title = {Unaccounted risk of cardiovascular disease: the role of the microbiome in lipid metabolism.}, journal = {Current opinion in lipidology}, volume = {}, number = {}, pages = {}, doi = {10.1097/MOL.0000000000000582}, pmid = {30664014}, issn = {1473-6535}, abstract = {PURPOSE OF REVIEW: Not all of the risk of cardiovascular disease can be explained by diet and genetics, and the human microbiome, which lies at the interface of these two factors, may help explain some of the unaccounted risk. This review examines some of the well established links between the microbiome and cardiovascular health, and proposes relatively unexplored associations.
RECENT FINDINGS: Byproducts of microbial metabolism are associated with health and disease: Trimethylamine N oxide is associated with atherosclerosis; whereas short-chain fatty acids are associated with decreased inflammation and increased energy expenditure. More broadly, a large number of association studies have been conducted to explore the connections between bacterial taxa and metabolic syndrome. In contrast, the relationship between the microbiome and triglycerides levels remains poorly understood.
SUMMARY: We suggest that deeper understanding of the molecular mechanisms that drive linkages between the microbiome and disease can be determined by replacing 16S rRNA gene sequencing with shotgun metagenomic sequencing or other functional approaches. Furthermore, to ensure translatability and reproducibility of research findings, a combination of multiple different complementary '-omic' approaches should be employed.}, }
@article {pmid30661755, year = {2019}, author = {Pasolli, E and Asnicar, F and Manara, S and Zolfo, M and Karcher, N and Armanini, F and Beghini, F and Manghi, P and Tett, A and Ghensi, P and Collado, MC and Rice, BL and DuLong, C and Morgan, XC and Golden, CD and Quince, C and Huttenhower, C and Segata, N}, title = {Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle.}, journal = {Cell}, volume = {176}, number = {3}, pages = {649-662.e20}, doi = {10.1016/j.cell.2019.01.001}, pmid = {30661755}, issn = {1097-4172}, support = {MR/L015080/1//Medical Research Council/United Kingdom ; R01 HG005220/HG/NHGRI NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; }, abstract = {The body-wide human microbiome plays a role in health, but its full diversity remains uncharacterized, particularly outside of the gut and in international populations. We leveraged 9,428 metagenomes to reconstruct 154,723 microbial genomes (45% of high quality) spanning body sites, ages, countries, and lifestyles. We recapitulated 4,930 species-level genome bins (SGBs), 77% without genomes in public repositories (unknown SGBs [uSGBs]). uSGBs are prevalent (in 93% of well-assembled samples), expand underrepresented phyla, and are enriched in non-Westernized populations (40% of the total SGBs). We annotated 2.85 M genes in SGBs, many associated with conditions including infant development (94,000) or Westernization (106,000). SGBs and uSGBs permit deeper microbiome analyses and increase the average mappability of metagenomic reads from 67.76% to 87.51% in the gut (median 94.26%) and 65.14% to 82.34% in the mouth. We thus identify thousands of microbial genomes from yet-to-be-named species, expand the pangenomes of human-associated microbes, and allow better exploitation of metagenomic technologies.}, }
@article {pmid30661109, year = {2019}, author = {Liang, C and Huang, Y and Wang, Y and Ye, Q and Zhang, Z and Wang, H}, title = {Distribution of bacterial polycyclic aromatic hydrocarbon (PAH) ring-hydroxylating dioxygenases genes in oilfield soils and mangrove sediments explored by gene-targeted metagenomics.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00253-018-09613-x}, pmid = {30661109}, issn = {1432-0614}, support = {41773082//National Natural Science Foundation of China/ ; 41573065//National Natural Science Foundation of China/ ; No. 2017ZX07202002//Major Science and Technology Program for Water Pollution Control and Treatment (CN)/ ; }, abstract = {PAH ring-hydroxylating dioxygenases (PAH-RHDα) gene, a useful biomarker for PAH-degrading bacteria, has been widely used to examine PAH-degrading bacterial community in different contaminated sites. However, the distribution of PAH-RHDα genes in oilfield soils and mangrove sediments and their relationship with environmental factors still remain largely unclear. In this study, gene-targeted metagenomics was first used to investigate the diversity of PAH-degrading bacterial communities in oilfield soils and mangrove sediments. The results showed that higher diversity of PAH-degrading bacteria in the studied samples was revealed by gene-targeted metagenomics than traditional clone library analysis. Pseudomonas, Burkholderia, Ralstonia, Polymorphum gilvum, Mycobacterium, Sciscionella marina, Rhodococcus, and potential new degraders were prevailed in the oilfield area. For mangrove sediments, novel PAH degraders and Mycobacterium were predominated. The spatial distribution of PAH-RHDα gene was dependent on geographical location and regulated by local environmental variables. PAH content played a key role in shaping PAH-degrading bacterial communities in the studied samples, which would enrich PAH-degrading bacterial population and decrease PAH-degrading bacterial diversity. This work brings a more comprehensive and some new insights into the distribution and biodegradation potential of PAH-degrading bacteria in soil and sediments ecosystems.}, }
@article {pmid30660184, year = {2019}, author = {Keijser, BJF and Agamennone, V and van den Broek, TJ and Caspers, M and van de Braak, A and Bomers, R and Havekes, M and Schoen, E and van Baak, M and Mioch, D and Bomers, L and Montijn, RC}, title = {Dose-dependent impact of oxytetracycline on the veal calf microbiome and resistome.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {65}, doi = {10.1186/s12864-018-5419-x}, pmid = {30660184}, issn = {1471-2164}, support = {060.24960//Agentschap NL/ ; }, abstract = {BACKGROUND: Antibiotic therapy is commonly used in animal agriculture. Antibiotics excreted by the animals can contaminate farming environments, resulting in long term exposure of animals to sub-inhibitory levels of antibiotics. Little is known on the effect of this exposure on antibiotic resistance. In this study, we aimed to investigate the long term effects of sub-inhibitory levels of antibiotics on the gut microbiota composition and resistome of veal calves in vivo. Forty-two veal calves were randomly assigned to three groups. The first group (OTC-high) received therapeutic oral dosages of 1 g oxytetracycline (OTC), twice per day, during 5 days. The second group (OTC-low) received an oral dose of OTC of 100-200 μg per day during 7 weeks, mimicking animal exposure to environmental contamination. The third group (CTR) did not receive OTC, serving as unexposed control. Antibiotic residue levels were determined over time. The temporal effects on the gut microbiota and antibiotic resistance gene abundance was analysed by metagenomic sequencing.
RESULTS: In the therapeutic group, OTC levels exceeded MIC values. The low group remained at sub-inhibitory levels. The control group did not reach any significant OTC levels. 16S rRNA gene-based analysis revealed significant changes in the calf gut microbiota. Time-related changes accounted for most of the variation in the sequence data. Therapeutic application of OTC had transient effect, significantly impacting gut microbiota composition between day 0 and day 2. By metagenomic sequence analysis we identified six antibiotic resistance genes representing three gene classes (tetM, floR and mel) that differed in relative abundance between any of the intervention groups and the control. qPCR was used to validate observations made by metagenomic sequencing, revealing a peak of tetM abundance at day 28-35 in the OTC-high group. No increase in resistance genes abundance was seen in the OTC-low group.
CONCLUSIONS: Under the conditions tested, sub-therapeutic administration of OTC did not result in increased tetM resistance levels as observed in the therapeutic group.}, }
@article {pmid30659861, year = {2019}, author = {Hamza, IA and Bibby, K}, title = {Critical issues in application of molecular methods to environmental virology.}, journal = {Journal of virological methods}, volume = {266}, number = {}, pages = {11-24}, doi = {10.1016/j.jviromet.2019.01.008}, pmid = {30659861}, issn = {1879-0984}, abstract = {Waterborne diseases have significant public health and socioeconomic implications worldwide. Many viral pathogens are commonly associated with water-related diseases, namely enteric viruses. Also, novel recently discovered human-associated viruses have been shown to be a causative agent of gastroenteritis or other clinical symptoms. A wide range of analytical methods is available for virus detection in environmental water samples. Viral isolation is historically carried out via propagation on permissive cell lines; however, some enteric viruses are difficult or not able to propagate on existing cell lines. Real-time polymerase chain reaction (qPCR) screening of viral nucleic acid is routinely used to investigate virus contamination in water due to the high sensitivity and specificity. Additionally, the introduction of metagenomic approaches into environmental virology has facilitated the discovery of viruses that cannot be grown in cell culture. This review (i) highlights the applications of molecular techniques in environmental virology such as PCR and its modifications to overcome the critical issues associated with the inability to discriminate between infectious viruses and nonviable viruses, (ii) outlines the strengths and weaknesses of Nucleic Acid Sequence Based Amplification (NASBA) and microarray, (iii) discusses the role of digital PCR as an emerging water quality monitoring assay and its advantages over qPCR, (iv) addresses the viral metagenomics in terms of detecting emerging viral pathogens and diversity in aquatic environment. Indeed, there are many challenges for selecting methods to detect classic and emerging viruses in environmental samples. While the existing techniques have revealed the importance and diversity of viruses in the water environment, further developments are necessary to enable more rapid and accurate methodologies for viral water quality monitoring and regulation.}, }
@article {pmid30659857, year = {2019}, author = {Hu, HL and Guo, LY and Wu, HL and Feng, WY and Chen, TM and Liu, G}, title = {Evaluation of next-generation sequencing for the pathogenic diagnosis of children brain abscesses.}, journal = {The Journal of infection}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jinf.2019.01.003}, pmid = {30659857}, issn = {1532-2742}, abstract = {In this study, we applied metagenomic next-generation sequencing (mNGS) to detect the causative pathogens in brain abscess samples from 4 pediatric patients. NGS could offer unbiased sequencing and rapid diagnosis of causative pathogens, moreover, it could detect multiple pathogenic microorganisms from abscess samples. In our study, Fusobacterium nucleatum, and Streptococcus intermedius or combinations of them were found in 3/4 of polymicrobial brain abscesses. Internal organ abscesses are illustrative of the shortcomings of bacterial culture. NGS has the ability to identify both common and rare pathogens without any prior suspicious needed, and is able to offer a new platform for quantification of all detected microorganisms. Our study displayed the possible potential that NGS is about to provide the diagnostic tools that can characterize even the most complex microbial communities during brain abscesses and is less affected by prior antibiotic exposure.}, }
@article {pmid30659724, year = {2019}, author = {Turgay, E and Steinum, TM and Colquhoun, D and Karataş, S}, title = {Environmental biofilm communities associated with early-stage common dentex (Dentex dentex) culture.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jam.14205}, pmid = {30659724}, issn = {1365-2672}, support = {20950//Scientific Research Project Coordination Unit of Istanbul University/ ; }, abstract = {AIMS: To describe the biofilm microbiota associated with various feeding phases during larval common dentex (Dentex dentex) culture.
METHODS AND RESULTS: A targeted metagenomic (metagenetic) study was performed by means of 16S rRNA gene-based PCR and NextGen pyrosequencing. The resulting dataset was scrutinized with microbial community analysis software (r packages) using r/Rstudio. While median observed and estimated alpha-diversities were 171 ± 38 and 207 ± 27 taxa, respectively, 72·1-85·8% of individual biofilm communities comprised only 27-46 taxa. Members of the genus Methylobacterium and family Rhodobacteraceae dominated biofilms formed during all feeding phases while genera Nannochloropsis and Tetraselmis microalgae were major constituents of biofilms during rotifer live feeding. Both potential fish pathogenic genera, for example, Vibrio and putatively probiotic taxa, for example, Phaeobacter gallaeciensis were identified.
CONCLUSIONS: Relatively stable biofilm communities were identified during each feeding phase but varied significantly between feeding phases, most likely in response to the introduction of live feed/microalgae-associated bacteria into rearing tanks.
The structure of the bacterial communities identified represents a 'template' for successful larval dentex culture and provides a foundation for future investigations into failed production cycles.}, }
@article {pmid30658995, year = {2019}, author = {Hildebrand, F and Moitinho-Silva, L and Blasche, S and Jahn, MT and Gossmann, TI and Heuerta-Cepas, J and Hercog, R and Luetge, M and Bahram, M and Pryszlak, A and Alves, RJ and Waszak, SM and Zhu, A and Ye, L and Costea, PI and Aalvink, S and Belzer, C and Forslund, SK and Sunagawa, S and Hentschel, U and Merten, C and Patil, KR and Benes, V and Bork, P}, title = {Antibiotics-induced monodominance of a novel gut bacterial order.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2018-317715}, pmid = {30658995}, issn = {1468-3288}, abstract = {OBJECTIVE: The composition of the healthy human adult gut microbiome is relatively stable over prolonged periods, and representatives of the most highly abundant and prevalent species have been cultured and described. However, microbial abundances can change on perturbations, such as antibiotics intake, enabling the identification and characterisation of otherwise low abundant species.
DESIGN: Analysing gut microbial time-series data, we used shotgun metagenomics to create strain level taxonomic and functional profiles. Community dynamics were modelled postintervention with a focus on conditionally rare taxa and previously unknown bacteria.
RESULTS: In response to a commonly prescribed cephalosporin (ceftriaxone), we observe a strong compositional shift in one subject, in which a previously unknown species, UBorkfalki ceftriaxensis, was identified, blooming to 92% relative abundance. The genome assembly reveals that this species (1) belongs to a so far undescribed order of Firmicutes, (2) is ubiquitously present at low abundances in at least one third of adults, (3) is opportunistically growing, being ecologically similar to typical probiotic species and (4) is stably associated to healthy hosts as determined by single nucleotide variation analysis. It was the first coloniser after the antibiotic intervention that led to a long-lasting microbial community shift and likely permanent loss of nine commensals.
CONCLUSION: The bloom of UB. ceftriaxensis and a subsequent one of Parabacteroides distasonis demonstrate the existence of monodominance community states in the gut. Our study points to an undiscovered wealth of low abundant but common taxa in the human gut and calls for more highly resolved longitudinal studies, in particular on ecosystem perturbations.}, }
@article {pmid30658982, year = {2019}, author = {Jiao, S and Chen, W and Wei, G}, title = {Resilience and Assemblage of Soil Microbiome in Response to Chemical Contamination Combined with Plant Growth.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02523-18}, pmid = {30658982}, issn = {1098-5336}, abstract = {Lacking knowledge of the microbial responses to environmental change at the species and functional levels hinders our ability to understand the intrinsic mechanisms underlying the maintenance of microbial ecosystems. Here, we present results from temporal microcosms that introduced inorganic and organic contaminants into agro-soils for 90 days, with three common legume plants. Temporal dynamics and assemblage of soil microbial communities and functions in response to contamination under the influence of different plant growth were explored via sequencing of the 16S rRNA amplicon and shotgun metagenomics. Soil microbial alpha-diversity and structure at the taxonomic and functional levels exhibited resilience patterns. Functional profiles showed greater resilience than taxonomic ones. Different legume plants imposed stronger selection on taxonomic profiles compared with functional ones. Network and random forest analyses revealed that the functional potential of soil microbial communities was fostered by various taxonomic groups. Betaproteobacteria were important predictors of key functional traits such as amino acid metabolism, nucleic acid metabolism, and hydrocarbon degradation. Our study reveals strong resilience of soil microbiome to chemical contamination and sensitive responses of taxonomic rather than functional profiles to selection processes induced by different legume plants. This is pivotal to develop approaches and policies for the protection of soil microbial diversity and functions in agro-ecosystems with different response strategies from global environmental drivers, such as soil contamination and plant invasion.Importance Exploring the microbial responses to environmental disturbances is a central issue in microbial ecology. Understanding the dynamic responses of soil microbial communities to chemical contamination and the microbe-soil-plant interactions is essential for forecasting the long-term changes in soil ecosystems. Nevertheless, few studies have applied multi-omics approaches to assess the microbial responses to soil contamination and the microbe-soil-plant interactions at the taxonomic and functional levels simultaneously. Our study reveals clear succession and resilience patterns of soil microbial diversity and structure in response to chemical contamination. Different legume plants exerted stronger selection processes on taxonomic than functional profiles in contaminated soils, which could benefit plant growth and fitness as well as foster the potential abilities of hydrocarbon-degradation and metal-tolerance. These results provide new insight into the resilience and assemblage of soil microbiome in response to environmental disturbances in agro-ecosystems at the species and functional levels.}, }
@article {pmid30658981, year = {2019}, author = {Williams, TJ and Allen, MA and Liao, Y and Raftery, MJ and Cavicchioli, R}, title = {Sucrose Metabolism in Haloarchaea: Reassessment Using Genomics, Proteomics and Metagenomics.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02935-18}, pmid = {30658981}, issn = {1098-5336}, abstract = {The canonical pathway for sucrose metabolism in haloarchaea utilizes a modified Embden-Meyerhof-Parnas pathway (EMP), in which ketohexokinase and 1-phosphofructokinase phosphorylate fructose released from sucrose hydrolysis. However, our survey of haloarchaeal genomes determined that ketohexokinase and 1-phosphofructokinase genes were not present in all species known to utilize fructose and sucrose, thereby indicating that alternative mechanisms exist for fructose metabolism. A fructokinase gene was identified in the majority of fructose- and sucrose-utilizing species, whereas only a small number possessed a ketohexokinase gene. Analysis of a range of hypersaline metagenomes revealed that haloarchaeal fructokinase genes were far more abundant (37 times) than haloarchaeal ketohexokinase genes. We used proteomics on Halohasta litchfieldiae (which encodes fructokinase) and identified changes in protein abundance that relate to growth on sucrose. Proteins inferred to be involved in sucrose metabolism included fructokinase, a carbohydrate primary transporter, a putative sucrose hydrolase, and two uncharacterized carbohydrate-related proteins encoded in the same gene cluster as fructokinase and the transporter. Homologs of these proteins were present in the genomes of all haloarchaea that use sugars for growth. Enzymes involved in the semi-phosphorylative Entner-Doudoroff pathway also had higher abundance in sucrose-grown Hht. litchfieldiae cells, consistent with this pathway functioning in the catabolism of the glucose moiety of sucrose. The study revises the current understanding of fundamental pathways for sugar utilization in haloarchaea, and proposes alternatives to the modified EMP pathway used by haloarchaea for sucrose and fructose utilization.IMPORTANCE Our ability to infer the function that microorganisms perform in the environment is predicated on assumptions about metabolic capacity. When using genomic or metagenomic data, metabolic capacity is inferred from genetic potential. Here we investigate the pathways by which haloarchaea utilize sucrose. The canonical haloarchaeal pathway for fructose metabolism involving ketohexokinase only occurs in a small proportion of haloarchaeal genomes and is underrepresented in metagenomes. Instead, fructokinase genes are present in the majority of genomes/metagenomes. In addition to genomic and metagenomic analyses, we used proteomics on Halohasta litchfieldiae (which encodes fructokinase but lacks ketohexokinase) and identified changes in protein abundance that related to growth on sucrose. In this way, we identified novel proteins implicated in sucrose metabolism in haloarchaea, comprising a transporter and various catabolic enzymes (including proteins that are annotated as hypothetical).}, }
@article {pmid30658973, year = {2019}, author = {Malmuthuge, N and Liang, G and Griebel, PJ and Guan, LL}, title = {Taxonomic and functional composition of the small intestinal microbiome in neonatal calves provide a framework for understanding early life gut health.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02534-18}, pmid = {30658973}, issn = {1098-5336}, abstract = {A lack of information on the intestinal microbiome of neonatal calves prevents the use of microbial intervention strategies to improve calf gut health. This study profiled the taxonomic and functional composition of the small intestinal luminal microbiome of neonatal calves using whole genome sequencing of metagenome, aiming to understand the dynamics of microbial establishment during the early life. Despite highly individualized microbial communities, we identified two distinct taxonomic-based clusters from the collective luminal microbiomes comprising either a high level of Lactobacillus or Bacteroides Among the clustered microbiomes, Lactobacillus-dominant ileal microbiomes had significantly lower abundances of Bacteroides, Prevotella, Roseburia, Ruminococcus, and Veillonella compared to the Bacteroides-dominated ileal microbiomes. In addition, the upregulated ileal genes of the Lactobacillus-dominant calves were related to leukocyte and lymphocyte chemotaxis, the cytokine/chemokine-mediated signaling pathway, and inflammatory responses, while the upregulated ileal genes of the Bacteroides-dominant calves were related to cell adhesion, response to stimulus, cell communication and regulation of MAPK cascades. The functional profiles of the luminal microbiomes also revealed two distinct clusters consisting of functions related to either high protein metabolism or sulfur metabolism. A lower abundance of Bifidobacterium and a higher abundance of sulfur-reducing bacteria (SRB) were observed in the sulfur metabolism-dominant cluster (0.2±0.1%) compared to the protein metabolism-dominant cluster (12.6±5.7%), suggesting an antagonistic relationship between SRB and Bifidobacterium, which both compete for cysteine. These distinct taxonomic and functional clusters may provide a framework to further analyze interactions between the intestinal microbiome and the immune function and health of neonatal calves.Importance Dietary interventions to manipulate neonatal gut microbiota have been proposed to generate long-term impacts on hosts. Currently, our understanding on early gut microbiome of neonatal calves is limited to 16S rRNA gene amplicon based microbial profiling, which is a barrier to develop dietary interventions to improve calf gut health. The use of metagenome sequencing based approach in the present study revealed high individual animal variation in taxonomic and functional abundance of intestinal microbiome and potential impacts of early microbiome on mucosal immune responses during the pre-weaning period. During this developmental period, age- and diet-related changes in microbial diversity, richness, density and the abundance taxa and functions were observed. A correlation based approach to further explore the individual animal variation revealed potential enterotypes that can be linked to calf gut health, which may pave the way to developing strategies to manipulate the microbiome and improve calf health.}, }
@article {pmid30658727, year = {2019}, author = {Sarin, SK and Pande, A and Schnabl, B}, title = {Microbiome as a therapeutic target in alcohol-related liver disease.}, journal = {Journal of hepatology}, volume = {70}, number = {2}, pages = {260-272}, doi = {10.1016/j.jhep.2018.10.019}, pmid = {30658727}, issn = {1600-0641}, abstract = {Alcohol-related liver disease is associated with significant changes in gut microbial composition. The transmissibility of ethanol-induced liver disease has been demonstrated using faecal microbiota transfer in preclinical models. This technique has also led to improved survival in patients with severe alcoholic hepatitis, suggesting that changes in the composition and function of the gut microbiota are causatively linked to alcohol-related liver disease. A major mechanism by which gut microbiota influence the development of alcohol-related liver disease is through a leaky intestinal barrier. This permits translocation of viable bacteria and microbial products to the liver, where they induce and promote inflammation, as well as contribute to hepatocyte death and the fibrotic response. In addition, gut dysbiosis is associated with changes in the metabolic function of the intestinal microbiota, bile acid composition and circulation, immune dysregulation during onset and progression of alcohol-related liver disease. Findings from preclinical and human studies will be used to demonstrate how alcohol causes intestinal pathology and contributes to alcohol-related liver disease and how the latter is self-perpetuating. Additionally, we summarise the effects of untargeted treatment approaches on the gut microbiota, such as diet, probiotics, antibiotics and faecal microbial transplantation in alcohol-related liver disease. We further discuss how targeted approaches can restore intestinal homeostasis and improve alcohol-related liver disease. These approaches are likely to add to the therapeutic options for alcohol-related liver disease independently or in conjunction with steroids.}, }
@article {pmid30658400, year = {2019}, author = {Liew, WP and Mohd-Redzwan, S and Than, LTL}, title = {Gut Microbiota Profiling of Aflatoxin B1-Induced Rats Treated with Lactobacillus casei Shirota.}, journal = {Toxins}, volume = {11}, number = {1}, pages = {}, doi = {10.3390/toxins11010049}, pmid = {30658400}, issn = {2072-6651}, support = {GP-IPS/2018/9613100//Universiti Putra Malaysia/ ; }, abstract = {Aflatoxin B1 (AFB1) is a ubiquitous carcinogenic food contaminant. Gut microbiota is of vital importance for the host's health, regrettably, limited studies have reported the effects of xenobiotic toxins towards gut microbiota. Thus, the present study aims to investigate the interactions between AFB1 and the gut microbiota. Besides, an AFB1-binding microorganism, Lactobacillus casei Shirota (Lcs) was tested on its ability to ameliorate the changes on gut microbiota induced by AFB1. The fecal contents of three groups of rats included an untreated control group, an AFB1 group, as well as an Lcs + AFB1 group, were analyzed. Using the MiSeq platform, the PCR products of 16S rDNA gene extracted from the feces were subjected to next-generation sequencing. The alpha diversity index (Shannon) showed that the richness of communities increased significantly in the Lcs + AFB1 group compared to the control and AFB1 groups. Meanwhile, beta diversity indices demonstrated that AFB1 group significantly deviated from the control and Lcs + AFB1 groups. AFB1-exposed rats were especially high in Alloprevotella spp. abundance. Such alteration in the bacterial composition might give an insight on the interactions of AFB1 towards gut microbiota and how Lcs plays its role in detoxification of AFB1.}, }
@article {pmid30658055, year = {2019}, author = {Pellock, SJ and Walton, WG and Ervin, SM and Torres-Rivera, D and Creekmore, BC and Bergan, G and Dunn, ZD and Li, B and Tripathy, A and Redinbo, MR}, title = {Discovery and Characterization of FMN-Binding β-Glucuronidases in the Human Gut Microbiome.}, journal = {Journal of molecular biology}, volume = {431}, number = {5}, pages = {970-980}, doi = {10.1016/j.jmb.2019.01.013}, pmid = {30658055}, issn = {1089-8638}, support = {R01 CA098468/CA/NCI NIH HHS/United States ; R01 CA161879/CA/NCI NIH HHS/United States ; R01 CA207416/CA/NCI NIH HHS/United States ; }, abstract = {The human gut microbiota encodes β-glucuronidases (GUSs) that play key roles in health and disease via the metabolism of glucuronate-containing carbohydrates and drugs. Hundreds of putative bacterial GUS enzymes have been identified by metagenomic analysis of the human gut microbiome, but less than 10% have characterized structures and functions. Here we describe a set of unique gut microbial GUS enzymes that bind flavin mononucleotide (FMN). First, we show using mass spectrometry, isothermal titration calorimetry, and x-ray crystallography that a purified GUS from the gut commensal microbe Faecalibacterium prausnitzii binds to FMN on a surface groove located 30 Å away from the active site. Second, utilizing structural and functional data from this FMN-binding GUS, we analyzed the 279 unique GUS sequences from the Human Microbiome Project database and identified 14 putative FMN-binding GUSs. We characterized four of these hits and solved the structure of two, the GUSs from Ruminococcus gnavus and Roseburia hominis, which confirmed that these are FMN binders. Third, binding and kinetic analysis of the FMN-binding site mutants of these five GUSs show that they utilize a conserved site to bind FMN that is not essential for GUS activity, but can affect KM. Lastly, a comprehensive structural review of the PDB reveals that the FMN-binding site employed by these enzymes is unlike any structurally characterized FMN binders to date. These findings reveal the first instance of an FMN-binding glycoside hydrolase and suggest a potential link between FMN and carbohydrate metabolism in the human gut microbiota.}, }
@article {pmid30657979, year = {2019}, author = {Liu, J and Lian, Q and Chen, Y and Qi, J}, title = {Amino acid based de Bruijn graph algorithm for identifying complete coding genes from metagenomic and metatranscriptomic short reads.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkz017}, pmid = {30657979}, issn = {1362-4962}, abstract = {Metagenomic studies, greatly promoted by the fast development of next-generation sequencing (NGS) technologies, uncover complex structures of microbial communities and their interactions with environment. As the majority of microbes lack information of genome sequences, it is essential to assemble prokaryotic genomes ab initio aiming to retrieve complete coding genes from various metabolic pathways. The complex nature of microbial composition and the burden of handling a vast amount of metagenomic data, bring great challenges to the development of effective and efficient bioinformatic tools. Here we present a protein assembler (MetaPA), based on de Bruijn graph searching on oligopeptide spaces and can be applied on both metagenomic and metatranscriptomic sequencing data. When public homologous protein sequences are involved to guide the assembling procedures, MetaPA assembles 85% of total proteins in complete sequences with high precision of 83% on real high-throughput sequencing datasets. Application of MetaPA on metatranscriptomic data successfully identifies the majority of actively transcribed genes validated in related studies. The results suggest that MetaPA has a good potential in both metagenomic and metatranscriptomic studies to characterize the composition and abundance of microbiota.}, }
@article {pmid30657007, year = {2019}, author = {Machiavelli, A and Duarte, RTD and Pires, MMS and Zárate-Bladés, CR and Pinto, AR}, title = {The impact of in utero HIV exposure on gut microbiota, inflammation, and microbial translocation.}, journal = {Gut microbes}, volume = {}, number = {}, pages = {1-16}, doi = {10.1080/19490976.2018.1560768}, pmid = {30657007}, issn = {1949-0984}, abstract = {HIV-exposed but uninfected (HEU) children represent a growing population and show a significantly higher number of infectious diseases, several immune alterations, compromised growth, and increased mortality rates when compared to HIV-unexposed children. Considering the impact that the gut microbiota has on general host homeostasis and immune system development and modulation, we hypothesized that HEU children present altered gut microbiota that is linked to the increased morbidity and the immune system disorders faced by them. Our experiments revealed no differences in beta and alpha diversity of the gut microbiota between HEU and unexposed children or between HIV-infected and uninfected mothers. However, there were differences in the abundance of several taxa from the gut microbiota between HEU and unexposed children and between HIV-infected and uninfected mothers. Functional prediction based on 16S rRNA sequences also indicated differences between HEU and unexposed children and between infected and uninfected mothers. In addition, we detected no differences between HEU and unexposed children in relation to weight, weight-for-age z scores, albumin serum levels, or microbial translocation and inflammation markers. In summary, HIV-infected mothers and their HIV-exposed children present alterations in the abundance of several taxa in the gut microbiome and the predicted functional metagenome when compared to uninfected mothers and unexposed children. Knowledge about the gut microbiome of HEU children in different settings is essential in order to determine better treatments for this susceptible population.}, }
@article {pmid30656204, year = {2019}, author = {Sadaiappan, B and Prasannakumar, C and Subramanian, K and Subramanian, M}, title = {Metagenomic data of vertical distribution and abundance of bacterial diversity in the hypersaline sediments of Mad Boon-mangrove ecosystem, Bay of Bengal.}, journal = {Data in brief}, volume = {22}, number = {}, pages = {716-721}, doi = {10.1016/j.dib.2018.12.028}, pmid = {30656204}, issn = {2352-3409}, abstract = {Bacterial diversity studies in hypersaline soil often yield novel organisms and contribute to our understanding of this extreme environment. Soil from Mad Boon is previously uncharacterized, with dense mangrove forest in one side and hypersaline soil in another side of backwater located in Southeast coast of Tamil Nadu, India. We surveyed to characterize the structure and diversity of the bacterial community. Samples were collected in a partially vegetated upland, exposed backwater sedimentation and water-logged location. In this study, we investigate the bacterial community structure using pyrosequence analysis of the V5- V9 gene region. After quality checks a total of 3919, 7298 and 7399 reads were obtained. About 42 phyla were observed, among them Proteobacteria were dominant phylum followed by Acidobacteria, Firmicutes and Chloroflexi. Classes including Deltaproteobacteria and Gammaproteobacteriawere observed. All sequences generated in this study were submitted to NCBI SRA under the accession numbers SRR627695, SRR63011 and SRR631012.}, }
@article {pmid30656069, year = {2019}, author = {Barajas, HR and Romero, MF and Martínez-Sánchez, S and Alcaraz, LD}, title = {Global genomic similarity and core genome sequence diversity of the Streptococcus genus as a toolkit to identify closely related bacterial species in complex environments.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e6233}, doi = {10.7717/peerj.6233}, pmid = {30656069}, issn = {2167-8359}, abstract = {Background: The Streptococcus genus is relevant to both public health and food safety because of its ability to cause pathogenic infections. It is well-represented (>100 genomes) in publicly available databases. Streptococci are ubiquitous, with multiple sources of isolation, from human pathogens to dairy products. The Streptococcus genus has traditionally been classified by morphology, serum types, the 16S ribosomal RNA (rRNA) gene, and multi-locus sequence types subject to in-depth comparative genomic analysis.
Methods: Core and pan-genomes described the genomic diversity of 108 strains belonging to 16 Streptococcus species. The core genome nucleotide diversity was calculated and compared to phylogenomic distances within the genus Streptococcus. The core genome was also used as a resource to recruit metagenomic fragment reads from streptococci dominated environments. A conventional 16S rRNA gene phylogeny reconstruction was used as a reference to compare the resulting dendrograms of average nucleotide identity (ANI) and genome similarity score (GSS) dendrograms.
Results: The core genome, in this work, consists of 404 proteins that are shared by all 108 Streptococcus. The average identity of the pairwise compared core proteins decreases proportionally to GSS lower scores, across species. The GSS dendrogram recovers most of the clades in the 16S rRNA gene phylogeny while distinguishing between 16S polytomies (unresolved nodes). The GSS is a distance metric that can reflect evolutionary history comparing orthologous proteins. Additionally, GSS resulted in the most useful metric for genus and species comparisons, where ANI metrics failed due to false positives when comparing different species.
Discussion: Understanding of genomic variability and species relatedness is the goal of tools like GSS, which makes use of the maximum pairwise shared orthologous sequences for its calculation. It allows for long evolutionary distances (above species) to be included because of the use of amino acid alignment scores, rather than nucleotides, and normalizing by positive matches. Newly sequenced species and strains could be easily placed into GSS dendrograms to infer overall genomic relatedness. The GSS is not restricted to ubiquitous conservancy of gene features; thus, it reflects the mosaic-structure and dynamism of gene acquisition and loss in bacterial genomes.}, }
@article {pmid30655087, year = {2019}, author = {Markowski, MC and Boorjian, SA and Burton, JP and Hahn, NM and Ingersoll, MA and Maleki Vareki, S and Pal, SK and Sfanos, KS}, title = {The Microbiome and Genitourinary Cancer: A Collaborative Review.}, journal = {European urology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.eururo.2018.12.043}, pmid = {30655087}, issn = {1873-7560}, abstract = {CONTEXT: The recent discovery of the existence of a human genitourinary microbiome has led to the investigation of its role in mediating the pathogenesis of genitourinary malignancies, including bladder, kidney, and prostate cancers. Furthermore, although it is largely recognized that members of the gastrointestinal microbiota are actively involved in drug metabolism, new studies demonstrate additional roles and the potential necessity of the gastrointestinal microbiota in dictating cancer treatment response.
OBJECTIVE: To summarize the current evidence of a mechanistic role for the genitourinary and gastrointestinal microbiome in genitourinary cancer initiation and treatment response.
EVIDENCE ACQUISITION: We conducted a literature search up to October 2018. Search terms included microbiome, microbiota, urinary microbiome, bladder cancer, urothelial carcinoma, renal cell carcinoma, kidney cancer, testicular cancer, and prostate cancer.
EVIDENCE SYNTHESIS: There is preliminary evidence to implicate the members of the genitourinary microbiota as causative factors or cofactors in genitourinary malignancy. Likewise, the current evidence for gastrointestinal microbes in dictating cancer treatment response is mainly correlative; however, we provide examples where therapeutic agents used for the treatment of genitourinary cancers are affected by the human-associated microbiota, or vice versa. Clinical trials, such as fecal microbiota transplant to increase the efficacy of immunotherapy, are currently underway.
CONCLUSIONS: The role of the microbiome in genitourinary cancer is an emerging field that merits further studies. Translating microbiome research into clinical action will require incorporation of microbiome surveillance into ongoing and future clinical trials as well as expansion of studies to include metagenomic sequencing and metabolomics.
PATIENT SUMMARY: This review covers recent evidence that microbial populations that reside in the genitourinary tract-and were previously not known to exist-may influence the development of genitourinary malignancies including bladder, kidney, and prostate cancers. Furthermore, microbial populations that exist at sites outside of the genitourinary tract, such as those that reside in our gut, may influence cancer development and/or treatment response.}, }
@article {pmid30167467, year = {2018}, author = {Dias, M and Pattabiraman, C and Siddappa, S and Gowda, M and Shet, A and Smith, D and Muehlemann, B and Tamma, K and Solomon, T and Jones, T and Krishna, S}, title = {Complete assembly of a dengue virus type 3 genome from a recent genotype III clade by metagenomic sequencing of serum.}, journal = {Wellcome open research}, volume = {3}, number = {}, pages = {44}, doi = {10.12688/wellcomeopenres.14438.2}, pmid = {30167467}, issn = {2398-502X}, abstract = {Background: Mosquito-borne flaviviruses, such as dengue and Japanese encephalitis virus (JEV), cause life-threatening diseases, particularly in the tropics. Methods: Here we performed unbiased metagenomic sequencing of RNA extracted from the serum of four patients and the plasma of one patient, all hospitalized at a tertiary care centre in South India with severe or prolonged febrile illness, together with the serum from one healthy control, in 2014. Results: We identified and assembled a complete dengue virus type 3 sequence from a case of severe dengue fever. We also identified a small number of JEV sequences in the serum of two adults with febrile illness, including one with severe dengue. Phylogenetic analysis revealed that the dengue sequence belonged to genotype III. It has an estimated divergence time of 13.86 years from the most highly related Indian strains. In total, 11 amino acid substitutions were predicted for this strain in the antigenic envelope protein, when compared to the parent strain used for development of the first commercial dengue vaccine. Conclusions: We demonstrate that both genome assembly and detection of a low number of viral sequences are possible through the unbiased sequencing of clinical material. These methods may help ascertain causal agents for febrile illnesses with no known cause.}, }
@article {pmid30654102, year = {2019}, author = {Akyol, Ç and Ince, O and Bozan, M and Ozbayram, EG and Ince, B}, title = {Fungal bioaugmentation of anaerobic digesters fed with lignocellulosic biomass: What to expect from anaerobic fungus Orpinomyces sp.}, journal = {Bioresource technology}, volume = {277}, number = {}, pages = {1-10}, doi = {10.1016/j.biortech.2019.01.024}, pmid = {30654102}, issn = {1873-2976}, abstract = {Energy-efficient biogas reactors are often designed and operated mimicking natural microbial ecosystems such as the digestive tracts of ruminants. Anaerobic fungi play a crucial role in the degradation of lignocellulose-rich fiber thanks to their high cellulolytic activity. Fungal bioaugmentation is therefore at the heart of our understanding of enhancing anaerobic digestion (AD). The efficiency of bioaugmentation with anaerobic fungus Orpinomyces sp. was evaluated in lignocellulose-based AD configurations. Fungal bioaugmentation increased the methane yield by 15-33% during anaerobic co-digestion of cow manure and selected cereal crops/straws. Harvesting stage of the crops was a decisive parameter to influence methane production together with fungal bioaugmentation. A more efficient fermentation process in the bioaugmented digesters was distinguished by relatively-higher abundance of Synergistetes, which was mainly represented by the genus Anaerobaculum. On the contrary, the composition of the methanogenic archaea did not change, and the majority of methanogens was assigned to Methanosarcina.}, }
@article {pmid30652494, year = {2019}, author = {Kalantar, KL and Moazed, F and Christenson, SC and Wilson, J and Deiss, T and Belzer, A and Vessel, K and Caldera, S and Jauregui, A and Bolourchi, S and DeRisi, JL and Calfee, CS and Langelier, C}, title = {A Metagenomic Comparison of Tracheal Aspirate and Mini-Bronchial Alveolar Lavage for Assessment of Respiratory Microbiota.}, journal = {American journal of physiology. Lung cellular and molecular physiology}, volume = {}, number = {}, pages = {}, doi = {10.1152/ajplung.00476.2018}, pmid = {30652494}, issn = {1522-1504}, abstract = {Accurate and informative microbiologic testing is essential for guiding diagnosis and management of pneumonia in critically ill patients. Sampling of tracheal aspirate (TA) is less invasive compared to mini-bronchoalveolar lavage (mBAL) and is now recommended as a frontline diagnostic approach in mechanically ventilated patients, despite the historical belief that TA was suboptimal due to contamination from oral microbes. Advancements in metagenomic next generation sequencing (mNGS) now permit assessment of airway microbiota without a need for culture, and as such provide an opportunity to examine differences between mBAL and TA at a resolution previously unachievable. Here, we engaged shotgun mNGS to quantitatively assess the airway microbiome in matched mBAL and TA specimens from a prospective cohort of critically ill adults. We observed moderate differences betweensampletypes across all subjects, however we found significant compositional similarity in subjects with bacterial pneumonia, whose microbial communities were characterized by a dominant pathogen. In addition, we found that both mBAL and TA were similar in terms of microbialrelative abundance, abundance of oropharyngeal taxa, and microbial diversity. Our findings suggest that TA sampling provides a similar assessment of airway microbiota as more invasive testing by mBAL, and that this similarity is most significant in the setting of bacterial pneumonia.}, }
@article {pmid30651609, year = {2019}, author = {Boyd, JA and Jungbluth, SP and Leu, AO and Evans, PN and Woodcroft, BJ and Chadwick, GL and Orphan, VJ and Amend, JP and Rappé, MS and Tyson, GW}, title = {Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-018-0343-2}, pmid = {30651609}, issn = {1751-7370}, support = {DE-SC0010580//U.S. Department of Energy (DOE)/ ; DE-SC0016440//U.S. Department of Energy (DOE)/ ; DE-SC0016469//U.S. Department of Energy (DOE)/ ; DE-SC0016469//U.S. Department of Energy (DOE)/ ; DE-170100428//Department of Education and Training | Australian Research Council (ARC)/ ; DE-160100248//Department of Education and Training | Australian Research Council (ARC)/ ; MCB06-04014//National Science Foundation (NSF)/ ; }, abstract = {The methyl-coenzyme M reductase (MCR) complex is a key enzyme in archaeal methane generation and has recently been proposed to also be involved in the oxidation of short-chain hydrocarbons including methane, butane, and potentially propane. The number of archaeal clades encoding the MCR continues to grow, suggesting that this complex was inherited from an ancient ancestor, or has undergone extensive horizontal gene transfer. Expanding the representation of MCR-encoding lineages through metagenomic approaches will help resolve the evolutionary history of this complex. Here, a near-complete Archaeoglobi metagenome-assembled genome (MAG; Ca. Polytropus marinifundus gen. nov. sp. nov.) was recovered from the deep subseafloor along the Juan de Fuca Ridge flank that encodes two divergent McrABG operons similar to those found in Ca. Bathyarchaeota and Ca. Syntrophoarchaeum MAGs. Ca. P. marinifundus is basal to members of the class Archaeoglobi, and encodes the genes for β-oxidation, potentially allowing an alkanotrophic metabolism similar to that proposed for Ca. Syntrophoarchaeum. Ca. P. marinifundus also encodes a respiratory electron transport chain that can potentially utilize nitrate, iron, and sulfur compounds as electron acceptors. Phylogenetic analysis suggests that the Ca. P. marinifundus MCR operons were horizontally transferred, changing our understanding of the evolution and distribution of this complex in the Archaea.}, }
@article {pmid30651402, year = {2019}, author = {Mu, A and Kwong, JC and Isles, NS and Gonçalves da Silva, A and Schultz, MB and Ballard, SA and Lane, CR and Carter, GP and Williamson, DA and Seemann, T and Stinear, TP and Howden, BP}, title = {Reconstruction of the Genomes of Drug-Resistant Pathogens for Outbreak Investigation through Metagenomic Sequencing.}, journal = {mSphere}, volume = {4}, number = {1}, pages = {}, doi = {10.1128/mSphere.00529-18}, pmid = {30651402}, issn = {2379-5042}, abstract = {Culture-independent methods that target genome fragments have shown promise in identifying certain pathogens, but the holy grail of comprehensive pathogen genome detection from microbiologically complex samples for subsequent forensic analyses remains a challenge. In the context of an investigation of a nosocomial outbreak, we used shotgun metagenomic sequencing of a human fecal sample and a neural network algorithm based on tetranucleotide frequency profiling to reconstruct microbial genomes and tested the same approach using rectal swabs from a second patient. The approach rapidly and readily detected the genome of Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae in the patient fecal specimen and in the rectal swab sample, achieving a level of strain resolution that was sufficient for confident transmission inference during a highly clonal outbreak. The analysis also detected previously unrecognized colonization of the patient by vancomycin-resistant Enterococcus faecium, another multidrug-resistant bacterium.IMPORTANCE The study results reported here perfectly demonstrate the power and promise of clinical metagenomics to recover genome sequences of important drug-resistant bacteria and to rapidly provide rich data that inform outbreak investigations and treatment decisions, independently of the need to culture the organisms.}, }
@article {pmid30649386, year = {2019}, author = {Van Gompel, L and Luiken, REC and Sarrazin, S and Munk, P and Knudsen, BE and Hansen, RB and Bossers, A and Aarestrup, FM and Dewulf, J and Wagenaar, JA and Mevius, DJ and Schmitt, H and Heederik, DJJ and Dorado-García, A and Smit, LAM and , }, title = {The antimicrobial resistome in relation to antimicrobial use and biosecurity in pig farming, a metagenome-wide association study in nine European countries.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {}, number = {}, pages = {}, doi = {10.1093/jac/dky518}, pmid = {30649386}, issn = {1460-2091}, abstract = {Objectives: Previous studies in food-producing animals have shown associations between antimicrobial use (AMU) and resistance (AMR) in specifically isolated bacterial species. Multi-country data are scarce and only describe between-country differences. Here we investigate associations between the pig faecal mobile resistome and characteristics at the farm-level across Europe.
Methods: A cross-sectional study was conducted among 176 conventional pig farms from nine European countries. Twenty-five faecal samples from fattening pigs were pooled per farm and acquired resistomes were determined using shotgun metagenomics and the Resfinder reference database, i.e. the full collection of horizontally acquired AMR genes (ARGs). Normalized fragments resistance genes per kilobase reference per million bacterial fragments (FPKM) were calculated. Specific farm-level data (AMU, biosecurity) were collected. Random-effects meta-analyses were performed by country, relating farm-level data to relative ARG abundances (FPKM).
Results: Total AMU during fattening was positively associated with total ARG (total FPKM). Positive associations were particularly observed between widely used macrolides and tetracyclines, and ARGs corresponding to the respective antimicrobial classes. Significant AMU-ARG associations were not found for β-lactams and only few colistin ARGs were found, despite high use of these antimicrobial classes in younger pigs. Increased internal biosecurity was directly related to higher abundances of ARGs mainly encoding macrolide resistance. These effects of biosecurity were independent of AMU in mutually adjusted models.
Conclusions: Using resistome data in association studies is unprecedented and adds accuracy and new insights to previously observed AMU-AMR associations. Major components of the pig resistome are positively and independently associated with on-farm AMU and biosecurity conditions.}, }
@article {pmid30649204, year = {2019}, author = {Saha, S and Johnson, J and Pal, S and Weinstock, G and Rajasekaran, S}, title = {MSC: a metagenomic sequence classification algorithm.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/bty1071}, pmid = {30649204}, issn = {1367-4811}, abstract = {Motivation: Metagenomics is the study of genetic materials directly sampled from natural habitats. It has the potential to reveal previously hidden diversity of microscopic life largely due to the existence of highly parallel and low-cost next-generation sequencing (NGS) technology. Conventional approaches align metagenomic reads onto known reference genomes to identify microbes in the sample. Since such a collection of reference genomes is very large, the approach often needs high-end computing machines with large memory which is not often available to researchers. Alternative approaches follow an alignment-free methodology where the presence of a microbe is predicted using the information about the unique k-mers present in the microbe genomes. However, such approaches suffer from high false positives due to trading off the value of k with the computational resources. In this article we propose a highly efficient metagenomic sequence classification algorithm (MSC) that is a hybrid of both approaches. Instead of aligning reads to the full genomes, MSC aligns reads onto a set of carefully chosen, shorter and highly discriminating model sequences built from the unique k-mers of each of the target sequences.
Results: Microbiome researchers are generally interested in two objectives of a taxonomic classifier: 1) to detect prevalence, i.e., the taxa present in a sample, and 2) to estimate their relative abundances. MSC is primarily designed to detect prevalence and experimental results show that MSC is indeed a more effective and efficient algorithm compared to the other state-of-the-art algorithms in terms of accuracy, memory, and runtime. Moreover, MSC outputs an approximate estimate of the abundances.
Availability: The implementations are freely available for non-commercial purposes. They can be downloaded from https://drive.google.com/open?id=1XirkAamkQ3ltWvI1W1igYQFusp9DHtVl.}, }
@article {pmid30649168, year = {2019}, author = {Griffith, JC and Morgan, XC}, title = {Invited Commentary: Improving accessibility of the Human Microbiome Project data through integration with R/Bioconductor.}, journal = {American journal of epidemiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/aje/kwz007}, pmid = {30649168}, issn = {1476-6256}, abstract = {Alterations in the composition of the microbiota have been implicated in many diseases. The Human Microbiome Project (HMP) provides a comprehensive reference dataset of the "normal" human microbiome of 242 healthy adults at five major body sites. The HMP used both 16S ribosomal RNA gene sequencing and whole-genome metagenomic sequencing to profile the subjects' microbial communities. However, accessing and analyzing the HMP dataset still presents technical and bioinformatic challenges, as researchers must import the microbiome data, integrate phylogenetic trees, and access and merge public and restricted metadata. In this issue, the HMP16SData R/Bioconductor package developed by Schiffer and colleagues (Am J Epidemiol. XXX; XX (XX): XX-XXX) greatly simplifies access to the HMP data by combining 16S taxonomic abundance data, public patient metadata, and phylogenetic trees as a single data object. The authors also provide an interface for users with approved dbGaP projects to easily retrieve and merge the controlled-access HMP metadata. This package has a broad range of appeal to researchers across disciplines and with various levels of expertise in using R and/or other statistical tools. This will translate to improved data accessibility for public health research, with data from healthy individuals serving as a reference for disease-associated studies.}, }
@article {pmid30649062, 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 ART-treated perinatally HIV-infected patients associated with cardiac and inflammatory biomarkers.}, journal = {AIDS (London, England)}, volume = {}, number = {}, pages = {}, doi = {10.1097/QAD.0000000000002131}, pmid = {30649062}, issn = {1473-5571}, abstract = {OBJECTIVE: Persistent inflammation and higher risk to develop cardiovascular diseases (CVDs) still represent a major complication for HIV-infected patients despite effective antiretroviral therapy (ART). We investigated the correlation between the gut microbiota (GM) profile, markers of inflammation, vascular endothelial activation (VEA) and microbial translocation (MT) in perinatally HIV-infected patients (PHIV) under ART.
DESIGN: Cross-sectional study including sixty-one ART-treated PHIV (age range 3-30 years old) and seventy-one age-matched healthy controls (CTRL). Blood and stool sample were collected at the same time and analyzed for GM composition and plasma biomarkers.
METHODS: GM composition was determined by 16S rRNA targeted-metagenomics. Soluble markers of MT, SI and VEA were quantified by ELISA or Luminex assay. Markers of immune activation were analyzed by flow cytometry on CD4+ and CD8+T-cells.
RESULTS: We identified two distinct GM profiles (group 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 (A.muciniphila), whereas GM of group B was characterized by a higher biodiversity. The analysis of soluble markers revealed a significantly higher level of sE-selectin (p = 0.0296), ICAM-1 (p = 0.0028), VCAM-1 (p = 0.0230), IL-6 (p = 0.0247) and sCD14 (p = 0.0142) in group A compared to group B.
CONCLUSIONS: Distinctive GM profiles are differently associated with inflammation, MT and VEA. Future studies are needed in order to understand the role of A.muciniphila and risk to develop CVDs in PHIV.}, }
@article {pmid30648419, year = {2019}, author = {BenIsrael, M and Wanner, P and Aravena, R and Parker, BL and Haack, EA and Tsao, DT and Dunfield, KE}, title = {Toluene biodegradation in the vadose zone of a poplar phytoremediation system identified using metagenomics and toluene-specific stable carbon isotope analysis.}, journal = {International journal of phytoremediation}, volume = {}, number = {}, pages = {1-10}, doi = {10.1080/15226514.2018.1523873}, pmid = {30648419}, issn = {1549-7879}, abstract = {Biodegradation is an important mechanism of action of phytoremediation systems, but performance evaluation is challenging. We applied metagenomic molecular approaches and compound-specific stable carbon isotope analysis to assess biodegradation of toluene in the vadose zone at an urban pilot field system where hybrid poplars were planted to remediate legacy impacts to an underlying shallow fractured bedrock aquifer. Carbon isotope ratios were compared spatio-temporally between toluene dissolved in groundwater and in the vapor phase. Enrichment of 13C from toluene in the vapor phase compared to groundwater provided evidence for biodegradation in the vadose zone. Total bacterial abundance (16S rRNA) and abundance and expression of degradation genes were determined in rhizosphere soil (DNA and RNA) and roots (DNA) using quantitative PCR. Relative abundances of degraders in the rhizosphere were on average higher at greater depths, except for enrichment of PHE-encoding communities that more strongly followed patterns of toluene concentrations detected. Quantification of RMO and PHE gene transcripts supported observations of active aerobic toluene degradation. Finally, spatially-variable numbers of toluene degraders were detected in poplar roots. We present multiple lines of evidence for biodegradation in the vadose zone at this site, contributing to our understanding of mechanisms of action of the phytoremediation system.}, }
@article {pmid30648011, year = {2019}, author = {Susi, H and Filloux, D and Frilander, MJ and Roumagnac, P and Laine, AL}, title = {Diverse and variable virus communities in wild plant populations revealed by metagenomic tools.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6140}, doi = {10.7717/peerj.6140}, pmid = {30648011}, issn = {2167-8359}, abstract = {Wild plant populations may harbour a myriad of unknown viruses. As the majority of research efforts have targeted economically important plant species, the diversity and prevalence of viruses in the wild has remained largely unknown. However, the recent shift towards metagenomics-based sequencing methodologies, especially those targeting small RNAs, is finally enabling virus discovery from wild hosts. Understanding this diversity of potentially pathogenic microbes in the wild can offer insights into the components of natural biodiversity that promotes long-term coexistence between hosts and parasites in nature, and help predict when and where risks of disease emergence are highest. Here, we used small RNA deep sequencing to identify viruses in Plantago lanceolata populations, and to understand the variation in their prevalence and distribution across the Åland Islands, South-West Finland. By subsequent design of PCR primers, we screened the five most common viruses from two sets of P. lanceolata plants: 164 plants collected from 12 populations irrespective of symptoms, and 90 plants collected from five populations showing conspicuous viral symptoms. In addition to the previously reported species Plantago lanceolata latent virus (PlLV), we found four potentially novel virus species belonging to Caulimovirus, Betapartitivirus, Enamovirus, and Closterovirus genera. Our results show that virus prevalence and diversity varied among the sampled host populations. In six of the virus infected populations only a single virus species was detected, while five of the populations supported between two to five of the studied virus species. In 20% of the infected plants, viruses occurred as coinfections. When the relationship between conspicuous viral symptoms and virus infection was investigated, we found that plants showing symptoms were usually infected (84%), but virus infections were also detected from asymptomatic plants (44%). Jointly, these results reveal a diverse virus community with newly developed tools and protocols that offer exciting opportunities for future studies on the eco-evolutionary dynamics of viruses infecting plants in the wild.}, }
@article {pmid30647460, year = {2019}, author = {Rubin-Blum, M and Antony, CP and Sayavedra, L and Martínez-Pérez, C and Birgel, D and Peckmann, J and Wu, YC and Cardenas, P and MacDonald, I and Marcon, Y and Sahling, H and Hentschel, U and Dubilier, N}, title = {Fueled by methane: deep-sea sponges from asphalt seeps gain their nutrition from methane-oxidizing symbionts.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0346-7}, pmid = {30647460}, issn = {1751-7370}, support = {N/A//Alexander von Humboldt-Stiftung (Alexander von Humboldt Foundation)/ ; 679849//EC | Horizon 2020 (Horizon 2020 - Research and Innovation Framework Programme)/ ; 679849//EC | European Research Council (ERC)/ ; GBMF3811//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; }, abstract = {Sponges host a remarkable diversity of microbial symbionts, however, the benefit their microbes provide is rarely understood. Here, we describe two new sponge species from deep-sea asphalt seeps and show that they live in a nutritional symbiosis with methane-oxidizing (MOX) bacteria. Metagenomics and imaging analyses revealed unusually high amounts of MOX symbionts in hosts from a group previously assumed to have low microbial abundances. These symbionts belonged to the Marine Methylotrophic Group 2 clade. They are host-specific and likely vertically transmitted, based on their presence in sponge embryos and streamlined genomes, which lacked genes typical of related free-living MOX. Moreover, genes known to play a role in host-symbiont interactions, such as those that encode eukaryote-like proteins, were abundant and expressed. Methane assimilation by the symbionts was one of the most highly expressed metabolic pathways in the sponges. Molecular and stable carbon isotope patterns of lipids confirmed that methane-derived carbon was incorporated into the hosts. Our results revealed that two species of sponges, although distantly related, independently established highly specific, nutritional symbioses with two closely related methanotrophs. This convergence in symbiont acquisition underscores the strong selective advantage for these sponges in harboring MOX bacteria in the food-limited deep sea.}, }
@article {pmid30645605, year = {2019}, author = {Kim, SH and Kang, PA and Han, K and Lee, SW and Rhee, S}, title = {Crystal structure of chloramphenicol-metabolizing enzyme EstDL136 from a metagenome.}, journal = {PloS one}, volume = {14}, number = {1}, pages = {e0210298}, doi = {10.1371/journal.pone.0210298}, pmid = {30645605}, issn = {1932-6203}, abstract = {Metagenomes often convey novel biological activities and therefore have gained considerable attention for use in biotechnological applications. Recently, metagenome-derived EstDL136 was found to possess chloramphenicol (Cm)-metabolizing features. Sequence analysis showed EstDL136 to be a member of the hormone-sensitive lipase (HSL) family with an Asp-His-Ser catalytic triad and a notable substrate specificity. In this study, we determined the crystal structures of EstDL136 and in a complex with Cm. Consistent with the high sequence similarity, the structure of EstDL136 is homologous to that of the HSL family. The active site of EstDL136 is a relatively shallow pocket that could accommodate Cm as a substrate as opposed to the long acyl chain substrates typical of the HSL family. Mutational analyses further suggested that several residues in the vicinity of the active site play roles in the Cm-binding of EstDL136. These results provide structural and functional insights into a metagenome-derived EstDL136.}, }
@article {pmid30644013, year = {2019}, author = {Wang, G and Ren, Y and Ng, TB and Streit, WR and Ye, X}, title = {High-throughput amplicon sequencing demonstrates extensive diversity of xylanase genes in the sediment of soda lake Dabusu.}, journal = {Biotechnology letters}, volume = {41}, number = {3}, pages = {409-418}, doi = {10.1007/s10529-019-02646-w}, pmid = {30644013}, issn = {1573-6776}, support = {31301406//National Natural Science Foundation of China/ ; 2014FJPT02//the Marine Biological Engineering Platform for Innovative Services/ ; 2017-3059//China Scholarship Council/ ; }, abstract = {OBJECTIVE: To explore the diversity of glycoside hydrolase family 10 xylanase genes in the sediment of soda lake Dabusu by using high-throughput amplicon sequencing based on the Illumina HiSeq2500 platform.
RESULTS: A total of 227,420 clean reads, representing approximately 49.5 M bp, were obtained. Operational taxonomic unit (OTU) classification, with a 95% sequence identity cut-off, resulted in 467 OTUs with 392 annotated as GH10 xylanase, exhibiting 35-99% protein sequence identity with their closest-related xylanases in GenBank. Above 75% of the total OTUs demonstrated less than 80% identity with known xylanases. In addition, xylanases derived from the sediment were found to be affiliated to 12 different phyla, with Bacteroidetes, Proteobacteria, Actinobacteria, Firmicutes, Verrucomicrobia, and Basidiomycota being the dominant phyla. Moreover, barcode sequence had a major effect on abundance with only a minor effect on diversity.
CONCLUSIONS: High-throughput amplicon sequencing offers insight into xylanase gene diversity at a substantially higher resolution and lesser cost than library cloning and Sanger sequencing, facilitating a more thorough understanding of xylanase distribution and ecology.}, }
@article {pmid30643883, year = {2019}, author = {Franco Filho, LC and Barata, RR and Cardoso, JF and Massafra, JMV and Lemos, PDS and Casseb, LMN and Cruz, ACR and Nunes, MRT}, title = {Metagenomic Analysis of Samples from Three Bat Species Collected in the Amazon Rain Forest.}, journal = {Microbiology resource announcements}, volume = {8}, number = {2}, pages = {}, doi = {10.1128/MRA.01422-18}, pmid = {30643883}, issn = {2576-098X}, abstract = {We report here the sequencing of five microbiome samples collected from different bat species in the Amazon rain forest. All contigs matching virus sequences were assigned to members of the Retroviridae family, while the bacterial contigs matched several bacterial species mostly belonging to the Proteobacteria phylum.}, }
@article {pmid30643240, year = {2019}, author = {Nakamoto, N and Sasaki, N and Aoki, R and Miyamoto, K and Suda, W and Teratani, T and Suzuki, T and Koda, Y and Chu, PS and Taniki, N and Yamaguchi, A and Kanamori, M and Kamada, N and Hattori, M and Ashida, H and Sakamoto, M and Atarashi, K and Narushima, S and Yoshimura, A and Honda, K and Sato, T and Kanai, T}, title = {Gut pathobionts underlie intestinal barrier dysfunction and liver T helper 17 cell immune response in primary sclerosing cholangitis.}, journal = {Nature microbiology}, volume = {4}, number = {3}, pages = {492-503}, doi = {10.1038/s41564-018-0333-1}, pmid = {30643240}, issn = {2058-5276}, abstract = {Primary sclerosing cholangitis (PSC) is a chronic inflammatory liver disease and its frequent complication with ulcerative colitis highlights the pathogenic role of epithelial barrier dysfunction. Intestinal barrier dysfunction has been implicated in the pathogenesis of PSC, yet its underlying mechanism remains unknown. Here, we identify Klebsiella pneumonia in the microbiota of patients with PSC and demonstrate that K. pneumoniae disrupts the epithelial barrier to initiate bacterial translocation and liver inflammatory responses. Gnotobiotic mice inoculated with PSC-derived microbiota exhibited T helper 17 (TH17) cell responses in the liver and increased susceptibility to hepatobiliary injuries. Bacterial culture of mesenteric lymph nodes in these mice isolated K. pneumoniae, Proteus mirabilis and Enterococcus gallinarum, which were prevalently detected in patients with PSC. A bacterial-organoid co-culture system visualized the epithelial-damaging effect of PSC-derived K. pneumoniae that was associated with bacterial translocation and susceptibility to TH17-mediated hepatobiliary injuries. We also show that antibiotic treatment ameliorated the TH17 immune response induced by PSC-derived microbiota. These results highlight the role of pathobionts in intestinal barrier dysfunction and liver inflammation, providing insights into therapeutic strategies for PSC.}, }
@article {pmid30643213, year = {2019}, author = {Ronda, C and Chen, SP and Cabral, V and Yaung, SJ and Wang, HH}, title = {Metagenomic engineering of the mammalian gut microbiome in situ.}, journal = {Nature methods}, volume = {16}, number = {2}, pages = {167-170}, doi = {10.1038/s41592-018-0301-y}, pmid = {30643213}, issn = {1548-7105}, support = {DP5 OD009172/OD/NIH HHS/United States ; F30 DK111145/DK/NIDDK NIH HHS/United States ; R01 AI132403/AI/NIAID NIH HHS/United States ; R01 DK118044/DK/NIDDK NIH HHS/United States ; }, abstract = {Engineering of microbial communities in open environments remains challenging. Here we describe a platform used to identify and modify genetically tractable mammalian microbiota by engineering community-wide horizontal gene transfer events in situ. With this approach, we demonstrate that diverse taxa in the mouse gut microbiome can be modified directly with a desired genetic payload. In situ microbiome engineering in living animals allows novel capabilities to be introduced into established communities in their native milieu.}, }
@article {pmid30643200, year = {2019}, author = {González, JM and Hernández, L and Manzano, I and Pedrós-Alió, C}, title = {Functional annotation of orthologs in metagenomes: a case study of genes for the transformation of oceanic dimethylsulfoniopropionate.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0347-6}, pmid = {30643200}, issn = {1751-7370}, abstract = {Dimethylsulfoniopropionate (DMSP) is produced mainly by phytoplankton and bacteria. It is relatively abundant and ubiquitous in the marine environment, where bacterioplankton make use of it readily as both carbon and sulfur sources. In one transformation pathway, part of the molecule becomes dimethylsulfide (DMS), which escapes into the atmosphere and plays an important role in the sulfur exchange between oceans and atmosphere. Through its other dominant catabolic pathway, bacteria are able to use it as sulfur source. During the past few years, a number of genes involved in its transformation have been characterized. Identifying genes in taxonomic groups not amenable to conventional methods of cultivation is challenging. Indeed, functional annotation of genes in environmental studies is not straightforward, considering that particular taxa are not well represented in the available sequence databases. Furthermore, many genes belong to families of paralogs with similar sequences but perhaps different functions. In this study, we develop in silico approaches to infer protein function of an environmentally important gene (dmdA) that carries out the first step in the sulfur assimilation from DMSP. The method combines a set of tools to annotate a targeted gene in genome databases and metagenome assemblies. The method will be useful to identify genes that carry out key biochemical processes in the environment.}, }
@article {pmid30642389, year = {2019}, author = {Li, F and Hitch, TCA and Chen, Y and Creevey, CJ and Guan, LL}, title = {Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {6}, doi = {10.1186/s40168-019-0618-5}, pmid = {30642389}, issn = {2049-2618}, support = {BB/E/W/10964A01 and BBS/OS/GC/000011B//BBSRC/ ; 2013R029R//Alberta Livestock and Meat Agency/ ; 2015P008R//Alberta Livestock and Meat Agency/ ; Discovery//Natural Sciences and Engineering Research Council of Canada/ ; Doctoral Scholarship//Alberta Innovates - Technology Futures/ ; Scholarship//GPLER/ ; }, abstract = {BACKGROUND: Microorganisms are responsible for fermentation within the rumen and have been reported to contribute to the variation in feed efficiency of cattle. However, to what extent the breed affects the rumen microbiome and its association with host feed efficiency is unknown. Here, rumen microbiomes of beef cattle (n = 48) from three breeds (Angus, Charolais, Kinsella composite hybrid) with high and low feed efficiency were explored using metagenomics and metatranscriptomics, aiming to identify differences between functional potentials and activities of same rumen microbiomes and to evaluate the effects of host breed and feed efficiency on the rumen microbiome.
RESULTS: Rumen metagenomes were more closely clustered together and thus more conserved among individuals than metatranscriptomes, suggesting that inter-individual functional variations at the RNA level were higher than those at the DNA level. However, while mRNA enrichment significantly increased the sequencing depth of mRNA and generated similar functional profiles to total RNA-based metatranscriptomics, it led to biased abundance estimation of several transcripts. We observed divergent rumen microbial composition (metatranscriptomic level) and functional potentials (metagenomic level) among three breeds, but differences in functional activity (metatranscriptomic level) were less apparent. Differential rumen microbial features (e.g., taxa, diversity indices, functional categories, and genes) were detected between cattle with high and low feed efficiency, and most of them were breed-specific.
CONCLUSIONS: Metatranscriptomes represent real-time functional activities of microbiomes and have the potential to better associate rumen microorganisms with host performances compared to metagenomics. As total RNA-based metatranscriptomics seem to avoid potential biases caused by mRNA enrichment and allow simultaneous use of rRNA for generation of compositional profiles, we suggest their use for linking the rumen microbiome with host phenotypes in future studies. However, if exploration of specific lowly expressed genes is desired, mRNA enrichment is recommended as it will enhance the resolution of mRNA. Finally, the differential microbial features observed between efficient and inefficient steers tended to be specific to breeds, suggesting that interactions between host breed genotype and the rumen microbiome contribute to the variations in feed efficiency observed. These breed-associated differences represent an opportunity to engineer specific rumen microbiomes through selective breeding of the hosts.}, }
@article {pmid30642268, year = {2019}, author = {Aiemjoy, K and Altan, E and Aragie, S and Fry, DM and Phan, TG and Deng, X and Chanyalew, M and Tadesse, Z and Callahan, EK and Delwart, E and Keenan, JD}, title = {Viral species richness and composition in young children with loose or watery stool in Ethiopia.}, journal = {BMC infectious diseases}, volume = {19}, number = {1}, pages = {53}, doi = {10.1186/s12879-019-3674-3}, pmid = {30642268}, issn = {1471-2334}, support = {F31 HD088070-01A1//National Institute of Child Health and Human Development/ ; U10 EY016214//National Eye Institute/ ; R01 HL105770//National Heart, Lung, and Blood Institute/ ; }, mesh = {Biodiversity ; Caliciviridae Infections/virology ; Child, Preschool ; Diarrhea/epidemiology/*virology ; Ethiopia/epidemiology ; Feces/*virology ; Female ; Humans ; Infant ; Infant, Newborn ; Male ; Metagenomics ; Norovirus/genetics/isolation & purification ; Picornaviridae/genetics/isolation & purification ; Picornaviridae Infections/virology ; Prevalence ; Viruses/genetics/*isolation & purification ; }, abstract = {BACKGROUND: Stool consistency is an important diagnostic criterion in both research and clinical medicine and is often used to define diarrheal disease.
METHODS: We examine the pediatric enteric virome across stool consistencies to evaluate differences in richness and community composition using fecal samples collected from children aged 0 to 5 years participating in a clinical trial in the Amhara region of Ethiopia. The consistency of each sample was graded according to the modified Bristol Stool Form Scale for children (mBSFS-C) before a portion of stool was preserved for viral metagenomic analysis. Stool samples were grouped into 29 pools according to stool consistency type. Differential abundance was determined using negative-binomial modeling.
RESULTS: Of 446 censused children who were eligible to participate, 317 presented for the study visit examination and 269 provided stool samples. The median age of children with stool samples was 36 months. Species richness was highest in watery-consistency stool and decreased as stool consistency became firmer (Spearman's r = - 0.45, p = 0.013). The greatest differential abundance comparing loose or watery to formed stool was for norovirus GII (7.64, 95% CI 5.8, 9.5) followed by aichivirus A (5.93, 95% CI 4.0, 7.89) and adeno-associated virus 2 (5.81, 95%CI 3.9, 7.7).
CONCLUSIONS: In conclusion, we documented a difference in pediatric enteric viromes according to mBSFS-C stool consistency category, both in species richness and composition.}, }
@article {pmid30640944, year = {2019}, author = {Hjelmsø, MH and Mollerup, S and Jensen, RH and Pietroni, C and Lukjancenko, O and Schultz, AC and Aarestrup, FM and Hansen, AJ}, title = {Metagenomic analysis of viruses in toilet waste from long distance flights-A new procedure for global infectious disease surveillance.}, journal = {PloS one}, volume = {14}, number = {1}, pages = {e0210368}, doi = {10.1371/journal.pone.0210368}, pmid = {30640944}, issn = {1932-6203}, abstract = {Human viral pathogens are a major public health threat. Reliable information that accurately describes and characterizes the global occurrence and transmission of human viruses is essential to support national and global priority setting, public health actions, and treatment decisions. However, large areas of the globe are currently without surveillance due to limited health care infrastructure and lack of international cooperation. We propose a novel surveillance strategy, using metagenomic analysis of toilet material from international air flights as a method for worldwide viral disease surveillance. The aim of this study was to design, implement, and evaluate a method for viral analysis of airplane toilet waste enabling simultaneous detection and quantification of a wide range of human viral pathogens. Toilet waste from 19 international airplanes was analyzed for viral content, using viral capture probes followed by high-throughput sequencing. Numerous human pathogens were detected including enteric and respiratory viruses. Several geographic trends were observed with samples originating from South Asia having significantly higher viral species richness as well as higher abundances of salivirus A, aichivirus A and enterovirus B, compared to samples originating from North Asia and North America. In addition, certain city specific trends were observed, including high numbers of rotaviruses in airplanes departing from Islamabad. Based on this study we believe that central sampling and analysis at international airports could be a useful supplement for global viral surveillance, valuable for outbreak detection and for guiding public health resources.}, }
@article {pmid30640905, year = {2019}, author = {Ravi, A and Ereqat, S and Al-Jawabreh, A and Abdeen, Z and Abu Shamma, O and Hall, H and Pallen, MJ and Nasereddin, A}, title = {Metagenomic profiling of ticks: Identification of novel rickettsial genomes and detection of tick-borne canine parvovirus.}, journal = {PLoS neglected tropical diseases}, volume = {13}, number = {1}, pages = {e0006805}, doi = {10.1371/journal.pntd.0006805}, pmid = {30640905}, issn = {1935-2735}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Anaplasma ovis/genetics/isolation & purification ; Animals ; Camelus ; Coxiella/classification/genetics/isolation & purification ; DNA, Bacterial/genetics ; Dogs ; Francisella/classification/genetics/isolation & purification ; Genome, Bacterial/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Insect Vectors/genetics/microbiology/virology ; Israel/epidemiology ; Ixodes/*microbiology/*virology ; Parvovirus, Canine/genetics/*isolation & purification ; RNA, Ribosomal, 16S/genetics ; Rickettsia/classification/genetics/*isolation & purification ; Sheep ; Tick-Borne Diseases/epidemiology ; }, abstract = {BACKGROUND: Across the world, ticks act as vectors of human and animal pathogens. Ticks rely on bacterial endosymbionts, which often share close and complex evolutionary links with tick-borne pathogens. As the prevalence, diversity and virulence potential of tick-borne agents remain poorly understood, there is a pressing need for microbial surveillance of ticks as potential disease vectors.
We developed a two-stage protocol that includes 16S-amplicon screening of pooled samples of hard ticks collected from dogs, sheep and camels in Palestine, followed by shotgun metagenomics on individual ticks to detect and characterise tick-borne pathogens and endosymbionts. Two ticks isolated from sheep yielded an abundance of reads from the genus Rickettsia, which were assembled into draft genomes. One of the resulting genomes was highly similar to Rickettsia massiliae strain MTU5. Analysis of signature genes showed that the other represents the first genome sequence of the potential pathogen Candidatus Rickettsia barbariae. Ticks from a dog and a sheep yielded draft genome sequences of Coxiella strains. A sheep tick yielded sequences from the sheep pathogen Anaplasma ovis, while Hyalomma ticks from camels yielded sequences belonging to Francisella-like endosymbionts. From the metagenome of a dog tick from Jericho, we generated a genome sequence of a canine parvovirus.
SIGNIFICANCE: Here, we have shown how a cost-effective two-stage protocol can be used to detect and characterise tick-borne pathogens and endosymbionts. In recovering genome sequences from an unexpected pathogen (canine parvovirus) and a previously unsequenced pathogen (Candidatus Rickettsia barbariae), we demonstrate the open-ended nature of metagenomics. We also provide evidence that ticks can carry canine parvovirus, raising the possibility that ticks might contribute to the spread of this troublesome virus.}, }
@article {pmid30640566, year = {2019}, author = {Dubourg, G and Raoult, D and Fenollar, F}, title = {Emerging methodologies for pathogen identification in bloodstream infections: an update.}, journal = {Expert review of molecular diagnostics}, volume = {19}, number = {2}, pages = {161-173}, doi = {10.1080/14737159.2019.1568241}, pmid = {30640566}, issn = {1744-8352}, abstract = {INTRODUCTION: Bloodstream infections (BSIs) remain a major public health burden worldwide, particularly in high-income countries as they are associated with a significant mortality rate. As early administration of appropriate antimicrobial therapy is a major prognostic factor, there remain unmet needs for shortening BSI diagnosis. Current blood cultures (BC) processing to identify pathogens involved in BSI is not compatible with such delays, although it remains the gold standard. Areas covered: Herein, we review and discuss emerging or ongoing assessed methodologies dedicated to shorten the identification of microorganisms involved in BSI and published since 2015. A particular focus on the economical and clinical impact of these approaches is provided when hindsight is sufficient. Methods to shorten antibiotic susceptibility testing are also reviewed. Expert commentary: Post-culture approaches have encountered a huge success as they are reliable, fast and easy to implement in the laboratory. In particular, the MALDI-TOF MS was shown to be a cost-effective method when combined with antimicrobial stewardship policies. However, further research is needed to optimize methods performed on whole blood in particular next-generation sequencing methods, as they represent an opportunity to substantially improve management of high-risk patients.}, }
@article {pmid30639767, year = {2019}, author = {Davis, WJ and Amses, KR and Benny, GL and Carter-House, D and Chang, Y and Grigoriev, I and Smith, ME and Spatafora, JW and Stajich, JE and James, TY}, title = {Genome-scale phylogenetics reveals a monophyletic Zoopagales (Zoopagomycota, Fungi).}, journal = {Molecular phylogenetics and evolution}, volume = {133}, number = {}, pages = {152-163}, doi = {10.1016/j.ympev.2019.01.006}, pmid = {30639767}, issn = {1095-9513}, abstract = {Previous genome-scale phylogenetic analyses of Fungi have under sampled taxa from Zoopagales; this order contains many predacious or parasitic genera, and most have never been grown in pure culture. We sequenced the genomes of 4 zoopagalean taxa that are predators of amoebae, nematodes, or rotifers and the genome of one taxon that is a parasite of amoebae using single cell sequencing methods with whole genome amplification. Each genome was a metagenome, which was assembled and binned using multiple techniques to identify the target genomes. We inferred phylogenies with both super matrix and coalescent approaches using 192 conserved proteins mined from the target genomes and performed ancestral state reconstructions to determine the ancestral trophic lifestyle of the clade. Our results indicate that Zoopagales is monophyletic. Ancestral state reconstructions provide moderate support for mycoparasitism being the ancestral state of the clade.}, }
@article {pmid30637962, year = {2019}, author = {Asante, J and Osei Sekyere, J}, title = {Understanding antimicrobial discovery and resistance from a metagenomic and metatranscriptomic perspective: advances and applications.}, journal = {Environmental microbiology reports}, volume = {}, number = {}, pages = {}, doi = {10.1111/1758-2229.12735}, pmid = {30637962}, issn = {1758-2229}, abstract = {Our inability to cultivate most microorganisms, specifically bacteria, in the laboratory has for many years restricted our view and understanding of the bacterial meta-resistome in all living and nonliving environments. As a result, reservoirs, sources and distribution of antibiotic resistance genes (ARGS) and antibiotic-producers, as well as the effects of human activity and antibiotics on the selection and dissemination of ARGs were not well comprehended. With the advances made in the fields of metagenomics and metatranscriptomics, many of the hitherto little-understood concepts are becoming clearer. Further, the discovery of antibiotics such as lugdinin and lactocillin from the human microbiota, buttressed the importance of these new fields. Metagenomics and metatranscriptomics are becoming important clinical diagnostic tools for screening and detecting pathogens and ARGs, assessing the effects of antibiotics, other xenobiotics and human activity on the environment, characterizing the microbiome and the environmental resistome with lesser turnaround time and decreasing cost, as well as discovering antibiotic-producers. However, challenges with accurate binning, skewed ARGs databases, detection of less abundant and allelic variants of ARGs and efficient mobilome characterization remain. Ongoing efforts in long-read, phased- and single-cell sequencing, strain-resolved binning, chromosomal-conformation capture, DNA-methylation binning and deep-learning bioinformatic approaches offer promising prospects in reconstructing complete strain-level genomes and mobilomes from metagenomes.}, }
@article {pmid30637337, year = {2018}, author = {Bayer, K and Jahn, MT and Slaby, BM and Moitinho-Silva, L and Hentschel, U}, title = {Marine Sponges as Chloroflexi Hot Spots: Genomic Insights and High-Resolution Visualization of an Abundant and Diverse Symbiotic Clade.}, journal = {mSystems}, volume = {3}, number = {6}, pages = {}, doi = {10.1128/mSystems.00150-18}, pmid = {30637337}, issn = {2379-5077}, abstract = {Members of the widespread bacterial phylum Chloroflexi can dominate high-microbial-abundance (HMA) sponge microbiomes. In the Sponge Microbiome Project, Chloroflexi sequences amounted to 20 to 30% of the total microbiome of certain HMA sponge genera with the classes/clades SAR202, Caldilineae, and Anaerolineae being the most prominent. We performed metagenomic and single-cell genomic analyses to elucidate the functional gene repertoire of Chloroflexi symbionts of Aplysina aerophoba. Eighteen draft genomes were reconstructed and placed into phylogenetic context of which six were investigated in detail. Common genomic features of Chloroflexi sponge symbionts were related to central energy and carbon converting pathways, amino acid and fatty acid metabolism, and respiration. Clade-specific metabolic features included a massively expanded genomic repertoire for carbohydrate degradation in Anaerolineae and Caldilineae genomes, but only amino acid utilization by SAR202. While Anaerolineae and Caldilineae import cofactors and vitamins, SAR202 genomes harbor genes encoding components involved in cofactor biosynthesis. A number of features relevant to symbiosis were further identified, including CRISPR-Cas systems, eukaryote-like repeat proteins, and secondary metabolite gene clusters. Chloroflexi symbionts were visualized in the sponge extracellular matrix at ultrastructural resolution by the fluorescence in situ hybridization-correlative light and electron microscopy (FISH-CLEM) method. Carbohydrate degradation potential was reported previously for "Candidatus Poribacteria" and SAUL, typical symbionts of HMA sponges, and we propose here that HMA sponge symbionts collectively engage in degradation of dissolved organic matter, both labile and recalcitrant. Thus, sponge microbes may not only provide nutrients to the sponge host, but they may also contribute to dissolved organic matter (DOM) recycling and primary productivity in reef ecosystems via a pathway termed the sponge loop. IMPORTANCEChloroflexi represent a widespread, yet enigmatic bacterial phylum with few cultivated members. We used metagenomic and single-cell genomic approaches to characterize the functional gene repertoire of Chloroflexi symbionts in marine sponges. The results of this study suggest clade-specific metabolic specialization and that Chloroflexi symbionts have the genomic potential for dissolved organic matter (DOM) degradation from seawater. Considering the abundance and dominance of sponges in many benthic environments, we predict that the role of sponge symbionts in biogeochemical cycles is larger than previously thought.}, }
@article {pmid30636420, year = {2019}, author = {Gunasekera, SP and Meyer, JL and Ding, Y and Abboud, KA and Luo, D and Campbell, JE and Angerhofer, A and Goodsell, JL and Raymundo, LJ and Liu, J and Ye, T and Luesch, H and Teplitski, M and Paul, VJ}, title = {Chemical and Metagenomic Studies of the Lethal Black Band Disease of Corals Reveal Two Broadly Distributed, Redox-Sensitive Mixed Polyketide/Peptide Macrocycles.}, journal = {Journal of natural products}, volume = {82}, number = {1}, pages = {111-121}, doi = {10.1021/acs.jnatprod.8b00804}, pmid = {30636420}, issn = {1520-6025}, support = {R01 CA172310/CA/NCI NIH HHS/United States ; R35 GM128742/GM/NIGMS NIH HHS/United States ; }, abstract = {Black band disease (BBD), a lethal, polymicrobial disease consortium dominated by the cyanobacterium Roseofilum reptotaenium, kills many species of corals worldwide. To uncover chemical signals or cytotoxins that could be important in proliferation of Roseofilum and the BBD layer, we examined the secondary metabolites present in geographically diverse collections of BBD from Caribbean and Pacific coral reefs. Looekeyolide A (1), a 20-membered macrocyclic compound formed by a 16-carbon polyketide chain, 2-deamino-2-hydroxymethionine, and d-leucine, and its autoxidation product looekeyolide B (2) were extracted as major compounds (∼1 mg g-1 dry wt) from more than a dozen field-collected BBD samples. Looekeyolides A and B were also produced by a nonaxenic R. reptotaenium culture under laboratory conditions at similar concentrations. R. reptotaenium genomes that were constructed from four different metagenomic data sets contained a unique nonribosomal peptide/polyketide biosynthetic cluster that is likely responsible for the biosynthesis of the looekeyolides. Looekeyolide A, which readily oxidizes to looekeyolide B, may play a biological role in reducing H2O2 and other reactive oxygen species that could occur in the BBD layer as it overgrows and destroys coral tissue.}, }
@article {pmid30635385, year = {2019}, author = {Fredriksen, L and Stokke, R and Jensen, MS and Westereng, B and Jameson, JK and Steen, IH and Eijsink, VGH}, title = {Discovery of a thermostable GH10 xylanase with broad substrate specificity from the Arctic Mid-Ocean Ridge vent system.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02970-18}, pmid = {30635385}, issn = {1098-5336}, abstract = {A two-domain GH10 xylanase encoding gene (amor_gh10a) was discovered from a metagenomic dataset, generated after in situ incubation of a lignocellulosic substrate in hot sediments on the sea floor of the Arctic Mid-Ocean Ridge (AMOR). AMOR_GH10A comprises a signal peptide, a carbohydrate-binding module belonging to a previously uncharacterized family, and a catalytic glycosyl hydrolase (GH10) domain. The enzyme shares the highest sequence identity (42%) with a hypothetical protein from Verrucomicrobia bacterium, and its GH10 domain shares low identity (24-28%) with functionally characterized xylanases. Purified AMOR_GH10A showed thermophilic and halophilic properties and was active towards various xylans. Uniquely, the enzyme showed high activity towards amorphous cellulose, glucomannan, and xyloglucan and was more active towards cellopentaose than towards xylopentaose. Binding assays showed that the N-terminal domain of this broad-specificity GH10 binds strongly to amorphous cellulose, as well as to microcrystalline cellulose, birchwood glucuronoxylan, barley β-glucan and konjac glucomannan, confirming its classification as a novel CBM (CBM85).ImportanceHot springs at the sea bottom harbor unique biodiversity and are a promising source of enzymes with interesting properties. We describe the functional characterization of a thermophilic and halophilic multi-domain xylanase originating from the Arctic Mid-Ocean Ridge vent system, belonging to the well-studied family 10 of glycosyl hydrolases (GH10). This xylanase, AMOR_GH10A, has a surprisingly wide substrate range and is more active towards cellopentaose compared to xylopentaose. This substrate promiscuity is unique for the GH10 family and could prove useful in industrial applications. Emphasizing the versatility of AMOR_GH10A, its N-terminal domain binds to both xylans and glycans, while not showing significant sequence similarities to any known carbohydrate-binding module (CBM) in the CAZy database. Thus, this N-terminal domain lays the foundation for the new CBM85 family.}, }
@article {pmid30635078, year = {2019}, author = {Zhao, L and Rosario, K and Breitbart, M and Duffy, S}, title = {Eukaryotic Circular Rep-Encoding Single-Stranded DNA (CRESS DNA) Viruses: Ubiquitous Viruses With Small Genomes and a Diverse Host Range.}, journal = {Advances in virus research}, volume = {103}, number = {}, pages = {71-133}, doi = {10.1016/bs.aivir.2018.10.001}, pmid = {30635078}, issn = {1557-8399}, abstract = {While single-stranded DNA (ssDNA) was once thought to be a relatively rare genomic architecture for viruses, modern metagenomics sequencing has revealed circular ssDNA viruses in most environments and in association with diverse hosts. In particular, circular ssDNA viruses encoding a homologous replication-associated protein (Rep) have been identified in the majority of eukaryotic supergroups, generating interest in the ecological effects and evolutionary history of circular Rep-encoding ssDNA viruses (CRESS DNA) viruses. This review surveys the explosion of sequence diversity and expansion of eukaryotic CRESS DNA taxonomic groups over the last decade, highlights similarities between the well-studied geminiviruses and circoviruses with newly identified groups known only through their genome sequences, discusses the ecology and evolution of eukaryotic CRESS DNA viruses, and speculates on future research horizons.}, }
@article {pmid30635058, year = {2019}, author = {Simon, JC and Marchesi, JR and Mougel, C and Selosse, MA}, title = {Host-microbiota interactions: from holobiont theory to analysis.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {5}, doi = {10.1186/s40168-019-0619-4}, pmid = {30635058}, issn = {2049-2618}, abstract = {In the recent years, the holobiont concept has emerged as a theoretical and experimental framework to study the interactions between hosts and their associated microbial communities in all types of ecosystems. The spread of this concept in many branches of biology results from the fairly recent realization of the ubiquitous nature of host-associated microbes and their central role in host biology, ecology, and evolution. Through this special series "Host-microbiota interactions: from holobiont theory to analysis," we wanted to promote this field of research which has considerable implications for human health, food production, and ecosystem protection. In this preface, we highlight a collection of articles selected for this special issue that show, use, or debate the concept of holobiont to approach taxonomically and ecologically diverse organisms, from humans and plants to sponges and insects. We also identify some theoretical and methodological challenges and propose directions for future research on holobionts.}, }
@article {pmid30635018, year = {2019}, author = {Akorli, J and Namaali, PA and Ametsi, GW and Egyirifa, RK and Pels, NAP}, title = {Generational conservation of composition and diversity of field-acquired midgut microbiota in Anopheles gambiae (sensu lato) during colonization in the laboratory.}, journal = {Parasites & vectors}, volume = {12}, number = {1}, pages = {27}, doi = {10.1186/s13071-019-3287-0}, pmid = {30635018}, issn = {1756-3305}, support = {DEL-15-007: Awandare//DELTAS Africa/ ; }, mesh = {Animals ; Anopheles/*microbiology ; Bacteria/*classification/genetics ; Gastrointestinal Microbiome/*genetics ; Genetic Variation ; Larva ; Pupa ; }, abstract = {BACKGROUND: The gut microbiota is known to play a role in a mosquito vector's life history, a subject of increasing research. Laboratory experiments are essential for such studies and require laboratory colonies. In this study, the conservation of field-obtained midgut microbiota was evaluated in laboratory-reared Anopheles gambiae (s.l.) mosquitoes continuously hatched in water from field breeding habitats.
METHODS: Pupae and late instars were obtained from the field and reared, and the emerged adults were blood-fed. The eggs obtained from them were hatched in either water from the field or in dechlorinated tap water. The mosquito colonies were maintained for 10 generations. Midguts of female adults from unfed F0 (emerging from field-caught pupae and larvae), F5 and F10 were dissected out and genomic DNA was extracted for 16S metagenomic sequencing. The sequences were compared to investigate the diversity and bacterial compositional differences using ANCOM and correlation clustering methods.
RESULTS: Less than 10% of the bacterial families identified had differential relative abundances between generational groups and accounted for 46% of the variation observed. Although diversity reduced in F10 mosquitoes during laboratory colonization (Shannon-Weaver; P-value < 0.05), 50% of bacterial genera were conserved in those bred continuously in field-water compared to 38% in those bred in dechlorinated tap water.
CONCLUSIONS: To our knowledge, this study is the first report on the assessment of gut bacterial community of mosquitoes during laboratory colonization and recommends the use of water from the natural breeding habitats if they are intended for microbiota research.}, }
@article {pmid30635006, year = {2019}, author = {Brinkmann, A and Hekimoğlu, O and Dinçer, E and Hagedorn, P and Nitsche, A and Ergünay, K}, title = {A cross-sectional screening by next-generation sequencing reveals Rickettsia, Coxiella, Francisella, Borrelia, Babesia, Theileria and Hemolivia species in ticks from Anatolia.}, journal = {Parasites & vectors}, volume = {12}, number = {1}, pages = {26}, doi = {10.1186/s13071-018-3277-7}, pmid = {30635006}, issn = {1756-3305}, support = {not applicable//Alexander von Humboldt-Stiftung (DE)/ ; }, mesh = {Animals ; Arthropod Vectors/microbiology ; Arthropods ; Babesia/genetics/isolation & purification ; Bacteria/*isolation & purification ; Borrelia/genetics/isolation & purification ; Coxiella/genetics/isolation & purification ; Cross-Sectional Studies ; Francisella/genetics/isolation & purification ; Humans ; Nucleic Acid Amplification Techniques/*methods ; Rickettsia/genetics/isolation & purification ; Species Specificity ; Theileria/genetics/isolation & purification ; Ticks/*microbiology ; Turkey ; }, abstract = {BACKGROUND: Ticks participate as arthropod vectors in the transmission of pathogenic microorganisms to humans. Several tick-borne infections have reemerged, along with newly described agents of unexplored pathogenicity. In an attempt to expand current information on tick-associated bacteria and protozoans, we performed a cross-sectional screening of ticks, using next-generation sequencing. Ticks seeking hosts and infesting domestic animals were collected in four provinces across the Aegean, Mediterranean and Central Anatolia regions of Turkey and analyzed by commonly used procedures and platforms.
RESULTS: Two hundred and eighty ticks comprising 10 species were evaluated in 40 pools. Contigs from tick-associated microorganisms were detected in 22 (55%) questing and 4 feeding (10%) tick pools, with multiple microorganisms identified in 12 pools. Rickettsia 16S ribosomal RNA gene, gltA, sca1 and ompA sequences were present in 7 pools (17.5%), comprising feeding Haemaphysalis parva and questing/hunting Rhipicephalus bursa, Rhipicephalus sanguineus (sensu lato) and Hyalomma marginatum specimens. A near-complete genome and conjugative plasmid of a Rickettsia hoogstraalii strain could be characterized in questing Ha. parva. Coxiella-like endosymbionts were identified in pools of questing (12/40) as well as feeding (4/40) ticks of the genera Rhipicephalus, Haemaphysalis and Hyalomma. Francisella-like endosymbionts were also detected in 22.5% (9/40) of the pools that comprise hunting Hyalomma ticks in 8 pools. Coxiella-like and Francisella-like endosymbionts formed phylogenetically distinct clusters associated with their tick hosts. Borrelia turcica was characterized in 5% (2/40) of the pools, comprising hunting Hyalomma aegyptium ticks. Co-infection of Coxiella-like endosymbiont and Babesia was noted in a questing R. sanguineus (s.l.) specimen. Furthermore, protozoan 18S rRNA gene sequences were detected in 4 pools of questing/hunting ticks (10%) and identified as Babesia ovis, Hemolivia mauritanica, Babesia and Theileria spp.
CONCLUSIONS: Our metagenomic approach enabled identification of diverse pathogenic and non-pathogenic microorganisms in questing and feeding ticks in Anatolia.}, }
@article {pmid30632960, year = {2019}, author = {Tangudu, CS and Charles, J and Hurt, SL and Dunphy, BM and Smith, RC and Bartholomay, LC and Blitvich, BJ}, title = {Skunk River virus, a novel orbivirus isolated from Aedes trivittatus in the United States.}, journal = {The Journal of general virology}, volume = {100}, number = {2}, pages = {295-300}, doi = {10.1099/jgv.0.001219}, pmid = {30632960}, issn = {1465-2099}, abstract = {The genomic organization and in vitro host range of a novel mosquito-associated orbivirus, designated Skunk River virus, is described. The virus was isolated from Aedes trivittatus collected in Iowa in the United States. Three recognized viruses were also recovered: Culex flavivirus (family Flaviviridae), Houston virus (family Mesoniviridae) and Umatilla virus (family Reoviridae). The genome of Skunk River virus contains 10 segments and its organization is characteristic of viruses in the genus Orbivirus (family Reoviridae). The coding region of each segment was fully sequenced, revealing that the greatest nucleotide identity was to the corresponding regions of Big Cypress orbivirus and Sathuvachari virus, two recently described mosquito-associated orbiviruses. The phylogenetic inference is in agreement with these findings. In vitro host range experiments revealed that Aedes, Anopheles and Culex cell lines, and select lepidopteran and rodent cell lines, are permissive to Skunk River virus replication. In conclusion, we provide evidence of a novel mosquito-associated orbivirus in Iowa.}, }
@article {pmid30632609, year = {2019}, author = {Hamada, T and Nowak, JA and Milner, DA and Song, M and Ogino, S}, title = {Integration of microbiology, molecular pathology, and epidemiology: a new paradigm to explore the pathogenesis of microbiome-driven neoplasms.}, journal = {The Journal of pathology}, volume = {}, number = {}, pages = {}, doi = {10.1002/path.5236}, pmid = {30632609}, issn = {1096-9896}, support = {K99 CA215314//US National Institutes of Health (NIH)/ ; R00 CA215314//US National Institutes of Health (NIH)/ ; R35 CA197735//US National Institutes of Health (NIH)/ ; MRSG-17-220-01-NEC//The American Cancer Society/ ; 2016-02//The Dana-Farber Harvard Cancer Center (Nodal Award)/ ; //The Friends of the Dana-Farber Cancer Institute/ ; }, abstract = {Molecular pathological epidemiology (MPE) is an integrative transdisciplinary field that addresses heterogeneous effects of exogenous and endogenous factors (collectively termed 'exposures'), including microorganisms, on disease occurrence and consequences, utilising molecular pathological signatures of the disease. In parallel with the paradigm of precision medicine, findings from MPE research can provide aetiological insights into tailored strategies of disease prevention and treatment. Due to the availability of molecular pathological tests on tumours, the MPE approach has been utilised predominantly in research on cancers including breast, lung, prostate, and colorectal carcinomas. Mounting evidence indicates that the microbiome (inclusive of viruses, bacteria, fungi, and parasites) plays an important role in a variety of human diseases including neoplasms. An alteration of the microbiome may be not only a cause of neoplasia but also an informative biomarker that indicates or mediates the association of an epidemiological exposure with health conditions and outcomes. To adequately educate and train investigators in this emerging area, we herein propose the integration of microbiology into the MPE model (termed 'microbiology-MPE'), which could improve our understanding of the complex interactions of environment, tumour cells, the immune system, and microbes in the tumour microenvironment during the carcinogenic process. Using this approach, we can examine how lifestyle factors, dietary patterns, medications, environmental exposures, and germline genetics influence cancer development and progression through impacting the microbial communities in the human body. Further integration of other disciplines (e.g. pharmacology, immunology, nutrition) into microbiology-MPE would expand this developing research frontier. With the advent of high-throughput next-generation sequencing technologies, researchers now have increasing access to large-scale metagenomics as well as other omics data (e.g. genomics, epigenomics, proteomics, and metabolomics) in population-based research. The integrative field of microbiology-MPE will open new opportunities for personalised medicine and public health. Copyright © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.}, }
@article {pmid30632017, year = {2019}, author = {Altan, E and Seguin, MA and Leutenegger, CM and Phan, TG and Deng, X and Delwart, E}, title = {Nasal virome of dogs with respiratory infection signs include novel taupapillomaviruses.}, journal = {Virus genes}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11262-019-01634-6}, pmid = {30632017}, issn = {1572-994X}, support = {5149.14//Blood Systems Research Institute/ ; }, abstract = {Using viral metagenomics, we characterized the mammalian virome of nasal swabs from 57 dogs with unexplained signs of respiratory infection showing mostly negative results using the IDEXX Canine Respiratory Disease RealPCR™ Panel. We identified canine parainfluenza virus 5, canine respiratory coronavirus, carnivore bocaparvovirus 3, canine circovirus and canine papillomavirus 9. Novel canine taupapillomaviruses (CPV21-23) were also identified in 3 dogs and their complete genome sequenced showing L1 nucleotide identity ranging from 68.4 to 70.3% to their closest taupapillomavirus relative. Taupapillomavirus were the only mammalian viral nucleic acids detected in two affected dogs, while a third dog was coinfected with low levels of canine parainfluenza 5. A role for these taupapillomavirues in canine respiratory disease remains to be determined.}, }
@article {pmid30631958, year = {2019}, author = {Haddad-Boubaker, S and Joffret, ML and Pérot, P and Bessaud, M and Meddeb, Z and Touzi, H and Delpeyroux, F and Triki, H and Eloit, M}, title = {Metagenomic analysis identifies human adenovirus 31 in children with acute flaccid paralysis in Tunisia.}, journal = {Archives of virology}, volume = {164}, number = {3}, pages = {747-755}, doi = {10.1007/s00705-018-04141-5}, pmid = {30631958}, issn = {1432-8798}, support = {ANR-10-LABX-62-IBEID//Instituto Nacional de Biotecnologia Estrutural e Química Medicinal em Doenças Infecciosas (BR)/ ; S-CM15010-05B//Fondation Total/ ; }, mesh = {Adenovirus Infections, Human/*virology ; Adenoviruses, Human/classification/*genetics/*isolation & purification ; Adolescent ; Child ; Child, Preschool ; Feces/virology ; Genotype ; Humans ; Infant ; Metagenomics ; Paraplegia/*virology ; Phylogeny ; Tunisia ; }, abstract = {A variety of viruses can cause acute flaccid paralysis (AFP). However, the causative agent, sometimes, remains undetermined. Metagenomics helps in identifying viruses not diagnosed by conventional methods. Stool samples from AFP (n = 104) and non-AFP (n = 114) cases that tested enterovirus-negative by WHO standard methods were investigated. A metagenomics approach, first used on five pools of four samples each, revealed the presence of adenovirus sequences. Amplification in A549 cells and full-genome sequencing were used for complete virus identification and for designing a PCR assay to screen individual related samples. Metagenomic analysis showed that adenovirus sequences that were closely to the A31 and A61 genotypes were the most abundant. Two out of the corresponding 20 individual samples were found positive by PCR, and isolates were obtained in cell culture. Phylogenetic analysis based on complete genome sequences showed that the viruses belong to HAdV-A31 genotype (98-100% nucleotide sequence identity). PCR analysis of stool samples from all AFP and non-AFP cases revealed that a larger proportion of the positive samples were from AFP cases (17.3%) than from non-AFP cases (2.4%). These results open the way to studies aiming to test a possible role of HAdV-A31 in the pathogenesis of AFP.}, }
@article {pmid30631769, year = {2018}, author = {Klaumann, F and Correa-Fiz, F and Franzo, G and Sibila, M and Núñez, JI and Segalés, J}, title = {Current Knowledge on Porcine circovirus 3 (PCV-3): A Novel Virus With a Yet Unknown Impact on the Swine Industry.}, journal = {Frontiers in veterinary science}, volume = {5}, number = {}, pages = {315}, doi = {10.3389/fvets.2018.00315}, pmid = {30631769}, issn = {2297-1769}, abstract = {Porcine circovirus 3 (PCV-3) is a recently described virus belonging to the family Circoviridae. It represents the third member of genus Circovirus able to infect swine, together with PCV-1, considered non-pathogenic, and PCV-2, one of the most economically relevant viruses for the swine worldwide industry. PCV-3 was originally found by metagenomics analyses in 2015 in tissues of pigs suffering from porcine dermatitis and nephropathy syndrome, reproductive failure, myocarditis and multisystemic inflammation. The lack of other common pathogens as potential infectious agents of these conditions prompted the suspicion that PCV-3 might etiologically be involved in disease occurrence. Subsequently, viral genome was detected in apparently healthy pigs, and retrospective studies indicated that PCV-3 was already present in pigs by early 1990s. In fact, current evidence suggests that PCV-3 is a rather widespread virus worldwide. Recently, the virus DNA has also been found in wild boar, expanding the scope of infection susceptibility among the Suidae family; also, the potential reservoir role of this species for the domestic pig has been proposed. Phylogenetic studies with available PCV-3 partial and complete sequences from around the world have revealed high nucleotide identity (>96%), although two main groups and several subclusters have been described as well. Moreover, it has been proposed the existence of a most common ancestor dated around 50 years ago. Taking into account the economic importance and the well-known effects of PCV-2 on the swine industry, a new member of the same family like PCV-3 should not be neglected. Studies on epidemiology, pathogenesis, immunity and diagnosis are guaranteed in the next few years. Therefore, the present review will update the current knowledge and future trends of research on PCV-3.}, }
@article {pmid30631651, year = {2019}, author = {Gardner, PP and Watson, RJ and Morgan, XC and Draper, JL and Finn, RD and Morales, SE and Stott, MB}, title = {Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6160}, doi = {10.7717/peerj.6160}, pmid = {30631651}, issn = {2167-8359}, abstract = {Metagenomic and meta-barcode DNA sequencing has rapidly become a widely-used technique for investigating a range of questions, particularly related to health and environmental monitoring. There has also been a proliferation of bioinformatic tools for analysing metagenomic and amplicon datasets, which makes selecting adequate tools a significant challenge. A number of benchmark studies have been undertaken; however, these can present conflicting results. In order to address this issue we have applied a robust Z-score ranking procedure and a network meta-analysis method to identify software tools that are consistently accurate for mapping DNA sequences to taxonomic hierarchies. Based upon these results we have identified some tools and computational strategies that produce robust predictions.}, }
@article {pmid30631318, year = {2018}, author = {Shao, L and Ling, Z and Chen, D and Liu, Y and Yang, F and Li, L}, title = {Disorganized Gut Microbiome Contributed to Liver Cirrhosis Progression: A Meta-Omics-Based Study.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3166}, doi = {10.3389/fmicb.2018.03166}, pmid = {30631318}, issn = {1664-302X}, abstract = {Early detection and effective interventions for liver cirrhosis (LC) remain an urgent unmet clinical need. Inspired from intestinal disorders in LC patients, we investigated the associations between gut microbiome and disease progression based on a raw metagenomic dataset of 47 healthy controls, 49 compensated, and 46 decompensated LC patients from our previous study, and a metabolomic dataset of urine samples from the same controls/patients using ultra-performance liquid chromatography/mass spectrophotometry system. It was found that the combination and relative abundance of gut microbiome, the inter-microbiome regulatory networks, and the microbiome-host correlation patterns varied during disease progression. The significant reduction of bacteria involved in fermentation of plant cell wall polysaccharides and resistant starch (such as Alistipes sp. HG5, Clostridium thermocellum) contributed to the reduced supply of energy sources, the disorganized self-feeding and cross-feeding networks and the thriving of some opportunistic pathogens in genus Veillonella. The marked decrease of butyrate-producing bacteria and increase of Ruminococcus gnavus implicated in degradation of elements from the mucus layer provided an explanation for the impaired intestinal barrier function and systematic inflammation in LC patients. Our results pave the way for further developments in early detection and intervention of LC targeting on gut microbiome.}, }
@article {pmid30631102, year = {2019}, author = {Weiland-Bräuer, N and Fischer, MA and Pinnow, N and Schmitz, RA}, title = {Potential role of host-derived quorum quenching in modulating bacterial colonization in the moon jellyfish Aurelia aurita.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {34}, doi = {10.1038/s41598-018-37321-z}, pmid = {30631102}, issn = {2045-2322}, abstract = {Multicellular organisms can be regarded as metaorganisms, comprising of a macroscopic host interacting with associated microorganisms. Within this alliance, the host has to ensure attracting beneficial bacteria and defending against pathogens to establish and maintain a healthy homeostasis. Here, we obtained several lines of evidence arguing that Aurelia aurita uses interference with bacterial quorum sensing (QS) - quorum quenching (QQ) - as one host defense mechanism. Three A. aurita-derived proteins interfering with bacterial QS were identified by functionally screening a metagenomic library constructed from medusa-derived mucus. Native expression patterns of these host open reading frames (ORFs) differed in the diverse life stages (associated with different microbiota) pointing to a specific role in establishing the developmental stage-specific microbiota. Highly increased expression of all QQ-ORFs in germ-free animals further indicates their impact on the microbiota. Moreover, incubation of native animals with pathogenic bacteria induced expression of the identified QQ-ORFs arguing for a host defense strategy against confronting bacteria by interference with bacterial QS. In agreement, immobilized recombinant QQ proteins induced restructuring of polyp-associated microbiota through changing abundance and operational taxonomic unit composition. Thus, we hypothesize that additional to the immune system host-derived QQ-activities potentially control bacterial colonization.}, }
@article {pmid30630933, year = {2019}, author = {Jiang, X and Hall, AB and Arthur, TD and Plichta, DR and Covington, CT and Poyet, M and Crothers, J and Moses, PL and Tolonen, AC and Vlamakis, H and Alm, EJ and Xavier, RJ}, title = {Invertible promoters mediate bacterial phase variation, antibiotic resistance, and host adaptation in the gut.}, journal = {Science (New York, N.Y.)}, volume = {363}, number = {6423}, pages = {181-187}, doi = {10.1126/science.aau5238}, pmid = {30630933}, issn = {1095-9203}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 AT009708/AT/NCCIH NIH HHS/United States ; }, abstract = {Phase variation, the reversible alternation between genetic states, enables infection by pathogens and colonization by commensals. However, the diversity of phase variation remains underexplored. We developed the PhaseFinder algorithm to quantify DNA inversion-mediated phase variation. A systematic search of 54,875 bacterial genomes identified 4686 intergenic invertible DNA regions (invertons), revealing an enrichment in host-associated bacteria. Invertons containing promoters often regulate extracellular products, underscoring the importance of surface diversity for gut colonization. We found invertons containing promoters regulating antibiotic resistance genes that shift to the ON orientation after antibiotic treatment in human metagenomic data and in vitro, thereby mitigating the cost of antibiotic resistance. We observed that the orientations of some invertons diverge after fecal microbiota transplant, potentially as a result of individual-specific selective forces.}, }
@article {pmid30629718, year = {2019}, author = {Gruenstaeudl, M and Hartmaring, Y}, title = {EMBL2checklists: A Python package to facilitate the user-friendly submission of plant and fungal DNA barcoding sequences to ENA.}, journal = {PloS one}, volume = {14}, number = {1}, pages = {e0210347}, doi = {10.1371/journal.pone.0210347}, pmid = {30629718}, issn = {1932-6203}, abstract = {BACKGROUND: The submission of DNA sequences to public sequence databases is an essential, but insufficiently automated step in the process of generating and disseminating novel DNA sequence data. Despite the centrality of database submissions to biological research, the range of available software tools that facilitate the preparation of sequence data for database submissions is low, especially for sequences generated via plant and fungal DNA barcoding. Current submission procedures can be complex and prohibitively time expensive for any but a small number of input sequences. A user-friendly software tool is needed that streamlines the file preparation for database submissions of DNA sequences that are commonly generated in plant and fungal DNA barcoding.
METHODS: A Python package was developed that converts DNA sequences from the common EMBL and GenBank flat file formats to submission-ready, tab-delimited spreadsheets (so-called 'checklists') for a subsequent upload to the annotated sequence section of the European Nucleotide Archive (ENA). The software tool, titled 'EMBL2checklists', automatically converts DNA sequences, their annotation features, and associated metadata into the idiosyncratic format of marker-specific ENA checklists and, thus, generates files that can be uploaded via the interactive Webin submission system of ENA.
RESULTS: EMBL2checklists provides a simple, platform-independent tool that automates the conversion of common DNA barcoding sequences into easily editable spreadsheets that require no further processing but their upload to ENA via the interactive Webin submission system. The software is equipped with an intuitive graphical as well as an efficient command-line interface for its operation. The utility of the software is illustrated by its application in four recent investigations, including plant phylogenetic and fungal metagenomic studies.
DISCUSSION: EMBL2checklists bridges the gap between common software suites for DNA sequence assembly and annotation and the interactive data submission process of ENA. It represents an easy-to-use solution for plant and fungal biologists without bioinformatics expertise to generate submission-ready checklists from common DNA sequence data. It allows the post-processing of checklists as well as work-sharing during the submission process and solves a critical bottleneck in the effort to increase participation in public data sharing.}, }
@article {pmid30629604, year = {2019}, author = {Mayday, MY and Khan, LM and Chow, ED and Zinter, MS and DeRisi, JL}, title = {Miniaturization and optimization of 384-well compatible RNA sequencing library preparation.}, journal = {PloS one}, volume = {14}, number = {1}, pages = {e0206194}, doi = {10.1371/journal.pone.0206194}, pmid = {30629604}, issn = {1932-6203}, abstract = {Preparation of high-quality sequencing libraries is a costly and time-consuming component of metagenomic next generation sequencing (mNGS). While the overall cost of sequencing has dropped significantly over recent years, the reagents needed to prepare sequencing samples are likely to become the dominant expense in the process. Furthermore, libraries prepared by hand are subject to human variability and needless waste due to limitations of manual pipetting volumes. Reduction of reaction volumes, combined with sub-microliter automated dispensing of reagents without consumable pipette tips, has the potential to provide significant advantages. Here, we describe the integration of several instruments, including the Labcyte Echo 525 acoustic liquid handler and the iSeq and NovaSeq Illumina sequencing platforms, to miniaturize and automate mNGS library preparation, significantly reducing the cost and the time required to prepare samples. Through the use of External RNA Controls Consortium (ERCC) spike-in RNAs, we demonstrated the fidelity of the miniaturized preparation to be equivalent to full volume reactions. Furthermore, detection of viral and microbial species from cell culture and patient samples was also maintained in the miniaturized libraries. For 384-well mNGS library preparations, we achieved cost savings of over 80% in materials and reagents alone, and reduced preparation time by 90% compared to manual approaches, without compromising quality or representation within the library.}, }
@article {pmid30629185, year = {2019}, author = {Stewart, CJ and Mansbach, JM and Ajami, NJ and Petrosino, JF and Zhu, Z and Liang, L and Camargo, CA and Hasegawa, K}, title = {Serum metabolome is associated with nasopharyngeal microbiota and disease severity among infants with bronchiolitis.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiz021}, pmid = {30629185}, issn = {1537-6613}, abstract = {Background: Emerging evidence suggests relations of nasopharyngeal metabolome and microbiota with bronchiolitis severity. However, the influence of host systemic metabolism on disease pathobiology remains unclear. We aimed to examine metabolome profiles and their association with higher severity, defined by use of positive pressure ventilation (PPV), in infants hospitalized for bronchiolitis.
Methods: In 140 infants with bronchiolitis, metabolomic profiling was performed on serum: n=70 in the training dataset and n=70 independent samples in the test dataset. We also profiled the nasopharyngeal airway microbiota and examined its association with the serum metabolites.
Results: Serum metabolome profiles differed by bronchiolitis severity (P<0.001). In total, 20 metabolites in the training dataset were significantly associated with the risk of PPV and 18 metabolites remained significant following adjustment for confounders (FDR<0.10). Phosphatidylcholine metabolites were associated with higher risks of PPV use, while metabolites from the plasmalogen sub-pathway were associated with lower risks. The test dataset validated these findings (FDR<0.05). Streptococcus abundance was positively associated with metabolites that are associated with higher risks of PPV.
Conclusions: Serum metabolomic signatures were associated with both the nasopharyngeal microbiota and bronchiolitis severity. Our findings advance research into the complex interrelations between airway microbiome, host systemic response, and pathobiology of bronchiolitis.}, }
@article {pmid30627872, year = {2019}, author = {Wang, Q and Wang, K and Wu, W and Giannoulatou, E and Ho, JWK and Li, L}, title = {Host and microbiome multi-omics integration: applications and methodologies.}, journal = {Biophysical reviews}, volume = {11}, number = {1}, pages = {55-65}, doi = {10.1007/s12551-018-0491-7}, pmid = {30627872}, issn = {1867-2450}, support = {81330011, 81330014, 81790631, 81790633, 81570512, and 81121002//National Natural Science Foundation of China/ ; 81721091//Science Fund for Creative Research Groups/ ; 100848//National Heart Foundation of Australia/ ; 101204//National Heart Foundation of Australia/ ; }, abstract = {The study of the microbial community-the microbiome-associated with a human host is a maturing research field. It is increasingly clear that the composition of the human's microbiome is associated with various diseases such as gastrointestinal diseases, liver diseases and metabolic diseases. Using high-throughput technologies such as next-generation sequencing and mass spectrometry-based metabolomics, we are able to comprehensively sequence the microbiome-the metagenome-and associate these data with the genomic, epigenomics, transcriptomic and metabolic profile of the host. Our review summarises the application of integrating host omics with microbiome as well as the analytical methods and related tools applied in these studies. In addition, potential future directions are discussed.}, }
@article {pmid30626904, year = {2019}, author = {Delgado, B and Bach, A and Guasch, I and González, C and Elcoso, G and Pryce, JE and Gonzalez-Recio, O}, title = {Whole rumen metagenome sequencing allows classifying and predicting feed efficiency and intake levels in cattle.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {11}, doi = {10.1038/s41598-018-36673-w}, pmid = {30626904}, issn = {2045-2322}, abstract = {The current research was carried out to determine the associations between the rumen microbiota and traits related with feed efficiency in a Holstein cattle population (n = 30) using whole metagenome sequencing. Improving feed efficiency (FE) is important for a more sustainable livestock production. The variability for the efficiency of feed utilization in ruminants is partially controlled by the gastrointestinal microbiota. Modulating the microbiota composition can promote a more sustainable and efficient livestock. This study revealed that most efficient cows had larger relative abundance of Bacteroidetes (P = 0.041) and Prevotella (P = 0.003), while lower, but non-significant (P = 0.119), relative abundance of Firmicutes. Methanobacteria (P = 0.004) and Methanobrevibacter (P = 0.003) were also less abundant in the high-efficiency cows. A de novo metagenome assembly was carried out using de Bruijn graphs in MEGAHIT resulting in 496,375 contigs. An agnostic pre-selection of microbial contigs allowed high classification accuracy for FE and intake levels using hierarchical classification. These microbial contigs were also able to predict FE and intake levels with accuracy of 0.19 and 0.39, respectively, in an independent population (n = 31). Nonetheless, a larger potential accuracy up to 0.69 was foreseen in this study for datasets that allowed a larger statistical power. Enrichment analyses showed that genes within these contigs were mainly involved in fatty acids and cellulose degradation pathways. The findings indicated that there are differences between the microbiota compositions of high and low-efficiency animals both at the taxonomical and gene levels. These differences are even more evident in terms of intake levels. Some of these differences remain even between populations under different diets and environments, and can provide information on the feed utilization performance without information on the individual intake level.}, }
@article {pmid30626868, year = {2019}, author = {Singh, R and Chandrashekharappa, S and Bodduluri, SR and Baby, BV and Hegde, B and Kotla, NG and Hiwale, AA and Saiyed, T and Patel, P and Vijay-Kumar, M and Langille, MGI and Douglas, GM and Cheng, X and Rouchka, EC and Waigel, SJ and Dryden, GW and Alatassi, H and Zhang, HG and Haribabu, B and Vemula, PK and Jala, VR}, title = {Enhancement of the gut barrier integrity by a microbial metabolite through the Nrf2 pathway.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {89}, doi = {10.1038/s41467-018-07859-7}, pmid = {30626868}, issn = {2041-1723}, support = {R21CA216090/NH/NIH HHS/United States ; P20GM125504-01/NH/NIH HHS/United States ; }, mesh = {Animals ; Basic Helix-Loop-Helix Transcription Factors/genetics/metabolism ; Caco-2 Cells ; Coumarins/chemistry/*pharmacology ; Epithelial Cells/metabolism ; Gene Expression Regulation/drug effects ; HT29 Cells ; Humans ; Intestinal Mucosa/metabolism ; Macrophages ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; NF-E2-Related Factor 2/genetics/*metabolism ; Receptors, Aryl Hydrocarbon/genetics/metabolism ; Specific Pathogen-Free Organisms ; Tight Junction Proteins/genetics/*metabolism ; }, abstract = {The importance of gut microbiota in human health and pathophysiology is undisputable. Despite the abundance of metagenomics data, the functional dynamics of gut microbiota in human health and disease remain elusive. Urolithin A (UroA), a major microbial metabolite derived from polyphenolics of berries and pomegranate fruits displays anti-inflammatory, anti-oxidative, and anti-ageing activities. Here, we show that UroA and its potent synthetic analogue (UAS03) significantly enhance gut barrier function and inhibit unwarranted inflammation. We demonstrate that UroA and UAS03 exert their barrier functions through activation of aryl hydrocarbon receptor (AhR)- nuclear factor erythroid 2-related factor 2 (Nrf2)-dependent pathways to upregulate epithelial tight junction proteins. Importantly, treatment with these compounds attenuated colitis in pre-clinical models by remedying barrier dysfunction in addition to anti-inflammatory activities. Cumulatively, the results highlight how microbial metabolites provide two-pronged beneficial activities at gut epithelium by enhancing barrier functions and reducing inflammation to protect from colonic diseases.}, }
@article {pmid30626052, year = {2019}, author = {Cheong, DE and Park, SY and Lim, HD and Kim, GJ}, title = {An Alternative Platform for Protein Expression Using an Innate Whole Expression Module from Metagenomic DNA.}, journal = {Microorganisms}, volume = {7}, number = {1}, pages = {}, doi = {10.3390/microorganisms7010009}, pmid = {30626052}, issn = {2076-2607}, support = {NRF-2017030616//The Intelligent Synthetic Biology Center program of the National Research Foundation (NRF) funded by the Ministry of Science/ ; 20170305//ICT & Future Planning and by a grant from the Marine Biotechnology Program funded by the Ministry of Oceans and Fisheries, Korea/ ; 2017R1D1A1B03035338//Basic Science Research Program through the National Research Foundation of Korea(NRF) funded by the Ministry of Education/ ; }, abstract = {Many integrated gene clusters beyond a single genetic element are commonly trapped as the result of promoter traps in (meta)genomic DNA libraries. Generally, a single element, which is mainly the promoter, is deduced from the resulting gene clusters and employed to construct a new expression vector. However, expression patterns of target proteins under the incorporated promoter are often inconsistent with those shown in clones harboring plasmids with gene clusters. These results suggest that the integrated set of gene clusters with diverse cis- and trans-acting elements is evolutionarily tuned as a complete set for gene expression, and is an expression module with all the components for the expression of a nested open reading frame (ORF). This possibility is further supported by truncation and/or serial deletion analysis of this module in which the expression of the nested ORF is highly fluctuated or reduced frequently, despite being supported by plentiful cis-acting elements in the spanning regions around the ORF such as the promoter, ribosome binding site (RBS), terminator, and 3'-/5'-UTRs for gene expression. Here, we examined whether an innate module with a naturally overexpressed gene could be considered as a scaffold for an expression system. For a proof-of-principle study, we mined a complete expression module with an innately overexpressed ORF in E. coli from a metagenomics DNA library, and incorporated it into a vector that had no regulatory element for expressing the insert. We obtained successful expression of several inserts such as MBP, GFPuv, β-glucosidase, and esterase using this simple construct without tuning and codon optimization of the target insert.}, }
@article {pmid30626002, year = {2019}, author = {Rechenberger, J and Samaras, P and Jarzab, A and Behr, J and Frejno, M and Djukovic, A and Sanz, J and González-Barberá, EM and Salavert, M and López-Hontangas, JL and Xavier, KB and Debrauwer, L and Rolain, JM and Sanz, M and Garcia-Garcera, M and Wilhelm, M and Ubeda, C and Kuster, B}, title = {Challenges in Clinical Metaproteomics Highlighted by the Analysis of Acute Leukemia Patients with Gut Colonization by Multidrug-Resistant Enterobacteriaceae.}, journal = {Proteomes}, volume = {7}, number = {1}, pages = {}, doi = {10.3390/proteomes7010002}, pmid = {30626002}, issn = {2227-7382}, support = {031L0089//Bundesministerium für Bildung und Forschung/ ; }, abstract = {The microbiome has a strong impact on human health and disease and is, therefore, increasingly studied in a clinical context. Metaproteomics is also attracting considerable attention, and such data can be efficiently generated today owing to improvements in mass spectrometry-based proteomics. As we will discuss in this study, there are still major challenges notably in data analysis that need to be overcome. Here, we analyzed 212 fecal samples from 56 hospitalized acute leukemia patients with multidrug-resistant Enterobactericeae (MRE) gut colonization using metagenomics and metaproteomics. This is one of the largest clinical metaproteomic studies to date, and the first metaproteomic study addressing the gut microbiome in MRE colonized acute leukemia patients. Based on this substantial data set, we discuss major current limitations in clinical metaproteomic data analysis to provide guidance to researchers in the field. Notably, the results show that public metagenome databases are incomplete and that sample-specific metagenomes improve results. Furthermore, biological variation is tremendous which challenges clinical study designs and argues that longitudinal measurements of individual patients are a valuable future addition to the analysis of patient cohorts.}, }
@article {pmid30625669, year = {2019}, author = {Costeira, R and Doherty, R and Allen, CCR and Larkin, MJ and Kulakov, LA}, title = {Analysis of viral and bacterial communities in groundwater associated with contaminated land.}, journal = {The Science of the total environment}, volume = {656}, number = {}, pages = {1413-1426}, doi = {10.1016/j.scitotenv.2018.11.429}, pmid = {30625669}, issn = {1879-1026}, mesh = {Bacteria/classification/*genetics ; Groundwater/*microbiology/virology ; *Metagenome ; *Microbiota ; Northern Ireland ; Soil Pollutants/*analysis ; Viruses/classification/*genetics ; }, abstract = {This work aimed at the comprehensive analysis of total microbial communities inhabiting a typical hydrocarbon-polluted site, where chemical characteristics of the groundwater were readily available. To achieve this, a joint metagenomic characterization of bacteria and viruses surrounding a contaminant plume was performed over a one-year period. The results presented demonstrated that both potential hydrocarbon degraders and their bacteriophages were dominant around the plume, and that the viral and bacterial diversities found at the site were probably influenced by the pH of the groundwater. Niche-specific and dispersed associations between phages and bacteria were identified. The niche phage-host associations were found at the edge of the site and at the core of the plume where pH was the highest (9.52). The identified host populations included several classes of bacteria (e.g. Clostridia and Proteobacteria). Thirty-six viral generalists were also discovered, with BGW-G9 having the broadest host range across 23 taxa, including Pseudomonas, Polycyclovorans, Methylocaldum and Candidatus Magnetobacterium species. The phages with broad host ranges are presumed to have significant effects on prokaryotic production and horizontal gene transfer, and therefore impact the biodegradation processes conducted by various bacteria of the environment studied. This study for the first time characterized the phages and their bacterial hosts associated with a contaminant plume.}, }
@article {pmid30625356, year = {2019}, author = {Jia, ML and Zhong, XL and Lin, ZW and Dong, BX and Li, G}, title = {Expression and characterization of an esterase belonging to a new family via isolation from a metagenomic library of paper mill sludge.}, journal = {International journal of biological macromolecules}, volume = {126}, number = {}, pages = {1192-1200}, doi = {10.1016/j.ijbiomac.2019.01.025}, pmid = {30625356}, issn = {1879-0003}, abstract = {A new bacterial lipolytic enzyme Est903 was obtained from paper mill sludge via metagenomic approach. Est903 displayed moderate similarities to two lipolytic enzymes from Rhodopirellula islandica and contained a distinctive pentapeptide motif (GFSAG) that differed from those of all known fourteen families of bacterial lipolytic enzymes. Est903 was regarded as from a new bacterial lipolytic enzyme family through multiple sequence alignment and phylogenetic analysis. The recombinant Est903 showed the highest activity for ρ-nitrophenol butyrate. The pH optimum and temperature optimum of the recombinant enzyme was 9.0 and 51 °C, respectively. Also, this enzyme displayed moderate thermostability, high activity under alkaline conditions, and good tolerance against several organic solvents. In addition, the compatibility test and washing performance analysis revealed that Est903 had good compatibility with commercial laundry detergent and high cleaning ability of oil stains. These good properties make Est903 a potential candidate in organic synthesis or detergent industry.}, }
@article {pmid30624643, year = {2019}, author = {Baldrian, P}, title = {The known and the unknown in soil microbial ecology.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {2}, pages = {}, doi = {10.1093/femsec/fiz005}, pmid = {30624643}, issn = {1574-6941}, abstract = {The methodical developments in the fields of molecular biology and analytical chemistry significantly increased the level of detail that we achieve when exploring soils and their microbial inhabitants. High-resolution description of microbial communities, detection of taxa with minor abundances, screening of gene expression or the detailed characterization of metabolomes are nowadays technically feasible. Despite all of this, our understanding of soil is limited in many ways. The imperfect tools to describe microbial communities and limited possibilities to assign traits to community members make it difficult to link microbes to functions. Also the analysis of processes exemplified by enzyme activity measurements is still imperfect. In the future, it is important to look at soil at a finer detail to obtain a better picture on the properties of individual microbes, their in situ interactions, metabolic rates and activity at a scale relevant to individual microbes. Scaling up is needed as well to get answers at ecosystem or biome levels and to enable global modelling. The recent development of novel tools including metabolomics, identification of genomes in metagenomics sequencing datasets or collection of trait data have the potential to bring soil ecology further. It will, however, always remain a highly demanding scientific discipline.}, }
@article {pmid30623484, year = {2019}, author = {Zhai, J and Knox, K and Twigg, HL and Zhou, H and Zhou, JJ}, title = {Exact variance component tests for longitudinal microbiome studies.}, journal = {Genetic epidemiology}, volume = {}, number = {}, pages = {}, doi = {10.1002/gepi.22185}, pmid = {30623484}, issn = {1098-2272}, support = {K01DK106116//National Institute of Diabetes and Digestive and Kidney Diseases/ ; DMS-1645093//National Science Foundation/ ; U01 HL098960/HL/NHLBI NIH HHS/United States ; GM053275//National Institute of General Medical Sciences/ ; HG006139//National Human Genome Research Institute/ ; GM105785//National Institute of General Medical Sciences/ ; K01 DK106116/DK/NIDDK NIH HHS/United States ; New Investigator Award//Arizona Biomedical Research Commission/ ; }, abstract = {In metagenomic studies, testing the association between microbiome composition and clinical outcomes translates to testing the nullity of variance components. Motivated by a lung human immunodeficiency virus (HIV) microbiome project, we study longitudinal microbiome data by using variance component models with more than two variance components. Current testing strategies only apply to models with exactly two variance components and when sample sizes are large. Therefore, they are not applicable to longitudinal microbiome studies. In this paper, we propose exact tests (score test, likelihood ratio test, and restricted likelihood ratio test) to (a) test the association of the overall microbiome composition in a longitudinal design and (b) detect the association of one specific microbiome cluster while adjusting for the effects from related clusters. Our approach combines the exact tests for null hypothesis with a single variance component with a strategy of reducing multiple variance components to a single one. Simulation studies demonstrate that our method has a correct type I error rate and superior power compared to existing methods at small sample sizes and weak signals. Finally, we apply our method to a longitudinal pulmonary microbiome study of HIV-infected patients and reveal two interesting genera Prevotella and Veillonella associated with forced vital capacity. Our findings shed light on the impact of the lung microbiome on HIV complexities. The method is implemented in the open-source, high-performance computing language Julia and is freely available at https://github.com/JingZhai63/VCmicrobiome.}, }
@article {pmid30623233, year = {2019}, author = {Kim, JY and Kim, EM and Yi, MH and Lee, J and Lee, S and Hwang, Y and Yong, D and Sohn, WM and Yong, TS}, title = {Chinese liver fluke Clonorchis sinensis infection changes the gut microbiome and increases probiotic Lactobacillus in mice.}, journal = {Parasitology research}, volume = {118}, number = {2}, pages = {693-699}, doi = {10.1007/s00436-018-6179-x}, pmid = {30623233}, issn = {1432-1955}, support = {NRF-2016R1A2B4016194//National Research Foundation of Korea/ ; 2011-0012166//National Research Foundation of Korea/ ; }, abstract = {Chinese liver fluke Clonorchis sinensis changes the host's immune system. Recently, it has been reported that helminths including C. sinensis can ameliorate immune-related diseases such as allergy. In addition, recent studies showed that helminth infection can alleviate immune-mediated disorders by altering the gut microbiome. However, changes in the gut microbiome due to C. sinensis have not been reported yet. In this study, changes in the gut microbiome of C57BL/6 mice infected with C. sinensis metacercariae were evaluated over time. Stool was analyzed by 16S rRNA amplicon analysis using high-throughput sequencing technology. There was no apparent difference in species richness and diversity between the infected and control groups. However, the composition of the microbiome was different between the infected and control groups at 20 days and 30 days post-infection, and the difference disappeared at 50 days post-infection. In particular, this microbiome alteration was associated with a change in the relative abundance of genus Lactobacillus and the probiotic Lactobacillus species that are known to have an immune-modulation role in immune-mediated diseases.}, }
@article {pmid30623212, year = {2019}, author = {de Sousa, AGG and Tomasino, MP and Duarte, P and Fernández-Méndez, M and Assmy, P and Ribeiro, H and Surkont, J and Leite, RB and Pereira-Leal, JB and Torgo, L and Magalhães, C}, title = {Diversity and Composition of Pelagic Prokaryotic and Protist Communities in a Thin Arctic Sea-Ice Regime.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-01314-2}, pmid = {30623212}, issn = {1432-184X}, support = {244646//Research Council of Norway/ ; NORTE-01-0145-FEDER-000031//Structured Program of R&D&I MarInfo/ ; Arktis 2030//Norwegian Ministries of Foreign Affairs and Climate and Environment/ ; NITROLIMIT - PTDC 2017 - PTDC/CTA-AMB/30997/2017//Funda??o para a Ci?ncia e a Tecnologia/ ; }, abstract = {One of the most prominent manifestations of climate change is the changing Arctic sea-ice regime with a reduction in the summer sea-ice extent and a shift from thicker, perennial multiyear ice towards thinner, first-year ice. These changes in the physical environment are likely to impact microbial communities, a key component of Arctic marine food webs and biogeochemical cycles. During the Norwegian young sea ICE expedition (N-ICE2015) north of Svalbard, seawater samples were collected at the surface (5 m), subsurface (20 or 50 m), and mesopelagic (250 m) depths on 9 March, 27 April, and 16 June 2015. In addition, several physical and biogeochemical data were recorded to contextualize the collected microbial communities. Through the massively parallel sequencing of the small subunit ribosomal RNA amplicon and metagenomic data, this work allows studying the Arctic's microbial community structure during the late winter to early summer transition. Results showed that, at compositional level, Alpha- (30.7%) and Gammaproteobacteria (28.6%) are the most frequent taxa across the prokaryotic N-ICE2015 collection, and also the most phylogenetically diverse. Winter to early summer trends were quite evident since there was a high relative abundance of thaumarchaeotes in the under-ice water column in late winter while this group was nearly absent during early summer. Moreover, the emergence of Flavobacteria and the SAR92 clade in early summer might be associated with the degradation of a spring bloom of Phaeocystis. High relative abundance of hydrocarbonoclastic bacteria, particularly Alcanivorax (54.3%) and Marinobacter (6.3%), was also found. Richness showed different patterns along the depth gradient for prokaryotic (highest at mesopelagic depth) and protistan communities (higher at subsurface depths). The microbial N-ICE2015 collection analyzed in the present study provides comprehensive new knowledge about the pelagic microbiota below drifting Arctic sea-ice. The higher microbial diversity found in late winter/early spring communities reinforces the need to continue with further studies to properly characterize the winter microbial communities under the pack-ice.}, }
@article {pmid30622518, year = {2018}, author = {Fujiwara, K and Iwanami, T and Fujikawa, T}, title = {Alterations of Candidatus Liberibacter asiaticus-Associated Microbiota Decrease Survival of Ca. L. asiaticus in in vitro Assays.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3089}, doi = {10.3389/fmicb.2018.03089}, pmid = {30622518}, issn = {1664-302X}, abstract = {Phloem-inhabiting bacterial phytopathogens often have smaller genomes than other bacterial phytopathogens. It is thought that they depend on both other phloem microbiota and phloem nutrients for colonization of the host. However, the mechanism underlying associations between phloem-inhabiting phytopathogens and other phloem microbiota are poorly understood. Here, we demonstrate that the survival of Candidatus Liberibacter asiaticus (CLas), a cause of huanglongbing (citrus greening disease), depends on interplay with a specific subset of CLas-associated microbiota. CLas was not susceptible to oxytetracycline in vitro. However, oxytetracycline treatment eliminated a particular sub-community dominated by the Comamonadaceae, Flavobacteriaceae, Microbacteriaceae, and Pseudomonadaceae, decreasing CLas survival. We speculate that CLas uses ecological services derived from CLas-associated microbiota to colonize the host and to construct a pathogen-associated community that stimulates disease development.}, }
@article {pmid30622259, year = {2019}, author = {Karkman, A and Pärnänen, K and Larsson, DGJ}, title = {Fecal pollution can explain antibiotic resistance gene abundances in anthropogenically impacted environments.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {80}, doi = {10.1038/s41467-018-07992-3}, pmid = {30622259}, issn = {2041-1723}, abstract = {Discharge of treated sewage leads to release of antibiotic resistant bacteria, resistance genes and antibiotic residues to the environment. However, it is unclear whether increased abundance of antibiotic resistance genes in sewage and sewage-impacted environments is due to on-site selection pressure by residual antibiotics, or is simply a result of fecal contamination with resistant bacteria. Here we analyze relative resistance gene abundance and accompanying extent of fecal pollution in publicly available metagenomic data, using crAssphage sequences as a marker of human fecal contamination (crAssphage is a bacteriophage that is exceptionally abundant in, and specific to, human feces). We find that the presence of resistance genes can largely be explained by fecal pollution, with no clear signs of selection in the environment, with the exception of environments polluted by very high levels of antibiotics from manufacturing, where selection is evident. Our results demonstrate the necessity to take into account fecal pollution levels to avoid making erroneous assumptions regarding environmental selection of antibiotic resistance.}, }
@article {pmid30622080, year = {2019}, author = {Cota-Ruiz, K and López de Los Santos, Y and Hernández-Viezcas, JA and Delgado-Rios, M and Peralta-Videa, JR and Gardea-Torresdey, JL}, title = {A comparative metagenomic and spectroscopic analysis of soils from an international point of entry between the US and Mexico.}, journal = {Environment international}, volume = {123}, number = {}, pages = {558-566}, doi = {10.1016/j.envint.2018.12.055}, pmid = {30622080}, issn = {1873-6750}, abstract = {The Paso del Norte region is characterized by its dynamic industries and active agriculture. Throughout the years, urban and agricultural soils from this region have been exposed to xenobiotics, heavy metals, and excess of hydrocarbons. In this study, samples of urban [domestic workshops (DW)] and agricultural-intended (AI) soils from different sites of Ciudad Juárez, Mexico were evaluated for their fertility, element content, and microbial diversity. Chemical analyses showed that nitrites, nitrates, P, K, Mg, and Mn were predominantly higher in AI soils, compared to DW soils (p ≤ 0.05). The composition of soil microbial communities showed that Proteobacteria phylum was the most abundant in both soils (67%, p ≤ 0.05). In AI soils, Paracoccus denitrificans was reduced (p ≤ 0.05), concurring with an increment in nitrates, while the content of nitrogen was negatively correlated with the rhizobium group (r2 = -0.65, p ≤ 0.05). In DW soils, the Firmicutes phylum represented up to ~25%, and the relative abundance of Proteobacteria strongly correlated with a higher Cu content (r2 = 0.99, p ≤ 0.0001). The monotypic genus Sulfuricurvum was found only in oil-contaminated soil samples. Finally, all samples showed the presence of the recently created phylum Candidatus saccharibacteria. These results describe the productivity parameters of AI soils and its correlation to the microbial diversity, which are very important to understand and potentiate the productivity of soils. The data also suggest that soils impacted with hydrocarbons and metal(oid)s allow the reproduction of microorganisms with the potential to alleviate contaminated sites.}, }
@article {pmid30621881, year = {2019}, author = {Jagadeesan, B and Gerner-Smidt, P and Allard, MW and Leuillet, S and Winkler, A and Xiao, Y and Chaffron, S and Van Der Vossen, J and Tang, S and Katase, M and McClure, P and Kimura, B and Ching Chai, L and Chapman, J and Grant, K}, title = {The use of next generation sequencing for improving food safety: Translation into practice.}, journal = {Food microbiology}, volume = {79}, number = {}, pages = {96-115}, doi = {10.1016/j.fm.2018.11.005}, pmid = {30621881}, issn = {1095-9998}, abstract = {Next Generation Sequencing (NGS) combined with powerful bioinformatic approaches are revolutionising food microbiology. Whole genome sequencing (WGS) of single isolates allows the most detailed comparison possible hitherto of individual strains. The two principle approaches for strain discrimination, single nucleotide polymorphism (SNP) analysis and genomic multi-locus sequence typing (MLST) are showing concordant results for phylogenetic clustering and are complementary to each other. Metabarcoding and metagenomics, applied to total DNA isolated from either food materials or the production environment, allows the identification of complete microbial populations. Metagenomics identifies the entire gene content and when coupled to transcriptomics or proteomics, allows the identification of functional capacity and biochemical activity of microbial populations. The focus of this review is on the recent use and future potential of NGS in food microbiology and on current challenges. Guidance is provided for new users, such as public health departments and the food industry, on the implementation of NGS and how to critically interpret results and place them in a broader context. The review aims to promote the broader application of NGS technologies within the food industry as well as highlight knowledge gaps and novel applications of NGS with the aim of driving future research and increasing food safety outputs from its wider use.}, }
@article {pmid30621868, year = {2019}, author = {Ottesen, A and Ramachandran, P and Reed, E and Gu, G and Gorham, S and Ducharme, D and Newell, M and Rideout, S and Turini, T and Hill, T and Strain, E and Brown, E}, title = {Metagenome tracking biogeographic agroecology: Phytobiota of tomatoes from Virginia, Maryland, North Carolina and California.}, journal = {Food microbiology}, volume = {79}, number = {}, pages = {132-136}, doi = {10.1016/j.fm.2018.12.001}, pmid = {30621868}, issn = {1095-9998}, abstract = {Describing baseline microbiota associated with agricultural commodities in the field is an important step towards improving our understanding of a wide range of important objectives from plant pathology and horticultural sustainability, to food safety. Environmental pressures on plants (wind, dust, drought, water, temperature) vary by geography and characterizing the impact of these variable pressures on phyllosphere microbiota will contribute to improved stewardship of fresh produce for both plant and human health. A higher resolution understanding of the incidence of human pathogens on food plants and co-occurring phytobiota using metagenomic approaches (metagenome tracking) may contribute to improved source attribution and risk assessment in cases where human pathogens become introduced to agro-ecologies. Between 1990 and 2007, as many as 1990 culture-confirmed Salmonella illnesses were linked to tomatoes from as many as 12 multistate outbreaks (Bell et al., 2012; Bell et al., 2015; Bennett et al., 2014; CDC, 2004; CDC, 2007; Greene et al., 2005a; Gruszynski et al., 2014). When possible, source attribution for these incidents revealed a biogeographic trend, most events were associated with eastern growing regions. To improve our understanding of potential biogeographically linked trends in contamination of tomatoes by Salmonella, we profiled microbiota from the surfaces of tomatoes from Virginia, Maryland, North Carolina and California. Bacterial profiles from California tomatoes were completely different than those of Maryland, Virginia and North Carolina (which were highly similar to each other). A statistically significant enrichment of Firmicutes taxa was observed in California phytobiota compared to the three eastern states. Rhizobiaceae, Sphingobacteriaceae and Xanthobacteraceae were the most abundant bacterial families associated with tomatoes grown in eastern states. These baseline metagenomic profiles of phyllosphere microbiota may contribute to improved understanding of how certain ecologies provide supportive resources for human pathogens on plants and how components of certain agro-ecologies may play a role in the introduction of human pathogens to plants.}, }
@article {pmid30621867, year = {2019}, author = {Marino, M and Dubsky de Wittenau, G and Saccà, E and Cattonaro, F and Spadotto, A and Innocente, N and Radovic, S and Piasentier, E and Marroni, F}, title = {Metagenomic profiles of different types of Italian high-moisture Mozzarella cheese.}, journal = {Food microbiology}, volume = {79}, number = {}, pages = {123-131}, doi = {10.1016/j.fm.2018.12.007}, pmid = {30621867}, issn = {1095-9998}, abstract = {The microbiota of different types of Italian high-moisture Mozzarella cheese produced using cow or buffalo milk, acidified with natural or selected cultures, and sampled at the dairy or at the mass market, was evaluated using a Next Generation Sequencing approach, in order to identify possible drivers of the bacterial diversity. Cow Mozzarella and buffalo Mozzarella acidified with commercial cultures were dominated by Streptococcus thermophilus, while buffalo samples acidified with natural whey cultures showed similar prevalence of L. delbrueckii subsp. bulgaricus, L. helveticus and S. thermophilus. Moreover, several species of non-starter lactic acid bacteria were frequently detected. The diversity in cow Mozzarella microbiota was much higher than that of water buffalo samples. Cluster analysis clearly separated cow's cheeses from buffalo's ones, the former having a higher prevalence of psychrophilic taxa, and the latter of Lactobacillus and Streptococcus. A higher prevalence of psychrophilic species and potential spoilers was observed in samples collected at the mass retail, suggesting that longer exposures to cooling temperatures and longer production-to-consumption times could significantly affect microbiota diversity. Our results could help in detecting some kind of thermal abuse during the production or storage of mozzarella cheese.}, }
@article {pmid30621760, year = {2018}, author = {Gerner, SM and Rattei, T and Graf, AB}, title = {Assessment of urban microbiome assemblies with the help of targeted in silico gold standards.}, journal = {Biology direct}, volume = {13}, number = {1}, pages = {22}, doi = {10.1186/s13062-018-0225-6}, pmid = {30621760}, issn = {1745-6150}, abstract = {BACKGROUND: Microbial communities play a crucial role in our environment and may influence human health tremendously. Despite being the place where human interaction is most abundant we still know little about the urban microbiome. This is highlighted by the large amount of unclassified DNA reads found in urban metagenome samples. The only in silico approach that allows us to find unknown species, is the assembly and classification of draft genomes from a metagenomic dataset. In this study we (1) investigate the applicability of an assembly and binning approach for urban metagenome datasets, and (2) develop a new method for the generation of in silico gold standards to better understand the specific challenges of such datasets and provide a guide in the selection of available software.
RESULTS: We applied combinations of three assembly (Megahit, SPAdes and MetaSPAdes) and three binning tools (MaxBin, MetaBAT and CONCOCT) to whole genome shotgun datasets from the CAMDA 2017 Challenge. Complex in silico gold standards with a simulated bacterial fraction were generated for representative samples of each surface type and city. Using these gold standards, we found the combination of SPAdes and MetaBAT to be optimal for urban metagenome datasets by providing the best trade-off between the number of high-quality genome draft bins (MIMAG standards) retrieved, the least amount of misassemblies and contamination. The assembled draft genomes included known species like Propionibacterium acnes but also novel species according to respective ANI values.
CONCLUSIONS: In our work, we showed that, even for datasets with high diversity and low sequencing depth from urban environments, assembly and binning-based methods can provide high-quality genome drafts. Of vital importance to retrieve high-quality genome drafts is sequence depth but even more so a high proportion of the bacterial sequence fraction too achieve high coverage for bacterial genomes. In contrast to read-based methods relying on database knowledge, genome-centric methods as applied in this study can provide valuable information about unknown species and strains as well as functional contributions of single community members within a sample. Furthermore, we present a method for the generation of sample-specific highly complex in silico gold standards.
REVIEWERS: This article was reviewed by Craig Herbold, Serghei Mangul and Yana Bromberg.}, }
@article {pmid30621600, year = {2019}, author = {Imhann, F and Van der Velde, KJ and Barbieri, R and Alberts, R and Voskuil, MD and Vich Vila, A and Collij, V and Spekhorst, LM and der Sloot Kwj, V and Peters, V and Van Dullemen, HM and Visschedijk, MC and Eam, F and Swertz, MA and Dijkstra, G and Weersma, RK}, title = {The 1000IBD project: multi-omics data of 1000 inflammatory bowel disease patients; data release 1.}, journal = {BMC gastroenterology}, volume = {19}, number = {1}, pages = {5}, doi = {10.1186/s12876-018-0917-5}, pmid = {30621600}, issn = {1471-230X}, support = {016.136.308//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 92.003.577//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; MLDS D16-14//Maag Lever Darm Stichting/ ; CD14-04//Maag Lever Darm Stichting (NL)/ ; }, mesh = {Adolescent ; Adult ; Aged ; Biomarkers ; Biopsy ; Diet ; Environment ; Female ; Gastrointestinal Microbiome ; Genotype ; Humans ; Inflammatory Bowel Diseases/*classification/drug therapy/*genetics/pathology ; Male ; Middle Aged ; Netherlands ; Phenotype ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Transcriptome ; Whole Exome Sequencing ; Young Adult ; }, abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a chronic complex disease of the gastrointestinal tract. Patients with IBD can experience a wide range of symptoms, but the pathophysiological mechanisms that cause these individual differences in clinical presentation remain largely unknown. In consequence, IBD is currently classified into subtypes using clinical characteristics. If we are to develop a more targeted treatment approach, molecular subtypes of IBD need to be discovered that can be used as new drug targets. To achieve this, we need multiple layers of molecular data generated from the same IBD patients.
CONSTRUCTION AND CONTENT: We initiated the 1000IBD project (https://1000ibd.org) to prospectively follow more than 1000 IBD patients from the Northern provinces of the Netherlands. For these patients, we have collected a uniquely large number of phenotypes and generated multi-omics profiles. To date, 1215 participants have been enrolled in the project and enrolment is on-going. Phenotype data collected for these participants includes information on dietary and environmental factors, drug responses and adverse drug events. Genome information has been generated using genotyping (ImmunoChip, Global Screening Array and HumanExomeChip) and sequencing (whole exome sequencing and targeted resequencing of IBD susceptibility loci), transcriptome information generated using RNA-sequencing of intestinal biopsies and microbiome information generated using both sequencing of the 16S rRNA gene and whole genome shotgun metagenomic sequencing.
UTILITY AND DISCUSSION: All molecular data generated within the 1000IBD project will be shared on the European Genome-Phenome Archive (https://ega-archive.org , accession no: EGAS00001002702). The first data release, detailed in this announcement and released simultaneously with this publication, will contain basic phenotypes for 1215 participants, genotypes of 314 participants and gut microbiome data from stool samples (315 participants) and biopsies (107 participants) generated by tag sequencing the 16S gene. Future releases will comprise many more additional phenotypes and -omics data layers. 1000IBD data can be used by other researchers as a replication cohort, a dataset to test new software tools, or a dataset for applying new statistical models.
CONCLUSIONS: We report on the establishment and future development of the 1000IBD project: the first comprehensive multi-omics dataset aimed at discovering IBD biomarker profiles and treatment targets.}, }
@article {pmid30620035, year = {2019}, author = {Huo, L and Hug, JJ and Fu, C and Bian, X and Zhang, Y and Müller, R}, title = {Heterologous expression of bacterial natural product biosynthetic pathways.}, journal = {Natural product reports}, volume = {}, number = {}, pages = {}, doi = {10.1039/c8np00091c}, pmid = {30620035}, issn = {1460-4752}, abstract = {Covering: 2013 to June 2018Heterologous expression of natural product biosynthetic pathways is of increasing interest in microbial biotechnology, drug discovery and optimization. It empowers not only the robust production of valuable biomolecules in more amenable heterologous hosts but also permits the generation of novel analogs through biosynthetic engineering. This strategy also facilitates the discovery of novel bioactive compounds following the functional expression of cryptic biosynthetic gene clusters (BGCs) from fastidious original producers or metagenomic DNA in surrogate hosts, thus facilitating genome mining in the post-genomic era. This review discusses recent advances and trends pertaining to the heterologous production of bacterial natural products, with an emphasis on new techniques, heterologous hosts, and novel chemistry since 2013.}, }
@article {pmid30619927, year = {2019}, author = {Kadnikov, VV and Mardanov, AV and Frank, YA and Beletsky, AV and Karnachuk, OV and Ravin, NV}, title = {Genomes of three bacteriophages from the deep subsurface aquifer.}, journal = {Data in brief}, volume = {22}, number = {}, pages = {488-491}, doi = {10.1016/j.dib.2018.12.045}, pmid = {30619927}, issn = {2352-3409}, abstract = {Viral particles have been detected in the underground biosphere where they could be one of the main factors impacting microbial diversity, biogeochemistry and evolution. To characterize the viral component in the deep subsurface biosphere, we sequenced the metagenome of subsurface aquifer located in the Tomsk region of Russia, sampled via 2.8-km-deep borehole 5P. The de novo assembly of metagenomics sequences yielded three circular genomes assigned to bacteriophages of the order Caudovirales. The annotated genome sequences of these bacteriophages have been deposited in the GenBank database under the accession numbers MK113949, MK113950 and MK113951.}, }
@article {pmid30619848, year = {2018}, author = {Nishiyama, E and Higashi, K and Mori, H and Suda, K and Nakamura, H and Omori, S and Maruyama, S and Hongoh, Y and Kurokawa, K}, title = {The Relationship Between Microbial Community Structures and Environmental Parameters Revealed by Metagenomic Analysis of Hot Spring Water in the Kirishima Area, Japan.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {6}, number = {}, pages = {202}, doi = {10.3389/fbioe.2018.00202}, pmid = {30619848}, issn = {2296-4185}, abstract = {Diverse microorganisms specifically inhabit extreme environments, such as hot springs and deep-sea hydrothermal vents. To test the hypothesis that the microbial community structure is predictable based on environmental factors characteristic of such extreme environments, we conducted correlation analyses of microbial taxa/functions and environmental factors using metagenomic and 61 types of physicochemical data of water samples from nine hot springs in the Kirishima area (Kyusyu, Japan), where hot springs with diverse chemical properties are distributed in a relatively narrow area. Our metagenomic analysis revealed that the samples can be classified into two major types dominated by either phylum Crenarchaeota or phylum Aquificae. The correlation analysis showed that Crenarchaeota dominated in nutrient-rich environments with high concentrations of ions and total carbons, whereas Aquificae dominated in nutrient-poor environments with low ion concentrations. These environmental factors were also important explanatory variables in the generalized linear models constructed to predict the abundances of Crenarchaeota or Aquificae. Functional enrichment analysis of genes also revealed that the separation of the two major types is primarily attributable to genes involved in autotrophic carbon fixation, sulfate metabolism and nitrate reduction. Our results suggested that Aquificae and Crenarchaeota play a vital role in the Kirishima hot spring water ecosystem through their metabolic pathways adapted to each environment. Our findings provide a basis to predict microbial community structures in hot springs from environmental parameters, and also provide clues for the exploration of biological resources in extreme environments.}, }
@article {pmid30619804, year = {2018}, author = {Bachmann, NL and Rockett, RJ and Timms, VJ and Sintchenko, V}, title = {Advances in Clinical Sample Preparation for Identification and Characterization of Bacterial Pathogens Using Metagenomics.}, journal = {Frontiers in public health}, volume = {6}, number = {}, pages = {363}, doi = {10.3389/fpubh.2018.00363}, pmid = {30619804}, issn = {2296-2565}, abstract = {Whole genome sequencing (WGS) plays an increasing role in communicable disease control through high-resolution outbreak tracing, laboratory surveillance and diagnostics. However, WGS has traditionally relied on microbial culture in order to obtain pathogen specific DNA for sequencing. This has severely limited the application of whole genome sequencing on pathogens with fastidious culturing requirements. In addition, the widespread adoption of culture-independent diagnostic tests has reduced availability of cultured isolates for confirmatory testing and surveillance. These recent developments have created demand for the implementation of techniques enabling direct sequencing of microbial genomes in clinical samples without having to culture an isolate. However, sequencing of specific organisms from clinical samples can be affected by high levels of contaminating DNA from the host and other commensal microorganisms. Several methods have been introduced for selective lysis of host cells and/or separate specific organisms from a clinical sample. This review examines the different approaches for sample preparation that have been used in diagnostic and public health laboratories for metagenomic sequencing.}, }
@article {pmid30619779, year = {2018}, author = {Hu, YL and Pang, W and Huang, Y and Zhang, Y and Zhang, CJ}, title = {The Gastric Microbiome Is Perturbed in Advanced Gastric Adenocarcinoma Identified Through Shotgun Metagenomics.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {433}, doi = {10.3389/fcimb.2018.00433}, pmid = {30619779}, issn = {2235-2988}, abstract = {Objective: Dysbiosis of gastric microbiota such as Helicobacter pylori plays a significant role in pathogenesis and progression of gastric cancer. Our aim was to evaluate the composition and functional effects of gastric microbiota in superficial gastritis (SG) and advanced gastric adenocarcinoma (GC). Methods: We carried out shotgun metagenomic sequencing on gastric wash samples from 6 patients with GC and 5 patients with SG. The taxonomic composition was profiled using MetaPhlAn2 and functional gene pathway was profiled using HUMAnN2. Differences in microbial composition and pathways between the two patient groups were assessed via LEfSe. Results: The gastric microbiota in GC patients was characterized by reduced species richness, enrichment of 13 bacterial taxa and depletion of 31 taxa (q < 0.05). The most representative taxa which were abundant in GC corresponded to the commensals or opportunistic pathogens that usually colonize the oral cavity, including genera Neisseria, Alloprevotella, and Aggregatibacter, species Streptococcus_mitis_oralis_pneumoniae and strain Porphyromonas_endodontalis.t_GCF_000174815. Each of the three GC-associated genera could separate GC from SG completely. In particular, Sphingobium yanoikuyae, a bacterium capable of degrading carcinogenic compounds, was depleted in GC. Functionally, pathways associated with the biosynthesis of lipopolysaccharide (LPS) and L-arginine were enriched in GC, whereas pathways involved in the fermentation of short chain fatty acids (SCFAs) and branched amino acid metabolism were more abundant in SG. Conclusions: Our results present new alterations in the gastric microbiome in patients with GC from a whole-genome perspective, suggesting that microbiome composition and function can be used for prognosis and diagnosis of GC.}, }
@article {pmid30619503, year = {2018}, author = {Cai, FF and Zhou, WJ and Wu, R and Su, SB}, title = {Systems biology approaches in the study of Chinese herbal formulae.}, journal = {Chinese medicine}, volume = {13}, number = {}, pages = {65}, doi = {10.1186/s13020-018-0221-x}, pmid = {30619503}, issn = {1749-8546}, abstract = {Systems biology is an academic field that attempts to integrate different levels of information to understand how biological systems function. It is the study of the composition of all components of a biological system and their interactions under specific conditions. The core of systems biology is holistic and systematic research, which is different from the manner of thinking and research of all other branches of biology to date. Chinese herbal formulae (CHF) are the main form of Chinese medicine and are composed of single Chinese herbal medicines (CHMs) with pharmacological and pharmacodynamic compatibility. When single CHMs are combined into CHF, the result is different from the original effect of a single drug and can be better adapted to more diseases with complex symptoms. CHF represent a complex system with multiple components, targets and effects. Therefore, the use of systems biology is conducive to revealing the complex characteristics of CHF. With the rapid development of omics technologies, systems biology has been widely and increasingly applied to the study of the basis of the pharmacological substances, action targets and mechanisms of CHF. To meet the challenges of multiomics synthesis-intensive studies and system dynamics research in CHF, this paper reviews the common techniques of genomics, transcriptomics, proteomics, metabolomics, and metagenomics and their applications in research on CHF.}, }
@article {pmid30619215, year = {2018}, author = {Han, M and Yang, P and Zhong, C and Ning, K}, title = {The Human Gut Virome in Hypertension.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3150}, doi = {10.3389/fmicb.2018.03150}, pmid = {30619215}, issn = {1664-302X}, abstract = {Objectives: Previous studies have reported that the gut microbiome has an important link with the development of hypertension. Though previous researches have focused on the links of gut bacteria with hypertension, little has been known about the linkage of gut viruses to hypertension and the development of hypertension, largely due to the lack of data mining tools for such investigation. In this work, we have analyzed 196 fecal metagenomic data related to hypertension aiming to profile the gut virome and link the gut virome to pre-hypertension and hypertension. Design: Here, we have applied a statistically sound method for mining of gut virome data and linking gut virome to hypertension. We characterized the viral composition and bacterial composition of 196 samples, identified the viral-type of each sample and linked gut virome to hypertension. Results: We stratified these 196 fecal samples into two viral-types and selected 32 viruses as the biomarkers for these groups. We found that viruses could have a superior resolution and discrimination power than bacteria for differentiation of healthy samples and pre-hypertension samples, as well as hypertension samples. Moreover, as to the co-occurrence networks linking viruses and bacteria, we found increasingly pervasive virus-bacteria linkages from healthy people to pre-hypertension people to hypertension patients. Conclusion: Overall, our results have shown ample indications of the link between human gut virome and hypertension, and could help provide microbial solutions toward early diagnoses of hypertension.}, }
@article {pmid30619209, year = {2018}, author = {Suzuki, S and Nealson, KH and Ishii, S}, title = {Genomic and in-situ Transcriptomic Characterization of the Candidate Phylum NPL-UPL2 From Highly Alkaline Highly Reducing Serpentinized Groundwater.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3141}, doi = {10.3389/fmicb.2018.03141}, pmid = {30619209}, issn = {1664-302X}, abstract = {Serpentinization is a process whereby water interacts with reduced mantle rock called peridotite to produce a new suite of minerals (e.g., serpentine), a highly alkaline fluid, and hydrogen. In previous reports, we identified abundance of microbes of the candidate phylum NPL-UPA2 in a serpentinization site called The Cedars. Here, we report the first metagenome assembled genome (MAG) of the candidate phylum as well as the in-situ gene expression. The MAG of the phylum NPL-UPA2, named Unc8, is only about 1 Mbp and its biosynthetic properties suggest it should be capable of independent growth. In keeping with the highly reducing niche of Unc8, its genome encodes none of the known oxidative stress response genes including superoxide dismutases. With regard to energy metabolism, the MAG of Unc8 encodes all enzymes for Wood-Ljungdahl acetogenesis pathway, a ferredoxin:NAD+ oxidoreductase (Rnf) and electron carriers for flavin-based electron bifurcation (Etf, Hdr). Furthermore, the transcriptome of Unc8 in the waters of The Cedars showed enhanced levels of gene expression in the key enzymes of the Wood-Ljungdahl pathway [e.g., Carbon monoxide dehydrogenase /Acetyl-CoA synthase complex (CODH/ACS), Rnf, Acetyl-CoA synthetase (Acd)], which indicated that the Unc8 is an acetogen. However, the MAG of Unc8 encoded no well-known hydrogenase genes, suggesting that the energy metabolism of Unc8 might be focused on CO as the carbon and energy sources for the acetate formation. Given that CO could be supplied via abiotic reaction associated with deep subsurface serpentinization, while available CO2 would be at extremely low concentrations in this high pH environment, CO-associated metabolism could provide advantageous approach. The CODH/ACS in Unc8 is a Bacteria/Archaea hybrid type of six-subunit complex and the electron carriers, Etf and Hdr, showed the highest similarity to those in Archaea, suggesting that archaeal methanogenic energy metabolism was incorporated into the bacterial acetogenesis in NPL-UPA2. Given that serpentinization systems are viewed as potential habitats for early life, and that acetogenesis via the Wood-Ljungdahl pathway is proposed as an energy metabolism of Last Universal Common Ancestor, a phylogenetically distinct acetogen from an early earth analog site may provide important insights in primordial lithotrophs and their habitat.}, }
@article {pmid30619206, year = {2018}, author = {Guo, M and Chen, J and Li, Q and Fu, Y and Fan, G and Ma, J and Peng, L and Zeng, L and Chen, J and Wang, Y and Lee, SM}, title = {Dynamics of Gut Microbiome in Giant Panda Cubs Reveal Transitional Microbes and Pathways in Early Life.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3138}, doi = {10.3389/fmicb.2018.03138}, pmid = {30619206}, issn = {1664-302X}, abstract = {Adult giant pandas (Ailuropoda melanoleuca) express transitional characteristics in that they consume bamboos, despite their carnivore-like digestive tracts. Their genome contains no cellulolytic enzymes; therefore, understanding the development of the giant panda gut microbiome, especially in early life, is important for decoding the rules underlying gut microbial formation, inheritance and dietary transitions. With deep metagenomic sequencing, we investigated the gut microbiomes of two newborn giant panda brothers and their parents living in Macao, China, from 2016 to 2017. Both giant panda cubs exhibited progressive increases in gut microbial richness during growth, particularly from the 6th month after birth. Enterobacteriaceae dominated the gut microbial compositions in both adult giant pandas and cubs. A total of 583 co-abundance genes (CAGs) and about 79 metagenomic species (MGS) from bacteria or viruses displayed significant changes with age. Seven genera (Shewanella, Oblitimonas, Helicobacter, Haemophilus, Aeromonas, Listeria, and Fusobacterium) showed great importance with respect to gut microbial structural determination in the nursing stage of giant panda cubs. Furthermore, 10 orthologous gene functions and 44 pathways showed significant changes with age. Of the significant pathways, 16 from Escherichia, Klebsiella, Propionibacterium, Lactobacillus, and Lactococcus displayed marked differences between parents and their cubs at birth, while 29 pathways from Escherichia, Campylobacter and Lactobacillus exhibited significant increase in cubs from 6 to 9 months of age. In addition, oxidoreductases, transferases, and hydrolases dominated the significantly changed gut microbial enzymes during the growth of giant panda cubs, while few of them were involved in cellulose degradation. The findings indicated diet-stimulated gut microbiome transitions and the important role of Enterobacteriaceae in the guts of giant panda in early life.}, }
@article {pmid30619174, year = {2018}, author = {Sharma, A and Schmidt, M and Kiesel, B and Mahato, NK and Cralle, L and Singh, Y and Richnow, HH and Gilbert, JA and Arnold, W and Lal, R}, title = {Bacterial and Archaeal Viruses of Himalayan Hot Springs at Manikaran Modulate Host Genomes.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3095}, doi = {10.3389/fmicb.2018.03095}, pmid = {30619174}, issn = {1664-302X}, abstract = {Hot spring-associated viruses, particularly the archaeal viruses, remain under-examined compared to bacteriophages. Previous metagenomic studies of the Manikaran hot springs in India suggested an abundance of viral DNA, which prompted us to examine the virus-host (bacterial and archaeal) interactions in sediment and microbial mat samples collected from the thermal discharges. Here, we characterize the viruses (both bacterial and archaeal) from this Himalayan hot spring using both metagenomics assembly and electron microscopy. We utilized four shotgun samples from sediment (78-98°C) and two from microbial mats (50°C) to reconstruct 65 bacteriophage genomes (24-200 kb). We also identified 59 archaeal viruses that were notably abundant across the sediment samples. Whole-genome analyses of the reconstructed bacteriophage genomes revealed greater genomic conservation in sediments (65%) compared to microbial mats (49%). However, a minimal phage genome was still maintained across both sediment and microbial mats suggesting a common origin. To complement the metagenomic data, scanning-electron and helium-ion microscopy were used to reveal diverse morphotypes of Caudovirales and archaeal viruses. The genome level annotations provide further evidence for gene-level exchange between virus and host in these hot springs, and augments our knowledgebase for bacteriophages, archaeal viruses and Clustered Regularly Interspaced Short Palindromic Repeat cassettes, which provide a critical resource for studying viromes in extreme natural environments.}, }
@article {pmid30619142, year = {2018}, author = {Nasko, DJ and Chopyk, J and Sakowski, EG and Ferrell, BD and Polson, SW and Wommack, KE}, title = {Family A DNA Polymerase Phylogeny Uncovers Diversity and Replication Gene Organization in the Virioplankton.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3053}, doi = {10.3389/fmicb.2018.03053}, pmid = {30619142}, issn = {1664-302X}, support = {P20 GM103446/GM/NIGMS NIH HHS/United States ; }, abstract = {Shotgun metagenomics, which allows for broad sampling of viral diversity, has uncovered genes that are widely distributed among virioplankton populations and show linkages to important biological features of unknown viruses. Over 25% of known dsDNA phage carry the DNA polymerase I (polA) gene, making it one of the most widely distributed phage genes. Because of its pivotal role in DNA replication, this enzyme is linked to phage lifecycle characteristics. Previous research has suggested that a single amino acid substitution might be predictive of viral lifestyle. In this study Chesapeake Bay virioplankton were sampled by shotgun metagenomic sequencing (using long and short read technologies). More polA sequences were predicted from this single viral metagenome (virome) than from 86 globally distributed virome libraries (ca. 2,100, and 1,200, respectively). The PolA peptides predicted from the Chesapeake Bay virome clustered with 69% of PolA peptides from global viromes; thus, remarkably the Chesapeake Bay virome captured the majority of known PolA peptide diversity in viruses. This deeply sequenced virome also expanded the diversity of PolA sequences, increasing the number of PolA clusters by 44%. Contigs containing polA sequences were also used to examine relationships between phylogenetic clades of PolA and other genes within unknown viral populations. Phylogenic analysis revealed five distinct groups of phages distinguished by the amino acids at their 762 (Escherichia coli IAI39 numbering) positions and replication genes. DNA polymerase I sequences from Tyr762 and Phe762 groups were most often neighbored by ring-shaped superfamily IV helicases and ribonucleotide reductases (RNRs). The Leu762 groups had non-ring shaped helicases from superfamily II and were further distinguished by an additional helicase gene from superfamily I and the lack of any identifiable RNR genes. Moreover, we found that the inclusion of ribonucleotide reductase associated with PolA helped to further differentiate phage diversity, chiefly within lytic podovirus populations. Altogether, these data show that DNA Polymerase I is a useful marker for observing the diversity and composition of the virioplankton and may be a driving factor in the divergence of phage replication components.}, }
@article {pmid30619134, year = {2018}, author = {Porcar, M and Louie, KB and Kosina, SM and Van Goethem, MW and Bowen, BP and Tanner, K and Northen, TR}, title = {Microbial Ecology on Solar Panels in Berkeley, CA, United States.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3043}, doi = {10.3389/fmicb.2018.03043}, pmid = {30619134}, issn = {1664-302X}, abstract = {Solar panels can be found practically all over the world and represent a standard surface that can be colonized by microbial communities that are resistant to harsh environmental conditions, including high irradiation, temperature fluctuations and desiccation. These properties make them not only ideal sources of stress-resistant bacteria, but also standard devices to study the microbial communities and their colonization process from different areas of Earth. We report here a comprehensive description of the microbial communities associated with solar panels in Berkeley, CA, United States. Cultivable bacteria were isolated to characterize their adhesive capabilities, and UV- and desiccation-resistance properties. Furthermore, a parallel culture-independent metagenomic and metabolomic approach has allowed us to gain insight on the taxonomic and functional nature of these communities. Metagenomic analysis was performed using the Illumina HiSeq2500 sequencing platform, revealing that the bacterial population of the Berkeley solar panels is composed mainly of Actinobacteria, Bacteroidetes and Proteobacteria, as well as lower amounts of Deinococcus-Thermus and Firmicutes. Furthermore, a clear predominance of Hymenobacter sp. was also observed. A functional analysis revealed that pathways involved in the persistence of microbes on solar panels (i.e., stress response, capsule development, and metabolite repair) and genes assigned to carotenoid biosynthesis were common to all metagenomes. On the other hand, genes involved in photosynthetic pathways and general autotrophic subsystems were rare, suggesting that these pathways are not critical for persistence on solar panels. Metabolomics was performed using a liquid chromatography tandem mass spectrometry (LC-MS/MS) approach. When comparing the metabolome of the solar panels from Berkeley and from Valencia (Spain), a very similar composition in polar metabolites could be observed, although some metabolites appeared to be differentially represented (for example, trigonelline, pantolactone and 5-valerolactone were more abundant in the samples from Valencia than in the ones from Berkeley). Furthermore, triglyceride metabolites were highly abundant in all the solar panel samples, and both locations displayed similar profiles. The comparison of the taxonomic profile of the Californian solar panels with those previously described in Spain revealed striking similarities, highlighting the central role of both selective pressures and the ubiquity of microbial populations in the colonization and establishment of microbial communities.}, }
@article {pmid30619130, year = {2018}, author = {Timmers, PHA and Vavourakis, CD and Kleerebezem, R and Damsté, JSS and Muyzer, G and Stams, AJM and Sorokin, DY and Plugge, CM}, title = {Metabolism and Occurrence of Methanogenic and Sulfate-Reducing Syntrophic Acetate Oxidizing Communities in Haloalkaline Environments.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3039}, doi = {10.3389/fmicb.2018.03039}, pmid = {30619130}, issn = {1664-302X}, support = {322551//European Research Council/International ; 323009//European Research Council/International ; }, abstract = {Anaerobic syntrophic acetate oxidation (SAO) is a thermodynamically unfavorable process involving a syntrophic acetate oxidizing bacterium (SAOB) that forms interspecies electron carriers (IECs). These IECs are consumed by syntrophic partners, typically hydrogenotrophic methanogenic archaea or sulfate reducing bacteria. In this work, the metabolism and occurrence of SAOB at extremely haloalkaline conditions were investigated, using highly enriched methanogenic (M-SAO) and sulfate-reducing (S-SAO) cultures from south-western Siberian hypersaline soda lakes. Activity tests with the M-SAO and S-SAO cultures and thermodynamic calculations indicated that H2 and formate are important IECs in both SAO cultures. Metagenomic analysis of the M-SAO cultures showed that the dominant SAOB was 'Candidatus Syntrophonatronum acetioxidans,' and a near-complete draft genome of this SAOB was reconstructed. 'Ca. S. acetioxidans' has all genes necessary for operating the Wood-Ljungdahl pathway, which is likely employed for acetate oxidation. It also encodes several genes essential to thrive at haloalkaline conditions; including a Na+-dependent ATP synthase and marker genes for 'salt-out' strategies for osmotic homeostasis at high soda conditions. Membrane lipid analysis of the M-SAO culture showed the presence of unusual bacterial diether membrane lipids which are presumably beneficial at extreme haloalkaline conditions. To determine the importance of SAO in haloalkaline environments, previously obtained 16S rRNA gene sequencing data and metagenomic data of five different hypersaline soda lake sediment samples were investigated, including the soda lakes where the enrichment cultures originated from. The draft genome of 'Ca. S. acetioxidans' showed highest identity with two metagenome-assembled genomes (MAGs) of putative SAOBs that belonged to the highly abundant and diverse Syntrophomonadaceae family present in the soda lake sediments. The 16S rRNA gene amplicon datasets of the soda lake sediments showed a high similarity of reads to 'Ca. S. acetioxidans' with abundance as high as 1.3% of all reads, whereas aceticlastic methanogens and acetate oxidizing sulfate-reducers were not abundant (≤0.1%) or could not be detected. These combined results indicate that SAO is the primary anaerobic acetate oxidizing pathway at extreme haloalkaline conditions performed by haloalkaliphilic syntrophic consortia.}, }
@article {pmid30619117, year = {2018}, author = {López-García, A and Pineda-Quiroga, C and Atxaerandio, R and Pérez, A and Hernández, I and García-Rodríguez, A and González-Recio, O}, title = {Comparison of Mothur and QIIME for the Analysis of Rumen Microbiota Composition Based on 16S rRNA Amplicon Sequences.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3010}, doi = {10.3389/fmicb.2018.03010}, pmid = {30619117}, issn = {1664-302X}, abstract = {Background: Microbiome studies need to analyze massive sequencing data, which requires the use of sophisticated bioinformatics pipelines. Up to date, several tools are available, although the literature is scarce on studies that compare the performance of different bioinformatics pipelines on rumen microbiota when 16S rRNA amplicons are analyzed. The impact of the pipeline on the outcome of the results is also unknown, mainly in terms of the output from studies using these tools as an intermediate phenotype (pseudophenotypes). This study compares two commonly used software (Quantitative Insights Into Microbial Ecology) (QIIME) and mothur, and two microbial gene data bases (GreenGenes and SILVA) for 16S rRNA gene analysis, using metagenome read data collected from rumen content of a cohort of dairy cows. Results: We compared the relative abundance (RA) of the identified OTUs at the genus level. Both tools presented a high degree of agreement at identifying the most abundant genera: Bifidobacterium, Butyrivibrio, Methanobrevibacter, Prevotella, and Succiniclasticum (RA > 1%), regardless the database. There were no statistical differences between mothur and QIIME (P > 0.05) at estimating the overall RA of the most abundant (RA > 10%) genera, either using SILVA or GreenGenes. However, differences were found at RA < 10% (P < 0.05) when using GreenGenes as database, with mothur assigning OTUs to a larger number of genera and in larger RA for these less frequent microorganisms. With this database mothur resulted in larger richness (P < 0.05), more favorable rarefaction curves and a larger analytic sensitivity. These differences caused significant and relevant differences between tools at identifying the dissimilarity of microbiotas between pairs of animals. However, these differences were attenuated, but not erased, when SILVA was used as the reference database. Conclusion: The findings showed that the SILVA database seemed a preferred reference dataset for classifying OTUs from rumen microbiota. If this database was used, both QIIME and mothur produced comparable richness and diversity, and also in the RA of most common rumen microbes. However, important differences were found for less common microorganisms which impacted on the beta diversity calculated between pipelines. This may have relevant implications at studying global rumen microbiota.}, }
@article {pmid30619102, year = {2018}, author = {Gupta, A and Dutta, A and Sarkar, J and Panigrahi, MK and Sar, P}, title = {Low-Abundance Members of the Firmicutes Facilitate Bioremediation of Soil Impacted by Highly Acidic Mine Drainage From the Malanjkhand Copper Project, India.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2882}, doi = {10.3389/fmicb.2018.02882}, pmid = {30619102}, issn = {1664-302X}, abstract = {Sulfate- and iron-reducing heterotrophic bacteria represented minor proportion of the indigenous microbial community of highly acidic, oligotrophic acid mine drainage (AMD), but they can be successfully stimulated for in situ bioremediation of an AMD impacted soil (AIS). These anaerobic microorganisms although played central role in sulfate- and metal-removal, they remained inactive in the AIS due to the paucity of organic carbon and extreme acidity of the local environment. The present study investigated the scope for increasing the abundance and activity of inhabitant sulfate- and iron-reducing bacterial populations of an AIS from Malanjkhand Copper Project. An AIS of pH 3.5, high soluble SO42- (7838 mg/l) and Fe (179 mg/l) content was amended with nutrients (cysteine and lactate). Thorough geochemical analysis, 16S rRNA gene amplicon sequencing and qPCR highlighted the intrinsic metabolic abilities of native bacteria in AMD bioremediation. Following 180 days incubation, the nutrient amended AIS showed marked increase in pH (to 6.6) and reduction in soluble -SO42- (95%), -Fe (50%) and other heavy metals. Concomitant to physicochemical changes a vivid shift in microbial community composition was observed. Members of the Firmicutes present as a minor group (1.5% of total community) in AIS emerged as the single most abundant taxon (∼56%) following nutrient amendments. Organisms affiliated to Clostridiaceae, Peptococcaceae, Veillonellaceae, Christensenellaceae, Lachnospiraceae, Bacillaceae, etc. known for their fermentative, iron and sulfate reducing abilities were prevailed in the amended samples. qPCR data corroborated with this change and further revealed an increase in abundance of dissimilatory sulfite reductase gene (dsrB) and specific bacterial taxa. Involvement of these enhanced populations in reductive processes was validated by further enrichments and growth in sulfate- and iron-reducing media. Amplicon sequencing of these enrichments confirmed growth of Firmicutes members and proved their sulfate- and iron-reduction abilities. This study provided a better insight on ecological perspective of Firmicutes members within the AMD impacted sites, particularly their involvement in sulfate- and iron-reduction processes, in situ pH management and bioremediation.}, }
@article {pmid30618066, year = {2019}, author = {Flores-Uribe, J and Hevroni, G and Ghai, R and Pushkarev, A and Inoue, K and Kandori, H and Béjà, O}, title = {Heliorhodopsins are absent in diderm (Gram-negative) bacteria: Some thoughts and possible implications for activity.}, journal = {Environmental microbiology reports}, volume = {}, number = {}, pages = {}, doi = {10.1111/1758-2229.12730}, pmid = {30618066}, issn = {1758-2229}, support = {545/17//Israel Science Foundation/ ; }, abstract = {Microbial heliorhodopsins are a new type of rhodopsins, currently believed to engage in light sensing, with an opposite membrane topology compared to type-1 and type-2 rhodopsins. We determined heliorhodopsins presence/absence is monoderms and diderms representatives from the Tara Oceans and freshwater metagenomes as well as metagenome assembled genome collections. Heliorhodopsins are absent in diderms, confirming our previous observations in cultured Proteobacteria. We do not rule out the possibility that heliorhodopsins serve as light sensors. However, this does not easily explain their absence from diderms. Based on these observations, we speculate on the putative role of heliorhodopsins in light-driven transport of amphiphilic molecules.}, }
@article {pmid30616913, year = {2019}, author = {Martinez, MA and Woodcroft, BJ and Ignacio Espinoza, JC and Zayed, AA and Singleton, CM and Boyd, JA and Li, YF and Purvine, S and Maughan, H and Hodgkins, SB and Anderson, D and Sederholm, M and Temperton, B and Bolduc, B and Saleska, SR and Tyson, GW and Rich, VI and , and Saleska, SR and Tyson, GW and Rich, VI}, title = {Discovery and ecogenomic context of a global Caldiserica-related phylum active in thawing permafrost, Candidatus Cryosericota phylum nov., Ca. Cryosericia class nov., Ca. Cryosericales ord. nov., Ca. Cryosericaceae fam. nov., comprising the four species Cryosericum septentrionale gen. nov. sp. nov., Ca. C. hinesii sp. nov., Ca. C. odellii sp. nov., Ca. C. terrychapinii sp. nov.}, journal = {Systematic and applied microbiology}, volume = {42}, number = {1}, pages = {54-66}, doi = {10.1016/j.syapm.2018.12.003}, pmid = {30616913}, issn = {1618-0984}, mesh = {Bacteria/*classification/genetics/isolation & purification ; Bacterial Typing Techniques ; Cold Temperature ; DNA, Bacterial/genetics ; Metagenome ; Permafrost/*microbiology ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sweden ; }, abstract = {The phylum Caldiserica was identified from the hot spring 16S rRNA gene lineage 'OP5' and named for the sole isolate Caldisericum exile, a hot spring sulfur-reducing chemoheterotroph. Here we characterize 7 Caldiserica metagenome-assembled genomes (MAGs) from a thawing permafrost site in Stordalen Mire, Arctic Sweden. By 16S rRNA and marker gene phylogenies, and average nucleotide and amino acid identities, these Stordalen Mire Caldiserica (SMC) MAGs form part of a divergent clade from C. exile. Genome and meta-transcriptome and proteome analyses suggest that unlike Caldisericum, the SMCs (i) are carbohydrate- and possibly amino acid fermenters that can use labile plant compounds and peptides, and (ii) encode adaptations to low temperature. The SMC clade rose to community dominance within permafrost, with a peak metagenome-based relative abundance of ∼60%. It was also physiologically active in the upper seasonally-thawed soil. Beyond Stordalen Mire, analysis of 16S rRNA gene surveys indicated a global distribution of this clade, predominantly in anaerobic, carbon-rich and cold environments. These findings establish the SMCs as four novel phenotypically and ecologically distinct species within a single novel genus, distinct from C. exile clade at the phylum level. The SMCs are thus part of a novel cold-habitat phylum for an understudied, globally-distributed superphylum encompassing the Caldiserica. We propose the names Candidatus Cryosericota phylum nov., Ca. Cryosericia class nov., Ca. Cryosericales ord. nov., Ca. Cryosericaceae fam. nov., Ca. Cryosericum gen. nov., Ca. Cryosericum septentrionale sp. nov., Ca. C. hinesii sp. nov., Ca. C. odellii sp. nov., and Ca. C. terrychapinii sp. nov.}, }
@article {pmid30616051, year = {2019}, author = {Zhao, R and Feng, J and Liu, J and Fu, W and Li, X and Li, B}, title = {Deciphering of microbial community and antibiotic resistance genes in activated sludge reactors under high selective pressure of different antibiotics.}, journal = {Water research}, volume = {151}, number = {}, pages = {388-402}, doi = {10.1016/j.watres.2018.12.034}, pmid = {30616051}, issn = {1879-2448}, abstract = {Currently, the effects of high antibiotic concentrations on the performance of microbiota and antibiotic resistance genes (ARGs) in activated sludge (AS) process are not well characterized. Lab-scale batch reactors were performed to evaluate the dynamics of microbial community and ARGs in response to six antibiotics at different concentrations using high-throughput sequencing-based 16S rRNA gene and metagenomic analyses. The presence of antibiotics remarkably decreased the microbial diversity, caused a great change of the microbiota structure, and exerted a selective pressure on the enrichment of potential antibiotic resistant bacteria (ARB), such as Arthrobacter, Thauera, Geothrix, Rudaea, Aridibacter, Conexibacter, Terrimonas, etc. High antibiotic selective pressures increased ARG abundance but simultaneously reduced ARG number. In total, 491 ARG subtypes belonging to 20 ARG types were detected and kanamycin treatment showed the highest ARG abundances. A core set of 54 ARG subtypes that accounted for 66.7%-99.6% of the total ARG abundances were shared by all samples. The increase of the abundances of both corresponding and non-corresponding ARGs under a specific antibiotic treatment revealed the collateral effects of antibiotic selective pressure. Microbial community may play an important role in the composition of ARGs. Network analysis indicated that both internal-type and external-type of ARGs exhibited higher non-random co-occurrence incidences and 18 genera were speculated as the possible hosts for multiple ARGs. This study deciphered the profiles and relationships between microbial community and ARGs in AS process treating wastewater with high antibiotic concentrations and could provide helpful guidance for controlling the development and dissemination of ARB and ARGs.}, }
@article {pmid30612540, year = {2019}, author = {Singh, I and Kuscuoglu, M and Harkins, DM and Sutton, G and Fouts, DE and Nelson, KE}, title = {OMeta: an ontology-based, data-driven metadata tracking system.}, journal = {BMC bioinformatics}, volume = {20}, number = {1}, pages = {8}, doi = {10.1186/s12859-018-2580-9}, pmid = {30612540}, issn = {1471-2105}, support = {HHSN272200900007C/AI/NIAID NIH HHS/United States ; U19 AI110819/AI/NIAID NIH HHS/United States ; HHSN272200900007C,U19AI110819//National Institute of Allergy and Infectious Diseases/ ; }, mesh = {*Biological Ontologies ; Databases, Factual ; *Metadata ; Metagenomics ; Phylogeny ; *Software ; User-Computer Interface ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: The development of high-throughput sequencing and analysis has accelerated multi-omics studies of thousands of microbial species, metagenomes, and infectious disease pathogens. Omics studies are enabling genotype-phenotype association studies which identify genetic determinants of pathogen virulence and drug resistance, as well as phylogenetic studies designed to track the origin and spread of disease outbreaks. These omics studies are complex and often employ multiple assay technologies including genomics, metagenomics, transcriptomics, proteomics, and metabolomics. To maximize the impact of omics studies, it is essential that data be accompanied by detailed contextual metadata (e.g., specimen, spatial-temporal, phenotypic characteristics) in clear, organized, and consistent formats. Over the years, many metadata standards developed by various metadata standards initiatives have arisen; the Genomic Standards Consortium's minimal information standards (MIxS), the GSCID/BRC Project and Sample Application Standard. Some tools exist for tracking metadata, but they do not provide event based capabilities to configure, collect, validate, and distribute metadata. To address this gap in the scientific community, an event based data-driven application, OMeta, was created that allows users to quickly configure, collect, validate, distribute, and integrate metadata.
RESULTS: A data-driven web application, OMeta, has been developed for use by researchers consisting of a browser-based interface, a command-line interface (CLI), and server-side components that provide an intuitive platform for configuring, capturing, viewing, and sharing metadata. Project and sample metadata can be set based on existing standards or based on projects goals. Recorded information includes details on the biological samples, procedures, protocols, and experimental technologies, etc. This information can be organized based on events, including sample collection, sample quantification, sequencing assay, and analysis results. OMeta enables configuration in various presentation types: checkbox, file, drop-box, ontology, and fields can be configured to use the National Center for Biomedical Ontology (NCBO), a biomedical ontology server. Furthermore, OMeta maintains a complete audit trail of all changes made by users and allows metadata export in comma separated value (CSV) format for convenient deposition of data into public databases.
CONCLUSIONS: We present, OMeta, a web-based software application that is built on data-driven principles for configuring and customizing data standards, capturing, curating, and sharing metadata.}, }
@article {pmid30612183, year = {2019}, author = {Ding, W and Zhang, W and Alikunhi, NM and Batang, Z and Pei, B and Wang, R and Chen, L and Al-Suwailem, A and Qian, PY}, title = {Metagenomic Analysis of Zinc Surface-Associated Marine Biofilms.}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {406-416}, doi = {10.1007/s00248-018-01313-3}, pmid = {30612183}, issn = {1432-184X}, mesh = {Bacteria/classification/*genetics/isolation & purification ; Bacterial Physiological Phenomena ; Biodiversity ; *Biofilms ; Indian Ocean ; Metagenomics ; Phylogeny ; Seawater/analysis/*microbiology ; Zinc/analysis/*metabolism ; }, abstract = {Biofilms are a significant source of marine biofouling. Marine biofilm communities are established when microorganisms adhere to immersed surfaces. Despite the microbe-inhibiting effect of zinc surfaces, microbes can still attach to the surface and form biofilms. However, the diversity of biofilm-forming microbes that can attach to zinc surfaces and their common functional features remain elusive. Here, by analyzing 9,000,000 16S rRNA gene amplicon sequences and 270 Gb of metagenomic data, we comprehensively explored the taxa and functions related to biofilm formation in subtidal zones of the Red Sea. A clear difference was observed between the biofilm and adjacent seawater microbial communities in terms of the taxonomic structure at phylum and genus levels, and a huge number of genera were only present in the biofilms. Saturated alpha-diversity curves suggested the existence of more than 14,000 operational taxonomic units in one biofilm sample, which is much higher than previous estimates. Remarkably, the biofilms contained abundant and diverse transposase genes, which were localized along microbial chromosomal segments and co-existed with genes related to metal ion transport and resistance. Genomic analyses of two cyanobacterial strains that were abundant in the biofilms revealed a variety of metal ion transporters and transposases. Our analyses revealed the high diversity of biofilm-forming microbes that can attach to zinc surfaces and the ubiquitous role of transposase genes in microbial adaptation to toxic metal surfaces.}, }
@article {pmid30612083, year = {2019}, author = {Zhu, X and Campanaro, S and Treu, L and Kougias, PG and Angelidaki, I}, title = {Novel ecological insights and functional roles during anaerobic digestion of saccharides unveiled by genome-centric metagenomics.}, journal = {Water research}, volume = {151}, number = {}, pages = {271-279}, doi = {10.1016/j.watres.2018.12.041}, pmid = {30612083}, issn = {1879-2448}, abstract = {In typical anaerobic digestion (AD) systems, the microbial functional assertion is hampered by synchronised versatile metabolism required for heterogeneous substrates degradation. Thus, the intricate methanogenic process from organic compounds remains an enigma after decades of empirical operation. In this study, simplified AD microbial communities were obtained with substrate specifications and continuous reactor operation. Genome-centric metagenomic approach was followed to holistically investigate the metabolic pathways of the AD and the microbial synergistic networks. In total, 63 metagenome assembled genomes (MAGs) were assembled from 8 metagenomes acquired in specific methanogenic niches. The metabolic pathways were reconstructed from the annotated genes and their dynamicity under experimental conditions. The results show that the methanogenic niches nourish unique metabolism beyond current knowledge acquired from cultivation-based methods. A novel glucose mineralization model without acetate formation was proposed and asserted in a pair of syntrophs: Clostridiaceae sp. and Methanoculleus thermophilus. Moreover, the catabolic pathway was elucidated in uncharacterized syntrophic acetate oxidizers, Synergistaceae spp. A remarkable evolutionary insight is the discovery that electron transport and energy conservation mechanisms impose selective pressure on syntrophic partners. Overall, the functional roles of the individual microbes tightly rely on the catabolic pathways and cannot always be physiologically defined in accordance with conventional four-step AD concept. The substrate-specific systems provided a traceable microbial community to dissecting the AD process. The genome-centric metagenomics successfully constructed genomes of microbes that have not been previously isolated and illustrated metabolic pathways that beyond the current knowledge of AD process. This study provides new perspectives to unravel the AD microbial ecology and suggests more attention should be paid on uncharacterized metabolism specifically harboured by AD microbial communities.}, }
@article {pmid30612042, year = {2019}, author = {Gahan, ME and Bowman, S and Chevalier, R and Rossi, R and Nelson, M and Roffey, P and Xu, B and Power, D and McNevin, D}, title = {Bacillus species at the Canberra Airport: A comparison of real-time polymerase chain reaction and massively parallel sequencing for identification.}, journal = {Forensic science international}, volume = {295}, number = {}, pages = {169-178}, doi = {10.1016/j.forsciint.2018.12.011}, pmid = {30612042}, issn = {1872-6283}, mesh = {*Airports ; Animals ; Australia ; Bacillus/*genetics ; DNA, Bacterial/genetics ; Forensic Sciences ; *High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 16S ; *Real-Time Polymerase Chain Reaction ; Security Measures ; Sequence Analysis, DNA ; }, abstract = {Anthrax, caused by the Gram-positive, spore forming bacterium Bacillus anthracis, is a disease with naturally occurring outbreaks in many parts of the world, primarily in domestic and wild herbivores. Due to the movement of people and stock, B. anthracis could, however, be at transportation hubs including airports. The continuous threat to national and international security from a biological agent release, or hoax attack, is a very real concern. Sensitive, robust and rapid (hours-day) methods to identify biological agents, including B. anthracis, and distinguish pathogenic from non-pathogenic species, is an essential cornerstone to national security. The aim of this project was to determine the presence of Bacillus species at the Canberra Airport using two massively parallel sequencing (MPS) approaches and compare with previous results using real-time polymerase chain reaction (qPCR). Samples were collected daily for seven days each month from August 2011-July 2012 targeting movement of people, luggage and freight into and out of the Canberra Airport. Extracted DNA was analysed using qPCR specific for B. anthracis. A subset of samples was analysed using two MPS approaches. Approach one, using the Ion PGM™ (Thermo Fisher Scientific; TFS) and an in-house assay, targeted the two B. anthracis virulence plasmids (cya and capB genes) and a single conserved region of the 16S rRNA gene. Approach two, using the Ion S5™ (TFS) and the commercial Ion 16S™ Metagenomics Kit (TFS), targeted multiple regions within the bacterial 16S rRNA gene. Overall there was consistency between the two MPS approaches and between MPS and qPCR, however, MPS was more sensitive, particularly for plasmid detection. Whilst the broad-range 16S genomic target(s) used in both MPS approaches in this study was able to generate a metagenomic fingerprint of the bacterial community at the Canberra Airport, it could not resolve Bacillus species beyond the level of the Bacillus cereus group. The inclusion of B. anthracis virulence plasmid targets in the in-house assay did allow for the potential presumptive identifications of pathogenic species. No plasmid targets were in the Ion 16S™ Metagenomics Kit. This study shows the choice of target(s) is key in MPS assay development and should be carefully considered to ensure the assay is fit for purpose, whether as an initial screening (presumptive) or a more specific (but not entirely confirmatory) test. Identification approaches may also benefit from a combination of MPS and qPCR as each has benefits and limitations.}, }
@article {pmid30610394, year = {2019}, author = {Feng, R and Xu, M and Li, J and Huang, S and Zhao, G and Tu, X and Sun, G and Guo, J}, title = {Structure and predictive functional profiling of microbial communities in two biotrickling filters treated with continuous/discontinuous waste gases.}, journal = {AMB Express}, volume = {9}, number = {1}, pages = {2}, doi = {10.1186/s13568-018-0726-9}, pmid = {30610394}, issn = {2191-0855}, support = {U1701243//National Natural Science Foundation of China/ ; 2014A020216022//Science and Technology Project of Guangdong Province, China/ ; 2016B070701017//Science and Technology Project of Guangdong Province, China/ ; 2016A030310314//Science and Technology Project of Guangdong Province, China/ ; 201504010014//Science and Technology Project of Guangzhou/ ; 201704020204//Science and Technology Project of Guangzhou/ ; 201707010377//Science and Technology Project of Guangzhou/ ; }, abstract = {Two biotrickling filters were operated in continuous (BTF1) and discontinuous (BTF2) modes at a constant empty bed residence time of 60 s for 60 days. From day 60, the operation mode of each BTF was oppositely switched. Higher removal efficiencies of five aromatic pollutants were recorded with BTF1 (> 77.2%). The switch in the operation mode did not alter the removal performance of BTF1. Comparatively, BTF2 was not successfully acclimated in the discontinuous operation mode. Once the mode had been switched to continuous mode, the removal efficiencies of BTF2 on all pollutants increased drastically and finally exceeded the values observed in BTF1, with the single exception of p-xylene. Principle coordinate analysis and analysis of similarities (ANOSIM) showed that the structure of the microbial communities differed considerably between both BTFs (R = 1.000, p < 0.01) as well as before and after the switch in BTF2 (R = 0.996, p < 0.01). The random forest model demonstrated that Mycobacterium, Burkholderia, and Comamonas were the three most important bacterial genera contributing to the differences in microbial communities between the two BTFs. Metagenomics inferred by PICUSt (phylogenetic investigation of communities by reconstruction of unobserved states) indicated that BTF2 had high degradation potential for aromatic pollutants, although those genes involved in biofilm formation were less active in BTF2 than those in BTF1.}, }
@article {pmid30610284, year = {2019}, author = {Xia, Y and Tan, D and Akbary, R and Kong, J and Seviour, R and Kong, Y}, title = {Aqueous raw and ripe Pu-erh tea extracts alleviate obesity and alter cecal microbiota composition and function in diet-induced obese rats.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {4}, pages = {1823-1835}, doi = {10.1007/s00253-018-09581-2}, pmid = {30610284}, issn = {1432-0614}, support = {ZD2015015//Yunnan Provincial Department of Education/ ; 2016FA052//Yunnan Provincial Science and Technology Department/ ; 31860029//National Natural Science Foundation of China/ ; }, abstract = {Pu-erh tea is attracting increased attention worldwide because of its unique flavor and health effects, but its impact on the composition and function of the gut microbiota remains unclear. The aim of this study was to investigate the effects of aqueous extracts of fermented (ripe) and non-fermented (raw) Pu-erh teas on the composition and function of the intestinal microbiota of rats with diet-induced obesity. We conducted a comparative metagenomic and meta-proteomic investigation of the microbial communities in cecal samples taken from obese rats treated with or without extracts of raw or ripe Pu-erh teas. By analyzing the composition and diversity of 16S rRNA amplicons and expression profiles of 814 distinct proteins, we found that despite differences in the chemical compositions of raw and ripe Pu-erh teas, administration of either tea at two doses (0.15- and 0.40-g/kg body weight) significantly (P < 0.05) increased microbial diversity and changed the composition of cecal microbiota by increasing the relative abundances of Firmicutes and decreasing those of Bacteroidetes. Community metabolic processes, including sucrose metabolism, glycolysis, and syntheses of proteins, rRNAs, and antibiotics were significantly (P < 0.05) promoted or had a tendency (0.10 < P < 0.05) to be promoted due to the enrichment of relevant enzymes. Furthermore, evidence at population, molecular, and metabolic levels indicated that polyphenols of raw Pu-erh tea and their metabolites potentially promote Akkermansia muciniphila growth by stimulating a type II and III secretion system protein, the elongation factor Tu, and a glyceraldehyde-3-phosphate dehydrogenase. This study provides new evidence for the prebiotic effects of Pu-erh tea.}, }
@article {pmid30609942, year = {2019}, author = {Yang, SH and Tandon, K and Lu, CY and Wada, N and Shih, CJ and Hsiao, SS and Jane, WN and Lee, TC and Yang, CM and Liu, CT and Denis, V and Wu, YT and Wang, LT and Huang, L and Lee, DC and Wu, YW and Yamashiro, H and Tang, SL}, title = {Metagenomic, phylogenetic, and functional characterization of predominant endolithic green sulfur bacteria in the coral Isopora palifera.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {3}, doi = {10.1186/s40168-018-0616-z}, pmid = {30609942}, issn = {2049-2618}, support = {MOST 105-2621-B-001-004-MY3//Ministry of Science and Technology, Taiwan/ ; }, abstract = {BACKGROUND: Endolithic microbes in coral skeletons are known to be a nutrient source for the coral host. In addition to aerobic endolithic algae and Cyanobacteria, which are usually described in the various corals and form a green layer beneath coral tissues, the anaerobic photoautotrophic green sulfur bacteria (GSB) Prosthecochloris is dominant in the skeleton of Isopora palifera. However, due to inherent challenges in studying anaerobic microbes in coral skeleton, the reason for its niche preference and function are largely unknown.
RESULTS: This study characterized a diverse and dynamic community of endolithic microbes shaped by the availability of light and oxygen. In addition, anaerobic bacteria isolated from the coral skeleton were cultured for the first time to experimentally clarify the role of these GSB. This characterization includes GSB's abundance, genetic and genomic profiles, organelle structure, and specific metabolic functions and activity. Our results explain the advantages endolithic GSB receive from living in coral skeletons, the potential metabolic role of a clade of coral-associated Prosthecochloris (CAP) in the skeleton, and the nitrogen fixation ability of CAP.
CONCLUSION: We suggest that the endolithic microbial community in coral skeletons is diverse and dynamic and that light and oxygen are two crucial factors for shaping it. This study is the first to demonstrate the ability of nitrogen uptake by specific coral-associated endolithic bacteria and shed light on the role of endolithic bacteria in coral skeletons.}, }
@article {pmid30609941, year = {2019}, author = {Zhong, H and Penders, J and Shi, Z and Ren, H and Cai, K and Fang, C and Ding, Q and Thijs, C and Blaak, EE and Stehouwer, CDA and Xu, X and Yang, H and Wang, J and Wang, J and Jonkers, DMAE and Masclee, AAM and Brix, S and Li, J and Arts, ICW and Kristiansen, K}, title = {Impact of early events and lifestyle on the gut microbiota and metabolic phenotypes in young school-age children.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {2}, doi = {10.1186/s40168-018-0608-z}, pmid = {30609941}, issn = {2049-2618}, support = {ID0E5LAG8456//European Foundation for the Study of Diabetes (DE)/ ; ID0EGNAG8457//Netherlands Asthma Foundation/ ; ID0EQOAG8458//Shenzhen Municipal Government of China/ ; ID0E1PAG8459//ZonMW/JPI HDHL Intestinal Microbiomics/ ; ID0EERAG8460//Stichting Astma Bestrijding/ ; ID0E1PAG8461//Dutch Biobanking and Biomolecular Resources Infrastructure (BBMRI-NL)/ ; ID0E1PAG8462//Netherlands Asthma Foundation/ ; }, abstract = {BACKGROUND: The gut microbiota evolves from birth and is in early life influenced by events such as birth mode, type of infant feeding, and maternal and infant antibiotics use. However, we still have a gap in our understanding of gut microbiota development in older children, and to what extent early events and pre-school lifestyle modulate the composition of the gut microbiota, and how this impinges on whole body metabolic regulation in school-age children.
RESULTS: Taking advantage of the KOALA Birth Cohort Study, a long-term prospective birth cohort in the Netherlands with extensive collection of high-quality host metadata, we applied shotgun metagenomics sequencing and systematically investigated the gut microbiota of children at 6-9 years of age. We demonstrated an overall adult-like gut microbiota in the 281 Dutch school-age children and identified 3 enterotypes dominated by the genera Bacteroides, Prevotella, and Bifidobacterium, respectively. Importantly, we found that breastfeeding duration in early life and pre-school dietary lifestyle correlated with the composition and functional competences of the gut microbiota in the children at school age. The correlations between pre-school dietary lifestyle and metabolic phenotypes exhibited a striking enterotype dependency. Thus, an inverse correlation between high dietary fiber consumption and low plasma insulin levels was only observed in individuals with the Bacteroides and Prevotella enterotypes, but not in Bifidobacterium enterotype individuals in whom the gut microbiota displayed overall lower microbial gene richness, alpha-diversity, functional potential for complex carbohydrate fermentation, and butyrate and succinate production. High total fat consumption and elevated plasma free fatty acid levels in the Bifidobacterium enterotype are associated with the co-occurrence of Streptococcus.
CONCLUSIONS: Our work highlights the persistent effects of breastfeeding duration and pre-school dietary lifestyle in affecting the gut microbiota in school-age children and reveals distinct compositional and functional potential in children according to enterotypes. The findings underscore enterotype-specific links between the host metabolic phenotypes and dietary patterns, emphasizing the importance of microbiome-based stratification when investigating metabolic responses to diets. Future diet intervention studies are clearly warranted to examine gut microbe-diet-host relationships to promote knowledge-based recommendations in relation to improving metabolic health in children.}, }
@article {pmid30609847, year = {2019}, author = {Bustamante-Brito, R and Vera-Ponce de León, A and Rosenblueth, M and Martínez-Romero, JC and Martínez-Romero, E}, title = {Metatranscriptomic Analysis of the Bacterial Symbiont Dactylopiibacterium carminicum from the Carmine Cochineal Dactylopius coccus (Hemiptera: Coccoidea: Dactylopiidae).}, journal = {Life (Basel, Switzerland)}, volume = {9}, number = {1}, pages = {}, doi = {10.3390/life9010004}, pmid = {30609847}, issn = {2075-1729}, support = {IN207718//Universidad Nacional Autónoma de México/ ; 253116//Consejo Nacional de Ciencia y Tecnología/ ; }, abstract = {The scale insect Dactylopius coccus produces high amounts of carminic acid, which has historically been used as a pigment by pre-Hispanic American cultures. Nowadays carmine is found in food, cosmetics, and textiles. Metagenomic approaches revealed that Dactylopius spp. cochineals contain two Wolbachia strains, a betaproteobacterium named Candidatus Dactylopiibacterium carminicum and Spiroplasma, in addition to different fungi. We describe here a transcriptomic analysis indicating that Dactylopiibacterium is metabolically active inside the insect host, and estimate that there are over twice as many Dactylopiibacterium cells in the hemolymph than in the gut, with even fewer in the ovary. Albeit scarce, the transcripts in the ovaries support the presence of Dactylopiibacterium in this tissue and a vertical mode of transmission. In the cochineal, Dactylopiibacterium may catabolize plant polysaccharides, and be active in carbon and nitrogen provisioning through its degradative activity and by fixing nitrogen. In most insects, nitrogen-fixing bacteria are found in the gut, but in this study they are shown to occur in the hemolymph, probably delivering essential amino acids and riboflavin to the host from nitrogen substrates derived from nitrogen fixation.}, }
@article {pmid30608881, year = {2019}, author = {Kayser, BD and Lhomme, M and Prifti, E and Da Cunha, C and Marquet, F and Chain, F and Naas, I and Pelloux, V and Dao, MC and Kontush, A and Rizkalla, SW and Aron-Wisnewsky, J and Bermúdez-Humarán, LG and Oakley, F and Langella, P and Clément, K and Dugail, I}, title = {Phosphatidylglycerols are induced by gut dysbiosis and inflammation, and favorably modulate adipose tissue remodeling in obesity.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {}, number = {}, pages = {fj201801897R}, doi = {10.1096/fj.201801897R}, pmid = {30608881}, issn = {1530-6860}, abstract = {Lipidomic techniques can improve our understanding of complex lipid interactions that regulate metabolic diseases. Here, a serum phospholipidomics analysis identified associations between phosphatidylglycerols (PGs) and gut microbiota dysbiosis. Compared with the other phospholipids, serum PGs were the most elevated in patients with low microbiota gene richness, which were normalized after a dietary intervention that restored gut microbial diversity. Serum PG levels were positively correlated with metagenomic functional capacities for bacterial LPS synthesis and host markers of low-grade inflammation; transcriptome databases identified PG synthase, the first committed enzyme in PG synthesis, as a potential mediator. Experiments in mice and cultured human-derived macrophages demonstrated that LPS induces PG release. Acute PG treatment in mice altered adipose tissue gene expression toward remodeling and inhibited ex vivo lipolysis in adipose tissue, suggesting that PGs favor lipid storage. Indeed, several PG species were associated with the severity of obesity in mice and humans. Finally, despite enrichment in PGs in bacterial membranes, experiments employing gnotobiotic mice colonized with recombinant PG overproducing Lactococcus lactis showed limited direct contribution of microbial PGs to the host. In summary, PGs are inflammation-responsive lipids indirectly regulated by the gut microbiota via endotoxins and regulate adipose tissue homeostasis in obesity.-Kayser, B. D., Lhomme, M., Prifti, E., Da Cunha, C., Marquet, F., Chain, F., Naas, I., Pelloux, V., Dao, M.-C., Kontush, A., Rizkalla, S. W., Aron-Wisnewsky, J., Bermúdez-Humarán, L. G., Oakley, F., Langella, P., Clément, K., Dugail, I. Phosphatidylglycerols are induced by gut dysbiosis and inflammation, and favorably modulate adipose tissue remodeling in obesity.}, }
@article {pmid30606844, year = {2019}, author = {Kafetzopoulou, LE and Pullan, ST and Lemey, P and Suchard, MA and Ehichioya, DU and Pahlmann, M and Thielebein, A and Hinzmann, J and Oestereich, L and Wozniak, DM and Efthymiadis, K and Schachten, D and Koenig, F and Matjeschk, J and Lorenzen, S and Lumley, S and Ighodalo, Y and Adomeh, DI and Olokor, T and Omomoh, E and Omiunu, R and Agbukor, J and Ebo, B and Aiyepada, J and Ebhodaghe, P and Osiemi, B and Ehikhametalor, S and Akhilomen, P and Airende, M and Esumeh, R and Muoebonam, E and Giwa, R and Ekanem, A and Igenegbale, G and Odigie, G and Okonofua, G and Enigbe, R and Oyakhilome, J and Yerumoh, EO and Odia, I and Aire, C and Okonofua, M and Atafo, R and Tobin, E and Asogun, D and Akpede, N and Okokhere, PO and Rafiu, MO and Iraoyah, KO and Iruolagbe, CO and Akhideno, P and Erameh, C and Akpede, G and Isibor, E and Naidoo, D and Hewson, R and Hiscox, JA and Vipond, R and Carroll, MW and Ihekweazu, C and Formenty, P and Okogbenin, S and Ogbaini-Emovon, E and Günther, S and Duraffour, S}, title = {Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak.}, journal = {Science (New York, N.Y.)}, volume = {363}, number = {6422}, pages = {74-77}, doi = {10.1126/science.aau9343}, pmid = {30606844}, issn = {1095-9203}, support = {//European Research Council/International ; //Wellcome Trust/United Kingdom ; }, abstract = {The 2018 Nigerian Lassa fever season saw the largest ever recorded upsurge of cases, raising concerns over the emergence of a strain with increased transmission rate. To understand the molecular epidemiology of this upsurge, we performed, for the first time at the epicenter of an unfolding outbreak, metagenomic nanopore sequencing directly from patient samples, an approach dictated by the highly variable genome of the target pathogen. Genomic data and phylogenetic reconstructions were communicated immediately to Nigerian authorities and the World Health Organization to inform the public health response. Real-time analysis of 36 genomes and subsequent confirmation using all 120 samples sequenced in the country of origin revealed extensive diversity and phylogenetic intermingling with strains from previous years, suggesting independent zoonotic transmission events and thus allaying concerns of an emergent strain or extensive human-to-human transmission.}, }
@article {pmid30606832, year = {2019}, author = {Bhadelia, N}, title = {Understanding Lassa fever.}, journal = {Science (New York, N.Y.)}, volume = {363}, number = {6422}, pages = {30}, doi = {10.1126/science.aav8958}, pmid = {30606832}, issn = {1095-9203}, mesh = {Disease Outbreaks ; Humans ; Lassa Fever/*epidemiology ; *Lassa virus ; Metagenomics ; Nigeria ; }, }
@article {pmid30606403, year = {2019}, author = {Gong, J and Noel, S and Pluznick, JL and Hamad, ARA and Rabb, H}, title = {Gut Microbiota-Kidney Cross-Talk in Acute Kidney Injury.}, journal = {Seminars in nephrology}, volume = {39}, number = {1}, pages = {107-116}, doi = {10.1016/j.semnephrol.2018.10.009}, pmid = {30606403}, issn = {1558-4488}, support = {R01 DK111209/DK/NIDDK NIH HHS/United States ; }, abstract = {The recent surge in research on the intestinal microbiota has greatly changed our understanding of human biology. Significant technical advances in DNA sequencing analysis and its application to metagenomics and metatranscriptomics has profoundly enhanced our ability to quantify and track complex microbial communities and to begin understanding their impact on human health and disease. This has led to a better understanding of the relationships between the intestinal microbiome and renal physiology/pathophysiology. In this review, we discuss the interactions between intestinal microbiota and kidney. We focus on select aspects including the intestinal barrier, immunologic and soluble mediators of microbiome effects, and effects of dysbiosis on acute kidney injury. Relevant studies on microbiome changes in other renal diseases are highlighted. We also introduce potential mechanisms of intervention with regard to gut microbiota in renal diseases.}, }
@article {pmid30606162, year = {2019}, author = {Xue, F and Nan, X and Li, Y and Pan, X and Guo, Y and Jiang, L and Xiong, B}, title = {Metagenomic insights into effects of thiamine supplementation on ruminal non-methanogen archaea in high-concentrate diets feeding dairy cows.}, journal = {BMC veterinary research}, volume = {15}, number = {1}, pages = {7}, doi = {10.1186/s12917-018-1745-0}, pmid = {30606162}, issn = {1746-6148}, support = {Grant No. 31572435//Project of National Nature Science Foundation of China/ ; 2016YFD0700205//National Key Research and Development Plan/ ; }, mesh = {Animal Feed ; Animals ; Archaea/*drug effects/genetics ; Cattle ; Diet/*veterinary ; *Dietary Supplements ; Eating/drug effects ; Female ; Gastrointestinal Microbiome/drug effects ; Hydrogen-Ion Concentration ; Lactation/drug effects ; Metagenomics ; Rumen/chemistry/*microbiology ; Thiamine/analysis/*pharmacology ; }, abstract = {BACKGROUND: Overfeeding of high-concentrate diet (HC) frequently leads to subacute ruminal acidosis (SARA) in modern dairy cows' production. Thiamine supplementation has been confirmed to attenuate HC induced SARA by increasing ruminal pH and ratio of acetate to propionate, and decreasing rumen lactate, biogenic amines and lipopolysaccharide (LPS). The effects of thiamine supplementation in HC on rumen bacteria and fungi profile had been detected in our previous studies, however, effects of thiamine supplementation in HC on rumen non-methanogen archaea is still unclear. The objective of the present study was therefore to investigate the effects of thiamine supplementation on ruminal archaea, especially non-methanogens in HC induced SARA cows.
RESULTS: HC feeding significantly decreased dry matter intake, milk production, milk fat content, ruminal pH and the concentrations of thiamine and acetate in rumen fluid compared with control diet (CON) (P < 0.05), while the concentrations of propionate and ammonia-nitrogen (NH3-N) were significantly increased compared with CON (P < 0.05). These changes caused by HC were inversed by thiamine supplementation (P < 0.05). The taxonomy results showed that ruminal archaea ranged from 0.37 to 0.47% of the whole microbiota. Four characterized phyla, a number of Candidatus archaea and almost 660 species were identified in the present study. In which Euryarchaeota occupied the largest proportion of the whole archaea. Furthermore, thiamine supplementation treatment significantly increased the relative abundance of non-methanogens compared with CON and HC treatments. Thaumarchaeota was increased in HC compared with CON. Thiamine supplementation significantly increased Crenarchaeota, Nanoarchaeota and the Candidatus phyla, however decreased Thaumarchaeota compared with HC treatment.
CONCLUSIONS: HC feeding significantly decreased ruminal pH and increased the content of NH3-N which led to N loss and the increase of the relative abundance of Thaumarchaeota. Thiamine supplementation increased ruminal pH, improved the activity of ammonia utilizing bacteria, and decreased Thaumarchaeota abundance to reduce the ruminal NH3 content and finally reduced N loss. Overall, these findings contributed to the understanding of thiamine's function in dairy cows and provided new strategies to improve dairy cows' health under high-concentrate feeding regime.}, }
@article {pmid30605809, year = {2019}, author = {Bai, Y and Ruan, X and Wang, F and Antoine, G and van der Hoek, JP}, title = {Sulfonamides removal under different redox conditions and microbial response to sulfonamides stress during riverbank filtration: A laboratory column study.}, journal = {Chemosphere}, volume = {220}, number = {}, pages = {668-677}, doi = {10.1016/j.chemosphere.2018.12.167}, pmid = {30605809}, issn = {1879-1298}, abstract = {Riverbank filtration (RBF) as a barrier of pathogenic microorganisms and organic micropollutants recently has been proven capable of removing sulfonamides. However, the study about the effect of redox conditions on biodegradation of common and persistent sulfonamides in RBF is limited and the response of microbial communities to sulfonamides stress during RBF is unknown. In this study, two column set-ups (with residence time 5 days and 11 days respectively), simulating different redox conditions of riverbank filtration systems, were operated for seven months to investigate 1) the long-term effect of redox conditions on ng∙L-1 level sulfonamides (sulfapyridine, sulfadiazine, sulfamethoxazole, sulfamethazine, sulfaquinoxaline) removal, and 2) the microbial community evolution represented by the phylogenetic and metabolic function shift under non-lethal selective pressures of sulfonamides. The results showed that sulfonamides were more degradable under anoxic conditions than oxic and suboxic conditions. In the sulfonamides stressed community, the phylogenetic diversity increased slightly. Relative abundance of an intrinsic sulfonamides resistant bacteria Bacillus spp. increased, suggesting that sulfonamide resistance developed in specific bacteria under sulfonamides contamination pressure in RBF systems. At the same time, an activated transport function in the stressed microbial community was noticed. The predicted relative abundance of gene folP, which encodes dihydropteroate synthase, also increased significantly, indicating a detoxification mechanism and sulfonamides resistance potential under non-lethal selective pressures of sulfonamides in RBF systems.}, }
@article {pmid30605153, year = {2019}, author = {Xiao, L and Feng, Q and Liang, S and Sonne, SB and Xia, Z and Qiu, X and Li, X and Long, H and Zhang, J and Zhang, D and Liu, C and Fang, Z and Chou, J and Glanville, J and Hao, Q and Kotowska, D and Colding, C and Licht, TR and Wu, D and Yu, J and Sung, JJY and Liang, Q and Li, J and Jia, H and Lan, Z and Tremaroli, V and Dworzynski, P and Nielsen, HB and Bäckhed, F and Doré, J and Le Chatelier, E and Ehrlich, SD and Lin, JC and Arumugam, M and Wang, J and Madsen, L and Kristiansen, K}, title = {Amendments: Author Correction: A catalog of the mouse gut metagenome.}, journal = {Nature biotechnology}, volume = {37}, number = {1}, pages = {102}, doi = {10.1038/nbt0119-102a}, pmid = {30605153}, issn = {1546-1696}, }
@article {pmid30604012, year = {2019}, author = {Tyagi, A and Singh, B and Billekallu Thammegowda, NK and Singh, NK}, title = {Shotgun metagenomics offers novel insights into taxonomic compositions, metabolic pathways and antibiotic resistance genes in fish gut microbiome.}, journal = {Archives of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00203-018-1615-y}, pmid = {30604012}, issn = {1432-072X}, support = {YSS/2014/000269//Science and Engineering Research Board/ ; }, abstract = {Gut microbiota of freshwater carp (Labeo rohita) was investigated by shotgun metagenomics to understand its taxonomic composition and functional capabilities. With the presence of 36 phyla, 326 families and 985 genera, the fish gut microbiota was found to be quite diverse in nature. However, at the phylum level, more than three-fourths of gut microbes belonged to Proteobacteria. Very low prevalence of commonly used probiotic bacteria (Bacillus, Lactobacillus, Streptococcus, and Lactococcus) in fish gut suggested the need to search for alternative probiotics for aquaculture use. Biosynthesis pathways were found to be the most dominant (51%) followed by degradation (39%), energy metabolism (4%) and fermentation (2%). In conformity with herbivorous feeding habit of L. rohita, gut microbiome also had pathways for the degradation of cellulose, hemicellulose, chitin, pectin, starch, and other complex carbohydrates. High prevalence of Actinobacteria and antibiotic biosynthesis pathways in the fish gut microbiome indicated its potential for bioprospecting of potentially novel natural antibiotics. Fifty-one different types of antibiotic resistance genes (ARGs) belonging to 15 antimicrobial resistance (AMR) gene families and conferring resistance against 24 antibiotic types were detected in fish gut. Some of the ARGs for multi-drug resistance were also found to be located on sequences of plasmid origin. The presence of pathogenic bacteria and ARGs on plasmid sequences suggested the potential risk due to horizontal gene transfer in the confined gut environment. The role of ARGs in fish gut microbiome needs further investigations.}, }
@article {pmid30602367, year = {2019}, author = {Chen, YY and Chen, DQ and Chen, L and Liu, JR and Vaziri, ND and Guo, Y and Zhao, YY}, title = {Microbiome-metabolome reveals the contribution of gut-kidney axis on kidney disease.}, journal = {Journal of translational medicine}, volume = {17}, number = {1}, pages = {5}, doi = {10.1186/s12967-018-1756-4}, pmid = {30602367}, issn = {1479-5876}, support = {81673578//National Natural Science Foundation of China/ ; 81603271//National Natural Science Foundation of China/ ; 81872985//National Natural Science Foundation of China/ ; }, abstract = {Dysbiosis represents changes in composition and structure of the gut microbiome community (microbiome), which may dictate the physiological phenotype (health or disease). Recent technological advances and efforts in metagenomic and metabolomic analyses have led to a dramatical growth in our understanding of microbiome, but still, the mechanisms underlying gut microbiome-host interactions in healthy or diseased state remain elusive and their elucidation is in infancy. Disruption of the normal gut microbiota may lead to intestinal dysbiosis, intestinal barrier dysfunction, and bacterial translocation. Excessive uremic toxins are produced as a result of gut microbiota alteration, including indoxyl sulphate, p-cresyl sulphate, and trimethylamine-N-oxide, all implicated in the variant processes of kidney diseases development. This review focuses on the pathogenic association between gut microbiota and kidney diseases (the gut-kidney axis), covering CKD, IgA nephropathy, nephrolithiasis, hypertension, acute kidney injury, hemodialysis and peritoneal dialysis in clinic. Targeted interventions including probiotic, prebiotic and symbiotic measures are discussed for their potential of re-establishing symbiosis, and more effective strategies for the treatment of kidney diseases patients are suggested. The novel insights into the dysbiosis of the gut microbiota in kidney diseases are helpful to develop novel therapeutic strategies for preventing or attenuating kidney diseases and complications.}, }
@article {pmid30602085, year = {2018}, author = {Park, SC and Won, S}, title = {Evaluation of 16S rRNA Databases for Taxonomic Assignments Using Mock Community.}, journal = {Genomics & informatics}, volume = {16}, number = {4}, pages = {e24}, doi = {10.5808/GI.2018.16.4.e24}, pmid = {30602085}, issn = {1598-866X}, abstract = {Taxonomy identification is fundamental to all microbiology studies. Particularly in metagenomics, which identify the composition of microorganisms using thousands of sequences, its importance is even greater. Identification is inevitably affected by the choice of database. This study was conducted to evaluate the accuracy of three widely used 16S databases, Greengenes, Silva, and EzBioCloud, and to suggest basic guidelines for selecting reference databases. Using public mock community data, each database was used to assign taxonomy and to test its accuracy. We showed that EzBioCloud performs well compared to other existing databases.}, }
@article {pmid30602083, year = {2018}, author = {Kang, S and Kim, YC}, title = {The Genome-Based Virus Taxonomy with ICTV Database Extension.}, journal = {Genomics & informatics}, volume = {16}, number = {4}, pages = {e22}, doi = {10.5808/GI.2018.16.4.e22}, pmid = {30602083}, issn = {1598-866X}, abstract = {In 1966, the International Classification of Viruses (ICNV) was established to standardize the naming of viruses. In 1975, the organization was renamed 'ICTV', by which it is still known today. The primary virus classification provided by ICTV in 1971 was for viruses infecting vertebrates, which includes 19 genera, 2 families, and a further 24 unclassified groups. Presently, the 10th virus taxonomy has been published. However, early classification of viruses was based on the clinical results of "in vivo" and "in vitro", as well as on the shape of PhynoType virus. However, due to the development of next-generation sequencing (NGS) and the accompanying bioinformatics analysis pipelines, a reconstruction of the classification system has been proposed. At a meeting held in Boston, USA between June 9-11, 2016, even there was an in-depth discussion regarding the classification of viruses using Metagenomic data. One suggested activity that arose from the meeting was that viral taxonomy should be reconstructed, based on genotype and bioinformatics analysis "in silico". This article describes our efforts to achieve this goal by construction of a web-based system and extension of an associated database, based on ICTV taxonomy. This virus taxonomy web system was specifically designed to extend the virus taxonomy up to strain and isolation, which was then connected with the NCBI database to facilitate searching for specific viral genes; there are also links to journals provided by the EMBL RESTful API that improve accessibility for academic groups.}, }
@article {pmid30602082, year = {2018}, author = {Jeon, SJ and Galvão, KN}, title = {An Advanced Understanding of Uterine Microbial Ecology Associated with Metritis in Dairy Cows.}, journal = {Genomics & informatics}, volume = {16}, number = {4}, pages = {e21}, doi = {10.5808/GI.2018.16.4.e21}, pmid = {30602082}, issn = {1598-866X}, abstract = {Metritis, the inflammation of the uterus caused by polymicrobial infections, is a prevalent and costly disease to the dairy industry as it decreases milk yield, survival, and the welfare of dairy cows. Although the antibiotic ceftiofur is widely used for the treatment of metritis, endometrium and ovary function is compromised, resulting in subfertility and infertility. According to culture-dependent studies, uterine pathogens include Escherichia coli, Trueperella pyogenes, Fusobacterium necrophorum, and Prevotella melaninogenica. Recent studies using high-throughput sequencing claimed that metritis is a microbiota-associated disease. Herein, we propose that metritis is associated with uterine microbiota with high abundance of Bacteroides, Porphyromonas, and Fusobacterium, but rare bacteria such as Escherichia coli and Helcococcus ovis cannot be ignored.}, }
@article {pmid30601862, year = {2019}, author = {Thornbury, M and Sicheri, J and Slaine, P and Getz, LJ and Finlayson-Trick, E and Cook, J and Guinard, C and Boudreau, N and Jakeman, D and Rohde, J and McCormick, C}, title = {Characterization of novel lignocellulose-degrading enzymes from the porcupine microbiome using synthetic metagenomics.}, journal = {PloS one}, volume = {14}, number = {1}, pages = {e0209221}, doi = {10.1371/journal.pone.0209221}, pmid = {30601862}, issn = {1932-6203}, abstract = {Plant cell walls are composed of cellulose, hemicellulose, and lignin, collectively known as lignocellulose. Microorganisms degrade lignocellulose to liberate sugars to meet metabolic demands. Using a metagenomic sequencing approach, we previously demonstrated that the microbiome of the North American porcupine (Erethizon dorsatum) is replete with genes that could encode lignocellulose-degrading enzymes. Here, we report the identification, synthesis and partial characterization of four novel genes from the porcupine microbiome encoding putative lignocellulose-degrading enzymes: β-glucosidase, α-L-arabinofuranosidase, β-xylosidase, and endo-1,4-β-xylanase. These genes were identified via conserved catalytic domains associated with cellulose- and hemicellulose-degradation. Phylogenetic trees were created for each of these putative enzymes to depict genetic relatedness to known enzymes. Candidate genes were synthesized and cloned into plasmid expression vectors for inducible protein expression and secretion. The putative β-glucosidase fusion protein was efficiently secreted but did not permit Escherichia coli (E. coli) to use cellobiose as a sole carbon source, nor did the affinity purified enzyme cleave p-Nitrophenyl β-D-glucopyranoside (p-NPG) substrate in vitro over a range of physiological pH levels (pH 5-7). The putative hemicellulose-degrading β-xylosidase and α-L-arabinofuranosidase enzymes also lacked in vitro enzyme activity, but the affinity purified endo-1,4-β-xylanase protein cleaved a 6-chloro-4-methylumbelliferyl xylobioside substrate in acidic and neutral conditions, with maximal activity at pH 7. At this optimal pH, KM, Vmax, and kcat were determined to be 32.005 ± 4.72 μM, 1.16x10-5 ± 3.55x10-7 M/s, and 94.72 s-1, respectively. Thus, our pipeline enabled successful identification and characterization of a novel hemicellulose-degrading enzyme from the porcupine microbiome. Progress towards the goal of introducing a complete lignocellulose-degradation pathway into E. coli will be accelerated by combining synthetic metagenomic approaches with functional metagenomic library screening, which can identify novel enzymes unrelated to those found in available databases.}, }
@article {pmid30600356, year = {2019}, author = {Kadnikov, VV and Mardanov, AV and Beletsky, AV and Karnachuk, OV and Ravin, NV}, title = {Genome of the candidate phylum Aminicenantes bacterium from a deep subsurface thermal aquifer revealed its fermentative saccharolytic lifestyle.}, journal = {Extremophiles : life under extreme conditions}, volume = {23}, number = {2}, pages = {189-200}, doi = {10.1007/s00792-018-01073-5}, pmid = {30600356}, issn = {1433-4909}, support = {14-14-01016//Russian Science Foundation/ ; }, abstract = {Bacteria of candidate phylum OP8 (Aminicenantes) have been identified in various terrestrial and marine ecosystems as a result of molecular analysis of microbial communities. So far, none of the representatives of Aminicenantes have been isolated in a pure culture. We assembled the near-complete genome of a member of Aminicenantes from the metagenome of the 2-km-deep subsurface thermal aquifer in Western Siberia and used genomic data to analyze the metabolic pathways of this bacterium and its ecological role. This bacterium, designated BY38, was predicted to be rod shaped, it lacks flagellar machinery but twitching motility is encoded. Analysis of the BY38 genome revealed a variety of glycosyl hydrolases that can enable utilization of carbohydrates, including chitin, cellulose, starch, mannose, galactose, fructose, fucose, rhamnose, maltose and arabinose. The reconstructed central metabolic pathways suggested that Aminicenantes bacterium BY38 is an anaerobic organotroph capable of fermenting carbohydrates and proteinaceous substrates and performing anaerobic respiration with nitrite. In the deep subsurface aquifer Aminicenantes probably act as destructors of buried organic matter and produce hydrogen and acetate. Based on phylogenetic and genomic analyses, the novel bacterium is proposed to be classified as Candidatus Saccharicenans subterraneum.}, }
@article {pmid30599960, year = {2019}, author = {Xie, M and Wu, J and An, F and Yue, X and Tao, D and Wu, R and Lee, Y}, title = {An integrated metagenomic/metaproteomic investigation of microbiota in dajiang-meju, a traditional fermented soybean product in Northeast China.}, journal = {Food research international (Ottawa, Ont.)}, volume = {115}, number = {}, pages = {414-424}, doi = {10.1016/j.foodres.2018.10.076}, pmid = {30599960}, issn = {1873-7145}, abstract = {Dajiang-meju have been used as major ingredients for the preparation of traditional spontaneously fermented soybean paste in Northeast China. In this work, we sequenced and analyzed the metagenome of 12 dajiang-meju samples. To complement the metagenome analysis, we analyzed the taxonomic and functional diversity of the microbiota by metaproteomics (LC-MS/MS). The analysis of metagenomic data revealed that the communities were primarily dominated by Enterobacter, Enterococcus, Leuconostoc, Lactobacillus, Citrobacter and Leclercia. Moreover, changes in the functional levels were monitored, and metaproteomic analysis revealed that most of the proteins were mainly expressed by members of Rhizopus, Penicillium and Geotrichum. The number of sequences allocated to fungi in the fermentation process decreased, whereas the number of sequences assigned to bacteria increased with time of fermentation. In addition, functional metagenomic profiling indicated that a series of sequences related to carbohydrates and amino acids metabolism were enriched. Additionally, enzymes associated with glycolysis metabolic pathways were presumed to contribute to the generation of flavor in dajiang-meju. Proteins from different dajiang-meju samples involved in global and overview maps, carbohydrate metabolism, nucleic acid metabolism and energy metabolism were differentially expressed. This information improves the understanding of microbial metabolic patterns with respect to the metaproteomes of dajiang-meju and provides a powerful tool for studying the fermentation process of soybean products.}, }
@article {pmid30599936, year = {2019}, author = {Danneskiold-Samsøe, NB and Dias de Freitas Queiroz Barros, H and Santos, R and Bicas, JL and Cazarin, CBB and Madsen, L and Kristiansen, K and Pastore, GM and Brix, S and Maróstica Júnior, MR}, title = {Interplay between food and gut microbiota in health and disease.}, journal = {Food research international (Ottawa, Ont.)}, volume = {115}, number = {}, pages = {23-31}, doi = {10.1016/j.foodres.2018.07.043}, pmid = {30599936}, issn = {1873-7145}, abstract = {Numerous microorganisms colonize the human gastrointestinal tract playing pivotal roles in relation to digestion and absorption of dietary components. They biotransform food components and produce metabolites, which in combination with food components shape and modulate the host immune system and metabolic responses. Reciprocally, the diet modulates the composition and functional capacity of the gut microbiota, which subsequently influence host biochemical processes establishing a system of mutual interaction and inter-dependency. Macronutrients, fibers, as well as polyphenols and prebiotics are strong drivers shaping the composition of the gut microbiota. Especially, short-chain fatty acids produced from ingested fibers and tryptophan metabolites are key in modulating host immune responses. Since reciprocal interactions between diet, host, and microbiota are personal, understanding this complex network of interactions calls for novel use of large datasets and the implementation of machine learning algorithms and artificial intelligence. In this review, we aim to provide a base for future investigations of how interactions between food components and gut microbiota may influence or even determine human health and disease.}, }
@article {pmid30599328, year = {2019}, author = {Yun, YM and Kim, M and Kim, H and Kim, DH and Kwon, EE and Kang, S}, title = {Increased biodegradability of low-grade coal wastewater in anaerobic membrane bioreactor by adding yeast wastes.}, journal = {Journal of environmental management}, volume = {234}, number = {}, pages = {36-43}, doi = {10.1016/j.jenvman.2018.12.083}, pmid = {30599328}, issn = {1095-8630}, abstract = {Demineralization is required in upgrading low-grade coal to serve as an alternative energy resource for the production of fuel and valuable chemicals but generates a large amount of low-grade coal wastewater (LCWW). The objective of this study was to investigate the effects of a co-substrate on an anaerobic membrane bioreactor (AnMBR) treating LCWW. CH4 was not produced during the operation fed by LCWW alone. When yeast wastes (YW) were supplemented, there was a gradual increase in the biodegradability of LCWW, achieving 182 CH4 mL/g COD with 58% COD removal efficiency. The analysis of physicochemical characteristics in the effluent of AnMBR, done by excitation-emission matrix (EEM) and size exclusion chromatography (SEC), showed that the proportion of soluble microbial products (SMPs) and aromatic group with high-molecular weight (>1 kDa) increased. Microbial analysis revealed that the increased dominance of bacteria Comamonas, Methanococcus, and Methanosarcina facilitated biodegradation of LCWW in the presence of YW.}, }
@article {pmid30598099, year = {2018}, author = {Abe, K and Hirayama, M and Ohno, K and Shimamura, T}, title = {A latent allocation model for the analysis of microbial composition and disease.}, journal = {BMC bioinformatics}, volume = {19}, number = {Suppl 19}, pages = {519}, doi = {10.1186/s12859-018-2530-6}, pmid = {30598099}, issn = {1471-2105}, abstract = {BACKGROUND: Establishing the relationship between microbiota and specific diseases is important but requires appropriate statistical methodology. A specialized feature of microbiome count data is the presence of a large number of zeros, which makes it difficult to analyze in case-control studies. Most existing approaches either add a small number called a pseudo-count or use probability models such as the multinomial and Dirichlet-multinomial distributions to explain the excess zero counts, which may produce unnecessary biases and impose a correlation structure taht is unsuitable for microbiome data.
RESULTS: The purpose of this article is to develop a new probabilistic model, called BERnoulli and MUltinomial Distribution-based latent Allocation (BERMUDA), to address these problems. BERMUDA enables us to describe the differences in bacteria composition and a certain disease among samples. We also provide a simple and efficient learning procedure for the proposed model using an annealing EM algorithm.
CONCLUSION: We illustrate the performance of the proposed method both through both the simulation and real data analysis. BERMUDA is implemented with R and is available from GitHub (https://github.com/abikoushi/Bermuda).}, }
@article {pmid30598080, year = {2018}, author = {Chen, HM and Chang, TH and Lin, FM and Liang, C and Chiu, CM and Yang, TL and Yang, T and Huang, CY and Cheng, YN and Chang, YA and Chang, PY and Weng, SL}, title = {Vaginal microbiome variances in sample groups categorized by clinical criteria of bacterial vaginosis.}, journal = {BMC genomics}, volume = {19}, number = {Suppl 10}, pages = {876}, doi = {10.1186/s12864-018-5284-7}, pmid = {30598080}, issn = {1471-2164}, abstract = {BACKGROUND: One of the most common and recurrent vaginal infections is bacterial vaginosis (BV). The diagnosis is based on changes to the "normal" vaginal microbiome; however, the normal microbiome appears to differ according to reproductive status and ethnicity, and even among individuals within these groups. The Amsel criteria and Nugent score test are widely used for diagnosing BV; however, these tests are based on different criteria, and so may indicate distinct changes in the vaginal microbial community. Nevertheless, few studies have compared the results of these test against metagenomics analysis.
METHODS: Vaginal flora samples from 77 participants were classified according to the Amsel criteria and Nugent score test. The microbiota composition was analyzed using 16S ribosome RNA gene amplicon sequencing. Bioinformatics analysis and multivariate statistical analysis were used to evaluate the microbial diversity and function.
RESULTS: Only 3 % of the participants diagnosed BV negative using the Amsel criteria (A-) were BV-positive according to the Nugent score test (N+), while over half of the BV-positive patients using the Amsel criteria (A+) were BV-negative according to the Nugent score test (N-). Thirteen genera showed significant differences in distribution among BV status defined by BV tests (e.g., A - N-, A + N- and A + N+). Variations in the four most abundant taxa, Lactobacillus, Gardnerella, Prevotella, and Escherichia, were responsible for most of this dissimilarity. Furthermore, vaginal microbial diversity differed significantly among the three groups classified by the Nugent score test (N-, N+, and intermediate flora), but not between the Amsel criteria groups. Numerous predictive microbial functions, such as bacterial chemotaxis and bacterial invasion of epithelial cells, differed significantly among multiple BV test, but not between the A- and A+ groups.
CONCLUSIONS: Metagenomics analysis can greatly expand our current understanding of vaginal microbial diversity in health and disease. Metagenomics profiling may also provide more reliable diagnostic criteria for BV testing.}, }
@article {pmid30597257, year = {2018}, author = {Ngara, TR and Zhang, H}, title = {Recent Advances in Function-based Metagenomic Screening.}, journal = {Genomics, proteomics & bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.gpb.2018.01.002}, pmid = {30597257}, issn = {2210-3244}, abstract = {Metagenomes from uncultured microorganisms are rich resources for novel enzyme genes. The methods used to screen the metagenomic libraries fall into two categories, which are based on sequence or function of the enzymes. The sequence-based approaches rely on the known sequences of the target gene families. In contrast, the function-based approaches do not involve the incorporation of metagenomic sequencing data and, therefore, may lead to the discovery of novel gene sequences with desired functions. In this review, we discuss the function-based screening strategies that have been used in the identification of enzymes from metagenomes. Because of its simplicity, agar plate screening is most commonly used in the identification of novel enzymes with diverse functions. Other screening methods with higher sensitivity are also employed, such as microtiter plate screening. Furthermore, several ultra-high-throughput methods were developed to deal with large metagenomic libraries. Among these are the FACS-based screening, droplet-based screening, and the in vivo reporter-based screening methods. The application of these novel screening strategies has increased the chance for the discovery of novel enzyme genes.}, }
@article {pmid30597002, year = {2019}, author = {Choi, I and Ponsero, AJ and Bomhoff, M and Youens-Clark, K and Hartman, JH and Hurwitz, BL}, title = {Libra: scalable k-mer-based tool for massive all-vs-all metagenome comparisons.}, journal = {GigaScience}, volume = {8}, number = {2}, pages = {}, doi = {10.1093/gigascience/giy165}, pmid = {30597002}, issn = {2047-217X}, abstract = {Background: Shotgun metagenomics provides powerful insights into microbial community biodiversity and function. Yet, inferences from metagenomic studies are often limited by dataset size and complexity and are restricted by the availability and completeness of existing databases. De novo comparative metagenomics enables the comparison of metagenomes based on their total genetic content.
Results: We developed a tool called Libra that performs an all-vs-all comparison of metagenomes for precise clustering based on their k-mer content. Libra uses a scalable Hadoop framework for massive metagenome comparisons, Cosine Similarity for calculating the distance using sequence composition and abundance while normalizing for sequencing depth, and a web-based implementation in iMicrobe (http://imicrobe.us) that uses the CyVerse advanced cyberinfrastructure to promote broad use of the tool by the scientific community.
Conclusions: A comparison of Libra to equivalent tools using both simulated and real metagenomic datasets, ranging from 80 million to 4.2 billion reads, reveals that methods commonly implemented to reduce compute time for large datasets, such as data reduction, read count normalization, and presence/absence distance metrics, greatly diminish the resolution of large-scale comparative analyses. In contrast, Libra uses all of the reads to calculate k-mer abundance in a Hadoop architecture that can scale to any size dataset to enable global-scale analyses and link microbial signatures to biological processes.}, }
@article {pmid30596893, year = {2018}, author = {Gonnella, G and Niehus, N and Kurtz, S}, title = {GfaViz: Flexible and interactive visualization of GFA sequence graphs.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/bty1046}, pmid = {30596893}, issn = {1367-4811}, abstract = {Summary: The Graphical Fragment Assembly (GFA) formats are emerging standard formats for the representation of sequence graphs. While GFA 1 was primarely targeting assembly graphs, the newer GFA 2 format introduces several features, which makes it suitable for representing other kinds of information, such as scaffolding graphs, variation graphs, alignment graphs, and colored metagenomic graphs. Here, we present GfaViz, an interactive graphical tool for the visualization of sequence graphs in GFA format. The software supports all new features of GFA 2 and introduces conventions for their visualization. The user can choose between two different layouts and multiple styles for representing single elements or groups. All customizations can be stored in custom tags of the GFA format itself, without requiring external configuration files. Stylesheets are supported for storing standard configuration options for groups of files. The visualizations can be exported to raster and vector graphics formats. A command line interface allows for batch generation of images.
GfaViz is available at https://github.com/ggonnella/gfaviz.
Supplementary information: Supplementary data are available at Bioinformatics online.}, }
@article {pmid30592753,