@article {pmid31731121,
year = {2019},
author = {Liu, YR and Delgado-Baquerizo, M and Yang, Z and Feng, J and Zhu, J and Huang, Q},
title = {Microbial taxonomic and functional attributes consistently predict soil CO2 emissions across contrasting croplands.},
journal = {The Science of the total environment},
volume = {702},
number = {},
pages = {134885},
doi = {10.1016/j.scitotenv.2019.134885},
pmid = {31731121},
issn = {1879-1026},
abstract = {Despite distinct roles of soil microbes in regulating carbon (C) respiration in diverse environments, it remains unclear whether microbial taxonomic and functional attributes can consistently predict soil C emissions across contrasting ecosystems. Here, we conducted a large-scale sampling event across two contrasting croplands (rice and wheat-corn crop rotation) to identify specific soil microbial phylotypes and functional genes associated with soil respiration rates. The results of structural equation modeling indicated that bacterial community composition had a strong link with C respiration rates in the two contrasting cropland types; however, this link was weaker for fungal communities. More importantly, we found that the relative abundances of bacterial Solirubrobacterales_480-2, Myxococcales_mle1-27 and fungal Westerdykella had consistently negative correlation with respiration rates across paddy and upland soils. We also identified taxa that are significantly correlated to C respiration in the paddy (e.g. Methylocaldum) and upland soils (e.g. Kribbella), respectively. Further, we found multiple associations between functional genes involved in microbial C metabolism and soil respiration rates. Our findings provide novel insights into understanding microbial predictors of soil CO2 emissions in diverse croplands, which have important implications for improving C emission predictions in terrestrial ecosystems.},
}

@article {pmid31730850,
year = {2019},
author = {Salazar, G and Paoli, L and Alberti, A and Huerta-Cepas, J and Ruscheweyh, HJ and Cuenca, M and Field, CM and Coelho, LP and Cruaud, C and Engelen, S and Gregory, AC and Labadie, K and Marec, C and Pelletier, E and Royo-Llonch, M and Roux, S and Sánchez, P and Uehara, H and Zayed, AA and Zeller, G and Carmichael, M and Dimier, C and Ferland, J and Kandels, S and Picheral, M and Pisarev, S and Poulain, J and , and Acinas, SG and Babin, M and Bork, P and Bowler, C and de Vargas, C and Guidi, L and Hingamp, P and Iudicone, D and Karp-Boss, L and Karsenti, E and Ogata, H and Pesant, S and Speich, S and Sullivan, MB and Wincker, P and Sunagawa, S},
title = {Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome.},
journal = {Cell},
volume = {179},
number = {5},
pages = {1068-1083.e21},
doi = {10.1016/j.cell.2019.10.014},
pmid = {31730850},
issn = {1097-4172},
abstract = {Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms. VIDEO ABSTRACT.},
}

@article {pmid31730200,
year = {2019},
author = {Esposito, A and Borruso, L and Rattray, JE and Brusetti, L and Ahmed, E},
title = {Taxonomic and functional insights into rock varnish microbiome using shotgun metagenomics.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiz180},
pmid = {31730200},
issn = {1574-6941},
abstract = {Rock varnish is a microbial habitat, characterized by thin (5-500 μm) and shiny coatings of iron (Fe) and manganese (Mn) oxides associated with clay minerals. This structure is well studied by geologists, and recently there have been reports about the taxonomical composition of its microbiome. In this study, we investigated the rock varnish microbiome using shotgun metagenomics together with analyses of elemental composition, lipid and small molecule biomarkers, and rock surface analyses to explore the biogeography of microbial communities and their functional features. We report taxa and encoded functions represented in metagenomes retrieved from varnish or non-varnish samples, additionally, 8 nearly-complete genomes have been reconstructed spanning four phyla (Acidobacteria, Actinobacteria, Chloroflexi and TM7). The functional and taxonomic analyses presented in this study provide new insights into the ecosystem dynamics and survival strategies of microbial communities inhabiting varnish and non-varnish rock surfaces.},
}

@article {pmid31730192,
year = {2019},
author = {Chaumeil, PA and Mussig, AJ and Hugenholtz, P and Parks, DH},
title = {GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btz848},
pmid = {31730192},
issn = {1367-4811},
abstract = {SUMMARY: The GTDB Toolkit (GTDB-Tk) provides objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB). GTDB-Tk is computationally efficient and able to classify thousands of draft genomes in parallel. Here we demonstrate the accuracy of the GTDB-Tk taxonomic assignments by evaluating its performance on a phylogenetically diverse set of 10,156 bacterial and archaeal metagenome-assembled genomes.

AVAILABILITY: GTDB-Tk is implemented in Python and licensed under the GNU General Public License v3.0. Source code and documentation are available at: https://github.com/ecogenomics/gtdbtk.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid31729183,
year = {2019},
author = {Manasson, J and Wallach, DS and Guggino, G and Stapylton, M and Badri, MH and Solomon, G and Reddy, SM and Coras, R and Aksenov, AA and Jones, DR and Girija, PV and Neimann, AL and Heguy, A and Segal, LN and Dorrestein, PC and Bonneau, R and Guma, M and Ciccia, F and Ubeda, C and Clemente, JC and Scher, JU},
title = {IL-17 Inhibition in Spondyloarthritis Associates with Subclinical Gut Microbiome Perturbations and a Distinctive IL-25-Driven Intestinal Inflammation.},
journal = {Arthritis & rheumatology (Hoboken, N.J.)},
volume = {},
number = {},
pages = {},
doi = {10.1002/art.41169},
pmid = {31729183},
issn = {2326-5205},
abstract = {OBJECTIVE: To characterize the ecological effects of biologic therapies on the gut bacterial and fungal microbiome of psoriatic arthritis (PsA)/spondyloarthritis (SpA) patients.

METHODS: Fecal samples from PsA/SpA patients pre- and post-treatment with tumor necrosis factor inhibitors (TNFi; n=15) or an anti-interleukin (IL)-17A monoclonal antibody inhibitor (IL-17i; n=14) underwent sequencing (16S, ITS and shotgun metagenomics) and computational microbiome analysis. Fecal levels of fatty acid metabolites and cytokines/proteins implicated in PsA/SpA pathogenesis or intestinal inflammation were correlated with sequence data. Additionally, ileal biopsies obtained from SpA patients who developed clinically overt Crohn's disease (CD) after treatment with IL-17i (n=5) were analyzed for expression of IL-23/Th-17 related cytokines, IL-25/IL-17E-producing cells and type-2 innate lymphoid cells (ILC2s).

RESULTS: There were significant shifts in abundance of specific taxa after treatment with IL-17i compared to TNFi, particularly Clostridiales (p=0.016) and Candida albicans (p=0.041). These subclinical alterations correlated with changes in bacterial community co-occurrence, metabolic pathways, IL-23/Th17-related cytokines and various fatty acids. Ileal biopsies showed that clinically overt CD was associated with expansion of IL-25/IL-17E-producing tuft cells and ILC2s (p<0.05) compared to pre-IL-17i treatment levels.

CONCLUSION: In a subgroup of SpA patients, the initiation of IL-17A blockade correlated with features of subclinical gut inflammation and intestinal dysbiosis of certain bacterial and fungal taxa, most notably C. albicans. Further, IL-17i-related CD was associated with overexpression of IL-25/IL-17E-producing tuft cells and ILC2s. These results may help to explain the potential link between inhibition of a specific IL-17 pathway and the (sub)clinical gut inflammation observed in SpA.},
}

@article {pmid31728602,
year = {2019},
author = {Quero, GM and Celussi, M and Relitti, F and Kovačević, V and Del Negro, P and Luna, GM},
title = {Inorganic and Organic Carbon Uptake Processes and Their Connection to Microbial Diversity in Meso- and Bathypelagic Arctic Waters (Eastern Fram Strait).},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-019-01451-2},
pmid = {31728602},
issn = {1432-184X},
abstract = {The deep Arctic Ocean is increasingly vulnerable to climate change effects, yet our understanding of its microbial processes is limited. We collected samples from shelf waters, mesopelagic Atlantic Waters (AW) and bathypelagic Norwegian Sea Deep Waters (NSDW) in the eastern Fram Strait, along coast-to-offshore transects off Svalbard during boreal summer. We measured community respiration, heterotrophic carbon production (HCP), and dissolved inorganic carbon utilization (DICu) together with prokaryotic abundance, diversity, and metagenomic predictions. In deep samples, HCP was significantly faster in AW than in NSDW, while we observed no differences in DICu rates. Organic carbon uptake was higher than its inorganic counterpart, suggesting a major reliance of deep microbial Arctic communities on heterotrophic metabolism. Community structure and spatial distribution followed the hydrography of water masses. Distinct from other oceans, the most abundant OTU in our deep samples was represented by the archaeal MG-II. To address the potential biogeochemical role of each water mass-specific microbial community, as well as their link with the measured rates, PICRUSt-based predicted metagenomes were built. The results showed that pathways of auto- and heterotrophic carbon utilization differed between the deep water masses, although this was not reflected in measured DICu rates. Our findings provide new insights to understand microbial processes and diversity in the dark Arctic Ocean and to progress toward a better comprehension of the biogeochemical cycles and their trends in light of climate changes.},
}

@article {pmid31728526,
year = {2019},
author = {Corrêa, FB and Saraiva, JP and Stadler, PF and da Rocha, UN},
title = {TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkz994},
pmid = {31728526},
issn = {1362-4962},
abstract = {Microbiome studies focused on the genetic potential of microbial communities (metagenomics) became standard within microbial ecology. MG-RAST and the Sequence Read Archive (SRA), the two main metagenome repositories, contain over 202 858 public available metagenomes and this number has increased exponentially. However, mining databases can be challenging due to misannotated, misleading and decentralized data. The main goal of TerrestrialMetagenomeDB is to make it easier for scientists to find terrestrial metagenomes of interest that could be compared with novel datasets in meta-analyses. We defined terrestrial metagenomes as those that do not belong to marine environments. Further, we curated the database using text mining to assign potential descriptive keywords that better contextualize environmental aspects of terrestrial metagenomes, such as biomes and materials. TerrestrialMetagenomeDB release 1.0 includes 15 022 terrestrial metagenomes from SRA and MG-RAST. Together, the downloadable data amounts to 68 Tbp. In total, 199 terrestrial terms were divided into 14 categories. These metagenomes span 83 countries, 30 biomes and 7 main source materials. The TerrestrialMetagenomeDB is publicly available at https://webapp.ufz.de/tmdb.},
}

@article {pmid31728072,
year = {2019},
author = {Wu, L and Ning, D and Zhang, B and Li, Y and Zhang, P and Shan, X and Zhang, Q and Brown, MR and Li, Z and Van Nostrand, JD and Ling, F and Xiao, N and Zhang, Y and Vierheilig, J and Wells, GF and Yang, Y and Deng, Y and Tu, Q and Wang, A and , and Zhang, T and He, Z and Keller, J and Nielsen, PH and Alvarez, PJJ and Criddle, CS and Wagner, M and Tiedje, JM and He, Q and Curtis, TP and Stahl, DA and Alvarez-Cohen, L and Rittmann, BE and Wen, X and Zhou, J},
title = {Author Correction: Global diversity and biogeography of bacterial communities in wastewater treatment plants.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41564-019-0617-0},
pmid = {31728072},
issn = {2058-5276},
abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.},
}

@article {pmid31727980,
year = {2019},
author = {Kim, HJ and Kim, JJ and Myeong, NR and Kim, T and Kim, D and An, S and Kim, H and Park, T and Jang, SI and Yeon, JH and Kwack, I and Sul, WJ},
title = {Segregation of age-related skin microbiome characteristics by functionality.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {16748},
doi = {10.1038/s41598-019-53266-3},
pmid = {31727980},
issn = {2045-2322},
support = {2016R1A6A3A11933991//National Research Foundation of Korea (NRF)/ ; 2019R1C1C1009360//National Research Foundation of Korea (NRF)/ ; },
abstract = {Although physiological changes are the most evident indicators of skin aging by alteration of the skin's structure and function, we question whether skin aging is also affected by the structure and assembly process of the skin microbiome. We analysed the skin microbiomes of 73 healthy Chinese women in two age groups (25-35 years old and 56-63 years old) using 16S rRNA gene amplicon sequencing; the overall microbiome structure was significantly different between the two age groups. An analysis using ecological theory to evaluate the process of microbial community assembly processes revealed that the microbiomes of the older group were formed under a greater influence of the niche-based process, with the network of microbes being more collapsed than that of the younger group. Inferred metagenomic functional pathways associated with replication and repair were relatively more predominant in the younger group whereas, among the various metabolism-related pathways, those associated with biodegradation were more predominant in the older group. Interestingly, we found two segregated sub-typing patterns in the younger group which were also observed in the skin microbiomes of young Chinese women living in four other cities in China. The results of our study highlights candidate microbes and functional pathways that are important for future research into preventing skin aging and which could lead to a comprehensive understanding of age-related skin microbiome characteristics.},
}

@article {pmid31727712,
year = {2019},
author = {Rusley, C and Onstott, TC and Vishnivetskaya, TA and Layton, A and Chauhan, A and Pfiffner, SM and Whyte, LG and Lau, MCY},
title = {Metagenome-Assembled Genome of USCα AHI, a Potential High-Affinity Methanotroph from Axel Heiberg Island, Canadian High Arctic.},
journal = {Microbiology resource announcements},
volume = {8},
number = {46},
pages = {},
doi = {10.1128/MRA.01178-19},
pmid = {31727712},
issn = {2576-098X},
abstract = {Metagenomic sequencing of active-layer cryosols from the Canadian High Arctic has yielded a nearly complete genome for an atmospheric CH4-oxidizing bacterium belonging to upland soil cluster α (USCα). This genome contains genes involved in CH4 metabolism, H2 metabolism, and multiple carbon assimilation pathways.},
}

@article {pmid31727697,
year = {2019},
author = {Kamau, E and Luka, MM and de Laurent, ZR and Adema, I and Agoti, CN and Nokes, DJ},
title = {Genome Sequences of Human Coronavirus OC43 and NL63, Associated with Respiratory Infections in Kilifi, Kenya.},
journal = {Microbiology resource announcements},
volume = {8},
number = {46},
pages = {},
doi = {10.1128/MRA.00730-19},
pmid = {31727697},
issn = {2576-098X},
abstract = {Coding-complete genomes of two human coronavirus OC43 strains and one NL63 strain were obtained by metagenomic sequencing of clinical samples collected in 2017 and 2018 in Kilifi, Kenya. Maximum likelihood phylogenies showed that the OC43 strains were genetically dissimilar and that the NL63 strain was closely related to NL63 genotype B viruses.},
}

@article {pmid30471158,
year = {2019},
author = {Saarman, NP and Opiro, R and Hyseni, C and Echodu, R and Opiyo, EA and Dion, K and Johnson, T and Aksoy, S and Caccone, A},
title = {The population genomics of multiple tsetse fly (Glossina fuscipes fuscipes) admixture zones in Uganda.},
journal = {Molecular ecology},
volume = {28},
number = {1},
pages = {66-85},
doi = {10.1111/mec.14957},
pmid = {30471158},
issn = {1365-294X},
support = {5T32AI007404-24//Foundation for the National Institutes of Health/International ; AI068932//Foundation for the National Institutes of Health/International ; D43TW0/TW/FIC NIH HHS/United States ; },
mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; *Genetic Speciation ; Genome, Insect/genetics ; Haplotypes/genetics ; Hybridization, Genetic ; *Metagenomics ; Microsatellite Repeats/*genetics ; Tsetse Flies/*genetics/pathogenicity ; Uganda/epidemiology ; },
abstract = {Understanding the mechanisms that enforce, maintain or reverse the process of speciation is an important challenge in evolutionary biology. This study investigates the patterns of divergence and discusses the processes that form and maintain divergent lineages of the tsetse fly Glossina fuscipes fuscipes in Uganda. We sampled 251 flies from 18 sites spanning known genetic lineages and the four admixture zones between them. We apply population genomics, hybrid zone and approximate Bayesian computation to the analysis of three types of genetic markers: 55,267 double-digest restriction site-associated DNA (ddRAD) SNPs to assess genome-wide admixture, 16 microsatellites to provide continuity with published data and accurate biogeographic modelling, and a 491-bp fragment of mitochondrial cytochrome oxidase I and II to infer maternal inheritance patterns. Admixture zones correspond with regions impacted by the reorganization of Uganda's river networks that occurred during the formation of the West African Rift system over the last several hundred thousand years. Because tsetse fly population distributions are defined by rivers, admixture zones likely represent both old and new regions of secondary contact. Our results indicate that older hybrid zones contain mostly parental types, while younger zones contain variable hybrid types resulting from multiple generations of interbreeding. These findings suggest that reproductive barriers are nearly complete in the older admixture zones, while nearly absent in the younger admixture zones. Findings are consistent with predictions of hybrid zone theory: Populations in zones of secondary contact transition rapidly from early to late stages of speciation or collapse all together.},
}

Animals
Bayes Theorem
DNA, Mitochondrial/genetics
*Genetic Speciation
Genome, Insect/genetics
Haplotypes/genetics
Hybridization, Genetic
*Metagenomics
Microsatellite Repeats/*genetics
Tsetse Flies/*genetics/pathogenicity
Uganda/epidemiology

@article {pmid31726395,
year = {2019},
author = {Chopyk, J and Nasko, DJ and Allard, S and Bui, A and Treangen, T and Pop, M and Mongodin, EF and Sapkota, AR},
title = {Comparative metagenomic analysis of microbial taxonomic and functional variations in untreated surface and reclaimed waters used in irrigation applications.},
journal = {Water research},
volume = {169},
number = {},
pages = {115250},
doi = {10.1016/j.watres.2019.115250},
pmid = {31726395},
issn = {1879-2448},
abstract = {The use of irrigation water sourced from reclamation facilities and untreated surface water bodies may be a practical solution to attenuate the burden on diminishing groundwater aquifers. However, comprehensive microbial characterizations of these water sources are generally lacking, especially with regard to variations through time and across multiple water types. To address this knowledge gap we used a shotgun metagenomic approach to characterize the taxonomic and functional variations of microbial communities within two agricultural ponds, two freshwater creeks, two brackish rivers, and three water reclamation facilities located in the Mid-Atlantic, United States. Water samples (n = 24) were collected from all sites between October and November 2016, and filtered onto 0.2 μm membrane filters. Filters were then subjected to total DNA extraction and shotgun sequencing on the Illumina HiSeq platform. From these data, we found that Betaproteobacteria dominated the majority of freshwater sites, while Alphaproteobacteria were abundant at times in the brackish waters. One of these brackish sites was also host to a greater abundance of the bacterial genera Gimesia and Microcystis. Furthermore, predicted microbial features (e.g. antibiotic resistance genes (ARGs) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) arrays) varied based on specific site and sampling date. ARGs were found across samples, with the diversity and abundance highest in those from a reclamation facility and a wastewater-impacted freshwater creek. Additionally, we identified over 600 CRISPR arrays, containing ∼2600 unique spacers, suggestive of a diverse and often site-specific phage community. Overall, these results provide a better understanding of the complex microbial community in untreated surface and reclaimed waters, while highlighting possible environmental and human health impacts associated with their use in agriculture.},
}

@article {pmid31726394,
year = {2019},
author = {Cotto, I and Dai, Z and Huo, L and Anderson, CL and Vilardi, KJ and Ijaz, U and Khunjar, W and Wilson, C and De Clippeleir, H and Gilmore, K and Bailey, E and Pinto, AJ},
title = {Long solids retention times and attached growth phase favor prevalence of comammox bacteria in nitrogen removal systems.},
journal = {Water research},
volume = {169},
number = {},
pages = {115268},
doi = {10.1016/j.watres.2019.115268},
pmid = {31726394},
issn = {1879-2448},
abstract = {The discovery of the complete ammonia oxidizing (comammox) bacteria overturns the traditional two-organism nitrification paradigm which largely underpins the design and operation of nitrogen removal during wastewater treatment. Quantifying the abundance, diversity, and activity of comammox bacteria in wastewater treatment systems is important for ensuring a clear understanding of the nitrogen biotransformations responsible for ammonia removal. To this end, we conducted a yearlong survey of 14 full-scale nitrogen removal systems including mainstream conventional and simultaneous nitrification-denitrification and side-stream partial nitrification-anammox systems with varying process configurations. Metagenomics and genome-resolved metagenomics identified comammox bacteria in mainstream conventional and simultaneous nitrification-denitrification systems, with no evidence for their presence in side-stream partial nitrification-anammox systems. Further, comammox bacterial diversity was restricted to clade A and these clade A comammox bacteria were detected in systems with long solids retention times (>10 days) and/or in the attached growth phase. Using a newly designed qPCR assay targeting the amoB gene of clade A comammox bacteria in combination with quantitation of other canonical nitrifiers, we show that long solids retention time is the key process parameter associated with the prevalence and abundance of comammox bacteria. The increase in comammox bacterial abundance was not associated with concomitant decrease in the abundance of canonical nitrifiers; however, systems with comammox bacteria showed significantly better and temporally stable ammonia removal compared to systems where they were not detected. Finally, in contrast to recent studies, we do not find any significant association of comammox bacterial prevalence and abundance with dissolved oxygen concentrations in this study.},
}

@article {pmid31726316,
year = {2019},
author = {Fiers, WD and Gao, IH and Iliev, ID},
title = {Gut mycobiota under scrutiny: fungal symbionts or environmental transients?.},
journal = {Current opinion in microbiology},
volume = {50},
number = {},
pages = {79-86},
doi = {10.1016/j.mib.2019.09.010},
pmid = {31726316},
issn = {1879-0364},
abstract = {The human gastrointestinal tract is home to a thriving community of microbes including the fungal 'mycobiota'. Although sequencing methodology has enumerated diverse fungal genera within this niche, discerning persistent symbiotic residents from contaminants and purely environmental transients remains a challenge. Recent advances in culturomics and sequencing employing metagenomics, metatranscriptomics and longitudinal studies have begun to reveal a human symbiont 'core mycobiome' that may contribute to human health and disease. Trans-kingdom interactions between the bacterial microbiota and evolution within the niche have defined C. albicans as a true symbiont, setting a bar for defining other fungi. Additionally, elegant investigations of mammalian antifungal immunity have examined mononuclear phagocytes, neutrophils, antigen-specific recognition by T cells and other mechanisms important for local and systemic effects on the host, providing further evidence supporting gut persistence. In this review we discuss current research aimed at investigating the symbiotic mycobiota and propose four criteria aiding in the differentiation of fungal symbionts from environmental transients.},
}

@article {pmid31726162,
year = {2019},
author = {Guo, WL and Chen, M and Pan, WL and Zhang, Q and Xu, JX and Lin, YC and Li, L and Liu, B and Bai, WD and Zhang, YY and Ni, L and Rao, PF and Lv, XC},
title = {Hypoglycemic and hypolipidemic mechanism of organic chromium derived from chelation of Grifola frondosa polysaccharide-chromium (III) and its modulation of intestinal microflora in high fat-diet and STZ-induced diabetic mice.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ijbiomac.2019.09.206},
pmid = {31726162},
issn = {1879-0003},
abstract = {Polysaccharide from Grifola frondosa is an excellent metal-ion chelating agent owing to its distinctive structure and outstanding functional activities. Our previous research has successfully synthesized novel organic chromium derived from the chelation ofG. frondosapolysaccharide-chromium (III) [GFP-Cr(III)]. The purpose of present research was to reveal the hypoglycemic and hypolipidemic mechanism of GFP-Cr(III), and its relationship with the modulation of intestinal microflora. Successful fabrication of GFP-Cr(III) was verified by thermogravimetric analysis (TGA), powder X-ray diffraction (XRD) and 1H NMR spectrum.The hypoglycemic and hypolipidemic effects were examined using type 2 diabetic mice induced by a high-fat diet (HFD) and streptozocin (STZ). Results indicated that GFP-Cr(III) intervention improved abnormal serum biochemical indicators (triglyceride (TG), cholesterol (TC), low-density lipoprotein cholesterol (LDL-C) and glucose), inhibited lipid accumulation and steatosis in the liver. Metagenomic analysis revealed that GFP-Cr(III) treatment produced obvious changes on the intestinal microflora in T2DM mice. Thecorrelationnetwork analysis further revealed that the serum and hepatic lipid profiles were positively correlated with Streptococcus and Enterococcus, but negatively correlated with Enterorhabdus, Ruminococcaceae-UCG-011, Coriobacteriaceae and Micrococcaceae. Meanwhile, oral administration with GFP-Cr(III) regulated the mRNA expression related to glucose and lipid metabolism. These results of present study suggest that GFP-Cr(III) could be used as potential functional food ingredients for the amelioration of hyperglycemia and hyperlipidemia.},
}

@article {pmid31726030,
year = {2019},
author = {Fehlner-Peach, H and Magnabosco, C and Raghavan, V and Scher, JU and Tett, A and Cox, LM and Gottsegen, C and Watters, A and Wiltshire-Gordon, JD and Segata, N and Bonneau, R and Littman, DR},
title = {Distinct Polysaccharide Utilization Profiles of Human Intestinal Prevotella copri Isolates.},
journal = {Cell host & microbe},
volume = {26},
number = {5},
pages = {680-690.e5},
doi = {10.1016/j.chom.2019.10.013},
pmid = {31726030},
issn = {1934-6069},
abstract = {Gut-dwelling Prevotella copri (P. copri), the most prevalent Prevotella species in the human gut, have been associated with diet and disease. However, our understanding of their diversity and function remains rudimentary because studies have been limited to 16S and metagenomic surveys and experiments using a single type strain. Here, we describe the genomic diversity of 83 P. copri isolates from 11 human donors. We demonstrate that genomically distinct isolates, which can be categorized into different P. copri complex clades, utilize defined sets of polysaccharides. These differences are exemplified by variations in susC genes involved in polysaccharide transport as well as polysaccharide utilization loci (PULs) that were predicted in part from genomic and metagenomic data. Functional validation of these PULs showed that P. copri isolates utilize distinct sets of polysaccharides from dietary plant, but not animal, sources. These findings reveal both genomic and functional differences in polysaccharide utilization across human intestinal P. copri strains.},
}

@article {pmid31725875,
year = {2019},
author = {Hellmann, J and Andersen, H and Fei, L and Linn, A and Bezold, R and Lake, K and Jackson, K and Meyer, D and Dirksing, K and Bonkowski, E and Ollberding, NJ and Haslam, DB and Denson, L},
title = {Microbial Shifts and Shorter Time to Bowel Resection Surgery Associated with C. difficile in Pediatric Crohn's Disease.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izz263},
pmid = {31725875},
issn = {1536-4844},
abstract = {BACKGROUND: Clostridioides difficile infection and colonization are common in pediatric Crohn's disease (CD). Our aims were to test the relationship between C. difficile positivity and bowel resection surgery and to characterize microbial shifts associated with C. difficile carriage and surgery.

METHODS: A retrospective single-center study of 75 pediatric CD patients tested for association between C. difficile carriage and bowel resection surgery. A prospective single-center study of 70 CD patients utilized C. difficile testing and shotgun metagenomic sequencing of fecal samples to define microbiota variation stratified by C. difficile carriage or history of surgery.

RESULTS: The rate of bowel resection surgery increased from 21% in those without C. difficile to 67% in those with (P = 0.003). From a Kaplan-Meier survival model, the hazard ratio for time to first surgery was 4.4 (95% CI, 1.2-16.2; P = 0.00) in patients with positive C. difficile testing in the first year after diagnosis. Multivariable logistic regression analysis confirmed this association (odds ratio 16.2; 95% CI, 2.2-120; P = 0.006). Larger differences in microbial abundance and metabolic pathways were observed in patients with prior surgery than in those with C. difficile carriage. Depletion of Alistipes and Ruminococcus species and reduction in methionine biosynthesis were noted in patients with both C. difficile carriage and past surgery.

CONCLUSIONS: A positive C. difficile test during the first year after diagnosis is associated with decreased time to first bowel resection surgery in pediatric Crohn's disease. Depletion of beneficial commensals and methionine biosynthesis in patients with C. difficile carriage may contribute to increased risk for surgery.},
}

@article {pmid31724125,
year = {2019},
author = {Sharma, V and Kumar, R and Sharma, VK and Yadav, AK and Tiirola, M and Sharma, PK},
title = {Expression, purification, characterization and in silico analysis of newly isolated hydrocarbon degrading bleomycin resistance dioxygenase.},
journal = {Molecular biology reports},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11033-019-05159-x},
pmid = {31724125},
issn = {1573-4978},
support = {SB/YS/LS-63/2013//Science and Engineering Research Board/ ; },
abstract = {In the present investigation, we report cloning, expression, purification and characterization of a novel Bleomycin Resistance Dioxygenase (BRPD). His-tagged fusion protein was purified to homogeneity using Ni-NTA affinity chromatography, yielding 1.2 mg of BRPD with specific activity of 6.25 U mg-1 from 600 ml of E. coli culture. Purified enzyme was a dimer with molecular weight ~ 26 kDa in SDS-PAGE and ~ 73 kDa in native PAGE analysis. The protein catalyzed breakdown of hydrocarbon substrates, including catechol and hydroquinone, in the presence of metal ions, as characterized via spectrophotometric analysis of the enzymatic reactions. Bleomycin binding was proven using the EMSA gel retardation assay, and the putative bleomycin binding site was further determined by in silico analysis. Molecular dynamic simulations revealed that BRPD attains octahedral configuration in the presence of Fe2+ ion, forming six co-ordinate complexes to degrade hydroquinone-like molecules. In contrary, in the presence of Zn2+ ion BRPD adopts tetrahedral configuration, which enables degradation of catechol-like molecules.},
}

@article {pmid31723319,
year = {2019},
author = {Griswold, CK},
title = {Properties of Samples With Segregating Polymerase Chain Reaction (PCR) Dropout Mutations Within a Species.},
journal = {Evolutionary bioinformatics online},
volume = {15},
number = {},
pages = {1176934319883612},
doi = {10.1177/1176934319883612},
pmid = {31723319},
issn = {1176-9343},
abstract = {In polymerase chain reaction (PCR)-based DNA sequencing studies, there is the possibility that mutations at the binding sites of primers result in no primer binding and therefore no amplification. In this article, we call such mutations PCR dropouts and present a coalescent-based theory of the distribution of segregating PCR dropout mutations within a species. We show that dropout mutations typically occur along branch sections that are at or near the base of a coalescent tree, if at all. Given that a dropout mutation occurs along a branch section near the base of a tree, there is a good chance that it causes the alleles of a large fraction of a species to go unamplified, which distorts the tree shape. Expected coalescence times and distributions of pairwise sequence differences in the presence of PCR dropout mutations are derived under the assumptions of both neutrality and background selection. These expectations differ from when PCR dropout mutations are absent and may form the basis of inferential approaches to detect the presence of dropout mutations, as well as the development of unbiased estimators of statistics associated with population-level genetic variation.},
}

@article {pmid31723038,
year = {2019},
author = {Kundu, P and Lee, HU and Garcia-Perez, I and Tay, EXY and Kim, H and Faylon, LE and Martin, KA and Purbojati, R and Drautz-Moses, DI and Ghosh, S and Nicholson, JK and Schuster, S and Holmes, E and Pettersson, S},
title = {Neurogenesis and prolongevity signaling in young germ-free mice transplanted with the gut microbiota of old mice.},
journal = {Science translational medicine},
volume = {11},
number = {518},
pages = {},
doi = {10.1126/scitranslmed.aau4760},
pmid = {31723038},
issn = {1946-6242},
abstract = {The gut microbiota evolves as the host ages, yet the effects of these microbial changes on host physiology and energy homeostasis are poorly understood. To investigate these potential effects, we transplanted the gut microbiota of old or young mice into young germ-free recipient mice. Both groups showed similar weight gain and skeletal muscle mass, but germ-free mice receiving a gut microbiota transplant from old donor mice unexpectedly showed increased neurogenesis in the hippocampus of the brain and increased intestinal growth. Metagenomic analysis revealed age-sensitive enrichment in butyrate-producing microbes in young germ-free mice transplanted with the gut microbiota of old donor mice. The higher concentration of gut microbiota-derived butyrate in these young transplanted mice was associated with an increase in the pleiotropic and prolongevity hormone fibroblast growth factor 21 (FGF21). An increase in FGF21 correlated with increased AMPK and SIRT-1 activation and reduced mTOR signaling. Young germ-free mice treated with exogenous sodium butyrate recapitulated the prolongevity phenotype observed in young germ-free mice receiving a gut microbiota transplant from old donor mice. These results suggest that gut microbiota transplants from aged hosts conferred beneficial effects in responsive young recipients.},
}

@article {pmid31722729,
year = {2019},
author = {Kawulok, J and Kawulok, M and Deorowicz, S},
title = {Environmental metagenome classification for constructing a microbiome fingerprint.},
journal = {Biology direct},
volume = {14},
number = {1},
pages = {20},
doi = {10.1186/s13062-019-0251-z},
pmid = {31722729},
issn = {1745-6150},
abstract = {BACKGROUND: Nowadays, not only are single genomes commonly analyzed, but also metagenomes, which are sets of, DNA fragments (reads) derived from microbes living in a given environment. Metagenome analysis is aimed at extracting crucial information on the organisms that have left their traces in an investigated environmental sample.In this study we focus on the MetaSUB Forensics Challenge (organized within the CAMDA 2018 conference) which consists in predicting the geographical origin of metagenomic samples. Contrary to the existing methods for environmental classification that are based on taxonomic or functional classification, we rely on the similarity between a sample and the reference database computed at a reads level.

RESULTS: We report the results of our extensive experimental study to investigate the behavior of our method and its sensitivity to different parameters. In our tests, we have followed the protocol of the MetaSUB Challenge, which allowed us to compare the obtained results with the solutions based on taxonomic and functional classification.

CONCLUSIONS: The results reported in the paper indicate that our method is competitive with those based on taxonomic classification. Importantly, by measuring the similarity at the reads level, we avoid the necessity of using large databases with annotated gene sequences. Hence our main finding is that environmental classification of metagenomic data can be proceeded without using large databases required for taxonomic or functional classification.

REVIEWERS: This article was reviewed by Eran Elhaik, Alexandra Bettina Graf, Chengsheng Zhu, and Andre Kahles.},
}

@article {pmid31722416,
year = {2019},
author = {Doster, E and Lakin, SM and Dean, CJ and Wolfe, C and Young, JG and Boucher, C and Belk, KE and Noyes, NR and Morley, PS},
title = {MEGARes 2.0: a database for classification of antimicrobial drug, biocide and metal resistance determinants in metagenomic sequence data.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkz1010},
pmid = {31722416},
issn = {1362-4962},
abstract = {Antimicrobial resistance (AMR) is a threat to global public health and the identification of genetic determinants of AMR is a critical component to epidemiological investigations. High-throughput sequencing (HTS) provides opportunities for investigation of AMR across all microbial genomes in a sample (i.e. the metagenome). Previously, we presented MEGARes, a hand-curated AMR database and annotation structure developed to facilitate the analysis of AMR within metagenomic samples (i.e. the resistome). Along with MEGARes, we released AmrPlusPlus, a bioinformatics pipeline that interfaces with MEGARes to identify and quantify AMR gene accessions contained within a metagenomic sequence dataset. Here, we present MEGARes 2.0 (https://megares.meglab.org), which incorporates previously published resistance sequences for antimicrobial drugs, while also expanding to include published sequences for metal and biocide resistance determinants. In MEGARes 2.0, the nodes of the acyclic hierarchical ontology include four antimicrobial compound types, 57 classes, 220 mechanisms of resistance, and 1,345 gene groups that classify the 7,868 accessions. In addition, we present an updated version of AmrPlusPlus (AMR ++ version 2.0), which improves accuracy of classifications, as well as expanding scalability and usability.},
}

@article {pmid31722286,
year = {2019},
author = {Hakim, S and Mirza, BS and Imran, A and Zaheer, A and Yasmin, S and Mubeen, F and Mclean, JE and Mirza, MS},
title = {Illumina sequencing of 16S rRNA tag shows disparity in rhizobial and non-rhizobial diversity associated with root nodules of mung bean (Vigna radiata L.) growing in different habitats in Pakistan.},
journal = {Microbiological research},
volume = {231},
number = {},
pages = {126356},
doi = {10.1016/j.micres.2019.126356},
pmid = {31722286},
issn = {1618-0623},
abstract = {In Rhizobium-legume symbiosis, the nodule is the most frequently studied compartment, where the endophytic/symbiotic microbiota demands critical investigation for development of specific inocula. We identified the bacterial diversity within root nodules of mung bean from different growing areas of Pakistan using Illumina sequencing of 16S rRNA gene. We observed specific OTUs related to specific site where Bradyrhizobium was found to be the dominant genus comprising of 82-94% of total rhizobia in nodules with very minor fraction of sequences from other rhizobia at three sites. In contrast, Ensifer (Sinorhizobium) was single dominant genus comprising 99.9% of total rhizobial sequences at site four. Among non-rhizobial sequences, the genus Acinetobacter was abundant (7-18% of total sequences), particularly in Bradyrhizobium-dominated nodule samples. Rhizobia and non-rhizobial PGPR isolated from nodule samples include Ensifer, Bradyrhizobium, Acinetobacter, Microbacterium and Pseudomonas strains. Co-inoculation of multi-trait PGPR Acinetobacter sp. VrB1 with either of the two rhizobia in field exhibited more positive effect on nodulation and plant growth than single-strain inoculation which favors the use of Acinetobacter as an essential component for development of mung bean inoculum. Furthermore, site-specific dominance of rhizobia and non-rhizobia revealed in this study may contribute towards decision making for development and application of specific inocula in different habitats.},
}

@article {pmid31722268,
year = {2019},
author = {Wollants, E and Beller, L and Beuselinck, K and Bloemen, M and Lagrou, K and Reynders, M and Van Ranst, M},
title = {A decade of enterovirus genetic diversity in Belgium.},
journal = {Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology},
volume = {121},
number = {},
pages = {104205},
doi = {10.1016/j.jcv.2019.104205},
pmid = {31722268},
issn = {1873-5967},
abstract = {BACKGROUND: Enteroviruses are responsible for a wide range of clinical symptoms.Enterovirus D68 was already known to cause mild to severe respiratory infections, but in the last few years, it has also been associated with neurological symptoms and acute flaccid paralysis.

OBJECTIVES: In this epidemiological surveillance in Belgium, 1521 enteroviruspositive samples were genotyped.

STUDY DESIGN: Enterovirus-positive patient samples were collected from the University Hospitals Leuven and other hospitals and medical practices in Belgium from 2007 to 2018. Molecular typing was done by RT-PCR using different primers sets. EV-A and EV-B were typed by sequencing part of VP1. For EVC and EV-D, the VP4/VP2 region was used together with the non-coding region.

RESULTS: In this epidemiological survey with samples collected over 12 years, 35 different EV types were detected in 1521 patient samples. Enterovirus species B was by far the most dominant species in our samples (93%). Echovirus 30 was most frequently found (24%), followed by echovirus 6 (8%) and echovirus 9 (7%). In 2018, there was an outbreak for the first time of enterovirus D68 with severe respiratory infections but no acute flaccid paralysis. Phylogenetic analyses showed that the collected outbreak strains coexist in different clades.

CONCLUSIONS: For more than a decade, the circulating enterovirus strains were investigated in Belgium. During this time span, echovirus 30 was the most frequently detected and peaked every 3 years. Enterovirus D68 began an upsurge in 2018, but thus far without being clinically associated with acute flaccid paralysis.},
}

@article {pmid31722195,
year = {2019},
author = {Hertel, J and Harms, AC and Heinken, A and Baldini, F and Thinnes, CC and Glaab, E and Vasco, DA and Pietzner, M and Stewart, ID and Wareham, NJ and Langenberg, C and Trenkwalder, C and Krüger, R and Hankemeier, T and Fleming, RMT and Mollenhauer, B and Thiele, I},
title = {Integrated Analyses of Microbiome and Longitudinal Metabolome Data Reveal Microbial-Host Interactions on Sulfur Metabolism in Parkinson's Disease.},
journal = {Cell reports},
volume = {29},
number = {7},
pages = {1767-1777.e8},
doi = {10.1016/j.celrep.2019.10.035},
pmid = {31722195},
issn = {2211-1247},
abstract = {Parkinson's disease (PD) exhibits systemic effects on the human metabolism, with emerging roles for the gut microbiome. Here, we integrate longitudinal metabolome data from 30 drug-naive, de novo PD patients and 30 matched controls with constraint-based modeling of gut microbial communities derived from an independent, drug-naive PD cohort, and prospective data from the general population. Our key results are (1) longitudinal trajectory of metabolites associated with the interconversion of methionine and cysteine via cystathionine differed between PD patients and controls; (2) dopaminergic medication showed strong lipidomic signatures; (3) taurine-conjugated bile acids correlated with the severity of motor symptoms, while low levels of sulfated taurolithocholate were associated with PD incidence in the general population; and (4) computational modeling predicted changes in sulfur metabolism, driven by A. muciniphila and B. wadsworthia, which is consistent with the changed metabolome. The multi-omics integration reveals PD-specific patterns in microbial-host sulfur co-metabolism that may contribute to PD severity.},
}

@article {pmid31722044,
year = {2019},
author = {Qian, J and Meng, Q and Feng, Y and Mao, X and Ling, Y and Li, J},
title = {Multiplexed Non-barcoded Long-Read Sequencing and Assembling Genomes of Bacillus Strains in Error-Free Simulations.},
journal = {Current microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00284-019-01808-3},
pmid = {31722044},
issn = {1432-0991},
support = {KYZ2018009Q//the Teachers' Research Start-up Fund from Changshu Institute of Technology/ ; BK20181034//the Natural Science Foundation of Jiangsu Province/ ; },
abstract = {The generation of genomic data from microorganisms has revolutionized our abilities to understand their biology, but it is still challenging to obtain complete genome sequences of microbes in an automated high-throughput and cost-effective manner. While the advent of second-generation sequencing technologies provided significantly higher throughput, their shorter lengths and more pronounced sequence-context bias led to a shift towards resequencing applications. Recently, single molecule real-time (SMRT) DNA sequencing has been used to generate sequencing reads that are much longer than other sequencing platforms, facilitating de novo genome assembly and genome finishing. Here we introduced a novel multiplex strategy to make full use of the capacity and characteristics of SMRT sequencing in microbe genome assembly. We used error-free simulations to evaluate the practicability of assembling SMRT genomic sequencing data from multiple microbes into finished genomes once at a time. Then we compared the influence of two key factors, including sequencing coverage and read length, on multiplex assembling. Our results showed that long-read genomic sequencing inherently provided the ability to assemble genomic sequencing data from multiple microbes into finished genomes due to its long length. This approach might be helpful for the various groups of microbial genome projects or metagenomics research.},
}

@article {pmid31721393,
year = {2019},
author = {Beraldi, EJ and Borges, SC and de Almeida, FLA and Dos Santos, A and Saad, MJA and Buttow, NC},
title = {Colonic neuronal loss and delayed motility induced by high-fat diet occur independently of changes in the major groups of microbiota in Swiss mice.},
journal = {Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society},
volume = {},
number = {},
pages = {e13745},
doi = {10.1111/nmo.13745},
pmid = {31721393},
issn = {1365-2982},
support = {//National Council for Scientific and Technological Development (CNPq, Brazil)/ ; },
abstract = {BACKGROUND: Obesity has been linked to gastrointestinal disorders, and the loss of myenteric neurons in the intestine caused by high-fat diets (HFD) has been attributed to changes in microbiota and lipotoxicity. We investigated whether the prebiotic inulin modulates bacterial populations and alleviates neuronal loss in mice fed HFD.

METHODS: Swiss mice were fed purified rodent diet or HFD (59% kcal fat), or both diets supplemented with inulin for 17 weeks. Intestinal motility was assessed and a metagenome analysis of the colonic microbiota was performed. The gene expression of inflammatory markers was evaluated, and immunofluorescence was performed for different types of myenteric neurons and glial cells in the distal colon.

KEY RESULTS: The HFD caused obesity and delayed colonic motility. The loss of myenteric neurons and glial cells in obese mice affected all of the studied neuronal populations, including neurons positive for myosin-V, neuronal nitric oxide synthase, vasoactive intestinal peptide, and calretinin. Although obese mice supplemented with inulin exhibited improvements in colonic motility, neuronal, and glial cell loss persisted. The HFD did not altered the expression levels of inflammatory cytokines in the intestine or the prevalence of the major groups in microbiota, but inulin increased the proportion of the genus Akkermansia in the obese mice.

CONCLUSIONS AND INFERENCES: In Swiss mice, the HFD-induced neuronal loss but did not change the major groups in microbiota. This suggests that, despite the increase in the beneficial bacteria, other factors that are directly linked to excess dietary lipid intake affect the enteric nervous system.},
}

@article {pmid31720799,
year = {2019},
author = {Thomas, P and Shaik, SP},
title = {Molecular Profiling on Surface-Disinfected Tomato Seeds Reveals High Diversity of Cultivation-Recalcitrant Endophytic Bacteria with Low Shares of Spore-Forming Firmicutes.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-019-01440-5},
pmid = {31720799},
issn = {1432-184X},
support = {AMAAS Project//National Bureau of Agriculturally Important Microorganisms/ ; },
abstract = {Seeds are known to harbor diverse microorganisms offering protective effects on them with the prospects of quick root colonization at germination, selective recruitment as endophytes, and possible vertical transmission. The study was undertaken to assess the gross seed-internal bacterial community in tomato and to confirm if spore-forming Firmicutes constituted major seed endophytes adopting cultivation versus molecular approach on surface-sterilized seeds. Testing the initial seed wash solutions of "Arka Vikas" and "Arka Abha" cultivars showed > 1000 bacterial cfu per dry seed, largely Bacillus spp. Tissue homogenates from surface-disinfected seeds did not show any cultivable bacteria on enriched media for 1-2 weeks, while 16S rRNA V3-V4 taxonomic profiling revealed a huge bacterial diversity (10-16 phyla per cultivar). Proteobacteria formed the dominant phylum (65.7-69.6% OTUs) followed by Firmicutes, Actinobacteria, Bacteroidetes, and a notable share of Euryarchaeota (1.1-3.1%). Five more phyla appeared common to both cultivars in minor shares (Acidobacteria, Planctomycetes, Chloroflexi, Spirochaetes, Verrucomicrobia) with the ten phyla together constituting 99.6-99.9% OTUs. Class level and family level, the cultivars displayed elevated bacterial diversity, but similar taxonomic profiles. Arka Vikas and Arka Abha showed 114 and 107 genera, respectively, with 63 common genera constituting 96-97% OTUs. Psychrobacter formed the dominant genus. Bacillus and related genera constituted only negligible OTU share (0.16-0.28%). KEGG functional analysis showed metabolism as the major bacterial community role. One-month-old in vitro seedlings showed the activation of some originally uncultivable bacteria uninfluenced by the OTU share. The study reveals a high diversity of cultivation-recalcitrant endophytic bacteria prevailing in tomato seeds with possible vertical transmission and significant roles in plant biology.},
}

@article {pmid31719228,
year = {2019},
author = {Kuntal, BK and Mande, SS},
title = {Visual exploration of microbiome data.},
journal = {Journal of biosciences},
volume = {44},
number = {5},
pages = {},
pmid = {31719228},
issn = {0973-7138},
abstract = {A dramatic increase in large-scale cross-sectional and temporal-level metagenomic experiments has led to an improved understanding of the microbiome and its role in human well-being. Consequently, a plethora of analytical methods has been developed to decipher microbial biomarkers for various diseases, cluster different ecosystems based on microbial content, and infer functional potential of the microbiome as well as analyze its temporal behavior. Development of user-friendly visualization methods and frameworks is necessary to analyze this data and infer taxonomic and functional patterns corresponding to a phenotype. Thus, new methods as well as application of pre-existing ones has gained importance in recent times pertaining to the huge volume of the generated microbiome data. In this review, we present a brief overview of some useful visualization techniques that have significantly enriched microbiome data analytics.},
}

@article {pmid31719223,
year = {2019},
author = {Auti, AM and Narwade, NP and Deshpande, NM and Dhotre, DP},
title = {Microbiome and imputed metagenome study of crude and refined petroleum-oil-contaminated soils: Potential for hydrocarbon degradation and plant-growth promotion.},
journal = {Journal of biosciences},
volume = {44},
number = {5},
pages = {},
pmid = {31719223},
issn = {0973-7138},
abstract = {Microbial community structure of crude petroleum oil (CP)- and refined petroleum oil (RP)-contaminated soil was investigated. The taxonomical and functional diversity of such soils can be a great source of information about microbial community and genes involved in petroleum hydrocarbon (PHC) degradation. In this study, microbial diversity of soils contaminated by RP from urban biome of Pune, India, and CP from agricultural biome of Gujarat, India, were assessed by 16S rRNA amplicon sequencing on Illumina MiSeq platform. Association between the soil microbial community and the physicochemical parameters were investigated for their potential role. In RP- and CP-contaminated soils, the microbiome analysis showed Proteobacteria as most dominant phylum followed by Actinobacteria. Interestingly, Firmicutes were most prevailing in a CP-contaminated sample while they were least prevailing in RP-contaminated soils. Soil moisture content, total organic carbon and organic nitrogen content influenced the taxa diversity in these soils. Species richness was more in RP as compared to CP soils. Further prediction of metagenome using PICRUSt revealed that the RP and CP soils contain microbial communities with excellent metabolic potential for PHC degradation. Microbial community contributing to genes essential for soil health improvement and plant growth promotion was also gauged. Our analysis showed promising results for future bioaugmentation assisted phytoremediation (BAP) strategies for treating such soils.},
}

@article {pmid31719221,
year = {2019},
author = {Chaudhari, D and Dhotre, D and Agarwal, D and Gondhali, A and Nagarkar, A and Lad, V and Patil, U and Juvekar, S and Sinkar, V and Shouche, Y},
title = {Understanding the association between the human gut, oral and skin microbiome and the Ayurvedic concept of prakriti.},
journal = {Journal of biosciences},
volume = {44},
number = {5},
pages = {},
pmid = {31719221},
issn = {0973-7138},
abstract = {Ayurveda is one of the ancient systems of medicine which is widely practised as a personalized scientific approach towards the general wellness. Ayurvedic prakriti is broadly defined as the phenotypes which are determined on the basis of physical, psychological and physiological traits irrespective of their social, ethnic, dietary and geographical stature. Prakriti is the constitution of a person, which comprises vata, pitta, and kapha and is a key determinant of how one individual is different from the other. Human microbiome is considered the 'latest discovered' human organ and microbiome research reiterates the fundamental principles of Ayurveda for creating a healthy gut environment by maintaining the individual-specific microbiome. Hence, it is important to understand the association of human microbiome with the Ayurvedic prakriti of an individual. Here, we provide a comprehensive analysis of human microbiome from the gut, oral and skin samples of healthy individuals (n=18) by 16S rRNA gene-based metagenomics using standard QIIME pipeline. In the three different prakriti samples differential abundance of Bacteroides, Desulfovibrio, Parabacteroides, Slackia, and Succinivibrio was observed in the gut microbiome. Analysis also revealed prakriti-specific presence of Mogibacterium, Propionibacterium, Pyramidobacter, Rhodococcus in the kapha prakriti individuals Planomicrobium, Hyphomicrobium, Novosphingobium in the pitta prakriti individuals and Carnobacterium, Robiginitalea, Cetobacterium, Psychrobacter in the vata prakriti individuals. Similarly, the oral and skin microbiome also revealed presence of prakriti-specific differential abundance of diverse bacterial genera. Prakriti-specific presence of bacterial taxa was recorded and only 42% microbiome in the oral samples and 52% microbiome in the skin samples were shared. Bacteria known for preventing gut inflammation by digesting the resistant starch were abundant in the pitta prakriti individuals, who are more prone to develop gut-inflammation-related disorders. In summary, human gut, oral and skin microbiome showed presence or high abundance of few bacterial taxa across three prakriti types, suggesting their specific physiological importance.},
}

@article {pmid31719220,
year = {2019},
author = {Holmes, S},
title = {Successful strategies for human microbiome data generation, storage and analyses.},
journal = {Journal of biosciences},
volume = {44},
number = {5},
pages = {},
pmid = {31719220},
issn = {0973-7138},
abstract = {Current interest in the potential for clinical use of new tools for improving human health are now focused on techniques for the study of the human microbiome and its interaction with environmental and clinical covariates. This review outlines the use of statistical strategies that have been developed in past studies and can inform successful design and analyses of controlled perturbation experiments performed in the human microbiome. We carefully outline what the data are, their imperfections and how we need to transform, decontaminate and denoise them. We show how to identify the important unknown parameters and how to can leverage variability we see to produce efficient models for prediction and uncertainty quantification. We encourage a reproducible strategy that builds on best practice principles that can be adapted for effective experimental design and reproducible workflows. Nonparametric, data-driven denoising strategies already provide the best strain identification and decontamination methods. Data driven models can be combined with uncertainty quantification to provide reproducible aids to decision making in the clinical context, as long as careful, separate, registered confirmatory testing are undertaken. Here we provide guidelines for effective longitudinal studies and their analyses. Lessons learned along the way are that visualizations at every step can pinpoint problems and outliers, normalization and filtering improve power in downstream testing. We recommend collecting and binding the metadata and covariates to sample descriptors and recording complete computer scripts into an R markdown supplement that can reduce opportunities for human error and enable collaborators and readers to replicate all the steps of the study. Finally, we note that optimizing the bioinformatic and statistical workflow involves adopting a wait-and-see approach that is particularly effective in cases where the features such as 'mass spectrometry peaks' and metagenomic tables can only be partially annotated.},
}

@article {pmid31719139,
year = {2019},
author = {Gupta, A and Dhakan, DB and Maji, A and Saxena, R and P K, VP and Mahajan, S and Pulikkan, J and Kurian, J and Gomez, AM and Scaria, J and Amato, KR and Sharma, AK and Sharma, VK},
title = {Association of Flavonifractor plautii, a Flavonoid-Degrading Bacterium, with the Gut Microbiome of Colorectal Cancer Patients in India.},
journal = {mSystems},
volume = {4},
number = {6},
pages = {},
doi = {10.1128/mSystems.00438-19},
pmid = {31719139},
issn = {2379-5077},
abstract = {Recently, dysbiosis in the human gut microbiome and shifts in the relative abundances of several bacterial species have been recognized as important factors in colorectal cancer (CRC). However, these studies have been carried out mainly in developed countries where CRC has a high incidence, and it is unclear whether the host-microbiome relationships deduced from these studies can be generalized to the global population. To test if the documented associations between the microbiome and CRC are conserved in a distinct context, we performed metagenomic and metabolomic association studies on fecal samples from 30 CRC patients and 30 healthy controls from two different locations in India, followed by a comparison of CRC data available from other populations. We confirmed the association of Bacteroides and other bacterial taxa with CRC that have been previously reported in other studies. However, the association of CRC with Flavonifractor plautii in Indian patients emerged as a novel finding. The plausible role of F. plautii appears to be linked with the degradation of beneficial anticarcinogenic flavonoids, which was also found to be significantly correlated with the enzymes and modules involved in flavonoid degradation within Indian CRC samples. Thus, we hypothesize that the degradation of beneficial flavonoids might be playing a role in cancer progression within this Indian cohort. We also identified 20 potential microbial taxonomic markers and 33 potential microbial gene markers that discriminate the Indian CRC from healthy microbiomes with high accuracy based on machine learning approaches.IMPORTANCE This study provides novel insights on the CRC-associated microbiome of a unique cohort in India, reveals the potential role of a new bacterium in CRC, and identifies cohort-specific biomarkers, which can potentially be used in noninvasive diagnosis of CRC. The study gains additional significance, as India is among the countries with a very low incidence of CRC, and the diet and lifestyle in India have been associated with a distinct gut microbiome in healthy Indians compared to other global populations. Thus, in this study, we hypothesize a unique relationship between CRC and the gut microbiome in an Indian population.},
}

@article {pmid31717688,
year = {2019},
author = {Wojciuk, B and Salabura, A and Grygorcewicz, B and Kędzierska, K and Ciechanowski, K and Dołęgowska, B},
title = {Urobiome: In Sickness and in Health.},
journal = {Microorganisms},
volume = {7},
number = {11},
pages = {},
doi = {10.3390/microorganisms7110548},
pmid = {31717688},
issn = {2076-2607},
abstract = {The human microbiome has been proven to contribute to the human condition, both in health and in disease. The metagenomic approach based on next-generation sequencing has challenged the dogma of urine sterility. The human urobiome consists of bacteria and eukaryotic viruses as well as bacteriophages, which potentially represent the key factor. There have been several significant findings with respect to the urobiome in the context of urological disorders. Still, the research on the urobiome in chronic kidney disease and kidney transplantation remains underrepresented, as does research on the role of the virome in the urinary microbiota. In this review, we present recent findings on the urobiome with a particular emphasis on chronic kidney disease and post-kidney transplantation status. Challenges and opportunities arising from the research on the human urobiome will also be discussed.},
}

@article {pmid31717640,
year = {2019},
author = {Sadeghpour Heravi, F and Zakrzewski, M and Vickery, K and G Armstrong, D and Hu, H},
title = {Bacterial Diversity of Diabetic Foot Ulcers: Current Status and Future Prospectives.},
journal = {Journal of clinical medicine},
volume = {8},
number = {11},
pages = {},
doi = {10.3390/jcm8111935},
pmid = {31717640},
issn = {2077-0383},
abstract = {Diabetic foot ulcers (DFUs) and diabetic foot infections (DFIs) are associated with reduced patient quality of life, lower-extremity amputation, hospitalization, and high morbidity and mortality. Diverse bacterial communities have been identified in DFUs/DFIs, playing a significant role in infection prognosis. However, due to the high heterogeneity of bacterial communities colonized in DFUs/DFIs, culture-based methods may not isolate all of the bacterial population or unexpected microorganisms. Recently, high sensitivity and specificity of DNA (metagenomics) and RNA (metatranscriptomics) technologies have addressed limitations of culture-based methods and have taken a step beyond bacterial identification. As a consequence, new advances obtained from DNA- and RNA-based techniques for bacterial identification can improve therapeutic approaches. This review evaluated the current state of play in aetiology of DFUs/DFIs on culture and molecular approaches, and discussed the impact of metagenomic and metatranscriptomic methods in bacterial identification approaches.},
}

@article {pmid31717498,
year = {2019},
author = {Gran-Stadniczeñko, S and Krabberød, AK and Sandaa, RA and Yau, S and Egge, E and Edvardsen, B},
title = {Seasonal Dynamics of Algae-Infecting Viruses and Their Inferred Interactions with Protists.},
journal = {Viruses},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/v11111043},
pmid = {31717498},
issn = {1999-4915},
abstract = {Viruses are a highly abundant, dynamic, and diverse component of planktonic communities that have key roles in marine ecosystems. We aimed to reveal the diversity and dynamics of marine large dsDNA viruses infecting algae in the Northern Skagerrak, South Norway through the year by metabarcoding, targeting the major capsid protein (MCP) and its correlation to protist diversity and dynamics. Metabarcoding results demonstrated a high diversity of algal viruses compared to previous metabarcoding surveys in Norwegian coastal waters. We obtained 313 putative algal virus operational taxonomic units (vOTUs), all classified by phylogenetic analyses to either the Phycodnaviridae or Mimiviridae families, most of them in clades without any cultured or environmental reference sequences. The viral community showed a clear temporal variation, with some vOTUs persisting for several months. The results indicate co-occurrences between abundant viruses and potential hosts during long periods. This study gives new insights into the virus-algal host dynamics and provides a baseline for future studies of algal virus diversity and temporal dynamics.},
}

@article {pmid31717432,
year = {2019},
author = {Dalmon, A and Gayral, P and Decante, D and Klopp, C and Bigot, D and Thomasson, M and Herniou, EA and Alaux, C and Le Conte, Y},
title = {Viruses in the Invasive Hornet Vespa velutina.},
journal = {Viruses},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/v11111041},
pmid = {31717432},
issn = {1999-4915},
abstract = {The Asian yellow-legged hornet Vespa velutina nigrithorax, a major predator of honeybees, is spreading in Europe in part due to a lack of efficient control methods. In this study, as a first step to identify biological control agents, we characterized viral RNA sequences present in asymptomatic or symptomatic hornets. Among 19 detected viruses, the honey bee virus Deformed wing virus-B was predominant in all the samples, particularly in muscles from the symptomatic hornet, suggesting a putative cause of the deformed wing symptom. Interestingly, two new viruses closely related to Acyrthosiphon pisumvirus and Himetobi Pvirus and viruses typically associated with honey bees, Acute bee paralysis virus and Black queen cell virus, were detected in the brain and muscles, and may correspond to the circulation and possible replication forms of these viruses in the hornet. Aphid lethal paralysis virus, Bee Macula-like virus, and Moku virus, which are known to infect honey bees, were also identified in the gut virus metagenome of hornets. Therefore, our study underlined the urgent need to study the host range of these newly discovered viruses in hornets to determine whether they represent a new threat for honey bees or a hope for the biocontrol of V. velutina.},
}

@article {pmid31715071,
year = {2019},
author = {Zhang, M and Hill, JE and Godson, DL and Ngeleka, M and Fernando, C and Huang, Y},
title = {The pulmonary virome, bacteriological and histopathological findings in bovine respiratory disease from western Canada.},
journal = {Transboundary and emerging diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/tbed.13419},
pmid = {31715071},
issn = {1865-1682},
abstract = {The etiology and pathogenesis of bovine respiratory disease (BRD) is complex and involves the interplay of infectious agents, management and environmental factors. Previous studies of BRD focused on ante mortem samples from the upper respiratory tract and identified several unconventional viruses. The lung, however, is the primary location where significant BRD lesions are usually found, and is a common post mortem diagnostic specimen. In this study, results of high throughput virome sequencing, bacterial culture, targeted real-time PCR and histological examination of 130 bovine pneumonic lungs from western Canadian cattle were combined to explore associations of microorganisms with different types of pneumonia. Fibrinous bronchopneumonia (FBP) was the predominant type of pneumonia (46.2%, 60/130), and was associated with the detection of Mannheimia haemolytica. Detection of Histophilus somni and Pasteurella multocida were associated with suppurative bronchopneumonia (SBP) and concurrent bronchopneumonia and bronchointerstitial pneumonia (BP&BIP), respectively. Sixteen viruses were identified, of which bovine parvovirus 2 (BPV2) was the most prevalent (11.5%, 15/130) followed by ungulate tetraparvovirus 1 (UTPV1, 8.5%, 11/130) and bovine respiratory syncytial virus (BRSV, 8.5%, 11/130). None of these viruses, however, were significantly associated with a particular type of pneumonia. Unconventional viruses such as influenza D virus (IDV) and bovine rhinitis B virus (BRBV) were detected, although sparsely, consistent with our previous findings in upper respiratory tract samples. Taken together, our results show that while virus detection in post mortem lung samples is of relatively little diagnostic value, the strong associations of H. somni and M. haemolytica with SBP and FBP, respectively, indicate that histopathology can be useful in differentiating bacterial etiologies.},
}

@article {pmid31713674,
year = {2019},
author = {Schröder, C and Eixenberger, D and Suleiman, M and Schäfers, C and Antranikian, G},
title = {Characterization of an extremely thermo-active archaeal β-glucosidase and its activity towards glucan and mannan in concert with an endoglucanase.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-019-10218-1},
pmid = {31713674},
issn = {1432-0614},
abstract = {A metagenome from an enrichment culture of a hydrothermal vent sample taken at Vulcano Island (Italy) was sequenced and an endoglucanase-encoding gene (vul_cel5A) was identified in a previous work. Vul_Cel5A with maximal activity at 115 °C was characterized as the most heat-active endoglucanase to date. Based on metagenome sequences, genomes were binned and bin4 included vul_cel5A as well as a putative GH1 β-glycosidase-encoding gene (vul_bgl1A) with highest identities to sequences from the archaeal genus Thermococcus. The recombinant β-glucosidase Vul_Bgl1A produced in E. coli BL21 pQE-80L exhibited highest activity at 105 °C and pH 7.0 (76.12 ± 5.4 U/mg, 100%) using 4NP β-D-glucopyranoside as substrate and 61% relative activity at 120 °C. Accordingly, Vul_Bgl1A represents one of the most heat-active β-glucosidases to date. The enzyme has a broad substrate specificity with 155% activity towards 4NP β-D-mannopyranoside in comparison with 4NP β-D-glucopyranoside. Moreover, nearly complete hydrolysis of cellobiose was demonstrated. The enzyme exhibited a high glucose tolerance with 26% residual activity in presence of 2 M glucose and was furthermore activated at glucose concentrations of up to 0.5 M. When the endoglucanase Vul_Cel5A and the β-glucosidase Vul_Bgl1A were applied simultaneously at 99 °C, 158% activity towards barley β-glucan and 215% towards mannan were achieved compared with the activity of Vul_Cel5A alone (100%). Consequently, a significant increase in glucose formation was observed when both enzymes were incubated with β-glucan and mannan suggesting a synergistic effect. Hence, the two archaeal extremozymes are ideal candidates for complete glucan and mannan saccharification at temperatures above the boiling point of water.},
}

@article {pmid31713420,
year = {2019},
author = {Heß, S and Kneis, D and Österlund, T and Li, B and Kristiansson, E and Berendonk, TU},
title = {Sewage from Airplanes Exhibits High Abundance and Diversity of Antibiotic Resistance Genes.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.9b03236},
pmid = {31713420},
issn = {1520-5851},
abstract = {Airplane sanitary facilities are shared by an international audience. We hypothesized the corresponding sewage to be an extraordinary source of antibiotic-resistant bacteria (ARB) and resistance genes (ARG) in terms of diversity and quantity. Accordingly, we analyzed ARG and ARB in airplane-borne sewage using complementary approaches: metagenomics, quantitative polymerase chain reaction (qPCR), and cultivation. For the purpose of comparison, we also quantified ARG and ARB in the inlets of municipal treatment plants with and without connection to airports. As expected, airplane sewage contained an extraordinarily rich set of mobile ARG, and the relative abundances of genes were mostly increased compared to typical raw sewage of municipal origin. Moreover, combined resistance against third-generation cephalosporins, fluorochinolones, and aminoglycosides was unusually common (28.9%) among Escherichia coli isolated from airplane sewage. This percentage exceeds the one reported for German clinical isolates by a factor of 8. Our findings suggest that airplane-borne sewage can effectively contribute to the fast and global spread of antibiotic resistance.},
}

@article {pmid31713170,
year = {2019},
author = {Astudillo-de la Vega, H and Alonso-Luna, O and Ali-Pérez, J and López-Camarillo, C and Ruiz-Garcia, E},
title = {Oncobiome at the Forefront of a Novel Molecular Mechanism to Understand the Microbiome and Cancer.},
journal = {Advances in experimental medicine and biology},
volume = {1168},
number = {},
pages = {147-156},
doi = {10.1007/978-3-030-24100-1_10},
pmid = {31713170},
issn = {0065-2598},
abstract = {The microbiome comprises all the genetic material within a microbiota, that represents tenfold higher than that of our cells. The microbiota it includes a wide variety of microorganisms such as bacteria, viruses, protozoans, fungi, and archaea, and this ecosystem is personalized in any body space of every individual. Balanced microbial communities can positively contribute to training the immune system and maintaining immune homeostasis. Dysbiosis is a change in the normal microbiome composition that can initiate chronic inflammation, epithelial barrier breaches, and overgrowth of harmful bacteria. The next-generation sequencing methods have revolutionized the study of the microbiome. Bioinformatic tools to manage large volumes of new information, it became possible to assess species diversity and measure dynamic fluctuations in microbial communities. The burden of infections that are associated to human cancer is increasing but is underappreciated by the cancer research community. The rich content in microbes of normal and tumoral tissue reflect could be defining diverse physiological or pathological states. Genomic research has emerged a new focus on the interplay between the human microbiome and carcinogenesis and has been termed the 'oncobiome'. The interactions among the microbiota in all epithelium, induce changes in the host immune interactions and can be a cause of cancer. Microbes have been shown to have systemic effects on the host that influence the efficacy of anticancer drugs. Metagenomics allows to investigate the composition of microbial community. Metatranscriptome analysis applies RNA sequencing to microbial samples to determine which species are present. Cancer can be caused by changes in the microbiome. The roles of individual microbial species in cancer progression have been identified long ago for various tissue types. The identification of microbiomes of drug resistance in the treatment of cancer patients has been the subject of numerous microbiome studies. The complexity of cancer genetic alterations becomes irrelevant in certain cancers to explain the origin, the cause or the oncogenic maintenance by the oncogene addiction theory.},
}

@article {pmid31712737,
year = {2019},
author = {Brewer, TE and Albertsen, M and Edwards, A and Kirkegaard, RH and Rocha, EPC and Fierer, N},
title = {Unlinked rRNA genes are widespread among bacteria and archaea.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-019-0552-3},
pmid = {31712737},
issn = {1751-7370},
support = {15510//Villum Fonden (Villum Foundation)/ ; RF-2017-652\2//Leverhulme Trust/ ; EAR1331828//National Science Foundation (NSF)/ ; },
abstract = {Ribosomes are essential to cellular life and the genes for their RNA components are the most conserved and transcribed genes in bacteria and archaea. Ribosomal RNA genes are typically organized into a single operon, an arrangement thought to facilitate gene regulation. In reality, some bacteria and archaea do not share this canonical rRNA arrangement-their 16S and 23S rRNA genes are separated across the genome and referred to as "unlinked". This rearrangement has previously been treated as an anomaly or a byproduct of genome degradation in intracellular bacteria. Here, we leverage complete genome and long-read metagenomic data to show that unlinked 16S and 23S rRNA genes are more common than previously thought. Unlinked rRNA genes occur in many phyla, most significantly within Deinococcus-Thermus, Chloroflexi, and Planctomycetes, and occur in differential frequencies across natural environments. We found that up to 41% of rRNA genes in soil were unlinked, in contrast to the human gut, where all sequenced rRNA genes were linked. The frequency of unlinked rRNA genes may reflect meaningful life history traits, as they tend to be associated with a mix of slow-growing free-living species and intracellular species. We speculate that unlinked rRNA genes may confer selective advantages in some environments, though the specific nature of these advantages remains undetermined and worthy of further investigation. More generally, the prevalence of unlinked rRNA genes in poorly-studied taxa serves as a reminder that paradigms derived from model organisms do not necessarily extend to the broader diversity of bacteria and archaea.},
}

@article {pmid31712445,
year = {2019},
author = {Sobhani, I and Bergsten, E and Couffin, S and Amiot, A and Nebbad, B and Barau, C and de'Angelis, N and Rabot, S and Canoui-Poitrine, F and Mestivier, D and Pédron, T and Khazaie, K and Sansonetti, PJ},
title = {Colorectal cancer-associated microbiota contributes to oncogenic epigenetic signatures.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1912129116},
pmid = {31712445},
issn = {1091-6490},
abstract = {Sporadic colorectal cancer (CRC) is a result of complex interactions between the host and its environment. Environmental stressors act by causing host cell DNA alterations implicated in the onset of cancer. Here we investigate the stressor ability of CRC-associated gut dysbiosis as causal agent of host DNA alterations. The epigenetic nature of these alterations was investigated in humans and in mice. Germ-free mice receiving fecal samples from subjects with normal colonoscopy or from CRC patients were monitored for 7 or 14 wk. Aberrant crypt foci, luminal microbiota, and DNA alterations (colonic exome sequencing and methylation patterns) were monitored following human feces transfer. CRC-associated microbiota induced higher numbers of hypermethylated genes in murine colonic mucosa (vs. healthy controls' microbiota recipients). Several gene promoters including SFRP1,2,3, PENK, NPY, ALX4, SEPT9, and WIF1 promoters were found hypermethylated in CRC but not in normal tissues or effluents from fecal donors. In a pilot study (n = 266), the blood methylation levels of 3 genes (Wif1, PENK, and NPY) were shown closely associated with CRC dysbiosis. In a validation study (n = 1,000), the cumulative methylation index (CMI) of these genes was significantly higher in CRCs than in controls. Further, CMI appeared as an independent risk factor for CRC diagnosis as shown by multivariate analysis that included fecal immunochemical blood test. Consequently, fecal bacterial species in individuals with higher CMI in blood were identified by whole metagenomic analysis. Thus, CRC-related dysbiosis induces methylation of host genes, and corresponding CMIs together with associated bacteria are potential biomarkers for CRC.},
}

@article {pmid31711703,
year = {2019},
author = {Even, G and Mottais, D and Morien, F and Pham, MD and Ostergaard, A and Martel, S and Merlin, S and Audebert, C},
title = {Porcine bacteriospermia examined by high-throughput sequencing.},
journal = {Theriogenology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.theriogenology.2019.10.034},
pmid = {31711703},
issn = {1879-3231},
}

@article {pmid31709946,
year = {2019},
author = {Doğan, Ö and Tunçkanat, F and Cinel, G and Şener, B and Özçelik, HU and Yalçın, EE and Doğru Ersöz, D and Kiper, EN},
title = {[Investigation of role of anaerobic bacteria in cystic fibrosis patients].},
journal = {Tuberkuloz ve toraks},
volume = {67},
number = {3},
pages = {151-161},
doi = {10.5578/tt.68358},
pmid = {31709946},
issn = {0494-1373},
abstract = {Introduction: Repetitive pulmonary infections are the main cause of morbidity and mortality in cystic fibrosis (CF) patients. In recent years, non-culture dependent metagenomic studies showed complex dynamics of the pulmonary environment of CF patients and pointed out the importance of anaerobic bacteria. Molecular-based studies indicate that anaerobic bacteria can be found more than aerobic or facultative anaerobic bacteria in CF lung environment. However, limited number of studies are far away to clarify the importance of anaerobic bacteria in CF pulmonary disease.

Materials and Methods: The aim of this study was to evaluate the role of anaerobic bacteria in CF patients admitted to Hacettepe University, Pediatric Respiratory Diseases Department, by using quantitative culture method for both aerobic and anaerobic bacteria. Anaerobic bacteria were identified by conventional and semi-automated methods. Antibiotic susceptibilities were performed by agar dilution method.

Result: Seventy-seven anaerobic bacteria were isolated from 35 (81.4%) of 43 patients. The total count of anaerobes and facultative bacteria (mean 16 x 106), was higher than aerobes and facultative bacteria (mean 14.1 x 106). If anaerobe culture were not performed merely 63.65% of all species could be obtained. In patients whose samples yielded intermediate or high numbers of PMNLs, significantly more obligate anaerobic bacteria were isolated (p= 0.046). Patients older than 18 years were colonized with higher number of anaerobic bacteria. Susceptibilities of 72 isolates out of 77, against ampicillin, sulbactam-ampicillin, piperacillin, piperacillin-tazobactam, moxifloxacin, metronidazole, imipenem, and clindamycin were also evaluated. Clindamycin was found to be the least effective antibiotic among all. None of the isolates was resistant to imipenem.

Conclusions: This is the first study to show the role and importance of anaerobic bacteria in CF patients in our country. The resistance rates in anaerobic bacteria isolated from CF patients is concerning. Therefore, intermittent anaerobic culture and follow-up of resistance rates will be helpful in the follow-up of these patients.},
}

@article {pmid31709683,
year = {2019},
author = {Mayneris-Perxachs, J and Fernández-Real, JM},
title = {How the joint study of the microbiota and metabolites in different body fluids may aid in the identification of novel disease mechanisms.},
journal = {The FEBS journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/febs.15130},
pmid = {31709683},
issn = {1742-4658},
abstract = {Thanks to the emergence and recent advances in high-throughput sequencing technologies, it is becoming more evident every day that changes in the microbiome composition are linked to a myriad of health conditions. Despite this, the mechanisms of host-microbiota signalling remain largely unknown. The microbiome has an extensive metabolic activity that leads to the generation of a large number of compounds that are likely to influence host health. Therefore, the microbiome-host cross-talk is in part mediated by microbial-derived metabolites. Unlike metagenomics, which only provides information about microbial genes and thus the microbiome functional potential, metabolic phenotyping is well suited to capture their actual metabolic activity. Here we provide an overview of these approaches and propose an integration of metagenomics, as a microbiome compositional readout, with faecal and plasma/urine metabolomics, as a functional readout, to unravel novel mechanisms linking the microbiome to host health and disease.},
}

@article {pmid31708944,
year = {2019},
author = {Lucaciu, R and Pelikan, C and Gerner, SM and Zioutis, C and Köstlbacher, S and Marx, H and Herbold, CW and Schmidt, H and Rattei, T},
title = {A Bioinformatics Guide to Plant Microbiome Analysis.},
journal = {Frontiers in plant science},
volume = {10},
number = {},
pages = {1313},
doi = {10.3389/fpls.2019.01313},
pmid = {31708944},
issn = {1664-462X},
abstract = {Recent evidence for intimate relationship of plants with their microbiota shows that plants host individual and diverse microbial communities that are essential for their survival. Understanding their relatedness using genome-based and high-throughput techniques remains a hot topic in microbiome research. Molecular analysis of the plant holobiont necessitates the application of specific sampling and preparatory steps that also consider sources of unwanted information, such as soil, co-amplified plant organelles, human DNA, and other contaminations. Here, we review state-of-the-art and present practical guidelines regarding experimental and computational aspects to be considered in molecular plant-microbiome studies. We discuss sequencing and "omics" techniques with a focus on the requirements needed to adapt these methods to individual research approaches. The choice of primers and sequence databases is of utmost importance for amplicon sequencing, while the assembly and binning of shotgun metagenomic sequences is crucial to obtain quality data. We discuss specific bioinformatic workflows to overcome the limitation of genome database resources and for covering large eukaryotic genomes such as fungi. In transcriptomics, it is necessary to account for the separation of host mRNA or dual-RNAseq data. Metaproteomics approaches provide a snapshot of the protein abundances within a plant tissue which requires the knowledge of complete and well-annotated plant genomes, as well as microbial genomes. Metabolomics offers a powerful tool to detect and quantify small molecules and molecular changes at the plant-bacteria interface if the necessary requirements with regard to (secondary) metabolite databases are considered. We highlight data integration and complementarity which should help to widen our understanding of the interactions among individual players of the plant holobiont in the future.},
}

@article {pmid31708903,
year = {2019},
author = {Mori, JF and Chen, LX and Jessen, GL and Rudderham, SB and McBeth, JM and Lindsay, MBJ and Slater, GF and Banfield, JF and Warren, LA},
title = {Putative Mixotrophic Nitrifying-Denitrifying Gammaproteobacteria Implicated in Nitrogen Cycling Within the Ammonia/Oxygen Transition Zone of an Oil Sands Pit Lake.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2435},
doi = {10.3389/fmicb.2019.02435},
pmid = {31708903},
issn = {1664-302X},
abstract = {Anthropogenically-impacted environments offer the opportunity to discover novel microbial species and metabolisms, which may be undetectable in natural systems. Here, a combined metagenomic and geochemical study in Base Mine Lake, Alberta, Canada, which is the only oil sands end pit lake to date, revealed that nitrification was performed by members from Nitrosomonadaceae, Chloroflexi and unclassified Gammaproteobacteria "MBAE14." While Nitrosomonadaceae and Chloroflexi groups were relatively abundant in the upper oxygenated zones, MBAE14 dominated the hypoxic hypolimnetic zones (approximately 30% of total microbial communities); MBAE14 was not detected in the underlying anoxic tailings. Replication rate analyses indicate that MBAE14 grew in metalimnetic and hypolimnetic water cap regions, most actively at the metalimnetic, ammonia/oxygen transition zone consistent with it putatively conducting nitrification. Detailed genomic analyses of MBAE14 evidenced both ammonia oxidation and denitrification into dinitrogen capabilities. However, the absence of known CO2-fixation genes suggests a heterotrophic denitrifying metabolism. Functional marker genes of ammonia oxidation (amo and hao) in the MBAE14 genome are homologous with those conserved in autotrophic nitrifiers, but not with those of known heterotrophic nitrifiers. We propose that this novel MBAE14 inhabits the specific ammonia-rich, oxygen and labile organic matter-limited conditions occurring in Base Mine Lake which selectively favors mixotrophic coupled nitrifier denitrification metabolism. Our results highlight the opportunities to better constrain biogeochemical cycles from the application of metagenomics to engineered systems associated with extractive resource sectors.},
}

@article {pmid31708889,
year = {2019},
author = {Tang, KY and Wang, ZW and Wan, QH and Fang, SG},
title = {Metagenomics Reveals Seasonal Functional Adaptation of the Gut Microbiome to Host Feeding and Fasting in the Chinese Alligator.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2409},
doi = {10.3389/fmicb.2019.02409},
pmid = {31708889},
issn = {1664-302X},
abstract = {As a natural hibernator, the Chinese alligator (Alligator sinensis) is an ideal and intriguing model to investigate changes in microbial community structure and function caused by hibernation. In this study, we used 16S rRNA profiling and metagenomic analysis to compare the composition, diversity, and functional capacity in the gut microbiome of hibernating vs. active Chinese alligators. Our results show that gut microbial communities undergo seasonal restructuring in response to seasonal cycles of feeding and fasting in the Chinese alligator, but this animal harbors a core gut microbial community primarily dominated by Proteobacteria, Fusobacteria, Bacteroidetes, and Firmicutes across the gut regions. During hibernation, there is an increase in the abundance of bacterial taxa (e.g., the genus Bacteroides) that can degrade host mucin glycans, which allows adaptation to winter fasting. This is accompanied by the enrichment of mucin oligosaccharide-degrading enzyme and carbohydrate-active enzyme families. In contrast, during the active phase (feeding), active Chinese alligators exhibit a carnivore gut microbiome dominated by Fusobacteria, and there is an increase in the relative abundance of bacteria (e.g., Cetobacterium somerae) with known proteolytic and amino acids-fermentating functions that improve host protein-rich food digestion efficiency. In addition, seasonal variations in the expression of β-defensins play a protective role in intestinal immunity. These findings provide insights into the functional adaptations of host-gut microbe symbioses to seasonal dietary shifts to maintain gut homeostasis and health, especially in extreme physiological states.},
}

@article {pmid31708885,
year = {2019},
author = {Géron, A and Werner, J and Wattiez, R and Lebaron, P and Matallana-Surget, S},
title = {Deciphering the Functioning of Microbial Communities: Shedding Light on the Critical Steps in Metaproteomics.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2395},
doi = {10.3389/fmicb.2019.02395},
pmid = {31708885},
issn = {1664-302X},
abstract = {Unraveling the complex structure and functioning of microbial communities is essential to accurately predict the impact of perturbations and/or environmental changes. From all molecular tools available today to resolve the dynamics of microbial communities, metaproteomics stands out, allowing the establishment of phenotype-genotype linkages. Despite its rapid development, this technology has faced many technical challenges that still hamper its potential power. How to maximize the number of protein identification, improve quality of protein annotation, and provide reliable ecological interpretation are questions of immediate urgency. In our study, we used a robust metaproteomic workflow combining two protein fractionation approaches (gel-based versus gel-free) and four protein search databases derived from the same metagenome to analyze the same seawater sample. The resulting eight metaproteomes provided different outcomes in terms of (i) total protein numbers, (ii) taxonomic structures, and (iii) protein functions. The characterization and/or representativeness of numerous proteins from ecologically relevant taxa such as Pelagibacterales, Rhodobacterales, and Synechococcales, as well as crucial environmental processes, such as nutrient uptake, nitrogen assimilation, light harvesting, and oxidative stress response, were found to be particularly affected by the methodology. Our results provide clear evidences that the use of different protein search databases significantly alters the biological conclusions in both gel-free and gel-based approaches. Our findings emphasize the importance of diversifying the experimental workflow for a comprehensive metaproteomic study.},
}

@article {pmid31708159,
year = {2019},
author = {Abendroth, C and Latorre-Pérez, A and Porcar, M and Simeonov, C and Luschnig, O and Vilanova, C and Pascual, J},
title = {Shedding light on biogas: Phototrophic biofilms in anaerobic digesters hold potential for improved biogas production.},
journal = {Systematic and applied microbiology},
volume = {},
number = {},
pages = {126024},
doi = {10.1016/j.syapm.2019.126024},
pmid = {31708159},
issn = {1618-0984},
abstract = {Conventional anaerobic digesters intended for the production of biogas usually operate in complete darkness. Therefore, little is known about the effect of light on their microbial communities. In the present work, 16S rRNA gene amplicon Nanopore sequencing and shotgun metagenomic sequencing were used to study the taxonomic and functional structure of the microbial community forming a biofilm on the inner wall of a laboratory-scale transparent anaerobic biodigester illuminated with natural sunlight. The biofilm was composed of microorganisms involved in the four metabolic processes needed for biogas production, and it was surprisingly rich in Rhodopseudomonas faecalis, a versatile bacterium able to carry out photoautotrophic metabolism when grown under anaerobic conditions. The results suggested that this bacterium, which is able to fix carbon dioxide, could be considered for use in transparent biogas fermenters in order to contribute to the production of optimized biogas with a higher CH4:CO2 ratio than the biogas produced in regular, opaque digesters. To the best of our knowledge, this is the first study characterising the phototrophic biofilm associated with illuminated bioreactors.},
}

@article {pmid31707781,
year = {2019},
author = {Li, Q and Chen, H and Zhang, M and Wu, T and Liu, R and Zhang, Z},
title = {Potential correlation between dietary fiber suppresses microbial conversion of choline to trimethylamine and formation of methylglyoxal.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.9b04860},
pmid = {31707781},
issn = {1520-5118},
abstract = {Dietary interventions alter the formation of the disease-associated metabolite, trimethylamine (TMA), via intestinal microbial TMA lyase activity. Nevertheless, the mechanisms regulating microbial enzyme production are still unclear. Sequencing of the gut bacteria 16S rDNA demonstrated that dietary intervention changed the composition of the gut microbiota and the functional metagenome involved in the choline utilization pathway. Characterization of the functional profile of the metagenomes and metabonomics analysis revealed that a series of Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologous (KO) groups and enzyme (EC) groups related to accumulation of methylglyoxal (MG) and glycine were enriched in red meat diet-fed animals, whereas fiber-rich diet suppressed glycine formation via the MG-dependent pathway. Our observations suggest associations between choline-TMA lyase expression and MG formation, which are indicative of a novel role of the gut microbiota in choline metabolism and highlight it as a potential target for inhibiting TMA production.},
}

@article {pmid31054477,
year = {2019},
author = {Wei, Z and Wu, Y and Feng, K and Yang, M and Zhang, Y and Tu, Q and Wang, J and Deng, Y},
title = {ARGA, a pipeline for primer evaluation on antibiotic resistance genes.},
journal = {Environment international},
volume = {128},
number = {},
pages = {137-145},
doi = {10.1016/j.envint.2019.04.030},
pmid = {31054477},
issn = {1873-6750},
mesh = {Anti-Bacterial Agents/*pharmacology ; Databases, Genetic ; *Drug Resistance, Microbial/genetics ; Metagenome ; },
abstract = {Molecular biology techniques have assisted in the investigation of antibiotic resistance genes (ARGs) from various environments. However, their accuracy relies on primer quality and data interpretation, both of which require a full-coverage sequence database for ARGs. Here, based upon the abandoned Antibiotic Resistance Genes Database (ARDB), we created an updated sequence database of antibiotic resistance genes (SDARG). A total of 1,260,069 protein sequences and 1,164,479 nucleotide sequences, 56 times more sequences than ARDB, from 448 types of ARGs (enabling resistance to 18 categories of antibiotics) were collected and integrated with different hierarchical credibility and full-scale taxonomic information. Based on this comprehensive sequence database, an online pipeline - ARG analyzer (ARGA, http://mem.rcees.ac.cn:8083/) was developed to assess current ARGs primers, as well as annotate ARGs from environmental metagenomes. Thereafter, a list of 658 published primer pairs, targeting 173 ARGs, was evaluated using ARGA and integrated in ARGA as ARGs primer database. The results showed that 65.05% primers are of high specificity (≥90%), while only 29.79% primers cover >50% of targeted sequences, indicating a divergence in the quality of current ARG primers. Hence, primer assessment or redesign is highly recommended to improve the accuracy of ARGs studies. ARGs primer database was attached in ARGA to provide researchers alternatives to better survey ARGs in the environment.},
}

Anti-Bacterial Agents/*pharmacology
Databases, Genetic
*Drug Resistance, Microbial/genetics
Metagenome

@article {pmid31707440,
year = {2019},
author = {Carabeo-Pérez, A and Guerra-Rivera, G and Ramos-Leal, M and Jiménez-Hernández, J},
title = {Correction to: Metagenomic approaches: effective tools for monitoring the structure and functionality of microbiomes in anaerobic digestion systems.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-019-10137-1},
pmid = {31707440},
issn = {1432-0614},
abstract = {The original version of this article was revised: After publication of this article, the publisher was notified that Michael Klocke has been listed as an author without his consent.},
}

@article {pmid31707285,
year = {2019},
author = {Huang, YC and Huang, LT and Sheen, JM and Hou, CY and Yeh, YT and Chiang, CP and Lin, IC and Tiao, MM and Tsai, CC and Lin, YJ and Chen, CC and Tain, YL and Yu, HR},
title = {Resveratrol treatment improves the altered metabolism and related dysbiosis of gut programed by prenatal high-fat diet and postnatal high-fat diet exposure.},
journal = {The Journal of nutritional biochemistry},
volume = {75},
number = {},
pages = {108260},
doi = {10.1016/j.jnutbio.2019.108260},
pmid = {31707285},
issn = {1873-4847},
abstract = {A maternal high-fat (HF) diet sensitizes offspring to the adverse effects of postnatal HF intake and can lead to metabolic dysregulation. Resveratrol, a natural polyphenolic compound found in grapes and red wine, could help to relieve metabolic syndrome dysregulation. Since the gut microbiota is known to be closely related to metabolic homeostasis, this study aimed to investigate the impact of a combination of maternal and postweaning HF diets on the gut microbiota and whether resveratrol could relieve the gut dysbiosis associated with metabolic dysregulation. Sprague-Dawley dams were sustained on either a chow or HF diet before mating, during pregnancy and during lactation. Their offspring were randomly fed chow or a HF diet after weaning. Four experimental groups were generated: CC (maternal/postnatal chow diet), HC (maternal HF/postnatal chow diet), CH (maternal chow/postnatal high-fat diet) and HH (maternal/postnatal HF diet). A fifth group consisted of HH with resveratrol treatment. We found that both maternal and postnatal HF exposure has a distinct effect on the gut microbiota metagenome of offspring. Maternal HF diet exposure decreased plasma acetate, propionate and butyrate level, while postnatal HF diet exposure decreased plasma acetate level in adult life. The metabolic dysregulation programed by the maternal and postnatal HF diets was related to the relevant gut microbiota. Resveratrol treatment ameliorated the altered plasma propionate level related to maternal HF and postnatal HF diet treatment. Resveratrol treatment also improved most of the altered metabolic dysregulation and related dysbiosis programmed by maternal and postnatal HF diet exposure.},
}

@article {pmid31706163,
year = {2019},
author = {Liu, X and Wang, H and Liu, X and Li, Y and Chen, J and Zhang, J and Wang, X and Shen, S and Wang, H and Deng, F and Wang, M and Guan, W and Hu, Z},
title = {Genomic and transcriptional analyses of novel parvoviruses identified from dead peafowl.},
journal = {Virology},
volume = {539},
number = {},
pages = {80-91},
doi = {10.1016/j.virol.2019.10.013},
pmid = {31706163},
issn = {1096-0341},
abstract = {To identify potential pathogens responsible for a disease outbreak of cultured peafowls in China in 2013, metagenomic sequencing was conducted. The genomes of two closely related parvoviruses, namely peafowl parvovirus 1 (PePV1) and PePV2, were identified with size of 4428 bp and 4348 bp, respectively. Phylogenetic analysis revealed that both viruses are novel parvoviruses, belonging to the proposed genus Chapparvovirus of Parvoviridae. The transcriptional profile of PePV1 was analyzed by transfecting a nearly complete PePV1 genome into HEK-293T cells. Results revealed that PePV1 employs one promoter and two polyadenylation sites to start and terminate its transcriptions, with one donor site and two acceptor sites for pre-mRNA splicing. PePV1 DNA and structural protein were detected in several tissues of a dead peafowl, which appeared to have suffered enteritis, pneumonia and viremia. These results provide novel information of chapparvoviruses, and call for attention to the potential pathogens.},
}

@article {pmid31706024,
year = {2019},
author = {Gui, Q and Hoffman, PS and Lewis, JP},
title = {Amixicile targets anaerobic bacteria within the oral microbiome.},
journal = {Journal of oral biosciences},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.job.2019.10.004},
pmid = {31706024},
issn = {1880-3865},
abstract = {OBJECTIVES: Anaerobic bacteria are the major causative agents of periodontal disease. However, so far, targeted therapy aimed at reducing those pathogens has not been widely implemented. We have previously reported on a novel antimicrobial, amixicile, that targets anaerobic bacteria through inhibition of the function of the major anaerobic metabolic enzyme pyruvate ferredoxin oxidoreductase (PFOR), while not affecting aerotolerant organisms. It effectively inhibited the growth of oral anaerobes both in monocultures as well as in mixed in vitro mixed cultured however, amixicile's activity in in vivo-like conditions remained to be established.

METHODS: Here, we expand our study using an ex vivo oral microbiome combined with metagenomic sequencing to determine the effect of amixicile treatment on the composition of the microbiome and compare it to that of metronidazole.

RESULTS: Our results show that in the complex microbiomes, anaerobic bacteria are selectively inhibited, while the growth of aerotolerant ones, such as Streptococcus, Klebsiella, Neisseria, and Rothia is unaffected. Veillonella was the most abundant anaerobic genus in our ex vivo microbiome, and we observed complete inhibition of its growth. In addition, growth of other anaerobes, Fusobacterium and Prevotella, was significantly inhibited. Lactobacillus was inhibited only at high concentrations of amixicile. It is noteworthy that a change in abundance of bacteriophages, such as Siphoviridae and Myoviridae, associated with the oral microbiome was observed.

CONCLUSIONS: Collectively, our data expand on the so far reported inhibitory spectrum of amixicile and demonstrates that it inhibits anaerobic bacteria, including both clinical isolates and laboratory strains.},
}

@article {pmid31705042,
year = {2019},
author = {Kundu, P and Manna, B and Majumder, S and Ghosh, A},
title = {Species-wide Metabolic Interaction Network for Understanding Natural Lignocellulose Digestion in Termite Gut Microbiota.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {16329},
doi = {10.1038/s41598-019-52843-w},
pmid = {31705042},
issn = {2045-2322},
abstract = {The structural complexity of lignocellulosic biomass hinders the extraction of cellulose, and it has remained a challenge for decades in the biofuel production process. However, wood-feeding organisms like termite have developed an efficient natural lignocellulolytic system with the help of specialized gut microbial symbionts. Despite having an enormous amount of high-throughput metagenomic data, specific contributions of each individual microbe to achieve this lignocellulolytic functionality remains unclear. The metabolic cross-communication and interdependence that drives the community structure inside the gut microbiota are yet to be explored. We have contrived a species-wide metabolic interaction network of the termite gut-microbiome to have a system-level understanding of metabolic communication. Metagenomic data of Nasutitermes corniger have been analyzed to identify microbial communities in different gut segments. A comprehensive metabolic cross-feeding network of 205 microbes and 265 metabolites was developed using published experimental data. Reconstruction of inter-species influence network elucidated the role of 37 influential microbes to maintain a stable and functional microbiota. Furthermore, in order to understand the natural lignocellulose digestion inside N. corniger gut, the metabolic functionality of each influencer was assessed, which further elucidated 15 crucial hemicellulolytic microbes and their corresponding enzyme machinery.},
}

@article {pmid31705027,
year = {2019},
author = {Ventura, RE and Iizumi, T and Battaglia, T and Liu, M and Perez-Perez, GI and Herbert, J and Blaser, MJ},
title = {Gut microbiome of treatment-naïve MS patients of different ethnicities early in disease course.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {16396},
doi = {10.1038/s41598-019-52894-z},
pmid = {31705027},
issn = {2045-2322},
abstract = {Although the intestinal microbiome has been increasingly implicated in autoimmune diseases, much is unknown about its roles in Multiple Sclerosis (MS). Our aim was to compare the microbiome between treatment-naïve MS subjects early in their disease course and controls, and between Caucasian (CA), Hispanic (HA), and African American (AA) MS subjects. From fecal samples, we performed 16S rRNA V4 sequencing and analysis from 45 MS subjects (15 CA, 16 HA, 14 AA) and 44 matched healthy controls, and whole metagenomic shotgun sequencing from 24 MS subjects (all newly diagnosed, treatment-naïve, and steroid-free) and 24 controls. In all three ethnic groups, there was an increased relative abundance of the same single genus, Clostridium, compared to ethnicity-matched controls. Analysis of microbiota networks showed significant changes in the network characteristics between combined MS cohorts and controls, suggesting global differences not restricted to individual taxa. Metagenomic analysis revealed significant enrichment of individual species within Clostridia as well as particular functional pathways in the MS subjects. The increased relative abundance of Clostridia in all three early MS cohorts compared to controls provides candidate taxa for further study as biomarkers or as etiologic agents in MS.},
}

@article {pmid31704413,
year = {2019},
author = {Rehman, ZU and Fortunato, L and Cheng, T and Leiknes, T},
title = {Metagenomic analysis of sludge and early-stage biofilm communities of a submerged membrane bioreactor.},
journal = {The Science of the total environment},
volume = {701},
number = {},
pages = {134682},
doi = {10.1016/j.scitotenv.2019.134682},
pmid = {31704413},
issn = {1879-1026},
abstract = {Biofilm formation on membranes in activated sludge membrane bioreactors (MBR), commonly identified as biofouling, is a significant problem for MBR operations. A better understanding of microbial species involved in the biofilm formation is needed to develop anti-biofilm measures. A read-based and genome-resolved shotgun metagenomic approach was applied to characterize the composition and functional potential of the sludge and early stage biofilm microbial communities in an MBR process. Read-based analysis revealed that the prevalence of different phyla are relatively similar in both the sludge and biofilm samples, with Proteobacteria as the most dominant, followed by Chloroflexi, Bacteroidetes and Planctomycetes. However, the relative abundance of these phyla slightly varies between the sludge and biofilm. Phyla such as Actinobacteria, bacterial candidate phyla, Chlamydiae, Cyanobacteria/Melainabacteria and Firmicutes are 2 to 4 times more abundant in the biofilm than in the sludge. At the genus level, genera belonging to Proteobacteria (Legionella, Caulobacter, Sphingomonas, Acinetobacter and Rhizobium), Cyanobacteria (Hassallia), and Spirochaetes (Turneriella) are at least twice more abundant in the biofilm. These genera, especially those belonging to Phylum Proteobacteria, are known to play an important role in the formation of biofilms on surfaces. The Alpha diversity is found slightly higher in the biofilm, compared with sludge samples. Functional classification of reads through the SEED subsystem shows that functional classes such as those involved in the metabolism of various molecules are significantly different in the biofilm and sludge. A phylogenomic analysis of the six extracted metagenome assembled genomes (MAGs) shows that three MAGs belong to Proteobacteria, and one MAG belong to each of Chloroflexi, Bacteroidetes and Planctomycetes. The relative abundance of the MAG belonging to Alphaproteobacteria is higher in the biofilm. A functional potential analysis of the MAGs reveals their potential to metabolize carbon and nitrogen sources, as well as the prevalence of antibiotic resistance genes.},
}

@article {pmid31703871,
year = {2020},
author = {Chen, C and Liu, Y and Tian, H and Ai, L and Yu, H},
title = {Metagenomic analysis reveals the impact of JIUYAO microbial diversity on fermentation and the volatile profile of Shaoxing-jiu.},
journal = {Food microbiology},
volume = {86},
number = {},
pages = {103326},
doi = {10.1016/j.fm.2019.103326},
pmid = {31703871},
issn = {1095-9998},
abstract = {This study focused on the microbial communities found in JIUYAO, the fermentation starter traditionally used in Shaoxing-jiu, and elucidated their relationship with the fermentation activities and volatile compounds involved in winemaking. The microbial communities found in all JIUYAO samples tested were dominated by Pediococcus and Weissella bacteria and Saccharomycopsis and Rhizopus fungi. Saccharifying power showed significant positive correlations with the presence of Pedioccoccus, Saccharomycopsis, and Rhizopus, whereas acid production capacity was strongly associated with Pedioccoccus, Weissella, and Rhizopus. Alcohol production capacity positively correlated with the presence of Pedioccoccus and Rhizopus. Fifteen important volatile compounds (odor-activity values ≥ 1) including esters, alcohols, acids, and aldehydes were identified in Huangjiu samples fermented with JIUYAO. Positive correlations were found between Saccharomycopsis and phenylethanol/ethyl butyrate, Rhizopus and ethyl propionate/ethyl laurate/ethyl butyrate, Pedioccoccus and ethyl laurate/acetic acid, and Weissella and decanoic acid/isopentanol. These results imply that these microorganisms significantly contribute to the fermentation activities and flavor of Shaoxing-jiu. Finally, the results showed that a combination of five core microbes with Saccharomyces cerevisiae could be used as a starter in winemaking. To conclude, this study provides a comprehensive overview of the core microbes found in JIUYAO and strategies for the selection of beneficial microorganisms to improve the quality and flavor of Shaoxing-jiu.},
}

@article {pmid31703868,
year = {2020},
author = {Chen, SH and Fegan, N and Kocharunchitt, C and Bowman, JP and Duffy, LL},
title = {Changes of the bacterial community diversity on chicken carcasses through an Australian poultry processing line.},
journal = {Food microbiology},
volume = {86},
number = {},
pages = {103350},
doi = {10.1016/j.fm.2019.103350},
pmid = {31703868},
issn = {1095-9998},
abstract = {Understanding the bacterial community profile through poultry processing could help the industry to produce better poultry products. In this study, 10 chicken carcasses were randomly sampled from before and after scalding, before and after immersion chilling, and after air chilling each through a modern commercial processing line, along with the contents of 10 caeca. The sampled processing line effectively reduced the bacterial counts by > 4.6 Log10 CFU/ml for each of Total Viable Counts, Escherichia coli and Campylobacter. However, the metagenomics results suggested that Lactobacillus, Staphylococcus and unclassified Lachnospiraceae persisted at all sampling stages. Pseudomonas, Paeniglutamicibacter, Chryseobacterium and Pseudarthrobacter comprised 47.2% in the bacterial community on samples after air chilling compared to 0.3% on samples after immersion chilling, whereas TVCs were the same. Overall, the current interventions of the investigated poultry processing line were unable to eliminate persistence of certain foodborne pathogens, despite a significant reduction of the overall bacterial counts. Chilling is an important controlling point in contamination/cross-contamination, particularly extended air chilling. Lastly, the large presence of Pseudomonas on chickens after air chilling may lead to downstream spoilage related issues, which needs more investigation to explore quantitatively the effect on the shelf life of poultry products.},
}

@article {pmid31703372,
year = {2019},
author = {Gowers, GF and Vince, O and Charles, JH and Klarenberg, I and Ellis, T and Edwards, A},
title = {Entirely Off-Grid and Solar-Powered DNA Sequencing of Microbial Communities during an Ice Cap Traverse Expedition.},
journal = {Genes},
volume = {10},
number = {11},
pages = {},
doi = {10.3390/genes10110902},
pmid = {31703372},
issn = {2073-4425},
abstract = {Microbial communities in remote locations remain under-studied. This is particularly true on glaciers and icecaps, which cover approximately 11% of the Earth's surface. The principal reason for this is the inaccessibility of most of these areas due to their extreme isolation and challenging environmental conditions. While remote research stations have significantly lowered the barrier to studying the microbial communities on icecaps, their use has led to a bias for data collection in the near vicinity of these institutions. Here, miniaturisation of a DNA sequencing lab suitable for off-grid metagenomic studies is demonstrated. Using human power alone, this lab was transported across Europe's largest ice cap (Vatnajökull, Iceland) by ski and sledge. After 11 days of unsupported polar-style travel, a metagenomic study of a geothermal hot spring gorge was conducted on the remote northern edge of the ice cap. This tent-based metagenomic study resulted in over 24 h of Nanopore sequencing, powered by solar power alone. This study demonstrates the ability to conduct DNA sequencing in remote locations, far from civilised resources (mechanised transport, external power supply, internet connection, etc.), whilst greatly reducing the time from sample collection to data acquisition.},
}

@article {pmid31703241,
year = {2019},
author = {Wang, F and Wan, Y and Yin, K and Wei, Y and Wang, B and Yu, X and Ni, Y and Zheng, J and Huang, T and Song, M and Li, D},
title = {Lower Circulating Branched-Chain Amino Acid Concentrations Among Vegetarians are Associated with Changes in Gut Microbial Composition and Function.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e1900612},
doi = {10.1002/mnfr.201900612},
pmid = {31703241},
issn = {1613-4133},
abstract = {SCOPE: Vegetarian diets confer health benefits to many cardiometabolic diseases, while whether and how gut microbiota in vegetarians contributes to host metabolism remains unclear. Thus, we aimed to explore the possible links between the gut microbiota and circulating gut microbiota-host co-metabolites among vegetarians and omnivores.

METHODS AND RESULTS: We collected fecal and serum samples from 36 adults following a vegan, a lacto-ovo vegetarian, or an omnivorous diet. A 16S rRNA gene, metagenome, metatranscriptome, and metabolome integrated multi-omics approach was adopted to profile fecal microbial composition and functionality and circulating gut microbiota-host co-metabolites. 16S rRNA gene and metagenomic sequencing suggested a significant difference in gut microbial composition between the two vegetarian groups and the omnivorous group, at the family, genus, and species level. Metabolomic analysis revealed that circulating branched-chain amino acids (BCAAs) - valine, leucine and isoleucine, were significantly lower in the two vegetarian groups than those in the omnivorous group. In line with the lower concentrations of BCAAs, metatranscriptomic analysis showed that the gut microbial pathway for the degradation of BCAAs was significantly upregulated among vegetarians compared with the omnivores.

CONCLUSIONS: Our results indicate that gut microbiota plays an important role in the modulation of circulating BCAAs among vegetarians. This article is protected by copyright. All rights reserved.},
}

@article {pmid31703093,
year = {2019},
author = {Kato, S and Hirai, M and Ohkuma, M and Suzuki, K},
title = {Microbial metabolisms in an abyssal ferromanganese crust from the Takuyo-Daigo Seamount as revealed by metagenomics.},
journal = {PloS one},
volume = {14},
number = {11},
pages = {e0224888},
doi = {10.1371/journal.pone.0224888},
pmid = {31703093},
issn = {1932-6203},
abstract = {Rocky outcrops covered with thick Fe and Mn oxide coatings, which are known as ferromanganese (Fe-Mn) crusts, are commonly found on slopes of aged seamounts in bathyal and abyssal zones. Although the presence of diverse microorganisms on these Fe-Mn crusts has been reported, little is known about their metabolism. Here, we report the metabolic potential of the microbial community in an abyssal crust collected in the Takuyo-Daigo Seamount, in the north-western Pacific. We performed shotgun metagenomic sequencing of the Fe-Mn crust, and detected putative genes involved in dissolution and precipitation of Fe and Mn, nitrification, sulfur oxidation, carbon fixation, and decomposition of organics in the metagenome. In addition, four metagenome-assembled genomes (MAGs) of abundant members in the microbial community were recovered from the metagenome. The MAGs were affiliated with Thaumarchaeota, Alphaproteobacteria, and Gammaproteobacteria, and were distantly related to previously reported genomes/MAGs of cultured and uncultured species. Putative genes involved in the above reactions were also found in the crust MAGs. Our results suggest that crust microbial communities play a role in biogeochemical cycling of C, N, S, Fe, and Mn, and imply that they contribute to the growth of Fe-Mn crusts.},
}

@article {pmid31703058,
year = {2019},
author = {Peto, L and Fawcett, NJ and Crook, DW and Peto, TEA and Llewelyn, MJ and Walker, AS},
title = {Selective culture enrichment and sequencing of feces to enhance detection of antimicrobial resistance genes in third-generation cephalosporin resistant Enterobacteriaceae.},
journal = {PloS one},
volume = {14},
number = {11},
pages = {e0222831},
doi = {10.1371/journal.pone.0222831},
pmid = {31703058},
issn = {1932-6203},
abstract = {Metagenomic sequencing of fecal DNA can usefully characterise an individual's intestinal resistome but is limited by its inability to detect important pathogens that may be present at low abundance, such as carbapenemase or extended-spectrum beta-lactamase producing Enterobacteriaceae. Here we aimed to develop a hybrid protocol to improve detection of resistance genes in Enterobacteriaceae by using a short period of culture enrichment prior to sequencing of DNA extracted directly from the enriched sample. Volunteer feces were spiked with carbapenemase-producing Enterobacteriaceae and incubated in selective broth culture for 6 hours before sequencing. Different DNA extraction methods were compared, including a plasmid extraction protocol to increase the detection of plasmid-associated resistance genes. Although enrichment prior to sequencing increased the detection of carbapenemase genes, the differing growth characteristics of the spike organisms precluded accurate quantification of their concentration prior to culture. Plasmid extraction increased detection of resistance genes present on plasmids, but the effects were heterogeneous and dependent on plasmid size. Our results demonstrate methods of improving the limit of detection of selected resistance mechanisms in a fecal resistome assay, but they also highlight the difficulties in using these techniques for accurate quantification and should inform future efforts to achieve this goal.},
}

@article {pmid31701197,
year = {2019},
author = {Tang, R and Ye, P and Alper, HS and Liu, Z and Zhao, X and Bai, F},
title = {Identification and characterization of novel xylose isomerases from a Bos taurus fecal metagenome.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-019-10161-1},
pmid = {31701197},
issn = {1432-0614},
support = {51561145014//National Natural Science Foundation of China/ ; MMLKF19-01//State Key Laboratory of Microbial Metabolism/ ; },
abstract = {Discovering sugar metabolism genes is of great interest for lignocellulosic biorefinery. Xylose isomerases (XIs) were commonly screened from metagenomes derived from bovine rumen, soil, and other sources. However, so far, XIs and other sugar-utilizing enzymes have not been discovered from fecal metagenomes. In this study, environmental DNA from the fecal samples collected from yellow cattle (Bos taurus) was sequenced and analyzed. In the whole 14.26 Gbp clean data, 92 putative XIs were annotated. After sequence analysis, seven putative XIs were heterologously expressed in Escherichia coli and characterized in vitro. The XIs 58444 and 58960 purified from E. coli exhibited 22% higher enzyme activity when compared with that of the native E. coli XI. The XI 58444, similar to the XI from Lachnospira multipara, exhibited a relatively stable activity profile across different pH conditions. Four XIs were further investigated in budding yeast Saccharomyces cerevisiae after codon optimization. Overexpression of the codon-optimized 58444 enabled S. cerevisiae to utilize 6.4 g/L xylose after 96 h without any other genetic manipulations, which is 56% higher than the control yeast strain overexpressing an optimized XI gene xylA*3 selected by three rounds of mutation. Our results provide evidence that a bovine fecal metagenome is a novel and valuable source of XIs and other industrial enzymes for biotechnology applications.},
}

@article {pmid31700955,
year = {2019},
author = {Bougnom, BP and Thiele-Bruhn, S and Ricci, V and Zongo, C and Piddock, LJV},
title = {High-throughput sequencing data and antibiotic resistance mechanisms of soil microbial communities in non-irrigated and irrigated soils with raw sewage in African cities.},
journal = {Data in brief},
volume = {27},
number = {},
pages = {104638},
doi = {10.1016/j.dib.2019.104638},
pmid = {31700955},
issn = {2352-3409},
abstract = {High-throughput sequencing data of soil microbial communities in non-irrigated and irrigated soils with raw sewage in African cities are presented in this report. These data were collected to study the potential of wastewater use in urban agriculture to disseminate bacterial resistance in soil. Soil samples were collected in three cities in two African countries. Each city had two sectors (irrigated and non-irrigated). After collection, biomass samples were purified, DNA from soil was extracted, quantified and sequenced using multiplex Illumina high-throughput sequencing. The sequence count of the six metagenome datasets ranges from 3,258,523,350 bp to 4,120,454,250 bp; the mean sequence length post quality control average was 149 ± 3 bp. The mechanisms of resistance encoded by the identified antibiotic resistance genes (ARGs) in the metagenomic data were dominated by antibiotic inactivation enzymes (64.7% and 71.9%), followed by antibiotic target replacement (14.7% and 12.5%), antibiotic target protection (11.8% and 9.4%) and efflux pumps (6.3% and 8.8%) in bacterial DNA isolated from irrigated and non-irrigated fields, respectively. The datasets will be useful for the scientific community working in the area of bacterial resistance dissemination from the environment. They can be used for further understanding of bacterial drug-resistance gene prevalence and acquisition in wastewater irrigated soils. The data reported herein was used for the article, titled "Raw wastewater irrigation for urban agriculture in three African cities increases the abundance of transferable antibiotic resistance genes in soil, including those encoding Extended spectrum β-lactamase (ESBLs)" Bougnom et al. (2020) [1].},
}

@article {pmid31700622,
year = {2019},
author = {He, J and Guo, H and Zheng, W and Xue, Y and Zhao, R and Yao, W},
title = {Heat stress affects fecal microbial and metabolic alterations of primiparous sows during late gestation.},
journal = {Journal of animal science and biotechnology},
volume = {10},
number = {},
pages = {84},
doi = {10.1186/s40104-019-0391-0},
pmid = {31700622},
issn = {1674-9782},
abstract = {Background: Heat stress (HS) jeopardizes intestinal barrier functions and augments intestinal permeability in pigs. However, whether HS-induced maternal microbial and metabolic changes in primiparous sows during late gestation remains elusive. We present here, a study investigating the fecal microbial and metabolic responses in late gestational primiparous sows when exposed to HS.

Methods: Twelve first-parity Landrace × Large White F1 sows were randomly assigned into two environmental treatments including the thermoneutral (TN) (18-22 °C; n = 6) and HS (28-32 °C; n = 6) conditions. Both treatments were applied from 85 d of gestation to farrowing. The serum and feces samples were collected on d 107 of gestation, for analyses including intestinal integrity biomarkers, high-throughput sequencing metagenomics, short-chain fatty acid (SCFA) profiles and nontargeted metabolomics.

Results: Our results show that HS group has higher serum Heat shock protein 70 (HSP70), lipopolysaccharide (LPS) and lipopolysaccharide-binding protein (LBP) levels. The gut microbial community can be altered upon HS by using β-diversity and taxon-based analysis. In particular, the relative abundance of genera and operational taxonomic units (OTUs) related to Clostridiales and Halomonas are higher in HS group, the relative abundance of genera and OTUs related to Bacteroidales and Streptococcus, however, are lower in HS group. Results of metabolic analysis reveal that HS lowers the concentrations of propionate, butyrate, total SCFA, succinate, fumarate, malate, lactate, aspartate, ethanolamine, β-alanine and niacin, whereas that of fructose and azelaic acid are higher in HS group. These metabolites mainly affect propanoate metabolism, alanine, aspartate and glutamate metabolism, phenylalanine metabolism, β-alanine metabolism, pantothenate and CoA biosynthesis, tricarboxylic acid cycle (TCA) and nicotinate and nicotinamide metabolism. Additionally, correlation analysis between significant microbes and metabolites indicated that the HS-induced microbiota shift is likely the cause of changes of intestinal metabolism.

Conclusions: Taken together, we reveal characteristic structural and metabolic changes in maternal gut microbiota as a result of late gestational HS, which could potentially provide the basis for further study on offspring gut microbiota and immune programming.},
}

@article {pmid31699813,
year = {2019},
author = {Kishikawa, T and Maeda, Y and Nii, T and Motooka, D and Matsumoto, Y and Matsushita, M and Matsuoka, H and Yoshimura, M and Kawada, S and Teshigawara, S and Oguro, E and Okita, Y and Kawamoto, K and Higa, S and Hirano, T and Narazaki, M and Ogata, A and Saeki, Y and Nakamura, S and Inohara, H and Kumanogoh, A and Takeda, K and Okada, Y},
title = {Metagenome-wide association study of gut microbiome revealed novel aetiology of rheumatoid arthritis in the Japanese population.},
journal = {Annals of the rheumatic diseases},
volume = {},
number = {},
pages = {},
doi = {10.1136/annrheumdis-2019-215743},
pmid = {31699813},
issn = {1468-2060},
abstract = {OBJECTIVE: The causality and pathogenic mechanism of microbiome composition remain elusive in many diseases, including autoimmune diseases such as rheumatoid arthritis (RA). This study aimed to elucidate gut microbiome's role in RA pathology by a comprehensive metagenome-wide association study (MWAS).

METHODS: We conducted MWAS of the RA gut microbiome in the Japanese population (ncase=82, ncontrol=42) by using whole-genome shotgun sequencing of high depth (average 13 Gb per sample). Our MWAS consisted of three major bioinformatic analytic pipelines (phylogenetic analysis, functional gene analysis and pathway analysis).

RESULTS: Phylogenetic case-control association tests showed high abundance of multiple species belonging to the genus Prevotella (e.g., Prevotella denticola) in the RA case metagenome. The non-linear machine learning method efficiently deconvoluted the case-control phylogenetic discrepancy. Gene functional assessments showed that the abundance of one redox reaction-related gene (R6FCZ7) was significantly decreased in the RA metagenome compared with controls. A variety of biological pathways including those related to metabolism (e.g., fatty acid biosynthesis and glycosaminoglycan degradation) were enriched in the case-control comparison. A population-specific link between the metagenome and host genome was identified by comparing biological pathway enrichment between the RA metagenome and the RA genome-wide association study results. No apparent discrepancy in alpha or beta diversities of metagenome was found between RA cases and controls.

CONCLUSION: Our shotgun sequencing-based MWAS highlights a novel link among the gut microbiome, host genome and pathology of RA, which contributes to our understanding of the microbiome's role in RA aetiology.},
}

@article {pmid31699767,
year = {2019},
author = {Ragab, A and Shaw, DR and Katuri, KP and Saikaly, PE},
title = {Draft Genome Sequence of Methanobacterium sp. Strain 34x, Reconstructed from an Enriched Electromethanogenic Biocathode.},
journal = {Microbiology resource announcements},
volume = {8},
number = {45},
pages = {},
doi = {10.1128/MRA.01138-19},
pmid = {31699767},
issn = {2576-098X},
abstract = {A draft genome sequence of Methanobacterium sp. strain 34x was reconstructed from the metagenome of an enriched electromethanogenic biocathode operated in a microbial electrosynthesis (MES) reactor. Methanobacterium sp. strain 34x has 68.98% nucleotide-level genomic similarity with the closest related methanogen available with a whole-genome assembly, Methanobacterium lacus strain AL-21. This genome will provide insight into the functional potential of methanogens at the biocathodes of MES systems.},
}

@article {pmid31698863,
year = {2019},
author = {Lugli, GA and Duranti, S and Milani, C and Mancabelli, L and Turroni, F and Sinderen, DV and Ventura, M},
title = {Uncovering Bifidobacteria via Targeted Sequencing of the Mammalian Gut Microbiota.},
journal = {Microorganisms},
volume = {7},
number = {11},
pages = {},
doi = {10.3390/microorganisms7110535},
pmid = {31698863},
issn = {2076-2607},
support = {15/JP-HDHL/3280//Joint Programming Initiative A healthy diet for a healthy life/ ; SFI/12/RC/2273a and SFI/12/RC/2273b//Science Fondation Ireland/ ; },
abstract = {Bifidobacteria are among the most prevalent gut commensals in mammals, playing crucial functional roles that start from their early colonization of the infant gastrointestinal tract and last throughout the life span of their host. Metagenomic approaches have been employed to unveil the genetic features of bifidobacteria in order to understand how they participate in the correct development of a healthy microbiome. Nevertheless, their low relative abundance in many environmental samples may represent a major limitation for metagenomics approaches. To overcome this restriction, we applied an enrichment method that allows amplification of bifidobacterial DNA obtained from human or animal fecal samples for up to 26,500-fold, resulting in the metagenomic reconstruction of genomes belonging to bifidobacterial strains, present at very low abundance in collected samples. Functional predictions of the genes from these reconstructed genomes allows us to identify unique signatures among members of the same bifidobacterial species, highlighting genes correlated with the uptake of nutrients and adhesion to the intestinal mucosa.},
}

@article {pmid31697678,
year = {2019},
author = {Srivathsan, A and Nagarajan, N and Meier, R},
title = {Boosting natural history research via metagenomic clean-up of crowdsourced feces.},
journal = {PLoS biology},
volume = {17},
number = {11},
pages = {e3000517},
doi = {10.1371/journal.pbio.3000517},
pmid = {31697678},
issn = {1545-7885},
abstract = {Biodiversity is in crisis due to habitat destruction and climate change. The conservation of many noncharismatic species is hampered by the lack of data. Yet, natural history research-a major source of information on noncharismatic species-is in decline. We here suggest a remedy for many mammal species, i.e., metagenomic clean-up of fecal samples that are "crowdsourced" during routine field surveys. Based on literature data, we estimate that this approach could yield natural history information for circa 1,000 species within a decade. Metagenomic analysis would simultaneously yield natural history data on diet and gut parasites while enhancing our understanding of host genetics, gut microbiome, and the functional interactions between traditional and new natural history data. We document the power of this approach by carrying out a "metagenomic clean-up" on fecal samples collected during a single night of small mammal trapping in one of Alfred Wallace's favorite collecting sites.},
}

@article {pmid31697231,
year = {2019},
author = {Sydenham, TV and Overballe-Petersen, S and Hasman, H and Wexler, H and Kemp, M and Justesen, US},
title = {Complete hybrid genome assembly of clinical multidrug-resistant Bacteroides fragilis isolates enables comprehensive identification of antimicrobial-resistance genes and plasmids.},
journal = {Microbial genomics},
volume = {},
number = {},
pages = {},
doi = {10.1099/mgen.0.000312},
pmid = {31697231},
issn = {2057-5858},
abstract = {Bacteroides fragilis constitutes a significant part of the normal human gut microbiota and can also act as an opportunistic pathogen. Antimicrobial resistance (AMR) and the prevalence of AMR genes are increasing, and prediction of antimicrobial susceptibility based on sequence information could support targeted antimicrobial therapy in a clinical setting. Complete identification of insertion sequence (IS) elements carrying promoter sequences upstream of resistance genes is necessary for prediction of AMR. However, de novo assemblies from short reads alone are often fractured due to repeat regions and the presence of multiple copies of identical IS elements. Identification of plasmids in clinical isolates can aid in the surveillance of the dissemination of AMR, and comprehensive sequence databases support microbiome and metagenomic studies. We tested several short-read, hybrid and long-lead assembly pipelines by assembling the type strain B. fragilis CCUG4856T (=ATCC25285=NCTC9343) with Illumina short reads and long reads generated by Oxford Nanopore Technologies (ONT) MinION sequencing. Hybrid assembly with Unicycler, using quality filtered Illumina reads and Filtlong filtered and Canu-corrected ONT reads, produced the assembly of highest quality. This approach was then applied to six clinical multidrug-resistant B. fragilis isolates and, with minimal manual finishing of chromosomal assemblies of three isolates, complete, circular assemblies of all isolates were produced. Eleven circular, putative plasmids were identified in the six assemblies, of which only three corresponded to a known cultured Bacteroides plasmid. Complete IS elements could be identified upstream of AMR genes; however, there was not complete correlation between the absence of IS elements and antimicrobial susceptibility. As our knowledge on factors that increase expression of resistance genes in the absence of IS elements is limited, further research is needed prior to implementing AMR prediction for B. fragilis from whole-genome sequencing.},
}

@article {pmid31696948,
year = {2019},
author = {Tamim, S and Heylen, E and Zeller, M and Ranst, MV and Matthijnssens, J and Salman, M and Aamir, UB and Sharif, S and Ikram, A and Hasan, F},
title = {Phylogenetic analysis of open reading frame of 11 gene segments of novel human-bovine reassortant RVA G6P[1] strain in Pakistan.},
journal = {Journal of medical virology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jmv.25625},
pmid = {31696948},
issn = {1096-9071},
abstract = {BACKGROUND: Multiple Rotavirus A (RVA) strains are linked with gastrointestinal infections in children that fall in age bracket of 0-60 months. However, the problem is augmented with emergence of unique strains that reassort with RVA strains of animal origin. The study describes the sequence analysis of a rare G6P[1] rotavirus strain isolated from a less than 1 year old child, during rotavirus surveillance in Rawalpindi district, Pakistan in 2010.

METHODS: Extracted RNA from fecal specimen was subjected to high throughput RT-PCR for structural and non-structural gene segments. The complete rotavirus genome of one isolate RVA/Human-wt/PAK/PAK99/2010/G6P[1] was sequenced for phylogenetic analysis to elucidate the evolutionary linkages and origin.

RESULTS: Full genome examination of novel strain RVA/Human-wt/PAK/PAK99/2010/G6P[1] revealed the unique genotype assemblage: G6-P[1]-I2-R2-C2-M2-A3-N2-T6-E2-H1. The evolutionary analyses of VP7, VP4, NSP1 and NSP3 gene segments revealed that PAK99 clustered with bovine, or cattle-like rotavirus strains from other closely related species, in the genotypes G6, P[1], A3 and T6 respectively. Gene segments VP6, VP1, VP2, VP3, NSP2 and NSP4 all possessed the DS-1-like bovine genotype 2 and bovine (-like) RVA strains instead of RVA strains having human origin. However, the NSP5 gene was found to cluster closely with contemporary human Wa-like rotavirus strains of H1 genotype.

CONCLUSION: This is the first report on bovine-human (Wa-like reassortant) genotype constellation of G6P[1] strain from a human case in Pakistan (and the second description worldwide). Our results emphasize the significance of incessant monitoring of circulating RVA strains in humans and animals for better understanding of RV evolution. This article is protected by copyright. All rights reserved.},
}

@article {pmid31696235,
year = {2019},
author = {Mitchell, AL and Almeida, A and Beracochea, M and Boland, M and Burgin, J and Cochrane, G and Crusoe, MR and Kale, V and Potter, SC and Richardson, LJ and Sakharova, E and Scheremetjew, M and Korobeynikov, A and Shlemov, A and Kunyavskaya, O and Lapidus, A and Finn, RD},
title = {MGnify: the microbiome analysis resource in 2020.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkz1035},
pmid = {31696235},
issn = {1362-4962},
abstract = {MGnify (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline with multiple analysis pipelines that are tailored according to the input data, and that are formally described using the Common Workflow Language, enabling greater provenance, reusability, and reproducibility. MGnify's new analysis pipelines offer additional approaches for taxonomic assertions based on ribosomal internal transcribed spacer regions (ITS1/2) and expanded protein functional annotations. Biochemical pathways and systems predictions have also been added for assembled contigs. MGnify's growing focus on the assembly of metagenomic data has also seen the number of datasets it has assembled and analysed increase six-fold. The non-redundant protein database constructed from the proteins encoded by these assemblies now exceeds 1 billion sequences. Meanwhile, a newly developed contig viewer provides fine-grained visualisation of the assembled contigs and their enriched annotations.},
}

@article {pmid31696023,
year = {2019},
author = {Amao, JA and Barooah, M and Omojasola, PF},
title = {Comparative 16S rDNA metagenomics study of two samples of cassava peel heap from Nigeria and India.},
journal = {3 Biotech},
volume = {9},
number = {11},
pages = {418},
doi = {10.1007/s13205-019-1941-z},
pmid = {31696023},
issn = {2190-572X},
abstract = {The microbiology of many cassava products and the wastes generated during the processing have been reported; however, majority of these reports used culture-dependent methods. This has resulted in a dearth of information on the bacterial diversity of cassava peels and peel heaps. Large amounts of cassava peels generated during the processing of cassava root are usually discharged on land or water as wastes and are allowed to rot in the open, especially in some developing countries. Culture-independent methods such as PCR-based amplification and sequencing of 16S rRNA genes, among others have been used in recent times to study the diversity of microbes in different environmental samples. In this study, bacterial isolates were screened for cellulase and xylanase enzyme activities on minimal agar and genomic DNA was isolated from cassava peel samples; metagenomics was carried out using MiSeq 2 × 300 with primers specific for V3-V4 bacterial region. Samples collected from Nigeria (AAG) had more species compared with samples from India (JHA) with 793 and 525 observed OTUs (operational taxonomic units), respectively. Five bacterial isolates from cassava peel-heap samples obtained from Ogbomoso, Nigeria showed no ability to produce cellulase enzyme, seven isolates from the Nigeria samples and three from Jorhat samples were positive for xylanase production; the highest amylase activity was shown by isolate AG18 (10,055 U/mL), while the lowest was recorded for isolate JA2 (2333 U/mL) with a significant difference observed in the amylase activities of isolates (p ≤ 0.05). Comparing the most abundant taxonomy for each of the samples at different taxonomic levels, the most abundant for sample AAG were phylum Firmicutes (42.11%), class Bacilli (41.27%), order Lactobacillales (33.11%), family Acetobacteraceae (31.30%), genus Acetobacter (30.02%) and unclassified species of Acetobacter (29.88%), while sample JHA had Actinobacteria (47.47%) as the highest phylum and class, order Actinomycetales (47.47%), family Brevibacteriaceae (46.97%), genus Brevibacterium (46.97%) and unclassified species of Brevibacterium (46.89%). This study provides an insight into the vast diversity of the bacteria associated with cassava peel heaps and the ability of some of the bacteria to produce selected extracellular enzymes.},
}

@article {pmid31695254,
year = {2019},
author = {Abby Philips, C and Agarwal, M and Phadke, N and Rajesh, S and Padsalgi, G and Ahamed, R and Augustine, P},
title = {A Novel Phosphoinositide-3-kinase Adapter Protein 1 Gene Missense Mutation in Familial Cirrhosis.},
journal = {Journal of clinical and experimental hepatology},
volume = {9},
number = {5},
pages = {652-656},
doi = {10.1016/j.jceh.2019.02.002},
pmid = {31695254},
issn = {0973-6883},
abstract = {Familial cirrhosis is a condition that is associated with the presence of liver disease with genetic linkage among multiple family members in a generation or in multiple generations. With cirrhosis, most of these disease pathogeneses are related to a defect of an enzyme/transport protein leading to a deranged metabolic pathway with variable prevalence. Many studies and high-quality metanalyses have shed light on genetic linkage associated with nonalcoholic fatty liver disease and steatohepatitis such as the PNPLA3, MBOAT7, and TM6SF2 variants. In this report, we shed light on a novel missense mutation associated with cirrhosis in a family of brothers associated with phosphoinositide-3-kinase adapter protein 1 gene through high-output whole exosome gene sequencing methodology.},
}

@article {pmid31694663,
year = {2019},
author = {Cai, L and Ma, R and Chen, H and Yang, Y and Jiao, N and Zhang, R},
title = {A newly isolated roseophage represents a distinct member of Siphoviridae family.},
journal = {Virology journal},
volume = {16},
number = {1},
pages = {128},
doi = {10.1186/s12985-019-1241-6},
pmid = {31694663},
issn = {1743-422X},
support = {DY135-E2-1-04//the China Ocean Mineral Resources R & D Association/ ; QNLM2016ORP0303//Qingdao National Laboratory for Marine Science and Technology/ ; 41706154//the National Natural Science Foundation of China/ ; 31570172//the National Natural Science Foundation of China/ ; 2017M622066//China Postdoctoral Science Foundation/ ; NA//the PhD Fellowship of the State Key Laboratory of Marine Environmental Science at Xiamen University/ ; },
abstract = {BACKGROUND: Members of the Roseobacter lineage are a major group of marine heterotrophic bacteria because of their wide distribution, versatile lifestyles and important biogeochemical roles. Bacteriophages, the most abundant biological entities in the ocean, play important roles in shaping their hosts' population structures and mediating genetic exchange between hosts. However, our knowledge of roseophages (bacteriophages that infect Roseobacter) is far behind that of their host counterparts, partly reflecting the need to isolate and analyze the phages associated with this ecologically important bacterial clade.

METHODS: vB_DshS-R4C (R4C), a novel virulent roseophage that infects Dinoroseobacter shibae DFL12T, was isolated with the double-layer agar method. The phage morphology was visualized with transmission electron microscopy. We characterized R4C in-depth with a genomic analysis and investigated the distribution of the R4C genome in different environments with a metagenomic recruitment analysis.

RESULTS: The double-stranded DNA genome of R4C consists of 36,291 bp with a high GC content of 66.75%. It has 49 genes with low DNA and protein homologies to those of other known phages. Morphological and phylogenetic analyses suggested that R4C is a novel member of the family Siphoviridae and is most closely related to phages in the genus Cronusvirus. However, unlike the Cronusvirus phages, R4C encodes an integrase, implying its ability to establish a lysogenic life cycle. A terminal analysis shows that, like that of λ phage, the R4C genome utilize the 'cohesive ends' DNA-packaging mechanism. Significantly, homologues of the R4C genes are more prevalent in coastal areas than in the open ocean.

CONCLUSIONS: Information about this newly discovered phage extends our understanding of bacteriophage diversity, evolution, and their roles in different environments.},
}

@article {pmid31694525,
year = {2019},
author = {LaPierre, N and Egan, R and Wang, W and Wang, Z},
title = {De novo Nanopore read quality improvement using deep learning.},
journal = {BMC bioinformatics},
volume = {20},
number = {1},
pages = {552},
doi = {10.1186/s12859-019-3103-z},
pmid = {31694525},
issn = {1471-2105},
abstract = {BACKGROUND: Long read sequencing technologies such as Oxford Nanopore can greatly decrease the complexity of de novo genome assembly and large structural variation identification. Currently Nanopore reads have high error rates, and the errors often cluster into low-quality segments within the reads. The limited sensitivity of existing read-based error correction methods can cause large-scale mis-assemblies in the assembled genomes, motivating further innovation in this area.

RESULTS: Here we developed a Convolutional Neural Network (CNN) based method, called MiniScrub, for identification and subsequent "scrubbing" (removal) of low-quality Nanopore read segments to minimize their interference in downstream assembly process. MiniScrub first generates read-to-read overlaps via MiniMap2, then encodes the overlaps into images, and finally builds CNN models to predict low-quality segments. Applying MiniScrub to real world control datasets under several different parameters, we show that it robustly improves read quality, and improves read error correction in the metagenome setting. Compared to raw reads, de novo genome assembly with scrubbed reads produces many fewer mis-assemblies and large indel errors.

CONCLUSIONS: MiniScrub is able to robustly improve read quality of Oxford Nanopore reads, especially in the metagenome setting, making it useful for downstream applications such as de novo assembly. We propose MiniScrub as a tool for preprocessing Nanopore reads for downstream analyses. MiniScrub is open-source software and is available at https://bitbucket.org/berkeleylab/jgi-miniscrub .},
}

@article {pmid31694288,
year = {2019},
author = {Castelán-Sánchez, HG and Elorrieta, P and Romoacca, P and Liñan-Torres, A and Sierra, JL and Vera, I and Batista-García, RA and Tenorio-Salgado, S and Lizama-Uc, G and Pérez-Rueda, E and Quispe-Ricalde, MA and Dávila-Ramos, S},
title = {Intermediate-Salinity Systems at High Altitudes in the Peruvian Andes Unveil a High Diversity and Abundance of Bacteria and Viruses.},
journal = {Genes},
volume = {10},
number = {11},
pages = {},
doi = {10.3390/genes10110891},
pmid = {31694288},
issn = {2073-4425},
support = {227-2015-FONDECYT//Fondo Nacional de Desarrollo Científico, Tecnológico y de Innovación Tecnológica/ ; 227229//Consejo Nacional de Ciencia y Tecnología/ ; NI-201117//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; UAEMOR-PTC-344//Secretaría de Educación Pública/ ; },
abstract = {Intermediate-salinity environments are distributed around the world. Here, we present a snapshot characterization of two Peruvian thalassohaline environments at high altitude, Maras and Acos, which provide an excellent opportunity to increase our understanding of these ecosystems. The main goal of this study was to assess the structure and functional diversity of the communities of microorganisms in an intermediate-salinity environment, and we used a metagenomic shotgun approach for this analysis. These Andean hypersaline systems exhibited high bacterial diversity and abundance of the phyla Proteobacteria, Bacteroidetes, Balneolaeota, and Actinobacteria; in contrast, Archaea from the phyla Euryarchaeota, Thaumarchaeota, and Crenarchaeota were identified in low abundance. Acos harbored a more diverse prokaryotic community and a higher number of unique species compared with Maras. In addition, we obtained the draft genomes of two bacteria, Halomonas elongata and Idiomarina loihiensis, as well as the viral genomes of Enterobacteria lambda-like phage and Halomonas elongata-like phage and 27 partial novel viral halophilic genomes. The functional metagenome annotation showed a high abundance of sequences associated with detoxification, DNA repair, cell wall and capsule formation, and nucleotide metabolism; sequences for these functions were overexpressed mainly in bacteria and also in some archaea and viruses. Thus, their metabolic profiles afford a decrease in oxidative stress as well as the assimilation of nitrogen, a critical energy source for survival. Our work represents the first microbial characterization of a community structure in samples collected from Peruvian hypersaline systems.},
}

@article {pmid31694175,
year = {2019},
author = {Öhlund, P and Hayer, J and Lundén, H and Hesson, JC and Blomström, AL},
title = {Viromics Reveal a Number of Novel RNA Viruses in Swedish Mosquitoes.},
journal = {Viruses},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/v11111027},
pmid = {31694175},
issn = {1999-4915},
support = {2016-01251//Vetenskapsrådet/ ; GFS2016-0033//Kungl. Skogs- och Lantbruksakademien/ ; 2015-ALB//Konung Carl XVI Gustafs 50- årsfond för Vetenskap, Teknik och miljö/ ; },
abstract = {Metagenomic studies of mosquitoes have revealed that their virome is far more diverse and includes many more viruses than just the pathogenic arboviruses vectored by mosquitoes. In this study, the virome of 953 female mosquitoes collected in the summer of 2017, representing six mosquito species from two geographic locations in Mid-Eastern Sweden, were characterized. In addition, the near-complete genome of nine RNA viruses were characterized and phylogenetically analysed. These viruses showed association to the viral orders Bunyavirales, Picornavirales, Articulavirales, and Tymovirales, and to the realm Ribovira. Hence, through this study, we expand the knowledge of the virome composition of different mosquito species in Sweden. In addition, by providing viral reference genomes from wider geographic regions and different mosquito species, future in silico recognition and assembly of viral genomes in metagenomic datasets will be facilitated.},
}

@article {pmid31693972,
year = {2019},
author = {Gao, S and He, Q and Wang, H},
title = {Research on the aerobic granular sludge under alkalinity in sequencing batch reactors: Removal efficiency, metagenomic and key microbes.},
journal = {Bioresource technology},
volume = {296},
number = {},
pages = {122280},
doi = {10.1016/j.biortech.2019.122280},
pmid = {31693972},
issn = {1873-2976},
abstract = {Effects of additional alkalinity on the performance of aerobic granular sludge (AGS) in sequencing batch reactors (SBR) performing simultaneous nitrification, denitrification, and phosphorus removal (SNDPR) were evaluated. Results showed that COD and ammonia-N (NH4+-N) were slightly stimulated and remained high and stable with the increase of alkalinity up to 750 mg/L, while denitrification was boosted and total inorganic nitrogen (TIN) removal efficiency increased from 60.46% to 98.62% with an additional alkalinity of 750 mg/L. However, total phosphorus (TP) removal stayed unaffected and efficient. Illumina MiSeq sequencing revealed that microbial diversity and richness shifted mostly with 500 mg/L exterior alkalinity addition. Additional alkalinity altered the bacterial compositions within aerobic granules at various levels and the enrichment of Thiothrix and Acinetobacter was accounted for the promotion of COD and TIN removal.},
}

@article {pmid31693506,
year = {2019},
author = {Yamaguchi, J and McArthur, C and Vallari, A and Sthreshley, L and Cloherty, GA and Berg, MG and Rodgers, MA},
title = {Complete genome sequence of CG-0018a-01 establishes HIV-1 subtype L.},
journal = {Journal of acquired immune deficiency syndromes (1999)},
volume = {},
number = {},
pages = {},
doi = {10.1097/QAI.0000000000002246},
pmid = {31693506},
issn = {1944-7884},
abstract = {BACKGROUND: The full spectrum of HIV-1 diversity can be found in central Africa, including two divergent HIV-1 strains collected in 1983 and 1990 in Democratic Republic of Congo (DRC) that were preliminarily classified as group M subtype L. However, a third epidemiologically distinct subtype L genome must be identified to designate L as a true subtype.

METHODS: Specimen CG-0018a-01 was collected in 2001 in DRC as part of an HIV prevention of mother to child transmission (PMTCT) study. Prior sub-genomic HIV-1 sequences from this specimen branched closely with proposed subtype L references. Metagenomic (mNGS) and HIV-specific target enriched (HIV-xGen) libraries were combined for next generation sequencing (NGS) to extend genome coverage. mNGS reads were analyzed for the presence of other co-infections with the SURPI bioinformatics pipeline.

RESULTS: A complete HIV-1 genome was generated with an average coverage depth of 47,783x. After bioinformatic analysis also identified Hepatitis B virus (HBV) reads, a complete HBV genotype A genome was assembled with an average coverage depth of 73,830x. The CG-0018a-01 HIV-1 genome branched basal to the two previous putative subtype L strains with strong bootstrap support of 100. With no evidence of recombination present, the strain was classified as subtype L.

CONCLUSIONS: The CG-0018a-01 HIV-1 genome establishes subtype L and confirms ongoing transmission in DRC as recently as 2001. Since CG-0018a-01 is more closely related to an ancestral strain than to isolates from 1983 or 1990, additional strains are likely circulating in DRC and possibly elsewhere.},
}

@article {pmid31693476,
year = {2019},
author = {Stormo, KA and Nygaard, RM and Bruvold, TS and Dimmen, G and Lindemann, PC and Jordal, S and Kommedal, Ø},
title = {Eikenella exigua sp. nov., isolated from brain abscess and blood.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1099/ijsem.0.003827},
pmid = {31693476},
issn = {1466-5034},
abstract = {We herein describe the first novel species within the genus Eikenella since it was established in 1972 by the reclassification of 'Bacteroides corrodens' to Eikenella corrodens. From a polymicrobial brain abscess, we encountered an Eikenella isolate, PXXT, that could not validly be named E. corrodens. The isolate grew on blood agar with small, translucent, pitting colonies after 3 days of anaerobic incubation. By reviewing previously collected invasive isolates, we found an additional Eikenella strain, EI-02, from a blood culture exhibiting the same properties as PXXT. Phylogenetic analyses based on both whole genome and individual house-keeping genes confirmed that the two strains allocate in a phylogenetic cluster separate from E. corrodens. Using specific amplification and sequencing of the Eikenella nusG gene, we further detected the novel Eikenella species in six historic brain abscesses previously reported to contain E. corrodens based on 16S metagenomics. Out of 24 Eikenella whole-genome projects available in GenBank, eight cluster together with PXXT and EI-02. These isolates were recovered from brain abscess (n=2), blood (n=1), bone/soft tissue (n=3), parotid gland (n=1) and unknown (n=1). It remains to be investigated whether the new species can cause endocarditis. The average nucleotide identity value between strain PXXT and the E. corrodens type strain ATCC 23834T was 92.1 % and the corresponding genome-to-genome distance value was 47.1 %, both supporting the classification of PXXT as a novel species. For this species we propose the name Eikenella exigua. The type strain of E. exigua is PXXT (DSM 109756T, NCTC 14318T).},
}

@article {pmid31693109,
year = {2019},
author = {Mangioni, D and Peri, AM and Rossolini, GM and Viaggi, B and Perno, CF and Gori, A and Bandera, A},
title = {Towards Rapid Sepsis Diagnosis and Patients Stratification: What's New From Microbiology and Omics Science.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiz585},
pmid = {31693109},
issn = {1537-6613},
abstract = {Early etiological diagnosis and characterization of host response to infection are becoming central in sepsis recognition and management. Still, limitations in conventional diagnosis and patient stratification contribute to the high mortality rates of septic patients despite new antimicrobials and resuscitation agents. Novel microbiological techniques and omics analyses have recently led to the development of several tests that are now commercially available or in the pipeline as rapid diagnostic tools. In this review, we first summarize emerging assays for the etiological diagnosis starting directly from whole blood, based on target-specific PCRs or metagenomics. We then investigate results of different omics approaches for both bedside diagnosis of immune dysfunction and detection of patients' signatures associated with different clinical outcomes or potential response to individualized therapies. Finally, we discuss about the translation of these novel laboratory tools into clinical practice, showing how their best performance is achieved when integrated within antimicrobial stewardship programs.},
}

@article {pmid31691607,
year = {2019},
author = {Han, D and Li, Z and Li, R and Tan, P and Zhang, R and Li, J},
title = {mNGS in clinical microbiology laboratories: on the road to maturity.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-18},
doi = {10.1080/1040841X.2019.1681933},
pmid = {31691607},
issn = {1549-7828},
abstract = {Metagenomic next-generation sequencing (mNGS) is increasingly being applied in clinical laboratories for unbiased culture-independent diagnosis. Whether it can be a next routine pathogen identification tool has become a topic of concern. We review the current implementation of this new technology for infectious disease diagnostics and discuss the feasibility of transforming mNGS into a routine diagnostic test. Since 2008, numerous studies from over 20 countries have revealed the practicality of mNGS in the work-up of undiagnosed infectious diseases. mNGS performs well in identifying rare, novel, difficult-to-detect and coinfected pathogens directly from clinical samples and presents great potential in resistance prediction by sequencing the antibiotic resistance genes, providing new diagnostic evidence that can be used to guide treatment options and improve antibiotic stewardship. Many physicians recognized mNGS as a last resort method to address clinical infection problems. Although several hurdles, such as workflow validation, quality control, method standardisation, and data interpretation, remain before mNGS can be implemented routinely in clinical laboratories, they are temporary and can be overcome by rapidly evolving technologies. With more validated workflows, lower cost and turnaround time, and simplified interpretation criteria, mNGS will be widely accepted in clinical practice. Overall, mNGS is transforming the landscape of clinical microbiology laboratories, and to ensure that it is properly utilised in clinical diagnosis, both physicians and microbiologists should have a thorough understanding of the power and limitations of this method.},
}

@article {pmid31691592,
year = {2019},
author = {Chan, WS and Au, CH and Leung, HC and Ho, DN and Li, D and Chan, TL and Lam, TW and Ma, ES and Tang, BS},
title = {Potential utility of metagenomic sequencing for improving etiologic diagnosis of infective endocarditis.},
journal = {Future cardiology},
volume = {},
number = {},
pages = {},
doi = {10.2217/fca-2018-0088},
pmid = {31691592},
issn = {1744-8298},
abstract = {Aim: To explore potential utility of metagenomic sequencing for improving etiologic diagnosis of infective endocarditis (IE) caused by fastidious bacteria. Materials & methods: Plasma and heart valves of two patients, who were diagnosed with IE caused by Bartonella quintana and Propionibacterium species, were sequenced by using Illumina MiSeq and Nanopore MinION. Results: For patient 1, B. quintana was detected in the plasma pool collected 4 days before valvular replacement surgery. For patient 2, Propionibacterium sp. oral taxon 193 was detected in the plasma sample collected on hospital day 1. Nearly complete bacterial genomes (>98%) were retrieved from resected heart valves of both patients, enabling detection of antibiotic resistance-associated features. Real-time sequencing of heart valves identified both pathogens within the first 16 min of sequencing runs. Conclusion: Metagenomic sequencing may be a helpful supplement to IE diagnostic workflow, especially when conventional tests fail to yield a diagnosis.},
}

@article {pmid31691434,
year = {2019},
author = {Liu, WW and Pan, J and Feng, X and Li, M and Xu, Y and Wang, F and Zhou, NY},
title = {Evidences of aromatic degradation dominantly via the phenylacetic acid pathway in marine benthic Thermoprofundales.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.14850},
pmid = {31691434},
issn = {1462-2920},
abstract = {By constructing high quality metagenome-assembled genomes (MAGs) of two new subgroups of Thermoprofundales from hydrothermal sediment and predicting their catabolic pathways, we here provide genomic evidences that Thermoprofundales are capable of degrading aromatics via the phenylacetic acid (PAA) pathway. Then, the gene sequences of phenylacetyl-CoA ligase (PCL), a key enzyme for the PAA pathway, were searched in reference genomes. The widespread distribution of PCL genes among 14.9% of archaea and 75.9% of Thermoprofundales further supports the importance of the PAA pathway in archaea, particularly in Thermoprofundales where no ring-cleavage dioxygenases were found. Two PCLs from Thermoprofundales MAGs, PCLM8-3 and PCLM10-15 , were able to convert PAA to phenylacetyl-CoA (PA-CoA) in vitro, demonstrating the involvement of Thermoprofundales in aromatics degradation through PAA via CoA activation. Their acid tolerance (pH 5-7), high optimum temperatures (60°C and 80°C), thermostability (stable at 60°C and 50°C for 48h), and broad substrate spectra imply that Thermoprofundales are capable of transforming aromatics under extreme conditions. Together with the evidence of in situ transcriptional activities for most genes related to the aromatics pathway in Thermoprofundales, these genomic, and biochemical evidences highlight the essential role of this ubiquitous and abundant archaeal order in the carbon cycle of marine sediments. This article is protected by copyright. All rights reserved.},
}

@article {pmid31690672,
year = {2019},
author = {Gülay, A and Fowler, SJ and Tatari, K and Thamdrup, B and Albrechtsen, HJ and Al-Soud, WA and Sørensen, SJ and Smets, BF},
title = {DNA- and RNA-SIP Reveal Nitrospira spp. as Key Drivers of Nitrification in Groundwater-Fed Biofilters.},
journal = {mBio},
volume = {10},
number = {6},
pages = {},
doi = {10.1128/mBio.01870-19},
pmid = {31690672},
issn = {2150-7511},
abstract = {Nitrification, the oxidative process converting ammonia to nitrite and nitrate, is driven by microbes and plays a central role in the global nitrogen cycle. Our earlier investigations based on 16S rRNA and amoA amplicon analysis, amoA quantitative PCR and metagenomics of groundwater-fed biofilters indicated a consistently high abundance of comammox Nitrospira Here, we hypothesized that these nonclassical nitrifiers drive ammonia-N oxidation. Hence, we used DNA and RNA stable isotope probing (SIP) coupled with 16S rRNA amplicon sequencing to identify the active members in the biofilter community when subjected to a continuous supply of NH4+ or NO2- in the presence of 13C-HCO3- (labeled) or 12C-HCO3- (unlabeled). Allylthiourea (ATU) and sodium chlorate were added to inhibit autotrophic ammonia- and nitrite-oxidizing bacteria, respectively. Our results confirmed that lineage II Nitrospira dominated ammonia oxidation in the biofilter community. A total of 78 (8 by RNA-SIP and 70 by DNA-SIP) and 96 (25 by RNA-SIP and 71 by DNA-SIP) Nitrospira phylotypes (at 99% 16S rRNA sequence similarity) were identified as complete ammonia- and nitrite-oxidizing, respectively. We also detected significant HCO3- uptake by Acidobacteria subgroup10, Pedomicrobium, Rhizobacter, and Acidovorax under conditions that favored ammonia oxidation. Canonical Nitrospira alone drove nitrite oxidation in the biofilter community, and activity of archaeal ammonia-oxidizing taxa was not detected in the SIP fractions. This study provides the first in situ evidence of ammonia oxidation by comammox Nitrospira in an ecologically relevant complex microbiome.IMPORTANCE With this study we provide the first in situ evidence of ecologically relevant ammonia oxidation by comammox Nitrospira in a complex microbiome and document an unexpectedly high H13CO3- uptake and growth of proteobacterial and acidobacterial taxa under ammonia selectivity. This finding raises the question of whether comammox Nitrospira is an equally important ammonia oxidizer in other environments.},
}

@article {pmid31690594,
year = {2019},
author = {Coutinho, FH and Rosselli, R and Rodríguez-Valera, F},
title = {Trends of Microdiversity Reveal Depth-Dependent Evolutionary Strategies of Viruses in the Mediterranean.},
journal = {mSystems},
volume = {4},
number = {6},
pages = {},
doi = {10.1128/mSystems.00554-19},
pmid = {31690594},
issn = {2379-5077},
abstract = {The evolutionary interactions between viruses and their prokaryotic hosts remain a little-known aspect of microbial evolution. Most studies on this topic were carried out in pure cultures that challenge one virus with one bacterial clone at a time, which is very removed from real-life situations. Few studies have addressed trends of microdiversity in marine viral communities throughout depth gradients. We analyzed metagenomes from both the cellular and viral fractions of Mediterranean seawater samples spanning the epipelagic to the bathypelagic zones at depths of 15, 45, 60, and 2,000 m during the summer stratification of the water column. We evaluated microdiversity patterns by measuring the accumulation of synonymous and nonsynonymous mutations in viral genes. Our results demonstrated clear depth-dependent trends in the frequency of polymorphic sites and nonsynonymous mutations among genes encoding metabolic, structural, and replication proteins. These differences were linked to changes in energy availability, host and viral densities, and the proportions of actively replicating viruses. We propose the hypothesis that in the energy-rich, high-host-density, euphotic depths, selection acts to favor diversity of the host recognition machinery to increase host range, while in energy-depleted aphotic waters, selection acts on viral replication fitness, enhancing diversity in auxiliary metabolic genes.IMPORTANCE Viruses are extremely abundant and diverse biological entities that contribute to the functioning of marine ecosystems. Despite their recognized importance, few studies have addressed trends of mutation accumulation in marine viral communities across depth gradients. By investigating these trends, we show that mutation frequencies differ among viral genes according to their molecular functions, with the highest microdiversity occurring among proteins related to host metabolism, followed by structural proteins and, lastly, genome replication proteins. This is in agreement with evolutionary theory that postulates that housekeeping genes are under strong purifying selection. We also observed a positive association between depth and microdiversity. One exception to this trend was the host recognition proteins from the deep chlorophyll maximum, which displayed strikingly high microdiversity, which we hypothesize to be associated with intraspecies competition for hosts. Finally, our data allowed us to propose a theoretical model for viral microdiversity across the depth gradient. These discoveries are of special relevance because many of the viral genomic sequences discovered here were predicted to infect some of the most abundant bacteria in marine ecosystems, such as "Candidatus Pelagibacter," Puniceispirillum, and Prochlorococcus.},
}

@article {pmid31690590,
year = {2019},
author = {Wang, Y and Wang, S and Wu, C and Chen, X and Duan, Z and Xu, Q and Jiang, W and Xu, L and Wang, T and Su, L and Wang, Y and Chen, Y and Zhang, J and Huang, Y and Tong, S and Zhou, C and Deng, S and Qin, N},
title = {Oral Microbiome Alterations Associated with Early Childhood Caries Highlight the Importance of Carbohydrate Metabolic Activities.},
journal = {mSystems},
volume = {4},
number = {6},
pages = {},
doi = {10.1128/mSystems.00450-19},
pmid = {31690590},
issn = {2379-5077},
abstract = {Globally, dental caries is the most prevalent chronic oral disease and affects roughly half of all children. The aim of this report was to use metagenomic analyses to investigate the relationship between the oral microbiome and caries in preschool children. A total of 25 preschoolers, aged 3 to 5 years old with severe early childhood caries (ECC), and 19 age-matched, caries-free children as controls were recruited. Saliva samples were collected from the participants and were subjected to metagenomic analyses, whereby the oral microbial communities were investigated. The metagenomic analyses revealed substantial microbiota differences between the two groups, indicating apparent shifts of the oral microbiome present in the ECC group. At the species level, the ECC-enriched microbes included Prevotella amnii, Shuttleworthia satelles, Olsenella uli, and Anaeroglobus geminatus Interestingly, Actinomyces odontolyticus and Actinomyces graevenitzii exhibited apparent differences at the strain level but not the species level between the ECC and control groups. Functional examination showed that the ECC group displayed extensive alterations in metabolic genes/pathways/modules, including enriched functions in sugar metabolism. Finally, an SVM (support vector machine) classifier comprising seven species was developed and generated a moderately good performance in predicting caries onset (area under the receiver operating characteristic curve [AUC] = 78.33%). Together, these findings indicate that caries is associated with considerable changes in the oral microbiome, some of which can potentially be exploited as therapeutic targets or diagnostic markers. (This study has been registered at ClinicalTrials.gov under registration no. NCT02341352.)IMPORTANCE Dental caries is a highly prevalent oral disease that can lead to severe dental damage and may greatly compromise the quality of life of the affected individuals. Previous studies, including those based on 16S rRNA gene, have revealed that the oral microbiota plays a prominent role in development of the disease. But the approach of those studies was limited in analyzing several key microbiome traits, including species- or strain-level composition and functional profile. Here, we performed metagenomic analyses for a cohort of preschool children with or without caries. Our results showed that caries was associated with extensive microbiota differences at various taxonomic and functional levels. Some caries-associated species had not been previously reported, some of which may have significant clinical implications. A microbiome gene catalogue from children with caries was constructed for the first time. The results demonstrated that caries is associated with alterations of the oral microbiome, including changes in microbial composition and metabolic functional profile.},
}

@article {pmid31690338,
year = {2019},
author = {Ondov, BD and Starrett, GJ and Sappington, A and Kostic, A and Koren, S and Buck, CB and Phillippy, AM},
title = {Mash Screen: high-throughput sequence containment estimation for genome discovery.},
journal = {Genome biology},
volume = {20},
number = {1},
pages = {232},
doi = {10.1186/s13059-019-1841-x},
pmid = {31690338},
issn = {1474-760X},
abstract = {The MinHash algorithm has proven effective for rapidly estimating the resemblance of two genomes or metagenomes. However, this method cannot reliably estimate the containment of a genome within a metagenome. Here, we describe an online algorithm capable of measuring the containment of genomes and proteomes within either assembled or unassembled sequencing read sets. We describe several use cases, including contamination screening and retrospective analysis of metagenomes for novel genome discovery. Using this tool, we provide containment estimates for every NCBI RefSeq genome within every SRA metagenome and demonstrate the identification of a novel polyomavirus species from a public metagenome.},
}

@article {pmid31690071,
year = {2019},
author = {Firrman, J and Liu, L and Tanes, C and Friedman, E and Bittinger, K and Daniel, S and van den Abbeele, P and Evans, BS},
title = {Metabolic analysis of regionally distinct gut microbial communities using an in vitro platform.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.9b05202},
pmid = {31690071},
issn = {1520-5118},
abstract = {The colon gut microbiota is responsible for complex chemical conversions of nutrients and subsequent release of metabolites that have diverse biological consequences. However, information on the metabolic dynamics that occur longitudinally through the colon is limited. Here, gas and liquid chromatography coupled with mass spectrometry were applied to generate metabolic profiles of the region-specific microbial communities cultured using an in vitro platform simulating the ascending (AC), transverse (TC), and descending (DC) colon regions. Comparative analysis revealed a large divergence between metabolic profiles of the AC to the TC and DC regions in terms of short chain fatty acid production, metabolic spectrum, and conversion of bile acids. Metagenomic evaluation revealed that the regionally derived metabolic profiles had strong correlation to community composition and genetic potential. Together, the results provide key insights regarding the metabolic divergence of the regional communities that are integral to understanding the structure-function relationship of the gut microbiota.},
}

@article {pmid31689942,
year = {2019},
author = {Sommers, P and Fontenele, RS and Kringen, T and Kraberger, S and Porazinska, DL and Darcy, JL and Schmidt, SK and Varsani, A},
title = {Single-Stranded DNA Viruses in Antarctic Cryoconite Holes.},
journal = {Viruses},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/v11111022},
pmid = {31689942},
issn = {1999-4915},
support = {1443578//United States National Science Foundation Polar Programs/ ; },
abstract = {Antarctic cryoconite holes, or small melt-holes in the surfaces of glaciers, create habitable oases for isolated microbial communities with tightly linked microbial population structures. Viruses may influence the dynamics of polar microbial communities, but the viromes of the Antarctic cryoconite holes have yet to be characterized. We characterize single-stranded DNA (ssDNA) viruses from three cryoconite holes in the Taylor Valley, Antarctica, using metagenomics. Half of the assembled metagenomes cluster with those in the viral family Microviridae (n = 7), and the rest with unclassified circular replication associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses (n = 7). An additional 18 virus-like circular molecules encoding either a Rep, a capsid protein gene, or other unidentified but viral-like open reading frames were identified. The samples from which the genomes were identified show a strong gradient in microbial diversity and abundances, and the number of viral genomes detected in each sample mirror that gradient. Additionally, one of the CRESS genomes assembled here shares ~90% genome-wide pairwise identity with a virus identified from a freshwater pond on the McMurdo Ice Shelf (Antarctica). Otherwise, the similarity of these viruses to those previously identified is relatively low. Together, these patterns are consistent with the presence of a unique regional virome present in fresh water host populations of the McMurdo Dry Valley region.},
}

@article {pmid31689572,
year = {2019},
author = {Forberg, K and Rodgers, MA and Dawson, GJ and Sauleda, S and Olivo, A and Vallari, A and Bes, M and Piron, M and Cloherty, GA and Berg, MG},
title = {Human pegivirus 2 exhibits minimal geographic and temporal genetic diversity.},
journal = {Virology},
volume = {539},
number = {},
pages = {69-79},
doi = {10.1016/j.virol.2019.10.012},
pmid = {31689572},
issn = {1096-0341},
abstract = {We applied an NGS based target capture approach to amplify HPgV-2 sequences from metagenomic libraries and enable full genome characterization. Despite expanded geographical sampling, sequence variability remains low, with diversity concentrated in approximately 3.3% of all amino acids. Serial samples from one HPgV-2 positive individual co-infected with comparable titers of HIV, HCV, and GBV-C showed that HPgV-2 remains highly stable over several weeks compared to other RNA viruses, despite a similarly error-prone polymerase. The consistent epidemiological association with and structural similarities to HCV, and the weak positive correlation of HCV and HPgV-2 titers shown here, suggests it may benefit from co-infection. While minimal selective pressure on HPgV-2 to evolve could suggest fitness, the rarity of HPgV-2 and the tight phylogenetic clustering of global strains likely indicates origination from a common source and a virus that is ill-suited to its host. Sporadic infections may explain the limited genetic diversity observed worldwide.},
}

@article {pmid31685046,
year = {2019},
author = {Lai, WT and Deng, WF and Xu, SX and Zhao, J and Xu, D and Liu, YH and Guo, YY and Wang, MB and He, FS and Ye, SW and Yang, QF and Liu, TB and Zhang, YL and Wang, S and Li, MZ and Yang, YJ and Xie, XH and Rong, H},
title = {Shotgun metagenomics reveals both taxonomic and tryptophan pathway differences of gut microbiota in major depressive disorder patients.},
journal = {Psychological medicine},
volume = {},
number = {},
pages = {1-12},
doi = {10.1017/S0033291719003027},
pmid = {31685046},
issn = {1469-8978},
abstract = {BACKGROUND: The microbiota-gut-brain axis, especially the microbial tryptophan (Trp) biosynthesis and metabolism pathway (MiTBamp), may play a critical role in the pathogenesis of major depressive disorder (MDD). However, studies on the MiTBamp in MDD are lacking. The aim of the present study was to analyze the gut microbiota composition and the MiTBamp in MDD patients.

METHODS: We performed shotgun metagenomic sequencing of stool samples from 26 MDD patients and 29 healthy controls (HCs). In addition to the microbiota community and the MiTBamp analyses, we also built a classification based on the Random Forests (RF) and Boruta algorithm to identify the gut microbiota as biomarkers for MDD.

RESULTS: The Bacteroidetes abundance was strongly reduced whereas that of Actinobacteria was significantly increased in the MDD patients compared with the abundance in the HCs. Most noteworthy, the MDD patients had increased levels of Bifidobacterium, which is commonly used as a probiotic. Four Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologies (KOs) (K01817, K11358, K01626, K01667) abundances in the MiTBamp were significantly lower in the MDD group. Furthermore, we found a negative correlation between the K01626 abundance and the HAMD scores in the MDD group. Finally, RF classification at the genus level can achieve an area under the receiver operating characteristic curve of 0.890.

CONCLUSIONS: The present findings enabled a better understanding of the changes in gut microbiota and the related Trp pathway in MDD. Alterations of the gut microbiota may have the potential as biomarkers for distinguishing MDD patients form HCs.},
}

@article {pmid31684172,
year = {2019},
author = {Lee, S and Suwa, M and Shigemura, H},
title = {Metagenomic Analysis of Infectious F-Specific RNA Bacteriophage Strains in Wastewater Treatment and Disinfection Processes.},
journal = {Pathogens (Basel, Switzerland)},
volume = {8},
number = {4},
pages = {},
doi = {10.3390/pathogens8040217},
pmid = {31684172},
issn = {2076-0817},
support = {18K13863//Japan Society for the Promotion of Science/ ; },
abstract = {F-specific RNA bacteriophages (FRNAPHs) can be used to indicate water contamination and the fate of viruses in wastewater treatment plants (WWTPs). However, the occurrence of FRNAPH strains in WWTPs is relatively unknown, whereas FRNAPH genotypes (GI-GIV) are well documented. This study investigated the diversity of infectious FRNAPH strains in wastewater treatment and disinfection processes using cell culture combined with next-generation sequencing (integrated culture-NGS (IC-NGS)). A total of 32 infectious strains belonging to FRNAPH GI (nine strains), GI-JS (two strains), GII (nine strains), GIII (seven strains), and GIV (five strains) were detected in wastewater samples. The strains of FRNAPH GI and GII exhibited greater resistance to wastewater treatment than those of GIII. The IC-NGS results in the disinfected samples successfully reflected the infectivity of FRNAPHs by evaluating the relationship between IC-NGS results and the integrated culture-reverse-transcription polymerase chain reaction combined with the most probable number assay, which can detect infectious FRNAPH genotypes. The diversity of infectious FRNAPH strains in the disinfected samples indicates that certain strains are more resistant to chlorine (DL52, GI-JS; T72, GII) and ultraviolet (T72, GII) disinfection. It is possible that investigating these disinfectant-resistant strains could reveal effective mechanisms of viral disinfection.},
}

@article {pmid31683878,
year = {2019},
author = {Vokou, D and Genitsaris, S and Karamanoli, K and Vareli, K and Zachari, M and Voggoli, D and Monokrousos, N and Halley, JM and Sainis, I},
title = {Metagenomic Characterization Reveals Pronounced Seasonality in the Diversity and Structure of the Phyllosphere Bacterial Community in a Mediterranean Ecosystem.},
journal = {Microorganisms},
volume = {7},
number = {11},
pages = {},
doi = {10.3390/microorganisms7110518},
pmid = {31683878},
issn = {2076-2607},
support = {4177//European Social Fund (ESF) and National resources/ ; },
abstract = {We explore how the phyllosphere microbial community responds to a very seasonal environment such as the Mediterranean. For this, we studied the epiphytic bacterial community of a Mediterranean ecosystem in summer and winter, expecting to detect seasonal differences at their maximum. With high-throughput sequencing (HTS), we detected the operational taxonomic units (OTUs) present in the phyllosphere and also in the surrounding air. The epiphytic community is approximately five orders of magnitude denser than the airborne one and is made almost exclusively by habitat specialists. The two communities differ considerably but Proteobacteria and Actinobacteria are dominant in both. Of the five most abundant phyllosphere OTUs, two were closely related to Sphingomonas strains, one to Methylobacterium and the other two to Rhizobiales and Burkholderiales. We found the epiphytic community to become much richer, more distinct, even and diverse, denser and more connected in summer. In contrast, there was no difference in the level of bacterial colonization of the phyllosphere between the two seasons, although there were seasonal differences for individual taxonomic groups: Firmicutes, Gemmatimonadetes and Chlroroflexi had a higher participation in summer, whereas the major Proteobacteria classes presented reverse patterns, with Betaproteobacteria increasing in summer at the expense of the prominent Alphaproteobacteria.},
}