@article {pmid31117025,
year = {2019},
author = {Shi, X and Shao, C and Luo, C and Chu, Y and Wang, J and Meng, Q and Yu, J and Gao, Z and Kang, Y},
title = {Microfluidics-Based Enrichment and Whole-Genome Amplification Enable Strain-Level Resolution for Airway Metagenomics.},
journal = {mSystems},
volume = {4},
number = {4},
pages = {},
doi = {10.1128/mSystems.00198-19},
pmid = {31117025},
issn = {2379-5077},
abstract = {Dysbiosis of airway microbiomes has been found in various respiratory diseases, but its molecular details in terms of taxonomic profile, metabolic characteristics, defensive function, and inhabit adaption are far from clear. Shotgun metagenome sequencing provides detailed information for microbes, whereas its application is rather limited in airways due to host DNA contaminants that overwhelm a minute amount of microbial content. Here, we describe a microfluidics-based enrichment device and an emulsion-based whole-genome amplification procedure (MEEA) for the preparation of DNA from sputa for shotgun sequencing in a metagenomics study. The two protocols coupled in MEEA are first separately assayed with mock samples and are both promising in efficiency and bias. The efficiency and consistency of MEEA are further evaluated in six clinical sputum samples against direct sequencing without enrichment, and MEEA enables 2 to 14 times enrichment for microbial reads, which take 14.68% to 33.52% of total reads. The dominant pathogens detected in MEEA are in excellent agreement with those from clinical etiological tests. Meanwhile, MEEA presents much more microbiome complexity and genome information at a strain level than direct sequencing, exhibiting high sensitivity for identifying prophages and DNA viruses. MEEA provides better microbiome profiling than direct sequencing without a preference for specific microorganisms. The more detailed functional and taxonomic characterization of their species constituents, including both bacterium and virus, facilitates metagenomics studies on the pathogenesis of respiratory microbiomes.IMPORTANCE The airway microbial community, which takes important pathogenic roles for respiratory diseases, is far from clear in terms of taxonomy and gene functions. One of the critical reasons is the heavy contamination of host cell/DNA in airway samples, which hinders the subsequent sequencing of the whole genomic contents of the microbial community-the metagenome. Here, we describe a protocol for airway sample preparation which couples a microbe enrichment microfluidic device and a DNA amplification method performed in numerous droplets. When evaluated with mock and clinical sputum samples, the microfluidics-based enrichment device and emulsion-based whole-genome amplification (MEEA) procedure efficiently removes host cells, amplifies the microbial genome, and shows no obvious bias among microbes. The efficiency of MEEA makes it a promising method in research of respiratory microbial communities and their roles in diseases.},
}

@article {pmid31117019,
year = {2019},
author = {Kleiner, M},
title = {Metaproteomics: Much More than Measuring Gene Expression in Microbial Communities.},
journal = {mSystems},
volume = {4},
number = {3},
pages = {},
doi = {10.1128/mSystems.00115-19},
pmid = {31117019},
issn = {2379-5077},
abstract = {Metaproteomics is the large-scale identification and quantification of proteins from microbial communities and thus provides direct insight into the phenotypes of microorganisms on the molecular level. Initially, metaproteomics was mainly used to assess the "expressed" metabolism and physiology of microbial community members. However, recently developed metaproteomic tools allow quantification of per-species biomass to determine community structure, in situ carbon sources of community members, and the uptake of labeled substrates by community members. In this perspective, I provide a brief overview of the questions that we can currently address, as well as new metaproteomics-based approaches that we and others are developing to address even more questions in the study of microbial communities and plant and animal microbiota. I also highlight some areas and technologies where I anticipate developments and potentially major breakthroughs in the next 5 years and beyond.},
}

@article {pmid31116375,
year = {2019},
author = {Ma, A and Sun, M and McDermaid, A and Liu, B and Ma, Q},
title = {MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btz414},
pmid = {31116375},
issn = {1367-4811},
abstract = {MOTIVATION: Metagenomic and metatranscriptomic analyses can provide an abundance of information related to microbial communities. However, straightforward analysis of this data does not provide optimal results, with a required integration of data types being needed to thoroughly investigate these microbiomes and their environmental interactions.

RESULTS: Here, we present MetaQUBIC, an integrated biclustering-based computational pipeline for gene module detection that integrates both metagenomic and metatranscriptomic data. Additionally, we used this pipeline to investigate 735 paired DNA and RNA human gut microbiome samples, resulting in a comprehensive hybrid gene expression matrix of 2.3 million cross-species genes in the 735 human faecal samples and 155 functional enriched gene modules. We believe both the MetaQUBIC pipeline and the generated comprehensive human gut hybrid expression matrix will facilitate further investigations into multiple levels of microbiome studies.

AVAILABILITY: The package is freely available at https://github.com/OSU-BMBL/metaqubic.

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

@article {pmid31114971,
year = {2019},
author = {de Assumpção, PP and Araújo, TMT and de Assumpção, PB and Barra, WF and Khayat, AS and Assumpção, CB and Ishak, G and Nunes, DN and Dias-Neto, E and Coelho, LGV},
title = {Suicide journey of H. pylori through gastric carcinogenesis: the role of non-H. pylori microbiome and potential consequences for clinical practice.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10096-019-03564-5},
pmid = {31114971},
issn = {1435-4373},
abstract = {Despite being one of the most studied cancer-related infections, the relationship between Helicobacter pylori infection and gastric adenocarcinoma (GC) remains, in some points, obscure. Based on a critical analysis of the available literature regarding stomach microbiota, we aimed to shed light to a possible new interpretation of the current understanding about the Helicobacter pylori-related GC carcinogenesis. We analyzed data from the literature on Helicobacter pylori and other potential carcinogenic pathogens, in both benignant conditions and gastric adenocarcinoma. Helicobacter pylori is the dominant microorganism in benignant conditions as non-complicated gastritis. In atrophic gastritis, metaplasia and, mainly, in gastric adenocarcinoma, a strong reduction in Helicobacter pylori abundance, and increased occurrence of other microorganisms is strongly demonstrated by metagenomic experiments. While causing peptic disease and keeping the stomach's high acidity, Helicobacter pylori infection avoids gastric infection by carcinogenic intestinal microbiota. Nevertheless, Helicobacter pylori persistence may also provoke an atrophic gastritis, a condition that causes its own decline, due to a microenvironment modification, including reduced acidity, resulting in Helicobacter pylori substitution by a cancer-prone microbiota. This new interpretation might result in a dramatic modification on clinical management of Helicobacter pylori-related gastric disease.},
}

@article {pmid31114866,
year = {2019},
author = {Quan, J and Langelier, C and Kuchta, A and Batson, J and Teyssier, N and Lyden, A and Caldera, S and McGeever, A and Dimitrov, B and King, R and Wilheim, J and Murphy, M and Ares, LP and Travisano, KA and Sit, R and Amato, R and Mumbengegwi, DR and Smith, JL and Bennett, A and Gosling, R and Mourani, PM and Calfee, CS and Neff, NF and Chow, ED and Kim, PS and Greenhouse, B and DeRisi, JL and Crawford, ED},
title = {FLASH: a next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkz418},
pmid = {31114866},
issn = {1362-4962},
abstract = {The growing prevalence of deadly microbes with resistance to previously life-saving drug therapies is a dire threat to human health. Detection of low abundance pathogen sequences remains a challenge for metagenomic Next Generation Sequencing (NGS). We introduce FLASH (Finding Low Abundance Sequences by Hybridization), a next-generation CRISPR/Cas9 diagnostic method that takes advantage of the efficiency, specificity and flexibility of Cas9 to enrich for a programmed set of sequences. FLASH-NGS achieves up to 5 orders of magnitude of enrichment and sub-attomolar gene detection with minimal background. We provide an open-source software tool (FLASHit) for guide RNA design. Here we applied it to detection of antimicrobial resistance genes in respiratory fluid and dried blood spots, but FLASH-NGS is applicable to all areas that rely on multiplex PCR.},
}

@article {pmid31114711,
year = {2019},
author = {Day, RL and Harper, AJ and Woods, RM and Davies, OG and Heaney, LM},
title = {Probiotics: current landscape and future horizons.},
journal = {Future science OA},
volume = {5},
number = {4},
pages = {FSO391},
doi = {10.4155/fsoa-2019-0004},
pmid = {31114711},
issn = {2056-5623},
abstract = {In recent years there has been a rapid rise in interest for the application of probiotic supplements to act as mediators in health and disease. This appeal is predominantly due to ever-increasing evidence of the interaction of the microbiota and pathophysiological processes of disease within the human host. This narrative review considers the current landscape of the probiotic industry and its research, and discusses current pitfalls in the lack of translation from laboratory science to clinical application. Future considerations into how industry and academia must adapt probiotic research to maximize success are suggested, including more targeted application of probiotic strains dependent on individual capabilities as well as application of multiple advanced analytical technologies to further understand and accelerate microbiome science.},
}

@article {pmid30193112,
year = {2018},
author = {Zmora, N and Zilberman-Schapira, G and Suez, J and Mor, U and Dori-Bachash, M and Bashiardes, S and Kotler, E and Zur, M and Regev-Lehavi, D and Brik, RB and Federici, S and Cohen, Y and Linevsky, R and Rothschild, D and Moor, AE and Ben-Moshe, S and Harmelin, A and Itzkovitz, S and Maharshak, N and Shibolet, O and Shapiro, H and Pevsner-Fischer, M and Sharon, I and Halpern, Z and Segal, E and Elinav, E},
title = {Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics Is Associated with Unique Host and Microbiome Features.},
journal = {Cell},
volume = {174},
number = {6},
pages = {1388-1405.e21},
doi = {10.1016/j.cell.2018.08.041},
pmid = {30193112},
issn = {1097-4172},
support = {/HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Adolescent ; Adult ; Aged ; Animals ; Bacteria/genetics/isolation & purification ; Feces/microbiology ; Female ; Gastric Mucosa/microbiology ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/microbiology ; Male ; Metagenomics ; Mice ; Mice, Inbred C57BL ; Middle Aged ; Placebo Effect ; Principal Component Analysis ; Probiotics/*administration & dosage ; RNA, Ribosomal, 16S/genetics/metabolism ; Transcriptome ; Young Adult ; },
abstract = {Empiric probiotics are commonly consumed by healthy individuals as means of life quality improvement and disease prevention. However, evidence of probiotic gut mucosal colonization efficacy remains sparse and controversial. We metagenomically characterized the murine and human mucosal-associated gastrointestinal microbiome and found it to only partially correlate with stool microbiome. A sequential invasive multi-omics measurement at baseline and during consumption of an 11-strain probiotic combination or placebo demonstrated that probiotics remain viable upon gastrointestinal passage. In colonized, but not germ-free mice, probiotics encountered a marked mucosal colonization resistance. In contrast, humans featured person-, region- and strain-specific mucosal colonization patterns, hallmarked by predictive baseline host and microbiome features, but indistinguishable by probiotics presence in stool. Consequently, probiotics induced a transient, individualized impact on mucosal community structure and gut transcriptome. Collectively, empiric probiotics supplementation may be limited in universally and persistently impacting the gut mucosa, meriting development of new personalized probiotic approaches.},
}

Adolescent
Adult
Aged
Animals
Bacteria/genetics/isolation & purification
Feces/microbiology
Female
Gastric Mucosa/microbiology
*Gastrointestinal Microbiome
Humans
Intestinal Mucosa/microbiology
Male
Metagenomics
Mice
Mice, Inbred C57BL
Middle Aged
Placebo Effect
Principal Component Analysis
Probiotics/*administration & dosage
RNA, Ribosomal, 16S/genetics/metabolism
Transcriptome
Young Adult

@article {pmid30046166,
year = {2018},
author = {Ma, B and Zhao, K and Lv, X and Su, W and Dai, Z and Gilbert, JA and Brookes, PC and Faust, K and Xu, J},
title = {Genetic correlation network prediction of forest soil microbial functional organization.},
journal = {The ISME journal},
volume = {12},
number = {10},
pages = {2492-2505},
pmid = {30046166},
issn = {1751-7370},
mesh = {*Forests ; Gene Regulatory Networks ; Metagenome ; Microbiota/*genetics ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {Soil ecological functions are largely determined by the activities of soil microorganisms, which, in turn, are regulated by relevant interactions between genes and their corresponding pathways. Therefore, the genetic network can theoretically elucidate the functional organization that supports complex microbial community functions, although this has not been previously attempted. We generated a genetic correlation network based on 5421 genes derived from metagenomes of forest soils, identifying 7191 positive and 123 negative correlation relationships. This network consisted of 27 clusters enriched with sets of genes within specific functions, represented with corresponding cluster hubs. The clusters revealed a hierarchical architecture, reflecting the functional organization in the soil metagenomes. Positive correlations mapped functional associations, whereas negative correlations often mapped regulatory processes. The potential functions of uncharacterized genes were predicted based on the functions of located clusters. The global genetic correlation network highlights the functional organization in soil metagenomes and provides a resource for predicting gene functions. We anticipate that the genetic correlation network may be exploited to comprehensively decipher soil microbial community functions.},
}

*Forests
Gene Regulatory Networks
Metagenome
Microbiota/*genetics
Soil/chemistry
*Soil Microbiology

@article {pmid29955139,
year = {2018},
author = {Singleton, CM and McCalley, CK and Woodcroft, BJ and Boyd, JA and Evans, PN and Hodgkins, SB and Chanton, JP and Frolking, S and Crill, PM and Saleska, SR and Rich, VI and Tyson, GW},
title = {Methanotrophy across a natural permafrost thaw environment.},
journal = {The ISME journal},
volume = {12},
number = {10},
pages = {2544-2558},
pmid = {29955139},
issn = {1751-7370},
mesh = {Atmosphere ; Bacteria/genetics/*metabolism ; Carbon/analysis ; Carbon Cycle ; Metagenome ; Metagenomics ; Methane/analysis ; Permafrost/*microbiology ; *Soil Microbiology ; Sweden ; Temperature ; },
abstract = {The fate of carbon sequestered in permafrost is a key concern for future global warming as this large carbon stock is rapidly becoming a net methane source due to widespread thaw. Methane release from permafrost is moderated by methanotrophs, which oxidise 20-60% of this methane before emission to the atmosphere. Despite the importance of methanotrophs to carbon cycling, these microorganisms are under-characterised and have not been studied across a natural permafrost thaw gradient. Here, we examine methanotroph communities from the active layer of a permafrost thaw gradient in Stordalen Mire (Abisko, Sweden) spanning three years, analysing 188 metagenomes and 24 metatranscriptomes paired with in situ biogeochemical data. Methanotroph community composition and activity varied significantly as thaw progressed from intact permafrost palsa, to partially thawed bog and fully thawed fen. Thirteen methanotroph population genomes were recovered, including two novel genomes belonging to the uncultivated upland soil cluster alpha (USCα) group and a novel potentially methanotrophic Hyphomicrobiaceae. Combined analysis of porewater δ13C-CH4 isotopes and methanotroph abundances showed methane oxidation was greatest below the oxic-anoxic interface in the bog. These results detail the direct effect of thaw on autochthonous methanotroph communities, and their consequent changes in population structure, activity and methane moderation potential.},
}

Atmosphere
Bacteria/genetics/*metabolism
Carbon/analysis
Carbon Cycle
Metagenome
Metagenomics
Methane/analysis
Permafrost/*microbiology
*Soil Microbiology
Sweden
Temperature

@article {pmid29180726,
year = {2018},
author = {Schulfer, AF and Battaglia, T and Alvarez, Y and Bijnens, L and Ruiz, VE and Ho, M and Robinson, S and Ward, T and Cox, LM and Rogers, AB and Knights, D and Sartor, RB and Blaser, MJ},
title = {Intergenerational transfer of antibiotic-perturbed microbiota enhances colitis in susceptible mice.},
journal = {Nature microbiology},
volume = {3},
number = {2},
pages = {234-242},
pmid = {29180726},
issn = {2058-5276},
support = {P30 CA016087/CA/NCI NIH HHS/United States ; P40 OD010995/OD/NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; P30 CA016086/CA/NCI NIH HHS/United States ; R01 DK090989/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; Anti-Bacterial Agents/*administration & dosage ; Colitis/chemically induced/*microbiology ; Colon/immunology/microbiology/pathology ; Diet, High-Fat ; Disease Models, Animal ; Disease Susceptibility/*microbiology ; Dysbiosis/chemically induced/microbiology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Inflammatory Bowel Diseases/chemically induced/*microbiology ; Interleukin-10 ; Metagenome/drug effects ; Mice ; Mice, Inbred C57BL ; Phenotype ; Pregnancy ; },
abstract = {Antibiotic exposure in children has been associated with the risk of inflammatory bowel disease (IBD). Antibiotic use in children or in their pregnant mother can affect how the intestinal microbiome develops, so we asked whether the transfer of an antibiotic-perturbed microbiota from mothers to their children could affect their risk of developing IBD. Here we demonstrate that germ-free adult pregnant mice inoculated with a gut microbial community shaped by antibiotic exposure transmitted their perturbed microbiota to their offspring with high fidelity. Without any direct or continued exposure to antibiotics, this dysbiotic microbiota in the offspring remained distinct from controls for at least 21 weeks. By using both IL-10-deficient and wild-type mothers, we showed that both inoculum and genotype shape microbiota populations in the offspring. Because IL10-/- mice are genetically susceptible to colitis, we could assess the risk due to maternal transmission of an antibiotic-perturbed microbiota. We found that the IL10-/- offspring that had received the perturbed gut microbiota developed markedly increased colitis. Taken together, our findings indicate that antibiotic exposure shaping the maternal gut microbiota has effects that extend to the offspring, with both ecological and long-term disease consequences.},
}

Animals
Anti-Bacterial Agents/*administration & dosage
Colitis/chemically induced/*microbiology
Colon/immunology/microbiology/pathology
Diet, High-Fat
Disease Models, Animal
Disease Susceptibility/*microbiology
Dysbiosis/chemically induced/microbiology
Feces/microbiology
Female
Gastrointestinal Microbiome/*drug effects
Inflammatory Bowel Diseases/chemically induced/*microbiology
Interleukin-10
Metagenome/drug effects
Mice
Mice, Inbred C57BL
Phenotype
Pregnancy

@article {pmid31112880,
year = {2019},
author = {Gopinath, D and Menon, RK and Banerjee, M and Su Yuxiong, R and Botelho, MG and Johnson, NW},
title = {Culture-independent studies on bacterial dysbiosis in oral and oropharyngeal squamous cell carcinoma: A systematic review.},
journal = {Critical reviews in oncology/hematology},
volume = {139},
number = {},
pages = {31-40},
doi = {10.1016/j.critrevonc.2019.04.018},
pmid = {31112880},
issn = {1879-0461},
abstract = {Imbalance within the resident bacterial community (dysbiosis), rather than the presence and activity of a single organism, has been proposed to be associated with, and to influence, the development and progression of various diseases; however, the existence and significance of dysbiosis in oral/oropharyngeal cancer is yet to be clearly established. A systematic search (conducted on 25/01/2018 and updated on 25/05/2018) was performed on three databases (Pubmed, Web of Science & Scopus) to identify studies employing culture-independent methods which investigated the bacterial community in oral/oropharyngeal cancer patients compared to control subjects. Of the 1546 texts screened, only fifteen publications met the pre-determined selection criteria. Data extracted from 731 cases and 809 controls overall, could not identify consistent enrichment of any particular taxon in oral/oropharyngeal cancers, although common taxa could be identified between studies. Six studies reported the enrichment of Fusobacteria in cancer at different taxonomic levels whereas four studies reported an increase in Parvimonas. Changes in microbial diversity remained inconclusive, with four studies showing a higher diversity in controls, three studies showing a higher diversity in tumors and three additional studies showing no difference between tumors and controls. Even though most studies identified a component of dysbiosis in oral/oropharyngeal cancer, methodological and analytical variations prevented a standardized summary, which highlights the necessity for studies of superior quality and magnitude employing standardized methodology and reporting. Indeed an holistic metagenomic approach is likely to be more meaningful, as is understanding of the overall metabolome, rather than a mere enumeration of the organisms present.},
}

@article {pmid31111267,
year = {2019},
author = {Jadeja, NB and Purohit, HJ and Kapley, A},
title = {Decoding microbial community intelligence through metagenomics for efficient wastewater treatment.},
journal = {Functional & integrative genomics},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10142-019-00681-4},
pmid = {31111267},
issn = {1438-7948},
abstract = {Activated sludge, a microbial ecosystem at industrial wastewater treatment plants, is an active collection of diverse gene pool that creates the intelligence required for coexistence at the cost of pollutants. This study has analyzed one such ecosystem from a site treating wastewater pooled from over 200 different industries. The metagenomics approach used could predict the degradative pathways of more than 30 dominating molecules commonly found in wastewater. Results were extended to design a bioremediation strategy using 4-methylphenol, 2-chlorobenzoate, and 4-chlorobenzoate as target compounds. Catabolic potential required to degrade four aromatic families, namely benzoate family, PAH family, phenol family, and PCB family, was mapped. Results demonstrated a network of diverse genera, where a few phylotypes were seen to contain diverse catabolic capacities and were seen to be present in multiple networks. The study highlights the importance of looking more closely at the microbial community of activated sludge to harness its latent potential. Conventionally treated as a black box, the activated biomass does not perform at its full potential. Metagenomics allows a clearer insight into the complex pathways operating at the site and the detailed documentation of genes allows the activated biomass to be used as a bioresource.},
}

@article {pmid31110365,
year = {2019},
author = {Low, SJ and Džunková, M and Chaumeil, PA and Parks, DH and Hugenholtz, P},
title = {Evaluation of a concatenated protein phylogeny for classification of tailed double-stranded DNA viruses belonging to the order Caudovirales.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41564-019-0448-z},
pmid = {31110365},
issn = {2058-5276},
abstract = {Viruses of bacteria and archaea are important players in global carbon cycling as well as drivers of host evolution, yet the taxonomic classification of viruses remains a challenge due to their genetic diversity and absence of universally conserved genes. Traditional classification approaches employ a combination of phenotypic and genetic information which is no longer scalable in the era of bulk viral genome recovery through metagenomics. Here, we evaluate a phylogenetic approach for the classification of tailed double-stranded DNA viruses from the order Caudovirales by inferring a phylogeny from the concatenation of 77 single-copy protein markers using a maximum-likelihood method. Our approach is largely consistent with the International Committee on Taxonomy of Viruses, with 72 and 89% congruence at the subfamily and genus levels, respectively. Discrepancies could be attributed to misclassifications and a small number of highly mosaic genera confounding the phylogenetic signal. We also show that confidently resolved nodes in the concatenated protein tree are highly reproducible across different software and models, and conclude that the approach can serve as a framework for a rank-normalized taxonomy of most tailed double-stranded DNA viruses.},
}

@article {pmid31110364,
year = {2019},
author = {Diamond, S and Andeer, PF and Li, Z and Crits-Christoph, A and Burstein, D and Anantharaman, K and Lane, KR and Thomas, BC and Pan, C and Northen, TR and Banfield, JF},
title = {Mediterranean grassland soil C-N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41564-019-0449-y},
pmid = {31110364},
issn = {2058-5276},
abstract = {Soil microbial activity drives the carbon and nitrogen cycles and is an important determinant of atmospheric trace gas turnover, yet most soils are dominated by microorganisms with unknown metabolic capacities. Even Acidobacteria, among the most abundant bacteria in soil, remain poorly characterized, and functions across groups such as Verrucomicrobia, Gemmatimonadetes, Chloroflexi and Rokubacteria are understudied. Here, we have resolved 60 metagenomic and 20 proteomic data sets from a Mediterranean grassland soil ecosystem and recovered 793 near-complete microbial genomes from 18 phyla, representing around one-third of all microorganisms detected. Importantly, this enabled extensive genomics-based metabolic predictions for these communities. Acidobacteria from multiple previously unstudied classes have genomes that encode large enzyme complements for complex carbohydrate degradation. Alternatively, most microorganisms encode carbohydrate esterases that strip readily accessible methyl and acetyl groups from polymers like pectin and xylan, forming methanol and acetate, the availability of which could explain the high prevalence of C1 metabolism and acetate utilization in genomes. Microorganism abundances among samples collected at three soil depths and under natural and amended rainfall regimes indicate statistically higher associations of inorganic nitrogen metabolism and carbon degradation in deep and shallow soils, respectively. This partitioning decreased in samples under extended spring rainfall, indicating that long-term climate alteration can affect both carbon and nitrogen cycling. Overall, by leveraging natural and experimental gradients with genome-resolved metabolic profiles, we link microorganisms lacking prior genomic characterization to specific roles in complex carbon, C1, nitrate and ammonia transformations, and constrain factors that impact their distributions in soil.},
}

@article {pmid31109866,
year = {2019},
author = {Chattopadhyay, I and Panda, M},
title = {Recent Trends of Saliva Omics Biomarkers for the Diagnosis and Treatment of Oral Cancer.},
journal = {Journal of oral biosciences},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.job.2019.03.002},
pmid = {31109866},
issn = {1880-3865},
abstract = {BACKGROUND: Recent advances in surgery, radiotherapy, and chemotherapy have no significant effect on oral cancer survival rates due to late diagnosis, poor tumor response to chemotherapy and radiotherapy, as well as a lack of effective biomarkers for early diagnosis.

HIGHLIGHTS: Therefore, an investigative study aimed at identifying genomics, proteomics, metagenomics, and, metabolomics derived biomarkers for early diagnosis may improve the survival rate of oral cancer patients. Identification and application of saliva-based ''omics'' biomarkers may overcome painful invasive procedures currently being used for the diagnosis of oral cancer. One single biomarker may not be able to differentiate between oral squamous cell carcinoma (OSCC) and controls. Thus, multiple sensitive and specific biomarkers may be needed for screening high-risk patients and following them up for early signs of OSCC occurrence. Validation of these biomarkers in large patient cohorts is, however, required before they can be used in clinical practice.

CONCLUSION: In this review, we summarize the potential of omics derived salivary biomarkers as diagnostic and prognostic tools in oral cancer detection and the future clinical benefits associated with these markers.},
}

@article {pmid31109865,
year = {2019},
author = {Takahashi, Y and Park, J and Hosomi, K and Yamada, T and Kobayashi, A and Yamaguchi, Y and Iketani, S and Kunisawa, J and Mizuguchi, K and Nobuko, M and Ohshima, T},
title = {Analysis of oral microbiota in Japanese oral cancer patients using 16S rRNA sequencing.},
journal = {Journal of oral biosciences},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.job.2019.03.003},
pmid = {31109865},
issn = {1880-3865},
abstract = {OBJECTIVES: It is important to determine the cause of increasing oral cancer occurrence and mortality rates in Japan, because the mortality rate has recently decreased in other developed countries. The impact of microbiota in carcinogenesis, especially in the digestive tract has been reported. This study aimed to clarify the relationship between oral cancer and oral microbiota in Japanese patients.

METHODS: DNA was extracted from salivary samples of 60 oral cancer patients and 80 non-cancer individuals as controls. We performed metagenomic analysis using 16S rRNA amplicon sequencing. Statistical analysis in this study was performed using R (version 3.5.0).

RESULTS: Oral cancer patients showed higher α-diversity compared to the control group, and the β-diversity between the two groups differed significantly. Further, there was a significant difference in the abundance ratio of bacterial genera between the two groups. Peptostreptococcus, Fusobacterium, Alloprevotella, and Capnocytophaga were more abundant in the cancer group compared to the control, whereas Rothia and Haemophilus were less abundant (p < 0.01). A negative correlation in the microbiota composition was confirmed between the operational taxonomic units (OTU) of genus Rothia and T-stage progression using the TNM classification method. We performed logistic regression analysis to investigate the impact factor for the oral cancer group, and the result showed that Chao 1 index and sex are statistically significant variables.

CONCLUSIONS: In this study, we observed an increased bacterial diversity in oral cancer patients and found distribution changes for some bacteria.},
}

@article {pmid30449351,
year = {2018},
author = {Amicucci, A and Barbieri, E and Sparvoli, V and Gioacchini, AM and Calcabrini, C and Palma, F and Stocchi, V and Zambonelli, A},
title = {Microbial and pigment profile of the reddish patch occurring within Tuber magnatum ascomata.},
journal = {Fungal biology},
volume = {122},
number = {12},
pages = {1134-1141},
doi = {10.1016/j.funbio.2018.07.007},
pmid = {30449351},
issn = {1878-6146},
mesh = {Ascomycota/*chemistry ; Bacteria/*classification/genetics/*isolation & purification/metabolism ; Fruiting Bodies, Fungal/*chemistry ; Italy ; Metagenome ; Pigments, Biological/*analysis/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Tandem Mass Spectrometry ; },
abstract = {Tuber magnatum Pico, the delectable white truffle, is the most prized truffle species. In this study, we examined the reddish pigmentation that frequently occurs in T. magnatum ascomata for the presence of pigment-producing bacteria. The inner part of the reddish-pigmented region of three T. magnatum ascomata collected in North-Central Italy was analysed. This reddish part was used to establish a bacterial culture collection and to extract the total genomic DNA in order to obtain a library of 16S rRNA genes representative of the bacterial community. The molecular approach revealed limited microbial diversity within the reddish-pigmented regions compared to the wider range of bacterial species commonly found at the same maturation stage and season in T. magnatum ascomata. The pigmented regions showed a prevalence of specific bacterial species belonging to α-, β- and γ- Proteobacteria, Actinobacteria and Firmicutes. From the tandem mass spectrometry analysis of the extracted pigment, four compounds were identified: i) bixin, ii) β-carotene, iii) cis-1-glycosyl-apo-8'- lycopene and iv) the fucoxanthin. Carotenoid producing species such as Microbacterium and Chryseobacterium emerged as the most likely cause of the peculiar reddish pigment production. Indeed, our findings suggest that the peculiar reddish pigment might be produced by these bacterial species.},
}

Ascomycota/*chemistry
Bacteria/*classification/genetics/*isolation & purification/metabolism
Fruiting Bodies, Fungal/*chemistry
Italy
Metagenome
Pigments, Biological/*analysis/isolation & purification
RNA, Ribosomal, 16S/genetics
Tandem Mass Spectrometry

@article {pmid29511332,
year = {2018},
author = {},
title = {A different view of the environment.},
journal = {Nature nanotechnology},
volume = {13},
number = {3},
pages = {177},
doi = {10.1038/s41565-018-0106-2},
pmid = {29511332},
issn = {1748-3395},
mesh = {Animals ; Environment ; *Environmental Exposure/adverse effects ; Environmental Pollutants/chemistry/*metabolism/*toxicity ; Gold/chemistry/metabolism/toxicity ; Humans ; Metagenomics ; Nanoparticles/chemistry/metabolism/toxicity ; Nanostructures/chemistry/*toxicity ; Nanotechnology ; Waste Water/microbiology ; },
}

Animals
Environment
*Environmental Exposure/adverse effects
Environmental Pollutants/chemistry/*metabolism/*toxicity
Gold/chemistry/metabolism/toxicity
Humans
Metagenomics
Nanoparticles/chemistry/metabolism/toxicity
Nanostructures/chemistry/*toxicity
Nanotechnology
Waste Water/microbiology

@article {pmid31108361,
year = {2019},
author = {Regar, RK and Gaur, VK and Bajaj, A and Tambat, S and Manickam, N},
title = {Comparative microbiome analysis of two different long-term pesticide contaminated soils revealed the anthropogenic influence on functional potential of microbial communities.},
journal = {The Science of the total environment},
volume = {681},
number = {},
pages = {413-423},
doi = {10.1016/j.scitotenv.2019.05.090},
pmid = {31108361},
issn = {1879-1026},
abstract = {Microbial communities play a crucial role in bioremediation of pollutants in contaminated ecosystem. In addition to pure culture isolation and bacterial 16S rRNA based community studies, the focus has now shifted employing the omics technologies enormously for understanding the microbial diversity and functional potential of soil samples. Our previous report on two pesticide-contaminated sites revealed the diversity of both culturable and unculturable bacteria. In the present study, we have observed distinct taxonomic and functional communities in contaminated soil with respect to an uncontaminated soil as control by using shotgun metagenomic sequencing method. Our data demonstrated that Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, and Acidobacteria significantly dominated the microbial diversity with their cumulative abundance percentage in the range of 98.61, 87.38, and 80.52 for Hindustan Insecticides Limited (HIL), India Pesticides Limited (IPL), and control respectively. Functional gene analysis demonstrated the presence of large number of both substrate specific upper pathway and common lower pathway degradative genes. Relatively lower number of genes was found encoding the degradation of styrene, atrazine, bisphenol, dioxin, and naphthalene. When three bacteria were augumentated with rhamnolipid (20-100 μM) and Triton X-100 (84-417 μM) surfactants in HIL soil, an enhanced degradation to 76%, 70%, and 58% of HCH, Endosulfan, and DDT respectively was achieved. The overall data obtained from two heavily contaminated soil suggest the versatility of the microbial communities for the xenobiotic pollutant degradation which may help in exploiting their potential applications in bioremediation.},
}

@article {pmid31107955,
year = {2019},
author = {Haston, JC and Rostad, CA and Jerris, RC and Milla, SS and McCracken, C and Pratt, C and Wiley, M and Prieto, K and Palacios, G and Shane, AL and McElroy, AK},
title = {Prospective Cohort Study of Next-Generation Sequencing as a Diagnostic Modality for Unexplained Encephalitis in Children.},
journal = {Journal of the Pediatric Infectious Diseases Society},
volume = {},
number = {},
pages = {},
doi = {10.1093/jpids/piz032},
pmid = {31107955},
issn = {2048-7207},
abstract = {BACKGROUND: Encephalitis is an inflammatory condition of the brain associated with long-term neurologic sequelae and even death in children. Although viruses are often implicated, an etiology is not identified in the majority of cases. Metagenomics-based next-generation sequencing (mNGS) is a high-throughput sequencing technique that can enhance the detection of novel or low-frequency pathogens.

METHODS: Hospitalized immunocompetent children aged 6 months to 18 years with encephalitis of unidentified etiology were eligible for enrollment. Demographic, historical, and clinical information was obtained, and residual blood and cerebrospinal fluid (CSF) samples were subjected to mNGS. Pathogens were identified by querying the sequence data against the NCBI GenBank database.

RESULTS: Twenty children were enrolled prospectively between 2013 and 2017. mNGS of CSF identified 7 nonhuman nucleic acid sequences of significant frequency in 6 patients, including that of Mycoplasma bovis, parvovirus B19, Neisseria meningitidis, and Balamuthia mandrillaris. mNGS also detected Cladophialophora species, tobacco mosaic virus, and human bocavirus, which were presumed to be contaminants or nonpathogenic organisms. One patient was found to have positive serology results for California encephalitis virus, but mNGS did not detect it. Patients for whom mNGS identified a diagnosis had a significantly higher CSF white blood cell count, a higher CSF protein concentration, and a lower CSF glucose level than patients for whom mNGS did not identify a diagnosis.

CONCLUSION: We describe here the results of a prospective cohort analysis to evaluate mNGS as a diagnostic tool for children with unexplained encephalitis. Although mNGS detected multiple nonpathogenic organisms, it also identified multiple pathogens successfully and was most useful in patients with a CSF abnormality.},
}

@article {pmid31107587,
year = {2019},
author = {Poghosyan, L and Koch, H and Lavy, A and Frank, J and van Kessel, MAHJ and Jetten, MSM and Banfield, JF and Lücker, S},
title = {Metagenomic recovery of two distinct comammox Nitrospira from the terrestrial subsurface.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.14691},
pmid = {31107587},
issn = {1462-2920},
abstract = {The recently discovered comammox process encompasses both nitrification steps, the aerobic oxidation of ammonia and nitrite, in a single organism. All known comammox bacteria are affiliated with Nitrospira sublineage II and can be grouped into two distinct clades, referred to as A and B, based on ammonia monooxygenase phylogeny. In this study, we report high-quality draft genomes of two novel comammox Nitrospira from the terrestrial subsurface, representing one clade A and one clade B comammox organism. The two metagenome-assembled genomes were compared to other representatives of Nitrospira sublineage II, including both canonical and comammox Nitrospira. Phylogenomic analyses confirmed the affiliation of the two novel Nitrospira with comammox clade A and B, respectively. Based on phylogenetic distance and pairwise average nucleotide identity values, both comammox Nitrospira were classified as novel species. Genomic comparison revealed high conservation of key metabolic features in sublineage II Nitrospira, including respiratory complexes I to V and the machineries for nitrite oxidation and carbon fixation via the reductive tricarboxylic acid cycle. In addition, the presence of the enzymatic repertoire for formate and hydrogen oxidation in the Rifle clade A and B comammox genomes, respectively, suggest a broader distribution of these metabolic features than previously anticipated. This article is protected by copyright. All rights reserved.},
}

@article {pmid31107251,
year = {2019},
author = {Chong, PP and Atmar, RL},
title = {Norovirus in health care and implications for the immunocompromised host.},
journal = {Current opinion in infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1097/QCO.0000000000000557},
pmid = {31107251},
issn = {1473-6527},
abstract = {PURPOSE OF REVIEW: The majority of norovirus outbreaks in the United States occur in healthcare facilities. With the growing population of immunocompromised hosts who are in frequent contact with healthcare facilities, norovirus is not only a threat to hospitals and nursing homes but also to these individuals. This review summarizes the impact of norovirus infection on healthcare facilities and immunocompromised hosts.

RECENT FINDINGS: The natural history of norovirus infection in immunocompromised individuals remains poorly understood. Although host immune responses play a critical role in reducing duration of viral shedding and viral load in norovirus-infected individuals, why some immunocompromised patients spontaneously recover while others develop a chronic and protracted course of illness remains unclear. Norovirus outbreaks occur in healthcare facilities because the virus is highly contagious, resistant to disinfection and efficiently transmitted. The use of real-time metagenomic next-generation sequencing and phylogenetic analyses has provided valuable information on transmission patterns in complex hospital-associated norovirus outbreaks. The development of human intestinal enteroid cultures enables the determination of effectiveness of disinfectants against human noroviruses, circumventing the validity questions with surrogate virus models due to differences in susceptibility to inactivation and disinfectants.

SUMMARY: Metagenomics next-generation sequencing can enhance our understanding of norovirus transmission and lead to more timely mitigation strategies to curb norovirus outbreaks in healthcare facilities. With new in-vitro cultivation methods for human noroviruses, candidate vaccines and effective antivirals could be available in the near future.},
}

@article {pmid31107235,
year = {2019},
author = {Fereidouni, S and Freimanis, GL and Orynbayev, M and Ribeca, P and Flannery, J and King, DP and Zuther, S and Beer, M and Höper, D and Kydyrmanov, A and Karamendin, K and Kock, R},
title = {Mass Die-Off of Saiga Antelopes, Kazakhstan, 2015.},
journal = {Emerging infectious diseases},
volume = {25},
number = {6},
pages = {1169-1176},
doi = {10.3201/eid2506.180990},
pmid = {31107235},
issn = {1080-6059},
abstract = {In 2015, a mass die-off of ≈200,000 saiga antelopes in central Kazakhstan was caused by hemorrhagic septicemia attributable to the bacterium Pasteurella multocida serotype B. Previous analyses have indicated that environmental triggers associated with weather conditions, specifically air moisture and temperature in the region of the saiga antelope calving during the 10-day period running up to the event, were critical to the proliferation of latent bacteria and were comparable to conditions accompanying historically similar die-offs in the same areas. We investigated whether additional viral or bacterial pathogens could be detected in samples from affected animals using 3 different high-throughput sequencing approaches. We did not identify pathogens associated with commensal bacterial opportunisms in blood, kidney, or lung samples and thus concluded that P. multocida serotype B was the primary cause of the disease.},
}

@article {pmid31105659,
year = {2019},
author = {Fuertes, A and Pérez-Burillo, S and Apaolaza, I and Vallès, Y and Francino, MP and Rufián-Henares, JÁ and Planes, FJ},
title = {Adaptation of the Human Gut Microbiota Metabolic Network During the First Year After Birth.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {848},
doi = {10.3389/fmicb.2019.00848},
pmid = {31105659},
issn = {1664-302X},
abstract = {Predicting the metabolic behavior of the human gut microbiota in different contexts is one of the most promising areas of constraint-based modeling. Recently, we presented a supra-organismal approach to build context-specific metabolic networks of bacterial communities using functional and taxonomic assignments of meta-omics data. In this work, this algorithm is applied to elucidate the metabolic changes induced over the first year after birth in the gut microbiota of a cohort of Spanish infants. We used metagenomics data of fecal samples and nutritional data of 13 infants at five time points. The resulting networks for each time point were analyzed, finding significant alterations once solid food is introduced in the diet. Our work shows that solid food leads to a different pattern of output metabolites that can be potentially released from the gut microbiota to the host. Experimental validation is presented for ferulate, a neuroprotective metabolite involved in the gut-brain axis.},
}

@article {pmid30628657,
year = {2019},
author = {Chen, L and Li, H and Li, J and Chen, Y and Yang, Y},
title = {Lactobacillus rhamnosus GG treatment improves intestinal permeability and modulates microbiota dysbiosis in an experimental model of sepsis.},
journal = {International journal of molecular medicine},
volume = {43},
number = {3},
pages = {1139-1148},
doi = {10.3892/ijmm.2019.4050},
pmid = {30628657},
issn = {1791-244X},
mesh = {Animals ; Apoptosis ; Biomarkers ; Cell Proliferation ; Colon/metabolism/microbiology/pathology ; Disease Models, Animal ; *Dysbiosis ; *Gastrointestinal Microbiome ; Lactobacillus rhamnosus/*physiology ; Male ; Metagenome ; Metagenomics/methods ; Mice ; Mortality ; Permeability ; Phylogeny ; Probiotics/*administration & dosage ; RNA, Ribosomal, 16S/genetics ; Sepsis/diagnosis/*metabolism/*microbiology/therapy ; },
abstract = {Decrease of 'health‑benefiting' microbes and increase of pathogenic bacteria (a condition termed dysbiosis) in intensive care unit patients is considered to induce or aggravate sepsis (gut‑origin sepsis). Orally administered probiotics have been effective in the prevention of nosocomial infections. However, the mechanisms of probiotic‑induced anti‑infection and anti‑sepsis remain to be explored. In the present study, 4‑week‑old C57BL6 mice were orally administrated with Lactobacillus rhamnosus GG (LGG) or normal saline (control) 4 weeks prior to cecal ligation and puncture (CLP). A subset of the mice were sacrificed at 24 h post‑CLP, and the others were used for survival studies. Ileum tissues, blood and fecal samples were collected. The survival rate of septic mice pretreated with LGG was significantly improved compared with untreated mice. The levels of inflammatory cytokines were reduced in LGG‑pretreated septic mice. A decrease of colonic proliferation and epithelial tight junctions and an increase of colonic apoptosis were observed in control septic CLP+saline mice. LGG pretreatment reversed the colonic proliferation, apoptosis and expression of tight junction proteins to the levels of the sham group. LGG pretreatment improved the richness and diversity of intestinal microbiota in septic mice. The principal coordinates analysis clustering plots revealed a significant separate clustering in microbiota structure between three groups. Bacteria associated with energy consumption, including Bacteroidetes, with opportunistic infection, including Proteobacteria, Staphylococcaceae and Enterococcaceae, lipopolysaccharide producers, including Enterobacteriaceae, and facultative anaerobes, such as Bacteroidaceae and Erysipelotrichaceae, increased in septic mice. By contrast, bacteria associated with energy harvest, including Firmicutes, intestinal barrier function regulators, including Akkermansia, hepatic function regulators, including Coprococcus and Oscillospira, and obligate anaerobes, including Prevotellaceae, decreased in septic mice. With LGG pretreatment, the sepsis‑induced microbiota dysbiosis was reversed. The present results elucidated the potential mechanism of LGG treatment in sepsis, by improving intestinal permeability and modulating microbiota dysbiosis.},
}

Animals
Apoptosis
Biomarkers
Cell Proliferation
Colon/metabolism/microbiology/pathology
Disease Models, Animal
*Dysbiosis
*Gastrointestinal Microbiome
Lactobacillus rhamnosus/*physiology
Male
Metagenome
Metagenomics/methods
Mice
Mortality
Permeability
Phylogeny
Probiotics/*administration & dosage
RNA, Ribosomal, 16S/genetics
Sepsis/diagnosis/*metabolism/*microbiology/therapy

@article {pmid30596703,
year = {2018},
author = {Quinn, O and Gruber, MAM and Brown, RL and Baty, JW and Bulgarella, M and Lester, PJ},
title = {A metatranscriptomic analysis of diseased social wasps (Vespula vulgaris) for pathogens, with an experimental infection of larvae and nests.},
journal = {PloS one},
volume = {13},
number = {12},
pages = {e0209589},
doi = {10.1371/journal.pone.0209589},
pmid = {30596703},
issn = {1932-6203},
mesh = {Animals ; Gene Expression Profiling/methods ; *Host-Pathogen Interactions ; Larva/microbiology ; *Metagenome ; *Metagenomics ; *Microbiota ; Phylogeny ; Wasps/*microbiology/ultrastructure ; },
abstract = {Social wasps are a major pest in many countries around the world. Pathogens may influence wasp populations and could provide an option for population management via biological control. We investigated the pathology of nests of apparently healthy common wasps, Vespula vulgaris, with nests apparently suffering disease. First, next-generation sequencing and metatranscriptomic analysis were used to examine pathogen presence. The transcriptome of healthy and diseased V. vulgaris showed 27 known microbial phylotypes. Four of these were observed in diseased larvae alone (Aspergillus fumigatus, Moellerella wisconsensis, Moku virus, and the microsporidian Vavraia culicis). Kashmir Bee Virus (KBV) was found to be present in both healthy and diseased larvae. Moellerella wisconsensis is a human pathogen that was potentially misidentified in our wasps by the MEGAN analysis: it is more likely to be the related bacteria Hafnia alvei that is known to infect social insects. The closest identification to the putative pathogen identified as Vavraia culicis was likely to be another microsporidian Nosema vulgaris. PCR and subsequent Sanger sequencing using published or our own designed primers, confirmed the identity of Moellerella sp. (which may be Hafnia alvei), Aspergillus sp., KBV, Moku virus and Nosema. Secondly, we used an infection study by homogenising diseased wasp larvae and feeding them to entire nests of larvae in the laboratory. Three nests transinfected with diseased larvae all died within 19 days. No pathogen that we monitored, however, had a significantly higher prevalence in diseased than in healthy larvae. RT-qPCR analysis indicated that pathogen infections were significantly correlated, such as between KBV and Aspergillus sp. Social wasps clearly suffer from an array of pathogens, which may lead to the collapse of nests and larval death.},
}

Animals
Gene Expression Profiling/methods
*Host-Pathogen Interactions
Larva/microbiology
*Metagenome
*Metagenomics
*Microbiota
Phylogeny
Wasps/*microbiology/ultrastructure

@article {pmid29808965,
year = {2019},
author = {Grönroos, M and Parajuli, A and Laitinen, OH and Roslund, MI and Vari, HK and Hyöty, H and Puhakka, R and Sinkkonen, A},
title = {Short-term direct contact with soil and plant materials leads to an immediate increase in diversity of skin microbiota.},
journal = {MicrobiologyOpen},
volume = {8},
number = {3},
pages = {e00645},
doi = {10.1002/mbo3.645},
pmid = {29808965},
issn = {2045-8827},
mesh = {Bacteria/*classification/*genetics ; *Environmental Exposure ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; *Microbiota ; Plants ; Skin/*microbiology ; Soil ; },
abstract = {Immune-mediated diseases have increased during the last decades in urban environments. The hygiene hypothesis suggests that increased hygiene level and reduced contacts with natural biodiversity are related to the increase in immune-mediated diseases. We tested whether short-time contact with microbiologically diverse nature-based materials immediately change bacterial diversity on human skin. We tested direct skin contact, as two volunteers rubbed their hands with sixteen soil and plant based materials, and an exposure via fabric packets filled with moss material. Skin swabs were taken before and after both exposures. Next-generation sequencing showed that exposures increased, at least temporarily, the total diversity of skin microbiota and the diversity of Acidobacteria, Actinobacteria, Bacteroidetes, Proteobacteria and Alpha-, Beta- and Gammaproteobacteria suggesting that contact with nature-based materials modify skin microbiome and increase skin microbial diversity. Until now, approaches to cure or prevent immune system disorders using microbe-based treatments have been limited to use of a few microbial species. We propose that nature-based materials with high natural diversity, such as the materials tested here, might be more effective in modifying human skin microbiome, and eventually, in reducing immune system disorders. Future studies should investigate how long-term changes in skin microbiota are achieved and if the exposure induces beneficial changes in the immune system markers.},
}

Bacteria/*classification/*genetics
*Environmental Exposure
High-Throughput Nucleotide Sequencing
Humans
Metagenome
*Microbiota
Plants
Skin/*microbiology
Soil

@article {pmid28883460,
year = {2017},
author = {Bridgewater, LC and Zhang, C and Wu, Y and Hu, W and Zhang, Q and Wang, J and Li, S and Zhao, L},
title = {Gender-based differences in host behavior and gut microbiota composition in response to high fat diet and stress in a mouse model.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {10776},
pmid = {28883460},
issn = {2045-2322},
mesh = {Animals ; *Behavior, Animal ; Computational Biology/methods ; *Diet, High-Fat ; Female ; *Gastrointestinal Microbiome ; Male ; Metagenome ; Metagenomics/methods ; Mice ; Sex Factors ; *Stress, Physiological ; },
abstract = {Obesity is associated with a high prevalence of mood disorders such as anxiety and depression. Both stress and high fat diet can alter the gut microbiota and contribute to obesity. To examine the interrelationships between obesity, stress, gut microbiota and mood disorders, obesity was induced in mice using a high fat diet, and the mice were subsequently stressed using a chronic unpredictable mild stress protocol. During the experiment, the composition of the gut microbiota was analyzed by 16 S rRNA gene high-throughput sequencing, and anxiety-like behaviors were measured. The results revealed distinct gender differences in the impacts of obesity and stress on anxiety-like behaviors, activity levels, and composition of the gut microbiota. Male mice were more vulnerable to the anxiogenic effects of the high fat diet, and obese male mice showed decreased locomotion activity in response to stress whereas obese female mice did not. In females, stress caused the gut microbiota of lean mice to more closely resemble that of obese mice. Taken together, these results suggest the importance of considering gender as a biological variable in studies on the role of gut microbiota in obesity-related mood disorders.},
}

Animals
*Behavior, Animal
Computational Biology/methods
*Diet, High-Fat
Female
*Gastrointestinal Microbiome
Male
Metagenome
Metagenomics/methods
Mice
Sex Factors
*Stress, Physiological

@article {pmid31104215,
year = {2019},
author = {Li, P and Wu, H and Jin, Y and Huang, X and Chen, Y and Yang, X and Wang, R and Zhang, W},
title = {Exploring the diversity and dynamic of bacterial community vertically distributed in Tongguling National Nature Reserve in Hainan Island, China.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
doi = {10.1007/s42770-019-00078-2},
pmid = {31104215},
issn = {1678-4405},
abstract = {National nature reserves are important for preserving ecological resources and constructing national ecological security barriers. Tongguling National Nature Reserve (TNNR) is known for its unique tropical island ecosystem and abundant biological resources. This study was conducted to characterize and compare its bacterial community diversity and composition in soils from 10, 20, and 30 cm in depth using high-throughput sequencing of 16S rDNA genes. We found that soils from 20 cm had the highest diversity and might serve as a "middle bridge" to the dynamic distribution between the 10- and 30-cm soil samples. The diversity pattern indicated that the main abundant groups varied distinctly and significantly among soils of different depths. Moreover, Chloroflexi was the most dynamic group in TNNR soils, together with another abundant but rarely reported group, Verrucomicrobia, which greatly enhanced the microbial diversity of TNNR soils. Overall, the results of this study emphasize the urgent need for greater understanding of bacterial community variations in response to human activities and climate change.},
}

@article {pmid31103724,
year = {2019},
author = {Scherler, A and Ardissone, S and Moran-Gilad, J and Greub, G},
title = {ESCMID/ESGMD postgraduate technical workshop on diagnostic microbiology.},
journal = {Microbes and infection},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.micinf.2019.04.006},
pmid = {31103724},
issn = {1769-714X},
abstract = {The European Society of Clinical Microbiology and Infectious Diseases (ESCMID) workshop on diagnostic microbiology was held in Lausanne from 25th to 28th September 2018. A total of 87 participants from 31 countries participated to this postgraduate technical workshop. Over 4 days, the mornings were dedicated to talks, which covered many subjects including MALDI-TOF, molecular diagnosis, genomics and metagenomics as well as new innovative approaches. The afternoons were dedicated to 12 different practicals covering various aspects of microbiological diagnosis. This ESCMID meeting provided a unique opportunity to exchange knowledge and ideas on the recent tools developed in diagnostic laboratories. This meeting report summarises the key messages of this four-day workshop.},
}

@article {pmid31102963,
year = {2019},
author = {Liu, S and Chen, Q and Zou, H and Yu, Y and Zhou, Z and Mao, J and Zhang, S},
title = {A metagenomic analysis of the relationship between microorganisms and flavor development in Shaoxing mechanized huangjiu fermentation mashes.},
journal = {International journal of food microbiology},
volume = {303},
number = {},
pages = {9-18},
doi = {10.1016/j.ijfoodmicro.2019.05.001},
pmid = {31102963},
issn = {1879-3460},
abstract = {Complex microbial metabolism is responsible for the unique flavor of Shaoxing mechanized huangjiu. However, the relationship between the microorganisms present during fermentation and the formation of specific flavor components is difficult to understand. In this study, gas chromatography-mass spectrometry and high-performance liquid chromatography were used to identify flavor components, and a metagenomic sequencing approach was used to characterize the taxonomic and functional attributes of the Shaoxing mechanized huangjiu fermentation microbiota. The metagenomic sequencing data were used to predict the relationship between microorganisms and flavor formation. The chromatographic analysis identified amino acids, alcohols, acids, phenols and esters as major flavor components, and six microbial genera (Saccharomyces, Aspergillus, Saccharopolyspora, Staphylococcus, Lactobacillus, and Lactococcus) were most closely related to the production of these flavor components. This study helps clarify the different metabolic roles of microorganisms in flavor formation during Shaoxing huangjiu fermentation.},
}

@article {pmid31102141,
year = {2019},
author = {Sahoo, K and Sahoo, RK and Gaur, M and Subudhi, E},
title = {Cellulolytic thermophilic microorganisms in white biotechnology: a review.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12223-019-00710-6},
pmid = {31102141},
issn = {1874-9356},
support = {YSS/2014/000413//Science and Engineering Research Board/ ; },
abstract = {Enzymes of microbial origin are of immense importance for organic material decomposition leading to bioremediation of organic waste, bioenergy generation, large-scale industrial bioprocesses, etc. The market demand for microbial cellulase enzyme is growing more rapidly which ultimately becomes the driving force towards research on this biocatalyst, widely used in various industrial activities. The use of novel cellulase genes obtained from various thermophiles through metagenomics and genetic engineering as well as following metabolic engineering pathways would be able to enhance the production of thermophilic cellulase at industrial scale. The present review is mainly focused on thermophilic cellulolytic bacteria, discoveries on cellulase gene, genetically modified cellulase, metabolic engineering, and their various industrial applications. A lot of lacunae are yet to overcome for thermophiles such as metagenome analysis, metabolic pathway modification study, search of heterologous hosts in gene expression system, and improved recombinant strain for better cellulase yield as well as value-added product formation.},
}

@article {pmid31102076,
year = {2019},
author = {Wu, S and Nan, F and Jiang, J and Qiu, J and Zhang, Y and Qiao, B and Li, S and Xin, Z},
title = {Molecular cloning, expression and characterization of a novel feruloyl esterase from a soil metagenomic library with phthalate-degrading activity.},
journal = {Biotechnology letters},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10529-019-02693-3},
pmid = {31102076},
issn = {1573-6776},
support = {KYYJ201708//the Fundamental Research Funds for the Central Universities/ ; },
abstract = {OBJECTIVES: To discover novel feruloyl esterases (FAEs) by the function-driven screening procedure from soil metagenome.

RESULTS: A novel FAE gene bds4 was isolated from a soil metagenomic library and over-expressed in Escherichia coli. The recombinant enzyme BDS4 was purified to homogeneity with a predicted molecular weight of 38.8 kDa. BDS4 exhibited strong activity (57.05 U/mg) toward methyl ferulate under the optimum pH and temperature of 8.0 and 37°C. Based on its amino acid sequence and model substrates specificity, BDS4 was classified as a type-C FAE. The quantity of the releasing ferulic acid can be enhanced significantly in the presence of xylanase compared with BDS4 alone from de-starched wheat bran. In addition, BDS4 can also hydrolyze several phthalates such as diethyl phthalate, dimethyl phthalate and dibutyl phthalate.

CONCLUSION: The current investigation discovered a novel FAE with phthalate-degrading activity and highlighted the usefulness of metagenomic approaches as a powerful tool for discovery of novel FAEs.},
}

@article {pmid31101866,
year = {2019},
author = {Cho, EJ and Leem, S and Kim, SA and Yang, J and Lee, YB and Kim, SS and Cheong, JY and Cho, SW and Kim, JW and Kim, SM and Yoon, JH and Park, T},
title = {Circulating Microbiota-Based Metagenomic Signature for Detection of Hepatocellular Carcinoma.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {7536},
doi = {10.1038/s41598-019-44012-w},
pmid = {31101866},
issn = {2045-2322},
support = {HI16C2037//Korea Health Industry Development Institute (KHIDI)/ ; NRF-2017R1D1A1B03034639//National Research Foundation of Korea (NRF)/ ; 04-2017-0640//Seoul National University Hospital (SNUH)/ ; },
abstract = {Circulating microbial dysbiosis is associated with chronic liver disease including nonalcoholic steatohepatitis and alcoholic liver disease. In this study, we evaluated whether disease-specific alterations of circulating microbiome are present in patients with cirrhosis and hepatocellular carcinoma (HCC), and their potential as diagnostic biomarkers for HCC. We performed cross-sectional metagenomic analyses of serum samples from 79 patients with HCC, 83 with cirrhosis, and 201 matching healthy controls, and validated the results in the same number of subjects. Serum bacterial DNA was analyzed using high-throughput pyrosequencing after amplification of the V3-V4 hypervariable regions of 16S rDNA. Blood microbial diversity was significantly reduced in HCC, compared with cirrhosis and control. There were significant differences in the relative abundances of several bacterial taxa that correlate with the presence of HCC, thus defining a specific blood microbiome-derived metagenomic signature of HCC. We identified 5 microbial gene markers-based model which distinguished HCC from controls with an area under the receiver-operating curve (AUC) of 0.879 and a balanced accuracy of 81.6%. In the validation, this model accurately distinguished HCC with an AUC of 0.875 and an accuracy of 79.8%. In conclusion, circulating microbiome-based signatures may be potential biomarkers for the detection HCC.},
}

@article {pmid31101811,
year = {2019},
author = {Sande, CJ and Njunge, JM and Mwongeli Ngoi, J and Mutunga, MN and Chege, T and Gicheru, ET and Gardiner, EM and Gwela, A and Green, CA and Drysdale, SB and Berkley, JA and Nokes, J and Pollard, AJ},
title = {Airway response to respiratory syncytial virus has incidental antibacterial effects.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {2218},
doi = {10.1038/s41467-019-10222-z},
pmid = {31101811},
issn = {2041-1723},
support = {WT105882MA//Wellcome Trust (Wellcome)/ ; },
abstract = {RSV infection is typically associated with secondary bacterial infection. We hypothesise that the local airway immune response to RSV has incidental antibacterial effects. Using coordinated proteomics and metagenomics analysis we simultaneously analysed the microbiota and proteomes of the upper airway and determined direct antibacterial activity in airway secretions of RSV-infected children. Here, we report that the airway abundance of Streptococcus was higher in samples collected at the time of RSV infection compared with samples collected one month later. RSV infection is associated with neutrophil influx into the airway and degranulation and is marked by overexpression of proteins with known antibacterial activity including BPI, EPX, MPO and AZU1. Airway secretions of children infected with RSV, have significantly greater antibacterial activity compared to RSV-negative controls. This RSV-associated, neutrophil-mediated antibacterial response in the airway appears to act as a regulatory mechanism that modulates bacterial growth in the airways of RSV-infected children.},
}

@article {pmid31101528,
year = {2019},
author = {Hagihara, M and Yamashita, R and Matsumoto, A and Mori, T and Inagaki, T and Nonogaki, T and Kuroki, Y and Higashi, S and Oka, K and Takahashi, M and Mikamo, H},
title = {The impact of probiotic Clostridium butyricum MIYAIRI 588 on murine gut metabolic alterations.},
journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jiac.2019.02.008},
pmid = {31101528},
issn = {1437-7780},
abstract = {INTRODUCTION: Clostridium butyricum MIYAIRI 588 (CBM 588) is a probiotic bacterium used in antidiarrheal medicine in Japan. A few studies analyzed the changes in gut microbiome in patients treated with antimicrobials based on metagenomics sequencing. However, the impact of CBM 588 on gut metabolic alterations has not been fully elucidated. This study was to reveal the impact of CBM 588 on gut metabolic alterations.

MATERIAL AND METHODS: In this in vivo study, mice were divided into four groups and CBM 588, clindamycin (CLDM), and normal saline (control) was orally administered (1. CLDM, 2. CBM 588, 3. CBM 588 + CLDM, 4. water) for 4 days. Fecal samples were collected to extract DNA for metagenomics analysis. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was used to obtain relative Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway abundance information derived from metagenomics data.

RESULTS: CLDM treatment resulted in a dramatic increase in Firmicutes phylum compared to non-CLDM-treated groups (control and CBM 588-treated group). Then, the CBM 588 + CLDM-treated group showed a trend similar in many metabolic pathways to the CLDM-treated group. On the other hand, the CBM 588 + CLDM-treated group showed higher relative abundance compared to the CLDM-treated group especially in starch and sucrose metabolism.

DISCUSSION: We concluded that CBM 588 caused a gut microbiome functional shift toward increased carbohydrate metabolism. These results support the hypothesis that CBM 588 treatment modulates gut microbiome under dysbiosis conditions due to antimicrobials.},
}

@article {pmid31100994,
year = {2019},
author = {Zhang, YZ and Chen, YM and Wang, W and Qin, XC and Holmes, EC},
title = {Expanding the RNA Virosphere by Unbiased Metagenomics.},
journal = {Annual review of virology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-virology-092818-015851},
pmid = {31100994},
issn = {2327-0578},
abstract = {Although viruses comprise the most abundant genetic material in the biosphere, to date only several thousand virus species have been formally defined. Such a limited perspective on virus diversity has in part arisen because viruses were traditionally considered only as etiologic agents of overt disease in humans or economically important species and were often difficult to identify using cell culture. This view has dramatically changed with the rise of metagenomics, which is transforming virus discovery and revealing a remarkable diversity of viruses sampled from diverse cellular organisms. These newly discovered viruses help fill major gaps in the evolutionary history of viruses, revealing a near continuum of diversity among genera, families, and even orders of RNA viruses. Herein, we review some of the recent advances in our understanding of the RNA virosphere that have stemmed from metagenomics, note future directions, and highlight some of the remaining challenges to this rapidly developing field. Expected final online publication date for the Annual Review of Virology Volume 6 is September 30, 2019. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.},
}

@article {pmid31100923,
year = {2019},
author = {Di Pietro, M and Filardo, S and Romano, S and Sessa, R},
title = {Chlamydia trachomatis and Chlamydia pneumoniae Interaction with the Host: Latest Advances and Future Prospective.},
journal = {Microorganisms},
volume = {7},
number = {5},
pages = {},
doi = {10.3390/microorganisms7050140},
pmid = {31100923},
issn = {2076-2607},
abstract = {Research in Chlamydia trachomatis and Chlamydia pneumoniae has gained new traction due to recent advances in molecular biology, namely the widespread use of the metagenomic analysis and the development of a stable genomic transformation system, resulting in a better understanding of Chlamydia pathogenesis. C. trachomatis, the leading cause of bacterial sexually transmitted diseases, is responsible of cervicitis and urethritis, and C. pneumoniae, a widespread respiratory pathogen, has long been associated with several chronic inflammatory diseases with great impact on public health. The present review summarizes the current evidence regarding the complex interplay between C. trachomatis and host defense factors in the genital micro-environment as well as the key findings in chronic inflammatory diseases associated to C. pneumoniae.},
}

@article {pmid31100576,
year = {2019},
author = {Tao, Y and Huang, X and Gao, D and Wang, X and Chen, C and Liang, H and van Loosdrecht, MCM},
title = {NanoSIMS reveals unusual enrichment of acetate and propionate by an anammox consortium dominated by Jettenia asiatica.},
journal = {Water research},
volume = {159},
number = {},
pages = {223-232},
doi = {10.1016/j.watres.2019.05.006},
pmid = {31100576},
issn = {1879-2448},
abstract = {Anaerobic ammonium-oxidizing (anammox) bacteria convert ammonium and nitrite into N2 in a chemolithoautotrophic way, meaning that they utilize CO2/HCO3 solely as their carbon sources. Such autotrophic behavior limits their competitiveness with heterotrophic microorganisms in both natural environments and engineered systems. Recently, environmental metagenomic results have indicated the capability of anammox bacteria to metabolize short-chain fatty acids, further confirmed by limited experimental evidence based on highly enriched cultures. However, clear evidence is difficult to get because of the limits of traditional methodologies which rely on the availability of a pure anammox culture. In this study, we identified and quantified the uptake of acetate and propionate, on a single-cell level, by an anammox consortium that was dominated by Candidatus Jettenia asiatica (relative abundance of 96%). The consortium, growing in granular form with an average relative abundance of anammox bacteria of 96.0%, was firstly incubated in a13C-labelled acetate or propionate medium; then microtome sections were scanned by a nanometer-scale secondary ion mass spectrometer (NanoSIMS). The NanoSIMS scannings revealed that the consortium enriched acetate and propionate at a >10 times higher efficiency than bicarbonate incorporation. Our results also suggest that acetate or propionate was likely not assimilated by J. asiatica directly, but firstly oxidized to CO2, which then served as carbon sources for the follow-up autotrophy in J. asiatica cells. Furthermore, more [15N]ammonium was enriched by the propionate-fed consortium than the acetate-fed consortium despite that exactly the same amount of 13C atoms were supplied. Our study strongly indicates an alternative lifestyle, namely organotrophy, in addition to chemolithoautotrophy of anammox bacteria, making it more versatile than often expected. It suggests that the niche of anammox bacteria in both natural and engineered ecosystems can be much broader than usual assumed. Recognising this is important for their role in wastewater treatment and the global nitrogen turn-over rates.},
}

@article {pmid31100040,
year = {2019},
author = {Ramadan, M and Solyman, S and Yones, M and Abdallah, Y and Halaby, H and Hanora, A},
title = {Skin Microbiome Differences in Atopic Dermatitis and Healthy Controls in Egyptian Children and Adults, and Association with Serum Immunoglobulin E.},
journal = {Omics : a journal of integrative biology},
volume = {23},
number = {5},
pages = {247-260},
doi = {10.1089/omi.2019.0011},
pmid = {31100040},
issn = {1557-8100},
abstract = {Atopic dermatitis (AD) is a complex, multifactorial, chronic pruritic inflammatory skin disease. We report the first microbiome study and new insights on the relationship between skin microbiota variation and AD susceptibility in a population sample from Egypt. We characterized the skin microbiome in 75 patients with AD and 20 healthy controls using Illumina MiSeq sequencing of 16S rRNA gene. Overall, bacterial diversity of skin microbiome in patients with AD was less than those of the healthy subjects. Genus level analysis revealed significant abundance variations by age, disease severity, locality, or immune response. Among these genera, Streptococcus, Cutibacterium, and Corynebacterium appeared to be specific signatures for AD in children, adolescents, and adults, respectively, while Staphylococcus was noted as a potential biomarker candidate for AD. Additionally, functional potential of metagenomes shifted the overall metabolic pathways to participate in the exacerbation of disease. Total immunoglobulin E (IgE) levels were positively correlated with relative enrichment of certain Staphylococcus aureus subspecies. Finally, AD-related differences in skin bacterial diversity appeared to be in part linked to the serum IgE level. These new observations attest to the promise of microbiome science and metagenomic analysis in AD specifically, and clinical dermatology broadly.},
}

@article {pmid31098412,
year = {2019},
author = {Sato, Y and Hori, T and Koike, H and Navarro, RR and Ogata, A and Habe, H},
title = {Transcriptome analysis of activated sludge microbiomes reveals an unexpected role of minority nitrifiers in carbon metabolism.},
journal = {Communications biology},
volume = {2},
number = {},
pages = {179},
doi = {10.1038/s42003-019-0418-2},
pmid = {31098412},
issn = {2399-3642},
abstract = {Although metagenomics researches have illuminated microbial diversity in numerous biospheres, understanding individual microbial functions is yet difficult due to the complexity of ecosystems. To address this issue, we applied a metagenome-independent, de novo assembly-based metatranscriptomics to a complex microbiome, activated sludge, which has been used for wastewater treatment for over a century. Even though two bioreactors were operated under the same conditions, their performances differed from each other with unknown causes. Metatranscriptome profiles in high- and low-performance reactors demonstrated that denitrifiers contributed to the anaerobic degradation of heavy oil; however, no marked difference in the gene expression was found. Instead, gene expression-based nitrification activities that fueled the denitrifiers by providing the respiratory substrate were notably high in the high-performance reactor only. Nitrifiers-small minorities with relative abundances of <0.25%-governed the heavy-oil degradation performances of the reactors, unveiling an unexpected linkage of carbon- and nitrogen-metabolisms of the complex microbiome.},
}

@article {pmid31098399,
year = {2019},
author = {Armour, CR and Nayfach, S and Pollard, KS and Sharpton, TJ},
title = {A Metagenomic Meta-analysis Reveals Functional Signatures of Health and Disease in the Human Gut Microbiome.},
journal = {mSystems},
volume = {4},
number = {4},
pages = {},
doi = {10.1128/mSystems.00332-18},
pmid = {31098399},
issn = {2379-5077},
abstract = {While recent research indicates that human health is affected by the gut microbiome, the functional mechanisms that underlie host-microbiome interactions remain poorly resolved. Metagenomic clinical studies can address this problem by revealing specific microbial functions that stratify healthy and diseased individuals. To improve our understanding of the relationship between the gut microbiome and health, we conducted the first integrative functional analysis of nearly 2,000 publicly available fecal metagenomic samples obtained from eight clinical studies. We identified characteristics of the gut microbiome that associate generally with disease, including functional alpha-diversity, beta-diversity, and beta-dispersion. Using regression modeling, we identified specific microbial functions that robustly stratify diseased individuals from healthy controls. Many of these functions overlapped multiple diseases, suggesting a general role in host health, while others were specific to a single disease and may indicate disease-specific etiologies. Our results clarify potential microbiome-mediated mechanisms of disease and reveal features of the microbiome that may be useful for the development of microbiome-based diagnostics. IMPORTANCE The composition of the gut microbiome associates with a wide range of human diseases, but the mechanisms underpinning these associations are not well understood. To shift toward a mechanistic understanding, we integrated distinct metagenomic data sets to identify functions encoded in the gut microbiome that associate with multiple diseases, which may be important to human health. Additionally, we identified functions that associate with specific diseases, which may elucidate disease-specific etiologies. We demonstrated that the functions encoded in the microbiome can be used to classify disease status, but the inclusion of additional patient covariates may be necessary to obtain sufficient accuracy. Ultimately, this analysis advances our understanding of the gut microbiome functions that constitute a healthy microbiome and identifies potential targets for microbiome-based diagnostics and therapeutics.},
}

@article {pmid31097033,
year = {2019},
author = {Lugli, GA and Milani, C and Duranti, S and Alessandri, G and Turroni, F and Mancabelli, L and Tatoni, D and Ossiprandi, MC and van Sinderen, D and Ventura, M},
title = {Isolation of novel gut bifidobacteria using a combination of metagenomic and cultivation approaches.},
journal = {Genome biology},
volume = {20},
number = {1},
pages = {96},
doi = {10.1186/s13059-019-1711-6},
pmid = {31097033},
issn = {1474-760X},
support = {15/JP-HDHL/3280//Science Foundation Ireland/Ireland ; SFI/12/RC/2273//Science Foundation Ireland/Ireland ; },
abstract = {Whole metagenome shotgun (WMGS) sequencing is a method that provides insights into the genomic composition and arrangement of complex microbial consortia. Here, we report how WMGS coupled with a cultivation approach allows the isolation of novel bifidobacteria from animal fecal samples. A combination of in silico analyses based on nucleotide and protein sequences facilitate the identification of genetic material belonging to putative novel species. Consequently, the prediction of metabolic properties by in silico analyses permits the identification of specific substrates that are then employed to isolate these species through a cultivation method.},
}

@article {pmid31097029,
year = {2019},
author = {Altan, E and Kubiski, SV and Burchell, J and Bicknese, E and Deng, X and Delwart, E},
title = {The first reptilian circovirus identified infects gut and liver tissues of black-headed pythons.},
journal = {Veterinary research},
volume = {50},
number = {1},
pages = {35},
doi = {10.1186/s13567-019-0653-z},
pmid = {31097029},
issn = {1297-9716},
support = {5419.18//Vitalant Research Institute/ ; },
abstract = {Viral metagenomic analysis of the liver of a black headed python (Aspidites melanocephalus) euthanized for a proliferative spinal lesion of unknown etiology yielded the first characterized genome of a reptile-infecting circovirus (black-headed python circovirus or BhPyCV). BhPyCV-specific in situ hybridization (ISH) showed that viral nucleic acids were strongly expressed in the intestinal lining and mucosa and multifocally in the liver. To investigate the presence of this virus in other snakes and its possible pathogenicity, 17 snakes in the python family with spinal disease were screened with ISH yielding a second BhP positive in intestinal tissue, and a Boelen's python (Morelia boeleni) positive in the liver. BhPyCV specific PCR was used to screen available frozen tissues from 13 of these pythons, four additional deceased pythons with and without spinal disease, and fecal samples from 37 live snakes of multiple species with unknown disease status. PCR detected multiple positive tissues in both of the ISH positive BhP and in the feces of another two live BhP and two live annulated tree boas (Corallus annulatus). Preliminary analysis indicates this circovirus can infect BhPs where it was found in 4/5 BhPs tested (2/2 with spinal disease, 2/3 live with unknown status), Boelen's python (1/2 with spinal disease), and annulated tree boa (2/6 live with unknown status) but was not detected in other python species with the same spinal lesions. This circovirus' causal or contributory role in spinal disease remains speculative and not well supported by these initial data.},
}

@article {pmid31096909,
year = {2019},
author = {Zhang, J and Lacroix, C and Wortmann, E and Ruscheweyh, HJ and Sunagawa, S and Sturla, SJ and Schwab, C},
title = {Gut microbial beta-glucuronidase and glycerol/diol dehydratase activity contribute to dietary heterocyclic amine biotransformation.},
journal = {BMC microbiology},
volume = {19},
number = {1},
pages = {99},
doi = {10.1186/s12866-019-1483-x},
pmid = {31096909},
issn = {1471-2180},
support = {ETH-41 16-1//ETHZ/ ; 201406320209//Chinese Government Scholarship/ ; },
abstract = {BACKGROUND: Consuming red and processed meat has been associated with an increased risk of colorectal cancer (CRC), which is partly attributed to exposure to carcinogens such as heterocyclic amines (HCA) formed during cooking and preservation processes. The interaction of gut microbes and HCA can result in altered bioactivities and it has been shown previously that human gut microbiota can transform mutagenic HCA to a glycerol conjugate with reduced mutagenic potential. However, the major form of HCA in the colon are glucuronides (HCA-G) and it is not known whether these metabolites, via stepwise microbial hydrolysis and acrolein conjugation, are viable precursors for glycerol conjugated metabolites. We hypothesized that such a process could be concurrently catalyzed by bacterial beta-glucuronidase (B-GUS) and glycerol/diol dehydratase (GDH) activity. We therefore investigated how the HCA-G PhIP-N2-β-D-glucuronide (PhIP-G), a representative liver metabolite of PhIP (2-Amino-1-methyl-6-phenylimidazo [4,5-b] pyridine), which is the most abundant carcinogenic HCA in well-cooked meat, is transformed by enzymatic activity of human gut microbial representatives of the phyla Firmicutes, Bacteroidetes, and Proteobacteria.

RESULTS: We employed a combination of growth and enzymatic assays, and a bioanalysis approach combined with metagenomics. B-GUS of Faecalibacterium prausnitzii converted PhIP-G to PhIP and GDH of Flavonifractor plautii, Blautia obeum, Eubacterium hallii, and Lactobacillus reuteri converted PhIP to PhIP-M1 in the presence of glycerol. In addition, B-GUS- and GDH-positive bacteria cooperatively converted PhIP-G to PhIP-M1. A screen of genes encoding B-GUS and GDH was performed for fecal microbiome data from healthy individuals (n = 103) and from CRC patients (n = 53), which revealed a decrease in abundance of taxa with confirmed GDH and HCA transformation activity in CRC patients.

CONCLUSIONS: This study for the first time demonstrates that gut microbes mediate the stepwise transformation of PhIP-G to PhIP-M1 via the intermediate production of PhIP. Findings from this study suggest that targeted manipulation with gut microbes bearing specific functions, or dietary glycerol supplementation might modify gut microbial activity to reduce HCA-induced CRC risk.},
}

@article {pmid31096848,
year = {2019},
author = {Arruda, B and Piñeyro, P and Derscheid, R and Hause, B and Byers, E and Dion, K and Long, D and Sievers, C and Tangen, J and Williams, T and Schwartz, K},
title = {PCV3-associated disease in the United States swine herd.},
journal = {Emerging microbes & infections},
volume = {8},
number = {1},
pages = {684-698},
doi = {10.1080/22221751.2019.1613176},
pmid = {31096848},
issn = {2222-1751},
abstract = {Porcine circovirus-associated disease encompasses multiple disease syndromes including porcine circovirus 2 systemic diseases, reproductive failure, and porcine dermatitis and nephropathy syndrome. Until recently, porcine circovirus 2 was the only species associated with the porcine circovirus-associated disease. In this report, diagnostic investigations of thirty-six field cases submitted from multiple production systems, numerous sites and varied geographic locations demonstrated porcine circovirus 3 within lesions by in situ hybridization including fetuses with myocarditis, weak-born neonatal piglets with encephalitis and myocarditis, from cases of porcine dermatitis and nephropathy syndrome, and in weaned pigs with systemic periarteritis. Porcine circovirus 3 was detected by PCR in numerous fetuses and perinatal piglets at high viral loads (trillions of genome copies per mL of tissue homogenate). Samples from all cases in this study were assayed and found negative for porcine circovirus 2 by PCR. Metagenomic sequencing was performed on a subset of reproductive cases, consisting of sixteen fetuses/fetal sample pools. PCV3 was identified in all pools and the only virus identified in fourteen pools. Based on these data, porcine circovirus 3 is considered a putative cause of reproductive failure, encephalitis and myocarditis in perinatal piglets, porcine dermatitis and nephropathy syndrome, and periarteritis in swine in the United States.},
}

@article {pmid30232678,
year = {2019},
author = {Osman, JR and Regeard, C and Badel, C and Fernandes, G and DuBow, MS},
title = {Variation of bacterial biodiversity from saline soils and estuary sediments present near the Mediterranean Sea coast of Camargue (France).},
journal = {Antonie van Leeuwenhoek},
volume = {112},
number = {3},
pages = {351-365},
doi = {10.1007/s10482-018-1164-z},
pmid = {30232678},
issn = {1572-9699},
mesh = {Bacteria/*classification/genetics/*isolation & purification ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Estuaries ; France ; Geologic Sediments/*microbiology ; Mediterranean Sea ; Metagenomics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; },
abstract = {Salinity is an important environmental factor influencing microbial community composition. To better understand this influence, we determined the bacterial communities present in 17 different sites of brackish sediment (underwater) and soil (surface) samples from the Camargue region (Rhône river delta) in southern France during the fall of 2013 and 2014 using pyrosequencing of the V3-V4 regions of the 16S rRNA genes amplified by PCR. This region is known for abundant flora and fauna and, though saline, 30% of rice consumed in France is grown here. We found that bacterial abundance in 1 g of soil or sediment, calculated by qPCR, was higher in sediments than in surface soil samples. Members belonging to the Proteobacteria, Bacteroidetes, Chloroflexi and Firmicutes phyla dominated the bacterial communities of sediment samples, while members belonging to the Proteobacteria, Bacteroidetes, Gemmatimonadetes, Actinobacteria, Firmicutes and Acidobacteria phyla dominated the bacterial communities of the soil samples. The most abundant bacterial genera present in the saline sediments and soils from the Camargue belonged mostly to halophilic and sulphate reducing bacteria, suggesting that the Camargue may be a valuable system to investigate saline, yet agriculturally productive, sediment and soil microbial ecosystem.},
}

Bacteria/*classification/genetics/*isolation & purification
*Biodiversity
Cluster Analysis
DNA, Bacterial/chemistry/genetics
DNA, Ribosomal/chemistry/genetics
*Estuaries
France
Geologic Sediments/*microbiology
Mediterranean Sea
Metagenomics
Phylogeny
Polymerase Chain Reaction
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
*Soil Microbiology

@article {pmid29878200,
year = {2018},
author = {Lee, FJ and Miller, KI and McKinlay, JB and Newton, ILG},
title = {Differential carbohydrate utilization and organic acid production by honey bee symbionts.},
journal = {FEMS microbiology ecology},
volume = {94},
number = {8},
pages = {},
doi = {10.1093/femsec/fiy113},
pmid = {29878200},
issn = {1574-6941},
mesh = {Acetates/metabolism ; Animals ; Bacteria/genetics/*metabolism ; Bees/*microbiology ; Carbohydrate Metabolism/*physiology ; Carbohydrates ; Fatty Acids, Volatile/biosynthesis/*metabolism ; Gastrointestinal Microbiome/genetics/*physiology ; Lactic Acid/metabolism ; Metagenome ; Symbiosis/physiology ; },
abstract = {The honey bee worker gut hosts a community of bacteria that comprises 8-10 core bacterial species, along with a set of more transient environmental microbes. Collectively, these microbes break down and ferment saccharides present in the host's diet, based on analyses of metagenomes, and metatranscriptomes from this environment. As part of this metabolism, the bacteria produce short-chain fatty acids that may serve as a food source for the host bee, stimulating biological processes that may contribute to host weight gain. To identify metabolic contributions of symbionts within the honey bee gut, we utilized a combination of molecular and biochemical approaches. We show significant variation in the metabolic capabilities of honey bee-associated taxa, highlighting the fact that honey bee gut microbiota members of the same clade are highly variable in their ability to use specific carbohydrates and produce organic acids. Finally, we confirm that the honey bee core microbes are active in vivo, expressing key enzymatic genes critical for utilizing plant-derived molecules and producing organic acids (i.e. acetate and lactate). These results suggest that core taxa may contribute significantly to weight gain in the honey bee, specifically through the production of organic acids.},
}

Acetates/metabolism
Animals
Bacteria/genetics/*metabolism
Bees/*microbiology
Carbohydrate Metabolism/*physiology
Carbohydrates
Fatty Acids, Volatile/biosynthesis/*metabolism
Gastrointestinal Microbiome/genetics/*physiology
Lactic Acid/metabolism
Metagenome
Symbiosis/physiology

@article {pmid31095619,
year = {2019},
author = {Motta, V and Luise, D and Bosi, P and Trevisi, P},
title = {Faecal microbiota shift during weaning transition in piglets and evaluation of AO blood types as shaping factor for the bacterial community profile.},
journal = {PloS one},
volume = {14},
number = {5},
pages = {e0217001},
doi = {10.1371/journal.pone.0217001},
pmid = {31095619},
issn = {1932-6203},
abstract = {The host-microbiota interplay is recognized as a key factor for the homeostatic maintenance in animals. In pigs, the weaning transition represents a drastic changes event leading to high risk of gut dysbiosis, which in most cases results in economic losses for swine industry. The blood type antigens expressed on mucosal surfaces can act as receptors for bacterial adhesion and the hypothesis of possible associations between blood groups and intestinal microbial profiles has been tested in human with contrasting results. Nevertheless, no studies testing the blood type as possible shaping factor for gut microbiota are available for pigs. The results of our previous study suggested the porcine AO blood types system as a possible factor influencing the microbiota composition. In the present study, the changes in fecal microbiota of 12 piglets were followed from 7 days after birth to 2 weeks post-weaning, testing the hypothesis that blood types may impact on its structure. No effects attributable to the difference in blood groups were detected, however, the sampling site (faeces) and the low statistical power might have masked the hypothesized impact. The data clearly showed the rearrangement of the bacterial ecosystem triggered by weaning transition; mainly consisting of a shift from a Bacteroidaceae-Enterobacteriaceae dominated community, to a Prevotellaceae-Ruminococcaceae dominated community. The functional analysis by metagenomic predictions suggested a role of the high levels of long-chain fatty acid in swine milk as energy source for Enterobacteriaceae (E. coli), in suckling piglets. This study provides a first insight for further investigations; indicating the need for larger sample size, preferably derived from intestinal mucosa, to test the potential effect of blood groups on gut microbiota profiles, and for analyses aimed at assessing the long-chain fatty acids degradation activity within the intestinal microbiota of suckling piglets, with particular attention to the role of E. coli.},
}

@article {pmid31095603,
year = {2019},
author = {Khan, MAW and Stephens, WZ and Mohammed, AD and Round, JL and Kubinak, JL},
title = {Does MHC heterozygosity influence microbiota form and function?.},
journal = {PloS one},
volume = {14},
number = {5},
pages = {e0215946},
doi = {10.1371/journal.pone.0215946},
pmid = {31095603},
issn = {1932-6203},
abstract = {MHC molecules are essential for the adaptive immune response, and they are the most polymorphic genetic loci in vertebrates. Extreme genetic variation at these loci is paradoxical given their central importance to host health. Classic models of MHC gene evolution center on antagonistic host-pathogen interactions to promote gene diversification and allelic diversity in host populations. However, all multicellular organisms are persistently colonized by their microbiota that perform essential metabolic functions for their host and protect from infection. Here, we provide data to support the hypothesis that MHC heterozygote advantage (a main force of selection thought to drive MHC gene evolution), may operate by enhancing fitness advantages conferred by the host's microbiome. We utilized fecal 16S rRNA gene sequences and their predicted metagenome datasets collected from multiple MHC congenic homozygote and heterozygote mouse strains to describe the influence of MHC heterozygosity on microbiome form and function. We find that in contrast to homozygosity at MHC loci, MHC heterozygosity promotes functional diversification of the microbiome, enhances microbial network connectivity, and results in enrichment for a variety of microbial functions that are positively associated with host fitness. We demonstrate that taxonomic and functional diversity of the microbiome is positively correlated in MHC heterozygote but not homozygote animals, suggesting that heterozygote microbiomes are more functionally adaptive under similar environmental conditions than homozygote microbiomes. Our data complement previous observations on the role of MHC polymorphism in sculpting microbiota composition, but also provide functional insights into how MHC heterozygosity may enhance host health by modulating microbiome form and function. We also provide evidence to support that MHC heterozygosity limits functional redundancy among commensal microbes and may enhance the metabolic versatility of their microbiome. Results from our analyses yield multiple testable predictions regarding the role of MHC heterozygosity on the microbiome that will help guide future research in the area of MHC-microbiome interactions.},
}

@article {pmid31095297,
year = {2019},
author = {Mhatre, SS and Kaufmann, S and Marshall, IPG and Obrochta, S and Andrèn, T and Jørgensen, BB and Lomstein, BAA},
title = {Microbial biomass turnover times and clues to cellular protein repair in energy-limited deep Baltic Sea sediments.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiz068},
pmid = {31095297},
issn = {1574-6941},
abstract = {The discovery of active microbial life deeply buried beneath the seafloor has opened important questions: how do microorganisms cope with extreme energy limitation, what is their metabolic activity, and how do they repair damages to essential biomolecules? We used a D:L-amino acid model to calculate microbial biomass turnover times. We used a metagenome and metatranscriptome analysis to investigate the distribution of the gene that encodes Protein-L-iso aspartate(D-aspartate) O-methyltransferase (PCMT), an enzyme which recognizes damaged L-isoapartyl and D-aspartyl residues in proteins and catalyzes their repair. Sediment was retrieved during the Integrated Ocean Drilling Program (IODP) Expedition 347 from Landsort Deep and the Little Belt in the Baltic Sea. The study covers the period from the Baltic Ice Lake ca. 13,000 years ago to the present. Our results provide new knowledge on microbial biomass turnover times and protein repair in relation to different regimes of organic matter input. For the first time, we show that the PCMT gene was widely distributed and expressed among phylogenetically diverse groups of microorganisms. Our findings suggest that microbial communities are capable of repairing D-amino acids within proteins using energy obtained from the degradation of a mixture of labile compounds in microbial necromass and more recalcitrant organic matter.},
}

@article {pmid31092601,
year = {2019},
author = {Hu, H and da Costa, RR and Pilgaard, B and Schiøtt, M and Lange, L and Poulsen, M},
title = {Fungiculture in Termites Is Associated with a Mycolytic Gut Bacterial Community.},
journal = {mSphere},
volume = {4},
number = {3},
pages = {},
doi = {10.1128/mSphere.00165-19},
pmid = {31092601},
issn = {2379-5042},
abstract = {Termites forage on a range of substrates, and it has been suggested that diet shapes the composition and function of termite gut bacterial communities. Through comparative analyses of gut metagenomes in nine termite species with distinct diets, we characterize bacterial community compositions and use peptide-based functional annotation method to determine biomass-degrading enzymes and the bacterial taxa that encode them. We find that fungus-growing termite guts have relatively more fungal cell wall-degrading enzyme genes, while wood-feeding termite gut communities have relatively more plant cell wall-degrading enzyme genes. Interestingly, wood-feeding termite gut bacterial genes code for abundant chitinolytic enzymes, suggesting that fungal biomass within the decaying wood likely contributes to gut bacterial or termite host nutrition. Across diets, the dominant biomass-degrading enzymes are predominantly coded for by the most abundant bacterial taxa, suggesting tight links between diet and gut community composition, with the most marked difference being the communities coding for the mycolytic capacity of the fungus-growing termite gut.IMPORTANCE Understanding functional capacities of gut microbiomes is important to improve our understanding of symbiotic associations. Here, we use peptide-based functional annotation to show that the gut microbiomes of fungus-farming termites code for a wealth of enzymes that likely target the fungal diet the termites eat. Comparisons to other termites showed that fungus-growing termite guts have relatively more fungal cell wall-degrading enzyme genes, whereas wood-feeding termite gut communities have relatively more plant cell wall-degrading enzyme genes. Across termites with different diets, the dominant biomass-degrading enzymes are predominantly coded for by the most abundant bacterial taxa, suggesting tight links between diet and gut community compositions.},
}

@article {pmid31092577,
year = {2019},
author = {Chen, Q and Godfrey, K and Liu, J and Mao, Q and Kuo, YW and Falk, BW},
title = {A nonstructural protein responsible for viral spread of a novel insect reovirus provides a safe channel for biparental virus transmission to progeny.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {},
doi = {10.1128/JVI.00702-19},
pmid = {31092577},
issn = {1098-5514},
abstract = {Diaphorina citri reovirus (DcRV) was previously identified based on metagenomics surveys for virus discovery. Here, we demonstrated that DcRV induces persistent infections in its psyllid host, Diaphorina citri DcRV was efficiently vertically passed to offspring in a biparental manner. Transmission electron microscopic and immunological analysis showed that the DcRV-encoded nonstructural protein, P10, assembled into a virion-packaging tubular structure which is associated with the spread of DcRV throughout the bodies of D. citri P10 tubules containing virions were associated with oocytes of female and sperm of male D. citri, suggesting a role in the highly efficient biparental transmission of DcRV. Knocking down P10 by RNA interference for males reduced the percentage of DcRV-infected progeny, and for females reduced the viral accumulation in progeny. These results, for the first time, show that a nonstructural protein of a novel insect reovirus provides a safe and pivotal channel for virus spread and biparental transmission to progeny.IMPORTANCE The Asian citrus psyllid, Diaphorina citri Kuwayama, is an important pest in the worldwide citrus industry. It is the vector of Candidatus Liberibacter asiaticus (CLas), the bacterial pathogen of Huanglongbing (HLB), which is currently considered to be the most destructive disease of citrus worldwide. Diaphorina citri reovirus (DcRV) was previously identified based on metagenomics surveys for virus discovery. Here, we found that this novel and persistent insect reovirus took advantage of a viral-encoded nonstructural protein, P10, for efficient vertical transmission from parents to progeny. The P10 assembled into a virion-packaging tubular structure, and was associated with oocytes of female D. citri and sperm of males. Consistently, knockdown of P10 for either male or female D. citri inhibited DcRV transmission to offspring. This tubular strategy for viral spread and biparental transmission might serve as a target for controlling viral vertical transmission and population expansion.},
}

@article {pmid31092280,
year = {2019},
author = {Heinken, A and Ravcheev, DA and Baldini, F and Heirendt, L and Fleming, RMT and Thiele, I},
title = {Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {75},
doi = {10.1186/s40168-019-0689-3},
pmid = {31092280},
issn = {2049-2618},
support = {FNR/A12/01//Fonds National de la Recherche Luxembourg (LU)/ ; FNR/O16/11402054//Fonds National de la Recherche Luxembourg/ ; 757922//H2020 European Research Council/ ; },
abstract = {BACKGROUND: The human gut microbiome performs important functions in human health and disease. A classic example for host-gut microbial co-metabolism is host biosynthesis of primary bile acids and their subsequent deconjugation and transformation by the gut microbiome. To understand these system-level host-microbe interactions, a mechanistic, multi-scale computational systems biology approach that integrates the different types of omic data is needed. Here, we use a systematic workflow to computationally model bile acid metabolism in gut microbes and microbial communities.

RESULTS: Therefore, we first performed a comparative genomic analysis of bile acid deconjugation and biotransformation pathways in 693 human gut microbial genomes and expanded 232 curated genome-scale microbial metabolic reconstructions with the corresponding reactions (available at https://vmh.life). We then predicted the bile acid biotransformation potential of each microbe and in combination with other microbes. We found that each microbe could produce maximally six of the 13 secondary bile acids in silico, while microbial pairs could produce up to 12 bile acids, suggesting bile acid biotransformation being a microbial community task. To investigate the metabolic potential of a given microbiome, publicly available metagenomics data from healthy Western individuals, as well as inflammatory bowel disease patients and healthy controls, were mapped onto the genomes of the reconstructed strains. We constructed for each individual a large-scale personalized microbial community model that takes into account strain-level abundances. Using flux balance analysis, we found considerable variation in the potential to deconjugate and transform primary bile acids between the gut microbiomes of healthy individuals. Moreover, the microbiomes of pediatric inflammatory bowel disease patients were significantly depleted in their bile acid production potential compared with that of controls. The contributions of each strain to overall bile acid production potential across individuals were found to be distinct between inflammatory bowel disease patients and controls. Finally, bottlenecks limiting secondary bile acid production potential were identified in each microbiome model.

CONCLUSIONS: This large-scale modeling approach provides a novel way of analyzing metagenomics data to accelerate our understanding of the metabolic interactions between the host and gut microbiomes in health and diseases states. Our models and tools are freely available to the scientific community.},
}

@article {pmid31089513,
year = {2017},
author = {Cavallari, JF and Schertzer, JD},
title = {Intestinal Microbiota Contributes to Energy Balance, Metabolic Inflammation, and Insulin Resistance in Obesity.},
journal = {Journal of obesity & metabolic syndrome},
volume = {26},
number = {3},
pages = {161-171},
doi = {10.7570/jomes.2017.26.3.161},
pmid = {31089513},
issn = {2508-7576},
abstract = {Obesity is associated with increased risk of developing metabolic diseases such as type 2 diabetes. The origins of obesity are multi-factorial, but ultimately rooted in increased host energy accumulation or retention. The gut microbiota has been implicated in control of host energy balance and nutrient extraction from dietary sources. The microbiota also impacts host immune status and dysbiosis-related inflammation can augment insulin resistance, independently of obesity. Advances in microbial metagenomic analyses and directly manipulating bacterial-host models of obesity have contributed to our understanding of the relationship between gut bacteria and metabolic disease. Foodborne, or drug-mediated perturbations to the gut microbiota can increase metabolic inflammation, insulin resistance, and dysglycemia. There is now some evidence that specific bacterial species can influence obesity and related metabolic defects such as insulin sensitivity. Components of bacteria are sufficient to impact obesity-related changes in metabolism. In fact, different microbial components derived from the bacterial cell wall can increase or decrease insulin resistance. Improving our understanding of the how components of the microbiota alter host metabolism is positioned to aid in the development of dietary interventions, avoiding triggers of dysbiosis, and generating novel therapeutic strategies to combat increasing rates of obesity and diabetes.},
}

@article {pmid31084612,
year = {2019},
author = {Liekniņa, I and Kalniņš, G and Akopjana, I and Bogans, J and Šišovs, M and Jansons, J and Rūmnieks, J and Tārs, K},
title = {Production and characterization of novel ssRNA bacteriophage virus-like particles from metagenomic sequencing data.},
journal = {Journal of nanobiotechnology},
volume = {17},
number = {1},
pages = {61},
doi = {10.1186/s12951-019-0497-8},
pmid = {31084612},
issn = {1477-3155},
support = {1.1.1.1/16/A/104//European Research and Development Fund/ ; },
abstract = {BACKGROUND: Protein shells assembled from viral coat proteins are an attractive platform for development of new vaccines and other tools such as targeted bioimaging and drug delivery agents. Virus-like particles (VLPs) derived from the single-stranded RNA (ssRNA) bacteriophage coat proteins (CPs) have been important and successful contenders in the area due to their simplicity and robustness. However, only a few different VLP types are available that put certain limitations on continued developments and expanded adaptation of ssRNA phage VLP technology. Metagenomic studies have been a rich source for discovering novel viral sequences, and in recent years have unraveled numerous ssRNA phage genomes significantly different from those known before. Here, we describe the use of ssRNA CP sequences found in metagenomic data to experimentally produce and characterize novel VLPs.

RESULTS: Approximately 150 ssRNA phage CP sequences were sourced from metagenomic sequence data and grouped into 14 different clusters based on CP sequence similarity analysis. 110 CP-encoding sequences were obtained by gene synthesis and expressed in bacteria which in 80 cases resulted in VLP assembly. Production and purification of the VLPs was straightforward and compatible with established protocols, with the only exception that a considerable proportion of the CPs had to be produced at a lower temperature to ensure VLP assembly. The VLP morphology was similar to that of the previously studied phages, although a few deviations such as elongated or smaller particles were noted in certain cases. In addition, stabilizing inter-subunit disulfide bonds were detected in six VLPs and several possible candidate RNA structures in the phage genomes were identified that might bind to the coat protein and ensure specific RNA packaging.

CONCLUSIONS: Compared to the few types of ssRNA phage VLPs that were used before, several dozens of new particles representing ten distinct similarity groups are now available with a notable potential for biotechnological applications. It is believed that the novel VLPs described in this paper will provide the groundwork for future development of new vaccines and other applications based on ssRNA bacteriophage VLPs.},
}

@article {pmid29926341,
year = {2019},
author = {Lladó Fernández, S and Větrovský, T and Baldrian, P},
title = {The concept of operational taxonomic units revisited: genomes of bacteria that are regarded as closely related are often highly dissimilar.},
journal = {Folia microbiologica},
volume = {64},
number = {1},
pages = {19-23},
doi = {10.1007/s12223-018-0627-y},
pmid = {29926341},
issn = {1874-9356},
support = {18-25706S//Czech Science Foundation/ ; LTT17022//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; },
mesh = {Bacteria/*classification/*genetics ; DNA, Bacterial/genetics ; Databases, Nucleic Acid ; Genes, Bacterial/genetics ; Genetic Variation ; Genome, Bacterial/*genetics ; Glycoside Hydrolases/genetics ; *Metagenomics ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {The concept of operational taxonomic units (OTUs), which constructs "mathematically" defined taxa, is widely accepted and applied to describe bacterial communities using amplicon sequencing of 16S rRNA gene. OTUs are often used to infer functional traits since they are considered to fairly represent of community members. However, the link between molecular taxa, real taxa, and OTUs seems to be much more complicated. Strains of the same bacterial species (ideally belonging to the same OTU) typically only share some genes (the core genome), while other genes are strain-specific and unique. It is thus unclear to what extent are important functional traits homogeneous within an OTU and how correctly can functional traits be inferred for individual OTU members. Here, we have tested in silico the similarity of all genes and, more specifically, the set of genes encoding for glycoside hydrolases (GH) in bacterial genomes that belong to the same OTU. Genome similarity varied among OTUs, but as many as 5-78% of genes were not shared between the two bacterial genomes in the pair. The complement of GH families (the presence of gene families and the number of genes per family) differed in 95% of OTUs. In average, 43% of GH families either differed in gene counts or were present in one genome and absent in the other. These results show a serious limitation of the OTU-based approaches when used to infer the functional traits of bacterial communities and open the questions how to link environmental sequencing data and microbial functions.},
}

Bacteria/*classification/*genetics
DNA, Bacterial/genetics
Databases, Nucleic Acid
Genes, Bacterial/genetics
Genetic Variation
Genome, Bacterial/*genetics
Glycoside Hydrolases/genetics
*Metagenomics
Microbiota
Phylogeny
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA

@article {pmid31091345,
year = {2019},
author = {Riiser, ES and Haverkamp, THA and Varadharajan, S and Borgan, Ø and Jakobsen, KS and Jentoft, S and Star, B},
title = {Switching on the light: using metagenomic shotgun sequencing to characterize the intestinal microbiome of Atlantic cod.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.14652},
pmid = {31091345},
issn = {1462-2920},
abstract = {Atlantic cod (Gadus morhua) is an ecologically important species with a wide-spread distribution in the North Atlantic Ocean, yet little is known about the diversity of its intestinal microbiome in its natural habitat. No geographical differentiation in this microbiome was observed based on 16S rRNA amplicon analyses, yet such finding may result from an inherent lack of power of this method to resolve fine-scaled biological complexity. Here, we use metagenomic shotgun sequencing to investigate the intestinal microbiome of 19 adult Atlantic cod individuals from two coastal populations in Norway - located 470 km apart. Resolving the species community to unprecedented resolution, we identify two abundant species, P. iliopiscarium and P. kishitanii, which comprise over 50% of the classified reads. Interestingly, the intestinal P. kishitanii strains have functionally intact lux genes, and its high abundance suggests that fish intestines form an important part of its ecological niche. These observations support a hypothesis that bioluminescence plays an ecological role in the marine food web. Despite our improved taxonomical resolution, we identify no geographical differences in bacterial community structure, indicating that the intestinal microbiome of these coastal cod is colonized by a limited number of closely related bacterial species with a broad geographical distribution. This article is protected by copyright. All rights reserved.},
}

@article {pmid31091277,
year = {2019},
author = {Ribeiro, H and Martins, A and Gonçalves, M and Guedes, M and Tomasino, MP and Dias, N and Dias, A and Mucha, AP and Carvalho, MF and Almeida, CMR and Ramos, S and Almeida, JM and Silva, E and Magalhães, C},
title = {Development of an autonomous biosampler to capture in situ aquatic microbiomes.},
journal = {PloS one},
volume = {14},
number = {5},
pages = {e0216882},
doi = {10.1371/journal.pone.0216882},
pmid = {31091277},
issn = {1932-6203},
abstract = {The importance of planktonic microbial communities is well acknowledged, since they are fundamental for several natural processes of aquatic ecosystems. Microorganisms naturally control the flux of nutrients, and also degrade and recycle anthropogenic organic and inorganic contaminants. Nevertheless, climate change effects and/or the runoff of nutrients/pollutants can affect the equilibrium of natural microbial communities influencing the occurrence of microbial pathogens and/or microbial toxin producers, which can compromise ecosystem environmental status. Therefore, improved microbial plankton monitoring is essential to better understand how these communities respond to environmental shifts. The study of marine microbial communities typically involves highly cost and time-consuming sampling procedures, which can limit the frequency of sampling and data availability. In this context, we developed and validated an in situ autonomous biosampler (IS-ABS) able to collect/concentrate in situ planktonic communities of different size fractions (targeting prokaryotes and unicellular eukaryotes) for posterior genomic, metagenomic, and/or transcriptomic analysis at a home laboratory. The IS-ABS field prototype is a small size and compact system able to operate up to 150 m depth. Water is pumped by a micropump (TCS MG2000) through a hydraulic circuit that allows in situ filtration of environmental water in one or more Sterivex filters placed in a filter cartridge. The IS-ABS also includes an application to program sampling definitions, allowing pre-setting configuration of the sampling. The efficiency of the IS-ABS was tested against traditional laboratory filtration standardized protocols. Results showed a good performance in terms of DNA recovery, as well as prokaryotic (16S rDNA) and eukaryotic (18S rDNA) community diversity analysis, using either methodologies. The IS-ABS automates the process of collecting environmental DNA, and is suitable for integration in water observation systems, what will contribute to substantially increase biological surveillances. Also, the use of highly sensitive genomic approaches allows a further study of the diversity and functions of whole or specific microbial communities.},
}

@article {pmid31089679,
year = {2019},
author = {Nicholls, SM and Quick, JC and Tang, S and Loman, NJ},
title = {Ultra-deep, long-read nanopore sequencing of mock microbial community standards.},
journal = {GigaScience},
volume = {8},
number = {5},
pages = {},
doi = {10.1093/gigascience/giz043},
pmid = {31089679},
issn = {2047-217X},
abstract = {BACKGROUND: Long sequencing reads are information-rich: aiding de novo assembly and reference mapping, and consequently have great potential for the study of microbial communities. However, the best approaches for analysis of long-read metagenomic data are unknown. Additionally, rigorous evaluation of bioinformatics tools is hindered by a lack of long-read data from validated samples with known composition.

FINDINGS: We sequenced 2 commercially available mock communities containing 10 microbial species (ZymoBIOMICS Microbial Community Standards) with Oxford Nanopore GridION and PromethION. Both communities and the 10 individual species isolates were also sequenced with Illumina technology. We generated 14 and 16 gigabase pairs from 2 GridION flowcells and 150 and 153 gigabase pairs from 2 PromethION flowcells for the evenly distributed and log-distributed communities, respectively. Read length N50 ranged between 5.3 and 5.4 kilobase pairs over the 4 sequencing runs. Basecalls and corresponding signal data are made available (4.2 TB in total). Alignment to Illumina-sequenced isolates demonstrated the expected microbial species at anticipated abundances, with the limit of detection for the lowest abundance species below 50 cells (GridION). De novo assembly of metagenomes recovered long contiguous sequences without the need for pre-processing techniques such as binning.

CONCLUSIONS: We present ultra-deep, long-read nanopore datasets from a well-defined mock community. These datasets will be useful for those developing bioinformatics methods for long-read metagenomics and for the validation and comparison of current laboratory and software pipelines.},
}

@article {pmid31088928,
year = {2019},
author = {Schorn, MA and Jordan, PA and Podell, S and Blanton, JM and Agarwal, V and Biggs, JS and Allen, EE and Moore, BS},
title = {Comparative Genomics of Cyanobacterial Symbionts Reveals Distinct, Specialized Metabolism in Tropical Dysideidae Sponges.},
journal = {mBio},
volume = {10},
number = {3},
pages = {},
doi = {10.1128/mBio.00821-19},
pmid = {31088928},
issn = {2150-7511},
abstract = {Marine sponges are recognized as valuable sources of bioactive metabolites and renowned as petri dishes of the sea, providing specialized niches for many symbiotic microorganisms. Sponges of the family Dysideidae are well documented to be chemically talented, often containing high levels of polyhalogenated compounds, terpenoids, peptides, and other classes of bioactive small molecules. This group of tropical sponges hosts a high abundance of an uncultured filamentous cyanobacterium, Hormoscilla spongeliae Here, we report the comparative genomic analyses of two phylogenetically distinct Hormoscilla populations, which reveal shared deficiencies in essential pathways, hinting at possible reasons for their uncultivable status, as well as differing biosynthetic machinery for the production of specialized metabolites. One symbiont population contains clustered genes for expanded polybrominated diphenylether (PBDE) biosynthesis, while the other instead harbors a unique gene cluster for the biosynthesis of the dysinosin nonribosomal peptides. The hybrid sequencing and assembly approach utilized here allows, for the first time, a comprehensive look into the genomes of these elusive sponge symbionts.IMPORTANCE Natural products provide the inspiration for most clinical drugs. With the rise in antibiotic resistance, it is imperative to discover new sources of chemical diversity. Bacteria living in symbiosis with marine invertebrates have emerged as an untapped source of natural chemistry. While symbiotic bacteria are often recalcitrant to growth in the lab, advances in metagenomic sequencing and assembly now make it possible to access their genetic blueprint. A cell enrichment procedure, combined with a hybrid sequencing and assembly approach, enabled detailed genomic analysis of uncultivated cyanobacterial symbiont populations in two chemically rich tropical marine sponges. These population genomes reveal a wealth of secondary metabolism potential as well as possible reasons for historical difficulties in their cultivation.},
}

@article {pmid31087994,
year = {2019},
author = {Yu, X and Sun, HW and Li, WW and Qi, GP and Ma, J and Cheng, YZ and Lü, XT},
title = {[Effect of Temperature on the Activity Kinetics of Nitrobacter].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {40},
number = {3},
pages = {1426-1430},
doi = {10.13227/j.hjkx.201808261},
pmid = {31087994},
issn = {0250-3301},
abstract = {A sequencing batch reactor (SBR) was operated in this study to investigate the effect of temperature on the kinetics of Nitrobacter activity among nitrite oxidizing bacteria. At the beginning of the experiment, the NO2--N concentration in the influent was changed to enrich Nitrobacter. Then, the sludge with enriched Nitrobacter was employed to determine the variation of the specific nitrite oxidation rate (SNiOR) during the nitrite oxidation process in batch tests. Metagenomics species annotation and abundance analysis showed that Nitrobacter accounted for 40.3% of the total bacterial population. The variation of SNiOR in the nitrite oxidation process was investigated under different NO2--N concentrations. The effect of temperature on the kinetics of Nitrobacter was investigated using the Monod model. Furthermore, the kinetics model of the effect of temperature on Nitrobacter activity was fitted for statistical analysis. The results showed that SNiOR reached its maximum at 30℃, which was 1.31 g·(g·d)-1. Statistical analysis showed that the Monod equation could describe the effect of substrate concentration on Nitrobacter activity under different temperature conditions. Calculating the temperature coefficient (θ) in different temperature intervals based on the Phelps equation, showed that when the system temperature is lower than 25℃ or higher than 30℃, the reaction rate is more sensitive to temperature changes.},
}

@article {pmid31087993,
year = {2019},
author = {Liu, ZQ and Zhang, Y and Ma, XS and Zhang, BK and Cao, MJ and Chen, CM},
title = {[Nitrogen Removal Characteristics and Analysis of Microbial Community Structure in an IEM-UF Simultaneous Separation and Denitrification System].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {40},
number = {3},
pages = {1419-1425},
doi = {10.13227/j.hjkx.201808051},
pmid = {31087993},
issn = {0250-3301},
abstract = {A system that combines an ion exchange membrane and ultrafiltration membrane (IEM-UF) to form a simultaneous separation and denitrification system was proposed for domestic sewage with a low carbon/nitrogen ratio. The removal of nitrogen and COD in the system was studied under a three phase operating condition. The characteristics of the microbial community in each reactor were analyzed using metagenomics. The results show that, the average rate of ammonia nitrogen enrichment in the separator reached above 116.1% when the current intensity was 0.2 A. When the system was at C/N 2.80 and operating well, the average removal rates of COD and TN reached above 90% and 50%, respectively. The maximum removal rate of TN was above 65.4%. The results of metagenomics showed a genus of phylum Nitrospirae (Nitrospira) and a genus of phylum Proteobacteria (Nitrosomonas), with the proportions of 12.23% and 2.31%, respectively. In the denitrifying reactor, Dechloromonas, Thauera, and Azospira were detected in the proportions 4.57%, 1.76%, and 1.03%, respectively. These proportions were far larger than those of other bacteria in this reactor. Meanwhile, the presence of iron autotrophic denitrifying bacteria increased the denitrification efficiency of the system.},
}

@article {pmid31087742,
year = {2019},
author = {Geiger, RA and Junghare, M and Mergelsberg, M and Ebenau-Jehle, C and Jesenofsky, VJ and Jehmlich, N and von Bergen, M and Schink, B and Boll, M},
title = {Enzymes involved in phthalate degradation in sulfate-reducing bacteria.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.14681},
pmid = {31087742},
issn = {1462-2920},
abstract = {The complete degradation of the xenobiotic and environmentally harmful phthalate esters is initiated by hydrolysis to alcohols and o-phthalate (phthalate) by esterases. While further catabolism of phthalate has been studied in aerobic and denitrifying microorganisms, the degradation in obligately anaerobic bacteria has remained obscure. Here we demonstrate a previously overseen growth of the δ-proteobacterium Desulfosarcina cetonica with phthalate/sulfate as only carbon and energy sources. Differential proteome and CoA ester pool analyses together with in vitro enzyme assays identified the genes, enzymes and metabolites involved in phthalate uptake and degradation in D. cetonica. Phthalate is initially activated to the short-lived phthaloyl-CoA by an ATP-dependent phthalate CoA ligase (PCL) followed by decarboxylation to the central intermediate benzoyl-CoA by an UbiD-like phthaloyl-CoA decarboxylase (PCD) containing a prenylated flavin cofactor. Genome/metagenome analyses predicted phthalate degradation capacity also in the sulfate-reducing Desulfobacula toluolica, strain NaphS2, and other δ-proteobacteria. Our results suggest that phthalate degradation proceeds in all anaerobic bacteria via the labile phthaloyl-CoA that is captured and decarboxylated by highly abundant PCDs. In contrast, two alternative strategies have been established for the formation of phthaloyl-CoA, the possibly most unstable CoA ester in biology. This article is protected by copyright. All rights reserved.},
}

@article {pmid31087616,
year = {2019},
author = {Martin-Cuadrado, AB and Senel, E and Martínez-García, M and Cifuentes, A and Santos, F and Almansa, C and Moreno-Paz, M and Blanco, Y and García-Villadangos, M and García Del Cura, MÁ and Sanz-Montero, ME and Rodríguez-Aranda, JP and Rosselló-Móra, R and Antón, J and Parro, V},
title = {Prokaryotic and viral community of the sulfate-rich crust from Peñahueca ephemeral lake, an astrobiology analogue.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.14680},
pmid = {31087616},
issn = {1462-2920},
abstract = {Peñahueca is an athalassohaline hypersaline inland ephemeral lake originated under semiarid conditions in the central Iberian Peninsula (Spain). Its chemical composition makes it extreme for microbial life as well as a terrestrial analogue of other planetary environments. To investigate the persistence of microbial life associated with sulfate-rich crusts, we applied cultivation-independent methods (optical and electron microscopy, 16S rRNA gene profiling and metagenomics) to describe the prokaryotic community and its associated viruses. The diversity for Bacteria was very low and was vastly dominated by endospore formers related to Pontibacillus marinus of the Firmicutes phylum. The archaeal assemblage was more diverse and included taxa related to those normally found in hypersaline environments. Several "metagenome assembled genomes" were recovered, corresponding to new species of Pontibacillus, several species from the Halobacteria and one new member of the Nanohaloarchaeota. The viral assemblage, although composed of the morphotypes typical of high salt systems, showed little similarity to previously isolated/reconstructed halophages. Several putative prophages of Pontibacillus and haloarchaeal hosts were identified. Remarkably, the Peñahueca sulfate-rich metagenome contained CRISPR-associated proteins and repetitions which were over 10-fold higher than in most hypersaline systems analyzed so far. This article is protected by copyright. All rights reserved.},
}

@article {pmid31087436,
year = {2019},
author = {Akiyama, K and Nishioka, K and Khan, KN and Tanaka, Y and Mori, T and Nakaya, T and Kitawaki, J},
title = {Molecular detection of microbial colonization in cervical mucus of women with and without endometriosis.},
journal = {American journal of reproductive immunology (New York, N.Y. : 1989)},
volume = {},
number = {},
pages = {e13147},
doi = {10.1111/aji.13147},
pmid = {31087436},
issn = {1600-0897},
abstract = {PROBLEM: Intrauterine microbial colonization and its association with the pathogenesis of endometriosis via an innate immune cascade have been reported. As a potential source of microbial transmission, information on microbial colonization in cervical mucus is unknown. We investigated pattern of microbiota in the cervical mucus collected from women with and without endometriosis using next-generation sequencing (NGS) technology.

METHOD OF STUDY: Cervical mucus samples were collected from women with (n = 30) and without (n = 39) endometriosis. The communities of microbiota in cervical mucus in the endometriosis group and the control group were examined by Gram staining and NGS targeting the V5-V6 region of 16S ribosomal RNA gene. Copy number of some target bacteria was detected by real-time PCR. Results We confirmed visual presence of bacteria in cervical mucus by Gram staining. NGS analysis showed that distribution of microbiota was similar in cervical mucus of women with and without endometriosis regardless of the phases of the menstrual cycle. In addition to predominant Lactobacilli spp. the populations of Corynebacterium, Enterobacteriaceae, Flavobacterium, Pseudomonas, and Streptococcus were increased in the endometriosis group. Of them, Enterobacteriaceae and Streptococcus were identified as the more significant candidates in the endometriosis group than in controls by real-time PCR (P < 0.05 for each). Conclusions Our NGS analysis of cervical mucus indicated that among a variable microbiota, two candidates (Enterobacteriaceae and Streptococcus) were more frequently detected in women with endometriosis. Further investigation is needed to elucidate a mechanistic link of these bacteria in the pathophysiology of endometriosis. This article is protected by copyright. All rights reserved.},
}

@article {pmid31086829,
year = {2019},
author = {Burgsdorf, I and Handley, KM and Bar-Shalom, R and Erwin, PM and Steindler, L},
title = {Life at Home and on the Roam: Genomic Adaptions Reflect the Dual Lifestyle of an Intracellular, Facultative Symbiont.},
journal = {mSystems},
volume = {4},
number = {4},
pages = {},
doi = {10.1128/mSystems.00057-19},
pmid = {31086829},
issn = {2379-5077},
abstract = {"Candidatus Synechococcus feldmannii" is a facultative intracellular symbiont of the Atlanto-Mediterranean sponge Petrosia ficiformis. Genomic information of sponge-associated cyanobacteria derives thus far from the obligate and extracellular symbiont "Candidatus Synechococcus spongiarum." Here we utilized a differential methylation-based approach for bacterial DNA enrichment combined with metagenomics to obtain the first draft genomes of "Ca. Synechococcus feldmannii." By comparative genomics, we revealed that some genomic features (e.g., iron transport mediated by siderophores, eukaryotic-like proteins, and defense mechanisms, like CRISPR-Cas [clustered regularly interspaced short palindromic repeats-associated proteins]) are unique to both symbiont types and absent or rare in the genomes of taxonomically related free-living cyanobacteria. These genomic features likely enable life under the conditions found inside the sponge host. Interestingly, there are many genomic features that are shared by "Ca. Synechococcus feldmannii" and free-living cyanobacteria, while they are absent in the obligate symbiont "Ca. Synechococcus spongiarum." These include genes related to cell surface structures, genetic regulation, and responses to environmental stress, as well as the composition of photosynthetic genes and DNA metabolism. We speculate that the presence of these genes confers on "Ca. Synechococcus feldmannii" its facultative nature (i.e., the ability to respond to a less stable environment when free-living). Our comparative analysis revealed that distinct genomic features depend on the nature of the symbiotic interaction: facultative and intracellular versus obligate and extracellular. IMPORTANCE Given the evolutionary position of sponges as one of the earliest phyla to depart from the metazoan stem lineage, studies on their distinct and exceptionally diverse microbial communities should yield a better understanding of the origin of animal-bacterium interactions. While genomes of several extracellular sponge symbionts have been published, the intracellular symbionts have, so far, been elusive. Here we compare the genomes of two unicellular cyanobacterial sponge symbionts that share an ancestor but followed different evolutionary paths-one became intracellular and the other extracellular. Counterintuitively, the intracellular cyanobacteria are facultative, while the extracellular ones are obligate. By sequencing the genomes of the intracellular cyanobacteria and comparing them to the genomes of the extracellular symbionts and related free-living cyanobacteria, we show how three different cyanobacterial lifestyles are reflected by adaptive genomic features.},
}

@article {pmid31086738,
year = {2019},
author = {Warwick-Dugdale, J and Solonenko, N and Moore, K and Chittick, L and Gregory, AC and Allen, MJ and Sullivan, MB and Temperton, B},
title = {Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e6800},
doi = {10.7717/peerj.6800},
pmid = {31086738},
issn = {2167-8359},
abstract = {Marine viruses impact global biogeochemical cycles via their influence on host community structure and function, yet our understanding of viral ecology is constrained by limitations in host culturing and a lack of reference genomes and 'universal' gene markers to facilitate community surveys. Short-read viral metagenomic studies have provided clues to viral function and first estimates of global viral gene abundance and distribution, but their assemblies are confounded by populations with high levels of strain evenness and nucleotide diversity (microdiversity), limiting assembly of some of the most abundant viruses on Earth. Such features also challenge assembly across genomic islands containing niche-defining genes that drive ecological speciation. These populations and features may be successfully captured by single-virus genomics and fosmid-based approaches, at least in abundant taxa, but at considerable cost and technical expertise. Here we established a low-cost, low-input, high throughput alternative sequencing and informatics workflow to improve viral metagenomic assemblies using short-read and long-read technology. The 'VirION' (Viral, long-read metagenomics via MinION sequencing) approach was first validated using mock communities where it was found to be as relatively quantitative as short-read methods and provided significant improvements in recovery of viral genomes. We then then applied VirION to the first metagenome from a natural viral community from the Western English Channel. In comparison to a short-read only approach, VirION: (i) increased number and completeness of assembled viral genomes; (ii) captured abundant, highly microdiverse virus populations, and (iii) captured more and longer genomic islands. Together, these findings suggest that VirION provides a high throughput and cost-effective alternative to fosmid and single-virus genomic approaches to more comprehensively explore viral communities in nature.},
}

@article {pmid31086312,
year = {2019},
author = {Wu, L and Ning, D and Zhang, B and Li, Y and Zhang, P and Shan, X and Zhang, Q and Brown, M and Li, Z and Van Nostrand, JD and Ling, F and Xiao, N and Zhang, Y and Vierheilig, J and Wells, GF and Yang, Y and Deng, Y and Tu, Q and Wang, A and , and Zhang, T and He, Z and Keller, J and Nielsen, PH and Alvarez, PJJ and Criddle, CS and Wagner, M and Tiedje, JM and He, Q and Curtis, TP and Stahl, DA and Alvarez-Cohen, L and Rittmann, BE and Wen, X and Zhou, J},
title = {Global diversity and biogeography of bacterial communities in wastewater treatment plants.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41564-019-0426-5},
pmid = {31086312},
issn = {2058-5276},
abstract = {Microorganisms in wastewater treatment plants (WWTPs) are essential for water purification to protect public and environmental health. However, the diversity of microorganisms and the factors that control it are poorly understood. Using a systematic global-sampling effort, we analysed the 16S ribosomal RNA gene sequences from ~1,200 activated sludge samples taken from 269 WWTPs in 23 countries on 6 continents. Our analyses revealed that the global activated sludge bacterial communities contain ~1 billion bacterial phylotypes with a Poisson lognormal diversity distribution. Despite this high diversity, activated sludge has a small, global core bacterial community (n = 28 operational taxonomic units) that is strongly linked to activated sludge performance. Meta-analyses with global datasets associate the activated sludge microbiomes most closely to freshwater populations. In contrast to macroorganism diversity, activated sludge bacterial communities show no latitudinal gradient. Furthermore, their spatial turnover is scale-dependent and appears to be largely driven by stochastic processes (dispersal and drift), although deterministic factors (temperature and organic input) are also important. Our findings enhance our mechanistic understanding of the global diversity and biogeography of activated sludge bacterial communities within a theoretical ecology framework and have important implications for microbial ecology and wastewater treatment processes.},
}

@article {pmid31086216,
year = {2019},
author = {Agamennone, V and Le, NG and van Straalen, NM and Brouwer, A and Roelofs, D},
title = {Antimicrobial activity and carbohydrate metabolism in the bacterial metagenome of the soil-living invertebrate Folsomia candida.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {7308},
doi = {10.1038/s41598-019-43828-w},
pmid = {31086216},
issn = {2045-2322},
abstract = {The microbiome associated with an animal's gut and other organs is considered an integral part of its ecological functions and adaptive capacity. To better understand how microbial communities influence activities and capacities of the host, we need more information on the functions that are encoded in a microbiome. Until now, the information about soil invertebrate microbiomes is mostly based on taxonomic characterization, achieved through culturing and amplicon sequencing. Using shotgun sequencing and various bioinformatics approaches we explored functions in the bacterial metagenome associated with the soil invertebrate Folsomia candida, an established model organism in soil ecology with a fully sequenced, high-quality genome assembly. Our metagenome analysis revealed a remarkable diversity of genes associated with antimicrobial activity and carbohydrate metabolism. The microbiome also contains several homologs to F. candida genes that were previously identified as candidates for horizontal gene transfer (HGT). We suggest that the carbohydrate- and antimicrobial-related functions encoded by Folsomia's metagenome play a role in the digestion of recalcitrant soil-born polysaccharides and the defense against pathogens, thereby significantly contributing to the adaptation of these animals to life in the soil. Furthermore, the transfer of genes from the microbiome may constitute an important source of new functions for the springtail.},
}

@article {pmid31086023,
year = {2019},
author = {McLaughlin, J and Watterson, S and Layton, AM and Bjourson, AJ and Barnard, E and McDowell, A},
title = {Propionibacterium acnes and Acne Vulgaris: New Insights from the Integration of Population Genetic, Multi-Omic, Biochemical and Host-Microbe Studies.},
journal = {Microorganisms},
volume = {7},
number = {5},
pages = {},
doi = {10.3390/microorganisms7050128},
pmid = {31086023},
issn = {2076-2607},
support = {025/s/16//British Skin Foundation/ ; },
abstract = {The anaerobic bacterium Propionibacterium acnes is believed to play an important role in the pathophysiology of the common skin disease acne vulgaris. Over the last 10 years our understanding of the taxonomic and intraspecies diversity of this bacterium has increased tremendously, and with it the realisation that particular strains are associated with skin health while others appear related to disease. This extensive review will cover our current knowledge regarding the association of P. acnes phylogroups, clonal complexes and sequence types with acne vulgaris based on multilocus sequence typing of isolates, and direct ribotyping of the P. acnes strain population in skin microbiome samples based on 16S rDNA metagenomic data. We will also consider how multi-omic and biochemical studies have facilitated our understanding of P. acnes pathogenicity and interactions with the host, thus providing insights into why certain lineages appear to have a heightened capacity to contribute to acne vulgaris development, while others are positively associated with skin health. We conclude with a discussion of new therapeutic strategies that are currently under investigation for acne vulgaris, including vaccination, and consider the potential of these treatments to also perturb beneficial lineages of P. acnes on the skin.},
}

@article {pmid31085071,
year = {2019},
author = {Jansson, JK and Hofmockel, KS},
title = {Corrigendum to "The soil microbiome - from metagenomics to metaphenomics" [Curr Opin Micrbiol 43 (June 2018) 162-168].},
journal = {Current opinion in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.mib.2019.04.004},
pmid = {31085071},
issn = {1879-0364},
}

@article {pmid31085022,
year = {2019},
author = {Tsementzi, D and Rodriguez-R, LM and Ruiz-Perez, CA and Meziti, A and Hatt, JK and Konstantinidis, K},
title = {Ecogenomic characterization of widespread, closely-related SAR11 clades of the freshwater genus "Candidatus Fonsibacter" and proposal of Ca. Fonsibacter lacus sp. nov.},
journal = {Systematic and applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.syapm.2019.03.007},
pmid = {31085022},
issn = {1618-0984},
abstract = {The ubiquitous alpha-proteobacteria of the order "Candidatus Pelagibacterales" (SAR11) are highly abundant in aquatic environments, and among them, members of the monophyletic lineage LD12 (also known as SAR11 clade IIIb) are specifically found in lacustrine ecosystems. Clade IIIb bacteria are some of the most prominent members of freshwater environments, but little is known about their biology due to the lack of genome representatives. Only recently, the first non-marine isolate was cultured and described as "Candidatus Fonsibacter ubiquis". Here, we expand the collection of freshwater IIIb representatives and describe a new IIIb species of the genus "Ca. Fonsibacter". Specifically, we assembled a collection of 67 freshwater metagenomic datasets from the interconnected lakes of the Chattahoochee River basin (GA, USA) and obtained nearly complete metagenome-assembled genomes (MAGs) representing 5 distinct IIIb subclades, roughly equivalent to species based on genomic standards, including the previously described "Ca. F. ubiquis". Genomic comparisons between members of the IIIb species revealed high similarity in gene content. However, when comparing their abundance profiles in the Chattahoochee basin and various aquatic environments, differences in temporal and spatial distributions among the distinct species were observed implying niche differentiation might be underlying the coexistence of the highly functionally similar representatives. The name Ca. Fonsibacter lacus sp. nov. is proposed for the most abundant and widespread species in the Chattahoochee River basin and various freshwater ecosystems.},
}

@article {pmid31081896,
year = {2019},
author = {Rastelli, M and Cani, PD and Knauf, C},
title = {The gut microbiome influences host endocrine functions.},
journal = {Endocrine reviews},
volume = {},
number = {},
pages = {},
doi = {10.1210/er.2018-00280},
pmid = {31081896},
issn = {1945-7189},
abstract = {The gut microbiome is now considered as an organ contributing to the regulation of host metabolism. Since the finding of the existence of a relationship between the gut microbiome and specific diseases, numerous studies have also deciphered molecular mechanisms explaining how gut bacteria dialogue with host cells and eventually shape metabolism. Both metagenomic and metabolomic analyses have contributed to the discovery of bacterial-derived metabolites acting on host cells. In this review, we examine the molecular mechanisms by which bacterial metabolites are acting as paracrine or endocrine factors thereby regulating host metabolism. We highlight the impact of specific short chain fatty acids on the secretion of gut peptides (i.e., GLP-1, PYY) as well as other metabolites produced from different amino acids and regulating inflammation, glucose metabolism or energy homeostasis. We also discuss the role of gut microbes on the regulation of bioactive lipids that belong to the endocannabinoid system as well as specific neurotransmitters (e.g., GABA, serotonin, NO). Finally, we review the role of specific bacterial components (i.e., ClpB, Amuc_1100) also acting as endocrine factors and eventually controlling host metabolism. In conclusion, this review summarizes recent state-of-the art aiming at providing evidence that the gut microbiome influences host endocrine functions via several bacterial-derived metabolites.},
}

@article {pmid31081685,
year = {2019},
author = {Thombre, RS and Shivakarthik, E and Sivaraman, B and Vaishampayan, PA and Seuylemezian, A and Meka, JK and Vijayan, S and Kulkarni, PP and Pataskar, T and Patil, BS},
title = {Survival of Extremotolerant Bacteria from the Mukundpura Meteorite Impact Crater.},
journal = {Astrobiology},
volume = {},
number = {},
pages = {},
doi = {10.1089/ast.2018.1928},
pmid = {31081685},
issn = {1557-8070},
abstract = {Carbonaceous meteorites provide clues with regard to prebiotic chemistry and the origin of life. Geological Survey of India recorded a carbonaceous chondrite meteorite fall in Mukundpura, India, on June 6, 2017. We conducted a study to investigate the microbial community that survived the meteorite impact. 16S rRNA metagenomic sequencing indicates the presence of Actinobacteria, Proteobacteria, and Acidobacteria in meteorite impact soil. Comparative phylogenetic analysis revealed an intriguing abundance of class Bacilli in the impact soil. Bacillus thermocopriae IR-1, a moderately thermotolerant organism, was isolated from a rock, impacted by the Mukundpura meteorite. We investigated the resilience of B. thermocopriae IR-1 to environmental stresses and impact shock in a Reddy shock tube. B. thermocopriae IR-1 survived (28.82% survival) the effect of shock waves at a peak shock pressure of 300 kPa, temperature 400 K, and Mach number of 1.47. This investigation presents the first report on the effect of impact shock on B. thermocopriae IR-1. The study is also the first report on studying the microbial diversity and isolation of bacteria from impact crater soil immediately after meteorite impact event.},
}

@article {pmid31081473,
year = {2019},
author = {Suryawanshi, PR and Badapanda, C and Singh, KM and Rathore, A},
title = {Exploration of the rumen microbial diversity and carbohydrate active enzyme profile of black Bengal goat using metagenomic approach.},
journal = {Animal biotechnology},
volume = {},
number = {},
pages = {1-14},
doi = {10.1080/10495398.2019.1609489},
pmid = {31081473},
issn = {1532-2378},
abstract = {Black Bengal goats possess a rich source of rumen microbiota that helps them to adapt for the better utilization of plant biomaterial into energy and nutrients, a task largely performed by enzymes encoded by the rumen microbiota. Therefore the study was designed in order to explore the taxonomic profile of rumen microbial communities and potential biomass degradation enzymes present in the rumen of back Bengal goat using Illumina Nextseq-500 platform. A total of 83.18 million high-quality reads were generated and bioinformatics analysis was performed using various tools and subsequently, the predicted ORFs along with the rRNA containing contigs were then uploaded to MG-RAST to analyze taxonomic and functional profiling. The results highlighted that Bacteriodetes (41.38-59.74%) were the most abundant phyla followed by Firmicutes (30.59-39.96%), Proteobacteria (5.07-7.61%), Euryarcheaota (0.71-7.41%), Actinobacteria (2.05-2.75%). Genes that encode glycoside hydrolases (GHs) had the highest number of CAZymes, and accounted for (39.73-37.88%) of all CAZymes in goat rumen. The GT families were the second-most abundant in CAZymes (23.73-23.11%) and followed by Carbohydrate Binding module Domain (17.65-15.61%), Carbohydrate Esterase (12.90-11.95%). This study indicated that goat rumen had complex functional microorganisms produce numerous CAZymes, and that can be further effectively utilised for applied ruminant research and industry based applications.},
}

@article {pmid31080075,
year = {2019},
author = {Macdonald, SS and Armstrong, Z and Morgan-Lang, C and Osowiecka, M and Robinson, K and Hallam, SJ and Withers, SG},
title = {Development and Application of a High-Throughput Functional Metagenomic Screen for Glycoside Phosphorylases.},
journal = {Cell chemical biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chembiol.2019.03.017},
pmid = {31080075},
issn = {2451-9448},
abstract = {Glycoside phosphorylases (GPs) catalyze the reversible phosphorolysis of glycosidic bonds, releasing sugar 1-phosphates. To identify a greater range of these under-appreciated enzymes, we have developed a high-throughput functional screening method based on molybdenum blue formation. In a proof-of-principle screen focused on cellulose-degrading GPs we interrogated ∼23,000 large insert (fosmid) clones sourced from microbial communities inhabiting two separate environments and identified seven novel GPs from carbohydrate active enzyme family GH94 and one from GH149. Characterization identified cellobiose phosphorylases, cellodextrin phosphorylases, laminaribiose phosphorylases, and a β-1,3-glucan phosphorylase. To demonstrate the versatility of the screening method, varying substrate combinations were used to identify GP activity from families GH13, GH65, GH112, and GH130 in addition to GH94 and GH149. These pilot screen and substrate versatility results provide a screening paradigm platform for recovering diverse GPs from uncultivated microbial communities acting on different substrates with considerable potential to unravel previously unknown degradative pathways within microbiomes.},
}

@article {pmid30535578,
year = {2019},
author = {Zhang, F and Zheng, W and Xue, Y and Yao, W},
title = {Suhuai suckling piglet hindgut microbiome-metabolome responses to different dietary copper levels.},
journal = {Applied microbiology and biotechnology},
volume = {103},
number = {2},
pages = {853-868},
doi = {10.1007/s00253-018-9533-0},
pmid = {30535578},
issn = {1432-0614},
support = {JATS[2018]287//The earmarked fund for Jiangsu Agricultural Industry Technology System/ ; 31372321//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Animals, Newborn ; Blood Chemical Analysis ; Copper/*administration & dosage ; Diet/*methods ; Feces/chemistry ; Gas Chromatography-Mass Spectrometry ; Gastrointestinal Microbiome/*drug effects ; High-Throughput Nucleotide Sequencing ; Metabolome/*drug effects ; Metabolomics ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Swine ; Trace Elements/*administration & dosage ; },
abstract = {Unabsorbed copper accumulates in the hindgut of pigs that consume high levels of dietary copper, which enhances the coselection of antibiotic-resistant bacteria and is considered detrimental to the environment and to porcine health. In our study, a combination of 16S rRNA pyrosequencing and nontargeted metabolomics was used to investigate the microbiome-metabolome responses to dietary copper levels in the hindgut of suckling piglets. The results showed that the dietary copper level affected the abundance of several Clostridia genera and that the relative abundance of butyrate-producing bacteria, such as Coprococcus, Roseburia, and Acidaminococcus, was reduced in the 300 mg kg-1 (high) Cu group. Metabolomic analysis revealed that dietary copper levels affected protein and carbohydrate metabolites, protein biosynthesis, the urea cycle, galactose metabolism, gluconeogenesis, and amino acid metabolism (including the metabolism of arginine, proline, β-alanine, phenylalanine, tyrosine, and methionine). Furthermore, Pearson's correlation analysis showed that the abundance levels of Coprococcus (family Lachnospiraceae) and operational taxonomic unit (OTU) 18 (family Ruminococcaceae) were positively correlated with energy metabolism pathways (gluconeogenesis, glycolysis, and the pentose phosphate pathway). The abundance of Streptococcus was negatively correlated with amino acid metabolism pathways (protein biosynthesis, glycine, serine, threonine, methionine, phenylalanine, and tyrosine metabolism), and OTU583 and OTU1067 (family Rikenellaceae) were positively correlated with amino acid metabolism pathways. These results suggest that the copper levels consumed by LC (low-copper group) versus HC (high-copper group) animals alter the composition of the gut microbiota and modulate microbial metabolic pathways, which may further affect the health of suckling piglets.},
}

Animals
Animals, Newborn
Blood Chemical Analysis
Copper/*administration & dosage
Diet/*methods
Feces/chemistry
Gas Chromatography-Mass Spectrometry
Gastrointestinal Microbiome/*drug effects
High-Throughput Nucleotide Sequencing
Metabolome/*drug effects
Metabolomics
Metagenomics
RNA, Ribosomal, 16S/genetics
Swine
Trace Elements/*administration & dosage

@article {pmid30474727,
year = {2019},
author = {Meng, H and Zhou, Z and Wu, R and Wang, Y and Gu, JD},
title = {Diazotrophic microbial community and abundance in acidic subtropical natural and re-vegetated forest soils revealed by high-throughput sequencing of nifH gene.},
journal = {Applied microbiology and biotechnology},
volume = {103},
number = {2},
pages = {995-1005},
doi = {10.1007/s00253-018-9466-7},
pmid = {30474727},
issn = {1432-0614},
support = {31470562//National Natural Science Foundation of China/ ; 701913//Hong Kong RGC GRF grant/ ; },
mesh = {Acids/analysis ; Archaea/*classification/enzymology/genetics/metabolism ; Bacteria/*classification/enzymology/genetics/metabolism ; Chemical Phenomena ; Forests ; *Genetic Variation ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Microbiota ; *Nitrogen Fixation ; Oxidoreductases/*genetics ; Seasons ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {Biological nitrogen fixation (BNF) is an important natural biochemical process converting the inert dinitrogen gas (N2) in the atmosphere to ammonia (NH3) in the N cycle. In this study, the nifH gene was chosen to detect the diazotrophic microorganisms with high-throughput sequencing from five acidic forest soils, including three natural forests and two re-vegetated forests. Soil samples were taken in two seasons (summer and winter) at two depth layers (surface and lower depths). A dataset of 179,600 reads obtained from 20 samples were analyzed to provide the microbial community structure, diversity, abundance, and relationship with physiochemical parameters. Both archaea and bacteria were detected in these samples and diazotrophic bacteria were the dominant members contributing to the biological dinitrogen fixation in the acidic forest soils. Cyanobacteria, Firmicutes, Proteobacteria, Spirocheates, and Verrucomicrobia were observed, especially the Proteobacteria as the most abundant phylum. The core genera were Bradyrhizobium and Methylobacterium from α-Proteobacteia, and Desulfovibrio from δ-Proteobacteia in the phylum of Proteobacteia of these samples. The diversity indices and the gene abundances of all samples were higher in the surface layer than the lower layer. Diversity was apparently higher in re-vegetated forests than the natural forests. Significant positive correlation to the organic matter and nitrogen-related parameters was observed, but there was no significant seasonal variation on the community structure and diversity in these samples between the summer and winter. The application of high-throughput sequencing method provides a better understanding and more comprehensive information of diazotrophs in acidic forest soils than conventional and PCR-based ones.},
}

Acids/analysis
Archaea/*classification/enzymology/genetics/metabolism
Bacteria/*classification/enzymology/genetics/metabolism
Chemical Phenomena
Forests
*Genetic Variation
High-Throughput Nucleotide Sequencing
Metagenomics
*Microbiota
*Nitrogen Fixation
Oxidoreductases/*genetics
Seasons
Soil/chemistry
*Soil Microbiology

@article {pmid30377368,
year = {2018},
author = {McDonald, D and Vázquez-Baeza, Y and Koslicki, D and McClelland, J and Reeve, N and Xu, Z and Gonzalez, A and Knight, R},
title = {Striped UniFrac: enabling microbiome analysis at unprecedented scale.},
journal = {Nature methods},
volume = {15},
number = {11},
pages = {847-848},
doi = {10.1038/s41592-018-0187-8},
pmid = {30377368},
issn = {1548-7105},
mesh = {*Algorithms ; Bacteria/*classification/*genetics ; Computational Biology/*methods ; Computer Simulation ; Humans ; *Metagenome ; *Microbiota ; Models, Statistical ; Phylogeny ; },
}

*Algorithms
Bacteria/*classification/*genetics
Computational Biology/*methods
Computer Simulation
Humans
*Metagenome
*Microbiota
Models, Statistical
Phylogeny

@article {pmid30275573,
year = {2018},
author = {Gonzalez, A and Navas-Molina, JA and Kosciolek, T and McDonald, D and Vázquez-Baeza, Y and Ackermann, G and DeReus, J and Janssen, S and Swafford, AD and Orchanian, SB and Sanders, JG and Shorenstein, J and Holste, H and Petrus, S and Robbins-Pianka, A and Brislawn, CJ and Wang, M and Rideout, JR and Bolyen, E and Dillon, M and Caporaso, JG and Dorrestein, PC and Knight, R},
title = {Qiita: rapid, web-enabled microbiome meta-analysis.},
journal = {Nature methods},
volume = {15},
number = {10},
pages = {796-798},
pmid = {30275573},
issn = {1548-7105},
support = {R01 HG004872/HG/NHGRI NIH HHS/United States ; R01 HL140976/HL/NHLBI NIH HHS/United States ; R01 MD011389/MD/NIMHD NIH HHS/United States ; },
mesh = {Computational Biology/*methods ; Humans ; *Internet ; *Metagenomics ; *Microbiota ; *Software ; User-Computer Interface ; },
abstract = {Multi-omic insights into microbiome function and composition typically advance one study at a time. However, in order for relationships across studies to be fully understood, data must be aggregated into meta-analyses. This makes it possible to generate new hypotheses by finding features that are reproducible across biospecimens and data layers. Qiita dramatically accelerates such integration tasks in a web-based microbiome-comparison platform, which we demonstrate with Human Microbiome Project and Integrative Human Microbiome Project (iHMP) data.},
}

Computational Biology/*methods
Humans
*Internet
*Metagenomics
*Microbiota
*Software
User-Computer Interface

@article {pmid28883464,
year = {2017},
author = {Pettersson, JH and Shi, M and Bohlin, J and Eldholm, V and Brynildsrud, OB and Paulsen, KM and Andreassen, Å and Holmes, EC},
title = {Characterizing the virome of Ixodes ricinus ticks from northern Europe.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {10870},
pmid = {28883464},
issn = {2045-2322},
mesh = {Animals ; Computational Biology/methods ; Disease Vectors ; Europe ; Evolution, Molecular ; Humans ; Ixodes/*virology ; *Metagenome ; *Metagenomics/methods ; Molecular Sequence Annotation ; Phylogeny ; Viruses/*classification/*genetics ; },
abstract = {RNA viruses are abundant infectious agents and present in all domains of life. Arthropods, including ticks, are well known as vectors of many viruses of concern for human and animal health. Despite their obvious importance, the extent and structure of viral diversity in ticks is still poorly understood, particularly in Europe. Using a bulk RNA-sequencing approach that captures the complete transcriptome, we analysed the virome of the most common tick in Europe - Ixodes ricinus. In total, RNA sequencing was performed on six libraries consisting of 33 I. ricinus nymphs and adults sampled in Norway. Despite the small number of animals surveyed, our virus identification pipeline revealed nine diverse and novel viral species, phylogenetically positioned within four different viral groups - bunyaviruses, luteoviruses, mononegavirales and partitiviruses - and sometimes characterized by extensive genetic diversity including a potentially novel genus of bunyaviruses. This work sheds new light on the virus diversity in I. ricinus, expands our knowledge of potential host/vector-associations and tick-transmitted viruses within several viral groups, and pushes the latitudinal limit where it is likely to find tick-associated viruses. Notably, our phylogenetic analysis revealed the presence of tick-specific virus clades that span multiple continents, highlighting the role of ticks as important virus reservoirs.},
}

Animals
Computational Biology/methods
Disease Vectors
Europe
Evolution, Molecular
Humans
Ixodes/*virology
*Metagenome
*Metagenomics/methods
Molecular Sequence Annotation
Phylogeny
Viruses/*classification/*genetics

@article {pmid31079214,
year = {2019},
author = {Tamim, S and Matthijnssens, J and Heylen, E and Zeller, M and Van Ranst, M and Salman, M and Hasan, F},
title = {Evidence of zoonotic transmission of VP6 and NSP4 genes into human species A rotaviruses isolated in Pakistan in 2010.},
journal = {Archives of virology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00705-019-04271-4},
pmid = {31079214},
issn = {1432-8798},
abstract = {Introduction of animal group A rotavirus (RVA) gene segments into the human RVA population is a major factor shaping the genetic landscape of human RVA strains. The VP6 and NSP4 genes of 74 G/P-genotyped RVA isolates collected in Rawalpindi during 2010 were analyzed, revealing the presence of VP6 genotypes I1 (60.8%) and I2 (39.2%) and NSP4 genotypes E1 (60.8%), E2 (28.3%) and E-untypable (10.8%) among the circulating human RVA strains. The typical human RVA combinations I1E1 and I2E2 were found in 59.4% and 24.3% of the cases, respectively, whereas 5.4% of the RVA strains were reassortants, i.e., either I1E2 or I2E1. The phylogeny of the NSP4 gene showed that one G2P[4] and two G1P[6] RVA strains clustered with porcine E1 RVA strains or RVA strains that were considered to be (partially) of porcine origin. In addition, the NSP4 gene segment of the unusual human G6P[1] RVA strains clustered closely with bovine E2 RVA strains, further strengthening the hypothesis of an interspecies transmission event. The study further demonstrates the role of genomic re-assortment and the involvement of interspecies transmission in the evolution of human RVA strains. The VP6 and NSP4 nucleotide sequences analyzed in the study received the GenBank accession numbers KC846908- KC846971 and KC846972-KC847037, respectively.},
}

@article {pmid31078243,
year = {2019},
author = {Koliani-Pace, JL and Siegel, CA},
title = {Prognosticating the Course of Inflammatory Bowel Disease.},
journal = {Gastrointestinal endoscopy clinics of North America},
volume = {29},
number = {3},
pages = {395-404},
doi = {10.1016/j.giec.2019.02.003},
pmid = {31078243},
issn = {1558-1950},
abstract = {Both Crohn's disease and ulcerative colitis are inflammatory bowel diseases (IBD) that can lead to progressive irreversible bowel damage. Selecting the most appropriate therapy for patients is a challenge because not all patients diagnosed with IBD have complications, and the amount of time to develop a complication is different for individuals. Models using patient characteristics, genetics, and immune responses help identify those patients who require early aggressive therapy with a goal to modify their disease course. Future research will help identify the role that the microbiome, metagenomics, metaproteomics, and microRNAs play in a patient prognosis.},
}

@article {pmid31077935,
year = {2019},
author = {Trotter, AJ and Aydin, A and Strinden, MJ and O'Grady, J},
title = {Recent and emerging technologies for the rapid diagnosis of infection and antimicrobial resistance.},
journal = {Current opinion in microbiology},
volume = {51},
number = {},
pages = {39-45},
doi = {10.1016/j.mib.2019.03.001},
pmid = {31077935},
issn = {1879-0364},
abstract = {The rise in antimicrobial resistance (AMR) is predicted to cause 10 million deaths per year by 2050 unless steps are taken to prevent this looming crisis. Microbiological culture is the gold standard for the diagnosis of bacterial/fungal pathogens and antimicrobial resistance and takes 48 hours or longer. Hence, antibiotic prescriptions are rarely based on a definitive diagnosis and patients often receive inappropriate treatment. Rapid diagnostic tools are urgently required to guide appropriate antimicrobial therapy, thereby improving patient outcomes and slowing AMR development. We discuss new technologies for rapid infection diagnosis including: sample-in-answer-out PCR-based tests, BioFire FilmArray and Curetis Unyvero; rapid susceptibility tests, Accelerate Pheno and microfluidic tests; and sequencing-based approaches, focusing on targeted and clinical metagenomic nanopore sequencing.},
}

@article {pmid31076501,
year = {2019},
author = {Toivonen, L and Hasegawa, K and Waris, M and Ajami, NJ and Petrosino, JF and Camargo, CA and Peltola, V},
title = {Early nasal microbiota and acute respiratory infections during the first years of life.},
journal = {Thorax},
volume = {},
number = {},
pages = {},
doi = {10.1136/thoraxjnl-2018-212629},
pmid = {31076501},
issn = {1468-3296},
abstract = {BACKGROUND: Emerging evidence shows that airway microbiota may modulate local immune responses, thereby contributing to the susceptibility and severity of acute respiratory infections (ARIs). However, there are little data on the longitudinal relationships between airway microbiota and susceptibility to ARIs in children.

OBJECTIVE: We aimed to investigate the association of early nasal microbiota and the subsequent risk of ARIs during the first years of life.

METHODS: In this prospective population-based birth-cohort study in Finland, we followed 839 healthy infants for ARIs from birth to age 24 months. Nasal microbiota was tested using 16S rRNA gene sequencing at age 2 months. We applied an unsupervised clustering approach to identify early nasal microbiota profiles, and examined the association of profiles with the rate of ARIs during age 2-24 months.

RESULTS: We identified five nasal microbiota profiles dominated by Moraxella, Streptococcus, Dolosigranulum, Staphylococcus and Corynebacteriaceae, respectively. Incidence rate of ARIs was highest in children with an early Moraxella-dominant profile and lowest in those with a Corynebacteriaceae-dominant profile (738 vs 552/100 children years; unadjusted incidence rate ratio (IRR), 1.34; 95% CI 1.16 to 1.54; p < 0.001). After adjusting for nine potential confounders, the Moraxella-dominant profile-ARI association persisted (adjusted IRR (aIRR), 1.19; 95% CI 1.04 to 1.37; p = 0.01). Similarly, the incidence rate of lower respiratory tract infections (a subset of all ARIs) was significantly higher in children with an early Moraxella-dominant profile (aIRR, 2.79; 95% CI 1.04 to 8.09; p = 0.04).

CONCLUSION: Moraxella-dominant nasal microbiota profile in early infancy was associated with an increased rate of ARIs during the first 2 years of life.},
}

@article {pmid31075586,
year = {2019},
author = {Zhang, L and Zhang, Y and Gamal El-Din, M},
title = {Integrated mild ozonation with biofiltration can effectively enhance the removal of naphthenic acids from hydrocarbon-contaminated water.},
journal = {The Science of the total environment},
volume = {678},
number = {},
pages = {197-206},
doi = {10.1016/j.scitotenv.2019.04.302},
pmid = {31075586},
issn = {1879-1026},
abstract = {An innovative biofiltration-ozonation-biofiltration process was established and applied for the treatment of oil sands process water (OSPW). With an equivalent hydraulic retention time (HRT) of 8 h, the biofiltration pretreatment removed 24.4% of classical naphthenic acids (NAs) and 3.3% of oxidized NAs from raw OSPW with removal rate of 0.4 mg/L/h and 0.1 mg/L. Oxidized NAs showed higher resistance to the biofiltration process than classical NAs. The mild ozonation process (with utilized ozone dose of 30 mg/L) removed 84.8% of classical NAs and 11.5% of oxidized NAs from the biofiltrated OSPW with a degradation efficiency of 0.3 mg classical NAs/mg O3 and 0.1 mg oxidized NAs/mg O3. However, by using the same utilized ozone dose, the degradation of classical NAs and oxidized NAs from raw OSPW was 32.1% and 3.9% with ozonation efficiency of 0.1 mg classical NAs/mg O3 and 0.0 mg oxidized NAs/mg O3, respectively. Compared with the biofiltration pretreatment, the post biofiltration process (with HRT of 8 h) showed higher degradation effect on oxidized NAs with removal ratio of 22.9% and removal rate of 0.4 mg/L/h, but showed lower degradation effect on classical NAs with removal ratio of 6.7% and removal rate of 0.0 mg/L/h. After biofiltration-ozonation-biofiltration treatment, the microbial community structure in the biofilter was investigated by next generation sequencing. Proteobacteria and Rhodococcus were dominant bacterial phyla and genus in the biofilter, the abundance of which were 47.21% and 9.50% which were different from those in raw OSPW (62.88% and 0.72%). The change of microbial community structure could be resulted from the interaction between microbial community and the circulating OSPW. The ozonation integrated biodegradation process removed 89.3% and 34.0% of classical and oxidized NAs from OSPW which shows high potential to be applied by the oil and gas industry.},
}

@article {pmid31073898,
year = {2019},
author = {Zhao, H and Yan, B and Mo, S and Nie, S and Li, Q and Ou, Q and Wu, B and Jiang, G and Tang, J and Li, N and Jiang, C},
title = {Carbohydrate metabolism genes dominant in a subtropical marine mangrove ecosystem revealed by metagenomics analysis.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12275-019-8679-5},
pmid = {31073898},
issn = {1976-3794},
abstract = {Mangrove sediment microorganisms play a vital role in the energy transformation and element cycling in marine wetland ecosystems. Using metagenomics analysis strategy, we compared the taxonomic structure and gene profile of the mangrove and non-mangrove sediment samples at the subtropical estuary in Beibu Gulf, South China Sea. Proteobacteria, Bacteroidetes, and Firmicutes were the most abundant bacterial phyla. Archaeal family Methanosarcinaceae and bacterial genera Vibrio and Dehalococcoides were significantly higher in the mangrove sediments than in the nonmangrove sediments. Functional analysis showed that "Carbohydrate metabolism" was the most abundant metabolic category. The feature of carbohydrate-active enzymes (CZs) was analyzed using the Carbohydrate-Active EnZymes Database. The significant differences of CZs between mangrove and non-mangrove sediments, were attributed to the amounts of polyphenol oxidase (EC 1.10.3.-), hexosyltransferase (EC 2.4.1.-), and β-N-acetylhexosaminidase (EC 3.2.1.52), which were higher in the mangrove sediment samples. Principal component analysis indicated that the microbial community and gene profile between mangrove and non-mangrove sediments were distinct. Redundancy analysis showed that total organic carbon is a significant factor that affects the microbial community and gene distribution. The results indicated that the mangrove ecosystem with massive amounts of organic carbon may promote the richness of carbohydrate metabolism genes and enhance the degradation and utilization of carbohydrates in the mangrove sediments.},
}

@article {pmid31073691,
year = {2019},
author = {Bersanelli, M and Santoni, M and Ticinesi, A and Buti, S},
title = {The Urinary Microbiome and Anticancer Immunotherapy: The Potentially Hidden Role of Unculturable Microbes.},
journal = {Targeted oncology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11523-019-00643-7},
pmid = {31073691},
issn = {1776-260X},
abstract = {Several urinary disorders, including overactive bladder, urinary incontinence, and interstitial cystitis, are often characterized by negative urine cultures. The application of metagenomics (i.e., 16S rRNA microbial profiling or whole-genome shotgun sequencing) to urine samples has enabled the identification of previously undetected bacteria, contributing to the discovery and characterization of the urinary microbiome. The most frequent species isolated are Lactobacillus (15%), Corynebacterium (14.2%), Streptococcus (11.9%), Actinomyces (6.9%), and Staphylococcus (6.9%). Although several studies are emerging in this context, the role of urinary microbiota in the pathogenesis of infections and in tumor carcinogenesis remains unclear. Furthermore, data on the activity of gut microbiota in modulating sensitivity to immune checkpoint inhibitors in advanced cancer patients suggest that the influence of urinary microbiota on tumor response to anticancer therapy should also be investigated. Moreover, its possible relationship with tumor mutational burden, which is in turn correlated with response to immunotherapy, should be the focus of future studies. Of note, the effect of antibiotics on this complex scenario seems to deserve careful consideration.},
}

@article {pmid31071993,
year = {2019},
author = {Ziko, L and Adel, M and Malash, MN and Siam, R},
title = {Insights into Red Sea Brine Pool Specialized Metabolism Gene Clusters Encoding Potential Metabolites for Biotechnological Applications and Extremophile Survival.},
journal = {Marine drugs},
volume = {17},
number = {5},
pages = {},
doi = {10.3390/md17050273},
pmid = {31071993},
issn = {1660-3397},
support = {NA//AUC Faculty Support Grant to RS/ ; },
abstract = {The recent rise in antibiotic and chemotherapeutic resistance necessitates the search for novel drugs. Potential therapeutics can be produced by specialized metabolism gene clusters (SMGCs). We mined for SMGCs in metagenomic samples from Atlantis II Deep, Discovery Deep and Kebrit Deep Red Sea brine pools. Shotgun sequence assembly and secondary metabolite analysis shell (antiSMASH) screening unraveled 2751 Red Sea brine SMGCs, pertaining to 28 classes. Predicted categorization of the SMGC products included those (1) commonly abundant in microbes (saccharides, fatty acids, aryl polyenes, acyl-homoserine lactones), (2) with antibacterial and/or anticancer effects (terpenes, ribosomal peptides, non-ribosomal peptides, polyketides, phosphonates) and (3) with miscellaneous roles conferring adaptation to the environment/special structure/unknown function (polyunsaturated fatty acids, ectoine, ladderane, others). Saccharide (80.49%) and putative (7.46%) SMGCs were the most abundant. Selected Red Sea brine pool sites had distinct SMGC profiles, e.g., for bacteriocins and ectoine. Top promising candidates, SMs with pharmaceutical applications, were addressed. Prolific SM-producing phyla (Proteobacteria, Actinobacteria, Cyanobacteria), were ubiquitously detected. Sites harboring the largest numbers of bacterial and archaeal phyla, had the most SMGCs. Our results suggest that the Red Sea brine niche constitutes a rich biological mine, with the predicted SMs aiding extremophile survival and adaptation.},
}

@article {pmid31071918,
year = {2019},
author = {Dai, L and Zhang, G and Yu, Z and Ding, H and Xu, Y and Zhang, Z},
title = {Effect of Drought Stress and Developmental Stages on Microbial Community Structure and Diversity in Peanut Rhizosphere Soil.},
journal = {International journal of molecular sciences},
volume = {20},
number = {9},
pages = {},
doi = {10.3390/ijms20092265},
pmid = {31071918},
issn = {1422-0067},
support = {2018YFD0201007//National Key Research and Development Program of China/ ; SDAIT-04-06//Modern Agricultural Industry Technical System of Shandong Province/ ; },
abstract = {BACKGROUND: Peanut (Arachis hypogaea L.), an important oilseed and food legume, is widely cultivated in the semi-arid tropics. Drought is the major stress in this region which limits productivity. Microbial communities in the rhizosphere are of special importance to stress tolerance. However, relatively little is known about the relationship between drought and microbial communities in peanuts.

METHOD: In this study, deep sequencing of the V3-V4 region of the 16S rRNA gene was performed to characterize the microbial community structure of drought-treated and untreated peanuts.

RESULTS: Taxonomic analysis showed that Actinobacteria, Proteobacteria, Saccharibacteria, Chloroflexi, Acidobacteria and Cyanobacteria were the dominant phyla in the peanut rhizosphere. Comparisons of microbial community structure of peanuts revealed that the relative abundance of Actinobacteria and Acidobacteria dramatically increased in the seedling and podding stages in drought-treated soil, while that of Cyanobacteria and Gemmatimonadetes increased in the flowering stage in drought-treated rhizospheres. Metagenomic profiling indicated that sequences related to metabolism, signaling transduction, defense mechanism and basic vital activity were enriched in the drought-treated rhizosphere, which may have implications for plant survival and drought tolerance.

CONCLUSION: This microbial communities study will form the foundation for future improvement of drought tolerance of peanuts via modification of the soil microbes.},
}

@article {pmid31069047,
year = {2017},
author = {Agafonov, A and Mattila, K and Tuan, CD and Tiede, L and Raknes, IA and Bongo, LA},
title = {META-pipe cloud setup and execution.},
journal = {F1000Research},
volume = {6},
number = {},
pages = {},
doi = {10.12688/f1000research.13204.1},
pmid = {31069047},
issn = {2046-1402},
abstract = {META-pipe is a complete service for the analysis of marine metagenomic data. It provides assembly of high-throughput sequence data, functional annotation of predicted genes, and taxonomic profiling. The functional annotation is computationally demanding and is therefore currently run on a high-performance computing cluster in Norway. However, additional compute resources are necessary to open the service to all ELIXIR users. We describe our approach for setting up and executing the functional analysis of META-pipe on additional academic and commercial clouds. Our goal is to provide a powerful analysis service that is easy to use and to maintain. Our design therefore uses a distributed architecture where we combine central servers with multiple distributed backends that execute the computationally intensive jobs. We believe our experiences developing and operating META-pipe provides a useful model for others that plan to provide a portal based data analysis service in ELIXIR and other organizations with geographically distributed compute and storage resources.},
}

@article {pmid31071295,
year = {2019},
author = {Abbas, AA and Taylor, LJ and Dothard, MI and Leiby, JS and Fitzgerald, AS and Khatib, LA and Collman, RG and Bushman, FD},
title = {Redondoviridae, a Family of Small, Circular DNA Viruses of the Human Oro-Respiratory Tract Associated with Periodontitis and Critical Illness.},
journal = {Cell host & microbe},
volume = {25},
number = {5},
pages = {719-729.e4},
doi = {10.1016/j.chom.2019.04.001},
pmid = {31071295},
issn = {1934-6069},
abstract = {The global virome is largely uncharacterized but is now being unveiled by metagenomic DNA sequencing. Exploring the human respiratory virome, in particular, can provide insights into oro-respiratory diseases. Here, we use metagenomics to identify a family of small circular DNA viruses-named Redondoviridae-associated with human diseases. We first identified two redondovirus genomes from bronchoalveolar lavage samples from human lung donors. We then queried thousands of metagenomic samples and recovered 17 additional complete redondovirus genomes. Detections were exclusively in human samples and mostly from respiratory tract and oro-pharyngeal sites, where Redondoviridae was the second most prevalent eukaryotic DNA virus family. Redondovirus sequences were associated with periodontal disease, and abundances decreased with treatment. Some critically ill patients in a medical intensive care unit were found to harbor high levels of redondoviruses in respiratory samples. These results suggest that redondoviruses colonize human oro-respiratory sites and can bloom in several human disorders.},
}

@article {pmid31071293,
year = {2019},
author = {MacLeod, AS},
title = {Bad "Staph" in the Wound Environment of Diabetic Foot Ulcers.},
journal = {Cell host & microbe},
volume = {25},
number = {5},
pages = {638-640},
doi = {10.1016/j.chom.2019.04.006},
pmid = {31071293},
issn = {1934-6069},
abstract = {Diabetic foot ulcers (DFUs) are a leading cause of high morbidity among diabetic patients. In this issue of Cell Host & Microbe, Kalan et al. (2019) examine the microbial bio-burden of DFUs and reveal biofilm and virulence pathways in the microbial metagenome that are linked to clinical healing outcomes.},
}

@article {pmid31071291,
year = {2019},
author = {Noell, K and Kolls, JK},
title = {Further Defining the Human Virome using NGS: Identification of Redondoviridae.},
journal = {Cell host & microbe},
volume = {25},
number = {5},
pages = {634-635},
doi = {10.1016/j.chom.2019.04.010},
pmid = {31071291},
issn = {1934-6069},
abstract = {In this issue of Cell Host & Microbe, Abbas et al. (2019) uncover a previously undefined family of single-stranded DNA viruses, Redondoviridae, in human ororespiratory sites. The presence of Redondoviridae associates with critical illness such as respiratory failure and periodontitis, illustrating the power of metagenomics to define the human virome.},
}

@article {pmid31069462,
year = {2019},
author = {Mahapatra, GP and Raman, S and Nayak, S and Gouda, S and Das, G and Patra, JK},
title = {Metagenomics Approaches in Discovery and Development of New Bioactive Compounds from Marine Actinomycetes.},
journal = {Current microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00284-019-01698-5},
pmid = {31069462},
issn = {1432-0991},
abstract = {Marine actinomycetes are prolific sources of marine drug discovery system contributing for several bioactive compounds of biomedical prominence. Metagenomics, a culture-independent technique through its sequence- and function-based screening has led to the discovery and synthesis of numerous biologically significant compounds like polyketide synthase, Non-ribosomal peptide synthetase, antibiotics, and biocatalyst. While metagenomics offers different advantages over conventional sequencing techniques, they also have certain limitations including bias classification, non-availability of quality DNA samples, heterologous expression, and host selection. The assimilation of advanced amplification and screening methods such as φ29 DNA polymerase, Next-Generation Sequencing, Cosmids, and recent bioinformatics tools like automated genome mining, anti-SMASH have shown promising results to overcome these constrains. Consequently, functional genomics and bioinformatics along with synthetic biology will be crucial for the success of the metagenomic approach and indeed for exploring new possibilities among the microbial consortia for the future drug discovery process.},
}

@article {pmid31068916,
year = {2019},
author = {Zhang, X and Payne, M and Lan, R},
title = {In silico Identification of Serovar-Specific Genes for Salmonella Serotyping.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {835},
doi = {10.3389/fmicb.2019.00835},
pmid = {31068916},
issn = {1664-302X},
abstract = {Salmonella enterica subspecies enterica is a highly diverse subspecies with more than 1500 serovars and the ability to distinguish serovars within this group is vital for surveillance. With the development of whole-genome sequencing technology, serovar prediction by traditional serotyping is being replaced by molecular serotyping. Existing in silico serovar prediction approaches utilize surface antigen encoding genes, core genome MLST and serovar-specific gene markers or DNA fragments for serotyping. However, these serovar-specific gene markers or DNA fragments only distinguished a small number of serovars. In this study, we compared 2258 Salmonella accessory genomes to identify 414 candidate serovar-specific or lineage-specific gene markers for 106 serovars which includes 24 polyphyletic serovars and the paraphyletic serovar Enteritidis. A combination of several lineage-specific gene markers can be used for the clear identification of the polyphyletic serovars and the paraphyletic serovar. We designed and evaluated an in silico serovar prediction approach by screening 1089 genomes representing 106 serovars against a set of 131 serovar-specific gene markers. The presence or absence of one or more serovar-specific gene markers was used to predict the serovar of an isolate from genomic data. We show that serovar-specific gene markers have comparable accuracy to other in silico serotyping methods with 84.8% of isolates assigned to the correct serovar with no false positives (FP) and false negatives (FN) and 10.5% of isolates assigned to a small subset of serovars containing the correct serovar with varied FP. Combined, 95.3% of genomes were correctly assigned to a serovar. This approach would be useful as diagnosis moves to culture-independent and metagenomic methods as well as providing a third alternative to confirm other genome-based analyses. The identification of a set of gene markers may also be useful in the development of more cost-effective molecular assays designed to detect specific gene markers of the all major serovars in a region. These assays would be useful in serotyping isolates where cultures are no longer obtained and traditional serotyping is therefore impossible.},
}

@article {pmid31068913,
year = {2019},
author = {Ai, D and Pan, H and Li, X and Gao, Y and Liu, G and Xia, LC},
title = {Identifying Gut Microbiota Associated With Colorectal Cancer Using a Zero-Inflated Lognormal Model.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {826},
doi = {10.3389/fmicb.2019.00826},
pmid = {31068913},
issn = {1664-302X},
abstract = {Colorectal cancer (CRC) is the third most common cancer worldwide. Its incidence is still increasing, and the mortality rate is high. New therapeutic and prognostic strategies are urgently needed. It became increasingly recognized that the gut microbiota composition differs significantly between healthy people and CRC patients. Thus, identifying the difference between gut microbiota of the healthy people and CRC patients is fundamental to understand these microbes' functional roles in the development of CRC. We studied the microbial community structure of a CRC metagenomic dataset of 156 patients and healthy controls, and analyzed the diversity, differentially abundant bacteria, and co-occurrence networks. We applied a modified zero-inflated lognormal (ZIL) model for estimating the relative abundance. We found that the abundance of genera: Anaerostipes, Bilophila, Catenibacterium, Coprococcus, Desulfovibrio, Flavonifractor, Porphyromonas, Pseudoflavonifractor, and Weissella was significantly different between the healthy and CRC groups. We also found that bacteria such as Streptococcus, Parvimonas, Collinsella, and Citrobacter were uniquely co-occurring within the CRC patients. In addition, we found that the microbial diversity of healthy controls is significantly higher than that of the CRC patients, which indicated a significant negative correlation between gut microbiota diversity and the stage of CRC. Collectively, our results strengthened the view that individual microbes as well as the overall structure of gut microbiota were co-evolving with CRC.},
}

@article {pmid31068624,
year = {2019},
author = {Catron, TR and Swank, A and Wehmas, LC and Phelps, D and Keely, SP and Brinkman, NE and McCord, J and Singh, R and Sobus, J and Wood, CE and Strynar, M and Wheaton, E and Tal, T},
title = {Microbiota alter metabolism and mediate neurodevelopmental toxicity of 17β-estradiol.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {7064},
doi = {10.1038/s41598-019-43346-9},
pmid = {31068624},
issn = {2045-2322},
abstract = {Estrogenic chemicals are widespread environmental contaminants associated with diverse health and ecological effects. During early vertebrate development, estrogen receptor signaling is critical for many different physiologic responses, including nervous system function. Recently, host-associated microbiota have been shown to influence neurodevelopment. Here, we hypothesized that microbiota may biotransform exogenous 17-βestradiol (E2) and modify E2 effects on swimming behavior. Colonized zebrafish were continuously exposed to non-teratogenic E2 concentrations from 1 to 10 days post-fertilization (dpf). Changes in microbial composition and predicted metagenomic function were evaluated. Locomotor activity was assessed in colonized and axenic (microbe-free) zebrafish exposed to E2 using a standard light/dark behavioral assay. Zebrafish tissue was collected for chemistry analyses. While E2 exposure did not alter microbial composition or putative function, colonized E2-exposed larvae showed reduced locomotor activity in the light, in contrast to axenic E2-exposed larvae, which exhibited normal behavior. Measured E2 concentrations were significantly higher in axenic relative to colonized zebrafish. Integrated peak area for putative sulfonated and glucuronidated E2 metabolites showed a similar trend. These data demonstrate that E2 locomotor effects in the light phase are dependent on the presence of microbiota and suggest that microbiota influence chemical E2 toxicokinetics. More broadly, this work supports the concept that microbial colonization status may influence chemical toxicity.},
}

@article {pmid31068435,
year = {2019},
author = {Guron, GKP and Arango-Argoty, G and Zhang, L and Pruden, A and Ponder, MA},
title = {Effects of Dairy Manure-Based Amendments and Soil Texture on Lettuce- and Radish-Associated Microbiota and Resistomes.},
journal = {mSphere},
volume = {4},
number = {3},
pages = {},
doi = {10.1128/mSphere.00239-19},
pmid = {31068435},
issn = {2379-5042},
abstract = {Dairy cattle are routinely treated with antibiotics, and the resulting manure or composted manure is commonly used as a soil amendment for crop production, raising questions regarding the potential for antibiotic resistance to propagate from "farm to fork." The objective of this study was to compare the microbiota and "resistomes" (i.e., carriage of antibiotic resistance genes [ARGs]) associated with lettuce leaf and radish taproot surfaces grown in different soils amended with dairy manure, compost, or chemical fertilizer only (control). Manure was collected from antibiotic-free dairy cattle (DC) or antibiotic-treated dairy cattle (DA), with a portion composted for parallel comparison. Amendments were applied to loamy sand or silty clay loam, and lettuce and radishes were cultivated to maturity in a greenhouse. Metagenomes were profiled via shotgun Illumina sequencing. Radishes carried a distinct ARG composition compared to that of lettuce, with greater relative abundance of total ARGs. Taxonomic species richness was also greater for radishes by 1.5-fold. The resistomes of lettuce grown with DC compost were distinct from those grown with DA compost, DC manure, or fertilizer only. Further, compost applied to loamy sand resulted in twofold-greater relative abundance of total ARGs on lettuce than when applied to silty clay loam. The resistomes of radishes grown with biological amendments were distinct from the corresponding fertilizer controls, but effects of composting or antibiotic use were not measureable. Cultivation in loamy sand resulted in higher species richness for both lettuce and radishes than when grown in silty clay loam by 2.2-fold and 1.2-fold, respectively, when amended with compost.IMPORTANCE A controlled, integrated, and replicated greenhouse study, along with comprehensive metagenomic analysis, revealed that multiple preharvest factors, including antibiotic use during manure collection, composting, biological soil amendment, and soil type, influence vegetable-borne resistomes. Here, radishes, a root vegetable, carried a greater load of ARGs and species richness than lettuce, a leafy vegetable. However, the lettuce resistome was more noticeably influenced by upstream antibiotic use and composting. Network analysis indicated that cooccurring ARGs and mobile genetic elements were almost exclusively associated with conditions receiving raw manure amendments, suggesting that composting could alleviate the mobility of manure-derived resistance traits. Effects of preharvest factors on associated microbiota and resistomes of vegetables eaten raw are worthy of further examination in terms of potential influence on human microbiomes and spread of antibiotic resistance. This research takes a step toward identifying on-farm management practices that can help mitigate the spread of agricultural sources of antibiotic resistance.},
}