@article {pmid31307536, year = {2019}, author = {Chen, J and McIlroy, SE and Archana, A and Baker, DM and Panagiotou, G}, title = {A pollution gradient contributes to the taxonomic, functional, and resistome diversity of microbial communities in marine sediments.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {104}, doi = {10.1186/s40168-019-0714-6}, pmid = {31307536}, issn = {2049-2618}, support = {2016-67//Environment and Conservation Fund/ ; }, abstract = {BACKGROUND: Coastal marine environments are one of the most productive ecosystems on Earth. However, anthropogenic impacts exert significant pressure on coastal marine biodiversity, contributing to functional shifts in microbial communities and human health risk factors. However, relatively little is known about the impact of eutrophication-human-derived nutrient pollution-on the marine microbial biosphere.<br><br>RESULTS: Here, we tested the hypothesis that benthic microbial diversity and function varies along a pollution gradient, with a focus on human pathogens and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG annotation revealed that zinc, lead, total volatile solids, and ammonia nitrogen were correlated with microbial diversity and function. We propose several microbes, including Planctomycetes and sulfate-reducing microbes as candidates to reflect pollution concentration. Annotation of antibiotic resistance genes showed that the highest abundance of efflux pumps was found at the most polluted site, corroborating the relationship between pollution and human health risk factors. This result suggests that sediments at polluted sites harbor microbes with a higher capacity to reduce intracellular levels of antibiotics, heavy metals, or other environmental contaminants.<br><br>CONCLUSIONS: Our findings suggest a correlation between pollution and the marine sediment microbiome and provide insight into the role of high-turnover microbial communities as well as potential pathogenic organisms as real-time indicators of water quality, with implications for human health and demonstrate the inner functional shifts contributed by the microcommunities.}, }
@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}, mesh = {Chromatography, High Pressure Liquid ; *Fermentation ; Fermented Foods/*microbiology ; Gas Chromatography-Mass Spectrometry ; *Metagenomics ; *Microbiota/genetics ; Taste ; }, 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 {pmid31051396, year = {2019}, author = {Cabral, L and Noronha, MF and de Sousa, STP and Lacerda-Júnior, GV and Richter, L and Fostier, AH and Andreote, FD and Hess, M and Oliveira, VM}, title = {The metagenomic landscape of xenobiotics biodegradation in mangrove sediments.}, journal = {Ecotoxicology and environmental safety}, volume = {179}, number = {}, pages = {232-240}, doi = {10.1016/j.ecoenv.2019.04.044}, pmid = {31051396}, issn = {1090-2414}, mesh = {Biodegradation, Environmental ; Drug Resistance, Microbial/genetics ; Gene Library ; *Geologic Sediments/chemistry/microbiology ; Hydrolases/genetics ; Metagenomics/*methods ; Metals, Heavy/*analysis/toxicity ; Microbiota/drug effects/*genetics ; Petroleum/analysis/toxicity ; *Wetlands ; Xenobiotics/*analysis/toxicity ; }, abstract = {Metagenomics is a powerful approach to study microorganisms present in any given environment and their potential to maintain and improve ecosystem health without the need of cultivating these microorganisms in the laboratory. In this study, we combined a cultivation-independent metagenomics approach with functional assays to identify the detoxification potential of microbial genes evaluating their potential to contribute to xenobiotics resistance in oil-impacted mangrove sediments. A metagenomic fosmid library containing 12,960 clones from highly contaminated mangrove sediment was used in this study. For assessment of metal resistance, clones were grown in culture medium with increasing concentrations of mercury. The analyses metagenomic library sequences revealed the presence of genes related to heavy metals and antibiotics resistance in the oil-impacted mangrove microbiome. The taxonomic profiling of these sequences suggests that at the genus level, Geobacter was the most abundant genus in our dataset. A functional screening assessment of the metagenomic library successfully detected 24 potential heavy metal tolerant clones, six of which were capable of growing with increased concentrations of mercury. The genetic characterization of selected clones allowed the detection of genes related to detoxification processes, such as chromate transport protein ChrA, haloacid dehalogenase-like hydrolase, lipopolysaccharide transport system, and 3-oxoacyl-[acyl-carrier-protein] reductase. Clones were capable of growing in medium containing increased concentrations of metals and antibiotics, but none manifested strong mercury removal from culture medium characteristic of mercuric reductase activity. These results suggest that resistance to xenobiotic stress varies greatly and that additional studies to elucidate the potential of metal biotransformation need to be carried out with the goal of improving bioremediation application.}, }
@article {pmid30901843, year = {2019}, author = {Cortes, L and Wopereis, H and Tartiere, A and Piquenot, J and Gouw, JW and Tims, S and Knol, J and Chelsky, D}, title = {Metaproteomic and 16S rRNA Gene Sequencing Analysis of the Infant Fecal Microbiome.}, journal = {International journal of molecular sciences}, volume = {20}, number = {6}, pages = {}, doi = {10.3390/ijms20061430}, pmid = {30901843}, issn = {1422-0067}, mesh = {Anti-Bacterial Agents/pharmacology ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome/drug effects ; Humans ; Infant ; Informatics/methods ; Male ; Metagenome ; *Metagenomics/methods ; Proteome ; *Proteomics/methods ; *RNA, Ribosomal, 16S ; }, abstract = {A metaproteomic analysis was conducted on the fecal microbiome of eight infants to characterize global protein and pathway expression. Although mass spectrometry-based proteomics is now a routine tool, analysis of the microbiome presents specific technical challenges, including the complexity and dynamic range of member taxa, the need for well-annotated metagenomic databases, and high inter-protein sequence redundancy and similarity. In this study, an approach was developed for assessment of biological phenotype and metabolic status, as a functional complement to DNA sequence analysis. Fecal samples were prepared and analysed by tandem mass spectrometry and a homology-based meta-clustering strategy was used to combine peptides from multiple species into representative proteins. In total, 15,250 unique peptides were sequenced and assigned to 2154 metaclusters, which were then assigned to pathways and functional groups. Differences were noted in several pathways, consistent with the dominant genera observed in different subjects. Although this study was not powered to draw conclusions from the comparisons, the results obtained demonstrate the applicability of this approach and provide the methods needed for performing semi-quantitative comparisons of human fecal microbiome composition, physiology and metabolism, as well as a more detailed assessment of microbial composition in comparison to 16S rRNA gene sequencing.}, }
@article {pmid29196717, year = {2017}, author = {Hamad, I and Ranque, S and Azhar, EI and Yasir, M and Jiman-Fatani, AA and Tissot-Dupont, H and Raoult, D and Bittar, F}, title = {Culturomics and Amplicon-based Metagenomic Approaches for the Study of Fungal Population in Human Gut Microbiota.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {16788}, pmid = {29196717}, issn = {2045-2322}, mesh = {Ascomycota/classification/genetics/isolation &amp; purification ; Basidiomycota/classification/genetics/isolation &amp; purification ; Case-Control Studies ; DNA, Fungal/analysis ; DNA, Ribosomal Spacer/*analysis ; Feces/microbiology ; Fungi/*classification/genetics/isolation &amp; purification ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; Microbiological Techniques ; Mycobiome ; Mycoses/*microbiology ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Herein, the mycobiota was characterized in fecal samples from sick patients and healthy subjects, collected from different geographical locations and using both culturomics and amplicon-based metagenomics approaches. Using the culturomics approach, a total of 17,800 fungal colonies were isolated from 14 fecal samples, and resulted in the isolation of 41 fungal species, of which 10 species had not been previously reported in the human gut. Deep sequencing of fungal-directed ITS1 and ITS2 amplicons led to the detection of a total of 142 OTUs and 173 OTUs from the ITS1 and ITS2 regions, respectively. Ascomycota composed the largest fraction of the total OTUs analyzed (78.9% and 68.2% of the OTUs from the ITS1 and ITS2 regions, respectively), followed by Basidiomycota (16.9% and 30.1% of the OTUs from the ITS1 and ITS2 regions, respectively). Interestingly, the results demonstrate that the ITS1/ITS2 amplicon sequencing provides different information about gut fungal communities compared to culturomics, though both approaches complete each other in assessing fungal diversity in fecal samples. We also report higher fungal diversity and abundance in patients compared to healthy subjects. In conclusion, combining both culturomic and amplicon-based metagenomic approaches may be a novel strategy towards analyzing fungal compositions in the human gut.}, }
@article {pmid28947833, year = {2017}, author = {Thomas, M and Webb, M and Ghimire, S and Blair, A and Olson, K and Fenske, GJ and Fonder, AT and Christopher-Hennings, J and Brake, D and Scaria, J}, title = {Metagenomic characterization of the effect of feed additives on the gut microbiome and antibiotic resistome of feedlot cattle.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {12257}, pmid = {28947833}, issn = {2045-2322}, mesh = {*Animal Feed ; Animals ; Anti-Bacterial Agents/*administration &amp; dosage ; Bacteria/classification/genetics ; Cattle ; *Dietary Supplements ; Drug Resistance, Bacterial/*drug effects ; Gastrointestinal Microbiome/*drug effects ; Genes, Bacterial ; Metagenomics ; North America ; }, abstract = {In North America, antibiotic feed additives such as monensin and tylosin are added to the finishing diets of feedlot cattle to counter the ill-effects of feeding diets with rapidly digestible carbohydrates. While these feed additives have been proven to improve feed efficiency and reduce liver abscess incidence, how these products impact the gastrointestinal microbiota is not completely understood. In this study, we analyzed the impact of providing antibiotic feed additives to feedlot cattle using metagenome sequencing of treated and control animals. Our results indicate that use of antibiotic feed additives does not produce discernable changes at the phylum level. However, treated cattle had reduced abundance of gram-positive bacteria at the genus level. The abundance of Ruminococcus, Erysipelotrichaceae and Lachnospiraceae in the gut of treated steers was reduced. Functional analysis of the data indicates that there was only minimal impact due to the treatment in the rumen. Genes involved in detoxification were significantly increased in the rumen of AB steers. But the relative abundance of these genes was < 0.3%. However, our results did not show any correlation between the presence of antimicrobial resistance genes in the gut microbiota and the administration of antibiotic feed additives.}, }
@article {pmid28947818, year = {2017}, author = {Stat, M and Huggett, MJ and Bernasconi, R and DiBattista, JD and Berry, TE and Newman, SJ and Harvey, ES and Bunce, M}, title = {Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {12240}, pmid = {28947818}, issn = {2045-2322}, mesh = {Animals ; Aquatic Organisms/*classification/*genetics ; DNA/analysis/genetics ; Environmental Monitoring/*methods ; Metagenomics/*methods ; Seawater/chemistry ; Sensitivity and Specificity ; Sequence Analysis, DNA ; Tropical Climate ; }, abstract = {Effective marine management requires comprehensive data on the status of marine biodiversity. However, efficient methods that can document biodiversity in our oceans are currently lacking. Environmental DNA (eDNA) sourced from seawater offers a new avenue for investigating the biota in marine ecosystems. Here, we investigated the potential of eDNA to inform on the breadth of biodiversity present in a tropical marine environment. Directly sequencing eDNA from seawater using a shotgun approach resulted in only 0.34% of 22.3 million reads assigning to eukaryotes, highlighting the inefficiency of this method for assessing eukaryotic diversity. In contrast, using 'tree of life' (ToL) metabarcoding and 20-fold fewer sequencing reads, we could detect 287 families across the major divisions of eukaryotes. Our data also show that the best performing 'universal' PCR assay recovered only 44% of the eukaryotes identified across all assays, highlighting the need for multiple metabarcoding assays to catalogue biodiversity. Lastly, focusing on the fish genus Lethrinus, we recovered intra- and inter-specific haplotypes from seawater samples, illustrating that eDNA can be used to explore diversity beyond taxon identifications. Given the sensitivity and low cost of eDNA metabarcoding we advocate this approach be rapidly integrated into biomonitoring programs.}, }
@article {pmid31171880, year = {2019}, author = {Yachida, S and Mizutani, S and Shiroma, H and Shiba, S and Nakajima, T and Sakamoto, T and Watanabe, H and Masuda, K and Nishimoto, Y and Kubo, M and Hosoda, F and Rokutan, H and Matsumoto, M and Takamaru, H and Yamada, M and Matsuda, T and Iwasaki, M and Yamaji, T and Yachida, T and Soga, T and Kurokawa, K and Toyoda, A and Ogura, Y and Hayashi, T and Hatakeyama, M and Nakagama, H and Saito, Y and Fukuda, S and Shibata, T and Yamada, T}, title = {Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer.}, journal = {Nature medicine}, volume = {25}, number = {6}, pages = {968-976}, doi = {10.1038/s41591-019-0458-7}, pmid = {31171880}, issn = {1546-170X}, mesh = {Adult ; Aged ; Case-Control Studies ; Colorectal Neoplasms/genetics/*metabolism/*microbiology ; Disease Progression ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Male ; Metabolomics ; Metagenomics ; Middle Aged ; Neoplasm Staging ; Young Adult ; }, abstract = {In most cases of sporadic colorectal cancers, tumorigenesis is a multistep process, involving genomic alterations in parallel with morphologic changes. In addition, accumulating evidence suggests that the human gut microbiome is linked to the development of colorectal cancer. Here we performed fecal metagenomic and metabolomic studies on samples from a large cohort of 616 participants who underwent colonoscopy to assess taxonomic and functional characteristics of gut microbiota and metabolites. Microbiome and metabolome shifts were apparent in cases of multiple polypoid adenomas and intramucosal carcinomas, in addition to more advanced lesions. We found two distinct patterns of microbiome elevations. First, the relative abundance of Fusobacterium nucleatum spp. was significantly (P < 0.005) elevated continuously from intramucosal carcinoma to more advanced stages. Second, Atopobium parvulum and Actinomyces odontolyticus, which co-occurred in intramucosal carcinomas, were significantly (P < 0.005) increased only in multiple polypoid adenomas and/or intramucosal carcinomas. Metabolome analyses showed that branched-chain amino acids and phenylalanine were significantly (P < 0.005) increased in intramucosal carcinomas and bile acids, including deoxycholate, were significantly (P < 0.005) elevated in multiple polypoid adenomas and/or intramucosal carcinomas. We identified metagenomic and metabolomic markers to discriminate cases of intramucosal carcinoma from the healthy controls. Our large-cohort multi-omics data indicate that shifts in the microbiome and metabolome occur from the very early stages of the development of colorectal cancer, which is of possible etiological and diagnostic importance.}, }
@article {pmid31142849, year = {2019}, author = {Fettweis, JM and Serrano, MG and Brooks, JP and Edwards, DJ and Girerd, PH and Parikh, HI and Huang, B and Arodz, TJ and Edupuganti, L and Glascock, AL and Xu, J and Jimenez, NR and Vivadelli, SC and Fong, SS and Sheth, NU and Jean, S and Lee, V and Bokhari, YA and Lara, AM and Mistry, SD and Duckworth, RA and Bradley, SP and Koparde, VN and Orenda, XV and Milton, SH and Rozycki, SK and Matveyev, AV and Wright, ML and Huzurbazar, SV and Jackson, EM and Smirnova, E and Korlach, J and Tsai, YC and Dickinson, MR and Brooks, JL and Drake, JI and Chaffin, DO and Sexton, AL and Gravett, MG and Rubens, CE and Wijesooriya, NR and Hendricks-Muñoz, KD and Jefferson, KK and Strauss, JF and Buck, GA}, title = {The vaginal microbiome and preterm birth.}, journal = {Nature medicine}, volume = {25}, number = {6}, pages = {1012-1021}, doi = {10.1038/s41591-019-0450-2}, pmid = {31142849}, issn = {1546-170X}, mesh = {Adult ; African Americans ; Biodiversity ; Cohort Studies ; Cytokines/metabolism ; Female ; Host Microbial Interactions/immunology ; Humans ; Infant, Newborn ; Inflammation Mediators/metabolism ; Longitudinal Studies ; Metagenomics ; *Microbiota/genetics/immunology ; Premature Birth/etiology/immunology/*microbiology ; Risk Factors ; United States ; Vagina/immunology/*microbiology ; Young Adult ; }, abstract = {The incidence of preterm birth exceeds 10% worldwide. There are significant disparities in the frequency of preterm birth among populations within countries, and women of African ancestry disproportionately bear the burden of risk in the United States. In the present study, we report a community resource that includes 'omics' data from approximately 12,000 samples as part of the integrative Human Microbiome Project. Longitudinal analyses of 16S ribosomal RNA, metagenomic, metatranscriptomic and cytokine profiles from 45 preterm and 90 term birth controls identified harbingers of preterm birth in this cohort of women predominantly of African ancestry. Women who delivered preterm exhibited significantly lower vaginal levels of Lactobacillus crispatus and higher levels of BVAB1, Sneathia amnii, TM7-H1, a group of Prevotella species and nine additional taxa. The first representative genomes of BVAB1 and TM7-H1 are described. Preterm-birth-associated taxa were correlated with proinflammatory cytokines in vaginal fluid. These findings highlight new opportunities for assessment of the risk of preterm birth.}, }
@article {pmid30719705, year = {2019}, author = {Cheng, L and Chen, Y and Zhang, X and Zheng, X and Cao, J and Wu, Z and Qin, W and Cheng, K}, title = {A metagenomic analysis of the modulatory effect of Cyclocarya paliurus flavonoids on the intestinal microbiome in a high-fat diet-induced obesity mouse model.}, journal = {Journal of the science of food and agriculture}, volume = {99}, number = {8}, pages = {3967-3975}, doi = {10.1002/jsfa.9622}, pmid = {30719705}, issn = {1097-0010}, support = {//K. C. Wong Magna Fund of Ningbo University/ ; 2017C02039//Key Research and Development Project of Zhejiang Province/ ; 2018C02047//Key Research and Development Project of Zhejiang Province/ ; LY19C200006//Zhejiang Provincial Natural Science Foundation of China/ ; }, mesh = {Adult ; Animals ; Bacteria/classification/drug effects/*genetics/isolation &amp; purification ; Diet, High-Fat/adverse effects ; Disease Models, Animal ; Dysbiosis/drug therapy/metabolism/microbiology ; Female ; Flavonoids/*administration &amp; dosage/analysis ; Gastrointestinal Microbiome/*drug effects ; Humans ; Intestines/*microbiology ; Juglandaceae/*chemistry ; Male ; Metagenomics ; Mice ; Mice, Inbred C57BL ; Obesity/*drug therapy/microbiology ; Plant Extracts/*administration &amp; dosage/analysis ; }, abstract = {BACKGROUND: As a result of a low bioavailability, the majority of Cyclocarya paliurus flavonoids (CPF) remain in the large intestine where they accumulate to exert a modulatory effect on the intestinal micro-ecology. Therefore, the present study investigated the modulatory effect of CPF on intestinal microbiota.<br><br>RESULTS: CPF dramatically ameliorated the obesity-induced gut dysbiosis. A significant decrease (P < 0.05) was observed in the ratio of Firmicutes/Bacteroidetes after CPF treatment for 8 weeks. Moreover, Kyoto Encyclopedia of Genes and Genomes pathways of biosynthesis of amino acids, the two-component system and ATP-binding cassette transporters enriched the most differentially expressed genes after CPF intervention.<br><br>CONCLUSION: The results of the present study indicate that CPF might have prebiotic-like activity and could be used as a functional food component with potential therapeutic utility to prevent obesity-related metabolic disorders by manipulating the gut flora and affecting certain metabolic pathways, thus contributing to the improvement of human health. © 2019 Society of Chemical Industry.}, }
@article {pmid29539432, year = {2018}, author = {Fujisaka, S and Avila-Pacheco, J and Soto, M and Kostic, A and Dreyfuss, JM and Pan, H and Ussar, S and Altindis, E and Li, N and Bry, L and Clish, CB and Kahn, CR}, title = {Diet, Genetics, and the Gut Microbiome Drive Dynamic Changes in Plasma Metabolites.}, journal = {Cell reports}, volume = {22}, number = {11}, pages = {3072-3086}, pmid = {29539432}, issn = {2211-1247}, support = {P30 DK040561/DK/NIDDK NIH HHS/United States ; U01 CA210171/CA/NCI NIH HHS/United States ; P30 DK036836/DK/NIDDK NIH HHS/United States ; R01 DK033201/DK/NIDDK NIH HHS/United States ; R37 DK031036/DK/NIDDK NIH HHS/United States ; R01 DK031036/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Diet, High-Fat/*methods ; Gastrointestinal Microbiome/*genetics ; Humans ; Metabolomics/*methods ; Mice ; Obesity/*genetics/pathology ; }, abstract = {Diet, genetics, and the gut microbiome are determinants of metabolic status, in part through production of metabolites by the gut microbiota. To understand the mechanisms linking these factors, we performed LC-MS-based metabolomic analysis of cecal contents and plasma from C57BL/6J, 129S1/SvImJ, and 129S6/SvEvTac mice on chow or a high-fat diet (HFD) and HFD-treated with vancomycin or metronidazole. Prediction of the functional metagenome of gut bacteria by PICRUSt analysis of 16S sequences revealed dramatic differences in microbial metabolism. Cecal and plasma metabolites showed multifold differences reflecting the combined and integrated effects of diet, antibiotics, host background, and the gut microbiome. Eighteen plasma metabolites correlated positively or negatively with host insulin resistance across strains and diets. Over 1,000 still-unidentified metabolite peaks were also highly regulated by diet, antibiotics, and genetic background. Thus, diet, host genetics, and the gut microbiota interact to create distinct responses in plasma metabolites, which can contribute to regulation of metabolism and insulin resistance.}, }
@article {pmid29463537, year = {2018}, author = {Ajami, NJ and Cope, JL and Wong, MC and Petrosino, JF and Chesnel, L}, title = {Impact of Oral Fidaxomicin Administration on the Intestinal Microbiota and Susceptibility to Clostridium difficile Colonization in Mice.}, journal = {Antimicrobial agents and chemotherapy}, volume = {62}, number = {5}, pages = {}, pmid = {29463537}, issn = {1098-6596}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Clostridium Infections/*drug therapy/prevention &amp; control ; Clostridium difficile/*drug effects ; Cross Infection/drug therapy/microbiology/prevention &amp; control ; Disease Models, Animal ; Feces/microbiology ; Female ; Fidaxomicin/*pharmacology ; Gastrointestinal Microbiome/*drug effects ; Mice ; Mice, Inbred C57BL ; RNA, Ribosomal, 16S/genetics ; Vancomycin/*pharmacology ; }, abstract = {Clostridium difficile infection (CDI), a common cause of hospital-acquired infections, typically occurs after disruption of the normal gut microbiome by broad-spectrum antibiotics. Fidaxomicin is a narrow-spectrum antibiotic that demonstrates a reduced impact on the normal gut microbiota and is approved for the treatment of CDI. To further explore the benefits of this property, we used a murine model to examine the effects of fidaxomicin versus vancomycin on gut microbiota and susceptibility to C. difficile colonization while tracking microbiota recovery over time. Mice were exposed to fidaxomicin or vancomycin by oral gavage for 3 days and subsequently challenged with C. difficile spores at predetermined time points up to 21 days postexposure to antibiotics. Fecal samples were subsequently collected for analysis. Twenty-four hours postchallenge, mice were euthanized and the colon contents harvested. The microbiota was characterized using 16S rRNA gene sequencing. All fidaxomicin-exposed mice (except for one at day 8) were resistant to C. difficile colonization. However, 9 of 15 vancomycin-exposed mice were susceptible to C. difficile colonization until day 12. All vancomycin-exposed mice recovered colonization resistance by day 16. Bacterial diversity was similar prior to antibiotic exposure in both arms and decreased substantially after exposure. A shift in taxonomic structure and composition occurred after both exposures; however, the shift was greater in vancomycin-exposed than in fidaxomicin-exposed mice. In summary, compared with vancomycin, fidaxomicin exposure had less impact on microbiota composition, promoted faster microbial recovery, and had less impact on the loss of C. difficile colonization resistance.}, }
@article {pmid29194524, year = {2018}, author = {Zhu, C and Miller, M and Marpaka, S and Vaysberg, P and Rühlemann, MC and Wu, G and Heinsen, FA and Tempel, M and Zhao, L and Lieb, W and Franke, A and Bromberg, Y}, title = {Functional sequencing read annotation for high precision microbiome analysis.}, journal = {Nucleic acids research}, volume = {46}, number = {4}, pages = {e23}, pmid = {29194524}, issn = {1362-4962}, mesh = {Algorithms ; Bacterial Proteins/physiology ; Child ; Crohn Disease/microbiology ; Humans ; Metagenomics/*methods ; *Microbiota ; Molecular Sequence Annotation/*methods ; Prader-Willi Syndrome/microbiology ; Sequence Alignment ; }, abstract = {The vast majority of microorganisms on Earth reside in often-inseparable environment-specific communities-microbiomes. Meta-genomic/-transcriptomic sequencing could reveal the otherwise inaccessible functionality of microbiomes. However, existing analytical approaches focus on attributing sequencing reads to known genes/genomes, often failing to make maximal use of available data. We created faser (functional annotation of sequencing reads), an algorithm that is optimized to map reads to molecular functions encoded by the read-correspondent genes. The mi-faser microbiome analysis pipeline, combining faser with our manually curated reference database of protein functions, accurately annotates microbiome molecular functionality. mi-faser's minutes-per-microbiome processing speed is significantly faster than that of other methods, allowing for large scale comparisons. Microbiome function vectors can be compared between different conditions to highlight environment-specific and/or time-dependent changes in functionality. Here, we identified previously unseen oil degradation-specific functions in BP oil-spill data, as well as functional signatures of individual-specific gut microbiome responses to a dietary intervention in children with Prader-Willi syndrome. Our method also revealed variability in Crohn's Disease patient microbiomes and clearly distinguished them from those of related healthy individuals. Our analysis highlighted the microbiome role in CD pathogenicity, demonstrating enrichment of patient microbiomes in functions that promote inflammation and that help bacteria survive it.}, }
@article {pmid29142285, year = {2017}, author = {Mehrpouya-Bahrami, P and Chitrala, KN and Ganewatta, MS and Tang, C and Murphy, EA and Enos, RT and Velazquez, KT and McCellan, J and Nagarkatti, M and Nagarkatti, P}, title = {Blockade of CB1 cannabinoid receptor alters gut microbiota and attenuates inflammation and diet-induced obesity.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {15645}, pmid = {29142285}, issn = {2045-2322}, support = {K01 AT007824/AT/NCCIH NIH HHS/United States ; P01 AT003961/AT/NCCIH NIH HHS/United States ; P20 GM103641/GM/NIGMS NIH HHS/United States ; R01 AT006888/AT/NCCIH NIH HHS/United States ; R01 ES019313/ES/NIEHS NIH HHS/United States ; R01 MH094755/MH/NIMH NIH HHS/United States ; }, mesh = {Adipose Tissue/metabolism/pathology ; Animals ; Cannabinoid Receptor Antagonists/*pharmacology ; Cell Movement/drug effects ; Cytokines/metabolism ; Gastrointestinal Microbiome/*drug effects ; Inflammation/drug therapy/metabolism/pathology ; Macrophages/metabolism ; Male ; Mice ; Obesity/*drug therapy/etiology/metabolism ; Receptor, Cannabinoid, CB1/*antagonists &amp; inhibitors/metabolism ; Rimonabant/*pharmacology ; }, abstract = {Obesity is characterized by chronic low-grade, systemic inflammation, altered gut microbiota, and gut barrier disruption. Additionally, obesity is associated with increased activity of endocannabinoid system (eCB). However, the clear connection between gut microbiota and the eCB system in the regulation of energy homeostasis and adipose tissue inflammation and metabolism, remains to be established. We investigated the effect of treatment of mice with a cannabinoid receptor 1 (CB1) antagonist on Diet-Induced Obesity (DIO), specifically whether such a treatment that blocks endocannabinoid activity can induce changes in gut microbiota and anti-inflammatory state in adipose tissue. Blockade of CB1 attenuated DIO, inflammatory cytokines and trafficking of M1 macrophages into adipose tissue. Decreased inflammatory tone was associated with a lower intestinal permeability and decreased metabolic endotoxemia as evidenced by reduced plasma LPS level, and improved hyperglycemia and insulin resistance. 16S rRNA metagenomics sequencing revealed that CB1 blockade dramatically increased relative abundance of Akkermansia muciniphila and decreased Lanchnospiraceae and Erysipelotrichaceae in the gut. Together, the current study suggests that blocking of CB1 ameliorates Diet-Induced Obesity and metabolic disorder by modulating macrophage inflammatory mediators, and that this effect is associated with alterations in gut microbiota and their metabolites.}, }
@article {pmid29097759, year = {2017}, author = {Meiser, A and Otte, J and Schmitt, I and Grande, FD}, title = {Sequencing genomes from mixed DNA samples - evaluating the metagenome skimming approach in lichenized fungi.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {14881}, pmid = {29097759}, issn = {2045-2322}, mesh = {DNA, Fungal/*genetics ; *Genome, Fungal ; Lichens/classification/*genetics ; Metagenomics ; Sequence Analysis, DNA ; Transcriptome ; }, abstract = {The metagenome skimming approach, i.e. low coverage shotgun sequencing of multi-species assemblages and subsequent reconstruction of individual genomes, is increasingly used for in-depth genomic characterization of ecological communities. This approach is a promising tool for reconstructing genomes of facultative symbionts, such as lichen-forming fungi, from metagenomic reads. However, no study has so far tested accuracy and completeness of assemblies based on metagenomic sequences compared to assemblies based on pure culture strains of lichenized fungi. Here we assembled the genomes of Evernia prunastri and Pseudevernia furfuracea based on metagenomic sequences derived from whole lichen thalli. We extracted fungal contigs using two different taxonomic binning methods, and performed gene prediction on the fungal contig subsets. We then assessed quality and completeness of the metagenome-based assemblies using genome assemblies as reference which are based on pure culture strains of the two fungal species. Our comparison showed that we were able to reconstruct fungal genomes from uncultured lichen thalli, and also cover most of the gene space (86-90%). Metagenome skimming will facilitate genome mining, comparative (phylo)genomics, and population genetics of lichen-forming fungi by circumventing the time-consuming, sometimes unfeasible, step of aposymbiotic cultivation.}, }
@article {pmid31301473, year = {2019}, author = {Bengtsson-Palme, J and Milakovic, M and Švecová, H and Ganjto, M and Jonsson, V and Grabic, R and Udikovic-Kolic, N}, title = {Industrial wastewater treatment plant enriches antibiotic resistance genes and alters the structure of microbial communities.}, journal = {Water research}, volume = {162}, number = {}, pages = {437-445}, doi = {10.1016/j.watres.2019.06.073}, pmid = {31301473}, issn = {1879-2448}, abstract = {Antibiotic resistance is an emerging global health crisis, driven largely by overuse and misuse of antibiotics. However, there are examples in which the production of these antimicrobial agents has polluted the environment with active antibiotic residues, selecting for antibiotic resistant bacteria and the genes they carry. In this work, we have used shotgun metagenomics to investigate the taxonomic structure and resistance gene composition of sludge communities in a treatment plant in Croatia receiving wastewater from production of the macrolide antibiotic azithromycin. We found that the total abundance of antibiotic resistance genes was three times higher in sludge from the treatment plant receiving wastewater from pharmaceutical production than in municipal sludge from a sewage treatment plant in Zagreb. Surprisingly, macrolide resistance genes did not have higher abundances in the industrial sludge, but genes associated with mobile genetic elements such as integrons had. We conclude that at high concentrations of antibiotics, selection may favor taxonomic shifts towards intrinsically resistant species or strains harboring chromosomal resistance mutations rather than acquisition of mobile resistance determinants. Our results underscore the need for regulatory action also within Europe to avoid release of antibiotics into the environment.}, }
@article {pmid30826606, year = {2019}, author = {Bai, Y and Ruan, X and Xie, X and Yan, Z}, title = {Antibiotic resistome profile based on metagenomics in raw surface drinking water source and the influence of environmental factor: A case study in Huaihe River Basin, China.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {248}, number = {}, pages = {438-447}, doi = {10.1016/j.envpol.2019.02.057}, pmid = {30826606}, issn = {1873-6424}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacitracin/pharmacology ; Burkholderiaceae/drug effects/*genetics ; China ; Drinking Water/*microbiology ; Drug Resistance, Microbial/*genetics ; Flavobacterium/drug effects/*genetics ; Genes, Bacterial/genetics ; Humans ; Metagenomics ; Microbiota/drug effects ; Rivers/*microbiology ; Tetracyclines/pharmacology ; Verrucomicrobia/drug effects/*genetics ; beta-Lactams/pharmacology ; }, abstract = {The contamination with antibiotic resistance genes (ARGs) in raw drinking water source may pose a direct threat to human health. In this study, metagenomics sequencing and analysis were applied to investigate the ARG pattern in 12 drinking water sources in upper and middle reach of Huaihe River Basin, China. Based on the redundant analysis and multi-linear regression model, location, specific microbial taxa, number of livestock and health facilities significantly influenced the ARG profile in drinking water sources. Besides the cluster effect of ARG in samples from plain and bedrock mountain areas, the samples from fracture aquifer areas also showed a distinctive biogeographic pattern with that from porous aquifer areas. Putative ARGs host Opitutus and Flavobacterium were the enriched biomarkers in plain and fracture aquifer area respectively, which mainly carried bacitracin, multidrug, beta-lactam and tetracycline ARGs. This result illuminated that both natural background and anthropogenic activities in the watershed influenced the ARG profile in natural freshwater system significantly. The low MGEs abundance and absence of pathogen revealed a low ARG dissemination risk in sampled drinking water sources, while Polynucleobacter was an abundant ARGs host and was significantly related to the ARG profile, which indicated that specific bacteria was responsible for ARGs propagation and accumulation in surface freshwater system. Further researches are needed to assess human exposure to raw drinking water source and the potential risk, as well as the species interaction in microbial community and its impact on ARG propagation under oligotrophic condition.}, }
@article {pmid30311571, year = {2018}, author = {Shillitoe, EJ}, title = {The Microbiome of Oral Cancer.}, journal = {Critical reviews in oncogenesis}, volume = {23}, number = {3-4}, pages = {153-160}, doi = {10.1615/CritRevOncog.2018027422}, pmid = {30311571}, issn = {0893-9675}, mesh = {Animals ; Bacterial Infections/complications/microbiology ; Cell Transformation, Neoplastic ; Disease Susceptibility ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; Mouth Neoplasms/*etiology ; Mycoses/complications/microbiology ; Virus Diseases/complications/virology ; }, abstract = {The pathogenesis of oral cancer is complex, and not all relevant factors involved in it have been determined. In particular, the role of the microbiota is not well understood because of difficulties in isolating and culturing its organisms. However, the recent development of metagenomic sequencing allows the discovery of all the DNA sequences in a specimen, and thus, the microbiome is now under intensive investigation. Studies of the bacteriome, the mycobiome, and the virome have revealed new organisms and have uncovered various differences between healthy persons and patients with oral cancer. In addition, sequencing of human samples shows the existence of DNA sequences that may be from novel microbes but are actually of unknown origin and so are referred to as the dark matter. The large volumes of data that are being produced by sequencing projects must be studied further to reveal novel pathogens and new pathways in the development of oral cancer.}, }
@article {pmid30257633, year = {2018}, author = {White, LS and Van den Bogaerde, J and Kamm, M}, title = {The gut microbiota: cause and cure of gut diseases.}, journal = {The Medical journal of Australia}, volume = {209}, number = {7}, pages = {312-317}, pmid = {30257633}, issn = {1326-5377}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Diseases/microbiology/physiopathology/therapy ; *Gastrointestinal Microbiome/drug effects/genetics/physiology ; Humans ; Inflammatory Bowel Diseases/microbiology/physiopathology/therapy ; Liver Diseases/microbiology/physiopathology/therapy ; Metabolic Syndrome/microbiology/physiopathology/therapy ; Metagenomics ; Mice ; *Obesity/microbiology/physiopathology/therapy ; }, abstract = {The gastrointestinal microbiota is emerging as a central factor in the pathogenesis of a range of gastrointestinal and hepatic disorders. Epidemiological studies, and experimental studies in animals and humans, have highlighted a likely causative role of this microbial community in the modern global epidemics of inflammatory bowel disease, non-alcoholic fatty liver disease, non-alcoholic steato-hepatitis, obesity and metabolic syndrome. New techniques for microbial culture and gene sequencing are enabling the identification of specific pathogens and protective organisms in these conditions. Factors that change the microbiota are being defined: dietary pattern, specific foods, food additives in processed food and drinks, such as emulsifiers and non-sugar sweeteners, and antibiotics. Microbiota changes in early life appear critical to the later development of a range of inflammatory disorders. For many of these conditions, the treatment paradigm will change, at least in part, from immune suppression and drug therapy to treatments that reshape the microbiota or restore its integrity. These treatments include dietary changes, specific microbial manipulation and faecal microbiota transplantation. A dialogue is needed regarding population strategies that target disease prevention. This will include how food is produced, what additives it contains, and how it is processed. Widespread use of antibiotics, from agricultural and veterinary to medicinal settings, needs more attention. At the individual level, microbial profiles may be able to predict who is at risk of disease when subjected to particular environmental influences, and what microbial restoration is needed to minimise risk.}, }
@article {pmid30250051, year = {2019}, author = {Ju, F and Beck, K and Yin, X and Maccagnan, A and McArdell, CS and Singer, HP and Johnson, DR and Zhang, T and Bürgmann, H}, title = {Wastewater treatment plant resistomes are shaped by bacterial composition, genetic exchange, and upregulated expression in the effluent microbiomes.}, journal = {The ISME journal}, volume = {13}, number = {2}, pages = {346-360}, doi = {10.1038/s41396-018-0277-8}, pmid = {30250051}, issn = {1751-7370}, mesh = {Anti-Bacterial Agents/analysis ; Bacteria/drug effects/genetics/metabolism ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Metagenome ; Metagenomics ; *Microbiota ; Transcriptome ; Up-Regulation ; Waste Disposal, Fluid ; Waste Water/chemistry/*microbiology ; }, abstract = {Wastewater treatment plants (WWTPs) are implicated as hotspots for the dissemination of antibacterial resistance into the environment. However, the in situ processes governing removal, persistence, and evolution of resistance genes during wastewater treatment remain poorly understood. Here, we used quantitative metagenomic and metatranscriptomic approaches to achieve a broad-spectrum view of the flow and expression of genes related to antibacterial resistance to over 20 classes of antibiotics, 65 biocides, and 22 metals. All compartments of 12 WWTPs share persistent resistance genes with detectable transcriptional activities that were comparatively higher in the secondary effluent, where mobility genes also show higher relative abundance and expression ratios. The richness and abundance of resistance genes vary greatly across metagenomes from different treatment compartments, and their relative and absolute abundances correlate with bacterial community composition and biomass concentration. No strong drivers of resistome composition could be identified among the chemical stressors analyzed, although the sub-inhibitory concentration (hundreds of ng/L) of macrolide antibiotics in wastewater correlates with macrolide and vancomycin resistance genes. Contig-based analysis shows considerable co-localization between resistance and mobility genes and implies a history of substantial horizontal resistance transfer involving human bacterial pathogens. Based on these findings, we propose future inclusion of mobility incidence (M%) and host pathogenicity of antibiotic resistance genes in their quantitative health risk ranking models with an ultimate goal to assess the biological significance of wastewater resistomes with regard to disease control in humans or domestic livestock.}, }
@article {pmid30158571, year = {2018}, author = {Caussy, C and Loomba, R}, title = {Gut microbiome, microbial metabolites and the development of NAFLD.}, journal = {Nature reviews. Gastroenterology &amp; hepatology}, volume = {15}, number = {12}, pages = {719-720}, doi = {10.1038/s41575-018-0058-x}, pmid = {30158571}, issn = {1759-5053}, mesh = {Female ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; *Non-alcoholic Fatty Liver Disease ; Obesity ; }, }
@article {pmid30136922, year = {2018}, author = {Cornet, L and Bertrand, AR and Hanikenne, M and Javaux, EJ and Wilmotte, A and Baurain, D}, title = {Metagenomic assembly of new (sub)polar Cyanobacteria and their associated microbiome from non-axenic cultures.}, journal = {Microbial genomics}, volume = {4}, number = {9}, pages = {}, pmid = {30136922}, issn = {2057-5858}, mesh = {Antarctic Regions ; Arctic Regions ; Cyanobacteria/*classification/*genetics/isolation &amp; purification ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Cyanobacteria form one of the most diversified phyla of Bacteria. They are important ecologically as primary producers, for Earth evolution and biotechnological applications. Yet, Cyanobacteria are notably difficult to purify and grow axenically, and most strains in culture collections contain heterotrophic bacteria that were probably associated with Cyanobacteria in the environment. Obtaining cyanobacterial DNA without contaminant sequences is thus a challenging and time-consuming task. Here, we describe a metagenomic pipeline that enables the easy recovery of genomes from non-axenic cultures. We tested this pipeline on 17 cyanobacterial cultures from the BCCM/ULC public collection and generated novel genome sequences for 12 polar or subpolar strains and three temperate ones, including three early-branching organisms that will be useful for phylogenomics. In parallel, we assembled 31 co-cultivated bacteria (12 nearly complete) from the same cultures and showed that they mostly belong to Bacteroidetes and Proteobacteria, some of them being very closely related in spite of geographically distant sampling sites.}, }
@article {pmid29184122, year = {2017}, author = {Lee, WH and Chen, HM and Yang, SF and Liang, C and Peng, CY and Lin, FM and Tsai, LL and Wu, BC and Hsin, CH and Chuang, CY and Yang, T and Yang, TL and Ho, SY and Chen, WL and Ueng, KC and Huang, HD and Huang, CN and Jong, YJ}, title = {Bacterial alterations in salivary microbiota and their association in oral cancer.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {16540}, pmid = {29184122}, issn = {2045-2322}, mesh = {Biodiversity ; Carcinoma, Squamous Cell/diagnosis/epidemiology/etiology ; Computational Biology/methods ; Disease Susceptibility ; Female ; Humans ; Male ; Metagenomics ; *Microbiota ; Mouth Mucosa/microbiology/pathology ; Mouth Neoplasms/diagnosis/*epidemiology/*etiology ; RNA, Ribosomal, 16S ; Saliva/*microbiology ; Taiwan/epidemiology ; }, abstract = {Oral squamous cell carcinoma (OSCC) is the most common malignant neoplasm of the oral cavity and the fourth leading malignancy and cause of cancer-related death in the male population of Taiwan. Most cases are detected at advanced stages, resulting in poor prognosis. Therefore, improved detection of early oral health disorders is indispensable. The involvement of oral bacteria in inflammation and their association with OSCC progression provide a feasible target for diagnosis. Due to the nature of oral neoplasms, the diagnosis of epithelial precursor lesions is relatively easy compared with that of other types of cancer. However, the transition from an epithelial precursor lesion to cancer is slow and requires further and continuous follow-up. In this study, we investigated microbiota differences between normal individuals, epithelial precursor lesion patients, and cancer patients with different lifestyle habits, such as betel chewing and smoking, using next-generation sequencing. Overall, the oral microbiome compositions of five genera, Bacillus, Enterococcus, Parvimonas, Peptostreptococcus, and Slackia, revealed significant differences between epithelial precursor lesion and cancer patients and correlated with their classification into two clusters. These composition changes might have the potential to constitute a biomarker to help in monitoring the oral carcinogenesis transition from epithelial precursor lesion to cancer.}, }
@article {pmid29184093, year = {2017}, author = {Stearns, JC and Simioni, J and Gunn, E and McDonald, H and Holloway, AC and Thabane, L and Mousseau, A and Schertzer, JD and Ratcliffe, EM and Rossi, L and Surette, MG and Morrison, KM and Hutton, EK}, title = {Intrapartum antibiotics for GBS prophylaxis alter colonization patterns in the early infant gut microbiome of low risk infants.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {16527}, pmid = {29184093}, issn = {2045-2322}, support = {MSH-136665//CIHR/Canada ; }, mesh = {Adult ; Anti-Bacterial Agents/*administration &amp; dosage ; *Antibiotic Prophylaxis ; Bifidobacterium/drug effects ; Delivery, Obstetric ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Infant ; Infant, Newborn ; Male ; *Maternal Exposure ; Metagenome ; Metagenomics ; Pregnancy ; Streptococcal Infections/*microbiology/*prevention &amp; control ; Streptococcus agalactiae/*drug effects/physiology ; }, abstract = {Early life microbial colonization and succession is critically important to healthy development with impacts on metabolic and immunologic processes throughout life. A longitudinal prospective cohort was recruited from midwifery practices to include infants born at full term gestation to women with uncomplicated pregnancies. Here we compare bacterial community succession in infants born vaginally, with no exposure to antibiotics (n = 53), with infants who were exposed to intrapartum antibiotic prophylaxis (IAP) for Group B Streptococcus (GBS; n = 14), and infants born by C-section (n = 7). Molecular profiles of the 16 S rRNA genes indicate that there is a delay in the expansion of Bifidobacterium, which was the dominate infant gut colonizer, over the first 12 weeks and a persistence of Escherichia when IAP for GBS exposure is present during vaginal labour. Longer duration of IAP exposure increased the magnitude of the effect on Bifidobacterium populations, suggesting a longer delay in microbial community maturation. As with prior studies, we found altered gut colonisation following C-section that included a notable lack of Bacteroidetes. This study found that exposure of infants to IAP for GBS during vaginal birth affected aspects of gut microbial ecology that, although dramatic at early time points, disappeared by 12 weeks of age in most infants.}, }
@article {pmid29463904, year = {2018}, author = {Lavelle, A and Sokol, H}, title = {Gut microbiota: Beyond metagenomics, metatranscriptomics illuminates microbiome functionality in IBD.}, journal = {Nature reviews. Gastroenterology &amp; hepatology}, volume = {15}, number = {4}, pages = {193-194}, pmid = {29463904}, issn = {1759-5053}, mesh = {*Gastrointestinal Microbiome ; Humans ; *Inflammatory Bowel Diseases ; Metagenomics ; *Microbiota ; }, }
@article {pmid29018275, year = {2017}, author = {Ray, K}, title = {Gut microbiota: Human faecal sample processing in metagenomic studies: striving for standards.}, journal = {Nature reviews. Gastroenterology &amp; hepatology}, volume = {14}, number = {11}, pages = {631}, pmid = {29018275}, issn = {1759-5053}, mesh = {Feces ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; }, }
@article {pmid28513633, year = {2017}, author = {Thomas, H}, title = {NAFLD: A gut microbiome signature for advanced fibrosis diagnosis in NAFLD.}, journal = {Nature reviews. Gastroenterology &amp; hepatology}, volume = {14}, number = {7}, pages = {388}, pmid = {28513633}, issn = {1759-5053}, mesh = {Dysbiosis ; Fibrosis ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; *Non-alcoholic Fatty Liver Disease ; }, }
@article {pmid28406159, year = {2017}, author = {Hatzenbuhler, C and Kelly, JR and Martinson, J and Okum, S and Pilgrim, E}, title = {Sensitivity and accuracy of high-throughput metabarcoding methods for early detection of invasive fish species.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {46393}, pmid = {28406159}, issn = {2045-2322}, mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; Fish Proteins/genetics ; Fishes/*classification/embryology/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Introduced Species ; Limit of Detection ; Metagenomics ; Sequence Analysis, DNA/methods ; }, abstract = {High-throughput DNA metabarcoding has gained recognition as a potentially powerful tool for biomonitoring, including early detection of aquatic invasive species (AIS). DNA based techniques are advancing, but our understanding of the limits to detection for metabarcoding complex samples is inadequate. For detecting AIS at an early stage of invasion when the species is rare, accuracy at low detection limits is key. To evaluate the utility of metabarcoding in future fish community monitoring programs, we conducted several experiments to determine the sensitivity and accuracy of routine metabarcoding methods. Experimental mixes used larval fish tissue from multiple &quot;common&quot; species spiked with varying proportions of tissue from an additional &quot;rare&quot; species. Pyrosequencing of genetic marker, COI (cytochrome c oxidase subunit I) and subsequent sequence data analysis provided experimental evidence of low-level detection of the target &quot;rare&quot; species at biomass percentages as low as 0.02% of total sample biomass. Limits to detection varied interspecifically and were susceptible to amplification bias. Moreover, results showed some data processing methods can skew sequence-based biodiversity measurements from corresponding relative biomass abundances and increase false absences. We suggest caution in interpreting presence/absence and relative abundance in larval fish assemblages until metabarcoding methods are optimized for accuracy and precision.}, }
@article {pmid27876768, year = {2017}, author = {Dickson, I}, title = {Gut microbiota: Culturomics: illuminating microbial dark matter.}, journal = {Nature reviews. Gastroenterology &amp; hepatology}, volume = {14}, number = {1}, pages = {3}, pmid = {27876768}, issn = {1759-5053}, mesh = {*Gastrointestinal Microbiome ; *Gastrointestinal Tract ; Humans ; Metagenomics ; }, }
@article {pmid31178526, year = {2019}, author = {Wang, N and Guo, Y and Li, G and Xia, Y and Ma, M and Zang, J and Ma, Y and Yin, X and Han, W and Lv, J and Cao, H}, title = {Geochemical-Compositional-Functional Changes in Arctic Soil Microbiomes Post Land Submergence Revealed by Metagenomics.}, journal = {Microbes and environments}, volume = {34}, number = {2}, pages = {180-190}, doi = {10.1264/jsme2.ME18091}, pmid = {31178526}, issn = {1347-4405}, mesh = {Archaea/classification/genetics ; Archaeal Proteins/genetics/metabolism ; Arctic Regions ; Bacteria/classification/genetics ; Bacterial Proteins/genetics/metabolism ; Biodiversity ; Geologic Sediments/chemistry/*microbiology ; Lakes ; *Metagenomics ; Methane/metabolism ; *Microbiota/genetics ; Nitrogen/metabolism ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Lakes of meltwater in the Artic have become one of the transforming landscape changes under global warming. We herein compared microbial communities between sediments and bank soils at an arctic lake post land submergence using geochemistry, 16S rRNA amplicons, and metagenomes. The results obtained showed that each sample had approximately 2,609 OTUs on average and shared 1,716 OTUs based on the 16S rRNA gene V3-V4 region. Dominant phyla in sediments and soils included Proteobacteria, Acidobacteria, Actinobacteria, Gemmatimonadetes, and Nitrospirae; sediments contained a unique phylum, Euryarchaeota, with the phylum Thaumarchaeota being primarily present in bank soils. Among the top 35 genera across all sites, 17 were more abundant in sediments, while the remaining 18 were more abundant in bank soils; seven out of the top ten genera across all sites were only from sediments. A redundancy analysis separated sediment samples from soil samples based on the components of nitrite and ammonium. Metagenome results supported the role of nitrite because most of the genes for denitrification and methane metabolic genes were more abundant in sediments than in soils, while the abundance of phosphorus-utilizing genes was similar and, thus, was not a significant explanatory factor. We identified several modules from the global networks of OTUs that were closely related to some geochemical factors, such as pH and nitrite. Collectively, the present results showing consistent changes in geochemistry, microbiome compositions, and functional genes suggest an ecological mechanism across molecular and community levels that structures microbiomes post land submergence.}, }
@article {pmid30871224, year = {2019}, author = {Gurwara, S and Ajami, NJ and Jang, A and Hessel, FC and Chen, L and Plew, S and Wang, Z and Graham, DY and Hair, C and White, DL and Kramer, J and Kourkoumpetis, T and Hoffman, K and Cole, R and Hou, J and Husain, N and Jarbrink-Sehgal, M and Hernaez, R and Kanwal, F and Ketwaroo, G and Shah, R and Velez, M and Natarajan, Y and El-Serag, HB and Petrosino, JF and Jiao, L}, title = {Dietary Nutrients Involved in One-Carbon Metabolism and Colonic Mucosa-Associated Gut Microbiome in Individuals with an Endoscopically Normal Colon.}, journal = {Nutrients}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/nu11030613}, pmid = {30871224}, issn = {2072-6643}, support = {RP#140767//Cancer Prevention and Research Institute of Texas/ ; 1000//Gillson Longenbaugh Foundation/ ; 0000//Golfers Against Cancer/ ; }, mesh = {Aged ; Bacteria/*metabolism ; Colon/*microbiology ; Cross-Sectional Studies ; *Diet ; Food Analysis ; Gastrointestinal Microbiome/*drug effects/physiology ; Humans ; Intestinal Mucosa/*microbiology ; Male ; Middle Aged ; Prospective Studies ; }, abstract = {One carbon (1C) metabolism nutrients influence epigenetic regulation and they are supplied by diet and synthesized by gut microbiota. We examined the association between dietary consumption of methyl donors (methionine, betaine and choline) and B vitamins (folate, B2, B6, and B12) and the community composition and structure of the colonic mucosa-associated gut microbiota determined by 16S rRNA gene sequencing in 97 colonic biopsies of 35 men. We used the food frequency questionnaire to assess daily consumption of nutrients, and the UPARSE and SILVA databases for operational taxonomic unit classification. The difference in bacterial diversity and taxonomic relative abundance were compared between low versus high consumption of these nutrients. False discover rate (FDR) adjusted p value < 0.05 indicated statistical significance. The bacterial richness and composition differed significantly by the consumption of folate and B vitamins (p < 0.001). Compared with higher consumption, a lower consumption of these nutrients was associated with a lower abundance of Akkermansia (folate), Roseburia (vitamin B2), and Faecalibacterium (vitamins B2, B6, and B12) but a higher abundance of Erysipelatoclostridium (vitamin B2) (FDR p values < 0.05). The community composition and structure of the colonic bacteria differed significantly by dietary consumption of folate and B vitamins.}, }
@article {pmid30763538, year = {2019}, author = {Gogokhia, L and Buhrke, K and Bell, R and Hoffman, B and Brown, DG and Hanke-Gogokhia, C and Ajami, NJ and Wong, MC and Ghazaryan, A and Valentine, JF and Porter, N and Martens, E and O'Connell, R and Jacob, V and Scherl, E and Crawford, C and Stephens, WZ and Casjens, SR and Longman, RS and Round, JL}, title = {Expansion of Bacteriophages Is Linked to Aggravated Intestinal Inflammation and Colitis.}, journal = {Cell host &amp; microbe}, volume = {25}, number = {2}, pages = {285-299.e8}, doi = {10.1016/j.chom.2019.01.008}, pmid = {30763538}, issn = {1934-6069}, support = {//Wellcome Trust/United Kingdom ; DP2 GM111099/GM/NIGMS NIH HHS/United States ; R00 HL102228/HL/NHLBI NIH HHS/United States ; R01 GM114817/GM/NIGMS NIH HHS/United States ; R01 DK114252/DK/NIDDK NIH HHS/United States ; DP2 AT008746/AT/NCCIH NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*virology ; *Bacteriophages ; CD4-Positive T-Lymphocytes/metabolism ; Colitis, Ulcerative/*immunology/*microbiology/pathology ; Colorectal Neoplasms/*immunology/*microbiology/pathology ; Disease Models, Animal ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; Humans ; Interferon-gamma/metabolism ; Intestinal Mucosa/*immunology/*microbiology/pathology ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Pilot Projects ; Prospective Studies ; Specific Pathogen-Free Organisms ; }, abstract = {Bacteriophages are the most abundant members of the microbiota and have the potential to shape gut bacterial communities. Changes to bacteriophage composition are associated with disease, but how phages impact mammalian health remains unclear. We noted an induction of host immunity when experimentally treating bacterially driven cancer, leading us to test whether bacteriophages alter immune responses. Treating germ-free mice with bacteriophages leads to immune cell expansion in the gut. Lactobacillus, Escherichia, and Bacteroides bacteriophages and phage DNA stimulated IFN-γ via the nucleotide-sensing receptor TLR9. The resultant immune responses were both phage and bacteria specific. Additionally, increasing bacteriophage levels exacerbated colitis via TLR9 and IFN-γ. Similarly, ulcerative colitis (UC) patients responsive to fecal microbiota transplantation (FMT) have reduced phages compared to non-responders, and mucosal IFN-γ positively correlates with bacteriophage levels. Bacteriophages from active UC patients induced more IFN-γ compared to healthy individuals. Collectively, these results indicate that bacteriophages can alter mucosal immunity to impact mammalian health.}, }
@article {pmid29176730, year = {2017}, author = {Junqueira, ACM and Ratan, A and Acerbi, E and Drautz-Moses, DI and Premkrishnan, BNV and Costea, PI and Linz, B and Purbojati, RW and Paulo, DF and Gaultier, NE and Subramanian, P and Hasan, NA and Colwell, RR and Bork, P and Azeredo-Espin, AML and Bryant, DA and Schuster, SC}, title = {The microbiomes of blowflies and houseflies as bacterial transmission reservoirs.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {16324}, pmid = {29176730}, issn = {2045-2322}, mesh = {Animals ; Feces/microbiology ; Helicobacter pylori/isolation &amp; purification ; Houseflies/*microbiology ; Metagenomics ; Microbiota/physiology ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Blowflies and houseflies are mechanical vectors inhabiting synanthropic environments around the world. They feed and breed in fecal and decaying organic matter, but the microbiome they harbour and transport is largely uncharacterized. We sampled 116 individual houseflies and blowflies from varying habitats on three continents and subjected them to high-coverage, whole-genome shotgun sequencing. This allowed for genomic and metagenomic analyses of the host-associated microbiome at the species level. Both fly host species segregate based on principal coordinate analysis of their microbial communities, but they also show an overlapping core microbiome. Legs and wings displayed the largest microbial diversity and were shown to be an important route for microbial dispersion. The environmental sequencing approach presented here detected a stochastic distribution of human pathogens, such as Helicobacter pylori, thereby demonstrating the potential of flies as proxies for environmental and public health surveillance.}, }
@article {pmid29138475, year = {2017}, author = {Lin, JJ and Wang, FY and Li, WH and Wang, TY}, title = {The rises and falls of opsin genes in 59 ray-finned fish genomes and their implications for environmental adaptation.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {15568}, pmid = {29138475}, issn = {2045-2322}, mesh = {Animals ; *Evolution, Molecular ; Fishes/*genetics ; Genome/genetics ; Metagenomics ; Opsins/classification/*genetics ; Phylogeny ; Rod Opsins/classification/*genetics ; Synteny/genetics ; }, abstract = {We studied the evolution of opsin genes in 59 ray-finned fish genomes. We identified the opsin genes and adjacent genes (syntenies) in each genome. Then we inferred the changes in gene copy number (N), syntenies, and tuning sites along each phylogenetic branch during evolution. The Exorh (rod opsin) gene has been retained in 56 genomes. Rh1, the intronless rod opsin gene, first emerged in ancestral Actinopterygii, and N increased to 2 by the teleost-specific whole genome duplication, but then decreased to 1 in the ancestor of Neoteleostei fishes. For cone opsin genes, the rhodopsin-like (Rh2) and long-wave-sensitive (LWS) genes showed great variation in N among species, ranging from 0 to 5 and from 0 to 4, respectively. The two short-wave-sensitive genes, SWS1 and SWS2, were lost in 23 and 6 species, respectively. The syntenies involving LWS, SWS2 and Rh2 underwent complex changes, while the evolution of the other opsin gene syntenies was much simpler. Evolutionary adaptation in tuning sites under different living environments was discussed. Our study provides a detailed view of opsin gene gains and losses, synteny changes and tuning site changes during ray-finned fish evolution.}, }
@article {pmid29123168, year = {2017}, author = {Zheng, S and Shao, S and Qiao, Z and Chen, X and Piao, C and Yu, Y and Gao, F and Zhang, J and Du, J}, title = {Clinical Parameters and Gut Microbiome Changes Before and After Surgery in Thoracic Aortic Dissection in Patients with Gastrointestinal Complications.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {15228}, pmid = {29123168}, issn = {2045-2322}, mesh = {Aneurysm, Dissecting/*surgery ; Bacteria/*classification/genetics ; Blood Chemical Analysis ; Cytokines/blood ; Gastrointestinal Diseases/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; *Microbiota ; Postoperative Complications/*microbiology ; }, abstract = {Thoracic aortic dissection (TAAD) is one of the most common types of aortic diseases. Although surgery remains the main method of treatment, the high rate of postoperative gastrointestinal complications significantly influences the effects of surgery and the recovery process. Moreover, the mechanisms underlying this disease remain unclear. To address these problems, we examined changes in the gut microbiota in 40 thoracic aortic dissection patients with abdominal complications after surgery. Levels of white blood cells (WBC), neutrophile granulocytes (NE), alanine aminotransferase (ALT), and aspartate aminotransferase (AST) were higher in all patients after surgery. Levels of inflammatory cytokines, including interleukin (IL)-2, IL-6, IL-8, and IL-10, were also higher after surgery. A metagenome analysis revealed that levels of Oscillibacter, Anaerotruncus, Alistipes, and Clostridium difficile were higher after the operation. The abundance of functional genes, such as the spermidine/putrescine transport system permease protein, the flagellar motor switch protein, and branched-chain amino acid transport system proteins, was also higher post-surgery. These changes likely contribute to diarrhea, bloating, gastrointestinal bleeding, and other abdominal complications after surgery, and our research opens up new treatment possibilities for patients suffering from abdominal complications after surgical treatment.}, }
@article {pmid29042583, year = {2017}, author = {Xie, K and Deng, Y and Zhang, S and Zhang, W and Liu, J and Xie, Y and Zhang, X and Huang, H}, title = {Prokaryotic Community Distribution along an Ecological Gradient of Salinity in Surface and Subsurface Saline Soils.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {13332}, pmid = {29042583}, issn = {2045-2322}, mesh = {Biodiversity ; Environment ; Geologic Sediments/*chemistry/*microbiology ; Metagenome ; Metagenomics/methods ; Microbiota ; *Prokaryotic Cells ; RNA, Ribosomal, 16S/genetics ; *Salinity ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Salinity effects on microbial communities in saline soils is still unclear, and little is known about subsurface soil microbial communities especially in saline or hypersaline ecosystems. Here we presented the survey of the prokaryotic community in saline soils along a salinity gradient (17.3-148.3 dS/m) in surface (0-10 cm) and subsurface (15-30 cm) saline soils of Qarhan Salt Lake, China. Moreover, we compared them with three paired nonsaline normal soils. Using the high-throughput sequencing technology and several statistical methods, we observed no significant community difference between surface soils and subsurface soils. For environmental factors, we found that TOC was the primary driver of the prokaryotic community distribution in surface saline soils, so was pH in subsurface saline soils. Salinity had more effects on the prokaryotic community in subsurface saline soils than in surface saline soils and played a less important role in saline soils than in saline waters or saline sediments. Our research provided references for the prokaryotic community distribution along a salinity gradient in both surface and subsurface saline soils of arid playa areas.}, }
@article {pmid29026883, year = {2017}, author = {Martinez, KA and Devlin, JC and Lacher, CR and Yin, Y and Cai, Y and Wang, J and Dominguez-Bello, MG}, title = {Increased weight gain by C-section: Functional significance of the primordial microbiome.}, journal = {Science advances}, volume = {3}, number = {10}, pages = {eaao1874}, pmid = {29026883}, issn = {2375-2548}, support = {P30 CA016087/CA/NCI NIH HHS/United States ; T32 AI007180/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Biodiversity ; Body Weight ; *Cesarean Section ; Feces/microbiology ; Female ; Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; Mice ; *Microbiota ; Obesity/etiology ; *Weight Gain ; }, abstract = {Epidemiological evidence supports a direct association between early microbiota impact-including C-section-and obesity. We performed antibiotic-free, fostered C-sections and determined the impact on the early microbiota and body weight during development. Mice in the C-section group gained more body mass after weaning, with a stronger phenotype in females. C-section-born mice lacked the dynamic developmental gut microbiota changes observed in control mice. The results demonstrate a causal relationship between C-section and increased body weight, supporting the involvement of maternal vaginal bacteria in normal metabolic development.}, }
@article {pmid30470178, year = {2018}, author = {Griffith, BC and Weiss, BL and Aksoy, E and Mireji, PO and Auma, JE and Wamwiri, FN and Echodu, R and Murilla, G and Aksoy, S}, title = {Analysis of the gut-specific microbiome from field-captured tsetse flies, and its potential relevance to host trypanosome vector competence.}, journal = {BMC microbiology}, volume = {18}, number = {Suppl 1}, pages = {146}, pmid = {30470178}, issn = {1471-2180}, support = {D43 TW007391/TW/FIC NIH HHS/United States ; R01 AI051584/AI/NIAID NIH HHS/United States ; R01 AI068932/AI/NIAID NIH HHS/United States ; U01 AI115648/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*classification ; *Gastrointestinal Microbiome ; Geography ; High-Throughput Nucleotide Sequencing ; Insect Vectors/*microbiology/parasitology ; Kenya ; Symbiosis ; Trypanosoma/*physiology ; Tsetse Flies/*microbiology/parasitology ; Uganda ; }, abstract = {BACKGROUND: The tsetse fly (Glossina sp.) midgut is colonized by maternally transmitted and environmentally acquired bacteria. Additionally, the midgut serves as a niche in which pathogenic African trypanosomes reside within infected flies. Tsetse's bacterial microbiota impacts many aspects of the fly's physiology. However, little is known about the structure of tsetse's midgut-associated bacterial communities as they relate to geographically distinct fly habitats in east Africa and their contributions to parasite infection outcomes. We utilized culture dependent and independent methods to characterize the taxonomic structure and density of bacterial communities that reside within the midgut of tsetse flies collected at geographically distinct locations in Kenya and Uganda.<br><br>RESULTS: Using culture dependent methods, we isolated 34 strains of bacteria from four different tsetse species (G. pallidipes, G. brevipalpis, G. fuscipes and G. fuscipleuris) captured at three distinct locations in Kenya. To increase the depth of this study, we deep sequenced midguts from individual uninfected and trypanosome infected G. pallidipes captured at two distinct locations in Kenya and one in Uganda. We found that tsetse's obligate endosymbiont, Wigglesworthia, was the most abundant bacterium present in the midgut of G. pallidipes, and the density of this bacterium remained largely consistent regardless of whether or not its tsetse host was infected with trypanosomes. These fly populations also housed the commensal symbiont Sodalis, which was found at significantly higher densities in trypanosome infected compared to uninfected flies. Finally, midguts of field-captured G. pallidipes were colonized with distinct, low density communities of environmentally acquired microbes that differed in taxonomic structure depending on parasite infection status and the geographic location from which the flies were collected.<br><br>CONCLUSIONS: The results of this study will enhance our understanding of the tripartite relationship between tsetse, its microbiota and trypanosome vector competence. This information may be useful for developing novel disease control strategies or enhancing the efficacy of those already in use.}, }
@article {pmid30427574, year = {2019}, author = {Barnes, RC and Kim, H and Fang, C and Bennett, W and Nemec, M and Sirven, MA and Suchodolski, JS and Deutz, N and Britton, RA and Mertens-Talcott, SU and Talcott, ST}, title = {Body Mass Index as a Determinant of Systemic Exposure to Gallotannin Metabolites during 6-Week Consumption of Mango (Mangifera indica L.) and Modulation of Intestinal Microbiota in Lean and Obese Individuals.}, journal = {Molecular nutrition &amp; food research}, volume = {63}, number = {2}, pages = {e1800512}, doi = {10.1002/mnfr.201800512}, pmid = {30427574}, issn = {1613-4133}, mesh = {Adult ; *Body Mass Index ; Fatty Acids, Volatile/biosynthesis ; Feces/chemistry ; Female ; *Gastrointestinal Microbiome ; Humans ; Hydrolyzable Tannins/*metabolism ; Male ; *Mangifera/chemistry ; Obesity/*metabolism/microbiology ; Phenols/analysis ; Polymerase Chain Reaction ; }, abstract = {SCOPE: This human clinical pilot trial investigated pharmacokinetics of gallotannin-metabolites and modulation of intestinal microbiota in healthy lean and obese individuals after 6 weeks of daily mango consumption.<br><br>METHODS AND RESULTS: Participants are divided into three groups: Lean Mango (LM: n = 12; BMI = 22.9 kg m-2), Obese Mango (OM: n = 9; BMI = 34.6 kg m-2), and Lean Control (LC: n = 11; BMI = 22.1 kg m-2). LM and OM consumed 400 g of mango per day for 6 weeks. LC consumed mango only on Days 0 and 42. After 6 weeks, LM experienced increased systemic exposure (AUC0-8h) to gallotannin-metabolites, 1.4-fold (p = 0.043). The greatest increase is 4-O-methyl-gallic acid, 3.3-fold (p = 0.0026). Cumulative urinary excretion of gallotannin-metabolites significantly increased in LM and OM, but not LC. For OM, qPCR data show increased levels of tannase-producing Lactococcus lactis and decreased levels of Clostridium leptum and Bacteroides thetaiotaomicron, bacteria associated with obesity. LM experienced an increased trend of fecal levels of butyric (1.3-fold; p = 0.09) and valeric acids (1.5-fold; p = 0.056). Plasma endotoxins showed a decreased trend in LM and OM.<br><br>CONCLUSION: Continuous mango intake significantly increased systemic exposure to gallotannin- metabolites and induced an increased trend for fecal short-chain fatty acids in lean but not obese individuals. This pharmacokinetic discrepancy may result in BMI-associated reduced gallotannin-derived health benefits.}, }
@article {pmid30355340, year = {2018}, author = {Mailhe, M and Ricaboni, D and Vitton, V and Gonzalez, JM and Bachar, D and Dubourg, G and Cadoret, F and Robert, C and Delerce, J and Levasseur, A and Fournier, PE and Angelakis, E and Lagier, JC and Raoult, D}, title = {Repertoire of the gut microbiota from stomach to colon using culturomics and next-generation sequencing.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {157}, pmid = {30355340}, issn = {1471-2180}, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/*classification/isolation &amp; purification ; Colon/*microbiology ; Colonoscopy ; Colony Count, Microbial ; DNA, Bacterial/genetics ; Endoscopy, Digestive System ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Hydrogen-Ion Concentration ; Male ; *Metagenomics ; Middle Aged ; Proton Pump Inhibitors/administration &amp; dosage ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Stomach/*microbiology ; Young Adult ; }, abstract = {BACKGROUND: Most studies on the human microbiota have analyzed stool samples, although a large proportion of the absorption of nutrients takes place in upper gut tract. We collected samples from different locations along the entire gastrointestinal tract from six patients who had simultaneously undergone upper endoscopy and colonoscopy, to perform a comprehensive analysis using culturomics with matrix assisted laser desorption ionisation - time of flight (MALDI-TOF) identification and by metagenomics targeting the 16S ribosomal ribonucleic acid (rRNA) gene.<br><br>RESULTS: Using culturomics, we isolated 368 different bacterial species, including 37 new species. Fewer species were isolated in the upper gut: 110 in the stomach and 106 in the duodenum, while 235 were isolated from the left colon (p < 0.02). We isolated fewer aero-intolerant species in the upper gut: 37 from the stomach and 150 from the left colon (p < 0.004). Using metagenomics, 1,021 species were identified. The upper gut microbiota was revealed to be less rich than the lower gut microbiota, with 37,622 reads from the stomach, 28,390 from the duodenum, and 79,047 from the left colon (p < 0.009). There were fewer reads for aero-intolerant species in the upper gut (8,656 in the stomach, 5,188 in the duodenum and 72,262 in the left colon, p < 0.02). Patients taking proton pump inhibitors (PPI) were then revealed to have a higher stomach pH and a greater diversity of species in the upper digestive tract than patients not receiving treatment (p < 0.001).<br><br>CONCLUSION: Significant modifications in bacterial composition and diversity exist throughout the gastrointestinal tract. We suggest that the upper gut may be key to understanding the relationship between the gut microbiota and health.}, }
@article {pmid28125344, year = {2017}, author = {Walsh, AM and Crispie, F and Claesson, MJ and Cotter, PD}, title = {Translating Omics to Food Microbiology.}, journal = {Annual review of food science and technology}, volume = {8}, number = {}, pages = {113-134}, doi = {10.1146/annurev-food-030216-025729}, pmid = {28125344}, issn = {1941-1413}, mesh = {*Food Microbiology ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenomics ; Probiotics ; *Transcriptome ; }, abstract = {This review examines the applications of omics technologies in food microbiology, with a primary focus on high-throughput sequencing (HTS) technologies. We discuss the different sequencing approaches applicable to the study of food-related microbial isolates and mixed microbial communities in foods, and we provide an overview of the sequencing platforms suitable for each approach. We highlight the potential for genomics, metagenomics, and metatranscriptomics to guide efforts to optimize food fermentations. Additionally, we explore the use of comparative and functional genomics to further our understanding of the mechanisms of probiotic action and we describe the applicability of HTS as a food safety measure. Finally, we consider the use of HTS to investigate the effects that ingested microbes have on the human gut microbiota.}, }
@article {pmid31126262, year = {2019}, author = {Ke, S and Fang, S and He, M and Huang, X and Yang, H and Yang, B and Chen, C and Huang, L}, title = {Age-based dynamic changes of phylogenetic composition and interaction networks of health pig gut microbiome feeding in a uniformed condition.}, journal = {BMC veterinary research}, volume = {15}, number = {1}, pages = {172}, doi = {10.1186/s12917-019-1918-5}, pmid = {31126262}, issn = {1746-6148}, support = {31772579//National Natural Science Foundation of China/ ; 31472071//National Natural Science Foundation of China/ ; }, mesh = {*Age Factors ; Animals ; Bacteria/*classification/genetics ; Bacterial Typing Techniques ; Female ; Gastrointestinal Microbiome/*physiology ; Male ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sus scrofa/*microbiology ; }, abstract = {BACKGROUND: The gut microbiota impacts on a range of host biological processes, and the imbalances in its composition are associated with pathology. Though the understanding of contribution of the many factors, e.g. gender, diet and age, in the development of gut microbiota has been well established, the dynamic changes of the phylogenetic composition and the interaction networks along with the age remain unclear in pigs.<br><br>RESULTS: Here we applied 16S ribosomal RNA gene sequencing, enterotype-like clustering (Classification of the gut microbiome into distinct types) and phylogenetic co-occurrence network to explore the dynamic changes of pig gut microbiome following the ages with a successive investigation at four ages in a cohort of 953 pigs. We found that Firmicutes and Bacteroidetes are two predominant phyla throughout the experimental period. The richness of gut microbiota was significantly increased from 25 to 240 days of age. Principal coordinates analysis showed a clear difference in the gut microbial community compositions between pre-weaning piglets and the pigs at the other three age groups. The gut microbiota of pre-weaning piglets was clearly classified into two enterotypes, which were dominated by Fusobacterium and p-75-a5, respectively. However, Prevotella and Treponema were the main drivers of the enterotypes for pigs at the age of 80, 120 and 240 days. Besides the piglets, even some adult pigs switched putative enterotypes between ages. We confirmed that the topological features of phylogenetic co-occurrence networks, including scale, stability and complexity were increased along with the age. The biological significance for modules in the network of piglets were mainly associated with the utilization of simple carbohydrate and lactose, whereas the sub-networks identified at the ages of 80, 120 and 240 days may be involved in the digestion of complex dietary polysaccharide. The modules related to the metabolism of protein and amino acids could be identified in the networks at 120 and 240 days. This dynamic change of the functional capacities of gut microbiome was further supported by functional prediction analysis.<br><br>CONCLUSIONS: The present study provided meaningful biological insights into the age-based dynamic shifts of ecological community of porcine gut microbiota.}, }
@article {pmid30298261, year = {2018}, author = {Adeolu, M and Parkinson, J and Xiong, X}, title = {Analyzing Metabolic Pathways in Microbiomes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1849}, number = {}, pages = {291-307}, doi = {10.1007/978-1-4939-8728-3_18}, pmid = {30298261}, issn = {1940-6029}, mesh = {High-Throughput Nucleotide Sequencing/*methods ; Humans ; *Metabolic Networks and Pathways ; Metagenomics ; *Microbiota ; *Transcriptome ; }, abstract = {Understanding the metabolic activity of a microbial community, at both the level of the individual microbe and the whole microbiome, provides fundamental biological, biochemical, and clinical insights into the nature of the microbial community and interactions with their hosts in health and disease. Here, we discuss a method to examine the expression of metabolic pathways in microbial communities using data from metatranscriptomic next-generation sequencing data. The methodology described here encompasses enzyme function annotation, differential enzyme expression and pathway enrichment analyses, and visualization of metabolic networks with differential enzyme expression levels.}, }
@article {pmid30298260, year = {2018}, author = {Dunn, KA and Andrews, K and Bashwih, RO and Bielawski, JP}, title = {Bayesian Inference of Microbial Community Structure from Metagenomic Data Using BioMiCo.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1849}, number = {}, pages = {267-289}, doi = {10.1007/978-1-4939-8728-3_17}, pmid = {30298260}, issn = {1940-6029}, mesh = {*Algorithms ; *Bayes Theorem ; Computational Biology/*methods ; Metagenomics/*methods ; *Microbiota ; }, abstract = {Microbial samples taken from an environment often represent mixtures of communities, where each community is composed of overlapping assemblages of species. Such data represent a serious analytical challenge, as the community structures will be present as complex mixtures, there will be very large numbers of component species, and the species abundance will often be sparse over samples. The structure and complexity of these samples will vary according to both biotic and abiotic factors, and classical methods of data analysis will have a limited value in this setting. A novel Bayesian modeling framework, called BioMiCo, was developed to meet this challenge. BioMiCo takes abundance data derived from environmental DNA, and models each sample by a two-level mixture, where environmental OTUs contribute community structures, and those structures are related to the known biotic and abiotic features of each sample. The model is constrained by Dirichlet priors, which induces compact structures, minimizes variance, and maximizes model interpretability. BioMiCo is trained on a portion of the data, and once trained a BioMiCo model can be employed to make predictions about the features of new samples. This chapter provides a set of protocols that illustrate the application of BioMiCo to real inference problems. Each protocol is designed around the analysis of a real dataset, which was carefully chosen to illustrate specific aspects of real data analysis. With these protocols, users of BioMiCo will be able to undertake basic research into the properties of complex microbial systems, as well as develop predictive models for applied microbiomics.}, }
@article {pmid30298257, year = {2018}, author = {Hug, LA}, title = {Subsampled Assemblies and Hybrid Nucleotide Composition/Differential Coverage Binning for Genome-Resolved Metagenomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1849}, number = {}, pages = {215-225}, doi = {10.1007/978-1-4939-8728-3_14}, pmid = {30298257}, issn = {1940-6029}, mesh = {Algorithms ; *Genome, Microbial ; Metagenomics/*methods ; *Microbiota ; Nucleotides/*genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Metagenomic analyses for reconstruction of genomes from mixed microbial community datasets now routinely allow rapid, accurate genome recovery for tens to hundreds of organisms from environmental samples. This chapter provides a step-by-step protocol for reconstructing genomes from metagenomic datasets, with a focus on the most abundant community members. Subsampling assembly approaches are implemented to improve assembly of abundant genome sequences, an iterative process that targets progressively less abundant populations and improves total community representation in the final merged assembly. A hybrid approach to genome binning is described, combining differential coverage information from a series of metagenomic samples with nucleotide composition information. This approach strengthens binning through application of multiple independent variables for contig clustering. Genome curation through error correction and gap closure leads to high-quality draft genomes, and, for some community members, closed and complete genome sequences reconstructed directly from environmental samples.}, }
@article {pmid30298255, year = {2018}, author = {Zhang, Q}, title = {Metagenome Assembly and Contig Assignment.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1849}, number = {}, pages = {179-192}, doi = {10.1007/978-1-4939-8728-3_12}, pmid = {30298255}, issn = {1940-6029}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Computational Biology/methods ; DNA Barcoding, Taxonomic/*methods ; High-Throughput Nucleotide Sequencing/*methods ; *Metagenome ; Microbiota ; Molecular Sequence Annotation ; *Software ; }, abstract = {The recent development of metagenomic assembly has revolutionized metagenomic data analysis, thanks to the improvement of sequencing techniques, more powerful computational infrastructure and the development of novel algorithms and methods. Using longer assembled contigs rather than raw reads improves the process of metagenomic binning and annotation significantly, ultimately resulting in a deeper understanding of the microbial dynamics of the metagenomic samples being analyzed. In this chapter, we demonstrate a typical metagenomic analysis pipeline including raw read quality evaluation and trimming, assembly and contig binning. Alternative tools that can be used for each step are also discussed.}, }
@article {pmid30298253, year = {2018}, author = {McMurdie, PJ}, title = {Normalization of Microbiome Profiling Data.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1849}, number = {}, pages = {143-168}, doi = {10.1007/978-1-4939-8728-3_10}, pmid = {30298253}, issn = {1940-6029}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Computational Biology/*methods ; Data Analysis ; High-Throughput Nucleotide Sequencing/*methods ; *Metagenome ; *Microbiota ; Phylogeny ; *Software ; }, abstract = {Normalization is a term that is often used but rarely defined and poorly understood. The number of choices of normalization procedure is large-some are inappropriate or inadmissible-and all are narrowly relevant to a specific analysis that depends on both the nature of the data and the question being asked. This chapter describes key definitions of normalization as they apply in metagenomics, mainly for taxonomic profiling data; while also demonstrating specific, reproducible examples of normalization procedures in the context of analysis techniques for which they were intended. The analysis and graphics code is distributed as a supplemental companion to this chapter so that the motivated reader can re-use it on new data.}, }
@article {pmid30298244, year = {2018}, author = {Daly, RA and Wrighton, KC and Wilkins, MJ}, title = {Characterizing the Deep Terrestrial Subsurface Microbiome.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1849}, number = {}, pages = {1-15}, doi = {10.1007/978-1-4939-8728-3_1}, pmid = {30298244}, issn = {1940-6029}, mesh = {Bacteria/*classification/*genetics ; Biomass ; DNA, Bacterial/*analysis ; Gene Library ; Geologic Sediments/*microbiology ; Metagenomics ; *Microbiota ; Soil Microbiology ; Water Microbiology ; }, abstract = {A large portion of the earth's biomass resides in the subsurface and recent studies have expanded our knowledge of indigenous microbial life. Advances in the field of metagenomics now allow analysis of microbial communities from low-biomass samples such as deep (>2.5 km) shale core samples. Here we present protocols for the best practices in contamination control, handling core material, extraction of nucleic acids, and low-input library preparation for subsequent metagenomic sequencing.}, }
@article {pmid31267680, year = {2019}, author = {Taubert, M and Grob, C and Crombie, A and Howat, AM and Burns, OJ and Weber, M and Lott, C and Kaster, AK and Vollmers, J and Jehmlich, N and von Bergen, M and Chen, Y and Murrell, JC}, title = {Communal metabolism by Methylococcaceae and Methylophilaceae is driving rapid aerobic methane oxidation in sediments of a shallow seep near Elba, Italy.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14728}, pmid = {31267680}, issn = {1462-2920}, abstract = {Release of abiotic methane from marine seeps into the atmosphere is a major source of this potent greenhouse gas. Methanotrophic microorganisms in methane seeps use methane as carbon and energy source, thus significantly mitigating global methane emissions. Here we investigated microbial methane oxidation at the sediment-water interface of a shallow marine methane seep. Metagenomics and metaproteomics, combined with 13 C-methane stable isotope probing, demonstrated that various members of the gammaproteobacterial family Methylococcaceae were the key players for methane oxidation, catalyzing the first reaction step to methanol. We observed a transfer of carbon to methanol-oxidizing methylotrophs of the betaproteobacterial family Methylophilaceae, suggesting an interaction between methanotrophic and methylotrophic microorganisms that allowed for rapid methane oxidation. From our microcosms, we estimated methane oxidation rates of up to 871 nmol of methane per gram sediment and day. This implies that more than 50% of methane at the seep is removed by microbial oxidation at the sediment-water interface, based on previously reported in situ methane fluxes. The organic carbon produced was further assimilated by different heterotrophic microbes, demonstrating that the methane-oxidizing community supported a complex trophic network. Our results provide valuable eco-physiological insights into this specialized microbial community performing an ecosystem function of global relevance. This article is protected by copyright. All rights reserved.}, }
@article {pmid31266971, year = {2019}, author = {Fernández-Correa, I and Truchado, DA and Gomez-Lucia, E and Doménech, A and Pérez-Tris, J and Schmidt-Chanasit, J and Cadar, D and Benítez, L}, title = {A novel group of avian astroviruses from Neotropical passerine birds broaden the diversity and host range of Astroviridae.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {9513}, doi = {10.1038/s41598-019-45889-3}, pmid = {31266971}, issn = {2045-2322}, support = {CGL2017-82117-P//Ministry of Economy and Competitiveness | Agencia Estatal de Investigaci&amp;#x00F3;n (Spanish Agencia Estatal de Investigaci&amp;#x00F3;n)/ ; CGL2017-82117-P//Ministry of Economy and Competitiveness | Agencia Estatal de Investigaci&amp;#x00F3;n (Spanish Agencia Estatal de Investigaci&amp;#x00F3;n)/ ; CT27/16-CT28/16//Universidad Complutense de Madrid (Complutense University of Madrid)/ ; }, abstract = {Metagenomics is helping to expand the known diversity of viruses, especially of those with poorly studied hosts in remote areas. The Neotropical region harbors a considerable diversity of avian species that may play a role as both host and short-distance vectors of unknown viruses. Viral metagenomics of cloacal swabs from 50 Neotropical birds collected in French Guiana revealed the presence of four complete astrovirus genomes. They constitute an early diverging novel monophyletic clade within the Avastrovirus phylogeny, representing a putative new astrovirus species (provisionally designated as Avastrovirus 5) according to the International Committee on Taxonomy of Viruses (ICTV) classification criteria. Their genomic organization shares some characteristics with Avastrovirus but also with Mamastrovirus. The pan-astrovirus RT-PCR analysis of the cloacal samples of 406 wild Neotropical birds showed a community-level prevalence of 4.9% (5.1% in passerines, the highest described so far in this order of birds). By screening birds of a remote region, we expanded the known host range of astroviruses to the avian families Cardinalidae, Conopophagidae, Furnariidae, Thamnophilidae, Turdidae and Tyrannidae. Our results provide important first insights into the unexplored viral communities, the ecology, epidemiology and features of host-pathogen interactions that shape the evolution of avastroviruses in a remote Neotropical rainforest.}, }
@article {pmid31036930, year = {2019}, author = {Zhang, J and Liu, YX and Zhang, N and Hu, B and Jin, T and Xu, H and Qin, Y and Yan, P and Zhang, X and Guo, X and Hui, J and Cao, S and Wang, X and Wang, C and Wang, H and Qu, B and Fan, G and Yuan, L and Garrido-Oter, R and Chu, C and Bai, Y}, title = {NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice.}, journal = {Nature biotechnology}, volume = {37}, number = {6}, pages = {676-684}, doi = {10.1038/s41587-019-0104-4}, pmid = {31036930}, issn = {1546-1696}, mesh = {Alleles ; Anion Transport Proteins/chemistry/*genetics ; Bacteria/classification/*genetics ; Genotype ; Metagenomics ; Microbiota/*genetics ; Nitrogen/metabolism ; Oryza/*genetics/growth &amp; development/metabolism/microbiology ; Phylogeny ; Plant Breeding ; Plant Roots/genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Nitrogen-use efficiency of indica varieties of rice is superior to that of japonica varieties. We apply 16S ribosomal RNA gene profiling to characterize root microbiota of 68 indica and 27 japonica varieties grown in the field. We find that indica and japonica recruit distinct root microbiota. Notably, indica-enriched bacterial taxa are more diverse, and contain more genera with nitrogen metabolism functions, than japonica-enriched taxa. Using genetic approaches, we provide evidence that NRT1.1B, a rice nitrate transporter and sensor, is associated with the recruitment of a large proportion of indica-enriched bacteria. Metagenomic sequencing reveals that the ammonification process is less abundant in the root microbiome of the nrt1.1b mutant. We isolated 1,079 pure bacterial isolates from indica and japonica roots and derived synthetic communities (SynComs). Inoculation of IR24, an indica variety, with an indica-enriched SynCom improved rice growth in organic nitrogen conditions compared with a japonica-enriched SynCom. The links between plant genotype and root microbiota membership established in this study will inform breeding strategies to improve nitrogen use in crops.}, }
@article {pmid31264806, year = {2019}, author = {Pereira, O and Hochart, C and Auguet, JC and Debroas, D and Galand, PE}, title = {Genomic ecology of Marine Group II, the most common marine planktonic Archaea across the surface ocean.}, journal = {MicrobiologyOpen}, volume = {}, number = {}, pages = {e852}, doi = {10.1002/mbo3.852}, pmid = {31264806}, issn = {2045-8827}, support = {ANR-14-CE02-0004-01//Agence Nationale de la Recherche/ ; }, abstract = {Planktonic Archaea have been detected in all the world's oceans and are found from surface waters to the deep sea. The two most common Archaea phyla are Thaumarchaeota and Euryarchaeota. Euryarchaeota are generally more common in surface waters, but very little is known about their ecology and their potential metabolisms. In this study, we explore the genomic ecology of the Marine Group II (MGII), the main marine planktonic Euryarchaeota, and test if it is composed of different ecologically relevant units. We re-analyzed Tara Oceans metagenomes from the photic layer and the deep ocean by annotating sequences against a custom MGII database and by mapping gene co-occurrences. Our data provide a global view of the distribution of Euryarchaeota, and more specifically of MGII subgroups, and reveal their association to a number of gene-coding sequences. In particular, we show that MGII proteorhodopsins were detected in both the surface and the deep chlorophyll maximum layer and that different clusters of these light harvesting proteins were present. Our approach helped describing the set of genes found together with specific MGII subgroups. We could thus define genomic environments that could theoretically describe ecologically meaningful units and the ecological niche that they occupy.}, }
@article {pmid30606403, year = {2019}, author = {Gong, J and Noel, S and Pluznick, JL and Hamad, ARA and Rabb, H}, title = {Gut Microbiota-Kidney Cross-Talk in Acute Kidney Injury.}, journal = {Seminars in nephrology}, volume = {39}, number = {1}, pages = {107-116}, doi = {10.1016/j.semnephrol.2018.10.009}, pmid = {30606403}, issn = {1558-4488}, support = {R01 DK111209/DK/NIDDK NIH HHS/United States ; }, mesh = {Acute Kidney Injury/immunology/*microbiology ; Animals ; Blood Pressure ; Dysbiosis/*complications ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*immunology ; Humans ; Methylamines/metabolism ; Prebiotics ; Probiotics/therapeutic use ; Uremia/microbiology ; }, abstract = {The recent surge in research on the intestinal microbiota has greatly changed our understanding of human biology. Significant technical advances in DNA sequencing analysis and its application to metagenomics and metatranscriptomics has profoundly enhanced our ability to quantify and track complex microbial communities and to begin understanding their impact on human health and disease. This has led to a better understanding of the relationships between the intestinal microbiome and renal physiology/pathophysiology. In this review, we discuss the interactions between intestinal microbiota and kidney. We focus on select aspects including the intestinal barrier, immunologic and soluble mediators of microbiome effects, and effects of dysbiosis on acute kidney injury. Relevant studies on microbiome changes in other renal diseases are highlighted. We also introduce potential mechanisms of intervention with regard to gut microbiota in renal diseases.}, }
@article {pmid31034867, year = {2019}, author = {Tsiaoussis, J and Antoniou, MN and Koliarakis, I and Mesnage, R and Vardavas, CI and Izotov, BN and Psaroulaki, A and Tsatsakis, A}, title = {Effects of single and combined toxic exposures on the gut microbiome: Current knowledge and future directions.}, journal = {Toxicology letters}, volume = {312}, number = {}, pages = {72-97}, doi = {10.1016/j.toxlet.2019.04.014}, pmid = {31034867}, issn = {1879-3169}, mesh = {Environmental Pollutants/*toxicity ; Gastrointestinal Microbiome/*drug effects ; Hazardous Substances/*toxicity ; Humans ; }, abstract = {Human populations are chronically exposed to mixtures of toxic chemicals. Predicting the health effects of these mixtures require a large amount of information on the mode of action of their components. Xenobiotic metabolism by bacteria inhabiting the gastrointestinal tract has a major influence on human health. Our review aims to explore the literature for studies looking to characterize the different modes of action and outcomes of major chemical pollutants, and some components of cosmetics and food additives, on gut microbial communities in order to facilitate an estimation of their potential mixture effects. We identified good evidence that exposure to heavy metals, pesticides, nanoparticles, polycyclic aromatic hydrocarbons, dioxins, furans, polychlorinated biphenyls, and non-caloric artificial sweeteners affect the gut microbiome and which is associated with the development of metabolic, malignant, inflammatory, or immune diseases. Answering the question 'Who is there?' is not sufficient to define the mode of action of a toxicant in predictive modeling of mixture effects. Therefore, we recommend that new studies focus to simulate real-life exposure to diverse chemicals (toxicants, cosmetic/food additives), including as mixtures, and which combine metagenomics, metatranscriptomics and metabolomic analytical methods achieving in that way a comprehensive evaluation of effects on human health.}, }
@article {pmid30866822, year = {2019}, author = {Lee, Y and Schmidt, H and Collier, TC and Conner, WR and Hanemaaijer, MJ and Slatkin, M and Marshall, JM and Chiu, JC and Smartt, CT and Lanzaro, GC and Mulligan, FS and Cornel, AJ}, title = {Genome-wide divergence among invasive populations of Aedes aegypti in California.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {204}, doi = {10.1186/s12864-019-5586-4}, pmid = {30866822}, issn = {1471-2164}, support = {U01CK000516//ACL HHS/United States ; HR0011-17-2-0047//Defense Sciences Office, DARPA/ ; 1U01CK000516//Centers for Disease Control and Prevention/ ; }, mesh = {Aedes/*classification/genetics ; Animals ; California ; Evolution, Molecular ; Genetic Variation ; Genetics, Population ; Genome Size ; *Genome, Insect ; Introduced Species ; Metagenomics ; Mosquito Vectors/classification/genetics ; Phylogeny ; Phylogeography ; Whole Genome Sequencing/*veterinary ; }, abstract = {BACKGROUND: In the summer of 2013, Aedes aegypti Linnaeus was first detected in three cities in central California (Clovis, Madera and Menlo Park). It has now been detected in multiple locations in central and southern CA as far south as San Diego and Imperial Counties. A number of published reports suggest that CA populations have been established from multiple independent introductions.<br><br>RESULTS: Here we report the first population genomics analyses of Ae. aegypti based on individual, field collected whole genome sequences. We analyzed 46 Ae. aegypti genomes to establish genetic relationships among populations from sites in California, Florida and South Africa. Based on 4.65 million high quality biallelic SNPs, we identified 3 major genetic clusters within California; one that includes all sample sites in the southern part of the state (South of Tehachapi mountain range) plus the town of Exeter in central California and two additional clusters in central California.<br><br>CONCLUSIONS: A lack of concordance between mitochondrial and nuclear genealogies suggests that the three founding populations were polymorphic for two main mitochondrial haplotypes prior to being introduced to California. One of these has been lost in the Clovis populations, possibly by a founder effect. Genome-wide comparisons indicate extensive differentiation between genetic clusters. Our observations support recent introductions of Ae. aegypti into California from multiple, genetically diverged source populations. Our data reveal signs of hybridization among diverged populations within CA. Genetic markers identified in this study will be of great value in pursuing classical population genetic studies which require larger sample sizes.}, }
@article {pmid30866812, year = {2019}, author = {Das, P and Babaei, P and Nielsen, J}, title = {Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {208}, doi = {10.1186/s12864-019-5591-7}, pmid = {30866812}, issn = {1471-2164}, support = {HEALTH-F4-2012-305312//METACARDIS/ ; }, mesh = {Bacteria/*classification/genetics/isolation &amp; purification/metabolism ; Bacterial Proteins/*genetics ; China ; Feces/microbiology ; Gastrointestinal Microbiome ; Gene Expression Profiling ; Humans ; Metagenomics/*methods ; Phylogeny ; Phylogeography ; United States ; Vitamins/*metabolism ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: Human gut microbial communities have been known to produce vitamins, which are subsequently absorbed by the host in the large intestine. However, the relationship between species with vitamin pathway associated functional features or their gene abundance in different states of health and disease is lacking. Here, we analyzed shotgun fecal metagenomes of individuals from four different countries for genes that are involved in vitamin biosynthetic pathways and transport mechanisms and corresponding species' abundance.<br><br>RESULTS: We found that the prevalence of these genes were found to be distributed across the dominant phyla of gut species. The number of positive correlations were high between species harboring genes related to vitamin biosynthetic pathways and transporter mechanisms than that with either alone. Although, the range of total gene abundances remained constant across healthy populations at the global level, species composition and their presence for metabolic pathway related genes determine the abundance and functional genetic content of vitamin metabolism. Based on metatranscriptomics data, the equation between abundance of vitamin-biosynthetic enzymes and vitamin-dependent enzymes suggests that the production and utilization potential of these enzymes seems way more complex usage allocations than just mere direct linear associations.<br><br>CONCLUSIONS: Our findings provide a rationale to examine and disentangle the interrelationship between B-vitamin dosage (dietary or microbe-mediated) on gut microbial members and the host, in the gut microbiota of individuals with under- or overnutrition.}, }
@article {pmid30452938, year = {2018}, author = {Bilal, T and Malik, B and Hakeem, KR}, title = {Metagenomic analysis of uncultured microorganisms and their enzymatic attributes.}, journal = {Journal of microbiological methods}, volume = {155}, number = {}, pages = {65-69}, doi = {10.1016/j.mimet.2018.11.014}, pmid = {30452938}, issn = {1872-8359}, mesh = {Bioengineering/methods ; Biofuels ; Biotechnology ; Enzyme Activation ; *Enzymes/genetics/metabolism ; Extremophiles/*enzymology/*genetics ; Genome, Microbial/*genetics ; Genomics ; Metagenomics/*methods ; Microbiological Techniques/methods ; Microbiota/genetics ; }, abstract = {Although second generation biofuel technology is a sustainable route for bioethanol production it is not currently a robust technology because of certain hindrances viz., unavailability of potential enzyme resources, low efficiency of enzymes and restricted availability of potent enzymes that work under harsh conditions in industrial processes. Therefore, bioprospecting of extremophilic microorganisms using metagenomics is a promising alternative to discover novel microbes and enzymes with efficient tolerance to unfavourable conditions and thus could revolutionize the energy sector. Metagenomics a recent field in &quot;omics&quot; technology enables the genomic study of uncultured microorganisms with the goal of better understanding microbial dynamics. Metagenomics in conjunction with NextGen Sequencing technology facilitates the sequencing of microbial DNA directly from environmental samples and has expanded, and transformed our knowledge of the microbial world. However, filtering the meaningful information from the millions of genomic sequences offers a serious challenge to bioinformaticians. The current review holds the opinion tool 'know- how' to unravel the secrets of nature while expediting the bio-industrial world. We also discuss the novel biocatalytic agents discovered through metagenomics and how bioengineering plays a pivotal role to enhance their efficiency.}, }
@article {pmid30287354, year = {2018}, author = {Staley, C and Sadowsky, MJ}, title = {Practical considerations for sampling and data analysis in contemporary metagenomics-based environmental studies.}, journal = {Journal of microbiological methods}, volume = {154}, number = {}, pages = {14-18}, doi = {10.1016/j.mimet.2018.09.020}, pmid = {30287354}, issn = {1872-8359}, mesh = {Algorithms ; Biodiversity ; Biostatistics/methods ; Computational Biology/methods ; DNA/analysis/isolation &amp; purification ; *Data Analysis ; Ecology ; Ecosystem ; Environment ; *Environmental Microbiology ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Metagenome ; Metagenomics/*methods ; Microbiota/genetics ; Phylogeography ; Sequence Analysis, DNA/methods ; Specimen Handling/*methods ; }, abstract = {Recent advancements in metagenomic-based studies, especially analyses of amplicon-based DNA sequencing targeting taxonomic marker genes, has led to an unprecedented characterization of microbial communities from diverse ecosystems around the world. While originally constrained by a lack of appropriate analytical tools and sequencing depth, new technologies and computational and statistical algorithms have been developed to handle highly dimensional, next-generation sequencing datasets. Both these tools allow for the robust analysis of structural and distributional patterns of microbiota essential for the understanding of microbial ecology and biogeography. Furthermore, consortia of individual laboratories working on large interdisciplinary research programs, like the Human and Earth Microbiome Projects, have developed standardized protocols for DNA extraction, sequencing pipelines, and bioinformatics. These approaches provide large repositories of publicly available data to serve as references for on-going and future, hypothesis-driven studies to better characterize the roles of microbial communities in diverse ecosystems. In this review, we outline the currently available statistical approaches and tools to aid in statistically powered study designs and analyses. Given what is now known about the enormous diversity and variability of the microbial communities in aquatic and terrestrial habitats, we also discuss practical considerations for sample collection. Due to the extensive advances made in the field of metagenomics over the last decade, rigorous, well replicated, hypothesis-driven studies are: 1) needed, 2) now possible, and 3) essential to make best use of sequencing-based technologies to characterize the roles of microbial communities in the structure and function of diverse ecosystems.}, }
@article {pmid29770137, year = {2018}, author = {Stanisavljević, S and Dinić, M and Jevtić, B and Đedović, N and Momčilović, M and Đokić, J and Golić, N and Mostarica Stojković, M and Miljković, Đ}, title = {Gut Microbiota Confers Resistance of Albino Oxford Rats to the Induction of Experimental Autoimmune Encephalomyelitis.}, journal = {Frontiers in immunology}, volume = {9}, number = {}, pages = {942}, pmid = {29770137}, issn = {1664-3224}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Cytokines/metabolism ; Disease Models, Animal ; *Disease Resistance/immunology ; Encephalomyelitis, Autoimmune, Experimental/*etiology/metabolism/therapy ; Fecal Microbiota Transplantation/methods ; Female ; *Gastrointestinal Microbiome/drug effects/immunology ; Lymph Nodes/immunology/metabolism ; Metagenome ; Metagenomics/methods ; Peyer's Patches/immunology/metabolism ; Rats ; }, abstract = {Albino Oxford (AO) rats are extremely resistant to induction of experimental autoimmune encephalomyelitis (EAE). EAE is an animal model of multiple sclerosis, a chronic inflammatory disease of the central nervous system (CNS), with established autoimmune pathogenesis. The autoimmune response against the antigens of the CNS is initiated in the peripheral lymphoid tissues after immunization of AO rats with CNS antigens. Subsequently, limited infiltration of the CNS occurs, yet without clinical sequels. It has recently become increasingly appreciated that gut-associated lymphoid tissues (GALT) and gut microbiota play an important role in regulation and propagation of encephalitogenic immune response. Therefore, modulation of AO gut microbiota by antibiotics was performed in this study. The treatment altered composition of gut microbiota in AO rats and led to a reduction in the proportion of regulatory T cells in Peyer's patches, mesenteric lymph nodes, and in lymph nodes draining the site of immunization. Upregulation of interferon-γ and interleukin (IL)-17 production was observed in the draining lymph nodes. The treatment led to clinically manifested EAE in AO rats with more numerous infiltrates and higher production of IL-17 observed in the CNS. Importantly, transfer of AO gut microbiota into EAE-prone Dark Agouti rats ameliorated the disease. These results clearly imply that gut microbiota is an important factor in AO rat resistance to EAE and that gut microbiota transfer is an efficacious way to treat CNS autoimmunity. These findings also support the idea that gut microbiota modulation has a potential as a future treatment of multiple sclerosis.}, }
@article {pmid28125788, year = {2017}, author = {Yang, Y and Chen, N and Chen, T}, title = {Inference of Environmental Factor-Microbe and Microbe-Microbe Associations from Metagenomic Data Using a Hierarchical Bayesian Statistical Model.}, journal = {Cell systems}, volume = {4}, number = {1}, pages = {129-137.e5}, doi = {10.1016/j.cels.2016.12.012}, pmid = {28125788}, issn = {2405-4712}, mesh = {Algorithms ; Animals ; Bacteria/classification/genetics ; Bayes Theorem ; Computational Biology/methods ; Computer Simulation ; Gene-Environment Interaction ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Models, Statistical ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; }, abstract = {The inference of associations between environmental factors and microbes and among microbes is critical to interpreting metagenomic data, but compositional bias, indirect associations resulting from common factors, and variance within metagenomic sequencing data limit the discovery of associations. To account for these problems, we propose metagenomic Lognormal-Dirichlet-Multinomial (mLDM), a hierarchical Bayesian model with sparsity constraints, to estimate absolute microbial abundance and simultaneously infer both conditionally dependent associations among microbes and direct associations between microbes and environmental factors. We empirically show the effectiveness of the mLDM model using synthetic data, data from the TARA Oceans project, and a colorectal cancer dataset. Finally, we apply mLDM to 16S sequencing data from the western English Channel and report several associations. Our model can be used on both natural environmental and human metagenomic datasets, promoting the understanding of associations in the microbial community.}, }
@article {pmid31250077, year = {2019}, author = {Goss-Souza, D and Mendes, LW and Rodrigues, JLM and Tsai, SM}, title = {Ecological Processes Shaping Bulk Soil and Rhizosphere Microbiome Assembly in a Long-Term Amazon Forest-to-Agriculture Conversion.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01401-y}, pmid = {31250077}, issn = {1432-184X}, support = {2008/58114-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2014/50320-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 140317/2014-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico (BR)/ ; 311008/2016-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {Forest-to-agriculture conversion has been identified as a major threat to soil biodiversity and soil processes resilience, although the consequences of long-term land use change to microbial community assembly and ecological processes have been often neglected. Here, we combined metagenomic approach with a large environmental dataset, to (i) identify the microbial assembly patterns and, (ii) to evaluate the ecological processes governing microbial assembly, in bulk soil and soybean rhizosphere, along a long-term forest-to-agriculture conversion chronosequence, in Eastern Amazon. We hypothesized that (i) microbial communities in bulk soil and rhizosphere have different assembly patterns and (ii) the weight of the four ecological processes governing assembly differs between bulk soil and rhizosphere and along the chronosequence in the same fraction. Community assembly in bulk soil fitted most the zero-sum multinomial (ZSM) neutral-based model, regardless of time. Low to intermediate dispersal was observed. Decreasing influence of abiotic factors was counterbalanced by increasing influence of biotic factors, as the chronosequence advanced. Undominated ecological processes of dispersal limitation and variable selection governing community assembly were observed in this soil fraction. For soybean rhizosphere, community assembly fitted most the lognormal niche-based model in all chronosequence areas. High dispersal and an increasing influence of abiotic factors coupled with a decreasing influence of biotic factors were found along the chronosequence. Thus, we found a dominant role of dispersal process governing microbial assembly with a secondary effect of homogeneous selection process, mainly driven by decreasing aluminum and increased cations saturation in soil solution, due to long-term no-till cropping. Together, our results indicate that long-term no-till lead community abundances in bulk soil to be in a transient and conditional state, while for soybean rhizosphere, community abundances reach a periodic and permanent distribution state. Dominant dispersal process in rhizosphere, coupled with homogeneous selection, brings evidences that soybean root system selects microbial taxa via trade-offs in order to keep functional resilience of soil processes.}, }
@article {pmid30838598, year = {2019}, author = {Divaris, K and Shungin, D and Rodríguez-Cortés, A and Basta, PV and Roach, J and Cho, H and Wu, D and Ferreira Zandoná, AG and Ginnis, J and Ramamoorthy, S and Kinchen, JM and Kwintkiewicz, J and Butz, N and Ribeiro, AA and Azcarate-Peril, MA}, title = {The Supragingival Biofilm in Early Childhood Caries: Clinical and Laboratory Protocols and Bioinformatics Pipelines Supporting Metagenomics, Metatranscriptomics, and Metabolomics Studies of the Oral Microbiome.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1922}, number = {}, pages = {525-548}, doi = {10.1007/978-1-4939-9012-2_40}, pmid = {30838598}, issn = {1940-6029}, mesh = {Bacteria/*genetics/isolation &amp; purification/metabolism ; *Biofilms ; Child, Preschool ; DNA, Bacterial/genetics ; Dental Caries/etiology/*microbiology ; Gene Expression Profiling/methods ; Gingiva/microbiology ; Humans ; Metabolomics/*methods ; Metagenomics/*methods ; Microbiota ; RNA, Bacterial/genetics ; Sequence Analysis, DNA/methods ; Sequence Analysis, RNA/methods ; Software ; Specimen Handling/methods ; Tooth, Deciduous/*microbiology ; Transcriptome ; }, abstract = {Early childhood caries (ECC) is a biofilm-mediated disease. Social, environmental, and behavioral determinants as well as innate susceptibility are major influences on its incidence; however, from a pathogenetic standpoint, the disease is defined and driven by oral dysbiosis. In other words, the disease occurs when the natural equilibrium between the host and its oral microbiome shifts toward states that promote demineralization at the biofilm-tooth surface interface. Thus, a comprehensive understanding of dental caries as a disease requires the characterization of both the composition and the function or metabolic activity of the supragingival biofilm according to well-defined clinical statuses. However, taxonomic and functional information of the supragingival biofilm is rarely available in clinical cohorts, and its collection presents unique challenges among very young children. This paper presents a protocol and pipelines available for the conduct of supragingival biofilm microbiome studies among children in the primary dentition, that has been designed in the context of a large-scale population-based genetic epidemiologic study of ECC. The protocol is being developed for the collection of two supragingival biofilm samples from the maxillary primary dentition, enabling downstream taxonomic (e.g., metagenomics) and functional (e.g., transcriptomics and metabolomics) analyses. The protocol is being implemented in the assembly of a pediatric precision medicine cohort comprising over 6000 participants to date, contributing social, environmental, behavioral, clinical, and biological data informing ECC and other oral health outcomes.}, }
@article {pmid29523365, year = {2017}, author = {Lagier, JC and Dubourg, G and Amrane, S and Raoult, D}, title = {Koch Postulate: Why Should we Grow Bacteria?.}, journal = {Archives of medical research}, volume = {48}, number = {8}, pages = {774-779}, doi = {10.1016/j.arcmed.2018.02.003}, pmid = {29523365}, issn = {1873-5487}, mesh = {Anti-Bacterial Agents/therapeutic use ; Bacteria/drug effects/genetics/*isolation &amp; purification ; *Bacterial Infections/diagnosis/drug therapy/microbiology ; *Bacteriological Techniques ; *Cell Culture Techniques ; Humans ; Metagenomics ; Microbial Sensitivity Tests ; Microbiota/*physiology ; }, }
@article {pmid28835919, year = {2017}, author = {Dickson, LB and Jiolle, D and Minard, G and Moltini-Conclois, I and Volant, S and Ghozlane, A and Bouchier, C and Ayala, D and Paupy, C and Moro, CV and Lambrechts, L}, title = {Carryover effects of larval exposure to different environmental bacteria drive adult trait variation in a mosquito vector.}, journal = {Science advances}, volume = {3}, number = {8}, pages = {e1700585}, pmid = {28835919}, issn = {2375-2548}, mesh = {Animals ; Antibiosis ; *Bacteria ; *Biological Variation, Population ; Breeding ; Dengue/transmission ; Ecosystem ; Environment ; *Environmental Microbiology ; Gastrointestinal Microbiome ; Host-Pathogen Interactions ; Humans ; Larva ; Life Cycle Stages ; Metagenome ; Metagenomics ; Microbiota ; Mosquito Vectors/*growth &amp; development/*microbiology/virology ; *Quantitative Trait, Heritable ; }, abstract = {Conditions experienced during larval development of holometabolous insects can affect adult traits, but whether differences in the bacterial communities of larval development sites contribute to variation in the ability of insect vectors to transmit human pathogens is unknown. We addressed this question in the mosquito Aedes aegypti, a major arbovirus vector breeding in both sylvatic and domestic habitats in Sub-Saharan Africa. Targeted metagenomics revealed differing bacterial communities in the water of natural breeding sites in Gabon. Experimental exposure to different native bacterial isolates during larval development resulted in significant differences in pupation rate and adult body size but not life span. Larval exposure to an Enterobacteriaceae isolate resulted in decreased antibacterial activity in adult hemolymph and reduced dengue virus dissemination titer. Together, these data provide the proof of concept that larval exposure to different bacteria can drive variation in adult traits underlying vectorial capacity. Our study establishes a functional link between larval ecology, environmental microbes, and adult phenotypic variation in a holometabolous insect vector.}, }
@article {pmid30725462, year = {2019}, author = {Morales, E and Chen, J and Greathouse, KL}, title = {Compositional Analysis of the Human Microbiome in Cancer Research.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1928}, number = {}, pages = {299-335}, doi = {10.1007/978-1-4939-9027-6_16}, pmid = {30725462}, issn = {1940-6029}, mesh = {Biological Evolution ; Gastrointestinal Microbiome ; Humans ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S ; *Research ; }, abstract = {Gut microbial composition has shown to be associated with obesity, diabetes mellitus, inflammatory bowel disease, colitis, autoimmune disorders, and cancer, among other diseases. Microbiome research has significantly evolved through the years and continues to advance as we develop new and better strategies to more accurately measure its composition and function. Careful selection of study design, inclusion and exclusion criteria of participants, and methodology are paramount to accurately analyze microbial structure. Here we present the most up-to-date available information on methods for gut microbial collection and analysis.}, }
@article {pmid30685386, year = {2019}, author = {Liu, J and Johnson, R and Dillon, S and Kroehl, M and Frank, DN and Tuncil, YE and Zhang, X and Ir, D and Robertson, CE and Seifert, S and Higgins, J and Hamaker, B and Wilson, CC and Erlandson, KM}, title = {Among older adults, age-related changes in the stool microbiome differ by HIV-1 serostatus.}, journal = {EBioMedicine}, volume = {40}, number = {}, pages = {583-594}, doi = {10.1016/j.ebiom.2019.01.033}, pmid = {30685386}, issn = {2352-3964}, support = {K23 AG050260/AG/NIA NIH HHS/United States ; P30 DK048520/DK/NIDDK NIH HHS/United States ; T32 AG000279/AG/NIA NIH HHS/United States ; UL1 TR002535/TR/NCATS NIH HHS/United States ; }, mesh = {Age Factors ; Aged ; Aged, 80 and over ; Biomarkers ; Case-Control Studies ; Computational Biology/methods ; Diet ; Dysbiosis ; Fatty Acids, Volatile/metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome ; HIV Infections/*epidemiology/*virology ; HIV Seropositivity ; *HIV-1 ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; }, abstract = {BACKGROUND: HIV-1 infection and physiological aging are independently linked to elevated systemic inflammation and changes in enteric microbial communities (dysbiosis). However, knowledge of the direct effect of HIV infection on the aging microbiome and potential links to systemic inflammation is lacking.<br><br>METHODS: In a cross-sectional study of older people living with HIV (PLWH) (median age 61.5 years, N = 14) and uninfected controls (median 58 years, n = 22) we compared stool microbiota, levels of microbial metabolites (short-chain fatty acid levels, SCFA) and systemic inflammatory biomarkers by HIV serostatus and age.<br><br>FINDINGS: HIV and age were independently associated with distinct changes in the stool microbiome. For example, abundances of Enterobacter and Paraprevotella were higher and Eggerthella and Roseburia lower among PLWH compared to uninfected controls. Age-related microbiome changes also differed by HIV serostatus. Some bacteria with inflammatory potential (e.g. Escherichia) increased with age among PLWH, but not controls. Stool SCFA levels were similar between the two groups yet patterns of associations between individual microbial taxa and SCFA levels differed. Abundance of various genera including Escherichia and Bifidobacterium positively associated with inflammatory biomarkers (e.g. soluble Tumor Necrosis Factor Receptors) among PLWH, but not among controls.<br><br>INTERPRETATION: The age effect on the gut microbiome and associations between microbiota and microbial metabolites or systemic inflammation differed based on HIV serostatus, raising important implications for the impact of therapeutic interventions, dependent on HIV serostatus or age.}, }
@article {pmid30584008, year = {2019}, author = {Liu, X and Shao, L and Liu, X and Ji, F and Mei, Y and Cheng, Y and Liu, F and Yan, C and Li, L and Ling, Z}, title = {Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer.}, journal = {EBioMedicine}, volume = {40}, number = {}, pages = {336-348}, doi = {10.1016/j.ebiom.2018.12.034}, pmid = {30584008}, issn = {2352-3964}, mesh = {Aged ; Biodiversity ; Cohort Studies ; Combined Modality Therapy ; Computational Biology/methods ; Dysbiosis ; Female ; Gastric Mucosa/*microbiology/pathology ; Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Neoplasm Grading ; Neoplasm Staging ; RNA, Ribosomal, 16S ; Stomach Neoplasms/*etiology/pathology/therapy ; }, abstract = {BACKGROUND: As part of the tumor microenvironment, the gastric microbiota play vital roles in tumor initiation, progression and metastasis, but stomach microhabitats are not always uniform. We aimed to characterize differences of gastric microbiota in stomach microhabitats associated with gastric cancer (GC) development.<br><br>METHODS: A cohort of 276 GC patients without preoperative chemotherapy was enrolled retrospectively, and 230 normal, 247 peritumoral and 229 tumoral tissues were obtained for gastric microbiota analysis targeting the 16S rRNA gene by MiSeq sequencing. The microbial diversity and composition, bacterial co-occurrence correlations and predictive functional profiles were compared across different microhabitats.<br><br>FINDINGS: GC-specific stomach microhabitats, not GC stages or types, determine the composition and diversity of the gastric microbiota. Most notably, bacterial richness was decreased in peritumoral and tumoral microhabitats, and the correlation network of abundant gastric bacteria was simplified in tumoral microhabitat. Helicobacter pylori (HP), Prevotella copri and Bacteroides uniformis were significantly decreased, whereas Prevotella melaninogenica, Streptococcus anginosus and Propionibacterium acnes were increased in tumoral microhabitat. Higher HP colonisation influenced the overall structure of the gastric microbiota in normal and peritumoral microhabitats. PiCRUSt analysis revealed that genes associated with nucleotide transport and metabolism and amino acid transport and metabolism were significantly enriched in tumoral microbiota, while gastric acid secretion was significantly higher in HP positive group of the tumoral microbiota.<br><br>INTERPRETATION: Our present study provided new insights into the roles of gastric microbiota in different stomach microhabitats in gastric carcinogenesis, especially the pathogenesis of HP. FUND: National Natural Science Foundation of China.}, }
@article {pmid30155556, year = {2019}, author = {Ma, ZS}, title = {Sketching the Human Microbiome Biogeography with DAR (Diversity-Area Relationship) Profiles.}, journal = {Microbial ecology}, volume = {77}, number = {3}, pages = {821-838}, doi = {10.1007/s00248-018-1245-6}, pmid = {30155556}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; Humans ; Metagenomics ; *Microbiota ; Models, Biological ; }, abstract = {SAR (species area relationship) is a classic ecological theory that has been extensively investigated and applied in the studies of global biogeography and biodiversity conservation in macro-ecology. It has also found important applications in microbial ecology in recent years thanks to the breakthroughs in metagenomic sequencing technology. Nevertheless, SAR has a serious limitation for practical applications-ignoring the species abundance and treating all species as equally abundant. This study aims to explore the biogeography discoveries of human microbiome over 18 sites of 5 major microbiome habitats, establish the baseline DAR (diversity-area scaling relationship) parameters, and perform comparisons with the classic SAR. The extension from SAR to DAR by adopting the Hill numbers as diversity measures not only overcomes the previously mentioned flaw of SAR but also allows for obtaining a series of important findings on the human microbiome biodiversity and biogeography. Specifically, two types of DAR models were built, the traditional power law (PL) and power law with exponential cutoff (PLEC), using comprehensive datasets from the HMP (human microbiome project). Furthermore, the biogeography &quot;maps&quot; for 18 human microbiome sites using their DAR profiles for assessing and predicting the diversity scaling across individuals, PDO profiles (pair-wise diversity overlap) for measuring diversity overlap (similarity), and MAD profile (for predicting the maximal accrual diversity in a population) were sketched out. The baseline biogeography maps for the healthy human microbiome diversity can offer guidelines for conserving human microbiome diversity and investigating the health implications of the human microbiome diversity and heterogeneity.}, }
@article {pmid30068938, year = {2018}, author = {Hoedt, EC and Parks, DH and Volmer, JG and Rosewarne, CP and Denman, SE and McSweeney, CS and Muir, JG and Gibson, PR and Cuív, PÓ and Hugenholtz, P and Tyson, GW and Morrison, M}, title = {Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size.}, journal = {The ISME journal}, volume = {12}, number = {12}, pages = {2942-2953}, pmid = {30068938}, issn = {1751-7370}, mesh = {Animals ; Cattle ; Feces/microbiology ; *Gastrointestinal Microbiome ; Genome Size/*genetics ; Humans ; *Metagenomics ; Methanobacteriaceae/*genetics/physiology ; Methanobrevibacter/genetics/physiology ; Phylogeny ; Rumen/microbiology ; }, abstract = {The genus Methanosphaera is a well-recognized but poorly characterized member of the mammalian gut microbiome, and distinctive from Methanobrevibacter smithii for its ability to induce a pro-inflammatory response in humans. Here we have used a combination of culture- and metagenomics-based approaches to expand the representation and information for the genus, which has supported the examination of their phylogeny and physiological capacity. Novel isolates of the genus Methanosphaera were recovered from bovine rumen digesta and human stool, with the bovine isolate remarkable for its large genome size relative to other Methanosphaera isolates from monogastric hosts. To substantiate this observation, we then recovered seven high-quality Methanosphaera-affiliated population genomes from ruminant and human gut metagenomic datasets. Our analyses confirm a monophyletic origin of Methanosphaera spp. and that the colonization of monogastric and ruminant hosts favors representatives of the genus with different genome sizes, reflecting differences in the genome content needed to persist in these different habitats.}, }
@article {pmid30050163, year = {2018}, author = {Ishii, S and Suzuki, S and Tenney, A and Nealson, KH and Bretschger, O}, title = {Comparative metatranscriptomics reveals extracellular electron transfer pathways conferring microbial adaptivity to surface redox potential changes.}, journal = {The ISME journal}, volume = {12}, number = {12}, pages = {2844-2863}, pmid = {30050163}, issn = {1751-7370}, mesh = {Carbon/metabolism ; Cytochrome c Group/genetics/metabolism ; Electric Conductivity ; Electrodes ; Electron Transport ; Geobacter/*genetics/metabolism ; Heme ; *Metabolic Networks and Pathways ; Metagenomics ; *Microbiota ; Oxidation-Reduction ; *Transcriptome ; }, abstract = {Some microbes can capture energy through redox reactions with electron flow to solid-phase electron acceptors, such as metal-oxides or poised electrodes, via extracellular electron transfer (EET). While diverse oxide minerals, exhibiting different surface redox potentials, are widely distributed on Earth, little is known about how microbes sense and use the minerals. Here we show electrochemical, metabolic, and transcriptional responses of EET-active microbial communities established on poised electrodes to changes in the surface redox potentials (as electron acceptors) and surrounding substrates (as electron donors). Combination of genome-centric stimulus-induced metatranscriptomics and metabolic pathway investigation revealed that nine Geobacter/Pelobacter microbes performed EET activity differently according to their preferable surface potentials and substrates. While the Geobacter/Pelobacter microbes coded numerous numbers of multi-heme c-type cytochromes and conductive e-pili, wide variations in gene expression were seen in response to altering surrounding substrates and surface potentials, accelerating EET via poised electrode or limiting EET via an open circuit system. These flexible responses suggest that a wide variety of EET-active microbes utilizing diverse EET mechanisms may work together to provide such EET-active communities with an impressive ability to handle major changes in surface potential and carbon source availability.}, }
@article {pmid28924190, year = {2017}, author = {Cornejo-Granados, F and Lopez-Zavala, AA and Gallardo-Becerra, L and Mendoza-Vargas, A and Sánchez, F and Vichido, R and Brieba, LG and Viana, MT and Sotelo-Mundo, RR and Ochoa-Leyva, A}, title = {Microbiome of Pacific Whiteleg shrimp reveals differential bacterial community composition between Wild, Aquacultured and AHPND/EMS outbreak conditions.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11783}, pmid = {28924190}, issn = {2045-2322}, mesh = {Animals ; *Aquaculture ; *Bacteria/classification/genetics ; *Gastrointestinal Microbiome ; Metagenomics ; Penaeidae/growth &amp; development/*microbiology ; }, abstract = {Crustaceans form the second largest subphylum on Earth, which includes Litopeneaus vannamei (Pacific whiteleg shrimp), one of the most cultured shrimp worldwide. Despite efforts to study the shrimp microbiota, little is known about it from shrimp obtained from the open sea and the role that aquaculture plays in microbiota remodeling. Here, the microbiota from the hepatopancreas and intestine of wild type (wt) and aquacultured whiteleg shrimp and pond sediment from hatcheries were characterized using sequencing of seven hypervariable regions of the 16S rRNA gene. Cultured shrimp with AHPND/EMS disease symptoms were also included. We found that (i) microbiota and their predicted metagenomic functions were different between wt and cultured shrimp; (ii) independent of the shrimp source, the microbiota of the hepatopancreas and intestine was different; (iii) the microbial diversity between the sediment and intestines of cultured shrimp was similar; and (iv) associated to an early development of AHPND/EMS disease, we found changes in the microbiome and the appearance of disease-specific bacteria. Notably, under cultured conditions, we identified bacterial taxa enriched in healthy shrimp, such as Faecalibacterium prausnitzii and Pantoea agglomerans, and communities enriched in diseased shrimp, such as Aeromonas taiwanensis, Simiduia agarivorans and Photobacterium angustum.}, }
@article {pmid31012060, year = {2019}, author = {Lorenzi, AS and Chia, MA and Lopes, FAC and Silva, GGZ and Edwards, RA and Bittencourt-Oliveira, MDC}, title = {Cyanobacterial biodiversity of semiarid public drinking water supply reservoirs assessed via next-generation DNA sequencing technology.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {57}, number = {6}, pages = {450-460}, doi = {10.1007/s12275-019-8349-7}, pmid = {31012060}, issn = {1976-3794}, mesh = {Bacterial Toxins/analysis/genetics/isolation &amp; purification ; *Biodiversity ; Brazil ; Cyanobacteria/*classification/genetics/*isolation &amp; purification ; DNA, Bacterial/analysis ; Drinking Water/*microbiology ; Environmental Monitoring/methods ; Genes, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Microcystis/genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Saxitoxin/genetics ; Seasons ; Sequence Analysis, DNA/*methods ; Uracil/analogs &amp; derivatives ; *Water Microbiology ; *Water Supply ; }, abstract = {Next-generation DNA sequencing technology was applied to generate molecular data from semiarid reservoirs during well-defined seasons. Target sequences of 16S-23S rRNA ITS and cpcBA-IGS were used to reveal the taxonomic groups of cyanobacteria present in the samples, and genes coding for cyanotoxins such as microcystins (mcyE), saxitoxins (sxtA), and cylindrospermopsins (cyrJ) were investigated. The presence of saxitoxins in the environmental samples was evaluated using ELISA kit. Taxonomic analyses of high-throughput DNA sequencing data showed the dominance of the genus Microcystis in Mundaú reservoir. Furthermore, it was the most abundant genus in the dry season in Ingazeira reservoir. In the rainy season, 16S-23S rRNA ITS analysis revealed that Cylindrospermopsis raciborskii comprised 46.8% of the cyanobacterial community in Ingazeira reservoir, while the cpcBAIGS region revealed that C. raciborskii (31.8%) was the most abundant taxon followed by Sphaerospermopsis aphanizomenoides (17.3%) and Planktothrix zahidii (16.6%). Despite the presence of other potential toxin-producing genera, the detected sxtA gene belonged to C. raciborskii, while the mcyE gene belonged to Microcystis in both reservoirs. The detected mcyE gene had good correlation with MC content, while the amplification of the sxtA gene was related to the presence of STX. The cyrJ gene was not detected in these samples. Using DNA analyses, our results showed that the cyanobacterial composition of Mundaú reservoir was similar in successive dry seasons, and it varied between seasons in Ingazeira reservoir. In addition, our data suggest that some biases of analysis influenced the cyanobacterial communities seen in the NGS output of Ingazeira reservoir.}, }
@article {pmid30992350, year = {2019}, author = {Cobián Güemes, AG and Lim, YW and Quinn, RA and Conrad, DJ and Benler, S and Maughan, H and Edwards, R and Brettin, T and Cantú, VA and Cuevas, D and Hamidi, R and Dorrestein, P and Rohwer, F}, title = {Cystic Fibrosis Rapid Response: Translating Multi-omics Data into Clinically Relevant Information.}, journal = {mBio}, volume = {10}, number = {2}, pages = {}, doi = {10.1128/mBio.00431-19}, pmid = {30992350}, issn = {2150-7511}, mesh = {Adult ; Case-Control Studies ; Coinfection/complications ; Cystic Fibrosis/*complications/microbiology ; Disease Management ; *Disease Progression ; Escherichia coli Infections/*diagnosis ; Fatal Outcome ; Gene Expression Profiling ; *Genomics ; Humans ; Lung/*microbiology/physiopathology ; Male ; Metabolome ; *Metabolomics ; Metagenome ; Microbiota ; Shiga Toxin/genetics ; Shiga-Toxigenic Escherichia coli/genetics/pathogenicity ; }, abstract = {Pulmonary exacerbations are the leading cause of death in cystic fibrosis (CF) patients. To track microbial dynamics during acute exacerbations, a CF rapid response (CFRR) strategy was developed. The CFRR relies on viromics, metagenomics, metatranscriptomics, and metabolomics data to rapidly monitor active members of the viral and microbial community during acute CF exacerbations. To highlight CFRR, a case study of a CF patient is presented, in which an abrupt decline in lung function characterized a fatal exacerbation. The microbial community in the patient's lungs was closely monitored through the multi-omics strategy, which led to the identification of pathogenic shigatoxigenic Escherichia coli (STEC) expressing Shiga toxin. This case study illustrates the potential for the CFRR to deconstruct complicated disease dynamics and provide clinicians with alternative treatments to improve the outcomes of pulmonary exacerbations and expand the life spans of individuals with CF.IMPORTANCE Proper management of polymicrobial infections in patients with cystic fibrosis (CF) has extended their life span. Information about the composition and dynamics of each patient's microbial community aids in the selection of appropriate treatment of pulmonary exacerbations. We propose the cystic fibrosis rapid response (CFRR) as a fast approach to determine viral and microbial community composition and activity during CF pulmonary exacerbations. The CFRR potential is illustrated with a case study in which a cystic fibrosis fatal exacerbation was characterized by the presence of shigatoxigenic Escherichia coli The incorporation of the CFRR within the CF clinic could increase the life span and quality of life of CF patients.}, }
@article {pmid28912589, year = {2017}, author = {Naghoni, A and Emtiazi, G and Amoozegar, MA and Cretoiu, MS and Stal, LJ and Etemadifar, Z and Shahzadeh Fazeli, SA and Bolhuis, H}, title = {Microbial diversity in the hypersaline Lake Meyghan, Iran.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11522}, pmid = {28912589}, issn = {2045-2322}, mesh = {Archaea/*classification/genetics/growth &amp; development ; Bacteria/*classification/genetics/growth &amp; development ; *Biota ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Iran ; Lakes/chemistry/*microbiology ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Saline Waters ; Sequence Analysis, DNA ; }, abstract = {Lake Meyghan is one of the largest and commercially most important salt lakes in Iran. Despite its inland location and high altitude, Lake Meyghan has a thalassohaline salt composition suggesting a marine origin. Inputs of fresh water by rivers and rainfall formed various basins characterized by different salinities. We analyzed the microbial community composition of three basins by isolation and culturing of microorganisms and by analysis of the metagenome. The basins that were investigated comprised a green ~50 g kg-1 salinity brine, a red ~180 g kg-1 salinity brine and a white ~300 g kg-1 salinity brine. Using different growth media, 57 strains of Bacteria and 48 strains of Archaea were isolated. Two bacterial isolates represent potential novel species with less than 96% 16S rRNA gene sequence identity to known species. Abundant isolates were also well represented in the metagenome. Bacteria dominated the low salinity brine, with Alteromonadales (Gammaproteobacteria) as a particularly important taxon, whereas the high salinity brines were dominated by haloarchaea. Although the brines of Lake Meyghan differ in geochemical composition, their ecosystem function appears largely conserved amongst each other while being driven by different microbial communities.}, }
@article {pmid30915691, year = {2019}, author = {Akyol, Ç and Ozbayram, EG and Demirel, B and Onay, TT and Ince, O and Ince, B}, title = {Linking nano-ZnO contamination to microbial community profiling in sanitary landfill simulations.}, journal = {Environmental science and pollution research international}, volume = {26}, number = {13}, pages = {13580-13591}, doi = {10.1007/s11356-019-04906-8}, pmid = {30915691}, issn = {1614-7499}, support = {112Y322//TUBITAK/ ; 13081//Boğaziçi University Research Fund Project/ ; }, mesh = {Archaea ; Bacteria ; Biofuels ; Bioreactors/*microbiology ; Microbiota ; RNA, Ribosomal, 16S/*chemistry ; Refuse Disposal/methods ; Solid Waste/*analysis ; Waste Disposal Facilities ; Zinc Oxide/*analysis/chemistry ; }, abstract = {Nanomaterials (NMs) commercially used for various activities mostly end up in landfills. Reduced biogas productions reported in landfill reactors create a need for more comprehensive research on these greatly-diverse microbial pools. In order to evaluate the impact of one of the most widely-used NMs, namely nano-zinc oxide (nano-ZnO), simulated bioreactor and conventional landfills were operated using real municipal solid waste (MSW) for 300 days with addition nano-ZnO. Leachate samples were taken at different phases and analyzed by 16S rRNA gene amplicon sequencing. The bacterial communities were distinctly characterized by Cloacamonaceae (phylum WWE1), Rhodocyclaceae (phylum Proteobacteria), Porphyromonadaceae (phylum Bacteroidetes), and Synergistaceae (phylum Synergistetes). The bacterial community in the bioreactors shifted at the end of the operation and was dominated by Rhodocyclaceae. There was not a major change in the bacterial community in the conventional reactors. The methanogenic archaeal diversity highly differed between the bioreactors and conventional reactors. The dominance of Methanomicrobiaceae was observed in the bioreactors during the peak methane-production period; however, their prominence shifted to WSA2 in the nano-ZnO-added bioreactor and to Methanocorpusculaceae in the control bioreactor towards the end. Methanocorpusculaceae was the most abundant family in both conventional control and nano-ZnO-containing reactors.}, }
@article {pmid30526624, year = {2018}, author = {Wu, G and Niu, M and Tang, W and Hu, J and Wei, G and He, Z and Chen, Y and Jiang, Y and Chen, P}, title = {L-Fucose ameliorates high-fat diet-induced obesity and hepatic steatosis in mice.}, journal = {Journal of translational medicine}, volume = {16}, number = {1}, pages = {344}, pmid = {30526624}, issn = {1479-5876}, support = {2016A030306043//Natural Science Foundation of Guangdong Province/International ; 2017B030314034//Natural Science Foundation of Guangdong Province/International ; 2016A020216015//China Association for Science and Technology/International ; }, mesh = {Adiposity/drug effects ; Animals ; Cecum/drug effects/microbiology ; *Diet, High-Fat ; Dysbiosis/complications/microbiology/pathology ; Feeding Behavior ; Fucose/pharmacology/*therapeutic use ; Gastrointestinal Microbiome/drug effects ; Glucose Tolerance Test ; Insulin ; Metagenomics ; Mice, Inbred C57BL ; Non-alcoholic Fatty Liver Disease/*complications/*drug therapy/microbiology ; Obesity/*complications/*drug therapy/microbiology ; Weight Gain/drug effects ; }, abstract = {BACKGROUND: L-Fucose (Fuc), a six-deoxy hexose monosaccharide, is present endogenously in humans and animals and has a wide range of biological functions. In the present study, we aimed to examine the effect of Fuc on obesity and hepatic steatosis in mice fed a high-fat diet (HFD).<br><br>METHODS: C57BL/6 mice were fed a normal chow (NC) or HFD for 18 weeks to induce obesity and fatty liver. Fuc was administered intragastrically from the 8th week to the end of the experiment (18 weeks).<br><br>RESULTS: Metagenomic analysis showed that HFD altered the genomic profile of gut microbiota in the mice; specifically, expression of alpha-L-fucosidase, the gene responsible for Fuc generation, was markedly reduced in the HFD group compared with that in the NC group. Fuc treatment decreased body weight gain, fat accumulation, and hepatic triglyceride elevation in HFD-fed mice. In addition, Fuc decreased the levels of endotoxin-producing bacteria of the Desulfovibrionaceae family and restored HFD-induced enteric dysbiosis at both compositional and functional levels.<br><br>CONCLUSION: Our findings suggest that Fuc might be a novel strategy to treat HFD-induced obesity and fatty liver.}, }
@article {pmid30449316, year = {2018}, author = {Guerin, E and Shkoporov, A and Stockdale, SR and Clooney, AG and Ryan, FJ and Sutton, TDS and Draper, LA and Gonzalez-Tortuero, E and Ross, RP and Hill, C}, title = {Biology and Taxonomy of crAss-like Bacteriophages, the Most Abundant Virus in the Human Gut.}, journal = {Cell host &amp; microbe}, volume = {24}, number = {5}, pages = {653-664.e6}, doi = {10.1016/j.chom.2018.10.002}, pmid = {30449316}, issn = {1934-6069}, mesh = {Bacteriophages/*classification/*genetics/*physiology/ultrastructure ; Base Sequence ; Capsid Proteins/genetics ; DNA Viruses ; Feces/virology ; Fermentation ; *Gastrointestinal Microbiome ; Genome, Viral/genetics ; Genomics ; Humans ; Metagenomics/methods ; *Phylogeny ; Sequence Analysis ; Viral Proteins/genetics ; }, abstract = {CrAssphages represent the most abundant virus in the human gut microbiota, but the lack of available genome sequences for comparison has kept them enigmatic. Recently, sequence-based classification of distantly related crAss-like phages from multiple environments was reported, leading to a proposed familial-level taxonomic group. Here, we assembled the metagenomic sequencing reads from 702 human fecal virome/phageome samples and analyzed 99 complete circular crAss-like phage genomes and 150 contigs ≥70 kb. In silico comparative genomics and taxonomic analysis enabled a classification scheme of crAss-like phages from human fecal microbiomes into four candidate subfamilies composed of ten candidate genera. Laboratory analysis was performed on fecal samples from an individual harboring seven distinct crAss-like phages. We achieved crAss-like phage propagation in ex vivo human fecal fermentations and visualized short-tailed podoviruses by electron microscopy. Mass spectrometry of a crAss-like phage capsid protein could be linked to metagenomic sequencing data, confirming crAss-like phage structural annotations.}, }
@article {pmid29961061, year = {2018}, author = {Lee, J and Lim, JH and Park, J and Kim, IN}, title = {Temporal and Vertical Variation in Microbial Community Composition in Response to Physicochemical Characteristics in a Water Column of Highly Eutrophied Jinhae Bay, South Korea.}, journal = {Journal of molecular microbiology and biotechnology}, volume = {28}, number = {2}, pages = {65-77}, doi = {10.1159/000489633}, pmid = {29961061}, issn = {1660-2412}, mesh = {Bacteroidetes/genetics/isolation &amp; purification ; Bays/*microbiology ; Cyanobacteria/genetics/isolation &amp; purification ; DNA, Bacterial/genetics/isolation &amp; purification ; *Eutrophication ; *Microbiota ; Proteobacteria/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics/isolation &amp; purification ; Republic of Korea ; Seasons ; Sequence Analysis, DNA ; Water Microbiology ; }, abstract = {Microbial communities play an essential role in marine biogeochemical cycles. Physical and biogeochemical changes in Jinhae Bay, the most anthropogenically eutrophied bay on the coasts of South Korea, are well described, but less is known about the associated changes in microbial communities. Temporal and vertical variation in microbial communities at three depths (surface, middle, and bottom) at seven time points (June to December) at the J1 sampling site were investigated on the MiSeq platform based on the 16S rRNA gene. Overall, the microbial community was dominated by Proteobacteria, Cyanobacteria, and Bacteroidetes from June to November, whereas Firmicutes were dominant in December, especially in the middle and bottom layers. The results indicate that the microbial community composition strongly varied with temporal changes in the physicochemical water properties. Moreover, the community composition differed markedly between the surface and middle layers and the bottom layer in the summer, when the water column was strongly stratified and bottom water hypoxia developed. A redundancy analysis suggested a significant correlation between physicochemical variables (i.e., temperature, salinity, and oxygen concentration) and microbial community composition. This study indicates that temporal changes in water conditions and eutrophication-induced hypoxia effectively shape the structure of the microbial community.}, }
@article {pmid29715508, year = {2018}, author = {Lamichhane, S and Sen, P and Dickens, AM and Orešič, M and Bertram, HC}, title = {Gut metabolome meets microbiome: A methodological perspective to understand the relationship between host and microbe.}, journal = {Methods (San Diego, Calif.)}, volume = {149}, number = {}, pages = {3-12}, doi = {10.1016/j.ymeth.2018.04.029}, pmid = {29715508}, issn = {1095-9130}, mesh = {Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/immunology/metabolism ; Host Microbial Interactions/*physiology ; Humans ; Metabolome/*physiology ; Metabolomics/*methods/trends ; }, abstract = {It is well established that gut microbes and their metabolic products regulate host metabolism. The interactions between the host and its gut microbiota are highly dynamic and complex. In this review we present and discuss the metabolomic strategies to study the gut microbial ecosystem. We highlight the metabolic profiling approaches to study faecal samples aimed at deciphering the metabolic product derived from gut microbiota. We also discuss how metabolomics data can be integrated with metagenomics data derived from gut microbiota and how such approaches may lead to better understanding of the microbial functions. Finally, the emerging approaches of genome-scale metabolic modelling to study microbial co-metabolism and host-microbe interactions are highlighted.}, }
@article {pmid28912574, year = {2017}, author = {Purcell, RV and Visnovska, M and Biggs, PJ and Schmeier, S and Frizelle, FA}, title = {Distinct gut microbiome patterns associate with consensus molecular subtypes of colorectal cancer.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11590}, pmid = {28912574}, issn = {2045-2322}, mesh = {Adult ; Aged ; Aged, 80 and over ; *Biomarkers, Tumor ; Colorectal Neoplasms/*etiology/metabolism/*pathology ; Computational Biology ; Female ; *Gastrointestinal Microbiome ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Humans ; Male ; Metagenome ; Metagenomics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Transcriptome ; }, abstract = {Colorectal cancer (CRC) is a heterogeneous disease and recent advances in subtype classification have successfully stratified the disease using molecular profiling. The contribution of bacterial species to CRC development is increasingly acknowledged, and here, we sought to analyse CRC microbiomes and relate them to tumour consensus molecular subtypes (CMS), in order to better understand the relationship between bacterial species and the molecular mechanisms associated with CRC subtypes. We classified 34 tumours into CRC subtypes using RNA-sequencing derived gene expression and determined relative abundances of bacterial taxonomic groups using 16S rRNA amplicon metabarcoding. 16S rRNA analysis showed enrichment of Fusobacteria and Bacteroidetes, and decreased levels of Firmicutes and Proteobacteria in CMS1. A more detailed analysis of bacterial taxa using non-human RNA-sequencing reads uncovered distinct bacterial communities associated with each molecular subtype. The most highly enriched species associated with CMS1 included Fusobacterium hwasookii and Porphyromonas gingivalis. CMS2 was enriched for Selenomas and Prevotella species, while CMS3 had few significant associations. Targeted quantitative PCR validated these findings and also showed an enrichment of Fusobacterium nucleatum, Parvimonas micra and Peptostreptococcus stomatis in CMS1. In this study, we have successfully associated individual bacterial species to CRC subtypes for the first time.}, }
@article {pmid28900280, year = {2017}, author = {Zhang, J and Mao, L and Zhang, L and Loh, KC and Dai, Y and Tong, YW}, title = {Metagenomic insight into the microbial networks and metabolic mechanism in anaerobic digesters for food waste by incorporating activated carbon.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11293}, pmid = {28900280}, issn = {2045-2322}, mesh = {*Anaerobiosis ; Computational Biology/methods ; *Energy Metabolism ; Fermentation ; Food ; Metabolic Networks and Pathways ; *Metagenome ; *Metagenomics/methods ; Methane/biosynthesis ; *Microbiota ; Waste Disposal, Fluid ; }, abstract = {Powdered activated carbon (AC) is commonly used as an effective additive to enhance anaerobic digestion (AD), but little is known about how the metabolic pathways resulting from adding AC change the microbial association network and enhance food waste treatment. In this work, the use of AC in an anaerobic digestion system for food waste was explored. Using bioinformatics analysis, taxonomic trees and the KEGG pathway analysis, changes in microbial network and biometabolic pathways were tracked. The overall effect of these changes were used to explain and validate improved digestion performance. The results showed that AC accelerated the decomposition of edible oil in food waste, enhancing the conversion of food waste to methane with the optimized dosage of 12 g AC per reactor. Specifically, when AC was added, the proponoate metabolic pathway that converts propanoic acid to acetic acid became more prominent, as measured by 16S rRNA in the microbial community. The other two metabolic pathways, Lipid Metabolism and Methane Metabolism, were also enhanced. Bioinformatics analysis revealed that AC promoted the proliferation of syntrophic microorganisms such as Methanosaeta and Geobacter, forming a highly intensive syntrophic microbial network.}, }
@article {pmid28900257, year = {2017}, author = {Potter, C and Freeman, C and Golyshin, PN and Ackermann, G and Fenner, N and McDonald, JE and Ehbair, A and Jones, TG and Murphy, LM and Creer, S}, title = {Subtle shifts in microbial communities occur alongside the release of carbon induced by drought and rewetting in contrasting peatland ecosystems.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11314}, pmid = {28900257}, issn = {2045-2322}, support = {BB/M029085/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Biodiversity ; Carbon/*metabolism ; *Droughts ; *Ecosystem ; Environment ; Metagenome ; Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Peat represents a globally significant pool of sequestered carbon. However, peatland carbon stocks are highly threatened by anthropogenic climate change, including drought, which leads to a large release of carbon dioxide. Although the enzymatic mechanisms underlying drought-driven carbon release are well documented, the effect of drought on peatland microbial communities has been little studied. Here, we carried out a replicated and controlled drought manipulation using intact peat 'mesocosm cores' taken from bog and fen habitats, and used a combination of community fingerprinting and sequencing of marker genes to identify community changes associated with drought. Community composition varied with habitat and depth. Moreover, community differences between mesocosm cores were stronger than the effect of the drought treatment, emphasising the importance of replication in microbial marker gene studies. While the effect of drought on the overall composition of prokaryotic and eukaryotic communities was weak, a subset of the microbial community did change in relative abundance, especially in the fen habitat at 5 cm depth. 'Drought-responsive' OTUs were disproportionately drawn from the phyla Bacteroidetes and Proteobacteria. Collectively, the data provide insights into the microbial community changes occurring alongside drought-driven carbon release from peatlands, and suggest a number of novel avenues for future research.}, }
@article {pmid28900198, year = {2017}, author = {Wu, X and Zhang, H and Chen, J and Shang, S and Yan, J and Chen, Y and Tang, X and Zhang, H}, title = {Analysis and comparison of the wolf microbiome under different environmental factors using three different data of Next Generation Sequencing.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11332}, pmid = {28900198}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; Computational Biology/methods ; Dogs ; *Environment ; Feces/microbiology ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/methods ; *Microbiota ; Phylogeny ; *Wolves ; }, abstract = {Next Generation Sequencing has been widely used to characterize the prevalence of fecal bacteria in many different species. In this study, we attempted to employ a low-cost and high-throughput sequencing model to discern information pertaining to the wolf microbiota. It is hoped that this model will allow researchers to elucidate potential protective factors in relation to endangered wolf species. We propose three high-throughput sequencing models to reveal information pertaining to the micro-ecology of the wolf. Our analyses advised that, among the three models, more than 100,000 sequences are more appropriate to retrieve the communities' richness and diversity of micro-ecology. In addition, the top five wolf microbiome OTUs (99%) were members of the following five phyla: Bacteroidetes, Fusobacteria, Firmicutes, Proteobacteria, and Actinobacteria. While Alloprevotella, Clostridium_sensu_stricto_1, Anaerobiospirillum, Faecalibactreium and Streptococcus were shared by all samples, their relative abundances were differentially represented between domestic dogs and other wolves. Our findings suggest that altitude, human interference, age, and climate all contribute towards the micro-ecology of the wolf. Specifically, we observed that genera Succinivibrio and Turicibacter are significantly related to altitude and human interference (including hunting practices).}, }
@article {pmid28623321, year = {2017}, author = {Deng, ZL and Szafrański, SP and Jarek, M and Bhuju, S and Wagner-Döbler, I}, title = {Dysbiosis in chronic periodontitis: Key microbial players and interactions with the human host.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {3703}, pmid = {28623321}, issn = {2045-2322}, mesh = {Archaea ; Case-Control Studies ; Chronic Periodontitis/*microbiology/parasitology/virology ; Computational Biology/methods ; *Dysbiosis ; Gene Expression Regulation, Bacterial ; Host-Pathogen Interactions ; Humans ; Metagenome ; Metagenomics/methods ; Microbiota ; RNA, Ribosomal, 18S/genetics ; RNA, Viral ; Virulence Factors ; }, abstract = {Periodontitis is an extremely prevalent disease worldwide and is driven by complex dysbiotic microbiota. Here we analyzed the transcriptional activity of the periodontal pocket microbiota from all domains of life as well as the human host in health and chronic periodontitis. Bacteria showed strong enrichment of 18 KEGG functional modules in chronic periodontitis, including bacterial chemotaxis, flagellar assembly, type III secretion system, type III CRISPR-Cas system, and two component system proteins. Upregulation of these functions was driven by the red-complex pathogens and candidate pathogens, e.g. Filifactor alocis, Prevotella intermedia, Fretibacterium fastidiosum and Selenomonas sputigena. Nine virulence factors were strongly up-regulated, among them the arginine deiminase arcA from Porphyromonas gingivalis and Mycoplasma arginini. Viruses and archaea accounted for about 0.1% and 0.22% of total putative mRNA reads, respectively, and a protozoan, Entamoeba gingivalis, was highly enriched in periodontitis. Fourteen human transcripts were enriched in periodontitis, including a gene for a ferric iron binding protein, indicating competition with the microbiota for iron, and genes associated with cancer, namely nucleolar phosphoprotein B23, ankyrin-repeat domain 30B-like protein and beta-enolase. The data provide evidence on the level of gene expression in vivo for the potentially severe impact of the dysbiotic microbiota on human health.}, }
@article {pmid31015324, year = {2019}, author = {Easton, AV and Quiñones, M and Vujkovic-Cvijin, I and Oliveira, RG and Kepha, S and Odiere, MR and Anderson, RM and Belkaid, Y and Nutman, TB}, title = {The Impact of Anthelmintic Treatment on Human Gut Microbiota Based on Cross-Sectional and Pre- and Postdeworming Comparisons in Western Kenya.}, journal = {mBio}, volume = {10}, number = {2}, pages = {}, doi = {10.1128/mBio.00519-19}, pmid = {31015324}, issn = {2150-7511}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Anthelmintics/*administration &amp; dosage ; Ascariasis/*drug therapy ; Bacteria/*classification/genetics ; Child ; Child, Preschool ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects ; Humans ; Kenya ; Metagenomics ; Microbiota/*drug effects ; Middle Aged ; Necatoriasis/*drug therapy ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Rural Population ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {Murine studies suggest that the presence of some species of intestinal helminths is associated with changes in host microbiota composition and diversity. However, studies in humans have produced varied conclusions, and the impact appears to vary widely depending on the helminth species present. To demonstrate how molecular approaches to the human gut microbiome can provide insights into the complex interplay among disparate organisms, DNA was extracted from cryopreserved stools collected from residents of 5 rural Kenyan villages prior to and 3 weeks and 3 months following albendazole (ALB) therapy. Samples were analyzed by quantitative PCR (qPCR) for the presence of 8 species of intestinal parasites and by MiSeq 16S rRNA gene sequencing. Based on pretreatment results, the presence of neither Ascaris lumbricoides nor Necator americanus infection significantly altered the overall diversity of the microbiota in comparison with age-matched controls. Following ALB therapy and clearance of soil-transmitted helminths (STH), there were significant increases in the proportion of the microbiota made up by Clostridiales (P = 0.0002; average fold change, 0.57) and reductions in the proportion made up by Enterobacteriales (P = 0.0004; average fold change, -0.58). There was a significant posttreatment decrease in Chao1 richness, even among individuals who were uninfected pretreatment, suggesting that antimicrobial effects must be considered in any posttreatment setting. Nevertheless, the helminth-associated changes in Clostridiales and Enterobacteriales suggest that clearance of STH, and of N. americanus in particular, alters the gut microbiota.IMPORTANCE The gut microbiome is an important factor in human health. It is affected by what we eat, what medicines we take, and what infections we acquire. In turn, it affects the way we absorb nutrients and whether we have excessive intestinal inflammation. Intestinal worms may have an important impact on the composition of the gut microbiome. Without a complete understanding of the impact of mass deworming programs on the microbiome, it is impossible to accurately calculate the cost-effectiveness of such public health interventions and to guard against any possible deleterious side effects. Our research examines this question in a &quot;real-world&quot; setting, using a longitudinal cohort, in which individuals with and without worm infections are treated with deworming medication and followed up at both three weeks and three months posttreatment. We quantify the impact of roundworms and hookworms on gut microbial composition, suggesting that the impact is small, but that treatment of hookworm infection results in significant changes. This work points to the need for follow-up studies to further examine the impact of hookworm on the gut microbiota and determine the health consequences of the observed changes.}, }
@article {pmid30953542, year = {2019}, author = {Raymond, F and Boissinot, M and Ouameur, AA and Déraspe, M and Plante, PL and Kpanou, SR and Bérubé, È and Huletsky, A and Roy, PH and Ouellette, M and Bergeron, MG and Corbeil, J}, title = {Culture-enriched human gut microbiomes reveal core and accessory resistance genes.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {56}, doi = {10.1186/s40168-019-0669-7}, pmid = {30953542}, issn = {2049-2618}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/*classification/drug effects/genetics/growth &amp; development ; Bacterial Proteins/genetics ; Bacteriological Techniques/*methods ; *Drug Resistance, Microbial ; Escherichia coli/genetics/growth &amp; development/isolation &amp; purification ; Feces/cytology/microbiology ; Gastrointestinal Microbiome ; Gene Transfer, Horizontal ; Humans ; Metagenomics ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: Low-abundance microorganisms of the gut microbiome are often referred to as a reservoir for antibiotic resistance genes. Unfortunately, these less-abundant bacteria can be overlooked by deep shotgun sequencing. In addition, it is a challenge to associate the presence of resistance genes with their risk of acquisition by pathogens. In this study, we used liquid culture enrichment of stools to assemble the genome of lower-abundance bacteria from fecal samples. We then investigated the gene content recovered from these culture-enriched and culture-independent metagenomes in relation with their taxonomic origin, specifically antibiotic resistance genes. We finally used a pangenome approach to associate resistance genes with the core or accessory genome of Enterobacteriaceae and inferred their propensity to horizontal gene transfer.<br><br>RESULTS: Using culture-enrichment approaches with stools allowed assembly of 187 bacterial species with an assembly size greater than 1 million nucleotides. Of these, 67 were found only in culture-enriched conditions, and 22 only in culture-independent microbiomes. These assembled metagenomes allowed the evaluation of the gene content of specific subcommunities of the gut microbiome. We observed that differentially distributed metabolic enzymes were associated with specific culture conditions and, for the most part, with specific taxa. Gene content differences between microbiomes, for example, antibiotic resistance, were for the most part not associated with metabolic enzymes, but with other functions. We used a pangenome approach to determine if the resistance genes found in Enterobacteriaceae, specifically E. cloacae or E. coli, were part of the core genome or of the accessory genome of this species. In our healthy volunteer cohort, we found that E. cloacae contigs harbored resistance genes that were part of the core genome of the species, while E. coli had a large accessory resistome proximal to mobile elements.<br><br>CONCLUSION: Liquid culture of stools contributed to an improved functional and comparative genomics study of less-abundant gut bacteria, specifically those associated with antibiotic resistance. Defining whether a gene is part of the core genome of a species helped in interpreting the genomes recovered from culture-independent or culture-enriched microbiomes.}, }
@article {pmid30914068, year = {2019}, author = {Wang, W and Hu, H and Zijlstra, RT and Zheng, J and Gänzle, MG}, title = {Metagenomic reconstructions of gut microbial metabolism in weanling pigs.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {48}, doi = {10.1186/s40168-019-0662-1}, pmid = {30914068}, issn = {2049-2618}, mesh = {Animals ; Bacteria/*classification/genetics/isolation &amp; purification ; Bacteroidetes/genetics/isolation &amp; purification/metabolism ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Dietary Carbohydrates/*metabolism ; Firmicutes/genetics/isolation &amp; purification/metabolism ; Gastrointestinal Microbiome ; Lactobacillus/genetics/isolation &amp; purification/metabolism ; Male ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; Swine ; }, abstract = {BACKGROUND: The piglets' transition from milk to solid feed induces a succession of bacterial communities, enhancing the hosts' ability to harvest energy from dietary carbohydrates. To reconstruct microbial carbohydrate metabolism in weanling pigs, this study combined 16S rRNA gene sequencing (n = 191) and shotgun metagenomics (n = 72).<br><br>RESULTS: Time and wheat content in feed explained most of the variation of the microbiota as assessed by 16S rRNA gene sequencing in weanling pigs. De novo metagenomic binning reconstructed 360 high-quality genomes that represented 11 prokaryotic and 1 archaeal phylum. Analysis of carbohydrate metabolism in these genomes revealed that starch fermentation is carried out by a consortium of Firmicutes expressing extracellular α-(1 → 4)-glucan branching enzyme (GH13) and Bacteroidetes expressing periplasmic neopullulanase (GH13) and α-glucosidase (GH97). Fructans were degraded by extracellular GH32 enzymes from Bacteriodetes and Lactobacillus. Lactose fermentation by β-galactosidases (GH2 and GH42) was identified in Firmicutes. In conclusion, the assembly of 360 high-quality genomes as the first metagenomic reference for swine intestinal microbiota allowed identification of key microbial contributors to degradation of starch, fructans, and lactose.<br><br>CONCLUSIONS: Microbial consortia that are responsible for degradation of these glycans differ substantially from the microbial consortia that degrade the same glycans in humans. Our study thus enables improvement of feeding models with higher feed efficiency and better pathogen control for weanling pigs.}, }
@article {pmid30694507, year = {2019}, author = {Delafont, V and Perrin, Y and Bouchon, D and Moulin, L and Héchard, Y}, title = {Targeted Metagenomics of Microbial Diversity in Free-Living Amoebae and Water Samples.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1921}, number = {}, pages = {421-428}, doi = {10.1007/978-1-4939-9048-1_26}, pmid = {30694507}, issn = {1940-6029}, mesh = {Amoeba/*microbiology ; Biodiversity ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S ; *Water Microbiology ; }, abstract = {The presence of Legionella spp. in natural and man-made water systems is a great public health concern and heavily depends on the presence of free-living amoebae. Taking advantage of the development and affordability of next-generation sequencing technology, we present here a method to characterize the whole bacterial community directly from water samples, as well as from isolated free-living amoebae.}, }
@article {pmid30678352, year = {2019}, author = {Yang, Q and Gao, C and Jiang, Y and Wang, M and Zhou, X and Shao, H and Gong, Z and McMinn, A}, title = {Metagenomic Characterization of the Viral Community of the South Scotia Ridge.}, journal = {Viruses}, volume = {11}, number = {2}, pages = {}, doi = {10.3390/v11020095}, pmid = {30678352}, issn = {1999-4915}, mesh = {Antarctic Regions ; Bacteriophages/genetics ; *Genetic Variation ; *Genome, Viral ; *Metagenome ; Metagenomics ; *Microbiota ; Phylogeny ; Podoviridae/genetics/isolation &amp; purification ; Seawater/virology ; Viruses/*classification ; Water Microbiology ; }, abstract = {Viruses are the most abundant biological entities in aquatic ecosystems and harbor an enormous amount of genetic diversity. Whereas their influence on marine ecosystems is widely acknowledged, current information about their diversity remains limited. We conducted a viral metagenomic analysis of water samples collected during the austral summer of 2016 from the South Scotia Ridge (SSR), near the Antarctic Peninsula. The taxonomic composition and diversity of the viral communities were investigated, and a functional assessment of the sequences was performed. Phylotypic analysis showed that most viruses belonged to the order Caudovirales, especially the family Podoviridae (41.92⁻48.7%), which is similar to the situation in the Pacific Ocean. Functional analysis revealed a relatively high frequency of phage-associated and metabolism genes. Phylogenetic analyses of phage TerL and Capsid_NCLDV (nucleocytoplasmic large DNA viruses) marker genes indicated that many sequences associated with Caudovirales and NCLDV were novel and distinct from known phage genomes. High Phaeocystis globosa virus virophage (Pgvv) signatures were found and complete and partial Pgvv-like were obtained, which influence host⁻virus interactions. Our study expands existing knowledge of viral communities and their diversities from the Antarctic region and provides basic data for further exploring polar microbiomes.}, }
@article {pmid30525950, year = {2019}, author = {Hibberd, AA and Yde, CC and Ziegler, ML and Honoré, AH and Saarinen, MT and Lahtinen, S and Stahl, B and Jensen, HM and Stenman, LK}, title = {Probiotic or synbiotic alters the gut microbiota and metabolism in a randomised controlled trial of weight management in overweight adults.}, journal = {Beneficial microbes}, volume = {10}, number = {2}, pages = {121-135}, doi = {10.3920/BM2018.0028}, pmid = {30525950}, issn = {1876-2891}, mesh = {Adult ; Aged ; Bacteria/classification/metabolism ; Body Fat Distribution ; Double-Blind Method ; Feces/chemistry/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metabolomics ; Metagenomics ; *Microbiota ; Middle Aged ; Obesity/*therapy ; Overweight/*therapy ; Placebos/administration &amp; dosage ; Probiotics/*administration &amp; dosage ; Synbiotics/*administration &amp; dosage ; Treatment Outcome ; }, abstract = {The gut microbiota contributes to host energy metabolism, and altered gut microbiota has been associated with obesity-related metabolic disorders. We previously reported that a probiotic alone or together with a prebiotic controls body fat mass in healthy overweight or obese individuals in a randomised, double-blind, placebo controlled clinical study (ClinicalTrials.gov NCT01978691). We now aimed to investigate whether changes in the gut microbiota may be associated with the observed clinical benefits. Faecal and plasma samples were obtained from a protocol compliant subset (n=134) of participants from a larger clinical study where participants were randomised (1:1:1:1) into four groups: (1) placebo, 12 g/d microcrystalline cellulose; (2) Litesse® Ultra™ polydextrose (LU), 12 g/day; (3) Bifidobacterium animalis subsp. lactis 420™ (B420), 1010 cfu/d in 12 g microcrystalline cellulose; (4) LU+B420, 1010 cfu/d of B420 in 12 g/d LU for 6 months of intervention. The faecal microbiota composition and metabolites were assessed as exploratory outcomes at baseline, 2, 4, 6 months, and +1 month post-intervention and correlated to obesity-related clinical outcomes. Lactobacillus and Akkermansia were more abundant with B420 at the end of the intervention. LU+B420 increased Akkermansia, Christensenellaceae and Methanobrevibacter, while Paraprevotella was reduced. Christensenellaceae was consistently increased in the LU and LU+B420 groups across the intervention time points, and correlated negatively to waist-hip ratio and energy intake at baseline, and waist-area body fat mass after 6 months treatment with LU+B420. Functional metagenome predictions indicated alterations in pathways related to cellular processes and metabolism. Plasma bile acids glycocholic acid, glycoursodeoxycholic acid, and taurohyodeoxycholic acid and tauroursodeoxycholic acid were reduced in LU+B420 compared to Placebo. Consumption of B420 and its combination with LU resulted in alterations of the gut microbiota and its metabolism, and may support improved gut barrier function and obesity-related markers.}, }
@article {pmid30390805, year = {2018}, author = {Wang, Q and Yang, F and Jia, H}, title = {Mining the Microbiome for Drug Targets.}, journal = {Methods in enzymology}, volume = {610}, number = {}, pages = {59-72}, doi = {10.1016/bs.mie.2018.09.014}, pmid = {30390805}, issn = {1557-7988}, mesh = {Drug Discovery/*methods ; Humans ; Metagenome/drug effects ; Metagenomics/*methods ; Microbiota/*drug effects ; Molecular Targeted Therapy/methods ; }, abstract = {The human microbiome is our &quot;other genome.&quot; Implicated in a growing list of complex diseases, for which genomic studies typically explain a portion of the disease susceptibility, the human gut microbiome has been at the spotlight for our understanding of human diseases. As the microbiome is intrinsically more variable than the human genome, it is important to take careful considerations at each step of a study. Here, we put forward our recommendations, which we envision would facilitate identification of true drug targets in the human microbiome in the colon as well as at other body sites.}, }
@article {pmid30269123, year = {2018}, author = {Hattori, M}, title = {[Ecology and function of human microbiomes.].}, journal = {Clinical calcium}, volume = {28}, number = {10}, pages = {1398-1405}, doi = {CliCa181013981405}, pmid = {30269123}, issn = {0917-5857}, mesh = {Bacteria ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; }, abstract = {Hundreds of trillions of bacteria consisting of ~1,000 species reside in various human body sites to form bacterial communities(microbiomes)specific for the sites. In the past decade, the human microbiome research in the world incredibly advanced by development of a culture-independent metagenomic analysis based on next-generation sequencing technologies. Particularly, current studies have revealed that the human gut microbiome is profoundly associated with the host's health and disease.}, }
@article {pmid28449106, year = {2017}, author = {Dhariwal, A and Chong, J and Habib, S and King, IL and Agellon, LB and Xia, J}, title = {MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data.}, journal = {Nucleic acids research}, volume = {45}, number = {W1}, pages = {W180-W188}, pmid = {28449106}, issn = {1362-4962}, mesh = {Computational Biology/*methods ; Computer Graphics ; DNA Barcoding, Taxonomic/methods ; Datasets as Topic ; Female ; Gastrointestinal Tract/microbiology ; Humans ; Internet ; Male ; Meta-Analysis as Topic ; Metabolic Networks and Pathways/*genetics ; Metagenomics/methods/*statistics &amp; numerical data ; Microbiota/*genetics ; Mouth/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Skin/microbiology ; *Software ; Vagina/microbiology ; }, abstract = {The widespread application of next-generation sequencing technologies has revolutionized microbiome research by enabling high-throughput profiling of the genetic contents of microbial communities. How to analyze the resulting large complex datasets remains a key challenge in current microbiome studies. Over the past decade, powerful computational pipelines and robust protocols have been established to enable efficient raw data processing and annotation. The focus has shifted toward downstream statistical analysis and functional interpretation. Here, we introduce MicrobiomeAnalyst, a user-friendly tool that integrates recent progress in statistics and visualization techniques, coupled with novel knowledge bases, to enable comprehensive analysis of common data outputs produced from microbiome studies. MicrobiomeAnalyst contains four modules - the Marker Data Profiling module offers various options for community profiling, comparative analysis and functional prediction based on 16S rRNA marker gene data; the Shotgun Data Profiling module supports exploratory data analysis, functional profiling and metabolic network visualization of shotgun metagenomics or metatranscriptomics data; the Taxon Set Enrichment Analysis module helps interpret taxonomic signatures via enrichment analysis against >300 taxon sets manually curated from literature and public databases; finally, the Projection with Public Data module allows users to visually explore their data with a public reference data for pattern discovery and biological insights. MicrobiomeAnalyst is freely available at http://www.microbiomeanalyst.ca.}, }
@article {pmid30978480, year = {2019}, author = {Reddy, B and Pandey, J and Dubey, SK}, title = {Assessment of environmental gene tags linked with carbohydrate metabolism and chemolithotrophy associated microbial community in River Ganga.}, journal = {Gene}, volume = {704}, number = {}, pages = {31-41}, doi = {10.1016/j.gene.2019.04.004}, pmid = {30978480}, issn = {1879-0038}, mesh = {Animals ; Bacteria/classification/genetics/growth &amp; development ; Carbohydrate Metabolism/*genetics ; Chemoautotrophic Growth/*genetics ; DNA Barcoding, Taxonomic ; Environment ; Geologic Sediments/*microbiology ; Humans ; India ; Metabolic Networks and Pathways/genetics ; Metagenome ; *Metagenomics/methods ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; }, abstract = {The microbial community mediated biogeochemical cycles play important role in global C-cycle and display a sensitive response to environmental changes. Limited information is available on microbial composition and functional diversity controlling biogeochemical cycles in the riverine environment. The Ganga River water and sediment samples were studied for environmental gene tags with reference to carbohydrate metabolism, photoheterotrophy and chemolithotrophy using high throughput shotgun metagenomic sequencing and functional annotation. The diversity of environmental gene tags specific microbial community was annotated against reference sequence database using Kaiju taxonomic classifier. The metagenomic analyses revealed that the river harbored a broad range of carbohydrate and energy metabolism genes. The in-depth investigation of metagenomic data revealed that the enzymes associated with reverse TCA cycle, Calvin-Benson cycle enzyme RuBisCO, starch and sucrose metabolism genes were highly abundant. The enzymes associated with sulfur metabolism such as EC:2.7.7.4 (sulfate to ammonium per sulfate), EC:1.8.1.2, EC:1.8.7.1 (sulfite to H2S) were prevalent in both the class of samples. The principal component analysis of the functional profiles revealed that the water and sediment samples were clustered distinctly suggesting that both the sites had variable abundance of functional genes and associated microbiota. The taxonomic classification showed abundance of Proteobacteria, Actinobacteria and Bacteroidetes phyla. Also, the metagenomic study showed the presence of purple sulfur bacteria viz. Thiodictyon, Nitrosococcus and purple non-sulfur bacteria viz. Bradyrhozobium and Rhodobacter. The study demonstrates that the Ganga River microbiome has prevalence of functional genes involved in carbohydrate anabolism and catabolism, and CO2 fixation with great prospects in cellulose and sulfide degrading enzyme production and characterization.}, }
@article {pmid30010747, year = {2018}, author = {Nusbaum, DJ and Sun, F and Ren, J and Zhu, Z and Ramsy, N and Pervolarakis, N and Kunde, S and England, W and Gao, B and Fiehn, O and Michail, S and Whiteson, K}, title = {Gut microbial and metabolomic profiles after fecal microbiota transplantation in pediatric ulcerative colitis patients.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {9}, pages = {}, doi = {10.1093/femsec/fiy133}, pmid = {30010747}, issn = {1574-6941}, support = {R01 GM120624/GM/NIGMS NIH HHS/United States ; R01 HD081197/HD/NICHD NIH HHS/United States ; T32 EB009418/EB/NIBIB NIH HHS/United States ; R56 HL126754/HL/NHLBI NIH HHS/United States ; }, mesh = {Child ; Clostridiaceae/classification/genetics/*isolation &amp; purification ; Colitis, Ulcerative/*microbiology/*therapy ; *Fecal Microbiota Transplantation ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Male ; Metabolomics ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Ulcerative colitis is a chronic inflammatory disease of the colon that carries a significant disease burden in children. Therefore, new therapeutic approaches are being explored to help children living with this disease. Fecal microbiota transplantation (FMT) has been successful in some children with ulcerative colitis. However, the mechanism of its therapeutic effect in this patient population is not well understood. To characterize changes in gut microbial and metabolomic profiles after FMT, we performed 16S rRNA gene sequencing, shotgun metagenomic sequencing, virome analysis and untargeted metabolomics by gas chromatography-time of flight-mass spectrometry on stool samples collected before and after FMT from four children with ulcerative colitis who responded to this treatment. Alpha diversity of the gut microbiota increased after intervention, with species richness rising from 251 (S.D. 125) to 358 (S.D. 27). In responders, the mean relative abundance of bacteria in the class Clostridia shifted toward donor levels, increasing from 33% (S.D. 11%) to 54% (S.D. 16%). Patient metabolomic and viromic profiles exhibited a similar but less pronounced shift toward donor profiles after FMT. The fecal concentrations of several metabolites were altered after FMT, correlating with clinical improvement. Larger studies using a similar multi-omics approach may suggest novel strategies for the treatment of pediatric ulcerative colitis.}, }
@article {pmid29028181, year = {2018}, author = {Fosso, B and Pesole, G and Rosselló, F and Valiente, G}, title = {Unbiased Taxonomic Annotation of Metagenomic Samples.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {25}, number = {3}, pages = {348-360}, pmid = {29028181}, issn = {1557-8666}, mesh = {DNA Barcoding, Taxonomic/*methods/standards ; Humans ; *Metagenome ; Microbiota ; *Phylogeny ; *Software ; }, abstract = {The classification of reads from a metagenomic sample using a reference taxonomy is usually based on first mapping the reads to the reference sequences and then classifying each read at a node under the lowest common ancestor of the candidate sequences in the reference taxonomy with the least classification error. However, this taxonomic annotation can be biased by an imbalanced taxonomy and also by the presence of multiple nodes in the taxonomy with the least classification error for a given read. In this article, we show that the Rand index is a better indicator of classification error than the often used area under the receiver operating characteristic (ROC) curve and F-measure for both balanced and imbalanced reference taxonomies, and we also address the second source of bias by reducing the taxonomic annotation problem for a whole metagenomic sample to a set cover problem, for which a logarithmic approximation can be obtained in linear time and an exact solution can be obtained by integer linear programming. Experimental results with a proof-of-concept implementation of the set cover approach to taxonomic annotation in a next release of the TANGO software show that the set cover approach further reduces ambiguity in the taxonomic annotation obtained with TANGO without distorting the relative abundance profile of the metagenomic sample.}, }
@article {pmid30580413, year = {2019}, author = {Bridier, A}, title = {Exploring Foodborne Pathogen Ecology and Antimicrobial Resistance in the Light of Shotgun Metagenomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1918}, number = {}, pages = {229-245}, doi = {10.1007/978-1-4939-9000-9_19}, pmid = {30580413}, issn = {1940-6029}, mesh = {Anti-Infective Agents/pharmacology ; Bacteria/classification/genetics ; Biodiversity ; *Drug Resistance, Microbial ; Food Microbiology ; Food Safety ; Foodborne Diseases/diagnosis/*microbiology ; Genome ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; *Metagenomics/methods ; Whole Genome Sequencing ; }, abstract = {In this chapter, applications of shotgun metagenomics for taxonomic profiling and functional investigation of food microbial communities with a focus on antimicrobial resistance (AMR) were overviewed in the light of last data in the field. Potentialities of metagenomic approach, along with the challenges encountered for a wider and routinely use in food safety was discussed.}, }
@article {pmid30580412, year = {2019}, author = {Feye, KM and Ricke, SC}, title = {Establishment of a Standardized 16S rDNA Library Preparation to Enable Analysis of Microbiome in Poultry Processing Using Illumina MiSeq Platform.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1918}, number = {}, pages = {213-227}, doi = {10.1007/978-1-4939-9000-9_18}, pmid = {30580412}, issn = {1940-6029}, mesh = {Animals ; Data Analysis ; *Gene Library ; High-Throughput Nucleotide Sequencing ; Metagenome ; *Metagenomics/methods ; *Microbiota ; Polymerase Chain Reaction ; Poultry/*microbiology ; Quality Control ; *RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; }, abstract = {The standardization of the microbiome sequencing of poultry rinsates is essential for generating comparable microbial composition data among poultry processing facilities if this technology is to be adopted by the industry. Samples must first be acquired, DNA must be extracted, and libraries must be constructed. In order to proceed to library sequencing, the samples should meet quality control standards. Finally, data must be analyzed using computer bioinformatics pipelines. This data can subsequently be incorporated into more advanced computer algorithms for risk assessment. Ultimately, a uniform sequencing pipeline will enable both the government regulatory agencies and the poultry industry to identify potential weaknesses in food safety. This chapter presents the different steps for monitoring the population dynamics of the microbiome in poultry processing using 16S rDNA sequencing.}, }
@article {pmid30038310, year = {2018}, author = {Duerkop, BA and Kleiner, M and Paez-Espino, D and Zhu, W and Bushnell, B and Hassell, B and Winter, SE and Kyrpides, NC and Hooper, LV}, title = {Murine colitis reveals a disease-associated bacteriophage community.}, journal = {Nature microbiology}, volume = {3}, number = {9}, pages = {1023-1031}, pmid = {30038310}, issn = {2058-5276}, support = {K01 DK102436/DK/NIDDK NIH HHS/United States ; R01 DK070855/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteriophages/genetics/*isolation &amp; purification ; Cells, Cultured ; Colitis/*pathology/*virology ; Disease Models, Animal ; Dysbiosis/*virology ; Gastrointestinal Microbiome/*physiology ; Genome, Viral/genetics ; Humans ; Intestinal Mucosa/*virology ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; }, abstract = {The dysregulation of intestinal microbial communities is associated with inflammatory bowel diseases (IBD). Studies aimed at understanding the contribution of the microbiota to inflammatory diseases have primarily focused on bacteria, yet the intestine harbours a viral component dominated by prokaryotic viruses known as bacteriophages (phages). Phage numbers are elevated at the intestinal mucosal surface and phages increase in abundance during IBD, suggesting that phages play an unidentified role in IBD. We used a sequence-independent approach for the selection of viral contigs and then applied quantitative metagenomics to study intestinal phages in a mouse model of colitis. We discovered that during colitis the intestinal phage population is altered and transitions from an ordered state to a stochastic dysbiosis. We identified phages specific to pathobiotic hosts associated with intestinal disease, whose abundances are altered during colitis. Additionally, phage populations in healthy and diseased mice overlapped with phages from healthy humans and humans with IBD. Our findings indicate that intestinal phage communities are altered during inflammatory disease, establishing a platform for investigating phage involvement in IBD.}, }
@article {pmid31123265, year = {2019}, author = {Li, Y and Fu, X and Ma, J and Zhang, J and Hu, Y and Dong, W and Wan, Z and Li, Q and Kuang, YQ and Lan, K and Jin, X and Wang, JH and Zhang, C}, title = {Altered respiratory virome and serum cytokine profile associated with recurrent respiratory tract infections in children.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {2288}, doi = {10.1038/s41467-019-10294-x}, pmid = {31123265}, issn = {2041-1723}, mesh = {Acute Disease ; Bacteriophages/genetics/*isolation &amp; purification ; Child ; Child, Preschool ; Cytokines/*blood/immunology ; Disease Susceptibility/blood/immunology/microbiology ; Female ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Infant ; Longitudinal Studies ; Male ; Metagenomics/methods ; Microbiota/genetics ; Propionibacterium/virology ; Proteomics/methods ; Recurrence ; Respiratory System/immunology/*virology ; Respiratory Tract Infections/*blood/immunology/microbiology ; Retrospective Studies ; }, abstract = {Recurrent acute respiratory tract infections (ARTIs) affect a large population, yet the specific decisive factors are largely unknown. Here we study a population of 4407 children diagnosed with ARTI, comparing respiratory virome and serum cytokine profiles associated with multiple ARTIs and single ARTI during a six-year period. The relative abundance of Propionibacterium phages is significantly elevated in multiple ARTIs compared to single ARTI group. Serum levels of TIMP-1 and PDGF-BB are markedly increased in multiple ARTIs compared to single-ARTI and non-ARTI controls, making these two cytokines potential predictors for multiple ARTIs. The presence of Propionibacterium phages is associated with higher levels of TIMP-1 and PDGF-BB. Receiver operating characteristic (ROC) curve analyses show that the combination of TIMP-1, PDGF-BB and Propionibacterium phages could be a strong predictor for multiple ARTIs. These findings indicate that respiratory microbe homeostasis and specific cytokines are associated with the onset of multiple ARTIs over time.}, }
@article {pmid30890181, year = {2019}, author = {Zheng, T and Li, J and Ni, Y and Kang, K and Misiakou, MA and Imamovic, L and Chow, BKC and Rode, AA and Bytzer, P and Sommer, M and Panagiotou, G}, title = {Mining, analyzing, and integrating viral signals from metagenomic data.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {42}, doi = {10.1186/s40168-019-0657-y}, pmid = {30890181}, issn = {2049-2618}, mesh = {Algorithms ; Anti-Bacterial Agents/*administration &amp; dosage ; Bacteria/*classification/isolation &amp; purification/virology ; Bacteriophages/*genetics ; CRISPR-Cas Systems ; Data Mining/*methods ; Feces/microbiology ; Gastrointestinal Microbiome ; Healthy Volunteers ; Humans ; Metagenomics/*methods ; Random Allocation ; }, abstract = {BACKGROUND: Viruses are important components of microbial communities modulating community structure and function; however, only a couple of tools are currently available for phage identification and analysis from metagenomic sequencing data. Here we employed the random forest algorithm to develop VirMiner, a web-based phage contig prediction tool especially sensitive for high-abundances phage contigs, trained and validated by paired metagenomic and phagenomic sequencing data from the human gut flora.<br><br>RESULTS: VirMiner achieved 41.06% ± 17.51% sensitivity and 81.91% ± 4.04% specificity in the prediction of phage contigs. In particular, for the high-abundance phage contigs, VirMiner outperformed other tools (VirFinder and VirSorter) with much higher sensitivity (65.23% ± 16.94%) than VirFinder (34.63% ± 17.96%) and VirSorter (18.75% ± 15.23%) at almost the same specificity. Moreover, VirMiner provides the most comprehensive phage analysis pipeline which is comprised of metagenomic raw reads processing, functional annotation, phage contig identification, and phage-host relationship prediction (CRISPR-spacer recognition) and supports two-group comparison when the input (metagenomic sequence data) includes different conditions (e.g., case and control). Application of VirMiner to an independent cohort of human gut metagenomes obtained from individuals treated with antibiotics revealed that 122 KEGG orthology and 118 Pfam groups had significantly differential abundance in the pre-treatment samples compared to samples at the end of antibiotic administration, including clustered regularly interspaced short palindromic repeats (CRISPR), multidrug resistance, and protein transport. The VirMiner webserver is available at http://sbb.hku.hk/VirMiner/ .<br><br>CONCLUSIONS: We developed a comprehensive tool for phage prediction and analysis for metagenomic samples. Compared to VirSorter and VirFinder-the most widely used tools-VirMiner is able to capture more high-abundance phage contigs which could play key roles in infecting bacteria and modulating microbial community dynamics.<br><br>TRIAL REGISTRATION: The European Union Clinical Trials Register, EudraCT Number: 2013-003378-28 . Registered on 9 April 2014.}, }
@article {pmid30885266, year = {2019}, author = {Westreich, ST and Ardeshir, A and Alkan, Z and Kable, ME and Korf, I and Lemay, DG}, title = {Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {41}, doi = {10.1186/s40168-019-0664-z}, pmid = {30885266}, issn = {2049-2618}, support = {P51 OD011107/OD/NIH HHS/United States ; S10 OD010786/OD/NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics ; Diarrhea/*genetics/metabolism/microbiology/parasitology ; Feces/microbiology ; Fucose/*metabolism ; Gastrointestinal Microbiome ; Gene Expression Profiling/*veterinary ; Gene Expression Regulation ; Macaca mulatta ; Metagenomics/*methods ; Mucins/*metabolism ; Proteolysis ; Sequence Analysis, RNA/veterinary ; Trichomonas/classification/genetics ; }, abstract = {BACKGROUND: Idiopathic chronic diarrhea (ICD) is a common cause of morbidity and mortality among juvenile rhesus macaques. Characterized by chronic inflammation of the colon and repeated bouts of diarrhea, ICD is largely unresponsive to medical interventions, including corticosteroid, antiparasitic, and antibiotic treatments. Although ICD is accompanied by large disruptions in the composition of the commensal gut microbiome, no single pathogen has been concretely identified as responsible for the onset and continuation of the disease.<br><br>RESULTS: Fecal samples were collected from 12 ICD-diagnosed macaques and 12 age- and sex-matched controls. RNA was extracted for metatranscriptomic analysis of organisms and functional annotations associated with the gut microbiome. Bacterial, fungal, archaeal, protozoan, and macaque (host) transcripts were simultaneously assessed. ICD-afflicted animals were characterized by increased expression of host-derived genes involved in inflammation and increased transcripts from bacterial pathogens such as Campylobacter and Helicobacter and the protozoan Trichomonas. Transcripts associated with known mucin-degrading organisms and mucin-degrading enzymes were elevated in the fecal microbiomes of ICD-afflicted animals. Assessment of colon sections using immunohistochemistry and of the host transcriptome suggests differential fucosylation of mucins between control and ICD-afflicted animals. Interrogation of the metatranscriptome for fucose utilization genes reveals possible mechanisms by which opportunists persist in ICD. Bacteroides sp. potentially cross-fed fucose to Haemophilus whereas Campylobacter expressed a mucosa-associated transcriptome with increased expression of adherence genes.<br><br>CONCLUSIONS: The simultaneous profiling of bacterial, fungal, archaeal, protozoan, and macaque transcripts from stool samples reveals that ICD of rhesus macaques is associated with increased gene expression by pathogens, increased mucin degradation, and altered fucose utilization. The data suggest that the ICD-afflicted host produces fucosylated mucins that are leveraged by potentially pathogenic microbes as a carbon source or as adhesion sites.}, }
@article {pmid30878035, year = {2019}, author = {Rowe, WP and Carrieri, AP and Alcon-Giner, C and Caim, S and Shaw, A and Sim, K and Kroll, JS and Hall, LJ and Pyzer-Knapp, EO and Winn, MD}, title = {Streaming histogram sketching for rapid microbiome analytics.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {40}, doi = {10.1186/s40168-019-0653-2}, pmid = {30878035}, issn = {2049-2618}, support = {BB/M011216/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; //Wellcome Trust/United Kingdom ; 100/974/C/13/Z//Wellcome Trust/United Kingdom ; BB/R012490/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004529/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Anti-Bacterial Agents/therapeutic use ; Bacteria/*classification ; Bacterial Infections/drug therapy ; Cohort Studies ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; Infant, Premature ; Machine Learning ; Metagenomics/*methods ; Sequence Analysis, DNA ; Software ; }, abstract = {BACKGROUND: The growth in publically available microbiome data in recent years has yielded an invaluable resource for genomic research, allowing for the design of new studies, augmentation of novel datasets and reanalysis of published works. This vast amount of microbiome data, as well as the widespread proliferation of microbiome research and the looming era of clinical metagenomics, means there is an urgent need to develop analytics that can process huge amounts of data in a short amount of time. To address this need, we propose a new method for tyrhe compact representation of microbiome sequencing data using similarity-preserving sketches of streaming k-mer spectra. These sketches allow for dissimilarity estimation, rapid microbiome catalogue searching and classification of microbiome samples in near real time.<br><br>RESULTS: We apply streaming histogram sketching to microbiome samples as a form of dimensionality reduction, creating a compressed 'histosketch' that can efficiently represent microbiome k-mer spectra. Using public microbiome datasets, we show that histosketches can be clustered by sample type using the pairwise Jaccard similarity estimation, consequently allowing for rapid microbiome similarity searches via a locality sensitive hashing indexing scheme. Furthermore, we use a 'real life' example to show that histosketches can train machine learning classifiers to accurately label microbiome samples. Specifically, using a collection of 108 novel microbiome samples from a cohort of premature neonates, we trained and tested a random forest classifier that could accurately predict whether the neonate had received antibiotic treatment (97% accuracy, 96% precision) and could subsequently be used to classify microbiome data streams in less than 3 s.<br><br>CONCLUSIONS: Our method offers a new approach to rapidly process microbiome data streams, allowing samples to be rapidly clustered, indexed and classified. We also provide our implementation, Histosketching Using Little K-mers (HULK), which can histosketch a typical 2 GB microbiome in 50 s on a standard laptop using four cores, with the sketch occupying 3000 bytes of disk space. (https://github.com/will-rowe/hulk).}, }
@article {pmid30853028, year = {2019}, author = {Yason, JA and Liang, YR and Png, CW and Zhang, Y and Tan, KSW}, title = {Interactions between a pathogenic Blastocystis subtype and gut microbiota: in vitro and in vivo studies.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {30}, doi = {10.1186/s40168-019-0644-3}, pmid = {30853028}, issn = {2049-2618}, mesh = {Animals ; Bacterial Proteins/genetics ; Bifidobacterium longum/genetics/growth &amp; development ; Blastocystis/classification/*growth &amp; development/isolation &amp; purification/pathogenicity ; Blastocystis Infections/*microbiology ; Coculture Techniques ; Disease Models, Animal ; Feces/microbiology ; Gastrointestinal Diseases/*microbiology ; *Gastrointestinal Microbiome ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Bacterial ; HT29 Cells ; Humans ; Lactobacillus/genetics/growth &amp; development ; Metagenomics ; Mice ; }, abstract = {BACKGROUND: Blastocystis is a common gut eukaryote detected in humans and animals. It has been associated with gastrointestinal disease in the past although recent metagenomic studies also suggest that it is a member of normal microbiota. This study investigates interactions between pathogenic human isolates belonging to Blastocystis subtype 7 (ST7) and bacterial representatives of the gut microbiota.<br><br>RESULTS: Generally, Blastocystis ST7 exerts a positive effect on the viability of representative gut bacteria except on Bifidobacterium longum. Gene expression analysis and flow cytometry indicate that the bacterium may be undergoing oxidative stress in the presence of Blastocystis. In vitro assays demonstrate that Blastocystis-induced host responses are able to decrease Bifidobacterium counts. Mice infected with Blastocystis also reveal a decrease in beneficial bacteria Bifidobacterium and Lactobacillus.<br><br>CONCLUSIONS: This study shows that particular isolates of Blastocystis ST7 cause changes in microbiota populations and potentially lead to an imbalance of the gut microbiota. This study suggests that certain isolates of Blastocystis exert their pathogenic effects through disruption of the gut microbiota and provides a counterpoint to the increasing reports indicating the commensal nature of this ubiquitous parasite.}, }
@article {pmid30844070, year = {2019}, author = {Fritz, B and Stavnsbjerg, C and Markvart, M and Damgaard, PB and Nielsen, SH and Bjørndal, L and Qvortrup, K and Bjarnsholt, T}, title = {Shotgun sequencing of clinical biofilm following scanning electron microscopy identifies bacterial community composition.}, journal = {Pathogens and disease}, volume = {77}, number = {1}, pages = {}, doi = {10.1093/femspd/ftz013}, pmid = {30844070}, issn = {2049-632X}, mesh = {Bacteria/*classification/*genetics/ultrastructure ; Biodiversity ; *Biofilms ; Humans ; *Metagenome ; *Metagenomics ; }, abstract = {Bacterial biofilm infections often involve aggregates of bacteria heterogeneously distributed throughout a tissue or on a surface (such as an implanted medical device). Identification of a biofilm infection requires direct visualization via microscopy, followed by characterization of the microbial community by culturing or sequencing-based approaches. A sample, therefore, must be divided prior to analysis, often leading to inconsistent results. We demonstrate a combined approach, using scanning electron microscopy and next-generation shotgun sequencing, to visually identify a biofilm and characterize the microbial community, without dividing the sample. A clinical sample recovered from a patient following a dental root-filling procedure was prepared and visualized by scanning electron microscopy. DNA was then extracted from the sample several years later and analyzed by shotgun sequencing. The method was subsequently validated on in vitro cultures of Pseudomonas aeruginosa biofilm. Between 19 and 21 different genera and species were identified in the clinical sample with an estimated relative abundance greater than 1% by two different estimation approaches. Only eight genera identified were not associated with endodontic infections. This provides a proof-of-concept for a dual, microscopy and sequencing-based approach to identify and characterize bacterial biofilms, which could also easily be implemented in other scientific fields.}, }
@article {pmid30808411, year = {2019}, author = {, }, title = {A review of 10 years of human microbiome research activities at the US National Institutes of Health, Fiscal Years 2007-2016.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {31}, doi = {10.1186/s40168-019-0620-y}, pmid = {30808411}, issn = {2049-2618}, mesh = {Biomedical Research/*economics/*organization &amp; administration ; Humans ; Metagenomics/economics/organization &amp; administration ; Microbiota ; National Institutes of Health (U.S.) ; United States ; }, abstract = {The National Institutes of Health (NIH) is the primary federal government agency for biomedical research in the USA. NIH provides extensive support for human microbiome research with 21 of 27 NIH Institutes and Centers (ICs) currently funding this area through their extramural research programs. This analysis of the NIH extramural portfolio in human microbiome research briefly reviews the early history of this field at NIH, summarizes the program objectives and the resources developed in the recently completed 10-year (fiscal years 2007-2016) $215 M Human Microbiome Project (HMP) program, evaluates the scope and range of the $728 M NIH investment in extramural human microbiome research activities outside of the HMP over fiscal years 2012-2016, and highlights some specific areas of research which emerged from this investment. This analysis closes with a few comments on the technical needs and knowledge gaps which remain for this field to be able to advance over the next decade and for the outcomes of this research to be able to progress to microbiome-based interventions for treating disease and supporting health.}, }
@article {pmid30782206, year = {2019}, author = {Lagkouvardos, I and Lesker, TR and Hitch, TCA and Gálvez, EJC and Smit, N and Neuhaus, K and Wang, J and Baines, JF and Abt, B and Stecher, B and Overmann, J and Strowig, T and Clavel, T}, title = {Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {28}, doi = {10.1186/s40168-019-0637-2}, pmid = {30782206}, issn = {2049-2618}, mesh = {Animals ; Bacteriological Techniques/*methods ; Bacteroides/*classification/genetics/growth &amp; development ; Biodiversity ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Gastrointestinal Microbiome ; Metagenomics/*methods ; Mice ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {BACKGROUND: Bacteria within family S24-7 (phylum Bacteroidetes) are dominant in the mouse gut microbiota and detected in the intestine of other animals. Because they had not been cultured until recently and the family classification is still ambiguous, interaction with their host was difficult to study and confusion still exists regarding sequence data annotation.<br><br>METHODS: We investigated family S24-7 by combining data from large-scale 16S rRNA gene analysis and from functional and taxonomic studies of metagenomic and cultured species.<br><br>RESULTS: A total of 685 species was inferred by full-length 16S rRNA gene sequence clustering. While many species could not be assigned ecological habitats (93,045 samples analyzed), the mouse was the most commonly identified host (average of 20% relative abundance and nine co-occurring species). Shotgun metagenomics allowed reconstruction of 59 molecular species, of which 34 were representative of the 16S rRNA gene-derived species clusters. In addition, cultivation efforts allowed isolating five strains representing three species, including two novel taxa. Genome analysis revealed that S24-7 spp. are functionally distinct from neighboring families and versatile with respect to complex carbohydrate degradation.<br><br>CONCLUSIONS: We provide novel data on the diversity, ecology, and description of bacterial family S24-7, for which the name Muribaculaceae is proposed.}, }
@article {pmid30622080, year = {2019}, author = {Cota-Ruiz, K and López de Los Santos, Y and Hernández-Viezcas, JA and Delgado-Rios, M and Peralta-Videa, JR and Gardea-Torresdey, JL}, title = {A comparative metagenomic and spectroscopic analysis of soils from an international point of entry between the US and Mexico.}, journal = {Environment international}, volume = {123}, number = {}, pages = {558-566}, doi = {10.1016/j.envint.2018.12.055}, pmid = {30622080}, issn = {1873-6750}, support = {G12 MD007592/MD/NIMHD NIH HHS/United States ; }, mesh = {Agriculture ; Bacteria/classification ; Environmental Pollution ; Hydrocarbons/toxicity ; Metagenomics ; Metals, Heavy/toxicity ; Mexico ; *Microbiota ; Nitrogen/analysis ; Soil/*chemistry ; *Soil Microbiology ; Soil Pollutants/*toxicity ; Spectrum Analysis ; }, abstract = {The Paso del Norte region is characterized by its dynamic industries and active agriculture. Throughout the years, urban and agricultural soils from this region have been exposed to xenobiotics, heavy metals, and excess of hydrocarbons. In this study, samples of urban [domestic workshops (DW)] and agricultural-intended (AI) soils from different sites of Ciudad Juárez, Mexico were evaluated for their fertility, element content, and microbial diversity. Chemical analyses showed that nitrites, nitrates, P, K, Mg, and Mn were predominantly higher in AI soils, compared to DW soils (p ≤ 0.05). The composition of soil microbial communities showed that Proteobacteria phylum was the most abundant in both soils (67%, p ≤ 0.05). In AI soils, Paracoccus denitrificans was reduced (p ≤ 0.05), concurring with an increment in nitrates, while the content of nitrogen was negatively correlated with the rhizobium group (r2 = -0.65, p ≤ 0.05). In DW soils, the Firmicutes phylum represented up to ~25%, and the relative abundance of Proteobacteria strongly correlated with a higher Cu content (r2 = 0.99, p ≤ 0.0001). The monotypic genus Sulfuricurvum was found only in oil-contaminated soil samples. Finally, all samples showed the presence of the recently created phylum Candidatus saccharibacteria. These results describe the productivity parameters of AI soils and its correlation to the microbial diversity, which are very important to understand and potentiate the productivity of soils. The data also suggest that soils impacted with hydrocarbons and metal(oid)s allow the reproduction of microorganisms with the potential to alleviate contaminated sites.}, }
@article {pmid30502597, year = {2019}, author = {Yang, Y and Liu, G and Song, W and Ye, C and Lin, H and Li, Z and Liu, W}, title = {Plastics in the marine environment are reservoirs for antibiotic and metal resistance genes.}, journal = {Environment international}, volume = {123}, number = {}, pages = {79-86}, doi = {10.1016/j.envint.2018.11.061}, pmid = {30502597}, issn = {1873-6750}, mesh = {Anti-Bacterial Agents ; Drug Resistance, Bacterial/*genetics ; Drug Resistance, Microbial ; *Genes, Bacterial ; Metagenomics ; Metals ; *Microbiota ; Pacific Ocean ; *Plastics ; RNA, Ribosomal, 16S ; Seawater/microbiology ; Water Pollution/*analysis ; }, abstract = {Plastics have been accumulated offshore and in the deep oceans at an unprecedented scale. Microbial communities have colonized the plastisphere, which has become a reservoir for both antibiotic and metal resistance genes (ARGs and MRGs). This is the first analysis of the diversity, abundance, and co-occurrence of ARGs and MRGs, and their relationships within the microbial community, using metagenomic data of plastic particles observed in the North Pacific Gyre obtained from the National Centre for Biotechnology Information Sequence Read Archive database. The abundance of ARGs and MRGs in microbial communities on the plastics were in the ranges 7.07 × 10-4-1.21 × 10-2 and 5.51 × 10-3-4.82 × 10-2 copies per 16S rRNA, respectively. Both the Shannon-Wiener indices and richness of ARGs and MRGs in plastics microbiota were significantly greater than those of ARGs and MRGs in seawater microbiota in the North Pacific Gyre via one-way analysis of variance. Multidrug resistance genes and multi-metal resistance genes were the main classes of genes detected in plastic microbiota. There were no significant differences in the abundance or diversity of ARGs and MRGs between macroplastics biota and microplastics biota, indicating that particle size had no effect on resistance genes. Procrustes analysis suggested that microbial community composition was the determining factor of the ARG profile but not for MRG. Some ARGs and MRGs had a higher incidence of non-random co-occurrence, suggesting that the co-effects of selection for antibiotic or metal resistance are important factors influencing the resistome of the microbiota on the plastic particles.}, }
@article {pmid30270610, year = {2018}, author = {Fan, Y and Ya-E, Z and Ji-Dong, W and Yu-Fan, L and Ying, Z and Ya-Lun, S and Meng-Yu, M and Rui-Ling, Z}, title = {Comparison of Microbial Diversity and Composition in Jejunum and Colon of the Alcohol-dependent Rats.}, journal = {Journal of microbiology and biotechnology}, volume = {28}, number = {11}, pages = {1883-1895}, doi = {10.4014/jmb.1806.06050}, pmid = {30270610}, issn = {1738-8872}, mesh = {Alcoholism/*microbiology ; Animals ; Bacteria/classification/genetics ; *Biodiversity ; Colon/*microbiology ; Disease Models, Animal ; Dysbiosis/*microbiology ; Ethanol/adverse effects ; Gastrointestinal Microbiome/genetics ; Jejunum/*microbiology ; Male ; Metabolic Networks and Pathways/genetics ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Wistar ; }, abstract = {Alcohol dependence is a global public health problem, yet the mechanisms of alcohol dependence are incompletely understood. The traditional view has been that ethanol alters various neurotransmitters and their receptors in the brain and causes the addiction. However, an increasing amount of experimental evidence suggests that gut microbiota also influence brain functions via gut-to-brain interactions, and may therefore induce the development of alcohol use disorders. In this study, a rat model of alcohol dependence and withdrawal was employed, the gut microbiota composition was analyzed by high-throughput 16S rRNA gene sequencing, and the metagenome function was predicted by PICRUSt software. The results suggested that chronic alcohol consumption did not significantly alter the diversity and richness of gut microbiota in the jejunum and colon, but rather markedly changed the microbiota composition structure in the colon. The phyla Bacteroidetes and eight genera including Bacteroidales S24-7, Ruminococcaceae, Parabacteroides, Butyricimonas, et al were drastically increased, however the genus Lactobacillus and gauvreauii in the colon were significantly decreased in the alcohol dependence group compared with the withdrawal and control groups. The microbial functional prediction analysis revealed that the proportions of amino acid metabolism, polyketide sugar unit biosynthesis and peroxisome were significantly increased in the AD group. This study demonstrated that chronic alcohol consumption has a dramatic effect on the microbiota composition structure in the colon but few effects on the jejunum. Inducement of colonic microbiota dysbiosis due to alcohol abuse seems to be a factor of alcohol dependence, which suggests that modulating colonic microbiota composition might be a potentially new target for treating alcohol addiction.}, }
@article {pmid30038308, year = {2018}, author = {Munk, P and Knudsen, BE and Lukjancenko, O and Duarte, ASR and Van Gompel, L and Luiken, REC and Smit, LAM and Schmitt, H and Garcia, AD and Hansen, RB and Petersen, TN and Bossers, A and Ruppé, E and ,  and Lund, O and Hald, T and Pamp, SJ and Vigre, H and Heederik, D and Wagenaar, JA and Mevius, D and Aarestrup, FM}, title = {Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries.}, journal = {Nature microbiology}, volume = {3}, number = {8}, pages = {898-908}, doi = {10.1038/s41564-018-0192-9}, pmid = {30038308}, issn = {2058-5276}, mesh = {Animals ; Bacteria/*classification/drug effects/genetics ; Bacterial Proteins/*genetics ; Biodiversity ; Chickens ; *Drug Resistance, Bacterial ; Europe ; Feces/*microbiology ; Gene Expression Profiling/veterinary ; Metagenomics/methods ; Sequence Analysis, DNA/veterinary ; Species Specificity ; Swine ; }, abstract = {Antimicrobial resistance (AMR) in bacteria and associated human morbidity and mortality is increasing. The use of antimicrobials in livestock selects for AMR that can subsequently be transferred to humans. This flow of AMR between reservoirs demands surveillance in livestock and in humans. We quantified and characterized the acquired resistance gene pools (resistomes) of 181 pig and 178 poultry farms from nine European countries, sequencing more than 5,000 Gb of DNA using shotgun metagenomics. We quantified acquired AMR using the ResFinder database and a second database constructed for this study, consisting of AMR genes identified through screening environmental DNA. The pig and poultry resistomes were very different in abundance and composition. There was a significant country effect on the resistomes, more so in pigs than in poultry. We found higher AMR loads in pigs, whereas poultry resistomes were more diverse. We detected several recently described, critical AMR genes, including mcr-1 and optrA, the abundance of which differed both between host species and between countries. We found that the total acquired AMR level was associated with the overall country-specific antimicrobial usage in livestock and that countries with comparable usage patterns had similar resistomes. However, functionally determined AMR genes were not associated with total drug use.}, }
@article {pmid29922970, year = {2018}, author = {Li, J and Li, L and Jiang, H and Yuan, L and Zhang, L and Ma, JE and Zhang, X and Cheng, M and Chen, J}, title = {Fecal Bacteriome and Mycobiome in Bats with Diverse Diets in South China.}, journal = {Current microbiology}, volume = {75}, number = {10}, pages = {1352-1361}, pmid = {29922970}, issn = {1432-0991}, support = {2016B070701016//PlanningFunds of Science and Technology of Guangdong Province/ ; 2013B031500006//PlanningFunds of Science and Technology of Guangdong Province/ ; 2016GDASPT-0107//Funds for Environment Construction and Capacity Building of GDAS' Research Platform/ ; 2017GDASCX-0107//GDAS Special Project of Science and Technology Development/ ; }, mesh = {*Animal Feed ; Animals ; Bacteria/classification/genetics ; Biodiversity ; China ; *Chiroptera ; Feces/*microbiology ; Female ; Fungi/classification/genetics ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; }, abstract = {Bats can be divided into frugivory, nectarivory, insectivory, and sanguivory based on their diets, and are therefore ideal wild animal models to study the relationship between diets and intestinal microflora. Early studies of bat gut bacteria showed that the diversity and structure of intestinal bacterial communities in bats are closely related to dietary changes. Worthy of note, intestinal microbes are composed of bacteria, fungi, protozoa, and archaea. Although the number of gut fungi is much lower than that of gut bacteria, they also play an important role in maintaining the host homeostasis. However, there are still few reports on the relationship between the gut mycobiota and the dietary habits of the host. In addition, bats have also been shown to naturally transmit pathogenic viruses and bacteria through their feces and saliva, but fungal infections from bat are less studied. Here, we used high-throughput sequencing of bacterial 16S and eukaryotic 18S rRNA genes in the V4 and V9 regions to characterize fecal bacterial and fungal microbiota in phytophagous and insectivorous bats in South China. The results show that the gut microbiota in bats were dominated by bacterial phyla Proteobacteria, Firmicutes, Tenericutes and Bacteroidetes, and fungal phyla Ascomycota and Basidiomycota. There was a significant difference in the diversity of bacterial and fungal microbiota between the groups, in addition to specific bacteria and fungi populations on each of them. Of note, the number of fungi in the feces of herbivorous bats is relatively higher. Most of these fungi are foodborne and are also pathogens of humans and other animals. Thus, bats are natural carriers of fungal pathogens. The current study expands the understanding of the bat gut bacterial and fungal mycobiota and provides further insight into the transmission of fungal pathogens.}, }
@article {pmid29885225, year = {2017}, author = {Chase, MA and Stankowski, S and Streisfeld, MA}, title = {Genomewide variation provides insight into evolutionary relationships in a monkeyflower species complex (Mimulus sect. Diplacus).}, journal = {American journal of botany}, volume = {104}, number = {10}, pages = {1510-1521}, doi = {10.3732/ajb.1700234}, pmid = {29885225}, issn = {1537-2197}, mesh = {Biological Evolution ; *Gene Flow ; *Genetics, Population ; Genome, Plant/*genetics ; Hybridization, Genetic ; *Metagenomics ; Mimulus/*genetics ; Phylogeny ; }, abstract = {PREMISE OF THE STUDY: Evolutionary radiations provide excellent opportunities to study the origins of biodiversity, but rapid divergence and ongoing gene flow make inferring evolutionary relationships among taxa difficult. Consequently, combining morphological and genomic analyses will be necessary to clarify the evolutionary history of radiations. We used an integrative approach to shed light on relationships within a diverse radiation of monkeyflowers (Mimulus section Diplacus) with a controversial taxonomic history.<br><br>METHODS: We used genomewide single nucleotide polymorphism data and a combination of phylogenetic and population genomic analyses to infer the evolutionary relationships within the group. Tests for hybridization were performed to reveal sources of shared variation, and multivariate analyses of floral trait data were conducted to examine the correspondence between phenotypic and phylogenetic data.<br><br>KEY RESULTS: We identified four primary clades with evidence for some shared variation among them. We also detected evidence for recent gene flow between closely related subclades and populations. Strong discordance between floral trait and molecular data provides evidence for divergent and convergent phenotypic evolution.<br><br>CONCLUSIONS: Mimulus section Diplacus has all the hallmarks of a rapid radiation, including diverse taxa that are at different stages of divergence, extensive shared variation among taxa, and complex patterns of phenotypic evolution. Our findings will direct future evolutionary research and have important taxonomic implications that highlight the need for a new revision of section Diplacus.}, }
@article {pmid29807988, year = {2018}, author = {Sieber, CMK and Probst, AJ and Sharrar, A and Thomas, BC and Hess, M and Tringe, SG and Banfield, JF}, title = {Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy.}, journal = {Nature microbiology}, volume = {3}, number = {7}, pages = {836-843}, doi = {10.1038/s41564-018-0171-1}, pmid = {29807988}, issn = {2058-5276}, support = {5R01AI092531/NH/NIH HHS/United States ; }, mesh = {Algorithms ; Animals ; Computational Biology/*methods ; Data Curation ; Gastrointestinal Microbiome ; Genome, Bacterial ; Humans ; Metagenomics/*methods ; Microbiota ; Soil Microbiology ; User-Computer Interface ; Water Microbiology ; }, abstract = {Microbial communities are critical to ecosystem function. A key objective of metagenomic studies is to analyse organism-specific metabolic pathways and reconstruct community interaction networks. This requires accurate assignment of assembled genome fragments to genomes. Existing binning methods often fail to reconstruct a reasonable number of genomes and report many bins of low quality and completeness. Furthermore, the performance of existing algorithms varies between samples and biotopes. Here, we present a dereplication, aggregation and scoring strategy, DAS Tool, that combines the strengths of a flexible set of established binning algorithms. DAS Tool applied to a constructed community generated more accurate bins than any automated method. Indeed, when applied to environmental and host-associated samples of different complexity, DAS Tool recovered substantially more near-complete genomes, including previously unreported lineages, than any single binning method alone. The ability to reconstruct many near-complete genomes from metagenomics data will greatly advance genome-centric analyses of ecosystems.}, }
@article {pmid29501688, year = {2018}, author = {Ravi, A and Avershina, E and Angell, IL and Ludvigsen, J and Manohar, P and Padmanaban, S and Nachimuthu, R and Snipen, L and Rudi, K}, title = {Comparison of reduced metagenome and 16S rRNA gene sequencing for determination of genetic diversity and mother-child overlap of the gut associated microbiota.}, journal = {Journal of microbiological methods}, volume = {149}, number = {}, pages = {44-52}, doi = {10.1016/j.mimet.2018.02.016}, pmid = {29501688}, issn = {1872-8359}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/*classification/*genetics ; Cohort Studies ; DNA, Bacterial/genetics/isolation &amp; purification ; Drug Resistance, Bacterial/genetics ; Female ; Gastrointestinal Microbiome/drug effects/*genetics ; Genes, Bacterial/genetics ; *Genetic Variation ; Humans ; Infant, Newborn ; Metagenome/*genetics ; Metagenomics/methods ; *Mother-Child Relations ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {Use of the 16S rRNA gene in microbiota studies is limited by the lack of taxonomic and functional resolution. High resolution analyses are particularly important for understanding transmission and persistence of bacteria. The aim of our work was therefore to compare a novel reduced metagenome sequencing (RMS) approach with 16S rRNA gene sequencing to determine both the metagenome genetic diversity and the mother-to-child sharing of the microbiota in a cohort of 17 mother-child pairs. We found that although both approaches gave comparable results with respect to sample separation and taxonomy, RMS gave higher resolution and the potential for genomic-/functional assignment. Using RMS we estimated that the metagenome size increased from about 60 Mbp for 4-day-old children to about 225 Mbp for mothers. The 4-day-old children shared 7% of the metagenome sequences with the mothers, while the metagenome sequence sharing was >30% among the mothers. We found 15 genomes shared across >50% of the mothers, of which 10 belonged to Clostridia. Only Bacteroides showed a direct mother-child association, with B. vulgatus being abundant in both 4-day-old children and mothers. For the functional assignments, we identified a significant association between antibiotic usage during labor, and quantity of Fosfomycin resistance genes. In conclusion, our results show a higher functional and taxonomic resolution for RMS compared to 16S rRNA gene sequencing, where RMS enabled a detailed description of mother to child gut microbiota transmission - supporting a late recruitment of most gut bacteria and an effect of antibiotic treatment during labor on infant antibiotic resistance gene patterns.}, }
@article {pmid29471034, year = {2018}, author = {Andermann, TM and Peled, JU and Ho, C and Reddy, P and Riches, M and Storb, R and Teshima, T and van den Brink, MRM and Alousi, A and Balderman, S and Chiusolo, P and Clark, WB and Holler, E and Howard, A and Kean, LS and Koh, AY and McCarthy, PL and McCarty, JM and Mohty, M and Nakamura, R and Rezvani, K and Segal, BH and Shaw, BE and Shpall, EJ and Sung, AD and Weber, D and Whangbo, J and Wingard, JR and Wood, WA and Perales, MA and Jenq, RR and Bhatt, AS and , }, title = {The Microbiome and Hematopoietic Cell Transplantation: Past, Present, and Future.}, journal = {Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation}, volume = {24}, number = {7}, pages = {1322-1340}, pmid = {29471034}, issn = {1523-6536}, support = {U10 HL069294/HL/NHLBI NIH HHS/United States ; P30 CA016672/CA/NCI NIH HHS/United States ; UG1 HL069301/HL/NHLBI NIH HHS/United States ; K08 CA184420/CA/NCI NIH HHS/United States ; U24 HL138660/HL/NHLBI NIH HHS/United States ; UG1 HL069315/HL/NHLBI NIH HHS/United States ; U10 HL069330/HL/NHLBI NIH HHS/United States ; R01 HL124112/HL/NHLBI NIH HHS/United States ; UG1 HL069278/HL/NHLBI NIH HHS/United States ; UL1 TR001085/TR/NCATS NIH HHS/United States ; UG1 HL069330/HL/NHLBI NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; }, mesh = {*Hematopoietic Stem Cell Transplantation ; Humans ; *Microbiota ; }, }
@article {pmid29235707, year = {2018}, author = {Brewer, TE and Fierer, N}, title = {Tales from the tomb: the microbial ecology of exposed rock surfaces.}, journal = {Environmental microbiology}, volume = {20}, number = {3}, pages = {958-970}, doi = {10.1111/1462-2920.14024}, pmid = {29235707}, issn = {1462-2920}, mesh = {Bacteria/*classification/genetics ; Biodiversity ; *Calcium Carbonate ; *Metagenomics ; *Microbiota ; *Silicon Dioxide ; }, abstract = {Although a broad diversity of eukaryotic and bacterial taxa reside on rock surfaces where they can influence the weathering of rocks and minerals, these communities and their contributions to mineral weathering remain poorly resolved. To build a more comprehensive understanding of the diversity, ecology and potential functional attributes of microbial communities living on rock, we sampled 149 tombstones across three continents and analysed their bacterial and eukaryotic communities via marker gene and shotgun metagenomic sequencing. We found that geographic location and climate were important factors structuring the composition of these communities. Moreover, the tombstone-associated microbial communities varied as a function of rock type, with granite and limestone tombstones from the same cemeteries harbouring taxonomically distinct microbial communities. The granite and limestone-associated communities also had distinct functional attributes, with granite-associated bacteria having more genes linked to acid tolerance and chemotaxis, while bacteria on limestone were more likely to be lichen associated and have genes involved in photosynthesis and radiation resistance. Together these results indicate that rock-dwelling microbes exhibit adaptations to survive the stresses of the rock surface, differ based on location, climate and rock type, and seem pre-disposed to different ecological strategies (symbiotic versus free-living lifestyles) depending on the rock type.}, }
@article {pmid29225146, year = {2018}, author = {Hahn, A and Warnken, S and Pérez-Losada, M and Freishtat, RJ and Crandall, KA}, title = {Microbial diversity within the airway microbiome in chronic pediatric lung diseases.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {63}, number = {}, pages = {316-325}, pmid = {29225146}, issn = {1567-7257}, support = {K12 HL119994/HL/NHLBI NIH HHS/United States ; KL2 TR001877/TR/NCATS NIH HHS/United States ; UL1 TR001876/TR/NCATS NIH HHS/United States ; }, mesh = {Asthma/*microbiology/pathology ; Bacteria/classification/*genetics/isolation &amp; purification ; Biodiversity ; Child ; Cystic Fibrosis/*microbiology/pathology ; Humans ; Infant, Newborn ; Lung/microbiology/pathology ; *Metagenome ; Metagenomics/methods ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Respiratory Distress Syndrome, Newborn/*microbiology/pathology ; Severity of Illness Index ; Sputum/microbiology ; }, abstract = {The study of the airway microbiome in children is an area of emerging research, especially in relation to the role microbial diversity may play in acute and chronic inflammation. Three such pediatric airway diseases include cystic fibrosis, asthma, and chronic lung disease of prematurity. In cystic fibrosis, the presence of Pseudomonas spp. is associated with decreased microbial diversity. Decreasing microbial diversity is also associated with poor lung function. In asthma, early viral infections appear to drive changes in bacterial diversity which may be associated with asthma risk. Premature infants with Ureaplasma spp. are at higher risk for chronic lung disease due to inflammation. Microbiome changes due to prematurity also appear to affect the inflammatory response to viral infections post-natally. Importantly, microbial diversity can be measured using metataxonomic (e.g., 16S rRNA sequencing) and metagenomic (e.g., shotgun sequencing) approaches. A metagenomics approach may be preferable as it can provide further granularity of the sample composition, identifying the bacterial species or strain, information on additional microbial components, including fungal and viral components, information about functional genomics of the microbiome, and information about antimicrobial resistance mutations. Future studies of pediatric airway diseases incorporating these techniques may provide evidence for new treatment approaches for these vulnerable patient populations.}, }
@article {pmid28894273, year = {2017}, author = {Chen, L and Feng, Q and Li, C and Wei, Y and Zhao, Y and Feng, Y and Zheng, H and Li, F and Li, H}, title = {Impacts of aquaculture wastewater irrigation on soil microbial functional diversity and community structure in arid regions.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11193}, pmid = {28894273}, issn = {2045-2322}, mesh = {Agricultural Irrigation/*methods ; *Aquaculture ; Bacteria/*classification/genetics/*isolation &amp; purification ; Bacterial Typing Techniques ; *Biota ; Desert Climate ; Metagenomics ; Soil/chemistry ; *Soil Microbiology ; *Waste Water ; }, abstract = {Aquaculture wastewater is one of the most important alternative water resources in arid regions where scarcity of fresh water is common. Irrigation with this kind of water may affect soil microbial functional diversity and community structure as changes of soil environment would be significant. Here, we conducted a field sampling to investigate these effects using Biolog and metagenomic methods. The results demonstrated that irrigation with aquaculture wastewater could dramatically reduce soil microbial functional diversity. The values of diversity indices and sole carbon source utilization were all significantly decreased. Increased soil salinity, especially Cl concentration, appeared primarily associated with the decreases. Differently, higher bacterial community diversity was obtained in aquaculture wastewater irrigated soils. More abundant phyla Actinobacteria, Chloroflexi, Acidobacteria, Gemmatimonadetes and fewer members of Proteobacteria, Bacteroidetes and Planctomycetes were found in this kind of soils. Changes in the concentration of soil Cl mainly accounted for the shifts of bacterial community composition. This research can improve our understanding of how aquaculture wastewater irrigation changes soil microbial process and as a result, be useful to manage soil and wastewater resources in arid regions.}, }
@article {pmid28894183, year = {2017}, author = {Ticinesi, A and Milani, C and Lauretani, F and Nouvenne, A and Mancabelli, L and Lugli, GA and Turroni, F and Duranti, S and Mangifesta, M and Viappiani, A and Ferrario, C and Maggio, M and Ventura, M and Meschi, T}, title = {Gut microbiota composition is associated with polypharmacy in elderly hospitalized patients.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11102}, pmid = {28894183}, issn = {2045-2322}, mesh = {Aged ; Aged, 80 and over ; Biodiversity ; Biological Variation, Population ; Comorbidity ; Female ; Gastrointestinal Microbiome/*drug effects ; *Hospitalization ; Humans ; Male ; Metagenome ; Metagenomics ; Patient Outcome Assessment ; Phenotype ; *Polypharmacy ; RNA, Ribosomal, 16S ; Survival Analysis ; Symptom Assessment ; }, abstract = {Reduced biodiversity and increased representation of opportunistic pathogens are typical features of gut microbiota composition in aging. Few studies have investigated their correlation with polypharmacy, multimorbidity and frailty. To assess it, we analyzed the fecal microbiota from 76 inpatients, aged 83 ± 8. Microbiome biodiversity (Chao1 index) and relative abundance of individual bacterial taxa were determined by next-generation 16S rRNA microbial profiling. Their correlation with number of drugs, and indexes of multimorbidity and frailty were verified using multivariate linear regression models. The impact of gut microbiota biodiversity on mortality, rehospitalizations and incident sepsis was also assessed after a 2-year follow-up, using Cox regression analysis. We found a significant negative correlation between the number of drugs and Chao1 Index at multivariate analysis. The number of drugs was associated with the average relative abundance of 15 taxa. The drug classes exhibiting the strongest association with single taxa abundance were proton pump inhibitors, antidepressants and antipsychotics. Conversely, frailty and multimorbidity were not significantly associated with gut microbiota biodiversity. Very low Chao1 index was also a significant predictor of mortality, but not of rehospitalizations and sepsis, at follow-up. In aging, polypharmacy may thus represent a determinant of gut microbiota composition, with detrimental clinical consequences.}, }
@article {pmid28894161, year = {2017}, author = {Parnell, LA and Briggs, CM and Cao, B and Delannoy-Bruno, O and Schrieffer, AE and Mysorekar, IU}, title = {Microbial communities in placentas from term normal pregnancy exhibit spatially variable profiles.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11200}, pmid = {28894161}, issn = {2045-2322}, support = {T32 GM007067/GM/NIGMS NIH HHS/United States ; T32 HL130357/HL/NHLBI NIH HHS/United States ; UL1 TR000448/TR/NCATS NIH HHS/United States ; UL1 TR002345/TR/NCATS NIH HHS/United States ; }, mesh = {Bacteria/*classification/*genetics ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Female ; Humans ; *Metagenomics ; *Microbiota ; Phylogeny ; Placenta/*microbiology ; Polymerase Chain Reaction ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spatial Analysis ; }, abstract = {The placenta is the principal organ nurturing the fetus during pregnancy and was traditionally considered to be sterile. Recent work has suggested that the placenta harbours microbial communities, however the location and possible function of these microbes remain to be confirmed and elucidated. Here, we employed genomic DNA sequencing of multiple variable (V) regions of the bacterial 16S ribosomal gene, to interrogate microbial profiles in term pregnancies, from the basal plate, which is in direct contact with maternal uterine, endothelial, and immune cells; placental villi, which are bathed in maternal blood, and fetal membranes, which encapsulate the amniotic cavity. QIIME, R package &quot;Phyloseq&quot; analysis was used to assess alpha and beta diversity and absolute abundance of the 16S rRNA gene per location. We demonstrate that (1) microbiota exhibit spatially distinct profiles depending on the location within the placenta and (2) &quot;semi-composite&quot; 16S profiles using multiple V regions validated by quantitative PCR analysis confirmed that distinct bacterial taxa dominate in different placental niches. Finally, profiles are not altered by mode of delivery. Together these findings suggest that there is niche-specificity to the placental microbiota and placental microbiome studies should consider regional differences, which may affect maternal, fetal, and/or neonatal health and physiology.}, }
@article {pmid28887527, year = {2017}, author = {Kim, Y and Koh, I and Young Lim, M and Chung, WH and Rho, M}, title = {Pan-genome analysis of Bacillus for microbiome profiling.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {10984}, pmid = {28887527}, issn = {2045-2322}, mesh = {Bacillus/classification/*genetics ; Evolution, Molecular ; Genes, Bacterial ; *Genome, Bacterial ; *Genomics/methods ; Metagenome ; Metagenomics/methods ; *Microbiota ; Multilocus Sequence Typing ; Phylogeny ; }, abstract = {Recent advances in high-throughput sequencing technology allow for in-depth studies on microbial genomes and their communities. While multiple strains of the same species could display genomic variations with different gene contents in diverse habitats and hosts, the essential functions for a specific species are conserved as core genes that are shared among strains. We have comprehensively analyzed 238 strains of five different Bacillus species to identify the properties of core and strain-specific genes. Core and strain-specific genes in each Bacillus species show significant differences in their functions and genomic signatures. Using the core genes defined in this study, we have precisely identified the Bacillus species that exist in food microbiomes. Without resorting to culture-based whole genome sequencing, an unexpectedly large portion of the core genes, 98.22% of core genes in B. amyloliquefaciens and 97.77% of B. subtilis, were reconstructed from the microbiome. We have performed a pan-genome analysis on the core gene data of multiple Bacillus species to investigate the Bacillus species in food microbiome. Our findings provide a comprehensive genetic landscape of the Bacillus species, which is also consistent with previous studies on a limited number of strains and species. Analysis based on comprehensive core genes should thus serve as a powerful profiling tool to better understand major constituents in fermented food microbiomes.}, }
@article {pmid28855542, year = {2017}, author = {Shin, JM and Luo, T and Kamarajan, P and Fenno, JC and Rickard, AH and Kapila, YL}, title = {Microbial Communities Associated with Primary and Metastatic Head and Neck Squamous Cell Carcinoma - A High Fusobacterial and Low Streptococcal Signature.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {9934}, pmid = {28855542}, issn = {2045-2322}, support = {T32 DE007057/DE/NIDCR NIH HHS/United States ; }, mesh = {Aged ; Aged, 80 and over ; Bacteria/*classification/genetics ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Female ; Fusobacteria/isolation &amp; purification ; Head and Neck Neoplasms/*microbiology/secondary ; Humans ; Larynx/microbiology ; Lymph Nodes/microbiology ; Male ; Metagenomics/*methods ; Microbiota ; Middle Aged ; Mouth/microbiology ; Pharynx/microbiology ; RNA, Ribosomal, 16S/genetics ; Sample Size ; Sequence Analysis, DNA/*methods ; Squamous Cell Carcinoma of Head and Neck/*microbiology/secondary ; Streptococcus/isolation &amp; purification ; }, abstract = {Given the potential relationship between head and neck squamous cell carcinoma (HNSCC) and microbial dysbiosis, we profiled the microbiome within healthy normal and tumorous (primary and metastatic) human tissues from the oral cavity, larynx-pharynx, and lymph nodes using 16S rRNA sequencing. Alpha and beta diversity analyses revealed that normal tissues had the greatest richness in community diversity, while the metastatic populations were most closely related to one another. Compared to the normal, the microbiota associated with tumors supported altered abundances in the phyla Fusobacteria, Firmicutes, Actinobacteria and Proteobacteria. Most notably, the relative abundance of Fusobacterium increased whereas Streptococcus decreased in both primary and metastatic samples. Principal coordinate analysis indicated a separation and clustering of samples by tissue status. However, random forest analysis revealed that the microbial profiles alone were a poor predictor for primary and metastatic HNSCC samples. Here, we report that the microbial communities residing in the tumorous tissues are compositionally distinct compared to the normal adjacent tissues. However, likely due to the smaller sample size and sample-to-sample heterogeneity, our prediction models were not able to distinguish by sample types. This work provides a foundation for future studies aimed at understanding the role of the dysbiotic tissue microbiome in HNSCC.}, }
@article {pmid28810737, year = {2018}, author = {Cohen, LJ and Han, S and Huang, YH and Brady, SF}, title = {Identification of the Colicin V Bacteriocin Gene Cluster by Functional Screening of a Human Microbiome Metagenomic Library.}, journal = {ACS infectious diseases}, volume = {4}, number = {1}, pages = {27-32}, doi = {10.1021/acsinfecdis.7b00081}, pmid = {28810737}, issn = {2373-8227}, support = {K08 DK109287/DK/NIDDK NIH HHS/United States ; T32 GM007739/GM/NIGMS NIH HHS/United States ; U01 GM110714/GM/NIGMS NIH HHS/United States ; }, mesh = {Colicins/*genetics ; Gene Library ; Humans ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; *Multigene Family ; Sequence Analysis, DNA ; }, abstract = {The forces that shape human microbial ecology are complex. It is likely that human microbiota, similarly to other microbiomes, use antibiotics as one way to establish an ecological niche. In this study, we use functional metagenomics to identify human microbial gene clusters that encode for antibiotic functions. Screening of a metagenomic library prepared from a healthy patient stool sample led to the identification of a family of clones with inserts that are 99% identical to a region of a virulence plasmid found in avian pathogenic Escherichia coli. Characterization of the metagenomic DNA sequence identified a colicin V biosynthetic cluster as being responsible for the observed antibiotic effect of the metagenomic clone against E. coli. This study presents a scalable method to recover antibiotic gene clusters from humans using functional metagenomics and highlights a strategy to study bacteriocins in the human microbiome which can provide a resource for therapeutic discovery.}, }
@article {pmid31185897, year = {2019}, author = {Chen, CY and Tang, SL and Chou, ST}, title = {Taxonomy based performance metrics for evaluating taxonomic assignment methods.}, journal = {BMC bioinformatics}, volume = {20}, number = {1}, pages = {310}, doi = {10.1186/s12859-019-2896-0}, pmid = {31185897}, issn = {1471-2105}, support = {105-2410-H-002-101-MY3//The Ministry of Science and Technology of Taiwan/ ; }, abstract = {BACKGROUND: Metagenomics experiments often make inferences about microbial communities by sequencing 16S and 18S rRNA, and taxonomic assignment is a fundamental step in such studies. This paper addresses the weaknesses in two types of metrics commonly used by previous studies for measuring the performance of existing taxonomic assignment methods: Sequence count based metrics and Binary error measurement. These metrics made performance evaluation results biased, less informative and mutually incomparable.<br><br>RESULTS: We investigated weaknesses in two types of metrics and proposed new performance metrics including Average Taxonomy Distance (ATD) and ATD_by_Taxa, together with the visualized ATD plot.<br><br>CONCLUSIONS: By comparing the evaluation results from four popular taxonomic assignment methods across three test data sets, we found the new metrics more robust, informative and comparable.}, }
@article {pmid31167633, year = {2019}, author = {Zhong, C and Yang, Y and Yooseph, S}, title = {GRASP2: fast and memory-efficient gene-centric assembly and homolog search for metagenomic sequencing data.}, journal = {BMC bioinformatics}, volume = {20}, number = {Suppl 11}, pages = {276}, doi = {10.1186/s12859-019-2818-1}, pmid = {31167633}, issn = {1471-2105}, abstract = {BACKGROUND: A crucial task in metagenomic analysis is to annotate the function and taxonomy of the sequencing reads generated from a microbiome sample. In general, the reads can either be assembled into contigs and searched against reference databases, or individually searched without assembly. The first approach may suffer from fragmentary and incomplete assembly, while the second is hampered by the reduced functional signal contained in the short reads. To tackle these issues, we have previously developed GRASP (Guided Reference-based Assembly of Short Peptides), which accepts a reference protein sequence as input and aims to assemble its homologs from a database containing fragmentary protein sequences. In addition to a gene-centric assembly tool, GRASP also serves as a homolog search tool when using the assembled protein sequences as templates to recruit reads. GRASP has significantly improved recall rate (60-80% vs. 30-40%) compared to other homolog search tools such as BLAST. However, GRASP is both time- and space-consuming. Subsequently, we developed GRASPx, which is 30X faster than GRASP. Here, we present a completely redesigned algorithm, GRASP2, for this computational problem.<br><br>RESULTS: GRASP2 utilizes Burrows-Wheeler Transformation (BWT) and FM-index to perform assembly graph generation, and reduces the search space by employing a fast ungapped alignment strategy as a filter. GRASP2 also explicitly generates candidate paths prior to alignment, which effectively uncouples the iterative access of the assembly graph and alignment matrix. This strategy makes the execution of the program more efficient under current computer architecture, and contributes to GRASP2's speedup. GRASP2 is 8-fold faster than GRASPx (and 250-fold faster than GRASP) and uses 8-fold less memory while maintaining the original high recall rate of GRASP. GRASP2 reaches ~ 80% recall rate compared to that of ~ 40% generated by BLAST, both at a high precision level (> 95%). With such a high performance, GRASP2 is only ~3X slower than BLASTP.<br><br>CONCLUSION: GRASP2 is a high-performance gene-centric and homolog search tool with significant speedup compared to its predecessors, which makes GRASP2 a useful tool for metagenomics data analysis, GRASP2 is implemented in C++ and is freely available from http://www.sourceforge.net/projects/grasp2 .}, }
@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)/International ; }, mesh = {Bacterial Infections/*immunology/microbiology ; Cell Degranulation/immunology ; Child, Preschool ; Humans ; Infant ; Infant, Newborn ; Kenya ; Metagenomics/methods ; Microbiota/immunology ; Neutrophils/*immunology ; Proteomics/methods ; Respiratory Mucosa/cytology/*immunology/microbiology ; Respiratory Syncytial Virus Infections/*immunology/virology ; Respiratory Syncytial Virus, Human/*immunology/isolation &amp; purification ; Streptococcus/immunology/isolation &amp; purification ; }, 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 {pmid31030156, year = {2019}, author = {Darlison, J and Mogren, L and Rosberg, AK and Grudén, M and Minet, A and Liné, C and Mieli, M and Bengtsson, T and Håkansson, Å and Uhlig, E and Becher, PG and Karlsson, M and Alsanius, BW}, title = {Leaf mineral content govern microbial community structure in the phyllosphere of spinach (Spinacia oleracea) and rocket (Diplotaxis tenuifolia).}, journal = {The Science of the total environment}, volume = {675}, number = {}, pages = {501-512}, doi = {10.1016/j.scitotenv.2019.04.254}, pmid = {31030156}, issn = {1879-1026}, mesh = {Biodiversity ; Brassicaceae/chemistry/*microbiology ; *Environmental Monitoring ; Microbiota ; Minerals/*analysis ; Plant Leaves/chemistry/*microbiology ; Spinacia oleracea/chemistry/*microbiology ; }, abstract = {The plant microbiome is an important factor for plant health and productivity. While the impact of nitrogen (N) availability for plant growth and development is well established, its influence on the microbial phyllosphere community structure is unknown. We hypothesize that nitrogen impacts the growth and abundance of several microorganisms on the leaf surface. The bacterial and fungal communities of baby leaf spinach (Spinacia oleracea), and rocket (Diplotaxis tenuifolia) were investigated in a field trial for two years in a commercial setting. Nitrogen fertilizer was tested in four doses (basic nitrogen, basic + suboptimal, basic + commercial, basic + excess) with six replicates in each. Culture-independent (Illumina sequencing) and culture-dependent (viable count and identification of bacterial isolates) community studies were combined with monitoring of plant physiology and site weather conditions. This study found that alpha diversity of bacterial communities decreased in response to increasing nitrogen fertilizer dose, whereas viable counts showed no differences. Correspondingly, fungal communities of the spinach phyllosphere showed a decreasing pattern, whereas the decreasing diversity of fungal communities of rocket was not significant. Plant species and effects of annual variations on microbiome structure were observed for bacterial and fungal communities on both spinach and rocket. This study provides novel insights on the impact of nitrogen fertilizer regime on a nutrient scarce habitat, the phyllosphere.}, }
@article {pmid30927638, year = {2019}, author = {Wei, Z and Yu, S and Huang, Z and Xiao, X and Tang, M and Li, B and Zhang, X}, title = {Simultaneous removal of elemental mercury and NO by mercury induced thermophilic community in membrane biofilm reactor.}, journal = {Ecotoxicology and environmental safety}, volume = {176}, number = {}, pages = {170-177}, doi = {10.1016/j.ecoenv.2019.03.082}, pmid = {30927638}, issn = {1090-2414}, mesh = {Biofilms/*growth &amp; development ; Bioreactors/*microbiology ; Denitrification ; Mercury/*analysis ; Metagenomics ; Microbiota/drug effects/genetics ; Nitric Oxide/*analysis ; Nitrification ; Oxidation-Reduction ; }, abstract = {Thermophilic membrane biofilm reactor (TMBR) for elemental mercury (Hg0) and NO removal in simulated flue gas was investigated at oxygen content of 6% and 60 °C. The performance, the microbial community structures, gene function and the mechanism for Hg0 and NO removal in the TMBR were evaluated. TMBR achieved effective simultaneous Hg0 and NO removal in 210 days of operation, Hg0 and NO removal efficiency were up to 88.9% and 85.3%, respectively. Mercury induced thermophilic community had been formed significantly. Comamonas, Pseudomonas, Desulfomicrobium, Burkholderia and Halomonas were thermophilic mercury resistant bacteria. Brucella, Paracoccus, Tepidiphilus, Proteobacteria, Pseudomonas and Symbiobacterium were nitrifying/denitrifying genera, and had functional genes of mercury and nitrogen metabolism, as shown by16S rDNA and metagenomic sequencing. The biofilm in TMBR was characterized by XPS, HPLC. XPS and HPLC spectra indicate the formation of a mercuric species (Hg2+) from mercury oxidation. TMBR used oxygen as electron acceptor, NO and Hg0 as electron donor in nitrification; O2, NO and NO3- could be used as electron acceptor and Hg0 as electron donor in denitrification.}, }
@article {pmid30370682, year = {2019}, author = {Nogueira, T and David, PHC and Pothier, J}, title = {Antibiotics as both friends and foes of the human gut microbiome: The microbial community approach.}, journal = {Drug development research}, volume = {80}, number = {1}, pages = {86-97}, doi = {10.1002/ddr.21466}, pmid = {30370682}, issn = {1098-2299}, mesh = {Animals ; Anti-Bacterial Agents/adverse effects/*therapeutic use ; Bacterial Infections/drug therapy/genetics/metabolism ; Databases, Genetic/trends ; Dysbiosis/drug therapy/genetics/metabolism ; Gastrointestinal Microbiome/*drug effects/physiology ; Humans ; Metagenomics/*methods/trends ; Microbiota/*drug effects ; }, abstract = {The exposure of the human gut to antibiotics can have a great impact on human health. Antibiotics pertain to the preservation of human health and are useful tools for fighting bacterial infections. They can be used for curing infections and can play a critical role in immunocompromised or chronic patients, or in fighting childhood severe malnutrition. Yet, the genomic and phylogenetic diversity of the human gut changes under antibiotic exposure. Antibiotics can also have severe side effects on human gut health, due to the spreading of potential antibiotic resistance genetic traits and to their correlation with virulence of some bacterial pathogens. They can shape, and even disrupt, the composition and functioning diversity of the human gut microbiome. Traditionally bacterial antibiotic resistances have been evaluated at clone or population level. However, the understanding of these two apparently disparate perspectives as both friends and foes may come from the study of microbiomes as a whole and from the evaluation of both positive and negative effects of antibiotics on microbial community dynamics and diversity. In this review we present some metagenomic tools and databases that enable the studying of antibiotic resistance in human gut metagenomes, promoting the development of personalized medicine strategies, new antimicrobial therapy protocols and patient follow-up.}, }
@article {pmid30342083, year = {2018}, author = {De Mol, ML and Snoeck, N and De Maeseneire, SL and Soetaert, WK}, title = {Hidden antibiotics: Where to uncover?.}, journal = {Biotechnology advances}, volume = {36}, number = {8}, pages = {2201-2218}, doi = {10.1016/j.biotechadv.2018.10.008}, pmid = {30342083}, issn = {1873-1899}, mesh = {Animals ; *Anti-Bacterial Agents/isolation &amp; purification/pharmacology ; Bacteria/chemistry/drug effects/genetics ; *Drug Discovery ; Gastrointestinal Microbiome/genetics ; Humans ; *Metagenomics ; Mice ; *Synthetic Biology ; }, abstract = {The struggle of humans versus pathogens is a never ending battle. Since the discovery of antibiotics humans have tipped the scales in their favour, but today bacteria are nullifying this advantage by developing resistance mechanisms against these molecules. The plethora of different antibiotics active against pathogens is shrinking while the discovery of new molecules is arduous. Especially the development of drugs active against Gram- pathogens continues slowly. New strategies to discover novel, potent antibiotics are hence needed. Adopting the optimistic view of technological singularity, innovative and disruptive approaches are required and hence proposed to lift the current conundrum. In this review, questions are answered on where and how to look for new natural product hit molecules with antibacterial activity, on how the field of synthetic biology can aid the contemporary pharmaceutical challenge and whether we are ready to make the transition towards other approaches, such as narrow-spectrum antibiotics and phage therapy.}, }
@article {pmid29554272, year = {2018}, author = {Rodriguez-Palacios, A and Harding, A and Menghini, P and Himmelman, C and Retuerto, M and Nickerson, KP and Lam, M and Croniger, CM and McLean, MH and Durum, SK and Pizarro, TT and Ghannoum, MA and Ilic, S and McDonald, C and Cominelli, F}, title = {The Artificial Sweetener Splenda Promotes Gut Proteobacteria, Dysbiosis, and Myeloperoxidase Reactivity in Crohn's Disease-Like Ileitis.}, journal = {Inflammatory bowel diseases}, volume = {24}, number = {5}, pages = {1005-1020}, pmid = {29554272}, issn = {1536-4844}, support = {S10 RR026820/RR/NCRR NIH HHS/United States ; P01 DK091222/DK/NIDDK NIH HHS/United States ; P30 DK097948/DK/NIDDK NIH HHS/United States ; R01 DK042191/DK/NIDDK NIH HHS/United States ; R01 DK082437/DK/NIDDK NIH HHS/United States ; R01 DK055812/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteroidetes/drug effects/genetics ; Crohn Disease/metabolism/*pathology ; Disease Models, Animal ; Dysbiosis/*physiopathology ; Female ; Humans ; Ileitis/metabolism/*pathology ; In Situ Hybridization, Fluorescence ; Intestinal Mucosa/metabolism/*pathology ; Male ; Mice ; Mice, Inbred AKR ; Microbiota ; Peroxidase/metabolism ; Proteobacteria/drug effects/genetics ; RNA, Ribosomal, 16S/genetics ; Sucrose/adverse effects/*analogs &amp; derivatives ; Sweetening Agents/*adverse effects ; }, abstract = {Background: Epidemiological studies indicate that the use of artificial sweeteners doubles the risk for Crohn's disease (CD). Herein, we experimentally quantified the impact of 6-week supplementation with a commercial sweetener (Splenda; ingredients sucralose maltodextrin, 1:99, w/w) on both the severity of CD-like ileitis and the intestinal microbiome alterations using SAMP1/YitFc (SAMP) mice.<br><br>Methods: Metagenomic shotgun DNA sequencing was first used to characterize the microbiome of ileitis-prone SAMP mice. Then, 16S rRNA microbiome sequencing, quantitative polymerase chain reaction, fluorescent in situ hybridization (FISH), bacterial culture, stereomicroscopy, histology, and myeloperoxidase (MPO) activity analyses were then implemented to compare the microbiome and ileitis phenotype in SAMP with that of control ileitis-free AKR/J mice after Splenda supplementation.<br><br>Results: Metagenomics indicated that SAMP mice have a gut microbial phenotype rich in Bacteroidetes, and experiments showed that Helicobacteraceae did not have an exacerbating effect on ileitis. Splenda did not increase the severity of (stereomicroscopic/histological) ileitis; however, biochemically, ileal MPO activity was increased in SAMP treated with Splenda compared with nonsupplemented mice (P < 0.022) and healthy AKR mice. Splenda promoted dysbiosis with expansion of Proteobacteria in all mice, and E. coli overgrowth with increased bacterial infiltration into the ileal lamina propria of SAMP mice. FISH showed increase malX gene-carrying bacterial clusters in the ilea of supplemented SAMP (but not AKR) mice.<br><br>Conclusions: Splenda promoted gut Proteobacteria, dysbiosis, and biochemical MPO reactivity in a spontaneous model of (Bacteroidetes-rich) ileal CD. Our results indicate that although Splenda may promote parallel microbiome alterations in CD-prone and healthy hosts, this did not result in elevated MPO levels in healthy mice, only CD-prone mice. The consumption of sucralose/maltodextrin-containing foods might exacerbate MPO intestinal reactivity only in individuals with a pro-inflammatory predisposition, such as CD.}, }
@article {pmid29319528, year = {2017}, author = {Wang, H and Wei, Q and Gui, S and Feng, Y and Zhang, Y and Liu, Y and Lu, F}, title = {Metagenomic Profiling of the Bacterial Community Changes from Koji to Mash Stage in the Brewing of Soy Sauce.}, journal = {Polish journal of microbiology}, volume = {66}, number = {4}, pages = {537-541}, doi = {10.5604/01.3001.0010.7097}, pmid = {29319528}, issn = {1733-1331}, mesh = {Bacteria/*classification ; Biodiversity ; *Fermentation ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; *Microbiota ; Polymerase Chain Reaction ; Soy Foods/*microbiology ; Soybeans/microbiology ; Staphylococcus/classification ; Weissella/classification ; }, abstract = {The improvement of soy sauce fermentation is restricted by the insufficient information on bacterial community. In this study, bacterial communities in the koji and mash stage were compared based on next-generation sequencing technology. A total of 29 genera were identified in the koji stage, while 34 in the mash stage. After koji stage, 7 genera disappeared and 12 new genera appeared in the mash stage. The dominant bacteria were Kurthia, Weissella and Staphylococcus in the koji stage and Staphylococcus, Kurthia, Enterococcus and Leuconostoc in the mash stage. The results provided insights into the microbial communities involved in soy sauce fermentation.}, }
@article {pmid30643240, year = {2019}, author = {Nakamoto, N and Sasaki, N and Aoki, R and Miyamoto, K and Suda, W and Teratani, T and Suzuki, T and Koda, Y and Chu, PS and Taniki, N and Yamaguchi, A and Kanamori, M and Kamada, N and Hattori, M and Ashida, H and Sakamoto, M and Atarashi, K and Narushima, S and Yoshimura, A and Honda, K and Sato, T and Kanai, T}, title = {Gut pathobionts underlie intestinal barrier dysfunction and liver T helper 17 cell immune response in primary sclerosing cholangitis.}, journal = {Nature microbiology}, volume = {4}, number = {3}, pages = {492-503}, doi = {10.1038/s41564-018-0333-1}, pmid = {30643240}, issn = {2058-5276}, mesh = {Adult ; Aged ; Animals ; Bacterial Translocation ; Cholangitis, Sclerosing/*immunology/microbiology ; Colitis, Ulcerative/complications ; Enterococcus/isolation &amp; purification ; Epithelial Cells/microbiology/pathology ; Female ; *Gastrointestinal Microbiome ; Germ-Free Life ; Humans ; Intestines/immunology/*pathology ; Klebsiella pneumoniae/isolation &amp; purification/*pathogenicity ; Liver/*immunology/pathology ; Lymph Nodes/microbiology ; Male ; Mice ; Mice, Inbred C57BL ; Middle Aged ; Organoids/microbiology ; Proteus mirabilis/isolation &amp; purification ; Th17 Cells/*immunology ; }, abstract = {Primary sclerosing cholangitis (PSC) is a chronic inflammatory liver disease and its frequent complication with ulcerative colitis highlights the pathogenic role of epithelial barrier dysfunction. Intestinal barrier dysfunction has been implicated in the pathogenesis of PSC, yet its underlying mechanism remains unknown. Here, we identify Klebsiella pneumonia in the microbiota of patients with PSC and demonstrate that K. pneumoniae disrupts the epithelial barrier to initiate bacterial translocation and liver inflammatory responses. Gnotobiotic mice inoculated with PSC-derived microbiota exhibited T helper 17 (TH17) cell responses in the liver and increased susceptibility to hepatobiliary injuries. Bacterial culture of mesenteric lymph nodes in these mice isolated K. pneumoniae, Proteus mirabilis and Enterococcus gallinarum, which were prevalently detected in patients with PSC. A bacterial-organoid co-culture system visualized the epithelial-damaging effect of PSC-derived K. pneumoniae that was associated with bacterial translocation and susceptibility to TH17-mediated hepatobiliary injuries. We also show that antibiotic treatment ameliorated the TH17 immune response induced by PSC-derived microbiota. These results highlight the role of pathobionts in intestinal barrier dysfunction and liver inflammation, providing insights into therapeutic strategies for PSC.}, }
@article {pmid30559407, year = {2019}, author = {Vatanen, T and Plichta, DR and Somani, J and Münch, PC and Arthur, TD and Hall, AB and Rudolf, S and Oakeley, EJ and Ke, X and Young, RA and Haiser, HJ and Kolde, R and Yassour, M and Luopajärvi, K and Siljander, H and Virtanen, SM and Ilonen, J and Uibo, R and Tillmann, V and Mokurov, S and Dorshakova, N and Porter, JA and McHardy, AC and Lähdesmäki, H and Vlamakis, H and Huttenhower, C and Knip, M and Xavier, RJ}, title = {Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life.}, journal = {Nature microbiology}, volume = {4}, number = {3}, pages = {470-479}, doi = {10.1038/s41564-018-0321-5}, pmid = {30559407}, issn = {2058-5276}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; UM1 AI110498/AI/NIAID NIH HHS/United States ; }, mesh = {*Adaptation, Physiological ; Age Factors ; Bacteriophages/genetics ; Bacteroides/genetics/virology ; Bifidobacterium bifidum/genetics ; Bifidobacterium longum/genetics ; Child Development ; Child, Preschool ; Estonia ; Feces/microbiology ; Female ; Finland ; Gastrointestinal Microbiome/*genetics ; *Genetic Variation ; *Genome, Bacterial ; Humans ; Infant ; Longitudinal Studies ; Male ; Metabolic Networks and Pathways ; Metagenomics ; Polymorphism, Single Nucleotide ; Probiotics ; Russia ; }, abstract = {The human gut microbiome matures towards the adult composition during the first years of life and is implicated in early immune development. Here, we investigate the effects of microbial genomic diversity on gut microbiome development using integrated early childhood data sets collected in the DIABIMMUNE study in Finland, Estonia and Russian Karelia. We show that gut microbial diversity is associated with household location and linear growth of children. Single nucleotide polymorphism- and metagenomic assembly-based strain tracking revealed large and highly dynamic microbial pangenomes, especially in the genus Bacteroides, in which we identified evidence of variability deriving from Bacteroides-targeting bacteriophages. Our analyses revealed functional consequences of strain diversity; only 10% of Finnish infants harboured Bifidobacterium longum subsp. infantis, a subspecies specialized in human milk metabolism, whereas Russian infants commonly maintained a probiotic Bifidobacterium bifidum strain in infancy. Groups of bacteria contributing to diverse, characterized metabolic pathways converged to highly subject-specific configurations over the first two years of life. This longitudinal study extends the current view of early gut microbial community assembly based on strain-level genomic variation.}, }
@article {pmid30559406, year = {2019}, author = {Kintses, B and Méhi, O and Ari, E and Számel, M and Györkei, Á and Jangir, PK and Nagy, I and Pál, F and Fekete, G and Tengölics, R and Nyerges, Á and Likó, I and Bálint, A and Molnár, T and Bálint, B and Vásárhelyi, BM and Bustamante, M and Papp, B and Pál, C}, title = {Phylogenetic barriers to horizontal transfer of antimicrobial peptide resistance genes in the human gut microbiota.}, journal = {Nature microbiology}, volume = {4}, number = {3}, pages = {447-458}, doi = {10.1038/s41564-018-0313-5}, pmid = {30559406}, issn = {2058-5276}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Antimicrobial Cationic Peptides/*genetics ; Bacteria/*genetics ; Escherichia coli/genetics ; Gastrointestinal Microbiome/*genetics ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome, Bacterial ; Humans ; Metagenomics ; *Phylogeny ; }, abstract = {The human gut microbiota has adapted to the presence of antimicrobial peptides (AMPs), which are ancient components of immune defence. Despite its medical importance, it has remained unclear whether AMP resistance genes in the gut microbiome are available for genetic exchange between bacterial species. Here, we show that AMP resistance and antibiotic resistance genes differ in their mobilization patterns and functional compatibilities with new bacterial hosts. First, whereas AMP resistance genes are widespread in the gut microbiome, their rate of horizontal transfer is lower than that of antibiotic resistance genes. Second, gut microbiota culturing and functional metagenomics have revealed that AMP resistance genes originating from phylogenetically distant bacteria have only a limited potential to confer resistance in Escherichia coli, an intrinsically susceptible species. Taken together, functional compatibility with the new bacterial host emerges as a key factor limiting the genetic exchange of AMP resistance genes. Finally, our results suggest that AMPs induce highly specific changes in the composition of the human microbiota, with implications for disease risks.}, }
@article {pmid30414158, year = {2019}, author = {Bosch, TCG}, title = {Hydra as Model to Determine the Role of FOXO in Longevity.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1890}, number = {}, pages = {231-238}, doi = {10.1007/978-1-4939-8900-3_19}, pmid = {30414158}, issn = {1940-6029}, mesh = {Aging/genetics/metabolism ; Animals ; Animals, Genetically Modified ; Forkhead Transcription Factors/*genetics/metabolism ; Gene Expression Profiling ; Gene Expression Regulation ; Genes, Reporter ; Genetic Vectors/genetics ; Hydra/classification/*genetics/metabolism ; Longevity/*genetics ; Metagenome ; Metagenomics/methods ; Microbiota ; Molecular Imaging ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Recombinant Fusion Proteins ; Stem Cells/metabolism ; }, abstract = {In non-senescent Hydra, continuously high activity of transcription factor FOXO contributes to continuous stem cell proliferation. Here, we describe how genetic manipulation of Hydra polyps using embryo-microinjection allows uncovering the role of FOXO in coordinating both stem cell proliferation and antimicrobial peptide0073 , effector molecules of the innate immune system, and regulators of the microbiome.}, }
@article {pmid29319531, year = {2017}, author = {Czarny, J and Staninska-Pięta, J and Powierska-Czarny, J and Nowak, J and Wolko, Ł and Piotrowska-Cyplik, A}, title = {Metagenomic Analysis of Soil Bacterial Community and Level of Genes Responsible for Biodegradation of Aromatic Hydrocarbons.}, journal = {Polish journal of microbiology}, volume = {66}, number = {3}, pages = {345-352}, doi = {10.5604/01.3001.0010.4865}, pmid = {29319531}, issn = {1733-1331}, mesh = {Alphaproteobacteria/classification/*genetics/*metabolism ; *Biodegradation, Environmental ; DNA, Bacterial/genetics ; Dioxygenases/analysis ; Gammaproteobacteria/classification/*genetics/*metabolism ; Gasoline/analysis ; Metagenomics ; Poland ; Polycyclic Aromatic Hydrocarbons/*metabolism ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Soil Microbiology ; Soil Pollutants/*metabolism ; }, abstract = {The aim of the studies was to compare the composition of soil bacterial metabiomes originating from urbanized areas and areas con¬taminated with hydrocarbons with those from agricultural soil and forest soil obtained from a protected wild-life park area. It should be noted that hydrocarbons are everywhere therefore bacteria capable of their utilization are present in every soil type. In the hydrocarbon-contaminated soil and in the soil of anthropogenic origin, the bacteria belonging to Gammaproteobacteria were dominant (28.4-36.6%), whereas in the case of agricultural soil and protected wild-life park soil their ratios decreased (22.8-23.0%) and were similar to that of Alphaproteobacteria. No statistically significant changes were observed in terms of the Operational Taxonomic Unit identified in the studies soils, however, based on the determined alpha-diversity it can be established that contaminated soils were characterized by lower biodiversity indices compared to agricultural and forest soils. Furthermore, the dioxygenase level was also evaluated in the studied soils, which are genes encoding crucial enzymes for the decomposition of mono- and polycyclic aromatic hydrocarbons during the biodegradation of diesel oil (PAHRHDαGN, PAHRHDαGP, xylE, Cat 2,3, ndoB). It was concluded that both the population structure of the soil metabiome and the number of genes crucial for biodegradation processes differed significantly between the soils. The level of analysed genes showed a similar trend, as their highest number in relations to genes encoding 16S RNA was determined in urban and hydrocarbon-contaminated soil.}, }
@article {pmid30791436, year = {2019}, author = {Jaimes, JD and Jarosova, V and Vesely, O and Mekadim, C and Mrazek, J and Marsik, P and Killer, J and Smejkal, K and Kloucek, P and Havlik, J}, title = {Effect of Selected Stilbenoids on Human Fecal Microbiota.}, journal = {Molecules (Basel, Switzerland)}, volume = {24}, number = {4}, pages = {}, doi = {10.3390/molecules24040744}, pmid = {30791436}, issn = {1420-3049}, support = {16-07193S//Grantová Agentura České Republiky/ ; CIGA 20172031//Česká Zemědělská Univerzita v Praze/ ; }, mesh = {Feces/*microbiology ; Fermentation ; Gastrointestinal Microbiome/*drug effects ; Humans ; Metagenome ; Metagenomics/methods ; Molecular Structure ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Stilbenes/*pharmacology ; }, abstract = {Dietary phenolics or polyphenols are mostly metabolized by the human gut microbiota. These metabolites appear to confer the beneficial health effects attributed to phenolics. Microbial composition affects the type of metabolites produced. Reciprocally, phenolics modulate microbial composition. Understanding this relationship could be used to positively impact health by phenolic supplementation and thus create favorable colonic conditions. This study explored the effect of six stilbenoids (batatasin III, oxyresveratrol, piceatannol, pinostilbene, resveratrol, thunalbene) on the gut microbiota composition. Stilbenoids were anaerobically fermented with fecal bacteria from four donors, samples were collected at 0 and 24 h, and effects on the microbiota were assessed by 16S rRNA gene sequencing. Statistical tests identified affected microbes at three taxonomic levels. Observed microbial composition modulation by stilbenoids included a decrease in the Firmicutes to Bacteroidetes ratio, a decrease in the relative abundance of strains from the genus Clostridium, and effects on the family Lachnospiraceae. A frequently observed effect was a further decrease of the relative abundance when compared to the control. An opposite effect to the control was observed for Faecalibacterium prausnitzii, whose relative abundance increased. Observed effects were more frequently attributed to resveratrol and piceatannol, followed by thunalbene and batatasin III.}, }
@article {pmid28620208, year = {2017}, author = {Xu, Y and Xie, Z and Wang, H and Shen, Z and Guo, Y and Gao, Y and Chen, X and Wu, Q and Li, X and Wang, K}, title = {Bacterial Diversity of Intestinal Microbiota in Patients with Substance Use Disorders Revealed by 16S rRNA Gene Deep Sequencing.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {3628}, pmid = {28620208}, issn = {2045-2322}, mesh = {Adult ; Bacteria/*classification/*genetics ; Biodiversity ; Case-Control Studies ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenome ; Metagenomics ; Middle Aged ; Phylogeny ; *RNA, Ribosomal, 16S ; Substance-Related Disorders/*etiology ; Young Adult ; }, abstract = {Substance abuse and addiction are worldwide concerns. In China, populated with over 1.3 billion people, emerging studies show a steady increase in substance abuse and substance-related problems. Some of the major challenges include a lack of an effective evaluation platform to determine the health status of substance-addicted subjects. It is known that the intestinal microbiota is associated to the occurrence and development of human diseases. However, the changes of bacterial diversity of intestinal microbiota in substance-addicted subjects have not been clearly characterized. Herein, we examined the composition and diversity of intestinal microbiota in 45 patients with substance use disorders (SUDs) and in 48 healthy controls (HCs). The results show that the observed species diversity index and the abundance of Thauera, Paracoccus, and Prevotella are significantly higher in SUDs compared to HCs. The functional diversity of the putative metagenomes analysis reveals that pathways including translation, DNA replication and repair, and cell growth and death are over-represented while cellular processes and signaling, and metabolism are under-represented in SUDs. Overall, the analyses show that there seem to be changes in the microbiota that are associated with substance use across an array of SUDs, providing fundamental knowledge for future research in substance-addiction assessment tests.}, }
@article {pmid31043514, year = {2019}, author = {Escudeiro, P and Pothier, J and Dionisio, F and Nogueira, T}, title = {Antibiotic Resistance Gene Diversity and Virulence Gene Diversity Are Correlated in Human Gut and Environmental Microbiomes.}, journal = {mSphere}, volume = {4}, number = {3}, pages = {}, doi = {10.1128/mSphere.00135-19}, pmid = {31043514}, issn = {2379-5042}, mesh = {Adolescent ; Adult ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics ; Child ; Child, Preschool ; Drug Resistance, Microbial/*genetics ; *Environmental Microbiology ; Gastrointestinal Microbiome/*drug effects ; Gastrointestinal Tract/microbiology ; *Genetic Variation ; Humans ; Infant ; Metagenome ; Metagenomics ; Microbiota/*drug effects ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Virulence ; Virulence Factors/genetics ; Young Adult ; }, abstract = {Human beings have used large amounts of antibiotics, not only in medical contexts but also, for example, as growth factors in agriculture and livestock, resulting in the contamination of the environment. Even when pathogenic bacteria are the targets of antibiotics, hundreds of nonpathogenic bacterial species are affected as well. Therefore, both pathogenic and nonpathogenic bacteria have gradually become resistant to antibiotics. We tested whether there is still cooccurrence of resistance and virulence determinants. We performed a comparative study of environmental and human gut metagenomes from different individuals and from distinct human populations across the world. We found a great diversity of antibiotic resistance determinants (AR diversity [ARd]) and virulence factors (VF diversity [VFd]) in metagenomes. Importantly there is a correlation between ARd and VFd, even after correcting for protein family richness. In the human gut, there are less ARd and VFd than in more diversified environments, and yet correlations between the ARd and VFd are stronger. They can vary from very high in Malawi, where antibiotic consumption is unattended, to nonexistent in the uncontacted Amerindian population. We conclude that there is cooccurrence of resistance and virulence determinants in human gut microbiomes, suggesting a possible coselective mechanism.IMPORTANCE Every year, thousands of tons of antibiotics are used, not only in human and animal health but also as growth promoters in livestock. Consequently, during the last 75 years, antibiotic-resistant bacterial strains have been selected in human and environmental microbial communities. This implies that, even when pathogenic bacteria are the targets of antibiotics, hundreds of nonpathogenic bacterial species are also affected. Here, we performed a comparative study of environmental and human gut microbial communities issuing from different individuals and from distinct human populations across the world. We found that antibiotic resistance and pathogenicity are correlated and speculate that, by selecting for resistant bacteria, we may be selecting for more virulent strains as a side effect of antimicrobial therapy.}, }
@article {pmid30747914, year = {2019}, author = {Gastauer, M and Vera, MPO and de Souza, KP and Pires, ES and Alves, R and Caldeira, CF and Ramos, SJ and Oliveira, G}, title = {A metagenomic survey of soil microbial communities along a rehabilitation chronosequence after iron ore mining.}, journal = {Scientific data}, volume = {6}, number = {}, pages = {190008}, doi = {10.1038/sdata.2019.8}, pmid = {30747914}, issn = {2052-4463}, mesh = {Archaea/genetics ; Bacteria/genetics ; Brazil ; Environmental Monitoring/*methods ; High-Throughput Nucleotide Sequencing ; Iron ; Metagenomics/*methods ; *Microbiota/genetics ; Mining ; *Soil Microbiology ; Viruses/genetics ; }, abstract = {Microorganisms are useful environmental indicators, able to deliver essential insights to processes regarding mine land rehabilitation. To compare microbial communities from a chronosequence of mine land rehabilitation to pre-disturbance levels from references sites covered by native vegetation, we sampled non-rehabilitated, rehabilitating and reference study sites from the Urucum Massif, Southwestern Brazil. From each study site, three composed soil samples were collected for chemical, physical, and metagenomics analysis. We used a paired-end library sequencing technology (NextSeq 500 Illumina); the reads were assembled using MEGAHIT. Coding DNA sequences (CDS) were identified using Kaiju in combination with non-redundant NCBI BLAST reference sequences containing archaea, bacteria, and viruses. Additionally, a functional classification was performed by EMG v2.3.2. Here, we provide the raw data and assembly (reads and contigs), followed by initial functional and taxonomic analysis, as a base-line for further studies of this kind. Further investigation is needed to fully understand the mechanisms of environmental rehabilitation in tropical regions, inspiring further researchers to explore this collection for hypothesis testing.}, }
@article {pmid30720800, year = {2019}, author = {Bukin, YS and Galachyants, YP and Morozov, IV and Bukin, SV and Zakharenko, AS and Zemskaya, TI}, title = {The effect of 16S rRNA region choice on bacterial community metabarcoding results.}, journal = {Scientific data}, volume = {6}, number = {}, pages = {190007}, doi = {10.1038/sdata.2019.7}, pmid = {30720800}, issn = {2052-4463}, mesh = {Bacteria/genetics ; Computational Biology/methods ; DNA Barcoding, Taxonomic/*methods ; High-Throughput Nucleotide Sequencing ; Lakes ; Metagenomics/*methods ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*genetics ; Russia ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {In this work, we compare the resolution of V2-V3 and V3-V4 16S rRNA regions for the purposes of estimating microbial community diversity using paired-end Illumina MiSeq reads, and show that the fragment, including V2 and V3 regions, has higher resolution for lower-rank taxa (genera and species). It allows for a more precise distance-based clustering of reads into species-level OTUs. Statistically convergent estimates of the diversity of major species (defined as those that together are covered by 95% of reads) can be achieved at the sample sizes of 10000 to 15000 reads. The relative error of the Shannon index estimate for this condition is lower than 4%.}, }
@article {pmid30144516, year = {2018}, author = {Nguyen, D and Khanal, SK}, title = {A little breath of fresh air into an anaerobic system: How microaeration facilitates anaerobic digestion process.}, journal = {Biotechnology advances}, volume = {36}, number = {7}, pages = {1971-1983}, doi = {10.1016/j.biotechadv.2018.08.007}, pmid = {30144516}, issn = {1873-1899}, mesh = {Anaerobiosis ; Bacteria/*metabolism ; Bioreactors ; Fermentation ; Gene Expression Profiling ; Hydrogen Sulfide/*metabolism ; Hydrolysis ; Metabolic Networks and Pathways ; Metagenomics ; Methane/*metabolism ; Methanomicrobiales/*metabolism ; Microbial Consortia/*physiology ; Oxidation-Reduction ; Oxygen/*metabolism ; Proteomics ; }, abstract = {Exposure of a small amount of oxygen/air (microaeration) has been reported to benefit the anaerobic digestion (AD) process in enhancing hydrolysis, improving methane yield, stabilizing the process and scavenging hydrogen sulfide among others. The underlying mechanism of enhancing AD process via microaeration is the augmentation of activity and diversity of the microbial consortia that promotes syntrophic interactions among different microbial groups, thereby creating a more stable process. To design and implement a microaeration-based AD process, fundamental insights about the mechanism of the AD system at process, microbial and molecular levels must be fully explored. This review critically examines microaeration-based AD processes through our recent understandings of the effect of oxygen on microbial community structure, enzymatic, energetic, physiological, and biochemical aspects of the microbial-mediated process. Syntrophic interactions between hydrolytic, fermentative, sulfate reducing, syntrophic bacteria and methanogens under microaerobic conditions are examined to reveal putative mechanism and factors that need to be considered when implementing microaeration in AD process. Further studies are needed to better understand the microbial pathways and bioenergetics of the microaerobic AD process by adopting advanced molecular techniques such as metagenomics, transcriptomics, and proteomics.}, }
@article {pmid30001854, year = {2018}, author = {Berry, D and Loy, A}, title = {Stable-Isotope Probing of Human and Animal Microbiome Function.}, journal = {Trends in microbiology}, volume = {26}, number = {12}, pages = {999-1007}, pmid = {30001854}, issn = {1878-4380}, mesh = {Animals ; Bacterial Physiological Phenomena ; DNA/chemistry ; Gastrointestinal Microbiome/*physiology ; Host Microbial Interactions/*physiology ; Humans ; Isotope Labeling/*methods ; *Isotopes ; Metagenome ; Metagenomics/methods ; Molecular Probes ; RNA/chemistry ; Spectrum Analysis, Raman/methods ; }, abstract = {Humans and animals host diverse communities of microorganisms important to their physiology and health. Despite extensive sequencing-based characterization of host-associated microbiomes, there remains a dramatic lack of understanding of microbial functions. Stable-isotope probing (SIP) is a powerful strategy to elucidate the ecophysiology of microorganisms in complex host-associated microbiotas. Here, we suggest that SIP methodologies should be more frequently exploited as part of a holistic functional microbiomics approach. We provide examples of how SIP has been used to study host-associated microbes in vivo and ex vivo. We highlight recent developments in SIP technologies and discuss future directions that will facilitate deeper insights into the function of human and animal microbiomes.}, }
@article {pmid29436230, year = {2018}, author = {Xiao, J and Tanca, A and Jia, B and Yang, R and Wang, B and Zhang, Y and Li, J}, title = {Metagenomic Taxonomy-Guided Database-Searching Strategy for Improving Metaproteomic Analysis.}, journal = {Journal of proteome research}, volume = {17}, number = {4}, pages = {1596-1605}, doi = {10.1021/acs.jproteome.7b00894}, pmid = {29436230}, issn = {1535-3907}, mesh = {Classification/methods ; Computer Simulation ; Data Mining/*methods ; Databases, Protein ; Metagenomics/*standards ; *Microbiota ; Proteins/*analysis ; Proteomics/*standards ; }, abstract = {Metaproteomics provides a direct measure of the functional information by investigating all proteins expressed by a microbiota. However, due to the complexity and heterogeneity of microbial communities, it is very hard to construct a sequence database suitable for a metaproteomic study. Using a public database, researchers might not be able to identify proteins from poorly characterized microbial species, while a sequencing-based metagenomic database may not provide adequate coverage for all potentially expressed protein sequences. To address this challenge, we propose a metagenomic taxonomy-guided database-search strategy (MT), in which a merged database is employed, consisting of both taxonomy-guided reference protein sequences from public databases and proteins from metagenome assembly. By applying our MT strategy to a mock microbial mixture, about two times as many peptides were detected as with the metagenomic database only. According to the evaluation of the reliability of taxonomic attribution, the rate of misassignments was comparable to that obtained using an a priori matched database. We also evaluated the MT strategy with a human gut microbial sample, and we found 1.7 times as many peptides as using a standard metagenomic database. In conclusion, our MT strategy allows the construction of databases able to provide high sensitivity and precision in peptide identification in metaproteomic studies, enabling the detection of proteins from poorly characterized species within the microbiota.}, }
@article {pmid31141902, year = {2019}, author = {Kallies, R and Hölzer, M and Brizola Toscan, R and Nunes da Rocha, U and Anders, J and Marz, M and Chatzinotas, A}, title = {Evaluation of Sequencing Library Preparation Protocols for Viral Metagenomic Analysis from Pristine Aquifer Groundwaters.}, journal = {Viruses}, volume = {11}, number = {6}, pages = {}, doi = {10.3390/v11060484}, pmid = {31141902}, issn = {1999-4915}, support = {CRC 1076//Deutsche Forschungsgemeinschaft/ ; SPP-1596//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Viral ecology of terrestrial habitats is yet-to be extensively explored, in particular the terrestrial subsurface. One problem in obtaining viral sequences from groundwater aquifer samples is the relatively low amount of virus particles. As a result, the amount of extracted DNA may not be sufficient for direct sequencing of such samples. Here we compared three DNA amplification methods to enrich viral DNA from three pristine limestone aquifer assemblages of the Hainich Critical Zone Exploratory to evaluate potential bias created by the different amplification methods as determined by viral metagenomics. Linker amplification shotgun libraries resulted in lowest redundancy among the sequencing reads and showed the highest diversity, while multiple displacement amplification produced the highest number of contigs with the longest average contig size, suggesting a combination of these two methods is suitable for the successful enrichment of viral DNA from pristine groundwater samples. In total, we identified 27,173, 5,886 and 32,613 viral contigs from the three samples from which 11.92 to 18.65% could be assigned to taxonomy using blast. Among these, members of the Caudovirales order were the most abundant group (52.20 to 69.12%) dominated by Myoviridae and Siphoviridae. Those, and the high number of unknown viral sequences, substantially expand the known virosphere.}, }
@article {pmid30804518, year = {2019}, author = {Monnahan, P and Kolář, F and Baduel, P and Sailer, C and Koch, J and Horvath, R and Laenen, B and Schmickl, R and Paajanen, P and Šrámková, G and Bohutínská, M and Arnold, B and Weisman, CM and Marhold, K and Slotte, T and Bomblies, K and Yant, L}, title = {Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa.}, journal = {Nature ecology &amp; evolution}, volume = {3}, number = {3}, pages = {457-468}, doi = {10.1038/s41559-019-0807-4}, pmid = {30804518}, issn = {2397-334X}, mesh = {Arabidopsis/*genetics ; Evolution, Molecular ; *Gene Duplication ; *Gene Flow ; *Genome, Plant ; Metagenomics ; }, abstract = {Ploidy-variable species allow direct inference of the effects of chromosome copy number on fundamental evolutionary processes. While an abundance of theoretical work suggests polyploidy should leave distinct population genomic signatures, empirical data remains sparse. We sequenced ~300 individuals from 39 populations of Arabidopsis arenosa, a naturally diploid-autotetraploid species. We find that the impacts of polyploidy on population genomic processes are subtle yet pervasive, such as reduced efficiency of purifying selection, differences in linked selection and rampant gene flow from diploids. Initial masking of deleterious mutations, faster rates of nucleotide substitution and interploidy introgression likely conspire to shape the evolutionary potential of polyploids.}, }
@article {pmid30013164, year = {2018}, author = {Armstrong, Z and Mewis, K and Liu, F and Morgan-Lang, C and Scofield, M and Durno, E and Chen, HM and Mehr, K and Withers, SG and Hallam, SJ}, title = {Metagenomics reveals functional synergy and novel polysaccharide utilization loci in the Castor canadensis fecal microbiome.}, journal = {The ISME journal}, volume = {12}, number = {11}, pages = {2757-2769}, pmid = {30013164}, issn = {1751-7370}, mesh = {Animals ; Biomass ; Feces/microbiology ; Gastrointestinal Tract/microbiology ; Glycoside Hydrolases/genetics ; Metagenomics ; *Microbiota/genetics ; Polysaccharides/*metabolism ; Rodentia/*microbiology ; }, abstract = {The North American beaver (Castor canadensis) has long been considered an engineering marvel, transforming landscapes and shaping biological diversity through its dam building behavior. While the beaver possesses conspicuous morphological features uniquely adapted for the use of woody plants as construction materials and dietary staples, relatively little is known about the specialized microorganisms inhabiting the beaver gastrointestinal tract and their functional roles in determining host nutrition. Here we use a combination of shotgun metagenomics, functional screening and carbohydrate biochemistry to chart the community structure and metabolic power of the beaver fecal microbiome. We relate this information to the metabolic capacity of other wood feeding and hindgut fermenting organisms and profile the functional repertoire of glycoside hydrolase (GH) families distributed among and between population genome bins. Metagenomic screening revealed novel mechanisms of xylan oligomer degradation involving GH43 enzymes from uncharacterized subfamilies and divergent polysaccharide utilization loci, indicating the potential for synergistic biomass deconstruction. Together, these results open a functional metagenomic window on less conspicuous adaptations enabling the beaver microbiome to efficiently convert woody plants into host nutrition and point toward rational design of enhanced enzyme mixtures for biorefining process streams.}, }
@article {pmid29980796, year = {2018}, author = {Wong, HL and White, RA and Visscher, PT and Charlesworth, JC and Vázquez-Campos, X and Burns, BP}, title = {Disentangling the drivers of functional complexity at the metagenomic level in Shark Bay microbial mat microbiomes.}, journal = {The ISME journal}, volume = {12}, number = {11}, pages = {2619-2639}, pmid = {29980796}, issn = {1751-7370}, mesh = {Animals ; Archaea/genetics/isolation &amp; purification/metabolism ; Bacteria/genetics/isolation &amp; purification/metabolism ; Bays ; Carbon/metabolism ; Carbon Cycle/genetics ; *Metagenome ; Metagenomics ; Microbial Interactions ; *Microbiota ; Nitrogen/metabolism ; Phosphorus/metabolism ; Sulfur/metabolism ; }, abstract = {The functional metagenomic potential of Shark Bay microbial mats was examined for the first time at a millimeter scale, employing shotgun sequencing of communities via the Illumina NextSeq 500 platform in conjunction with defined chemical analyses. A detailed functional metagenomic profile has elucidated key pathways and facilitated inference of critical microbial interactions. In addition, 87 medium-to-high-quality metagenome-assembled genomes (MAG) were assembled, including potentially novel bins under the deep-branching archaeal Asgard group (Thorarchaetoa and Lokiarchaeota). A range of pathways involved in carbon, nitrogen, sulfur, and phosphorus cycles were identified in mat metagenomes, with the Wood-Ljungdahl pathway over-represented and inferred as a major carbon fixation mode. The top five sets of genes were affiliated to sulfate assimilation (cysNC cysNCD, sat), methanogenesis (hdrABC), Wood-Ljungdahl pathways (cooS, coxSML), phosphate transport (pstB), and copper efflux (copA). Polyhydroxyalkanoate (PHA) synthase genes were over-represented at the surface, with PHA serving as a potential storage of fixed carbon. Sulfur metabolism genes were highly represented, in particular complete sets of genes responsible for both assimilatory and dissimilatory sulfate reduction. Pathways of environmental adaptation (UV, hypersalinity, oxidative stress, and heavy metal resistance) were also delineated, as well as putative viral defensive mechanisms (core genes of the CRISPR, BREX, and DISARM systems). This study provides new metagenome-based models of how biogeochemical cycles and adaptive responses may be partitioned in the microbial mats of Shark Bay.}, }
@article {pmid29681906, year = {2018}, author = {Iino, C and Shimoyama, T and Chinda, D and Arai, T and Chiba, D and Nakaji, S and Fukuda, S}, title = {Infection of Helicobacter pylori and Atrophic Gastritis Influence Lactobacillus in Gut Microbiota in a Japanese Population.}, journal = {Frontiers in immunology}, volume = {9}, number = {}, pages = {712}, pmid = {29681906}, issn = {1664-3224}, mesh = {Adult ; Aged ; Biomarkers ; Female ; Gastritis, Atrophic/etiology/*immunology ; *Gastrointestinal Microbiome/immunology ; Helicobacter Infections/complications/diagnosis/*immunology/*microbiology ; *Helicobacter pylori/immunology ; Humans ; Japan ; *Lactobacillus/immunology ; Male ; Metagenome ; Metagenomics ; Middle Aged ; Public Health Surveillance ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Background: Suppression of gastric acid by proton pump inhibitors is associated with the increase of Lactobacillus in human gut microbiota. Gastric acid secretion is also suppressed by Helicobacter pylori infection and following atrophic gastritis. However, few studies have examined the association between H. pylori infection and Lactobacillus species in gut microbiota particularly in Japan.<br><br>Methods: A total of 1,123 adult subjects who participated in a health survey in Hirosaki City were studied. Infection of H. pylori was defined by both serum antibody and stool antigen test. The presence and the severity of atrophic gastritis were defined by the serum level of serum pepsinogens. Using 16S ribosomal RNA amplification from fecal samples, the relative abundance of Lactobacillus was calculated, and the composition ratio of each Lactobacillus species was surveyed.<br><br>Results: The relative abundance of the Lactobacillus in H. pylori-infected subjects with severe atrophic gastritis was higher comparing with those in subjects with mild atrophic gastritis and without atrophic gastritis (0.591 vs 0.068% and 0.033%, respectively; p < 0.001) and also that of non-infected subjects (0.033%; p < 0.001). In H. pylori non-infected subjects, both gender and age were not associated with the relative abundance of Lactobacillus in fecal samples. The proportion of Lactobacillus salivarius was high in H. pylori-infected subjects while that of Lactobacillus acidophilus was high in non-infected subjects.<br><br>Conclusion: Lactobacillus in human gut microbiota could be influenced by H. pylori infection and severity of atrophic gastritis in Japanese subjects.}, }
@article {pmid30664775, year = {2019}, author = {Lin, M and Kussell, E}, title = {Inferring bacterial recombination rates from large-scale sequencing datasets.}, journal = {Nature methods}, volume = {16}, number = {2}, pages = {199-204}, doi = {10.1038/s41592-018-0293-7}, pmid = {30664775}, issn = {1548-7105}, mesh = {Computational Biology/*methods ; Computer Simulation ; *DNA, Ancient ; DNA, Bacterial ; Databases, Genetic ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/genetics ; Gastrointestinal Microbiome ; Genetic Techniques ; Genetic Variation ; Helicobacter pylori/genetics ; History, Medieval ; Humans ; Metagenomics/*methods ; Models, Genetic ; Mutation ; Plague/history/microbiology ; *Recombination, Genetic ; *Sequence Analysis, DNA ; Yersinia pestis/genetics ; }, abstract = {We present a robust, computationally efficient method (https://github.com/kussell-lab/mcorr) for inferring the parameters of homologous recombination in bacteria, which can be applied in diverse datasets, from whole-genome sequencing to metagenomic shotgun sequencing data. Using correlation profiles of synonymous substitutions, we determine recombination rates and diversity levels of the shared gene pool that has contributed to a given sample. We validated the recombination parameters using data from laboratory experiments. We determined the recombination parameters for a wide range of bacterial species, and inferred the distribution of shared gene pools for global Helicobacter pylori isolates. Using metagenomics data of the infant gut microbiome, we measured the recombination parameters of multidrug-resistant Escherichia coli ST131. Lastly, we analyzed ancient samples of bacterial DNA from the Copper Age 'Iceman' mummy and from 14th century victims of the Black Death, obtaining measurements of bacterial recombination rates and gene pool diversity of earlier eras.}, }
@article {pmid30643213, year = {2019}, author = {Ronda, C and Chen, SP and Cabral, V and Yaung, SJ and Wang, HH}, title = {Metagenomic engineering of the mammalian gut microbiome in situ.}, journal = {Nature methods}, volume = {16}, number = {2}, pages = {167-170}, doi = {10.1038/s41592-018-0301-y}, pmid = {30643213}, issn = {1548-7105}, support = {DP5 OD009172/OD/NIH HHS/United States ; T32 GM007367/GM/NIGMS NIH HHS/United States ; R01 DK118044/DK/NIDDK NIH HHS/United States ; R01 AI132403/AI/NIAID NIH HHS/United States ; F30 DK111145/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Cell Separation ; Escherichia coli/genetics ; Female ; Flow Cytometry ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology/physiology ; Gene Transfer Techniques ; Genome ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; Mice ; Mice, Inbred C57BL ; Microbiota/*genetics ; Plasmids/genetics ; Protein Engineering/*methods ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Engineering of microbial communities in open environments remains challenging. Here we describe a platform used to identify and modify genetically tractable mammalian microbiota by engineering community-wide horizontal gene transfer events in situ. With this approach, we demonstrate that diverse taxa in the mouse gut microbiome can be modified directly with a desired genetic payload. In situ microbiome engineering in living animals allows novel capabilities to be introduced into established communities in their native milieu.}, }
@article {pmid29870921, year = {2018}, author = {Zou, Y and Lin, M and Xiong, W and Wang, M and Zhang, J and Wang, M and Sun, Y}, title = {Metagenomic insights into the effect of oxytetracycline on microbial structures, functions and functional genes in sediment denitrification.}, journal = {Ecotoxicology and environmental safety}, volume = {161}, number = {}, pages = {85-91}, doi = {10.1016/j.ecoenv.2018.05.045}, pmid = {29870921}, issn = {1090-2414}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics/growth &amp; development/metabolism ; Bacterial Proteins/metabolism ; Bradyrhizobium ; *Denitrification ; Farms ; Genes, Bacterial ; Geologic Sediments ; Metagenomics ; Microbiota ; Nitrate Reductase/metabolism ; Nitrite Reductases/metabolism ; Nitrogen/*metabolism ; Nitrous Oxide/metabolism ; Oxytetracycline/*pharmacology ; Ponds ; Proteobacteria/metabolism ; Pseudomonas ; Sewage ; Water Microbiology ; Water Pollutants, Chemical/metabolism/*pharmacology ; }, abstract = {Denitrification is an indispensable pathway of nitrogen removal in aquatic ecosystems, and plays an important role in decreasing eutrophication induced by excessive reactive nitrogen pollution. Aquatic environments also suffer from antibiotic pollution due to runoff from farms and sewage systems. The aim of this study was to investigate the effect of oxytetracycline stress on denitrifying functional genes, the microbial community and metabolic pathways in sediments using high-throughput sequencing and metagenomic analysis. The oxytetracycline was observed to significantly inhibit the abundance of nirK and nosZ genes (P < 0.001). KEGG pathway annotation indicated that oxytetracycline treatment decreased the abundance of nitrate reductase, nitrite reductase and N2O reductase. Functional annotations revealed that oxytetracycline exposure decreased the abundance of the protein metabolism subsystem in the bacterial community. Metagenomic sequencing demonstrated that the abundance of Proteobacteria and Firmicutes increased with oxytetracycline exposure while the Actinobacteria decreased. In sediments, Pseudomonas and Bradyrhizobium were major contributors to denitrification and oxytetracycline exposure resulted in a decreased abundance of Bradyrhizobium. These results indicated that oxytetracycline residues influences the denitrifier community and may heighten occurrence of reactive nitrogen in aquatic ecosystems.}, }
@article {pmid31000700, year = {2019}, author = {Dong, X and Greening, C and Rattray, JE and Chakraborty, A and Chuvochina, M and Mayumi, D and Dolfing, J and Li, C and Brooks, JM and Bernard, BB and Groves, RA and Lewis, IA and Hubert, CRJ}, title = {Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1816}, doi = {10.1038/s41467-019-09747-0}, pmid = {31000700}, issn = {2041-1723}, mesh = {Acetates/metabolism ; Archaea/genetics/isolation &amp; purification/*metabolism ; Bacteria/genetics/isolation &amp; purification/*metabolism ; Geologic Sediments/chemistry/*microbiology ; Hydrocarbons/metabolism ; Hydrogen/metabolism ; Metagenome ; Metagenomics/methods ; Mexico ; Microbial Interactions/physiology ; Microbiota/*physiology ; Petroleum/*metabolism ; }, abstract = {The lack of microbial genomes and isolates from the deep seabed means that very little is known about the ecology of this vast habitat. Here, we investigate energy and carbon acquisition strategies of microbial communities from three deep seabed petroleum seeps (3 km water depth) in the Eastern Gulf of Mexico. Shotgun metagenomic analysis reveals that each sediment harbors diverse communities of chemoheterotrophs and chemolithotrophs. We recovered 82 metagenome-assembled genomes affiliated with 21 different archaeal and bacterial phyla. Multiple genomes encode enzymes for anaerobic oxidation of aliphatic and aromatic compounds, including those of candidate phyla Aerophobetes, Aminicenantes, TA06 and Bathyarchaeota. Microbial interactions are predicted to be driven by acetate and molecular hydrogen. These findings are supported by sediment geochemistry, metabolomics, and thermodynamic modelling. Overall, we infer that deep-sea sediments experiencing thermogenic hydrocarbon inputs harbor phylogenetically and functionally diverse communities potentially sustained through anaerobic hydrocarbon, acetate and hydrogen metabolism.}, }
@article {pmid30552020, year = {2018}, author = {Castellanos, JG and Woo, V and Viladomiu, M and Putzel, G and Lima, S and Diehl, GE and Marderstein, AR and Gandara, J and Perez, AR and Withers, DR and Targan, SR and Shih, DQ and Scherl, EJ and Longman, RS}, title = {Microbiota-Induced TNF-like Ligand 1A Drives Group 3 Innate Lymphoid Cell-Mediated Barrier Protection and Intestinal T Cell Activation during Colitis.}, journal = {Immunity}, volume = {49}, number = {6}, pages = {1077-1089.e5}, doi = {10.1016/j.immuni.2018.10.014}, pmid = {30552020}, issn = {1097-4180}, support = {R03 DK111852/DK/NIDDK NIH HHS/United States ; K08 DK099381/DK/NIDDK NIH HHS/United States ; UL1 TR002384/TR/NCATS NIH HHS/United States ; R01 AI125264/AI/NIAID NIH HHS/United States ; T32 GM007739/GM/NIGMS NIH HHS/United States ; K08 DK093578/DK/NIDDK NIH HHS/United States ; R01 DK114252/DK/NIDDK NIH HHS/United States ; R01 DK056328/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Aged ; Animals ; Colitis/genetics/*immunology/metabolism ; Female ; Humans ; Immunity, Innate/genetics/*immunology ; Interleukins/genetics/immunology/metabolism ; Intestinal Mucosa/immunology/metabolism/microbiology ; Lymphocyte Activation/genetics/immunology ; Lymphocytes/*immunology/metabolism ; Male ; Mice, Inbred C57BL ; Mice, Knockout ; Mice, Transgenic ; Microbiota/*immunology/physiology ; Middle Aged ; Phagocytes/cytology/immunology/metabolism ; T-Lymphocytes/immunology/metabolism ; Tumor Necrosis Factor Ligand Superfamily Member 15/genetics/*immunology/metabolism ; Young Adult ; }, abstract = {Inflammatory bowel disease (IBD) results from a dysregulated interaction between the microbiota and a genetically susceptible host. Genetic studies have linked TNFSF15 polymorphisms and its protein TNF-like ligand 1A (TL1A) with IBD, but the functional role of TL1A is not known. Here, we found that adherent IBD-associated microbiota induced TL1A release from CX3CR1+ mononuclear phagocytes (MNPs). Using cell-specific genetic deletion models, we identified an essential role for CX3CR1+MNP-derived TL1A in driving group 3 innate lymphoid cell (ILC3) production of interleukin-22 and mucosal healing during acute colitis. In contrast to this protective role in acute colitis, TL1A-dependent expression of co-stimulatory molecule OX40L in MHCII+ ILC3s during colitis led to co-stimulation of antigen-specific T cells that was required for chronic T cell colitis. These results identify a role for ILC3s in activating intestinal T cells and reveal a central role for TL1A in promoting ILC3 barrier immunity during colitis.}, }
@article {pmid30396006, year = {2019}, author = {Velikonja, A and Lipoglavšek, L and Zorec, M and Orel, R and Avguštin, G}, title = {Alterations in gut microbiota composition and metabolic parameters after dietary intervention with barley beta glucans in patients with high risk for metabolic syndrome development.}, journal = {Anaerobe}, volume = {55}, number = {}, pages = {67-77}, doi = {10.1016/j.anaerobe.2018.11.002}, pmid = {30396006}, issn = {1095-8274}, mesh = {Adult ; Aged ; Cholesterol/blood ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Diet Therapy/*methods ; Dietary Fiber/*administration &amp; dosage ; Double-Blind Method ; Fatty Acids, Volatile/analysis ; Feces/chemistry ; Female ; Gastrointestinal Microbiome/*drug effects ; Healthy Volunteers ; Hordeum/*chemistry ; Humans ; Male ; Metabolic Syndrome/*therapy ; Middle Aged ; Phylogeny ; Placebos/administration &amp; dosage ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Treatment Outcome ; beta-Glucans/*administration &amp; dosage ; }, abstract = {Metabolic syndrome is a complex disease that is exponentially increasing in the western world, and diet is one of the possible ways to improve the metabolic status of patients. Barley beta glucans are dietary fibres that show promise for improvement cholesterol levels and postprandial glucose response, but they have been rarely investigated in human trials with concurrent focus on gut microbiota. A double-blind, placebo-controlled, randomised clinical trial was conducted with 43 volunteers with high risk for metabolic syndrome development or with diagnosed metabolic syndrome. During a four-week intervention study, participants consumed experimental bread containing 6 g of barley beta glucans or equal bread but without beta glucans. After dietary intervention, total plasma cholesterol decreased in the test group (-0.26 ± 0.54, p = 0.019), but not in the control group. Short chain fatty acids (SCFA) composition in faeces significantly changed with increase of propionic acid in test group (43.2%, p = 0.045) and with decrease of acetic acid in control group (41.8%, p = 0.011). The microbiome analysis based on Illumina paired end sequencing of 16S rRNA genes showed a decrease in microbial diversity and richness in the test group. The pre-intervention gut microbiota composition showed higher abundance of health associated Bifidobacterium spp. and Akkermansia municiphila within cholesterol-responsive group, showing that diet-induced metabolic response is possibly dependent on individual gut microbiota composition.}, }
@article {pmid30356154, year = {2018}, author = {Solden, LM and Naas, AE and Roux, S and Daly, RA and Collins, WB and Nicora, CD and Purvine, SO and Hoyt, DW and Schückel, J and Jørgensen, B and Willats, W and Spalinger, DE and Firkins, JL and Lipton, MS and Sullivan, MB and Pope, PB and Wrighton, KC}, title = {Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem.}, journal = {Nature microbiology}, volume = {3}, number = {11}, pages = {1274-1284}, doi = {10.1038/s41564-018-0225-4}, pmid = {30356154}, issn = {2058-5276}, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Carbon/*metabolism ; Host Microbial Interactions ; Metabolic Networks and Pathways ; Metagenomics ; *Microbial Consortia ; Phylogeny ; Proteomics ; *Rumen/metabolism/microbiology/virology ; Ruminants ; Viruses/classification/genetics/isolation &amp; purification/metabolism ; Wood/metabolism ; }, abstract = {Because of their agricultural value, there is a great body of research dedicated to understanding the microorganisms responsible for rumen carbon degradation. However, we lack a holistic view of the microbial food web responsible for carbon processing in this ecosystem. Here, we sampled rumen-fistulated moose, allowing access to rumen microbial communities actively degrading woody plant biomass in real time. We resolved 1,193 viral contigs and 77 unique, near-complete microbial metagenome-assembled genomes, many of which lacked previous metabolic insights. Plant-derived metabolites were measured with NMR and carbohydrate microarrays to quantify the carbon nutrient landscape. Network analyses directly linked measured metabolites to expressed proteins from these unique metagenome-assembled genomes, revealing a genome-resolved three-tiered carbohydrate-fuelled trophic system. This provided a glimpse into microbial specialization into functional guilds defined by specific metabolites. To validate our proteomic inferences, the catalytic activity of a polysaccharide utilization locus from a highly connected metabolic hub genome was confirmed using heterologous gene expression. Viral detected proteins and linkages to microbial hosts demonstrated that phage are active controllers of rumen ecosystem function. Our findings elucidate the microbial and viral members, as well as their metabolic interdependencies, that support in situ carbon degradation in the rumen ecosystem.}, }
@article {pmid30349083, year = {2018}, author = {Palleja, A and Mikkelsen, KH and Forslund, SK and Kashani, A and Allin, KH and Nielsen, T and Hansen, TH and Liang, S and Feng, Q and Zhang, C and Pyl, PT and Coelho, LP and Yang, H and Wang, J and Typas, A and Nielsen, MF and Nielsen, HB and Bork, P and Wang, J and Vilsbøll, T and Hansen, T and Knop, FK and Arumugam, M and Pedersen, O}, title = {Recovery of gut microbiota of healthy adults following antibiotic exposure.}, journal = {Nature microbiology}, volume = {3}, number = {11}, pages = {1255-1265}, doi = {10.1038/s41564-018-0257-9}, pmid = {30349083}, issn = {2058-5276}, mesh = {Adolescent ; Adult ; Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/drug effects/genetics/isolation &amp; purification ; *Bacterial Physiological Phenomena ; Biodiversity ; Drug Resistance, Bacterial/genetics ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects/*physiology ; Genes, Bacterial ; Healthy Volunteers ; Humans ; Male ; Metagenomics ; Virulence Factors/genetics ; Young Adult ; }, abstract = {To minimize the impact of antibiotics, gut microorganisms harbour and exchange antibiotics resistance genes, collectively called their resistome. Using shotgun sequencing-based metagenomics, we analysed the partial eradication and subsequent regrowth of the gut microbiota in 12 healthy men over a 6-month period following a 4-day intervention with a cocktail of 3 last-resort antibiotics: meropenem, gentamicin and vancomycin. Initial changes included blooms of enterobacteria and other pathobionts, such as Enterococcus faecalis and Fusobacterium nucleatum, and the depletion of Bifidobacterium species and butyrate producers. The gut microbiota of the subjects recovered to near-baseline composition within 1.5 months, although 9 common species, which were present in all subjects before the treatment, remained undetectable in most of the subjects after 180 days. Species that harbour β-lactam resistance genes were positively selected for during and after the intervention. Harbouring glycopeptide or aminoglycoside resistance genes increased the odds of de novo colonization, however, the former also decreased the odds of survival. Compositional changes under antibiotic intervention in vivo matched results from in vitro susceptibility tests. Despite a mild yet long-lasting imprint following antibiotics exposure, the gut microbiota of healthy young adults are resilient to a short-term broad-spectrum antibiotics intervention and their antibiotics resistance gene carriage modulates their recovery processes.}, }
@article {pmid30126689, year = {2019}, author = {Schiattarella, GG and Sannino, A and Esposito, G and Perrino, C}, title = {Diagnostics and therapeutic implications of gut microbiota alterations in cardiometabolic diseases.}, journal = {Trends in cardiovascular medicine}, volume = {29}, number = {3}, pages = {141-147}, doi = {10.1016/j.tcm.2018.08.003}, pmid = {30126689}, issn = {1873-2615}, mesh = {Animals ; Anti-Bacterial Agents/administration &amp; dosage ; Bacteria/drug effects/enzymology/*metabolism ; Cardiovascular Diseases/diagnosis/*microbiology/therapy ; Dysbiosis ; Enzyme Inhibitors/therapeutic use ; Exercise ; *Gastrointestinal Microbiome/drug effects ; Healthy Diet ; Host-Pathogen Interactions ; Humans ; Metabolic Diseases/diagnosis/*microbiology/therapy ; Prebiotics/administration &amp; dosage ; Probiotics/administration &amp; dosage ; Risk Reduction Behavior ; }, abstract = {Alterations in gut microbiota composition and its metabolic activity are emerging as one of the most powerful determinants of cardiovascular disease. Although our knowledge of the precise molecular mechanisms by which gut microbiota influences cardiometabolic homeostasis is still limited, a growing body of knowledge has recently been uncovered about the potential modulation of microbiome for cardiovascular diagnostic and therapeutic aspects. The multitude of interactions between the microorganisms inhabiting the digestive tract and the host has been recognized crucial in the development and progression of atherosclerosis, obesity, diabetes and hypertension. Here, we summarize the role of gut microbiota in host physiology as well as in the pathophysiology of the most common cardio-metabolic disorders, discussing the potential therapeutic opportunities offered by interventions aimed at modifying microbiome composition and activity.}, }
@article {pmid30095241, year = {2019}, author = {Leis, ML and Costa, MO}, title = {Initial description of the core ocular surface microbiome in dogs: Bacterial community diversity and composition in a defined canine population.}, journal = {Veterinary ophthalmology}, volume = {22}, number = {3}, pages = {337-344}, doi = {10.1111/vop.12599}, pmid = {30095241}, issn = {1463-5224}, support = {419248//U of S Faculty Recruitment and Retention Program/ ; 100008920//U of S Faculty Recruitment and Retention Program/ ; }, mesh = {Animals ; Bacteria/*isolation &amp; purification ; Conjunctiva/*microbiology ; DNA, Bacterial/analysis ; Dogs/*microbiology ; Female ; High-Throughput Nucleotide Sequencing/veterinary ; Male ; Microbiota ; }, abstract = {OBJECTIVE: To characterize the bacterial community residing on the conjunctiva of clinically healthy dogs.<br><br>METHODS: Bacterial DNA from conjunctival swabs of 10 dogs with normal ocular examinations (both OD and OS, n = 20) was extracted, and 16S rRNA amplicons were sequenced using Illumina MiSeq 600. Resulting data were subjected to quality control steps, and analyzed for bacterial community richness and diversity, within- and between-group dissimilarity, and relative taxonomic composition.<br><br>RESULTS: High-quality reads (2.22 million bp) resulted in a mean of 159 068 sequences per sample. Bacterial community evenness and diversity was high when compared to other species, and did not significantly differ when samples were grouped by dogs or eyes. As expected, within-dog samples were more similar than between-dog samples. Taxonomic classification revealed that >95% of the community consisted of Firmicutes (34.9 ± 8.8%), Actinobacteria (26.3 ± 7.1%), Proteobacteria (26.2 ± 6.6%), and Bacteroidetes (9.4 ± 2.4%). Key members of the dog ocular surface microbiome, found in all dogs and corresponding to >25% of all identified OTUs (operational taxonomic units), were part of the Bifidobacteriaceae, Lachnospiraceae, Moraxellaceae, Corynebacteriaceae families. Genera previously thought to account for the majority of the core ocular surface microbiome in the dog (Staphylococcus sp., Streptococcus sp., and Bacillus sp.) were associated with only 2.63% of overall reads.<br><br>CONCLUSIONS: This study shows the feasibility of conjunctival swabs and high-throughput sequencing to profile the bacterial community structure of the canine ocular surface. A core ocular surface microbiome was identified for this canine population.}, }
@article {pmid29102544, year = {2018}, author = {Kang, Y and Cai, Y}, title = {Gut microbiota and hypertension: From pathogenesis to new therapeutic strategies.}, journal = {Clinics and research in hepatology and gastroenterology}, volume = {42}, number = {2}, pages = {110-117}, doi = {10.1016/j.clinre.2017.09.006}, pmid = {29102544}, issn = {2210-741X}, mesh = {*Gastrointestinal Microbiome ; Humans ; Hypertension/*microbiology/*therapy ; Probiotics/*therapeutic use ; }, abstract = {Hypertension (HTN) has become a global public health concern and a major risk factor for cardiovascular, cerebrovascular, and kidney diseases. The complex interplay of genetic and environmental influences is important for the development of the disease. Accumulating evidence has illustrated the association of dysbiosis of gut microbiota with hypertension. Certain gut microbial strains may play either a pathogenic or a protective role in the development of hypertension. Oral probiotics can therefore represent a therapeutic approach for hypertension treatment. However, the relevant scientific work has only just begun, and the available data in this field remain limited. Fortunately, recent technological developments that permit identification of microbes and their products using culture-independent molecular detection techniques. In this review, we summarize the role of gut microbiota in hypertension progression, and probiotics in the treatment of hypertension.}, }
@article {pmid28882888, year = {2017}, author = {Versalovic, J and Dore, J and Guarner, F and Luna, RA and Ringel, Y}, title = {Microbiome-Based Diagnostics: Ready for Applications in Laboratory Medicine?.}, journal = {Clinical chemistry}, volume = {63}, number = {11}, pages = {1674-1679}, doi = {10.1373/clinchem.2016.264473}, pmid = {28882888}, issn = {1530-8561}, mesh = {Communicable Diseases/*diagnosis ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome/drug effects/genetics/physiology ; Humans ; Noncommunicable Diseases/prevention &amp; control/therapy ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA ; }, }
@article {pmid29335555, year = {2018}, author = {Abu-Ali, GS and Mehta, RS and Lloyd-Price, J and Mallick, H and Branck, T and Ivey, KL and Drew, DA and DuLong, C and Rimm, E and Izard, J and Chan, AT and Huttenhower, C}, title = {Metatranscriptome of human faecal microbial communities in a cohort of adult men.}, journal = {Nature microbiology}, volume = {3}, number = {3}, pages = {356-366}, doi = {10.1038/s41564-017-0084-4}, pmid = {29335555}, issn = {2058-5276}, support = {K24 DK098311/DK/NIDDK NIH HHS/United States ; R01 CA202704/CA/NCI NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; U54 DK102557/DK/NIDDK NIH HHS/United States ; }, mesh = {Aged ; Aged, 80 and over ; Feces/*microbiology ; Follow-Up Studies ; Gastrointestinal Microbiome ; *Gene Expression Profiling ; Gene Regulatory Networks ; Humans ; Longitudinal Studies ; Male ; *Metagenome ; Metagenomics ; *Microbiota ; Phylogeny ; Prospective Studies ; }, abstract = {The gut microbiome is intimately related to human health, but it is not yet known which functional activities are driven by specific microorganisms' ecological configurations or transcription. We report a large-scale investigation of 372 human faecal metatranscriptomes and 929 metagenomes from a subset of 308 men in the Health Professionals Follow-Up Study. We identified a metatranscriptomic 'core' universally transcribed over time and across participants, often by different microorganisms. In contrast to the housekeeping functions enriched in this core, a 'variable' metatranscriptome included specialized pathways that were differentially expressed both across participants and among microorganisms. Finally, longitudinal metagenomic profiles allowed ecological interaction network reconstruction, which remained stable over the six-month timespan, as did strain tracking within and between participants. These results provide an initial characterization of human faecal microbial ecology into core, subject-specific, microorganism-specific and temporally variable transcription, and they differentiate metagenomically versus metatranscriptomically informative aspects of the human faecal microbiome.}, }
@article {pmid29335554, year = {2018}, author = {Mehta, RS and Abu-Ali, GS and Drew, DA and Lloyd-Price, J and Subramanian, A and Lochhead, P and Joshi, AD and Ivey, KL and Khalili, H and Brown, GT and DuLong, C and Song, M and Nguyen, LH and Mallick, H and Rimm, EB and Izard, J and Huttenhower, C and Chan, AT}, title = {Stability of the human faecal microbiome in a cohort of adult men.}, journal = {Nature microbiology}, volume = {3}, number = {3}, pages = {347-355}, pmid = {29335554}, issn = {2058-5276}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; K01 DK110267/DK/NIDDK NIH HHS/United States ; R01 CA202704/CA/NCI NIH HHS/United States ; U01 CA152904/CA/NCI NIH HHS/United States ; K24 DK098311/DK/NIDDK NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; UM1 CA167552/CA/NCI NIH HHS/United States ; R01 HL035464/HL/NHLBI NIH HHS/United States ; }, mesh = {Adult ; Aged ; Bacteria/classification ; Cohort Studies ; Feces/*microbiology ; Follow-Up Studies ; *Gastrointestinal Microbiome ; *Gene Expression ; Gene Expression Profiling ; Health Personnel/statistics &amp; numerical data ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenomics ; *Microbiota ; Middle Aged ; Prospective Studies ; }, abstract = {Characterizing the stability of the gut microbiome is important to exploit it as a therapeutic target and diagnostic biomarker. We metagenomically and metatranscriptomically sequenced the faecal microbiomes of 308 participants in the Health Professionals Follow-Up Study. Participants provided four stool samples-one pair collected 24-72 h apart and a second pair ~6 months later. Within-person taxonomic and functional variation was consistently lower than between-person variation over time. In contrast, metatranscriptomic profiles were comparably variable within and between subjects due to higher within-subject longitudinal variation. Metagenomic instability accounted for ~74% of corresponding metatranscriptomic instability. The rest was probably attributable to sources such as regulation. Among the pathways that were differentially regulated, most were consistently over- or under-transcribed at each time point. Together, these results suggest that a single measurement of the faecal microbiome can provide long-term information regarding organismal composition and functional potential, but repeated or short-term measures may be necessary for dynamic features identified by metatranscriptomics.}, }
@article {pmid29311644, year = {2018}, author = {Schirmer, M and Franzosa, EA and Lloyd-Price, J and McIver, LJ and Schwager, R and Poon, TW and Ananthakrishnan, AN and Andrews, E and Barron, G and Lake, K and Prasad, M and Sauk, J and Stevens, B and Wilson, RG and Braun, J and Denson, LA and Kugathasan, S and McGovern, DPB and Vlamakis, H and Xavier, RJ and Huttenhower, C}, title = {Dynamics of metatranscription in the inflammatory bowel disease gut microbiome.}, journal = {Nature microbiology}, volume = {3}, number = {3}, pages = {337-346}, pmid = {29311644}, issn = {2058-5276}, support = {U54 DK102557/DK/NIDDK NIH HHS/United States ; U01 DK062413/DK/NIDDK NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; P30 DK078392/DK/NIDDK NIH HHS/United States ; R01 DK092405/DK/NIDDK NIH HHS/United States ; P01 DK046763/DK/NIDDK NIH HHS/United States ; UL1 TR001881/TR/NCATS NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Child ; Colitis, Ulcerative/microbiology ; Crohn Disease/microbiology ; Dysbiosis ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Gene Expression Profiling ; Humans ; Inflammatory Bowel Diseases/*microbiology ; Longitudinal Studies ; Male ; *Metagenomics ; Phenotype ; *Transcription, Genetic ; Young Adult ; }, abstract = {Inflammatory bowel disease (IBD) is a group of chronic diseases of the digestive tract that affects millions of people worldwide. Genetic, environmental and microbial factors have been implicated in the onset and exacerbation of IBD. However, the mechanisms associating gut microbial dysbioses and aberrant immune responses remain largely unknown. The integrative Human Microbiome Project seeks to close these gaps by examining the dynamics of microbiome functionality in disease by profiling the gut microbiomes of >100 individuals sampled over a 1-year period. Here, we present the first results based on 78 paired faecal metagenomes and metatranscriptomes, and 222 additional metagenomes from 59 patients with Crohn's disease, 34 with ulcerative colitis and 24 non-IBD control patients. We demonstrate several cases in which measures of microbial gene expression in the inflamed gut can be informative relative to metagenomic profiles of functional potential. First, although many microbial organisms exhibited concordant DNA and RNA abundances, we also detected species-specific biases in transcriptional activity, revealing predominant transcription of pathways by individual microorganisms per host (for example, by Faecalibacterium prausnitzii). Thus, a loss of these organisms in disease may have more far-reaching consequences than suggested by their genomic abundances. Furthermore, we identified organisms that were metagenomically abundant but inactive or dormant in the gut with little or no expression (for example, Dialister invisus). Last, certain disease-specific microbial characteristics were more pronounced or only detectable at the transcript level, such as pathways that were predominantly expressed by different organisms in patients with IBD (for example, Bacteroides vulgatus and Alistipes putredinis). This provides potential insights into gut microbial pathway transcription that can vary over time, inducing phenotypical changes that are complementary to those linked to metagenomic abundances. The study's results highlight the strength of analysing both the activity and the presence of gut microorganisms to provide insight into the role of the microbiome in IBD.}, }
@article {pmid30521551, year = {2018}, author = {Vernocchi, P and Del Chierico, F and Russo, A and Majo, F and Rossitto, M and Valerio, M and Casadei, L and La Storia, A and De Filippis, F and Rizzo, C and Manetti, C and Paci, P and Ercolini, D and Marini, F and Fiscarelli, EV and Dallapiccola, B and Lucidi, V and Miccheli, A and Putignani, L}, title = {Gut microbiota signatures in cystic fibrosis: Loss of host CFTR function drives the microbiota enterophenotype.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0208171}, doi = {10.1371/journal.pone.0208171}, pmid = {30521551}, issn = {1932-6203}, mesh = {Anti-Bacterial Agents/adverse effects ; Bacteria/*isolation &amp; purification ; Child, Preschool ; Cohort Studies ; Cystic Fibrosis/drug therapy/genetics/*physiopathology ; Cystic Fibrosis Transmembrane Conductance Regulator/*genetics ; Dysbiosis/microbiology/physiopathology ; Exocrine Pancreatic Insufficiency/genetics/physiopathology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/drug effects/*physiology ; Host Microbial Interactions/physiology ; Humans ; Intestinal Mucosa/microbiology/*physiopathology ; Male ; Metabolomics ; Metagenomics ; Phenotype ; }, abstract = {BACKGROUND: Cystic fibrosis (CF) is a disorder affecting the respiratory, digestive, reproductive systems and sweat glands. This lethal hereditary disease has known or suspected links to the dysbiosis gut microbiota. High-throughput meta-omics-based approaches may assist in unveiling this complex network of symbiosis modifications.<br><br>OBJECTIVES: The aim of this study was to provide a predictive and functional model of the gut microbiota enterophenotype of pediatric patients affected by CF under clinical stability.<br><br>METHODS: Thirty-one fecal samples were collected from CF patients and healthy children (HC) (age range, 1-6 years) and analysed using targeted-metagenomics and metabolomics to characterize the ecology and metabolism of CF-linked gut microbiota. The multidimensional data were low fused and processed by chemometric classification analysis.<br><br>RESULTS: The fused metagenomics and metabolomics based gut microbiota profile was characterized by a high abundance of Propionibacterium, Staphylococcus and Clostridiaceae, including Clostridium difficile, and a low abundance of Eggerthella, Eubacterium, Ruminococcus, Dorea, Faecalibacterium prausnitzii, and Lachnospiraceae, associated with overexpression of 4-aminobutyrate (GABA), choline, ethanol, propylbutyrate, and pyridine and low levels of sarcosine, 4-methylphenol, uracil, glucose, acetate, phenol, benzaldehyde, and methylacetate. The CF gut microbiota pattern revealed an enterophenotype intrinsically linked to disease, regardless of age, and with dysbiosis uninduced by reduced pancreatic function and only partially related to oral antibiotic administration or lung colonization/infection.<br><br>CONCLUSIONS: All together, the results obtained suggest that the gut microbiota enterophenotypes of CF, together with endogenous and bacterial CF biomarkers, are direct expression of functional alterations at the intestinal level. Hence, it's possible to infer that CFTR impairment causes the gut ecosystem imbalance.This new understanding of CF host-gut microbiota interactions may be helpful to rationalize novel clinical interventions to improve the affected children's nutritional status and intestinal function.}, }
@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 &amp; 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 &amp; 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.}, }
@article {pmid29925880, year = {2018}, author = {Galand, PE and Pereira, O and Hochart, C and Auguet, JC and Debroas, D}, title = {A strong link between marine microbial community composition and function challenges the idea of functional redundancy.}, journal = {The ISME journal}, volume = {12}, number = {10}, pages = {2470-2478}, pmid = {29925880}, issn = {1751-7370}, mesh = {Bacteria/*classification/*genetics ; Metagenome ; Metagenomics ; Microbiota/*genetics/*physiology ; Time Factors ; }, abstract = {Marine microbes have tremendous diversity, but a fundamental question remains unanswered: why are there so many microbial species in the sea? The idea of functional redundancy for microbial communities has long been assumed, so that the high level of richness is often explained by the presence of different taxa that are able to conduct the exact same set of metabolic processes and that can readily replace each other. Here, we refute the hypothesis of functional redundancy for marine microbial communities by showing that a shift in the community composition altered the overall functional attributes of communities across different temporal and spatial scales. Our metagenomic monitoring of a coastal northwestern Mediterranean site also revealed that diverse microbial communities harbor a high diversity of potential proteins. Working with all information given by the metagenomes (all reads) rather than relying only on known genes (annotated orthologous genes) was essential for revealing the similarity between taxonomic and functional community compositions. Our finding does not exclude the possibility for a partial redundancy where organisms that share some specific function can coexist when they differ in other ecological requirements. It demonstrates, however, that marine microbial diversity reflects a tremendous diversity of microbial metabolism and highlights the genetic potential yet to be discovered in an ocean of microbes.}, }
@article {pmid30958827, year = {2019}, author = {Martí, JM}, title = {Recentrifuge: Robust comparative analysis and contamination removal for metagenomics.}, journal = {PLoS computational biology}, volume = {15}, number = {4}, pages = {e1006967}, doi = {10.1371/journal.pcbi.1006967}, pmid = {30958827}, issn = {1553-7358}, mesh = {Algorithms ; Big Data ; Computational Biology/methods ; DNA Contamination ; High-Throughput Nucleotide Sequencing ; Humans ; Internet ; Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA/*methods ; Software ; Whole Genome Sequencing/methods ; }, abstract = {Metagenomic sequencing is becoming widespread in biomedical and environmental research, and the pace is increasing even more thanks to nanopore sequencing. With a rising number of samples and data per sample, the challenge of efficiently comparing results within a specimen and between specimens arises. Reagents, laboratory, and host related contaminants complicate such analysis. Contamination is particularly critical in low microbial biomass body sites and environments, where it can comprise most of a sample if not all. Recentrifuge implements a robust method for the removal of negative-control and crossover taxa from the rest of samples. With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications. In addition to contamination-subtracted samples, Recentrifuge provides shared and exclusive taxa per sample, thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics. Regarding the first area, Recentrifuge's novel approach has already demonstrated its benefits showing that microbiomes of Arctic and Antarctic solar panels display similar taxonomic profiles. In the clinical field, to confirm Recentrifuge's ability to analyze complex metagenomes, we challenged it with data coming from a metagenomic investigation of RNA in plasma that suffered from critical contamination to the point of preventing any positive conclusion. Recentrifuge provided results that yielded new biological insight into the problem, supporting the growing evidence of a blood microbiota even in healthy individuals, mostly translocated from the gut, the oral cavity, and the genitourinary tract. We also developed a synthetic dataset carefully designed to rate the robust contamination removal algorithm, which demonstrated a significant improvement in specificity while retaining a high sensitivity even in the presence of cross-contaminants. Recentrifuge's official website is www.recentrifuge.org. The data and source code are anonymously and freely available on GitHub and PyPI. The computing code is licensed under the AGPLv3. The Recentrifuge Wiki is the most extensive and continually-updated source of documentation for Recentrifuge, covering installation, use cases, testing, and other useful topics.}, }
@article {pmid30955749, year = {2019}, author = {Fernandes, C and Kankonkar, H and Meena, RM and Menezes, G and Shenoy, BD and Khandeparker, R}, title = {Metagenomic analysis of tarball-associated bacteria from Goa, India.}, journal = {Marine pollution bulletin}, volume = {141}, number = {}, pages = {398-403}, doi = {10.1016/j.marpolbul.2019.02.040}, pmid = {30955749}, issn = {1879-3363}, mesh = {Biodegradation, Environmental ; Environmental Monitoring/*methods ; Humans ; India ; Marinobacter/genetics/isolation &amp; purification ; Metagenome/*genetics ; Metagenomics ; Microbiota/*genetics ; Petroleum/*analysis ; Polycyclic Aromatic Hydrocarbons/*analysis ; Proteobacteria/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Water Pollutants, Chemical/*analysis ; }, abstract = {The beaches of Goa state in India are frequently polluted with tarballs, specifically during pre-monsoon and monsoon seasons. Tarballs contain hydrocarbons, including polycyclic aromatic hydrocarbons, which pose significant environmental risks. Microbes associated with tarballs reportedly possess capabilities to degrade toxic hydrocarbons present in tarballs. In this study, bacterial diversity associated with tarballs from Vagator and Morjim beaches of north Goa was analysed based on V3-V4 regions of 16S rRNA gene sequenced using Illumina Miseq Platform. The Proteobacterial members were dominant in both Vagator (≥85.5%) and Morjim (≥94.0%) samples. Many of the identified taxa have been previously reported as hydrocarbon degraders (e.g. Halomonas, Marinobacter) or possible human pathogens (e.g. Acinetobacter, Klebsiella, Rhodococcus, Staphylococcus, Vibrio). This is the first study reported on a metagenomic analysis of bacteria associated with tarballs from Goa.}, }
@article {pmid29335567, year = {2018}, author = {Metch, JW and Burrows, ND and Murphy, CJ and Pruden, A and Vikesland, PJ}, title = {Metagenomic analysis of microbial communities yields insight into impacts of nanoparticle design.}, journal = {Nature nanotechnology}, volume = {13}, number = {3}, pages = {253-259}, doi = {10.1038/s41565-017-0029-3}, pmid = {29335567}, issn = {1748-3395}, mesh = {Acrylic Resins/chemistry/metabolism ; Bacteria/*genetics/metabolism ; Cetrimonium/chemistry/metabolism ; Gold/chemistry/*metabolism ; Metagenomics ; *Microbiota ; Nanoparticles/chemistry/*metabolism/ultrastructure ; Nanotubes/chemistry/ultrastructure ; Phylogeny ; Sewage/*microbiology ; Surface Properties ; }, abstract = {Next-generation DNA sequencing and metagenomic analysis provide powerful tools for the environmentally friendly design of nanoparticles. Herein we demonstrate this approach using a model community of environmental microbes (that is, wastewater-activated sludge) dosed with gold nanoparticles of varying surface coatings and morphologies. Metagenomic analysis was highly sensitive in detecting the microbial community response to gold nanospheres and nanorods with either cetyltrimethylammonium bromide or polyacrylic acid surface coatings. We observed that the gold-nanoparticle morphology imposes a stronger force in shaping the microbial community structure than does the surface coating. Trends were consistent in terms of the compositions of both taxonomic and functional genes, which include antibiotic resistance genes, metal resistance genes and gene-transfer elements associated with cell stress that are relevant to public health. Given that nanoparticle morphology remained constant, the potential influence of gold dissolution was minimal. Surface coating governed the nanoparticle partitioning between the bioparticulate and aqueous phases.}, }
@article {pmid30955771, year = {2019}, author = {Cotta, SR and Cadete, LL and van Elsas, JD and Andreote, FD and Dias, ACF}, title = {Exploring bacterial functionality in mangrove sediments and its capability to overcome anthropogenic activity.}, journal = {Marine pollution bulletin}, volume = {141}, number = {}, pages = {586-594}, doi = {10.1016/j.marpolbul.2019.03.001}, pmid = {30955771}, issn = {1879-3363}, mesh = {Bacteria/genetics/metabolism ; Biodiversity ; Brazil ; Carbon/metabolism ; Ecosystem ; Gene Transfer, Horizontal ; Geologic Sediments/*microbiology ; Metagenomics ; *Microbiota/genetics ; Sulfur/metabolism ; *Wetlands ; }, abstract = {Mangrove forests are highly productive yet vulnerable ecosystems that act as important carbon sinks (&quot;blue carbon&quot;). The objective of this work was to analyze the impact of anthropogenic activities on microbiome structure and functioning. The metagenomic analysis revealed that the taxonomic compositions were grossly similar across all mangrove microbiomes. Remarkably, these microbiomes, along the gradient of anthropogenic impact, showed fluctuations in the relative abundances of bacterial taxa predicted to be involved in sulfur cycling processes. Functions involved in sulfur metabolism, such as APS pathways (associated with sulfate reduction and sulfur oxidation processes) were prevalent across the microbiomes, being sox and dsrAB genes highly expressed on anthropogenically-impacted areas. Apparently, the oil-impacted microbiomes were more affected in taxonomic than in functional terms, as high functional redundancies were noted across them. The microbial gene diversity found was typical for a functional system, even following the previous disturbance.}, }
@article {pmid30918057, year = {2019}, author = {Thomas, M and Wongkuna, S and Ghimire, S and Kumar, R and Antony, L and Doerner, KC and Singery, A and Nelson, E and Woyengo, T and Chankhamhaengdecha, S and Janvilisri, T and Scaria, J}, title = {Gut Microbial Dynamics during Conventionalization of Germfree Chicken.}, journal = {mSphere}, volume = {4}, number = {2}, pages = {}, doi = {10.1128/mSphere.00035-19}, pmid = {30918057}, issn = {2379-5042}, mesh = {Animals ; Bacteria/*classification/isolation &amp; purification ; Bacteroidetes/classification/isolation &amp; purification ; Chickens/growth &amp; development ; DNA, Bacterial/genetics ; Firmicutes/classification/isolation &amp; purification ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; *Germ-Free Life ; *Host Microbial Interactions ; Metagenomics ; Phylogeny ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {A gnotobiotic Gallus gallus (chicken) model was developed to study the dynamics of intestinal microflora from hatching to 18 days of age employing metagenomics. Intestinal samples were collected from a local population of feral chickens and administered orally to germfree 3-day-old chicks. Animals were euthanized on days 9 and 18 postinoculation, and intestinal samples were collected and subjected to metagenomic analysis. On day 18, the five most prevalent phyla were Bacteroidetes (43.03 ± 3.19%), Firmicutes (38.51 ± 2.67%), Actinobacteria (6.77 ± 0.7%), Proteobacteria (6.38 ± 0.7%), and Spirochaetes (2.71 ± 0.55%). Principal-coordinate analysis showed that the day 18 variables clustered more closely than the day 9 variables, suggesting that the microbial communities had changed temporally. The Morista-Horn index values ranged from 0.7 to 1, indicating that the communities in the inoculum and in the day 9 and day 18 samples were more similar than dissimilar. The predicted functional profiles of the microbiomes of the inoculum and the day 9 and day 18 samples were also similar (values of 0.98 to 1). These results indicate that the gnotobiotic chicks stably maintained the phylogenetic diversity and predicted metabolic functionality of the inoculum community.IMPORTANCE The domestic chicken is the cornerstone of animal agriculture worldwide, with a flock population exceeding 40 billion birds/year. It serves as an economically valuable source of protein globally. The microbiome of poultry has important effects on chicken growth, feed conversion, immune status, and pathogen resistance. The aim of our research was to develop a gnotobiotic chicken model appropriate for the study chicken gut microbiota function. Our experimental model shows that young germfree chicks are able to colonize diverse sets of gut bacteria. Therefore, besides the use of this model to study mechanisms of gut microbiota interactions in the chicken gut, it could be also used for applied aspects such as determining the safety and efficacy of new probiotic strains derived from chicken gut microbiota.}, }
@article {pmid30894435, year = {2019}, author = {Majta, J and Odrzywolek, K and Milanovic, B and Hubar, V and Wrobel, S and Strycharz-Angrecka, E and Wojciechowski, S and Milanowska, K}, title = {Identification of Differentiating Metabolic Pathways between Infant Gut Microbiome Populations Reveals Depletion of Function-Level Adaptation to Human Milk in the Finnish Population.}, journal = {mSphere}, volume = {4}, number = {2}, pages = {}, doi = {10.1128/mSphereDirect.00152-19}, pmid = {30894435}, issn = {2379-5042}, mesh = {*Adaptation, Physiological ; Bacteroides/genetics/*metabolism ; Bifidobacterium/genetics/*metabolism ; Feces/microbiology ; Finland ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Genome, Bacterial ; Humans ; Infant ; *Metabolic Networks and Pathways ; Metagenomics ; Milk, Human/*chemistry ; Oligosaccharides/metabolism ; }, abstract = {A variety of autoimmune and allergy events are becoming increasingly common, especially in Western countries. Some pieces of research link such conditions with the composition of microbiota during infancy. In this period, the predominant form of nutrition for gut microbiota is oligosaccharides from human milk (HMO). A number of gut-colonizing strains, such as Bifidobacterium and Bacteroides, are able to utilize HMO, but only some Bifidobacterium strains have evolved to digest the specific composition of human oligosaccharides. Differences in the proportions of the two genera that are able to utilize HMO have already been associated with the frequency of allergies and autoimmune diseases in the Finnish and the Russian populations. Our results show that differences in terms of the taxonomic annotation do not explain the reason for the differences in the Bifidobacterium/Bacteroides ratio between the Finnish and the Russian populations. In this paper, we present the results of function-level analysis. Unlike the typical workflow for gene abundance analysis, BiomeScout technology explains the differences in the Bifidobacterium/Bacteroides ratio. Our research shows the differences in the abundances of the two enzymes that are crucial for the utilization of short type 1 oligosaccharides.IMPORTANCE Knowing the limitations of taxonomy-based research, there is an emerging need for the development of higher-resolution techniques. The significance of this research is demonstrated by the novel method used for the analysis of function-level metagenomes. BiomeScout-the presented technology-utilizes proprietary algorithms for the detection of differences between functionalities present in metagenomic samples.}, }
@article {pmid30628657, year = {2019}, author = {Chen, L and Li, H and Li, J and Chen, Y and Yang, Y}, title = {Lactobacillus rhamnosus GG treatment improves intestinal permeability and modulates microbiota dysbiosis in an experimental model of sepsis.}, journal = {International journal of molecular medicine}, volume = {43}, number = {3}, pages = {1139-1148}, doi = {10.3892/ijmm.2019.4050}, pmid = {30628657}, issn = {1791-244X}, mesh = {Animals ; Apoptosis ; Biomarkers ; Cell Proliferation ; Colon/metabolism/microbiology/pathology ; Disease Models, Animal ; *Dysbiosis ; *Gastrointestinal Microbiome ; Lactobacillus rhamnosus/*physiology ; Male ; Metagenome ; Metagenomics/methods ; Mice ; Mortality ; Permeability ; Phylogeny ; Probiotics/*administration &amp; dosage ; RNA, Ribosomal, 16S/genetics ; Sepsis/diagnosis/*metabolism/*microbiology/therapy ; }, abstract = {Decrease of 'health‑benefiting' microbes and increase of pathogenic bacteria (a condition termed dysbiosis) in intensive care unit patients is considered to induce or aggravate sepsis (gut‑origin sepsis). Orally administered probiotics have been effective in the prevention of nosocomial infections. However, the mechanisms of probiotic‑induced anti‑infection and anti‑sepsis remain to be explored. In the present study, 4‑week‑old C57BL6 mice were orally administrated with Lactobacillus rhamnosus GG (LGG) or normal saline (control) 4 weeks prior to cecal ligation and puncture (CLP). A subset of the mice were sacrificed at 24 h post‑CLP, and the others were used for survival studies. Ileum tissues, blood and fecal samples were collected. The survival rate of septic mice pretreated with LGG was significantly improved compared with untreated mice. The levels of inflammatory cytokines were reduced in LGG‑pretreated septic mice. A decrease of colonic proliferation and epithelial tight junctions and an increase of colonic apoptosis were observed in control septic CLP+saline mice. LGG pretreatment reversed the colonic proliferation, apoptosis and expression of tight junction proteins to the levels of the sham group. LGG pretreatment improved the richness and diversity of intestinal microbiota in septic mice. The principal coordinates analysis clustering plots revealed a significant separate clustering in microbiota structure between three groups. Bacteria associated with energy consumption, including Bacteroidetes, with opportunistic infection, including Proteobacteria, Staphylococcaceae and Enterococcaceae, lipopolysaccharide producers, including Enterobacteriaceae, and facultative anaerobes, such as Bacteroidaceae and Erysipelotrichaceae, increased in septic mice. By contrast, bacteria associated with energy harvest, including Firmicutes, intestinal barrier function regulators, including Akkermansia, hepatic function regulators, including Coprococcus and Oscillospira, and obligate anaerobes, including Prevotellaceae, decreased in septic mice. With LGG pretreatment, the sepsis‑induced microbiota dysbiosis was reversed. The present results elucidated the potential mechanism of LGG treatment in sepsis, by improving intestinal permeability and modulating microbiota dysbiosis.}, }
@article {pmid30596703, year = {2018}, author = {Quinn, O and Gruber, MAM and Brown, RL and Baty, JW and Bulgarella, M and Lester, PJ}, title = {A metatranscriptomic analysis of diseased social wasps (Vespula vulgaris) for pathogens, with an experimental infection of larvae and nests.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0209589}, doi = {10.1371/journal.pone.0209589}, pmid = {30596703}, issn = {1932-6203}, mesh = {Animals ; Gene Expression Profiling/methods ; *Host-Pathogen Interactions ; Larva/microbiology ; *Metagenome ; *Metagenomics ; *Microbiota ; Phylogeny ; Wasps/*microbiology/ultrastructure ; }, abstract = {Social wasps are a major pest in many countries around the world. Pathogens may influence wasp populations and could provide an option for population management via biological control. We investigated the pathology of nests of apparently healthy common wasps, Vespula vulgaris, with nests apparently suffering disease. First, next-generation sequencing and metatranscriptomic analysis were used to examine pathogen presence. The transcriptome of healthy and diseased V. vulgaris showed 27 known microbial phylotypes. Four of these were observed in diseased larvae alone (Aspergillus fumigatus, Moellerella wisconsensis, Moku virus, and the microsporidian Vavraia culicis). Kashmir Bee Virus (KBV) was found to be present in both healthy and diseased larvae. Moellerella wisconsensis is a human pathogen that was potentially misidentified in our wasps by the MEGAN analysis: it is more likely to be the related bacteria Hafnia alvei that is known to infect social insects. The closest identification to the putative pathogen identified as Vavraia culicis was likely to be another microsporidian Nosema vulgaris. PCR and subsequent Sanger sequencing using published or our own designed primers, confirmed the identity of Moellerella sp. (which may be Hafnia alvei), Aspergillus sp., KBV, Moku virus and Nosema. Secondly, we used an infection study by homogenising diseased wasp larvae and feeding them to entire nests of larvae in the laboratory. Three nests transinfected with diseased larvae all died within 19 days. No pathogen that we monitored, however, had a significantly higher prevalence in diseased than in healthy larvae. RT-qPCR analysis indicated that pathogen infections were significantly correlated, such as between KBV and Aspergillus sp. Social wasps clearly suffer from an array of pathogens, which may lead to the collapse of nests and larval death.}, }
@article {pmid28883460, year = {2017}, author = {Bridgewater, LC and Zhang, C and Wu, Y and Hu, W and Zhang, Q and Wang, J and Li, S and Zhao, L}, title = {Gender-based differences in host behavior and gut microbiota composition in response to high fat diet and stress in a mouse model.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {10776}, pmid = {28883460}, issn = {2045-2322}, mesh = {Animals ; *Behavior, Animal ; Computational Biology/methods ; *Diet, High-Fat ; Female ; *Gastrointestinal Microbiome ; Male ; Metagenome ; Metagenomics/methods ; Mice ; Sex Factors ; *Stress, Physiological ; }, abstract = {Obesity is associated with a high prevalence of mood disorders such as anxiety and depression. Both stress and high fat diet can alter the gut microbiota and contribute to obesity. To examine the interrelationships between obesity, stress, gut microbiota and mood disorders, obesity was induced in mice using a high fat diet, and the mice were subsequently stressed using a chronic unpredictable mild stress protocol. During the experiment, the composition of the gut microbiota was analyzed by 16 S rRNA gene high-throughput sequencing, and anxiety-like behaviors were measured. The results revealed distinct gender differences in the impacts of obesity and stress on anxiety-like behaviors, activity levels, and composition of the gut microbiota. Male mice were more vulnerable to the anxiogenic effects of the high fat diet, and obese male mice showed decreased locomotion activity in response to stress whereas obese female mice did not. In females, stress caused the gut microbiota of lean mice to more closely resemble that of obese mice. Taken together, these results suggest the importance of considering gender as a biological variable in studies on the role of gut microbiota in obesity-related mood disorders.}, }
@article {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 {pmid30232678, year = {2019}, author = {Osman, JR and Regeard, C and Badel, C and Fernandes, G and DuBow, MS}, title = {Variation of bacterial biodiversity from saline soils and estuary sediments present near the Mediterranean Sea coast of Camargue (France).}, journal = {Antonie van Leeuwenhoek}, volume = {112}, number = {3}, pages = {351-365}, doi = {10.1007/s10482-018-1164-z}, pmid = {30232678}, issn = {1572-9699}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Estuaries ; France ; Geologic Sediments/*microbiology ; Mediterranean Sea ; Metagenomics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Salinity is an important environmental factor influencing microbial community composition. To better understand this influence, we determined the bacterial communities present in 17 different sites of brackish sediment (underwater) and soil (surface) samples from the Camargue region (Rhône river delta) in southern France during the fall of 2013 and 2014 using pyrosequencing of the V3-V4 regions of the 16S rRNA genes amplified by PCR. This region is known for abundant flora and fauna and, though saline, 30% of rice consumed in France is grown here. We found that bacterial abundance in 1 g of soil or sediment, calculated by qPCR, was higher in sediments than in surface soil samples. Members belonging to the Proteobacteria, Bacteroidetes, Chloroflexi and Firmicutes phyla dominated the bacterial communities of sediment samples, while members belonging to the Proteobacteria, Bacteroidetes, Gemmatimonadetes, Actinobacteria, Firmicutes and Acidobacteria phyla dominated the bacterial communities of the soil samples. The most abundant bacterial genera present in the saline sediments and soils from the Camargue belonged mostly to halophilic and sulphate reducing bacteria, suggesting that the Camargue may be a valuable system to investigate saline, yet agriculturally productive, sediment and soil microbial ecosystem.}, }
@article {pmid29630505, year = {2018}, author = {Panebianco, C and Potenza, A and Andriulli, A and Pazienza, V}, title = {Exploring the microbiota to better understand gastrointestinal cancers physiology.}, journal = {Clinical chemistry and laboratory medicine}, volume = {56}, number = {9}, pages = {1400-1412}, doi = {10.1515/cclm-2017-1163}, pmid = {29630505}, issn = {1437-4331}, mesh = {Antineoplastic Agents/therapeutic use ; Colorectal Neoplasms/microbiology/pathology ; Drug Resistance, Neoplasm ; Esophageal Neoplasms/microbiology/pathology ; Gastrointestinal Neoplasms/drug therapy/microbiology/*pathology ; Humans ; Liver Neoplasms/metabolism/pathology ; *Microbiota ; Pancreatic Neoplasms/microbiology/pathology ; Stomach Neoplasms/microbiology/pathology ; }, abstract = {Gastrointestinal cancers account for around 40% of cancer-related deaths worldwide, representing a global health burden. There is a growing body of evidence highlighting the link between microbiota and gastrointestinal tumorigenesis and/or resistance to therapy. In the present manuscript, we reviewed the published studies on the relationship between the microbiota and the different gastrointestinal tumors, namely, gastric, colorectal and esophageal, including also the cancer of accessory organs such as liver and pancreas. There is an emergent interest in the manipulation of gastrointestinal microflora in order to understand the gastrointestinal tumorigenesis' processes and the establishment of chemoresistance mechanisms.}, }
@article {pmid30683956, year = {2019}, author = {Mahato, NK and Sharma, A and Singh, Y and Lal, R}, title = {Comparative metagenomic analyses of a high-altitude Himalayan geothermal spring revealed temperature-constrained habitat-specific microbial community and metabolic dynamics.}, journal = {Archives of microbiology}, volume = {201}, number = {3}, pages = {377-388}, doi = {10.1007/s00203-018-01616-6}, pmid = {30683956}, issn = {1432-072X}, support = {BT/PR15118/BCE/8/1141/2015//Department of Biotechnology, Ministry of Science and Technology/ ; }, mesh = {Altitude ; Archaea/classification/*genetics ; Bacteria/classification/*genetics ; Flagella/genetics ; Geologic Sediments/*microbiology ; Hot Springs/*microbiology ; Hot Temperature ; India ; Metagenome/*genetics ; Metagenomics/methods ; Microbiota/*genetics ; Phylogeny ; Temperature ; Type IV Secretion Systems/genetics ; }, abstract = {Metagenomic surveys across microbial mat (~ 55 °C) samples of high-altitude (1760 m above sea level) Himalayan geothermal springs have revealed specialized community enriched with niche-specific functions. In this study, we have performed metagenomic sequence-based analyses to get insights into taxonomic composition and functional potential of hyperthermophiles in water (~ 95 °C) and sediment samples (78-98 °C). Community analyses revealed predominance of thermophilic bacterial and archeal genera dwelling in water in contrast to microbial mats (55 °C), namely Methylophilus, Methyloversatilis, Emticicia, Caulobacter, Thermus, Enhydrobacter and Pyrobaculum. Sediment samples having surface temperature (~ 78 °C) were colonized by Pyrobaculum and Chloroflexus while genus Massilia was found to be inhabited in high-temperature sediments (~ 98 °C). Functional analyses of metagenomic sequences revealed genetic enrichment of genes such as type IV secretion system, flagellar assembly and two-component system in contrast to mats. Furthermore, inter-sample comparison of enriched microbial diversity among water, sediment and microbial mats revealed habitat-specific clustering of the samples within same environment highlighting the role of temperature dynamics in modulating community structure across different habitats in same niche. However, function-based analysis demonstrated site-specific clustering among sediment, microbial mat and water samples. Furthermore, a novel thermophilic genotype of the genus Emticicia (designated as strain MM) was reconstructed from metagenome data. This is a correlative study between three major habitats present in geothermal spring environment, i.e., water, sediment and microbial mats revealing greater phylogenetic and functional dispersion emphasizing changing habitat-specific dynamics with temperature.}, }
@article {pmid30604012, year = {2019}, author = {Tyagi, A and Singh, B and Billekallu Thammegowda, NK and Singh, NK}, title = {Shotgun metagenomics offers novel insights into taxonomic compositions, metabolic pathways and antibiotic resistance genes in fish gut microbiome.}, journal = {Archives of microbiology}, volume = {201}, number = {3}, pages = {295-303}, doi = {10.1007/s00203-018-1615-y}, pmid = {30604012}, issn = {1432-072X}, support = {YSS/2014/000269//Science and Engineering Research Board/ ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Aquaculture ; *Bacteria/classification/drug effects/genetics ; Carps/*microbiology ; Drug Resistance, Multiple, Bacterial/*genetics ; Fishes ; Gastrointestinal Microbiome/*genetics ; Gene Transfer, Horizontal ; Metabolic Networks and Pathways ; Metagenomics/methods ; Probiotics ; }, abstract = {Gut microbiota of freshwater carp (Labeo rohita) was investigated by shotgun metagenomics to understand its taxonomic composition and functional capabilities. With the presence of 36 phyla, 326 families and 985 genera, the fish gut microbiota was found to be quite diverse in nature. However, at the phylum level, more than three-fourths of gut microbes belonged to Proteobacteria. Very low prevalence of commonly used probiotic bacteria (Bacillus, Lactobacillus, Streptococcus, and Lactococcus) in fish gut suggested the need to search for alternative probiotics for aquaculture use. Biosynthesis pathways were found to be the most dominant (51%) followed by degradation (39%), energy metabolism (4%) and fermentation (2%). In conformity with herbivorous feeding habit of L. rohita, gut microbiome also had pathways for the degradation of cellulose, hemicellulose, chitin, pectin, starch, and other complex carbohydrates. High prevalence of Actinobacteria and antibiotic biosynthesis pathways in the fish gut microbiome indicated its potential for bioprospecting of potentially novel natural antibiotics. Fifty-one different types of antibiotic resistance genes (ARGs) belonging to 15 antimicrobial resistance (AMR) gene families and conferring resistance against 24 antibiotic types were detected in fish gut. Some of the ARGs for multi-drug resistance were also found to be located on sequences of plasmid origin. The presence of pathogenic bacteria and ARGs on plasmid sequences suggested the potential risk due to horizontal gene transfer in the confined gut environment. The role of ARGs in fish gut microbiome needs further investigations.}, }
@article {pmid29926341, year = {2019}, author = {Lladó Fernández, S and Větrovský, T and Baldrian, P}, title = {The concept of operational taxonomic units revisited: genomes of bacteria that are regarded as closely related are often highly dissimilar.}, journal = {Folia microbiologica}, volume = {64}, number = {1}, pages = {19-23}, doi = {10.1007/s12223-018-0627-y}, pmid = {29926341}, issn = {1874-9356}, support = {18-25706S//Czech Science Foundation/ ; LTT17022//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; }, mesh = {Bacteria/*classification/*genetics ; DNA, Bacterial/genetics ; Databases, Nucleic Acid ; Genes, Bacterial/genetics ; Genetic Variation ; Genome, Bacterial/*genetics ; Glycoside Hydrolases/genetics ; *Metagenomics ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The concept of operational taxonomic units (OTUs), which constructs &quot;mathematically&quot; defined taxa, is widely accepted and applied to describe bacterial communities using amplicon sequencing of 16S rRNA gene. OTUs are often used to infer functional traits since they are considered to fairly represent of community members. However, the link between molecular taxa, real taxa, and OTUs seems to be much more complicated. Strains of the same bacterial species (ideally belonging to the same OTU) typically only share some genes (the core genome), while other genes are strain-specific and unique. It is thus unclear to what extent are important functional traits homogeneous within an OTU and how correctly can functional traits be inferred for individual OTU members. Here, we have tested in silico the similarity of all genes and, more specifically, the set of genes encoding for glycoside hydrolases (GH) in bacterial genomes that belong to the same OTU. Genome similarity varied among OTUs, but as many as 5-78% of genes were not shared between the two bacterial genomes in the pair. The complement of GH families (the presence of gene families and the number of genes per family) differed in 95% of OTUs. In average, 43% of GH families either differed in gene counts or were present in one genome and absent in the other. These results show a serious limitation of the OTU-based approaches when used to infer the functional traits of bacterial communities and open the questions how to link environmental sequencing data and microbial functions.}, }
@article {pmid29803134, year = {2018}, author = {Duru, IC and Laine, P and Andreevskaya, M and Paulin, L and Kananen, S and Tynkkynen, S and Auvinen, P and Smolander, OP}, title = {Metagenomic and metatranscriptomic analysis of the microbial community in Swiss-type Maasdam cheese during ripening.}, journal = {International journal of food microbiology}, volume = {281}, number = {}, pages = {10-22}, doi = {10.1016/j.ijfoodmicro.2018.05.017}, pmid = {29803134}, issn = {1879-3460}, mesh = {Cheese/analysis/*microbiology ; Cold Temperature ; Fermentation ; Food Handling ; Gene Expression Regulation, Bacterial ; *Metagenomics ; Microbiota/genetics/*physiology ; Taste ; *Transcriptome ; }, abstract = {In Swiss-type cheeses, characteristic nut-like and sweet flavor develops during the cheese ripening due to the metabolic activities of cheese microbiota. Temperature changes during warm and cold room ripening, and duration of ripening can significantly change the gene expression of the cheese microbiota, which can affect the flavor formation. In this study, a metagenomic and metatranscriptomic analysis of Swiss-type Maasdam cheese was performed on samples obtained during ripening in the warm and cold rooms. We reconstructed four different bacterial genomes (Lactococcus lactis, Lactobacillus rhamnosus, Lactobacillus helveticus, and Propionibacterium freudenreichii subsp. shermanii strain JS) from the Maasdam cheese to near completeness. Based on the DNA and RNA mean coverage, Lc. lactis strongly dominated (~80-90%) within the cheese microbial community. Genome annotation showed the potential for the presence of several flavor forming pathways in these species, such as production of methanethiol, free fatty acids, acetoin, diacetyl, acetate, ethanol, and propionate. Using the metatranscriptomic data, we showed that, with the exception of Lc. lactis, the central metabolism of the microbiota was downregulated during cold room ripening suggesting that fewer flavor compounds such as acetoin and propionate were produced. In contrast, Lc. lactis genes related to the central metabolism, including the vitamin biosynthesis and homolactic fermentation, were upregulated during cold room ripening.}, }
@article {pmid29322618, year = {2018}, author = {Kato, S and Shibuya, T and Takaki, Y and Hirai, M and Nunoura, T and Suzuki, K}, title = {Genome-enabled metabolic reconstruction of dominant chemosynthetic colonizers in deep-sea massive sulfide deposits.}, journal = {Environmental microbiology}, volume = {20}, number = {2}, pages = {862-877}, doi = {10.1111/1462-2920.14032}, pmid = {29322618}, issn = {1462-2920}, mesh = {Carbon Dioxide/*metabolism ; Deltaproteobacteria/*genetics/*metabolism ; Ecosystem ; Geologic Sediments/*microbiology ; Metagenome/genetics ; Metagenomics ; Microbiota ; Nitrogen Fixation/genetics/*physiology ; Seawater/microbiology ; Sulfides/*metabolism ; Sulfur/*metabolism ; }, abstract = {Deep-sea massive sulfide deposits remaining after ceasing of hydrothermal activity potentially provide energy for a chemosynthetic ecosystem in the dark, cold marine environments. Although yet-uncultivated bacteria in the phylum Nitrospirae and the class Deltaproteobacteria are known to dominate the microbial communities of sulfide deposits at and below the seafloor, their metabolic capabilities remain largely elusive. Here, we reveal the metabolic potential of these yet-uncultivated bacteria in hydrothermally inactive sulfide deposits collected at the Southern Mariana Trough by seafloor drilling. Near-complete genomes of the predominant bacterial members were recovered from shotgun metagenomic sequences. The genomic capabilities for CO2 and N2 fixation suggest that these bacteria are primary producers in the microbial ecosystem. Their genomes also encode versatile chemolithotrophic energy metabolisms, such as the oxidation of H2 , sulfide and intermediate sulfur species including thiosulfate, all of which can be supplied by chemical reactions between seawater and metal sulfides. Notably, the presence of genes involved in thiosulfate oxidation in Nitrospirae and Deltaproteobacteria genomes is unusual. Our study strongly support the presence of a chemosynthetic ecosystem fuelled by the Earth's internal energy in the deep-sea massive sulfide deposits, and illustrates the unexpected metabolic capability of known bacterial taxonomic groups.}, }
@article {pmid29205750, year = {2018}, author = {Fortunato, CS and Larson, B and Butterfield, DA and Huber, JA}, title = {Spatially distinct, temporally stable microbial populations mediate biogeochemical cycling at and below the seafloor in hydrothermal vent fluids.}, journal = {Environmental microbiology}, volume = {20}, number = {2}, pages = {769-784}, doi = {10.1111/1462-2920.14011}, pmid = {29205750}, issn = {1462-2920}, mesh = {Archaea/*genetics/isolation &amp; purification/*metabolism ; Bacteria/*genetics/isolation &amp; purification/*metabolism ; Carbon/metabolism ; Chemoautotrophic Growth/*genetics ; Geologic Sediments/*microbiology ; Hydrogen/metabolism ; Hydrothermal Vents/*microbiology ; Metagenomics ; Microbiota/genetics ; Nitrogen/metabolism ; Pacific Ocean ; Phylogeny ; Population Dynamics ; Seawater/chemistry/microbiology ; Sulfur/metabolism ; }, abstract = {At deep-sea hydrothermal vents, microbial communities thrive across geochemical gradients above, at, and below the seafloor. In this study, we determined the gene content and transcription patterns of microbial communities and specific populations to understand the taxonomy and metabolism both spatially and temporally across geochemically different diffuse fluid hydrothermal vents. Vent fluids were examined via metagenomic, metatranscriptomic, genomic binning, and geochemical analyses from Axial Seamount, an active submarine volcano on the Juan de Fuca Ridge in the NE Pacific Ocean, from 2013 to 2015 at three different vents: Anemone, Marker 33, and Marker 113. Results showed that individual vent sites maintained microbial communities and specific populations over time, but with spatially distinct taxonomic, metabolic potential, and gene transcription profiles. The geochemistry and physical structure of each vent both played important roles in shaping the dominant organisms and metabolisms present at each site. Genomic binning identified key populations of SUP05, Aquificales and methanogenic archaea carrying out important transformations of carbon, sulfur, hydrogen, and nitrogen, with groups that appear unique to individual sites. This work highlights the connection between microbial metabolic processes, fluid chemistry, and microbial population dynamics at and below the seafloor and increases understanding of the role of hydrothermal vent microbial communities in deep ocean biogeochemical cycles.}, }
@article {pmid29088129, year = {2017}, author = {Pasolli, E and Schiffer, L and Manghi, P and Renson, A and Obenchain, V and Truong, DT and Beghini, F and Malik, F and Ramos, M and Dowd, JB and Huttenhower, C and Morgan, M and Segata, N and Waldron, L}, title = {Accessible, curated metagenomic data through ExperimentHub.}, journal = {Nature methods}, volume = {14}, number = {11}, pages = {1023-1024}, pmid = {29088129}, issn = {1548-7105}, support = {P41 HG004059/HG/NHGRI NIH HHS/United States ; R21 AI121784/AI/NIAID NIH HHS/United States ; U24 CA180996/CA/NCI NIH HHS/United States ; U41 HG004059/HG/NHGRI NIH HHS/United States ; }, mesh = {Computational Biology/*methods ; Gastrointestinal Microbiome/genetics ; Genome, Archaeal/genetics ; Genome, Bacterial/genetics ; Genome, Fungal/genetics ; Genome, Human/genetics ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; *Software ; Species Specificity ; }, }
@article {pmid30535578, year = {2019}, author = {Zhang, F and Zheng, W and Xue, Y and Yao, W}, title = {Suhuai suckling piglet hindgut microbiome-metabolome responses to different dietary copper levels.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {2}, pages = {853-868}, doi = {10.1007/s00253-018-9533-0}, pmid = {30535578}, issn = {1432-0614}, support = {JATS[2018]287//The earmarked fund for Jiangsu Agricultural Industry Technology System/ ; 31372321//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Animals, Newborn ; Blood Chemical Analysis ; Copper/*administration &amp; dosage ; Diet/*methods ; Feces/chemistry ; Gas Chromatography-Mass Spectrometry ; Gastrointestinal Microbiome/*drug effects ; High-Throughput Nucleotide Sequencing ; Metabolome/*drug effects ; Metabolomics ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Swine ; Trace Elements/*administration &amp; dosage ; }, abstract = {Unabsorbed copper accumulates in the hindgut of pigs that consume high levels of dietary copper, which enhances the coselection of antibiotic-resistant bacteria and is considered detrimental to the environment and to porcine health. In our study, a combination of 16S rRNA pyrosequencing and nontargeted metabolomics was used to investigate the microbiome-metabolome responses to dietary copper levels in the hindgut of suckling piglets. The results showed that the dietary copper level affected the abundance of several Clostridia genera and that the relative abundance of butyrate-producing bacteria, such as Coprococcus, Roseburia, and Acidaminococcus, was reduced in the 300 mg kg-1 (high) Cu group. Metabolomic analysis revealed that dietary copper levels affected protein and carbohydrate metabolites, protein biosynthesis, the urea cycle, galactose metabolism, gluconeogenesis, and amino acid metabolism (including the metabolism of arginine, proline, β-alanine, phenylalanine, tyrosine, and methionine). Furthermore, Pearson's correlation analysis showed that the abundance levels of Coprococcus (family Lachnospiraceae) and operational taxonomic unit (OTU) 18 (family Ruminococcaceae) were positively correlated with energy metabolism pathways (gluconeogenesis, glycolysis, and the pentose phosphate pathway). The abundance of Streptococcus was negatively correlated with amino acid metabolism pathways (protein biosynthesis, glycine, serine, threonine, methionine, phenylalanine, and tyrosine metabolism), and OTU583 and OTU1067 (family Rikenellaceae) were positively correlated with amino acid metabolism pathways. These results suggest that the copper levels consumed by LC (low-copper group) versus HC (high-copper group) animals alter the composition of the gut microbiota and modulate microbial metabolic pathways, which may further affect the health of suckling piglets.}, }
@article {pmid30474727, year = {2019}, author = {Meng, H and Zhou, Z and Wu, R and Wang, Y and Gu, JD}, title = {Diazotrophic microbial community and abundance in acidic subtropical natural and re-vegetated forest soils revealed by high-throughput sequencing of nifH gene.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {2}, pages = {995-1005}, doi = {10.1007/s00253-018-9466-7}, pmid = {30474727}, issn = {1432-0614}, support = {31470562//National Natural Science Foundation of China/ ; 701913//Hong Kong RGC GRF grant/ ; }, mesh = {Acids/analysis ; Archaea/*classification/enzymology/genetics/metabolism ; Bacteria/*classification/enzymology/genetics/metabolism ; Chemical Phenomena ; Forests ; *Genetic Variation ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Microbiota ; *Nitrogen Fixation ; Oxidoreductases/*genetics ; Seasons ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Biological nitrogen fixation (BNF) is an important natural biochemical process converting the inert dinitrogen gas (N2) in the atmosphere to ammonia (NH3) in the N cycle. In this study, the nifH gene was chosen to detect the diazotrophic microorganisms with high-throughput sequencing from five acidic forest soils, including three natural forests and two re-vegetated forests. Soil samples were taken in two seasons (summer and winter) at two depth layers (surface and lower depths). A dataset of 179,600 reads obtained from 20 samples were analyzed to provide the microbial community structure, diversity, abundance, and relationship with physiochemical parameters. Both archaea and bacteria were detected in these samples and diazotrophic bacteria were the dominant members contributing to the biological dinitrogen fixation in the acidic forest soils. Cyanobacteria, Firmicutes, Proteobacteria, Spirocheates, and Verrucomicrobia were observed, especially the Proteobacteria as the most abundant phylum. The core genera were Bradyrhizobium and Methylobacterium from α-Proteobacteia, and Desulfovibrio from δ-Proteobacteia in the phylum of Proteobacteia of these samples. The diversity indices and the gene abundances of all samples were higher in the surface layer than the lower layer. Diversity was apparently higher in re-vegetated forests than the natural forests. Significant positive correlation to the organic matter and nitrogen-related parameters was observed, but there was no significant seasonal variation on the community structure and diversity in these samples between the summer and winter. The application of high-throughput sequencing method provides a better understanding and more comprehensive information of diazotrophs in acidic forest soils than conventional and PCR-based ones.}, }
@article {pmid30368579, year = {2019}, author = {Zhu, L and Liao, R and Wu, N and Zhu, G and Yang, C}, title = {Heat stress mediates changes in fecal microbiome and functional pathways of laying hens.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {1}, pages = {461-472}, doi = {10.1007/s00253-018-9465-8}, pmid = {30368579}, issn = {1432-0614}, support = {CARS-40-K03//Agriculture Research System of China/ ; }, mesh = {Animals ; Chickens/*microbiology ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Heat-Shock Response/*physiology ; Lipids/blood ; Metabolic Networks and Pathways ; }, abstract = {Chicken gastrointestinal microbiota plays important roles in health, productivity, and disease. However, knowledge of the relationship between heat stress and the gut microbial ecosystem of poultry, especially laying hens, is still limited. Here, we aimed to provide important knowledge for heat stress intervention in the egg industry. We performed high-throughput sequencing metagenomics on fecal contents to unravel the microbial taxa and functional capacity of the gut microbiome of caged laying hens under heat stress. Results showed that the fecal microbial communities of laying hens were dominated by Firmicutes, Bacteroidetes, and Proteobacteria phyla. The Firmicutes were significantly decreased, and Bacteroidetes were increased in the fecal microbiota under heat stress. Functional prediction of these changes in microbiota revealed that metabolism-related pathways, including cysteine and methionine metabolism and benzoate degradation, were more abundant. Conversely, retinol metabolism and phenylpropanoid biosynthesis were decreased by heat stress, suggesting differences in metabolism between layers in different temperature environments. Clear contributions were identified between active taxa (genus level) and metabolic pathways, which were associated with the liver and intestinal dysfunction in layers. These data revealed that heat stress induced a significant taxonomic perturbation in the gut microbiome of caged laying hens. This was related to the negative effects of heat stress in poultry and provided important basic knowledge for heat stress intervention.}, }
@article {pmid30362076, year = {2019}, author = {Almeida, OGG and De Martinis, ECP}, title = {Bioinformatics tools to assess metagenomic data for applied microbiology.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {1}, pages = {69-82}, doi = {10.1007/s00253-018-9464-9}, pmid = {30362076}, issn = {1432-0614}, support = {17/13759-6//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 6762/2006-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico (BR)/ ; }, mesh = {Biodiversity ; Computational Biology/*methods ; Gene Library ; High-Throughput Nucleotide Sequencing/methods ; Industrial Microbiology/*methods ; Metagenomics/*methods/statistics &amp; numerical data ; Phylogeny ; Quality Control ; }, abstract = {The reduction of the price of DNA sequencing has resulted in the emergence of large data sets to handle and analyze, especially in microbial ecosystems, which are characterized by high taxonomic and functional diversities. To assess the properties of these complex ecosystems, a conceptual background of the application of NGS technology and bioinformatics analysis to metagenomics is required. Accordingly, this article presents an overview of the evolution of knowledge of microbial ecology from traditional culture-dependent methods to culture-independent methods and the last frontier in knowledge, metagenomics. Topics that will be covered include sample preparation for NGS, starting with total DNA extraction and library preparation, followed by a brief discussion of the chemistry of NGS to help provide an understanding of which bioinformatics pipeline approach may be helpful for achieving a researcher's goals. The importance of selecting appropriate sequencing coverage and depth parameters to obtain a suitable measure of microbial diversity is discussed. As all DNA sequencing processes produce base-calling errors that compromise data analysis, including genome assembly and microbial functional analysis, dedicated software is presented and conceptually discussed with regard to potential applications in the general microbial ecology field.}, }
@article {pmid30354816, year = {2018}, author = {Ganesh, BP and Nelson, JW and Eskew, JR and Ganesan, A and Ajami, NJ and Petrosino, JF and Bryan, RM and Durgan, DJ}, title = {Prebiotics, Probiotics, and Acetate Supplementation Prevent Hypertension in a Model of Obstructive Sleep Apnea.}, journal = {Hypertension (Dallas, Tex. : 1979)}, volume = {72}, number = {5}, pages = {1141-1150}, pmid = {30354816}, issn = {1524-4563}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; R01 HL134838/HL/NHLBI NIH HHS/United States ; R01 NS080531/NS/NINDS NIH HHS/United States ; }, mesh = {Acetates/*therapeutic use ; Animals ; Blood Pressure/physiology ; Disease Models, Animal ; Gastrointestinal Microbiome/physiology ; Hypertension/complications/*prevention &amp; control ; Male ; *Prebiotics ; *Probiotics ; Rats ; Rats, Long-Evans ; Sleep Apnea, Obstructive/*complications ; }, abstract = {Disruption of the gut microbiota, termed gut dysbiosis, has been described in animal models of hypertension and hypertensive patients. We have shown that gut dysbiosis plays a causal role in the development of hypertension in a rat model of obstructive sleep apnea (OSA). Functional analysis of the dysbiotic microbiota in OSA demonstrates a loss of short chain fatty acid-producing bacteria. However, measurements of short chain fatty acid concentrations and testing of their role in blood pressure regulation are lacking. We hypothesized that reduced short chain fatty acids in the gut are responsible for OSA-induced hypertension. OSA significantly increased systolic blood pressure at 7 and 14 days (P<0.05), an effect that was abolished by the probiotic Clostridium butyricum or the prebiotic Hylon VII. The 16S rRNA analysis identified several short chain fatty acid-producing bacteria that were significantly increased by Cbutyricum and Hylon treatment. Acetate concentration in the cecum was decreased by 48% after OSA (P<0.05), an effect that was prevented by Cbutyricum and Hylon. Cbutyricum and Hylon reduced OSA-induced dysbiosis, epithelial goblet cell loss, mucus barrier thinning, and activation of brain microglia (P<0.05 for each). To examine the role of acetate in OSA-induced hypertension, we chronically infused acetate into the cecum during 2 weeks of sham or OSA. Restoring cecal acetate concentration prevented OSA-induced gut inflammation and hypertension (P<0.05). These studies identify acetate as a key player in OSA-induced hypertension. We demonstrate that various methods to increase cecal acetate concentrations are protective from the adverse effects of OSA on the microbiota, gut, brain, and blood pressure.}, }
@article {pmid30275573, year = {2018}, author = {Gonzalez, A and Navas-Molina, JA and Kosciolek, T and McDonald, D and Vázquez-Baeza, Y and Ackermann, G and DeReus, J and Janssen, S and Swafford, AD and Orchanian, SB and Sanders, JG and Shorenstein, J and Holste, H and Petrus, S and Robbins-Pianka, A and Brislawn, CJ and Wang, M and Rideout, JR and Bolyen, E and Dillon, M and Caporaso, JG and Dorrestein, PC and Knight, R}, title = {Qiita: rapid, web-enabled microbiome meta-analysis.}, journal = {Nature methods}, volume = {15}, number = {10}, pages = {796-798}, pmid = {30275573}, issn = {1548-7105}, support = {R01 HG004872/HG/NHGRI NIH HHS/United States ; R01 HL140976/HL/NHLBI NIH HHS/United States ; R01 MD011389/MD/NIMHD NIH HHS/United States ; }, mesh = {Computational Biology/*methods ; Humans ; *Internet ; *Metagenomics ; *Microbiota ; *Software ; User-Computer Interface ; }, abstract = {Multi-omic insights into microbiome function and composition typically advance one study at a time. However, in order for relationships across studies to be fully understood, data must be aggregated into meta-analyses. This makes it possible to generate new hypotheses by finding features that are reproducible across biospecimens and data layers. Qiita dramatically accelerates such integration tasks in a web-based microbiome-comparison platform, which we demonstrate with Human Microbiome Project and Integrative Human Microbiome Project (iHMP) data.}, }
@article {pmid29556105, year = {2018}, author = {Beller, HR and Rodrigues, AV and Zargar, K and Wu, YW and Saini, AK and Saville, RM and Pereira, JH and Adams, PD and Tringe, SG and Petzold, CJ and Keasling, JD}, title = {Discovery of enzymes for toluene synthesis from anoxic microbial communities.}, journal = {Nature chemical biology}, volume = {14}, number = {5}, pages = {451-457}, doi = {10.1038/s41589-018-0017-4}, pmid = {29556105}, issn = {1552-4469}, mesh = {Acidobacteria/enzymology/genetics/isolation &amp; purification ; Anaerobiosis ; Bacteria/*enzymology/genetics ; Biomass ; Carboxy-Lyases/metabolism ; Catalysis ; Genes, Bacterial ; Geologic Sediments/microbiology ; Lakes/microbiology ; Lignin/chemistry ; Likelihood Functions ; Metagenomics ; *Microbiota ; Phenylacetates/chemistry ; Phylogeny ; Proteomics ; Recombinant Proteins/metabolism ; Sewage/microbiology ; Toluene/*metabolism ; }, abstract = {Microbial toluene biosynthesis was reported in anoxic lake sediments more than three decades ago, but the enzyme catalyzing this biochemically challenging reaction has never been identified. Here we report the toluene-producing enzyme PhdB, a glycyl radical enzyme of bacterial origin that catalyzes phenylacetate decarboxylation, and its cognate activating enzyme PhdA, a radical S-adenosylmethionine enzyme, discovered in two distinct anoxic microbial communities that produce toluene. The unconventional process of enzyme discovery from a complex microbial community (>300,000 genes), rather than from a microbial isolate, involved metagenomics- and metaproteomics-enabled biochemistry, as well as in vitro confirmation of activity with recombinant enzymes. This work expands the known catalytic range of glycyl radical enzymes (only seven reaction types had been characterized previously) and aromatic-hydrocarbon-producing enzymes, and will enable first-time biochemical synthesis of an aromatic fuel hydrocarbon from renewable resources, such as lignocellulosic biomass, rather than from petroleum.}, }
@article {pmid30936548, year = {2019}, author = {Thomas, AM and Manghi, P and Asnicar, F and Pasolli, E and Armanini, F and Zolfo, M and Beghini, F and Manara, S and Karcher, N and Pozzi, C and Gandini, S and Serrano, D and Tarallo, S and Francavilla, A and Gallo, G and Trompetto, M and Ferrero, G and Mizutani, S and Shiroma, H and Shiba, S and Shibata, T and Yachida, S and Yamada, T and Wirbel, J and Schrotz-King, P and Ulrich, CM and Brenner, H and Arumugam, M and Bork, P and Zeller, G and Cordero, F and Dias-Neto, E and Setubal, JC and Tett, A and Pardini, B and Rescigno, M and Waldron, L and Naccarati, A and Segata, N}, title = {Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation.}, journal = {Nature medicine}, volume = {25}, number = {4}, pages = {667-678}, doi = {10.1038/s41591-019-0405-7}, pmid = {30936548}, issn = {1546-170X}, mesh = {Biomarkers, Tumor/metabolism ; Choline/*metabolism ; Cohort Studies ; Colorectal Neoplasms/diagnosis/*metabolism/*microbiology ; Databases, Genetic ; Gastrointestinal Microbiome ; Humans ; Lyases/genetics/metabolism ; *Metagenomics ; Species Specificity ; }, abstract = {Several studies have investigated links between the gut microbiome and colorectal cancer (CRC), but questions remain about the replicability of biomarkers across cohorts and populations. We performed a meta-analysis of five publicly available datasets and two new cohorts and validated the findings on two additional cohorts, considering in total 969 fecal metagenomes. Unlike microbiome shifts associated with gastrointestinal syndromes, the gut microbiome in CRC showed reproducibly higher richness than controls (P < 0.01), partially due to expansions of species typically derived from the oral cavity. Meta-analysis of the microbiome functional potential identified gluconeogenesis and the putrefaction and fermentation pathways as being associated with CRC, whereas the stachyose and starch degradation pathways were associated with controls. Predictive microbiome signatures for CRC trained on multiple datasets showed consistently high accuracy in datasets not considered for model training and independent validation cohorts (average area under the curve, 0.84). Pooled analysis of raw metagenomes showed that the choline trimethylamine-lyase gene was overabundant in CRC (P = 0.001), identifying a relationship between microbiome choline metabolism and CRC. The combined analysis of heterogeneous CRC cohorts thus identified reproducible microbiome biomarkers and accurate disease-predictive models that can form the basis for clinical prognostic tests and hypothesis-driven mechanistic studies.}, }
@article {pmid29942096, year = {2018}, author = {Hoyles, L and Fernández-Real, JM and Federici, M and Serino, M and Abbott, J and Charpentier, J and Heymes, C and Luque, JL and Anthony, E and Barton, RH and Chilloux, J and Myridakis, A and Martinez-Gili, L and Moreno-Navarrete, JM and Benhamed, F and Azalbert, V and Blasco-Baque, V and Puig, J and Xifra, G and Ricart, W and Tomlinson, C and Woodbridge, M and Cardellini, M and Davato, F and Cardolini, I and Porzio, O and Gentileschi, P and Lopez, F and Foufelle, F and Butcher, SA and Holmes, E and Nicholson, JK and Postic, C and Burcelin, R and Dumas, ME}, title = {Molecular phenomics and metagenomics of hepatic steatosis in non-diabetic obese women.}, journal = {Nature medicine}, volume = {24}, number = {7}, pages = {1070-1080}, pmid = {29942096}, issn = {1546-170X}, support = {MR/L01632X/1//Medical Research Council/United Kingdom ; MR/M501797/1//Medical Research Council/United Kingdom ; }, mesh = {Animals ; Cells, Cultured ; Cohort Studies ; Confounding Factors (Epidemiology) ; Diabetes Mellitus/*genetics ; Fecal Microbiota Transplantation ; Female ; Hepatocytes/metabolism ; Humans ; Metabolome ; Metabolomics ; *Metagenomics ; Mice ; Microbiota ; Non-alcoholic Fatty Liver Disease/*genetics ; Obesity/*genetics ; Phenotype ; Transcriptome/genetics ; }, abstract = {Hepatic steatosis is a multifactorial condition that is often observed in obese patients and is a prelude to non-alcoholic fatty liver disease. Here, we combine shotgun sequencing of fecal metagenomes with molecular phenomics (hepatic transcriptome and plasma and urine metabolomes) in two well-characterized cohorts of morbidly obese women recruited to the FLORINASH study. We reveal molecular networks linking the gut microbiome and the host phenome to hepatic steatosis. Patients with steatosis have low microbial gene richness and increased genetic potential for the processing of dietary lipids and endotoxin biosynthesis (notably from Proteobacteria), hepatic inflammation and dysregulation of aromatic and branched-chain amino acid metabolism. We demonstrated that fecal microbiota transplants and chronic treatment with phenylacetic acid, a microbial product of aromatic amino acid metabolism, successfully trigger steatosis and branched-chain amino acid metabolism. Molecular phenomic signatures were predictive (area under the curve = 87%) and consistent with the gut microbiome having an effect on the steatosis phenome (>75% shared variation) and, therefore, actionable via microbiome-based therapies.}, }
@article {pmid29702634, year = {2018}, author = {Eisenstein, M}, title = {Microbiology: making the best of PCR bias.}, journal = {Nature methods}, volume = {15}, number = {5}, pages = {317-320}, pmid = {29702634}, issn = {1548-7105}, mesh = {DNA, Bacterial/genetics ; *Metagenomics ; Microbiota/*genetics ; Polymerase Chain Reaction/*methods ; Selection Bias ; }, }
@article {pmid29045670, year = {2018}, author = {Houghton, D and Stewart, CJ and Stamp, C and Nelson, A and Aj Ami, NJ and Petrosino, JF and Wipat, A and Trenell, MI and Turnbull, DM and Greaves, LC}, title = {Impact of Age-Related Mitochondrial Dysfunction and Exercise on Intestinal Microbiota Composition.}, journal = {The journals of gerontology. Series A, Biological sciences and medical sciences}, volume = {73}, number = {5}, pages = {571-578}, pmid = {29045670}, issn = {1758-535X}, support = {G0700718//Medical Research Council/United Kingdom ; MR/L016354/1//Medical Research Council/United Kingdom ; P30 DK056338/DK/NIDDK NIH HHS/United States ; SRF-2011-04-017//Department of Health/United Kingdom ; //Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Aging/*physiology ; Animals ; Feces/microbiology ; *Gastrointestinal Microbiome ; Mice ; Mitochondrial Diseases/*physiopathology ; *Physical Conditioning, Animal ; Random Allocation ; Sedentary Behavior ; }, abstract = {Mitochondrial dysfunction is prevalent in the aging gastrointestinal tract. We investigated whether mitochondrial function in aging colonic crypts and exercise influences microbial gut communities in mice. Twelve PolgAmut/mut mice were randomly divided into a sedentary and exercise group at 4 months. Seven-aged matched PolgA+/+ mice remained sedentary throughout. Stool samples were collected at 4, 7, and 11 months, and bacterial profiling was achieved through 16S rRNA sequencing profiling. Mitochondrial enzyme activity was assessed in colonic epithelial crypts at 11 months for PolgAmut/mut and PolgA+/+ mice. Sedentary and exercised PolgAmut/mut mice had significantly higher levels of mitochondrial dysfunction than PolgA+/+ mice (78%, 77%, and 1% of crypts, respectively). Bacterial profiles of sedentary PolgAmut/mut mice were significantly different from the sedentary PolgA+/+ mice, with increases in Lactobacillus and Mycoplasma, and decreases in Alistipes, Odoribacter, Anaeroplasma, Rikenella, Parabacteroides, and Allobaculum in the PolgAmut/mut mice. Exercise did not have any impact upon gut mitochondrial dysfunction; however, exercise did increase gut microbiota diversity and significantly increased bacterial genera Mucispirillum and Desulfovibrio. Mitochondrial dysfunction is associated with changes in the gut microbiota. Endurance exercise moderated some of these changes, establishing that environmental factors can influence gut microbiota, despite mitochondrial dysfunction.}, }
@article {pmid28967193, year = {2018}, author = {De Corte, D and Srivastava, A and Koski, M and Garcia, JAL and Takaki, Y and Yokokawa, T and Nunoura, T and Elisabeth, NH and Sintes, E and Herndl, GJ}, title = {Metagenomic insights into zooplankton-associated bacterial communities.}, journal = {Environmental microbiology}, volume = {20}, number = {2}, pages = {492-505}, pmid = {28967193}, issn = {1462-2920}, support = {268595//European Research Council/International ; }, mesh = {Animals ; Atlantic Ocean ; Bacteria/classification/*genetics/isolation &amp; purification/*metabolism ; *Metagenome ; Metagenomics ; Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Zooplankton/*microbiology ; }, abstract = {Zooplankton and microbes play a key role in the ocean's biological cycles by releasing and consuming copious amounts of particulate and dissolved organic matter. Additionally, zooplankton provide a complex microhabitat rich in organic and inorganic nutrients in which bacteria thrive. In this study, we assessed the phylogenetic composition and metabolic potential of microbial communities associated with crustacean zooplankton species collected in the North Atlantic. Using Illumina sequencing of the 16S rRNA gene, we found significant differences between the microbial communities associated with zooplankton and those inhabiting the surrounding seawater. Metagenomic analysis of the zooplankton-associated microbial community revealed a highly specialized bacterial community able to exploit zooplankton as microhabitat and thus, mediating biogeochemical processes generally underrepresented in the open ocean. The zooplankton-associated bacterial community is able to colonize the zooplankton's internal and external surfaces using a large set of adhesion mechanisms and to metabolize complex organic compounds released or exuded by the zooplankton such as chitin, taurine and other complex molecules. Moreover, the high number of genes involved in iron and phosphorus metabolisms in the zooplankton-associated microbiome suggests that this zooplankton-associated bacterial community mediates specific biogeochemical processes (through the proliferation of specific taxa) that are generally underrepresented in the ambient waters.}, }
@article {pmid28874832, year = {2017}, author = {Minter, MR and Hinterleitner, R and Meisel, M and Zhang, C and Leone, V and Zhang, X and Oyler-Castrillo, P and Zhang, X and Musch, MW and Shen, X and Jabri, B and Chang, EB and Tanzi, RE and Sisodia, SS}, title = {Antibiotic-induced perturbations in microbial diversity during post-natal development alters amyloid pathology in an aged APPSWE/PS1ΔE9 murine model of Alzheimer's disease.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {10411}, pmid = {28874832}, issn = {2045-2322}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; }, mesh = {Alzheimer Disease/*etiology/metabolism/pathology ; Amyloid beta-Protein Precursor/*genetics/metabolism ; Amyloidosis/*genetics/metabolism/pathology ; Animals ; Anti-Bacterial Agents/*pharmacology ; Biodiversity ; Biomarkers ; Brain/metabolism/pathology ; Disease Models, Animal ; Gastrointestinal Microbiome ; Inflammation Mediators/metabolism ; Male ; Metagenome ; Metagenomics/methods ; Mice ; Mice, Transgenic ; Microbiota/*drug effects ; Neuroimmunomodulation/drug effects/genetics/immunology ; Plaque, Amyloid/etiology/metabolism/pathology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Recent evidence suggests the commensal microbiome regulates host immunity and influences brain function; findings that have ramifications for neurodegenerative diseases. In the context of Alzheimer's disease (AD), we previously reported that perturbations in microbial diversity induced by life-long combinatorial antibiotic (ABX) selection pressure in the APPSWE/PS1ΔE9 mouse model of amyloidosis is commensurate with reductions in amyloid-β (Aβ) plaque pathology and plaque-localised gliosis. Considering microbiota-host interactions, specifically during early post-natal development, are critical for immune- and neuro-development we now examine the impact of microbial community perturbations induced by acute ABX exposure exclusively during this period in APPSWE/PS1ΔE9 mice. We show that early post-natal (P) ABX treatment (P14-P21) results in long-term alterations of gut microbial genera (predominantly Lachnospiraceae and S24-7) and reduction in brain Aβ deposition in aged APPSWE/PS1ΔE9 mice. These mice exhibit elevated levels of blood- and brain-resident Foxp3+ T-regulatory cells and display an alteration in the inflammatory milieu of the serum and cerebrospinal fluid. Finally, we confirm that plaque-localised microglia and astrocytes are reduced in ABX-exposed mice. These findings suggest that ABX-induced microbial diversity perturbations during post-natal stages of development coincide with altered host immunity mechanisms and amyloidosis in a murine model of AD.}, }
@article {pmid28860611, year = {2017}, author = {Bhat, M and Pasini, E and Copeland, J and Angeli, M and Husain, S and Kumar, D and Renner, E and Teterina, A and Allard, J and Guttman, DS and Humar, A}, title = {Impact of Immunosuppression on the Metagenomic Composition of the Intestinal Microbiome: a Systems Biology Approach to Post-Transplant Diabetes.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {10277}, pmid = {28860611}, issn = {2045-2322}, mesh = {Animals ; Computational Biology/methods ; Diabetes Mellitus/etiology ; Gastrointestinal Microbiome/*immunology ; Gene Ontology ; Humans ; Hyperglycemia/etiology ; Immunosuppression/*adverse effects ; Immunosuppressive Agents/adverse effects/therapeutic use ; Insulin Resistance ; Male ; *Metagenome ; *Metagenomics/methods ; RNA, Ribosomal, 16S ; Rats ; Sirolimus/adverse effects/therapeutic use ; Systems Biology/methods ; Tacrolimus/adverse effects/therapeutic use ; Transplantation/adverse effects ; }, abstract = {Solid organ transplantation (SOT) outcomes have continued to improve, although long-term use of immunosuppressants can lead to complications such as diabetes, compromising post-transplant outcomes. In this study, we have characterized the intestinal microbiome (IM) composition at the metagenomic level in the context of hyperglycemia induced by immunosuppressants. Sprague-Dawley rats were subjected to doses of tacrolimus and sirolimus that reliably induce hyperglycemia and an insulin-resistant state. Subsequent exposure to probiotics resulted in reversal of hyperglycemia. 16S rRNA and metagenomic sequencing of stool were done to identify the bacterial genes and pathways enriched in immunosuppression. Bacterial diversity was significantly decreased in sirolimus-treated rats, with 9 taxa significantly less present in both immunosuppression groups: Roseburia, Oscillospira, Mollicutes, Rothia, Micrococcaceae, Actinomycetales and Staphylococcus. Following probiotics, these changes were reversed to baseline. At the metagenomic level, the balance of metabolism was shifted towards the catabolic side with an increase of genes involved in sucrose degradation, similar to diabetes. Conversely, the control rats had greater abundance of anabolic processes and genes involved in starch degradation. Immunosuppression leads to a more catabolic microbial profile, which may influence development of diabetes after SOT. Modulation of the microbiome with probiotics may help in minimizing adverse long-term effects of immunosuppression.}, }
@article {pmid30582999, year = {2019}, author = {Snowdon, RJ and Schiessl, S}, title = {Illuminating Crop Adaptation Using Population Genomics.}, journal = {Molecular plant}, volume = {12}, number = {1}, pages = {27-29}, doi = {10.1016/j.molp.2018.12.014}, pmid = {30582999}, issn = {1752-9867}, mesh = {Adaptation, Physiological/genetics ; Brassica rapa/*genetics ; Ecotype ; Genome ; Genomics ; Metagenomics ; }, }
@article {pmid30397356, year = {2018}, author = {Sun, L and Xie, C and Wang, G and Wu, Y and Wu, Q and Wang, X and Liu, J and Deng, Y and Xia, J and Chen, B and Zhang, S and Yun, C and Lian, G and Zhang, X and Zhang, H and Bisson, WH and Shi, J and Gao, X and Ge, P and Liu, C and Krausz, KW and Nichols, RG and Cai, J and Rimal, B and Patterson, AD and Wang, X and Gonzalez, FJ and Jiang, C}, title = {Gut microbiota and intestinal FXR mediate the clinical benefits of metformin.}, journal = {Nature medicine}, volume = {24}, number = {12}, pages = {1919-1929}, doi = {10.1038/s41591-018-0222-4}, pmid = {30397356}, issn = {1546-170X}, support = {T32 LM012415/LM/NLM NIH HHS/United States ; Z01 BC005561-20//NULL/International ; Z01 BC005561-21//NULL/International ; }, mesh = {Bacteroides/drug effects/pathogenicity ; Bile Acids and Salts/metabolism ; Diabetes Mellitus, Type 2/*drug therapy/genetics/microbiology/pathology ; Diet, High-Fat/adverse effects ; Gastrointestinal Microbiome/*drug effects/genetics ; Gene Expression Regulation, Bacterial/drug effects ; Glucose Intolerance/drug therapy/genetics/microbiology ; Humans ; Hyperglycemia/drug therapy/genetics/microbiology/pathology ; Metabolome/drug effects/genetics ; Metagenomics/methods ; Metformin/*administration &amp; dosage ; Obesity/*drug therapy/genetics/microbiology/pathology ; Receptors, Cytoplasmic and Nuclear/*genetics ; Ursodeoxycholic Acid/analogs &amp; derivatives ; }, abstract = {The anti-hyperglycemic effect of metformin is believed to be caused by its direct action on signaling processes in hepatocytes, leading to lower hepatic gluconeogenesis. Recently, metformin was reported to alter the gut microbiota community in humans, suggesting that the hyperglycemia-lowering action of the drug could be the result of modulating the population of gut microbiota. However, the critical microbial signaling metabolites and the host targets associated with the metabolic benefits of metformin remained elusive. Here, we performed metagenomic and metabolomic analysis of samples from individuals with newly diagnosed type 2 diabetes (T2D) naively treated with metformin for 3 d, which revealed that Bacteroides fragilis was decreased and the bile acid glycoursodeoxycholic acid (GUDCA) was increased in the gut. These changes were accompanied by inhibition of intestinal farnesoid X receptor (FXR) signaling. We further found that high-fat-diet (HFD)-fed mice colonized with B. fragilis were predisposed to more severe glucose intolerance, and the metabolic benefits of metformin treatment on glucose intolerance were abrogated. GUDCA was further identified as an intestinal FXR antagonist that improved various metabolic endpoints in mice with established obesity. Thus, we conclude that metformin acts in part through a B. fragilis-GUDCA-intestinal FXR axis to improve metabolic dysfunction, including hyperglycemia.}, }
@article {pmid29531366, year = {2018}, author = {Garza, DR and van Verk, MC and Huynen, MA and Dutilh, BE}, title = {Towards predicting the environmental metabolome from metagenomics with a mechanistic model.}, journal = {Nature microbiology}, volume = {3}, number = {4}, pages = {456-460}, doi = {10.1038/s41564-018-0124-8}, pmid = {29531366}, issn = {2058-5276}, mesh = {Bacteria/classification/genetics/*metabolism ; Colon/*microbiology ; Female ; Humans ; Metabolome/*genetics ; Metagenomics/methods ; Microbiota/*genetics ; Models, Biological ; Molecular Sequence Annotation ; Mouth/*microbiology ; Skin/*microbiology ; Vagina/*microbiology ; }, abstract = {The environmental metabolome and metabolic potential of microorganisms are dominant and essential factors shaping microbial community composition. Recent advances in genome annotation and systems biology now allow us to semiautomatically reconstruct genome-scale metabolic models (GSMMs) of microorganisms based on their genome sequence 1 . Next, growth of these models in a defined metabolic environment can be predicted in silico, mechanistically linking the metabolic fluxes of individual microbial populations to the community dynamics. A major advantage of GSMMs is that no training data is needed, besides information about the metabolic capacity of individual genes (genome annotation) and knowledge of the available environmental metabolites that allow the microorganism to grow. However, the composition of the environment is often not fully determined and remains difficult to measure 2 . We hypothesized that the relative abundance of different bacterial species, as measured by metagenomics, can be combined with GSMMs of individual bacteria to reveal the metabolic status of a given biome. Using a newly developed algorithm involving over 1,500 GSMMs of human-associated bacteria, we inferred distinct metabolomes for four human body sites that are consistent with experimental data. Together, we link the metagenome to the metabolome in a mechanistic framework towards predictive microbiome modelling.}, }
@article {pmid30736849, year = {2019}, author = {Fritz, A and Hofmann, P and Majda, S and Dahms, E and Dröge, J and Fiedler, J and Lesker, TR and Belmann, P and DeMaere, MZ and Darling, AE and Sczyrba, A and Bremges, A and McHardy, AC}, title = {CAMISIM: simulating metagenomes and microbial communities.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {17}, doi = {10.1186/s40168-019-0633-6}, pmid = {30736849}, issn = {2049-2618}, mesh = {Algorithms ; Animals ; *Computer Simulation ; Gastrointestinal Microbiome/*genetics ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; Mice ; Models, Biological ; Sequence Analysis, DNA/methods ; Software ; }, abstract = {BACKGROUND: Shotgun metagenome data sets of microbial communities are highly diverse, not only due to the natural variation of the underlying biological systems, but also due to differences in laboratory protocols, replicate numbers, and sequencing technologies. Accordingly, to effectively assess the performance of metagenomic analysis software, a wide range of benchmark data sets are required.<br><br>RESULTS: We describe the CAMISIM microbial community and metagenome simulator. The software can model different microbial abundance profiles, multi-sample time series, and differential abundance studies, includes real and simulated strain-level diversity, and generates second- and third-generation sequencing data from taxonomic profiles or de novo. Gold standards are created for sequence assembly, genome binning, taxonomic binning, and taxonomic profiling. CAMSIM generated the benchmark data sets of the first CAMI challenge. For two simulated multi-sample data sets of the human and mouse gut microbiomes, we observed high functional congruence to the real data. As further applications, we investigated the effect of varying evolutionary genome divergence, sequencing depth, and read error profiles on two popular metagenome assemblers, MEGAHIT, and metaSPAdes, on several thousand small data sets generated with CAMISIM.<br><br>CONCLUSIONS: CAMISIM can simulate a wide variety of microbial communities and metagenome data sets together with standards of truth for method evaluation. All data sets and the software are freely available at https://github.com/CAMI-challenge/CAMISIM.}, }
@article {pmid30728080, year = {2019}, author = {Yu, K and Yi, S and Li, B and Guo, F and Peng, X and Wang, Z and Wu, Y and Alvarez-Cohen, L and Zhang, T}, title = {An integrated meta-omics approach reveals substrates involved in synergistic interactions in a bisphenol A (BPA)-degrading microbial community.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {16}, doi = {10.1186/s40168-019-0634-5}, pmid = {30728080}, issn = {2049-2618}, mesh = {Alcaligenaceae/genetics/isolation &amp; purification/*metabolism ; Benzhydryl Compounds/*metabolism ; *Biodegradation, Environmental ; Metagenomics ; Microbial Interactions/physiology ; Microbiota/physiology ; Phenols/*metabolism ; Pseudomonas/genetics/isolation &amp; purification/*metabolism ; RNA, Ribosomal, 16S/genetics ; Sphingomonas/genetics/isolation &amp; purification/*metabolism ; }, abstract = {BACKGROUND: Understanding microbial interactions in engineering bioprocesses is important to enhance and optimize performance outcomes and requires dissection of the multi-layer complexities of microbial communities. However, unraveling microbial interactions as well as substrates involved in complex microbial communities is a challenging task. Here, we demonstrate an integrated approach of metagenomics, metatranscriptomics, and targeted metabolite analysis to identify the substrates involved in interspecies interactions from a potential cross-feeding model community-bisphenol A (BPA)-biodegrading community, aiming to establish an identification method of microbial interactions in engineering or environmental bioprocesses.<br><br>RESULTS: The community-level BPA-metabolic pathway was constructed using integrated metagenomics and targeted metabolite analyses. The dynamics of active functions and metabolism of major community members were identified using metagenomic and metatranscriptomic analyses in concert. Correlating the community BPA biodegradation performance to the individual bacterial activities enabled the discovery of substrates involved in a synergistic interaction of cross-feeding between BPA-degrading Sphingonomas species and intermediate users, Pseudomonas sp. and Pusillimonas sp. This proposed synergistic interaction was confirmed by the co-culture of a Sphingonomas sp. and Pseudomonas sp. isolates, which demonstrated enhanced BPA biodegradation compared to the isolate of Sphingonomas sp. alone.<br><br>CONCLUSION: The three types of integrated meta-omics analyses effectively revealed the metabolic capability at both community-wide and individual bacterial levels. The correlation between these two levels revealed the hidden connection between apparent overall community performance and the contributions of individual community members and their interactions in a BPA-degrading microbial community. In addition, we demonstrated that using integrated multi-omics in conjunction with culture-based confirmation approach is effective to elucidate the microbial interactions affecting the performance outcome. We foresee this approach would contribute the future application and operation of environmental bioprocesses on a knowledge-based control.}, }
@article {pmid30696492, year = {2019}, author = {Cernava, T and Erlacher, A and Soh, J and Sensen, CW and Grube, M and Berg, G}, title = {Enterobacteriaceae dominate the core microbiome and contribute to the resistome of arugula (Eruca sativa Mill.).}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {13}, doi = {10.1186/s40168-019-0624-7}, pmid = {30696492}, issn = {2049-2618}, mesh = {Anti-Bacterial Agents/pharmacology ; Base Sequence ; Brassicaceae/*microbiology ; Drug Resistance, Bacterial/genetics ; Enterobacteriaceae/*classification/genetics/*isolation &amp; purification ; Foodborne Diseases/microbiology ; Metagenome/*genetics ; Microbial Sensitivity Tests ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Arugula is a traditional medicinal plant and popular leafy green today. It is mainly consumed raw in the Western cuisine and known to contain various bioactive secondary metabolites. However, arugula has been also associated with high-profile outbreaks causing severe food-borne human diseases. A multiphasic approach integrating data from metagenomics, amplicon sequencing, and arugula-derived bacterial cultures was employed to understand the specificity of the indigenous microbiome and resistome of the edible plant parts.<br><br>RESULTS: Our results indicate that arugula is colonized by a diverse, plant habitat-specific microbiota. The indigenous phyllosphere bacterial community was shown to be dominated by Enterobacteriaceae, which are well-equipped with various antibiotic resistances. Unexpectedly, the prevalence of specific resistance mechanisms targeting therapeutic antibiotics (fluoroquinolone, chloramphenicol, phenicol, macrolide, aminocoumarin) was only surpassed by efflux pump assignments.<br><br>CONCLUSIONS: Enterobacteria, being core microbiome members of arugula, have a substantial implication in the overall resistome. Detailed insights into the natural occurrence of antibiotic resistances in arugula-associated microorganisms showed that the plant is a hotspot for distinctive defense mechanisms. The specific functioning of microorganisms in this unusual ecosystem provides a unique model to study antibiotic resistances in an ecological context.}, }
@article {pmid30529583, year = {2019}, author = {Paramsothy, S and Nielsen, S and Kamm, MA and Deshpande, NP and Faith, JJ and Clemente, JC and Paramsothy, R and Walsh, AJ and van den Bogaerde, J and Samuel, D and Leong, RWL and Connor, S and Ng, W and Lin, E and Borody, TJ and Wilkins, MR and Colombel, JF and Mitchell, HM and Kaakoush, NO}, title = {Specific Bacteria and Metabolites Associated With Response to Fecal Microbiota Transplantation in Patients With Ulcerative Colitis.}, journal = {Gastroenterology}, volume = {156}, number = {5}, pages = {1440-1454.e2}, doi = {10.1053/j.gastro.2018.12.001}, pmid = {30529583}, issn = {1528-0012}, mesh = {Bacteria/classification/genetics/growth &amp; development/*metabolism ; Biomarkers/metabolism ; Colitis, Ulcerative/diagnosis/microbiology/*therapy ; Double-Blind Method ; Fecal Microbiota Transplantation/adverse effects ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Metabolomics ; New South Wales ; Remission Induction ; Ribotyping ; Time Factors ; Treatment Outcome ; }, abstract = {BACKGROUND &amp; AIMS: Fecal microbiota transplantation (FMT) can induce remission in patients with ulcerative colitis (UC). In a randomized controlled trial of FMT in patients with active UC, we aimed to identify bacterial taxonomic and functional factors associated with response to therapy.<br><br>METHODS: We performed a double-blind trial of 81 patients with active UC randomly assigned to groups that received an initial colonoscopic infusion and then intensive multidonor FMT or placebo enemas, 5 d/wk for 8 weeks. Patients in the FMT group received blended homogenized stool from 3-7 unrelated donors. Patients in the placebo group were eligible to receive open-label FMT after the double-blind study period. We collected 314 fecal samples from the patients at screening, every 4 weeks during treatment, and 8 weeks after the blinded or open-label FMT therapy. We also collected 160 large-bowel biopsy samples from the patients at study entry, at completion of 8 weeks of blinded therapy, and at the end of open-label FMT, if applicable. We analyzed 105 fecal samples from the 14 individual donors (n = 55), who in turn contributed to 21 multidonor batches (n = 50). Bacteria in colonic and fecal samples were analyzed by both 16S ribosomal RNA gene and transcript amplicon sequencing; 285 fecal samples were analyzed by shotgun metagenomics, and 60 fecal samples were analyzed for metabolome features.<br><br>RESULTS: FMT increased microbial diversity and altered composition, based on analyses of colon and fecal samples collected before vs after FMT. Diversity was greater in fecal and colon samples collected before and after FMT treatment from patients who achieved remission compared with patients who did not. Patients in remission after FMT had enrichment of Eubacterium hallii and Roseburia inulivorans compared with patients who did not achieve remission after FMT and had increased levels of short-chain fatty acid biosynthesis and secondary bile acids. Patients who did not achieve remission had enrichment of Fusobacterium gonidiaformans, Sutterella wadsworthensis, and Escherichia species and increased levels of heme and lipopolysaccharide biosynthesis. Bacteroides in donor stool were associated with remission in patients receiving FMT, and Streptococcus species in donor stool was associated with no response to FMT.<br><br>CONCLUSIONS: In an analysis of fecal and colonic mucosa samples from patients receiving FMT for active UC and stool samples from donors, we associated specific bacteria and metabolic pathways with induction of remission. These findings may be of value in the design of microbe-based therapies for UC. ClinicalTrials.gov, Number NCT01896635.}, }
@article {pmid29783945, year = {2018}, author = {Westreich, ST and Treiber, ML and Mills, DA and Korf, I and Lemay, DG}, title = {SAMSA2: a standalone metatranscriptome analysis pipeline.}, journal = {BMC bioinformatics}, volume = {19}, number = {1}, pages = {175}, pmid = {29783945}, issn = {1471-2105}, support = {T32-GM008799/NH/NIH HHS/United States ; T32 GM008799/GM/NIGMS NIH HHS/United States ; R01AT008759/NH/NIH HHS/United States ; R01 AT008759/AT/NCCIH NIH HHS/United States ; }, mesh = {Gene Expression Profiling/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/*methods ; Microbiota/genetics ; Sequence Analysis, RNA/*methods ; *Software ; }, abstract = {BACKGROUND: Complex microbial communities are an area of growing interest in biology. Metatranscriptomics allows researchers to quantify microbial gene expression in an environmental sample via high-throughput sequencing. Metatranscriptomic experiments are computationally intensive because the experiments generate a large volume of sequence data and each sequence must be compared with reference sequences from thousands of organisms.<br><br>RESULTS: SAMSA2 is an upgrade to the original Simple Annotation of Metatranscriptomes by Sequence Analysis (SAMSA) pipeline that has been redesigned for standalone use on a supercomputing cluster. SAMSA2 is faster due to the use of the DIAMOND aligner, and more flexible and reproducible because it uses local databases. SAMSA2 is available with detailed documentation, and example input and output files along with examples of master scripts for full pipeline execution.<br><br>CONCLUSIONS: SAMSA2 is a rapid and efficient metatranscriptome pipeline for analyzing large RNA-seq datasets in a supercomputing cluster environment. SAMSA2 provides simplified output that can be examined directly or used for further analyses, and its reference databases may be upgraded, altered or customized to fit the needs of any experiment.}, }
@article {pmid29779275, year = {2018}, author = {Sun, TZ and Teng, F and Jia, SB and Tang, YP and Jiang, M and Huang, S and Yuan, X and Li, XL and Yang, F}, title = {[Salivary microbial communities associated with severe early childhood caries].}, journal = {Hua xi kou qiang yi xue za zhi = Huaxi kouqiang yixue zazhi = West China journal of stomatology}, volume = {36}, number = {2}, pages = {150-155}, doi = {10.7518/hxkq.2018.02.007}, pmid = {29779275}, issn = {1000-1182}, mesh = {Child ; Child, Preschool ; *Dental Caries/microbiology ; Humans ; Metagenomics ; *Microbiota/genetics ; RNA, Ribosomal, 16S ; Saliva ; }, abstract = {OBJECTIVE: To compare the salivary microbial profiles of healthy subjects and those with severe early childhood caries (S-ECC) by using high-throughput sequencing.<br><br>METHODS: Salivary samples were obtained from children with S-ECC (group C, n=24) and healthy children (group H, n=24). Total metagenomic DNA was extracted, and DNA amplicons of the V1-V3 hypervariable region of the 16S rRNA gene were generated and subjected to 454 sequencing. The characteristics of oral microbial communities from the two groups were compared based on microbial diversity and taxonomy assignment.<br><br>RESULTS: First, the microbial richness was significantly higher in group C than group H (P<0.05). Second, the microbial community structure was significantly different for the groups H and C (P<0.01). In addition, caries microbiota was significantly conserved in group C (P<0.001). High expression of suspected cariogenic microorganisms in group C (P<0.1) and health related microorganisms in group H (P<0.1) were identified. Finally, models of caries risk assessment were proposed to distinguish caries from healthy subjects with over 70% accuracy.<br><br>CONCLUSIONS: Salivary microbiota and certain taxa, such as caries-associated taxa (Prevotella), may be useful to screen/assess the children's risk of developing caries.}, }
@article {pmid29689301, year = {2018}, author = {Connelly, S and Subramanian, P and Hasan, NA and Colwell, RR and Kaleko, M}, title = {Distinct consequences of amoxicillin and ertapenem exposure in the porcine gut microbiome.}, journal = {Anaerobe}, volume = {53}, number = {}, pages = {82-93}, doi = {10.1016/j.anaerobe.2018.04.012}, pmid = {29689301}, issn = {1095-8274}, mesh = {Administration, Intravenous ; Administration, Oral ; Amoxicillin/*administration &amp; dosage ; Animals ; Anti-Bacterial Agents/*administration &amp; dosage ; Drug Resistance, Bacterial/drug effects ; Ertapenem/*administration &amp; dosage ; Gastrointestinal Microbiome/*drug effects ; Genes, Bacterial ; Membrane Transport Proteins/genetics ; Metagenomics ; Swine ; beta-Lactamases/genetics ; }, abstract = {The gut microbiome influences many, if not all, aspects of human health. Antibiotics, while lifesaving, have the unintended consequence of killing commensal microbiota inhabiting the gastrointestinal (GI) tract, which can lead to overgrowth of opportunistic pathogens such as Clostridium difficile and emergence of antibiotic-resistant organisms. Here, porcine models were developed to evaluate changes to the gut microbiome caused by two distinct types of beta-lactam antibiotics delivered via common administration routes, oral amoxicillin and intravenous ertapenem. Amoxicillin is one of the most often used broad-spectrum antibiotics, frequently prescribed to young children. Ertapenem, a carbapenem considered a last resort antibiotic, is used sparingly in humans and prohibited for use in animals. Cohorts of normal pigs (n = 5) were treated with amoxicillin (20 mg/kg, PO, BID) or ertapenem (30 mg/kg, IV, SID) for seven days. Microbiomes were evaluated using whole genome shotgun metagenomics analyses of fecal DNA collected prior to, during, and after antibiotic treatment. Each antibiotic resulted in significant and distinct changes in the microbiome, causing elimination of key commensal bacterial species and overgrowth of other, potentially pathogenic taxa. In addition, amoxicillin promoted propagation of a broad range of antibiotic resistance genes, many encoding efflux pump components and beta-lactamases, while ertapenem triggered emergence of genes encoding vancomycin resistance, and beta-lactamases, including the carbapenemase, IMP-27. Notably, microbiota alterations and antibiotic resistance gene propagation displayed unique patterns following exposure to amoxicillin or ertapenem. These data underscore the importance of understanding consequences of individual antibiotic use to predict and potentially mitigate adverse outcomes. The porcine models developed here can facilitate evaluation of therapeutic interventions to prevent antibiotic-mediated microbiome disruption.}, }
@article {pmid29494275, year = {2018}, author = {Humphries, A and Daud, A}, title = {The gut microbiota and immune checkpoint inhibitors.}, journal = {Human vaccines &amp; immunotherapeutics}, volume = {14}, number = {9}, pages = {2178-2182}, pmid = {29494275}, issn = {2164-554X}, mesh = {Animals ; CTLA-4 Antigen/*antagonists &amp; inhibitors ; Cancer Vaccines/*immunology ; Gastrointestinal Microbiome/*immunology ; Humans ; Immunotherapy/*methods ; Programmed Cell Death 1 Receptor/*antagonists &amp; inhibitors ; }, abstract = {Although immunotherapy has been remarkably effective across multiple cancer types, there continues to be a significant number of non-responding patients. A possible factor proposed to influence the efficacy of immunotherapies is the gut microbiome. We discuss the results and implications of recent research on the relationship between the gut microbiome, our immune systems, and immune checkpoint inhibitor therapies including anti-CTLA-4 Ab and anti-PD-1 Ab. While the investigations all exhibit interesting results and conclusions, we find little congruence in the specific bacteria that were found favorable for antitumor responses. It is unclear whether the inconsistencies are due to differential approaches in study design (pre-clinical or clinical subjects, anti-CTLA-4 Ab or anti-PD-1 Ab), experimental methods and measurements (metagenomics sequencing and clustering variations) or subject population dynamics (differential cancer types and baseline characteristics). Moreover, we note studies regarding particular bacterial commensals and autoimmune diseases, which challenge findings from these investigations. We conclude that with the current research, clinical investigators can appreciate the critical role of gut microbiota in mediating immunostimulant response. However, prospective research exploring the biochemical mechanisms which commensal bacteria communicate with each other and the immune system is imperative to understand how they can be adjusted properly for higher immunotherapy response.}, }
@article {pmid29291350, year = {2018}, author = {Smith, TE and Pond, CD and Pierce, E and Harmer, ZP and Kwan, J and Zachariah, MM and Harper, MK and Wyche, TP and Matainaho, TK and Bugni, TS and Barrows, LR and Ireland, CM and Schmidt, EW}, title = {Accessing chemical diversity from the uncultivated symbionts of small marine animals.}, journal = {Nature chemical biology}, volume = {14}, number = {2}, pages = {179-185}, pmid = {29291350}, issn = {1552-4469}, support = {R01 GM102602/GM/NIGMS NIH HHS/United States ; R01 GM107557/GM/NIGMS NIH HHS/United States ; U01 TW006671/TW/FIC NIH HHS/United States ; }, mesh = {Animals ; Anti-HIV Agents/*pharmacology ; Bacteria ; Biological Products/*pharmacology ; DNA/analysis ; *Drug Discovery ; Drug Evaluation, Preclinical ; Genomics ; HIV Infections/*drug therapy ; Humans ; Lysinoalanine/chemistry ; Metagenome ; Metagenomics ; *Microbiota ; Multigene Family ; Peptides/pharmacology ; Structure-Activity Relationship ; *Symbiosis ; Synthetic Biology ; T-Lymphocytes/drug effects ; Urochordata ; }, abstract = {Chemistry drives many biological interactions between the microbiota and host animals, yet it is often challenging to identify the chemicals involved. This poses a problem, as such small molecules are excellent sources of potential pharmaceuticals, pretested by nature for animal compatibility. We discovered anti-HIV compounds from small, marine tunicates from the Eastern Fields of Papua New Guinea. Tunicates are a reservoir for new bioactive chemicals, yet their small size often impedes identification or even detection of the chemicals within. We solved this problem by combining chemistry, metagenomics, and synthetic biology to directly identify and synthesize the natural products. We show that these anti-HIV compounds, the divamides, are a novel family of lanthipeptides produced by symbiotic bacteria living in the tunicate. Neighboring animal colonies contain structurally related divamides that differ starkly in their biological properties, suggesting a role for biosynthetic plasticity in a native context wherein biological interactions take place.}, }
@article {pmid29176696, year = {2017}, author = {}, title = {Overcoming hurdles in sharing microbiome data.}, journal = {Nature microbiology}, volume = {2}, number = {12}, pages = {1573}, doi = {10.1038/s41564-017-0077-3}, pmid = {29176696}, issn = {2058-5276}, mesh = {Computational Biology/*methods ; Information Dissemination/*methods ; Metagenomics/*methods ; *Microbiota ; }, }
@article {pmid28843021, year = {2018}, author = {Heintz-Buschart, A and Pandey, U and Wicke, T and Sixel-Döring, F and Janzen, A and Sittig-Wiegand, E and Trenkwalder, C and Oertel, WH and Mollenhauer, B and Wilmes, P}, title = {The nasal and gut microbiome in Parkinson's disease and idiopathic rapid eye movement sleep behavior disorder.}, journal = {Movement disorders : official journal of the Movement Disorder Society}, volume = {33}, number = {1}, pages = {88-98}, pmid = {28843021}, issn = {1531-8257}, mesh = {Aged ; Case-Control Studies ; Cohort Studies ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Male ; Middle Aged ; Nose/*microbiology ; Parkinson Disease/*microbiology ; REM Sleep Behavior Disorder/*microbiology ; RNA, Ribosomal, 16S/genetics/metabolism ; RNA, Ribosomal, 18S/genetics/metabolism ; }, abstract = {BACKGROUND: Increasing evidence connects the gut microbiota and the onset and/or phenotype of Parkinson's disease (PD). Differences in the abundances of specific bacterial taxa have been reported in PD patients. It is, however, unknown whether these differences can be observed in individuals at high risk, for example, with idiopathic rapid eye movement sleep behavior disorder, a prodromal condition of α-synuclein aggregation disorders including PD.<br><br>OBJECTIVES: To compare microbiota in carefully preserved nasal wash and stool samples of subjects with idiopathic rapid eye movement sleep behavior disorder, manifest PD, and healthy individuals.<br><br>METHODS: Microbiota of flash-frozen stool and nasal wash samples from 76 PD patients, 21 idiopathic rapid eye movement sleep behavior disorder patients, and 78 healthy controls were assessed by 16S and 18S ribosomal RNA amplicon sequencing. Seventy variables, related to demographics, clinical parameters including nonmotor symptoms, and sample processing, were analyzed in relation to microbiome variability and controlled differential analyses were performed.<br><br>RESULTS: Differentially abundant gut microbes, such as Akkermansia, were observed in PD, but no strong differences in nasal microbiota. Eighty percent of the differential gut microbes in PD versus healthy controls showed similar trends in idiopathic rapid eye movement sleep behavior disorder, for example, Anaerotruncus and several Bacteroides spp., and correlated with nonmotor symptoms. Metagenomic sequencing of select samples enabled the reconstruction of genomes of so far uncharacterized differentially abundant organisms.<br><br>CONCLUSION: Our study reveals differential abundances of gut microbial taxa in PD and its prodrome idiopathic rapid eye movement sleep behavior disorder in comparison to the healthy controls, and highlights the potential of metagenomics to identify and characterize microbial taxa, which are enriched or depleted in PD and/or idiopathic rapid eye movement sleep behavior disorder. © 2017 The Authors. Movement Disorders published by Wiley Periodicals, Inc. on behalf of International Parkinson and Movement Disorder Society.}, }
@article {pmid28349932, year = {2017}, author = {Nunes-Alves, C}, title = {Microbial communities rock.}, journal = {Nature microbiology}, volume = {2}, number = {}, pages = {17041}, doi = {10.1038/nmicrobiol.2017.41}, pmid = {28349932}, issn = {2058-5276}, mesh = {Biotransformation ; *Environmental Microbiology ; Metabolic Networks and Pathways ; Metagenomics/methods/trends ; Microbiological Techniques/methods/trends ; Microbiology/trends ; *Microbiota ; Minerals/metabolism ; }, }
@article {pmid28120929, year = {2017}, author = {Soppa, J}, title = {Polyploidy and community structure.}, journal = {Nature microbiology}, volume = {2}, number = {}, pages = {16261}, doi = {10.1038/nmicrobiol.2016.261}, pmid = {28120929}, issn = {2058-5276}, mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics ; *Biota ; Eukaryota/classification/*genetics ; Metagenomics/methods ; *Polyploidy ; }, }
@article {pmid30871469, year = {2019}, author = {Perz, AI and Giles, CB and Brown, CA and Porter, H and Roopnarinesingh, X and Wren, JD}, title = {MNEMONIC: MetageNomic Experiment Mining to create an OTU Network of Inhabitant Correlations.}, journal = {BMC bioinformatics}, volume = {20}, number = {Suppl 2}, pages = {96}, doi = {10.1186/s12859-019-2623-x}, pmid = {30871469}, issn = {1471-2105}, support = {P20 GM103636/GM/NIGMS NIH HHS/United States ; P30 AG050911/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; Metagenomics/*methods ; Microbiota/*genetics ; }, abstract = {BACKGROUND: The number of publicly available metagenomic experiments in various environments has been rapidly growing, empowering the potential to identify similar shifts in species abundance between different experiments. This could be a potentially powerful way to interpret new experiments, by identifying common themes and causes behind changes in species abundance.<br><br>RESULTS: We propose a novel framework for comparing microbial shifts between conditions. Using data from one of the largest human metagenome projects to date, the American Gut Project (AGP), we obtain differential abundance vectors for microbes using experimental condition information provided with the AGP metadata, such as patient age, dietary habits, or health status. We show it can be used to identify similar and opposing shifts in microbial species, and infer putative interactions between microbes. Our results show that groups of shifts with similar effects on microbiome can be identified and that similar dietary interventions display similar microbial abundance shifts.<br><br>CONCLUSIONS: Without comparison to prior data, it is difficult for experimentalists to know if their observed changes in species abundance have been observed by others, both in their conditions and in others they would never consider comparable. Yet, this can be a very important contextual factor in interpreting the significance of a shift. We've proposed and tested an algorithmic solution to this problem, which also allows for comparing the metagenomic signature shifts between conditions in the existing body of data.}, }
@article {pmid30808753, year = {2019}, author = {Ramírez-Flandes, S and González, B and Ulloa, O}, title = {Redox traits characterize the organization of global microbial communities.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {9}, pages = {3630-3635}, doi = {10.1073/pnas.1817554116}, pmid = {30808753}, issn = {1091-6490}, mesh = {Ecology ; *Ecosystem ; Humans ; *Metagenomics ; Microbiota/*genetics ; *Oxidation-Reduction ; Soil Microbiology ; }, abstract = {The structure of biological communities is conventionally described as profiles of taxonomic units, whose ecological functions are assumed to be known or, at least, predictable. In environmental microbiology, however, the functions of a majority of microorganisms are unknown and expected to be highly dynamic and collectively redundant, obscuring the link between taxonomic structure and ecosystem functioning. Although genetic trait-based approaches at the community level might overcome this problem, no obvious choice of gene categories can be identified as appropriate descriptive units in a general ecological context. We used 247 microbial metagenomes from 18 biomes to determine which set of genes better characterizes the differences among biomes on the global scale. We show that profiles of oxidoreductase genes support the highest biome differentiation compared with profiles of other categories of enzymes, general protein-coding genes, transporter genes, and taxonomic gene markers. Based on oxidoreductases' description of microbial communities, the role of energetics in differentiation and particular ecosystem function of different biomes become readily apparent. We also show that taxonomic diversity is decoupled from functional diversity, e.g., grasslands and rhizospheres were the most diverse biomes in oxidoreductases but not in taxonomy. Considering that microbes underpin biogeochemical processes and nutrient recycling through oxidoreductases, this functional diversity should be relevant for a better understanding of the stability and conservation of biomes. Consequently, this approach might help to quantify the impact of environmental stressors on microbial ecosystems in the context of the global-scale biome crisis that our planet currently faces.}, }
@article {pmid30669548, year = {2019}, author = {Chávez-Carbajal, A and Nirmalkar, K and Pérez-Lizaur, A and Hernández-Quiroz, F and Ramírez-Del-Alto, S and García-Mena, J and Hernández-Guerrero, C}, title = {Gut Microbiota and Predicted Metabolic Pathways in a Sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome.}, journal = {International journal of molecular sciences}, volume = {20}, number = {2}, pages = {}, doi = {10.3390/ijms20020438}, pmid = {30669548}, issn = {1422-0067}, support = {11a Convocatoria Para Proyectos de Investigación Básica.//Universidad Iberoamericana Ciudad de México/ ; CONACyT-163235 INFR-2011-01//Consejo Nacional de Ciencia y Tecnología/ ; FONSEC SS/IMSS/ISSSTE-CONACYT-233361.//Consejo Nacional de Ciencia y Tecnología/ ; }, mesh = {Adult ; Biodiversity ; Female ; *Gastrointestinal Microbiome ; Humans ; *Metabolic Networks and Pathways ; Metabolic Syndrome/complications/*etiology/*metabolism ; Metagenome ; Metagenomics/methods ; Mexico ; Middle Aged ; Obesity/complications/*etiology/*metabolism ; RNA, Ribosomal, 16S ; Sex Factors ; Young Adult ; }, abstract = {Obesity is an excessive fat accumulation that could lead to complications like metabolic syndrome. There are reports on gut microbiota and metabolic syndrome in relation to dietary, host genetics, and other environmental factors; however, it is necessary to explore the role of the gut microbiota metabolic pathways in populations like Mexicans, where the prevalence of obesity and metabolic syndrome is high. This study identify alterations of the gut microbiota in a sample of healthy Mexican women (CO), women with obesity (OB), and women with obesity plus metabolic syndrome (OMS). We studied 67 women, characterizing their anthropometric and biochemical parameters along with their gut bacterial diversity by high-throughput DNA sequencing. Our results indicate that in OB or OMS women, Firmicutes was the most abundant bacterial phylum. We observed significant changes in abundances of bacteria belonging to the Ruminococcaceae, Lachnospiraceae, and Erysipelotrichaceae families and significant enrichment of gut bacteria from 16 different taxa that might explain the observed metabolic alterations between the groups. Finally, the predicted functional metagenome of the gut microbiota found in each category shows differences in metabolic pathways related to lipid metabolism. We demonstrate that Mexican women have a particular bacterial gut microbiota characteristic of each phenotype. There are bacteria that potentially explain the observed metabolic differences between the groups, and gut bacteria in OMS and OB conditions carry more genes of metabolic pathways implicated in lipid metabolism.}, }
@article {pmid29767724, year = {2018}, author = {Magnabosco, C and Timmers, PHA and Lau, MCY and Borgonie, G and Linage-Alvarez, B and Kuloyo, O and Alleva, R and Kieft, TL and Slater, GF and van Heerden, E and Sherwood Lollar, B and Onstott, TC}, title = {Fluctuations in populations of subsurface methane oxidizers in coordination with changes in electron acceptor availability.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {7}, pages = {}, doi = {10.1093/femsec/fiy089}, pmid = {29767724}, issn = {1574-6941}, mesh = {Archaea/classification/genetics/*metabolism ; Bacteria/classification/genetics/*metabolism ; Electrons ; Geologic Sediments/*microbiology ; Metagenomics/methods ; Methane/*metabolism ; Microbiota/*physiology ; Oxidation-Reduction ; Proteomics/methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The concentrations of electron donors and acceptors in the terrestrial subsurface biosphere fluctuate due to migration and mixing of subsurface fluids, but the mechanisms and rates at which microbial communities respond to these changes are largely unknown. Subsurface microbial communities exhibit long cellular turnover times and are often considered relatively static-generating just enough ATP for cellular maintenance. Here, we investigated how subsurface populations of CH4 oxidizers respond to changes in electron acceptor availability by monitoring the biological and geochemical composition in a 1339 m-below-land-surface (mbls) fluid-filled fracture over the course of both longer (2.5 year) and shorter (2-week) time scales. Using a combination of metagenomic, metatranscriptomic, and metaproteomic analyses, we observe that the CH4 oxidizers within the subsurface microbial community change in coordination with electron acceptor availability over time. We then validate these findings through a series of 13C-CH4 laboratory incubation experiments, highlighting a connection between composition of subsurface CH4 oxidizing communities and electron acceptor availability.}, }
@article {pmid29490879, year = {2019}, author = {Wu, WK and Chen, CC and Panyod, S and Chen, RA and Wu, MS and Sheen, LY and Chang, SC}, title = {Optimization of fecal sample processing for microbiome study - The journey from bathroom to bench.}, journal = {Journal of the Formosan Medical Association = Taiwan yi zhi}, volume = {118}, number = {2}, pages = {545-555}, doi = {10.1016/j.jfma.2018.02.005}, pmid = {29490879}, issn = {0929-6646}, mesh = {DNA/*isolation &amp; purification ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; Reagent Kits, Diagnostic ; Sequence Analysis, DNA ; Specimen Handling/*methods/*standards ; }, abstract = {Although great interest has been displayed by researchers in the contribution of gut microbiota to human health, there is still no standard protocol with consensus to guarantee the sample quality of metagenomic analysis. Here we reviewed existing methodology studies and present suggestions for optimizing research pipeline from fecal sample collection to DNA extraction. First, we discuss strategies of clinical metadata collection as common confounders for microbiome research. Second, we propose general principles for freshly collected fecal sample and its storage and share a DIY stool collection kit protocol based on the manual procedure of Human Microbiome Project (HMP). Third, we provide a useful information of collection kit with DNA stabilization buffers and compare their pros and cons for multi-omic study. Fourth, we offer technical strategies as well as information of novel tools for sample aliquoting before long-term storage. Fifth, we discuss the substantial impact of different DNA extraction protocols on technical variations of metagenomic analysis. And lastly, we point out the limitation of current methods and the unmet needs for better quality control of metagenomic analysis. We hope the information provided here will help investigators in this exciting field to advance their studies while avoiding experimental artifacts.}, }
@article {pmid29194980, year = {2018}, author = {Tanner, K and Martí, JM and Belliure, J and Fernández-Méndez, M and Molina-Menor, E and Peretó, J and Porcar, M}, title = {Polar solar panels: Arctic and Antarctic microbiomes display similar taxonomic profiles.}, journal = {Environmental microbiology reports}, volume = {10}, number = {1}, pages = {75-79}, doi = {10.1111/1758-2229.12608}, pmid = {29194980}, issn = {1758-2229}, mesh = {Adaptation, Physiological ; Antarctic Regions ; Arctic Regions ; Bacteria/*classification/genetics/radiation effects ; Biodiversity ; Desiccation ; *Ecosystem ; Metagenomics ; *Microbiota ; *Solar Energy ; Ultraviolet Rays ; }, abstract = {Solar panels located on high (Arctic and Antarctic) latitudes combine the harshness of the climate with that of the solar exposure. We report here that these polar solar panels are inhabited by similar microbial communities in taxonomic terms, dominated by Hymenobacter spp., Sphingomonas spp. and Ascomycota. Our results suggest that solar panels, even on high latitudes, can shape a microbial ecosystem adapted to irradiation and desiccation.}, }
@article {pmid28874721, year = {2017}, author = {Shibagaki, N and Suda, W and Clavaud, C and Bastien, P and Takayasu, L and Iioka, E and Kurokawa, R and Yamashita, N and Hattori, Y and Shindo, C and Breton, L and Hattori, M}, title = {Aging-related changes in the diversity of women's skin microbiomes associated with oral bacteria.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {10567}, pmid = {28874721}, issn = {2045-2322}, mesh = {Adult ; Age Factors ; Aged ; Female ; Humans ; *Microbiota ; Middle Aged ; Mouth Mucosa/growth &amp; development/*microbiology ; Propionibacterium/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Skin/growth &amp; development/*microbiology ; }, abstract = {Skin aging is associated with changes in cutaneous physiology including interactions with a skin microbial community. A striking alteration and diversification in the skin microbiome with aging was observed between two different age groups of 37 healthy Japanese women, i.e. younger adults of 21-37 years old and older adults of 60-76 years old, using bacterial 16S rRNA gene sequencing. The analyses revealed that the alpha diversity/species richness was significantly higher in the older than the younger group for the cheek and forehead microbiomes, while the beta diversity in the overall structure significantly differed particularly for the forearm and scalp microbiomes between the two age groups. Taxonomic profiling showed a striking reduction in the relative abundance of the majority skin genus Propionibacterium in the cheek, forearm and forehead microbiomes of the older adults, and identified 38 species including many oral bacteria that significantly differentiated the two age groups with a skin site dependency. Furthermore, we found chronological age-related and unrelated skin clinical parameters that correlate with the observed changes in the skin microbiome diversity. Thus, our data suggested that the diversification of skin microbiomes in adult women was largely affected by chronological and physiological skin aging in association with oral bacteria.}, }
@article {pmid30902785, year = {2019}, author = {Kumar, R and Mishra, A and Jha, B}, title = {Bacterial community structure and functional diversity in subsurface seawater from the western coastal ecosystem of the Arabian Sea, India.}, journal = {Gene}, volume = {701}, number = {}, pages = {55-64}, doi = {10.1016/j.gene.2019.02.099}, pmid = {30902785}, issn = {1879-0038}, mesh = {*Bacteria/classification/genetics/growth &amp; development ; *Biodiversity ; India ; Microbial Consortia/*physiology ; Oceans and Seas ; Seawater/*microbiology ; *Water Microbiology ; }, abstract = {The present study revealed the spatial variability of bacteria in relation to physicochemical variations at four different locations (Diu - DIU, Veraval - VER, Porbandar - POR and Okha - OKH) along the Gujarat coast (Arabian Sea, India). The natural habitat was analyzed for temperature, salinity, pH, total dissolved solids, total organic content, total inorganic content, biological oxygen demand, conductivity and total dissolved oxygen. The lowest salinity and conductivity were observed at the VER site, whereas the highest salinity and conductivity were measured with OKH samples. In contrast, the pH was slightly alkaline at all of the sites. The VER site contained the maximum total dissolved solids (TDS), total carbon (TC), total organic carbon (TOC), and total inorganic carbon (TIC), while OKH showed the maximum dissolve oxygen (DO), biological oxygen demand (BOD), pH, temperature, conductivity, and salinity. The physicochemical characteristics showed that the Gujarat coast is alkaline and has a nutrient heterogeneous nature. Average well color development (AWCD) values, calculated using Biolog EcoPlates, showed that the microbial community from VER contained the highest metabolic activities and could metabolize all 31 substrates, followed by DIU > OKH > POR samples. In contrast, the abundance of the bacterial community, determined by qRT-PCR, was maximum in VER samples, followed by OKH > POR > DIU samples. The Shannon and Simpson indices showed that DIU, POR and OKH seawater clone libraries were more diverse. Furthermore, Chao estimator revealed the high diversity of POR and DIU clone libraries. Interestingly, DIU and OKH did not share any common operational taxonomic units (OTUs), and overall, the maximum bacterial diversity was observed with the POR seawater sample. Moreover, these observations were supported by statistical analysis, such as canonical correspondence analysis (CCA) and principal component analysis (PCA). The molecular phylogeny revealed the dominance of Proteobacteria followed by Firmicutes. Within the Proteobacteria phylum, most of the sequences were affiliated with the Gammaproteobacteria class. In total, about 726 OTUs were observed from all four sites which covers 59.79% DIU, 87.5% VER, 50% POR and 98.83% OKH of samples. This study is the first report to describe physicochemical attributes and the bacterial diversity of the coastal area of Gujarat. The study will provide useful insights about bacterial diversity, distribution, and abundance, as well as their relationships with the habitat.}, }
@article {pmid30574802, year = {2019}, author = {Murphy, R and Morgan, XC and Wang, XY and Wickens, K and Purdie, G and Fitzharris, P and Otal, A and Lawley, B and Stanley, T and Barthow, C and Crane, J and Mitchell, EA and Tannock, GW}, title = {Eczema-protective probiotic alters infant gut microbiome functional capacity but not composition: sub-sample analysis from a RCT.}, journal = {Beneficial microbes}, volume = {10}, number = {1}, pages = {5-17}, doi = {10.3920/BM2017.0191}, pmid = {30574802}, issn = {1876-2891}, mesh = {Adult ; Age Factors ; Biological Transport ; Breast Feeding ; Child, Preschool ; Dermatitis, Atopic/microbiology/*prevention &amp; control ; Dietary Supplements ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Glycerophosphates/metabolism ; Humans ; Infant ; Infant, Newborn ; Lactobacillus rhamnosus/*physiology ; Metagenomics ; Mothers ; Postpartum Period ; *Probiotics ; }, abstract = {Probiotic Lactobacillus rhamnosus HN001 given in early life has been shown to reduce infant eczema risk, but its effect on gut microbiota development has not been quantitatively and functionally examined. The aim of this study was to investigate the impact of early life probiotic exposure on the composition and functional capacity of infant gut microbiota from birth to 2 years considering the effects of age, delivery mode, antibiotics, pets and eczema. We performed shotgun metagenomic sequencing analysis of 650 infant faecal samples, collected at birth, 3, 12, and 24 months, as part of a randomised, controlled, 3-arm trial assessing the effect of L. rhamnosus HN001, Bifidobacterium animalis subsp. lactis HN019 supplementation on eczema development in 474 infants. There was a 50% reduced eczema risk in the HN001 probiotic group compared to placebo. Both mothers (from 35 weeks gestation until 6 months post-partum if breastfeeding) and infants (from birth to 2 years) received either a placebo or one of two probiotics, L. rhamnosus HN001 (6×109 cfu), or B. animalis subsp. lactis HN019 (9×109 cfu). L. rhamnosus HN001 probiotic supplementation was associated with increased overall glycerol-3 phosphate transport capacity and enrichment of L. rhamnosus. There were no other significant changes in infant gut microbiota composition or diversity. Increased capacity to transport glycerol-3-phosphate was positively correlated with relative abundance of L. rhamnosus. Children who developed eczema had gut microbiota with increased capacity for glycosaminoglycan degradation and flagellum assembly but had no significant differences in microbiota composition or diversity. Early life HN001 probiotic use is associated with both increased L. rhamnosus and increased infant gut microbiota functional capacity to transport glycerol-3 phosphate. The mechanistic relationship of such functional alteration in gut microbiota with reduced eczema risk and long-term health merits further investigation.}, }
@article {pmid30369115, year = {2018}, author = {Sivakala, KK and Jose, PA and Anandham, R and Thinesh, T and Jebakumar, SRD and Samaddar, S and Chatterjee, P and Sivakumar, N and Sa, T}, title = {Spatial Physiochemical and Metagenomic Analysis of Desert Environment.}, journal = {Journal of microbiology and biotechnology}, volume = {28}, number = {9}, pages = {1517-1526}, doi = {10.4014/jmb.1804.04005}, pmid = {30369115}, issn = {1738-8872}, mesh = {Bacteria/*chemistry/classification/*genetics/metabolism ; Biodiversity ; *Desert Climate ; India ; Metabolic Networks and Pathways ; *Metagenomics ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; Spatial Analysis ; }, abstract = {Investigating the bacterial diversity and their metabolic capabilities are crucial for interpreting ecological patterns in desert environment, and assessing the presence of exploitable microbial resources. In this study, we evaluated the spatial heterogeneity of physico-chemical parameters, soil bacterial diversity and metabolic adaptation at meter scale. Soil samples were collected from two quadrates a desert environment (Thar Desert, India) which face hot arid climate with very little rainfall and extreme temperatures. Analysis of physico-chemical parameters and subsequent variance analysis (p-values < 0.05) revealed that sulfate, potassium and magnesium ions were the most variable between the quadrates. Microbial diversity of the two quadrates was studied using Illumina bar coded sequencing by targeting V3-V4 regions of 16S rDNA. As the results, 702504 high-quality sequence reads, assigned to 173 operationaltaxonomic units (OTUs) at species level. The most abundant phyla in both quadrates were Actinobacteria (38.72%), Proteobacteria (32.94%), and Acidobacteria (9.24%). At genus level, Gaiellarepresented highest prevalence, followed by Streptomyces, Solirubrobacter, Aciditerrimonas, Geminicoccus, Geodermatophilus, Microvirga, and Rubrobacter. Between the quadrates, significant difference (p-values < 0.05) was found in the abundance of Aciditerrimonas, Geodermatophilus Geminicoccus, Ilumatobacter, Marmoricola, Nakamurella and Solirubrobacter. Metabolic functional mapping revealed diverse biological activities, and was significantly correlated with physico-chemical parameters. The results revealed spatial variation of ions, microbial abundance and functional attributes in the studied quadrates, and patchy nature in local scale. Interestingly, abundance ofthe biotechnologically important phylum Actinobacteria, with large proposition of unclassified speciesin the desert suggested that this arid environment is the promising site for bioprospection.}, }
@article {pmid31031001, year = {2019}, author = {Gregory, AC and Zayed, AA and Conceição-Neto, N and Temperton, B and Bolduc, B and Alberti, A and Ardyna, M and Arkhipova, K and Carmichael, M and Cruaud, C and Dimier, C and Domínguez-Huerta, G and Ferland, J and Kandels, S and Liu, Y and Marec, C and Pesant, S and Picheral, M and Pisarev, S and Poulain, J and Tremblay, JÉ and Vik, D and ,  and Babin, M and Bowler, C and Culley, AI and de Vargas, C and Dutilh, BE and Iudicone, D and Karp-Boss, L and Roux, S and Sunagawa, S and Wincker, P and Sullivan, MB}, title = {Marine DNA Viral Macro- and Microdiversity from Pole to Pole.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2019.03.040}, pmid = {31031001}, issn = {1097-4172}, abstract = {Microbes drive most ecosystems and are modulated by viruses that impact their lifespan, gene flow, and metabolic outputs. However, ecosystem-level impacts of viral community diversity remain difficult to assess due to classification issues and few reference genomes. Here, we establish an ∼12-fold expanded global ocean DNA virome dataset of 195,728 viral populations, now including the Arctic Ocean, and validate that these populations form discrete genotypic clusters. Meta-community analyses revealed five ecological zones throughout the global ocean, including two distinct Arctic regions. Across the zones, local and global patterns and drivers in viral community diversity were established for both macrodiversity (inter-population diversity) and microdiversity (intra-population genetic variation). These patterns sometimes, but not always, paralleled those from macro-organisms and revealed temperate and tropical surface waters and the Arctic as biodiversity hotspots and mechanistic hypotheses to explain them. Such further understanding of ocean viruses is critical for broader inclusion in ecosystem models.}, }
@article {pmid30887686, year = {2019}, author = {Weyrich, LS and Farrer, AG and Eisenhofer, R and Arriola, LA and Young, J and Selway, CA and Handsley-Davis, M and Adler, CJ and Breen, J and Cooper, A}, title = {Laboratory contamination over time during low-biomass sample analysis.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13011}, pmid = {30887686}, issn = {1755-0998}, support = {DECRA 150101574//Australian Research Council/ ; }, abstract = {Bacteria are not only ubiquitous on earth but can also be incredibly diverse within clean laboratories and reagents. The presence of both living and dead bacteria in laboratory environments and reagents is especially problematic when examining samples with low endogenous content (e.g., skin swabs, tissue biopsies, ice, water, degraded forensic samples or ancient material), where contaminants can outnumber endogenous microorganisms within samples. The contribution of contaminants within high-throughput studies remains poorly understood because of the relatively low number of contaminant surveys. Here, we examined 144 negative control samples (extraction blank and no-template amplification controls) collected in both typical molecular laboratories and an ultraclean ancient DNA laboratory over 5 years to characterize long-term contaminant diversity. We additionally compared the contaminant content within a home-made silica-based extraction method, commonly used to analyse low endogenous content samples, with a widely used commercial DNA extraction kit. The contaminant taxonomic profile of the ultraclean ancient DNA laboratory was unique compared to modern molecular biology laboratories, and changed over time according to researcher, month and season. The commercial kit also contained higher microbial diversity and several human-associated taxa in comparison to the home-made silica extraction protocol. We recommend a minimum of two strategies to reduce the impacts of laboratory contaminants within low-biomass metagenomic studies: (a) extraction blank controls should be included and sequenced with every batch of extractions and (b) the contributions of laboratory contamination should be assessed and reported in each high-throughput metagenomic study.}, }
@article {pmid30660184, year = {2019}, author = {Keijser, BJF and Agamennone, V and van den Broek, TJ and Caspers, M and van de Braak, A and Bomers, R and Havekes, M and Schoen, E and van Baak, M and Mioch, D and Bomers, L and Montijn, RC}, title = {Dose-dependent impact of oxytetracycline on the veal calf microbiome and resistome.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {65}, doi = {10.1186/s12864-018-5419-x}, pmid = {30660184}, issn = {1471-2164}, support = {060.24960//Agentschap NL/ ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Cattle ; Dose-Response Relationship, Drug ; Drug Resistance, Microbial/*drug effects/genetics ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects/genetics ; Genes, Bacterial/genetics ; Metagenomics/*methods ; Microbial Sensitivity Tests/methods ; Oxytetracycline/*pharmacology ; RNA, Ribosomal, 16S/chemistry/genetics ; Random Allocation ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Antibiotic therapy is commonly used in animal agriculture. Antibiotics excreted by the animals can contaminate farming environments, resulting in long term exposure of animals to sub-inhibitory levels of antibiotics. Little is known on the effect of this exposure on antibiotic resistance. In this study, we aimed to investigate the long term effects of sub-inhibitory levels of antibiotics on the gut microbiota composition and resistome of veal calves in vivo. Forty-two veal calves were randomly assigned to three groups. The first group (OTC-high) received therapeutic oral dosages of 1 g oxytetracycline (OTC), twice per day, during 5 days. The second group (OTC-low) received an oral dose of OTC of 100-200 μg per day during 7 weeks, mimicking animal exposure to environmental contamination. The third group (CTR) did not receive OTC, serving as unexposed control. Antibiotic residue levels were determined over time. The temporal effects on the gut microbiota and antibiotic resistance gene abundance was analysed by metagenomic sequencing.<br><br>RESULTS: In the therapeutic group, OTC levels exceeded MIC values. The low group remained at sub-inhibitory levels. The control group did not reach any significant OTC levels. 16S rRNA gene-based analysis revealed significant changes in the calf gut microbiota. Time-related changes accounted for most of the variation in the sequence data. Therapeutic application of OTC had transient effect, significantly impacting gut microbiota composition between day 0 and day 2. By metagenomic sequence analysis we identified six antibiotic resistance genes representing three gene classes (tetM, floR and mel) that differed in relative abundance between any of the intervention groups and the control. qPCR was used to validate observations made by metagenomic sequencing, revealing a peak of tetM abundance at day 28-35 in the OTC-high group. No increase in resistance genes abundance was seen in the OTC-low group.<br><br>CONCLUSIONS: Under the conditions tested, sub-therapeutic administration of OTC did not result in increased tetM resistance levels as observed in the therapeutic group.}, }
@article {pmid29988145, year = {2018}, author = {Delzenne, NM and Bindels, LB}, title = {Microbiome metabolomics reveals new drivers of human liver steatosis.}, journal = {Nature medicine}, volume = {24}, number = {7}, pages = {906-907}, doi = {10.1038/s41591-018-0126-3}, pmid = {29988145}, issn = {1546-170X}, mesh = {*Fatty Liver ; Female ; Humans ; Metabolomics ; Metagenomics ; *Microbiota ; Obesity ; }, }
@article {pmid29937307, year = {2018}, author = {Coutinho, FH and Gregoracci, GB and Walter, JM and Thompson, CC and Thompson, FL}, title = {Metagenomics Sheds Light on the Ecology of Marine Microbes and Their Viruses.}, journal = {Trends in microbiology}, volume = {26}, number = {11}, pages = {955-965}, doi = {10.1016/j.tim.2018.05.015}, pmid = {29937307}, issn = {1878-4380}, mesh = {Archaea/genetics/physiology ; Bacteria/genetics ; Bacterial Physiological Phenomena/genetics ; Biodiversity ; Biological Evolution ; Classification ; Cyanobacteria/physiology ; *Ecology ; Ecosystem ; Genomics ; Host Microbial Interactions/physiology ; Marine Biology ; *Metagenomics ; Seawater/*microbiology/*virology ; Virus Physiological Phenomena/genetics ; Viruses/genetics ; }, abstract = {Advances brought about by omics-based approaches have revolutionized our understanding of the diversity and ecological processes involving marine archaea, bacteria, and their viruses. This broad review discusses recent examples of how genomics, metagenomics, and ecogenomics have been applied to reveal the ecology of these biological entities. Three major topics are covered in this revision: (i) the novel roles of microorganisms in ecosystem processes; (ii) virus-host associations; and (iii) ecological associations of microeukaryotes and other microbes. We also briefly comment on the discovery of novel taxa from marine ecosystems; development of a robust taxonomic framework for prokaryotes; breakthroughs on the diversity and ecology of cyanobacteria; and advances on ecological modelling. We conclude by discussing limitations of the field and suggesting directions for future research.}, }
@article {pmid31024486, year = {2019}, author = {Sirén, K and Mak, SST and Melkonian, C and Carøe, C and Swiegers, JH and Molenaar, D and Fischer, U and Gilbert, MTP}, title = {Taxonomic and Functional Characterization of the Microbial Community During Spontaneous in vitro Fermentation of Riesling Must.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {697}, doi = {10.3389/fmicb.2019.00697}, pmid = {31024486}, issn = {1664-302X}, abstract = {Although there is an extensive tradition of research into the microbes that underlie the winemaking process, much remains to be learnt. We combined the high-throughput sequencing (HTS) tools of metabarcoding and metagenomics, to characterize how microbial communities of Riesling musts sampled at four different vineyards, and their subsequent spontaneously fermented derivatives, vary. We specifically explored community variation relating to three points: (i) how microbial communities vary by vineyard; (ii) how community biodiversity changes during alcoholic fermentation; and (iii) how microbial community varies between musts that successfully complete alcoholic fermentation and those that become 'stuck' in the process. Our metabarcoding data showed a general influence of microbial composition at the vineyard level. Two of the vineyards (4 and 5) had strikingly a change in the differential abundance of Metschnikowia. We therefore additionally performed shotgun metagenomic sequencing on a subset of the samples to provide preliminary insights into the potential relevance of this observation, and used the data to both investigate functional potential and reconstruct draft genomes (bins). At these two vineyards, we also observed an increase in non-Saccharomycetaceae fungal functions, and a decrease in bacterial functions during the early fermentation stage. The binning results yielded 11 coherent bins, with both vineyards sharing the yeast bins Hanseniaspora and Saccharomyces. Read recruitment and functional analysis of this data revealed that during fermentation, a high abundance of Metschnikowia might serve as a biocontrol agent against bacteria, via a putative iron depletion pathway, and this in turn could help Saccharomyces dominate the fermentation. During alcoholic fermentation, we observed a general decrease in biodiversity in both the metabarcoding and metagenomic data. Unexpected Micrococcus behavior was observed in vineyard 4 according to metagenomic analyses based on reference-based read mapping. Analysis of open reading frames using these data showed an increase of functions assigned to class Actinobacteria in the end of fermentation. Therefore, we hypothesize that bacteria might sit-and-wait until Saccharomyces activity slows down. Complementary approaches to annotation instead of relying a single database provide more coherent information true species. Lastly, our metabarcoding data enabled us to identify a relationship between stuck fermentations and Starmerella abundance. Given that robust chemical analysis indicated that although the stuck samples contained residual glucose, all fructose had been consumed, we hypothesize that this was because fructophilic Starmerella, rather than Saccharomyces, dominated these fermentations. Overall, our results showcase the different ways in which metagenomic analyses can improve our understanding of the wine alcoholic fermentation process.}, }
@article {pmid30659724, year = {2019}, author = {Turgay, E and Steinum, TM and Colquhoun, D and Karataş, S}, title = {Environmental biofilm communities associated with early-stage common dentex (Dentex dentex) culture.}, journal = {Journal of applied microbiology}, volume = {126}, number = {4}, pages = {1032-1043}, doi = {10.1111/jam.14205}, pmid = {30659724}, issn = {1365-2672}, support = {20950//Scientific Research Project Coordination Unit of Istanbul University/ ; }, mesh = {Animal Feed/analysis ; Animals ; Bacteria/classification/genetics/isolation &amp; purification ; Biofilms/classification/*growth &amp; development ; *Life Cycle Stages ; Metagenomics ; Microbiota/*genetics ; Perciformes/*growth &amp; development/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {AIMS: To describe the biofilm microbiota associated with various feeding phases during larval common dentex (Dentex dentex) culture.<br><br>METHODS AND RESULTS: A targeted metagenomic (metagenetic) study was performed by means of 16S rRNA gene-based PCR and NextGen pyrosequencing. The resulting dataset was scrutinized with microbial community analysis software (r packages) using r/Rstudio. While median observed and estimated alpha-diversities were 171 ± 38 and 207 ± 27 taxa, respectively, 72·1-85·8% of individual biofilm communities comprised only 27-46 taxa. Members of the genus Methylobacterium and family Rhodobacteraceae dominated biofilms formed during all feeding phases while genera Nannochloropsis and Tetraselmis microalgae were major constituents of biofilms during rotifer live feeding. Both potential fish pathogenic genera, for example, Vibrio and putatively probiotic taxa, for example, Phaeobacter gallaeciensis were identified.<br><br>CONCLUSIONS: Relatively stable biofilm communities were identified during each feeding phase but varied significantly between feeding phases, most likely in response to the introduction of live feed/microalgae-associated bacteria into rearing tanks.<br><br>The structure of the bacterial communities identified represents a 'template' for successful larval dentex culture and provides a foundation for future investigations into failed production cycles.}, }
@article {pmid30440093, year = {2019}, author = {Park, CH and Lee, AR and Lee, YR and Eun, CS and Lee, SK and Han, DS}, title = {Evaluation of gastric microbiome and metagenomic function in patients with intestinal metaplasia using 16S rRNA gene sequencing.}, journal = {Helicobacter}, volume = {24}, number = {1}, pages = {e12547}, doi = {10.1111/hel.12547}, pmid = {30440093}, issn = {1523-5378}, support = {//National Research Foundation of Korea (NRF)/ ; NRF-2017R1C1B5015928//Korea government (MSIP; Ministry of Science, ICT &amp; Future Planning)/ ; }, mesh = {Adult ; Aged ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria/classification/genetics/isolation &amp; purification ; Disease Progression ; Female ; Gastritis/microbiology/pathology ; Gastritis, Atrophic/drug therapy/microbiology/pathology ; Gastrointestinal Microbiome/drug effects/*genetics ; Helicobacter Infections/drug therapy/*microbiology/*pathology ; Helicobacter pylori/drug effects/genetics/isolation &amp; purification ; Humans ; Intestines/*microbiology/*pathology ; Male ; Metagenomics ; Metaplasia/*microbiology ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Stomach Neoplasms/microbiology/pathology ; Type IV Secretion Systems/genetics ; Young Adult ; }, abstract = {BACKGROUND: Despite recent advances in studies on the gastric microbiome, the role of the non-Helicobacter pylori gastric microbiome in gastric carcinogenesis remains unclear. We evaluated the characteristics of the gastric microbiome and metagenomic functions in patients with IM.<br><br>METHODS: Participants were classified into six groups according to disease status (chronic superficial gastritis [CSG], intestinal metaplasia [IM], and cancer) and H. pylori- infection status (H. pylori-positive and H. pylori-negative). The gastric microbiome was analyzed in mucosal tissues at the gastric antrum by 16S rRNA gene sequencing. Moreover, we assessed the metagenome including the type IV secretion system (T4SS) gene, as T4SS proteins are essential for transferring CagA from H. pylori- into the human gastric epithelium.<br><br>RESULTS: Among the 138 included patients, 48, 9, 23, 14, 12, and 32 were classified into the H. pylori-negative CSG, H. pylori-negative IM, H. pylori-negative cancer, H. pylori-positive CSG, H. pylori-positive IM, and H. pylori-positive cancer groups, respectively. Cyanobacteria were predominant in the H. pylori-negative CSG group compared to in the H. pylori-negative IM and H. pylori-negative cancer groups (H. pylori-negative CSG vs H. pylori-negative IM vs H. pylori-negative cancer: 14.0% vs 4.2% vs 0.04%, P < 0.001). In contrast, Rhizobiales were commonly observed in the H. pylori-negative IM group (H. pylori-negative CSG vs H. pylori-negative IM vs H. pylori-negative cancer: 1.9% vs 15.4% vs 2.8%, P < 0.001). The relative abundance of Rhizobiales increased as H. pylori-infected stomachs progressed from gastritis to IM. In the H. pylori-negative IM group, genes encoding T4SS were prevalent among the metagenome. Additionally, after H. pylori- eradication therapy, the gastric microbiome was similar to the microbiome observed after spontaneous clearance of H. pylori-.<br><br>CONCLUSIONS: The relative abundance of Rhizobiales was higher in patients with H. pylori-negative IM than in those with H. pylori-negative CSG or cancer. Additionally, T4SS genes were highly observed in the metagenome of patients with IM. Highly abundant T4SS proteins in these patients may promote gastric carcinogenesis.}, }
@article {pmid30286722, year = {2018}, author = {Mancini, MV and Damiani, C and Accoti, A and Tallarita, M and Nunzi, E and Cappelli, A and Bozic, J and Catanzani, R and Rossi, P and Valzano, M and Serrao, A and Ricci, I and Spaccapelo, R and Favia, G}, title = {Estimating bacteria diversity in different organs of nine species of mosquito by next generation sequencing.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {126}, pmid = {30286722}, issn = {1471-2180}, mesh = {Animal Structures/*microbiology ; Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; Culicidae/classification/*microbiology ; DNA, Bacterial/genetics ; Female ; High-Throughput Nucleotide Sequencing ; Male ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Symbiosis in insects is accumulating significant amount of studies: the description of a wide array of mutualistic associations across the evolutionary history of insects suggests that resident microbiota acts as a driving force by affecting several aspects of hosts biology. Among arthropods, mosquito midgut microbiota has been largely investigated, providing crucial insights on the role and implications of host-symbiont relationships. However, limited amount of studies addressed their efforts on the investigation of microbiota colonizing salivary glands and reproductive tracts, crucial organs for pathogen invasion and vertical transmission of symbiotic microorganisms. Using 16S rRNA gene sequencing-based approach, we analysed the microbiota of gut, salivary glands and reproductive tracts of several mosquito species, representing some of the main vectors of diseases, aiming at describing the dynamics of bacterial communities within the individual.<br><br>RESULTS: We identified a shared core microbiota between different mosquito species, although interesting inter- and intra-species differences were detected. Additionally, our results showed deep divergences between genera, underlining microbiota specificity and adaptation to their host.<br><br>CONCLUSIONS: The comprehensive landscape of the bacterial microbiota components may ultimately provide crucial insights and novel targets for possible application of symbionts in innovative strategies for the control of vector borne diseases, globally named Symbiotic Control (SC), and suggesting that the holobiont of different mosquito species may significantly vary. Moreover, mosquito species are characterized by distinctive microbiota in different organs, likely reflecting different functions and/or adaptation processes.}, }
@article {pmid30285625, year = {2018}, author = {Pacchioni, F and Esposito, A and Giacobazzi, E and Bettua, C and Struffi, P and Jousson, O}, title = {Air and waterborne microbiome of a pharmaceutical plant provide insights on spatiotemporal variations and community resilience after disturbance.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {124}, pmid = {30285625}, issn = {1471-2180}, mesh = {Air Microbiology ; Bacteria/classification/genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; Fresh Water/*microbiology ; Groundwater/*microbiology ; *Microbiota ; Phylogeny ; Plants, Medicinal/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: The presence of microrganisms in pharmaceutical production plant environments is typically monitored by cultural methods, however these cannot detect the unculturable fraction of the microbial community. To get more accurate information on the composition of these indoor microbial communities, both water and air microbiome from a pharmaceutical production plant were profiled by 16S amplicon sequencing.<br><br>RESULTS: In the water system, we found taxa which typically characterize surface freshwater, groundwater and oligotrophic environments. The airborne microbiome resulted dominated by taxa usually found in outdoor air in combination with human-associated taxa. The alpha- and beta- diversity values showed that the heat-based sanitization process of the water plant affects the composition of the water microbiome by transiently increasing both diversity and evenness. Taxonomic compositional shifts were also detected in response to sanitization, consisting in an increase of Firmicutes and α-Proteobacteria. On the other hand, seasonality seems to be the main driver of bacterial community composition in air of this work environment.<br><br>CONCLUSIONS: This approach resulted useful to describe the taxonomy of these indoor microbiomes and could be further applied to other built environments, in which the knowledge of the microbiome composition is of relevance. In addition, this study could assist in the design of new guidelines to improve microbiological quality control in indoor work environments.}, }
@article {pmid30833550, year = {2019}, author = {Milanese, A and Mende, DR and Paoli, L and Salazar, G and Ruscheweyh, HJ and Cuenca, M and Hingamp, P and Alves, R and Costea, PI and Coelho, LP and Schmidt, TSB and Almeida, A and Mitchell, AL and Finn, RD and Huerta-Cepas, J and Bork, P and Zeller, G and Sunagawa, S}, title = {Microbial abundance, activity and population genomic profiling with mOTUs2.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1014}, doi = {10.1038/s41467-019-08844-4}, pmid = {30833550}, issn = {2041-1723}, mesh = {Algorithms ; Cluster Analysis ; Computational Biology/methods ; Gene Expression Profiling ; Genes, Essential ; Genetic Markers ; Genome ; Host Microbial Interactions ; Humans ; *Metagenomics ; Microbiota/*genetics ; Molecular Sequence Annotation ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Metagenomic sequencing has greatly improved our ability to profile the composition of environmental and host-associated microbial communities. However, the dependency of most methods on reference genomes, which are currently unavailable for a substantial fraction of microbial species, introduces estimation biases. We present an updated and functionally extended tool based on universal (i.e., reference-independent), phylogenetic marker gene (MG)-based operational taxonomic units (mOTUs) enabling the profiling of >7700 microbial species. As more than 30% of them could not previously be quantified at this taxonomic resolution, relative abundance estimates based on mOTUs are more accurate compared to other methods. As a new feature, we show that mOTUs, which are based on essential housekeeping genes, are demonstrably well-suited for quantification of basal transcriptional activity of community members. Furthermore, single nucleotide variation profiles estimated using mOTUs reflect those from whole genomes, which allows for comparing microbial strain populations (e.g., across different human body sites).}, }
@article {pmid30128993, year = {2018}, author = {Mitchell, AB and Glanville, AR}, title = {Introduction to Techniques and Methodologies for Characterizing the Human Respiratory Virome.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1838}, number = {}, pages = {111-123}, doi = {10.1007/978-1-4939-8682-8_9}, pmid = {30128993}, issn = {1940-6029}, mesh = {Animals ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; *Metagenomics ; *Microbiota ; Polymerase Chain Reaction ; Respiratory Tract Infections/*virology ; Sequence Analysis, DNA ; Viruses/*genetics ; }, abstract = {There have been great advances in the methodologies available for the detection of respiratory viruses. Accompanying this, our knowledge surrounding the impact of these viruses has also made a great leap forward. We have come a long way from the once commonly accepted belief that the lower respiratory tract was sterile and that the detection of any microbial species must represent a breach in host defence and likely be associated with symptomatic infection. With the advent of molecular detection techniques and improvements in sequencing-based methodologies to make these tools more accessible and cost effective, we now know that there is an abundant and diverse ecosystem within the lower-respiratory tract. This chapter will outline the clinical impact of the human respiratory virome, techniques for sampling the lower respiratory tract, the evolution of the diagnostic tools available, and the current limitations in our instruments and knowledge in this area. The human respiratory virome is an exciting new area of research that will continue to grow with the aid of the methodologies outlined in the following chapters and the advent of even more efficient tools in the future.}, }
@article {pmid30128992, year = {2018}, author = {Mayo-Muñoz, D}, title = {Viral Genome Isolation from Human Faeces for Succession Assessment of the Human Gut Virome.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1838}, number = {}, pages = {97-108}, doi = {10.1007/978-1-4939-8682-8_8}, pmid = {30128992}, issn = {1940-6029}, mesh = {Feces/*virology ; *Gastrointestinal Microbiome ; *Genome, Viral ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; *Metagenomics/methods ; Whole Genome Sequencing ; }, abstract = {Despite the important role of the microbiota in the human gastrointestinal tract (GIT) and its impact on life-long health, the successional process through which this microbial community develops during infancy is still poorly understood. Specially, little is known about how the amount and type of viruses present in the GIT, i.e., the virome, varies throughout this period and about the role this collection of viruses may play in the assembly of the GIT microbiota.The patterns of taxonomic change of the GIT viral community can be analyzed in a birth cohort of infants during the first year of life. The present chapter presents a detailed protocol for the isolation and extraction of viral nucleic acids from collected human faecal samples, whole genome amplification (WGA) using phi29 DNA polymerase and preparation for sequencing through high-throughput 454 pyrosequencing. The sequencing data can be posteriorly used for taxonomic classification in order to establish the composition of the virome present in each sample and to assess the process of viral dynamics through time.}, }
@article {pmid30128990, year = {2018}, author = {Kramná, L and Cinek, O}, title = {Virome Sequencing of Stool Samples.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1838}, number = {}, pages = {59-83}, doi = {10.1007/978-1-4939-8682-8_6}, pmid = {30128990}, issn = {1940-6029}, mesh = {Bacteriophages/*classification/*genetics/isolation &amp; purification ; DNA, Viral/genetics/isolation &amp; purification ; Feces/*virology ; *Gastrointestinal Microbiome ; Gene Library ; *Metagenome ; *Metagenomics/methods ; Polymerase Chain Reaction ; RNA, Viral/genetics/isolation &amp; purification ; Ultracentrifugation ; }, abstract = {Next-generation sequencing has opened avenues to studying complex populations such as the bacteriome (all bacteria), mycobiome (all fungi), and virome (all viruses in a given sample). Viromes are less often investigated as compared to bacteriomes. The reasons are mostly methodological: because no common pan-viral sequence signature exists, metagenomic sequencing remains the only option. This brings about the need of laborious virus enrichment, multiple signal amplification steps with virtually no possibility of interim quality control, and complicated bioinformatic analysis of the ensuing sequence data. Nevertheless, over the past decade virome sequencing has been enormously successful in identifying new agents in human and animal diseases, and in characterizing viruses in various ecological niches. Recently, virome sequencing has been also employed in studies of non-infectious diseases, which has brought about new challenges of sensitivity, costs, and reproducibility in testing of large sets of samples. Here, we present a detailed protocol that has been utilized in virome studies where hundreds of samples had to be reliably tested in order to assess the association of the stool virome with susceptibility to type 1 diabetes, a non-infectious autoimmune disease.}, }
@article {pmid30128989, year = {2018}, author = {Castro-Mejía, JL and Deng, L and Vogensen, FK and Reyes, A and Nielsen, DS}, title = {Extraction and Purification of Viruses from Fecal Samples for Metagenome and Morphology Analyses.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1838}, number = {}, pages = {49-57}, doi = {10.1007/978-1-4939-8682-8_5}, pmid = {30128989}, issn = {1940-6029}, mesh = {Feces/*virology ; *Gastrointestinal Microbiome ; Humans ; *Metagenome ; *Metagenomics/methods ; Microscopy, Fluorescence ; Ultracentrifugation ; Viruses/*genetics/*isolation &amp; purification/ultrastructure ; }, abstract = {The human enteric virome consists of endogenous retro elements and viruses that infect the host and members of the gut microbiome (GM). Mounting evidence suggests that the gut virome plays a central role in maintaining homeostasis and via the GM influences immunology of the host. To thoroughly characterize the gut virome, it is often very useful to first separate and concentrate extracellular viral-like particles (eVLPs) enabling an integrative characterization of them. Here, we describe a detailed protocol for extraction and concentration of the viral fraction from fecal samples based on a polyethylene glycol precipitation (PEG) approach. These procedures maximize the yields of eVLPs (and their DNA) with high purity well suited for down-stream analysis such as quantification and morphological assessment, determination of phage-host pairs as well as virome sequencing.}, }
@article {pmid28852195, year = {2017}, author = {Ozkan, J and Nielsen, S and Diez-Vives, C and Coroneo, M and Thomas, T and Willcox, M}, title = {Temporal Stability and Composition of the Ocular Surface Microbiome.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {9880}, pmid = {28852195}, issn = {2045-2322}, mesh = {Adult ; Conjunctiva/*microbiology ; Eyelids/*microbiology ; Female ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; RNA, Ribosomal, 16S ; }, abstract = {To determine if there is a core ocular surface microbiome and whether there are microbial community changes over time, the conjunctiva of 45 healthy subjects were sampled at three time points over three months and processed using culture-dependent and -independent methods. Contaminant taxa were removed using a linear regression model using taxa abundances in negative controls as predictor of taxa abundances in subject samples. Both cultured cell counts and sequencing indicated low microbial biomass on the ocular surface. No cultured species was found in all subjects at all times or in all subjects at any one time. After removal of contaminant taxa identified in negative controls using a statistical model, the most commonly detected taxon was Corynebacterium (11.1%). No taxa were found in all subjects at all times or in all subjects in any one time, but there were 26 taxa present in at least one or more subjects at all times including Corynebacterium and Streptococcus. The ocular surface contains a low diversity of microorganisms. Using culture dependent and independent methods, the ocular surface does not appear to support a substantial core microbiome. However, consistently present taxa could be observed within individuals suggesting the possibility of individual-specific core microbiomes.}, }
@article {pmid28852182, year = {2017}, author = {Mancabelli, L and Milani, C and Lugli, GA and Turroni, F and Mangifesta, M and Viappiani, A and Ticinesi, A and Nouvenne, A and Meschi, T and van Sinderen, D and Ventura, M}, title = {Unveiling the gut microbiota composition and functionality associated with constipation through metagenomic analyses.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {9879}, pmid = {28852182}, issn = {2045-2322}, mesh = {Case-Control Studies ; Constipation/*etiology/metabolism ; *Gastrointestinal Microbiome ; Gene Amplification ; Humans ; *Metagenome ; *Metagenomics/methods ; RNA, Ribosomal, 16S ; }, abstract = {Functional constipation (FC) is a gastrointestinal disorder with a high prevalence among the general population. The precise causes of FC are still unknown and are most likely multifactorial. Growing evidence indicates that alterations of gut microbiota composition contribute to constipation symptoms. Nevertheless, many discrepancies exist in literature and no clear link between FC and gut microbiota composition has as yet been identified. In this study, we performed 16 S rRNA-based microbial profiling analysis of 147 stool samples from 68 FC individuals and compared their microbial profiles with those of 79 healthy subjects (HS). Notably, the gut microbiota of FC individuals was shown to be depleted of members belonging to Bacteroides, Roseburia and Coprococcus 3. Furthermore, the metabolic capabilities of the gut microbiomes of five FC and five HS individuals were evaluated through shotgun metagenomics using a MiSeq platform, indicating that HS are enriched in pathways involved in carbohydrate, fatty acid and lipid metabolism as compared to FC. In contrast, the microbiomes corresponding to FC were shown to exhibit high abundance of genes involved in hydrogen production, methanogenesis and glycerol degradation. The identified differences in bacterial composition and metabolic capabilities may play an important role in development of FC symptoms.}, }
@article {pmid28852143, year = {2017}, author = {Gribben, PE and Nielsen, S and Seymour, JR and Bradley, DJ and West, MN and Thomas, T}, title = {Microbial communities in marine sediments modify success of an invasive macrophyte.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {9845}, pmid = {28852143}, issn = {2045-2322}, mesh = {Australia ; Bacteria ; *Biodiversity ; Ecosystem ; Geologic Sediments/*microbiology ; *Introduced Species ; Metagenome ; Metagenomics/methods ; *Microbiota ; *Oceans and Seas ; *Plants ; }, abstract = {Invasive plants have extensive impacts on ecosystem function and biodiversity globally. Our inability to manage invasive species stems in part from a lack of understanding of the processes that control their successful establishment and spread. To date, studies have largely considered how above-ground processes control native/invasive plant interactions. Emerging research from terrestrial and wetland ecosystems demonstrates that below-ground processes under microbial control can determine the outcome of interactions between native and invasive plants. Whether sediment microbes modify the success of invasive macrophytes in marine ecosystems is untested, despite marine sediment microbes controlling many ecological processes (e.g. nutrient cycling) comparable to those in terrestrial ecosystems. We first show that sediment bacterial communities differ between the native seagrass Zostera capricorni and the invasive alga Caulerpa taxifolia and that those differences relate to functional changes in sulfur cycling between the macrophytes. Second, by experimentally manipulating the microbial communities we show that intact microbial communities in Z. capricorni sediments provide biotic resistance by reducing C. taxifolia fragment growth 119% compared to when they are inactive, and intact microbial communities in C. taxifolia sediments have positive feedbacks by increasing fragment growth 200%. Thus, similar to terrestrial ecosystems, microorganisms appear to indirectly control the success of invasive macrophytes in marine ecosystems.}, }
@article {pmid30504642, year = {2019}, author = {Nakagawa, T and Tsuchiya, Y and Ueda, S and Fukui, M and Takahashi, R}, title = {Eelgrass Sediment Microbiome as a Nitrous Oxide Sink in Brackish Lake Akkeshi, Japan.}, journal = {Microbes and environments}, volume = {34}, number = {1}, pages = {13-22}, doi = {10.1264/jsme2.ME18103}, pmid = {30504642}, issn = {1347-4405}, mesh = {Ammonia/metabolism ; Archaea/classification/genetics/isolation &amp; purification/metabolism ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Geologic Sediments/*microbiology ; Japan ; Lakes/*microbiology ; Metagenomics ; *Microbiota/genetics ; Nitrous Oxide/*metabolism ; Oxidation-Reduction ; Oxidoreductases/genetics ; *Saline Waters ; *Water Microbiology ; Zosteraceae/*microbiology ; }, abstract = {Nitrous oxide (N2O) is a powerful greenhouse gas; however, limited information is currently available on the microbiomes involved in its sink and source in seagrass meadow sediments. Using laboratory incubations, a quantitative PCR (qPCR) analysis of N2O reductase (nosZ) and ammonia monooxygenase subunit A (amoA) genes, and a metagenome analysis based on the nosZ gene, we investigated the abundance of N2O-reducing microorganisms and ammonia-oxidizing prokaryotes as well as the community compositions of N2O-reducing microorganisms in in situ and cultivated sediments in the non-eelgrass and eelgrass zones of Lake Akkeshi, Japan. Laboratory incubations showed that N2O was reduced by eelgrass sediments and emitted by non-eelgrass sediments. qPCR analyses revealed that the abundance of nosZ gene clade II in both sediments before and after the incubation as higher in the eelgrass zone than in the non-eelgrass zone. In contrast, the abundance of ammonia-oxidizing archaeal amoA genes increased after incubations in the non-eelgrass zone only. Metagenome analyses of nosZ genes revealed that the lineages Dechloromonas-Magnetospirillum-Thiocapsa and Bacteroidetes (Flavobacteriia) within nosZ gene clade II were the main populations in the N2O-reducing microbiome in the in situ sediments of eelgrass zones. Sulfur-oxidizing Gammaproteobacteria within nosZ gene clade II dominated in the lineage Dechloromonas-Magnetospirillum-Thiocapsa. Alphaproteobacteria within nosZ gene clade I were predominant in both zones. The proportions of Epsilonproteobacteria within nosZ gene clade II increased after incubations in the eelgrass zone microcosm supplemented with N2O only. Collectively, these results suggest that the N2O-reducing microbiome in eelgrass meadows is largely responsible for coastal N2O mitigation.}, }
@article {pmid30459201, year = {2018}, author = {Hannigan, GD and Duhaime, MB and Ruffin, MT and Koumpouras, CC and Schloss, PD}, title = {Diagnostic Potential and Interactive Dynamics of the Colorectal Cancer Virome.}, journal = {mBio}, volume = {9}, number = {6}, pages = {}, pmid = {30459201}, issn = {2150-7511}, support = {P30 DK034933/DK/NIDDK NIH HHS/United States ; T32 AI007528/AI/NIAID NIH HHS/United States ; U01 CA086400/CA/NCI NIH HHS/United States ; }, mesh = {Bacteria/genetics/virology ; Bacteriophages/*genetics/isolation &amp; purification ; Cohort Studies ; Colorectal Neoplasms/*diagnosis/microbiology/*virology ; Feces/microbiology/virology ; Humans ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Viruses/*genetics ; }, abstract = {Human viruses (those that infect human cells) have been associated with many cancers, largely due to their mutagenic and functionally manipulative abilities. Despite this, cancer microbiome studies have focused almost exclusively on bacteria instead of viruses. We began evaluating the cancer virome by focusing on colorectal cancer, a primary cause of morbidity and mortality throughout the world and a cancer linked to altered colonic bacterial community compositions but with an unknown association with the gut virome. We used 16S rRNA gene, whole shotgun metagenomic, and purified virus metagenomic sequencing of stool to evaluate the differences in human colorectal cancer virus and bacterial community composition. Through random forest modeling, we identified differences in the healthy and colorectal cancer viromes. The cancer-associated virome consisted primarily of temperate bacteriophages that were also predicted to be bacterium-virus community network hubs. These results provide foundational evidence that bacteriophage communities are associated with colorectal cancer and potentially impact cancer progression by altering the bacterial host communities.IMPORTANCE Colorectal cancer is a leading cause of cancer-related death in the United States and worldwide. Its risk and severity have been linked to colonic bacterial community composition. Although human-specific viruses have been linked to other cancers and diseases, little is known about colorectal cancer virus communities. We addressed this knowledge gap by identifying differences in colonic virus communities in the stool of colorectal cancer patients and how they compared to bacterial community differences. The results suggested an indirect role for the virome in impacting colorectal cancer by modulating the associated bacterial community. These findings both support the idea of a biological role for viruses in colorectal cancer and provide a new understanding of basic colorectal cancer etiology.}, }
@article {pmid30401779, year = {2018}, author = {Bratburd, JR and Keller, C and Vivas, E and Gemperline, E and Li, L and Rey, FE and Currie, CR}, title = {Gut Microbial and Metabolic Responses to Salmonella enterica Serovar Typhimurium and Candida albicans.}, journal = {mBio}, volume = {9}, number = {6}, pages = {}, pmid = {30401779}, issn = {2150-7511}, support = {U19 AI109673/AI/NIAID NIH HHS/United States ; R56 DK071801/DK/NIDDK NIH HHS/United States ; R01 DK108259/DK/NIDDK NIH HHS/United States ; S10 RR029531/RR/NCRR NIH HHS/United States ; T32 AI055397/AI/NIAID NIH HHS/United States ; R01 DK071801/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Biosynthetic Pathways ; Candida albicans/pathogenicity ; Candidiasis/*microbiology ; Cecum/microbiology ; Disease Models, Animal ; Enterobacteriaceae/isolation &amp; purification ; *Gastrointestinal Microbiome ; Germ-Free Life ; Humans ; Male ; Metabolomics ; Metagenomics ; Mice ; Mice, Inbred C57BL ; *Microbiota ; Oxidative Stress ; Salmonella Infections, Animal/*microbiology ; Salmonella typhimurium/pathogenicity ; }, abstract = {The gut microbiota confers resistance to pathogens of the intestinal ecosystem, yet the dynamics of pathogen-microbiome interactions and the metabolites involved in this process remain largely unknown. Here, we use gnotobiotic mice infected with the virulent pathogen Salmonella enterica serovar Typhimurium or the opportunistic pathogen Candida albicans in combination with metagenomics and discovery metabolomics to identify changes in the community and metabolome during infection. To isolate the role of the microbiota in response to pathogens, we compared mice monocolonized with the pathogen, uninfected mice &quot;humanized&quot; with a synthetic human microbiome, or infected humanized mice. In Salmonella-infected mice, by 3 days into infection, microbiome community structure and function changed substantially, with a rise in Enterobacteriaceae strains and a reduction in biosynthetic gene cluster potential. In contrast, Candida-infected mice had few microbiome changes. The LC-MS metabolomic fingerprint of the cecum differed between mice monocolonized with either pathogen and humanized infected mice. Specifically, we identified an increase in glutathione disulfide, glutathione cysteine disulfide, inosine 5'-monophosphate, and hydroxybutyrylcarnitine in mice infected with Salmonella in contrast to uninfected mice and mice monocolonized with Salmonella These metabolites potentially play a role in pathogen-induced oxidative stress. These results provide insight into how the microbiota community members interact with each other and with pathogens on a metabolic level.IMPORTANCE The gut microbiota is increasingly recognized for playing a critical role in human health and disease, especially in conferring resistance to both virulent pathogens such as Salmonella, which infects 1.2 million people in the United States every year (E. Scallan, R. M. Hoekstra, F. J. Angulo, R. V. Tauxe, et al., Emerg Infect Dis 17:7-15, 2011, https://doi.org/10.3201/eid1701.P11101), and opportunistic pathogens like Candida, which causes an estimated 46,000 cases of invasive candidiasis each year in the United States (Centers for Disease Control and Prevention, Antibiotic Resistance Threats in the United States, 2013, 2013). Using a gnotobiotic mouse model, we investigate potential changes in gut microbial community structure and function during infection using metagenomics and metabolomics. We observe that changes in the community and in biosynthetic gene cluster potential occur within 3 days for the virulent Salmonella enterica serovar Typhimurium, but there are minimal changes with a poorly colonizing Candida albicans In addition, the metabolome shifts depending on infection status, including changes in glutathione metabolites in response to Salmonella infection, potentially in response to host oxidative stress.}, }
@article {pmid29507058, year = {2018}, author = {Kim, S and Goel, R and Kumar, A and Qi, Y and Lobaton, G and Hosaka, K and Mohammed, M and Handberg, EM and Richards, EM and Pepine, CJ and Raizada, MK}, title = {Imbalance of gut microbiome and intestinal epithelial barrier dysfunction in patients with high blood pressure.}, journal = {Clinical science (London, England : 1979)}, volume = {132}, number = {6}, pages = {701-718}, pmid = {29507058}, issn = {1470-8736}, support = {R01 HL033610/HL/NHLBI NIH HHS/United States ; R01 HL056921/HL/NHLBI NIH HHS/United States ; R01 HL132448/HL/NHLBI NIH HHS/United States ; R37 HL033610/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/immunology/*metabolism ; *Blood Pressure ; Butyrates/blood ; Case-Control Studies ; Cholera Toxin/blood ; Disease Models, Animal ; Epithelial Cells/immunology/metabolism/*microbiology ; Fatty Acid-Binding Proteins/blood ; Feces/microbiology ; *Gastrointestinal Microbiome ; Host-Pathogen Interactions ; Humans ; Hypertension/blood/immunology/*microbiology/physiopathology ; Intestinal Mucosa/immunology/metabolism/*microbiology/physiopathology ; Lipopolysaccharides/blood ; Mice, Inbred C57BL ; Permeability ; Rats, Sprague-Dawley ; Th17 Cells/immunology/metabolism ; }, abstract = {Recent evidence indicates a link between gut pathology and microbiome with hypertension (HTN) in animal models. However, whether this association exists in humans is unknown. Thus, our objectives in the present study were to test the hypotheses that high blood pressure (BP) patients have distinct gut microbiomes and that gut-epithelial barrier function markers and microbiome composition could predict systolic BP (SBP). Fecal samples, analyzed by shotgun metagenomics, displayed taxonomic and functional changes, including altered butyrate production between patients with high BP and reference subjects. Significant increases in plasma of intestinal fatty acid binding protein (I-FABP), lipopolysaccharide (LPS), and augmented gut-targetting proinflammatory T helper 17 (Th17) cells in high BP patients demonstrated increased intestinal inflammation and permeability. Zonulin, a gut epithelial tight junction protein regulator, was markedly elevated, further supporting gut barrier dysfunction in high BP. Zonulin strongly correlated with SBP (R2 = 0.5301, P<0.0001). Two models predicting SBP were built using stepwise linear regression analysis of microbiome data and circulating markers of gut health, and validated in a separate cohort by prediction of SBP from zonulin in plasma (R2 = 0.4608, P<0.0001). The mouse model of HTN, chronic angiotensin II (Ang II) infusion, was used to confirm the effects of butyrate and gut barrier function on the cardiovascular system and BP. These results support our conclusion that intestinal barrier dysfunction and microbiome function are linked to HTN in humans. They suggest that manipulation of gut microbiome and its barrier functions could be the new therapeutic and diagnostic avenues for HTN.}, }
@article {pmid29089173, year = {2018}, author = {Turroni, F and Milani, C and Duranti, S and Mahony, J and van Sinderen, D and Ventura, M}, title = {Glycan Utilization and Cross-Feeding Activities by Bifidobacteria.}, journal = {Trends in microbiology}, volume = {26}, number = {4}, pages = {339-350}, doi = {10.1016/j.tim.2017.10.001}, pmid = {29089173}, issn = {1878-4380}, mesh = {Adaptation, Biological ; Bifidobacterium/genetics/*physiology ; Biological Evolution ; Carbohydrate Metabolism/physiology ; Ecology ; Gastrointestinal Microbiome/genetics/*physiology ; Gastrointestinal Tract/microbiology ; Genome, Bacterial ; Humans ; Metagenomics ; Polysaccharides/*metabolism ; Probiotics ; }, abstract = {Bifidobacteria represent one of the first colonizers of the mammalian gut, where such colonization is facilitated by their saccharolytic capabilities. Genomic analyses of bifidobacteria have revealed intriguing genetic strategies employed by these bacteria to access a variety of dietary and host-produced glycans. Bifidobacterial genome evolution therefore represents a fascinating example of how their chromosomes were molded to contain a large number of genes involved in carbohydrate metabolism. One of the reasons as to why bifidobacteria are such dominant and prevalent members of the (early) microbiota is that they may access glycans in the gut through mutualistic cross-feeding or resource-sharing activities, which is indicative of 'social behavior' among bifidobacterial strains.}, }
@article {pmid31004827, year = {2019}, author = {Sung, CM and Lin, YF and Chen, KF and Ke, HM and Huang, HY and Gong, YN and Tsai, WS and Lu, MJ and Cheng, HT and Lin, CY and Kuo, CJ and Tsai, IJ and Hsieh, SY}, title = {Predicting clinical outcomes of cirrhosis patients with hepatic encephalopathy from the fecal microbiome.}, journal = {Cellular and molecular gastroenterology and hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jcmgh.2019.04.008}, pmid = {31004827}, issn = {2352-345X}, abstract = {BACKGROUND &amp; AIMS: Gut dysbiosis plays a role in hepatic encephalopathy (HE), while its relationship at the acute episode of overt HE (AHE), the disease progression and clinical outcomes remains unclear. We aimed to identify AHE-specific microbiome and its association to patients' outcomes.<br><br>METHODS: We profiled fecal microbiome changes for a cohort of 62 patients with cirrhosis and AHE i) before treatment, ii) 2-3 days after medication and iii) 2-3 months after recovery, and three control cohorts i) healthy individuals, patients with ii) compensated or iii) decompensated cirrhosis.<br><br>RESULTS: Comparison of the microbiome shift from compensated, decompensated cirrhosis, AHE to recovery revealed the AHE-specific gut-dysbiosis. The gut microbiome diversity was decreased during AHE, further reduced after medication, and only partially reversed during the recovery. The relative abundance of Bacteroidetes phylum in the microbiome decreased, whereas that of Firmicute, Proteobacteria and Actinobacteria increased in patients during AHE compared to those with compensated cirrhosis. A total of 70 operational taxonomic units (OTUs) were significantly different between AHE and decompensated cirrhosis abundances. Of them, the abundance of Veillonella parvula increased the most during AHE via a metagenomics recovery of the genomes. Moreover, the relative abundances of three (Alistipes, Bacteroides, Phascolarctobacterium) and five OTUs (Clostridium-XI, Bacteroides, Bacteroides, Lactobacillus, Clostridium-sedis) at AHE were respectively associated with HE recurrence and overall survival during the subsequent one-year follow-up.<br><br>CONCLUSIONS: AHE-specific gut OTUs were identified that may be involved in HE development and able to predict clinical outcomes, providing new strategies for the prevention and treatment of HE recurrence in patients with cirrhosis.}, }
@article {pmid30979963, year = {2019}, author = {Singer, GAC and Fahner, NA and Barnes, JG and McCarthy, A and Hajibabaei, M}, title = {Comprehensive biodiversity analysis via ultra-deep patterned flow cell technology: a case study of eDNA metabarcoding seawater.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {5991}, doi = {10.1038/s41598-019-42455-9}, pmid = {30979963}, issn = {2045-2322}, abstract = {The characterization of biodiversity is a crucial element of ecological investigations as well as environmental assessment and monitoring activities. Increasingly, amplicon-based environmental DNA metabarcoding (alternatively, marker gene metagenomics) is used for such studies given its ability to provide biodiversity data from various groups of organisms simply from analysis of bulk environmental samples such as water, soil or sediments. The Illumina MiSeq is currently the most popular tool for carrying out this work, but we set out to determine whether typical studies were reading enough DNA to detect rare organisms (i.e., those that may be of greatest interest such as endangered or invasive species) present in the environment. We collected sea water samples along two transects in Conception Bay, Newfoundland and analyzed them on the MiSeq with a sequencing depth of 100,000 reads per sample (exceeding the 60,000 per sample that is typical of similar studies). We then analyzed these same samples on Illumina's newest high-capacity platform, the NovaSeq, at a depth of 7 million reads per sample. Not surprisingly, the NovaSeq detected many more taxa than the MiSeq thanks to its much greater sequencing depth. However, contrary to our expectations this pattern was true even in depth-for-depth comparisons. In other words, the NovaSeq can detect more DNA sequence diversity within samples than the MiSeq, even at the exact same sequencing depth. Even when samples were reanalyzed on the MiSeq with a sequencing depth of 1 million reads each, the MiSeq's ability to detect new sequences plateaued while the NovaSeq continued to detect new sequence variants. These results have important biological implications. The NovaSeq found 40% more metazoan families in this environment than the MiSeq, including some of interest such as marine mammals and bony fish so the real-world implications of these findings are significant. These results are most likely associated to the advances incorporated in the NovaSeq, especially a patterned flow cell, which prevents similar sequences that are neighbours on the flow cell (common in metabarcoding studies) from being erroneously merged into single spots by the sequencing instrument. This study sets the stage for incorporating eDNA metabarcoding in comprehensive analysis of oceanic samples in a wide range of ecological and environmental investigations.}, }
@article {pmid30962514, year = {2019}, author = {Tan, S and Liu, J and Fang, Y and Hedlund, BP and Lian, ZH and Huang, LY and Li, JT and Huang, LN and Li, WJ and Jiang, HC and Dong, HL and Shu, WS}, title = {Insights into ecological role of a new deltaproteobacterial order Candidatus Acidulodesulfobacterales by metagenomics and metatranscriptomics.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0415-y}, pmid = {30962514}, issn = {1751-7370}, support = {U1501232//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31570506//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41603074//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31600077//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41773132//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41622106//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31570500//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41630103//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2016A030312003//Natural Science Foundation of Guangdong Province (Guangdong Natural Science Foundation)/ ; DEB-1557042//National Science Foundation (NSF)/ ; }, abstract = {Several abundant but yet uncultivated bacterial groups exist in extreme iron- and sulfur-rich environments, and the physiology, biodiversity, and ecological roles of these bacteria remain a mystery. Here we retrieved four metagenome-assembled genomes (MAGs) from an artificial acid mine drainage (AMD) system, and propose they belong to a new deltaproteobacterial order, Candidatus Acidulodesulfobacterales. The distribution pattern of Ca. Acidulodesulfobacterales in AMDs across Southeast China correlated strongly with ferrous iron. Reconstructed metabolic pathways and gene expression profiles showed that they were likely facultatively anaerobic autotrophs capable of nitrogen fixation. In addition to dissimilatory sulfate reduction, encoded by dsrAB, dsrD, dsrL, and dsrEFH genes, these microorganisms might also oxidize sulfide, depending on oxygen concentration and/or oxidation reduction potential. Several genes with homology to those involved in iron metabolism were also identified, suggesting their potential role in iron cycling. In addition, the expression of abundant resistance genes revealed the mechanisms of adaptation and response to the extreme environmental stresses endured by these organisms in the AMD environment. These findings shed light on the distribution, diversity, and potential ecological role of the new order Ca. Acidulodesulfobacterales in nature.}, }
@article {pmid30962029, year = {2019}, author = {Brink, M and Rhode, C and Macey, BM and Christison, KW and Roodt-Wilding, R}, title = {Metagenomic assessment of body surface bacterial communities of the sea urchin, Tripneustes gratilla.}, journal = {Marine genomics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.margen.2019.03.010}, pmid = {30962029}, issn = {1876-7478}, abstract = {Sea urchins, including Tripneustes gratilla, are susceptible to a disease known as bald sea urchin disease, which has the potential to lead to economic losses in this emerging aquaculture industry in South Africa. This disease is characterized by lesions that form on sea urchin exoskeletal surfaces. This study aimed to characterize the body surface bacterial communities associated with T. gratilla, using a 16S rDNA gene metagenomics approach, to provide insight into the bacterial agents associated with this aquaculture species, as well as with this balding disease. Bacterial samples were collected from non-lesioned healthy animals obtained from natural locations along the eastern coast of South Africa, as well as from different cultured cohorts: non-lesioned healthy-, lesioned diseased- and non-lesioned stressed animals. A total of 1,067,515 individual bacterial operational taxonomic units (OTUs) were identified, belonging to 133 family-, 123 genus- and 113 species level OTU groups. Alpha diversity analyses, based on Chao1, Shannon and Simpson indices, showed that there were no statistically significant differences (ANOVA; P > 0.05) between the respective cohorts, as all cohorts displayed a high degree of bacterial diversity. Similarly, beta diversity analyses (Non-metric multidimensional scaling) showed a large degree of overlapping OTUs across the four cohorts. Within each cohort, various OTUs commonly associated with marine environments were found, predominantly belonging to the families Vibrionaceae, Saprospiraceae, Flavobacteriaceae and Sphingomonadaceae. Differential abundance analysis (DESeq2) revealed that OTUs that are differentially abundant across cohorts were likely not responsible for this balding disease, suggesting that complex bacterial agents, rather than a specific pathogenic agent, are likely causing this disease. Furthermore, the putative metabolic functions assigned to the bacterial communities showed that heterotrophic bacteria appear to be responsible for tissue lysis of degrading animal matter. The results from this study, obtained through univariate and multivariate-based approaches, contributes to future management strategies of this emerging aquaculture species by providing insight into the bacterial communities associated with both natural and cultured environments.}, }
@article {pmid30946154, year = {2019}, author = {Sessa, L and Reddel, S and Manno, E and Quagliariello, A and Cotugno, N and Del Chierico, F and Amodio, D and Capponi, C and Leone, F and Bernardi, S and Rossi, P and Putignani, L and Palma, P}, title = {Distinct gut microbiota profile in antiretroviral therapy-treated perinatally HIV-infected patients associated with cardiac and inflammatory biomarkers.}, journal = {AIDS (London, England)}, volume = {33}, number = {6}, pages = {1001-1011}, doi = {10.1097/QAD.0000000000002131}, pmid = {30946154}, issn = {1473-5571}, abstract = {OBJECTIVE: Persistent inflammation and higher risk to develop cardiovascular diseases still represent a major complication for HIV-infected patients despite effective antiretroviral therapy (ART). We investigated the correlation between the gut microbiota profile, markers of inflammation, vascular endothelial activation (VEA) and microbial translocation (MT) in perinatally HIV-infected patients (PHIV) under ART.<br><br>DESIGN: Cross-sectional study including 61 ART-treated PHIV (age range 3-30 years old) and 71 age-matched healthy controls. Blood and stool sample were collected at the same time and analyzed for gut microbiota composition and plasma biomarkers.<br><br>METHODS: Gut microbiota composition was determined by 16S rRNA targeted-metagenomics. Soluble markers of MT, inflammation and VEA were quantified by ELISA or Luminex assay. Markers of immune activation were analyzed by flow cytometry on CD4 and CD8T cells.<br><br>RESULTS: We identified two distinct gut microbiota profiles (groups A and B) among PHIV. No different clinical parameters (age, sex, ethnicity, clinical class), dietary and sexual habits were found between the groups. The group A showed a relative dominance of Akkermansia muciniphila, whereas gut microbiota of group B was characterized by a higher biodiversity. The analysis of soluble markers revealed a significantly higher level of soluble E-selectine (P = 0.0296), intercellular adhesion molecule-1 (P = 0.0028), vascular adhesion molecule-1 (P = 0.0230), IL-6 (P = 0.0247) and soluble CD14 (P = 0.0142) in group A compared with group B.<br><br>CONCLUSION: Distinctive gut microbiota profiles are differently associated with inflammation, microbial translocation and VEA. Future studies are needed to understand the role of A. muciniphila and risk to develop cardiovascular diseases in PHIV.}, }
@article {pmid30927421, year = {2019}, author = {Ding, GC and Bai, M and Han, H and Li, H and Ding, X and Yang, H and Xu, T and Li, J}, title = {Microbial taxonomic, nitrogen cycling and phosphorus recycling community composition during long-term organic greenhouse farming.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {5}, pages = {}, doi = {10.1093/femsec/fiz042}, pmid = {30927421}, issn = {1574-6941}, abstract = {Understanding the interplay between the farming system and soil microbiomes could aid the design of a sustainable and efficient farming system. A comparative greenhouse experiment consisting of organic (ORG), integrated (INT) and conventional (CON) farming systems was established in northern China in 2002. The effects of 12 years of organic farming on soil microbiomes were explored by metagenomic and 16S rRNA gene amplicon sequencing analyses. Long-term ORG shifted the community composition of dominant phyla, especially Acidobacteria, increased the relative abundance of Ignavibacteria and Acidobacteria Gp6 and decreased the relative abundance of Nitrosomonas, Bacillus and Paenibacillus. Metagenomic analysis further revealed that relative abundance of ammonia oxidizing microorganisms (Bacteria and Archaea) and anaerobic ammonium oxidation bacteria decreased during ORG. Conversely, the relative abundance of bacteria-carrying periplasmic nitrate reductases (napA) was slightly higher for ORG. Long-term organic farming also caused significant alterations to the community composition of functional groups associated with ammonia oxidation, denitrification and phosphorus recycling. In summary, this study provides key insights into the composition of soil microbiomes and long-term organic farming under greenhouse conditions.}, }
@article {pmid30906284, year = {2019}, author = {Cycoń, M and Mrozik, A and Piotrowska-Seget, Z}, title = {Antibiotics in the Soil Environment-Degradation and Their Impact on Microbial Activity and Diversity.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {338}, doi = {10.3389/fmicb.2019.00338}, pmid = {30906284}, issn = {1664-302X}, abstract = {Antibiotics play a key role in the management of infectious diseases in humans, animals, livestock, and aquacultures all over the world. The release of increasing amount of antibiotics into waters and soils creates a potential threat to all microorganisms in these environments. This review addresses issues related to the fate and degradation of antibiotics in soils and the impact of antibiotics on the structural, genetic and functional diversity of microbial communities. Due to the emergence of bacterial resistance to antibiotics, which is considered a worldwide public health problem, the abundance and diversity of antibiotic resistance genes (ARGs) in soils are also discussed. When antibiotic residues enter the soil, the main processes determining their persistence are sorption to organic particles and degradation/transformation. The wide range of DT50 values for antibiotic residues in soils shows that the processes governing persistence depend on a number of different factors, e.g., physico-chemical properties of the residue, characteristics of the soil, and climatic factors (temperature, rainfall, and humidity). The results presented in this review show that antibiotics affect soil microorganisms by changing their enzyme activity and ability to metabolize different carbon sources, as well as by altering the overall microbial biomass and the relative abundance of different groups (i.e., Gram-negative bacteria, Gram-positive bacteria, and fungi) in microbial communities. Studies using methods based on analyses of nucleic acids prove that antibiotics alter the biodiversity of microbial communities and the presence of many types of ARGs in soil are affected by agricultural and human activities. It is worth emphasizing that studies on ARGs in soil have resulted in the discovery of new genes and enzymes responsible for bacterial resistance to antibiotics. However, many ambiguous results indicate that precise estimation of the impact of antibiotics on the activity and diversity of soil microbial communities is a great challenge.}, }
@article {pmid30886779, year = {2019}, author = {Eisenhofer, R and Weyrich, LS}, title = {Assessing alignment-based taxonomic classification of ancient microbial DNA.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6594}, doi = {10.7717/peerj.6594}, pmid = {30886779}, issn = {2167-8359}, abstract = {The field of palaeomicrobiology-the study of ancient microorganisms-is rapidly growing due to recent methodological and technological advancements. It is now possible to obtain vast quantities of DNA data from ancient specimens in a high-throughput manner and use this information to investigate the dynamics and evolution of past microbial communities. However, we still know very little about how the characteristics of ancient DNA influence our ability to accurately assign microbial taxonomies (i.e. identify species) within ancient metagenomic samples. Here, we use both simulated and published metagenomic data sets to investigate how ancient DNA characteristics affect alignment-based taxonomic classification. We find that nucleotide-to-nucleotide, rather than nucleotide-to-protein, alignments are preferable when assigning taxonomies to short DNA fragment lengths routinely identified within ancient specimens (<60 bp). We determine that deamination (a form of ancient DNA damage) and random sequence substitutions corresponding to ∼100,000 years of genomic divergence minimally impact alignment-based classification. We also test four different reference databases and find that database choice can significantly bias the results of alignment-based taxonomic classification in ancient metagenomic studies. Finally, we perform a reanalysis of previously published ancient dental calculus data, increasing the number of microbial DNA sequences assigned taxonomically by an average of 64.2-fold and identifying microbial species previously unidentified in the original study. Overall, this study enhances our understanding of how ancient DNA characteristics influence alignment-based taxonomic classification of ancient microorganisms and provides recommendations for future palaeomicrobiological studies.}, }
@article {pmid30871459, year = {2019}, author = {Thrash, A and Arick, M and Barbato, RA and Jones, RM and Douglas, TA and Esdale, J and Perkins, EJ and Garcia-Reyero, N}, title = {Keanu: a novel visualization tool to explore biodiversity in metagenomes.}, journal = {BMC bioinformatics}, volume = {20}, number = {Suppl 2}, pages = {103}, doi = {10.1186/s12859-019-2629-4}, pmid = {30871459}, issn = {1471-2105}, abstract = {BACKGROUND: One of the main challenges when analyzing complex metagenomics data is the fact that large amounts of information need to be presented in a comprehensive and easy-to-navigate way. In the process of analyzing FASTQ sequencing data, visualizing which organisms are present in the data can be useful, especially with metagenomics data or data suspected to be contaminated. Here, we describe the development and application of a command-line tool, Keanu, for visualizing and exploring sample content in metagenomics data. We developed Keanu as an interactive tool to make viewing complex data easier.<br><br>RESULTS: Keanu, a tool for exploring sequence content, helps a user to understand the presence and abundance of organisms in a sample by analyzing alignments against a database that contains taxonomy data and displaying them in an interactive web page. The content of a sample can be presented either as a collapsible tree, with node size indicating abundance, or as a bilevel partition graph, with arc size indicating abundance. Here, we illustrate how Keanu works by exploring shotgun metagenomics data from a sample collected from a bluff that contained paleosols and a krotovina in an alpine site in Ft. Greely, Alaska.<br><br>CONCLUSIONS: Keanu provides a simple means by which researchers can explore and visualize species present in sequence data generated from complex communities and environments. Keanu is written in Python and is freely available at https://github.com/IGBB/keanu .}, }
@article {pmid30868805, year = {2019}, author = {Liu, ZX and Xu, J and Sun, W and Shi, YH and Chen, SL}, title = {[Application of DNA metabarcoding in species identification of Chinese herbal medicines].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {44}, number = {1}, pages = {1-8}, doi = {10.19540/j.cnki.cjcmm.2019.0001}, pmid = {30868805}, issn = {1001-5302}, abstract = {DNA metabarcoding,one rapid and robust method using specific standard DNA fragments,has been widely used for rapid species identification of a bulk sample through high-throughput sequencing technologies.While it has been widely used in the studies of metagenomics,animal and plant biodiversity,it has gradually come to be used as a profitable method in species identification of mixed Chinese herbal medicines.In this paper,we mainly summarize the current studies of the application of DNA metabarcoding in species identification of mixed Chinese herbal medicines.Moreover,high-throughput sequencing technologies adopted in those studies,such as Sanger,the next-generation,and third-generation sequencing technologies,are discussed.It is conducted to provide a theoretical guidance for the application of DNA metabarcoding in species identification of mixed Chinese herbal medicines and in more other biodiversity studies.}, }
@article {pmid30850636, year = {2019}, author = {Hendriksen, RS and Munk, P and Njage, P and van Bunnik, B and McNally, L and Lukjancenko, O and Röder, T and Nieuwenhuijse, D and Pedersen, SK and Kjeldgaard, J and Kaas, RS and Clausen, PTLC and Vogt, JK and Leekitcharoenphon, P and van de Schans, MGM and Zuidema, T and de Roda Husman, AM and Rasmussen, S and Petersen, B and ,  and Amid, C and Cochrane, G and Sicheritz-Ponten, T and Schmitt, H and Alvarez, JRM and Aidara-Kane, A and Pamp, SJ and Lund, O and Hald, T and Woolhouse, M and Koopmans, MP and Vigre, H and Petersen, TN and Aarestrup, FM}, title = {Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1124}, doi = {10.1038/s41467-019-08853-3}, pmid = {30850636}, issn = {2041-1723}, mesh = {Africa ; Asia ; Bacteria/classification/*drug effects/genetics/isolation &amp; purification ; Drug Resistance, Multiple, Bacterial/*genetics ; Epidemiological Monitoring ; Europe ; *Genes, Bacterial ; Humans ; *Metagenome ; Metagenomics/methods ; Microbial Consortia/drug effects/genetics ; North America ; Oceania ; Population Health ; Sewage/*microbiology ; Socioeconomic Factors ; South America ; }, abstract = {Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use metagenomic analysis of untreated sewage to characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data and bacterial taxonomy only explains a minor part of the AMR variation that we observe. We find no evidence for cross-selection between antimicrobial classes, or for effect of air travel between sites. However, AMR gene abundance strongly correlates with socio-economic, health and environmental factors, which we use to predict AMR gene abundances in all countries in the world. Our findings suggest that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR. We propose metagenomic analysis of sewage as an ethically acceptable and economically feasible approach for continuous global surveillance and prediction of AMR.}, }
@article {pmid30841395, year = {2019}, author = {Cordeiro, MC and Garcia, GD and Rocha, AM and Tschoeke, DA and Campeão, ME and Appolinario, LR and Soares, AC and Leomil, L and Froes, A and Bahiense, L and Rezende, CE and de Almeida, MG and Rangel, TP and De Oliveira, BCV and de Almeida, DQR and Thompson, MC and Thompson, CC and Thompson, FL}, title = {Insights on the freshwater microbiomes metabolic changes associated with the world's largest mining disaster.}, journal = {The Science of the total environment}, volume = {654}, number = {}, pages = {1209-1217}, doi = {10.1016/j.scitotenv.2018.11.112}, pmid = {30841395}, issn = {1879-1026}, mesh = {*Chemical Hazard Release ; Disasters ; *Environmental Monitoring ; Fresh Water/*microbiology ; Microbiota ; Mining ; *Water Microbiology ; Water Pollutants, Chemical/*analysis ; }, abstract = {To evaluate the impacts of the Fundão tailings dam failure (Minas Gerais, Brazil) on water quality of the Doce River, we analyzed metagenomics and physicochemical parameters during the month of the disaster and again 6 and 10 months after the disaster. To compare dam conditions before and after the failure, we performed a meta-analysis of physicochemical data from a public database. Immediately after the failure, suspended particulate matter (SPM) in the Doce River was 225-1877 mg L-1. Turbidity and dissolved aluminum and iron concentrations were extremely high, whereas dissolved oxygen was below Brazilian legislation norm (<5 mg L-1) in several locations. Six months later, physicochemical values were below thresholds set by Brazilian guidelines (e.g., SPM = 8-166 mg L-1). Short-term impacts on microbial communities included an increase in Actinobacteria and Bacteroidetes and gene sequences related to microbial virulence, motility, respiration, membrane transport, iron and nitrogen metabolism, suggesting changes in microbial metabolic profiles. The 11 recovered partial genomes from metagenomes (MAGs) had genes related to Fe cycle and metal resistance.}, }
@article {pmid30814504, year = {2019}, author = {Mahnert, A and Moissl-Eichinger, C and Zojer, M and Bogumil, D and Mizrahi, I and Rattei, T and Martinez, JL and Berg, G}, title = {Man-made microbial resistances in built environments.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {968}, doi = {10.1038/s41467-019-08864-0}, pmid = {30814504}, issn = {2041-1723}, mesh = {Biodiversity ; *Built Environment ; *Drug Resistance, Microbial/genetics ; *Environmental Microbiology ; Gram-Negative Bacteria/drug effects/genetics/isolation &amp; purification ; Gram-Positive Bacteria/drug effects/genetics/isolation &amp; purification ; Humans ; Metagenome ; *Microbiota/drug effects/genetics ; }, abstract = {Antimicrobial resistance is a serious threat to global public health, but little is known about the effects of microbial control on the microbiota and its associated resistome. Here we compare the microbiota present on surfaces of clinical settings with other built environments. Using state-of-the-art metagenomics approaches and genome and plasmid reconstruction, we show that increased confinement and cleaning is associated with a loss of microbial diversity and a shift from Gram-positive bacteria, such as Actinobacteria and Firmicutes, to Gram-negative such as Proteobacteria. Moreover, the microbiome of highly maintained built environments has a different resistome when compared to other built environments, as well as a higher diversity in resistance genes. Our results highlight that the loss of microbial diversity correlates with an increase in resistance, and the need for implementing strategies to restore bacterial diversity in certain built environments.}, }
@article {pmid30808694, year = {2019}, author = {Feng, J and Penton, CR and He, Z and Van Nostrand, JD and Yuan, MM and Wu, L and Wang, C and Qin, Y and Shi, ZJ and Guo, X and Schuur, EAG and Luo, Y and Bracho, R and Konstantinidis, KT and Cole, JR and Tiedje, JM and Yang, Y and Zhou, J}, title = {Long-Term Warming in Alaska Enlarges the Diazotrophic Community in Deep Soils.}, journal = {mBio}, volume = {10}, number = {1}, pages = {}, doi = {10.1128/mBio.02521-18}, pmid = {30808694}, issn = {2150-7511}, mesh = {Alaska ; *Biota ; *Global Warming ; Metagenomics ; Microarray Analysis ; *Nitrogen Fixation ; Oxidoreductases/genetics ; Plant Development ; *Soil Microbiology ; Tundra ; }, abstract = {Tundra ecosystems are typically carbon (C) rich but nitrogen (N) limited. Since biological N2 fixation is the major source of biologically available N, the soil N2-fixing (i.e., diazotrophic) community serves as an essential N supplier to the tundra ecosystem. Recent climate warming has induced deeper permafrost thaw and adversely affected C sequestration, which is modulated by N availability. Therefore, it is crucial to examine the responses of diazotrophic communities to warming across the depths of tundra soils. Herein, we carried out one of the deepest sequencing efforts of nitrogenase gene (nifH) to investigate how 5 years of experimental winter warming affects Alaskan soil diazotrophic community composition and abundance spanning both the organic and mineral layers. Although soil depth had a stronger influence on diazotrophic community composition than warming, warming significantly (P < 0.05) enhanced diazotrophic abundance by 86.3% and aboveground plant biomass by 25.2%. Diazotrophic composition in the middle and lower organic layers, detected by nifH sequencing and a microarray-based tool (GeoChip), was markedly altered, with an increase of α-diversity. Changes in diazotrophic abundance and composition significantly correlated with soil moisture, soil thaw duration, and plant biomass, as shown by structural equation modeling analyses. Therefore, more abundant diazotrophic communities induced by warming may potentially serve as an important mechanism for supplementing biologically available N in this tundra ecosystem.IMPORTANCE With the likelihood that changes in global climate will adversely affect the soil C reservoir in the northern circumpolar permafrost zone, an understanding of the potential role of diazotrophic communities in enhancing biological N2 fixation, which constrains both plant production and microbial decomposition in tundra soils, is important in elucidating the responses of soil microbial communities to global climate change. A recent study showed that the composition of the diazotrophic community in a tundra soil exhibited no change under a short-term (1.5-year) winter warming experiment. However, it remains crucial to examine whether the lack of diazotrophic community responses to warming is persistent over a longer time period as a possibly important mechanism in stabilizing tundra soil C. Through a detailed characterization of the effects of winter warming on diazotrophic communities, we showed that a long-term (5-year) winter warming substantially enhanced diazotrophic abundance and altered community composition, though soil depth had a stronger influence on diazotrophic community composition than warming. These changes were best explained by changes in soil moisture, soil thaw duration, and plant biomass. These results provide crucial insights into the potential factors that may impact future C and N availability in tundra regions.}, }
@article {pmid30808380, year = {2019}, author = {DeMaere, MZ and Darling, AE}, title = {bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {46}, doi = {10.1186/s13059-019-1643-1}, pmid = {30808380}, issn = {1474-760X}, mesh = {Computer Simulation ; Feces/microbiology ; *Genome, Bacterial ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA ; *Software ; }, abstract = {Most microbes cannot be easily cultured, and metagenomics provides a means to study them. Current techniques aim to resolve individual genomes from metagenomes, so-called metagenome-assembled genomes (MAGs). Leading approaches depend upon time series or transect studies, the efficacy of which is a function of community complexity, target abundance, and sequencing depth. We describe an unsupervised method that exploits the hierarchical nature of Hi-C interaction rates to resolve MAGs using a single time point. We validate the method and directly compare against a recently announced proprietary service, ProxiMeta. bin3C is an open-source pipeline and makes use of the Infomap clustering algorithm (https://github.com/cerebis/bin3C).}, }
@article {pmid30793504, year = {2019}, author = {Kwon, YM and Patra, AK and Chiura, HX and Kim, SJ}, title = {Production of extracellular vesicles with light-induced proton pump activity by proteorhodopsin-containing marine bacteria.}, journal = {MicrobiologyOpen}, volume = {}, number = {}, pages = {e808}, doi = {10.1002/mbo3.808}, pmid = {30793504}, issn = {2045-8827}, support = {2019M00700//MABIK/ ; }, abstract = {The production and release of extracellular vesicles (EVs) is a common process occurring in various types of bacteria. However, little is known regarding the functions of EVs derived from marine bacteria. We observed that during cell growth, Sediminicola sp. YIK13, a proteorhodopsin (PR)-containing marine flavobacterium, produces EVs (S13EVs). Transmission electron microscopy showed that Sediminicola sp. YIK13 released two spherical vesicle types, with mono- and/or bi-layered membranes, in the culture. Interestingly, the S13EVs have an orange pigment, indicating the presence of putative carotenoid and PR pigments ascribed to the parental cells. The S13EVs demonstrated the same PR-derived absorption peak spectrum and light-induced proton pump activity as the parental cells. Western blot (immunoblot) analysis of the S13EVs revealed the presence of PR. We confirmed the 16S rRNA gene, pro gene, and genes required for chromophore retinal synthesis, namely blh and crtI, in the DNA packaged into these vesicles. In addition, by metagenomic sequencing, we found microbial rhodopsin-related genes in vesicles derived from natural aquatic environments. Our results suggest that EVs as well potentially pursue horizontal gene transfer of diverse microbial rhodopsin genes in marine ecosystems.}, }
@article {pmid30782660, year = {2019}, author = {López-Pérez, M and Jayakumar, JM and Haro-Moreno, JM and Zaragoza-Solas, A and Reddi, G and Rodriguez-Valera, F and Shapiro, OH and Alam, M and Almagro-Moreno, S}, title = {Evolutionary Model of Cluster Divergence of the Emergent Marine Pathogen Vibrio vulnificus: From Genotype to Ecotype.}, journal = {mBio}, volume = {10}, number = {1}, pages = {}, doi = {10.1128/mBio.02852-18}, pmid = {30782660}, issn = {2150-7511}, mesh = {Aquaculture ; Aquatic Organisms/microbiology ; Cluster Analysis ; Computational Biology ; *Ecotype ; Evolution, Molecular ; Gene Flow ; Gene Transfer, Horizontal ; *Genetic Variation ; Genome, Bacterial ; *Genotype ; Phenotype ; Recombination, Genetic ; Vibrio vulnificus/*classification/*genetics/isolation &amp; purification/physiology ; }, abstract = {Vibrio vulnificus, an opportunistic pathogen, is the causative agent of a life-threatening septicemia and a rising problem for aquaculture worldwide. The genetic factors that differentiate its clinical and environmental strains remain enigmatic. Furthermore, clinical strains have emerged from every clade of V. vulnificus In this work, we investigated the underlying genomic properties and population dynamics of the V. vulnificus species from an evolutionary and ecological point of view. Genome comparisons and bioinformatic analyses of 113 V. vulnificus isolates indicate that the population of V. vulnificus is made up of four different clusters. We found evidence that recombination and gene flow between the two largest clusters (cluster 1 [C1] and C2) have drastically decreased to the point where they are diverging independently. Pangenome and phenotypic analyses showed two markedly different lifestyles for these two clusters, indicating commensal (C2) and bloomer (C1) ecotypes, with differences in carbohydrate utilization, defense systems, and chemotaxis, among other characteristics. Nonetheless, we identified frequent intra- and interspecies exchange of mobile genetic elements (e.g., antibiotic resistance plasmids, novel &quot;chromids,&quot; or two different and concurrent type VI secretion systems) that provide high levels of genetic diversity in the population. Surprisingly, we identified strains from both clusters in the mucosa of aquaculture species, indicating that manmade niches are bringing strains from the two clusters together. We propose an evolutionary model of V. vulnificus that could be broadly applicable to other pathogenic vibrios and facultative bacterial pathogens to pursue strategies to prevent their infections and emergence.IMPORTANCEVibrio vulnificus is an emergent marine pathogen and is the cause of a deadly septicemia. However, the genetic factors that differentiate its clinical and environmental strains and its several biotypes remain mostly enigmatic. In this work, we investigated the underlying genomic properties and population dynamics of the V. vulnificus species to elucidate the traits that make these strains emerge as a human pathogen. The acquisition of different ecological determinants could have allowed the development of highly divergent clusters with different lifestyles within the same environment. However, we identified strains from both clusters in the mucosa of aquaculture species, indicating that manmade niches are bringing strains from the two clusters together, posing a potential risk of recombination and of emergence of novel variants. We propose a new evolutionary model that provides a perspective that could be broadly applicable to other pathogenic vibrios and facultative bacterial pathogens to pursue strategies to prevent their infections.}, }
@article {pmid30782659, year = {2019}, author = {Klein, C and Gonzalez, D and Samwel, K and Kahesa, C and Mwaiselage, J and Aluthge, N and Fernando, S and West, JT and Wood, C and Angeletti, PC}, title = {Relationship between the Cervical Microbiome, HIV Status, and Precancerous Lesions.}, journal = {mBio}, volume = {10}, number = {1}, pages = {}, doi = {10.1128/mBio.02785-18}, pmid = {30782659}, issn = {2150-7511}, mesh = {Bacteria/*classification/genetics ; Cervix Uteri/*microbiology/*pathology ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Female ; HIV Infections/*complications ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; *Microbiota ; Phylogeny ; Precancerous Conditions/*epidemiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Tanzania/epidemiology ; Uterine Cervical Neoplasms/*epidemiology ; }, abstract = {Nearly all cervical cancers are causally associated with human papillomavirus (HPV). The burden of HPV-associated dysplasias in sub-Saharan Africa is influenced by HIV. To investigate the role of the bacterial microbiome in cervical dysplasia, cytobrush samples were collected directly from cervical lesions of 144 Tanzanian women. The V4 hypervariable region of the 16S rRNA gene was amplified and deep sequenced. Alpha diversity metrics (Chao1, PD whole tree, and operational taxonomic unit [OTU] estimates) displayed significantly higher bacterial richness in HIV-positive patients (P = 0.01) than in HIV-negative patients. In HIV-positive patients, there was higher bacterial richness in patients with high-grade squamous intraepithelial lesions (HSIL) (P = 0.13) than those without lesions. The most abundant OTUs associated with high-grade squamous intraepithelial lesions were Mycoplasmatales, Pseudomonadales, and Staphylococcus We suggest that a chronic mycoplasma infection of the cervix may contribute to HPV-dependent dysplasia by sustained inflammatory signals.IMPORTANCE HPV is known to be the causal agent in the majority of cervical cancers. However, the role of the cervical bacterial microbiome in cervical cancer is not clear. To investigate that possibility, we collected cervical cytobrush samples from 144 Tanzanian women and performed deep sequencing of bacterial 16S rRNA genes. We found that HIV-positive patients had greater bacterial richness (P = 0.01) than HIV-negative patients. We also observed that women with high-grade squamous intraepithelial lesions (HSIL) had greater cervical bacterial diversity than women with cytologically normal cervices. Data from our precise sampling of cervical lesions leads us to propose that Mycoplasma contributes to a cervical microbiome status that promotes HPV-related cervical lesions. These results suggest a greater influence of the bacterial microbiota on the outcome of HPV infection than previously thought.}, }
@article {pmid30777011, year = {2019}, author = {Feng, Y and Ramnarine, VR and Bell, R and Volik, S and Davicioni, E and Hayes, VM and Ren, S and Collins, CC}, title = {Metagenomic and metatranscriptomic analysis of human prostate microbiota from patients with prostate cancer.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {146}, doi = {10.1186/s12864-019-5457-z}, pmid = {30777011}, issn = {1471-2164}, support = {CSC201606325044//China Scholarship Council/ ; 201012TFF//Terry Fox Foundation/ ; T2013-01//Prostate Cancer Canada/ ; 81472397//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Prostate cancer (PCa) is the most common malignant neoplasm among men in many countries. Since most precancerous and cancerous tissues show signs of inflammation, chronic bacterial prostatitis has been hypothesized to be a possible etiology. However, establishing a causal relationship between microbial inflammation and PCa requires a comprehensive analysis of the prostate microbiome. The aim of this study was to characterize the microbiome in prostate tissue of PCa patients and investigate its association with tumour clinical characteristics as well as host expression profiles.<br><br>RESULTS: The metagenome and metatranscriptome of tumour and the adjacent benign tissues were assessed in 65 Chinese radical prostatectomy specimens. Escherichia, Propionibacterium, Acinetobacter and Pseudomonas were abundant in both metagenome and metatranscriptome, thus constituting the core of the prostate microbiome. The biodiversity of the microbiomes could not be differentiated between the matched tumour/benign specimens or between the tumour specimens of low and high Gleason Scores. The expression profile of ten Pseudomonas genes was strongly correlated with that of eight host small RNA genes; three of the RNA genes may negatively associate with metastasis. Few viruses could be identified from the prostate microbiomes.<br><br>CONCLUSIONS: This is the first study of the human prostate microbiome employing an integrated metagenomics and metatranscriptomics approach. In this Chinese cohort, both metagenome and metatranscriptome analyses showed a non-sterile microenvironment in the prostate of PCa patients, but we did not find links between the microbiome and local progression of PCa. However, the correlated expression of Pseudomonas genes and human small RNA genes may provide tantalizing preliminary evidence that Pseudomonas infection may impede metastasis.}, }
@article {pmid30764497, year = {2019}, author = {Plaza-Díaz, J and Gómez-Fernández, A and Chueca, N and Torre-Aguilar, MJ and Gil, Á and Perez-Navero, JL and Flores-Rojas, K and Martín-Borreguero, P and Solis-Urra, P and Ruiz-Ojeda, FJ and Garcia, F and Gil-Campos, M}, title = {Autism Spectrum Disorder (ASD) with and without Mental Regression is Associated with Changes in the Fecal Microbiota.}, journal = {Nutrients}, volume = {11}, number = {2}, pages = {}, doi = {10.3390/nu11020337}, pmid = {30764497}, issn = {2072-6643}, support = {404 Research Grant INVEST from the Spanish Society of Pediatrics and Red de Salud Materno Infantil (RED SAMID)//FUNDACIÓ AGRUPACIÓ Àmbit de la Infància/ ; }, mesh = {Autism Spectrum Disorder/*microbiology ; Bacteria/*classification/genetics ; Child, Preschool ; DNA, Bacterial/genetics ; Diet ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenomics ; }, abstract = {New microbiome sequencing technologies provide novel information about the potential interactions among intestinal microorganisms and the host in some neuropathologies as autism spectrum disorders (ASD). The microbiota⁻gut⁻brain axis is an emerging aspect in the generation of autistic behaviors; evidence from animal models suggests that intestinal microbial shifts may produce changes fitting the clinical picture of autism. The aim of the present study was to evaluate the fecal metagenomic profiles in children with ASD and compare them with healthy participants. This comparison allows us to ascertain how mental regression (an important variable in ASD) could influence the intestinal microbiota profile. For this reason, a subclassification in children with ASD by mental regression (AMR) and no mental regression (ANMR) phenotype was performed. The present report was a descriptive observational study. Forty-eight children aged 2⁻6 years with ASD were included: 30 with ANMR and 18 with AMR. In addition, a control group of 57 normally developing children was selected and matched to the ASD group by sex and age. Fecal samples were analyzed with a metagenomic approach using a next-generation sequencing platform. Several differences between children with ASD, compared with the healthy group, were detected. Namely, Actinobacteria and Proteobacteria at phylum level, as well as, Actinobacteria, Bacilli, Erysipelotrichi, and Gammaproteobacteria at class level were found at higher proportions in children with ASD. Additionally, Proteobacteria levels showed to be augmented exclusively in AMR children. Preliminary results, using a principal component analysis, showed differential patterns in children with ASD, ANMR and AMR, compared to healthy group, both for intestinal microbiota and food patterns. In this study, we report, higher levels of Actinobacteria, Proteobacteria and Bacilli, aside from Erysipelotrichi, and Gammaproteobacteria in children with ASD compared to healthy group. Furthermore, AMR children exhibited higher levels of Proteobacteria. Further analysis using these preliminary results and mixing metagenomic and other &quot;omic&quot; technologies are needed in larger cohorts of children with ASD to confirm these intestinal microbiota changes.}, }
@article {pmid30761108, year = {2019}, author = {Ulloa, R and Moya-Beltrán, A and Rojas-Villalobos, C and Nuñez, H and Chiacchiarini, P and Donati, E and Giaveno, A and Quatrini, R}, title = {Domestication of Local Microbial Consortia for Efficient Recovery of Gold Through Top-Down Selection in Airlift Bioreactors.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {60}, doi = {10.3389/fmicb.2019.00060}, pmid = {30761108}, issn = {1664-302X}, abstract = {Extreme acidophiles play central roles in the geochemical cycling of diverse elements in low pH environments. This has been harnessed in biotechnologies such as biomining, where microorganisms facilitate the recovery of economically important metals such as gold. By generating both extreme acidity and a chemical oxidant (ferric iron) many species of prokaryotes that thrive in low pH environments not only catalyze mineral dissolution but also trigger both community and individual level adaptive changes. These changes vary in extent and direction depending on the ore mineralogy, water availability and local climate. The use of indigenous versus introduced microbial consortia in biomining practices is still a matter of debate. Yet, indigenous microbial consortia colonizing sulfidic ores that have been domesticated, i.e., selected for their ability to survive under specific polyextreme conditions, are claimed to outperform un-adapted foreign consortia. Despite this, little is known on the domestication of acidic microbial communities and the changes elicited in their members. In this study, high resolution targeted metagenomic techniques were used to analyze the changes occurring in the community structure of local microbial consortia acclimated to growing under extreme acidic conditions and adapted to endure the conditions imposed by the target mineral during biooxidation of a gold concentrate in an airlift reactor over a period of 2 years. The results indicated that operative conditions evolving through biooxidation of the mineral concentrate exerted strong selective pressures that, early on, purge biodiversity in favor of a few Acidithiobacillus spp. over other iron oxidizing acidophiles. Metagenomic analysis of the domesticated consortium present at the end of the adaptation experiment enabled reconstruction of the RVS1-MAG, a novel representative of Acidithiobacillus ferrooxidans from the Andacollo gold mineral district. Comparative genomic analysis performed with this genome draft revealed a net enrichment of gene functions related to heavy metal transport and stress management that are likely to play a significant role in adaptation and survival to adverse conditions experienced by these acidophiles during growth in presence of gold concentrates.}, }
@article {pmid30759800, year = {2019}, author = {Tremblay, ÉD and Kimoto, T and Bérubé, JA and Bilodeau, GJ}, title = {High-Throughput Sequencing to Investigate Phytopathogenic Fungal Propagules Caught in Baited Insect Traps.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {5}, number = {1}, pages = {}, doi = {10.3390/jof5010015}, pmid = {30759800}, issn = {2309-608X}, support = {OLF-P-1304, GRDI, QIS and CFIA OFL-P-1411, Genome Canada, and Genome BC (LSARP2112), CFIA-RPS and CFIA-TD and GRDI-CFIA mandated//Canadian Food Inspection Agency/ ; }, abstract = {Studying the means of dispersal of plant pathogens is crucial to better understand the dynamic interactions involved in plant infections. On one hand, entomologists rely mostly on both traditional molecular methods and morphological characteristics, to identify pests. On the other hand, high-throughput sequencing (HTS) is becoming the go-to avenue for scientists studying phytopathogens. These organisms sometimes infect plants, together with insects. Considering the growing number of exotic insect introductions in Canada, forest pest-management efforts would benefit from the development of a high-throughput strategy to investigate the phytopathogenic fungal and oomycete species interacting with wood-boring insects. We recycled formerly discarded preservative fluids from the Canadian Food Inspection Agency annual survey using insect traps and analysed more than one hundred samples originating from across Canada. Using the Ion Torrent Personal Genome Machine (PGM) HTS technology and fusion primers, we performed metabarcoding to screen unwanted fungi and oomycetes species, including Phytophthora spp. Community profiling was conducted on the four different wood-boring, insect-attracting semiochemicals; although the preservative (contained ethanol) also attracted other insects. Phytopathogenic fungi (e.g., Leptographium spp. and Merialaricis in the pine sawyer semiochemical) and oomycetes (mainly Peronospora spp. and Pythium aff. hypogynum in the General Longhorn semiochemical), solely associated with one of the four types of semiochemicals, were detected. This project demonstrated that the insect traps' semiochemical microbiome represents a new and powerful matrix for screening phytopathogens. Compared to traditional diagnostic techniques, the fluids allowed for a faster and higher throughput assessment of the biodiversity contained within. Additionally, minimal modifications to this approach would allow it to be used in other phytopathology fields.}, }
@article {pmid30759613, year = {2019}, author = {Wang, X and Li, X and Yu, L and Huang, L and Xiu, J and Lin, W and Zhang, Y}, title = {Characterizing the microbiome in petroleum reservoir flooded by different water sources.}, journal = {The Science of the total environment}, volume = {653}, number = {}, pages = {872-885}, doi = {10.1016/j.scitotenv.2018.10.410}, pmid = {30759613}, issn = {1879-1026}, mesh = {Betaproteobacteria/genetics/*metabolism ; China ; Environmental Monitoring ; Gammaproteobacteria/genetics/*metabolism ; Metagenomics ; *Microbiota/genetics ; Oil and Gas Fields/*microbiology ; Petroleum/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S ; Water Microbiology ; *Water Resources/supply &amp; distribution ; }, abstract = {Petroleum reservoir is an unusual subsurface biosphere, where indigenous microbes lived and evolved for million years. However, continual water injection changed the situation by introduction of new electron acceptors, donors and exogenous microbes. In this study, 16S-rRNA gene sequencing, comparative metagenomics and genomic bins reconstruction were employed to investigate the microbial community and metabolic potential in three typical water-flooded blocks of the Shen84 oil reservoir in Liaohe oil field, China. The results showed significant difference of microbial community compositions and metabolic characteristics existed between the injected water and the produced water/oil mixtures; however, there was considerable uniformity between the produced samples in different blocks. Microbial communities in the produced fluids were dominated by exogenous facultative microbes such as Pseudomonas and Thauera members from Proteobacteria phylum. Metabolic potentials for O2-dependent hydrocarbon degradation, dissimilarly nitrate reduction, and thiosulfate‑sulfur oxidation were much more abundant, whereas genes involved in dissimilatory sulfate reduction, anaerobic hydrocarbon degradation and methanogenesis were less abundant in the oil reservoir. Statistical analysis indicated the water composition had an obvious influence on microbial community composition and metabolic potential. The water-flooding process accompanied with introduction of nitrate or nitrite, and dissolved oxygen promoted the alteration of microbiome in oil reservoir from slow-growing anaerobic indigenous microbes (such as Thermotoga, Clostridia, and Syntrophobacter) to fast-growing opportunists as Beta- and Gama- Proteobacteria. The findings of this study shed light on the microbial ecology change in water flooded petroleum reservoir.}, }
@article {pmid30755506, year = {2019}, author = {Hausmann, B and Pelikan, C and Rattei, T and Loy, A and Pester, M}, title = {Long-Term Transcriptional Activity at Zero Growth of a Cosmopolitan Rare Biosphere Member.}, journal = {mBio}, volume = {10}, number = {1}, pages = {}, doi = {10.1128/mBio.02189-18}, pmid = {30755506}, issn = {2150-7511}, mesh = {Bacterial Load ; Biomass ; Gene Expression Profiling ; Genome, Bacterial ; Metagenomics ; Peptococcaceae/*genetics/*growth &amp; development ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Soil Microbiology ; *Transcription, Genetic ; }, abstract = {Microbial diversity in the environment is mainly concealed within the rare biosphere (all species with <0.1% relative abundance). While dormancy explains a low-abundance state very well, the mechanisms leading to rare but active microorganisms remain elusive. We used environmental systems biology to genomically and transcriptionally characterize &quot;Candidatus Desulfosporosinus infrequens,&quot; a low-abundance sulfate-reducing microorganism cosmopolitan to freshwater wetlands, where it contributes to cryptic sulfur cycling. We obtained its near-complete genome by metagenomics of acidic peat soil. In addition, we analyzed anoxic peat soil incubated under in situ-like conditions for 50 days by Desulfosporosinus-targeted qPCR and metatranscriptomics. The Desulfosporosinus population stayed at a constant low abundance under all incubation conditions, averaging 1.2 × 106 16S rRNA gene copies per cm³ soil. In contrast, transcriptional activity of &quot;Ca. Desulfosporosinus infrequens&quot; increased at day 36 by 56- to 188-fold when minor amendments of acetate, propionate, lactate, or butyrate were provided with sulfate, compared to the no-substrate-control. Overall transcriptional activity was driven by expression of genes encoding ribosomal proteins, energy metabolism, and stress response but not by expression of genes encoding cell growth-associated processes. Since our results did not support growth of these highly active microorganisms in terms of biomass increase or cell division, they had to invest their sole energy for maintenance, most likely counterbalancing acidic pH conditions. This finding explains how a rare biosphere member can contribute to a biogeochemically relevant process while remaining in a zero-growth state over a period of 50 days.IMPORTANCE The microbial rare biosphere represents the largest pool of biodiversity on Earth and constitutes, in sum of all its members, a considerable part of a habitat's biomass. Dormancy or starvation is typically used to explain the persistence of low-abundance microorganisms in the environment. We show that a low-abundance microorganism can be highly transcriptionally active while remaining in a zero-growth state for at least 7 weeks. Our results provide evidence that this zero growth at a high cellular activity state is driven by maintenance requirements. We show that this is true for a microbial keystone species, in particular a cosmopolitan but permanently low-abundance sulfate-reducing microorganism in wetlands that is involved in counterbalancing greenhouse gas emissions. In summary, our results provide an important step forward in understanding time-resolved activities of rare biosphere members relevant for ecosystem functions.}, }
@article {pmid30740092, year = {2019}, author = {Grządziel, J and Gałązka, A}, title = {Fungal Biodiversity of the Most Common Types of Polish Soil in a Long-Term Microplot Experiment.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {6}, doi = {10.3389/fmicb.2019.00006}, pmid = {30740092}, issn = {1664-302X}, abstract = {The aim of the study was to investigate fungal genetic diversity in eight different types of soil in a long-term microplot experiment founded in 1881 in Puławy, Poland. The experiment consists of eight plots (14 m2), each 1 m deep with concrete walls, filled with profiles of different soils. The soils represent the most common Polish soil types (Cambic Leptosol, Fluvic Cambisol, Gleyic Chernozem, Cambisol and Haplic Cambisol, two Brunic Arenosols and Haplic Luvisol). Each soil was characterized by different pH (from 4.0 to 7.5) and organic carbon content (4.5-21.3 g kg-1). The soil structure was not destroyed by compaction because the soils had always been cultivated by hand. The same plant species were always grown in all plots at the same time and the soils received the same fertilization. Moreover, the soils were always under the same weather conditions. Ascomycota was the most abundant phylum in all samples, ranging from 70 to 90% of total fungi. Some genera (Mortierella, Solicoccozyma, and Mycosphaerella) were found to be adapted to a wide range of pH. Acidic soils were dominated by Talaromyces, Cladophialophora, Devriesia, and Saitozyma, while good quality soils primarily consisted of Plectosphaerella, Tetracladium, and Mortierella. The study confirmed previous reports that pH has a decisive influence on soil fungal diversity, but also indicated the strong impact of soil type itself. These studies have launched a new cycle of research in these historical soil profiles.}, }
@article {pmid30718869, year = {2019}, author = {Forster, SC and Kumar, N and Anonye, BO and Almeida, A and Viciani, E and Stares, MD and Dunn, M and Mkandawire, TT and Zhu, A and Shao, Y and Pike, LJ and Louie, T and Browne, HP and Mitchell, AL and Neville, BA and Finn, RD and Lawley, TD}, title = {A human gut bacterial genome and culture collection for improved metagenomic analyses.}, journal = {Nature biotechnology}, volume = {37}, number = {2}, pages = {186-192}, doi = {10.1038/s41587-018-0009-7}, pmid = {30718869}, issn = {1546-1696}, mesh = {Bacteria/classification ; Computational Biology/methods ; Contig Mapping ; Gastrointestinal Microbiome ; *Genome, Bacterial ; Genome, Human ; Humans ; *Metagenome ; *Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/metabolism ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Understanding gut microbiome functions requires cultivated bacteria for experimental validation and reference bacterial genome sequences to interpret metagenome datasets and guide functional analyses. We present the Human Gastrointestinal Bacteria Culture Collection (HBC), a comprehensive set of 737 whole-genome-sequenced bacterial isolates, representing 273 species (105 novel species) from 31 families found in the human gastrointestinal microbiota. The HBC increases the number of bacterial genomes derived from human gastrointestinal microbiota by 37%. The resulting global Human Gastrointestinal Bacteria Genome Collection (HGG) classifies 83% of genera by abundance across 13,490 shotgun-sequenced metagenomic samples, improves taxonomic classification by 61% compared to the Human Microbiome Project (HMP) genome collection and achieves subspecies-level classification for almost 50% of sequences. The improved resource of gastrointestinal bacterial reference sequences circumvents dependence on de novo assembly of metagenomes and enables accurate and cost-effective shotgun metagenomic analyses of human gastrointestinal microbiota.}, }
@article {pmid30718868, year = {2019}, author = {Zou, Y and Xue, W and Luo, G and Deng, Z and Qin, P and Guo, R and Sun, H and Xia, Y and Liang, S and Dai, Y and Wan, D and Jiang, R and Su, L and Feng, Q and Jie, Z and Guo, T and Xia, Z and Liu, C and Yu, J and Lin, Y and Tang, S and Huo, G and Xu, X and Hou, Y and Liu, X and Wang, J and Yang, H and Kristiansen, K and Li, J and Jia, H and Xiao, L}, title = {1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses.}, journal = {Nature biotechnology}, volume = {37}, number = {2}, pages = {179-185}, doi = {10.1038/s41587-018-0008-8}, pmid = {30718868}, issn = {1546-1696}, mesh = {Bacteria/classification ; Cluster Analysis ; Computational Biology/*methods ; Conserved Sequence ; Feces ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Genomics ; Humans ; *Metagenome ; Metagenomics ; Phylogeny ; Polymorphism, Single Nucleotide ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Reference genomes are essential for metagenomic analyses and functional characterization of the human gut microbiota. We present the Culturable Genome Reference (CGR), a collection of 1,520 nonredundant, high-quality draft genomes generated from >6,000 bacteria cultivated from fecal samples of healthy humans. Of the 1,520 genomes, which were chosen to cover all major bacterial phyla and genera in the human gut, 264 are not represented in existing reference genome catalogs. We show that this increase in the number of reference bacterial genomes improves the rate of mapping metagenomic sequencing reads from 50% to >70%, enabling higher-resolution descriptions of the human gut microbiome. We use the CGR genomes to annotate functions of 338 bacterial species, showing the utility of this resource for functional studies. We also carry out a pan-genome analysis of 38 important human gut species, which reveals the diversity and specificity of functional enrichment between their core and dispensable genomes.}, }
@article {pmid30717665, year = {2019}, author = {Jayasundara, D and Herath, D and Senanayake, D and Saeed, I and Yang, CY and Sun, Y and Chang, BC and Tang, SL and Halgamuge, SK}, title = {ENVirT: inference of ecological characteristics of viruses from metagenomic data.}, journal = {BMC bioinformatics}, volume = {19}, number = {Suppl 13}, pages = {377}, doi = {10.1186/s12859-018-2398-5}, pmid = {30717665}, issn = {1471-2105}, support = {LP140100670//Australian Research Council/ ; DP150103512//Australian Research Council/ ; }, mesh = {*Algorithms ; Computer Simulation ; *Ecological and Environmental Phenomena ; Fermented Foods ; Gastrointestinal Microbiome ; Genome, Viral ; Humans ; Lakes/virology ; *Metagenomics ; Time Factors ; Viruses/genetics ; }, abstract = {BACKGROUND: Estimating the parameters that describe the ecology of viruses,particularly those that are novel, can be made possible using metagenomic approaches. However, the best-performing existing methods require databases to first estimate an average genome length of a viral community before being able to estimate other parameters, such as viral richness. Although this approach has been widely used, it can adversely skew results since the majority of viruses are yet to be catalogued in databases.<br><br>RESULTS: In this paper, we present ENVirT, a method for estimating the richness of novel viral mixtures, and for the first time we also show that it is possible to simultaneously estimate the average genome length without a priori information. This is shown to be a significant improvement over database-dependent methods, since we can now robustly analyze samples that may include novel viral types under-represented in current databases. We demonstrate that the viral richness estimates produced by ENVirT are several orders of magnitude higher in accuracy than the estimates produced by existing methods named PHACCS and CatchAll when benchmarked against simulated data. We repeated the analysis of 20 metavirome samples using ENVirT, which produced results in close agreement with complementary in virto analyses.<br><br>CONCLUSIONS: These insights were previously not captured by existing computational methods. As such, ENVirT is shown to be an essential tool for enhancing our understanding of novel viral populations.}, }
@article {pmid30715365, year = {2019}, author = {Goss-Souza, D and Mendes, LW and Borges, CD and Rodrigues, JLM and Tsai, SM}, title = {Amazon forest-to-agriculture conversion alters rhizosphere microbiome composition while functions are kept.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {3}, pages = {}, doi = {10.1093/femsec/fiz009}, pmid = {30715365}, issn = {1574-6941}, abstract = {The conversion of native forest to agriculture is the main cause of microbial biodiversity loss in Amazon soils. In order to better understand this effect, we used metagenomics to investigate microbial patterns and functions in bulk soil and rhizosphere of soybean, in a long-term forest-to-agriculture conversion. Long-term forest-to-agriculture led to microbial homogenization and loss of diversity in both bulk soil and rhizosphere, mainly driven by decreasing aluminum concentration and increased cations saturation in soil, due to liming and fertilization in long-term no-till cropping. Data revealed that long-term no-till cropping culminated in a decrease in Acidobacteria, Actinobacteria and Proteobacteria abundances. However, α- and β-Proteobacteria abundances were higher in the rhizosphere than in bulk soil, regardless of the time after forest-to-agriculture conversion. Changes in functional potential occurred predominantly in bulk soil, with decreases in functions related to potassium metabolism and virulence, disease and defense, while functions related to nucleic acids metabolism increased. Functions in the soybean rhizosphere remained stable, except for those related to potassium metabolism, which decreased after 20-year no-till cropping. Together, our results show that the soybean root system selects microbial taxa via trade-offs, to maintain functional resilience in the rhizosphere microbiome over time.}, }
@article {pmid30712189, year = {2019}, author = {Brito, EMS and Romero-Núñez, VM and Caretta, CA and Bertin, P and Valerdi-Negreros, JC and Guyoneaud, R and Goñi-Urriza, M}, title = {The bacterial diversity on steam vents from Paricutín and Sapichu volcanoes.}, journal = {Extremophiles : life under extreme conditions}, volume = {23}, number = {2}, pages = {249-263}, doi = {10.1007/s00792-019-01078-8}, pmid = {30712189}, issn = {1433-4909}, support = {0627/15//Convocatoria de Apoyo a la Investigacion de la UG (DAIP)/ ; ANR-CONACyT-188775//Biometal Project/ ; }, abstract = {Vapor steam vents are prevailing structures on geothermal sites in which local geochemical conditions allow the development of extremophilic microorganisms. We describe the structure of the prokaryotic community able to grow on the walls and rocks of such microecosystems in two terrestrial Mexican volcanoes: Paricutín (PI and PII samples) and its satellite Sapichu (S sample). The investigated samples showed similar diversity indices, with few dominant OTUs (abundance > 1%): 21, 16 and 23, respectively for PI, PII and S. However, each steam vent showed a particular community profile: PI was dominated by photosynthetic bacteria (Cyanobacteria and Chloroflexia class), PII by Actinobacteria and Proteobacteria, and S by Ktedonobacteria class, Acidobacteria and Cyanobacteria phyla. Concerning the predicted metabolic potential, we found a dominance of cellular pathways, especially the ones for energy generation with metabolisms for sulfur respiration, nitrogen fixation, methanogenesis, carbon fixation, photosynthesis, and metals, among others. We suggest a different maturity stage for the three studied fumaroles, from the youngest (PI) to the oldest (S and PII), also influenced by the temperature and other geochemical parameters. Furthermore, four anaerobic strains were isolated, belonging to Clostridia class (Clostridium sphenoides, C. swellfunanium and Anaerocolumna cellulosilytica) and to Bacilli class (Paenibacillus azoreducens).}, }
@article {pmid30704595, year = {2019}, author = {Kamimura, BA and De Filippis, F and Sant'Ana, AS and Ercolini, D}, title = {Large-scale mapping of microbial diversity in artisanal Brazilian cheeses.}, journal = {Food microbiology}, volume = {80}, number = {}, pages = {40-49}, doi = {10.1016/j.fm.2018.12.014}, pmid = {30704595}, issn = {1095-9998}, mesh = {Animals ; *Biodiversity ; Brazil ; Cheese/*microbiology ; Cluster Analysis ; DNA, Bacterial/genetics ; *Food Microbiology ; Geography ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Brazilian artisanal cheeses are characterized by the use of raw milk and in some cases, natural starter cultures, known as &quot;pingo&quot;, as well as following simple and traditional manufacturing technology. In this study, a large-scale screening of the microbial ecology of 11 different types of artisanal cheeses produced in five geographical areas of Brazil was performed. Besides, the specific origin-related microbial signatures were identified. Clear geography- and technology-based differences in the microbiota were observed. Lactic acid bacteria dominated in all cheeses although Enterobacteriaceae and Staphylococcus also occurred in North, Northeast and Central cheeses. Differences in the lactic acid bacteria patterns were also highlighted: Streptococcus, Leuconostoc, Lactococcus and Lactobacillus were differently combined in terms of relative abundance according to product type and region of production. This study provides a comprehensive, unprecedented microbiological mapping of Brazilian cheeses, highlighting the impact of geographical origin and mode of production on microbial diversity. The results obtained will help to plan an evaluation of microbial contamination sources that will need to be studied for the improvement of cheese quality and safety.}, }
@article {pmid30701707, year = {2019}, author = {Jerde, CL and Wilson, EA and Dressler, TL}, title = {Measuring global fish species richness with eDNA metabarcoding.}, journal = {Molecular ecology resources}, volume = {19}, number = {1}, pages = {19-22}, doi = {10.1111/1755-0998.12929}, pmid = {30701707}, issn = {1755-0998}, support = {AID-OAA-A-16-00057//United States Agency for International Development/ ; }, mesh = {Animals ; *Biodiversity ; Computational Biology ; DNA/chemistry/genetics/isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; Fishes/*classification/*genetics ; French Guiana ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; Water/chemistry ; }, abstract = {Despite mounting threats to global freshwater and marine biodiversity, including climate change, habitat alteration, overharvesting and pollution, we struggle to know which species are present below the water's surface that are suffering from these stressors. However, the idea that a water sample containing environmental DNA (eDNA) can be screened using high-throughput sequencing and bioinformatics to reveal the identity of aquatic species is a revolutionary advance for studying the patterns of species extirpation, invasive species establishment and the dynamics of species richness. To date, many of the critical tests of fisheries diversity using this metabarcoding approach have been conducted in lower diversity systems (<40 fish species), but in this issue of Molecular Ecology Resources, Cilleros et al. (2018) described their eDNA application in the species-rich French Guiana fishery (>200 fish species) and showed the greater potential and some limitations of using eDNA in species-rich environments.}, }
@article {pmid30696735, year = {2019}, author = {Baxter, NT and Schmidt, AW and Venkataraman, A and Kim, KS and Waldron, C and Schmidt, TM}, title = {Dynamics of Human Gut Microbiota and Short-Chain Fatty Acids in Response to Dietary Interventions with Three Fermentable Fibers.}, journal = {mBio}, volume = {10}, number = {1}, pages = {}, doi = {10.1128/mBio.02566-18}, pmid = {30696735}, issn = {2150-7511}, support = {52008119/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Adolescent ; Adult ; Biostatistics ; Chemistry Techniques, Analytical ; Chicory ; Dietary Fiber/*administration &amp; dosage ; Fatty Acids, Volatile/*metabolism ; Feces/*chemistry/*microbiology ; Gastrointestinal Microbiome/*drug effects ; Humans ; Inulin/administration &amp; dosage ; Metagenomics ; Solanum tuberosum ; Starch/administration &amp; dosage ; Young Adult ; Zea mays ; }, abstract = {Production of short-chain fatty acids (SCFAs), especially butyrate, in the gut microbiome is required for optimal health but is frequently limited by the lack of fermentable fiber in the diet. We attempted to increase butyrate production by supplementing the diets of 174 healthy young adults for 2 weeks with resistant starch from potatoes (RPS), resistant starch from maize (RMS), inulin from chicory root, or an accessible corn starch control. RPS resulted in the greatest increase in total SCFAs, including butyrate. Although the majority of microbiomes responded to RPS with increases in the relative abundance of bifidobacteria, those that responded with an increase in Ruminococcus bromii or Clostridium chartatabidum were more likely to yield higher butyrate concentrations, especially when their microbiota were replete with populations of the butyrate-producing species Eubacterium rectale RMS and inulin induced different changes in fecal communities, but they did not generate significant increases in fecal butyrate levels.IMPORTANCE These results reveal that not all fermentable fibers are equally capable of stimulating SCFA production, and they highlight the importance of the composition of an individual's microbiota in determining whether or not they respond to a specific dietary supplement. In particular, R. bromii or C. chartatabidum may be required for enhanced butyrate production in response to RS. Bifidobacteria, though proficient at degrading RS and inulin, may not contribute to the butyrogenic effect of those fermentable fibers in the short term.}, }
@article {pmid30690359, year = {2019}, author = {Qiao, R and Sheng, C and Lu, Y and Zhang, Y and Ren, H and Lemos, B}, title = {Microplastics induce intestinal inflammation, oxidative stress, and disorders of metabolome and microbiome in zebrafish.}, journal = {The Science of the total environment}, volume = {662}, number = {}, pages = {246-253}, doi = {10.1016/j.scitotenv.2019.01.245}, pmid = {30690359}, issn = {1879-1026}, mesh = {Animals ; Dose-Response Relationship, Drug ; Dysbiosis/chemically induced/immunology/*physiopathology ; Fish Diseases/chemically induced/*immunology/physiopathology ; Gastrointestinal Microbiome/drug effects ; Inflammation/chemically induced/*immunology ; Intestines/immunology/physiology ; Metabolome/drug effects ; Metagenomics ; Oxidative Stress/drug effects ; Polystyrenes/*adverse effects/metabolism ; Random Allocation ; Toxicity Tests, Chronic ; Water Pollutants, Chemical/*adverse effects/metabolism ; *Zebrafish/metabolism/microbiology ; }, abstract = {Microplastics (MPs) can be ingested by a variety of species and mainly accumulate in the gut. However, the consequences of MPs exposure in the gut are largely unknown. Here we evaluated the impacts of MPs exposure in zebrafish gut. Animals were experimentally exposed to polystyrene MPs (5-μm beads; 50 μg/L and 500 μg/L) for 21 days and monitored for alterations in tissue histology, enzymatic biomarkers, gut microbiome and metabolomic responses. Inflammation and oxidative stress were observed in the zebrafish gut after exposed to MPs. Furthermore, significant alterations in the gut microbiome and tissue metabolic profiles were observed, with most of these were associated with oxidative stress, inflammation and lipid metabolism. This study provides evidence that MPs exposure causes gut damage as well as alterations in gut metabolome and microbiome, yielding novel insights into the consequences of MPs exposure.}, }
@article {pmid30683856, year = {2019}, author = {Ellegaard, KM and Engel, P}, title = {Genomic diversity landscape of the honey bee gut microbiota.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {446}, doi = {10.1038/s41467-019-08303-0}, pmid = {30683856}, issn = {2041-1723}, mesh = {Age Factors ; Animals ; Bees/*microbiology ; Bifidobacterium/classification/*genetics/isolation &amp; purification ; *Biological Variation, Individual ; DNA, Bacterial/genetics ; Firmicutes/classification/*genetics/isolation &amp; purification ; Gammaproteobacteria/classification/*genetics/isolation &amp; purification ; Gastrointestinal Microbiome/*genetics ; Genetic Variation ; Metagenomics ; Microbial Consortia/genetics ; Phylogeny ; Symbiosis/physiology ; }, abstract = {The structure and distribution of genomic diversity in natural microbial communities is largely unexplored. Here, we used shotgun metagenomics to assess the diversity of the honey bee gut microbiota, a community consisting of few bacterial phylotypes. Our results show that most phylotypes are composed of sequence-discrete populations, which co-exist in individual bees and show age-specific abundance profiles. In contrast, strains present within these sequence-discrete populations were found to segregate into individual bees. Consequently, despite a conserved phylotype composition, each honey bee harbors a distinct community at the functional level. While ecological differentiation seems to facilitate coexistence at higher taxonomic levels, our findings suggest that, at the level of strains, priority effects during community assembly result in individualized profiles, despite the social lifestyle of the host. Our study underscores the need to move beyond phylotype-level characterizations to understand the function of this community, and illustrates its potential for strain-level analysis.}, }
@article {pmid30680877, year = {2019}, author = {Alessandri, G and Milani, C and Mancabelli, L and Mangifesta, M and Lugli, GA and Viappiani, A and Duranti, S and Turroni, F and Ossiprandi, MC and van Sinderen, D and Ventura, M}, title = {Metagenomic dissection of the canine gut microbiota: insights into taxonomic, metabolic and nutritional features.}, journal = {Environmental microbiology}, volume = {21}, number = {4}, pages = {1331-1343}, doi = {10.1111/1462-2920.14540}, pmid = {30680877}, issn = {1462-2920}, support = {//EU Joint Programming Initiative - A Healthy Diet for a Healthy Life/ ; //Fondazione Cariparma/ ; //Ministero dell'Istruzione, dell'Università e della Ricerca/ ; 15/JP-HDHL/3280//Science Foundation Ireland/Ireland ; //JPI HDHL/ ; }, abstract = {Domestication of dogs from wolves is the oldest known example of ongoing animal selection, responsible for generating more than 300 dog breeds worldwide. In order to investigate the taxonomic and functional evolution of the canine gut microbiota, a multi-omics approach was applied to six wild wolves and 169 dog faecal samples, the latter encompassing 51 breeds, which fully covers currently known canine genetic biodiversity. Specifically, 16S rRNA gene and bifidobacterial Internally Transcribed Spacer (ITS) profiling were employed to reconstruct and then compare the canine core gut microbiota to those of wolves and humans, revealing that artificial selection and subsequent cohabitation of dogs with their owners influenced the microbial population of canine gut through loss and acquisition of specific bacterial taxa. Moreover, comparative analysis of the intestinal bacterial population of dogs fed on Bones and Raw Food (BARF) or commercial food (CF) diet, coupled with shotgun metagenomics, highlighted that both bacterial composition and metabolic repertoire of the canine gut microbiota have evolved to adapt to high-protein or high-carbohydrates intake. Altogether, these data indicate that artificial selection and domestication not only affected the canine genome, but also shaped extensively the bacterial population harboured by the canine gut.}, }
@article {pmid30680143, year = {2019}, author = {Rytkönen, S and Vesterinen, EJ and Westerduin, C and Leviäkangas, T and Vatka, E and Mutanen, M and Välimäki, P and Hukkanen, M and Suokas, M and Orell, M}, title = {From feces to data: A metabarcoding method for analyzing consumed and available prey in a bird-insect food web.}, journal = {Ecology and evolution}, volume = {9}, number = {1}, pages = {631-639}, doi = {10.1002/ece3.4787}, pmid = {30680143}, issn = {2045-7758}, abstract = {Diets play a key role in understanding trophic interactions. Knowing the actual structure of food webs contributes greatly to our understanding of biodiversity and ecosystem functioning. The research of prey preferences of different predators requires knowledge not only of the prey consumed, but also of what is available. In this study, we applied DNA metabarcoding to analyze the diet of 4 bird species (willow tits Poecile montanus, Siberian tits Poecile cinctus, great tits Parus major and blue tits Cyanistes caeruleus) by using the feces of nestlings. The availability of their assumed prey (Lepidoptera) was determined from feces of larvae (frass) collected from the main foraging habitat, birch (Betula spp.) canopy. We identified 53 prey species from the nestling feces, of which 11 (21%) were also detected from the frass samples (eight lepidopterans). Approximately 80% of identified prey species in the nestling feces represented lepidopterans, which is in line with the earlier studies on the parids' diet. A subsequent laboratory experiment showed a threshold for fecal sample size and the barcoding success, suggesting that the smallest frass samples do not contain enough larval DNA to be detected by high-throughput sequencing. To summarize, we apply metabarcoding for the first time in a combined approach to identify available prey (through frass) and consumed prey (via nestling feces), expanding the scope and precision for future dietary studies on insectivorous birds.}, }
@article {pmid30649062, year = {2019}, author = {Sessa, L and Reddel, S and Manno, E and Quagliariello, A and Cotugno, N and Del Chierico, F and Amodio, D and Capponi, C and Leone, F and Bernardi, S and Rossi, P and Putignani, L and Palma, P}, title = {Distinct gut microbiota profile in ART-treated perinatally HIV-infected patients associated with cardiac and inflammatory biomarkers.}, journal = {AIDS (London, England)}, volume = {}, number = {}, pages = {}, doi = {10.1097/QAD.0000000000002131}, pmid = {30649062}, issn = {1473-5571}, abstract = {OBJECTIVE: Persistent inflammation and higher risk to develop cardiovascular diseases (CVDs) still represent a major complication for HIV-infected patients despite effective antiretroviral therapy (ART). We investigated the correlation between the gut microbiota (GM) profile, markers of inflammation, vascular endothelial activation (VEA) and microbial translocation (MT) in perinatally HIV-infected patients (PHIV) under ART.<br><br>DESIGN: Cross-sectional study including sixty-one ART-treated PHIV (age range 3-30 years old) and seventy-one age-matched healthy controls (CTRL). Blood and stool sample were collected at the same time and analyzed for GM composition and plasma biomarkers.<br><br>METHODS: GM composition was determined by 16S rRNA targeted-metagenomics. Soluble markers of MT, SI and VEA were quantified by ELISA or Luminex assay. Markers of immune activation were analyzed by flow cytometry on CD4+ and CD8+T-cells.<br><br>RESULTS: We identified two distinct GM profiles (group A and B) among PHIV. No different clinical parameters (age, sex, ethnicity, clinical class), dietary and sexual habits were found between the groups. The group A showed a relative dominance of Akkermansia muciniphila (A.muciniphila), whereas GM of group B was characterized by a higher biodiversity. The analysis of soluble markers revealed a significantly higher level of sE-selectin (p = 0.0296), ICAM-1 (p = 0.0028), VCAM-1 (p = 0.0230), IL-6 (p = 0.0247) and sCD14 (p = 0.0142) in group A compared to group B.<br><br>CONCLUSIONS: Distinctive GM profiles are differently associated with inflammation, MT and VEA. Future studies are needed in order to understand the role of A.muciniphila and risk to develop CVDs in PHIV.}, }
@article {pmid30648011, year = {2019}, author = {Susi, H and Filloux, D and Frilander, MJ and Roumagnac, P and Laine, AL}, title = {Diverse and variable virus communities in wild plant populations revealed by metagenomic tools.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6140}, doi = {10.7717/peerj.6140}, pmid = {30648011}, issn = {2167-8359}, abstract = {Wild plant populations may harbour a myriad of unknown viruses. As the majority of research efforts have targeted economically important plant species, the diversity and prevalence of viruses in the wild has remained largely unknown. However, the recent shift towards metagenomics-based sequencing methodologies, especially those targeting small RNAs, is finally enabling virus discovery from wild hosts. Understanding this diversity of potentially pathogenic microbes in the wild can offer insights into the components of natural biodiversity that promotes long-term coexistence between hosts and parasites in nature, and help predict when and where risks of disease emergence are highest. Here, we used small RNA deep sequencing to identify viruses in Plantago lanceolata populations, and to understand the variation in their prevalence and distribution across the Åland Islands, South-West Finland. By subsequent design of PCR primers, we screened the five most common viruses from two sets of P. lanceolata plants: 164 plants collected from 12 populations irrespective of symptoms, and 90 plants collected from five populations showing conspicuous viral symptoms. In addition to the previously reported species Plantago lanceolata latent virus (PlLV), we found four potentially novel virus species belonging to Caulimovirus, Betapartitivirus, Enamovirus, and Closterovirus genera. Our results show that virus prevalence and diversity varied among the sampled host populations. In six of the virus infected populations only a single virus species was detected, while five of the populations supported between two to five of the studied virus species. In 20% of the infected plants, viruses occurred as coinfections. When the relationship between conspicuous viral symptoms and virus infection was investigated, we found that plants showing symptoms were usually infected (84%), but virus infections were also detected from asymptomatic plants (44%). Jointly, these results reveal a diverse virus community with newly developed tools and protocols that offer exciting opportunities for future studies on the eco-evolutionary dynamics of viruses infecting plants in the wild.}, }
@article {pmid30642268, year = {2019}, author = {Aiemjoy, K and Altan, E and Aragie, S and Fry, DM and Phan, TG and Deng, X and Chanyalew, M and Tadesse, Z and Callahan, EK and Delwart, E and Keenan, JD}, title = {Viral species richness and composition in young children with loose or watery stool in Ethiopia.}, journal = {BMC infectious diseases}, volume = {19}, number = {1}, pages = {53}, doi = {10.1186/s12879-019-3674-3}, pmid = {30642268}, issn = {1471-2334}, support = {F31 HD088070-01A1//National Institute of Child Health and Human Development/ ; U10 EY016214//National Eye Institute/ ; R01 HL105770//National Heart, Lung, and Blood Institute/ ; }, mesh = {Biodiversity ; Caliciviridae Infections/virology ; Child, Preschool ; Diarrhea/epidemiology/*virology ; Ethiopia/epidemiology ; Feces/*virology ; Female ; Humans ; Infant ; Infant, Newborn ; Male ; Metagenomics ; Norovirus/genetics/isolation &amp; purification ; Picornaviridae/genetics/isolation &amp; purification ; Picornaviridae Infections/virology ; Prevalence ; Viruses/genetics/*isolation &amp; purification ; }, abstract = {BACKGROUND: Stool consistency is an important diagnostic criterion in both research and clinical medicine and is often used to define diarrheal disease.<br><br>METHODS: We examine the pediatric enteric virome across stool consistencies to evaluate differences in richness and community composition using fecal samples collected from children aged 0 to 5 years participating in a clinical trial in the Amhara region of Ethiopia. The consistency of each sample was graded according to the modified Bristol Stool Form Scale for children (mBSFS-C) before a portion of stool was preserved for viral metagenomic analysis. Stool samples were grouped into 29 pools according to stool consistency type. Differential abundance was determined using negative-binomial modeling.<br><br>RESULTS: Of 446 censused children who were eligible to participate, 317 presented for the study visit examination and 269 provided stool samples. The median age of children with stool samples was 36 months. Species richness was highest in watery-consistency stool and decreased as stool consistency became firmer (Spearman's r = - 0.45, p = 0.013). The greatest differential abundance comparing loose or watery to formed stool was for norovirus GII (7.64, 95% CI 5.8, 9.5) followed by aichivirus A (5.93, 95% CI 4.0, 7.89) and adeno-associated virus 2 (5.81, 95%CI 3.9, 7.7).<br><br>CONCLUSIONS: In conclusion, we documented a difference in pediatric enteric viromes according to mBSFS-C stool consistency category, both in species richness and composition.}, }
@article {pmid30635058, year = {2019}, author = {Simon, JC and Marchesi, JR and Mougel, C and Selosse, MA}, title = {Host-microbiota interactions: from holobiont theory to analysis.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {5}, doi = {10.1186/s40168-019-0619-4}, pmid = {30635058}, issn = {2049-2618}, mesh = {Animals ; Food Microbiology ; *Host Microbial Interactions ; Humans ; *Microbiota ; Plants/microbiology ; Symbiosis ; }, abstract = {In the recent years, the holobiont concept has emerged as a theoretical and experimental framework to study the interactions between hosts and their associated microbial communities in all types of ecosystems. The spread of this concept in many branches of biology results from the fairly recent realization of the ubiquitous nature of host-associated microbes and their central role in host biology, ecology, and evolution. Through this special series &quot;Host-microbiota interactions: from holobiont theory to analysis,&quot; we wanted to promote this field of research which has considerable implications for human health, food production, and ecosystem protection. In this preface, we highlight a collection of articles selected for this special issue that show, use, or debate the concept of holobiont to approach taxonomically and ecologically diverse organisms, from humans and plants to sponges and insects. We also identify some theoretical and methodological challenges and propose directions for future research on holobionts.}, }
@article {pmid30625669, year = {2019}, author = {Costeira, R and Doherty, R and Allen, CCR and Larkin, MJ and Kulakov, LA}, title = {Analysis of viral and bacterial communities in groundwater associated with contaminated land.}, journal = {The Science of the total environment}, volume = {656}, number = {}, pages = {1413-1426}, doi = {10.1016/j.scitotenv.2018.11.429}, pmid = {30625669}, issn = {1879-1026}, mesh = {Bacteria/classification/*genetics ; Groundwater/*microbiology/virology ; *Metagenome ; *Microbiota ; Northern Ireland ; Soil Pollutants/*analysis ; Viruses/classification/*genetics ; }, abstract = {This work aimed at the comprehensive analysis of total microbial communities inhabiting a typical hydrocarbon-polluted site, where chemical characteristics of the groundwater were readily available. To achieve this, a joint metagenomic characterization of bacteria and viruses surrounding a contaminant plume was performed over a one-year period. The results presented demonstrated that both potential hydrocarbon degraders and their bacteriophages were dominant around the plume, and that the viral and bacterial diversities found at the site were probably influenced by the pH of the groundwater. Niche-specific and dispersed associations between phages and bacteria were identified. The niche phage-host associations were found at the edge of the site and at the core of the plume where pH was the highest (9.52). The identified host populations included several classes of bacteria (e.g. Clostridia and Proteobacteria). Thirty-six viral generalists were also discovered, with BGW-G9 having the broadest host range across 23 taxa, including Pseudomonas, Polycyclovorans, Methylocaldum and Candidatus Magnetobacterium species. The phages with broad host ranges are presumed to have significant effects on prokaryotic production and horizontal gene transfer, and therefore impact the biodegradation processes conducted by various bacteria of the environment studied. This study for the first time characterized the phages and their bacterial hosts associated with a contaminant plume.}, }
@article {pmid30623233, year = {2019}, author = {Kim, JY and Kim, EM and Yi, MH and Lee, J and Lee, S and Hwang, Y and Yong, D and Sohn, WM and Yong, TS}, title = {Chinese liver fluke Clonorchis sinensis infection changes the gut microbiome and increases probiotic Lactobacillus in mice.}, journal = {Parasitology research}, volume = {118}, number = {2}, pages = {693-699}, doi = {10.1007/s00436-018-6179-x}, pmid = {30623233}, issn = {1432-1955}, support = {NRF-2016R1A2B4016194//National Research Foundation of Korea/ ; 2011-0012166//National Research Foundation of Korea/ ; }, mesh = {Animals ; Clonorchiasis/*immunology/parasitology ; Clonorchis sinensis/growth &amp; development/*immunology ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; High-Throughput Nucleotide Sequencing ; Lactobacillus/classification/cytology/*growth &amp; development ; Metacercariae/cytology ; Mice ; Mice, Inbred C57BL ; Probiotics/*analysis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Chinese liver fluke Clonorchis sinensis changes the host's immune system. Recently, it has been reported that helminths including C. sinensis can ameliorate immune-related diseases such as allergy. In addition, recent studies showed that helminth infection can alleviate immune-mediated disorders by altering the gut microbiome. However, changes in the gut microbiome due to C. sinensis have not been reported yet. In this study, changes in the gut microbiome of C57BL/6 mice infected with C. sinensis metacercariae were evaluated over time. Stool was analyzed by 16S rRNA amplicon analysis using high-throughput sequencing technology. There was no apparent difference in species richness and diversity between the infected and control groups. However, the composition of the microbiome was different between the infected and control groups at 20 days and 30 days post-infection, and the difference disappeared at 50 days post-infection. In particular, this microbiome alteration was associated with a change in the relative abundance of genus Lactobacillus and the probiotic Lactobacillus species that are known to have an immune-modulation role in immune-mediated diseases.}, }
@article {pmid30621868, year = {2019}, author = {Ottesen, A and Ramachandran, P and Reed, E and Gu, G and Gorham, S and Ducharme, D and Newell, M and Rideout, S and Turini, T and Hill, T and Strain, E and Brown, E}, title = {Metagenome tracking biogeographic agroecology: Phytobiota of tomatoes from Virginia, Maryland, North Carolina and California.}, journal = {Food microbiology}, volume = {79}, number = {}, pages = {132-136}, doi = {10.1016/j.fm.2018.12.001}, pmid = {30621868}, issn = {1095-9998}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; California ; *Food Microbiology ; Food Safety ; Lycopersicon esculentum/*microbiology ; Maryland ; Metagenomics ; Microbiota/*genetics ; North Carolina ; RNA, Ribosomal, 16S/genetics ; Salmonella/classification/genetics/isolation &amp; purification ; Virginia ; }, abstract = {Describing baseline microbiota associated with agricultural commodities in the field is an important step towards improving our understanding of a wide range of important objectives from plant pathology and horticultural sustainability, to food safety. Environmental pressures on plants (wind, dust, drought, water, temperature) vary by geography and characterizing the impact of these variable pressures on phyllosphere microbiota will contribute to improved stewardship of fresh produce for both plant and human health. A higher resolution understanding of the incidence of human pathogens on food plants and co-occurring phytobiota using metagenomic approaches (metagenome tracking) may contribute to improved source attribution and risk assessment in cases where human pathogens become introduced to agro-ecologies. Between 1990 and 2007, as many as 1990 culture-confirmed Salmonella illnesses were linked to tomatoes from as many as 12 multistate outbreaks (Bell et al., 2012; Bell et al., 2015; Bennett et al., 2014; CDC, 2004; CDC, 2007; Greene et al., 2005a; Gruszynski et al., 2014). When possible, source attribution for these incidents revealed a biogeographic trend, most events were associated with eastern growing regions. To improve our understanding of potential biogeographically linked trends in contamination of tomatoes by Salmonella, we profiled microbiota from the surfaces of tomatoes from Virginia, Maryland, North Carolina and California. Bacterial profiles from California tomatoes were completely different than those of Maryland, Virginia and North Carolina (which were highly similar to each other). A statistically significant enrichment of Firmicutes taxa was observed in California phytobiota compared to the three eastern states. Rhizobiaceae, Sphingobacteriaceae and Xanthobacteraceae were the most abundant bacterial families associated with tomatoes grown in eastern states. These baseline metagenomic profiles of phyllosphere microbiota may contribute to improved understanding of how certain ecologies provide supportive resources for human pathogens on plants and how components of certain agro-ecologies may play a role in the introduction of human pathogens to plants.}, }
@article {pmid30621867, year = {2019}, author = {Marino, M and Dubsky de Wittenau, G and Saccà, E and Cattonaro, F and Spadotto, A and Innocente, N and Radovic, S and Piasentier, E and Marroni, F}, title = {Metagenomic profiles of different types of Italian high-moisture Mozzarella cheese.}, journal = {Food microbiology}, volume = {79}, number = {}, pages = {123-131}, doi = {10.1016/j.fm.2018.12.007}, pmid = {30621867}, issn = {1095-9998}, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Buffaloes ; Cattle ; Cheese/analysis/*microbiology ; Cluster Analysis ; DNA, Bacterial/genetics ; *Food Microbiology ; Metagenomics ; Microbiota/*genetics ; Milk/microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The microbiota of different types of Italian high-moisture Mozzarella cheese produced using cow or buffalo milk, acidified with natural or selected cultures, and sampled at the dairy or at the mass market, was evaluated using a Next Generation Sequencing approach, in order to identify possible drivers of the bacterial diversity. Cow Mozzarella and buffalo Mozzarella acidified with commercial cultures were dominated by Streptococcus thermophilus, while buffalo samples acidified with natural whey cultures showed similar prevalence of L. delbrueckii subsp. bulgaricus, L. helveticus and S. thermophilus. Moreover, several species of non-starter lactic acid bacteria were frequently detected. The diversity in cow Mozzarella microbiota was much higher than that of water buffalo samples. Cluster analysis clearly separated cow's cheeses from buffalo's ones, the former having a higher prevalence of psychrophilic taxa, and the latter of Lactobacillus and Streptococcus. A higher prevalence of psychrophilic species and potential spoilers was observed in samples collected at the mass retail, suggesting that longer exposures to cooling temperatures and longer production-to-consumption times could significantly affect microbiota diversity. Our results could help in detecting some kind of thermal abuse during the production or storage of mozzarella cheese.}, }
@article {pmid30619130, year = {2018}, author = {Timmers, PHA and Vavourakis, CD and Kleerebezem, R and Damsté, JSS and Muyzer, G and Stams, AJM and Sorokin, DY and Plugge, CM}, title = {Metabolism and Occurrence of Methanogenic and Sulfate-Reducing Syntrophic Acetate Oxidizing Communities in Haloalkaline Environments.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3039}, doi = {10.3389/fmicb.2018.03039}, pmid = {30619130}, issn = {1664-302X}, support = {322551//European Research Council/International ; 323009//European Research Council/International ; }, abstract = {Anaerobic syntrophic acetate oxidation (SAO) is a thermodynamically unfavorable process involving a syntrophic acetate oxidizing bacterium (SAOB) that forms interspecies electron carriers (IECs). These IECs are consumed by syntrophic partners, typically hydrogenotrophic methanogenic archaea or sulfate reducing bacteria. In this work, the metabolism and occurrence of SAOB at extremely haloalkaline conditions were investigated, using highly enriched methanogenic (M-SAO) and sulfate-reducing (S-SAO) cultures from south-western Siberian hypersaline soda lakes. Activity tests with the M-SAO and S-SAO cultures and thermodynamic calculations indicated that H2 and formate are important IECs in both SAO cultures. Metagenomic analysis of the M-SAO cultures showed that the dominant SAOB was 'Candidatus Syntrophonatronum acetioxidans,' and a near-complete draft genome of this SAOB was reconstructed. 'Ca. S. acetioxidans' has all genes necessary for operating the Wood-Ljungdahl pathway, which is likely employed for acetate oxidation. It also encodes several genes essential to thrive at haloalkaline conditions; including a Na+-dependent ATP synthase and marker genes for 'salt-out' strategies for osmotic homeostasis at high soda conditions. Membrane lipid analysis of the M-SAO culture showed the presence of unusual bacterial diether membrane lipids which are presumably beneficial at extreme haloalkaline conditions. To determine the importance of SAO in haloalkaline environments, previously obtained 16S rRNA gene sequencing data and metagenomic data of five different hypersaline soda lake sediment samples were investigated, including the soda lakes where the enrichment cultures originated from. The draft genome of 'Ca. S. acetioxidans' showed highest identity with two metagenome-assembled genomes (MAGs) of putative SAOBs that belonged to the highly abundant and diverse Syntrophomonadaceae family present in the soda lake sediments. The 16S rRNA gene amplicon datasets of the soda lake sediments showed a high similarity of reads to 'Ca. S. acetioxidans' with abundance as high as 1.3% of all reads, whereas aceticlastic methanogens and acetate oxidizing sulfate-reducers were not abundant (≤0.1%) or could not be detected. These combined results indicate that SAO is the primary anaerobic acetate oxidizing pathway at extreme haloalkaline conditions performed by haloalkaliphilic syntrophic consortia.}, }
@article {pmid30612183, year = {2019}, author = {Ding, W and Zhang, W and Alikunhi, NM and Batang, Z and Pei, B and Wang, R and Chen, L and Al-Suwailem, A and Qian, PY}, title = {Metagenomic Analysis of Zinc Surface-Associated Marine Biofilms.}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {406-416}, doi = {10.1007/s00248-018-01313-3}, pmid = {30612183}, issn = {1432-184X}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Bacterial Physiological Phenomena ; Biodiversity ; *Biofilms ; Indian Ocean ; Metagenomics ; Phylogeny ; Seawater/analysis/*microbiology ; Zinc/analysis/*metabolism ; }, abstract = {Biofilms are a significant source of marine biofouling. Marine biofilm communities are established when microorganisms adhere to immersed surfaces. Despite the microbe-inhibiting effect of zinc surfaces, microbes can still attach to the surface and form biofilms. However, the diversity of biofilm-forming microbes that can attach to zinc surfaces and their common functional features remain elusive. Here, by analyzing 9,000,000 16S rRNA gene amplicon sequences and 270 Gb of metagenomic data, we comprehensively explored the taxa and functions related to biofilm formation in subtidal zones of the Red Sea. A clear difference was observed between the biofilm and adjacent seawater microbial communities in terms of the taxonomic structure at phylum and genus levels, and a huge number of genera were only present in the biofilms. Saturated alpha-diversity curves suggested the existence of more than 14,000 operational taxonomic units in one biofilm sample, which is much higher than previous estimates. Remarkably, the biofilms contained abundant and diverse transposase genes, which were localized along microbial chromosomal segments and co-existed with genes related to metal ion transport and resistance. Genomic analyses of two cyanobacterial strains that were abundant in the biofilms revealed a variety of metal ion transporters and transposases. Our analyses revealed the high diversity of biofilm-forming microbes that can attach to zinc surfaces and the ubiquitous role of transposase genes in microbial adaptation to toxic metal surfaces.}, }
@article {pmid30609942, year = {2019}, author = {Yang, SH and Tandon, K and Lu, CY and Wada, N and Shih, CJ and Hsiao, SS and Jane, WN and Lee, TC and Yang, CM and Liu, CT and Denis, V and Wu, YT and Wang, LT and Huang, L and Lee, DC and Wu, YW and Yamashiro, H and Tang, SL}, title = {Metagenomic, phylogenetic, and functional characterization of predominant endolithic green sulfur bacteria in the coral Isopora palifera.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {3}, doi = {10.1186/s40168-018-0616-z}, pmid = {30609942}, issn = {2049-2618}, mesh = {Animals ; Anthozoa/*microbiology ; Chlorobi/*classification/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Endolithic microbes in coral skeletons are known to be a nutrient source for the coral host. In addition to aerobic endolithic algae and Cyanobacteria, which are usually described in the various corals and form a green layer beneath coral tissues, the anaerobic photoautotrophic green sulfur bacteria (GSB) Prosthecochloris is dominant in the skeleton of Isopora palifera. However, due to inherent challenges in studying anaerobic microbes in coral skeleton, the reason for its niche preference and function are largely unknown.<br><br>RESULTS: This study characterized a diverse and dynamic community of endolithic microbes shaped by the availability of light and oxygen. In addition, anaerobic bacteria isolated from the coral skeleton were cultured for the first time to experimentally clarify the role of these GSB. This characterization includes GSB's abundance, genetic and genomic profiles, organelle structure, and specific metabolic functions and activity. Our results explain the advantages endolithic GSB receive from living in coral skeletons, the potential metabolic role of a clade of coral-associated Prosthecochloris (CAP) in the skeleton, and the nitrogen fixation ability of CAP.<br><br>CONCLUSION: We suggest that the endolithic microbial community in coral skeletons is diverse and dynamic and that light and oxygen are two crucial factors for shaping it. This study is the first to demonstrate the ability of nitrogen uptake by specific coral-associated endolithic bacteria and shed light on the role of endolithic bacteria in coral skeletons.}, }
@article {pmid30609875, year = {2019}, author = {Waseem, H and Jameel, S and Ali, J and Saleem Ur Rehman, H and Tauseef, I and Farooq, U and Jamal, A and Ali, MI}, title = {Contributions and Challenges of High Throughput qPCR for Determining Antimicrobial Resistance in the Environment: A Critical Review.}, journal = {Molecules (Basel, Switzerland)}, volume = {24}, number = {1}, pages = {}, doi = {10.3390/molecules24010163}, pmid = {30609875}, issn = {1420-3049}, mesh = {Anti-Infective Agents/*pharmacology ; Computational Biology/methods ; Data Analysis ; *Drug Resistance, Microbial ; *Environmental Microbiology ; Gastrointestinal Microbiome ; Genes, Bacterial ; *High-Throughput Screening Assays ; Humans ; Metagenome ; Metagenomics/methods ; Quality Control ; *Real-Time Polymerase Chain Reaction ; }, abstract = {Expansion in whole genome sequencing and subsequent increase in antibiotic resistance targets have paved the way of high throughput qPCR (HT-qPCR) for analyzing hundreds of antimicrobial resistance genes (ARGs) in a single run. A meta-analysis of 51 selected studies is performed to evaluate ARGs abundance trends over the last 7 years. WaferGenTM SmartChip is found to be the most widely used HT-qPCR platform among others for evaluating ARGs. Up till now around 1000 environmental samples (excluding biological replicates) from different parts of the world have been analyzed on HT-qPCR. Calculated detection frequency and normalized ARGs abundance (ARGs/16S rRNA gene) reported in gut microbiome studies have shown a trend of low ARGs as compared to other environmental matrices. Disparities in the HT-qPCR data analysis which are causing difficulties to researchers in precise interpretation of results have been highlighted and a possible way forward for resolving them is also suggested. The potential of other amplification technologies and point of care or field deployable devices for analyzing ARGs have also been discussed in the review. Our review has focused on updated information regarding the role, current status and future perspectives of HT-qPCR in the field of antimicrobial resistance.}, }
@article {pmid30606162, year = {2019}, author = {Xue, F and Nan, X and Li, Y and Pan, X and Guo, Y and Jiang, L and Xiong, B}, title = {Metagenomic insights into effects of thiamine supplementation on ruminal non-methanogen archaea in high-concentrate diets feeding dairy cows.}, journal = {BMC veterinary research}, volume = {15}, number = {1}, pages = {7}, doi = {10.1186/s12917-018-1745-0}, pmid = {30606162}, issn = {1746-6148}, support = {Grant No. 31572435//Project of National Nature Science Foundation of China/ ; 2016YFD0700205//National Key Research and Development Plan/ ; }, mesh = {Animal Feed ; Animals ; Archaea/*drug effects/genetics ; Cattle ; Diet/*veterinary ; *Dietary Supplements ; Eating/drug effects ; Female ; Gastrointestinal Microbiome/drug effects ; Hydrogen-Ion Concentration ; Lactation/drug effects ; Metagenomics ; Rumen/chemistry/*microbiology ; Thiamine/analysis/*pharmacology ; }, abstract = {BACKGROUND: Overfeeding of high-concentrate diet (HC) frequently leads to subacute ruminal acidosis (SARA) in modern dairy cows' production. Thiamine supplementation has been confirmed to attenuate HC induced SARA by increasing ruminal pH and ratio of acetate to propionate, and decreasing rumen lactate, biogenic amines and lipopolysaccharide (LPS). The effects of thiamine supplementation in HC on rumen bacteria and fungi profile had been detected in our previous studies, however, effects of thiamine supplementation in HC on rumen non-methanogen archaea is still unclear. The objective of the present study was therefore to investigate the effects of thiamine supplementation on ruminal archaea, especially non-methanogens in HC induced SARA cows.<br><br>RESULTS: HC feeding significantly decreased dry matter intake, milk production, milk fat content, ruminal pH and the concentrations of thiamine and acetate in rumen fluid compared with control diet (CON) (P < 0.05), while the concentrations of propionate and ammonia-nitrogen (NH3-N) were significantly increased compared with CON (P < 0.05). These changes caused by HC were inversed by thiamine supplementation (P < 0.05). The taxonomy results showed that ruminal archaea ranged from 0.37 to 0.47% of the whole microbiota. Four characterized phyla, a number of Candidatus archaea and almost 660 species were identified in the present study. In which Euryarchaeota occupied the largest proportion of the whole archaea. Furthermore, thiamine supplementation treatment significantly increased the relative abundance of non-methanogens compared with CON and HC treatments. Thaumarchaeota was increased in HC compared with CON. Thiamine supplementation significantly increased Crenarchaeota, Nanoarchaeota and the Candidatus phyla, however decreased Thaumarchaeota compared with HC treatment.<br><br>CONCLUSIONS: HC feeding significantly decreased ruminal pH and increased the content of NH3-N which led to N loss and the increase of the relative abundance of Thaumarchaeota. Thiamine supplementation increased ruminal pH, improved the activity of ammonia utilizing bacteria, and decreased Thaumarchaeota abundance to reduce the ruminal NH3 content and finally reduced N loss. Overall, these findings contributed to the understanding of thiamine's function in dairy cows and provided new strategies to improve dairy cows' health under high-concentrate feeding regime.}, }
@article {pmid30598099, year = {2018}, author = {Abe, K and Hirayama, M and Ohno, K and Shimamura, T}, title = {A latent allocation model for the analysis of microbial composition and disease.}, journal = {BMC bioinformatics}, volume = {19}, number = {Suppl 19}, pages = {519}, doi = {10.1186/s12859-018-2530-6}, pmid = {30598099}, issn = {1471-2105}, mesh = {*Algorithms ; Bacteria/*classification ; Case-Control Studies ; Colorectal Neoplasms/*microbiology ; Computer Simulation ; Humans ; *Microbiota ; *Models, Statistical ; Parkinson Disease/*microbiology ; }, abstract = {BACKGROUND: Establishing the relationship between microbiota and specific diseases is important but requires appropriate statistical methodology. A specialized feature of microbiome count data is the presence of a large number of zeros, which makes it difficult to analyze in case-control studies. Most existing approaches either add a small number called a pseudo-count or use probability models such as the multinomial and Dirichlet-multinomial distributions to explain the excess zero counts, which may produce unnecessary biases and impose a correlation structure taht is unsuitable for microbiome data.<br><br>RESULTS: The purpose of this article is to develop a new probabilistic model, called BERnoulli and MUltinomial Distribution-based latent Allocation (BERMUDA), to address these problems. BERMUDA enables us to describe the differences in bacteria composition and a certain disease among samples. We also provide a simple and efficient learning procedure for the proposed model using an annealing EM algorithm.<br><br>CONCLUSION: We illustrate the performance of the proposed method both through both the simulation and real data analysis. BERMUDA is implemented with R and is available from GitHub (https://github.com/abikoushi/Bermuda).}, }
@article {pmid30598080, year = {2018}, author = {Chen, HM and Chang, TH and Lin, FM and Liang, C and Chiu, CM and Yang, TL and Yang, T and Huang, CY and Cheng, YN and Chang, YA and Chang, PY and Weng, SL}, title = {Vaginal microbiome variances in sample groups categorized by clinical criteria of bacterial vaginosis.}, journal = {BMC genomics}, volume = {19}, number = {Suppl 10}, pages = {876}, doi = {10.1186/s12864-018-5284-7}, pmid = {30598080}, issn = {1471-2164}, mesh = {Adult ; DNA, Bacterial/genetics ; Female ; *Genetic Variation ; Humans ; Microbiota/*genetics ; Vagina/*microbiology ; Vaginosis, Bacterial/microbiology ; }, abstract = {BACKGROUND: One of the most common and recurrent vaginal infections is bacterial vaginosis (BV). The diagnosis is based on changes to the &quot;normal&quot; vaginal microbiome; however, the normal microbiome appears to differ according to reproductive status and ethnicity, and even among individuals within these groups. The Amsel criteria and Nugent score test are widely used for diagnosing BV; however, these tests are based on different criteria, and so may indicate distinct changes in the vaginal microbial community. Nevertheless, few studies have compared the results of these test against metagenomics analysis.<br><br>METHODS: Vaginal flora samples from 77 participants were classified according to the Amsel criteria and Nugent score test. The microbiota composition was analyzed using 16S ribosome RNA gene amplicon sequencing. Bioinformatics analysis and multivariate statistical analysis were used to evaluate the microbial diversity and function.<br><br>RESULTS: Only 3 % of the participants diagnosed BV negative using the Amsel criteria (A-) were BV-positive according to the Nugent score test (N+), while over half of the BV-positive patients using the Amsel criteria (A+) were BV-negative according to the Nugent score test (N-). Thirteen genera showed significant differences in distribution among BV status defined by BV tests (e.g., A - N-, A + N- and A + N+). Variations in the four most abundant taxa, Lactobacillus, Gardnerella, Prevotella, and Escherichia, were responsible for most of this dissimilarity. Furthermore, vaginal microbial diversity differed significantly among the three groups classified by the Nugent score test (N-, N+, and intermediate flora), but not between the Amsel criteria groups. Numerous predictive microbial functions, such as bacterial chemotaxis and bacterial invasion of epithelial cells, differed significantly among multiple BV test, but not between the A- and A+ groups.<br><br>CONCLUSIONS: Metagenomics analysis can greatly expand our current understanding of vaginal microbial diversity in health and disease. Metagenomics profiling may also provide more reliable diagnostic criteria for BV testing.}, }
@article {pmid30597002, year = {2019}, author = {Choi, I and Ponsero, AJ and Bomhoff, M and Youens-Clark, K and Hartman, JH and Hurwitz, BL}, title = {Libra: scalable k-mer-based tool for massive all-vs-all metagenome comparisons.}, journal = {GigaScience}, volume = {8}, number = {2}, pages = {}, doi = {10.1093/gigascience/giy165}, pmid = {30597002}, issn = {2047-217X}, abstract = {Background: Shotgun metagenomics provides powerful insights into microbial community biodiversity and function. Yet, inferences from metagenomic studies are often limited by dataset size and complexity and are restricted by the availability and completeness of existing databases. De novo comparative metagenomics enables the comparison of metagenomes based on their total genetic content.<br><br>Results: We developed a tool called Libra that performs an all-vs-all comparison of metagenomes for precise clustering based on their k-mer content. Libra uses a scalable Hadoop framework for massive metagenome comparisons, Cosine Similarity for calculating the distance using sequence composition and abundance while normalizing for sequencing depth, and a web-based implementation in iMicrobe (http://imicrobe.us) that uses the CyVerse advanced cyberinfrastructure to promote broad use of the tool by the scientific community.<br><br>Conclusions: A comparison of Libra to equivalent tools using both simulated and real metagenomic datasets, ranging from 80 million to 4.2 billion reads, reveals that methods commonly implemented to reduce compute time for large datasets, such as data reduction, read count normalization, and presence/absence distance metrics, greatly diminish the resolution of large-scale comparative analyses. In contrast, Libra uses all of the reads to calculate k-mer abundance in a Hadoop architecture that can scale to any size dataset to enable global-scale analyses and link microbial signatures to biological processes.}, }
@article {pmid30594064, year = {2019}, author = {Procopio, N and Ghignone, S and Williams, A and Chamberlain, A and Mello, A and Buckley, M}, title = {Metabarcoding to investigate changes in soil microbial communities within forensic burial contexts.}, journal = {Forensic science international. Genetics}, volume = {39}, number = {}, pages = {73-85}, doi = {10.1016/j.fsigen.2018.12.002}, pmid = {30594064}, issn = {1878-0326}, mesh = {Animals ; Burial ; DNA Barcoding, Taxonomic/*methods ; Forensic Sciences ; Metagenomics/methods ; Microbiota/*genetics ; Models, Animal ; Polymerase Chain Reaction ; *Postmortem Changes ; RNA, Ribosomal, 16S ; *Soil Microbiology ; Swine ; }, abstract = {The estimation of the time elapsed since death (post-mortem interval, or PMI) is one of the key themes that forensic scientists have to address frequently. However, the estimation of PMI still suffers from poor accuracy and biases especially when decomposition stages are prolonged, so further improvements in methods for PMI estimation are desirable. Soil microbial communities associated with decomposing bodies have been shown to be good candidates for the estimation of the PMI of exposed bodies. Nevertheless, further research is required to better understand the bacterial succession associated with decomposition of buried carcasses in order to test its reliability and applicability for the estimation of PMI and to better understand the dynamics involved with decomposition within this particular scenario. Therefore we explored the succession of soil microbial communities associated with four decomposing pig carcasses (from one to six months PMI) using a metabarcoding approach. The sequencing of the bacterial 16S rRNA variable region 4 (V4) revealed trends linking particular microbial taxa with specific PMIs, and notably an increase in Proteobacteria, Firmicutes and Bacteroidetes at specific PMIs as well as a decrease in Acidobacteria. Our results, in accordance with previous studies conducted on exposed bodies of different mammalian species (including humans), also showed a general reduction of the taxonomic richness from two months PMI onwards, as well as an incomplete re-establishment of the starting soil microbial conditions after six months PMI. We also found specific mammal-derived taxa, such as Bacteroides spp., being still present in the soil after six months PMI. As such, this study serves as a baseline for additional research to allow the characterisation of biomarkers associated with specific PMIs. Due to the similarity between the results presented here and those reported in other types of decomposition studies we believe that the metabarcoding approach has considerable potential in the estimation of the PMI, particularly to clarify cases involving heavily skeletonised bodies or for the investigation of clandestine graves in which the carcass has been moved from its original place of deposition.}, }
@article {pmid30589606, year = {2019}, author = {Yasir, M and Qureshi, AK and Khan, I and Bibi, F and Rehan, M and Khan, SB and Azhar, EI}, title = {Culturomics-Based Taxonomic Diversity of Bacterial Communities in the Hot Springs of Saudi Arabia.}, journal = {Omics : a journal of integrative biology}, volume = {23}, number = {1}, pages = {17-27}, doi = {10.1089/omi.2018.0176}, pmid = {30589606}, issn = {1557-8100}, mesh = {Bacteria/*genetics ; Biodiversity ; Hot Springs/*microbiology ; Hot Temperature ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Saudi Arabia ; Sequence Analysis, DNA/methods ; }, abstract = {Hot springs are natural habitats for thermophilic microorganisms and provide a significant opportunity for bioprospecting thermostable biomolecules. However, the scientific community has only a fragmented understanding of the microbial diversity and composition in these biotopes. In this study, bacterial diversity in sediment samples from six hot springs of Saudi Arabia was investigated using an improved culture-dependent approach. High-throughput MALDI-TOF MS (matrix assisted laser desorption/ionization mass spectrometry) and 16S rRNA genes sequencing were used for the identification of purified isolates. Most of the hot springs had a neutral pH and a temperature range of 45-89°C. Relatively higher colony-forming units (1.9 ± 0.45 × 104) were observed with 60°C incubation of an 89°C sediment sample from the hot spring at Ain al Harra1. Among the 536 purified isolates, 6 novel candidate species were found, and the remaining isolates represented 139 distinct species. Several species, such as Bacillus cereus, Bacillus subtilis, and Bacillus schlegelii, were ubiquitous in the hot springs sampled, but 102 of the identified species were uniquely distributed among the hot springs. Sixteen of the isolated thermophilic bacteria, including Geobacillus kaustophilus, Thermus oshimai, and Brevibacillus thermoruber, grew at ≥60°C. In addition, 21 species exhibited hydrolytic enzymatic activity. Most of these species belonged to Bacillus and Brevibacillus. Overall, this study contributes to global knowledgebase on bacterial communities by comprehensively profiling culture-based bacterial diversity in the hot springs of Saudi Arabia. Further studies are required for investigating bacteria from hot springs by a metagenomic approach.}, }
@article {pmid30588764, year = {2019}, author = {Woyke, T and Schulz, F}, title = {Entities inside one another - a matryoshka doll in biology?.}, journal = {Environmental microbiology reports}, volume = {11}, number = {1}, pages = {26-28}, doi = {10.1111/1758-2229.12716}, pmid = {30588764}, issn = {1758-2229}, mesh = {*Biological Evolution ; Eukaryota/physiology ; Giant Viruses/physiology ; Metagenomics ; Microbial Consortia ; Organelles/physiology ; *Symbiosis ; Thiothrix/physiology ; }, }
@article {pmid30587114, year = {2018}, author = {Tyakht, AV and Manolov, AI and Kanygina, AV and Ischenko, DS and Kovarsky, BA and Popenko, AS and Pavlenko, AV and Elizarova, AV and Rakitina, DV and Baikova, JP and Ladygina, VG and Kostryukova, ES and Karpova, IY and Semashko, TA and Larin, AK and Grigoryeva, TV and Sinyagina, MN and Malanin, SY and Shcherbakov, PL and Kharitonova, AY and Khalif, IL and Shapina, MV and Maev, IV and Andreev, DN and Belousova, EA and Buzunova, YM and Alexeev, DG and Govorun, VM}, title = {Genetic diversity of Escherichia coli in gut microbiota of patients with Crohn's disease discovered using metagenomic and genomic analyses.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {968}, doi = {10.1186/s12864-018-5306-5}, pmid = {30587114}, issn = {1471-2164}, support = {16-15-00258//Russian Science Foundation/ ; }, mesh = {Cluster Analysis ; Crohn Disease/microbiology/*pathology ; Escherichia coli/*genetics/isolation &amp; purification ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Genetic Variation ; Genome, Bacterial ; Humans ; Intestinal Mucosa/microbiology ; Metagenomics/*methods ; }, abstract = {BACKGROUND: Crohn's disease is associated with gut dysbiosis. Independent studies have shown an increase in the abundance of certain bacterial species, particularly Escherichia coli with the adherent-invasive pathotype, in the gut. The role of these species in this disease needs to be elucidated.<br><br>METHODS: We performed a metagenomic study investigating the gut microbiota of patients with Crohn's disease. A metagenomic reconstruction of the consensus genome content of the species was used to assess the genetic variability.<br><br>RESULTS: The abnormal shifts in the microbial community structures in Crohn's disease were heterogeneous among the patients. The metagenomic data suggested the existence of multiple E. coli strains within individual patients. We discovered that the genetic diversity of the species was high and that only a few samples manifested similarity to the adherent-invasive varieties. The other species demonstrated genetic diversity comparable to that observed in the healthy subjects. Our results were supported by a comparison of the sequenced genomes of isolates from the same microbiota samples and a meta-analysis of published gut metagenomes.<br><br>CONCLUSIONS: The genomic diversity of Crohn's disease-associated E. coli within and among the patients paves the way towards an understanding of the microbial mechanisms underlying the onset and progression of the Crohn's disease and the development of new strategies for the prevention and treatment of this disease.}, }
@article {pmid30584534, year = {2018}, author = {Ranjan, R and Rani, A and Finn, PW and Perkins, DL}, title = {Multiomic Strategies Reveal Diversity and Important Functional Aspects of Human Gut Microbiome.}, journal = {BioMed research international}, volume = {2018}, number = {}, pages = {6074918}, doi = {10.1155/2018/6074918}, pmid = {30584534}, issn = {2314-6141}, support = {R01 AI053878/AI/NIAID NIH HHS/United States ; R01 HL081663/HL/NHLBI NIH HHS/United States ; }, mesh = {Adult ; Bacteria/genetics ; Biodiversity ; Dysbiosis/genetics/microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Male ; Metagenome/genetics ; Metagenomics/methods ; Microbiota/*genetics ; Sequence Analysis, DNA/methods ; Transcriptome/genetics ; }, abstract = {It is well accepted that dysbiosis of microbiota is associated with disease; however, the biological mechanisms that promote susceptibility or resilience to disease remain elusive. One of the major limitations of previous microbiome studies has been the lack of complementary metatranscriptomic (functional) data to complement the interpretation of metagenomics (bacterial abundance). The purpose of this study was twofold, first to evaluate the bacterial diversity and differential gene expression of gut microbiota using complementary shotgun metagenomics (MG) and metatranscriptomics (MT) from same fecal sample. Second, to compare sequence data using different Illumina platforms and with different sequencing parameters as new sequencers are introduced, and to determine if the data are comparable on different platforms. In this study, we perform ultradeep metatranscriptomic shotgun sequencing for a sample that we previously analyzed with metagenomics shotgun sequencing. We performed sequencing analysis using different Illumina platforms, with different sequencing and analysis parameters. Our results suggest that use of different Illumina platform did not lead to detectable bias in the sequencing data. The analysis of the sample using MG and MT approach shows that some species genes are highly represented in the MT than in the MG, indicating that some species are highly metabolically active. Our analysis also shows that ~52% of the genes in the metagenome are in the metatranscriptome and therefore are robustly expressed. The functions of the low and rare abundance bacterial species remain poorly understood. Our observations indicate that among the low abundant species analyzed in this study some were found to be more metabolically active compared to others, and can contribute distinct profiles of biological functions that may modulate the host-microbiota and bacteria-bacteria interactions.}, }
@article {pmid30581850, year = {2018}, author = {Chen, WP and Chang, SH and Tang, CY and Liou, ML and Tsai, SJ and Lin, YL}, title = {Composition Analysis and Feature Selection of the Oral Microbiota Associated with Periodontal Disease.}, journal = {BioMed research international}, volume = {2018}, number = {}, pages = {3130607}, doi = {10.1155/2018/3130607}, pmid = {30581850}, issn = {2314-6141}, mesh = {Bacteria/*genetics ; Chronic Periodontitis/*microbiology ; Gingiva/*microbiology ; Humans ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Tooth/microbiology ; }, abstract = {Periodontitis is an inflammatory disease involving complex interactions between oral microorganisms and the host immune response. Understanding the structure of the microbiota community associated with periodontitis is essential for improving classifications and diagnoses of various types of periodontal diseases and will facilitate clinical decision-making. In this study, we used a 16S rRNA metagenomics approach to investigate and compare the compositions of the microbiota communities from 76 subgingival plagues samples, including 26 from healthy individuals and 50 from patients with periodontitis. Furthermore, we propose a novel feature selection algorithm for selecting features with more information from many variables with a combination of these features and machine learning methods were used to construct prediction models for predicting the health status of patients with periodontal disease. We identified a total of 12 phyla, 124 genera, and 355 species and observed differences between health- and periodontitis-associated bacterial communities at all phylogenetic levels. We discovered that the genera Porphyromonas, Treponema, Tannerella, Filifactor, and Aggregatibacter were more abundant in patients with periodontal disease, whereas Streptococcus, Haemophilus, Capnocytophaga, Gemella, Campylobacter, and Granulicatella were found at higher levels in healthy controls. Using our feature selection algorithm, random forests performed better in terms of predictive power than other methods and consumed the least amount of computational time.}, }
@article {pmid30581574, year = {2019}, author = {Angelakis, E and Bachar, D and Yasir, M and Musso, D and Djossou, F and Melenotte, C and Robert, C and Davoust, B and Gaborit, B and Azhar, EI and Bibi, F and Dutour, A and Raoult, D}, title = {Comparison of the gut microbiota of obese individuals from different geographic origins.}, journal = {New microbes and new infections}, volume = {27}, number = {}, pages = {40-47}, doi = {10.1016/j.nmni.2018.11.005}, pmid = {30581574}, issn = {2052-2975}, abstract = {Few studies have examined the interaction of human geography, microbial community structure and obesity. We tested obese adult volunteers from France, Saudi Arabia, French Polynesia and from a traditional population in the village of Trois-Sauts in French Guiana by sequencing the V3-V4 region. We also sequenced homemade fermented cachiri beers that were obtained from the traditional Amazonian population and are highly consumed by this population. We found that French and Saudis had significantly less richness and biodiversity in their gut microbiota than Amazonians and Polynesians (p <0.05). Principle coordinate analysis of the overall composition of the genera communities revealed that the microbiomes of Amazonians clustered independently from the other obese individuals. Moreover, we found that Amazonians presented significantly stricter anaerobic genera than the Saudis, French and Polynesians (p < 0.001). Polynesians presented significantly lower relative abundance of Lactobacillus sp. than French (p 0.01) and Saudis (p 0.05). Treponema berlinense and Treponema succinifaciens were only present in the gut microbiome of Amazonians. The cachiri beers presented significantly more bacterial species in common with the gut microbiome of Amazonians (p < 0.005). Obese individuals with different origins present modifications in their gut microbiota, and we provide evidence that the cachiri beers influenced the gut microbiome of Amazonians.}, }
@article {pmid30579193, year = {2019}, author = {Deng, Y and Wang, Y and Xia, Y and Zhang, AN and Zhao, Y and Zhang, T}, title = {Genomic resolution of bacterial populations in saccharin and cyclamate degradation.}, journal = {The Science of the total environment}, volume = {658}, number = {}, pages = {357-366}, doi = {10.1016/j.scitotenv.2018.12.162}, pmid = {30579193}, issn = {1879-1026}, mesh = {Alphaproteobacteria/genetics/isolation &amp; purification/metabolism ; *Biodegradation, Environmental ; Biodiversity ; Cyclamates/*metabolism ; *Genome, Bacterial ; Metagenomics/methods ; Methylobacteriaceae/genetics/isolation &amp; purification/metabolism ; Rhodocyclaceae/genetics/isolation &amp; purification/metabolism ; Saccharin/*metabolism ; Sphingomonadaceae/genetics/isolation &amp; purification/metabolism ; Water Microbiology ; Water Pollutants, Chemical/*metabolism ; }, abstract = {The benefits of extensive artificial sweeteners use come at a cost of their ubiquitous occurrence in the aquatic environment. Biodegradation is crucial for the removal of artificial sweeteners in the environment, yet comprehensive characterizations of the degradation consortia that degrade these compounds have not been initiated. Here, we performed metagenomic analysis of microbial communities fulfilling complete mineralization of two typical artificial sweeteners, i.e. saccharin and cyclamate. Genome-resolved metagenomics enabled the recovery and metabolic characterization of total 23 population genomes from 8 phyla in the two consortia, most of which represented novel species. The saccharin-degrading consortia was notably dominated by a betaproteobacterial genome from the family Rhodocyclaceae, accounting for 15.5% of total sequences. For the cyclamate enrichment, 28.1% of the total sequences were assigned to three similarly abundant Alphaproteobacteria population genomes belonging to the family Sphingomonadaceae and Methylobacteriaceae. The metabolic potential of these population genomes were examined to potentially identify the roles of these populations in biodegradation of artificial sweeteners, and focusing on the energy and nutrient metabolisms.}, }
@article {pmid30578263, year = {2019}, author = {Wegner, CE and Gaspar, M and Geesink, P and Herrmann, M and Marz, M and Küsel, K}, title = {Biogeochemical Regimes in Shallow Aquifers Reflect the Metabolic Coupling of the Elements Nitrogen, Sulfur, and Carbon.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {5}, pages = {}, doi = {10.1128/AEM.02346-18}, pmid = {30578263}, issn = {1098-5336}, abstract = {Near-surface groundwaters are prone to receive (in)organic matter input from their recharge areas and are known to harbor autotrophic microbial communities linked to nitrogen and sulfur metabolism. Here, we use multi-omic profiling to gain holistic insights into the turnover of inorganic nitrogen compounds, carbon fixation processes, and organic matter processing in groundwater. We sampled microbial biomass from two superimposed aquifers via monitoring wells that follow groundwater flow from its recharge area through differences in hydrogeochemical settings and land use. Functional profiling revealed that groundwater microbiomes are mainly driven by nitrogen (nitrification, denitrification, and ammonium oxidation [anammox]) and to a lesser extent sulfur cycling (sulfur oxidation and sulfate reduction), depending on local hydrochemical differences. Surprisingly, the differentiation potential of the groundwater microbiome surpasses that of hydrochemistry for individual monitoring wells. Being dominated by a few phyla (Bacteroidetes, Proteobacteria, Planctomycetes, and Thaumarchaeota), the taxonomic profiling of groundwater metagenomes and metatranscriptomes revealed pronounced differences between merely present microbiome members and those actively participating in community gene expression and biogeochemical cycling. Unexpectedly, we observed a constitutive expression of carbohydrate-active enzymes encoded by different microbiome members, along with the groundwater flow path. The turnover of organic carbon apparently complements for lithoautotrophic carbon assimilation pathways mainly used by the groundwater microbiome depending on the availability of oxygen and inorganic electron donors, like ammonium.IMPORTANCE Groundwater is a key resource for drinking water production and irrigation. The interplay between geological setting, hydrochemistry, carbon storage, and groundwater microbiome ecosystem functioning is crucial for our understanding of these important ecosystem services. We targeted the encoded and expressed metabolic potential of groundwater microbiomes along an aquifer transect that diversifies in terms of hydrochemistry and land use. Our results showed that the groundwater microbiome has a higher spatial differentiation potential than does hydrochemistry.}, }
@article {pmid30577803, year = {2018}, author = {Chappell, T and Geva, S and Hogan, JM and Huygens, F and Rathnayake, IU and Rudd, S and Kelly, W and Perrin, D}, title = {Rapid analysis of metagenomic data using signature-based clustering.}, journal = {BMC bioinformatics}, volume = {19}, number = {Suppl 20}, pages = {509}, doi = {10.1186/s12859-018-2540-4}, pmid = {30577803}, issn = {1471-2105}, mesh = {Algorithms ; Cluster Analysis ; *Data Analysis ; Humans ; Metagenomics/*methods ; Microbiota/genetics ; }, abstract = {BACKGROUND: Sequencing highly-variable 16S regions is a common and often effective approach to the study of microbial communities, and next-generation sequencing (NGS) technologies provide abundant quantities of data for analysis. However, the speed of existing analysis pipelines may limit our ability to work with these quantities of data. Furthermore, the limited coverage of existing 16S databases may hamper our ability to characterise these communities, particularly in the context of complex or poorly studied environments.<br><br>RESULTS: In this article we present the SigClust algorithm, a novel clustering method involving the transformation of sequence reads into binary signatures. When compared to other published methods, SigClust yields superior cluster coherence and separation of metagenomic read data, while operating within substantially reduced timeframes. We demonstrate its utility on published Illumina datasets and on a large collection of labelled wound reads sourced from patients in a wound clinic. The temporal analysis is based on tracking the dominant clusters of wound samples over time. The analysis can identify markers of both healing and non-healing wounds in response to treatment. Prominent clusters are found, corresponding to bacterial species known to be associated with unfavourable healing outcomes, including a number of strains of Staphylococcus aureus.<br><br>CONCLUSIONS: SigClust identifies clusters rapidly and supports an improved understanding of the wound microbiome without reliance on a reference database. The results indicate a promising use for a SigClust-based pipeline in wound analysis and prediction, and a possible novel method for wound management and treatment.}, }
@article {pmid30576077, year = {2019}, author = {Jeunen, GJ and Knapp, M and Spencer, HG and Lamare, MD and Taylor, HR and Stat, M and Bunce, M and Gemmell, NJ}, title = {Environmental DNA (eDNA) metabarcoding reveals strong discrimination among diverse marine habitats connected by water movement.}, journal = {Molecular ecology resources}, volume = {19}, number = {2}, pages = {426-438}, doi = {10.1111/1755-0998.12982}, pmid = {30576077}, issn = {1755-0998}, mesh = {Aquatic Organisms/*classification/genetics/growth &amp; development ; *Biota ; Cluster Analysis ; *DNA Barcoding, Taxonomic ; DNA, Ribosomal/chemistry/genetics ; *Ecosystem ; Electron Transport Complex IV/genetics ; Eukaryota/*classification/genetics/growth &amp; development ; *Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Water Movements ; }, abstract = {While in recent years environmental DNA (eDNA) metabarcoding surveys have shown great promise as an alternative monitoring method, the integration into existing marine monitoring programs may be confounded by the dispersal of the eDNA signal. Currents and tidal influences could transport eDNA over great distances, inducing false-positive species detection, leading to inaccurate biodiversity assessments and, ultimately, mismanagement of marine environments. In this study, we determined the ability of eDNA metabarcoding surveys to distinguish localized signals obtained from four marine habitats within a small spatial scale (<5 km) subject to significant tidal and along-shore water flow. Our eDNA metabarcoding survey detected 86 genera, within 77 families and across 11 phyla using three established metabarcoding assays targeting fish (16S rRNA gene), crustacean (16S rRNA gene) and eukaryotic (cytochrome oxidase subunit 1) diversity. Ordination and cluster analyses for both taxonomic and OTU data sets show distinct eDNA signals between the sampled habitats, suggesting dispersal of eDNA among habitats was limited. Individual taxa with strong habitat preferences displayed localized eDNA signals in accordance with their respective habitat, whereas taxa known to be less habitat-specific generated more ubiquitous signals. Our data add to evidence that eDNA metabarcoding surveys in marine environments detect a broad range of taxa that are spatially discrete. Our work also highlights that refinement of assay choice is essential to realize the full potential of eDNA metabarcoding surveys in marine biodiversity monitoring programs.}, }
@article {pmid30565880, year = {2019}, author = {Thorn, CE and Bergesch, C and Joyce, A and Sambrano, G and McDonnell, K and Brennan, F and Heyer, R and Benndorf, D and Abram, F}, title = {A robust, cost-effective method for DNA, RNA and protein co-extraction from soil, other complex microbiomes and pure cultures.}, journal = {Molecular ecology resources}, volume = {19}, number = {2}, pages = {439-455}, doi = {10.1111/1755-0998.12979}, pmid = {30565880}, issn = {1755-0998}, support = {//NUI Galway/ ; }, mesh = {Cost-Benefit Analysis ; DNA/genetics/*isolation &amp; purification ; Metagenomics/economics/*methods ; *Microbiota ; Proteins/analysis/*isolation &amp; purification ; Proteomics/economics/*methods ; RNA/genetics/*isolation &amp; purification ; *Soil Microbiology ; }, abstract = {The soil microbiome is inherently complex with high biological diversity, and spatial heterogeneity typically occurring on the submillimetre scale. To study the microbial ecology of soils, and other microbiomes, biomolecules, that is, nucleic acids and proteins, must be efficiently and reliably co-recovered from the same biological samples. Commercial kits are currently available for the co-extraction of DNA, RNA and proteins but none has been developed for soil samples. We present a new protocol drawing on existing phenol-chloroform-based methods for nucleic acids co-extraction but incorporating targeted precipitation of proteins from the phenol phase. The protocol is cost-effective and robust, and easily implemented using reagents commonly available in laboratories. The method is estimated to be eight times cheaper than using disparate commercial kits for the isolation of DNA and/or RNA, and proteins, from soil. The method is effective, providing good quality biomolecules from a diverse range of soil types, with clay contents varying from 9.5% to 35.1%, which we successfully used for downstream, high-throughput gene sequencing and metaproteomics. Additionally, we demonstrate that the protocol can also be easily implemented for biomolecule co-extraction from other complex microbiome samples, including cattle slurry and microbial communities recovered from anaerobic bioreactors, as well as from Gram-positive and Gram-negative pure cultures.}, }
@article {pmid30562947, year = {2018}, author = {Ishii, C and Nakanishi, Y and Murakami, S and Nozu, R and Ueno, M and Hioki, K and Aw, W and Hirayama, A and Soga, T and Ito, M and Tomita, M and Fukuda, S}, title = {A Metabologenomic Approach Reveals Changes in the Intestinal Environment of Mice Fed on American Diet.}, journal = {International journal of molecular sciences}, volume = {19}, number = {12}, pages = {}, doi = {10.3390/ijms19124079}, pmid = {30562947}, issn = {1422-0067}, support = {15H01522//Japan Society for the Promotion of Science/ ; 16H04901//Japan Society for the Promotion of Science/ ; 17H05654//Japan Society for the Promotion of Science/ ; 18H04805//Japan Society for the Promotion of Science/ ; JPMJPR1537//Japan Science and Technology Agency/ ; }, mesh = {Animals ; *Diet ; *Gastrointestinal Microbiome ; Humans ; Male ; *Metabolome ; *Metagenomics ; Mice ; *Ruminococcus/genetics/growth &amp; development ; }, abstract = {Intestinal microbiota and their metabolites are strongly associated with host physiology. Developments in DNA sequencing and mass spectrometry technologies have allowed us to obtain additional data that enhance our understanding of the interactions among microbiota, metabolites, and the host. However, the strategies used to analyze these datasets are not yet well developed. Here, we describe an original analytical strategy, metabologenomics, consisting of an integrated analysis of mass spectrometry-based metabolome data and high-throughput-sequencing-based microbiome data. Using this approach, we compared data obtained from C57BL/6J mice fed an American diet (AD), which contained higher amounts of fat and fiber, to those from mice fed control rodent diet. The feces of the AD mice contained higher amounts of butyrate and propionate, and higher relative abundances of Oscillospira and Ruminococcus. The amount of butyrate positively correlated with the abundance of these bacterial genera. Furthermore, integrated analysis of the metabolome data and the predicted metagenomic data from Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) indicated that the abundance of genes associated with butyrate metabolism positively correlated with butyrate amounts. Thus, our metabologenomic approach is expected to provide new insights and understanding of intestinal metabolic dynamics in complex microbial ecosystems.}, }
@article {pmid30559737, year = {2018}, author = {Gong, Z and Liang, Y and Wang, M and Jiang, Y and Yang, Q and Xia, J and Zhou, X and You, S and Gao, C and Wang, J and He, J and Shao, H and McMinn, A}, title = {Viral Diversity and Its Relationship With Environmental Factors at the Surface and Deep Sea of Prydz Bay, Antarctica.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2981}, doi = {10.3389/fmicb.2018.02981}, pmid = {30559737}, issn = {1664-302X}, abstract = {A viral metagenomic analysis of five surface and two bottom water (878 meters below surface, mbs, and 3,357 mbs) samples from Prydz Bay, was conducted during February-March 2015. The results demonstrated that most of the DNA viruses were dsDNA viruses (79.73-94.06%, except at PBI1, 37.51%). Of these, Caudovirales (Siphoviridae, Myoviridae, and Podoviridae) phages were most abundant in surface seawater (67.67-71.99%), while nucleocytoplasmic large DNA viruses (NCLDVs) (Phycodnaviridae, Mimiviridae, and Pandoraviridae accounted for >30% of dsDNA viruses) were most abundant in the bottom water (3,357 mbs). Of the ssDNA viruses, Microviridae was the dominant family in PBI2, PBI3, PBOs, and PBI4b (57.09-87.55%), while Inoviridae (58.16%) was the dominant family in PBI1. Cellulophaga phages (phi38:1 and phi10:1) and Flavobacterium phage 11b, infecting the possible host strains affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes, were abundant in surface water dsDNA viromes. The long contig (PBI2_1_C) from the viral metagenomes were most similar to the genome architectures of Cellulophaga phage phi10:1 and Flavobacterium phage 11b from the Arctic Ocean. Comparative analysis showed that the surface viral community of Prydz Bay could be clearly separated from other marine and freshwater environments. The deep sea viral community was similar to the deep sea viral metagenome at A Long-term Oligotrophic Habitat Assessment Station (ALOHA, at 22°45'N, 158°00'W). The multivariable analysis indicated that nutrients probably played an important role in shaping the local viral community structure. This study revealed the preliminary characteristics of the viral community in Prydz Bay, from both the surface and the deep sea. It provided evidence of the relationships between the virome and the environment in Prydz Bay and provided the first data from the deep sea viral community of the Southern Ocean.}, }
@article {pmid30558682, year = {2018}, author = {Sirová, D and Bárta, J and Šimek, K and Posch, T and Pech, J and Stone, J and Borovec, J and Adamec, L and Vrba, J}, title = {Hunters or farmers? Microbiome characteristics help elucidate the diet composition in an aquatic carnivorous plant.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {225}, doi = {10.1186/s40168-018-0600-7}, pmid = {30558682}, issn = {2049-2618}, mesh = {Aquatic Organisms/microbiology/physiology ; Bacteria/*classification/genetics/isolation &amp; purification ; DNA, Algal/genetics ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; Fungi/*classification/genetics/isolation &amp; purification ; Gene Expression Profiling/methods ; Lamiales/*microbiology/physiology ; Metagenomics/*methods ; Microbial Consortia ; Phylogeny ; }, abstract = {BACKGROUND: Utricularia are rootless aquatic carnivorous plants which have recently attracted the attention of researchers due to the peculiarities of their miniaturized genomes. Here, we focus on a novel aspect of Utricularia ecophysiology-the interactions with and within the complex communities of microorganisms colonizing their traps and external surfaces.<br><br>RESULTS: Bacteria, fungi, algae, and protozoa inhabit the miniature ecosystem of the Utricularia trap lumen and are involved in the regeneration of nutrients from complex organic matter. By combining molecular methods, microscopy, and other approaches to assess the trap-associated microbial community structure, diversity, function, as well as the nutrient turn-over potential of bacterivory, we gained insight into the nutrient acquisition strategies of the Utricularia hosts.<br><br>CONCLUSIONS: We conclude that Utricularia traps can, in terms of their ecophysiological function, be compared to microbial cultivators or farms, which center around complex microbial consortia acting synergistically to convert complex organic matter, often of algal origin, into a source of utilizable nutrients for the plants.}, }
@article {pmid30545401, year = {2018}, author = {Forbes, JD and Chen, CY and Knox, NC and Marrie, RA and El-Gabalawy, H and de Kievit, T and Alfa, M and Bernstein, CN and Van Domselaar, G}, title = {A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {221}, doi = {10.1186/s40168-018-0603-4}, pmid = {30545401}, issn = {2049-2618}, mesh = {Adult ; Arthritis, Rheumatoid/microbiology ; Bacteria/*classification/genetics/isolation &amp; purification ; Case-Control Studies ; Colitis, Ulcerative/microbiology ; Crohn Disease/*microbiology ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Dysbiosis/*diagnosis ; Female ; Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/*microbiology ; Machine Learning ; Male ; Metagenomics/*methods ; Middle Aged ; Multiple Sclerosis/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Immune-mediated inflammatory disease (IMID) represents a substantial health concern. It is widely recognized that IMID patients are at a higher risk for developing secondary inflammation-related conditions. While an ambiguous etiology is common to all IMIDs, in recent years, considerable knowledge has emerged regarding the plausible role of the gut microbiome in IMIDs. This study used 16S rRNA gene amplicon sequencing to compare the gut microbiota of patients with Crohn's disease (CD; N = 20), ulcerative colitis (UC; N = 19), multiple sclerosis (MS; N = 19), and rheumatoid arthritis (RA; N = 21) versus healthy controls (HC; N = 23). Biological replicates were collected from participants within a 2-month interval. This study aimed to identify common (or unique) taxonomic biomarkers of IMIDs using both differential abundance testing and a machine learning approach.<br><br>RESULTS: Significant microbial community differences between cohorts were observed (pseudo F = 4.56; p = 0.01). Richness and diversity were significantly different between cohorts (pFDR < 0.001) and were lowest in CD while highest in HC. Abundances of Actinomyces, Eggerthella, Clostridium III, Faecalicoccus, and Streptococcus (pFDR < 0.001) were significantly higher in all disease cohorts relative to HC, whereas significantly lower abundances were observed for Gemmiger, Lachnospira, and Sporobacter (pFDR < 0.001). Several taxa were found to be differentially abundant in IMIDs versus HC including significantly higher abundances of Intestinibacter in CD, Bifidobacterium in UC, and unclassified Erysipelotrichaceae in MS and significantly lower abundances of Coprococcus in CD, Dialister in MS, and Roseburia in RA. A machine learning approach to classify disease versus HC was highest for CD (AUC = 0.93 and AUC = 0.95 for OTU and genus features, respectively) followed by MS, RA, and UC. Gemmiger and Faecalicoccus were identified as important features for classification of subjects to CD and HC. In general, features identified by differential abundance testing were consistent with machine learning feature importance.<br><br>CONCLUSIONS: This study identified several gut microbial taxa with differential abundance patterns common to IMIDs. We also found differentially abundant taxa between IMIDs. These taxa may serve as biomarkers for the detection and diagnosis of IMIDs and suggest there may be a common component to IMID etiology.}, }
@article {pmid30543873, year = {2019}, author = {Lima, DA and Cibulski, SP and Tochetto, C and Varela, APM and Finkler, F and Teixeira, TF and Loiko, MR and Cerva, C and Junqueira, DM and Mayer, FQ and Roehe, PM}, title = {The intestinal virome of malabsorption syndrome-affected and unaffected broilers through shotgun metagenomics.}, journal = {Virus research}, volume = {261}, number = {}, pages = {9-20}, doi = {10.1016/j.virusres.2018.12.005}, pmid = {30543873}, issn = {1872-7492}, mesh = {Animals ; Chickens ; Feces/*virology ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Malabsorption Syndromes/*veterinary/virology ; Metagenomics ; Poultry Diseases/*virology ; Viruses/*classification/*genetics ; }, abstract = {Malabsorption syndrome (MAS) is an economically important disease of young, commercially reared broilers, characterized by growth retardation, defective feather development and diarrheic faeces. Several viruses have been tentatively associated to such syndrome. Here, in order to examine potential associations between enteric viruses and MAS, the faecal viromes of 70 stool samples collected from diseased (n = 35) and healthy (n = 35) chickens from seven flocks were characterized and compared. Following high-throughput sequencing, a total of 8,347,319 paired end reads, with an average of 231 nt, were generated. Through analysis of de novo assembled contigs, 144 contigs > 1000 nt were identified with hits to eukaryotic viral sequences, as determined by GenBank database. A number of known and unknown representatives of Adenoviridae, Anelloviridae, Astroviridae, Caliciviridae, Circoviridae, Parvoviridae, Picobirnaviridae, Picornaviridae and Reoviridae, as well as novel uncharacterized CRESS-DNA viruses, were identified. However, the distribution of sequence reads of viral genomes identified in diseased or healthy birds revealed no statistically significant differences. These findings indicate no association between the occurrence of MAS and enteric viruses. The viral genomes reported in the present study, including a variety of novel viruses, seem part of the normal intestinal microbiota of chickens.}, }
@article {pmid30522530, year = {2018}, author = {Edlund, A and Yang, Y and Yooseph, S and He, X and Shi, W and McLean, JS}, title = {Uncovering complex microbiome activities via metatranscriptomics during 24 hours of oral biofilm assembly and maturation.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {217}, pmid = {30522530}, issn = {2049-2618}, support = {R00 DE024543/DE/NIDCR NIH HHS/United States ; K99 DE024543/DE/NIDCR NIH HHS/United States ; R01 DE023810/DE/NIDCR NIH HHS/United States ; R01 DE020102/DE/NIDCR NIH HHS/United States ; R01 DE026186/DE/NIDCR NIH HHS/United States ; R01 GM095373/GM/NIGMS NIH HHS/United States ; }, mesh = {Adult ; Bacteria/*classification/genetics/growth &amp; development ; Bacterial Proteins/genetics ; Biofilms ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Dental Plaque/*microbiology ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Bacterial ; Humans ; Hydrogen-Ion Concentration ; Metabolic Networks and Pathways ; Metagenomics/*methods ; Mouth/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Dental plaque is composed of hundreds of bacterial taxonomic units and represents one of the most diverse and stable microbial ecosystems associated with the human body. Taxonomic composition and functional capacity of mature plaque is gradually shaped during several stages of community assembly via processes such as co-aggregation, competition for space and resources, and by bacterially produced reactive agents. Knowledge on the dynamics of assembly within complex communities is very limited and derives mainly from studies composed of a limited number of bacterial species. To fill current knowledge gaps, we applied parallel metagenomic and metatranscriptomic analyses during assembly and maturation of an in vitro oral biofilm. This model system has previously demonstrated remarkable reproducibility in taxonomic composition across replicate samples during maturation.<br><br>RESULTS: Time course analysis of the biofilm maturation was performed by parallel sampling every 2-3 h for 24 h for both DNA and RNA. Metagenomic analyses revealed that community taxonomy changed most dramatically between three and six hours of growth when pH dropped from 6.5 to 5.5. By applying comparative metatranscriptome analysis we could identify major shifts in overall community activities between six and nine hours of growth when pH dropped below 5.5, as 29,015 genes were significantly up- or down- expressed. Several of the differentially expressed genes showed unique activities for individual bacterial genomes and were associated with pyruvate and lactate metabolism, two-component signaling pathways, production of antibacterial molecules, iron sequestration, pH neutralization, protein hydrolysis, and surface attachment. Our analysis also revealed several mechanisms responsible for the niche expansion of the cariogenic pathogen Lactobacillus fermentum.<br><br>CONCLUSION: It is highly regarded that acidic conditions in dental plaque cause a net loss of enamel from teeth. Here, as pH drops below 5.5 pH to 4.7, we observe blooms of cariogenic lactobacilli, and a transition point of many bacterial gene expression activities within the community. To our knowledge, this represents the first study of the assembly and maturation of a complex oral bacterial biofilm community that addresses gene level functional responses over time.}, }
@article {pmid30537931, year = {2018}, author = {Benavides, A and Isaza, JP and Niño-García, JP and Alzate, JF and Cabarcas, F}, title = {CLAME: a new alignment-based binning algorithm allows the genomic description of a novel Xanthomonadaceae from the Colombian Andes.}, journal = {BMC genomics}, volume = {19}, number = {Suppl 8}, pages = {858}, pmid = {30537931}, issn = {1471-2164}, mesh = {*Algorithms ; Colombia ; Genes, Bacterial ; Genetic Markers ; *Genome, Bacterial ; *Metagenomics ; Microbiota ; Phylogeny ; Sequence Analysis, DNA/*methods ; Xanthomonadaceae/*classification/*genetics ; }, abstract = {BACKGROUND: Hot spring bacteria have unique biological adaptations to survive the extreme conditions of these environments; these bacteria produce thermostable enzymes that can be used in biotechnological and industrial applications. However, sequencing these bacteria is complex, since it is not possible to culture them. As an alternative, genome shotgun sequencing of whole microbial communities can be used. The problem is that the classification of sequences within a metagenomic dataset is very challenging particularly when they include unknown microorganisms since they lack genomic reference. We failed to recover a bacterium genome from a hot spring metagenome using the available software tools, so we develop a new tool that allowed us to recover most of this genome.<br><br>RESULTS: We present a proteobacteria draft genome reconstructed from a Colombian's Andes hot spring metagenome. The genome seems to be from a new lineage within the family Rhodanobacteraceae of the class Gammaproteobacteria, closely related to the genus Dokdonella. We were able to generate this genome thanks to CLAME. CLAME, from Spanish &quot;CLAsificador MEtagenomico&quot;, is a tool to group reads in bins. We show that most reads from each bin belong to a single chromosome. CLAME is very effective recovering most of the reads belonging to the predominant species within a metagenome.<br><br>CONCLUSIONS: We developed a tool that can be used to extract genomes (or parts of them) from a complex metagenome.}, }
@article {pmid30532085, year = {2018}, author = {Chen, B and Yu, T and Xie, S and Du, K and Liang, X and Lan, Y and Sun, C and Lu, X and Shao, Y}, title = {Comparative shotgun metagenomic data of the silkworm Bombyx mori gut microbiome.}, journal = {Scientific data}, volume = {5}, number = {}, pages = {180285}, pmid = {30532085}, issn = {2052-4463}, mesh = {Acinetobacter/genetics ; Animals ; Bombyx/*microbiology ; Enterobacter/genetics ; Enterococcus/genetics ; *Gastrointestinal Microbiome ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; }, abstract = {Lepidoptera (butterflies and moths) is a major insect order including important pollinators and agricultural pests, however their microbiomes are little studied. Here, using next-generation sequencing (NGS)-based shotgun metagenomics, we characterize both the biodiversity and functional potential of gut microbiota of a lepidopteran model insect, the silkworm Bombyx mori. Two metagenomes, including the standard inbred strain Dazao (P50) and an improved hybrid strain Qiufeng × Baiyu (QB) widely used in commercial silk production, were generated, containing 45,505,084 and 69,127,002 raw reads, respectively. Taxonomic analysis revealed that a total of 663 bacterial species were identified in P50 silkworms, while 322 unique species in QB silkworms. Notably, Enterobacter, Acinetobacter and Enterococcus were dominated in both strains. The further functional annotation was performed by both BlastP and MG-RAST against various databases including Nr, COG, KEGG, CAZy and SignalP, which revealed >5 × 106 protein-coding genes. These datasets not only provide first insights into all bacterial genes in silkworm guts, but also help to generate hypotheses for subsequently testing functional traits of gut microbiota in an important insect group.}, }
@article {pmid30528276, year = {2019}, author = {Ramos-Barbero, MD and Martin-Cuadrado, AB and Viver, T and Santos, F and Martinez-Garcia, M and Antón, J}, title = {Recovering microbial genomes from metagenomes in hypersaline environments: The Good, the Bad and the Ugly.}, journal = {Systematic and applied microbiology}, volume = {42}, number = {1}, pages = {30-40}, doi = {10.1016/j.syapm.2018.11.001}, pmid = {30528276}, issn = {1618-0984}, mesh = {Archaea/genetics/isolation &amp; purification ; Bacteria/genetics/isolation &amp; purification ; *Genome, Microbial ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; *Salinity ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {Current metagenomic tools allow the recovery of microbial genomes directly from the environment. This can be accomplished by binning metagenomic contigs according to their coverage and tetranucleotide frequency, followed by an estimation of the bin quality. The public availability of bioinformatics tools, together with the decreasing cost of next generation sequencing, are democratizing this powerful approach that is spreading from specialized research groups to the general public. Using metagenomes from hypersaline environments, as well as mock metagenomes composed of Archaea and Bacteria frequently found in these systems, we have analyzed the advantages and difficulties of the binning process in these extreme environments to tackle microbial population diversity. These extreme systems harbor relatively low species diversity but high intraspecific diversity, which can compromise metagenome assembly and therefore the whole binning process. The main goal is to compare the output of the binning process with what is previously known from the analyzed samples, based on years of study using different approaches. Several scenarios have been analyzed in detail: (i) a good quality bin from a species highly abundant in the environment; (ii) an intermediate quality bin with incongruences that can be solved by further analyses and manual curation, and (iii) a low-quality bin to investigate the failure to recover a very abundant microbial genome as well as some possible solutions. The latter can be considered the &quot;great metagenomics anomaly&quot; and is mainly due to assembly problems derived from the microdiversity of naturally co-existing populations in nature.}, }
@article {pmid30518415, year = {2018}, author = {Alonso, L and Creuzé-des-Châtelliers, C and Trabac, T and Dubost, A and Moënne-Loccoz, Y and Pommier, T}, title = {Rock substrate rather than black stain alterations drives microbial community structure in the passage of Lascaux Cave.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {216}, pmid = {30518415}, issn = {2049-2618}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Carbon Dioxide/analysis ; Caves/*microbiology ; DNA, Fungal/genetics ; France ; Fungi/*classification/genetics/isolation &amp; purification ; Geologic Sediments/microbiology ; High-Throughput Nucleotide Sequencing ; Human Activities ; Humans ; Metagenomics ; Microbiota ; Phylogeny ; Seasons ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: The World-famous UNESCO heritage from the Paleolithic human society, Lascaux Cave (France), has endeavored intense microclimatic perturbations, in part due to high touristic pressure. These perturbations have resulted in numerous disturbances of the cave ecosystem, including on its microbial compartment, which resulted in the formation of black stains especially on the rock faces of the passage. We investigated the cave microbiome in this part of Lascaux by sampling three mineral substrates (soil, banks, and inclined planes) on and outside stains to assess current cave microbial assemblage and explore the possibility that pigmented microorganisms involved in stain development occur as microbial consortia.<br><br>METHODS: Microbial abundance and diversity were assessed by means of quantitative PCR and high-throughput sequencing (Illumina MiSeq) of several DNA and cDNA taxonomic markers. Five sampling campaigns were carried out during winter and summer to embrace potential seasonal effect in this somewhat stable environment (based on measurements of temperature and CO2 concentration).<br><br>RESULTS: While the season or type of mineral substrate did not affect the abundances of bacteria and micro-eukaryotes on or outside stains, mineral substrate rather than stain presence appears to be the most significant factor determining microbial diversity and structuring microbial community, regardless of whether DNA or cDNA markers were considered. A phylogenetic signal was also detected in relation to substrate types, presence of stains but not with season among the OTUs common to the three substrates. Co-occurrence network analyses showed that most bacterial and fungal interactions were positive regardless of the factor tested (season, substrate, or stain), but these networks varied according to ecological conditions and time. Microorganisms known to harbor pigmentation ability were well established inside but also outside black stains, which may be prerequisite for subsequent stain formation.<br><br>CONCLUSIONS: This first high throughput sequencing performed in Lascaux Cave showed that black stains were secondary to mineral substrate in determining microbiome community structure, regardless of whether total or transcriptionally active bacterial and micro-eukaryotic communities were considered. These results revealed the potential for new stain formation and highlight the need for careful microbiome management to avoid further cave wall degradation.}, }
@article {pmid30518356, year = {2018}, author = {Bin, P and Tang, Z and Liu, S and Chen, S and Xia, Y and Liu, J and Wu, H and Zhu, G}, title = {Intestinal microbiota mediates Enterotoxigenic Escherichia coli-induced diarrhea in piglets.}, journal = {BMC veterinary research}, volume = {14}, number = {1}, pages = {385}, pmid = {30518356}, issn = {1746-6148}, mesh = {Animals ; Bacteria/classification/genetics ; Diarrhea/microbiology/*veterinary ; Dysbiosis/immunology/microbiology/*veterinary ; Enterotoxigenic Escherichia coli/immunology/physiology ; Escherichia coli Infections/veterinary ; Fecal Microbiota Transplantation ; Gastrointestinal Microbiome/*genetics/*immunology ; Intestinal Diseases/immunology/microbiology/*veterinary ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Swine ; Swine Diseases/immunology/*microbiology ; }, abstract = {BACKGROUND: Enterotoxigenic Escherichia coli (ETEC) causes diarrhea in humans, cows, and pigs. The gut microbiota underlies pathology of several infectious diseases yet the role of the gut microbiota in the pathogenesis of ETEC-induced diarrhea is unknown.<br><br>RESULTS: By using an ETEC induced diarrheal model in piglet, we profiled the jejunal and fecal microbiota using metagenomics and 16S rRNA sequencing. A jejunal microbiota transplantation experiment was conducted to determine the role of the gut microbiota in ETEC-induced diarrhea. ETEC-induced diarrhea influenced the structure and function of gut microbiota. Diarrheal piglets had lower Bacteroidetes: Firmicutes ratio and microbiota diversity in the jejunum and feces, and lower percentage of Prevotella in the feces, but higher Lactococcus in the jejunum and higher Escherichia-Shigella in the feces. The transplantation of the jejunal microbiota from diarrheal piglets to uninfected piglets leaded to diarrhea after transplantation. Microbiota transplantation experiments also supported the notion that dysbiosis of gut microbiota is involved in the immune responses in ETEC-induced diarrhea.<br><br>CONCLUSION: We conclude that ETEC infection influences the gut microbiota and the dysbiosis of gut microbiota after ETEC infection mediates the immune responses in ETEC infection.}, }
@article {pmid30518125, year = {2018}, author = {Raimundo, I and Silva, SG and Costa, R and Keller-Costa, T}, title = {Bioactive Secondary Metabolites from Octocoral-Associated Microbes-New Chances for Blue Growth.}, journal = {Marine drugs}, volume = {16}, number = {12}, pages = {}, doi = {10.3390/md16120485}, pmid = {30518125}, issn = {1660-3397}, support = {EXPL/MAR-EST/1664/2013//Fundação para a Ciência e a Tecnologia/ ; PTDC/MAR-BIO/1547/2014//Fundação para a Ciência e a Tecnologia/ ; }, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/genetics/*metabolism ; Biological Products/isolation &amp; purification/metabolism/*pharmacology ; Biosynthetic Pathways/*genetics ; Fungi/genetics/*metabolism ; Industrial Microbiology/methods ; Microbiota/physiology ; Multigene Family ; Symbiosis ; Technology, Pharmaceutical/methods ; }, abstract = {Octocorals (Cnidaria, Anthozoa Octocorallia) are magnificent repositories of natural products with fascinating and unusual chemical structures and bioactivities of interest to medicine and biotechnology. However, mechanistic understanding of the contribution of microbial symbionts to the chemical diversity of octocorals is yet to be achieved. This review inventories the natural products so-far described for octocoral-derived bacteria and fungi, uncovering a true chemical arsenal of terpenes, steroids, alkaloids, and polyketides with antibacterial, antifungal, antiviral, antifouling, anticancer, anti-inflammatory, and antimalarial activities of enormous potential for blue growth. Genome mining of 15 bacterial associates (spanning 12 genera) cultivated from Eunicella spp. resulted in the identification of 440 putative and classifiable secondary metabolite biosynthetic gene clusters (BGCs), encompassing varied terpene-, polyketide-, bacteriocin-, and nonribosomal peptide-synthase BGCs. This points towards a widespread yet uncharted capacity of octocoral-associated bacteria to synthetize a broad range of natural products. However, to extend our knowledge and foster the near-future laboratory production of bioactive compounds from (cultivatable and currently uncultivatable) octocoral symbionts, optimal blending between targeted metagenomics, DNA recombinant technologies, improved symbiont cultivation, functional genomics, and analytical chemistry are required. Such a multidisciplinary undertaking is key to achieving a sustainable response to the urgent industrial demand for novel drugs and enzyme varieties.}, }
@article {pmid30507071, year = {2019}, author = {Alsammar, HF and Naseeb, S and Brancia, LB and Gilman, RT and Wang, P and Delneri, D}, title = {Targeted metagenomics approach to capture the biodiversity of Saccharomyces genus in wild environments.}, journal = {Environmental microbiology reports}, volume = {11}, number = {2}, pages = {206-214}, doi = {10.1111/1758-2229.12724}, pmid = {30507071}, issn = {1758-2229}, support = {BB/L021471/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {The species of the genus Saccharomyces are commonly inhabiting tree bark and the surrounding soil, but their abundance have likely been underestimated due to biases in culturing methods. Metagenomic studies have so far been unable to detect Saccharomyces species in wild environments. Here, we sequenced the mycobiome of soils surrounding different trees at various altitudes in the Italian Alps. To survey for yeasts species belonging to Saccharomyces genus rather than other fungal species, we performed a selectivity step involving the isolation of the internal transcribed spacer (ITS) region that is specific to this yeast group. Reads mapping to Saccharomyces species were detected in all soil samples, including reads for S. mikatae and for S. eubayanus. ITS1 alignment of the S. cerevisiae, S. paradoxus and S. kudriavzevii sequences showed up to three base pair polymorphisms with other known strains, indicating possible new lineages. Basidiomycetous fungi were still the dominant species, compared to the Ascomycota, but the selectivity step allowed for the first time the detection and study of the biodiversity of the Saccharomyces species in their natural environment.}, }
@article {pmid30504906, year = {2018}, author = {Wampach, L and Heintz-Buschart, A and Fritz, JV and Ramiro-Garcia, J and Habier, J and Herold, M and Narayanasamy, S and Kaysen, A and Hogan, AH and Bindl, L and Bottu, J and Halder, R and Sjöqvist, C and May, P and Andersson, AF and de Beaufort, C and Wilmes, P}, title = {Birth mode is associated with earliest strain-conferred gut microbiome functions and immunostimulatory potential.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {5091}, doi = {10.1038/s41467-018-07631-x}, pmid = {30504906}, issn = {2041-1723}, mesh = {Cesarean Section ; Delivery, Obstetric ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; In Vitro Techniques ; Infant, Newborn ; Infectious Disease Transmission, Vertical ; Interleukin-18/metabolism ; Lipopolysaccharides/metabolism ; Metagenomics/methods ; Pregnancy ; Tumor Necrosis Factor-alpha/metabolism ; }, abstract = {The rate of caesarean section delivery (CSD) is increasing worldwide. It remains unclear whether disruption of mother-to-neonate transmission of microbiota through CSD occurs and whether it affects human physiology. Here we perform metagenomic analysis of earliest gut microbial community structures and functions. We identify differences in encoded functions between microbiomes of vaginally delivered (VD) and CSD neonates. Several functional pathways are over-represented in VD neonates, including lipopolysaccharide (LPS) biosynthesis. We link these enriched functions to individual-specific strains, which are transmitted from mothers to neonates in case of VD. The stimulation of primary human immune cells with LPS isolated from early stool samples of VD neonates results in higher levels of tumour necrosis factor (TNF-α) and interleukin 18 (IL-18). Accordingly, the observed levels of TNF-α and IL-18 in neonatal blood plasma are higher after VD. Taken together, our results support that CSD disrupts mother-to-neonate transmission of specific microbial strains, linked functional repertoires and immune-stimulatory potential during a critical window for neonatal immune system priming.}, }
@article {pmid30504145, year = {2018}, author = {Tokuda, G and Mikaelyan, A and Fukui, C and Matsuura, Y and Watanabe, H and Fujishima, M and Brune, A}, title = {Fiber-associated spirochetes are major agents of hemicellulose degradation in the hindgut of wood-feeding higher termites.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {51}, pages = {E11996-E12004}, doi = {10.1073/pnas.1810550115}, pmid = {30504145}, issn = {1091-6490}, mesh = {Animals ; Cellulases/genetics/metabolism ; Cellulose/metabolism ; Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract/microbiology ; Gene Expression Regulation, Bacterial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Glycoside Hydrolases/genetics/metabolism ; Isoptera/*microbiology ; Metagenome/genetics ; Metagenomics ; Phylogeny ; Polysaccharides/*metabolism ; Sequence Analysis, DNA ; Spirochaetales/*enzymology/*genetics/*metabolism ; Symbiosis ; Wood/*metabolism ; Xylans/metabolism ; Xylosidases/classification/genetics/metabolism ; }, abstract = {Symbiotic digestion of lignocellulose in wood-feeding higher termites (family Termitidae) is a two-step process that involves endogenous host cellulases secreted in the midgut and a dense bacterial community in the hindgut compartment. The genomes of the bacterial gut microbiota encode diverse cellulolytic and hemicellulolytic enzymes, but the contributions of host and bacterial symbionts to lignocellulose degradation remain ambiguous. Our previous studies of Nasutitermes spp. documented that the wood fibers in the hindgut paunch are consistently colonized not only by uncultured members of Fibrobacteres, which have been implicated in cellulose degradation, but also by unique lineages of Spirochaetes. Here, we demonstrate that the degradation of xylan, the major component of hemicellulose, is restricted to the hindgut compartment, where it is preferentially hydrolyzed over cellulose. Metatranscriptomic analysis documented that the majority of glycoside hydrolase (GH) transcripts expressed by the fiber-associated bacterial community belong to family GH11, which consists exclusively of xylanases. The substrate specificity was further confirmed by heterologous expression of the gene encoding the predominant homolog. Although the most abundant transcripts of GH11 in Nasutitermes takasagoensis were phylogenetically placed among their homologs of Firmicutes, immunofluorescence microscopy, compositional binning of metagenomics contigs, and the genomic context of the homologs indicated that they are encoded by Spirochaetes and were most likely obtained by horizontal gene transfer among the intestinal microbiota. The major role of spirochetes in xylan degradation is unprecedented and assigns the fiber-associated Treponema clades in the hindgut of wood-feeding higher termites a prominent part in the breakdown of hemicelluloses.}, }
@article {pmid30503454, year = {2018}, author = {Hwang, J and Park, SY and Lee, S and Lee, TK}, title = {High diversity and potential translocation of DNA viruses in ballast water.}, journal = {Marine pollution bulletin}, volume = {137}, number = {}, pages = {449-455}, doi = {10.1016/j.marpolbul.2018.10.053}, pmid = {30503454}, issn = {1879-3363}, mesh = {Animals ; DNA Viruses/*genetics/*isolation &amp; purification ; Introduced Species ; Metagenomics ; Mexico ; New York ; Panama ; Republic of Korea ; Saudi Arabia ; *Ships ; Water/*analysis/chemistry ; Water Microbiology ; }, abstract = {Ballast water is a common vector for the transport of invasive species to new marine and aquatic environments. We used a metagenomics approach to examine the composition and diversity of viral communities in ballast water from ships originating in Mexico, Saudi Arabia, New York, and Panama, and in water from the port of their destination in Busan, Korea. Myoviridae was the most abundant virus family in ballast water, followed Podoviridae and Siphoviridae. We also identified viruses that infect invertebrates, amoebas, and algae in ballast water and in the Busan port water. Interestingly, there were several viruses that infect humans or other animals (Swinepox virus, Raccoonpox virus, Suid herpesvirus, and Human endogenous retrovirus) in the samples from New York and Panama. In addition, there were giant viruses in all the ballast water samples, especially, identified Megavirus chilensis in New York and Panama, and Pandoravirus salinus in Mexico and Saudi Arabia. These results provide detailed descriptions of the characteristics of the viruses present in ballast water, document significant viral diversity, and indicate the potential translocation of viruses via ballast water.}, }
@article {pmid30513942, year = {2018}, author = {Pinho, CJ and Santos, B and Mata, VA and Seguro, M and Romeiras, MM and Lopes, RJ and Vasconcelos, R}, title = {What Is the Giant Wall Gecko Having for Dinner? Conservation Genetics for Guiding Reserve Management in Cabo Verde.}, journal = {Genes}, volume = {9}, number = {12}, pages = {}, doi = {10.3390/genes9120599}, pmid = {30513942}, issn = {2073-4425}, support = {MP/EAM/2016/06//Fondation Ensemble/ ; NA//Club 300 Foundation for Bird Protection/ ; NA//Monaco Explorations/ ; Fellowships PD/BD/106055/2015 (to BS), PD/BD/113462/2015 (to VAM), SFRH/BPD/84141/2012 (to RJL), and SFRH/BPD/79913/2011 (to RV) were funded by FCT/MEC and POPH/QREN/FSE//Fundação para a Ciência e a Tecnologia/ ; (NORTE-01-0145-FEDER-AGRIGEN)//NORTE2020/PORTUGAL/ ; VAM by ERA Chair in Environmental Metagenomics (EU Horizon 2020 Research and Innovation Programme Grant agreement No 668981)//Horizon 2020/ ; MACDIV-FCT-PTDC/BIABIC/0054/2014, and CVAgrobiodiversity/333111699 (to MMR)//Aga Khan Development Network (AKDN) and FCT/ ; }, abstract = {Knowledge on diet composition of a species is an important step to unveil its ecology and guide conservation actions. This is especially important for species that inhabit remote areas within biodiversity hotspots, with little information about their ecological roles. The emblematic giant wall gecko of Cabo Verde, Tarentola gigas, is restricted to the uninhabited Branco and Raso islets, and presents two subspecies. It is classified as Endangered, and locally Extinct on Santa Luzia Island; however, little information is known about its diet and behaviour. In this study, we identified the main plant, arthropods, and vertebrates consumed by both gecko subspecies using next generation sequencing (NGS) (metabarcoding of faecal pellets), and compared them with the species known to occur on Santa Luzia. Results showed that plants have a significant role as diet items and identified vertebrate and invertebrate taxa with higher taxonomic resolution than traditional methods. With this study, we now have data on the diet of both subspecies for evaluating the reintroduction of this threatened gecko on Santa Luzia as potentially successful, considering the generalist character of both populations. The information revealed by these ecological networks is important for the development of conservation plans by governmental authorities, and reinforces the essential and commonly neglected role of reptiles on island systems.}, }
@article {pmid30509257, year = {2018}, author = {He, F and Liu, D and Zhang, L and Zhai, J and Ma, Y and Xu, Y and Jiang, G and Rong, K and Ma, J}, title = {Metagenomic analysis of captive Amur tiger faecal microbiome.}, journal = {BMC veterinary research}, volume = {14}, number = {1}, pages = {379}, pmid = {30509257}, issn = {1746-6148}, support = {31372209//National Natural Science Foundation of China/ ; 2572017AA20//The Fundamental Research Funds for the Central Universities/ ; }, mesh = {Animals ; Animals, Zoo/*microbiology ; Bacteria/*classification/genetics/metabolism ; Endangered Species ; Feces/*microbiology ; *Gastrointestinal Microbiome ; *Metagenome ; Tigers/*microbiology ; }, abstract = {BACKGROUND: The gastrointestinal tracts of animals are home to large, complex communities of microbes. The compositions of these communities ultimately reflect the coevolution of microorganisms with their animal host and are influenced by the living environment, diet and immune status of the host. Gut microbes have been shown to be important for human disease and health, but little research exists in the gut microbiome of the Amur tiger, which is one of the most endangered species in the world.<br><br>RESULTS: In this study, we present the use of whole-metagenome shotgun sequencing to analyze the composition and functional structures of the gut microbiota in captive Amur tigers. Our results showed a high abundance of four major phyla in captive Amur tigers, including Proteobacteria, Firmicutes, Actinobacteria and Fusobacteria. Moreover, at the genus level, Escherichia, Collinsella and Fusobacterium were most abundant in the captive Amur tiger fecal metagenome. At the species level, Escherichia coli, Fusobacterium ulcerans and Fusobacterium varium were the species with highest abundances in the captive Amur tiger gut microbiota. The primary functional categories of the Amur tiger faecal metagenome were associated mainly with Carbohydrate metabolism, Membrane transport and Amino acid metabolism based on the KEGG pathway database. The comparative metagenomic analyses showed that the captive Amur tiger fecal metagenome had a lower abundance of Spirochaetes, Cyanobacteria and Ascomycota than other animals, and the primary functional categories were primarily associated with carbohydrate metabolism subsystems, clustering-based subsystems and protein metabolism.<br><br>CONCLUSIONS: We presented here for the first time the use of the shotgun metagenomic sequencing approach to study the composition and functional structures of the gut microbiota in captive Amur tiger.}, }
@article {pmid30489678, year = {2019}, author = {Vieira, FR and Pecchia, JA and Segato, F and Polikarpov, I}, title = {Exploring oyster mushroom (Pleurotus ostreatus) substrate preparation by varying phase I composting time: changes in bacterial communities and physicochemical composition of biomass impacting mushroom yields.}, journal = {Journal of applied microbiology}, volume = {126}, number = {3}, pages = {931-944}, doi = {10.1111/jam.14168}, pmid = {30489678}, issn = {1365-2672}, support = {005707/2012-05//Coordination for the Improvement of Higher Education Personnel/ ; 403090/2012-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; 490022/2009-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; 443916/2014-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; //University of São Paulo (USP) via NAP/ ; 2009/52840-7//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; 2013/21545-5//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; 2014/18714-2//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; 2015/13684-0//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; }, mesh = {*Bacteria/chemistry/metabolism ; Biodegradation, Environmental ; *Biomass ; *Composting ; *Microbial Consortia ; *Pleurotus/chemistry/metabolism ; }, abstract = {AIMS: To investigate characterization of the bacterial community composition and functionality and their impact on substrate biodegradation as well as mushroom yield.<br><br>METHODS AND RESULTS: Bacterial diversity, composition and functionality were accessed by DNA-derived analysis for a sugarcane straw-based substrate composted for either 5, 10 or 15 days. In addition, carbon and nitrogen losses, carbohydrate conversion and mushroom yields were measured for the different treatments. Changes were observed in the bacterial community diversity and composition after the process started, but not during the composting process itself. Following phase I, Acinetobacter sequences were recovered in high numbers, and selected genes associated with nitrogen metabolism and lignocellulose deconstruction were mapped. Substrate physicochemical composition showed elevated carbon and nitrogen losses after 10 and 15 days of phase I with reductions in mushroom yield.<br><br>CONCLUSIONS: Acinetobacter species appear to play an important role in substrate degradation processes, and a 5-day phase I period showed a significant higher mushroom yield compared to composting for either 10 or 15 days.<br><br>This study confers a better understanding of the bacterial community manipulation during the substrate preparation and their influence in substrate selectivity for the Pleurotus ostreatus cultivation.}, }
@article {pmid30489677, year = {2019}, author = {Sánchez-González, M and Álvarez-Uribe, H and Rivera-Solís, R and González-Burgos, A and Escalante-Réndiz, D and Rojas-Herrera, R}, title = {Analysis of a phenol-adapted microbial community: degradation capacity, taxonomy and metabolic description.}, journal = {Journal of applied microbiology}, volume = {126}, number = {3}, pages = {771-779}, doi = {10.1111/jam.14166}, pmid = {30489677}, issn = {1365-2672}, mesh = {Bacteria/classification/enzymology/genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biodegradation, Environmental ; Metagenomics ; *Microbiota ; Mixed Function Oxygenases/genetics/metabolism ; Phenol/*metabolism ; Phylogeny ; }, abstract = {AIMS: In this study, the ability of the consortium MR-01 to degrade phenol was determined. The effects of this chemical on the taxonomy and the metabolic behaviour were analysed through metagenomics.<br><br>METHODS AND RESULTS: Consortium MR-01 was acclimated in a sublethal concentration of phenol. After this process, the capacity to degrade this molecule was analysed. Results showed that degradation increased with the increment of the initial phenol concentration. Metagenomic analysis indicates that the consortium metabolized phenol under aerobic conditions using phenol 2-monooxygenase and the meta-cleavage pathway. Sequence of the enzymes involved in the phenol degradation was ascribed to the Actinomycetales and Chloroflexales orders, with relative abundances <1%. The most abundant genera were part of the Sphingomonadales order; however, the role of these species in the consortium is not clear.<br><br>CONCLUSIONS: Consortium MR-01 degrades efficiently high concentrations of phenol. The participation of extremophiles in the degradation process and the emergence of beneficial metabolic dependencies between the community members are some of the strategies used by the consortium to survive and develop under harsh environmental conditions.<br><br>This is one of the few studies describing the taxonomy and metabolic profile of a phenol degrading consortium.}, }
@article {pmid30486439, year = {2018}, author = {Yi, X and Yuan, J and Zhu, Y and Yi, X and Zhao, Q and Fang, K and Cao, L}, title = {Comparison of the Abundance and Community Structure of N-Cycling Bacteria in Paddy Rhizosphere Soil under Different Rice Cultivation Patterns.}, journal = {International journal of molecular sciences}, volume = {19}, number = {12}, pages = {}, doi = {10.3390/ijms19123772}, pmid = {30486439}, issn = {1422-0067}, mesh = {Bacteria/*classification/genetics/metabolism ; *Biodiversity ; Enzymes/genetics/metabolism ; Metagenome ; Metagenomics/methods ; Nitrogen ; Oryza/*microbiology ; Phylogeny ; *Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Eco-agricultural systems aim to reduce the use of chemical fertilizers in order to improve sustainable production and maintain a healthy ecosystem. The aim of this study was to explore the effects of rice-frog farming on the bacterial community and N-cycling microbes in paddy rhizosphere soil. This experiment involved three rice cultivation patterns: Conventionally cultivated rice (CR), green rice-frog farming (GR), and organic rice-frog farming (OR). The rice yield, paddy soil enzyme activities, physicochemical variables and bacterial and N-cycling bacterial abundances were quantitatively analyzed. Rice-frog cultivations significantly increased soil protease, nitrate and reductase activity. Additionally, the nirS gene copy number and the relative abundance of denitrifying bacteria also increased, however urease activity and the relative abundance of nitrifying bacteria significantly decreased. The bacterial community richness and diversity of OR soil was significantly higher than that of the GR or CR soil. Nitrogen use efficiency (NUE) of GR was highest. The N-cycling bacterial community was positively correlated with the total carbon (TC), total nitrogren (TN) and carbon to nitrogen (C:N) ratio. The present work strengthens our current understanding of the soil bacterial community structure and its functions under rice-frog farming. The present work also provides certain theoretical support for the selection of rational rice cultivation patterns.}, }
@article {pmid30486388, year = {2018}, author = {Labbé, M and Raymond, F and Lévesque, A and Thaler, M and Mohit, V and Audet, M and Corbeil, J and Culley, A}, title = {Communities of Phytoplankton Viruses across the Transition Zone of the St. Lawrence Estuary.}, journal = {Viruses}, volume = {10}, number = {12}, pages = {}, doi = {10.3390/v10120672}, pmid = {30486388}, issn = {1999-4915}, mesh = {Biodiversity ; Ecosystem ; Environment ; *Estuaries ; Evolution, Molecular ; Geography ; Metagenome ; Metagenomics/methods ; Phycodnaviridae/classification/genetics ; Phylogeny ; Phytoplankton/*virology ; RNA, Ribosomal, 18S ; *Water Microbiology ; }, abstract = {The St. Lawrence hydrographic system includes freshwater, brackish, and marine habitats, and is the largest waterway in North America by volume. The food-webs in these habitats are ultimately dependent on phytoplankton. Viral lysis is believed to be responsible for a major part of phytoplankton mortality. To better understand their role, we characterized the diversity and distribution of two viral taxa infecting phytoplankton: the picornaviruses and phycodnaviruses. Our study focused on the estuary transition zone, which is an important nursery for invertebrates and fishes. Both viral taxa were investigated by PCR amplification of conserved molecular markers and next-generation sequencing at six sites, ranging from freshwater to marine. Our results revealed few shared viral phylotypes between saltwater and freshwater sites. Salinity appeared to be the primary determinant of viral community composition. Moreover, our analysis indicated that the viruses identified in this region of the St. Lawrence diverge from classified viruses and homologous published environmental virotypes. These results suggest that DNA and RNA viruses infecting phytoplankton are likely active in the estuary transition zone, and that this region harbors its own unique viral assemblages.}, }
@article {pmid30486338, year = {2018}, author = {Amedei, A and Boem, F}, title = {I've Gut A Feeling: Microbiota Impacting the Conceptual and Experimental Perspectives of Personalized Medicine.}, journal = {International journal of molecular sciences}, volume = {19}, number = {12}, pages = {}, doi = {10.3390/ijms19123756}, pmid = {30486338}, issn = {1422-0067}, support = {FAS SALUTE 2014//Regione Toscana/ ; P2016.0808//Ente Cassa di Risparmio di Firenze/ ; }, mesh = {Animals ; Biodiversity ; Biological Therapy ; Disease Susceptibility ; Fecal Microbiota Transplantation ; Feces/microbiology ; *Gastrointestinal Microbiome ; Genomics/methods ; Humans ; Metagenomics/methods ; Microbiota ; Organ Specificity ; *Precision Medicine/methods ; Research ; Symbiosis ; }, abstract = {In recent years, the human microbiota has gained increasing relevance both in research and clinical fields. Increasing studies seem to suggest the centrality of the microbiota and its composition both in the development and maintenance of what we call &quot;health&quot; and in generating and/or favoring (those cases in which the microbiota's complex relational architecture is dysregulated) the onset of pathological conditions. The complex relationships between the microbiota and human beings, which invest core notions of biomedicine such as &quot;health&quot; and &quot;individual,&quot; do concern not only problems of an empirical nature but seem to require the need to adopt new concepts and new perspectives in order to be properly analysed and utilized, especially for their therapeutic implementation. In this contribution we report and discuss some of the theoretical proposals and innovations (from the ecological component to the notion of polygenomic organism) aimed at producing this change of perspective. In conclusion, we summarily analyze what impact and what new challenges these new approaches might have on personalized/person centred/precision medicine.}, }
@article {pmid30485662, year = {2019}, author = {Koziol, A and Stat, M and Simpson, T and Jarman, S and DiBattista, JD and Harvey, ES and Marnane, M and McDonald, J and Bunce, M}, title = {Environmental DNA metabarcoding studies are critically affected by substrate selection.}, journal = {Molecular ecology resources}, volume = {19}, number = {2}, pages = {366-376}, doi = {10.1111/1755-0998.12971}, pmid = {30485662}, issn = {1755-0998}, support = {LP160100839//Australian Research Council/ ; }, mesh = {Aquatic Organisms/*classification/*genetics ; Australia ; *Biodiversity ; DNA/chemistry/genetics/*isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; Kazakhstan ; Metagenomics/*methods ; Seawater ; }, abstract = {Effective biomonitoring is critical for driving management outcomes that ensure long-term sustainability of the marine environment. In recent years, environmental DNA (eDNA), coupled with metabarcoding methodologies, has emerged as a promising tool for generating biotic surveys of marine ecosystems, including those under anthropogenic pressure. However, more empirical data are needed on how to best implement eDNA field sampling approaches to maximize their utility for each specific application. The effect of the substrate chosen for eDNA sampling on the diversity of marine taxa detected by DNA metabarcoding has not yet been systematically analysed, despite aquatic systems being those most commonly targeted for eDNA studies. We investigated the effect of four commonly used eDNA substrates to explore taxonomic diversity: (a) surface water, (b) marine sediment, (c) settlement plates and (d) planktonic tows. With a focus on coastal ports, 332 eDNA samples from Australia (Indian and Southern oceans) and Kazakhstan (Caspian Sea) were collected and analysed by multi-assay DNA metabarcoding. Across study locations, between 30% and 52% of eukaryotic families detected were unique to a particular substrate and <6% of families were found in all four substrates. Taxonomic composition varied significantly depending on the substrate sampled implying that the suitability (and bias) of an eDNA substrate will depend on the focal taxa. These findings demonstrate that single substrate eDNA metabarcoding likely underestimates the total eukaryotic diversity. Future eDNA experimental design should consider incorporating multiple substrates or select substrate(s) best suited to the specific detection of target taxa.}, }
@article {pmid30482830, year = {2018}, author = {Espinoza, JL and Harkins, DM and Torralba, M and Gomez, A and Highlander, SK and Jones, MB and Leong, P and Saffery, R and Bockmann, M and Kuelbs, C and Inman, JM and Hughes, T and Craig, JM and Nelson, KE and Dupont, CL}, title = {Supragingival Plaque Microbiome Ecology and Functional Potential in the Context of Health and Disease.}, journal = {mBio}, volume = {9}, number = {6}, pages = {}, pmid = {30482830}, issn = {2150-7511}, support = {R01 DE019665/DE/NIDCR NIH HHS/United States ; R01 GM120624/GM/NIGMS NIH HHS/United States ; }, mesh = {Australia ; Bacteria/*classification/*genetics ; Child ; Child, Preschool ; Dental Caries/*microbiology ; Dental Plaque/*microbiology ; Humans ; Metabolic Networks and Pathways/genetics ; Metagenomics ; *Microbiota ; Sequence Analysis, DNA ; }, abstract = {To address the question of how microbial diversity and function in the oral cavities of children relates to caries diagnosis, we surveyed the supragingival plaque biofilm microbiome in 44 juvenile twin pairs. Using shotgun sequencing, we constructed a genome encyclopedia describing the core supragingival plaque microbiome. Caries phenotypes contained statistically significant enrichments in specific genome abundances and distinct community composition profiles, including strain-level changes. Metabolic pathways that are statistically associated with caries include several sugar-associated phosphotransferase systems, antimicrobial resistance, and metal transport. Numerous closely related previously uncharacterized microbes had substantial variation in central metabolism, including the loss of biosynthetic pathways resulting in auxotrophy, changing the ecological role. We also describe the first complete Gracilibacteria genomes from the human microbiome. Caries is a microbial community metabolic disorder that cannot be described by a single etiology, and our results provide the information needed for next-generation diagnostic tools and therapeutics for caries.IMPORTANCE Oral health has substantial economic importance, with over $100 billion spent on dental care in the United States annually. The microbiome plays a critical role in oral health, yet remains poorly classified. To address the question of how microbial diversity and function in the oral cavities of children relate to caries diagnosis, we surveyed the supragingival plaque biofilm microbiome in 44 juvenile twin pairs. Using shotgun sequencing, we constructed a genome encyclopedia describing the core supragingival plaque microbiome. This unveiled several new previously uncharacterized but ubiquitous microbial lineages in the oral microbiome. Caries is a microbial community metabolic disorder that cannot be described by a single etiology, and our results provide the information needed for next-generation diagnostic tools and therapeutics for caries.}, }
@article {pmid30482513, year = {2019}, author = {Díaz-Sánchez, S and Hernández-Jarguín, A and Torina, A and de Mera, IGF and Blanda, V and Caracappa, S and Gortazar, C and de la Fuente, J}, title = {Characterization of the bacterial microbiota in wild-caught Ixodes ventalloi.}, journal = {Ticks and tick-borne diseases}, volume = {10}, number = {2}, pages = {336-343}, doi = {10.1016/j.ttbdis.2018.11.014}, pmid = {30482513}, issn = {1877-9603}, mesh = {Anaplasma/genetics ; Animals ; Borrelia/genetics ; DNA, Bacterial/genetics ; Female ; High-Throughput Nucleotide Sequencing ; Ixodes/*microbiology ; Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sicily ; Symbiosis ; }, abstract = {Exploring the microbial diversity of ticks is crucial to understand geographical dispersion and pathogen transmission. Tick microbes participate in many biological processes implicated in the acquisition, maintenance, and transmission of pathogens, and actively promote host phenotypic changes, and adaptation to new environments. The microbial community of Ixodes ventalloi still remains unexplored. In this study, the bacterial microbiota of wild-caught I. ventalloi was characterized using shotgun-metagenomic sequencing in samples from unfed adults collected during December 2013-January 2014 in two locations from Sicily, Italy. The microbiota identified in I. ventalloi was mainly composed of symbiotic, commensal, and environmental bacteria. Interestingly, we identified the genera Anaplasma and Borrelia as members of the microbiota of I. ventalloi. These results advance our information on I. ventalloi microbiota composition, with potential implications in tick-host adaptation, geographic expansion, and vector competence.}, }
@article {pmid30479342, year = {2018}, author = {Ramani, S and Stewart, CJ and Laucirica, DR and Ajami, NJ and Robertson, B and Autran, CA and Shinge, D and Rani, S and Anandan, S and Hu, L and Ferreon, JC and Kuruvilla, KA and Petrosino, JF and Venkataram Prasad, BV and Bode, L and Kang, G and Estes, MK}, title = {Human milk oligosaccharides, milk microbiome and infant gut microbiome modulate neonatal rotavirus infection.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {5010}, pmid = {30479342}, issn = {2041-1723}, support = {R01 AI036040/AI/NIAID NIH HHS/United States ; R01 AI105101/AI/NIAID NIH HHS/United States ; R37 AI036040/AI/NIAID NIH HHS/United States ; }, mesh = {Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; Milk, Human/*chemistry/*microbiology ; Oligosaccharides/*metabolism ; Rotavirus/pathogenicity ; Rotavirus Infections/immunology/*microbiology ; Rotavirus Vaccines/immunology ; }, abstract = {Neonatal rotavirus infections are predominantly asymptomatic. While an association with gastrointestinal symptoms has been described in some settings, factors influencing differences in clinical presentation are not well understood. Using multidisciplinary approaches, we show that a complex interplay between human milk oligosaccharides (HMOs), milk microbiome, and infant gut microbiome impacts neonatal rotavirus infections. Validating in vitro studies where HMOs are not decoy receptors for neonatal strain G10P[11], population studies show significantly higher levels of Lacto-N-tetraose (LNT), 2'-fucosyllactose (2'FL), and 6'-siallylactose (6'SL) in milk from mothers of rotavirus-positive neonates with gastrointestinal symptoms. Further, these HMOs correlate with abundance of Enterobacter/Klebsiella in maternal milk and infant stool. Specific HMOs also improve the infectivity of a neonatal strain-derived rotavirus vaccine. This study provides molecular and translational insight into host factors influencing neonatal rotavirus infections and identifies maternal components that could promote the performance of live, attenuated rotavirus vaccines.}, }
@article {pmid30479272, year = {2018}, author = {Glover, AG and Wiklund, H and Chen, C and Dahlgren, TG}, title = {Managing a sustainable deep-sea 'blue economy' requires knowledge of what actually lives there.}, journal = {eLife}, volume = {7}, number = {}, pages = {}, pmid = {30479272}, issn = {2050-084X}, mesh = {*Biodiversity ; Conservation of Energy Resources/*methods ; *Ecosystem ; Metagenomics/*methods ; *Oceans and Seas ; }, abstract = {Ensuring that the wealth of resources contained in our oceans are managed and developed in a sustainable manner is a priority for the emerging 'blue economy'. However, modern ecosystem-based management approaches do not translate well to regions where we know almost nothing about the individual species found in the ecosystem. Here, we propose a new taxon-focused approach to deep-sea conservation that includes regulatory oversight to set targets for the delivery of taxonomic data. For example, a five-year plan to deliver taxonomic and genomic knowledge on a thousand species in regions of the ocean earmarked for industrial activity is an achievable target. High-throughput, integrative taxonomy can, therefore, provide the data that is needed to monitor various ecosystem services (such as the natural history, connectivity, value and function of species) and to help break the regulatory deadlock of high-seas conservation.}, }
@article {pmid30478343, year = {2018}, author = {Regan, T and Barnett, MW and Laetsch, DR and Bush, SJ and Wragg, D and Budge, GE and Highet, F and Dainat, B and de Miranda, JR and Watson, M and Blaxter, M and Freeman, TC}, title = {Characterisation of the British honey bee metagenome.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4995}, pmid = {30478343}, issn = {2041-1723}, support = {BB/I001107/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bees/*genetics/microbiology ; Contig Mapping ; Genetic Variation ; *Metagenome ; Metagenomics ; Microbiota/genetics ; Sequence Analysis, DNA ; Symbiosis/genetics ; United Kingdom ; }, abstract = {The European honey bee (Apis mellifera) plays a major role in pollination and food production. Honey bee health is a complex product of the environment, host genetics and associated microbes (commensal, opportunistic and pathogenic). Improved understanding of these factors will help manage modern challenges to bee health. Here we used DNA sequencing to characterise the genomes and metagenomes of 19 honey bee colonies from across Britain. Low heterozygosity was observed in many Scottish colonies which had high similarity to the native dark bee. Colonies exhibited high diversity in composition and relative abundance of individual microbiome taxa. Most non-bee sequences were derived from known honey bee commensal bacteria or pathogens. However, DNA was also detected from additional fungal, protozoan and metazoan species. To classify cobionts lacking genomic information, we developed a novel network analysis approach for clustering orphan DNA contigs. Our analyses shed light on microbial communities associated with honey bees and demonstrate the power of high-throughput, directed metagenomics for identifying novel biological threats in agroecosystems.}, }
@article {pmid30478001, year = {2018}, author = {Wei, S and Mortensen, MS and Stokholm, J and Brejnrod, AD and Thorsen, J and Rasmussen, MA and Trivedi, U and Bisgaard, H and Sørensen, SJ}, title = {Short- and long-term impacts of azithromycin treatment on the gut microbiota in children: A double-blind, randomized, placebo-controlled trial.}, journal = {EBioMedicine}, volume = {38}, number = {}, pages = {265-272}, doi = {10.1016/j.ebiom.2018.11.035}, pmid = {30478001}, issn = {2352-3964}, mesh = {Anti-Bacterial Agents/*pharmacology/therapeutic use ; Azithromycin/*pharmacology/therapeutic use ; Biodiversity ; Child, Preschool ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Infant ; Male ; Metagenome ; Metagenomics ; Time Factors ; }, abstract = {BACKGROUND: Macrolides are commonly prescribed for respiratory infections and asthma-like episodes in children. While their clinical benefits have been proved, concerns regarding the side-effects of their therapeutic use have been raised. Here we assess the short- and long-term impacts of azithromycin on the gut microbiota of young children.<br><br>METHODS: We performed a randomized, double-blind, placebo-controlled trial in a group of children aged 12-36 months, diagnosed with recurrent asthma-like symptoms from the COPSAC2010 cohort. Each acute asthma-like episode was randomized to a 3-day course of azithromycin oral solution of 10 mg/kg per day or placebo. Azithromycin reduced episode duration by half, which was the primary end-point and reported previously. The assessment of gut microbiota after treatment was the secondary end-point and reported in this study. Fecal samples were collected 14 days after randomization (N = 59, short-term) and again at age 4 years (N = 49, long-term, of whom N = 18 were placebo treated) and investigated by 16S rRNA gene amplicon sequencing.<br><br>FINDINGS: Short-term, azithromycin caused a 23% reduction in observed richness and 13% reduction in Shannon diversity. Microbiota composition was shifted primarily in the Actinobacteria phylum, especially a reduction of abundance in the genus Bifidobacterium. Long-term (13-39 months after treatment), we did not observe any differences between the azithromycin and placebo recipients in their gut microbiota composition.<br><br>INTERPRETATION: Azithromycin treatment induced a perturbation in the gut microbiota 14 days after randomization but did not have long-lasting effects on the gut microbiota composition. However, it should be noted that our analyses included a limited number of fecal samples for the placebo treated group at age 4 years. FUND: Lundbeck Foundation, Danish Ministry of Health, Danish Council for Strategic Research, Capital Region Research Foundation, China Scholarship Council.}, }
@article {pmid30477563, year = {2018}, author = {Sinha, R and Ahsan, H and Blaser, M and Caporaso, JG and Carmical, JR and Chan, AT and Fodor, A and Gail, MH and Harris, CC and Helzlsouer, K and Huttenhower, C and Knight, R and Kong, HH and Lai, GY and Hutchinson, DLS and Le Marchand, L and Li, H and Orlich, MJ and Shi, J and Truelove, A and Verma, M and Vogtmann, E and White, O and Willett, W and Zheng, W and Mahabir, S and Abnet, C}, title = {Next steps in studying the human microbiome and health in prospective studies, Bethesda, MD, May 16-17, 2017.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {210}, pmid = {30477563}, issn = {2049-2618}, mesh = {Computational Biology/*methods ; Humans ; Microbiota/*physiology ; Neoplasms/*etiology ; Prospective Studies ; Reproducibility of Results ; *Research Design ; }, abstract = {The National Cancer Institute (NCI) sponsored a 2-day workshop, &quot;Next Steps in Studying the Human Microbiome and Health in Prospective Studies,&quot; in Bethesda, Maryland, May 16-17, 2017. The workshop brought together researchers in the field to discuss the challenges of conducting microbiome studies, including study design, collection and processing of samples, bioinformatics and statistical methods, publishing results, and ensuring reproducibility of published results. The presenters emphasized the great potential of microbiome research in understanding the etiology of cancer. This report summarizes the workshop and presents practical suggestions for conducting microbiome studies, from workshop presenters, moderators, and participants.}, }
@article {pmid30474920, year = {2019}, author = {Bell, T}, title = {Next-generation experiments linking community structure and ecosystem functioning.}, journal = {Environmental microbiology reports}, volume = {11}, number = {1}, pages = {20-22}, doi = {10.1111/1758-2229.12711}, pmid = {30474920}, issn = {1758-2229}, mesh = {Bacteria/classification/genetics/metabolism ; Biodiversity ; *Ecosystem ; Metagenomics ; Microbiota ; Population Dynamics ; Reproducibility of Results ; }, }
@article {pmid30463925, year = {2018}, author = {Bulow, C and Langdon, A and Hink, T and Wallace, M and Reske, KA and Patel, S and Sun, X and Seiler, S and Jones, S and Kwon, JH and Burnham, CA and Dantas, G and Dubberke, ER}, title = {Impact of Amoxicillin-Clavulanate followed by Autologous Fecal Microbiota Transplantation on Fecal Microbiome Structure and Metabolic Potential.}, journal = {mSphere}, volume = {3}, number = {6}, pages = {}, pmid = {30463925}, issn = {2379-5042}, support = {KL2 TR002346/TR/NCATS NIH HHS/United States ; T32 HG000045/HG/NHGRI NIH HHS/United States ; TL1 TR000449/TR/NCATS NIH HHS/United States ; TL1 TR002344/TR/NCATS NIH HHS/United States ; }, mesh = {Adult ; Amoxicillin-Potassium Clavulanate Combination/*administration &amp; dosage ; Anti-Bacterial Agents/*administration &amp; dosage ; Enema ; Fecal Microbiota Transplantation/*methods ; Female ; *Gastrointestinal Microbiome ; Healthy Volunteers ; Humans ; Male ; *Metabolism ; *Microbiota ; Middle Aged ; Treatment Outcome ; Young Adult ; beta-Lactamase Inhibitors/*administration &amp; dosage ; }, abstract = {Strategies to prevent multidrug-resistant organism (MDRO) infections are scarce, but autologous fecal microbiota transplantation (autoFMT) may limit gastrointestinal MDRO expansion. AutoFMT involves banking one's feces during a healthy state for later use in restoring gut microbiota following perturbation. This pilot study evaluated the effect of autoFMT on gastrointestinal microbiome taxonomic composition, resistance gene content, and metabolic capacity after exposure to amoxicillin-clavulanic acid (Amox-Clav). Ten healthy participants were enrolled. All received 5 days of Amox-Clav. Half were randomized to autoFMT, derived from stool collected pre-antimicrobial exposure, by enema, and half to saline enema. Participants submitted stool samples pre- and post-Amox-Clav and enema and during a 90-day follow-up period. Shotgun metagenomic sequencing revealed taxonomic composition, resistance gene content, and metabolic capacity. Amox-Clav significantly altered gut taxonomic composition in all participants (n = 10, P < 0.01); however, only three participants exhibited major changes at the phylum level following exposure. In the cohort as a whole, beta-lactamase genes were enriched following Amox-Clav (P < 0.05), and predicted metabolic capacity was significantly altered (P < 0.01). Species composition, metabolic capacity, and beta-lactamase abundance returned to pre-antimicrobial exposure state 7 days after either autoFMT or saline enema (P > 0.05, compared to enrollment). Alterations to microbial metabolic capacity occurred following antimicrobial exposure even in participants without substantial taxonomic disruption, potentially creating open niches for pathogen colonization. Our findings suggest that metabolic potential is an important consideration for complete assessment of antimicrobial impact on the microbiome. AutoFMT was well tolerated and may have contributed to phylogenetic recovery. (This study has been registered at ClinicalTrials.gov under identifier NCT02046525.)IMPORTANCE The spread of multidrug resistance among pathogenic organisms threatens the efficacy of antimicrobial treatment options. The human gut serves as a reservoir for many drug-resistant organisms and their resistance genes, and perturbation of the gut microbiome by antimicrobial exposure can open metabolic niches to resistant pathogens. Once established in the gut, antimicrobial-resistant bacteria can persist even after antimicrobial exposure ceases. Strategies to prevent multidrug-resistant organism (MDRO) infections are scarce, but autologous fecal microbiota transplantation (autoFMT) may limit gastrointestinal MDRO expansion. AutoFMT involves banking one's feces during a healthy state for later use in restoring gut microbiota following perturbation. This pilot study evaluated the effect of amoxicillin-clavulanic acid (Amox-Clav) exposure and autoFMT on gastrointestinal microbiome taxonomic composition, resistance gene content, and metabolic capacity. Importantly, we found that metabolic capacity was perturbed even in cases where gross phylogeny remained unchanged and that autoFMT was safe and well tolerated.}, }
@article {pmid30459421, year = {2018}, author = {Xu, J and Zhang, Y and Zhang, P and Trivedi, P and Riera, N and Wang, Y and Liu, X and Fan, G and Tang, J and Coletta-Filho, HD and Cubero, J and Deng, X and Ancona, V and Lu, Z and Zhong, B and Roper, MC and Capote, N and Catara, V and Pietersen, G and Vernière, C and Al-Sadi, AM and Li, L and Yang, F and Xu, X and Wang, J and Yang, H and Jin, T and Wang, N}, title = {The structure and function of the global citrus rhizosphere microbiome.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4894}, pmid = {30459421}, issn = {2041-1723}, mesh = {Bacteria/classification/genetics ; Citrus/*microbiology ; DNA, Ribosomal Spacer/genetics ; Fungi/classification/genetics ; Metagenome/genetics ; Metagenomics/classification/methods ; Microbiota/*genetics ; Phylogeny ; Plant Roots/*microbiology ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; *Soil Microbiology ; }, abstract = {Citrus is a globally important, perennial fruit crop whose rhizosphere microbiome is thought to play an important role in promoting citrus growth and health. Here, we report a comprehensive analysis of the structural and functional composition of the citrus rhizosphere microbiome. We use both amplicon and deep shotgun metagenomic sequencing of bulk soil and rhizosphere samples collected across distinct biogeographical regions from six continents. Predominant taxa include Proteobacteria, Actinobacteria, Acidobacteria and Bacteroidetes. The core citrus rhizosphere microbiome comprises Pseudomonas, Agrobacterium, Cupriavidus, Bradyrhizobium, Rhizobium, Mesorhizobium, Burkholderia, Cellvibrio, Sphingomonas, Variovorax and Paraburkholderia, some of which are potential plant beneficial microbes. We also identify over-represented microbial functional traits mediating plant-microbe and microbe-microbe interactions, nutrition acquisition and plant growth promotion in citrus rhizosphere. The results provide valuable information to guide microbial isolation and culturing and, potentially, to harness the power of the microbiome to improve plant production and health.}, }
@article {pmid30459334, year = {2018}, author = {Jersie-Christensen, RR and Lanigan, LT and Lyon, D and Mackie, M and Belstrøm, D and Kelstrup, CD and Fotakis, AK and Willerslev, E and Lynnerup, N and Jensen, LJ and Cappellini, E and Olsen, JV}, title = {Quantitative metaproteomics of medieval dental calculus reveals individual oral health status.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4744}, pmid = {30459334}, issn = {2041-1723}, mesh = {Adult ; Archaeology/methods ; Bacteria/classification ; Bacterial Proteins/analysis ; DNA, Ancient/analysis ; DNA, Bacterial/analysis ; Denmark ; Dental Calculus/*microbiology ; Dental Plaque/microbiology ; Dietary Proteins ; Female ; *Health Status ; Humans ; Male ; Metagenomics/methods ; Microbiota/genetics ; Middle Aged ; *Oral Health ; Proteomics/*methods ; }, abstract = {The composition of ancient oral microbiomes has recently become accessible owing to advanced biomolecular methods such as metagenomics and metaproteomics, but the utility of metaproteomics for such analyses is less explored. Here, we use quantitative metaproteomics to characterize the dental calculus associated with the remains of 21 humans retrieved during the archeological excavation of the medieval (ca. 1100-1450 CE) cemetery of Tjærby, Denmark. We identify 3671 protein groups, covering 220 bacterial species and 81 genera across all medieval samples. The metaproteome profiles of bacterial and human proteins suggest two distinct groups of archeological remains corresponding to health-predisposed and oral disease-susceptible individuals, which is supported by comparison to the calculus metaproteomes of healthy living individuals. Notably, the groupings identified by metaproteomics are not apparent from the bioarchaeological analysis, illustrating that quantitative metaproteomics has the potential to provide additional levels of molecular information about the oral health status of individuals from archeological contexts.}, }
@article {pmid30458701, year = {2018}, author = {Banos, S and Lentendu, G and Kopf, A and Wubet, T and Glöckner, FO and Reich, M}, title = {A comprehensive fungi-specific 18S rRNA gene sequence primer toolkit suited for diverse research issues and sequencing platforms.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {190}, pmid = {30458701}, issn = {1471-2180}, abstract = {BACKGROUND: Several fungi-specific primers target the 18S rRNA gene sequence, one of the prominent markers for fungal classification. The design of most primers goes back to the last decades. Since then, the number of sequences in public databases increased leading to the discovery of new fungal groups and changes in fungal taxonomy. However, no reevaluation of primers was carried out and relevant information on most primers is missing. With this study, we aimed to develop an 18S rRNA gene sequence primer toolkit allowing an easy selection of the best primer pair appropriate for different sequencing platforms, research aims (biodiversity assessment versus isolate classification) and target groups.<br><br>RESULTS: We performed an intensive literature research, reshuffled existing primers into new pairs, designed new Illumina-primers, and annealing blocking oligonucleotides. A final number of 439 primer pairs were subjected to in silico PCRs. Best primer pairs were selected and experimentally tested. The most promising primer pair with a small amplicon size, nu-SSU-1333-5'/nu-SSU-1647-3' (FF390/FR-1), was successful in describing fungal communities by Illumina sequencing. Results were confirmed by a simultaneous metagenomics and eukaryote-specific primer approach. Co-amplification occurred in all sample types but was effectively reduced by blocking oligonucleotides.<br><br>CONCLUSIONS: The compiled data revealed the presence of an enormous diversity of fungal 18S rRNA gene primer pairs in terms of fungal coverage, phylum spectrum and co-amplification. Therefore, the primer pair has to be carefully selected to fulfill the requirements of the individual research projects. The presented primer toolkit offers comprehensive lists of 164 primers, 439 primer combinations, 4 blocking oligonucleotides, and top primer pairs holding all relevant information including primer's characteristics and performance to facilitate primer pair selection.}, }
@article {pmid30447983, year = {2019}, author = {Vasquez, AK and Ganda, EK and Capel, MB and Eicker, S and Virkler, PD and Bicalho, RC and Nydam, DV}, title = {The microbiome of Escherichia coli and culture-negative nonsevere clinical mastitis: Characterization and associations with linear score and milk production.}, journal = {Journal of dairy science}, volume = {102}, number = {1}, pages = {578-594}, doi = {10.3168/jds.2018-15062}, pmid = {30447983}, issn = {1525-3198}, mesh = {Animals ; Anti-Infective Agents/therapeutic use ; Bacteria/classification/genetics ; Biodiversity ; Cattle ; Escherichia coli/*isolation &amp; purification ; Female ; Lactation/*physiology ; Mastitis, Bovine/*microbiology ; Metagenomics ; Microbiota/*physiology ; Milk/microbiology ; RNA, Ribosomal, 16S/analysis ; }, abstract = {Culture-negative and Escherichia coli cases are uncommonly treated in pathogen-based protocols for nonsevere mastitis. High-throughput 16S rRNA sequencing might reveal the presence of other pathogens and can provide information on microbial diversity. The objective was to explore the milk microbiome at the time of the mastitis event (enrollment) and its association with survival in the herd, milk production, and postevent linear score (LS) for cows with clinical mastitis characterized as negative or E. coli by culture. Fifty E. coli-positive and 35 culture-negative samples from cases were enrolled. No cases were treated with antimicrobials. All E. coli-positive quarters were characterized as transient; microbiological culture of samples taken 15 d postmastitis were negative for this organism. However, a difference in α-diversity (Shannon index) was present between enrollment and follow-up samples (3.8 vs. 5.1). When α-diversity was explored for enrollment E. coli samples, no relationship was observed between the Shannon indices of these samples and postmastitis LS. Alpha-diversity of the enrollment samples was lower for E. coli-positive cows that subsequently had greater losses in milk production. This difference was explained by a greater relative abundance of the family Enterobacteriaceae (67.8 vs. 38.4%) for cows that dropped in production. Analysis of composition of the microbiome identified one phylum, Proteobacteria, that differed between E. coli-positive cows that dropped in production and those that did not. Evaluation of β -diversity found no statistical relationship between postmastitis LS and the microbiome. When evaluating α- and β-diversities and composition of the microbiomes for culture-negative quarters, no associations were found for milk production changes and postmastitis LS. Three cows did not remain in the herd, limiting the ability to analyze survival. The findings suggest that a contributing factor to negative outcomes in E. coli-positive cows is relative abundance of this pathogen, and that no single or collective group of bacterial families is associated with milk production changes or postmastitis LS in culture-negative quarters. Although additional studies should be performed, the absence of associations between outcomes explored and microbial profiles in this study suggests that we are not missing opportunities by not treating nonsevere E. coli or culture-negative mastitis cases.}, }
@article {pmid30446434, year = {2018}, author = {Lucking, EF and O'Connor, KM and Strain, CR and Fouhy, F and Bastiaanssen, TFS and Burns, DP and Golubeva, AV and Stanton, C and Clarke, G and Cryan, JF and O'Halloran, KD}, title = {Chronic intermittent hypoxia disrupts cardiorespiratory homeostasis and gut microbiota composition in adult male guinea-pigs.}, journal = {EBioMedicine}, volume = {38}, number = {}, pages = {191-205}, doi = {10.1016/j.ebiom.2018.11.010}, pmid = {30446434}, issn = {2352-3964}, mesh = {Age Factors ; Animals ; Apnea/metabolism/physiopathology ; Basal Metabolism ; Biomarkers ; Brain Stem/metabolism ; Carotid Body ; *Gastrointestinal Microbiome ; Guinea Pigs ; Heart/*physiology/*physiopathology ; Homeostasis ; Hypoxia/*metabolism ; Male ; Metagenome ; Metagenomics ; Models, Animal ; Morbidity ; *Respiratory Physiological Phenomena ; Respiratory System/*physiopathology ; Sex Factors ; }, abstract = {BACKGROUND: Carotid body (peripheral oxygen sensor) sensitisation is pivotal in the development of chronic intermittent hypoxia (CIH)-induced hypertension. We sought to determine if exposure to CIH, modelling human sleep apnoea, adversely affects cardiorespiratory control in guinea-pigs, a species with hypoxia-insensitive carotid bodies. We reasoned that CIH-induced disruption of gut microbiota would evoke cardiorespiratory morbidity.<br><br>METHODS: Adult male guinea-pigs were exposed to CIH (6.5% O2 at nadir, 6 cycles.hour-1) for 8 h.day-1 for 12 consecutive days.<br><br>FINDINGS: CIH-exposed animals established reduced faecal microbiota species richness, with increased relative abundance of Bacteroidetes and reduced relative abundance of Firmicutes bacteria. Urinary corticosterone and noradrenaline levels were unchanged in CIH-exposed animals, but brainstem noradrenaline concentrations were lower compared with sham. Baseline ventilation was equivalent in CIH-exposed and sham animals; however, respiratory timing variability, sigh frequency and ventilation during hypoxic breathing were all lower in CIH-exposed animals. Baseline arterial blood pressure was unaffected by exposure to CIH, but β-adrenoceptor-dependent tachycardia and blunted bradycardia during phenylephrine-induced pressor responses was evident compared with sham controls.<br><br>INTERPRETATION: Increased carotid body chemo-afferent signalling appears obligatory for the development of CIH-induced hypertension and elevated chemoreflex control of breathing commonly reported in mammals, with hypoxia-sensitive carotid bodies. However, we reveal that exposure to modest CIH alters gut microbiota richness and composition, brainstem neurochemistry, and autonomic control of heart rate, independent of carotid body sensitisation, suggesting modulation of breathing and autonomic homeostasis via the microbiota-gut-brainstem axis. The findings have relevance to human sleep-disordered breathing.<br><br>FUNDING: The Department of Physiology, and APC Microbiome Ireland, UCC.}, }
@article {pmid30446169, year = {2019}, author = {Kosek, K and Kozioł, K and Luczkiewicz, A and Jankowska, K and Chmiel, S and Polkowska, Ż}, title = {Environmental characteristics of a tundra river system in Svalbard. Part 2: Chemical stress factors.}, journal = {The Science of the total environment}, volume = {653}, number = {}, pages = {1585-1596}, doi = {10.1016/j.scitotenv.2018.11.012}, pmid = {30446169}, issn = {1879-1026}, mesh = {Bacteria/classification/*drug effects ; *Environmental Monitoring ; Formaldehyde/analysis ; Metagenomics ; Metals/analysis ; Microbiota/*drug effects ; Phenols/analysis ; Polycyclic Aromatic Hydrocarbons/analysis ; Rivers/*chemistry/*microbiology ; Svalbard ; Tundra ; Water Pollutants, Chemical/*analysis ; }, abstract = {Bacterial communities in the Arctic environment are subject to multiple stress factors, including contaminants, although typically their concentrations are small. The Arctic contamination research has focused on persistent organic pollutants (POPs) because they are bioaccumulative, resistant to degradation and toxic for all organisms. Pollutants have entered the Arctic predominantly by atmospheric and oceanic long-range transport, and this was facilitated by their volatile or semi-volatile properties, while their chemical stability extended their lifetimes following emission. Chemicals present in the Arctic at detectable and quantifiable concentrations testify to their global impact. Chemical contamination may induce serious disorders in the integrity of polar ecosystems influencing the growth of bacterial communities. In this study, the abundance and the types of bacteria in the Arctic freshwater were examined and the microbial characteristics were compared to the amount of potentially harmful chemical compounds in particular elements of the Arctic catchment. The highest concentrations of all determined PAHs were observed in two samples in the vicinity of the estuary both in June and September 2016 and were 1964 ng L-1 (R12) and 3901 ng L-1 (R13) in June, and 2179 ng L-1 (R12) and 1349 ng L-1 (R13) in September. Remarkable concentrations of the sum of phenols and formaldehyde were detected also at the outflow of the Revelva river into the sea (R12) and were 0.24 mg L-1 in June and 0.35 mg L-1 in September 2016. The elevated concentrations of chemical compounds near the estuary suggest a potential impact of the water from the lower tributaries (including the glacier-fed stream measured at R13) or the sea currents and the sea aerosol as pollutant sources. The POPs' degradation at low temperature is not well understood but bacteria capable to degrading such compounds were noted in each sampling point.}, }
@article {pmid30431224, year = {2019}, author = {Koskella, B}, title = {New approaches to characterizing bacteria-phage interactions in microbial communities and microbiomes.}, journal = {Environmental microbiology reports}, volume = {11}, number = {1}, pages = {15-16}, doi = {10.1111/1758-2229.12706}, pmid = {30431224}, issn = {1758-2229}, mesh = {Bacteria/classification/*virology ; Bacteriophages/classification/genetics/*physiology ; Biodiversity ; Genetic Variation ; Genome, Viral/genetics ; Metagenomics ; *Microbiota ; Single-Cell Analysis ; }, }
@article {pmid30427852, year = {2018}, author = {Brito, TL and Campos, AB and Bastiaan von Meijenfeldt, FA and Daniel, JP and Ribeiro, GB and Silva, GGZ and Wilke, DV and de Moraes, DT and Dutilh, BE and Meirelles, PM and Trindade-Silva, AE}, title = {The gill-associated microbiome is the main source of wood plant polysaccharide hydrolases and secondary metabolite gene clusters in the mangrove shipworm Neoteredo reynei.}, journal = {PloS one}, volume = {13}, number = {11}, pages = {e0200437}, pmid = {30427852}, issn = {1932-6203}, mesh = {Animals ; Bivalvia/*microbiology/physiology ; Gammaproteobacteria/*enzymology/genetics/*physiology ; Genomics ; Gills/microbiology ; Glycoside Hydrolases/genetics/*metabolism ; Metagenome ; Microbiota ; Multigene Family ; Phylogeny ; Polysaccharides/*metabolism ; Secondary Metabolism ; *Symbiosis ; Wood/metabolism/parasitology ; }, abstract = {Teredinidae are a family of highly adapted wood-feeding and wood-boring bivalves, commonly known as shipworms, whose evolution is linked to the acquisition of cellulolytic gammaproteobacterial symbionts harbored in bacteriocytes within the gills. In the present work we applied metagenomics to characterize microbiomes of the gills and digestive tract of Neoteredo reynei, a mangrove-adapted shipworm species found over a large range of the Brazilian coast. Comparative metagenomics grouped the gill symbiont community of different N. reynei specimens, indicating closely related bacterial types are shared. Similarly, the intestine and digestive gland communities were related, yet were more diverse than and showed no overlap with the gill community. Annotation of assembled metagenomic contigs revealed that the gill symbiotic community of N. reynei encodes a plethora of plant cell wall polysaccharides degrading glycoside hydrolase encoding genes, and Biosynthetic Gene Clusters (BGCs). In contrast, the digestive tract microbiomes seem to play little role in wood digestion and secondary metabolites biosynthesis. Metagenome binning recovered the nearly complete genome sequences of two symbiotic Teredinibacter strains from the gills, a representative of Teredinibacter turnerae &quot;clade I&quot; strain, and a yet to be cultivated Teredinibacter sp. type. These Teredinibacter genomes, as well as un-binned gill-derived gammaproteobacteria contigs, also include an endo-β-1,4-xylanase/acetylxylan esterase multi-catalytic carbohydrate-active enzyme, and a trans-acyltransferase polyketide synthase (trans-AT PKS) gene cluster with the gene cassette for generating β-branching on complex polyketides. Finally, we use multivariate analyses to show that the secondary metabolome from the genomes of Teredinibacter representatives, including genomes binned from N. reynei gills' metagenomes presented herein, stands out within the Cellvibrionaceae family by size, and enrichments for polyketide, nonribosomal peptide and hybrid BGCs. Results presented here add to the growing characterization of shipworm symbiotic microbiomes and indicate that the N. reynei gill gammaproteobacterial community is a prolific source of biotechnologically relevant enzymes for wood-digestion and bioactive compounds production.}, }
@article {pmid30425247, year = {2018}, author = {Hansen, LBS and Roager, HM and Søndertoft, NB and Gøbel, RJ and Kristensen, M and Vallès-Colomer, M and Vieira-Silva, S and Ibrügger, S and Lind, MV and Mærkedahl, RB and Bahl, MI and Madsen, ML and Havelund, J and Falony, G and Tetens, I and Nielsen, T and Allin, KH and Frandsen, HL and Hartmann, B and Holst, JJ and Sparholt, MH and Holck, J and Blennow, A and Moll, JM and Meyer, AS and Hoppe, C and Poulsen, JH and Carvalho, V and Sagnelli, D and Dalgaard, MD and Christensen, AF and Lydolph, MC and Ross, AB and Villas-Bôas, S and Brix, S and Sicheritz-Pontén, T and Buschard, K and Linneberg, A and Rumessen, JJ and Ekstrøm, CT and Ritz, C and Kristiansen, K and Nielsen, HB and Vestergaard, H and Færgeman, NJ and Raes, J and Frøkiær, H and Hansen, T and Lauritzen, L and Gupta, R and Licht, TR and Pedersen, O}, title = {A low-gluten diet induces changes in the intestinal microbiome of healthy Danish adults.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4630}, pmid = {30425247}, issn = {2041-1723}, mesh = {Adult ; Aged ; Body Mass Index ; Creatinine/urine ; Cross-Over Studies ; Cytokines/blood ; DNA, Bacterial/analysis ; Denmark ; *Diet ; Fasting ; Feces/microbiology ; Female ; Fermentation ; *Gastrointestinal Microbiome/genetics ; Glutens/*administration &amp; dosage/*adverse effects ; Humans ; Hydrogen ; Intestines/microbiology ; Male ; Metabolomics ; Metagenomics ; Middle Aged ; Postprandial Period ; Self Report ; Young Adult ; }, abstract = {Adherence to a low-gluten diet has become increasingly common in parts of the general population. However, the effects of reducing gluten-rich food items including wheat, barley and rye cereals in healthy adults are unclear. Here, we undertook a randomised, controlled, cross-over trial involving 60 middle-aged Danish adults without known disorders with two 8-week interventions comparing a low-gluten diet (2 g gluten per day) and a high-gluten diet (18 g gluten per day), separated by a washout period of at least six weeks with habitual diet (12 g gluten per day). We find that, in comparison with a high-gluten diet, a low-gluten diet induces moderate changes in the intestinal microbiome, reduces fasting and postprandial hydrogen exhalation, and leads to improvements in self-reported bloating. These observations suggest that most of the effects of a low-gluten diet in non-coeliac adults may be driven by qualitative changes in dietary fibres.}, }
@article {pmid30424821, year = {2018}, author = {Singh, NK and Wood, JM and Karouia, F and Venkateswaran, K}, title = {Succession and persistence of microbial communities and antimicrobial resistance genes associated with International Space Station environmental surfaces.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {204}, pmid = {30424821}, issn = {2049-2618}, mesh = {Archaea/drug effects/genetics/*isolation &amp; purification ; Azides/pharmacology ; Bacteria/drug effects/genetics/*isolation &amp; purification ; Drug Resistance, Bacterial/*genetics ; Fungi/drug effects/genetics/*isolation &amp; purification ; Humans ; Metagenome/genetics ; Microbiota/drug effects/genetics ; Propidium/analogs &amp; derivatives/pharmacology ; *Space Flight ; *Spacecraft ; Virulence/genetics ; }, abstract = {BACKGROUND: The International Space Station (ISS) is an ideal test bed for studying the effects of microbial persistence and succession on a closed system during long space flight. Culture-based analyses, targeted gene-based amplicon sequencing (bacteriome, mycobiome, and resistome), and shotgun metagenomics approaches have previously been performed on ISS environmental sample sets using whole genome amplification (WGA). However, this is the first study reporting on the metagenomes sampled from ISS environmental surfaces without the use of WGA. Metagenome sequences generated from eight defined ISS environmental locations in three consecutive flights were analyzed to assess the succession and persistence of microbial communities, their antimicrobial resistance (AMR) profiles, and virulence properties. Metagenomic sequences were produced from the samples treated with propidium monoazide (PMA) to measure intact microorganisms.<br><br>RESULTS: The intact microbial communities detected in Flight 1 and Flight 2 samples were significantly more similar to each other than to Flight 3 samples. Among 318 microbial species detected, 46 species constituting 18 genera were common in all flight samples. Risk group or biosafety level 2 microorganisms that persisted among all three flights were Acinetobacter baumannii, Haemophilus influenzae, Klebsiella pneumoniae, Salmonella enterica, Shigella sonnei, Staphylococcus aureus, Yersinia frederiksenii, and Aspergillus lentulus. Even though Rhodotorula and Pantoea dominated the ISS microbiome, Pantoea exhibited succession and persistence. K. pneumoniae persisted in one location (US Node 1) of all three flights and might have spread to six out of the eight locations sampled on Flight 3. The AMR signatures associated with β-lactam, cationic antimicrobial peptide, and vancomycin were detected. Prominent virulence factors were cobalt-zinc-cadmium resistance and multidrug-resistance efflux pumps.<br><br>CONCLUSIONS: There was an increase in AMR and virulence gene factors detected over the period sampled, and metagenome sequences of human pathogens persisted over time. Comparative analysis of the microbial compositions of ISS with Earth analogs revealed that the ISS environmental surfaces were different in microbial composition. Metagenomics coupled with PMA treatment would help future space missions to estimate problematic risk group microbial pathogens. Cataloging AMR/virulence characteristics, succession, accumulation, and persistence of microorganisms would facilitate the development of suitable countermeasures to reduce their presence in the closed built environment.}, }
@article {pmid30420843, year = {2018}, author = {Alves, LF and Meleiro, LP and Silva, RN and Westmann, CA and Guazzaroni, ME}, title = {Novel Ethanol- and 5-Hydroxymethyl Furfural-Stimulated β-Glucosidase Retrieved From a Brazilian Secondary Atlantic Forest Soil Metagenome.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2556}, pmid = {30420843}, issn = {1664-302X}, abstract = {Beta-glucosidases are key enzymes involved in lignocellulosic biomass degradation for bioethanol production, which complete the final step during cellulose hydrolysis by converting cellobiose into glucose. Currently, industry requires enzymes with improved catalytic performance or tolerance to process-specific parameters. In this sense, metagenomics has become a powerful tool for accessing and exploring the biochemical biodiversity present in different natural environments. Here, we report the identification of a novel β-glucosidase from metagenomic DNA isolated from soil samples enriched with decaying plant matter from a Secondary Atlantic Forest region. For this, we employed a functional screening approach using an optimized and synthetic broad host-range vector for library production. The novel β-glucosidase - named Lfa2 - displays three GH3-family conserved domains and conserved catalytic amino acids D283 and E487. The purified enzyme was most active in pH 5.5 and at 50°C, and showed hydrolytic activity toward several pNP synthetic substrates containing β-glucose, β-galactose, β-xylose, β-fucose, and α-arabinopyranose, as well as toward cellobiose. Lfa2 showed considerable glucose tolerance, exhibiting an IC50 of 300 mM glucose and 30% of remaining activity in 600 mM glucose. In addition, Lfa2 retained full or slightly enhanced activity in the presence of several metal ions. Further, β-glucosidase activity was increased by 1.7-fold in the presence of 10% (v/v) ethanol, a concentration that can be reached in conventional fermentation processes. Similarly, Lfa2 showed 1.7-fold enhanced activity at high concentrations of 5-hydroxymethyl furfural, one of the most important cellulase inhibitors in pretreated sugarcane bagasse hydrolysates. Moreover, the synergistic effect of Lfa2 on Bacillus subtilis GH5-CBM3 endoglucanase activity was demonstrated by the increased production of glucose (1.6-fold). Together, these results indicate that β-glucosidase Lfa2 is a promissory enzyme candidate for utilization in diverse industrial applications, such as cellulosic biomass degradation or flavor enhancement in winemaking and grape processing.}, }
@article {pmid30419949, year = {2018}, author = {Silverman, JD and Durand, HK and Bloom, RJ and Mukherjee, S and David, LA}, title = {Dynamic linear models guide design and analysis of microbiota studies within artificial human guts.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {202}, pmid = {30419949}, issn = {2049-2618}, support = {R01 DK116187/DK/NIDDK NIH HHS/United States ; }, mesh = {Artificial Organs/*microbiology ; Bacteroides/*growth &amp; development ; Enterobacteriaceae/*growth &amp; development ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Linear Models ; *Models, Anatomic ; }, abstract = {BACKGROUND: Artificial gut models provide unique opportunities to study human-associated microbiota. Outstanding questions for these models' fundamental biology include the timescales on which microbiota vary and the factors that drive such change. Answering these questions though requires overcoming analytical obstacles like estimating the effects of technical variation on observed microbiota dynamics, as well as the lack of appropriate benchmark datasets.<br><br>RESULTS: To address these obstacles, we created a modeling framework based on multinomial logistic-normal dynamic linear models (MALLARDs) and performed dense longitudinal sampling of four replicate artificial human guts over the course of 1 month. The resulting analyses revealed how the ratio of biological variation to technical variation from sample processing depends on sampling frequency. In particular, we find that at hourly sampling frequencies, 76% of observed variation could be ascribed to technical sources, which could also skew the observed covariation between taxa. We also found that the artificial guts demonstrated replicable trajectories even after a recovery from a transient feed disruption. Additionally, we observed irregular sub-daily oscillatory dynamics associated with the bacterial family Enterobacteriaceae within all four replicate vessels.<br><br>CONCLUSIONS: Our analyses suggest that, beyond variation due to sequence counting, technical variation from sample processing can obscure temporal variation from biological sources in artificial gut studies. Our analyses also supported hypotheses that human gut microbiota fluctuates on sub-daily timescales in the absence of a host and that microbiota can follow replicable trajectories in the presence of environmental driving forces. Finally, multiple aspects of our approach are generalizable and could ultimately be used to facilitate the design and analysis of longitudinal microbiota studies in vivo.}, }
@article {pmid30417889, year = {2018}, author = {Hyeon, JY and Mann, DA and Townsend, AM and Deng, X}, title = {Quasi-metagenomic Analysis of Salmonella from Food and Environmental Samples.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {140}, pages = {}, pmid = {30417889}, issn = {1940-087X}, mesh = {Animals ; Cattle ; Environmental Monitoring ; Food Microbiology/*methods ; High-Throughput Nucleotide Sequencing ; Immunomagnetic Separation/*methods ; Metagenomics/*methods ; Microbiota ; Polymerase Chain Reaction ; *Salmonella enterica ; }, abstract = {Quasi-metagenomics sequencing refers to the sequencing-based analysis of modified microbiomes of food and environmental samples. In this protocol, microbiome modification is designed to concentrate genomic DNA of a target foodborne pathogen contaminant to facilitate the detection and subtyping of the pathogen in a single workflow. Here, we explain and demonstrate the sample preparation steps for the quasi-metagenomics analysis of Salmonella enterica from representative food and environmental samples including alfalfa sprouts, ground black pepper, ground beef, chicken breast and environmental swabs. Samples are first subjected to the culture enrichment of Salmonella for a shortened and adjustable duration (4-24 h). Salmonella cells are then selectively captured from the enrichment culture by immunomagnetic separation (IMS). Finally, multiple displacement amplification (MDA) is performed to amplify DNA from IMS-captured cells. The DNA output of this protocol can be sequenced by high throughput sequencing platforms. An optional quantitative PCR analysis can be performed to replace sequencing for Salmonella detection or assess the concentration of Salmonella DNA before sequencing.}, }
@article {pmid30413473, year = {2019}, author = {Coscolín, C and Katzke, N and García-Moyano, A and Navarro-Fernández, J and Almendral, D and Martínez-Martínez, M and Bollinger, A and Bargiela, R and Gertler, C and Chernikova, TN and Rojo, D and Barbas, C and Tran, H and Golyshina, OV and Koch, R and Yakimov, MM and Bjerga, GEK and Golyshin, PN and Jaeger, KE and Ferrer, M}, title = {Bioprospecting Reveals Class III ω-Transaminases Converting Bulky Ketones and Environmentally Relevant Polyamines.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {2}, pages = {}, doi = {10.1128/AEM.02404-18}, pmid = {30413473}, issn = {1098-5336}, abstract = {Amination of bulky ketones, particularly in (R) configuration, is an attractive chemical conversion; however, known ω-transaminases (ω-TAs) show insufficient levels of performance. By applying two screening methods, we discovered 10 amine transaminases from the class III ω-TA family that were 38% to 76% identical to homologues. We present examples of such enzymes preferring bulky ketones over keto acids and aldehydes with stringent (S) selectivity. We also report representatives from the class III ω-TAs capable of converting (R) and (S) amines and bulky ketones and one that can convert amines with longer alkyl substituents. The preference for bulky ketones was associated with the presence of a hairpin region proximal to the conserved Arg414 and residues conforming and close to it. The outward orientation of Arg414 additionally favored the conversion of (R) amines. This configuration was also found to favor the utilization of putrescine as an amine donor, so that class III ω-TAs with Arg414 in outward orientation may participate in vivo in the catabolism of putrescine. The positioning of the conserved Ser231 also contributes to the preference for amines with longer alkyl substituents. Optimal temperatures for activity ranged from 45 to 65°C, and a few enzymes retained ≥50% of their activity in water-soluble solvents (up to 50% [vol/vol]). Hence, our results will pave the way to design, in the future, new class III ω-TAs converting bulky ketones and (R) amines for the production of high-value products and to screen for those converting putrescine.IMPORTANCE Amine transaminases of the class III ω-TAs are key enzymes for modification of chemical building blocks, but finding those capable of converting bulky ketones and (R) amines is still challenging. Here, by an extensive analysis of the substrate spectra of 10 class III ω-TAs, we identified a number of residues playing a role in determining the access and positioning of bulky ketones, bulky amines, and (R)- and (S) amines, as well as of environmentally relevant polyamines, particularly putrescine. The results presented can significantly expand future opportunities for designing (R)-specific class III ω-TAs to convert valuable bulky ketones and amines, as well as for deepening the knowledge into the polyamine catabolic pathways.}, }
@article {pmid30412889, year = {2019}, author = {Nathani, NM and Mootapally, C and Dave, BP}, title = {Antibiotic resistance genes allied to the pelagic sediment microbiome in the Gulf of Khambhat and Arabian Sea.}, journal = {The Science of the total environment}, volume = {653}, number = {}, pages = {446-454}, doi = {10.1016/j.scitotenv.2018.10.409}, pmid = {30412889}, issn = {1879-1026}, mesh = {Bacteria/classification/drug effects/*genetics/*isolation &amp; purification ; *Drug Resistance, Microbial ; Genes, Bacterial/*drug effects ; Geologic Sediments/*microbiology ; Indian Ocean ; *Microbiota ; }, abstract = {Antibiotics have been widely spread in the environments, imposing profound stress on the resistome of the residing microbes. Marine microbiomes are well established large reservoirs of novel antibiotics and corresponding resistance genes. The Gulf of Khambhat is known for its extreme tides and complex sedimentation process. We performed high throughput sequencing and applied bioinformatics techniques on pelagic sediment microbiome across four coordinates of the Gulf of Khambhat to assess the marine resistome, its corresponding bacterial community and compared with the open Arabian Sea sample. We identified a total of 2354 unique types of resistance genes, with most abundant and diverse gene profile in the area that had anthropogenic activities being carried out on-shore. The genes with >1% abundance in all samples included carA, macB, sav1866, tlrC, srmB, taeA, tetA, oleC and bcrA which belonged to the macrolides, glycopeptides and peptide drug classes. ARG enriched phyla distribution was quite varying between all the sites, with Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes among the dominant phyla. Based on the outcomes, we also propose potential biomarker candidates Desulfovibrio, Thermotaga and Pelobacter for antibiotic monitoring in the two of the Gulf samples probable contamination prone environments, and genera Nitrosocccus, Marinobacter and Streptomyces in the rest of the three studied samples. Outcomes support the concept that ARGs naturally originate in environments and human activities contribute to the dissemination of antibiotic resistance.}, }
@article {pmid30405577, year = {2018}, author = {Bertelli, C and Courtois, S and Rosikiewicz, M and Piriou, P and Aeby, S and Robert, S and Loret, JF and Greub, G}, title = {Reduced Chlorine in Drinking Water Distribution Systems Impacts Bacterial Biodiversity in Biofilms.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2520}, pmid = {30405577}, issn = {1664-302X}, abstract = {In drinking water distribution systems (DWDS), a disinfectant residual is usually applied to limit bacterial regrowth. However, delivering water with no or reduced chlorine residual could potentially decrease the selection for antimicrobial resistant microorganisms, favor bacterial regrowth and result in changes in bacterial populations. To evaluate the feasibility of water reduction in local DWDS while ensuring water safety, water quality was measured over 2 months in two different networks, each of them harboring sub-areas with normal and reduced chlorine. Water quality remained good in chlorine reduced samples, with limited development of total flora and absence of coliforms. Furthermore, 16S rRNA amplicon-based metagenomics was used to investigate the diversity and the composition of microbial communities in the sub-networks. Taxonomic classification of sequence reads showed a reduced bacterial diversity in sampling points with higher chlorine residuals. Chlorine disinfection created more homogeneous bacterial population, dominated by Pseudomonas, a genus that contains some major opportunistic pathogens such as P. aeruginosa. In the absence of chlorine, a larger and unknown biodiversity was unveiled, also highlighted by a decreased rate of taxonomic classification to the genus and species level. Overall, this experiment in a functional DWDS will facilitate the move toward potable water delivery systems without residual disinfectants and will improve water taste for consumers.}, }
@article {pmid30400812, year = {2018}, author = {Kumar, MS and Slud, EV and Okrah, K and Hicks, SC and Hannenhalli, S and Corrada Bravo, H}, title = {Analysis and correction of compositional bias in sparse sequencing count data.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {799}, pmid = {30400812}, issn = {1471-2164}, support = {K99 HG009007/HG/NHGRI NIH HHS/United States ; R01 RR021967/RR/NCRR NIH HHS/United States ; GM114267//National Institutes of Health/ ; R01 GM083084/GM/NIGMS NIH HHS/United States ; HG005220//National Institutes of Health/ ; R01 HG005220/HG/NHGRI NIH HHS/United States ; R21 GM107683/GM/NIGMS NIH HHS/United States ; 1564785//National Science Foundation (US)/ ; R01 GM114267/GM/NIGMS NIH HHS/United States ; GM083084//National Institutes of Health/ ; R01 GM103552/GM/NIGMS NIH HHS/United States ; }, mesh = {*Algorithms ; Bayes Theorem ; Computational Biology/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/*methods ; *Microbiota ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {BACKGROUND: Count data derived from high-throughput deoxy-ribonucliec acid (DNA) sequencing is frequently used in quantitative molecular assays. Due to properties inherent to the sequencing process, unnormalized count data is compositional, measuring relative and not absolute abundances of the assayed features. This compositional bias confounds inference of absolute abundances. Commonly used count data normalization approaches like library size scaling/rarefaction/subsampling cannot correct for compositional or any other relevant technical bias that is uncorrelated with library size.<br><br>RESULTS: We demonstrate that existing techniques for estimating compositional bias fail with sparse metagenomic 16S count data and propose an empirical Bayes normalization approach to overcome this problem. In addition, we clarify the assumptions underlying frequently used scaling normalization methods in light of compositional bias, including scaling methods that were not designed directly to address it.<br><br>CONCLUSIONS: Compositional bias, induced by the sequencing machine, confounds inferences of absolute abundances. We present a normalization technique for compositional bias correction in sparse sequencing count data, and demonstrate its improved performance in metagenomic 16s survey data. Based on the distribution of technical bias estimates arising from several publicly available large scale 16s count datasets, we argue that detailed experiments specifically addressing the influence of compositional bias in metagenomics are needed.}, }
@article {pmid30396371, year = {2018}, author = {Meisel, JS and Nasko, DJ and Brubach, B and Cepeda-Espinoza, V and Chopyk, J and Corrada-Bravo, H and Fedarko, M and Ghurye, J and Javkar, K and Olson, ND and Shah, N and Allard, SM and Bazinet, AL and Bergman, NH and Brown, A and Caporaso, JG and Conlan, S and DiRuggiero, J and Forry, SP and Hasan, NA and Kralj, J and Luethy, PM and Milton, DK and Ondov, BD and Preheim, S and Ratnayake, S and Rogers, SM and Rosovitz, MJ and Sakowski, EG and Schliebs, NO and Sommer, DD and Ternus, KL and Uritskiy, G and Zhang, SX and Pop, M and Treangen, TJ}, title = {Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {197}, pmid = {30396371}, issn = {2049-2618}, support = {R01 AI100947/AI/NIAID NIH HHS/United States ; U54 CA143924/CA/NCI NIH HHS/United States ; U54 CA143925/CA/NCI NIH HHS/United States ; R01 GM114267/GM/NIGMS NIH HHS/United States ; }, mesh = {*Biological Warfare Agents ; Computational Biology/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; Microbiota/physiology ; Sequence Analysis, DNA/methods ; }, abstract = {The Mid-Atlantic Microbiome Meet-up (M3) organization brings together academic, government, and industry groups to share ideas and develop best practices for microbiome research. In January of 2018, M3 held its fourth meeting, which focused on recent advances in biodefense, specifically those relating to infectious disease, and the use of metagenomic methods for pathogen detection. Presentations highlighted the utility of next-generation sequencing technologies for identifying and tracking microbial community members across space and time. However, they also stressed the current limitations of genomic approaches for biodefense, including insufficient sensitivity to detect low-abundance pathogens and the inability to quantify viable organisms. Participants discussed ways in which the community can improve software usability and shared new computational tools for metagenomic processing, assembly, annotation, and visualization. Looking to the future, they identified the need for better bioinformatics toolkits for longitudinal analyses, improved sample processing approaches for characterizing viruses and fungi, and more consistent maintenance of database resources. Finally, they addressed the necessity of improving data standards to incentivize data sharing. Here, we summarize the presentations and discussions from the meeting, identifying the areas where microbiome analyses have improved our ability to detect and manage biological threats and infectious disease, as well as gaps of knowledge in the field that require future funding and focus.}, }
@article {pmid30394664, year = {2019}, author = {Spang, A and Offre, P}, title = {Towards a systematic understanding of differences between archaeal and bacterial diversity.}, journal = {Environmental microbiology reports}, volume = {11}, number = {1}, pages = {9-12}, doi = {10.1111/1758-2229.12701}, pmid = {30394664}, issn = {1758-2229}, mesh = {Archaea/*classification/*genetics ; Bacteria/*classification/*genetics ; *Biodiversity ; Biological Evolution ; Genome, Archaeal/genetics ; Genome, Bacterial/genetics ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Single-Cell Analysis ; }, abstract = {In this crystal ball, we discuss emerging methodologies that can help reaching a synthesis on the biodiversity of Archaea and Bacteria and thereby inform a central enigma in microbiology, i.e. the fundamental split between these primary domains of life and the apparent lower diversity of the Archaea.}, }
@article {pmid30394652, year = {2018}, author = {Borton, MA and Daly, RA and O'Banion, B and Hoyt, DW and Marcus, DN and Welch, S and Hastings, SS and Meulia, T and Wolfe, RA and Booker, AE and Sharma, S and Cole, DR and Wunch, K and Moore, JD and Darrah, TH and Wilkins, MJ and Wrighton, KC}, title = {Comparative genomics and physiology of the genus Methanohalophilus, a prevalent methanogen in hydraulically fractured shale.}, journal = {Environmental microbiology}, volume = {20}, number = {12}, pages = {4596-4611}, doi = {10.1111/1462-2920.14467}, pmid = {30394652}, issn = {1462-2920}, support = {1342701//National Science Foundation Dimensions of Biodiversity/ ; FE0024297//Department of Energy's National Energy Technology Laboratory/ ; //U.S. Department of Energy Joint Genome Institute/ ; DE-AC02-05CH11231//Office of Science of the U.S. Department of Energy/ ; }, abstract = {About 60% of natural gas production in the United States comes from hydraulic fracturing of unconventional reservoirs, such as shales or organic-rich micrites. This process inoculates and enriches for halotolerant microorganisms in these reservoirs over time, resulting in a saline ecosystem that includes methane producing archaea. Here, we survey the biogeography of methanogens across unconventional reservoirs, and report that members of genus Methanohalophilus are recovered from every hydraulically fractured unconventional reservoir sampled by metagenomics. We provide the first genomic sequencing of three isolate genomes, as well as two metagenome assembled genomes (MAGs). Utilizing six other previously sequenced isolate genomes and MAGs, we perform comparative analysis of the 11 genomes representing this genus. This genomic investigation revealed distinctions between surface and subsurface derived genomes that are consistent with constraints encountered in each environment. Genotypic differences were also uncovered between isolate genomes recovered from the same well, suggesting niche partitioning among closely related strains. These genomic substrate utilization predictions were then confirmed by physiological investigation. Fine-scale microdiversity was observed in CRISPR-Cas systems of Methanohalophilus, with genomes from geographically distinct unconventional reservoirs sharing spacers targeting the same viral population. These findings have implications for augmentation strategies resulting in enhanced biogenic methane production in hydraulically fractured unconventional reservoirs.}, }
@article {pmid30384903, year = {2018}, author = {Huang, X and Zhu, J and Cai, Z and Lao, Y and Jin, H and Yu, K and Zhang, B and Zhou, J}, title = {Profiles of quorum sensing (QS)-related sequences in phycospheric microorganisms during a marine dinoflagellate bloom, as determined by a metagenomic approach.}, journal = {Microbiological research}, volume = {217}, number = {}, pages = {1-13}, doi = {10.1016/j.micres.2018.08.015}, pmid = {30384903}, issn = {1618-0623}, mesh = {Acyltransferases/genetics/metabolism ; Bacteria/classification/*genetics/*metabolism ; Bacterial Physiological Phenomena ; Bacterial Proteins/genetics/metabolism ; Carbon-Sulfur Lyases/genetics/metabolism ; China ; Dinoflagellida/growth &amp; development/*microbiology ; Eutrophication/physiology ; Marine Biology ; Metagenomics/*methods ; Microbiota/*genetics/*physiology ; Phylogeny ; Proteobacteria/genetics/metabolism ; Quorum Sensing/*genetics/*physiology ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sequence Analysis ; Sequence Analysis, Protein ; Sequence Homology ; Symbiosis ; Transcription Factors/genetics/metabolism ; }, abstract = {The complicated relationships among environmental microorganisms are regulated by quorum sensing (QS). Understanding QS-based signals could shed light on the interactions between microbial communities in certain environments. Although QS characteristics have been widely discussed, few studies have been conducted on the role of QS in phycospheric microorganisms. Here, we used metagenomics to examine the profile of AI-1 (AinS, HdtS, LuxI) and AI-2 (LuxS) autoinducers from a deeply sequenced microbial database, obtained from a complete dinoflagellate bloom. A total of 3001 putative AI-1 homologs and 130 AI-2 homologs were identified. The predominant member among the AI groups was HdtS. The abundance of HdtS, AinS, and LuxS increased as the bloom developed, whereas the abundance of LuxI showed the opposite trend. Phylogenetic analysis suggested that HdtS and LuxI synthase originated mainly from alpha-, beta-, and gamma-Proteobacteria, whereas AinS synthase originated solely from Vibrionales. In comparison to AI-1, the sequences related to AI-2 (LuxS) demonstrated a much wider taxonomic coverage. Some significant correlations were found between dominant species and QS signals. In addition to the QS, we also performed parallel analysis of the quorum quenching (QQ) sequences. In comparison to QS, the relative abundance of QQ signals was lower; however, an obvious frequency correlation was observed. These results suggested that QS and QQ signals co-participate in regulating microbial communities during an algal bloom. These data helped to reveal the characteristic behavior of algal symbiotic bacteria, and facilitated a better understanding of microbial dynamics during an algal bloom event from a chemical ecological perspective.}, }
@article {pmid30382616, year = {2019}, author = {Ganuza, M and Pastor, N and Boccolini, M and Erazo, J and Palacios, S and Oddino, C and Reynoso, MM and Rovera, M and Torres, AM}, title = {Evaluating the impact of the biocontrol agent Trichoderma harzianum ITEM 3636 on indigenous microbial communities from field soils.}, journal = {Journal of applied microbiology}, volume = {126}, number = {2}, pages = {608-623}, doi = {10.1111/jam.14147}, pmid = {30382616}, issn = {1365-2672}, support = {//Agencia Nacional de Promoción Científica y Tecnológica (MINCyT)/ ; }, mesh = {Agriculture ; Arachis ; Argentina ; Bacteria/genetics/isolation &amp; purification ; *Biological Control Agents ; Denaturing Gradient Gel Electrophoresis ; Fungi/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Microbiota ; Polymerase Chain Reaction ; Seeds ; Soil/chemistry ; *Soil Microbiology ; *Trichoderma ; }, abstract = {AIM: To investigate the impact of inoculating peanut seeds with the biocontrol agent Trichoderma harzianum ITEM 3636 on the structure of bacterial and fungal communities from agricultural soils.<br><br>METHODS AND RESULTS: Polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (PCR-DGGE) and next-generation sequencing (NGS) of amplicons (or marker gene amplification metagenomics) were performed to investigate potential changes in the structure of microbial communities from fields located in a peanut-producing area in the province of Córdoba, Argentina. Fields had history of peanut smut (caused by Thecaphora frezii) incidence. The Shannon indexes (H'), which estimate diversity, obtained from the PCR-DGGE assays did not show significant differences neither for bacterial nor for fungal communities between control and inoculation treatments. On the other hand, the number of operational taxonomic units obtained after NGS was similar between all the analysed samples. Moreover, results of alpha and beta diversity showed that there were no significant variations between the relative abundances of the most representative bacterial and fungal phyla and genera, in both fields.<br><br>CONCLUSIONS: Trichoderma harzianum ITEM 3636 decreases the incidence and severity of agriculturally relevant diseases without causing significant changes in the microbial communities of agricultural soils.<br><br>Our investigations provide information on the structure of bacterial and fungal communities in peanut-producing fields after inoculation of seeds with a biocontrol agent.}, }
@article {pmid30376898, year = {2018}, author = {Leiby, JS and McCormick, K and Sherrill-Mix, S and Clarke, EL and Kessler, LR and Taylor, LJ and Hofstaedter, CE and Roche, AM and Mattei, LM and Bittinger, K and Elovitz, MA and Leite, R and Parry, S and Bushman, FD}, title = {Lack of detection of a human placenta microbiome in samples from preterm and term deliveries.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {196}, pmid = {30376898}, issn = {2049-2618}, support = {P30 AI045008/AI/NIAID NIH HHS/United States ; T32 AI007632/AI/NIAID NIH HHS/United States ; T32 AI007324/AI/NIAID NIH HHS/United States ; }, mesh = {Adult ; Bacteria/genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; Female ; Humans ; Microbiota/*genetics ; Placenta/*microbiology ; Pregnancy ; Premature Birth ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Term Birth ; Uterus/*microbiology ; }, abstract = {BACKGROUND: Historically, the human womb has been thought to be sterile in healthy pregnancies, but this idea has been challenged by recent studies using DNA sequence-based methods, which have suggested that the womb is colonized with bacteria. For example, analysis of DNA from placenta samples yielded small proportions of microbial sequences which were proposed to represent normal bacterial colonization. However, an analysis by our group showed no distinction between background negative controls and placenta samples. Also supporting the idea that the womb is sterile is the observation that germ-free mammals can be generated by sterile delivery of neonates into a sterile isolator, after which neonates remain germ-free, which would seem to provide strong data in support of sterility of the womb.<br><br>RESULTS: To probe this further and to investigate possible placental colonization associated with spontaneous preterm birth, we carried out another study comparing microbiota in placenta samples from 20 term and 20 spontaneous preterm deliveries. Both 16S rRNA marker gene sequencing and shotgun metagenomic sequencing were used to characterize placenta and control samples. We first quantified absolute amounts of bacterial 16S rRNA gene sequences using 16S rRNA gene quantitative PCR (qPCR). As in our previous study, levels were found to be low in the placenta samples and indistinguishable from negative controls. Analysis by DNA sequencing did not yield a placenta microbiome distinct from negative controls, either using marker gene sequencing as in our previous work, or with shotgun metagenomic sequencing. Several types of artifacts, including erroneous read classifications and barcode misattribution, needed to be identified and removed from the data to clarify this point.<br><br>CONCLUSIONS: Our findings do not support the existence of a consistent placental microbiome, in either placenta from term deliveries or spontaneous preterm births.}, }
@article {pmid30372979, year = {2019}, author = {Park, SE and Seo, SH and Kim, EJ and Byun, S and Na, CS and Son, HS}, title = {Changes of microbial community and metabolite in kimchi inoculated with different microbial community starters.}, journal = {Food chemistry}, volume = {274}, number = {}, pages = {558-565}, doi = {10.1016/j.foodchem.2018.09.032}, pmid = {30372979}, issn = {1873-7072}, mesh = {Bacteria/metabolism ; Brassica/metabolism/*microbiology ; *Fermentation ; Fermented Foods/*microbiology ; *Food Microbiology ; *Microbiota ; }, abstract = {Gas chromatography mass spectrometry-based metabolomics and next generation sequencing-based metagenomics were applied to investigate the effect of different microbial community starters (MCSs) on kimchi fermentation. Profiles of metabolites and microbial community in kimchi were remarkably different from those on the first day of fermentation according to MCS used. Kimchi inoculated with MCS5 or MCS10 had relatively higher levels of lactic acid, leucine, propanedioic acid, serine, glycerol, erythritol, and sorbitol but lower levels of butanedioic acid, glyceric acid, myo-inositol, xylose, fructose, and talose compared to control kimchi or kimchi inoculated with MCS1. Microbial communities of kimchi inoculated with MCS1, MCS5, and MCS10 were characterized by high ratios of Leuconostoc, Lactobacillus plantarum, and Lactobacillus brevis, respectively. The microbial community of kimchi formed on the first day of fermentation was stable for 50 days, suggesting that microbial communities containing multiple microorganisms can be used as starters to obtain desired quality of kimchi.}, }
@article {pmid30362648, year = {2019}, author = {Larivière-Gauthier, G and Thibodeau, A and Letellier, A and Yergeau, É and Fravalo, P}, title = {Salmonella shedding status of the sow affects the microbiota of their piglets at weaning.}, journal = {Journal of applied microbiology}, volume = {126}, number = {2}, pages = {411-423}, doi = {10.1111/jam.14139}, pmid = {30362648}, issn = {1365-2672}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Animals ; *Bacterial Shedding ; Female ; *Microbiota ; Pregnancy ; Salmonella/*isolation &amp; purification ; Swine/growth &amp; development/*microbiology ; Weaning ; }, abstract = {AIM: To observe the transfer of the digestive microbiota from sow to piglet, describe the impact of the sow's Salmonella shedding on this transfer and identify transferred populations that could be associated with the future Salmonella status of the piglets.<br><br>METHODS AND RESULTS: Salmonella shedding status of 19 sows was determined at the beginning and end of gestation. Four piglets were randomly selected from each sow. Using MiSeq, the microbiotas of the sows at the end of gestation and of their piglets 1 day before weaning were described. Results showed that the Salmonella shedding of the sows, the birth mother, the lairage room, the parity and the contamination of the lairage environment were associated to the microbiota of the piglets (permanova P < 0·05). Several genera were associated with piglets born from negative or positive sows.<br><br>CONCLUSION: There is a link between the microbiota of the sows at the end of gestation and the microbiota of their piglets at weaning, and the Salmonella shedding of the sow is associated with the microbiota of the piglets.<br><br>Salmonella status of the sows affects the microbiota of their piglets and could affect the long-term Salmonella colonization resistance of these animals and their health.}, }
@article {pmid30359379, year = {2018}, author = {Bidot, WA and Ericsson, AC and Franklin, CL}, title = {Effects of water decontamination methods and bedding material on the gut microbiota.}, journal = {PloS one}, volume = {13}, number = {10}, pages = {e0198305}, pmid = {30359379}, issn = {1932-6203}, support = {K01 OD019924/OD/NIH HHS/United States ; U42 OD010918/OD/NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics/isolation &amp; purification ; Cecum/microbiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Housing, Animal ; Mice, Inbred ICR ; *Water Microbiology ; Water Purification/*methods ; }, abstract = {Rodent models are invaluable to understanding health and disease in many areas of biomedical research. Unfortunately, many models suffer from lack of phenotype reproducibility. Our laboratory has shown that differences in gut microbiota (GM) can modulate phenotypes of models of colon cancer and inflammatory bowel disease. We and others have also shown that a number of factors associated with rodent research, including vendor, cage system, and bedding can alter GM. The objective of this study was to expand these studies to examine the effect of additional bedding materials and methods of water decontamination on GM diversity and composition. To this end, Crl:CD1 (ICR) mice were housed on corn cob or compressed paper chip bedding and provided water that was decontaminated by four different methods: autoclaving with reverse osmosis, autoclaving with hydrochloric acid, autoclaving with sulfuric acid, and autoclaving alone. Feces was collected at day 0, and at day 28 (endpoint), fecal and cecal samples were collected. DNA was extracted from samples, amplified by PCR using conserved bacterial primer sets and subjected to next generation sequencing. Sequence data were analyzed using Qiime and groups were compared using principal coordinate analysis (PCoA) and permutational multivariate analysis of variance (PERMANOVA). Two factor PERMANOVA of cecal GM data revealed significant changes when comparing bedding and water decontamination methods, while no significant effects were noted in the fecal GM data. Subsequent PERMANOVA and PCoA of cecal data revealed that several combinations of bedding and water decontamination methods resulted in differing GM, highlighting the complexity by which environmental factors interact to modulate GM.}, }
@article {pmid30358106, year = {2019}, author = {Siegenthaler, A and Wangensteen, OS and Soto, AZ and Benvenuto, C and Corrigan, L and Mariani, S}, title = {Metabarcoding of shrimp stomach content: Harnessing a natural sampler for fish biodiversity monitoring.}, journal = {Molecular ecology resources}, volume = {19}, number = {1}, pages = {206-220}, doi = {10.1111/1755-0998.12956}, pmid = {30358106}, issn = {1755-0998}, support = {//Santander Advantage Fund/ ; //University of Salford Manchester/ ; NE/N005759/1//Natural Environment Research Council/ ; //Mersey Gateway Environmental Trust/ ; }, mesh = {Animals ; *Biodiversity ; Crangonidae/*physiology ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV ; Estuaries ; Europe ; Feeding Behavior ; Fishes/*classification/*genetics ; *Gastrointestinal Contents ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/*methods ; RNA, Ribosomal/genetics ; }, abstract = {Given their positioning and biological productivity, estuaries have long represented key providers of ecosystem services and consequently remain under remarkable pressure from numerous forms of anthropogenic impact. The monitoring of fish communities in space and time is one of the most widespread and established approaches to assess the ecological status of estuaries and other coastal habitats, but traditional fish surveys are invasive, costly, labour intensive and highly selective. Recently, the application of metabarcoding techniques, on either sediment or aqueous environmental DNA, has rapidly gained popularity. Here, we evaluate the application of a novel, high-throughput DNA-based monitoring tool to assess fish diversity, based on the analysis of the gut contents of a generalist predator/scavenger, the European brown shrimp, Crangon crangon. Sediment and shrimp samples were collected from eight European estuaries, and DNA metabarcoding (using both 12S and COI markers) was carried out to infer fish assemblage composition. We detected 32 teleost species (16 and 20, for 12S and COI, respectively). Twice as many species were recovered using metabarcoding than by traditional net surveys. By comparing and interweaving trophic, environmental DNA and traditional survey-based techniques, we show that the DNA-assisted gut content analysis of a ubiquitous, easily accessible, generalist species may serve as a powerful, rapid and cost-effective tool for large-scale, routine estuarine biodiversity monitoring.}, }
@article {pmid30356699, year = {2018}, author = {Weißbecker, C and Wubet, T and Lentendu, G and Kühn, P and Scholten, T and Bruelheide, H and Buscot, F}, title = {Experimental Evidence of Functional Group-Dependent Effects of Tree Diversity on Soil Fungi in Subtropical Forests.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2312}, pmid = {30356699}, issn = {1664-302X}, abstract = {Deconvoluting the relative contributions made by specific biotic and abiotic drivers to soil fungal community compositions facilitates predictions about the functional responses of ecosystems to environmental changes, such as losses of plant diversity, but it is hindered by the complex interactions involved. Experimental assembly of tree species allows separation of the respective effects of plant community composition (biotic components) and soil properties (abiotic components), enabling much greater statistical power than can be achieved in observational studies. We therefore analyzed these contributions by assessing, via pyrotag sequencing of the internal transcribed spacer (ITS2) rDNA region, fungal communities in young subtropical forest plots included in a large experiment on the effects of tree species richness. Spatial variables and soil properties were the main drivers of soil fungal alpha and beta-diversity, implying strong early-stage environmental filtering and dispersal limitation. Tree related variables, such as tree community composition, significantly affected arbuscular mycorrhizal and pathogen fungal community structure, while differences in tree host species and host abundance affected ectomycorrhizal fungal community composition. At this early stage of the experiment, only a limited amount of carbon inputs (rhizodeposits and leaf litter) was being provided to the ecosystem due to the size of the tree saplings, and persisting legacy effects were observed. We thus expect to find increasing tree related effects on fungal community composition as forest development proceeds.}, }
@article {pmid30356187, year = {2018}, author = {Stewart, CJ and Ajami, NJ and O'Brien, JL and Hutchinson, DS and Smith, DP and Wong, MC and Ross, MC and Lloyd, RE and Doddapaneni, H and Metcalf, GA and Muzny, D and Gibbs, RA and Vatanen, T and Huttenhower, C and Xavier, RJ and Rewers, M and Hagopian, W and Toppari, J and Ziegler, AG and She, JX and Akolkar, B and Lernmark, A and Hyoty, H and Vehik, K and Krischer, JP and Petrosino, JF}, title = {Temporal development of the gut microbiome in early childhood from the TEDDY study.}, journal = {Nature}, volume = {562}, number = {7728}, pages = {583-588}, doi = {10.1038/s41586-018-0617-x}, pmid = {30356187}, issn = {1476-4687}, support = {U01 DK063821/DK/NIDDK NIH HHS/United States ; UC4 DK063863/DK/NIDDK NIH HHS/United States ; UL1 TR000064/TR/NCATS NIH HHS/United States ; U01 DK063836/DK/NIDDK NIH HHS/United States ; U01 DK063829/DK/NIDDK NIH HHS/United States ; U01 DK063865/DK/NIDDK NIH HHS/United States ; UC4 DK095300/DK/NIDDK NIH HHS/United States ; UC4 DK063861/DK/NIDDK NIH HHS/United States ; UC4 DK063829/DK/NIDDK NIH HHS/United States ; HHSN267200700014C/LM/NLM NIH HHS/United States ; UC4 DK063821/DK/NIDDK NIH HHS/United States ; UC4 DK117483/DK/NIDDK NIH HHS/United States ; UC4 DK063836/DK/NIDDK NIH HHS/United States ; UC4 DK112243/DK/NIDDK NIH HHS/United States ; HHSN267200700014C/DK/NIDDK NIH HHS/United States ; U01 DK063861/DK/NIDDK NIH HHS/United States ; UC4 DK063865/DK/NIDDK NIH HHS/United States ; U01 DK063863/DK/NIDDK NIH HHS/United States ; U01 DK063790/DK/NIDDK NIH HHS/United States ; UC4 DK106955/DK/NIDDK NIH HHS/United States ; UC4 DK100238/DK/NIDDK NIH HHS/United States ; UL1 TR001082/TR/NCATS NIH HHS/United States ; }, mesh = {Adolescent ; Animals ; Bifidobacterium/classification/genetics/isolation &amp; purification ; Breast Feeding/statistics &amp; numerical data ; Case-Control Studies ; Child ; Child, Preschool ; Cluster Analysis ; Datasets as Topic ; Diabetes Mellitus, Type 1/immunology/microbiology ; Female ; Firmicutes/classification/genetics/isolation &amp; purification ; Gastrointestinal Microbiome/genetics/*immunology/*physiology ; Humans ; Infant ; Male ; Milk, Human/immunology/microbiology ; Pets ; RNA, Ribosomal, 16S/genetics ; Siblings ; *Surveys and Questionnaires ; Time Factors ; }, abstract = {The development of the microbiome from infancy to childhood is dependent on a range of factors, with microbial-immune crosstalk during this time thought to be involved in the pathobiology of later life diseases1-9 such as persistent islet autoimmunity and type 1 diabetes10-12. However, to our knowledge, no studies have performed extensive characterization of the microbiome in early life in a large, multi-centre population. Here we analyse longitudinal stool samples from 903 children between 3 and 46 months of age by 16S rRNA gene sequencing (n = 12,005) and metagenomic sequencing (n = 10,867), as part of the The Environmental Determinants of Diabetes in the Young (TEDDY) study. We show that the developing gut microbiome undergoes three distinct phases of microbiome progression: a developmental phase (months 3-14), a transitional phase (months 15-30), and a stable phase (months 31-46). Receipt of breast milk, either exclusive or partial, was the most significant factor associated with the microbiome structure. Breastfeeding was associated with higher levels of Bifidobacterium species (B. breve and B. bifidum), and the cessation of breast milk resulted in faster maturation of the gut microbiome, as marked by the phylum Firmicutes. Birth mode was also significantly associated with the microbiome during the developmental phase, driven by higher levels of Bacteroides species (particularly B. fragilis) in infants delivered vaginally. Bacteroides was also associated with increased gut diversity and faster maturation, regardless of the birth mode. Environmental factors including geographical location and household exposures (such as siblings and furry pets) also represented important covariates. A nested case-control analysis revealed subtle associations between microbial taxonomy and the development of islet autoimmunity or type 1 diabetes. These data determine the structural and functional assembly of the microbiome in early life and provide a foundation for targeted mechanistic investigation into the consequences of microbial-immune crosstalk for long-term health.}, }
@article {pmid30356183, year = {2018}, author = {Vatanen, T and Franzosa, EA and Schwager, R and Tripathi, S and Arthur, TD and Vehik, K and Lernmark, Å and Hagopian, WA and Rewers, MJ and She, JX and Toppari, J and Ziegler, AG and Akolkar, B and Krischer, JP and Stewart, CJ and Ajami, NJ and Petrosino, JF and Gevers, D and Lähdesmäki, H and Vlamakis, H and Huttenhower, C and Xavier, RJ}, title = {The human gut microbiome in early-onset type 1 diabetes from the TEDDY study.}, journal = {Nature}, volume = {562}, number = {7728}, pages = {589-594}, doi = {10.1038/s41586-018-0620-2}, pmid = {30356183}, issn = {1476-4687}, support = {U01 DK063821/DK/NIDDK NIH HHS/United States ; UC4 DK063863/DK/NIDDK NIH HHS/United States ; UL1 TR000064/TR/NCATS NIH HHS/United States ; U01 DK063836/DK/NIDDK NIH HHS/United States ; U01 DK063829/DK/NIDDK NIH HHS/United States ; U01 DK063865/DK/NIDDK NIH HHS/United States ; UC4 DK095300/DK/NIDDK NIH HHS/United States ; UC4 DK063861/DK/NIDDK NIH HHS/United States ; UC4 DK063829/DK/NIDDK NIH HHS/United States ; UL1 TR002535/TR/NCATS NIH HHS/United States ; UC4 DK063821/DK/NIDDK NIH HHS/United States ; UC4 DK117483/DK/NIDDK NIH HHS/United States ; UC4 DK063836/DK/NIDDK NIH HHS/United States ; UC4 DK112243/DK/NIDDK NIH HHS/United States ; HHSN267200700014C/DK/NIDDK NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; U01 DK063861/DK/NIDDK NIH HHS/United States ; UC4 DK063865/DK/NIDDK NIH HHS/United States ; U01 DK063863/DK/NIDDK NIH HHS/United States ; U01 DK063790/DK/NIDDK NIH HHS/United States ; UC4 DK106955/DK/NIDDK NIH HHS/United States ; UC4 DK100238/DK/NIDDK NIH HHS/United States ; UL1 TR001082/TR/NCATS NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; }, mesh = {Age of Onset ; Animals ; Bifidobacterium/enzymology/genetics/isolation &amp; purification ; Breast Feeding ; Child, Preschool ; Diabetes Mellitus, Type 1/*epidemiology/genetics/*microbiology/prevention &amp; control ; Disease Models, Animal ; European Continental Ancestry Group ; Fatty Acids, Volatile/pharmacology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/genetics/immunology/*physiology ; *Health Surveys ; Humans ; Infant ; Islets of Langerhans/immunology ; Longitudinal Studies ; Male ; Mice ; Milk, Human/immunology/microbiology ; Proteobacteria/enzymology/genetics/isolation &amp; purification ; }, abstract = {Type 1 diabetes (T1D) is an autoimmune disease that targets pancreatic islet beta cells and incorporates genetic and environmental factors1, including complex genetic elements2, patient exposures3 and the gut microbiome4. Viral infections5 and broader gut dysbioses6 have been identified as potential causes or contributing factors; however, human studies have not yet identified microbial compositional or functional triggers that are predictive of islet autoimmunity or T1D. Here we analyse 10,913 metagenomes in stool samples from 783 mostly white, non-Hispanic children. The samples were collected monthly from three months of age until the clinical end point (islet autoimmunity or T1D) in the The Environmental Determinants of Diabetes in the Young (TEDDY) study, to characterize the natural history of the early gut microbiome in connection to islet autoimmunity, T1D diagnosis, and other common early life events such as antibiotic treatments and probiotics. The microbiomes of control children contained more genes that were related to fermentation and the biosynthesis of short-chain fatty acids, but these were not consistently associated with particular taxa across geographically diverse clinical centres, suggesting that microbial factors associated with T1D are taxonomically diffuse but functionally more coherent. When we investigated the broader establishment and development of the infant microbiome, both taxonomic and functional profiles were dynamic and highly individualized, and dominated in the first year of life by one of three largely exclusive Bifidobacterium species (B. bifidum, B. breve or B. longum) or by the phylum Proteobacteria. In particular, the strain-specific carriage of genes for the utilization of human milk oligosaccharide within a subset of B. longum was present specifically in breast-fed infants. These analyses of TEDDY gut metagenomes provide, to our knowledge, the largest and most detailed longitudinal functional profile of the developing gut microbiome in relation to islet autoimmunity, T1D and other early childhood events. Together with existing evidence from human cohorts7,8 and a T1D mouse model9, these data support the protective effects of short-chain fatty acids in early-onset human T1D.}, }
@article {pmid30353943, year = {2018}, author = {Sonoda, A and Kamiyama, N and Ozaka, S and Gendo, Y and Ozaki, T and Hirose, H and Noguchi, K and Saechue, B and Sachi, N and Sakai, K and Mizukami, K and Hidano, S and Murakami, K and Kobayashi, T}, title = {Oral administration of antibiotics results in fecal occult bleeding due to metabolic disorders and defective proliferation of the gut epithelial cell in mice.}, journal = {Genes to cells : devoted to molecular &amp; cellular mechanisms}, volume = {23}, number = {12}, pages = {1043-1055}, doi = {10.1111/gtc.12649}, pmid = {30353943}, issn = {1365-2443}, support = {//Suzuken Memorial Foundation/ ; 15K08953//Japan Society for the Promotion of Science/ ; 15K19577//Japan Society for the Promotion of Science/ ; 16K01872//Japan Society for the Promotion of Science/ ; 17H04649//Japan Society for the Promotion of Science/ ; 17H17104//Japan Society for the Promotion of Science/ ; 17K08695//Japan Society for the Promotion of Science/ ; 17K08889//Japan Society for the Promotion of Science/ ; 17K15954//Japan Society for the Promotion of Science/ ; 17K16346//Japan Society for the Promotion of Science/ ; //GlaxoSmithKline/ ; }, mesh = {Administration, Oral ; Ampicillin/administration &amp; dosage/pharmacology ; Animals ; Anti-Bacterial Agents/*administration &amp; dosage/*adverse effects ; Antimicrobial Cationic Peptides/metabolism ; Butyric Acid/pharmacology ; Carbohydrate Metabolism/drug effects ; Cecum/microbiology ; Cell Line, Tumor ; Cell Proliferation/drug effects ; Colon/*pathology ; Colonic Neoplasms/pathology ; Cytokines/metabolism ; Epithelial Cells/*pathology ; Glutamine/administration &amp; dosage ; Lipid Metabolism/drug effects ; Macrophages/drug effects/metabolism ; Metabolic Diseases/*complications ; Metabolome/drug effects ; Metagenomics ; Mice ; Microbiota/drug effects/genetics ; *Occult Blood ; RAW 264.7 Cells ; Regeneration/drug effects ; Sodium Glutamate/administration &amp; dosage ; Species Specificity ; Vancomycin/administration &amp; dosage/pharmacology ; }, abstract = {Antibiotics sometimes exert adverse effects on the pathogenesis of colitis due to the dysbiosis resulting from the disruption of gut homeostasis. However, the precise mechanisms underlying colitogenic effects of antibiotic-induced colitis are largely unknown. Here, we show a novel murine fecal occult bleeding model induced by the combinatorial treatment of ampicillin and vancomycin, which is accompanied by an enlarged cecum, upregulation of pro-inflammatory cytokines IL-6 and IL-12, a reduction in Ki-67-positive epithelial cell number and an increase in the apoptotic cell number in the colon. Moreover, gas chromatography-tandem mass analysis showed that various kinds of metabolites, including glutamic acid and butyric acid, were significantly decreased in the cecal contents. In addition, abundance of butyric acid producer Clostridiales was dramatically reduced in the enlarged cecum. Interestingly, supplementation of monosodium glutamate or its precursor glutamine suppressed colonic IL-6 and IL-12, protected from cell apoptosis and prevented fecal occult blood indicating that the reduced level of glutamic acid is a possible mechanism of antibiotic-induced fecal occult bleeding. Our data showed a novel mechanism of antibiotic-induced fecal occult bleeding providing a new insight into the clinical application of glutamic acid for the treatment of antibiotic-induced colitis.}, }
@article {pmid30346155, year = {2018}, author = {Pérez-Burillo, S and Pastoriza, S and Jiménez-Hernández, N and D'Auria, G and Francino, MP and Rufián-Henares, JA}, title = {Effect of Food Thermal Processing on the Composition of the Gut Microbiota.}, journal = {Journal of agricultural and food chemistry}, volume = {66}, number = {43}, pages = {11500-11509}, doi = {10.1021/acs.jafc.8b04077}, pmid = {30346155}, issn = {1520-5118}, mesh = {Bacteria/classification ; *Cooking ; Edible Grain ; Fabaceae ; Fatty Acids, Volatile/analysis ; Fermentation ; Fruit ; Furaldehyde/analogs &amp; derivatives/analysis ; *Gastrointestinal Microbiome ; *Hot Temperature ; Humans ; Lysine/analogs &amp; derivatives/analysis ; Maillard Reaction ; Meat ; RNA, Ribosomal, 16S/genetics ; Vegetables ; }, abstract = {Cooking modifies food composition due to chemical reactions. Additionally, food composition shapes the human gut microbiota. Thus, the objective of this research was to unravel the effect of different food cooking methods on the structure and functionality of the gut microbiota. Common culinary techniques were applied to five foods, which were submitted to in vitro digestion-fermentation. Furosine, 5-(hydroxymethyl)furfural, and furfural were used as Maillard reaction indicators to control the heat treatment. Short-chain fatty acids production was quantified as indicator of healthy metabolic output. Gut microbial community structure was analyzed through 16S rRNA. Both food composition and cooking methods modified the microbiota composition and released short-chain fatty acids. In general, intense cooking technologies (roasting and grilling) increased the abundance of beneficial bacteria like Ruminococcus spp. or Bifidobacterium spp. compared to milder treatments (boiling). However, for some foods (banana or bread), intense cooking decreased the levels of healthy bacteria.}, }
@article {pmid30342053, year = {2018}, author = {Vallianou, NG and Stratigou, T and Tsagarakis, S}, title = {Microbiome and diabetes: Where are we now?.}, journal = {Diabetes research and clinical practice}, volume = {146}, number = {}, pages = {111-118}, doi = {10.1016/j.diabres.2018.10.008}, pmid = {30342053}, issn = {1872-8227}, mesh = {Animals ; Diabetes Mellitus, Type 2/*microbiology ; Dysbiosis/*microbiology ; Fecal Microbiota Transplantation/*methods ; Gastrointestinal Microbiome/*genetics ; Humans ; Mice ; Prebiotics/*microbiology ; Probiotics/*metabolism ; }, abstract = {Alterations in the diversity or structure of gut microbiota known as dysbiosis, may affect metabolic activities, resulting in metabolic disorders, such as obesity and diabetes. The development of more sophisticated methods, such as metagenomics sequencing, PCR-denaturing gradient gel electrophoresis, microarrays and fluorescence in situ hybridization, has expanded our knowledge on gut microbiome. Dysbiosis has been related to increased plasma concentrations of gut microbiota-derived lipopolysaccharide (LPS), which triggers the production of a variety of cytokines and the recruitment of inflammatory cells. Metabolomics have demonstrated that butyrate and propionate suppress weight gain in mice with high fat diet-induced obesity, and acetate has been proven to reduce food intake in healthy mice. The role of prebiotics, probiotics, genetically modified bacteria and fecal microbiota transplantation, as potential therapeutic challenges for type 2 diabetes will be discussed in this review.}, }
@article {pmid30338752, year = {2018}, author = {Abranches, J and Zeng, L and Kajfasz, JK and Palmer, SR and Chakraborty, B and Wen, ZT and Richards, VP and Brady, LJ and Lemos, JA}, title = {Biology of Oral Streptococci.}, journal = {Microbiology spectrum}, volume = {6}, number = {5}, pages = {}, pmid = {30338752}, issn = {2165-0497}, support = {R01 DE022559/DE/NIDCR NIH HHS/United States ; HHSN272200900007C/AI/NIAID NIH HHS/United States ; }, mesh = {Carbohydrate Metabolism ; Dental Caries/microbiology ; Endocarditis/microbiology ; Fermentation ; Humans ; Hydrogen Peroxide/metabolism ; Metagenomics ; Microbiota/physiology ; Mouth/*microbiology ; Phylogeny ; Streptococcus/classification/genetics/pathogenicity/*physiology ; Streptococcus gordonii/metabolism ; Streptococcus mutans ; Streptococcus salivarius/metabolism ; }, abstract = {Bacteria belonging to the genus Streptococcus are the first inhabitants of the oral cavity, which can be acquired right after birth and thus play an important role in the assembly of the oral microbiota. In this article, we discuss the different oral environments inhabited by streptococci and the species that occupy each niche. Special attention is given to the taxonomy of Streptococcus, because this genus is now divided into eight distinct groups, and oral species are found in six of them. Oral streptococci produce an arsenal of adhesive molecules that allow them to efficiently colonize different tissues in the mouth. Also, they have a remarkable ability to metabolize carbohydrates via fermentation, thereby generating acids as byproducts. Excessive acidification of the oral environment by aciduric species such as Streptococcus mutans is directly associated with the development of dental caries. However, less acid-tolerant species such as Streptococcus salivarius and Streptococcus gordonii produce large amounts of alkali, displaying an important role in the acid-base physiology of the oral cavity. Another important characteristic of certain oral streptococci is their ability to generate hydrogen peroxide that can inhibit the growth of S. mutans. Thus, oral streptococci can also be beneficial to the host by producing molecules that are inhibitory to pathogenic species. Lastly, commensal and pathogenic streptococci residing in the oral cavity can eventually gain access to the bloodstream and cause systemic infections such as infective endocarditis.}, }
@article {pmid30336790, year = {2018}, author = {Liu, YR and Delgado-Baquerizo, M and Bi, L and Zhu, J and He, JZ}, title = {Consistent responses of soil microbial taxonomic and functional attributes to mercury pollution across China.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {183}, pmid = {30336790}, issn = {2049-2618}, mesh = {Bacteroidetes/classification/genetics/*growth &amp; development ; Biodiversity ; China ; Environmental Monitoring ; Environmental Pollution/*analysis ; Firmicutes/classification/genetics/*growth &amp; development ; Mercury/*analysis ; Metagenome/genetics ; Methylmercury Compounds/*analysis ; Microbiota/genetics ; Soil/chemistry ; Soil Microbiology ; Soil Pollutants/*analysis ; }, abstract = {BACKGROUND: The ecological consequences of mercury (Hg) pollution-one of the major pollutants worldwide-on microbial taxonomic and functional attributes remain poorly understood and largely unexplored. Using soils from two typical Hg-impacted regions across China, here, we evaluated the role of Hg pollution in regulating bacterial abundance, diversity, and co-occurrence network. We also investigated the associations between Hg contents and the relative abundance of microbial functional genes by analyzing the soil metagenomes from a subset of those sites.<br><br>RESULTS: We found that soil Hg largely influenced the taxonomic and functional attributes of microbial communities in the two studied regions. In general, Hg pollution was negatively related to bacterial abundance, but positively related to the diversity of bacteria in two separate regions. We also found some consistent associations between soil Hg contents and the community composition of bacteria. For example, soil total Hg content was positively related to the relative abundance of Firmicutes and Bacteroidetes in both paddy and upland soils. In contrast, the methylmercury (MeHg) concentration was negatively correlated to the relative abundance of Nitrospirae in the two types of soils. Increases in soil Hg pollution correlated with drastic changes in the relative abundance of ecological clusters within the co-occurrence network of bacterial communities for the two regions. Using metagenomic data, we were also able to detect the effect of Hg pollution on multiple functional genes relevant to key soil processes such as element cycles and Hg transformations (e.g., methylation and reduction).<br><br>CONCLUSIONS: Together, our study provides solid evidence that Hg pollution has predictable and significant effects on multiple taxonomic and functional attributes including bacterial abundance, diversity, and the relative abundance of ecological clusters and functional genes. Our results suggest an increase in soil Hg pollution linked to human activities will lead to predictable shifts in the taxonomic and functional attributes in the Hg-impacted areas, with potential implications for sustainable management of agricultural ecosystems and elsewhere.}, }
@article {pmid30332487, year = {2018}, author = {Wyman, SK and Avila-Herrera, A and Nayfach, S and Pollard, KS}, title = {A most wanted list of conserved microbial protein families with no known domains.}, journal = {PloS one}, volume = {13}, number = {10}, pages = {e0205749}, pmid = {30332487}, issn = {1932-6203}, mesh = {Bacterial Proteins/*chemistry/genetics ; Computational Biology ; *Databases, Nucleic Acid ; Humans ; Metagenome/*genetics ; Metagenomics ; Microbiota/*genetics ; Phylogeny ; Protein Domains/*genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {The number and proportion of genes with no known function are growing rapidly. To quantify this phenomenon and provide criteria for prioritizing genes for functional characterization, we developed a bioinformatics pipeline that identifies robustly defined protein families with no annotated domains, ranks these with respect to phylogenetic breadth, and identifies them in metagenomics data. We applied this approach to 271 965 protein families from the SFams database and discovered many with no functional annotation, including >118 000 families lacking any known protein domain. From these, we prioritized 6 668 conserved protein families with at least three sequences from organisms in at least two distinct classes. These Function Unknown Families (FUnkFams) are present in Tara Oceans Expedition and Human Microbiome Project metagenomes, with distributions associated with sampling environment. Our findings highlight the extent of functional novelty in sequence databases and establish an approach for creating a &quot;most wanted&quot; list of genes to prioritize for further characterization.}, }
@article {pmid30326954, year = {2018}, author = {Korpela, K and Salonen, A and Vepsäläinen, O and Suomalainen, M and Kolmeder, C and Varjosalo, M and Miettinen, S and Kukkonen, K and Savilahti, E and Kuitunen, M and de Vos, WM}, title = {Probiotic supplementation restores normal microbiota composition and function in antibiotic-treated and in caesarean-born infants.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {182}, pmid = {30326954}, issn = {2049-2618}, mesh = {Anti-Bacterial Agents/*administration &amp; dosage ; Bifidobacterium/*classification ; Breast Feeding ; Cesarean Section ; Clostridium/isolation &amp; purification ; Dietary Supplements ; Double-Blind Method ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects/physiology ; Humans ; Infant ; Lactobacillus rhamnosus/*classification ; Male ; Pregnancy ; Probiotics/*administration &amp; dosage ; Propionibacterium/*classification ; Proteobacteria/isolation &amp; purification ; }, abstract = {BACKGROUND: Infants born by caesarean section or receiving antibiotics are at increased risk of developing metabolic, inflammatory and immunological diseases, potentially due to disruption of normal gut microbiota at a critical developmental time window. We investigated whether probiotic supplementation could ameliorate the effects of antibiotic use or caesarean birth on infant microbiota in a double blind, placebo-controlled randomized clinical trial. Mothers were given a multispecies probiotic, consisting of Bifidobacterium breve Bb99 (Bp99 2 × 108 cfu) Propionibacterium freundenreichii subsp. shermanii JS (2 × 109cfu), Lactobacillus rhamnosus Lc705 (5 × 109 cfu) and Lactobacillus rhamnosus GG (5 × 109 cfu) (N = 168 breastfed and 31 formula-fed), or placebo supplement (N = 201 breastfed and 22 formula-fed) during pregnancy, and the infants were given the same supplement. Faecal samples of the infants were collected at 3 months and analyzed using taxonomic, metagenomic and metaproteomic approaches.<br><br>RESULTS: The probiotic supplement had a strong overall impact on the microbiota composition, but the effect depended on the infant's diet. Only breastfed infants showed the expected increase in bifidobacteria and reduction in Proteobacteria and Clostridia. In the placebo group, both birth mode and antibiotic use were significantly associated with altered microbiota composition and function, particularly reduced Bifidobacterium abundance. In the probiotic group, the effects of antibiotics and birth mode were either completely eliminated or reduced.<br><br>CONCLUSIONS: The results indicate that it is possible to correct undesired changes in microbiota composition and function caused by antibiotic treatments or caesarean birth by supplementing infants with a probiotic mixture together with at least partial breastfeeding.<br><br>TRIAL REGISTRATION: clinicaltrials.gov NCT00298337 . Registered March 2, 2006.}, }
@article {pmid30325092, year = {2019}, author = {Zhang, SY and Tsementzi, D and Hatt, JK and Bivins, A and Khelurkar, N and Brown, J and Tripathi, SN and Konstantinidis, KT}, title = {Intensive allochthonous inputs along the Ganges River and their effect on microbial community composition and dynamics.}, journal = {Environmental microbiology}, volume = {21}, number = {1}, pages = {182-196}, doi = {10.1111/1462-2920.14439}, pmid = {30325092}, issn = {1462-2920}, support = {//Georgia Institute of Technology/ ; DEB 1241046//National Science Foundation/ ; }, abstract = {Little is known about microbial communities in the Ganges River, India and how they respond to intensive anthropogenic inputs. Here we applied shotgun metagenomics sequencing to study microbial community dynamics and function in planktonic samples collected along an approximately 700 km river transect, including urban cities and rural settings in upstream waters, before and after the monsoon rainy season. Our results showed that 11%-32% of the microbes represented terrestrial, sewage and human inputs (allochthonous). Sewage inputs significantly contributed to the higher abundance, by 13-fold of human gut microbiome (HG) associated sequences and 2-fold of antibiotic resistance genes (ARGs) in the Ganges relative to other riverine ecosystems in Europe, North and South America. Metagenome-assembled genome sequences (MAGs) representing allochthonous populations were detectable and tractable across the river after 1-2 days of (downstream) transport (> 200 km apart). Only approximately 8% of these MAGs were abundant in U.S. freshwater ecosystems, revealing distinct biodiversity for the Ganges. Microbial communities in the rainy season exhibited increased alpha-diversity and spatial heterogeneity and showed significantly weaker distance-decay patterns compared with the dry season. These results advance our understanding of the Ganges microbial communities and how they respond to anthropogenic pollution.}, }
@article {pmid30309375, year = {2018}, author = {Zepeda Mendoza, ML and Roggenbuck, M and Manzano Vargas, K and Hansen, LH and Brunak, S and Gilbert, MTP and Sicheritz-Pontén, T}, title = {Protective role of the vulture facial skin and gut microbiomes aid adaptation to scavenging.}, journal = {Acta veterinaria Scandinavica}, volume = {60}, number = {1}, pages = {61}, pmid = {30309375}, issn = {1751-0147}, support = {R52-A5062//Lundbeckfonden/ ; }, mesh = {Adaptation, Biological ; Animals ; Animals, Wild/microbiology ; Bacteria/classification/genetics/*isolation &amp; purification ; Falconiformes/*microbiology/physiology ; *Feeding Behavior ; Gastrointestinal Tract/*microbiology ; *Microbiota ; Skin/*microbiology ; }, abstract = {BACKGROUND: Vultures have adapted the remarkable ability to feed on carcasses that may contain microorganisms that would be pathogenic to most other animals. The holobiont concept suggests that the genetic basis of such adaptation may not only lie within their genomes, but additionally in their associated microbes. To explore this, we generated shotgun DNA sequencing datasets of the facial skin and large intestine microbiomes of the black vulture (Coragyps atratus) and the turkey vulture (Cathartes aura). We characterized the functional potential and taxonomic diversity of their microbiomes, the potential pathogenic challenges confronted by vultures, and the microbial taxa and genes that could play a protective role on the facial skin and in the gut.<br><br>RESULTS: We found microbial taxa and genes involved in diseases, such as dermatitis and pneumonia (more abundant on the facial skin), and gas gangrene and food poisoning (more abundant in the gut). Interestingly, we found taxa and functions with potential for playing beneficial roles, such as antilisterial bacteria in the gut, and genes for the production of antiparasitics and insecticides on the facial skin. Based on the identified phages, we suggest that phages aid in the control and possibly elimination, as in phage therapy, of microbes reported as pathogenic to a variety of species. Interestingly, we identified Adineta vaga in the gut, an invertebrate that feeds on dead bacteria and protozoans, suggesting a defensive predatory mechanism. Finally, we suggest a colonization resistance role through biofilm formation played by Fusobacteria and Clostridia in the gut.<br><br>CONCLUSIONS: Our results highlight the importance of complementing genomic analyses with metagenomics in order to obtain a clearer understanding of the host-microbial alliance and show the importance of microbiome-mediated health protection for adaptation to extreme diets, such as scavenging.}, }
@article {pmid30308944, year = {2018}, author = {Fehlbaum, S and Prudence, K and Kieboom, J and Heerikhuisen, M and van den Broek, T and Schuren, FHJ and Steinert, RE and Raederstorff, D}, title = {In Vitro Fermentation of Selected Prebiotics and Their Effects on the Composition and Activity of the Adult Gut Microbiota.}, journal = {International journal of molecular sciences}, volume = {19}, number = {10}, pages = {}, pmid = {30308944}, issn = {1422-0067}, mesh = {*Biodiversity ; Dietary Fiber ; Fatty Acids, Volatile/metabolism ; Feces/microbiology ; Fermentation ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; Metagenomics/methods ; *Prebiotics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Recently, the concept of prebiotics has been revisited to expand beyond non-digestible oligosaccharides, and the requirements for selective stimulation were extended to include microbial groups other than, and additional to, bifidobacteria and lactobacilli. Here, the gut microbiota-modulating effects of well-known and novel prebiotics were studied. An in vitro fermentation screening platform (i-screen) was inoculated with adult fecal microbiota, exposed to different dietary fibers that had a range of concentrations (inulin, alpha-linked galacto-oligosaccharides (alpha-GOS), beta-linked GOS, xylo-oligosaccharides (XOS) from corn cobs and high-fiber sugar cane, and beta-glucan from oats), and compared to a positive fructo-oligosaccharide (FOS) control and a negative control (no fiber addition). All dietary fibers displayed prebiotic activity, with beta-glucan showing more distinct effects on the microbial composition and metabolism compared to the other fibers. Beta-glucan induced the growth of Prevotella and Roseburia with a concomitant increase in propionate production. Inulin and both forms of GOS and XOS had a strong bifidogenic effect on the microbial composition. A dose-response effect was observed for butyrate when exposed to beta-glucan and inulin. The findings of this study support the potential for alpha-GOS, XOS, and oat beta-glucan to serve as novel prebiotics, due to their association with the positive shifts in microbiome composition and short-chain fatty acid production that point to potential health benefits.}, }
@article {pmid30308887, year = {2019}, author = {Coble, AA and Flinders, CA and Homyack, JA and Penaluna, BE and Cronn, RC and Weitemier, K}, title = {eDNA as a tool for identifying freshwater species in sustainable forestry: A critical review and potential future applications.}, journal = {The Science of the total environment}, volume = {649}, number = {}, pages = {1157-1170}, doi = {10.1016/j.scitotenv.2018.08.370}, pmid = {30308887}, issn = {1879-1026}, mesh = {Aquatic Organisms/*chemistry ; DNA/*analysis ; *Environment ; Environmental Monitoring/*methods ; *Forestry ; Fresh Water ; Hydrobiology/*methods ; }, abstract = {Environmental DNA (eDNA) is an emerging biological monitoring tool that can aid in assessing the effects of forestry and forest manufacturing activities on biota. Monitoring taxa across broad spatial and temporal scales is necessary to ensure forest management and forest manufacturing activities meet their environmental goals of maintaining biodiversity. Our objectives are to describe potential applications of eDNA across the wood products supply chain extending from regenerating forests, harvesting, and wood transport, to manufacturing facilities, and to review the current state of the science in this context. To meet our second objective, we summarize the taxa examined with targeted (PCR, qPCR or ddPCR) or metagenomic eDNA methods (eDNA metabarcoding), evaluate how estimated species richness compares between traditional field sampling and eDNA metabarcoding approaches, and compare the geographical representation of prior eDNA studies in freshwater ecosystems to global wood baskets. Potential applications of eDNA include evaluating the effects of forestry and forest manufacturing activities on aquatic biota, delineating fish-bearing versus non fish-bearing reaches, evaluating effectiveness of constructed road crossings for freshwater organism passage, and determining the presence of at-risk species. Studies using targeted eDNA approaches focused on fish, amphibians, and invertebrates, while metagenomic studies focused on fish, invertebrates, and microorganisms. Rare, threatened, or endangered species received the least attention in targeted eDNA research, but are arguably of greatest interest to sustainable forestry and forest manufacturing that seek to preserve freshwater biodiversity. Ultimately, using eDNA methods will enable forestry and forest manufacturing managers to have data-driven prioritization for conservation actions for all freshwater species.}, }
@article {pmid30308248, year = {2018}, author = {Hessler, T and Harrison, STL and Huddy, RJ}, title = {Stratification of microbial communities throughout a biological sulphate reducing up-flow anaerobic packed bed reactor, revealed through 16S metagenomics.}, journal = {Research in microbiology}, volume = {169}, number = {10}, pages = {543-551}, doi = {10.1016/j.resmic.2018.09.003}, pmid = {30308248}, issn = {1769-7123}, mesh = {Anaerobiosis ; Bacteria/classification/*genetics/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Biodiversity ; Bioreactors/*microbiology ; DNA, Bacterial/genetics ; Genome, Bacterial ; Metagenomics ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sulfur Compounds/*metabolism ; }, abstract = {Biological sulphate reduction (BSR) is a promising low-cost treatment of acid rock drainage effluents. In this paper, the system performance and microbial ecology of a lactate supplemented BSR up-flow anaerobic packed bed reactor (UAPBR) are evaluated across reactor height and compared to a continuous stirred tank reactor (CSTR). The biomass concentrations of planktonic and biofilm communities were quantified and subsequently characterised by 16S rRNA gene amplicon sequencing. The defined microbial communities were shown to correlate with differing availability of lactate, volatile fatty acids produced from lactate degradation and sulphate concentration. The UAPBR was able to achieve near complete sulphate conversion at a 4-day hydraulic residence time (HRT) at a sulphate feed concentration of 10.41 mM (1 g/L). The high volumetric sulphate reduction rate of 0.184 mM/L.h achieved in the first third of the reactor was attributed to OTUs present in the planktonic and biofilm communities. While the scavenging of sulphate within the final third of the UAPBR was attributed to an acetate oxidising genus of SRB which was not detected in the lactate-fed CSTR. The detailed analyses of the microbial communities throughout the UAPBR and CSTR contribute to the growing understanding of the impact of the microbial communities of BSR reactors on system performance.}, }
@article {pmid30305166, year = {2018}, author = {Guyomar, C and Legeai, F and Jousselin, E and Mougel, C and Lemaitre, C and Simon, JC}, title = {Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {181}, pmid = {30305166}, issn = {2049-2618}, mesh = {Animals ; Aphids/*microbiology ; Buchnera/classification/genetics/*isolation &amp; purification ; Genome, Bacterial/genetics ; Metagenome/genetics ; Metagenomics ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rickettsia/classification/genetics/*isolation &amp; purification ; Symbiosis/*physiology ; }, abstract = {BACKGROUND: Most metazoans are involved in durable relationships with microbes which can take several forms, from mutualism to parasitism. The advances of NGS technologies and bioinformatics tools have opened opportunities to shed light on the diversity of microbial communities and to give some insights into the functions they perform in a broad array of hosts. The pea aphid is a model system for the study of insect-bacteria symbiosis. It is organized in a complex of biotypes, each adapted to specific host plants. It harbors both an obligatory symbiont supplying key nutrients and several facultative symbionts bringing additional functions to the host, such as protection against biotic and abiotic stresses. However, little is known on how the symbiont genomic diversity is structured at different scales: across host biotypes, among individuals of the same biotype, or within individual aphids, which limits our understanding on how these multi-partner symbioses evolve and interact.<br><br>RESULTS: We present a framework well adapted to the study of genomic diversity and evolutionary dynamics of the pea aphid holobiont from metagenomic read sets, based on mapping to reference genomes and whole genome variant calling. Our results revealed that the pea aphid microbiota is dominated by a few heritable bacterial symbionts reported in earlier works, with no discovery of new microbial associates. However, we detected a large and heterogeneous genotypic diversity associated with the different symbionts of the pea aphid. Partitioning analysis showed that this fine resolution diversity is distributed across the three considered scales. Phylogenetic analyses highlighted frequent horizontal transfers of facultative symbionts between host lineages, indicative of flexible associations between the pea aphid and its microbiota. However, the evolutionary dynamics of symbiotic associations strongly varied depending on the symbiont, reflecting different histories and possible constraints. In addition, at the intra-host scale, we showed that different symbiont strains may coexist inside the same aphid host.<br><br>CONCLUSIONS: We present a methodological framework for the detailed analysis of NGS data from microbial communities of moderate complexity and gave major insights into the extent of diversity in pea aphid-symbiont associations and the range of evolutionary trajectories they could take.}, }
@article {pmid30301312, year = {2018}, author = {Yu, YC and Yum, SJ and Jeon, DY and Jeong, HG}, title = {Analysis of the Microbiota on Lettuce (Lactuca sativa L.) Cultivated in South Korea to Identify Foodborne Pathogens.}, journal = {Journal of microbiology and biotechnology}, volume = {28}, number = {8}, pages = {1318-1331}, doi = {10.4014/jmb.1803.03007}, pmid = {30301312}, issn = {1738-8872}, mesh = {Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; DNA, Bacterial/genetics ; *Food Microbiology ; Foodborne Diseases/*microbiology ; Geography ; Lettuce/*microbiology ; Metagenomics ; Microbial Interactions ; Microbiota/genetics/*physiology ; RNA, Ribosomal, 16S/genetics ; Seasons ; Sequence Analysis, DNA ; }, abstract = {Lettuce (Lactuca sativa L.) is a major ingredient used in many food recipes in South Korea. Lettuce samples were collected during their maximum production period between April and July in order to investigate the microbiota of lettuce during different seasons. 16S rRNA gene-based sequencing was conducted using Illumina MiSeq, and real-time PCR was performed for quantification. The number of total bacterial was greater in lettuce collected in July than in that collected in April, albeit with reduced diversity. The bacterial compositions varied according to the site and season of sample collection. Potential pathogenic species such as Bacillus spp., Enterococcus casseliflavus, Klebsiella pneumoniae, and Pseudomonas aeruginosa showed season-specific differences. Results of the network co-occurrence analysis with core genera correlations showed characteristics of bacterial species in lettuce, and provided clues regarding the role of different microbes, including potential pathogens, in this microbiota. Although further studies are needed to determine the specific effects of regional and seasonal characteristics on the lettuce microbiota, our results imply that the 16S rRNA gene-based sequencing approach can be used to detect pathogenic bacteria in lettuce.}, }
@article {pmid30291903, year = {2018}, author = {Matsumoto, A and Yamagishi, Y and Miyamoto, K and Oka, K and Takahashi, M and Mikamo, H}, title = {Characterization of the vaginal microbiota of Japanese women.}, journal = {Anaerobe}, volume = {54}, number = {}, pages = {172-177}, doi = {10.1016/j.anaerobe.2018.10.001}, pmid = {30291903}, issn = {1095-8274}, mesh = {Adult ; Bacteria/classification/genetics/*isolation &amp; purification ; Female ; Humans ; Japan ; Lactobacillus/classification/genetics/isolation &amp; purification ; *Microbiota ; Phylogeny ; Pregnancy ; Sex Work/statistics &amp; numerical data ; Vagina/*microbiology ; Young Adult ; }, abstract = {The composition of vaginal microbiota changes throughout life in response to health status, sexual activity, and pregnancy. Here the constitution of the vaginal microbiota among non-pregnant women, pregnant woman, and commercial sex workers (CSWs) in Japan were compared. Vaginal samples were obtained from 54 women between January 2014 and February 2015 and the microbiota of each was analyzed by 16S metagenomics as well as cluster and diversity analyses to identify differences. In addition, vaginal Lactobacillus spp. were isolated for comparison. Furthermore, data regarding the use of ritodrine hydrochloride by pregnant women was collected from medical charts. The vaginal microbiota were clustered into three groups. Group 1 was most often dominated by Lactobacillus spp., whereas groups 2 and 3 included not only Lactobacillus spp. but also Bifidobacterium, Atopobium, Prevotella, and Gardnerella spp., in addition to a few other taxa. In non-pregnant women, the proportions of microbes in groups 1, 2, and 3 were 31.8%, 36.4%, and 31.8%, respectively. In pregnant women, the abundance of group 1 microbes was notably greater than that of groups 2 and 3 (66.7% vs. 12.5% and 20.8%, respectively). In CSWs, the prevalence of group 3 microbes was far greater than that of group 1 (87.5% vs. 12.5%, respectively). The alpha diversity of non-pregnant women was significantly greater than that of pregnant women. The detection rate of live Lactobacillus spp. in CSWs was lower than in pregnant and non-pregnant women (25% vs. 50% and 68.2%, respectively). The vaginal microbiota of most pregnant women (60%) who received ritodrine hydrochloride was not dominated by Lactobacillus spp. These results suggest that there were clear differences in the colonization rate of Lactobacillus spp. among non-pregnant, pregnant, and CSW women groups. In addition, the dominance of Lactobacillus may influence the risk of preterm birth among women who received ritodrine hydrochloride during pregnancy.}, }
@article {pmid30285861, year = {2018}, author = {O'Neill, AM and Gallo, RL}, title = {Host-microbiome interactions and recent progress into understanding the biology of acne vulgaris.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {177}, pmid = {30285861}, issn = {2049-2618}, support = {R01 AR074302/AR/NIAMS NIH HHS/United States ; R01 AR069653/AR/NIAMS NIH HHS/United States ; U19 AI117673/AI/NIAID NIH HHS/United States ; R01 AR064781/AR/NIAMS NIH HHS/United States ; R01 AI116576/AI/NIAID NIH HHS/United States ; }, mesh = {Acne Vulgaris/drug therapy/*microbiology ; Dysbiosis/microbiology ; Hair Follicle/*microbiology ; Humans ; Metagenome/genetics ; Microbiota/genetics ; Propionibacterium acnes/*genetics/isolation &amp; purification ; Sebaceous Glands/*microbiology ; Staphylococcus epidermidis/*genetics/isolation &amp; purification ; }, abstract = {Acne is one of the most common skin diseases worldwide and results in major health care costs and significant morbidity to severely affected individuals. However, the pathophysiology of this disorder is not well understood. Host-microbiome interactions that affect both innate and adaptive immune homeostasis appear to be a central factor in this disease, with recent observations suggesting that the composition and activities of the microbiota in acne is perturbed. Staphylococcus epidermidis and Cutibacterium acnes (C. acnes; formerly Propionibacterium acnes) are two major inhabitants of the skin that are thought to contribute to the disease but are also known to promote health by inhibiting the growth and invasion of pathogens. Because C. acnes is ubiquitous in sebaceous-rich skin, it is typically labeled as the etiological agent of acne yet it fails to fulfill all of Koch's postulates. The outdated model of acne progression proposes that increased sebum production promotes over-proliferation of C. acnes in a plugged hair follicle, thereby driving inflammation. In contrast, growing evidence indicates that C. acnes is equally abundant in both unaffected and acne-affected follicles. Moreover, recent advances in metagenomic sequencing of the acne microbiome have revealed a diverse population structure distinct from healthy individuals, uncovering new lineage-specific virulence determinants. In this article, we review recent developments in the interactions of skin microbes with host immunity, discussing the contribution of dysbiosis to the immunobiology of acne and newly emerging skin microbiome-based therapeutics to treat acne.}, }
@article {pmid30281913, year = {2019}, author = {Jusino, MA and Banik, MT and Palmer, JM and Wray, AK and Xiao, L and Pelton, E and Barber, JR and Kawahara, AY and Gratton, C and Peery, MZ and Lindner, DL}, title = {An improved method for utilizing high-throughput amplicon sequencing to determine the diets of insectivorous animals.}, journal = {Molecular ecology resources}, volume = {19}, number = {1}, pages = {176-190}, doi = {10.1111/1755-0998.12951}, pmid = {30281913}, issn = {1755-0998}, support = {//United States Forest Service, Northern Research Station/ ; Hatch Formula Funds//University of Wisconsin-Madison, Wisconsin Agricultural Experiment Station/ ; IOS-1121739//National Science Foundation/ ; IOS-1121807//National Science Foundation/ ; }, mesh = {Animals ; *Chiroptera ; Computational Biology/*methods ; DNA/chemistry/genetics/isolation &amp; purification ; Electron Transport Complex IV/genetics ; Feces/chemistry ; *Feeding Behavior ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/*methods ; }, abstract = {DNA analysis of predator faeces using high-throughput amplicon sequencing (HTS) enhances our understanding of predator-prey interactions. However, conclusions drawn from this technique are constrained by biases that occur in multiple steps of the HTS workflow. To better characterize insectivorous animal diets, we used DNA from a diverse set of arthropods to assess PCR biases of commonly used and novel primer pairs for the mitochondrial gene, cytochrome oxidase C subunit 1 (COI). We compared diversity recovered from HTS of bat guano samples using a commonly used primer pair &quot;ZBJ&quot; to results using the novel primer pair &quot;ANML.&quot; To parameterize our bioinformatics pipeline, we created an arthropod mock community consisting of single-copy (cloned) COI sequences. To examine biases associated with both PCR and HTS, mock community members were combined in equimolar amounts both pre- and post-PCR. We validated our system using guano from bats fed known diets and using composite samples of morphologically identified insects collected in pitfall traps. In PCR tests, the ANML primer pair amplified 58 of 59 arthropod taxa (98%), whereas ZBJ amplified 24-40 of 59 taxa (41%-68%). Furthermore, in an HTS comparison of field-collected samples, the ANML primers detected nearly fourfold more arthropod taxa than the ZBJ primers. The additional arthropods detected include medically and economically relevant insect groups such as mosquitoes. Results revealed biases at both the PCR and sequencing levels, demonstrating the pitfalls associated with using HTS read numbers as proxies for abundance. The use of an arthropod mock community allowed for improved bioinformatics pipeline parameterization.}, }
@article {pmid30272305, year = {2018}, author = {Zhou, S and Cai, Y and Wang, M and Yang, WD and Duan, N}, title = {Oral microbial flora of patients with Sicca syndrome.}, journal = {Molecular medicine reports}, volume = {18}, number = {6}, pages = {4895-4903}, pmid = {30272305}, issn = {1791-3004}, mesh = {Biodiversity ; Case-Control Studies ; Computational Biology/methods ; Female ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Mouth/*microbiology ; Sjogren's Syndrome/*etiology ; }, abstract = {Primary sicca syndrome (pSS) is a systemic autoimmune disease. However, its exact etiology and pathogenesis remain elusive. Various infectious factors have been identified to be closely associated with the occurrence and development of PSS. The present study aimed to assess the composition of the oral microbial flora of patients with pSS in China in order to provide guidance for treatment. The microbial flora of nine patients with pSS and five healthy controls from East China was evaluated in saliva samples using high‑throughput sequencing. A high microbial diversity was detected in the pSS and control groups, with bacteroidetes, firmicutes and proteobacteria constituting the largest phyla in the two groups. Compared with the control group, bacteroidetes and actinobacteria were significantly more abundant in the pSS group, whereas proteobacteria were significantly less abundant. However, no significant differences in bacterial richness and diversity were observed between the two groups. According to a Kyoto Encyclopedia of Genes and Genomes linear discriminant analysis, genes regulating cell apoptosis and the immune and digestive systems were significantly upregulated in the pSS group compared with those in the control group. In conclusion, the present study provided basic data on the flora of the oral cavity in patients with pSS from East China and may serve as a reference for the treatment of this condition.}, }
@article {pmid30271256, year = {2018}, author = {Anslan, S and Nilsson, RH and Wurzbacher, C and Baldrian, P and Leho Tedersoo,  and Bahram, M}, title = {Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding.}, journal = {MycoKeys}, volume = {}, number = {39}, pages = {29-40}, pmid = {30271256}, issn = {1314-4049}, abstract = {Along with recent developments in high-throughput sequencing (HTS) technologies and thus fast accumulation of HTS data, there has been a growing need and interest for developing tools for HTS data processing and communication. In particular, a number of bioinformatics tools have been designed for analysing metabarcoding data, each with specific features, assumptions and outputs. To evaluate the potential effect of the application of different bioinformatics workflow on the results, we compared the performance of different analysis platforms on two contrasting high-throughput sequencing data sets. Our analysis revealed that the computation time, quality of error filtering and hence output of specific bioinformatics process largely depends on the platform used. Our results show that none of the bioinformatics workflows appears to perfectly filter out the accumulated errors and generate Operational Taxonomic Units, although PipeCraft, LotuS and PIPITS perform better than QIIME2 and Galaxy for the tested fungal amplicon dataset. We conclude that the output of each platform requires manual validation of the OTUs by examining the taxonomy assignment values.}, }
@article {pmid30267472, year = {2019}, author = {Suchan, T and Talavera, G and Sáez, L and Ronikier, M and Vila, R}, title = {Pollen metabarcoding as a tool for tracking long-distance insect migrations.}, journal = {Molecular ecology resources}, volume = {19}, number = {1}, pages = {149-162}, doi = {10.1111/1755-0998.12948}, pmid = {30267472}, issn = {1755-0998}, support = {CGL2016-76322//AEI/FEDER, UE/ ; IJCI-2016-29083//MINECO programme Juan de la Cierva Incorporación/ ; LRB16/1015//British Ecological Society/ ; //Polish Academy of Sciences statutory fund/ ; 622716//FP7/ ; WW1-300R-18//National Geographic Society/ ; }, mesh = {Africa ; *Animal Migration ; Animals ; Arabia ; Butterflies/*physiology ; DNA Barcoding, Taxonomic/*methods ; Entomology/*methods ; Mediterranean Region ; Metagenomics/*methods ; Pollen/*genetics ; Spain ; }, abstract = {Insects account for a large portion of Earth's biodiversity and are key players for ecosystems, notably as pollinators. While insect migration is suspected to represent a natural phenomenon of major importance, remarkably little is known about it, except for a few flagship species. The reason for this situation is mainly due to technical limitations in the study of insect movement. Here, we propose using metabarcoding of pollen carried by insects as a method for tracking their migrations. We developed a flexible and simple protocol allowing efficient multiplexing and not requiring DNA extraction, one of the most time-consuming part of metabarcoding protocols, and apply this method to the study of the long-distance migration of the butterfly Vanessa cardui, an emerging model for insect migration. We collected 47 butterfly samples along the Mediterranean coast of Spain in spring and performed metabarcoding of pollen collected from their bodies to test for potential arrivals from the African continent. In total, we detected 157 plant species from 23 orders, most of which (82.8%) were insect-pollinated. Taxa present in Africa-Arabia represented 73.2% of our data set, and 19.1% were endemic to this region, strongly supporting the hypothesis that migratory butterflies colonize southern Europe from Africa in spring. Moreover, our data suggest that a northwards trans-Saharan migration in spring is plausible for early arrivals (February) into Europe, as shown by the presence of Saharan floristic elements. Our results demonstrate the possibility of regular insect-mediated transcontinental pollination, with potential implications for ecosystem functioning, agriculture and plant phylogeography.}, }
@article {pmid30267313, year = {2018}, author = {Song, EJ and Lee, ES and Nam, YD}, title = {Progress of analytical tools and techniques for human gut microbiome research.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {56}, number = {10}, pages = {693-705}, pmid = {30267313}, issn = {1976-3794}, mesh = {Computational Biology/*trends ; Data Analysis ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Metagenomics/*trends ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Massive DNA sequencing studies have expanded our insights and understanding of the ecological and functional characteristics of the gut microbiome. Advanced sequencing technologies allow us to understand the close association of the gut microbiome with human health and critical illnesses. In the future, analyses of the gut microbiome will provide key information associating with human individual health, which will help provide personalized health care for diseases. Numerous molecular biological analysis tools have been rapidly developed and employed for the gut microbiome researches; however, methodological differences among researchers lead to inconsistent data, limiting extensive share of data. It is therefore very essential to standardize the current methodologies and establish appropriate pipelines for human gut microbiome research. Herein, we review the methods and procedures currently available for studying the human gut microbiome, including fecal sample collection, metagenomic DNA extraction, massive DNA sequencing, and data analyses with bioinformatics. We believe that this review will contribute to the progress of gut microbiome research in the clinical and practical aspects of human health.}, }
@article {pmid30266101, year = {2018}, author = {Alneberg, J and Karlsson, CMG and Divne, AM and Bergin, C and Homa, F and Lindh, MV and Hugerth, LW and Ettema, TJG and Bertilsson, S and Andersson, AF and Pinhassi, J}, title = {Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {173}, pmid = {30266101}, issn = {2049-2618}, support = {310039//European Research Council/International ; }, mesh = {Bacteria/classification/*genetics ; Genome, Bacterial/*genetics ; High-Throughput Nucleotide Sequencing ; Metagenome/*genetics ; Microbiota/*genetics ; *Nucleic Acid Amplification Techniques ; Oceans and Seas ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sweden ; Whole Genome Sequencing/*methods ; }, abstract = {BACKGROUND: Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms.<br><br>RESULTS: We compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (average 99.51% sequence identity; range 98.77-99.84%) across overlapping regions (30-80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs.<br><br>CONCLUSIONS: The strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies.}, }
@article {pmid30261940, year = {2018}, author = {Denman, SE and Morgavi, DP and McSweeney, CS}, title = {Review: The application of omics to rumen microbiota function.}, journal = {Animal : an international journal of animal bioscience}, volume = {12}, number = {s2}, pages = {s233-s245}, doi = {10.1017/S175173111800229X}, pmid = {30261940}, issn = {1751-732X}, mesh = {Animals ; Bacteria/*classification/genetics ; Gastrointestinal Microbiome/*genetics ; Gene Expression Profiling/veterinary ; *Genomics ; Livestock ; *Metagenome ; Metagenomics ; Methane/*metabolism ; RNA, Ribosomal, 16S/genetics ; Rumen/metabolism ; }, abstract = {Rumen microbiome profiling uses 16S rRNA (18S rRNA, internal transcribed spacer) gene sequencing, a method that usually sequences a small portion of a single gene and is often biased and varies between different laboratories. Functional information can be inferred from this data, but only for those that are closely related to known annotated species, and even then may not truly reflect the function performed within the environment being studied. Genome sequencing of isolates and metagenome-assembled genomes has now reached a stage where representation of the majority of rumen bacterial genera are covered, but this still only represents a portion of rumen microbial species. The creation of a microbial genome (bins) database with associated functional annotations will provide a consistent reference to allow mapping of RNA-Seq reads for functional gene analysis from within the rumen microbiome. The integration of multiple omic analytics is linking functional gene activity, metabolic pathways and rumen metabolites with the responsible microbiota, supporting our biological understanding of the rumen system. The application of these techniques has advanced our understanding of the major microbial populations and functional pathways that are used in relation to lower methane emissions, higher feed efficiencies and responses to different feeding regimes. Continued and more precise use of these tools will lead to a detailed and comprehensive understanding of compositional and functional capacity and design of techniques for the directed intervention and manipulation of the rumen microbiota towards a desired state.}, }
@article {pmid30260956, year = {2018}, author = {Hunt, KA and Jennings, RM and Inskeep, WP and Carlson, RP}, title = {Multiscale analysis of autotroph-heterotroph interactions in a high-temperature microbial community.}, journal = {PLoS computational biology}, volume = {14}, number = {9}, pages = {e1006431}, pmid = {30260956}, issn = {1553-7358}, support = {U01 EB019416/EB/NIBIB NIH HHS/United States ; }, mesh = {Autotrophic Processes ; Biomass ; Carbon/chemistry ; Computer Simulation ; Electron Transport ; Electrons ; Ferric Compounds/*chemistry ; Genome, Archaeal ; Heterotrophic Processes ; Hot Temperature ; Iron/chemistry ; Metagenomics ; *Microbiota ; Oxygen/chemistry ; Phylogeny ; Sulfides/chemistry ; Sulfolobaceae/*metabolism ; Transcriptome ; }, abstract = {Interactions among microbial community members can lead to emergent properties, such as enhanced productivity, stability, and robustness. Iron-oxide mats in acidic (pH 2-4), high-temperature (> 65 °C) springs of Yellowstone National Park contain relatively simple microbial communities and are well-characterized geochemically. Consequently, these communities are excellent model systems for studying the metabolic activity of individual populations and key microbial interactions. The primary goals of the current study were to integrate data collected in situ with in silico calculations across process-scales encompassing enzymatic activity, cellular metabolism, community interactions, and ecosystem biogeochemistry, as well as to predict and quantify the functional limits of autotroph-heterotroph interactions. Metagenomic and transcriptomic data were used to reconstruct carbon and energy metabolisms of an important autotroph (Metallosphaera yellowstonensis) and heterotroph (Geoarchaeum sp. OSPB) from the studied Fe(III)-oxide mat communities. Standard and hybrid elementary flux mode and flux balance analyses of metabolic models predicted cellular- and community-level metabolic acclimations to simulated environmental stresses, respectively. In situ geochemical analyses, including oxygen depth-profiles, Fe(III)-oxide deposition rates, stable carbon isotopes and mat biomass concentrations, were combined with cellular models to explore autotroph-heterotroph interactions important to community structure-function. Integration of metabolic modeling with in situ measurements, including the relative population abundance of autotrophs to heterotrophs, demonstrated that Fe(III)-oxide mat communities operate at their maximum total community growth rate (i.e. sum of autotroph and heterotroph growth rates), as opposed to net community growth rate (i.e. total community growth rate subtracting autotroph consumed by heterotroph), as predicted from the maximum power principle. Integration of multiscale data with ecological theory provides a basis for predicting autotroph-heterotroph interactions and community-level cellular organization.}, }
@article {pmid30258040, year = {2018}, author = {Taft, DH and Liu, J and Maldonado-Gomez, MX and Akre, S and Huda, MN and Ahmad, SM and Stephensen, CB and Mills, DA}, title = {Bifidobacterial Dominance of the Gut in Early Life and Acquisition of Antimicrobial Resistance.}, journal = {mSphere}, volume = {3}, number = {5}, pages = {}, pmid = {30258040}, issn = {2379-5042}, support = {S10 RR029668/RR/NCRR NIH HHS/United States ; S10 RR027303/RR/NCRR NIH HHS/United States ; F32 HD093185/HD/NICHD NIH HHS/United States ; R01 AT008759/AT/NCCIH NIH HHS/United States ; R01 AT007079/AT/NCCIH NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Bangladesh ; Bifidobacterium/genetics/*physiology ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/*genetics ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Male ; Metagenomics ; Probiotics/therapeutic use ; Regression Analysis ; }, abstract = {Bifidobacterium species are important commensals capable of dominating the infant gut microbiome, in part by producing acids that suppress growth of other taxa. Bifidobacterium species are less prone to possessing antimicrobial resistance (AMR) genes (ARGs) than other taxa that may colonize infants. Given that AMR is a growing public health crisis and ARGs are present in the gut microbiome of humans from early life, this study examines the correlation between a Bifidobacterium-dominated infant gut microbiome and AMR levels, measured by a culture-independent metagenomic approach both in early life and as infants become toddlers. In general, Bifidobacterium dominance is associated with a significant reduction in AMR in a Bangladeshi cohort, both in the number of acquired AMR genes present and in the abundance of AMR genes. However, by year 2, Bangladeshi infants had no significant differences in AMR related to their early-life Bifidobacterium levels. A generalized linear model including all infants in a previously published Swedish cohort found a significant negative association between log-transformed total AMR and Bifidobacterium levels, thus confirming the relationship between Bifidobacterium levels and AMR. In both cohorts, there was no change between early-life and later-life AMR abundance in high-Bifidobacterium infants but a significant reduction in AMR abundance in low-Bifidobacterium infants. These results support the hypothesis that early Bifidobacterium dominance of the infant gut microbiome may help reduce colonization by taxa containing ARGs.IMPORTANCE Infants are vulnerable to an array of infectious diseases, and as the gut microbiome may serve as a reservoir of AMR for pathogens, reducing the levels of AMR in infants is important to infant health. This study demonstrates that high levels of Bifidobacterium are associated with reduced levels of AMR in early life and suggests that probiotic interventions to increase infant Bifidobacterium levels have the potential to reduce AMR in infants. However, this effect is not sustained at year 2 of age in Bangladeshi infants, underscoring the need for more detailed studies of the biogeography and timing of infant AMR acquisition.}, }
@article {pmid30250208, year = {2018}, author = {Pärnänen, K and Karkman, A and Hultman, J and Lyra, C and Bengtsson-Palme, J and Larsson, DGJ and Rautava, S and Isolauri, E and Salminen, S and Kumar, H and Satokari, R and Virta, M}, title = {Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {3891}, pmid = {30250208}, issn = {2041-1723}, mesh = {Anti-Bacterial Agents/*adverse effects ; Antibiotic Prophylaxis/adverse effects ; Breast Feeding ; Drug Resistance, Bacterial/*genetics ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/drug effects/*genetics ; Humans ; Infant ; Interspersed Repetitive Sequences/*genetics ; Maternal Inheritance ; Metagenomics ; Milk, Human/*microbiology ; Phylogeny ; Time Factors ; }, abstract = {The infant gut microbiota has a high abundance of antibiotic resistance genes (ARGs) compared to adults, even in the absence of antibiotic exposure. Here we study potential sources of infant gut ARGs by performing metagenomic sequencing of breast milk, as well as infant and maternal gut microbiomes. We find that fecal ARG and mobile genetic element (MGE) profiles of infants are more similar to those of their own mothers than to those of unrelated mothers. MGEs in mothers' breast milk are also shared with their own infants. Termination of breastfeeding and intrapartum antibiotic prophylaxis of mothers, which have the potential to affect microbial community composition, are associated with higher abundances of specific ARGs, the composition of which is largely shaped by bacterial phylogeny in the infant gut. Our results suggest that infants inherit the legacy of past antibiotic consumption of their mothers via transmission of genes, but microbiota composition still strongly impacts the overall resistance load.}, }
@article {pmid30249182, year = {2018}, author = {Cavalcanti, GS and Shukla, P and Morris, M and Ribeiro, B and Foley, M and Doane, MP and Thompson, CC and Edwards, MS and Dinsdale, EA and Thompson, FL}, title = {Rhodoliths holobionts in a changing ocean: host-microbes interactions mediate coralline algae resilience under ocean acidification.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {701}, pmid = {30249182}, issn = {1471-2164}, mesh = {Biodiversity ; Hydrogen-Ion Concentration ; Metagenome ; *Microbiota/genetics ; Oceans and Seas ; Photosynthesis ; Rhodophyta/metabolism/*microbiology/physiology ; Seawater/chemistry/microbiology ; Stress, Physiological ; }, abstract = {BACKGROUND: Life in the ocean will increasingly have to contend with a complex matrix of concurrent shifts in environmental properties that impact their physiology and control their life histories. Rhodoliths are coralline red algae (Corallinales, Rhodophyta) that are photosynthesizers, calcifiers, and ecosystem engineers and therefore represent important targets for ocean acidification (OA) research. Here, we exposed live rhodoliths to near-future OA conditions to investigate responses in their photosynthetic capacity, calcium carbonate production, and associated microbiome using carbon uptake, decalcification assays, and whole genome shotgun sequencing metagenomic analysis, respectively. The results from our live rhodolith assays were compared to similar manipulations on dead rhodolith (calcareous skeleton) biofilms and water column microbial communities, thereby enabling the assessment of host-microbiome interaction under climate-driven environmental perturbations.<br><br>RESULTS: Under high pCO2 conditions, live rhodoliths exhibited positive physiological responses, i.e. increased photosynthetic activity, and no calcium carbonate biomass loss over time. Further, whereas the microbiome associated with live rhodoliths remained stable and resembled a healthy holobiont, the microbial community associated with the water column changed after exposure to elevated pCO2.<br><br>CONCLUSIONS: Our results suggest that a tightly regulated microbial-host interaction, as evidenced by the stability of the rhodolith microbiome recorded here under OA-like conditions, is important for host resilience to environmental stress. This study extends the scarce comprehension of microbes associated with rhodolith beds and their reaction to increased pCO2, providing a more comprehensive approach to OA studies by assessing the host holobiont.}, }
@article {pmid30248115, year = {2018}, author = {Kurobe, T and Lehman, PW and Hammock, BG and Bolotaolo, MB and Lesmeister, S and Teh, SJ}, title = {Biodiversity of cyanobacteria and other aquatic microorganisms across a freshwater to brackish water gradient determined by shotgun metagenomic sequencing analysis in the San Francisco Estuary, USA.}, journal = {PloS one}, volume = {13}, number = {9}, pages = {e0203953}, pmid = {30248115}, issn = {1932-6203}, mesh = {Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; Chlorophyta/classification/genetics ; Cyanobacteria/classification/*genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; Diatoms/classification/genetics/isolation &amp; purification ; Estuaries ; Fresh Water/microbiology ; Genotype ; Harmful Algal Bloom ; Metagenomics ; Microcystis/genetics/isolation &amp; purification ; Phylogeny ; Polymerase Chain Reaction ; Saline Waters ; Salinity ; San Francisco ; Spatio-Temporal Analysis ; *Water Microbiology ; }, abstract = {Blooms of Microcystis and other harmful cyanobacteria can degrade water quality by producing cyanotoxins or other toxic compounds. The goals of this study were (1) to facilitate understanding of community structure for various aquatic microorganisms in brackish water and freshwater regions with emphasis on cyanobacteria, and (2) to test a hypothesis that Microcystis genotypes that tolerate higher salinity were blooming in brackish water environments during the severe drought, 2014. Shotgun metagenomic analysis revealed that cyanobacteria dominated the brackish water region while bacteria dominated the freshwater region. A group of cyanobacteria (e.g., Aphanizomenon, Microcystis, Planktothrix, Pseudanabaena), bacteria (e.g., Bacillus, Porphyrobacter), and diatoms (Phaeodactylum and Thalassiosira) were abundant in the brackish water region. In contrast, Hassallia (cyanobacteria) and green algae (Nannochloropsis, Chlamydomonas, and Volvox) were abundant in the landward freshwater region. Station variation was also apparent. One landward sampling station located downstream of an urbanized area differed substantially from the other stations in terms of both water chemistry and community structure, with a higher percentage of arthropods, green algae, and eukaryotes. Screening of the Microcystis internal transcribed spacer region revealed six representative genotypes, and two of which were successfully quantified using qPCR (Genotypes I and VI). Both genotypes occurred predominantly in the freshwater region, so the data from this study did not support the hypothesis that salinity tolerant Microcystis genotypes bloomed in the brackish water region in 2014.}, }
@article {pmid30242595, year = {2018}, author = {Hemmat-Jou, MH and Safari-Sinegani, AA and Mirzaie-Asl, A and Tahmourespour, A}, title = {Analysis of microbial communities in heavy metals-contaminated soils using the metagenomic approach.}, journal = {Ecotoxicology (London, England)}, volume = {27}, number = {9}, pages = {1281-1291}, pmid = {30242595}, issn = {1573-3017}, mesh = {Environmental Monitoring/*methods ; Metagenome ; *Metagenomics ; Metals, Heavy/*toxicity ; Soil ; *Soil Microbiology ; Soil Pollutants/*toxicity ; }, abstract = {Soil pollution occurring at mining sites has adverse impacts on soil microbial diversity. New approaches, such as metagenomics approach, have become a powerful tool to investigate biodiversity of soil microbial communities. In the current study, metagenomics approach was used to investigate the microbial diversity of soils contaminated with different concentrations of lead (Pb) and zinc (Zn). The contaminated soils were collected from a Pb and Zn mine. The soil total DNA was extracted and 16S rDNA genes were amplified using universal primers. The PCR amplicons were sequenced and bioinformatic analysis of metagenomes was conducted to identify prokaryotic diversity in the Pb- and Zn-contaminated soils. The results indicated that the ten most abundant bacteria in all samples were Solirubrobacter (Actinobacteria), Geobacter (Proteobacteria), Edaphobacter (Acidobacteria), Pseudomonas (Proteobacteria), Gemmatiomonas (Gemmatimonadetes), Nitrosomonas, Xanthobacter, and Sphingomonas (Proteobacteria), Pedobacter (Bacterioidetes), and Ktedonobacter (Chloroflexi), descendingly. Archaea were also numerous, and Nitrososphaerales which are important in the nitrogen cycle had the highest abundance in the samples. Although, alpha and beta diversity showed negative effects of Pb and Zn contamination on soil microbial communities, microbial diversity of the contaminated soils was not subjected to a significant change. This study provided valuable insights into microbial composition in heavy metals-contaminated soils.}, }
@article {pmid30240699, year = {2018}, author = {Harris, L and van Zyl, LJ and Kirby-McCullough, BM and Damelin, LH and Tiemessen, CT and Trindade, M}, title = {Identification and sequence analysis of two novel cryptic plasmids isolated from the vaginal mucosa of South African women.}, journal = {Plasmid}, volume = {98}, number = {}, pages = {56-62}, doi = {10.1016/j.plasmid.2018.09.008}, pmid = {30240699}, issn = {1095-9890}, mesh = {DNA, Bacterial/*genetics ; Female ; Humans ; Lactobacillus/classification/*genetics/*isolation &amp; purification/metabolism ; Microbiota ; Mucous Membrane/*microbiology ; Phylogeny ; Plasmids/chemistry/*genetics ; Sequence Analysis, DNA ; South Africa/epidemiology ; Vagina/*microbiology ; Vaginosis, Bacterial/epidemiology/*microbiology ; }, abstract = {The vaginal mucosa is dominated by Gram positive, rod shaped lactobacilli which serve as a natural barrier against infection. In both healthy- and bacterial vaginosis (BV)-infected women Lactobacillus crispatus and Lactobacillus jensenii have been found to be the predominant Lactobacillus species. Many studies have been conducted to assess factors influencing lactobacilli dominance in the vaginal microbiome. In the present study two plasmids, pLc4 and pLc17, isolated from vaginal Lactobacillus strains of both healthy and BV-infected women were characterized. The smaller plasmid, pLc4 (4224 bp), was detected in both L. crispatus and L. jensenii strains, while pLc17 was only detected in L. crispatus. Based on its nucleotide sequence pLc4 appears highly novel, with its replication protein having 44% identity to the replication initiation protein of pSMQ173b_03. Phylogenetic analysis with other Rolling Circle Replication plasmids confirmed that pLc4 shows a low degree of similarity to these plasmids. Plasmid pLc17 (16,663 bp) appears to carry both a RCR replicon and a theta replicon, which is rare in naturally occurring plasmids. pLc4 was maintained at a high copy number of 29, while pLc17 appears to be a medium copy number plasmid maintained at 11 copies per chromosome. While sequence analysis is a valuable tool to study cryptic plasmids, further function-based analysis will be required in order to fully elucidate the role of these plasmids within the vaginal milieu.}, }
@article {pmid30240114, year = {2019}, author = {Bergner, LM and Orton, RJ and da Silva Filipe, A and Shaw, AE and Becker, DJ and Tello, C and Biek, R and Streicker, DG}, title = {Using noninvasive metagenomics to characterize viral communities from wildlife.}, journal = {Molecular ecology resources}, volume = {19}, number = {1}, pages = {128-143}, doi = {10.1111/1755-0998.12946}, pmid = {30240114}, issn = {1755-0998}, support = {//Wellcome Trust/United Kingdom ; 102507/Z/13/Z//Sir Henry Dale Fellowship, jointly funded by the Wellcome Trust and Royal Society/ ; 102507/Z/13/A//Wellcome-Beit Prize/ ; MC_UU_12014/12//Medical Research Council/United Kingdom ; }, mesh = {Animals ; Biodiversity ; Chiroptera/*virology ; Feces/virology ; Metagenomics/*methods ; Oropharynx/virology ; Peru ; Sequence Analysis, DNA/*methods ; Specimen Handling/*methods ; Virus Diseases/*veterinary/virology ; Viruses/*classification/*genetics ; }, abstract = {Microbial communities play an important role in organismal and ecosystem health. While high-throughput metabarcoding has revolutionized the study of bacterial communities, generating comparable viral communities has proven elusive, particularly in wildlife samples where the diversity of viruses and limited quantities of viral nucleic acid present distinctive challenges. Metagenomic sequencing is a promising solution for studying viral communities, but the lack of standardized methods currently precludes comparisons across host taxa or localities. Here, we developed an untargeted shotgun metagenomic sequencing protocol to generate comparable viral communities from noninvasively collected faecal and oropharyngeal swabs. Using samples from common vampire bats (Desmodus rotundus), a key species for virus transmission to humans and domestic animals, we tested how different storage media, nucleic acid extraction procedures and enrichment steps affect viral community detection. Based on finding viral contamination in foetal bovine serum, we recommend storing swabs in RNAlater or another nonbiological medium. We recommend extracting nucleic acid directly from swabs rather than from supernatant or pelleted material, which had undetectable levels of viral RNA. Results from a low-input RNA library preparation protocol suggest that ribosomal RNA depletion and light DNase treatment reduce host and bacterial nucleic acid, and improve virus detection. Finally, applying our approach to twelve pooled samples from seven localities in Peru, we showed that detected viral communities saturated at the attained sequencing depth, allowing unbiased comparisons of viral community composition. Future studies using the methods outlined here will elucidate the determinants of viral communities across host species, environments and time.}, }
@article {pmid30232167, year = {2018}, author = {Ingala, MR and Simmons, NB and Perkins, SL}, title = {Bats Are an Untapped System for Understanding Microbiome Evolution in Mammals.}, journal = {mSphere}, volume = {3}, number = {5}, pages = {}, pmid = {30232167}, issn = {2379-5042}, mesh = {Animals ; Chiroptera/*microbiology ; *Diet ; Ecology ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; *Metagenomics ; Phylogeny ; }, abstract = {Mammals evolved in a microbial world, and consequently, microbial symbionts have played a role in their evolution. An exciting new subdiscipline of metagenomics considers the ways in which microbes, particularly those found in the gut, have facilitated the ecological and phylogenetic radiation of mammals. However, the vast majority of such studies focus on domestic animals, laboratory models, or charismatic megafauna (e.g., pandas and chimpanzees). The result is a plethora of studies covering few taxa across the mammal tree of life, leaving broad patterns of microbiome function and evolution unclear. Wildlife microbiome research urgently needs a model system in which to test hypotheses about metagenomic involvement in host ecology and evolution. We propose that bats (Order: Chiroptera) represent a model system ideal for comparative microbiome research, affording opportunities to examine host phylogeny, diet, and other natural history characteristics in relation to the evolution of the gut microbiome.}, }
@article {pmid30231921, year = {2018}, author = {Vavourakis, CD and Andrei, AS and Mehrshad, M and Ghai, R and Sorokin, DY and Muyzer, G}, title = {A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {168}, pmid = {30231921}, issn = {2049-2618}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification/metabolism ; Carbon Cycle ; Genetic Variation ; Genome, Bacterial ; Geologic Sediments/analysis/*microbiology ; Lakes/analysis/*microbiology ; Metagenome ; Metagenomics ; Microbiota ; Nitrogen Cycle ; Phylogeny ; Sodium Chloride/analysis ; }, abstract = {BACKGROUND: Hypersaline soda lakes are characterized by extreme high soluble carbonate alkalinity. Despite the high pH and salt content, highly diverse microbial communities are known to be present in soda lake brines but the microbiome of soda lake sediments received much less attention of microbiologists. Here, we performed metagenomic sequencing on soda lake sediments to give the first extensive overview of the taxonomic diversity found in these complex, extreme environments and to gain novel physiological insights into the most abundant, uncultured prokaryote lineages.<br><br>RESULTS: We sequenced five metagenomes obtained from four surface sediments of Siberian soda lakes with a pH 10 and a salt content between 70 and 400 g L-1. The recovered 16S rRNA gene sequences were mostly from Bacteria, even in the salt-saturated lakes. Most OTUs were assigned to uncultured families. We reconstructed 871 metagenome-assembled genomes (MAGs) spanning more than 45 phyla and discovered the first extremophilic members of the Candidate Phyla Radiation (CPR). Five new species of CPR were among the most dominant community members. Novel dominant lineages were found within previously well-characterized functional groups involved in carbon, sulfur, and nitrogen cycling. Moreover, key enzymes of the Wood-Ljungdahl pathway were encoded within at least four bacterial phyla never previously associated with this ancient anaerobic pathway for carbon fixation and dissimilation, including the Actinobacteria.<br><br>CONCLUSIONS: Our first sequencing effort of hypersaline soda lake sediment metagenomes led to two important advances. First, we showed the existence and obtained the first genomes of haloalkaliphilic members of the CPR and several hundred other novel prokaryote lineages. The soda lake CPR is a functionally diverse group, but the most abundant organisms in this study are likely fermenters with a possible role in primary carbon degradation. Second, we found evidence for the presence of the Wood-Ljungdahl pathway in many more taxonomic groups than those encompassing known homo-acetogens, sulfate-reducers, and methanogens. Since only few environmental metagenomics studies have targeted sediment microbial communities and never to this extent, we expect that our findings are relevant not only for the understanding of haloalkaline environments but can also be used to set targets for future studies on marine and freshwater sediments.}, }
@article {pmid30227897, year = {2018}, author = {Arora-Williams, K and Olesen, SW and Scandella, BP and Delwiche, K and Spencer, SJ and Myers, EM and Abraham, S and Sooklal, A and Preheim, SP}, title = {Dynamics of microbial populations mediating biogeochemical cycling in a freshwater lake.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {165}, pmid = {30227897}, issn = {2049-2618}, mesh = {Bacteria/classification/isolation &amp; purification/metabolism ; Carbon/chemistry/metabolism ; Ecosystem ; Lakes/*chemistry/*microbiology ; Metagenome ; Metagenomics ; Methane/chemistry/metabolism ; *Microbiota ; Oxidation-Reduction ; Oxygen/chemistry/metabolism ; }, abstract = {BACKGROUND: Microbial processes are intricately linked to the depletion of oxygen in in-land and coastal water bodies, with devastating economic and ecological consequences. Microorganisms deplete oxygen during biomass decomposition, degrading the habitat of many economically important aquatic animals. Microbes then turn to alternative electron acceptors, which alter nutrient cycling and generate potent greenhouse gases. As oxygen depletion is expected to worsen with altered land use and climate change, understanding how chemical and microbial dynamics impact dead zones will aid modeling efforts to guide remediation strategies. More work is needed to understand the complex interplay between microbial genes, populations, and biogeochemistry during oxygen depletion.<br><br>RESULTS: Here, we used 16S rRNA gene surveys, shotgun metagenomic sequencing, and a previously developed biogeochemical model to identify genes and microbial populations implicated in major biogeochemical transformations in a model lake ecosystem. Shotgun metagenomic sequencing was done for one time point in Aug., 2013, and 16S rRNA gene sequencing was done for a 5-month time series (Mar.-Aug., 2013) to capture the spatiotemporal dynamics of genes and microorganisms mediating the modeled processes. Metagenomic binning analysis resulted in many metagenome-assembled genomes (MAGs) that are implicated in the modeled processes through gene content similarity to cultured organism and the presence of key genes involved in these pathways. The MAGs suggested some populations are capable of methane and sulfide oxidation coupled to nitrate reduction. Using the model, we observe that modulating these processes has a substantial impact on overall lake biogeochemistry. Additionally, 16S rRNA gene sequences from the metagenomic and amplicon libraries were linked to processes through the MAGs. We compared the dynamics of microbial populations in the water column to the model predictions. Many microbial populations involved in primary carbon oxidation had dynamics similar to the model, while those associated with secondary oxidation processes deviated substantially.<br><br>CONCLUSIONS: This work demonstrates that the unique capabilities of resident microbial populations will substantially impact the concentration and speciation of chemicals in the water column, unless other microbial processes adjust to compensate for these differences. It further highlights the importance of the biological aspects of biogeochemical processes, such as fluctuations in microbial population dynamics. Integrating gene and population dynamics into biogeochemical models has the potential to improve predictions of the community response under altered scenarios to guide remediation efforts.}, }
@article {pmid30225935, year = {2019}, author = {Drinkwater, R and Schnell, IB and Bohmann, K and Bernard, H and Veron, G and Clare, E and Gilbert, MTP and Rossiter, SJ}, title = {Using metabarcoding to compare the suitability of two blood-feeding leech species for sampling mammalian diversity in North Borneo.}, journal = {Molecular ecology resources}, volume = {19}, number = {1}, pages = {105-117}, doi = {10.1111/1755-0998.12943}, pmid = {30225935}, issn = {1755-0998}, support = {SAS-2016-100//The Leverhulme Trust/ ; NE/K016148/1//Natural Environment Research Council/ ; DFF 5051-00140//The Danish Council for Independent Research/ ; }, mesh = {Animals ; Borneo ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal/chemistry/genetics ; *Feeding Behavior ; High-Throughput Nucleotide Sequencing ; *Host Specificity ; Leeches/*physiology ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The application of high-throughput sequencing (HTS) for metabarcoding of mixed samples offers new opportunities in conservation biology. Recently, the successful detection of prey DNA from the guts of leeches has raised the possibility that these, and other blood-feeding invertebrates, might serve as useful samplers of mammals. Yet little is known about whether sympatric leech species differ in their feeding preferences, and whether this has a bearing on their relative suitability for monitoring local mammalian diversity. To address these questions, we collected spatially matched samples of two congeneric leech species Haemadipsa picta and Haemadipsa sumatrana from lowland rainforest in Borneo. For each species, we pooled ~500 leeches into batches of 10 individuals, performed PCR to target a section of the mammalian 16S rRNA locus and undertook sequencing of amplicon libraries using an Illumina MiSeq. In total, we identified sequences from 14 mammalian genera, spanning nine families and five orders. We found greater numbers of detections, and higher diversity of OTUs, in H. picta compared with H. sumatrana, with rodents only present in the former leech species. However, comparison of samples from across the landscape revealed no significant difference in mammal community composition between the leech species. We therefore suggest that H. picta is the more suitable iDNA sampler in this degraded Bornean forest. We conclude that the choice of invertebrate sampler can influence the detectability of different mammal groups and that this should be accounted for when designing iDNA studies.}, }
@article {pmid30219103, year = {2018}, author = {Uritskiy, GV and DiRuggiero, J and Taylor, J}, title = {MetaWRAP-a flexible pipeline for genome-resolved metagenomic data analysis.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {158}, pmid = {30219103}, issn = {2049-2618}, support = {R01 AI134384/AI/NIAID NIH HHS/United States ; T32 GM007231/GM/NIGMS NIH HHS/United States ; U41 HG006620/HG/NHGRI NIH HHS/United States ; }, mesh = {Algorithms ; Bacteria/classification/genetics/isolation &amp; purification ; Data Analysis ; Data Mining ; Gastrointestinal Microbiome ; *Genome, Bacterial ; Humans ; Metagenome ; Metagenomics/*methods ; *Software ; }, abstract = {BACKGROUND: The study of microbiomes using whole-metagenome shotgun sequencing enables the analysis of uncultivated microbial populations that may have important roles in their environments. Extracting individual draft genomes (bins) facilitates metagenomic analysis at the single genome level. Software and pipelines for such analysis have become diverse and sophisticated, resulting in a significant burden for biologists to access and use them. Furthermore, while bin extraction algorithms are rapidly improving, there is still a lack of tools for their evaluation and visualization.<br><br>RESULTS: To address these challenges, we present metaWRAP, a modular pipeline software for shotgun metagenomic data analysis. MetaWRAP deploys state-of-the-art software to handle metagenomic data processing starting from raw sequencing reads and ending in metagenomic bins and their analysis. MetaWRAP is flexible enough to give investigators control over the analysis, while still being easy-to-install and easy-to-use. It includes hybrid algorithms that leverage the strengths of a variety of software to extract and refine high-quality bins from metagenomic data through bin consolidation and reassembly. MetaWRAP's hybrid bin extraction algorithm outperforms individual binning approaches and other bin consolidation programs in both synthetic and real data sets. Finally, metaWRAP comes with numerous modules for the analysis of metagenomic bins, including taxonomy assignment, abundance estimation, functional annotation, and visualization.<br><br>CONCLUSIONS: MetaWRAP is an easy-to-use modular pipeline that automates the core tasks in metagenomic analysis, while contributing significant improvements to the extraction and interpretation of high-quality metagenomic bins. The bin refinement and reassembly modules of metaWRAP consistently outperform other binning approaches. Each module of metaWRAP is also a standalone component, making it a flexible and versatile tool for tackling metagenomic shotgun sequencing data. MetaWRAP is open-source software available at https://github.com/bxlab/metaWRAP .}, }
@article {pmid30217078, year = {2018}, author = {Li, Y and Hingamp, P and Watai, H and Endo, H and Yoshida, T and Ogata, H}, title = {Degenerate PCR Primers to Reveal the Diversity of Giant Viruses in Coastal Waters.}, journal = {Viruses}, volume = {10}, number = {9}, pages = {}, pmid = {30217078}, issn = {1999-4915}, support = {203143100025//Canon Foundation for Scientific Research/International ; 16KT0020//Japan Society for the Promotion of Science/International ; 17H03850//Japan Society for the Promotion of Science/International ; 26430184//Japan Society for the Promotion of Science/International ; 2016-28//Institute for Chemical Research, Kyoto University/International ; 2017-25//Institute for Chemical Research, Kyoto University/International ; ANR-11-BTBR-0008//French Investments for the Future program/International ; }, mesh = {*Biodiversity ; Computational Biology/methods ; Genome, Viral ; Giant Viruses/*classification/*genetics ; Metagenome ; Metagenomics/methods ; Phylogeny ; *Polymerase Chain Reaction/methods ; Seawater/*virology ; *Water Microbiology ; }, abstract = {&quot;Megaviridae&quot; is a proposed family of giant viruses infecting unicellular eukaryotes. These viruses are ubiquitous in the sea and have impact on marine microbial community structure and dynamics through their lytic infection cycle. However, their diversity and biogeography have been poorly characterized due to the scarce detection of Megaviridae sequences in metagenomes, as well as the limitation of reference sequences used to design specific primers for this viral group. Here, we propose a set of 82 degenerated primers (referred to as MEGAPRIMER), targeting DNA polymerase genes (polBs) of Megaviridae. MEGAPRIMER was designed based on 921 Megaviridae polBs from sequenced genomes and metagenomes. By applying this primer set to environmental DNA meta-barcoding of a coastal seawater sample, we report 5595 non-singleton operational taxonomic units (OTUs) of Megaviridae at 97% nucleotide sequence identity. The majority of the OTUs were found to form diverse clades, which were phylogenetically distantly phylogenetically related to known viruses such as Mimivirus. The Megaviridae OTUs detected in this study outnumber the giant virus OTUs identified in previous individual studies by more than an order of magnitude. Hence, MEGAPRIMER represents a useful tool to study the diversity of Megaviridae at the population level in natural environments.}, }
@article {pmid30213145, year = {2018}, author = {Gómez-Villegas, P and Vigara, J and León, R}, title = {Characterization of the Microbial Population Inhabiting a Solar Saltern Pond of the Odiel Marshlands (SW Spain).}, journal = {Marine drugs}, volume = {16}, number = {9}, pages = {}, pmid = {30213145}, issn = {1660-3397}, support = {0055_ALGARED_PLUS_5_E//INTERREG VA España-Portugal (POCTEP) 2014-2020 Cooperation Program/ ; }, mesh = {Bacteroidetes/*genetics/isolation &amp; purification ; Biodiversity ; Biotechnology/methods ; DNA, Bacterial/isolation &amp; purification ; Genetic Variation ; Halobacteriales/*genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Salinity ; Sequence Analysis, DNA ; Spain ; *Water Microbiology ; Wetlands ; }, abstract = {The solar salterns located in the Odiel marshlands, in southwest Spain, are an excellent example of a hypersaline environment inhabited by microbial populations specialized in thriving under conditions of high salinity, which remains poorly explored. Traditional culture-dependent taxonomic studies have usually under-estimated the biodiversity in saline environments due to the difficulties that many of these species have to grow at laboratory conditions. Here we compare two molecular methods to profile the microbial population present in the Odiel saltern hypersaline water ponds (33% salinity). On the one hand, the construction and characterization of two clone PCR amplified-16S rRNA libraries, and on the other, a high throughput 16S rRNA sequencing approach based on the Illumina MiSeq platform. The results reveal that both methods are comparable for the estimation of major genera, although massive sequencing provides more information about the less abundant ones. The obtained data indicate that Salinibacter ruber is the most abundant genus, followed by the archaea genera, Halorubrum and Haloquadratum. However, more than 100 additional species can be detected by Next Generation Sequencing (NGS). In addition, a preliminary study to test the biotechnological applications of this microbial population, based on its ability to produce and excrete haloenzymes, is shown.}, }
@article {pmid30209011, year = {2018}, author = {Shade, A and Dunn, RR and Blowes, SA and Keil, P and Bohannan, BJM and Herrmann, M and Küsel, K and Lennon, JT and Sanders, NJ and Storch, D and Chase, J}, title = {Macroecology to Unite All Life, Large and Small.}, journal = {Trends in ecology &amp; evolution}, volume = {33}, number = {10}, pages = {731-744}, doi = {10.1016/j.tree.2018.08.005}, pmid = {30209011}, issn = {1872-8383}, mesh = {*Biodiversity ; Ecology/classification/*methods ; }, abstract = {Macroecology is the study of the mechanisms underlying general patterns of ecology across scales. Research in microbial ecology and macroecology have long been detached. Here, we argue that it is time to bridge the gap, as they share a common currency of species and individuals, and a common goal of understanding the causes and consequences of changes in biodiversity. Microbial ecology and macroecology will mutually benefit from a unified research agenda and shared datasets that span the entirety of the biodiversity of life and the geographic expanse of the Earth.}, }
@article {pmid30205462, year = {2018}, author = {Hidalgo-Cantabrana, C and Sanozky-Dawes, R and Barrangou, R}, title = {Insights into the Human Virome Using CRISPR Spacers from Microbiomes.}, journal = {Viruses}, volume = {10}, number = {9}, pages = {}, pmid = {30205462}, issn = {1999-4915}, support = {support//North Carolina Agricultural Foundation/International ; internal support//North Carolina State University/International ; }, mesh = {*Biodiversity ; Clustered Regularly Interspaced Short Palindromic Repeats ; Humans ; Metagenomics ; *Microbiota ; Viruses/*classification/genetics/*isolation &amp; purification ; }, abstract = {Due to recent advances in next-generation sequencing over the past decade, our understanding of the human microbiome and its relationship to health and disease has increased dramatically. Yet, our insights into the human virome, and its interplay with important microbes that impact human health, is relatively limited. Prokaryotic and eukaryotic viruses are present throughout the human body, comprising a large and diverse population which influences several niches and impacts our health at various body sites. The presence of prokaryotic viruses like phages, has been documented at many different body sites, with the human gut being the richest ecological niche. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and associated proteins constitute the adaptive immune system of bacteria, which prevents attack by invasive nucleic acid. CRISPR-Cas systems function by uptake and integration of foreign genetic element sequences into the CRISPR array, which constitutes a genomic archive of iterative vaccination events. Consequently, CRISPR spacers can be investigated to reconstruct interplay between viruses and bacteria, and metagenomic sequencing data can be exploited to provide insights into host-phage interactions within a niche. Here, we show how the CRISPR spacer content of commensal and pathogenic bacteria can be used to determine the evidence of their phage exposure. This framework opens new opportunities for investigating host-virus dynamics in metagenomic data, and highlights the need to dedicate more efforts for virome sampling and sequencing.}, }
@article {pmid30192933, year = {2018}, author = {Li, F and Chen, C and Wei, W and Wang, Z and Dai, J and Hao, L and Song, L and Zhang, X and Zeng, L and Du, H and Tang, H and Liu, N and Yang, H and Wang, J and Madsen, L and Brix, S and Kristiansen, K and Xu, X and Li, J and Wu, R and Jia, H}, title = {The metagenome of the female upper reproductive tract.}, journal = {GigaScience}, volume = {7}, number = {10}, pages = {}, pmid = {30192933}, issn = {2047-217X}, mesh = {Biodiversity ; Computational Biology/methods ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Reproductive Tract Infections/*microbiology ; Vagina/microbiology ; }, abstract = {Background: The human uterus is traditionally believed to be sterile, while the vaginal microbiota plays an important role in fending off pathogens. Emerging evidence demonstrates the presence of bacteria beyond the vagina. However, a microbiome-wide metagenomic analysis characterizing the diverse microbial communities has been lacking.<br><br>Results: We performed shotgun-sequencing of 52 samples from the cervical canal and the peritoneal fluid of Chinese women of reproductive age using the Illumina platform. Direct annotation of sequencing reads identified the taxonomy of bacteria, archaea, fungi and viruses, confirming and extending the results from our previous study. We replicated our previous findings in another 24 samples from the vagina, the cervical canal, the uterus and the peritoneal fluid using the BGISEQ-500 platform revealing that microorganisms in the samples from the same individuals were largely shared in the entire reproductive tract. Human sequences made up more than 99% of the 20GB raw data. After filtering, vaginal microorganisms were well covered in the generated reproductive tract gene catalogue, while the more diverse upper reproductive tract microbiota would require greater depth of sequencing and more samples to meet the full coverage scale.<br><br>Conclusions: We provide novel detailed data on the microbial composition of a largely unchartered body site, the female reproductive tract. Our results indicated the presence of an intra-individual continuum of microorganisms that gradually changed from the vagina to the peritoneal fluid. This study also provides a framework for understanding the implications of the composition and functional potential of the distinct microbial ecosystems of the female reproductive tract in relation to health and disease.}, }
@article {pmid30185512, year = {2018}, author = {Rohwer, RR and Hamilton, JJ and Newton, RJ and McMahon, KD}, title = {TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution.}, journal = {mSphere}, volume = {3}, number = {5}, pages = {}, pmid = {30185512}, issn = {2379-5042}, mesh = {Algorithms ; Animals ; Bacteria/*classification ; DNA, Bacterial/genetics ; Databases as Topic ; *Databases, Genetic ; Ecosystem ; Fresh Water/*microbiology ; *Metagenomics ; Mice ; *Microbial Consortia ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Taxonomy assignment of freshwater microbial communities is limited by the minimally curated phylogenies used for large taxonomy databases. Here we introduce TaxAss, a taxonomy assignment workflow that classifies 16S rRNA gene amplicon data using two taxonomy reference databases: a large comprehensive database and a small ecosystem-specific database rigorously curated by scientists within a field. We applied TaxAss to five different freshwater data sets using the comprehensive SILVA database and the freshwater-specific FreshTrain database. TaxAss increased the percentage of the data set classified compared to using only SILVA, especially at fine-resolution family to species taxon levels, while across the freshwater test data sets classifications increased by as much as 11 to 40% of total reads. A similar increase in classifications was not observed in a control mouse gut data set, which was not expected to contain freshwater bacteria. TaxAss also maintained taxonomic richness compared to using only the FreshTrain across all taxon levels from phylum to species. Without TaxAss, most organisms not represented in the FreshTrain were unclassified, but at fine taxon levels, incorrect classifications became significant. We validated TaxAss using simulated amplicon data derived from full-length clone libraries and found that 96 to 99% of test sequences were correctly classified at fine resolution. TaxAss splits a data set's sequences into two groups based on their percent identity to reference sequences in the ecosystem-specific database. Sequences with high similarity to sequences in the ecosystem-specific database are classified using that database, and the others are classified using the comprehensive database. TaxAss is free and open source and is available at https://www.github.com/McMahonLab/TaxAssIMPORTANCE Microbial communities drive ecosystem processes, but microbial community composition analyses using 16S rRNA gene amplicon data sets are limited by the lack of fine-resolution taxonomy classifications. Coarse taxonomic groupings at the phylum, class, and order levels lump ecologically distinct organisms together. To avoid this, many researchers define operational taxonomic units (OTUs) based on clustered sequences, sequence variants, or unique sequences. These fine-resolution groupings are more ecologically relevant, but OTU definitions are data set dependent and cannot be compared between data sets. Microbial ecologists studying freshwater have curated a small, ecosystem-specific taxonomy database to provide consistent and up-to-date terminology. We created TaxAss, a workflow that leverages this database to assign taxonomy. We found that TaxAss improves fine-resolution taxonomic classifications (family, genus, and species). Fine taxonomic groupings are more ecologically relevant, so they provide an alternative to OTU-based analyses that is consistent and comparable between data sets.}, }
@article {pmid30179232, year = {2018}, author = {Biller, SJ and Berube, PM and Dooley, K and Williams, M and Satinsky, BM and Hackl, T and Hogle, SL and Coe, A and Bergauer, K and Bouman, HA and Browning, TJ and De Corte, D and Hassler, C and Hulston, D and Jacquot, JE and Maas, EW and Reinthaler, T and Sintes, E and Yokokawa, T and Chisholm, SW}, title = {Marine microbial metagenomes sampled across space and time.}, journal = {Scientific data}, volume = {5}, number = {}, pages = {180176}, pmid = {30179232}, issn = {2052-4463}, mesh = {Archaea/*genetics ; Atlantic Ocean ; Bacteria/*genetics ; Biodiversity ; Ecosystem ; Eukaryota/*genetics ; *Metagenome ; Metagenomics ; Pacific Ocean ; Viruses/*genetics ; Water Microbiology ; }, abstract = {Recent advances in understanding the ecology of marine systems have been greatly facilitated by the growing availability of metagenomic data, which provide information on the identity, diversity and functional potential of the microbial community in a particular place and time. Here we present a dataset comprising over 5 terabases of metagenomic data from 610 samples spanning diverse regions of the Atlantic and Pacific Oceans. One set of metagenomes, collected on GEOTRACES cruises, captures large geographic transects at multiple depths per station. The second set represents two years of time-series data, collected at roughly monthly intervals from 3 depths at two long-term ocean sampling sites, Station ALOHA and BATS. These metagenomes contain genomic information from a diverse range of bacteria, archaea, eukaryotes and viruses. The data's utility is strengthened by the availability of extensive physical, chemical, and biological measurements associated with each sample. We expect that these metagenomes will facilitate a wide range of comparative studies that seek to illuminate new aspects of marine microbial ecosystems.}, }
@article {pmid30177919, year = {2018}, author = {Lin, JD and Lemay, MA and Parfrey, LW}, title = {Diverse Bacteria Utilize Alginate Within the Microbiome of the Giant Kelp Macrocystis pyrifera.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1914}, pmid = {30177919}, issn = {1664-302X}, abstract = {Bacteria are integral to marine carbon cycling. They transfer organic carbon to higher trophic levels and remineralise it into inorganic forms. Kelp forests are among the most productive ecosystems within the global oceans, yet the diversity and metabolic capacity of bacteria that transform kelp carbon is poorly understood. Here, we use 16S amplicon and metagenomic shotgun sequencing to survey bacterial communities associated with the surfaces of the giant kelp Macrocystis pyrifera and assess the capacity of these bacteria for carbohydrate metabolism. We find that Macrocystis-associated communities are distinct from the water column, and that they become more diverse and shift in composition with blade depth, which is a proxy for tissue age. These patterns are also observed in metagenomic functional profiles, though the broader functional groups-carbohydrate active enzyme families-are largely consistent across samples and depths. Additionally, we assayed more than 250 isolates cultured from Macrocystis blades and the surrounding water column for the ability to utilize alginate, the primary polysaccharide in Macrocystis tissue. The majority of cultured bacteria (66%) demonstrated this capacity; we find that alginate utilization is patchily distributed across diverse genera in the Bacteroidetes and Proteobacteria, yet can also vary between isolates with identical 16S rRNA sequences. The genes encoding enzymes involved in alginate metabolism were detected in metagenomic data across taxonomically diverse bacterial communities, further indicating this capacity is likely widespread amongst bacteria in kelp forests. Overall, the M. pyrifera epibiota shifts across a depth gradient, demonstrating a connection between bacterial assemblage and host tissue state.}, }
@article {pmid30177915, year = {2018}, author = {Wu, YT and Yang, CY and Chiang, PW and Tseng, CH and Chiu, HH and Saeed, I and Baatar, B and Rogozin, D and Halgamuge, S and Degermendzhi, A and Tang, SL}, title = {Comprehensive Insights Into Composition, Metabolic Potentials, and Interactions Among Archaeal, Bacterial, and Viral Assemblages in Meromictic Lake Shunet in Siberia.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1763}, pmid = {30177915}, issn = {1664-302X}, abstract = {Microorganisms are critical to maintaining stratified biogeochemical characteristics in meromictic lakes; however, their community composition and potential roles in nutrient cycling are not thoroughly described. Both metagenomics and metaviromics were used to determine the composition and capacity of archaea, bacteria, and viruses along the water column in the landlocked meromictic Lake Shunet in Siberia. Deep sequencing of 265 Gb and high-quality assembly revealed a near-complete genome corresponding to Nonlabens sp. sh3vir. in a viral sample and 38 bacterial bins (0.2-5.3 Mb each). The mixolimnion (3.0 m) had the most diverse archaeal, bacterial, and viral communities, followed by the monimolimnion (5.5 m) and chemocline (5.0 m). The bacterial and archaeal communities were dominated by Thiocapsa and Methanococcoides, respectively, whereas the viral community was dominated by Siphoviridae. The archaeal and bacterial assemblages and the associated energy metabolism were significantly related to the various depths, in accordance with the stratification of physicochemical parameters. Reconstructed elemental nutrient cycles of the three layers were interconnected, including co-occurrence of denitrification and nitrogen fixation in each layer and involved unique processes due to specific biogeochemical properties at the respective depths. According to the gene annotation, several pre-dominant yet unknown and uncultured bacteria also play potentially important roles in nutrient cycling. Reciprocal BLAST analysis revealed that the viruses were specific to the host archaea and bacteria in the mixolimnion. This study provides insights into the bacterial, archaeal, and viral assemblages and the corresponding capacity potentials in Lake Shunet, one of the three meromictic lakes in central Asia. Lake Shunet was determined to harbor specific and diverse viral, bacterial, and archaeal communities that intimately interacted, revealing patterns shaped by indigenous physicochemical parameters.}, }
@article {pmid30177353, year = {2018}, author = {Rhoads, JM and Collins, J and Fatheree, NY and Hashmi, SS and Taylor, CM and Luo, M and Hoang, TK and Gleason, WA and Van Arsdall, MR and Navarro, F and Liu, Y}, title = {Infant Colic Represents Gut Inflammation and Dysbiosis.}, journal = {The Journal of pediatrics}, volume = {203}, number = {}, pages = {55-61.e3}, doi = {10.1016/j.jpeds.2018.07.042}, pmid = {30177353}, issn = {1097-6833}, mesh = {Acinetobacter/isolation &amp; purification ; Breast Feeding ; Case-Control Studies ; Colic/*complications ; Dysbiosis/*diagnosis ; Feces/*chemistry/microbiology ; Female ; Gastrointestinal Microbiome ; Humans ; Infant ; Infant Formula ; Infant, Newborn ; Inflammation/*diagnosis ; Lactobacillus/isolation &amp; purification ; Leukocyte L1 Antigen Complex/*analysis ; Male ; }, abstract = {OBJECTIVE: To dissect potential confounding effects of breast milk and formula feeding on crying + fussing, fecal calprotectin, and gut microbiota in babies with colic. We hypothesized that infant colic is associated with gut inflammation linked to intestinal dysbiosis.<br><br>STUDY DESIGN: A nested case-control design of 3 of our studies was used to analyze clinical and laboratory data at presentation, comparing babies with colic with controls. All investigators other than the biostatistician were blinded during data analysis. Subjects were recruited based on their age and crying + fussy time. We screened 65 infants, 37 with colic, as defined by Barr diary (crying + fussing time >3 hours daily), who were compared with 28 noncolicky infants.<br><br>RESULTS: Fecal calprotectin was elevated in babies with colic. For each mode of infant feeding (breast milk, formula, or breast + formula), infants' fecal calprotectin was higher in babies with colic. Infants with colic had similar levels of fecal alpha diversity (richness) when compared with controls, and alpha diversity was lower in breast-fed babies. Beta diversity at the phylum level revealed significant differences in microbial population. A phylum difference resulted from reduced Actinobacteria (95% of which are Bifidobacilli) in babies with colic. Species significantly associated with colic were Acinetobacter and Lactobacillus iners.<br><br>CONCLUSIONS: Colic is linked with gut inflammation (as determined by fecal calprotectin) and dysbiosis, independent of mode of feeding, with fewer Bifidobacilli.<br><br>TRIAL REGISTRATION: Clinicaltrials.gov: NCT01279265 and NCT01849991.}, }
@article {pmid30173738, year = {2018}, author = {Stroebel, C and Alexander, T and Workentine, ML and Timsit, E}, title = {Effects of transportation to and co-mingling at an auction market on nasopharyngeal and tracheal bacterial communities of recently weaned beef cattle.}, journal = {Veterinary microbiology}, volume = {223}, number = {}, pages = {126-133}, doi = {10.1016/j.vetmic.2018.08.007}, pmid = {30173738}, issn = {1873-2542}, mesh = {Animals ; Bacteria/genetics/*isolation &amp; purification ; Bovine Respiratory Disease Complex/*microbiology ; Cattle ; DNA, Bacterial/chemistry/genetics ; Female ; *Metagenomics ; *Microbiota ; Moraxella/genetics/isolation &amp; purification ; Mycoplasma/genetics/isolation &amp; purification ; Nasopharynx/microbiology ; RNA, Ribosomal, 16S/chemistry/genetics ; Trachea/microbiology ; Transportation ; Weaning ; }, abstract = {The objective was to study effects of transportation to and co-mingling at an auction market on nasopharyngeal and tracheal bacterial communities of feedlot cattle. Two groups of 30 Angus-cross heifers were studied from weaning to 28 d after arrival at a feedlot. For each group, half the heifers were either transported directly to a feedlot after weaning (RANC) or transported to and co-mingled at an auction market for 24 h before being placed in a feedlot (AUCT). Deep nasal swabs (DNS) and trans-tracheal aspirates (TTA) were collected at weaning (d0) and at on-arrival processing at the feedlot (d2). At 7 (d9) and 28 d (d30) after arrival, DNS were repeated. The DNA was extracted from DNS and TTA and the V4 region of the 16S rRNA gene sequenced (MiSeq). Alpha diversity analysis did not reveal differences between AUCT and RANC. However, bacterial diversity decreased over time in the nasopharynx, especially at d9. Although beta-diversity was not different between AUCT and RANC, interval after arrival and feedlot where heifers were placed affected composition of the nasopharyngeal bacterial communities. In both groups, a large increase in Mycoplasma was observed after arrival; in one group, Mycoplasma bovis was dominant at d9 and remained dominant until d30. However, in the other group, Mycoplasma dispar dominated at d9 and was replaced by Moraxella at d30. We concluded that transportation to and co-mingling at an auction market for 24 h did not significantly influence diversity or composition of nasopharyngeal or tracheal bacterial communities.}, }
@article {pmid30168288, year = {2018}, author = {Minich, JJ and Zhu, Q and Xu, ZZ and Amir, A and Ngochera, M and Simwaka, M and Allen, EE and Zidana, H and Knight, R}, title = {Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus).}, journal = {MicrobiologyOpen}, volume = {7}, number = {6}, pages = {e00716}, doi = {10.1002/mbo3.716}, pmid = {30168288}, issn = {2045-8827}, mesh = {Animal Feed/analysis/microbiology ; Animals ; Aquaculture ; Bacteria/classification/genetics/*isolation &amp; purification ; Catfishes/*growth &amp; development/metabolism ; Cattle ; Livestock ; Manure/analysis/*microbiology ; Microbiota ; Ponds/analysis/*microbiology ; Poultry ; Swine ; Tilapia/*growth &amp; development/metabolism ; }, abstract = {The majority of seafood is farmed, with most finfish coming from freshwater ponds. Ponds are often fertilized to promote microbial productivity as a natural feed source to fish. To understand if pond fertilization with livestock manure induces a probiotic or prebiotic effect, we communally reared tilapia (Oreochromis shiranus), and North African catfish (Clarias gariepinus), for 4 weeks under seven manure treatments including layer chicken, broiler chicken, guinea fowl, quail, pig, cow, vs. commercial feed to evaluate microbial community dynamics of the manure, pond water, and fish feces using 16S and 18S rRNA marker genes along with metagenome sequencing. Catfish growth, but not tilapia, was positively associated with plankton abundance (p = 0.0006, R2 = 0.4887) and greatest in ponds fertilized with quail manure (ANOVA, p < 0.05). Manure was unique and influenced the 16S microbiome in pond water, tilapia gut, and catfish gut and 18S community in pond water and catfish guts (PERMANOVA, p = 0.001). On average, 18.5%, 18.6%, and 45.3% of manure bacteria sOTUs, (sub-operational taxonomic units), were present in the water column, catfish feces, and tilapia feces which comprised 3.7%, 12.8%, and 10.9% of the total microbial richness of the communities, respectively. Antibiotic resistance genes were highest in the manure and water samples followed by tilapia feces and lowest in catfish feces (p < 0.0001). In this study, we demonstrate how the bacterial and eukaryotic microbial composition of fish ponds are influenced by specific livestock manure inputs and that the gut microbiome of tilapia is more sensitive and responsive than catfish to these changes. We conclude that animal manure used as fertilizer induces a primarily prebiotic effect on the pond ecosystem rather than a direct probiotic effect on fish.}, }
@article {pmid30166168, year = {2018}, author = {Li, Z and Feng, C and Luo, X and Yao, H and Zhang, D and Zhang, T}, title = {Revealing the influence of microbiota on the quality of Pu-erh tea during fermentation process by shotgun metagenomic and metabolomic analysis.}, journal = {Food microbiology}, volume = {76}, number = {}, pages = {405-415}, doi = {10.1016/j.fm.2018.07.001}, pmid = {30166168}, issn = {1095-9998}, mesh = {Aspergillus/classification/genetics/isolation &amp; purification/metabolism ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Camellia sinensis/chemistry/*microbiology ; Fermentation ; Flavoring Agents/chemistry/metabolism ; Metabolomics ; Metagenomics ; *Microbiota ; Phenols/chemistry/metabolism ; Quality Control ; Tea/*chemistry/microbiology ; }, abstract = {Multispecies microbial community in natural solid-state fermentation (SSF) is crucial for the formation of Chinese Pu-erh tea's unique quality. However, the association between microbiota and tea quality are still poorly understood. Herein, shotgun metagenomic and metabolomic analysis showed that significant variations in composition of microbiota, collective functional genes, and flavour compounds occurred during SSF process. Furthermore, the formation pathways of the dominant flavours including theabrownin, methoxy-phenolic compound, alcohol and carvone were proposed. Moreover, biological interaction networks analysis among functional core microbiota, functional genes, and dominant flavours indicated Aspergillus was the main flavour-producing microorganism in the early SSF, while many other genera including Bacillus, Rasamsonia, Lichtheimia, Debaryomyces were determined as the functional core microorganism for flavours production in the late SSF. This study provides a perspective for bridging the gap between the microbiota and quality in Pu-erh tea, and benefited for further optimizing production efficiency and product quality.}, }
@article {pmid30166158, year = {2018}, author = {Bouju-Albert, A and Pilet, MF and Guillou, S}, title = {Influence of lactate and acetate removal on the microbiota of French fresh pork sausages.}, journal = {Food microbiology}, volume = {76}, number = {}, pages = {328-336}, doi = {10.1016/j.fm.2018.06.011}, pmid = {30166158}, issn = {1095-9998}, mesh = {Acetates/*pharmacology ; Animals ; Brochothrix/drug effects/genetics/isolation &amp; purification ; Colony Count, Microbial ; Food Microbiology/methods ; Food Packaging/methods ; Food Preservation/methods ; Food Preservatives/chemistry/*pharmacology ; Hydrogen-Ion Concentration ; Lactic Acid/*pharmacology ; Lactobacillus/drug effects/genetics/isolation &amp; purification ; Leuconostoc/drug effects/genetics/isolation &amp; purification ; Meat Products/analysis/*microbiology ; Metagenomics ; Microbiota/*drug effects/genetics ; RNA, Ribosomal, 16S ; Red Meat/*microbiology ; Swine ; Vacuum ; }, abstract = {The microbiota of fresh French pork sausages were characterised in five batches of comminuted pork meat that were equally divided into two formulations either containing the acid-based preservatives lactate and acetate, or no preservatives. Conventional microbiological analysis and high-throughput 16S rDNA amplicon sequencing methods were performed on meat batches packed under modified atmosphere (70% oxygen and 30% carbon dioxide) during chilled storage. In addition, meat pH and colour, and gas composition of the packages were monitored until the end of the shelf-life. During storage, the population of mesophilic and lactic acid bacteria increased from 4 log CFU/g to 8 log CFU/g after 15 days of chilled storage, both with and without preservatives. Despite similar changes of the physical and chemical parameters, such as pH and package gas composition, spoilage was delayed in the meat containing the preservatives, suggesting that lactate and acetate are effective against spoilage. Metagenetic analysis showed that at the end of the shelf-life, the species distribution differed between both the formulations and the batches. Lactic acid bacteria were shown to dominate both with and without preservatives; however, samples containing no preservatives were characterised by the presence of an increased population of Brochothrix spp. and Pseudomonas spp. whereas, Leuconostoc mesenteroides/pseudomesenteroides and Lactobacillus curvatus/graminis were more abundant in the meat with preservatives.}, }
@article {pmid30166157, year = {2018}, author = {Jung, MJ and Kim, MS and Yun, JH and Lee, JY and Kim, PS and Lee, HW and Ha, JH and Roh, SW and Bae, JW}, title = {Viral community predicts the geographical origin of fermented vegetable foods more precisely than bacterial community.}, journal = {Food microbiology}, volume = {76}, number = {}, pages = {319-327}, doi = {10.1016/j.fm.2018.06.010}, pmid = {30166157}, issn = {1095-9998}, mesh = {Bacteria/genetics/isolation &amp; purification/virology ; Bacteriophages/genetics/isolation &amp; purification ; Brassica/microbiology ; DNA, Bacterial/genetics ; DNA, Viral/genetics ; Fermented Foods/*microbiology/*virology ; Food Microbiology ; Geography ; High-Throughput Nucleotide Sequencing ; Humans ; Lactobacillales/genetics/isolation &amp; purification/virology ; Metagenomics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Vegetables/*microbiology/*virology ; }, abstract = {Fermented foods are considered as an integral part of the global human diet. Fermented foods also have unique microbial communities such as bacteria, archaea, fungi, and viruses that are essential to the fermentation process and affect final product characteristics. Despite the ecological importance of virus, little is known about the diversity and ecological role of virus in the food ecosystem. In this study, the viral and host bacterial communities from 10 representative samples of Korean and Chinese kimchi were analyzed in triplicate using next-generation sequencing technology. The overall structures of bacterial and viral communities were dominated by lactic acid bacteria in phylum Firmicutes and bacteriophages in order Caudovirales, respectively. For the single-stranded DNA (ssDNA) viruses, bacteriophage in family Microviridae were dominant in Korean kimchi. After correction for multiple comparisons using false discovery rate (FDR, P < 0.05), the relative abundances of 6 bacterial taxa and 33 viral host taxa at the genus level were significantly different between Korean and Chinese kimchi. Notably, in beta-diversity analysis, viral communities were much more clearly separated according to their geographical origin (PERMANOVA pseudo-F = 11.57, P < 0.001 in Bray-Curtis PCoA) than bacterial communities (pseudo-F = 4.75, P < 0.001 in unweighted UniFrac PCoA). Thus, viral metagenomics represents a potentially useful in-depth analytical method for determining the geographical origins of fermented foods.}, }
@article {pmid30166151, year = {2018}, author = {Mataragas, M and Alessandria, V and Ferrocino, I and Rantsiou, K and Cocolin, L}, title = {A bioinformatics pipeline integrating predictive metagenomics profiling for the analysis of 16S rDNA/rRNA sequencing data originated from foods.}, journal = {Food microbiology}, volume = {76}, number = {}, pages = {279-286}, doi = {10.1016/j.fm.2018.05.009}, pmid = {30166151}, issn = {1095-9998}, mesh = {Algorithms ; Cheese/microbiology ; *Computational Biology ; DNA, Ribosomal ; Food Microbiology/methods ; High-Throughput Nucleotide Sequencing ; Metabolic Networks and Pathways ; Metagenomics/*methods ; Microbial Consortia/*genetics ; RNA, Ribosomal, 16S/*genetics ; *Sequence Analysis, DNA ; Software ; }, abstract = {The recent advances in molecular biology, such as the advent of next-generation sequencing (NGS) platforms, have paved the way to new exciting tools which rapidly transform food microbiology. Nowadays, NGS methods such as 16S rDNA/rRNA metagenomics or amplicon sequencing are used for the taxonomic profiling of the food microbial communities. Although 16S rDNA/rRNA NGS-based microbial data are not suited for the investigation of the functional potential of the identified operational taxonomic units as compared to shotgun metagenomics, advances in the bioinformatics discipline allow now the performance of such studies. In this paper, a bioinformatics workflow is described integrating predictive metagenomics profiling with specific application to food microbiology data. Bioinformatics tools pertinent to each sub-module of the pipeline are suggested as well. The published 16S rDNA/rRNA amplicon data originated from an Italian Grana-type cheese, using an NGS platform, was employed to demonstrate the predictive metagenomics profiling approach. The pipeline identified the microbial community and the changes that occurred in the microbial profile during manufacture of the food product studied (taxonomic profiling). The workflow also indicated significant changes in the functional profiling of the community. The tool may help to investigate the functional potential, alterations, and interactions of a microbial community. The proposed workflow may also find an application in the investigation of the ecology of foodborne pathogens encountered in various food products.}, }
@article {pmid30165813, year = {2018}, author = {Rotimi, AM and Pierneef, R and Reva, ON}, title = {Selection of marker genes for genetic barcoding of microorganisms and binning of metagenomic reads by Barcoder software tools.}, journal = {BMC bioinformatics}, volume = {19}, number = {1}, pages = {309}, pmid = {30165813}, issn = {1471-2105}, support = {93664//National Research Foundation/ ; }, mesh = {Algorithms ; Bacteria/*genetics ; Base Sequence ; DNA Barcoding, Taxonomic/*methods ; *Genes, Bacterial ; Genetic Markers ; Humans ; Metagenome/genetics ; Metagenomics/*methods ; Microbiota/genetics ; Phylogeny ; ROC Curve ; Reproducibility of Results ; Sample Size ; *Software ; Species Specificity ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: Metagenomic approaches have revealed the complexity of environmental microbiomes with the advancement in whole genome sequencing displaying a significant level of genetic heterogeneity on the species level. It has become apparent that patterns of superior bioactivity of bacteria applicable in biotechnology as well as the enhanced virulence of pathogens often requires distinguishing between closely related species or sub-species. Current methods for binning of metagenomic reads usually do not allow for identification below the genus level and generally stops at the family level.<br><br>RESULTS: In this work, an attempt was made to improve metagenomic binning resolution by creating genome specific barcodes based on the core and accessory genomes. This protocol was implemented in novel software tools available for use and download from http://bargene.bi.up.ac.za /. The most abundant barcode genes from the core genomes were found to encode for ribosomal proteins, certain central metabolic genes and ABC transporters. Performance of metabarcode sequences created by this package was evaluated using artificially generated and publically available metagenomic datasets. Furthermore, a program (Barcoding 2.0) was developed to align reads against barcode sequences and thereafter calculate various parameters to score the alignments and the individual barcodes. Taxonomic units were identified in metagenomic samples by comparison of the calculated barcode scores to set cut-off values. In this study, it was found that varying sample sizes, i.e. number of reads in a metagenome and metabarcode lengths, had no significant effect on the sensitivity and specificity of the algorithm. Receiver operating characteristics (ROC) curves were calculated for different taxonomic groups based on the results of identification of the corresponding genomes in artificial metagenomic datasets. The reliability of distinguishing between species of the same genus or family by the program was nearly perfect.<br><br>CONCLUSIONS: The results showed that the novel online tool BarcodeGenerator (http://bargene.bi.up.ac.za /) is an efficient approach for generating barcode sequences from a set of complete genomes provided by users. Another program, Barcoder 2.0 is available from the same resource to enable an efficient and practical use of metabarcodes for visualization of the distribution of organisms of interest in environmental and clinical samples.}, }
@article {pmid30158489, year = {2018}, author = {Garcia, R and La Clair, JJ and Müller, R}, title = {Future Directions of Marine Myxobacterial Natural Product Discovery Inferred from Metagenomics.}, journal = {Marine drugs}, volume = {16}, number = {9}, pages = {}, pmid = {30158489}, issn = {1660-3397}, support = {German Center for Infection Research//Deutsches Zentrum für Infektionsforschung/ ; X//Xenobe Research Institute/ ; }, mesh = {Aquatic Organisms/*genetics/metabolism ; Biodiversity ; Biological Products/metabolism/*pharmacology ; DNA, Bacterial/genetics ; *Metagenomics ; Myxococcales/*genetics/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Salt Tolerance/genetics ; Sequence Analysis, DNA ; }, abstract = {Over the last two decades, halophilic (organisms that thrive at high salt concentrations) and halotolerant (organisms that have adapted to high salt concentrations) myxobacteria emerged as an important source of structurally diverse secondary metabolites from the marine environment. This review explores the advance of metagenomics analysis and 16S rRNA gene phylogeny of the cultured and uncultured myxobacteria from marine and other salt-environments up to July 2018. The diversity of novel groups of myxobacteria in these environments appears unprecedented, especially in the Sorangiineae and Nannocystineae suborders. The Sandaracinaceae related clade in the Sorangiineae suborder seems more widely distributed compared to the exclusively marine myxobacterial cluster. Some of the previously identified clones from metagenomic studies were found to be related to the Nannocystineae suborder. This understanding provides the foundation for a vital, unexplored resource. Understanding the conditions required to cultivate these yet &quot;uncultured&quot; myxobacteria in the laboratory, while a key next step, offers a significant potential to further expand access to diverse secondary metabolites.}, }
@article {pmid30155977, year = {2018}, author = {Bálint, M and Nowak, C and Márton, O and Pauls, SU and Wittwer, C and Aramayo, JL and Schulze, A and Chambert, T and Cocchiararo, B and Jansen, M}, title = {Accuracy, limitations and cost efficiency of eDNA-based community survey in tropical frogs.}, journal = {Molecular ecology resources}, volume = {18}, number = {6}, pages = {1415-1426}, doi = {10.1111/1755-0998.12934}, pmid = {30155977}, issn = {1755-0998}, support = {//USGS Amphibian Research and Monitoring Initiative/ ; //Globetrotter/ ; //Erika and Walter Datz-Stiftung/ ; LOEWE - Landes-Offensive zur Entwicklung Wissens//Hessisches Ministerium für Wissenschaft und Kunst/ ; //Ministry of Higher Education/ ; }, mesh = {Amphibians/*classification/*genetics ; Animals ; *Biota ; Bolivia ; Costs and Cost Analysis ; DNA Barcoding, Taxonomic/economics/*methods ; Metagenomics/economics/*methods ; Tropical Climate ; }, abstract = {Rapid environmental change in highly biodiverse tropical regions demands efficient biomonitoring programmes. While existing metrics of species diversity and community composition rely on encounter-based survey data, eDNA recently emerged as alternative approach. Costs and ecological value of eDNA-based methods have rarely been evaluated in tropical regions, where high species richness is accompanied by high functional diversity (e.g., the use of different microhabitats by different species and life stages). We first tested whether estimation of tropical frogs' community structure derived from eDNA data is compatible with expert field assessments. Next, we evaluated whether eDNA is a financially viable solution for biodiversity monitoring in tropical regions. We applied eDNA metabarcoding to investigate frog species occurrence in five ponds in the Chiquitano dry forest region in Bolivia and compared our data with a simultaneous visual and audio encounter survey (VAES). We found that taxon lists and community structure generated with eDNA and VAES correspond closely, and most deviations are attributable to different species' life histories. Cost efficiency of eDNA surveys was mostly influenced by the richness of local fauna and the number of surveyed sites: VAES may be less costly in low-diversity regions, but eDNA quickly becomes more cost-efficient in high-diversity regions with many sites sampled. The results highlight that eDNA is suitable for large-scale biodiversity surveys in high-diversity areas if life history is considered, and certain precautions in sampling, genetic analyses and data interpretation are taken. We anticipate that spatially extensive, standardized eDNA biodiversity surveys will quickly emerge in the future.}, }
@article {pmid30153857, year = {2018}, author = {Ugarte, A and Vicedomini, R and Bernardes, J and Carbone, A}, title = {A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {149}, pmid = {30153857}, issn = {2049-2618}, mesh = {Algorithms ; Bacteria/classification/*genetics/isolation &amp; purification ; Bacterial Proteins/*chemistry/*genetics/metabolism ; Databases, Genetic ; Environmental Microbiology ; Gastrointestinal Microbiome ; Humans ; Metagenome ; Metagenomics/*methods ; Molecular Sequence Annotation/*methods ; Protein Domains ; }, abstract = {BACKGROUND: Biochemical and regulatory pathways have until recently been thought and modelled within one cell type, one organism and one species. This vision is being dramatically changed by the advent of whole microbiome sequencing studies, revealing the role of symbiotic microbial populations in fundamental biochemical functions. The new landscape we face requires the reconstruction of biochemical and regulatory pathways at the community level in a given environment. In order to understand how environmental factors affect the genetic material and the dynamics of the expression from one environment to another, we want to evaluate the quantity of gene protein sequences or transcripts associated to a given pathway by precisely estimating the abundance of protein domains, their weak presence or absence in environmental samples.<br><br>RESULTS: MetaCLADE is a novel profile-based domain annotation pipeline based on a multi-source domain annotation strategy. It applies directly to reads and improves identification of the catalog of functions in microbiomes. MetaCLADE is applied to simulated data and to more than ten metagenomic and metatranscriptomic datasets from different environments where it outperforms InterProScan in the number of annotated domains. It is compared to the state-of-the-art non-profile-based and profile-based methods, UProC and HMM-GRASPx, showing complementary predictions to UProC. A combination of MetaCLADE and UProC improves even further the functional annotation of environmental samples.<br><br>CONCLUSIONS: Learning about the functional activity of environmental microbial communities is a crucial step to understand microbial interactions and large-scale environmental impact. MetaCLADE has been explicitly designed for metagenomic and metatranscriptomic data and allows for the discovery of patterns in divergent sequences, thanks to its multi-source strategy. MetaCLADE highly improves current domain annotation methods and reaches a fine degree of accuracy in annotation of very different environments such as soil and marine ecosystems, ancient metagenomes and human tissues.}, }
@article {pmid30152883, year = {2018}, author = {Toivonen, L and Hasegawa, K and Ajami, NJ and Celedón, JC and Mansbach, JM and Petrosino, JF and Camargo, CA}, title = {Circulating 25-hydroxyvitamin D, nasopharyngeal microbiota, and bronchiolitis severity.}, journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology}, volume = {29}, number = {8}, pages = {877-880}, pmid = {30152883}, issn = {1399-3038}, support = {//Päivikki ja Sakari Sohlbergin Säätiö/International ; R01 AI134940/AI/NIAID NIH HHS/United States ; U01 AI087881/AI/NIAID NIH HHS/United States ; UH3 OD023253/OD/NIH HHS/United States ; R01 AI137091/AI/NIAID NIH HHS/United States ; //Suomen Lääketieteen Säätiö/International ; UG3 OD023253/OD/NIH HHS/United States ; }, mesh = {Bronchiolitis/*etiology ; Cohort Studies ; Female ; Humans ; Infant ; Male ; Microbiota/genetics/*immunology ; Nasopharynx/*microbiology ; Prospective Studies ; Risk Factors ; United States ; Vitamin D/*analogs &amp; derivatives/blood ; }, }
@article {pmid30149004, year = {2018}, author = {Kim, JY and Kim, EM and Yi, MH and Lee, J and Lee, S and Hwang, Y and Yong, D and Sohn, WM and Yong, TS}, title = {Intestinal fluke Metagonimus yokogawai infection increases probiotic Lactobacillus in mouse cecum.}, journal = {Experimental parasitology}, volume = {193}, number = {}, pages = {45-50}, doi = {10.1016/j.exppara.2018.08.002}, pmid = {30149004}, issn = {1090-2449}, mesh = {Animals ; Bacteria/classification/growth &amp; development ; Cecum/*microbiology ; Fish Diseases/parasitology ; Gastrointestinal Microbiome ; Heterophyidae/*physiology ; *Lactobacillus ; Mice ; Mice, Inbred ICR ; Osmeriformes/parasitology ; *Probiotics ; Trematode Infections/*microbiology ; }, abstract = {Helminth infection can alleviate immune-mediated disorders such as allergies and autoimmune diseases, by altering the gut microbiome. However, changes in gut microbiome due to intestinal trematodes remain unelucidated. Here, we evaluated the changes in the gut microbiome of ICR mice infected with Metagonimus yokogawai, a hypo-virulent intestinal trematode. Four weeks after infection, mouse cecal content was analyzed by 16S rRNA amplicon analysis. Although there was no apparent difference in species richness and diversity, the microbiome composition was different in the infected and control groups. Furthermore, several Lactobacillus species with known immunomodulatory role in immune-mediated diseases were increased in the infected group.}, }
@article {pmid30143202, year = {2018}, author = {Shikata, A and Sermsathanaswadi, J and Thianheng, P and Baramee, S and Tachaapaikoon, C and Waeonukul, R and Pason, P and Ratanakhanokchai, K and Kosugi, A}, title = {Characterization of an Anaerobic, Thermophilic, Alkaliphilic, High Lignocellulosic Biomass-Degrading Bacterial Community, ISHI-3, Isolated from Biocompost.}, journal = {Enzyme and microbial technology}, volume = {118}, number = {}, pages = {66-75}, doi = {10.1016/j.enzmictec.2018.07.001}, pmid = {30143202}, issn = {1879-0909}, mesh = {Alkalies/chemistry ; Animals ; Bacteria, Anaerobic/growth &amp; development ; *Biomass ; Cattle ; *Composting ; Lignin/*metabolism ; Metagenome ; *Microbial Consortia ; Oryza/*metabolism/microbiology ; Phylogeny ; Temperature ; Zea mays/*metabolism/microbiology ; }, abstract = {The generation of a complex microbial consortium is a promising approach for efficient biomass decomposition. An anaerobic thermophilic alkaliphilic microbial consortium with efficient degradation ability was screened from bovine manure compost using non-pretreated milling corn stover (CS) and rice straw (RS). A stable microbial consortium ISHI-3 with high degradation ability for CS and RS was isolated by the roll tube technique. ISHI-3 comprised Herbivorax saccincola and bacteria belonging to the classes Pelotomaculum, Tepidanaerobacter, and Tepidimicrobium, as determined by DGGE of the PCR-generated 16S rRNA genes. Furthermore, metagenomics analysis using a 16S rRNA library was carried out to determine the bacterial distribution during degradation of CS and RS. H. saccincola and bacteria belonging to Pelotomaculum were relatively abundant in the beginning to middle periods of culture with CS and RS whereas bacteria belonging to Tepidanaerobacter and Tepidimicrobium gradually increased in the population during the later stages. To understand the role of non-cellulolytic bacteria in the consortium, novel strains ET1 and GL4, which were most closely related to Tepidimicrobium ferriphilum and Tepidanaerobacter acetatoxydans, were isolated from ISHI-3. Based on their carbon source usage, morphology, and phylogenetic analysis, we propose that strains ET1 and GL4 should be classified as a novel genus or species. Bacteria ET1 and GL4 can utilize different organic compounds as carbon and energy sources such as organic acids, alcohols, sugars, and amino acids, showing a preference for organic acids and alcohols rather than sugars such as glucose and cellobiose. These results indicated that ET1 and GL4 help to accelerate efficient lignocellulose degradation of H. saccincola.}, }
@article {pmid30143055, year = {2018}, author = {Chiarello, M and Auguet, JC and Bettarel, Y and Bouvier, C and Claverie, T and Graham, NAJ and Rieuvilleneuve, F and Sucré, E and Bouvier, T and Villéger, S}, title = {Skin microbiome of coral reef fish is highly variable and driven by host phylogeny and diet.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {147}, pmid = {30143055}, issn = {2049-2618}, mesh = {Animal Feed ; Animals ; Bacteria/*classification/genetics ; Biodiversity ; Coral Reefs ; Fishes/classification/*microbiology ; Humans ; Metagenomics/*methods ; Microbiota ; Phylogeny ; Plankton/microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; Skin/microbiology ; Species Specificity ; }, abstract = {BACKGROUND: The surface of marine animals is covered by abundant and diversified microbial communities, which have major roles for the health of their host. While such microbiomes have been deeply examined in marine invertebrates such as corals and sponges, the microbiomes living on marine vertebrates have received less attention. Specifically, the diversity of these microbiomes, their variability among species, and their drivers are still mostly unknown, especially among the fish species living on coral reefs that contribute to key ecosystem services while they are increasingly affected by human activities. Here, we investigated these knowledge gaps analyzing the skin microbiome of 138 fish individuals belonging to 44 coral reef fish species living in the same area.<br><br>RESULTS: Prokaryotic communities living on the skin of coral reef fishes are highly diverse, with on average more than 600 OTUs per fish, and differ from planktonic microbes. Skin microbiomes varied between fish individual and species, and interspecific differences were slightly coupled to the phylogenetic affiliation of the host and its ecological traits.<br><br>CONCLUSIONS: These results highlight that coral reef biodiversity is greater than previously appreciated, since the high diversity of macro-organisms supports a highly diversified microbial community. This suggest that beyond the loss of coral reefs-associated macroscopic species, anthropic activities on coral reefs could also lead to a loss of still unexplored host-associated microbial diversity, which urgently needs to be assessed.}, }
@article {pmid30141128, year = {2019}, author = {Li, H and Mishra, M and Ding, S and Miyamoto, MM}, title = {Diversity and Dynamics of &quot;Candidatus Endobugula&quot; and Other Symbiotic Bacteria in Chinese Populations of the Bryozoan, Bugula neritina.}, journal = {Microbial ecology}, volume = {77}, number = {1}, pages = {243-256}, doi = {10.1007/s00248-018-1233-x}, pmid = {30141128}, issn = {1432-184X}, support = {201205024-2//Public Welfare Project of the State Oceanic Administration/ ; 2013FY110700//National Basic Research Foundation of China/ ; }, mesh = {Animals ; Biodiversity ; Bryostatins/metabolism ; Bryozoa/growth &amp; development/*microbiology ; China ; DNA, Bacterial/isolation &amp; purification ; Ecology ; Gammaproteobacteria/*classification/genetics/*isolation &amp; purification/*metabolism ; Geography ; Larva/microbiology ; Life Cycle Stages ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Symbiosis ; }, abstract = {Bugula neritina is a common invasive cosmopolitan bryozoan that harbors (like many sessile marine invertebrates) a symbiotic bacterial (SB) community. Among the SB of B. neritina, &quot;Candidatus Endobugula sertula&quot; continues to receive the greatest attention, because it is the source of bryostatins. The bryostatins are potent bioactive polyketides, which have been investigated for their therapeutic potential to treat various cancers, Alzheimer's disease, and AIDS. In this study, we compare the metagenomics sequences for the 16S ribosomal RNA gene of the SB communities from different geographic and life cycle samples of Chinese B. neritina. Using a variety of approaches for estimating alpha/beta diversity and taxonomic abundance, we find that the SB communities vary geographically with invertebrate and fish mariculture and with latitude and environmental temperature. During the B. neritina life cycle, we find that the diversity and taxonomic abundances of the SB communities change with the onset of host metamorphosis, filter feeding, colony formation, reproduction, and increased bryostatin production. &quot;Ca. Endobugula sertula&quot; is confirmed as the symbiont of the Chinese &quot;Ca. Endobugula&quot;/B. neritina symbiosis. Our study extends our knowledge about B. neritina symbiosis from the New to the Old World and offers new insights into the environmental and life cycle factors that can influence its SB communities, &quot;Ca. Endobugula,&quot; and bryostatins more globally.}, }
@article {pmid30138419, year = {2018}, author = {Oliveira, JL and Cury, JC and Gurgel-Gonçalves, R and Bahia, AC and Monteiro, FA}, title = {Field-collected Triatoma sordida from central Brazil display high microbiota diversity that varies with regard to developmental stage and intestinal segmentation.}, journal = {PLoS neglected tropical diseases}, volume = {12}, number = {8}, pages = {e0006709}, pmid = {30138419}, issn = {1935-2735}, mesh = {Animals ; Bacteria/*classification ; Brazil ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Male ; Nymph ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Triatoma/growth &amp; development/*microbiology ; }, abstract = {BACKGROUND/METHODOLOGY: Triatomine bugs are the vectors of Trypanosoma cruzi, the agent of Chagas disease. Vector control has for decades relied upon insecticide spraying, but insecticide resistance has recently emerged in several triatomine populations. One alternative strategy to reduce T. cruzi transmission is paratransgenesis, whereby symbiotic bacteria are genetically engineered to produce T. cruzi-killing proteins in the vector's gut. This approach requires in-depth knowledge of the vectors' natural gut microbiota. Here, we use metagenomics (16S rRNA 454 pyrosequencing) to describe the gut microbiota of field-caught Triatoma sordida-likely the most common peridomestic triatomine in Brazil. For large nymphs (4th and 5th stage) and adults, we also studied separately the three main digestive-tract segments-anterior midgut, posterior midgut, and hindgut.<br><br>PRINCIPAL FINDINGS: Bacteria of four phyla (12 genera) were present in both nymphs (all five stages) and adults, thus defining T. sordida's 'bacterial core': Actinobacteria (Brevibacterium, Corynebacterium, Dietzia, Gordonia, Nitriliruptor, Nocardia, Nocardiopsis, Rhodococcus, and Williamsia), Proteobacteria (Pseudomonas and Sphingobium), and Firmicutes (Staphylococcus). We found some clear differences in bacterial composition and relative abundance among development stages; overall, Firmicutes and Proteobacteria increased, but Actinobacteria decreased, through development. Finally, the bacterial microbiotas of the bugs' anterior midgut, posterior midgut, and hindgut were sharply distinct.<br><br>CONCLUSIONS/SIGNIFICANCE: Our results identify the 'bacterial core set' of T. sordida and reveal important gut microbiota differences among development stages-particularly between 1st-3rd stage nymphs and adults. Further, we show that, within any given development stage, the vectors' gut cannot be regarded as a single homogeneous environment. Cultivable, non-pathogenic 'core' bacterial species may now be tested as candidates for paratransgenic control of T. cruzi transmission by T. sordida.}, }
@article {pmid30138339, year = {2018}, author = {Whitfield-Cargile, CM and Chamoun-Emanuelli, AM and Cohen, ND and Richardson, LM and Ajami, NJ and Dockery, HJ}, title = {Differential effects of selective and non-selective cyclooxygenase inhibitors on fecal microbiota in adult horses.}, journal = {PloS one}, volume = {13}, number = {8}, pages = {e0202527}, pmid = {30138339}, issn = {1932-6203}, mesh = {4-Butyrolactone/administration &amp; dosage/adverse effects/analogs &amp; derivatives ; Adult ; Animals ; Anti-Inflammatory Agents, Non-Steroidal/*administration &amp; dosage/adverse effects ; Cyclooxygenase 2/genetics ; Cyclooxygenase 2 Inhibitors/*administration &amp; dosage/adverse effects ; Feces/microbiology ; Horses/microbiology ; Humans ; Metagenome/drug effects ; Microbiota/*drug effects ; Phenylbutazone/administration &amp; dosage/adverse effects ; RNA, Ribosomal, 16S/*genetics ; Sulfones/administration &amp; dosage/adverse effects ; }, abstract = {Non-steroidal anti-inflammatory drugs (NSAIDs) are routinely used in both veterinary and human medicine. Gastrointestinal injury is a frequent adverse event associated with NSAID use and evidence suggests that NSAIDs induce gastrointestinal microbial imbalance (i.e., dysbiosis) in both animals and people. It is unknown, however, whether cyclooxygenase (COX)-2-selective NSAIDs induce dysbiosis, or if this phenomenon occurs in horses administered any class of NSAIDs. Therefore, our objectives were to determine whether the composition and diversity of the fecal microbiota of adult horses were altered by NSAID use, and whether these effects differed between non-selective and COX-2-selective NSAIDs. Twenty-five adult horses were randomly assigned to 1 of 3 groups: control (n = 5); phenylbutazone (n = 10); or, firocoxib (n = 10). Treatments were administered for 10 days. Fecal samples were collected every 5 days for 25 days. DNA was extracted from feces and the 16S rRNA gene amplified and sequenced to determine the composition of the microbiota and the inferred metagenome. While the fecal microbiota profile of the control group remained stable over time, the phenylbutazone and firocoxib groups had decreased diversity, and alteration of their microbiota profiles was most pronounced at day 10. Similarly, there were clear alterations of the inferred metagenome at day 10 compared to all other days, indicating that use of both non-selective and selective COX inhibitors resulted in temporary alterations of the fecal microbiota and inferred metagenome. Dysbiosis associated with NSAID administration is clinically relevant because dysbiosis has been associated with several important diseases of horses including abdominal pain (colic), colitis, enteric infections, and laminitis.}, }
@article {pmid30137571, year = {2019}, author = {Chen, WL and Tang, SGH and Jahromi, MF and Candyrine, SCL and Idrus, Z and Abdullah, N and Liang, JB}, title = {Metagenomics analysis reveals significant modulation of cecal microbiota of broilers fed palm kernel expeller diets.}, journal = {Poultry science}, volume = {98}, number = {1}, pages = {56-68}, doi = {10.3382/ps/pey366}, pmid = {30137571}, issn = {1525-3171}, mesh = {Animal Feed/analysis ; Animal Nutritional Physiological Phenomena ; Animals ; Arecaceae/chemistry ; Cecum/*microbiology ; Chickens/*microbiology ; Diet/veterinary ; Firmicutes/isolation &amp; purification ; Gastrointestinal Microbiome/*drug effects/genetics ; Lactobacillus/isolation &amp; purification ; Male ; *Metagenome ; Oligosaccharides/pharmacology ; RNA, Ribosomal, 16S ; }, abstract = {The potential use of palm kernel expeller (PKE) as an alternative energy source in broiler diets is limited by the high fiber content. Although enzymatic treatment could alleviate the fiber component and increase the nutritive value of PKE, this apparent improvement is not reflected in the growth response of birds fed with the treated-PKE. As chicken's ceca are the most heavily populated with microflora within their gastrointestinal tract, it was hypothesized that any modulation of the intestinal environment by dietary treatments should be reflected by the composition and activities of the cecal microflora. There is a correlation between cecal microbiota composition and the efficiency of the host to extract energy from the diet and to deposit that energy into improved feed conversion ratio. At present, little is known about the changes on cecal microflora of broilers fed with PKE diets. Hence, this study was designed to assess the effects of feeding different forms of PKE; namely untreated PKE (UPKE), enzyme-treated PKE (EPKE), and oligosaccharides extracted from PKE (OligoPKE), on the cecal microbiota of broiler chickens at 14 d old (day 14) and 28 d old (day 28) using 16S rRNA gene high-throughput next-generation sequencing method. The results showed that temporal changes in cecal microbiota of broiler chickens were evident on day 14 and day 28. The relative abundance of phylum Firmicutes, known to be involved in nutrient uptake and absorption in both age groups was higher in the UPKE as compared to EPKE group. In addition, supplementation of OligoPKE increased (P < 0.05) the relative abundance of Lactobacillus on both D14 and D28, signifying its effect as prebiotics in enhancing growth of indigenous Lactobacillus. Our results showed that cecal microbiota was significantly modulated by dietary treatments and that the lower relative abundance of phylum Firmicutes in chickens fed with EPKE could be a reason why broiler chickens fed with EPKE of higher metabolizable energy (ME) content did not show improvement in their growth performance.}, }
@article {pmid30134786, year = {2018}, author = {Denning, NL and Prince, JM}, title = {Neonatal intestinal dysbiosis in necrotizing enterocolitis.}, journal = {Molecular medicine (Cambridge, Mass.)}, volume = {24}, number = {1}, pages = {4}, pmid = {30134786}, issn = {1528-3658}, mesh = {Animals ; Anti-Bacterial Agents/therapeutic use ; *Dysbiosis/chemically induced ; *Enterocolitis, Necrotizing/immunology/microbiology ; *Gastrointestinal Microbiome ; Histamine H2 Antagonists/therapeutic use ; Humans ; Infant, Newborn ; Toll-Like Receptors/immunology ; }, abstract = {Necrotizing Enterocolitis (NEC) is one of the most devastating gastrointestinal diseases in neonates, particularly among preterm infants in whom surgical NEC is the leading cause of morbidity. NEC pathophysiology occurs in the hyper-reactive milieu of the premature gut after bacterial colonization. The resultant activation of the TLR4 pathway appears to be a strongly contributing factor. Advancements in metagenomics may yield new clarity to the relationship between the neonatal intestinal microbiome and the development of NEC. After a century without effective directed treatments, microbiome manipulation offers a promising therapeutic target for the prevention and treatment of this devastating disease.}, }
@article {pmid30131068, year = {2018}, author = {Jiao, S and Chen, W and Wang, J and Du, N and Li, Q and Wei, G}, title = {Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {146}, pmid = {30131068}, issn = {2049-2618}, mesh = {Archaea/*classification/genetics/isolation &amp; purification/metabolism ; Bacteria/*classification/genetics/isolation &amp; purification/metabolism ; Biodiversity ; Fungi/*classification/genetics/isolation &amp; purification/metabolism ; Metagenomics ; Nutrients/metabolism ; Phylogeny ; Plant Roots/microbiology ; Sequence Analysis, DNA ; Soil/chemistry ; Soil Microbiology ; Trees/*growth &amp; development/microbiology ; }, abstract = {BACKGROUND: Soil microbiomes play an important role in the services and functioning of terrestrial ecosystems. However, little is known of their vertical responses to restoration process and their contributions to soil nutrient cycling in the subsurface profiles. Here, we investigated the community assembly of soil bacteria, archaea, and fungi along vertical (i.e., soil depths of 0-300 cm) and horizontal (i.e., distance from trees of 30-90 cm) profiles in a chronosequence of reforestation sites that represent over 30 years of restoration.<br><br>RESULTS: In the superficial layers (0-80 cm), bacterial and fungal diversity decreased, whereas archaeal diversity increased with increasing soil depth. As reforestation proceeded over time, the vertical spatial variation in bacterial communities decreased, while that in archaeal and fungal communities increased. Vertical distributions of the soil microbiomes were more related to the variation in soil properties, while their horizontal distributions may be driven by a gradient effect of roots extending from the tree. Bacterial and archaeal beta-diversity were strongly related to multi-nutrient cycling in the soil, respectively, playing major roles in deep and superficial layers.<br><br>CONCLUSIONS: Taken together, these results reveal a new perspective on the vertical and horizontal spatial variation in soil microbiomes at the fine scale of single trees. Distinct response patterns underpinned the contributions of soil bacteria, archaea, and fungi as a function of subsurface nutrient cycling during the reforestation of ex-arable land.}, }
@article {pmid30129704, year = {2018}, author = {Macher, JN and Vivancos, A and Piggott, JJ and Centeno, FC and Matthaei, CD and Leese, F}, title = {Comparison of environmental DNA and bulk-sample metabarcoding using highly degenerate cytochrome c oxidase I primers.}, journal = {Molecular ecology resources}, volume = {18}, number = {6}, pages = {1456-1468}, doi = {10.1111/1755-0998.12940}, pmid = {30129704}, issn = {1755-0998}, mesh = {Aquatic Organisms/classification/*genetics ; DNA/chemistry/*genetics/isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/*genetics ; Electron Transport Complex IV/*genetics ; *Fresh Water ; Metagenomics/*methods ; New Zealand ; Rivers ; }, abstract = {Freshwater biodiversity provides important ecosystem services and is at the core of water quality monitoring worldwide. To assess freshwater biodiversity, genetic methods such as metabarcoding are increasingly used as they are faster and allow better taxonomic resolution than manual identification methods. Either sampled organisms are used directly for &quot;bulk metabarcoding,&quot; or water is filtered and the extracted environmental DNA serves as a proxy for biodiversity via &quot;eDNA metabarcoding.&quot; Despite the advantages of both methods, questions remain regarding their comparability and applicability for routine biomonitoring and stressor impact assessment. Therefore, we compared metabarcoding results from bulk and eDNA samples taken from 19 streams spanning a wide gradient of farming intensities in New Zealand. We performed PCR with highly degenerate cytochrome c oxidase I primers and sequenced libraries on an Illumina MiSeq. The inferred community composition differed strongly between the two methods. More taxa were captured by eDNA than bulk-sample metabarcoding (5,819 vs. 1,483), but more of the commonly used invertebrate bioindicator taxa (mayflies, stoneflies and caddisflies) were found in bulk (47) than eDNA samples (37). Catchment-wide and local land use impacts on communities were detected better by eDNA metabarcoding, especially for non-metazoan taxa. Our findings imply that bulk-sample metabarcoding resembles classical freshwater biomonitoring approaches better, as more indicator macroinvertebrate taxa are captured. However, eDNA metabarcoding might be better suited to infer the impact of stressors on stream ecosystems at larger scales, as many new and potentially more informative taxa are registered. We therefore suggest exploring both methods in future assessments of stream biodiversity.}, }
@article {pmid30128756, year = {2018}, author = {Mukhtar, S and Mirza, BS and Mehnaz, S and Mirza, MS and Mclean, J and Malik, KA}, title = {Impact of soil salinity on the microbial structure of halophyte rhizosphere microbiome.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {34}, number = {9}, pages = {136}, pmid = {30128756}, issn = {1573-0972}, support = {Project # HEC (FD/2012/1843)//Higher Education Commission, Pakistan/ ; Project # 5-9/PAS/2012/969//Pakistan Academy of Sciences/ ; }, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; DNA, Bacterial ; Ecosystem ; Metagenomics ; Microbiota/genetics/*physiology ; Pakistan ; Phylogeny ; Plant Roots/microbiology ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; *Salinity ; Salt-Tolerant Plants/classification/*microbiology ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {The rhizosphere microbiome plays a significant role in the life of plants in promoting plant survival under adverse conditions. However, limited information is available about microbial diversity in saline environments. In the current study, we compared the composition of the rhizosphere microbiomes of the halophytes Urochloa, Kochia, Salsola, and Atriplex living in moderate and high salinity environments (Khewra salt mines; Pakistan) with that of the non-halophyte Triticum. Soil microbiomes analysis using pyrosequencing of 16S rRNA gene indicated that Actinobacteria were dominant in saline soil samples whereas Proteobacteria predominated in non-saline soil samples. Firmicutes, Acidobacteria, Bacteriodetes and Thaumarchaeota were predominant phyla in saline and non-saline soils, whereas Cyanobacteria, Verrucomicrobia, Gemmatimonadetes and the unclassified WPS-2 were less abundant. Sequences from Euryarchaeota, Ignavibacteriae, and Nanohaloarchaeota were identified only from the rhizosphere of halophytes. Dominant halophilic bacteria and archaea identified in this study included Agrococcus, Armatimonadetes gp4, Halalkalicoccus, Haloferula and Halobacterium. Our analysis showed that increases in soil salinity correlated with significant differences in the alpha and beta diversity of the microbial communities across saline and non-saline soil samples. Having a complete inventory of the soil bacteria from different saline environments in Pakistan will help in the discovery of potential inoculants for crops growing on salt-affected land.}, }
@article {pmid30126456, year = {2018}, author = {Milani, C and Casey, E and Lugli, GA and Moore, R and Kaczorowska, J and Feehily, C and Mangifesta, M and Mancabelli, L and Duranti, S and Turroni, F and Bottacini, F and Mahony, J and Cotter, PD and McAuliffe, FM and van Sinderen, D and Ventura, M}, title = {Tracing mother-infant transmission of bacteriophages by means of a novel analytical tool for shotgun metagenomic datasets: METAnnotatorX.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {145}, pmid = {30126456}, issn = {2049-2618}, mesh = {Bacteriophages/*classification/genetics/isolation &amp; purification ; Computational Biology/*methods/standards ; Feces/*virology ; Female ; Gastrointestinal Microbiome ; Genotype ; Humans ; Infant, Newborn ; Male ; Metagenomics/*methods/standards ; Mothers ; Sequence Analysis, DNA/methods ; Software ; }, abstract = {BACKGROUND: Despite the relevance of viral populations, our knowledge of (bacterio) phage populations, i.e., the phageome, suffers from the absence of a &quot;gold standard&quot; protocol for viral DNA extraction with associated in silico sequence processing analyses. To overcome this apparent hiatus, we present here a comprehensive performance evaluation of various protocols and propose an optimized pipeline that covers DNA extraction, sequencing, and bioinformatic analysis of phageome data.<br><br>RESULTS: Five widely used protocols for viral DNA extraction from fecal samples were tested for their performance in removal of non-viral DNA. Moreover, we developed a novel bioinformatic platform, METAnnotatorX, for metagenomic dataset analysis. This in silico tool facilitates a range of read- and assembly-based analyses, including taxonomic profiling using an iterative multi-database pipeline, classification of contigs at genus and species level, as well as functional characterizations of reads and assembled data. Performances of METAnnotatorX were assessed through investigation of seven mother-newborn pairs, leading to the identification of shared phage genotypes, of which two were genomically decoded and characterized. METAnnotatorX was furthermore employed to evaluate a protocol for the identification of contaminant non-viral DNA in sequenced datasets and was exploited to determine the amount of metagenomic data needed for robust evaluation of human adult-derived (fecal) phageomes.<br><br>CONCLUSIONS: Results obtained in this study demonstrate that a comprehensive pipeline for analysis of phageomes will be pivotal for future explorations of the ecology of phages in the gut environment as well as for understanding their impact on the physiology and bacterial community kinetics as players of dysbiosis and homeostasis in the gut microbiota.}, }
@article {pmid30124863, year = {2018}, author = {McGrath, C}, title = {Up in the Air: The Emerging Science of Dust and Sandstorm Microbes.}, journal = {Genome biology and evolution}, volume = {10}, number = {8}, pages = {2008-2009}, pmid = {30124863}, issn = {1759-6653}, mesh = {*Dust ; Health ; Humans ; Metagenomics ; *Microbiota ; Soil Microbiology ; }, }
@article {pmid30123190, year = {2018}, author = {Roscini, L and Tristezza, M and Corte, L and Colabella, C and Perrotta, C and Rampino, P and Robert, V and Vu, D and Cardinali, G and Grieco, F}, title = {Early Ongoing Speciation of Ogataea uvarum Sp. Nov. Within the Grape Ecosystem Revealed by the Internal Variability Among the rDNA Operon Repeats.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1687}, pmid = {30123190}, issn = {1664-302X}, abstract = {A yeast strain was isolated during a study on vineyard-associated yeast strains from Apulia in Southern Italy. ITS and LSU D1/D2 rDNA sequences showed this strain not to belong to any known species and was described as the type strain of Ogataea uvarum sp. nov., a close relative of O. philodendri. Several secondary peaks appeared in the sequences, suggesting internal heterogeneity among the copies of the rDNA. This hypothesis was tested by sequencing single clones of the marker region. The analyses showed different levels of variability throughout the operon with differences between the rRNA encoding genes and the internally transcribed regions. O. uvarum and O. philodendri share high frequency variants, i.e., variants frequently found in many clones, whereas there is a large variability of the low frequency polymorphisms, suggesting that the mechanism of homogenization is more active with the former than with the latter type of variation. These findings indicate that low frequency variants are detected in Sanger sequencing as secondary peaks whereas in Next Generation Sequencing (NGS) of metagenomics DNA would lead to an overestimate of the alpha diversity. For the first time in our knowledge, this investigation shed light on the variation of the copy number of the rDNA cistron during the yeast speciation process. These polymorphisms can be used to investigate on the processes occurring in these taxonomic markers during the separation of fungal species, it being a genetic process highly frequent in the complex microbial ecosystem existing in grape, must and wine.}, }
@article {pmid30122883, year = {2018}, author = {Zhao, Y and Mao, YF and Tang, YS and Ni, MZ and Liu, QH and Wang, Y and Feng, Q and Peng, JH and Hu, YY}, title = {Altered oral microbiota in chronic hepatitis B patients with different tongue coatings.}, journal = {World journal of gastroenterology}, volume = {24}, number = {30}, pages = {3448-3461}, pmid = {30122883}, issn = {2219-2840}, mesh = {Adult ; Bacteria/genetics/*isolation &amp; purification/metabolism ; Case-Control Studies ; DNA, Viral/isolation &amp; purification ; Female ; Gastrointestinal Microbiome/*physiology ; Healthy Volunteers ; Hepatitis B virus/genetics/*isolation &amp; purification ; Hepatitis B, Chronic/diagnosis/metabolism/*microbiology ; Humans ; Male ; Medicine, Chinese Traditional/methods ; Metagenomics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Tongue/*microbiology ; }, abstract = {AIM: To elucidate tongue coating microbiota and metabolic differences in chronic hepatitis B (CHB) patients with yellow or white tongue coatings.<br><br>METHODS: Tongue coating samples were collected from 53 CHB patients (28 CHB yellow tongue coating patients and 25 CHB white tongue coating patients) and 22 healthy controls. Microbial DNA was extracted from the tongue samples, and the bacterial 16S ribosomal RNA gene V3 region was amplified from all samples and sequenced with the Ion Torrent PGM™ sequencing platform according to the standard protocols. The metabolites in the tongue coatings were evaluated using a liquid chromatography-mass spectrometry (LC-MS) platform. Statistical analyses were then performed.<br><br>RESULTS: The relative compositions of the tongue coating microbiotas and metabolites in the CHB patients were significantly different from those of the healthy controls, but the tongue coating microbiota abundances and diversity levels were not significantly different. Compared with the CHB white tongue coating patients, the CHB yellow tongue coating patients had higher hepatitis B viral DNA (HBV-DNA) titers (median 21210 vs 500, respectively, P = 0.03) and a significantly lower level of Bacteroidetes (20.14% vs 27.93%, respectively, P = 0.013) and higher level of Proteobacteria (25.99% vs 18.17%, respectively, P = 0.045) in the microbial compositions at the phylum level. The inferred metagenomic pathways enriched in the CHB yellow tongue coating patients were mainly those involved in amino acid metabolism, which was consistent with the metabolic disorder. The abundances of bacteria from Bacteroidales at the order level were higher in the CHB white tongue coating patients (19.2% vs 27.22%, respectively, P = 0.011), whereas Neisseriales were enriched in the yellow tongue coating patients (21.85% vs 13.83%, respectively, P = 0.029). At the family level, the abundance of Neisseriaceae in the yellow tongue patients was positively correlated with the HBV-DNA level but negatively correlated with the S-adenosyl-L-methionine level.<br><br>CONCLUSION: This research illustrates specific clinical features and bacterial structures in CHB patients with different tongue coatings, which facilitates understanding of the traditional tongue diagnosis.}, }
@article {pmid30121535, year = {2019}, author = {Bedoya, K and Coltell, O and Cabarcas, F and Alzate, JF}, title = {Metagenomic assessment of the microbial community and methanogenic pathways in biosolids from a municipal wastewater treatment plant in Medellín, Colombia.}, journal = {The Science of the total environment}, volume = {648}, number = {}, pages = {572-581}, doi = {10.1016/j.scitotenv.2018.08.119}, pmid = {30121535}, issn = {1879-1026}, mesh = {Colombia ; *Metagenome ; Methane/*biosynthesis ; *Microbiota/genetics ; Solid Waste/*analysis ; *Waste Disposal, Fluid ; Waste Water/*microbiology ; }, abstract = {Abundance and diversity of microbial communities in biosolids are variable and poorly studied in the tropics, and it is known that rainfall is one of the events that could affect the phylogenetic and functional microbial structure. In the present study, using NGS technics, we studied the microbial diversity as well as the methanogenesis pathway in one of the largest WWTP in Colombia. Besides, we sampled and analyzed biosolids from rainy season and dry season. Phylogenetic classification showed a predominance of bacteria in both samples and difference in the dominant groups depending on the rainfall season. Whereas Pseudomonas was the dominant bacteria in the dry season, Coprothermobacter was in the rainy season. Archaea abundance was higher in the rainy season (11.5%) doubling dry season proportion. The bioreactor biogas production and total solids content showed similar results between rainy and dry season at the sampling dates. The most abundant Archaea related with methanogenesis was Methanosaeta, which is a methanogenic microorganism that exclusively uses acetate to produce methane. Moreover, annotation of the methanogenic pathway in the metagenome showed abundance in genes encoding Acetyl-CoA synthetases (ACSS), an enzyme that catalyzes acetate activation. Our results suggest that the microbial diversity was stable among the two time points tested, rainy season and dry season; and, although there were changes in the microbial abundance of dominant bacterial species, anaerobic digester performance is not affected.}, }
@article {pmid30118379, year = {2019}, author = {Ito, T and Sekizuka, T and Kishi, N and Yamashita, A and Kuroda, M}, title = {Conventional culture methods with commercially available media unveil the presence of novel culturable bacteria.}, journal = {Gut microbes}, volume = {10}, number = {1}, pages = {77-91}, doi = {10.1080/19490976.2018.1491265}, pmid = {30118379}, issn = {1949-0984}, mesh = {Bacteria/classification/genetics/*growth &amp; development/*isolation &amp; purification ; *Bacteriological Techniques ; Culture Media ; Feces/microbiology ; Gastrointestinal Microbiome/genetics/*physiology ; Genome, Bacterial/genetics ; Humans ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Recent metagenomic analysis has revealed that our gut microbiota plays an important role in not only the maintenance of our health but also various diseases such as obesity, diabetes, inflammatory bowel disease, and allergy. However, most intestinal bacteria are considered 'unculturable' bacteria, and their functions remain unknown. Although culture-independent genomic approaches have enabled us to gain insight into their potential roles, culture-based approaches are still required to understand their characteristic features and phenotypes. To date, various culturing methods have been attempted to obtain these 'unculturable' bacteria, but most such methods require advanced techniques. Here, we have tried to isolate possible unculturable bacteria from a healthy Japanese individual by using commercially available media. A 16S rRNA (ribosomal RNA) gene metagenomic analysis revealed that each culture medium showed bacterial growth depending on its selective features and a possibility of the presence of novel bacterial species. Whole genome sequencing of these candidate strains suggested the isolation of 8 novel bacterial species classified in the Actinobacteria and Firmicutes phyla. Our approach indicates that a number of intestinal bacteria hitherto considered unculturable are potentially culturable and can be cultured on commercially available media. We have obtained novel gut bacteria from a healthy Japanese individual using a combination of comprehensive genomics and conventional culturing methods. We would expect that the discovery of such novel bacteria could illuminate pivotal roles for the gut microbiota in association with human health.}, }
@article {pmid30110928, year = {2018}, author = {Wu, L and Wang, J and Wu, H and Chen, J and Xiao, Z and Qin, X and Zhang, Z and Lin, W}, title = {Comparative Metagenomic Analysis of Rhizosphere Microbial Community Composition and Functional Potentials under Rehmannia glutinosa Consecutive Monoculture.}, journal = {International journal of molecular sciences}, volume = {19}, number = {8}, pages = {}, pmid = {30110928}, issn = {1422-0067}, mesh = {*Bacteria/classification/genetics/growth &amp; development ; *Metagenome ; Microbial Consortia/*physiology ; Rehmannia/*microbiology ; *Rhizosphere ; *Soil Microbiology ; }, abstract = {Consecutive monoculture of Rehmannia glutinosa, highly valued in traditional Chinese medicine, leads to a severe decline in both quality and yield. Rhizosphere microbiome was reported to be closely associated with the soil health and plant performance. In this study, comparative metagenomics was applied to investigate the shifts in rhizosphere microbial structures and functional potentials under consecutive monoculture. The results showed R. glutinosa monoculture significantly decreased the relative abundances of Pseudomonadaceae and Burkholderiaceae, but significantly increased the relative abundances of Sphingomonadaceae and Streptomycetaceae. Moreover, the abundances of genera Pseudomonas, Azotobacter, Burkholderia, and Lysobacter, among others, were significantly lower in two-year monocultured soil than in one-year cultured soil. For potentially harmful/indicator microorganisms, the percentages of reads categorized to defense mechanisms (i.e., ATP-binding cassette (ABC) transporters, efflux transporter, antibiotic resistance) and biological metabolism (i.e., lipid transport and metabolism, secondary metabolites biosynthesis, transport and catabolism, nucleotide transport and metabolism, transcription) were significantly higher in two-year monocultured soil than in one-year cultured soil, but the opposite was true for potentially beneficial microorganisms, which might disrupt the equilibrium between beneficial and harmful microbes. Collectively, our results provide important insights into the shifts in genomic diversity and functional potentials of rhizosphere microbiome in response to R. glutinosa consecutive monoculture.}, }
@article {pmid30108167, year = {2018}, author = {Peura, S and Buck, M and Aalto, SL and Morales, SE and Nykänen, H and Eiler, A}, title = {Novel Autotrophic Organisms Contribute Significantly to the Internal Carbon Cycling Potential of a Boreal Lake.}, journal = {mBio}, volume = {9}, number = {4}, pages = {}, pmid = {30108167}, issn = {2150-7511}, mesh = {Anaerobiosis ; *Autotrophic Processes ; *Biota ; Carbon/*metabolism ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Finland ; Lakes/*microbiology ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Oxygen-stratified lakes are typical for the boreal zone and also a major source of greenhouse gas emissions in the region. Due to shallow light penetration, restricting the growth of phototrophic organisms, and large allochthonous organic carbon inputs from the catchment area, the lake metabolism is expected to be dominated by heterotrophic organisms. In this study, we test this assumption and show that the potential for autotrophic carbon fixation and internal carbon cycling is high throughout the water column. Further, we show that during the summer stratification carbon fixation can exceed respiration in a boreal lake even below the euphotic zone. Metagenome-assembled genomes and 16S profiling of a vertical transect of the lake revealed multiple organisms in an oxygen-depleted compartment belonging to novel or poorly characterized phyla. Many of these organisms were chemolithotrophic, potentially deriving their energy from reactions related to sulfur, iron, and nitrogen transformations. The community, as well as the functions, was stratified along the redox gradient. The autotrophic potential in the lake metagenome below the oxygenic zone was high, pointing toward a need for revising our concepts of internal carbon cycling in boreal lakes. Further, the importance of chemolithoautotrophy for the internal carbon cycling suggests that many predicted climate change-associated fluctuations in the physical properties of the lake, such as altered mixing patterns, likely have consequences for the whole-lake metabolism even beyond the impact to the phototrophic community.IMPORTANCE Autotrophic organisms at the base of the food web are the only life form capable of turning inorganic carbon into the organic form, facilitating the survival of all other organisms. In certain environments, the autotrophic production is limited by environmental conditions and the food web is supported by external carbon inputs. One such environment is stratified boreal lakes, which are one of the biggest natural sources of greenhouse gas emissions in the boreal region. Thus, carbon cycling in these habitats is of utmost importance for the future climate. Here, we demonstrate a high potential for internal carbon cycling via phototrophic and novel chemolithotrophic organisms in the anoxic, poorly illuminated layers of a boreal lake. Our results significantly increase our knowledge on the microbial communities and their metabolic potential in oxygen-depleted freshwaters and help to understand and predict how climate change-induced alterations could impact the lake carbon dynamics.}, }
@article {pmid30106226, year = {2018}, author = {Heeger, F and Bourne, EC and Baschien, C and Yurkov, A and Bunk, B and Spröer, C and Overmann, J and Mazzoni, CJ and Monaghan, MT}, title = {Long-read DNA metabarcoding of ribosomal RNA in the analysis of fungi from aquatic environments.}, journal = {Molecular ecology resources}, volume = {18}, number = {6}, pages = {1500-1514}, doi = {10.1111/1755-0998.12937}, pmid = {30106226}, issn = {1755-0998}, support = {SAW-2014-IGB-1//Leibniz Association/ ; }, mesh = {Aquatic Organisms/classification/genetics ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Fungi/*classification/*genetics ; Metagenomics/*methods ; Phylogeny ; RNA, Fungal/*genetics ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; }, abstract = {DNA metabarcoding is widely used to study prokaryotic and eukaryotic microbial diversity. Technological constraints limit most studies to marker lengths below 600 base pairs (bp). Longer sequencing reads of several thousand bp are now possible with third-generation sequencing. Increased marker lengths provide greater taxonomic resolution and allow for phylogenetic methods of classification, but longer reads may be subject to higher rates of sequencing error and chimera formation. In addition, most bioinformatics tools for DNA metabarcoding were designed for short reads and are therefore unsuitable. Here, we used Pacific Biosciences circular consensus sequencing (CCS) to DNA-metabarcode environmental samples using a ca. 4,500 bp marker that included most of the eukaryote SSU and LSU rRNA genes and the complete ITS region. We developed an analysis pipeline that reduced error rates to levels comparable to short-read platforms. Validation using a mock community indicated that our pipeline detected 98% of chimeras de novo. We recovered 947 OTUs from water and sediment samples from a natural lake, 848 of which could be classified to phylum, 397 to genus and 330 to species. By allowing for the simultaneous use of three databases (Unite, SILVA and RDP LSU), long-read DNA metabarcoding provided better taxonomic resolution than any single marker. We foresee the use of long reads enabling the cross-validation of reference sequences and the synthesis of ribosomal rRNA gene databases. The universal nature of the rRNA operon and our recovery of >100 nonfungal OTUs indicate that long-read DNA metabarcoding holds promise for studies of eukaryotic diversity more broadly.}, }
@article {pmid30102711, year = {2018}, author = {Watanabe, K and Igarashi, M and Li, X and Nakatani, A and Miyamoto, J and Inaba, Y and Sutou, A and Saito, T and Sato, T and Tachibana, N and Inoue, H and Kimura, I}, title = {Dietary soybean protein ameliorates high-fat diet-induced obesity by modifying the gut microbiota-dependent biotransformation of bile acids.}, journal = {PloS one}, volume = {13}, number = {8}, pages = {e0202083}, pmid = {30102711}, issn = {1932-6203}, mesh = {Animals ; Bile Acids and Salts/*metabolism ; Biodiversity ; Diet, High-Fat/adverse effects ; Dietary Supplements ; Gastrointestinal Microbiome/*drug effects ; Glucagon-Like Peptide 1/metabolism ; Intestinal Mucosa/drug effects/metabolism/microbiology ; Male ; Metabolic Networks and Pathways/*drug effects ; Metagenome ; Metagenomics/methods ; Mice ; Obesity/*etiology/*metabolism ; Soybean Proteins/*pharmacology ; }, abstract = {The consumption of soybean protein has well-known favorable metabolic effects (e.g., reduced body weight, body fat, hyperglycemia, insulin resistance, hepatic steatosis, and lipogenesis). These effects of soy protein have been linked to modulation by the gut microbiota; however, the dynamic interplay among these factors remains unclear. Accordingly, we examined the metabolic phenotype, intestinal BA pool, and the gut microbiome of male C57BL/6 mice that were randomized to receive either a regular high-fat diet (HFD) or HFD that contained soybean protein isolate (SPI) in place of dairy protein. The intake of SPI significantly reduced the HFD-induced weight gain and adipose tissue mass accumulation and attenuated hepatic steatosis. Along with an enhancement in the secretion of intestinal Glucagon-like peptide-1 (GLP-1), an enlarged cecal BA pool with an elevated secondary/primary BA ratio was observed in the mice that consumed SPI, while fecal BA excretion remained unaltered. SPI also elicited dramatic changes in the gut microbiome, characterized by an expansion of taxa that may be involved in the biotransformation of BAs. The observed effects were abolished in germ-free (GF) mice, indicating that they were dependent on the microbiota. These findings collectively indicate that the metabolic benefits of SPI under the HFD regime may arise from a microbiota-driven increase in BA transformation and increase in GLP-1 secretion.}, }
@article {pmid30092815, year = {2018}, author = {Murali, A and Bhargava, A and Wright, ES}, title = {IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {140}, pmid = {30092815}, issn = {2049-2618}, mesh = {Bacteria/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; Machine Learning ; Metagenomics/*methods ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Software ; }, abstract = {BACKGROUND: Microbiome studies often involve sequencing a marker gene to identify the microorganisms in samples of interest. Sequence classification is a critical component of this process, whereby sequences are assigned to a reference taxonomy containing known sequence representatives of many microbial groups. Previous studies have shown that existing classification programs often assign sequences to reference groups even if they belong to novel taxonomic groups that are absent from the reference taxonomy. This high rate of &quot;over classification&quot; is particularly detrimental in microbiome studies because reference taxonomies are far from comprehensive.<br><br>RESULTS: Here, we introduce IDTAXA, a novel approach to taxonomic classification that employs principles from machine learning to reduce over classification errors. Using multiple reference taxonomies, we demonstrate that IDTAXA has higher accuracy than popular classifiers such as BLAST, MAPSeq, QIIME, SINTAX, SPINGO, and the RDP Classifier. Similarly, IDTAXA yields far fewer over classifications on Illumina mock microbial community data when the expected taxa are absent from the training set. Furthermore, IDTAXA offers many practical advantages over other classifiers, such as maintaining low error rates across varying input sequence lengths and withholding classifications from input sequences composed of random nucleotides or repeats.<br><br>CONCLUSIONS: IDTAXA's classifications may lead to different conclusions in microbiome studies because of the substantially reduced number of taxa that are incorrectly identified through over classification. Although misclassification error is relatively minor, we believe that many remaining misclassifications are likely caused by errors in the reference taxonomy. We describe how IDTAXA is able to identify many putative mislabeling errors in reference taxonomies, enabling training sets to be automatically corrected by eliminating spurious sequences. IDTAXA is part of the DECIPHER package for the R programming language, available through the Bioconductor repository or accessible online (http://DECIPHER.codes).}, }
@article {pmid30091981, year = {2018}, author = {Bradley, PH and Nayfach, S and Pollard, KS}, title = {Phylogeny-corrected identification of microbial gene families relevant to human gut colonization.}, journal = {PLoS computational biology}, volume = {14}, number = {8}, pages = {e1006242}, pmid = {30091981}, issn = {1553-7358}, support = {T32 GM067547/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Gastrointestinal Microbiome/*genetics/physiology ; Gene Expression Regulation, Bacterial/genetics ; Genes, Microbial/genetics ; Humans ; Metagenome ; Metagenomics/*methods ; Microbiota/genetics ; Phylogeny ; }, abstract = {The mechanisms by which different microbes colonize the healthy human gut versus other body sites, the gut in disease states, or other environments remain largely unknown. Identifying microbial genes influencing fitness in the gut could lead to new ways to engineer probiotics or disrupt pathogenesis. We approach this problem by measuring the statistical association between a species having a gene and the probability that the species is present in the gut microbiome. The challenge is that closely related species tend to be jointly present or absent in the microbiome and also share many genes, only a subset of which are involved in gut adaptation. We show that this phylogenetic correlation indeed leads to many false discoveries and propose phylogenetic linear regression as a powerful solution. To apply this method across the bacterial tree of life, where most species have not been experimentally phenotyped, we use metagenomes from hundreds of people to quantify each species' prevalence in and specificity for the gut microbiome. This analysis reveals thousands of genes potentially involved in adaptation to the gut across species, including many novel candidates as well as processes known to contribute to fitness of gut bacteria, such as acid tolerance in Bacteroidetes and sporulation in Firmicutes. We also find microbial genes associated with a preference for the gut over other body sites, which are significantly enriched for genes linked to fitness in an in vivo competition experiment. Finally, we identify gene families associated with higher prevalence in patients with Crohn's disease, including Proteobacterial genes involved in conjugation and fimbria regulation, processes previously linked to inflammation. These gene targets may represent new avenues for modulating host colonization and disease. Our strategy of combining metagenomics with phylogenetic modeling is general and can be used to identify genes associated with adaptation to any environment.}, }
@article {pmid30086347, year = {2018}, author = {Miró-Abella, E and Torrell, H and Herrero, P and Canela, N and Arola, L and Borrull, F and Ras, R and Fontanals, N}, title = {Monitoring and evaluation of the interaction between deoxynivalenol and gut microbiota in Wistar rats by mass spectrometry-based metabolomics and next-generation sequencing.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {121}, number = {}, pages = {124-130}, doi = {10.1016/j.fct.2018.08.006}, pmid = {30086347}, issn = {1873-6351}, mesh = {Animals ; Chromatography, High Pressure Liquid/methods ; Feces/chemistry ; Gastrointestinal Microbiome/*drug effects ; High-Throughput Nucleotide Sequencing/*methods ; Metabolomics/*methods ; Metagenomics ; Mycotoxins/analysis/*toxicity ; No-Observed-Adverse-Effect Level ; RNA, Ribosomal, 16S/metabolism ; Rats ; Rats, Wistar ; Tandem Mass Spectrometry/*methods ; Trichothecenes/analysis/*toxicity ; }, abstract = {Published evidence has demonstrated the several toxic characteristics of mycotoxins and their considerable risk to human and animal health. One of the most common uncertainties regards whether if very low concentrations of the mycotoxin deoxynivalenol (DON), easily consumed within the Mediterranean Diet, can cause metabolic alterations; some of them produced by the interaction between DON and gut microbiota. Accordingly, faecal samples were collected from Wistar rats that had consumed the mycotoxin DON at low levels (60 and 120 μg kg-1 body weight of DON per day), and were analysed by ultra-high performance liquid chromatography coupled with tandem mass spectrometry detection, in order to monitor the mycotoxin DON and its metabolite de-epoxy deoxynivalenol (DOM-1). The obtained results showed an evolution in DON excretion and the metabolite DOM-1 which has less toxic properties, over the course of the days of the study. To elucidate whether intestinal microbiota had a role in the observed detoxification process, the changes in microbial gut biodiversity were explored through 16s rRNA high throughput sequencing. No main changes were detected but significant increase in Coprococcus genus relative abundance was found. Further studies are needed to confirm if intestinal microbiota composition and function are affected by low mycotoxin concentrations.}, }
@article {pmid30081953, year = {2018}, author = {Zhu, J and Liao, M and Yao, Z and Liang, W and Li, Q and Liu, J and Yang, H and Ji, Y and Wei, W and Tan, A and Liang, S and Chen, Y and Lin, H and Zhu, X and Huang, S and Tian, J and Tang, R and Wang, Q and Mo, Z}, title = {Breast cancer in postmenopausal women is associated with an altered gut metagenome.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {136}, pmid = {30081953}, issn = {2049-2618}, mesh = {Adult ; Bacteria/*classification/genetics ; Bacterial Proteins/genetics ; Breast Neoplasms/metabolism/*microbiology ; C-Reactive Protein/metabolism ; Case-Control Studies ; Estradiol/metabolism ; Female ; *Gastrointestinal Microbiome ; Gene Regulatory Networks ; Humans ; Metagenomics/*methods ; Middle Aged ; Phylogeny ; Postmenopause/metabolism ; Premenopause/metabolism ; }, abstract = {BACKGROUND: Increasing evidence suggests that gut microbiota play a role in the pathogenesis of breast cancer. The composition and functional capacity of gut microbiota associated with breast cancer have not been studied systematically.<br><br>METHODS: We performed a comprehensive shotgun metagenomic analysis of 18 premenopausal breast cancer patients, 25 premenopausal healthy controls, 44 postmenopausal breast cancer patients, and 46 postmenopausal healthy controls.<br><br>RESULTS: Microbial diversity was higher in breast cancer patients than in controls. Relative species abundance in gut microbiota did not differ significantly between premenopausal breast cancer patients and premenopausal controls. In contrast, relative abundance of 45 species differed significantly between postmenopausal patients and postmenopausal controls: 38 species were enriched in postmenopausal patients, including Escherichia coli, Klebsiella sp_1_1_55, Prevotella amnii, Enterococcus gallinarum, Actinomyces sp. HPA0247, Shewanella putrefaciens, and Erwinia amylovora, and 7 species were less abundant in postmenopausal patients, including Eubacterium eligens and Lactobacillus vaginalis. Acinetobacter radioresistens and Enterococcus gallinarum were positively but weakly associated with expression of high-sensitivity C-reactive protein; Shewanella putrefaciens and Erwinia amylovora were positively but weakly associated with estradiol levels. Actinomyces sp. HPA0247 negatively but weakly correlated with CD3+CD8+ T cell numbers. Further characterization of metagenome functional capacity indicated that the gut metagenomes of postmenopausal breast cancer patients were enriched in genes encoding lipopolysaccharide biosynthesis, iron complex transport system, PTS system, secretion system, and beta-oxidation.<br><br>CONCLUSION: The composition and functions of the gut microbial community differ between postmenopausal breast cancer patients and healthy controls. The gut microbiota may regulate or respond to host immunity and metabolic balance. Thus, while cause and effect cannot be determined, there is a reproducible change in the microbiota of treatment-naive patients relative to matched controls.}, }
@article {pmid30077182, year = {2018}, author = {Ye, Z and Zhang, N and Wu, C and Zhang, X and Wang, Q and Huang, X and Du, L and Cao, Q and Tang, J and Zhou, C and Hou, S and He, Y and Xu, Q and Xiong, X and Kijlstra, A and Qin, N and Yang, P}, title = {A metagenomic study of the gut microbiome in Behcet's disease.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {135}, pmid = {30077182}, issn = {2049-2618}, mesh = {Animals ; Bacteria/*classification/genetics/isolation &amp; purification ; Bacterial Capsules/genetics ; Behcet Syndrome/*microbiology ; Case-Control Studies ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Fecal Microbiota Transplantation ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Gene Expression Regulation, Bacterial ; Humans ; Male ; Metagenomics/*methods ; Mice ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Saliva/microbiology ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Behcet's disease (BD) is a recalcitrant, multisystemic inflammatory disease that can lead to irreversible blindness. Microbial agents have been considered to contribute to the pathogenesis of this disease, but the underlying mechanisms remain unclear. In this study, we investigated the association of gut microbiome composition with BD as well as its possible roles in the development of this disease.<br><br>METHODS: Fecal and saliva samples were collected from 32 active BD patients and 74 healthy controls. DNA extracted from fecal samples was subjected to metagenomic analysis, whereas DNA extracted from saliva samples was subjected to 16S rRNA gene sequencing analysis. The results were used to compare the composition and biological function of the microbiome between patients and healthy controls. Lastly, transplantation of pooled fecal samples from active BD patients into B10RIII mice undergoing experimental autoimmune uveitis (EAU) was performed to determine the causal relationship between the gut microbiome and BD.<br><br>RESULTS: Fecal samples from active BD patients were shown to be enriched in Bilophila spp., a sulfate-reducing bacteria (SRB) and several opportunistic pathogens (e.g., Parabacteroides spp. and Paraprevotella spp.) along with a lower level of butyrate-producing bacteria (BPB) Clostridium spp. and methanogens (Methanoculleus spp. Methanomethylophilus spp.). Analysis of microbial functions revealed that capsular polysaccharide transport system, oxidation-reduction process, type III, and type IV secretion systems were also increased in active BD patients. Network analysis showed that the BD-enriched SRB and opportunistic pathogens were positively correlated with each other, but they were negatively associated with the BPB and methanogens. Animal experiments revealed that fecal microbiota transplantation with feces from BD patients significantly exacerbated EAU activity and increased the production of inflammatory cytokines including IL-17 and IFN-γ.<br><br>CONCLUSIONS: Our findings revealed that BD is associated with considerable gut microbiome changes, which is corroborated by a mouse study of fecal microbiota transplants. A model explaining the association of the gut microbiome composition with BD pathogenesis is proposed.}, }
@article {pmid30076897,