@article {pmid29705928, year = {2018}, author = {Bonilla, JO and Kurth, DG and Cid, FD and Ulacco, JH and Gil, RA and Villegas, LB}, title = {Prokaryotic and eukaryotic community structure affected by the presence of an acid mine drainage from an abandoned gold mine.}, journal = {Extremophiles : life under extreme conditions}, volume = {22}, number = {5}, pages = {699-711}, doi = {10.1007/s00792-018-1030-y}, pmid = {29705928}, issn = {1433-4909}, support = {PICT 2013 No. 3170//Agencia Nacional de Promoción Científica y Tecnológica/ ; }, mesh = {Acids/analysis ; Actinobacteria/isolation & purification ; Diatoms/isolation & purification ; *Extreme Environments ; Fungi/isolation & purification ; Gammaproteobacteria/isolation & purification ; Geologic Sediments/chemistry/*microbiology ; Gold/analysis ; Metagenome ; Metals, Heavy/analysis ; *Microbiota ; Mining ; }, abstract = {The acid mine drainage that originates in the abandoned gold mine in San Luis, Argentina, is released into La Carolina stream. The aim of this study was to determine the influence of this mine drainage on the physicochemical parameters of the area studied and on both prokaryotic and eukaryotic community structure. In addition, specific relationships between microbial taxonomic groups and physicochemical parameters were established. The drainage that flows into La Carolina stream acidifies the stream and increases its sulfate, Zn, Cd and Te concentrations. Microbial analysis showed that prokaryotic community structure is mainly affected by pH values. Actinobacteria and Gammaproteobacteria were abundant in samples characterized by low pH values, while Nitrospirae, Chloroflexi, Deltaproteobacteria, Thaumarchaeota and Euryarchaeota were associated with high concentrations of heavy metals. Otherwise, Alphaproteobacteria was present in samples taken in sunlit areas. Regarding eukaryotic community structure, the sunlight had the greatest impact. Inside the mine, in the absence of light, fungi and protists members were the most abundant microorganisms, while those samples taken in the presence of light displayed algae (green algae and diatoms) as the most abundant ones. After receiving the mine drainage, the stream showed a decrease in the diatom abundance and green algae predominated.}, }
@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 = {}, doi = {10.3390/ijms19082394}, pmid = {30110928}, issn = {1422-0067}, mesh = {*Bacteria/classification/genetics/growth & 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 {pmid29040451, year = {2018}, author = {Chen, J and King, E and Deek, R and Wei, Z and Yu, Y and Grill, D and Ballman, K and Stegle, O}, title = {An omnibus test for differential distribution analysis of microbiome sequencing data.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {4}, pages = {643-651}, doi = {10.1093/bioinformatics/btx650}, pmid = {29040451}, issn = {1367-4811}, mesh = {Arthritis, Rheumatoid/microbiology ; Humans ; Inflammatory Bowel Diseases/microbiology ; Metagenomics/*methods ; Microbiota/*genetics ; *Models, Statistical ; *Software ; }, abstract = {Motivation: One objective of human microbiome studies is to identify differentially abundant microbes across biological conditions. Previous statistical methods focus on detecting the shift in the abundance and/or prevalence of the microbes and treat the dispersion (spread of the data) as a nuisance. These methods also assume that the dispersion is the same across conditions, an assumption which may not hold in presence of sample heterogeneity. Moreover, the widespread outliers in the microbiome sequencing data make existing parametric models not overly robust. Therefore, a robust and powerful method that allows covariate-dependent dispersion and addresses outliers is still needed for differential abundance analysis.
Results: We introduce a novel test for differential distribution analysis of microbiome sequencing data by jointly testing the abundance, prevalence and dispersion. The test is built on a zero-inflated negative binomial regression model and winsorized count data to account for zero-inflation and outliers. Using simulated data and real microbiome sequencing datasets, we show that our test is robust across various biological conditions and overall more powerful than previous methods.
R package is available at https://github.com/jchen1981/MicrobiomeDDA.
Contact: chen.jun2@mayo.edu or zhiwei@njit.edu.
Supplementary information: Supplementary data are available at Bioinformatics online.}, }
@article {pmid28322295, year = {2017}, author = {Li, TH and Qin, Y and Sham, PC and Lau, KS and Chu, KM and Leung, WK}, title = {Alterations in Gastric Microbiota After H. Pylori Eradication and in Different Histological Stages of Gastric Carcinogenesis.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {44935}, doi = {10.1038/srep44935}, pmid = {28322295}, issn = {2045-2322}, mesh = {Biodiversity ; *Cell Transformation, Neoplastic ; Female ; Gastric Mucosa/*microbiology/*physiology ; Helicobacter Infections/*complications/*microbiology ; *Helicobacter pylori ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Microbiota ; Stomach Neoplasms/*etiology/*pathology ; }, abstract = {The role of bacteria other than Helicobacter pylori (HP) in the stomach remains elusive. We characterized the gastric microbiota in individuals with different histological stages of gastric carcinogenesis and after receiving HP eradication therapy. Endoscopic gastric biopsies were obtained from subjects with HP gastritis, gastric intestinal metaplasia (IM), gastric cancer (GC) and HP negative controls. Gastric microbiota was characterized by Illumina MiSeq platform targeting the 16 S rDNA. Apart from dominant H. pylori, we observed other Proteobacteria including Haemophilus, Serratia, Neisseria and Stenotrophomonas as the major components of the human gastric microbiota. Although samples were largely converged according to the relative abundance of HP, a clear separation of GC and other samples was recovered. Whilst there was a strong inverse association between HP relative abundance and bacterial diversity, this association was weak in GC samples which tended to have lower bacterial diversity compared with other samples with similar HP levels. Eradication of HP resulted in an increase in bacterial diversity and restoration of the relative abundance of other bacteria to levels similar to individuals without HP. In conclusion, HP colonization results in alterations of gastric microbiota and reduction in bacterial diversity, which could be restored by antibiotic treatment.}, }
@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}, doi = {10.3389/fmicb.2018.02556}, 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 {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 & derivatives/analysis ; *Gastrointestinal Microbiome ; *Hot Temperature ; Humans ; Lysine/analogs & 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 {pmid29788417, year = {2018}, author = {Patil, RD and Ellison, MJ and Wolff, SM and Shearer, C and Wright, AM and Cockrum, RR and Austin, KJ and Lamberson, WR and Cammack, KM and Conant, GC}, title = {Poor feed efficiency in sheep is associated with several structural abnormalities in the community metabolic network of their ruminal microbes.}, journal = {Journal of animal science}, volume = {96}, number = {6}, pages = {2113-2124}, doi = {10.1093/jas/sky096}, pmid = {29788417}, issn = {1525-3163}, mesh = {Animal Feed/*analysis ; Animals ; Female ; *Gastrointestinal Microbiome ; *Metabolic Networks and Pathways ; *Metagenomics ; Rumen/metabolism/microbiology ; Sheep/microbiology/*physiology ; }, abstract = {Ruminant animals have a symbiotic relationship with the microorganisms in their rumens. In this relationship, rumen microbes efficiently degrade complex plant-derived compounds into smaller digestible compounds, a process that is very likely associated with host animal feed efficiency. The resulting simpler metabolites can then be absorbed by the host and converted into other compounds by host enzymes. We used a microbial community metabolic network inferred from shotgun metagenomics data to assess how this metabolic system differs between animals that are able to turn ingested feedstuffs into body mass with high efficiency and those that are not. We conducted shotgun sequencing of microbial DNA from the rumen contents of 16 sheep that differed in their residual feed intake (RFI), a measure of feed efficiency. Metagenomic reads from each sheep were mapped onto a database-derived microbial metabolic network, which was linked to the sheep metabolic network by interface metabolites (metabolites transferred from microbes to host). No single enzyme was identified as being significantly different in abundance between the low and high RFI animals (P > 0.05, Wilcoxon test). However, when we analyzed the metabolic network as a whole, we found several differences between efficient and inefficient animals. Microbes from low RFI (efficient) animals use a suite of enzymes closer in network space to the host's reactions than those of the high RFI (inefficient) animals. Similarly, low RFI animals have microbial metabolic networks that, on average, contain reactions using shorter carbon chains than do those of high RFI animals, potentially allowing the host animals to extract metabolites more efficiently. Finally, the efficient animals possess community networks with greater Shannon diversity among their enzymes than do inefficient ones. Thus, our system approach to the ruminal microbiome identified differences attributable to feed efficiency in the structure of the microbes' community metabolic network that were undetected at the level of individual microbial taxa or reactions.}, }
@article {pmid28349946, year = {2017}, author = {Yan, W and Sun, C and Yuan, J and Yang, N}, title = {Gut metagenomic analysis reveals prominent roles of Lactobacillus and cecal microbiota in chicken feed efficiency.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {45308}, doi = {10.1038/srep45308}, pmid = {28349946}, issn = {2045-2322}, mesh = {Amino Acids/metabolism ; Animal Feed ; Animals ; Bacteria/genetics/isolation & purification ; Biodiversity ; Cecum/microbiology ; Chickens ; Duodenum/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Lactobacillus/genetics/*isolation & purification ; *Metagenomics ; Phenotype ; RNA, Ribosomal, 16S/chemistry/genetics/metabolism ; Sequence Analysis, DNA ; }, abstract = {Interactions between the host and gut microbiota can affect gut metabolism. In this study, the individual performances of 252 hens were recorded to evaluate feed efficiency. Hens with contrasting feed efficiencies (14 birds per group) were selected to investigate their duodenal, cecal and fecal microbial composition by sequencing the 16S rRNA gene V4 region. The results showed that the microbial community in the cecum was quite different from those in the duodenum and feces. The highest biodiversity and all differentially abundant taxa between the different efficiency groups were observed in the cecal microbial community with false discovery rate (FDR) <0.05. Of these differentially abundant cecal microbes, Lactobacillus accounted for a greater proportion than the others. The abundances of Lactobacillus and Akkermansia were significantly higher while that of Faecalibacterium was lower (FDR < 0.05) in the better feed efficiency (BFE) group. Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis revealed that the functions relating to glycometabolism and amino acid metabolism were enriched in the cecal microbiota of the BFE group. These results indicated the prominent role of cecal microbiota in the feed efficiency of chickens and suggested plausible uses of Lactobacillus to improve the feed efficiency of host.}, }
@article {pmid28112173, year = {2017}, author = {Ji, P and Zhang, Y and Wang, J and Zhao, F}, title = {MetaSort untangles metagenome assembly by reducing microbial community complexity.}, journal = {Nature communications}, volume = {8}, number = {}, pages = {14306}, doi = {10.1038/ncomms14306}, pmid = {28112173}, issn = {2041-1723}, mesh = {Bacteria/*genetics ; Computational Biology ; Genome, Bacterial ; Genome, Microbial ; Kelp/*microbiology ; *Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA/methods ; *Software ; }, abstract = {Most current approaches to analyse metagenomic data rely on reference genomes. Novel microbial communities extend far beyond the coverage of reference databases and de novo metagenome assembly from complex microbial communities remains a great challenge. Here we present a novel experimental and bioinformatic framework, metaSort, for effective construction of bacterial genomes from metagenomic samples. MetaSort provides a sorted mini-metagenome approach based on flow cytometry and single-cell sequencing methodologies, and employs new computational algorithms to efficiently recover high-quality genomes from the sorted mini-metagenome by the complementary of the original metagenome. Through extensive evaluations, we demonstrated that metaSort has an excellent and unbiased performance on genome recovery and assembly. Furthermore, we applied metaSort to an unexplored microflora colonized on the surface of marine kelp and successfully recovered 75 high-quality genomes at one time. This approach will greatly improve access to microbial genomes from complex or novel communities.}, }
@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 = {}, doi = {10.3390/v10090479}, 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 & 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 {pmid28696003, year = {2018}, author = {Malanoski, AP and Lin, B and Eddie, BJ and Wang, Z and Hervey, WJ and Glaven, SM}, title = {Relative abundance of 'Candidatus Tenderia electrophaga' is linked to cathodic current in an aerobic biocathode community.}, journal = {Microbial biotechnology}, volume = {11}, number = {1}, pages = {98-111}, doi = {10.1111/1751-7915.12757}, pmid = {28696003}, issn = {1751-7915}, mesh = {*Bioelectric Energy Sources ; *Biota ; Carbon Dioxide/metabolism ; Chromatiaceae/classification/genetics/*isolation & purification/*metabolism ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Electrodes/*microbiology ; Metagenomics ; Oxidation-Reduction ; Oxygen/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Biocathode microbial communities are proposed to catalyse a range of useful reactions. Unlike bioanodes, model biocathode organisms have not yet been successfully cultivated in isolation highlighting the need for culture-independent approaches to characterization. Biocathode MCL (Marinobacter, Chromatiaceae, Labrenzia) is a microbial community proposed to couple CO2 fixation to extracellular electron transfer and O2 reduction. Previous metagenomic analysis of a single MCL bioelectrochemical system (BES) resulted in resolution of 16 bin genomes. To further resolve bin genomes and compare community composition across replicate MCL BES, we performed shotgun metagenomic and 16S rRNA gene (16S) sequencing at steady-state current. Clustering pooled reads from replicate BES increased the number of resolved bin genomes to 20, over half of which were > 90% complete. Direct comparison of unassembled metagenomic reads and 16S operational taxonomic units (OTUs) predicted higher community diversity than the assembled/clustered metagenome and the predicted relative abundances did not match. However, when 16S OTUs were mapped to bin genomes and genome abundance was scaled by 16S gene copy number, estimated relative abundance was more similar to metagenomic analysis. The relative abundance of the bin genome representing 'Ca. Tenderia electrophaga' was correlated with increasing current, further supporting the hypothesis that this organism is the electroautotroph.}, }
@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}, doi = {10.3748/wjg.v24.i30.3448}, pmid = {30122883}, issn = {2219-2840}, mesh = {Adult ; Bacteria/genetics/*isolation & purification/metabolism ; Case-Control Studies ; DNA, Viral/isolation & purification ; Female ; Gastrointestinal Microbiome/*physiology ; Healthy Volunteers ; Hepatitis B virus/genetics/*isolation & 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.
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.
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.
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 {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}, doi = {10.3389/fmicb.2018.02520}, 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 {pmid28255158, year = {2017}, author = {Jandhyala, SM and Madhulika, A and Deepika, G and Rao, GV and Reddy, DN and Subramanyam, C and Sasikala, M and Talukdar, R}, title = {Altered intestinal microbiota in patients with chronic pancreatitis: implications in diabetes and metabolic abnormalities.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {43640}, doi = {10.1038/srep43640}, pmid = {28255158}, issn = {2045-2322}, mesh = {Adult ; Biodiversity ; Case-Control Studies ; Diabetes Mellitus, Type 2/diagnosis/*etiology ; Disease Progression ; *Dysbiosis ; Energy Metabolism ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metabolic Diseases/diagnosis/*etiology ; Metagenome ; Metagenomics/methods ; Middle Aged ; Pancreatitis, Chronic/*complications/diagnosis ; }, abstract = {Intestinal dysbiosis and its functional implications in chronic pancreatitis (CP) have not been elaborately studied. We evaluated the taxonomic and functional alterations in intestinal microbiota in 30 well-characterised patients with CP (16 without, 14 with diabetes) and 10 healthy controls. The patients with CP and diabetes had significantly longer disease duration and greater degree of malnutrition. There was increase in plasma endotoxin concentrations from controls to CP non-diabetics to CP diabetics. We observed significant differences in richness and alpha diversity between the groups. We also observed increase in the Firmicutes:Bacteroidetes ratio in CP patients without and with diabetes. There was reduction in abundance of Faecalibacterium prausnitzii and Ruminococcus bromii from controls to CP non-diabetics to CP diabetics. On the other hand, there was increase in LPS (endotoxin) synthetic pathways (KEGG orthology) in the groups. Faecalibacterium prausnitzii abundance correlated negatively with plasma endotoxin and glycemic status; while plasma endotoxin correlated positively with blood glucose and negatively with plasma insulin. Our results have important implications for future studies exploring mechanistic insights on secondary diabetes in CP.}, }
@article {pmid28240318, year = {2017}, author = {Lee, ST and Davy, SK and Tang, SL and Kench, PS}, title = {Water flow buffers shifts in bacterial community structure in heat-stressed Acropora muricata.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {43600}, doi = {10.1038/srep43600}, pmid = {28240318}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*microbiology/*physiology ; Bacteria/*classification/genetics ; *Biodiversity ; Environment ; *Hot Temperature ; Metagenome ; Metagenomics/methods ; Seasons ; Seawater ; *Stress, Physiological ; *Symbiosis ; Temperature ; Vibrio/classification/genetics ; }, abstract = {Deterioration of coral health and associated change in the coral holobiont's bacterial community are often a result of different environmental stressors acting synergistically. There is evidence that water flow is important for a coral's resistance to elevated seawater temperature, but there is no information on how water flow affects the coral-associated bacterial community under these conditions. In a laboratory cross-design experiment, Acropora muricata nubbins were subjected to interactive effects of seawater temperature (27 °C to 31 °C) and water flow (0.20 m s-1 and 0.03 m s-1). In an in situ experiment, water flow manipulation was conducted with three colonies of A. muricata during the winter and summer, by partially enclosing each colony in a clear plastic mesh box. 16S rRNA amplicon pyrosequencing showed an increase in the relative abundance of Flavobacteriales and Rhodobacterales in the laboratory experiment, and Vibrio spp. in the in situ experiment when corals were exposed to elevated temperature and slow water flow. In contrast, corals that were exposed to faster water flow under laboratory and in situ conditions had a stable bacterial community. These findings indicate that water flow plays an important role in the maintenance of specific coral-bacteria associations during times of elevated thermal stress.}, }
@article {pmid29076296, year = {2017}, author = {de la Calle, F}, title = {Marine microbiome as source of natural products.}, journal = {Microbial biotechnology}, volume = {10}, number = {6}, pages = {1293-1296}, doi = {10.1111/1751-7915.12882}, pmid = {29076296}, issn = {1751-7915}, mesh = {Biological Products/*metabolism ; Biotechnology/methods ; Data Mining/methods ; Metabolic Networks and Pathways/genetics ; Metagenomics ; *Microbiota ; Seawater/*microbiology ; }, }
@article {pmid30041354, year = {2018}, author = {Tiralerdpanich, P and Sonthiphand, P and Luepromchai, E and Pinyakong, O and Pokethitiyook, P}, title = {Potential microbial consortium involved in the biodegradation of diesel, hexadecane and phenanthrene in mangrove sediment explored by metagenomics analysis.}, journal = {Marine pollution bulletin}, volume = {133}, number = {}, pages = {595-605}, doi = {10.1016/j.marpolbul.2018.06.015}, pmid = {30041354}, issn = {1879-3363}, mesh = {Alkanes/*metabolism ; Bacteria/genetics/metabolism ; Biodegradation, Environmental ; Environmental Pollutants/metabolism ; Gasoline ; Geologic Sediments/*microbiology ; Metagenomics/methods ; Microbial Consortia/genetics/*physiology ; Phenanthrenes/*metabolism ; RNA, Ribosomal, 16S/metabolism ; Thailand ; Wetlands ; }, abstract = {Hydrocarbon contamination is a serious problem that degrades the quality of mangrove ecosystems, and bioremediation using autochthonous bacteria is a promising technology to recover an impacted environment. This research investigates the biodegradation rates of diesel, hexadecane and phenanthrene, by conducting a microcosm study and survey of the autochthonous microbial community in contaminated mangrove sediment, using an Illumina MiSeq platform. The biodegradation rates of diesel, hexadecane and phenanthrene were 82, 86 and 8 mg kg-1 sediment day-1, respectively. The removal efficiencies of hexadecane and phenanthrene were >99%, whereas the removal efficiency of diesel was 88%. A 16S rRNA gene amplicon sequence analysis revealed that the major bacterial assemblages detected were Gammaproteobacteria, Deltaproteobacteria, Alphaproteobacteria. The bacterial compositions were relatively constant, while reductions of the supplemented hydrocarbons were observed. The results imply that the autochthonous microorganisms in the mangrove sediment were responsible for the degradation of the respective hydrocarbons. Diesel-, hexadecane- and phenanthrene-degrading bacteria, namely Bacillus sp., Pseudomonas sp., Acinetobacter sp. and Staphylococcus sp., were also isolated from the mangrove sediment. The mangrove sediment provides a potential resource of effective hydrocarbon-degrading bacteria that can be used as an inoculum or further developed as a ready-to-use microbial consortium for the purpose of bioremediation.}, }
@article {pmid28252037, year = {2017}, author = {Aoki, R and Kamikado, K and Suda, W and Takii, H and Mikami, Y and Suganuma, N and Hattori, M and Koga, Y}, title = {A proliferative probiotic Bifidobacterium strain in the gut ameliorates progression of metabolic disorders via microbiota modulation and acetate elevation.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {43522}, doi = {10.1038/srep43522}, pmid = {28252037}, issn = {2045-2322}, mesh = {Acetates/*metabolism ; Animals ; Bifidobacterium/*metabolism ; Disease Models, Animal ; *Gastrointestinal Microbiome ; Glucose/metabolism ; Glucose Intolerance/metabolism/therapy ; Male ; Metabolic Diseases/etiology/*metabolism/therapy ; Metagenome ; Metagenomics/methods ; Mice ; *Probiotics ; }, abstract = {The gut microbiota is an important contributor to the worldwide prevalence of metabolic syndrome (MS), which includes obesity and diabetes. The anti-MS effects exerted by Bifidobacterium animalis ssp. lactis GCL2505 (BlaG), a highly proliferative Bifidobacterium strain in the gut, and B. longum ssp. longum JCM1217T (BloJ) were comparatively examined. BlaG treatment reduced visceral fat accumulation and improved glucose tolerance, whereas BloJ had no effect on these parameters. Gut microbial analysis revealed that BlaG exerted stronger effects on the overall bacterial structure of the gut microbiota than BloJ, including enrichment of the genus Bifidobacterium. The levels of acetate and glucagon-like peptide-1 were increased by BlaG treatment in both the gut and plasma, but not by BloJ treatment. Correlation analysis suggested that the elevation of gut acetate levels by BlaG treatment plays a pivotal role in the BlaG-induced anti-MS effects. These findings indicated that BlaG, a highly viable and proliferative probiotic, improves metabolic disorders by modulating gut microbiota, which results in the elevation of SCFAs, especially acetate.}, }
@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 & purification/metabolism ; Bacteria/classification/genetics/isolation & 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 {pmid29471863, year = {2018}, author = {Petrosino, JF}, title = {The microbiome in precision medicine: the way forward.}, journal = {Genome medicine}, volume = {10}, number = {1}, pages = {12}, doi = {10.1186/s13073-018-0525-6}, pmid = {29471863}, issn = {1756-994X}, support = {R01 AI108588/AI/NIAID NIH HHS/United States ; HHSN267200700014C/DK/NIDDK NIH HHS/United States ; R01 MH112356/MH/NIMH NIH HHS/United States ; U19 AI116497/AI/NIAID NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; }, mesh = {Disease ; Humans ; *Microbiota ; Phenotype ; *Precision Medicine ; }, abstract = {Novel associations between the human microbiome and health and disease are routinely emerging, and important host-microbiome interactions are targets for new diagnostics and therapeutics. Understanding how broadly host-microbe associations are maintained across populations is revealing individualized host-microbiome phenotypes that can be integrated with other 'omics' data sets to enhance precision medicine.}, }
@article {pmid28396267, year = {2017}, author = {Puehler, A and Kalinowski, J}, title = {Microbial genomics and metagenomics in human health and disease.}, journal = {Journal of biotechnology}, volume = {250}, number = {}, pages = {1}, doi = {10.1016/j.jbiotec.2017.04.007}, pmid = {28396267}, issn = {1873-4863}, mesh = {Bacteria/genetics ; Bacterial Infections/*genetics ; Bacteriophages/genetics ; *Genome, Bacterial ; Genomics ; Humans ; Microbiota ; Sequence Analysis, DNA ; }, }
@article {pmid28785417, year = {2016}, author = {Jameson, E and Doxey, AC and Airs, R and Purdy, KJ and Murrell, JC and Chen, Y}, title = {Metagenomic data-mining reveals contrasting microbial populations responsible for trimethylamine formation in human gut and marine ecosystems.}, journal = {Microbial genomics}, volume = {2}, number = {9}, pages = {e000080}, doi = {10.1099/mgen.0.000080}, pmid = {28785417}, issn = {2057-5858}, mesh = {Actinobacteria/enzymology/*genetics ; *Data Mining ; *Ecosystem ; Gastrointestinal Microbiome/*genetics ; Geologic Sediments/microbiology ; Humans ; *Metagenomics ; Methylamines/*metabolism ; Oxidoreductases, N-Demethylating/genetics ; Proteobacteria/enzymology/*genetics ; }, abstract = {Existing metagenome datasets from many different environments contain untapped potential for understanding metabolic pathways and their biological impact. Our interest lies in the formation of trimethylamine (TMA), a key metabolite in both human health and climate change. Here, we focus on bacterial degradation pathways for choline, carnitine, glycine betaine and trimethylamine N-oxide (TMAO) to TMA in human gut and marine metagenomes. We found the TMAO reductase pathway was the most prevalent pathway in both environments. Proteobacteria were found to contribute the majority of the TMAO reductase pathway sequences, except in the stressed gut, where Actinobacteria dominated. Interestingly, in the human gut metagenomes, a high proportion of the Proteobacteria hits were accounted for by the genera Klebsiella and Escherichia. Furthermore Klebsiella and Escherichia harboured three of the four potential TMA-production pathways (choline, carnitine and TMAO), suggesting they have a key role in TMA cycling in the human gut. In addition to the intensive TMAO-TMA cycling in the marine environment, our data suggest that carnitine-to-TMA transformation plays an overlooked role in aerobic marine surface waters, whereas choline-to-TMA transformation is important in anaerobic marine sediments. Our study provides new insights into the potential key microbes and metabolic pathways for TMA formation in two contrasting environments.}, }
@article {pmid28211884, year = {2017}, author = {Li, Z and Lu, L and Guo, J and Yang, J and Zhang, J and He, B and Xu, L}, title = {Responses of spatial-temporal dynamics of bacterioplankton community to large-scale reservoir operation: a case study in the Three Gorges Reservoir, China.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {42469}, doi = {10.1038/srep42469}, pmid = {28211884}, issn = {2045-2322}, mesh = {*Bacteroidetes ; *Biodiversity ; China ; Chlorophyll/analysis ; Environment ; Geography ; Metagenome ; Metagenomics/methods ; *Plankton ; Rivers/*microbiology ; Spatio-Temporal Analysis ; *Water Microbiology ; }, abstract = {Large rivers are commonly regulated by damming, yet the effects of such disruption on bacterioplankton community structures have not been adequately studied. The aim of this study was to explore the biogeographical patterns present under dam regulation and to uncover the major drivers structuring bacterioplankton communities. Bacterioplankton assemblages in the Three Gorges Reservoir (TGR) were analyzed using Illumina Miseq sequencing by comparing seven sites located within the TGR before and after impoundment. This approach revealed ecological and spatial-temporal variations in bacterioplankton community composition along the longitudinal axis. The community was dynamic and dominated by Proteobacteria and Actinobacteria phyla, encompassing 39.26% and 37.14% of all sequences, respectively, followed by Bacteroidetes (8.67%) and Cyanobacteria (3.90%). The Shannon-Wiener index of the bacterioplankton community in the flood season (August) was generally higher than that in the impoundment season (November). Principal Component Analysis of the bacterioplankton community compositions showed separation between different seasons and sampling sites. Results of the relationship between bacterioplankton community compositions and environmental variables highlighted that ecological processes of element cycling and large dam disturbances are of prime importance in driving the assemblages of riverine bacterioplankton communities.}, }
@article {pmid28198425, year = {2017}, author = {Leite, MF and Pan, Y and Bloem, J and Berge, HT and Kuramae, EE}, title = {Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {42634}, doi = {10.1038/srep42634}, pmid = {28198425}, issn = {2045-2322}, mesh = {Bacteria ; Carbon/chemistry/metabolism ; Fungi ; Metagenome ; Metagenomics/methods ; Microbiota ; Nitrogen/*chemistry/*metabolism ; *Soil Microbiology ; }, abstract = {Use of organic amendments is a valuable strategy for crop production. However, it remains unclear how organic amendments shape both soil microbial community structure and activity, and how these changes impact nutrient mineralization rates. We evaluated the effect of various organic amendments, which range in Carbon/Nitrogen (C/N) ratio and degradability, on the soil microbiome in a mesocosm study at 32, 69 and 132 days. Soil samples were collected to determine community structure (assessed by 16S and 18S rRNA gene sequences), microbial biomass (fungi and bacteria), microbial activity (leucine incorporation and active hyphal length), and carbon and nitrogen mineralization rates. We considered the microbial soil DNA as the microbial seedbank. High C/N ratio favored fungal presence, while low C/N favored dominance of bacterial populations. Our results suggest that organic amendments shape the soil microbial community structure through a feedback mechanism by which microbial activity responds to changing organic inputs and rearranges composition of the microbial seedbank. We hypothesize that the microbial seedbank composition responds to changing organic inputs according to the resistance and resilience of individual species, while changes in microbial activity may result in increases or decreases in availability of various soil nutrients that affect plant nutrient uptake.}, }
@article {pmid28198423, year = {2017}, author = {Montella, S and Ventorino, V and Lombard, V and Henrissat, B and Pepe, O and Faraco, V}, title = {Discovery of genes coding for carbohydrate-active enzyme by metagenomic analysis of lignocellulosic biomasses.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {42623}, doi = {10.1038/srep42623}, pmid = {28198423}, issn = {2045-2322}, mesh = {Biodegradation, Environmental ; *Biomass ; Biotransformation ; Carbohydrate Metabolism/*genetics ; Cellulases/*genetics/*metabolism ; Computational Biology/methods ; Crops, Agricultural ; Gene Expression Profiling ; Glycoside Hydrolases/genetics/metabolism ; High-Throughput Nucleotide Sequencing ; Hydrolysis ; Lignin/*metabolism ; *Metagenome ; *Metagenomics/methods ; Microbiota ; Open Reading Frames ; Polysaccharides/metabolism ; }, abstract = {In this study, a high-throughput sequencing approach was applied to discover novel biocatalysts for lignocellulose hydrolysis from three dedicated energy crops, Arundo donax, Eucalyptus camaldulensis and Populus nigra, after natural biodegradation. The microbiomes of the three lignocellulosic biomasses were dominated by bacterial species (approximately 90%) with the highest representation by the Streptomyces genus both in the total microbial community composition and in the microbial diversity related to GH families of predicted ORFs. Moreover, the functional clustering of the predicted ORFs showed a prevalence of poorly characterized genes, suggesting these lignocellulosic biomasses are potential sources of as yet unknown genes. 1.2%, 0.6% and 3.4% of the total ORFs detected in A. donax, E. camaldulensis and P. nigra, respectively, were putative Carbohydrate-Active Enzymes (CAZymes). Interestingly, the glycoside hydrolases abundance in P. nigra (1.8%) was higher than that detected in the other biomasses investigated in this study. Moreover, a high percentage of (hemi)cellulases with different activities and accessory enzymes (mannanases, polygalacturonases and feruloyl esterases) was detected, confirming that the three analyzed samples were a reservoir of diversified biocatalysts required for an effective lignocellulose saccharification.}, }
@article {pmid29660711, year = {2018}, author = {Kotoky, R and Rajkumari, J and Pandey, P}, title = {The rhizosphere microbiome: Significance in rhizoremediation of polyaromatic hydrocarbon contaminated soil.}, journal = {Journal of environmental management}, volume = {217}, number = {}, pages = {858-870}, doi = {10.1016/j.jenvman.2018.04.022}, pmid = {29660711}, issn = {1095-8630}, mesh = {Biodegradation, Environmental ; Hydrocarbons/*metabolism ; Microbiota ; Plant Roots ; *Rhizosphere ; Soil ; *Soil Microbiology ; Soil Pollutants ; }, abstract = {Microbial communities are an essential part of plant rhizosphere and participate in the functioning of plants, including rhizoremediation of petroleum contaminants. Rhizoremediation is a promising technology for removal of polyaromatic hydrocarbons based on interactions between plants and microbiome in the rhizosphere. Root exudation in the rhizosphere provides better nutrient uptake for rhizosphere microbiome, and therefore it is considered to be one of the major factors of microbial community function in the rhizosphere that plays a key role in the enhanced PAH biodegradation. Although the importance of the rhizosphere microbiome for plant growth has been widely recognized, the interactions between microbiome and plant roots in the process of rhizosphere mediated remediation of PAH still needs attention. Most of the current researches target PAH degradation by plant or single microorganism, separately, whereas the interactions between plants and whole microbiome are overlooked and its role has been ignored. This review summarizes recent knowledge of PAH degradation in the rhizosphere in the process of plant-microbiome interactions based on emerging omics approaches such as metagenomics, metatranscriptomics, metabolomics and metaproteomics. These omics approaches with combinations to bioinformatics tools provide us a better understanding in integrated activity patterns between plants and rhizosphere microbes, and insight into the biochemical and molecular modification of the meta-organisms (plant-microbiome) to maximize rhizoremediation activity. Moreover, a better understanding of the interactions could lead to the development of techniques to engineer rhizosphere microbiome for better hydrocarbon degradation.}, }
@article {pmid29032502, year = {2018}, author = {Santoro, A and Ostan, R and Candela, M and Biagi, E and Brigidi, P and Capri, M and Franceschi, C}, title = {Gut microbiota changes in the extreme decades of human life: a focus on centenarians.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {75}, number = {1}, pages = {129-148}, doi = {10.1007/s00018-017-2674-y}, pmid = {29032502}, issn = {1420-9071}, mesh = {Aged ; Aged, 80 and over ; Aging/genetics/*physiology ; *Diet ; Female ; Gastrointestinal Microbiome/*physiology ; Genetics, Population ; Humans ; Longevity/genetics/*physiology ; Male ; }, abstract = {The gut microbiota (GM) is a complex, evolutionarily molded ecological system, which contributes to a variety of physiological functions. The GM is highly dynamic, being sensitive to environmental stimuli, and its composition changes over the host's entire lifespan. However, the basic question of how much these changes may be ascribed to variables such as population, diet, genetics and gender, and/or to the aging process per se is still largely unanswered. We argue that comparison among studies on centenarians-the best model of healthy aging and longevity-recruited from different geographical areas/populations (different genetics and dietary habits) can help to disentangle the contribution of aging and non-aging-related variables to GM remodeling with age. The current review focuses on the role of population, gender and host genetics as possible drivers of GM modification along the human aging process. The feedback impact of age-associated GM variation on the GM-brain axis and GM metabolomics is also discussed. We likewise address the role of GM in neurodegenerative diseases such as Parkinson's and Alzheimer's, and its possible therapeutic use, taking advantage of the fact that centenarians are characterized by an extreme (healthy) phenotype versus patients suffering from age-related pathologies. Finally, it is argued that longitudinal studies combining metagenomics sequencing and in-depth phylogenetic analysis with a comprehensive phenotypic characterization of centenarians and patients using up-to-date omics (metabolomics, transcriptomics and meta-transcriptomics) are urgently needed.}, }
@article {pmid28983638, year = {2018}, author = {Turroni, F and Milani, C and Duranti, S and Ferrario, C and Lugli, GA and Mancabelli, L and van Sinderen, D and Ventura, M}, title = {Bifidobacteria and the infant gut: an example of co-evolution and natural selection.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {75}, number = {1}, pages = {103-118}, doi = {10.1007/s00018-017-2672-0}, pmid = {28983638}, issn = {1420-9071}, mesh = {Bifidobacterium/genetics/*physiology ; Evolution, Molecular ; Gastrointestinal Microbiome/genetics/*physiology ; Gastrointestinal Tract/metabolism/*microbiology ; Humans ; Infant ; Microbial Interactions/genetics/*physiology ; Polysaccharides/metabolism ; Selection, Genetic ; Time Factors ; }, abstract = {Throughout the human life, the gut microbiota interacts with us in a number of different ways, thereby influencing our health status. The acquisition of such an interactive gut microbiota commences at birth. Medical and environmental factors including diet, antibiotic exposure and mode of delivery are major factors that shape the composition of the microbial communities in the infant gut. Among the most abundant members of the infant microbiota are species belonging to the Bifidobacterium genus, which are believed to confer beneficial effects upon their host. Bifidobacteria may be acquired directly from the mother by vertical transmission and their persistence in the infant gut is associated with their saccharolytic activity toward glycans that are abundant in the infant gut. Here, we discuss the establishment of the infant gut microbiota and the contribution of bifidobacteria to this early life microbial consortium.}, }
@article {pmid28176868, year = {2017}, author = {Yergeau, E and Michel, C and Tremblay, J and Niemi, A and King, TL and Wyglinski, J and Lee, K and Greer, CW}, title = {Metagenomic survey of the taxonomic and functional microbial communities of seawater and sea ice from the Canadian Arctic.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {42242}, doi = {10.1038/srep42242}, pmid = {28176868}, issn = {2045-2322}, mesh = {Arctic Regions ; Canada ; Databases, Genetic ; Geography ; Ice Cover/*microbiology ; Metagenomics/*methods ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; }, abstract = {Climate change has resulted in an accelerated decline of Arctic sea ice since 2001 resulting in primary production increases and prolongation of the ice-free season within the Northwest Passage. The taxonomic and functional microbial community composition of the seawater and sea ice of the Canadian Arctic is not very well known. Bacterial communities from the bottom layer of sea ice cores and surface water from 23 locations around Cornwallis Island, NU, Canada, were extensively screened. The bacterial 16S rRNA gene was sequenced for all samples while shotgun metagenomics was performed on selected samples. Bacterial community composition showed large variation throughout the sampling area both for sea ice and seawater. Seawater and sea ice samples harbored significantly distinct microbial communities, both at different taxonomic levels and at the functional level. A key difference between the two sample types was the dominance of algae in sea ice samples, as visualized by the higher relative abundance of algae and photosynthesis-related genes in the metagenomic datasets and the higher chl a concentrations. The relative abundance of various OTUs and functional genes were significantly correlated with multiple environmental parameters, highlighting many potential environmental drivers and ecological strategies.}, }
@article {pmid28169321, year = {2017}, author = {Xu, J and Wei, Y and Jia, H and Xiao, L and Gong, D}, title = {A new perspective on studying burial environment before archaeological excavation: analyzing bacterial community distribution by high-throughput sequencing.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {41691}, doi = {10.1038/srep41691}, pmid = {28169321}, issn = {2045-2322}, mesh = {*Archaeology ; Bacteria/classification/genetics ; Biodiversity ; *Burial ; High-Throughput Nucleotide Sequencing ; Hydrogen-Ion Concentration ; Metagenome ; Metagenomics/methods ; Microbiota ; Phylogeny ; Salinity ; Soil/chemistry ; *Soil Microbiology ; Water/chemistry ; }, abstract = {Burial conditions play a crucial role in archaeological heritage preservation. Especially, the microorganisms were considered as the leading causes which incurred degradation and vanishment of historic materials. In this article, we analyzed bacterial diversity and community structure from M1 of Wangshanqiao using 16 S rRNA gene amplicon sequencing. The results indicated that microbial communities in burial conditions were diverse among four different samples. The samples from the robber hole varied most obviously in community structure both in Alpha and Beta diversity. In addition, the dominant phylum in different samples were Proteobacteria, Actinobacteria and Bacteroidetes, respectively. Moreover, the study implied that historical materials preservation conditions had connections with bacterial community distribution. At the genus level, Acinetobacter might possess high ability in degrading organic culture heritage in burial conditions, while Bacteroides were associated closely with favorable preservation conditions. This method contributes to fetch information which would never recover after excavation, and it will help to explore microbial degradation on precious organic culture heritage and further our understanding of archaeological burial environment. The study also indicates that robbery has a serious negative impact on burial remains.}, }
@article {pmid28150710, year = {2017}, author = {Nguyen, D and Boberg, J and Cleary, M and Bruelheide, H and Hönig, L and Koricheva, J and Stenlid, J}, title = {Foliar fungi of Betula pendula: impact of tree species mixtures and assessment methods.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {41801}, doi = {10.1038/srep41801}, pmid = {28150710}, issn = {2045-2322}, mesh = {Betula/classification/*microbiology ; Biodiversity ; Ecosystem ; Fungi/*classification/*genetics ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/methods ; Plant Leaves/microbiology ; }, abstract = {Foliar fungi of silver birch (Betula pendula) in an experimental Finnish forest were investigated across a gradient of tree species richness using molecular high-throughput sequencing and visual macroscopic assessment. We hypothesized that the molecular approach detects more fungal taxa than visual assessment, and that there is a relationship among the most common fungal taxa detected by both techniques. Furthermore, we hypothesized that the fungal community composition, diversity, and distribution patterns are affected by changes in tree diversity. Sequencing revealed greater diversity of fungi on birch leaves than the visual assessment method. One species showed a linear relationship between the methods. Species-specific variation in fungal community composition could be partially explained by tree diversity, though overall fungal diversity was not affected by tree diversity. Analysis of specific fungal taxa indicated tree diversity effects at the local neighbourhood scale, where the proportion of birch among neighbouring trees varied, but not at the plot scale. In conclusion, both methods may be used to determine tree diversity effects on the foliar fungal community. However, high-throughput sequencing provided higher resolution of the fungal community, while the visual macroscopic assessment detected functionally active fungal species.}, }
@article {pmid28139751, year = {2017}, author = {Jia, HR and Dai, PL and Geng, LL and Jack, CJ and Li, YH and Wu, YY and Diao, QY and Ellis, JD}, title = {No effect of Bt Cry1Ie toxin on bacterial diversity in the midgut of the Chinese honey bees, Apis cerana cerana (Hymenoptera, Apidae).}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {41688}, doi = {10.1038/srep41688}, pmid = {28139751}, issn = {2045-2322}, mesh = {Animals ; Bacillus thuringiensis ; Bacterial Toxins/*pharmacology ; Bees/*drug effects/*microbiology ; *Biodiversity ; Cluster Analysis ; Gastrointestinal Microbiome/*drug effects ; Metagenome ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Cry1Ie protein derived from Bacillus thuringiensis (Bt) has been proposed as a promising candidate for the development of a new Bt-maize variety to control maize pests in China. We studied the response of the midgut bacterial community of Apis cerana cerana to Cry1Ie toxin under laboratory conditions. Newly emerged bees were fed one of the following treatments for 15 and 30 days: three concentrations of Cry1Ie toxin (20 ng/mL, 200 ng/mL, and 20 μg/mL) in sugar syrup, pure sugar syrup as a negative control and 48 ng/mL imidacloprid as a positive control. The relative abundance of 16S rRNA genes was measured by Quantitative Polymerase Chain Reaction and no apparent differences were found among treatments for any of these counts at any time point. Furthermore, the midgut bacterial structure and compositions were determined using high-throughput sequencing targeting the V3-V4 regions of the 16S rDNA. All core honey bee intestinal bacterial genera such as Lactobacillus, Bifidobacterium, Snodgrassella, and Gilliamella were detected, and no significant changes were found in the species diversity and richness for any bacterial taxa among treatments at different time points. These results suggest that Cry1Ie toxin may not affect gut bacterial communities of Chinese honey bees.}, }
@article {pmid28091525, year = {2017}, author = {Patrascu, O and Béguet-Crespel, F and Marinelli, L and Le Chatelier, E and Abraham, AL and Leclerc, M and Klopp, C and Terrapon, N and Henrissat, B and Blottière, HM and Doré, J and Béra-Maillet, C}, title = {A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {40248}, doi = {10.1038/srep40248}, pmid = {28091525}, issn = {2045-2322}, support = {322820//European Research Council/International ; }, mesh = {Bacteroides/metabolism ; Carbohydrate Metabolism ; Carboxymethylcellulose Sodium/metabolism ; Chromosome Mapping ; Clostridiales/metabolism ; Dietary Fiber/*metabolism/*microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Ileum/*microbiology ; Metagenome ; Metagenomics ; Xylans/metabolism ; }, abstract = {The digestion of dietary fibers is a major function of the human intestinal microbiota. So far this function has been attributed to the microorganisms inhabiting the colon, and many studies have focused on this distal part of the gastrointestinal tract using easily accessible fecal material. However, microbial fermentations, supported by the presence of short-chain fatty acids, are suspected to occur in the upper small intestine, particularly in the ileum. Using a fosmid library from the human ileal mucosa, we screened 20,000 clones for their activities against carboxymethylcellulose and xylans chosen as models of the major plant cell wall (PCW) polysaccharides from dietary fibres. Eleven positive clones revealed a broad range of CAZyme encoding genes from Bacteroides and Clostridiales species, as well as Polysaccharide Utilization Loci (PULs). The functional glycoside hydrolase genes were identified, and oligosaccharide break-down products examined from different polysaccharides including mixed-linkage β-glucans. CAZymes and PULs were also examined for their prevalence in human gut microbiome. Several clusters of genes of low prevalence in fecal microbiome suggested they belong to unidentified strains rather specifically established upstream the colon, in the ileum. Thus, the ileal mucosa-associated microbiota encompasses the enzymatic potential for PCW polysaccharide degradation in the small intestine.}, }
@article {pmid29439741, year = {2018}, author = {Xiong, W and Wang, Y and Sun, Y and Ma, L and Zeng, Q and Jiang, X and Li, A and Zeng, Z and Zhang, T}, title = {Antibiotic-mediated changes in the fecal microbiome of broiler chickens define the incidence of antibiotic resistance genes.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {34}, doi = {10.1186/s40168-018-0419-2}, pmid = {29439741}, issn = {2049-2618}, support = {31702290//the National Natural Science Foundation of China/International ; 31672608//the National Natural Science Foundation of China/International ; GRF7201/11E//Hong Kong/International ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*classification/drug effects/genetics/isolation & purification ; Bacterial Proteins/*genetics ; Bifidobacterium/classification/drug effects/genetics/isolation & purification ; Chickens ; Chlortetracycline/pharmacology ; *Drug Resistance, Bacterial ; Escherichia/classification/drug effects/genetics/isolation & purification ; Feces/*microbiology ; Gene Regulatory Networks ; Klebsiella/classification/drug effects/genetics/isolation & purification ; Metagenomics ; Microbiota/drug effects ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Antimicrobial agents have been widely used in animal farms to prevent and treat animal diseases and to promote growth. Antimicrobial agents may change the bacterial community and enhance the resistome in animal feces. We used metagenome-wide analysis to investigate the changes in bacterial community, variations in antibiotic resistance genes (ARGs), and their bacterial hosts in the feces of broiler chickens over a full-treatment course of chlortetracycline at low and therapeutic dose levels.
RESULTS: The effects of chlortetracycline on resistome were dependent on the specific ARG subtypes and not simply the overall community-level ARGs. Therapeutic dose of chlortetracycline promoted the abundance of tetracycline resistance genes (tetA and tetW) and inhibited multidrug resistance genes (mdtA, mdtC, mdtK, ompR, and TolC). The therapeutic dose of chlortetracycline led to loss of Proteobacteria mainly due to the decrease of Escherichia/Shigella (from 72 to 58%). Inhibition of Escherichia by chlortetracycline was the primary reason for the decrease of genes resistant to multiple drugs in the therapeutic dose group. The ARG host Bifidobacterium were enriched due to tetW harbored by Bifidobacterium under chlortetracycline treatment. Escherichia was always the major host for multidrug resistance genes, whereas the primary host was changed from Escherichia to Klebsiella for aminoglycoside resistance genes with the treatment of therapeutic dose of chlortetracycline.
CONCLUSIONS: We provided the first metagenomic insights into antibiotic-mediated alteration of ARG-harboring bacterial hosts at community-wide level in chicken feces. These results indicated that the changes in the structure of antibiotic-induced feces microbial communities accompany changes in the abundance of bacterial hosts carrying specific ARGs in the feces microbiota. These findings will help to optimize therapeutic schemes for the effective treatment of antibiotic resistant pathogens in poultry farms. Resistome variations in faecal microbiome of chickens exposed to chlortetracycline.}, }
@article {pmid29347966, year = {2018}, author = {Zhou, W and Gay, N and Oh, J}, title = {ReprDB and panDB: minimalist databases with maximal microbial representation.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {15}, doi = {10.1186/s40168-018-0399-2}, pmid = {29347966}, issn = {2049-2618}, support = {K22 AI119231/AI/NIAID NIH HHS/United States ; }, mesh = {Access to Information ; Algorithms ; Computational Biology/methods ; *Databases, Genetic ; *Gastrointestinal Microbiome ; Humans ; Metagenomics/*methods ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Skin/*microbiology ; }, abstract = {BACKGROUND: Profiling of shotgun metagenomic samples is hindered by a lack of unified microbial reference genome databases that (i) assemble genomic information from all open access microbial genomes, (ii) have relatively small sizes, and (iii) are compatible to various metagenomic read mapping tools. Moreover, computational tools to rapidly compile and update such databases to accommodate the rapid increase in new reference genomes do not exist. As a result, database-guided analyses often fail to profile a substantial fraction of metagenomic shotgun sequencing reads from complex microbiomes.
RESULTS: We report pipelines that efficiently traverse all open access microbial genomes and assemble non-redundant genomic information. The pipelines result in two species-resolution microbial reference databases of relatively small sizes: reprDB, which assembles microbial representative or reference genomes, and panDB, for which we developed a novel iterative alignment algorithm to identify and assemble non-redundant genomic regions in multiple sequenced strains. With the databases, we managed to assign taxonomic labels and genome positions to the majority of metagenomic reads from human skin and gut microbiomes, demonstrating a significant improvement over a previous database-guided analysis on the same datasets.
CONCLUSIONS: reprDB and panDB leverage the rapid increases in the number of open access microbial genomes to more fully profile metagenomic samples. Additionally, the databases exclude redundant sequence information to avoid inflated storage or memory space and indexing or analyzing time. Finally, the novel iterative alignment algorithm significantly increases efficiency in pan-genome identification and can be useful in comparative genomic analyses.}, }
@article {pmid29298732, year = {2018}, author = {Luna, PN and Hasegawa, K and Ajami, NJ and Espinola, JA and Henke, DM and Petrosino, JF and Piedra, PA and Sullivan, AF and Camargo, CA and Shaw, CA and Mansbach, JM}, title = {The association between anterior nares and nasopharyngeal microbiota in infants hospitalized for bronchiolitis.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {2}, doi = {10.1186/s40168-017-0385-0}, pmid = {29298732}, issn = {2049-2618}, support = {R01 AI-114552/NH/NIH HHS/United States ; UG3 OD-023253/NH/NIH HHS/United States ; R01 AI-108588/NH/NIH HHS/United States ; R01 AI108588/AI/NIAID NIH HHS/United States ; UG3 OD023253/OD/NIH HHS/United States ; U01 AI-087881/NH/NIH HHS/United States ; }, mesh = {Bronchiolitis/*microbiology ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Female ; Hospitalization ; Humans ; Infant ; Longitudinal Studies ; Male ; Microbiota ; Nasal Cavity/*microbiology ; Nasopharynx/*microbiology ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; Staphylococcus/classification/genetics/*isolation & purification ; }, abstract = {BACKGROUND: The airway microbiome is a subject of great interest for the study of respiratory disease. Anterior nare samples are more accessible than samples from deeper within the nasopharynx. However, the correlation between the microbiota found in the anterior nares and the microbiota found within the nasopharynx is unknown. We assessed the anterior nares and nasopharyngeal microbiota to determine (1) the relation of the microbiota from these two upper airway sites and (2) if associations were maintained between the microbiota from these two sites and two bronchiolitis severity outcomes.
RESULTS: Among 815 infants hospitalized at 17 US centers for bronchiolitis with optimal 16S rRNA gene sequence reads from both nasal swab and nasopharyngeal aspirate samples, there were strong intra-individual correlations in the microbial communities between the two sample types, especially relating to Haemophilus and Moraxella genera. By contrast, we found a high abundance of Staphylococcus genus in the nasal swabs-a pattern not found in the nasopharyngeal samples and not informative when predicting the dominant nasopharyngeal genera. While these disparities may have been due to sample processing differences (i.e., nasal swabs were mailed at ambient temperature to emulate processing of future parent collected swabs while nasopharyngeal aspirates were mailed on dry ice), a previously reported association between Haemophilus-dominant nasopharyngeal microbiota and the increased severity of bronchiolitis was replicated utilizing the nasal swab microbiota and the same outcome measures: intensive care use (adjusted OR 6.43; 95% CI 2.25-20.51; P < 0.001) and hospital length-of-stay (adjusted OR 4.31; 95% CI, 1.73-11.11; P = 0.002). Additionally, Moraxella-dominant nasopharyngeal microbiota was previously identified as protective against intensive care use, a result that was replicated when analyzing the nasal swab microbiota (adjusted OR 0.30; 95% CI, 0.11-0.64; P = 0.01).
CONCLUSIONS: While the microbiota of the anterior nares and the nasopharynx are distinct, there is considerable overlap between the bacterial community compositions from these two anatomic sites. Despite processing differences between the samples, these results indicate that microbiota severity associations from the nasopharynx are recapitulated in the anterior nares, suggesting that nasal swab samples not only are effective sample types, but also can be used to detect microbial risk markers.}, }
@article {pmid28323391, year = {2018}, author = {Martinez-Sañudo, I and Simonato, M and Squartini, A and Mori, N and Marri, L and Mazzon, L}, title = {Metagenomic analysis reveals changes of the Drosophila suzukii microbiota in the newly colonized regions.}, journal = {Insect science}, volume = {25}, number = {5}, pages = {833-846}, doi = {10.1111/1744-7917.12458}, pmid = {28323391}, issn = {1744-7917}, support = {613678//European Union's Seventh Framework Programme/ ; }, mesh = {*Animal Distribution ; Animals ; Bacteria/*classification ; China ; Drosophila/*microbiology ; Europe ; *Gastrointestinal Microbiome ; *Introduced Species ; Japan ; *Metagenome ; Metagenomics ; United States ; }, abstract = {The spotted wing drosophila, Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) is a highly polyphagous pest of a wide variety of wild or cultivated berry and stone fruit. Originating from Southeast Asia, it has recently invaded a wide range of regions in Europe and North America. It is well known that insect microbiotas may significantly influence several aspects of the host biology and play an important role in invasive species introduction into new areas. However, in spite of the great economic importance of D. suzukii, a limited attention has been given so far to its microbiota. In this study, we present the first in-depth characterization of gut bacterial diversity from field (native and invasive range) and lab-reared populations of this insect. The gut bacterial communities of field insects were dominated, regardless of their origin, by 2 families of the phylum Proteobacteria: Acetobacteraceae and Enterobacteriaceae, while Firmicutes, mainly represented by the family Staphylococcaceae, prevailed in lab-reared population. Locality was the most significant factor in shaping the microbiota of wild flies. Moreover, a negative correlation between diversity and abundance of Enterobacteriaceae and the time elapsed since the establishment of D. suzukii in a new region was observed. Altogether our results indicate that habitat, food resources as well as the colonization phase of a new region contribute to shape the bacterial communities of the invasive species which, in turn, by evolving more quickly, could influence host adaptation in a new environment.}, }
@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}, doi = {10.3389/fmicb.2018.02312}, 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 {pmid29555111, year = {2018}, author = {Pandit, RJ and Hinsu, AT and Patel, SH and Jakhesara, SJ and Koringa, PG and Bruno, F and Psifidi, A and Shah, SV and Joshi, CG}, title = {Microbiota composition, gene pool and its expression in Gir cattle (Bos indicus) rumen under different forage diets using metagenomic and metatranscriptomic approaches.}, journal = {Systematic and applied microbiology}, volume = {41}, number = {4}, pages = {374-385}, doi = {10.1016/j.syapm.2018.02.002}, pmid = {29555111}, issn = {1618-0984}, mesh = {Animal Feed/*analysis ; Animals ; Bacteria/*classification/genetics ; Cattle ; *Diet ; Metagenome/genetics ; Metagenomics/methods ; Microbiota/genetics ; Rumen/*microbiology ; }, abstract = {Zebu (Bos indicus) is a domestic cattle species originating from the Indian subcontinent and now widely domesticated on several continents. In this study, we were particularly interested in understanding the functionally active rumen microbiota of an important Zebu breed, the Gir, under different dietary regimes. Metagenomic and metatranscriptomic data were compared at various taxonomic levels to elucidate the differential microbial population and its functional dynamics in Gir cattle rumen under different roughage dietary regimes. Different proportions of roughage rather than the type of roughage (dry or green) modulated microbiome composition and the expression of its gene pool. Fibre degrading bacteria (i.e. Clostridium, Ruminococcus, Eubacterium, Butyrivibrio, Bacillus and Roseburia) were higher in the solid fraction of rumen (P<0.01) compared to the liquid fraction, whereas bacteria considered to be utilizers of the degraded product (i.e. Prevotella, Bacteroides, Parabacteroides, Paludibacter and Victivallis) were dominant in the liquid fraction (P<0.05). Likewise, expression of fibre degrading enzymes and related carbohydrate binding modules (CBMs) occurred in the solid fraction. When metagenomic and metatranscriptomic data were compared, it was found that some genera and species were transcriptionally more active, although they were in low abundance, making an important contribution to fibre degradation and its further metabolism in the rumen. This study also identified some of the transcriptionally active genera, such as Caldicellulosiruptor and Paludibacter, whose potential has been less-explored in rumen. Overall, the comparison of metagenomic shotgun and metatranscriptomic sequencing appeared to be a much richer source of information compared to conventional metagenomic analysis.}, }
@article {pmid28134326, year = {2017}, author = {Liu, H and Carvalhais, LC and Schenk, PM and Dennis, PG}, title = {Effects of jasmonic acid signalling on the wheat microbiome differ between body sites.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {41766}, doi = {10.1038/srep41766}, pmid = {28134326}, issn = {2045-2322}, mesh = {Biodiversity ; Biomass ; Cyclopentanes/*metabolism ; Metagenome ; Metagenomics/methods ; Microbiota/*genetics ; Oxylipins/*metabolism ; Plant Roots/metabolism/microbiology ; Plant Shoots/metabolism/microbiology ; Rhizosphere ; *Signal Transduction ; Soil Microbiology ; Triticum/genetics/*metabolism/*microbiology ; }, abstract = {Jasmonic acid (JA) signalling helps plants to defend themselves against necrotrophic pathogens and herbivorous insects and has been shown to influence the root microbiome of Arabidopsis thaliana. In this study, we determined whether JA signalling influences the diversity and functioning of the wheat (Triticum aestivum) microbiome and whether these effects are specific to particular parts of the plant. Activation of the JA pathway was achieved via exogenous application of methyl jasmonate and was confirmed by significant increases in the abundance of 10 JA-signalling-related gene transcripts. Phylogenetic marker gene sequencing revealed that JA signalling reduced the diversity and changed the composition of root endophytic but not shoot endophytic or rhizosphere bacterial communities. The total enzymatic activity and substrate utilisation profiles of rhizosphere bacterial communities were not affected by JA signalling. Our findings indicate that the effects of JA signalling on the wheat microbiome are specific to individual plant compartments.}, }
@article {pmid28134269, year = {2017}, author = {Zhou, X and Zhang, J and Gao, D and Gao, H and Guo, M and Li, L and Zhao, M and Wu, F}, title = {Conversion from long-term cultivated wheat field to Jerusalem artichoke plantation changed soil fungal communities.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {41502}, doi = {10.1038/srep41502}, pmid = {28134269}, issn = {2045-2322}, mesh = {Agriculture ; Biodiversity ; *Fungi/classification/genetics ; Helianthus/growth & development/*microbiology ; Metagenome ; Metagenomics/methods ; *Soil Microbiology ; *Triticum/growth & development/microbiology ; }, abstract = {Understanding soil microbial communities in agroecosystems has the potential to contribute to the improvement of agricultural productivity and sustainability. Effects of conversion from long-term wheat plantation to Jerusalem artichoke (JA) plantation on soil fungal communities were determined by amplicon sequencing of total fungal ITS regions. Quantitative PCR and PCR-denaturing gradient gel electrophoresis were also used to analyze total fungal and Trichoderma spp. ITS regions and Fusarium spp. Ef1α genes. Results showed that soil organic carbon was higher in the first cropping of JA and Olsen P was lower in the third cropping of JA. Plantation conversion changed soil total fungal and Fusarium but not Trichoderma spp. community structures and compositions. The third cropping of JA had the lowest total fungal community diversity and Fusarium spp. community abundance, but had the highest total fungal and Trichoderma spp. community abundances. The relative abundances of potential fungal pathogens of wheat were higher in the wheat field. Fungal taxa with plant growth promoting, plant pathogen or insect antagonistic potentials were enriched in the first and second cropping of JA. Overall, short-term conversion from wheat to JA plantation changed soil fungal communities, which is related to changes in soil organic carbon and Olsen P contents.}, }
@article {pmid29273717, year = {2017}, author = {Albanese, D and Donati, C}, title = {Strain profiling and epidemiology of bacterial species from metagenomic sequencing.}, journal = {Nature communications}, volume = {8}, number = {1}, pages = {2260}, doi = {10.1038/s41467-017-02209-5}, pmid = {29273717}, issn = {2041-1723}, mesh = {Bacteria/*genetics ; Bifidobacterium longum/genetics ; *Computational Biology ; Databases, Genetic ; Enterococcus faecalis/genetics ; Escherichia coli/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome/*genetics ; *Metagenomics ; Microbiota/*genetics ; Neisseria meningitidis/genetics ; Polymorphism, Single Nucleotide ; Propionibacterium acnes/genetics ; Staphylococcus aureus/genetics ; Staphylococcus epidermidis/genetics ; Streptococcus pneumoniae/genetics ; }, abstract = {Microbial communities are often composed by complex mixtures of multiple strains of the same species, characterized by a wide genomic and phenotypic variability. Computational methods able to identify, quantify and classify the different strains present in a sample are essential to fully exploit the potential of metagenomic sequencing in microbial ecology, with applications that range from the epidemiology of infectious diseases to the characterization of the dynamics of microbial colonization. Here we present a computational approach that uses the available genomic data to reconstruct complex strain profiles from metagenomic sequencing, quantifying the abundances of the different strains and cataloging them according to the population structure of the species. We validate the method on synthetic data sets and apply it to the characterization of the strain distribution of several important bacterial species in real samples, showing how its application provides novel insights on the structure and complexity of the microbiota.}, }
@article {pmid29950381, year = {2018}, author = {Jenior, ML and Leslie, JL and Young, VB and Schloss, PD}, title = {Clostridium difficile Alters the Structure and Metabolism of Distinct Cecal Microbiomes during Initial Infection To Promote Sustained Colonization.}, journal = {mSphere}, volume = {3}, number = {3}, pages = {}, doi = {10.1128/mSphere.00261-18}, pmid = {29950381}, issn = {2379-5042}, mesh = {Animals ; Anti-Bacterial Agents/*administration & dosage/adverse effects ; Cecum/*chemistry/*microbiology ; Clostridium Infections/*microbiology ; Clostridium difficile/*growth & development ; Disease Models, Animal ; *Gastrointestinal Microbiome ; Gene Expression Profiling ; Metabolomics ; Metagenomics ; Mice ; }, abstract = {Susceptibility to Clostridium difficile infection (CDI) is primarily associated with previous exposure to antibiotics, which compromise the structure and function of the gut bacterial community. Specific antibiotic classes correlate more strongly with recurrent or persistent C. difficile infection. As such, we utilized a mouse model of infection to explore the effect of distinct antibiotic classes on the impact that infection has on community-level transcription and metabolic signatures shortly following pathogen colonization and how those changes may associate with persistence of C. difficile Untargeted metabolomic analysis revealed that C. difficile infection had significantly larger impacts on the metabolic environment across cefoperazone- and streptomycin-pretreated mice, which became persistently colonized compared to clindamycin-pretreated mice, where infection quickly became undetectable. Through metagenome-enabled metatranscriptomics, we observed that transcripts for genes associated with carbon and energy acquisition were greatly reduced in infected animals, suggesting that those niches were instead occupied by C. difficile Furthermore, the largest changes in transcription were seen in the least abundant species, indicating that C. difficile may "attack the loser" in gut environments where sustained infection occurs more readily. Overall, our results suggest that C. difficile is able to restructure the nutrient-niche landscape in the gut to promote persistent infection.IMPORTANCEClostridium difficile has become the most common single cause of hospital-acquired infection over the last decade in the United States. Colonization resistance to the nosocomial pathogen is primarily provided by the gut microbiota, which is also involved in clearing the infection as the community recovers from perturbation. As distinct antibiotics are associated with different risk levels for CDI, we utilized a mouse model of infection with 3 separate antibiotic pretreatment regimens to generate alternative gut microbiomes that each allowed for C. difficile colonization but varied in clearance rate. To assess community-level dynamics, we implemented an integrative multi-omics approach that revealed that infection significantly changed many aspects of the gut community. The degree to which the community changed was inversely correlated with clearance during the first 6 days of infection, suggesting that C. difficile differentially modifies the gut environment to promote persistence. This is the first time that metagenome-enabled metatranscriptomics have been employed to study the behavior of a host-associated microbiota in response to an infection. Our results allow for a previously unseen understanding of the ecology associated with C. difficile infection and provide the groundwork for identification of context-specific probiotic therapies.}, }
@article {pmid29898983, year = {2018}, author = {Zhu, L and Yang, Z and Yao, R and Xu, L and Chen, H and Gu, X and Wu, T and Yang, X}, title = {Potential Mechanism of Detoxification of Cyanide Compounds by Gut Microbiomes of Bamboo-Eating Pandas.}, journal = {mSphere}, volume = {3}, number = {3}, pages = {}, doi = {10.1128/mSphere.00229-18}, pmid = {29898983}, issn = {2379-5042}, mesh = {Ailuridae/*microbiology/*physiology ; Animals ; Bacteria/classification/genetics/metabolism ; Biotransformation ; Cyanides/*metabolism ; *Gastrointestinal Microbiome ; Metagenomics ; Ursidae/*microbiology/*physiology ; }, abstract = {Gut microbes can enhance the ability of hosts to consume secondary plant compounds and, therefore, expand the dietary niche breadth of mammalian herbivores. The giant and red pandas are bamboo-eating specialists within the mammalian order Carnivora. Bamboo contains abundant plant secondary metabolites (e.g., cyanide-containing compounds). However, Carnivora species, including the giant panda, have deficient levels of rhodanese (one of the essential cyanide detoxification enzymes) in their tissues compared with the same tissues of herbivores. Here, we make a comparative analysis of 94 gut metagenomes, including 25 from bamboo-eating pandas (19 from giant pandas and 6 from red pandas), 30 from Père David's deer, and 39 from published data for other mammals. The bamboo-eating pandas' gut microbiomes had some common features, such as high proportions of Pseudomonas bacteria. The results revealed that bamboo-eating pandas' gut microbiomes were significantly enriched in putative genes coding for enzymes related to cyanide degradation (e.g., rhodanese) compared with the gut microbiomes of typical herbivorous mammals, which might have coevolved with their special bamboo diets. The enrichment of putative cyanide-digesting gut microbes, in combination with adaptations related to morphology (e.g., pseudothumbs) and genomic signatures, show that the giant panda and red panda have evolved some common traits to adapt to their bamboo diet.IMPORTANCE The giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens), two obligate bamboo feeders, have distinct phylogenetic positions in the order Carnivora. Bamboo is extraordinarily rich in plant secondary metabolites, such as allied phenolic and polyphenolic compounds and even toxic cyanide compounds. Here, the enrichment of putative cyanide-digesting gut microbes, in combination with adaptations related to morphology (e.g., pseudothumbs) and genomic signatures, show that the giant panda and red panda have evolved some common traits to adapt to their bamboo diet. Thus, here is another story of diet-driven gut microbiota in nature.}, }
@article {pmid29848762, year = {2018}, author = {Garcia, SL and Buck, M and Hamilton, JJ and Wurzbacher, C and Grossart, HP and McMahon, KD and Eiler, A}, title = {Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria.}, journal = {mSphere}, volume = {3}, number = {3}, pages = {}, doi = {10.1128/mSphere.00202-18}, pmid = {29848762}, issn = {2379-5042}, mesh = {Bacteria/*metabolism ; Fresh Water/*microbiology ; *Metabolism ; *Microbial Consortia ; Microbial Interactions ; }, abstract = {Genome streamlining is frequently observed in free-living aquatic microorganisms and results in physiological dependencies between microorganisms. However, we know little about the specificity of these microbial associations. In order to examine the specificity and extent of these associations, we established mixed cultures from three different freshwater environments and analyzed the cooccurrence of organisms using a metagenomic time series. Free-living microorganisms with streamlined genomes lacking multiple biosynthetic pathways showed no clear recurring pattern in their interaction partners. Free-living freshwater bacteria form promiscuous cooperative associations. This notion contrasts with the well-documented high specificities of interaction partners in host-associated bacteria. Considering all data together, we suggest that highly abundant free-living bacterial lineages are functionally versatile in their interactions despite their distinct streamlining tendencies at the single-cell level. This metabolic versatility facilitates interactions with a variable set of community members.}, }
@article {pmid29687353, year = {2018}, author = {Allali, I and Boukhatem, N and Bouguenouch, L and Hardi, H and Boudouaya, HA and Cadenas, MB and Ouldim, K and Amzazi, S and Azcarate-Peril, MA and Ghazal, H}, title = {Gut microbiome of Moroccan colorectal cancer patients.}, journal = {Medical microbiology and immunology}, volume = {207}, number = {3-4}, pages = {211-225}, doi = {10.1007/s00430-018-0542-5}, pmid = {29687353}, issn = {1432-1831}, mesh = {Adult ; Aged ; Cluster Analysis ; Colorectal Neoplasms/*complications/*microbiology ; Cytosol/chemistry ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Dysbiosis ; Fatty Acids/analysis ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics ; *Microbiota ; Middle Aged ; Morocco ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Surveys and Questionnaires ; Young Adult ; }, abstract = {Although colorectal cancer is the third leading cause of death in Morocco, there are no studies of the microbiome changes associated with the disease in the Moroccan population. The aim of our study was to compare the stool microbiome of Moroccan cancer patients with healthy individuals. We analyzed the microbiome composition of samples from 11 CRC patients and 12 healthy individuals by 16S rRNA amplicon sequencing. Principal coordinate analysis of samples revealed defined cancer versus healthy clusters. Our findings showed that cancer samples had higher proportions of Firmicutes (T = 50.5%; N = 28.4%; p = 0.04), specifically of Clostridia (T = 48.3%; N = 19.0%; p = 0.002), and Fusobacteria (T = 0.1%; N = 0.0%; p = 0.02), especially of Fusobacteriia (T = 0.1%; N = 0.0%; p = 0.02), while Bacteroidetes were enriched in healthy samples (T = 35.1%; N = 62.8%; p = 0.06), particularly the class Bacteroidia (T = 35.1%; N = 62.6%; p = 0.06). Porphyromonas, Clostridium, Ruminococcus, Selenomonas, and Fusobacterium were significantly overrepresented in diseased patients, similarly to other studies. Predicted functional information showed that bacterial motility proteins, flagellar assembly, and fatty acid biosynthesis metabolism were significantly overrepresented in cancer patients, while amino acid metabolism and glycan biosynthesis were overrepresented in controls. This suggests that involvement of these functional metagenomes is similar and relevant in the carcinogenesis process, independent of the origin of the samples. Results from this study allowed identification of bacterial taxa relevant to the Moroccan population and encourages larger studies to facilitate population-directed therapeutic approaches.}, }
@article {pmid29079861, year = {2018}, author = {Velásquez-Mejía, EP and de la Cuesta-Zuluaga, J and Escobar, JS}, title = {Impact of DNA extraction, sample dilution, and reagent contamination on 16S rRNA gene sequencing of human feces.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {1}, pages = {403-411}, doi = {10.1007/s00253-017-8583-z}, pmid = {29079861}, issn = {1432-0614}, mesh = {DNA/genetics/*isolation & purification ; *DNA Contamination ; DNA, Bacterial/genetics ; Feces/*microbiology ; Gastrointestinal Microbiome/*genetics ; *High-Throughput Nucleotide Sequencing ; Humans ; Indicators and Reagents ; Metagenomics/methods ; Microbial Consortia/genetics ; Microbiota/genetics ; RNA, Ribosomal, 16S/chemistry/*genetics ; Sequence Analysis, DNA ; }, abstract = {Culture-independent methods have granted the possibility to study microbial diversity in great detail, but technical issues pose a threat to the accuracy of new findings. Biases introduced during DNA extraction can result in erroneous representations of the microbial community, particularly in samples with low microbial biomass. We evaluated the DNA extraction method, initial sample biomass, and reagent contamination on the assessment of the human gut microbiota. Fecal samples of 200 mg were subjected to 1:10 serial dilutions; total DNA was obtained using two commercial kits and the microbiota assessed by 16S ribosomal RNA (rRNA) gene sequencing. In addition, we sequenced multiple technical controls. The two kits were efficient in extracting DNA from samples with as low as 2 mg of feces. However, in instances of lower biomass, only one kit performed well. The number of reads from negative controls was negligible. Both DNA extraction kits allowed inferring microbial consortia with similar membership but different abundances. Furthermore, we found differences in the taxonomic profile of the microbial community. Unexpectedly, the effect of sample dilution was moderate and did not introduce severe bias into the microbial inference. Indeed, the microbiota inferred from fecal samples was distinguishable from that of negative controls. In most cases, samples as low as 2 mg did not result in a dissimilar representation of the microbial community compared with the undiluted sample. Our results indicate that the gut microbiota inference is not much affected by contamination with laboratory reagents but largely impacted by the protocol to extract DNA.}, }
@article {pmid27530840, year = {2016}, author = {Jitwasinkul, T and Suriyaphol, P and Tangphatsornruang, S and Hansen, MA and Hansen, LH and Sørensen, SJ and Permpikul, C and Rongrungruang, Y and Tribuddharat, C}, title = {Plasmid metagenomics reveals multiple antibiotic resistance gene classes among the gut microbiomes of hospitalised patients.}, journal = {Journal of global antimicrobial resistance}, volume = {6}, number = {}, pages = {57-66}, doi = {10.1016/j.jgar.2016.03.001}, pmid = {27530840}, issn = {2213-7173}, mesh = {Animals ; Anti-Bacterial Agents ; Cattle ; Drug Resistance, Multiple, Bacterial/*genetics ; *Gastrointestinal Microbiome ; *Genes, Bacterial ; Humans ; Inpatients ; Metagenomics ; Microbial Sensitivity Tests ; Plasmids/*genetics ; Sequence Analysis, DNA ; Thailand ; }, abstract = {Antibiotic resistance genes are rapidly spread between pathogens and the normal flora, with plasmids playing an important role in their circulation. This study aimed to investigate antibiotic resistance plasmids in the gut microbiome of hospitalised patients. Stool samples were collected from seven inpatients at Siriraj Hospital (Bangkok, Thailand) and were compared with a sample from a healthy volunteer. Plasmids from the gut microbiomes extracted from the stool samples were subjected to high-throughput DNA sequencing (GS Junior). Newbler-assembled DNA reads were categorised into known and unknown sequences (using >80% alignment length as the cut-off), and ResFinder was used to classify the antibiotic resistance gene pools. Plasmid replicon modules were used for plasmid typing. Forty-six genes conferring resistance to several classes of antibiotics were identified in the stool samples. Several antibiotic resistance genes were shared by the patients; interestingly, most were reported previously in food animals and healthy humans. Four antibiotic resistance genes were found in the healthy subject. One gene (aph3-III) was identified in the patients and the healthy subject and was related to that in cattle. Uncommon genes of hospital origin such as blaTEM-124-like and fosA, which confer resistance to extended-spectrum β-lactams and fosfomycin, respectively, were identified. The resistance genes did not match the patients' drug treatments. In conclusion, several plasmid types were identified in the gut microbiome; however, it was difficult to link these to the antibiotic resistance genes identified. That the antibiotic resistance genes came from hospital and community environments is worrying.}, }
@article {pmid29934497, year = {2018}, author = {Ji, Y and Zhang, F and Zhang, R and Shen, Y and Liu, L and Wang, J and Yang, J and Tang, Q and Xun, J and Qi, T and Wang, Z and Song, W and Tang, Y and Chen, J and Lu, H}, title = {Changes in intestinal microbiota in HIV-1-infected subjects following cART initiation: influence of CD4+ T cell count.}, journal = {Emerging microbes & infections}, volume = {7}, number = {1}, pages = {113}, doi = {10.1038/s41426-018-0117-y}, pmid = {29934497}, issn = {2222-1751}, support = {81571977//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Adult ; Antiretroviral Therapy, Highly Active ; Biodiversity ; Biomarkers ; *CD4 Lymphocyte Count ; CD4-CD8 Ratio ; Computational Biology/methods ; Female ; *Gastrointestinal Microbiome/drug effects ; HIV Infections/drug therapy/*immunology/virology ; HIV-1/*immunology ; Humans ; Male ; Metagenome ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Viral Load ; }, abstract = {The roles of immunodeficiency and combined antiretroviral therapy (cART) in shaping the gut microbiota in HIV-1-infected subjects (HISs) have not been described thoroughly by time-series investigations. In this study, 36 antiretroviral-naïve HISs were enrolled to prospectively assess alterations in the fecal microbiota and plasma markers of microbial translocation and inflammation with cART. At baseline, the species α-diversity of the fecal microbiota was significantly lower in HISs with a CD4+ T cell count <300/mm3 than in HISs with a CD4+ T cell count >300/mm3 (Shannon index: Median 2.557 vs. 2.981, P = 0.006; Simpson index: Median 0.168 vs. 0.096, P = 0.004). Additionally, the baseline α-diversity indices correlated with CD4+ T cell counts (Shannon index: r = 0.474, P = 0.004; Simpson index: r = -0.467, P = 0.004) and the specific plasma biomarkers for microbial translocation and inflammation. After cART introduction, the species α-diversity of fecal microbiota in HISs with CD4+ T cell counts <300/mm3 was significantly restored (Shannon index: Median 2.557 vs. 2.791, P = 0.007; Simpson index: Median 0.168 vs. 0.112, P = 0.004), while the variances were insignificant among HISs with CD4+ T cell counts >300/mm3 (Shannon index: Median 2.981 vs. 2.934, P = 0.179; Simpson index: Median 0.096 vs. 0.119, P = 0.082). Meanwhile, with cART introduction, alterations in the gut microbial composition were more significant in the subgroup with CD4+ T cell counts >300/mm3, corresponding to increases in the specific plasma inflammatory markers. These findings implicated the interactive roles of immunodeficiency and cART for affecting gut microbiota in HIV-1-infected individuals, providing new insights into intestinal microbiome dysbiosis related to HIV-1 infection.}, }
@article {pmid29800328, year = {2018}, author = {Birkl, P and Bharwani, A and Kjaer, JB and Kunze, W and McBride, P and Forsythe, P and Harlander-Matauschek, A}, title = {Differences in cecal microbiome of selected high and low feather-pecking laying hens.}, journal = {Poultry science}, volume = {97}, number = {9}, pages = {3009-3014}, doi = {10.3382/ps/pey167}, pmid = {29800328}, issn = {1525-3171}, mesh = {*Aggression ; Animals ; Bacteria/classification ; Cecum/*microbiology ; Chickens/genetics/*microbiology/*physiology ; Feathers ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; *Selection, Genetic ; Sequence Analysis, RNA/veterinary ; }, abstract = {In mammals, it has become increasingly clear that the gut microbiota influences not only gastrointestinal physiology but also modulates behavior. In domestic birds, ceca have the greatest gastrointestinal microbial population. Feather-pecking (FP) behavior in laying hens is one of the most important unsolved behavioral issues in modern agriculture. The aim of the present study was to assess the cecal microbial community of divergently selected high (HFP; n = 20) and low (LFP; n = 20) feather-pecking birds at 60 wk of age. The cecal samples were subjected to community profiling of 16S rRNA and in silico metagenomics using a modified bar-coded Illumina sequencing method on a MiSeq Illumina sequencer. Our results revealed that compared to HFP birds, LFP birds are characterized by an increased overall microbial diversity (beta diversity) shown by a difference in the Bray-Curtis index (R2 = 0.171, P < 0.05). Furthermore, operational taxonomic unit comparisons showed an increased presence of Clostridiae and decreased presence of Lactobaccillacae in HFP birds when compared to LFP birds (False Discovery Rate < 0.05, Mann-Whitney comparisons). Our data indicate that there may be differences in the cecal profile between these 2 lines of laying hens. More research, building on this first study using sequencing technology for profiling the chicken cecal microbiome, will be needed in order to reveal if and how there exists a functional link between the performance of FP and the cecal microbial community.}, }
@article {pmid28094284, year = {2017}, author = {Murphy, K and Curley, D and O'Callaghan, TF and O'Shea, CA and Dempsey, EM and O'Toole, PW and Ross, RP and Ryan, CA and Stanton, C}, title = {The Composition of Human Milk and Infant Faecal Microbiota Over the First Three Months of Life: A Pilot Study.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {40597}, doi = {10.1038/srep40597}, pmid = {28094284}, issn = {2045-2322}, mesh = {Biodiversity ; Feces/*microbiology ; Humans ; Infant ; Infant, Newborn ; Metagenome ; Metagenomics/methods ; *Microbiota ; Milk, Human/*microbiology ; Pilot Projects ; }, abstract = {Human milk contains a diverse array of bioactives and is also a source of bacteria for the developing infant gut. The aim of this study was to characterize the bacterial communities in human milk and infant faeces over the first 3 months of life, in 10 mother-infant pairs. The presence of viable Bifidobacterium and Lactobacillus in human milk was also evaluated. MiSeq sequencing revealed a large diversity of the human milk microbiota, identifying over 207 bacterial genera in milk samples. The phyla Proteobacteria and Firmicutes and the genera Pseudomonas, Staphylococcus and Streptococcus were the predominant bacterial groups. A core of 12 genera represented 81% of the microbiota relative abundance in milk samples at week 1, 3 and 6, decreasing to 73% at week 12. Genera shared between infant faeces and human milk samples accounted for 70-88% of the total relative abundance in infant faecal samples, supporting the hypothesis of vertical transfer of bacteria from milk to the infant gut. In addition, identical strains of Bifidobacterium breve and Lactobacillus plantarum were isolated from the milk and faeces of one mother-infant pair. Vertical transfer of bacteria via breastfeeding may contribute to the initial establishment of the microbiota in the developing infant intestine.}, }
@article {pmid29028897, year = {2018}, author = {Guo, X and Li, Z and Yao, Q and Mueller, RS and Eng, JK and Tabb, DL and Hervey, WJ and Pan, C}, title = {Sipros Ensemble improves database searching and filtering for complex metaproteomics.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {5}, pages = {795-802}, doi = {10.1093/bioinformatics/btx601}, pmid = {29028897}, issn = {1367-4811}, abstract = {Motivation: Complex microbial communities can be characterized by metagenomics and metaproteomics. However, metagenome assemblies often generate enormous, and yet incomplete, protein databases, which undermines the identification of peptides and proteins in metaproteomics. This challenge calls for increased discrimination of true identifications from false identifications by database searching and filtering algorithms in metaproteomics.
Results: Sipros Ensemble was developed here for metaproteomics using an ensemble approach. Three diverse scoring functions from MyriMatch, Comet and the original Sipros were incorporated within a single database searching engine. Supervised classification with logistic regression was used to filter database searching results. Benchmarking with soil and marine microbial communities demonstrated a higher number of peptide and protein identifications by Sipros Ensemble than MyriMatch/Percolator, Comet/Percolator, MS-GF+/Percolator, Comet & MyriMatch/iProphet and Comet & MyriMatch & MS-GF+/iProphet. Sipros Ensemble was computationally efficient and scalable on supercomputers.
Freely available under the GNU GPL license at http://sipros.omicsbio.org.
Contact: cpan@utk.edu.
Supplementary information: Supplementary data are available at Bioinformatics online.}, }
@article {pmid30325092, year = {2018}, 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 = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14439}, pmid = {30325092}, issn = {1462-2920}, 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 a ~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 ~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 to the dry season. These results advance our understanding of the Ganges microbial communities and how they respond to anthropogenic pollution. This article is protected by copyright. All rights reserved.}, }
@article {pmid29524068, year = {2018}, author = {Wang, C and Li, Q and Li, J}, title = {Gut microbiota and its implications in small bowel transplantation.}, journal = {Frontiers of medicine}, volume = {12}, number = {3}, pages = {239-248}, doi = {10.1007/s11684-018-0617-0}, pmid = {29524068}, issn = {2095-0225}, mesh = {Biomarkers ; *Gastrointestinal Microbiome ; Graft Rejection/*immunology ; Humans ; Immunity, Mucosal ; Intestine, Small/*microbiology/*transplantation ; Metagenomics ; Transplantation Tolerance/*immunology ; }, abstract = {The gut microbiota is mainly composed of a diverse population of commensal bacterial species and plays a pivotal role in the maintenance of intestinal homeostasis, immune modulation and metabolism. The influence of the gut microbiota on solid organ transplantation has recently been recognized. In fact, several studies indicated that acute and chronic allograft rejection in small bowel transplantation (SBT) is closely associated with the alterations in microbial patterns in the gut. In this review, we focused on the recent findings regarding alterations in the microbiota following SBTand the potential roles of these alterations in the development of acute and chronic allograft rejection. We also reviewed important advances with respect to the interplays between the microbiota and host immune systems in SBT. Furthermore, we explored the potential of the gut microbiota as a microbial marker and/or therapeutic target for the predication and intervention of allograft rejection and chronic dysfunction. Given that current research on the gut microbiota has become increasingly sophisticated and comprehensive, large cohort studies employing metagenomic analysis and multivariate linkage should be designed for the characterization of host-microbe interaction and causality between microbiota alterations and clinical outcomes in SBT. The findings are expected to provide valuable insights into the role of gut microbiota in the development of allograft rejection and other transplant-related complications and introduce novel therapeutic targets and treatment approaches in clinical practice.}, }
@article {pmid29433401, year = {2018}, author = {Alex, CE and Kubiski, SV and Li, L and Sadeghi, M and Wack, RF and McCarthy, MA and Pesavento, JB and Delwart, E and Pesavento, PA}, title = {Amdoparvovirus Infection in Red Pandas (Ailurus fulgens).}, journal = {Veterinary pathology}, volume = {55}, number = {4}, pages = {552-561}, doi = {10.1177/0300985818758470}, pmid = {29433401}, issn = {1544-2217}, mesh = {Ailuridae/*virology ; Animals ; Endangered Species ; Feces/virology ; Female ; *Genetic Variation ; Genome, Viral/*genetics ; In Situ Hybridization/veterinary ; Male ; Metagenomics ; Microscopy, Electron/veterinary ; Parvoviridae Infections/diagnostic imaging/pathology/*veterinary/virology ; Parvovirinae/genetics/*isolation & purification ; Phylogeny ; Polymerase Chain Reaction/veterinary ; Virus Shedding ; }, abstract = {Aleutian mink disease virus is the type species in the genus Amdoparvovirus, and in mink and other Mustelidae can cause either subclinical disease or fatal chronic immune stimulation and immune complex disease. The authors describe a novel amdoparvovirus in the endangered red panda (Ailurus fulgens), discovered using viral metagenomics. The authors analyzed the prevalence, tissue distribution, and disease association by PCR, in situ hybridization, electron microscopy, and histology in a group of 6 red pandas from a single zoological collection. The study incorporates a fecal shedding survey and analysis of tissues from 4 necropsied animals over a 12-year span. The tentatively named red panda amdoparvovirus (RpAPV) was detected in the feces and/or tissues of all animals tested. At necropsy of 1 geriatric animal, infection was associated with pyogranulomatous peritonitis, pancreatitis, and myocarditis. Other animals had detectable low-level viral nucleic acid in lymph nodes and both oral and intestinal epithelium at the time of necropsy. Full-length genome sequences of RpAPV strains from 2 animals had 12% sequence divergence, demonstrating genetic diversity even among in-contact animals. RpAPV is a persistent infection in this cohort of red pandas, and has variable clinical expression.}, }
@article {pmid29346588, year = {2018}, author = {Cridland, JM and Ramirez, SR and Dean, CA and Sciligo, A and Tsutsui, ND}, title = {Genome Sequencing of Museum Specimens Reveals Rapid Changes in the Genetic Composition of Honey Bees in California.}, journal = {Genome biology and evolution}, volume = {10}, number = {2}, pages = {458-472}, doi = {10.1093/gbe/evy007}, pmid = {29346588}, issn = {1759-6653}, support = {S10 RR027303/RR/NCRR NIH HHS/United States ; S10 RR029668/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Bees/*genetics ; California ; Chromosome Mapping ; *Evolution, Molecular ; Genetics, Population ; *Genome, Insect ; Introduced Species ; Metagenomics ; Pollination ; Polymorphism, Single Nucleotide ; Population Dynamics ; }, abstract = {The western honey bee, Apis mellifera, is an enormously influential pollinator in both natural and managed ecosystems. In North America, this species has been introduced numerous times from a variety of different source populations in Europe and Africa. Since then, feral populations have expanded into many different environments across their broad introduced range. Here, we used whole genome sequencing of historical museum specimens and newly collected modern populations from California (USA) to analyze the impact of demography and selection on introduced populations during the past 105 years. We find that populations from both northern and southern California exhibit pronounced genetic changes, but have changed in different ways. In northern populations, honey bees underwent a substantial shift from western European to eastern European ancestry since the 1960s, whereas southern populations are dominated by the introgression of Africanized genomes during the past two decades. Additionally, we identify an isolated island population that has experienced comparatively little change over a large time span. Fine-scale comparison of different populations and time points also revealed SNPs that differ in frequency, highlighting a number of genes that may be important for recent adaptations in these introduced populations.}, }
@article {pmid29242367, year = {2017}, author = {Costea, PI and Coelho, LP and Sunagawa, S and Munch, R and Huerta-Cepas, J and Forslund, K and Hildebrand, F and Kushugulova, A and Zeller, G and Bork, P}, title = {Subspecies in the global human gut microbiome.}, journal = {Molecular systems biology}, volume = {13}, number = {12}, pages = {960}, pmid = {29242367}, issn = {1744-4292}, mesh = {Escherichia coli/physiology ; *Gastrointestinal Microbiome/genetics ; Genes, Bacterial ; Humans ; *Microbiota/genetics ; Phenotype ; Phylogeography ; Species Specificity ; }, abstract = {Population genomics of prokaryotes has been studied in depth in only a small number of primarily pathogenic bacteria, as genome sequences of isolates of diverse origin are lacking for most species. Here, we conducted a large-scale survey of population structure in prevalent human gut microbial species, sampled from their natural environment, with a culture-independent metagenomic approach. We examined the variation landscape of 71 species in 2,144 human fecal metagenomes and found that in 44 of these, accounting for 72% of the total assigned microbial abundance, single-nucleotide variation clearly indicates the existence of sub-populations (here termed subspecies). A single subspecies (per species) usually dominates within each host, as expected from ecological theory. At the global scale, geographic distributions of subspecies differ between phyla, with Firmicutes subspecies being significantly more geographically restricted. To investigate the functional significance of the delineated subspecies, we identified genes that consistently distinguish them in a manner that is independent of reference genomes. We further associated these subspecies-specific genes with properties of the microbial community and the host. For example, two of the three Eubacterium rectale subspecies consistently harbor an accessory pro-inflammatory flagellum operon that is associated with lower gut community diversity, higher host BMI, and higher blood fasting insulin levels. Using an additional 676 human oral samples, we further demonstrate the existence of niche specialized subspecies in the different parts of the oral cavity. Taken together, we provide evidence for subspecies in the majority of abundant gut prokaryotes, leading to a better functional and ecological understanding of the human gut microbiome in conjunction with its host.}, }
@article {pmid28079128, year = {2017}, author = {Jing, G and Sun, Z and Wang, H and Gong, Y and Huang, S and Ning, K and Xu, J and Su, X}, title = {Parallel-META 3: Comprehensive taxonomical and functional analysis platform for efficient comparison of microbial communities.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {40371}, doi = {10.1038/srep40371}, pmid = {28079128}, issn = {2045-2322}, support = {R34 AA021502/AA/NIAAA NIH HHS/United States ; }, mesh = {Adult ; Base Sequence ; Biodiversity ; Biomarkers/metabolism ; Child ; Computer Simulation ; Databases, Genetic ; Humans ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Time Factors ; }, abstract = {The number of metagenomes is increasing rapidly. However, current methods for metagenomic analysis are limited by their capability for in-depth data mining among a large number of microbiome each of which carries a complex community structure. Moreover, the complexity of configuring and operating computational pipeline also hinders efficient data processing for the end users. In this work we introduce Parallel-META 3, a comprehensive and fully automatic computational toolkit for rapid data mining among metagenomic datasets, with advanced features including 16S rRNA extraction for shotgun sequences, 16S rRNA copy number calibration, 16S rRNA based functional prediction, diversity statistics, bio-marker selection, interaction network construction, vector-graph-based visualization and parallel computing. Application of Parallel-META 3 on 5,337 samples with 1,117,555,208 sequences from diverse studies and platforms showed it could produce similar results as QIIME and PICRUSt with much faster speed and lower memory usage, which demonstrates its ability to unravel the taxonomical and functional dynamics patterns across large datasets and elucidate ecological links between microbiome and the environment. Parallel-META 3 is implemented in C/C++ and R, and integrated into an executive package for rapid installation and easy access under Linux and Mac OS X. Both binary and source code packages are available at http://bioinfo.single-cell.cn/parallel-meta.html.}, }
@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}, 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 {pmid29476620, year = {2018}, author = {Chappell, CR and Fukami, T}, title = {Nectar yeasts: a natural microcosm for ecology.}, journal = {Yeast (Chichester, England)}, volume = {35}, number = {6}, pages = {417-423}, doi = {10.1002/yea.3311}, pmid = {29476620}, issn = {1097-0061}, mesh = {Animals ; Bacteria ; Biota ; Flowers ; Models, Biological ; *Plant Nectar ; Pollination ; *Social Behavior ; *Social Environment ; *Yeasts ; }, abstract = {The species of yeasts that colonize floral nectar can modify the mutualistic relationships between plants and pollinators by changing the chemical properties of nectar. Recent evidence supporting this possibility has led to increased interest among ecologists in studying these fungi as well as the bacteria that interact with them in nectar. Although not fully explored, nectar yeasts also constitute a promising natural microcosm that can be used to facilitate development of general ecological theory. We discuss the methodological and conceptual advantages of using nectar yeasts from this perspective, including simplicity of communities, tractability of dispersal, replicability of community assembly, and the ease with which the mechanisms of species interactions can be studied in complementary experiments conducted in the field and the laboratory. To illustrate the power of nectar yeasts as a study system, we discuss several topics in community ecology, including environmental filtering, priority effects, and metacommunity dynamics. An exciting new direction is to integrate metagenomics and comparative genomics into nectar yeast research to address these fundamental ecological topics.}, }
@article {pmid29773467, year = {2018}, author = {Daliri, EB and Tango, CN and Lee, BH and Oh, DH}, title = {Human microbiome restoration and safety.}, journal = {International journal of medical microbiology : IJMM}, volume = {308}, number = {5}, pages = {487-497}, doi = {10.1016/j.ijmm.2018.05.002}, pmid = {29773467}, issn = {1618-0607}, mesh = {Anti-Bacterial Agents ; Bacteria/classification/isolation & purification ; Diet ; Dysbiosis/*therapy ; Fecal Microbiota Transplantation/*adverse effects/methods ; Gastrointestinal Microbiome/*physiology ; Humans ; Probiotics/*administration & dosage ; }, abstract = {The human gut microbiome consists of many bacteria which are in symbiotic relationship with human beings. The gut microbial metabolism, as well as the microbial-host co-metabolism, has been found to greatly influence health and disease. Factors such as diet, antibiotic use and lifestyle have been associated with alterations in the gut microbial community and may result in several pathological conditions. For this reason, several strategies including fecal microbiota transplant and probiotic administration have been applied and proven to be feasible and effective in restoring the gut microbiota in humans. Yet, safety concerns such as potential health risks that may arise from such interventions and how these strategies are regulated need to be addressed. Also, it will be important to know if these microbiome restoration strategies can have a profound impact on health. This review provides an overview of our current knowledge of the microbiome restoration strategies and safety issues on how these strategies are regulated.}, }
@article {pmid29588360, year = {2018}, author = {Corvelo, A and Clarke, WE and Robine, N and Zody, MC}, title = {taxMaps: comprehensive and highly accurate taxonomic classification of short-read data in reasonable time.}, journal = {Genome research}, volume = {28}, number = {5}, pages = {751-758}, doi = {10.1101/gr.225276.117}, pmid = {29588360}, issn = {1549-5469}, mesh = {Bacteria/classification/genetics ; Computational Biology/*methods ; Databases, Nucleic Acid ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; Microbiota/genetics ; Reproducibility of Results ; Rivers/microbiology ; *Software ; Species Specificity ; Water Microbiology ; }, abstract = {High-throughput sequencing is a revolutionary technology for the analysis of metagenomic samples. However, querying large volumes of reads against comprehensive DNA/RNA databases in a sensitive manner can be compute-intensive. Here, we present taxMaps, a highly efficient, sensitive, and fully scalable taxonomic classification tool. Using a combination of simulated and real metagenomics data sets, we demonstrate that taxMaps is more sensitive and more precise than widely used taxonomic classifiers and is capable of delivering classification accuracy comparable to that of BLASTN, but at up to three orders of magnitude less computational cost.}, }
@article {pmid29083504, year = {2018}, author = {Puri, P and Liangpunsakul, S and Christensen, JE and Shah, VH and Kamath, PS and Gores, GJ and Walker, S and Comerford, M and Katz, B and Borst, A and Yu, Q and Kumar, DP and Mirshahi, F and Radaeva, S and Chalasani, NP and Crabb, DW and Sanyal, AJ and , }, title = {The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis.}, journal = {Hepatology (Baltimore, Md.)}, volume = {67}, number = {4}, pages = {1284-1302}, doi = {10.1002/hep.29623}, pmid = {29083504}, issn = {1527-3350}, support = {U01 AA021883/AA/NIAAA NIH HHS/United States ; U01 AA021840/AA/NIAAA NIH HHS/United States ; R01 AA021171/AA/NIAAA NIH HHS/United States ; U01 AA021788/AA/NIAAA NIH HHS/United States ; K23 AA021179/AA/NIAAA NIH HHS/United States ; U01 AA021891/AA/NIAAA NIH HHS/United States ; }, mesh = {Adult ; Alcohol Drinking/adverse effects ; DNA, Bacterial/*blood/genetics ; Endotoxins/blood ; Female ; Hepatitis, Alcoholic/*microbiology ; Humans ; Liver/microbiology/pathology ; Liver Diseases, Alcoholic/*microbiology ; Male ; Metagenomics/*methods ; Microbiota/*genetics ; Middle Aged ; Monocytes/pathology ; }, abstract = {Intestinal dysbiosis is implicated in alcoholic hepatitis (AH). However, changes in the circulating microbiome, its association with the presence and severity of AH, and its functional relevance in AH is unknown. Qualitative and quantitative assessment of changes in the circulating microbiome were performed by sequencing bacterial DNA in subjects with moderate AH (MAH) (n = 18) or severe AH (SAH) (n = 19). These data were compared with heavy drinking controls (HDCs) without obvious liver disease (n = 19) and non-alcohol-consuming controls (NACs, n = 20). The data were related to endotoxin levels and markers of monocyte activation. Linear discriminant analysis effect size (LEfSe) analysis, inferred metagenomics, and predictive functional analysis using PICRUSt were performed. There was a significant increase in 16S copies/ng DNA both in MAH (P < 0.01) and SAH (P < 0.001) subjects. Compared with NACs, the relative abundance of phylum Bacteroidetes was significantly decreased in HDCs, MAH, and SAH (P < 0.001). In contrast, all alcohol-consuming groups had enrichment with Fusobacteria; this was greatest for HDCs and decreased progressively in MAH and SAH. Subjects with SAH had significantly higher endotoxemia (P = 0.01). Compared with alcohol-consuming groups, predictive functional metagenomics indicated an enrichment of bacteria with genes related to methanogenesis and denitrification. Furthermore, both HDCs and SAH showed activation of a type III secretion system that has been linked to gram-negative bacterial virulence. Metagenomics in SAH versus NACs predicted increased isoprenoid synthesis via mevalonate and anthranilate degradation, known modulators of gram-positive bacterial growth and biofilm production, respectively.
CONCLUSION: Heavy alcohol consumption appears to be the primary driver of changes in the circulating microbiome associated with a shift in its inferred metabolic functions. (Hepatology 2018;67:1284-1302).}, }
@article {pmid28232956, year = {2017}, author = {Marbouty, M and Baudry, L and Cournac, A and Koszul, R}, title = {Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay.}, journal = {Science advances}, volume = {3}, number = {2}, pages = {e1602105}, doi = {10.1126/sciadv.1602105}, pmid = {28232956}, issn = {2375-2548}, mesh = {Animals ; *Bacteria/genetics/metabolism/virology ; *Bacteriophages/genetics/metabolism ; *Gastrointestinal Microbiome ; *Genome, Bacterial ; *Genome, Viral ; Male ; Mice ; }, abstract = {The biochemical activities of microbial communities, or microbiomes, are essential parts of environmental and animal ecosystems. The dynamics, balance, and effects of these communities are strongly influenced by phages present in the population. Being able to characterize bacterium-phage relationships is therefore essential to investigate these ecosystems to the full extent of their complexity. However, this task is currently limited by (i) the ability to characterize complete bacterial and viral genomes from a complex mix of species and (ii) the difficulty to assign phage sequences to their bacterial hosts. We show that both limitations can be circumvented using meta3C, an experimental and computational approach that exploits the physical contacts between DNA molecules to infer their proximity. In a single experiment, dozens of bacterial and phage genomes present in a complex mouse gut microbiota were assembled and scaffolded de novo. The phage genomes were then assigned to their putative bacterial hosts according to the physical contacts between the different DNA molecules, opening new perspectives for a comprehensive picture of the genomic structure of the gut flora. Therefore, this work holds far-reaching implications for human health studies aiming to bridge the virome to the microbiome.}, }
@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 & 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 {pmid29654556, year = {2018}, author = {Jung, DH and Seo, DH and Kim, GY and Nam, YD and Song, EJ and Yoon, S and Park, CS}, title = {The effect of resistant starch (RS) on the bovine rumen microflora and isolation of RS-degrading bacteria.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {11}, pages = {4927-4936}, doi = {10.1007/s00253-018-8971-z}, pmid = {29654556}, issn = {1432-0614}, support = {no. 2017R1A2B4004218//National Research Foundation of Korea/ ; }, mesh = {Animals ; Bacteria/isolation & purification/metabolism ; Cattle ; Feces/microbiology ; Fermentation ; Gastrointestinal Microbiome/*drug effects ; Humans ; Rumen/*microbiology ; Starch/*metabolism/*pharmacology ; }, abstract = {Resistant starch (RS) in the diet reaches the large intestine without degradation, where it is decomposed by the commensal microbiota. The fermentation of RS produces secondary metabolites including short-chain fatty acids (SCFAs), which have been linked to a variety of physiological and health effects. Therefore, the availability of RS as a prebiotic is a current issue. The objectives of this study were (1) to use metagenomics to observe microbial flora changes in Bos taurus coreanae rumen fluid in the presence of RS and (2) to isolate RS-degrading microorganisms. The major microbial genus in a general rumen fluid was Succiniclasticum sp., whereas Streptococcus sp. immediately predominated after the addition of RS into the culture medium and was then drastically replaced by Lactobacillus sp. The presence of Bifidobacterium sp. was also observed continuously. Several microorganisms with high RS granule-degrading activity were identified and isolated, including B. choerinum FMB-1 and B. pseudolongum FMB-2. B. choerinum FMB-1 showed the highest RS-hydrolyzing activity and degraded almost 60% of all substrates tested. Coculture experiments demonstrated that Lactobacillus brevis ATCC 14869, which was isolated from human feces, could grow using reducing sugars generated from RS by B. choerinum FMB-1. These results suggest that Bifidobacterium spp., especially B. choerinum FMB-1, are the putative primary degrader of RS in rumen microbial flora and could be further studied as probiotic candidates.}, }
@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}, doi = {10.3897/mycokeys.39.28109}, 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 {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}, doi = {10.1186/s12859-018-2320-1}, 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.
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.
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 {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 & biotechnology}, volume = {34}, number = {9}, pages = {136}, doi = {10.1007/s11274-018-2509-5}, 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 {pmid29704757, year = {2018}, author = {Campanaro, S and Treu, L and Kougias, PG and Luo, G and Angelidaki, I}, title = {Metagenomic binning reveals the functional roles of core abundant microorganisms in twelve full-scale biogas plants.}, journal = {Water research}, volume = {140}, number = {}, pages = {123-134}, doi = {10.1016/j.watres.2018.04.043}, pmid = {29704757}, issn = {1879-2448}, mesh = {Anaerobiosis ; *Biofuels ; Bioreactors/*microbiology ; Manure ; *Metagenome ; Metagenomics/methods ; Microbiota/*physiology ; Sewage/microbiology ; Waste Disposal, Fluid ; Waste Water ; }, abstract = {The aim of this work was to elucidate the microbial ecology in twelve mesophilic and thermophilic full-scale biogas plants using a genome-centric metagenomic approach. In this study both biogas plants treating manure and those treating sludge from waste water treatment plants were considered. The identification of 132 Metagenome-Assembled Genomes (MAGs) and analysis of their abundance profile in different samples allowed the identification of the most abundant core members of the anaerobic digestion microbiome. Canonical correspondence analysis was used to determine the influence of biotic and environmental factors on MAGs abundance and to investigate the methanogenic performance of the biogas plants. Prediction of the functional properties of MAGs was obtained analyzing their KEGG pathways and their carbohydrate active domains. Network analysis allowed investigation of species-species associations and shed light on syntrophic interactions between members belonging to the anaerobic digestion dark matter (phylum Fermentibacteria). By stratifying and comparing different levels of information, it was predicted that some MAGs have a crucial role in the manure-supplemented thermophilic biogas plants and it was highlighted the importance of the glycine cleavage system in complementing the "truncated" Wood-Ljungdahl pathway.}, }
@article {pmid29676472, year = {2018}, author = {Hao, DC and Zhang, CR and Xiao, PG}, title = {The first Taxus rhizosphere microbiome revealed by shotgun metagenomic sequencing.}, journal = {Journal of basic microbiology}, volume = {58}, number = {6}, pages = {501-512}, doi = {10.1002/jobm.201700663}, pmid = {29676472}, issn = {1521-4028}, mesh = {Archaea/classification/genetics/isolation & purification ; Bacteria/classification/genetics/isolation & purification ; Biodegradation, Environmental ; Environmental Pollutants/adverse effects ; Fungi/classification/genetics/isolation & purification ; Genes, Archaeal/genetics ; Genes, Bacterial/genetics ; Genes, Fungal/genetics ; Genes, Viral/genetics ; Metagenomics/*methods ; *Microbiota ; Phylogeny ; Plant Roots/*microbiology ; *Rhizosphere ; *Soil Microbiology ; Taxus/*microbiology ; Viruses/classification/genetics/isolation & purification ; }, abstract = {In the present study, the shotgun high throughput metagenomic sequencing was implemented to globally capture the features of Taxus rhizosphere microbiome. Total reads could be assigned to 6925 species belonging to 113 bacteria phyla and 301 species of nine fungi phyla. For archaea and virus, 263 and 134 species were for the first time identified, respectively. More than 720,000 Unigenes were identified by clean reads assembly. The top five assigned phyla were Actinobacteria (363,941 Unigenes), Proteobacteria (182,053), Acidobacteria (44,527), Ascomycota (fungi; 18,267), and Chloroflexi (15,539). KEGG analysis predicted numerous functional genes; 7101 Unigenes belong to "Xenobiotics biodegradation and metabolism." A total of 12,040 Unigenes involved in defense mechanisms (e.g., xenobiotic metabolism) were annotated by eggNOG. Talaromyces addition could influence not only the diversity and structure of microbial communities of Taxus rhizosphere, but also the relative abundance of functional genes, including metabolic genes, antibiotic resistant genes, and genes involved in pathogen-host interaction, bacterial virulence, and bacterial secretion system. The structure and function of rhizosphere microbiome could be sensitive to non-native microbe addition, which could impact on the pollutant degradation. This study, complementary to the amplicon sequencing, more objectively reflects the native microbiome of Taxus rhizosphere and its response to environmental pressure, and lays a foundation for potential combination of phytoremediation and bioaugmentation.}, }
@article {pmid29567298, year = {2018}, author = {Stensvold, CR and van der Giezen, M}, title = {Associations between Gut Microbiota and Common Luminal Intestinal Parasites.}, journal = {Trends in parasitology}, volume = {34}, number = {5}, pages = {369-377}, doi = {10.1016/j.pt.2018.02.004}, pmid = {29567298}, issn = {1471-5007}, mesh = {Blastocystis/*physiology ; Dientamoeba/*physiology ; *Environmental Biomarkers ; Gastrointestinal Microbiome/*physiology ; Host-Parasite Interactions/*physiology ; Humans ; Intestinal Diseases, Parasitic/*microbiology ; Intestines/microbiology/parasitology ; }, abstract = {The development and integration of DNA-based methods in research and clinical microbiology laboratories have enabled standardised and comprehensive detection and differentiation of the microbes colonising our guts. For instance, the single-celled parasites Blastocystis and Dientamoeba appear to be much more common than previously thought, especially so in healthy individuals. While increasing evidence appears to suggest limited pathogenicity of these parasites, next-generation-sequencing-based studies have helped us to appreciate links between parasite colonisation and certain host phenotypical characteristics and gut microbial profiles. The fundamental question remains as to whether such parasites are merely indicators or active manipulators of gut microbiota structure and function. In this article, we collate existing evidence that these parasites are, at minimum, indicators of intestinal microbiota structure.}, }
@article {pmid29500689, year = {2018}, author = {Xia, H and Wang, Y and Shi, C and Atoni, E and Zhao, L and Yuan, Z}, title = {Comparative Metagenomic Profiling of Viromes Associated with Four Common Mosquito Species in China.}, journal = {Virologica Sinica}, volume = {33}, number = {1}, pages = {59-66}, doi = {10.1007/s12250-018-0015-4}, pmid = {29500689}, issn = {1995-820X}, mesh = {Animals ; *Biodiversity ; China ; Culicidae/*virology ; Host Specificity ; *Metagenomics ; Mosquito Vectors/*virology ; Viral Tropism ; Viruses/*classification/genetics/*isolation & purification ; }, abstract = {Vast viruses are thought to be associated with mosquitoes. Anopheles sinensis, Armigeres subalbatus, Culex quinquefasciatus, and Culex tritaeniorhynchus are very common mosquito species in China, and whether the virome structure in each species is species-specific has not been evaluated. In this study, a total of 2222 mosquitoes were collected from the same geographic location, and RNAs were sequenced using the Illumina Miseq platform. After querying to the Refseq database, a total of 3,435,781, 2,223,509, 5,727,523, and 6,387,867 paired-end reads were classified under viral sequences from An. sinensis, Ar. subalbatus, Cx. quinquefasciatus, and Cx. tritaeniorhynchus, respectively, with the highest prevalence of virus-associated reads being observed in Cx. quinquefasciatus. The metagenomic comparison analysis showed that the virus-related reads were distributed across 26 virus families, together with an unclassified group of viruses. Anelloviridae, Circoviridae, Genomoviridae, Iridoviridae, Mesoniviridae, Microviridae, Myoviridae, Parvoviridae, Phenuiviridae, and Podoviridae were the top ten significantly different viral families among the four species. Further analysis reveals that the virome is species-specific in four mosquito samples, and several viral sequences which maybe belong to novel viruses are discovered for the first time in those mosquitoes. This investigation provides a basis for a comprehensive knowledge on the mosquito virome status in China.}, }
@article {pmid29171095, year = {2018}, author = {Barko, PC and McMichael, MA and Swanson, KS and Williams, DA}, title = {The Gastrointestinal Microbiome: A Review.}, journal = {Journal of veterinary internal medicine}, volume = {32}, number = {1}, pages = {9-25}, doi = {10.1111/jvim.14875}, pmid = {29171095}, issn = {1939-1676}, mesh = {Animals ; Dysbiosis/*veterinary ; *Gastrointestinal Microbiome ; Mammals ; Metabolomics ; Metagenomics ; }, abstract = {The gastrointestinal microbiome is a diverse consortium of bacteria, archaea, fungi, protozoa, and viruses that inhabit the gut of all mammals. Studies in humans and other mammals have implicated the microbiome in a range of physiologic processes that are vital to host health including energy homeostasis, metabolism, gut epithelial health, immunologic activity, and neurobehavioral development. The microbial genome confers metabolic capabilities exceeding those of the host organism alone, making the gut microbiome an active participant in host physiology. Recent advances in DNA sequencing technology and computational biology have revolutionized the field of microbiomics, permitting mechanistic evaluation of the relationships between an animal and its microbial symbionts. Changes in the gastrointestinal microbiome are associated with diseases in humans and animals including inflammatory bowel disease, asthma, obesity, metabolic syndrome, cardiovascular disease, immune-mediated conditions, and neurodevelopmental conditions such as autism spectrum disorder. While there remains a paucity of data regarding the intestinal microbiome in small animals, recent studies have helped to characterize its role in host animal health and associated disease states. This review is intended to familiarize small animal veterinarians with recent advances in the field of microbiomics and to prime them for a future in which diagnostic tests and therapies will incorporate these developments into clinical practice.}, }
@article {pmid28891744, year = {2018}, author = {Fraumene, C and Manghina, V and Cadoni, E and Marongiu, F and Abbondio, M and Serra, M and Palomba, A and Tanca, A and Laconi, E and Uzzau, S}, title = {Caloric restriction promotes rapid expansion and long-lasting increase of Lactobacillus in the rat fecal microbiota.}, journal = {Gut microbes}, volume = {9}, number = {2}, pages = {104-114}, doi = {10.1080/19490976.2017.1371894}, pmid = {28891744}, issn = {1949-0984}, mesh = {Animals ; Bacteria/classification/genetics/*growth & development ; *Caloric Restriction ; Cluster Analysis ; DNA, Bacterial/genetics ; Diet ; Feces/*microbiology ; Gastrointestinal Microbiome/*physiology ; Lactobacillus/classification/*growth & development ; Models, Animal ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Inbred F344 ; }, abstract = {Previous studies indicated that caloric restricted diet enables to lower significantly the risk of cardiovascular and metabolic diseases. In experimental animal models, life-long lasting caloric restriction (CR) was demonstrated to induce changes of the intestinal microbiota composition, regardless of fat content and/or exercise. To explore the potential impact of short and long-term CR treatment on the gut microbiota, we conducted an analysis of fecal microbiota composition in young and adult Fisher 344 rats treated with a low fat feed under ad libitum (AL) or CR conditions (70%). We report here significant changes of the rat fecal microbiota that arise rapidly in young growing animals after short-term administration of a CR diet. In particular, Lactobacillus increased significantly after 8 weeks of CR treatment and its relative abundance was significantly higher in CR vs AL fed animals after 36 weeks of dietary intervention. Taken together, our data suggest that Lactobacillus intestinal colonization is hampered in AL fed young rats compared to CR fed ones, while health-promoting CR diet intervention enables the expansion of this genus rapidly and persistently up to adulthood.}, }
@article {pmid29453765, year = {2018}, author = {Mahajan, R and Attri, S and Sharma, K and Singh, N and Sharma, D and Goel, G}, title = {Statistical assessment of DNA extraction methodology for culture-independent analysis of microbial community associated with diverse environmental samples.}, journal = {Molecular biology reports}, volume = {45}, number = {3}, pages = {297-308}, doi = {10.1007/s11033-018-4162-3}, pmid = {29453765}, issn = {1573-4978}, support = {INT/RUS/RFBR/P-175//Department of Science and Technology, Ministry of Science and Technology/ ; }, mesh = {Animals ; DNA/genetics/*isolation & purification ; DNA, Bacterial/genetics/isolation & purification ; Feces/chemistry ; Humans ; Metagenomics/methods ; Microbiota/genetics ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA/methods ; Soil/chemistry ; }, abstract = {Cost-effectiveness, quality, time-effectiveness and ease of the methodology are the most crucial factors in isolating quality DNA from wide variety of samples. Thus, research efforts focusing on the development of an efficient DNA extraction protocol is the need of the hour. The present study therefore, focuses on development of an efficient, rapid and free of inhibitory substances based methodology for extracting metagenomic DNA from diverse environmental samples viz. anaerobic biogas digesta, ruminant stomach, human feces, soil, and microbial starter cultures used for preparation of fermented food. PCR-DGGE based analysis and quality metagenomic library preparation, using DNA extraction methodology, validates the developed protocol. The developed protocol is cost effective, capable of isolating DNA from small sample size (100-1000 µl), time efficient (1.5-2.0 h protocol) and results in significantly higher DNA yield (4-8 times increased yield) when compared to previously available DNA extraction method and a commercial DNA extraction kit. The DNA extracted from the samples using different protocols was evaluated based on its ability to identify diverse microbial species using PCR-DGGE profiles targeting variable region within the 16S rRNA gene. The results of microbial community analysis revealed comparability of the developed protocol to commercial kits, in effectively identifying dominant representatives of the microbial community in different samples. Using the DNA extracted from the presented methodology, metagenomic libraries were prepared, which were found suitable for sequencing on Illumina platform.}, }
@article {pmid28612429, year = {2017}, author = {Tanner, K and Vilanova, C and Porcar, M}, title = {Bioprospecting challenges in unusual environments.}, journal = {Microbial biotechnology}, volume = {10}, number = {4}, pages = {671-673}, doi = {10.1111/1751-7915.12723}, pmid = {28612429}, issn = {1751-7915}, mesh = {Bacteria/classification/genetics/isolation & purification/*metabolism ; Biodiversity ; Bioprospecting/*trends ; Biotechnology ; *Environmental Microbiology ; Metagenomics ; }, }
@article {pmid29858829, year = {2018}, author = {Gupta, SK and Shin, H and Han, D and Hur, HG and Unno, T}, title = {Metagenomic analysis reveals the prevalence and persistence of antibiotic- and heavy metal-resistance genes in wastewater treatment plant.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {56}, number = {6}, pages = {408-415}, doi = {10.1007/s12275-018-8195-z}, pmid = {29858829}, issn = {1976-3794}, mesh = {Anti-Bacterial Agents/*toxicity ; Bacteria/*classification/drug effects/*genetics/isolation & purification ; DNA, Bacterial/genetics ; Drug Resistance, Microbial/*genetics ; Genes, Bacterial ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; Metals, Heavy/*toxicity ; Microbial Consortia/genetics ; Phylogeny ; Republic of Korea ; Sequence Analysis ; Sewage/microbiology ; Waste Water/*microbiology ; Water Purification ; }, abstract = {The increased antibiotic resistance among microorganisms has resulted into growing interest for investigating the wastewater treatment plants (WWTPs) as they are reported to be the major source in the dissemination of antibiotic resistance genes (ARGs) and heavy metal resistance genes (HMRGs) in the environment. In this study, we investigated the prevalence and persistence of ARGs and HMRGs as well as bacterial diversity and mobile genetic elements (MGEs) in influent and effluent at the WWTP in Gwangju, South Korea, using high-throughput sequencing based metagenomic approach. A good number of broad-spectrum of resistance genes (both ARG and HMRG) were prevalent and likely persistent, although large portion of them were successfully removed at the wastewater treatment process. The relative abundance of ARGs and MGEs was higher in effluent as compared to that of influent. Our results suggest that the resistance genes with high abundance and bacteria harbouring ARGs and MGEs are likely to persist more through the treatment process. On analyzing the microbial community, the phylum Proteobacteria, especially potentially pathogenic species belonging to the genus Acinetobacter, dominated in WWTP. Overall, our study demonstrates that many ARGs and HMRGs may persist the treatment processes in WWTPs and their association to MGEs may contribute to the dissemination of resistance genes among microorganisms in the environment.}, }
@article {pmid29587819, year = {2018}, author = {Dickson, LB and Ghozlane, A and Volant, S and Bouchier, C and Ma, L and Vega-Rúa, A and Dusfour, I and Jiolle, D and Paupy, C and Mayanja, MN and Kohl, A and Lutwama, JJ and Duong, V and Lambrechts, L}, title = {Diverse laboratory colonies of Aedes aegypti harbor the same adult midgut bacterial microbiome.}, journal = {Parasites & vectors}, volume = {11}, number = {1}, pages = {207}, doi = {10.1186/s13071-018-2780-1}, pmid = {29587819}, issn = {1756-3305}, support = {ANR-16-CE35-0004-01//Agence Nationale de la Recherche/International ; ANR-17-ERC2-0016-01//Agence Nationale de la Recherche/International ; ANR-10-LABX-62-IBEID//Investissement d'Avenir program Laboratoire d'Excellence Integrative Biology of Emerging Infectious Diseases/International ; 734584//European Union's Horizon 2020 research and innovation programme under ZikaPLAN/International ; 2015-FED-192//Programme Opérationnel FEDER-Guadeloupe-Conseil Régional/International ; MC_UU_12014//Medical Research Council/United Kingdom ; ANR10-INBS-09-08//France Génomique consortium/International ; }, mesh = {Aedes/*microbiology ; Animals ; Bacteria/*classification/*genetics ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Host-associated microbes, collectively known as the microbiota, play an important role in the biology of multicellular organisms. In mosquito vectors of human pathogens, the gut bacterial microbiota influences vectorial capacity and has become the subject of intense study. In laboratory studies of vector biology, genetic effects are often inferred from differences between geographically and genetically diverse colonies of mosquitoes that are reared in the same insectary. It is unclear, however, to what extent genetic effects can be confounded by uncontrolled differences in the microbiota composition among mosquito colonies. To address this question, we used 16S metagenomics to compare the midgut bacterial microbiome of six laboratory colonies of Aedes aegypti recently derived from wild populations representing the geographical range and genetic diversity of the species.
RESULTS: We found that the diversity, abundance, and community structure of the midgut bacterial microbiome was remarkably similar among the six different colonies of Ae. aegypti, regardless of their geographical origin. We also confirmed the relatively low complexity of bacterial communities inhabiting the mosquito midgut.
CONCLUSIONS: Our finding that geographically diverse colonies of Ae. aegypti reared in the same insectary harbor a similar gut bacterial microbiome supports the conclusion that the gut microbiota of adult mosquitoes is environmentally determined regardless of the host genotype. Thus, uncontrolled differences in microbiota composition are unlikely to represent a significant confounding factor in genetic studies of vector biology.}, }
@article {pmid29497869, year = {2018}, author = {Tan, Z and Wang, Y and Yang, T and Ao, H and Chen, S and Xing, K and Zhang, F and Zhao, X and Liu, J and Wang, C}, title = {Differences in gut microbiota composition in finishing Landrace pigs with low and high feed conversion ratios.}, journal = {Antonie van Leeuwenhoek}, volume = {111}, number = {9}, pages = {1673-1685}, doi = {10.1007/s10482-018-1057-1}, pmid = {29497869}, issn = {1572-9699}, support = {BAIC02-2016//Beijing Innovation Consortium of Agriculture Research System/ ; }, mesh = {Amino Acids/metabolism ; Animal Feed/*analysis ; Animals ; Bacteria/*classification/genetics ; *Biodiversity ; Carbohydrate Metabolism ; Cecum/microbiology ; Colon/microbiology ; DNA, Bacterial/genetics ; Discriminant Analysis ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Intestine, Small/microbiology ; Metabolic Networks and Pathways ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Swine ; }, abstract = {The goal of this study was to evaluate the microbial communities in the gut and feces from female finishing Landrace pigs with high and low feed conversion ratio (FCR) by 16S rRNA gene amplicon sequencing. Many potential biomarkers can distinguish between high and low FCR groups in the duodenum, ileum, cecum, colon, and rectum, according to linear discriminant analysis effect sizes. The relative abundance of microbes were tested by Mann-Whitney test between the high and low FCR groups in different organs: Campylobacter, Prevotella and Sphaerochaeta were different in the duodenum (P < 0.05); Sanguibacter, Kingella and Anaeroplasma in jejunum; Anaeroplasma, Arthrobacter, Kingella, Megasphaera and SMB53 in the ileum; Butyricicoccus, Campylobacter, Mitsuokella, and Coprobacillus in the cecum; Lactococcus and Peptococcus in the colon; Staphylococcus in the rectum; and Rothia in feces. The prevalence of microbial genera in certain locations could potentially be used as biomarkers to distinguish between high and low FCR. Functional prediction clustering analysis suggested that bacteria in the hindgut mainly participated in carbohydrate metabolism and amino acid metabolism, and different in the relative abundance of metabolic pathways, as predicted from the microbial taxa present, were identified by comparing the high and low groups of each location. The results may provide insights for the alteration of the intestinal microbial communities to improve the growth rate of pigs.}, }
@article {pmid29268781, year = {2017}, author = {Carda-Diéguez, M and Ghai, R and Rodríguez-Valera, F and Amaro, C}, title = {Wild eel microbiome reveals that skin mucus of fish could be a natural niche for aquatic mucosal pathogen evolution.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {162}, doi = {10.1186/s40168-017-0376-1}, pmid = {29268781}, issn = {2049-2618}, support = {BES-2012-052361//Secretaría de Estado de Investigación, Desarrollo e Innovación/International ; AGL2014-58933-P (cofunded with FEDER funds)//Secretaría de Estado de Investigación, Desarrollo e Innovación/International ; 17-04828S//Grantová Agentura České Republiky/International ; CGL2016-76273-P [AEI/FEDER, EU]//AEI/FEDER/EU/International ; CGL2015-71523-REDC (Acciones de dinamización "REDES DE EXCELENCIA" CONSOLIDER)//Dirección General de Investigación Científica y Técnica/International ; Prometeo II/2014/012 "AQUAMET"//Generalitat Valenciana/International ; }, mesh = {Anguilla/anatomy & histology/*microbiology ; Animals ; Animals, Wild/microbiology ; Bacteria/genetics/isolation & purification/*pathogenicity ; DNA, Bacterial ; Evolution, Molecular ; Genomic Islands ; Genomics ; Humans ; Metagenomics ; Microbiota/*genetics ; Mucus/*microbiology ; Skin/*microbiology ; Vibrio/genetics/isolation & purification/pathogenicity ; *Water Microbiology ; }, abstract = {BACKGROUND: Fish skin mucosal surfaces (SMS) are quite similar in composition and function to some mammalian MS and, in consequence, could constitute an adequate niche for the evolution of mucosal aquatic pathogens in natural environments. We aimed to test this hypothesis by searching for metagenomic and genomic evidences in the SMS-microbiome of a model fish species (Anguilla Anguilla or eel), from different ecosystems (four natural environments of different water salinity and one eel farm) as well as the water microbiome (W-microbiome) surrounding the host.
RESULTS: Remarkably, potentially pathogenic Vibrio monopolized wild eel SMS-microbiome from natural ecosystems, Vibrio anguillarum/Vibrio vulnificus and Vibrio cholerae/Vibrio metoecus being the most abundant ones in SMS from estuary and lake, respectively. Functions encoded in the SMS-microbiome differed significantly from those in the W-microbiome and allowed us to predict that successful mucus colonizers should have specific genes for (i) attachment (mainly by forming biofilms), (ii) bacterial competence and communication, and (iii) resistance to mucosal innate immunity, predators (amoeba), and heavy metals/drugs. In addition, we found several mobile genetic elements (mainly integrative conjugative elements) as well as a series of evidences suggesting that bacteria exchange DNA in SMS. Further, we isolated and sequenced a V. metoecus strain from SMS. This isolate shares pathogenicity islands with V. cholerae O1 from intestinal infections that are absent in the rest of sequenced V. metoecus strains, all of them from water and extra-intestinal infections.
CONCLUSIONS: We have obtained metagenomic and genomic evidence in favor of the hypothesis on the role of fish mucosal surfaces as a specialized habitat selecting microbes capable of colonizing and persisting on other comparable mucosal surfaces, e.g., the human intestine.}, }
@article {pmid29246178, year = {2017}, author = {Razavi, M and Marathe, NP and Gillings, MR and Flach, CF and Kristiansson, E and Joakim Larsson, DG}, title = {Discovery of the fourth mobile sulfonamide resistance gene.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {160}, doi = {10.1186/s40168-017-0379-y}, pmid = {29246178}, issn = {2049-2618}, support = {942-2015-750//Svenska Forskningsrådet Formas/ ; 521-2013-8633//Vetenskapsrådet/ ; 2015-02492//Vetenskapsrådet (SE)/ ; }, mesh = {Aminoglycosides/pharmacology ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics ; Bioprospecting ; Cross Infection/microbiology ; Dihydropteroate Synthase/genetics/isolation & purification ; Drug Resistance, Microbial/*genetics ; Escherichia coli/drug effects/genetics ; Genes, Bacterial ; Humans ; India ; *Integrons/genetics ; Metagenomics ; Microbial Consortia/genetics ; Microbial Sensitivity Tests ; RNA, Ribosomal, 16S/genetics ; Rivers/microbiology ; Sulfonamides/*pharmacology ; beta-Lactams/pharmacology ; }, abstract = {BACKGROUND: Over the past 75 years, human pathogens have acquired antibiotic resistance genes (ARGs), often from environmental bacteria. Integrons play a major role in the acquisition of antibiotic resistance genes. We therefore hypothesized that focused exploration of integron gene cassettes from microbial communities could be an efficient way to find novel mobile resistance genes. DNA from polluted Indian river sediments were amplified using three sets of primers targeting class 1 integrons and sequenced by long- and short-read technologies to maintain both accuracy and context.
RESULTS: Up to 89% of identified open reading frames encode known resistance genes, or variations thereof (> 1000). We identified putative novel ARGs to aminoglycosides, beta-lactams, trimethoprim, rifampicin, and chloramphenicol, including several novel OXA variants, providing reduced susceptibility to carbapenems. One dihydropteroate synthase gene, with less than 34% amino acid identity to the three known mobile sulfonamide resistance genes (sul1-3), provided complete resistance when expressed in Escherichia coli. The mobilized gene, here named sul4, is the first mobile sulfonamide resistance gene discovered since 2003. Analyses of adjacent DNA suggest that sul4 has been decontextualized from a set of chromosomal genes involved in folate synthesis in its original host, likely within the phylum Chloroflexi. The presence of an insertion sequence common region element could provide mobility to the entire integron. Screening of 6489 metagenomic datasets revealed that sul4 is already widespread in seven countries across Asia and Europe.
CONCLUSIONS: Our findings show that exploring integrons from environmental communities with a history of antibiotic exposure can provide an efficient way to find novel, mobile resistance genes. The mobilization of a fourth sulfonamide resistance gene is likely to provide expanded opportunities for sulfonamide resistance to spread, with potential impacts on both human and animal health.}, }
@article {pmid29228991, year = {2017}, author = {Auffret, MD and Dewhurst, RJ and Duthie, CA and Rooke, JA and John Wallace, R and Freeman, TC and Stewart, R and Watson, M and Roehe, R}, title = {The rumen microbiome as a reservoir of antimicrobial resistance and pathogenicity genes is directly affected by diet in beef cattle.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {159}, doi = {10.1186/s40168-017-0378-z}, pmid = {29228991}, issn = {2049-2618}, support = {BB/N01720X/1 and BB/N016742/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animal Feed/adverse effects/*analysis ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacteriocins/pharmacology ; Bacteroidetes/drug effects/genetics/pathogenicity ; Cattle/*microbiology ; Chloramphenicol/pharmacology ; Drug Resistance, Multiple, Bacterial/*genetics ; Firmicutes/drug effects/genetics/pathogenicity ; *Genes, Bacterial ; Humans ; Metagenomics/methods ; *Microbiota ; Proteobacteria/drug effects/genetics/pathogenicity ; Red Meat/analysis ; Rumen/*microbiology ; Virulence ; }, abstract = {BACKGROUND: The emergence and spread of antimicrobial resistance is the most urgent current threat to human and animal health. An improved understanding of the abundance of antimicrobial resistance genes and genes associated with microbial colonisation and pathogenicity in the animal gut will have a major role in reducing the contribution of animal production to this problem. Here, the influence of diet on the ruminal resistome and abundance of pathogenicity genes was assessed in ruminal digesta samples taken from 50 antibiotic-free beef cattle, comprising four cattle breeds receiving two diets containing different proportions of concentrate.
RESULTS: Two hundred and four genes associated with antimicrobial resistance (AMR), colonisation, communication or pathogenicity functions were identified from 4966 metagenomic genes using KEGG identification. Both the diversity and abundance of these genes were higher in concentrate-fed animals. Chloramphenicol and microcin resistance genes were dominant in samples from forage-fed animals (P < 0.001), while aminoglycoside and streptomycin resistances were enriched in concentrate-fed animals. The concentrate-based diet also increased the relative abundance of Proteobacteria, which includes many animal and zoonotic pathogens. A high ratio of Proteobacteria to (Firmicutes + Bacteroidetes) was confirmed as a good indicator for rumen dysbiosis, with eight cases all from concentrate-fed animals. Finally, network analysis demonstrated that the resistance/pathogenicity genes are potentially useful as biomarkers for health risk assessment of the ruminal microbiome.
CONCLUSIONS: Diet has important effects on the complement of AMR genes in the rumen microbial community, with potential implications for human and animal health.}, }
@article {pmid29197424, year = {2017}, author = {Cheng, K and Ning, Z and Zhang, X and Li, L and Liao, B and Mayne, J and Stintzi, A and Figeys, D}, title = {MetaLab: an automated pipeline for metaproteomic data analysis.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {157}, doi = {10.1186/s40168-017-0375-2}, pmid = {29197424}, issn = {2049-2618}, support = {217066//Natural Sciences and Engineering Research Council of Canada/ ; 9408//Genome Canada/Ontario Genomics/ ; }, mesh = {*Computational Biology ; Databases, Protein ; Gastrointestinal Microbiome ; *Metagenomics ; Microbiota ; *Proteomics ; *Software ; Statistics as Topic ; }, abstract = {BACKGROUND: Research involving microbial ecosystems has drawn increasing attention in recent years. Studying microbe-microbe, host-microbe, and environment-microbe interactions are essential for the understanding of microbial ecosystems. Currently, metaproteomics provide qualitative and quantitative information of proteins, providing insights into the functional changes of microbial communities. However, computational analysis of large-scale data generated in metaproteomic studies remains a challenge. Conventional proteomic software have difficulties dealing with the extreme complexity and species diversity present in microbiome samples leading to lower rates of peptide and protein identification. To address this issue, we previously developed the MetaPro-IQ approach for highly efficient microbial protein/peptide identification and quantification.
RESULT: Here, we developed an integrated software platform, named MetaLab, providing a complete and automated, user-friendly pipeline for fast microbial protein identification, quantification, as well as taxonomic profiling, directly from mass spectrometry raw data. Spectral clustering adopted in the pre-processing step dramatically improved the speed of peptide identification from database searches. Quantitative information of identified peptides was used for estimating the relative abundance of taxa at all phylogenetic ranks. Taxonomy result files exported by MetaLab are fully compatible with widely used metagenomics tools. Herein, the potential of MetaLab is evaluated by reanalyzing a metaproteomic dataset from mouse gut microbiome samples.
CONCLUSION: MetaLab is a fully automatic software platform enabling an integrated data-processing pipeline for metaproteomics. The function of sample-specific database generation can be very advantageous for searching peptides against huge protein databases. It provides a seamless connection between peptide determination and taxonomic profiling; therefore, the peptide abundance is readily used for measuring the microbial variations. MetaLab is designed as a versatile, efficient, and easy-to-use tool which can greatly simplify the procedure of metaproteomic data analysis for researchers in microbiome studies.}, }
@article {pmid29036588, year = {2018}, author = {Liu, X and Yu, Y and Liu, J and Elliott, CF and Qian, C and Liu, J}, title = {A novel data structure to support ultra-fast taxonomic classification of metagenomic sequences with k-mer signatures.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {1}, pages = {171-178}, doi = {10.1093/bioinformatics/btx432}, pmid = {29036588}, issn = {1367-4811}, support = {P30 CA177558/CA/NCI NIH HHS/United States ; R01 HG006272/HG/NHGRI NIH HHS/United States ; }, mesh = {Algorithms ; Bacteria/genetics ; *Genome, Microbial ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {Motivation: Metagenomic read classification is a critical step in the identification and quantification of microbial species sampled by high-throughput sequencing. Although many algorithms have been developed to date, they suffer significant memory and/or computational costs. Due to the growing popularity of metagenomic data in both basic science and clinical applications, as well as the increasing volume of data being generated, efficient and accurate algorithms are in high demand.
Results: We introduce MetaOthello, a probabilistic hashing classifier for metagenomic sequencing reads. The algorithm employs a novel data structure, called l-Othello, to support efficient querying of a taxon using its k-mer signatures. MetaOthello is an order-of-magnitude faster than the current state-of-the-art algorithms Kraken and Clark, and requires only one-third of the RAM. In comparison to Kaiju, a metagenomic classification tool using protein sequences instead of genomic sequences, MetaOthello is three times faster and exhibits 20-30% higher classification sensitivity. We report comparative analyses of both scalability and accuracy using a number of simulated and empirical datasets.
MetaOthello is a stand-alone program implemented in C ++. The current version (1.0) is accessible via https://doi.org/10.5281/zenodo.808941.
Contact: liuj@cs.uky.edu.
Supplementary information: Supplementary data are available at Bioinformatics online.}, }
@article {pmid28597254, year = {2017}, author = {Gopal, M and Bhute, SS and Gupta, A and Prabhu, SR and Thomas, GV and Whitman, WB and Jangid, K}, title = {Changes in structure and function of bacterial communities during coconut leaf vermicomposting.}, journal = {Antonie van Leeuwenhoek}, volume = {110}, number = {10}, pages = {1339-1355}, doi = {10.1007/s10482-017-0894-7}, pmid = {28597254}, issn = {1572-9699}, support = {BT/PR/0054/NDB/52/94/2007//Department of Biotechnology , Ministry of Science and Technology/ ; }, mesh = {Animals ; Bacteria/classification/genetics ; Bacterial Proteins/metabolism ; *Biodiversity ; *Cocos ; *Composting ; DNA, Bacterial/genetics ; Metagenomics/methods ; *Microbiota ; Oligochaeta/*metabolism/microbiology ; Plant Leaves/*metabolism ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {To understand bacterial community dynamics during the vermicomposting of lignin-rich coconut leaves using an indigenous isolate of an epigeic earthworm, Eudrilus sp., we employed amplicon-based pyrosequencing of the V1 to V3 region of the 16S rRNA genes. Total community DNA was isolated from two separate vermicomposting tanks in triplicate at four different stages of the process: pre-decomposition (15th day), initial vermicomposting (45th day), 50-70% vermicomposting (75th day) and mature vermicompost (105th day). Alpha diversity measurements revealed an increase in bacterial diversity till the 75th day, which then declined in the mature vermicompost. Beta diversity comparisons showed formation of distinct, stage-specific communities. In terms of relative abundance, the Acidobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes, Nitrospirae, Planctomycetes, TM7 and WS3 groups increased until the 50-70% vermicomposting stage (p = 0.05). During the same time, the abundance of Bacteroidetes and Proteobacteria decreased. In contrast, the levels of Firmicutes increased throughout the 105-day vermicomposting process. The distribution of the most abundant OTUs revealed that each stage of the vermicomposting process possessed its own unique microbiome. Predictions based on the OTUs present by PICRUSt suggested a functional shift in the microbiome during vermicomposting. Enzymes and pathways of lipid and lignin metabolism were predicted to be initially abundant, but by the end of the process, biosynthesis of secondary metabolites and plant beneficial properties were enriched. The study revealed that bacterial communities undergo a continuous change throughout the vermicomposting process and that certain OTUs associated with specific stages could be targets for further improvements in the process.}, }
@article {pmid29540507, year = {2018}, author = {Succurro, A and Ebenhöh, O}, title = {Review and perspective on mathematical modeling of microbial ecosystems.}, journal = {Biochemical Society transactions}, volume = {46}, number = {2}, pages = {403-412}, doi = {10.1042/BST20170265}, pmid = {29540507}, issn = {1470-8752}, mesh = {*Ecosystem ; Metagenomics ; *Microbiota ; *Models, Biological ; }, abstract = {Understanding microbial ecosystems means unlocking the path toward a deeper knowledge of the fundamental mechanisms of life. Engineered microbial communities are also extremely relevant to tackling some of today's grand societal challenges. Advanced meta-omics experimental techniques provide crucial insights into microbial communities, but have been so far mostly used for descriptive, exploratory approaches to answer the initial 'who is there?'
QUESTION: An ecosystem is a complex network of dynamic spatio-temporal interactions among organisms as well as between organisms and the environment. Mathematical models with their abstraction capability are essential to capture the underlying phenomena and connect the different scales at which these systems act. Differential equation models and constraint-based stoichiometric models are deterministic approaches that can successfully provide a macroscopic description of the outcome from microscopic behaviors. In this mini-review, we present classical and recent applications of these modeling methods and illustrate the potential of their integration. Indeed, approaches that can capture multiple scales are needed in order to understand emergent patterns in ecosystems and their dynamics regulated by different spatio-temporal phenomena. We finally discuss promising examples of methods proposing the integration of differential equations with constraint-based stoichiometric models and argue that more work is needed in this direction.}, }
@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 = {}, number = {}, pages = {}, doi = {10.1007/s10646-018-1981-x}, pmid = {30242595}, issn = {1573-3017}, 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 {pmid30240114, year = {2018}, 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 non-invasive metagenomics to characterize viral communities from wildlife.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.12946}, pmid = {30240114}, issn = {1755-0998}, 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 present 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 non-invasively collected fecal 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 fetal bovine serum, we recommend storing swabs in RNALater or another non-biological 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. This article is protected by copyright. All rights reserved.}, }
@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}, doi = {10.1186/s40168-018-0548-7}, pmid = {30231921}, issn = {2049-2618}, support = {322551//European Research Council/International ; 322551//European Research Council/International ; L200961651//Czech Academy of Science/ ; 16-14-00121//Russian Science Support Foundation/ ; 24002002//Dutch Ministry of Education and Science/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; 17-04828S//Grant Agency of the Czech Republic/ ; 17-04828S//Grant Agency of the Czech Republic/ ; }, 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.
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.
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 {pmid29180750, year = {2017}, author = {Brooks, B and Olm, MR and Firek, BA and Baker, R and Thomas, BC and Morowitz, MJ and Banfield, JF}, title = {Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome.}, journal = {Nature communications}, volume = {8}, number = {1}, pages = {1814}, doi = {10.1038/s41467-017-02018-w}, pmid = {29180750}, issn = {2041-1723}, support = {R01 AI092531/AI/NIAID NIH HHS/United States ; S10 OD018174/OD/NIH HHS/United States ; }, mesh = {Cross Infection/*microbiology ; Environmental Exposure ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/microbiology/*physiology ; Humans ; Infant ; Infant, Newborn ; Infant, Premature/*physiology ; *Intensive Care Units, Neonatal ; Metagenomics/methods ; }, abstract = {Preterm infants exhibit different microbiome colonization patterns relative to full-term infants, and it is speculated that the hospital room environment may contribute to infant microbiome development. Here, we present a genome-resolved metagenomic study of microbial genotypes from the gastrointestinal tracts of infants and from the neonatal intensive care unit (NICU) room environment. Some strains detected in hospitalized infants also occur in sinks and on surfaces, and belong to species such as Staphylococcus epidermidis, Enterococcus faecalis, Pseudomonas aeruginosa, and Klebsiella pneumoniae, which are frequently implicated in nosocomial infection and preterm infant gut colonization. Of the 15 K. pneumoniae strains detected in the study, four were detected in both infant gut and room samples. Time series experiments showed that nearly all strains associated with infant gut colonization can be detected in the room after, and often before, detection in the gut. Thus, we conclude that a component of premature infant gut colonization is the cycle of microbial exchange between the room and the occupant.}, }
@article {pmid29404836, year = {2018}, author = {Boers, SA and de Zeeuw, M and Jansen, R and van der Schroeff, MP and van Rossum, AMC and Hays, JP and Verhaegh, SJC}, title = {Characterization of the nasopharyngeal and middle ear microbiota in gastroesophageal reflux-prone versus gastroesophageal reflux non-prone children.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {37}, number = {5}, pages = {851-857}, doi = {10.1007/s10096-017-3178-2}, pmid = {29404836}, issn = {1435-4373}, mesh = {Bacterial Typing Techniques ; Biodiversity ; Child ; Child, Preschool ; Ear, Middle/*microbiology ; Female ; Gastroesophageal Reflux/*complications ; Humans ; Infant ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Nasopharyngitis/diagnosis/*etiology ; Nasopharynx/*microbiology ; Otitis Media/diagnosis/*etiology ; RNA, Ribosomal, 16S ; }, abstract = {Otitis media (OM) is one of the most common pediatric infections worldwide, but the complex microbiology associated with OM is poorly understood. Previous studies have shown an association between OM and gastroesophageal reflux (GER) in children. Therefore, in order to bridge the gap in our current understanding of the interaction between GER and OM, we investigated the nasopharyngeal and middle ear microbiota of children suffering from GER-associated OM and OM only, using culture-independent 16S rRNA gene sequencing. Middle ear fluid, nasopharyngeal swabs, and clinical data were collected as part of a prospective pilot study conducted at the Department of Otorhinolaryngology of the Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands. A total of 30 children up to 12 years of age who suffered from recurrent acute otitis media (AOM) (5), chronic otitis media with effusion (OME) (23), or both (2), and who were listed for tympanostomy tube placement, were included in the study. Nine children were included in the GER-associated OM cohort and 21 in the OM-only cohort. We found no obvious effect of GER on the nasopharyngeal and middle ear microbiota between the two groups of children. However, our results highlight the need to assess the true role of Alloiococcus spp. and Turicella spp. in children presenting with a high prevalence of recurrent AOM and chronic OME.}, }
@article {pmid29340898, year = {2018}, author = {Mirande, C and Bizine, I and Giannetti, A and Picot, N and van Belkum, A}, title = {Epidemiological aspects of healthcare-associated infections and microbial genomics.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {37}, number = {5}, pages = {823-831}, doi = {10.1007/s10096-017-3170-x}, pmid = {29340898}, issn = {1435-4373}, mesh = {Bacteria/classification/genetics ; Bacterial Typing Techniques/methods ; Cross Infection/*epidemiology/*microbiology/prevention & control ; Disease Outbreaks ; Genome, Bacterial ; Humans ; *Metagenome ; *Metagenomics/methods ; Microbiota/*genetics ; Molecular Epidemiology ; Whole Genome Sequencing ; }, abstract = {Hospital-acquired infections (HAIs) are a cause of continuously increasing morbidity and mortality. Most of these infections are caused by a limited set of bacterial species, which share the capability to efficiently spread from patient to patient and to easily acquire antibiotic resistance determinants. This renders correct and rapid species identification and antibiotic susceptibility testing (AST) important and underscores the relevance of bacterial epidemiological typing. The latter is needed for the sensitive detection and exact tracing of nosocomial spread of these potentially multidrug-resistant microorganisms (MDRO). Many microbial typing technologies have been developed and put to some level of executive practice, but it seems that the continued evolution in methodology has currently reached an apex: there is likely to be scientific and practical consensus on the ultimate typing potential of bacterial whole-genome sequencing (WGS). The possibility to perform pan-genomic nucleotide-to-nucleotide comparisons between strains belonging to a single species and to detect even minute changes in nucleotide order will identify closely related organisms, while upon accumulation of such mutations, independent descend can be assumed. Calibration of difference levels [i.e. number of single nucleotide polymorphisms (SNPs)] into categories of inter-strain relatedness needs to be performed in order to generate robust, portable typing schemes. Here, we will briefly discuss the state of affairs regarding bacterial epidemiology based upon WGS, its relatedness with the nomenclature of former typing approaches and the continuing need for a global typing language.}, }
@article {pmid29334978, year = {2018}, author = {Wang, H and Li, S and Mahmood, A and Yang, S and Wang, X and Shen, Q and Shan, T and Deng, X and Li, J and Hua, X and Cui, L and Delwart, E and Zhang, W}, title = {Plasma virome of cattle from forest region revealed diverse small circular ssDNA viral genomes.}, journal = {Virology journal}, volume = {15}, number = {1}, pages = {11}, doi = {10.1186/s12985-018-0923-9}, pmid = {29334978}, issn = {1743-422X}, mesh = {Animals ; Biodiversity ; Cattle ; Cattle Diseases/*virology ; DNA Viruses/*genetics ; *DNA, Circular ; *DNA, Viral ; Forests ; *Genetic Variation ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/methods ; Phylogeny ; Sequence Analysis, DNA ; *Viral Load ; Virus Diseases/*veterinary ; }, abstract = {BACKGROUND: Free-range cattle are common in the Northeast China area, which have close contact with farmers and may carry virus threatening to cattle and farmers.
METHODS: Using viral metagenomics we analyzed the virome in plasma samples collected from 80 cattle from the forested region of Northeast China.
RESULTS: The virome of cattle plasma is composed of the viruses belonging to the families including Parvoviridae, Papillomaviridae, Picobirnaviridae, and divergent viral genomes showing sequence similarity to circular Rep-encoding single stranded (CRESS) DNA viruses. Five such CRESS-DNA genomes were full characterized, with Rep sequences related to circovirus and gemycircularvirus. Three bovine parvoviruses belonging to two different genera were also characterized.
CONCLUSION: The virome in plasma samples of cattle from the forested region of Northeast China was revealed, which further characterized the diversity of viruses in cattle plasma.}, }
@article {pmid28442730, year = {2017}, author = {Wang, S and Hou, X and Su, H}, title = {Exploration of the relationship between biogas production and microbial community under high salinity conditions.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {1149}, doi = {10.1038/s41598-017-01298-y}, pmid = {28442730}, issn = {2045-2322}, mesh = {Biofuels/*microbiology ; Biota/*drug effects ; Carbon Dioxide/metabolism ; High-Throughput Nucleotide Sequencing ; Hydrogen-Ion Concentration ; Metagenomics ; Methane/*metabolism ; *Salinity ; Sewage/*microbiology ; Sodium Chloride/metabolism ; }, abstract = {High salinity frequently causes inhibition and even failure in anaerobic digestion. To explore the impact of increasing NaCl concentrations on biogas production, and reveal the microbial community variations in response to high salinity stress, the Illumina high-throughput sequencing technology was employed. The results showed that a NaCl concentration of 20 g/L (H group) exhibited a similar level of VFAs and specific CO2 production rate with that in the blank group, thus indicating that the bacterial activity in acidogenesis might not be inhibited. However, the methanogenic activity in the H group was significantly affected compared with that in the blank group, causing a 42.2% decrease in CH4 production, a 37.12% reduction in the specific CH4 generation rate and a lower pH value. Illumina sequencing revealed that microbial communities between the blank and H groups were significantly different. Bacteroides, Clostridium and BA021 uncultured were the dominant species in the blank group while some halotolerant genera, such as Thermovirga, Soehngenia and Actinomyces, dominated and complemented the hydrolytic and acidogenetic abilities in the H group. Additionally, the most abundant archaeal species included Methanosaeta, Methanolinea, Methanospirillum and Methanoculleus in both groups, but hydrogenotrophic methanogens showed a lower resistance to high salinity than aceticlastic methanogens.}, }
@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 = {}, doi = {10.3390/md16090332}, pmid = {30213145}, issn = {1660-3397}, support = {0055_ALGARED_PLUS_5_E//INTERREG VA España-Portugal (POCTEP) 2014-2020 Cooperation Program/ ; }, 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 {pmid29526926, year = {2018}, author = {Do, TH and Le, NG and Dao, TK and Nguyen, TMP and Le, TL and Luu, HL and Nguyen, KHV and Nguyen, VL and Le, LA and Phung, TN and van Straalen, NM and Roelofs, D and Truong, NH}, title = {Metagenomic insights into lignocellulose-degrading genes through Illumina-based de novo sequencing of the microbiome in Vietnamese native goats' rumen.}, journal = {The Journal of general and applied microbiology}, volume = {64}, number = {3}, pages = {108-116}, doi = {10.2323/jgam.2017.08.004}, pmid = {29526926}, issn = {1349-8037}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/classification/*enzymology/*genetics ; Base Sequence ; DNA, Bacterial/genetics ; Databases, Genetic ; Gastrointestinal Microbiome/*genetics ; Genome, Bacterial/genetics ; Glycoside Hydrolases/*genetics/metabolism ; Goats/*microbiology ; Lignin/metabolism ; Metagenome/*genetics ; Metagenomics ; Open Reading Frames ; Rumen/*microbiology ; Vietnam ; }, abstract = {The scarcity of enzymes having an optimal activity in lignocellulose deconstruction is an obstacle for industrial-scale conversion of cellulosic biomass into biofuels. With the aim of mining novel lignocellulolytic enzymes, a ~9 Gb metagenome of bacteria in Vietnamese native goats' rumen was sequenced by Illumina platform. From the data, 821 ORFs encoding carbohydrate esterases (CEs) and polysaccharide lyases (PLs) serving for lignocellulose pre-treatment, 816 ORFs encoding 11 glycoside hydrolase families (GHs) of cellulases, and 2252 ORFs encoding 22 GHs of hemicellulases, were mined. The carbohydrate binding module (CBM) was also abundant with 763 ORFs, of which 480 ORFs are located with lignocellulolytic enzymes. The enzyme modularity analysis showed that CBMs are usually present in endoglucanase, endo 1,3-beta-D-glucosidase, and endoxylanase, whereas fibronectin 3-like module (FN3) mainly represents in GH3 and immunoglobulin-like domain (Ig) was located in GH9 only. Every domain located in each ORF was analyzed in detail to contribute enzymes' modularity which is valuable for modelling, to study the structure, and for recombinant production. With the aim of confirming the annotated results, a mined ORF encoding CBM63 was highly expressed in E. coli in soluble form. The purified recombinant CBM63 exhibited no cellulase activity, but enhanced a commercial cellulase activity in the destruction of a paper filter.}, }
@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 & evolution}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tree.2018.08.005}, pmid = {30209011}, issn = {1872-8383}, 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 {pmid28686571, year = {2017}, author = {Chistoserdova, L}, title = {Application of Omics Approaches to Studying Methylotrophs and Methylotroph Comunities.}, journal = {Current issues in molecular biology}, volume = {24}, number = {}, pages = {119-142}, doi = {10.21775/cimb.024.119}, pmid = {28686571}, issn = {1467-3045}, mesh = {Aerobiosis ; Anaerobiosis ; Bacteria/*metabolism ; Metabolomics/methods ; Metagenomics/*methods ; Methane/chemistry/*metabolism ; Methanol/chemistry/*metabolism ; *Microbial Consortia ; Proteomics/methods ; }, abstract = {This review covers some recent advances in application of omics technologies to studying methylotrophs, with special reference to their activities in natural environments. Some of the developments highlighted in this review are the new outlook at the role of the XoxF-type, lanthanum-dependent methanol dehydrogenase in natural habitats, new mechanistic details of methane oxidation through the reverse methanogenesis pathway, propensity of 'aerobic' methanotrophs to thrive in hypoxic environments and potential connection of this process to denitrification, and a novel outlook at methane oxidation as a community function.}, }
@article {pmid28686567, year = {2017}, author = {Sudarikov, K and Tyakht, A and Alexeev, D}, title = {Methods for The Metagenomic Data Visualization and Analysis.}, journal = {Current issues in molecular biology}, volume = {24}, number = {}, pages = {37-58}, doi = {10.21775/cimb.024.037}, pmid = {28686567}, issn = {1467-3045}, mesh = {Bacteria/*genetics ; *Computer Graphics ; Databases, Genetic ; *Metagenome ; Metagenomics/*methods ; *Microbiota ; }, abstract = {Surveys of environmental microbial communities using metagenomic approach produce vast volumes of multidimensional data regarding the phylogenetic and functional composition of the microbiota. Faced with such complex data, a metagenomic researcher needs to select the means for data analysis properly. Data visualization became an indispensable part of the exploratory data analysis and serves a key to the discoveries. While the molecular-genetic analysis of even a single bacterium presents multiple layers of data to be properly displayed and perceived, the studies of microbiota are significantly more challenging. Here we present a review of the state-of-art methods for the visualization of metagenomic data in a multi-level manner: from the methods applicable to an in-depth analysis of a single metagenome to the techniques appropriate for large-scale studies containing hundreds of environmental samples.}, }
@article {pmid28686566, year = {2017}, author = {Odintsova, V and Tyakht, A and Alexeev, D}, title = {Guidelines to Statistical Analysis of Microbial Composition Data Inferred from Metagenomic Sequencing.}, journal = {Current issues in molecular biology}, volume = {24}, number = {}, pages = {17-36}, doi = {10.21775/cimb.024.017}, pmid = {28686566}, issn = {1467-3045}, mesh = {Algorithms ; Computational Biology/*methods ; Data Interpretation, Statistical ; *Guidelines as Topic ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; *Microbiota ; *Software ; }, abstract = {Metagenomics, the application of high-throughput DNA sequencing for surveys of environmental samples, has revolutionized our view on the taxonomic and genetic composition of complex microbial communities. An enormous richness of microbiota keeps unfolding in the context of various fields ranging from biomedicine and food industry to geology. Primary analysis of metagenomic reads allows to infer semi-quantitative data describing the community structure. However, such compositional data possess statistical specific properties that are important to be considered during preprocessing, hypothesis testing and interpreting the results of statistical tests. Failure to account for these specifics may lead to essentially wrong conclusions as a result of the survey. Here we present a researcher introduced to the field of metagenomics with the basic properties of microbial compositional data including statistical power and proposed distribution models, perform a review of the publicly available software tools developed specifically for such data and outline the recommendations for the application of the methods.}, }
@article {pmid28686565, year = {2017}, author = {Marco, D}, title = {Integration of Ecology and Environmental Metagenomics Conceptual and Methodological Frameworks.}, journal = {Current issues in molecular biology}, volume = {24}, number = {}, pages = {1-16}, doi = {10.21775/cimb.024.001}, pmid = {28686565}, issn = {1467-3045}, mesh = {*Biodiversity ; Computational Biology/*methods ; Ecology/*methods ; Ecosystem ; Environment ; Humans ; Metagenomics/*methods ; Models, Theoretical ; }, abstract = {Although from its origin metagenomics was concerned with composition of communities of microbial OTUs (Operational Taxonomic Units) living in a given habitat and their diversity and functional heterogeneity (concepts already well rooted in ecology), the new field was more 'environmentally' than 'ecologically' oriented. Probably by circumstantial reasons, metagenomics and ecology followed rather independent trajectories and conceptual and methodological gaps appeared. Recently, calls for the need of integrating the theoretical basis and methodologies coming from metagenomics (and other meta-omics) and ecology have been made. Here I will address some of the principles and methods of field ecology that, although useful in the context of environmental metagenomic studies, have been rather disregarded. In particular, I will emphasize the contribution of some well established concepts and methods of field ecology to a an appropriate field sampling and experimental design of environmental metagenomic studies.}, }
@article {pmid27572648, year = {2016}, author = {Jansson, JK and Baker, ES}, title = {A multi-omic future for microbiome studies.}, journal = {Nature microbiology}, volume = {1}, number = {}, pages = {16049}, doi = {10.1038/nmicrobiol.2016.49}, pmid = {27572648}, issn = {2058-5276}, mesh = {*Gene Expression Profiling ; Humans ; *Metabolomics ; *Metagenomics ; *Microbiota ; *Proteomics ; }, }
@article {pmid29941576, year = {2018}, author = {Borton, MA and Hoyt, DW and Roux, S and Daly, RA and Welch, SA and Nicora, CD and Purvine, S and Eder, EK and Hanson, AJ and Sheets, JM and Morgan, DM and Wolfe, RA and Sharma, S and Carr, TR and Cole, DR and Mouser, PJ and Lipton, MS and Wilkins, MJ and Wrighton, KC}, title = {Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {28}, pages = {E6585-E6594}, doi = {10.1073/pnas.1800155115}, pmid = {29941576}, issn = {1091-6490}, mesh = {Bacteria/classification/*metabolism ; *Hydraulic Fracking ; Microbial Consortia/*physiology ; Natural Gas/*microbiology ; United States ; }, abstract = {Hydraulic fracturing is one of the industrial processes behind the surging natural gas output in the United States. This technology inadvertently creates an engineered microbial ecosystem thousands of meters below Earth's surface. Here, we used laboratory reactors to perform manipulations of persisting shale microbial communities that are currently not feasible in field scenarios. Metaproteomic and metabolite findings from the laboratory were then corroborated using regression-based modeling performed on metagenomic and metabolite data from more than 40 produced fluids from five hydraulically fractured shale wells. Collectively, our findings show that Halanaerobium, Geotoga, and Methanohalophilus strain abundances predict a significant fraction of nitrogen and carbon metabolites in the field. Our laboratory findings also exposed cryptic predatory, cooperative, and competitive interactions that impact microorganisms across fractured shales. Scaling these results from the laboratory to the field identified mechanisms underpinning biogeochemical reactions, yielding knowledge that can be harnessed to potentially increase energy yields and inform management practices in hydraulically fractured shales.}, }
@article {pmid29500976, year = {2018}, author = {Tang, X and Guo, Y and Jiang, B and Liu, S}, title = {Metagenomic approaches to understanding bacterial communication during the anammox reactor start-up.}, journal = {Water research}, volume = {136}, number = {}, pages = {95-103}, doi = {10.1016/j.watres.2018.02.054}, pmid = {29500976}, issn = {1879-2448}, mesh = {Ammonium Compounds/*metabolism ; Anaerobiosis ; Bacteria/genetics/*isolation & purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biodiversity ; Bioreactors/*microbiology ; Metagenomics ; Nitrogen/chemistry ; Waste Water/chemistry/*microbiology ; }, abstract = {Increasing attention has been paid to the anammox community for its significant function in high-efficiency wastewater treatment. However, bacterial interaction in terms of bacterial communication is still elusive. This study firstly explored the intra- and interspecific communication of bacteria in the anammox community using metagenomic sequence data obtained during bioreactor operation. We verified the existence of multiple bacterial communication gene (BCG) subtypes by alignment with the constructed BCG database containing 11 identified gene subtypes. Bacterial communication was more active at the initial start-up than in the high loading-rate phase, and was correlated with the gradually decreasing bacterial diversity. Hdts, one of the key genes that produced the intraspecific signaling molecule AHL, and RpfF, the key gene that produced the intra- and interspecific signaling molecule DSF, were the primary communication engines in the anammox community because of their high abundance. Anammox bacteria mainly used Hdts genes to communicate with others, while RpfF gene played a core role characterized by their multiple correlations with other BCG subtypes. Interestingly, bacteria with abundant BCGs were more inclined to interact with the bacteria with the same functional traits, indicating the potential communication-related interaction among these bacteria in addition to the frequently reported substrate co-utilization. This highlights the primary importance of AHL and DSF for the anammox community, and thereby hints at a potential strategy for the target regulation of the signals to improve anammox viability and competitive capacity in wastewater treatment.}, }
@article {pmid29729565, year = {2018}, author = {Chen, L and Hu, C and Lok-Shun Lai, N and Zhang, W and Hua, J and Lam, PKS and Lam, JCW and Zhou, B}, title = {Acute exposure to PBDEs at an environmentally realistic concentration causes abrupt changes in the gut microbiota and host health of zebrafish.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {240}, number = {}, pages = {17-26}, doi = {10.1016/j.envpol.2018.04.062}, pmid = {29729565}, issn = {1873-6424}, mesh = {Animals ; Bacteria ; Female ; Gastrointestinal Microbiome/*drug effects ; Halogenated Diphenyl Ethers/metabolism/*toxicity ; Intestines/metabolism ; Liver/metabolism ; Male ; Metagenomics ; Water Pollutants, Chemical/*toxicity ; Zebrafish/microbiology/*physiology ; }, abstract = {Contamination from lower brominated PBDEs is ubiquitous in the environments. However, their effects on gut microbiota and intestinal health have not yet been investigated. This study exposed adult zebrafish to an environmentally realistic concentration of pentaBDE mixture (DE-71) at 5.0 ng/L for 7 days, after which metagenomic sequencing of the intestinal microbiome was conducted and host physiological activities in the intestine and liver were also examined. The results showed that acute exposure to DE-71 significantly shifted the gut microbial community in a sex-specific manner. Certain genera (e.g., Mycoplasma, Ruminiclostridium, unclassified Firmicutes sensu stricto, and Fusobacterium) disappeared from the DE-71-exposed intestines, resulting in decreased bacterial diversity. Bacterial metabolic functions in guts were also affected by DE-71, namely those covering energy metabolism, virulence, respiration, cell division, cell signaling, and stress response. In addition, measurement of diverse sensitive biomarkers showed that the health of male intestines was remarkably compromised by the DE-71 exposure, as indicated by the disruption to its neural signaling (serotonin), epithelial barrier integrity (tight junction protein 2), inflammatory response (interleukin 1β), oxidative stress and antioxidant capacity, as well as detoxifying potential (ethoxyresorufin-O-deethylase activity). However, female intestines maintained intact physiological activities. Compared to the direct impact on intestines, a latent effect of DE-71 was observed in livers. Co-occurrence network analysis demonstrated that the gut bacteria vigorously interacted to establish the fittest community under DE-71 stress by promoting the reproduction of favorable genera, while diminishing the survival of unfavorable ones. Significant correlations between the zebrafish gut microbiota and physiological activities (e.g., oxidative stress, detoxification, neurotransmission, and epithelial integrity) were also observed. Overall, this study has demonstrated, for the first time, the high susceptibility of gut microbiota and intestinal health of zebrafish to DE-71, thus warranting more work to reveal its mode of toxicity.}, }
@article {pmid27262209, year = {2018}, author = {Tsai, CY and Tang, CY and Tan, TS and Chen, KH and Liao, KH and Liou, ML}, title = {Subgingival microbiota in individuals with severe chronic periodontitis.}, journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi}, volume = {51}, number = {2}, pages = {226-234}, doi = {10.1016/j.jmii.2016.04.007}, pmid = {27262209}, issn = {1995-9133}, mesh = {Bacteria/*classification/genetics/*isolation & purification ; Base Sequence ; Biodiversity ; Chronic Periodontitis/*microbiology ; Gingiva/*microbiology ; Humans ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Taiwan ; }, abstract = {BACKGROUND/PURPOSE: Subgingival microorganisms are potentially associated with periodontal diseases. However, the correlation between the variance in the periodontal microbiome and the prevalence and severity of periodontitis remains unclear. The aim of this study was to determine the subgingival microbiota in Taiwanese individuals with severe chronic periodontitis (SP).
METHODS: The composition of the subgingival microbiota in healthy and diseased individuals was compared using a 16S rRNA metagenomic approach and quantitative polymerase chain reaction (qPCR). A total of 20 samples, including 10 from healthy individuals and 10 from SP patients, were analyzed.
RESULTS: We found high microbial diversity, with an average of 774 classified phylotypes per sample and a total of six bacterial phyla across all samples. Cluster analysis by principal component analysis and heat map showed that the bacterial communities were different in the two groups. Streptococcus dominated across all the healthy samples, whereas Prevotella, Porphyromonas, and Treponema were highly abundant across all diseased samples. At least 13 bacterial genera were conserved among all the samples. Only eight genera, including Lautropia, Parvimonas, Actinomyces, Capnocytophaga, Paludibacter, Streptococcus, Haemophilus, and Corynebacterium, were significantly enriched in the healthy group, and six genera, including Porphyromonas, Treponema, Tannerella, Aggregatibacter, Peptostreptococcus, and Filifactor, were significantly enriched in the diseased group. Furthermore, a trend of abundance of bacteria at the species level measured by qPCR in all samples was consistent with the 16S rRNA metagenomics results.
CONCLUSION: This study is the first in Taiwan to provide a picture of the microbiome in SP via 16S rRNA metagenomics.}, }
@article {pmid29568746, year = {2018}, author = {Wu, H and Cai, L and Li, D and Wang, X and Zhao, S and Zou, F and Zhou, K}, title = {Metagenomics Biomarkers Selected for Prediction of Three Different Diseases in Chinese Population.}, journal = {BioMed research international}, volume = {2018}, number = {}, pages = {2936257}, doi = {10.1155/2018/2936257}, pmid = {29568746}, issn = {2314-6141}, mesh = {Algorithms ; Arthritis, Rheumatoid/*microbiology ; Asian Continental Ancestry Group/*genetics ; Biomarkers/*metabolism ; Diabetes Mellitus, Type 2/*microbiology ; Dysbiosis/genetics ; Female ; Humans ; Liver Cirrhosis/*microbiology ; Male ; Metagenome/*genetics ; Metagenomics/methods ; Microbiota/*genetics ; Middle Aged ; ROC Curve ; }, abstract = {The dysbiosis of human microbiome has been proven to be associated with the development of many human diseases. Metagenome sequencing emerges as a powerful tool to investigate the effects of microbiome on diseases. Identification of human gut microbiome markers associated with abnormal phenotypes may facilitate feature selection for multiclass classification. Compared with binary classifiers, multiclass classification models deploy more complex discriminative patterns. Here, we developed a pipeline to address the challenging characterization of multilabel samples. In this study, a total of 300 biomarkers were selected from the microbiome of 806 Chinese individuals (383 controls, 170 with type 2 diabetes, 130 with rheumatoid arthritis, and 123 with liver cirrhosis), and then logistic regression prediction algorithm was applied to those markers as the model intrinsic features. The estimated model produced an F1 score of 0.9142, which was better than other popular classification methods, and an average receiver operating characteristic (ROC) of 0.9475 showed a significant correlation between these selected biomarkers from microbiome and corresponding phenotypes. The results from this study indicate that machine learning is a vital tool in data mining from microbiome in order to identify disease-related biomarkers, which may contribute to the application of microbiome-based precision medicine in the future.}, }
@article {pmid29576590, year = {2018}, author = {Okamoto, H and Koizumi, S and Shimizu, H and Cho, O and Sugita, T}, title = {Characterization of the Axillary Microbiota of Japanese Male Subjects with Spicy and Milky Odor Types by Pyrosequencing.}, journal = {Biocontrol science}, volume = {23}, number = {1}, pages = {1-5}, doi = {10.4265/bio.23.1}, pmid = {29576590}, issn = {1884-0205}, mesh = {Adult ; Axilla/*microbiology ; Bacteria/classification/genetics ; Biodiversity ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing ; Humans ; Japan ; Male ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Middle Aged ; *Odorants ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {Malodorants in the human axilla are produced from human biogenic precursors by axillary bacterial enzymes. In the present study, we used pyrosequencing analysis to identify the axillary bacterial microbiota of 13 Japanese male subjects with cumin-like, spicy body odor (C type), and 9 with milky, skin-based body odor (M type). Anaerococcus, Corynebacterium, and Staphylococcus predominated in both C- and M-type subjects, followed by Moraxella and Peptoniphilus. These genera accounted for 96.2-99.9% of the total bacterial population, except in the microbiota of one C-type subject. However, the axillary bacteria in C-type subjects were more abundant than that in M-type subjects. These results suggest that the level of colonization by axillary bacteria is important for the production of malodorants.}, }
@article {pmid29432849, year = {2018}, author = {Joshi, A and Lanjekar, V and Dhakephalkar, PK and Dagar, SS}, title = {Cultivation of multiple genera of hydrogenotrophic methanogens from different environmental niches.}, journal = {Anaerobe}, volume = {50}, number = {}, pages = {64-68}, doi = {10.1016/j.anaerobe.2018.02.001}, pmid = {29432849}, issn = {1095-8274}, mesh = {Animals ; *Environmental Microbiology ; Feces/microbiology ; Geologic Sediments/microbiology ; Hydrogen/*metabolism ; Metagenome ; Metagenomics/methods ; Methane/*metabolism ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; Rumen/microbiology ; }, abstract = {Six genera of hydrogenotrophic methanogens, namely Methanobrevibacter, Methanobacterium, Methanocorpusculum, Methanothermobacter, Methanoculleus, and Methanospirillum were cultivated from diverse environmental niches like rumen, feces, gut, and sediments using BY medium. We also report a putative novel genus and two novel species of methanogens isolated from termite, Indian star tortoise, and green iguana.}, }
@article {pmid29330119, year = {2018}, author = {Jin, W and Wang, Y and Li, Y and Cheng, Y and Zhu, W}, title = {Temporal changes of the bacterial community colonizing wheat straw in the cow rumen.}, journal = {Anaerobe}, volume = {50}, number = {}, pages = {1-8}, doi = {10.1016/j.anaerobe.2018.01.004}, pmid = {29330119}, issn = {1095-8274}, mesh = {Animal Feed/*microbiology ; Animals ; *Bacteria/classification/ultrastructure ; Biodiversity ; Biomass ; Cattle ; *Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; Rumen/*microbiology ; Triticum/*microbiology ; }, abstract = {This study used Miseq pyrosequencing and scanning electron microscopy to investigate the temporal changes in the bacterial community tightly attached to wheat straw in the cow rumen. The wheat straw was incubated in the rumens and samples were recovered at various times. The wheat straw degradation exhibited three phases: the first degradation phase occurred within 0.5 h, and the second degradation phase occurred after 6 h, with a stalling phase occurring between 0.5 and 6 h. Scanning electron microscopy revealed the colonization of the microorganisms on the wheat straw over time. The bacterial communities at 0.5, 6, 24, and 72 h were determined, corresponding to the degradation phases. Firmicutes and Bacteroidetes were the two most dominant phyla in the bacterial communities at the four time points. Principal coordinate analysis (PCoA) showed that the bacterial communities at the four time points were distinct from each other. The wheat straw-associated bacteria stabilized at the phylum level after 0.5 h of rumen incubation, and only modest phylum-level and family-level changes were observed for most taxa between 0.5 h and 72 h. The relative abundance of the dominant genera, Butyrivibrio, Coprococcus, Ruminococcus, Succiniclasticum, Clostridium, Prevotella, YRC22, CF231, and Treponema, changed significantly over time (P < .05). However, at the genus level, unclassified taxa accounted for 70.3% ± 6.1% of the relative abundance, indicating their probable importance in the degradation of wheat straw as well as in the temporal changes of the bacterial community. Thus, understanding the function of these unclassified taxa is of great importance for targeted improvement of forage use efficiency in ruminants. Collectively, our results revealed distinct degradation phases of wheat straw and corresponding changes in the colonized bacterial community.}, }
@article {pmid29182421, year = {2018}, author = {McKenney, EA and O'Connell, TM and Rodrigo, A and Yoder, AD}, title = {Feeding strategy shapes gut metagenomic enrichment and functional specialization in captive lemurs.}, journal = {Gut microbes}, volume = {9}, number = {3}, pages = {202-217}, doi = {10.1080/19490976.2017.1408762}, pmid = {29182421}, issn = {1949-0984}, support = {S10 OD018164/OD/NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics/metabolism ; Biodiversity ; *Diet ; Feces/chemistry/microbiology ; Feeding Methods/veterinary ; Fermentation ; Fruit/chemistry/metabolism ; Gastrointestinal Tract/*microbiology/physiology ; Lemur/metabolism/*microbiology ; Metabolic Networks and Pathways ; *Metagenome ; Microbiota/genetics/*physiology ; Plant Leaves/chemistry/metabolism ; Species Specificity ; Strepsirhini/metabolism/microbiology ; }, abstract = {Many studies have demonstrated the effects of host diet on gut microbial membership, metagenomics, and fermentation individually; but few have attempted to interpret the relationship among these biological phenomena with respect to host features (e.g. gut morphology). We quantitatively compare the fecal microbial communities, metabolic pathways, and fermentation products associated with the nutritional intake of frugivorous (fruit-eating) and folivorous (leaf-eating) lemurs. Our results provide a uniquely multidimensional and comparative perspective on the adaptive dynamics between host and microbiome. Shotgun metagenomic sequencing revealed significant differential taxonomic and metabolic pathway enrichment, tailored to digest and detoxify different diets. Frugivorous metagenomes feature pathways to degrade simple carbohydrates and host-derived glycosaminoglycans, while folivorous metagenomes are equipped to break down phytic acid and other phytochemical compounds in an anaerobic environment. We used nuclear magnetic resonance based metabolic profiling of fecal samples to link metabolic pathways to fermentation products, confirming that the dissimilar substrates provided in each diet select for specific microbial functions. Fecal samples from frugivorous lemurs contained significantly different profiles of short chain fatty acids, alcohol fermentation products, amino acids, glucose, and glycerol compared to folivorous lemurs. We present the relationships between these datasets as an integrated visual framework, which we refer to as microbial geometry. We use microbial geometry to compare empirical gut microbial profiles across different feeding strategies, and suggest additional utility as a tool for hypothesis-generation.}, }
@article {pmid27739431, year = {2016}, author = {Bagnoud, A and Chourey, K and Hettich, RL and de Bruijn, I and Andersson, AF and Leupin, OX and Schwyn, B and Bernier-Latmani, R}, title = {Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {12770}, doi = {10.1038/ncomms12770}, pmid = {27739431}, issn = {2041-1723}, mesh = {*Aluminum Silicates ; Autotrophic Processes ; Bacteria/classification/genetics/metabolism ; Carbon Cycle ; Ecosystem ; Geography ; Heterotrophic Processes ; Hydrogen/*metabolism ; *Metabolic Networks and Pathways ; Metagenomics/*methods ; *Microbial Consortia ; RNA, Ribosomal, 16S/genetics ; Radioactive Waste ; *Soil Microbiology ; Switzerland ; }, abstract = {The Opalinus Clay formation will host geological nuclear waste repositories in Switzerland. It is expected that gas pressure will build-up due to hydrogen production from steel corrosion, jeopardizing the integrity of the engineered barriers. In an in situ experiment located in the Mont Terri Underground Rock Laboratory, we demonstrate that hydrogen is consumed by microorganisms, fuelling a microbial community. Metagenomic binning and metaproteomic analysis of this deep subsurface community reveals a carbon cycle driven by autotrophic hydrogen oxidizers belonging to novel genera. Necromass is then processed by fermenters, followed by complete oxidation to carbon dioxide by heterotrophic sulfate-reducing bacteria, which closes the cycle. This microbial metabolic web can be integrated in the design of geological repositories to reduce pressure build-up. This study shows that Opalinus Clay harbours the potential for chemolithoautotrophic-based system, and provides a model of microbial carbon cycle in deep subsurface environments where hydrogen and sulfate are present.}, }
@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}, doi = {10.3389/fmicb.2018.01914}, 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}, doi = {10.3389/fmicb.2018.01763}, 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 {pmid29760079, year = {2018}, author = {Wang, GD and Zhang, BL and Zhou, WW and Li, YX and Jin, JQ and Shao, Y and Yang, HC and Liu, YH and Yan, F and Chen, HM and Jin, L and Gao, F and Zhang, Y and Li, H and Mao, B and Murphy, RW and Wake, DB and Zhang, YP and Che, J}, title = {Selection and environmental adaptation along a path to speciation in the Tibetan frog Nanorana parkeri.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {22}, pages = {E5056-E5065}, doi = {10.1073/pnas.1716257115}, pmid = {29760079}, issn = {1091-6490}, mesh = {Animals ; Anura/*genetics/*physiology ; Gene Flow/*genetics ; *Genetic Speciation ; Hybridization, Genetic ; Metagenomics ; Phylogeny ; Selection, Genetic ; Tibet ; }, abstract = {Tibetan frogs, Nanorana parkeri, are differentiated genetically but not morphologically along geographical and elevational gradients in a challenging environment, presenting a unique opportunity to investigate processes leading to speciation. Analyses of whole genomes of 63 frogs reveal population structuring and historical demography, characterized by highly restricted gene flow in a narrow geographic zone lying between matrilines West (W) and East (E). A population found only along a single tributary of the Yalu Zangbu River has the mitogenome only of E, whereas nuclear genes of W comprise 89-95% of the nuclear genome. Selection accounts for 579 broadly scattered, highly divergent regions (HDRs) of the genome, which involve 365 genes. These genes fall into 51 gene ontology (GO) functional classes, 14 of which are likely to be important in driving reproductive isolation. GO enrichment analyses of E reveal many overrepresented functional categories associated with adaptation to high elevations, including blood circulation, response to hypoxia, and UV radiation. Four genes, including DNAJC8 in the brain, TNNC1 and ADORA1 in the heart, and LAMB3 in the lung, differ in levels of expression between low- and high-elevation populations. High-altitude adaptation plays an important role in maintaining and driving continuing divergence and reproductive isolation. Use of total genomes enabled recognition of selection and adaptation in and between populations, as well as documentation of evolution along a stepped cline toward speciation.}, }
@article {pmid29058768, year = {2018}, author = {Hernandez-Rodriguez, J and Arandjelovic, M and Lester, J and de Filippo, C and Weihmann, A and Meyer, M and Angedakin, S and Casals, F and Navarro, A and Vigilant, L and Kühl, HS and Langergraber, K and Boesch, C and Hughes, D and Marques-Bonet, T}, title = {The impact of endogenous content, replicates and pooling on genome capture from faecal samples.}, journal = {Molecular ecology resources}, volume = {18}, number = {2}, pages = {319-333}, doi = {10.1111/1755-0998.12728}, pmid = {29058768}, issn = {1755-0998}, support = {U01 MH106874/MH/NIMH NIH HHS/United States ; }, mesh = {Animals ; DNA/*genetics/*isolation & purification ; Feces/*chemistry ; Gabon ; Genetics, Population/*methods ; Metagenomics/*methods ; Pan troglodytes ; Sampling Studies ; Uganda ; }, abstract = {Target-capture approach has improved over the past years, proving to be very efficient tool for selectively sequencing genetic regions of interest. These methods have also allowed the use of noninvasive samples such as faeces (characterized by their low quantity and quality of endogenous DNA) to be used in conservation genomic, evolution and population genetic studies. Here we aim to test different protocols and strategies for exome capture using the Roche SeqCap EZ Developer kit (57.5 Mb). First, we captured a complex pool of DNA libraries. Second, we assessed the influence of using more than one faecal sample, extract and/or library from the same individual, to evaluate its effect on the molecular complexity of the experiment. We validated our experiments with 18 chimpanzee faecal samples collected from two field sites as a part of the Pan African Programme: The Cultured Chimpanzee. Those two field sites are in Kibale National Park, Uganda (N = 9) and Loango National Park, Gabon (N = 9). We demonstrate that at least 16 libraries can be pooled, target enriched through hybridization, and sequenced allowing for the genotyping of 951,949 exome markers for population genetic analyses. Further, we observe that molecule richness, and thus, data acquisition, increase when using multiple libraries from the same extract or multiple extracts from the same sample. Finally, repeated captures significantly decrease the proportion of off-target reads from 34.15% after one capture round to 7.83% after two capture rounds, supporting our conclusion that two rounds of target enrichment are advisable when using complex faecal samples.}, }
@article {pmid28439121, year = {2017}, author = {Mukherjee, A and Chettri, B and Langpoklakpam, JS and Basak, P and Prasad, A and Mukherjee, AK and Bhattacharyya, M and Singh, AK and Chattopadhyay, D}, title = {Bioinformatic Approaches Including Predictive Metagenomic Profiling Reveal Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {1108}, doi = {10.1038/s41598-017-01126-3}, pmid = {28439121}, issn = {2045-2322}, mesh = {Bacteria/classification/*drug effects ; Biota/*drug effects ; Cluster Analysis ; Computational Biology/*methods ; DNA, Ribosomal/chemistry/genetics ; *Environmental Microbiology ; Environmental Pollutants/*metabolism ; Metagenomics/*methods ; Petroleum/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Microbial remediation of oil polluted habitats remains one of the foremost methods for restoration of petroleum hydrocarbon contaminated environments. The development of effective bioremediation strategies however, require an extensive understanding of the resident microbiome of these habitats. Recent developments such as high-throughput sequencing has greatly facilitated the advancement of microbial ecological studies in oil polluted habitats. However, effective interpretation of biological characteristics from these large datasets remain a considerable challenge. In this study, we have implemented recently developed bioinformatic tools for analyzing 65 16S rRNA datasets from 12 diverse hydrocarbon polluted habitats to decipher metagenomic characteristics of the resident bacterial communities. Using metagenomes predicted from 16S rRNA gene sequences through PICRUSt, we have comprehensively described phylogenetic and functional compositions of these habitats and additionally inferred a multitude of metagenomic features including 255 taxa and 414 functional modules which can be used as biomarkers for effective distinction between the 12 oil polluted sites. Additionally, we show that significantly over-represented taxa often contribute to either or both, hydrocarbon degradation and additional important functions. Our findings reveal significant differences between hydrocarbon contaminated sites and establishes the importance of endemic factors in addition to petroleum hydrocarbons as driving factors for sculpting hydrocarbon contaminated bacteriomes.}, }
@article {pmid28285978, year = {2017}, author = {Raoult, D}, title = {The study of microbiota needs both microbiologists and medical doctors.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {23}, number = {8}, pages = {500-501}, doi = {10.1016/j.cmi.2017.03.002}, pmid = {28285978}, issn = {1469-0691}, mesh = {Bacteria, Aerobic/classification/growth & development ; Bacteria, Anaerobic/classification/growth & development ; Colon/microbiology ; Feces/microbiology ; Humans ; Metagenomics/methods ; *Microbiology/education/trends ; *Microbiota ; *Physicians ; }, }
@article {pmid28787780, year = {2017}, author = {Noronha, MF and Lacerda Júnior, GV and Gilbert, JA and de Oliveira, VM}, title = {Taxonomic and functional patterns across soil microbial communities of global biomes.}, journal = {The Science of the total environment}, volume = {609}, number = {}, pages = {1064-1074}, doi = {10.1016/j.scitotenv.2017.07.159}, pmid = {28787780}, issn = {1879-1026}, mesh = {Biodiversity ; Classification ; *Ecosystem ; Metagenomics ; Soil ; *Soil Microbiology ; }, }
@article {pmid29567068, year = {2018}, author = {Górska, A and Peter, S and Willmann, M and Autenrieth, I and Schlaberg, R and Huson, DH}, title = {Dynamics of the human gut phageome during antibiotic treatment.}, journal = {Computational biology and chemistry}, volume = {74}, number = {}, pages = {420-427}, doi = {10.1016/j.compbiolchem.2018.03.011}, pmid = {29567068}, issn = {1476-928X}, mesh = {Anti-Bacterial Agents/administration & dosage/*pharmacology ; Ciprofloxacin/administration & dosage/*pharmacology ; Gastrointestinal Microbiome/*drug effects/genetics ; Gastrointestinal Tract/*drug effects/microbiology ; Healthy Volunteers ; Humans ; Metagenomics ; }, abstract = {Bacterial viruses contribute to the dynamics of the microbiome communities, as they are involved in the horizontal gene transfer. Previously we studied changes in the gut microbiome of the two healthy individuals over the course of a 6-days antibiotics treatment and subsequent 28 days recovery time (Willmann et al., 2015). Now, from the same samples, the virus-like particles were isolated and sequenced. As the phage sequences are currently poorly represented in reference databases, the reads had to be assembled, annotated and their abundance had to be evaluated via reads mapping. We analyzed and compared patterns of changes in abundance of the phage scaffolds and scaffolds with antibiotics resistant genes, in both phage and whole-genome metagenomic sets. We observed an increase in abundance of scaffolds carrying antibiotic-resistant genes in response to the treatment.}, }
@article {pmid29899109, year = {2018}, author = {Russo, AG and Eden, JS and Enosi Tuipulotu, D and Shi, M and Selechnik, D and Shine, R and Rollins, LA and Holmes, EC and White, PA}, title = {Viral Discovery in the Invasive Australian Cane Toad (Rhinella marina) Using Metatranscriptomic and Genomic Approaches.}, journal = {Journal of virology}, volume = {92}, number = {17}, pages = {}, doi = {10.1128/JVI.00768-18}, pmid = {29899109}, issn = {1098-5514}, mesh = {Animals ; Bufo marinus/*virology ; Gene Expression Profiling ; Metagenomics ; Proviruses/*classification/genetics/*isolation & purification ; Viruses/*classification/genetics/*isolation & purification ; Western Australia ; }, abstract = {Cane toads are a notorious invasive species, inhabiting over 1.2 million km2 of Australia and threatening native biodiversity. The release of pathogenic cane toad viruses is one possible biocontrol strategy yet is currently hindered by the poorly described cane toad virome. Metatranscriptomic analysis of 16 cane toad livers revealed the presence of a novel and full-length picornavirus, Rhimavirus A (RhiV-A), a member of a reptile- and amphibian-specific cluster of the Picornaviridae basal to the Kobuvirus-like group. In the combined liver transcriptome, we also identified a complete genome sequence of a distinct epsilonretrovirus, Rhinella marina endogenous retrovirus (RMERV). The recently sequenced cane toad genome contains 8 complete RMERV proviruses as well as 21 additional truncated insertions. The oldest full-length RMERV provirus was estimated to have inserted 1.9 million years ago (MYA). To screen for these viral sequences in additional toads, we analyzed publicly available transcriptomes from six diverse Australian locations. RhiV-A transcripts were identified in toads sampled from three locations across 1,000 km of Australia, stretching to the current Western Australia (WA) invasion front, while RMERV transcripts were observed at all six sites. Finally, we scanned the cane toad genome for nonretroviral endogenous viral elements, finding three sequences related to small DNA viruses in the family Circoviridae This shows ancestral circoviral infection with subsequent genomic integration. The identification of these current and past viral infections enriches our knowledge of the cane toad virome, an understanding of which will facilitate future work on infection and disease in this important invasive species.IMPORTANCE Cane toads are poisonous amphibians that were introduced to Australia in 1935 for insect control. Since then, their population has increased dramatically, and they now threaten many native Australian species. One potential method to control the population is to release a cane toad virus with high mortality rates, yet few cane toad viruses have been characterized. This study samples cane toads from different Australian locations and uses an RNA sequencing and computational approach to find new viruses. We report novel complete picornavirus and retrovirus sequences that were genetically similar to viruses infecting frogs, reptiles, and fish. Using data generated in other studies, we show that these viral sequences are present in cane toads from distinct Australian locations. Three sequences related to circoviruses were also found in the toad genome. The identification of new viral sequences will aid future studies that investigate their prevalence and potential as agents for biocontrol.}, }
@article {pmid29495531, year = {2018}, author = {Chen, H and Wu, H and Yan, B and Zhao, H and Liu, F and Zhang, H and Sheng, Q and Miao, F and Liang, Z}, title = {Core Microbiome of Medicinal Plant Salvia miltiorrhiza Seed: A Rich Reservoir of Beneficial Microbes for Secondary Metabolism?.}, journal = {International journal of molecular sciences}, volume = {19}, number = {3}, pages = {}, doi = {10.3390/ijms19030672}, pmid = {29495531}, issn = {1422-0067}, mesh = {Biodiversity ; Genetic Variation ; Metagenome ; Metagenomics/methods ; *Microbiota ; Plants, Medicinal/classification/genetics/metabolism/*microbiology ; RNA, Ribosomal, 16S/genetics ; Salvia miltiorrhiza/classification/genetics/metabolism/*microbiology ; Seeds/metabolism/*microbiology ; }, abstract = {Seed microbiome includes special endophytic or epiphytic microbial taxa associated with seeds, which affects seed germination, plant growth, and health. Here, we analyzed the core microbiome of 21 Salvia miltiorrhiza seeds from seven different geographic origins using 16S rDNA and ITS amplicon sequencing, followed by bioinformatics analysis. The whole bacterial microbiome was classified into 17 microbial phyla and 39 classes. Gammaproteobacteria (67.6%), Alphaproteobacteria (15.6%), Betaproteobacteria (2.6%), Sphingobacteria (5.0%), Bacilli (4.6%), and Actinobacteria (2.9%) belonged to the core bacterial microbiome. Dothideomycetes comprised 94% of core fungal microbiome in S. miltiorrhiza seeds, and another two dominant classes were Leotiomycetes (3.0%) and Tremellomycetes (2.0%). We found that terpenoid backbone biosynthesis, degradation of limonene, pinene, and geraniol, and prenyltransferases, were overrepresented in the core bacterial microbiome using phylogenetic examination of communities by reconstruction of unobserved states (PICRUSt) software. We also found that the bacterial genera Pantoea, Pseudomonas, and Sphingomonas were enriched core taxa and overlapped among S. miltiorrhiza, maize, bean, and rice, while a fungal genus, Alternaria, was shared within S. miltiorrhiza, bean, and Brassicaceae families. These findings highlight that seed-associated microbiomeis an important component of plant microbiomes, which may be a gene reservoir for secondary metabolism in medicinal plants.}, }
@article {pmid28393285, year = {2018}, author = {Rowland, I and Gibson, G and Heinken, A and Scott, K and Swann, J and Thiele, I and Tuohy, K}, title = {Gut microbiota functions: metabolism of nutrients and other food components.}, journal = {European journal of nutrition}, volume = {57}, number = {1}, pages = {1-24}, doi = {10.1007/s00394-017-1445-8}, pmid = {28393285}, issn = {1436-6215}, mesh = {Bacteria/enzymology/*metabolism ; Bile Acids and Salts/metabolism ; Diet ; Dietary Carbohydrates/metabolism ; Dietary Proteins/metabolism ; Fatty Acids/metabolism ; *Food ; Gastrointestinal Microbiome/*physiology ; *Health Promotion ; Humans ; Metagenomics ; Models, Theoretical ; Phytochemicals/metabolism ; Plants, Edible/chemistry/metabolism ; Polyphenols/metabolism ; Proteomics ; Vitamins/biosynthesis ; }, abstract = {The diverse microbial community that inhabits the human gut has an extensive metabolic repertoire that is distinct from, but complements the activity of mammalian enzymes in the liver and gut mucosa and includes functions essential for host digestion. As such, the gut microbiota is a key factor in shaping the biochemical profile of the diet and, therefore, its impact on host health and disease. The important role that the gut microbiota appears to play in human metabolism and health has stimulated research into the identification of specific microorganisms involved in different processes, and the elucidation of metabolic pathways, particularly those associated with metabolism of dietary components and some host-generated substances. In the first part of the review, we discuss the main gut microorganisms, particularly bacteria, and microbial pathways associated with the metabolism of dietary carbohydrates (to short chain fatty acids and gases), proteins, plant polyphenols, bile acids, and vitamins. The second part of the review focuses on the methodologies, existing and novel, that can be employed to explore gut microbial pathways of metabolism. These include mathematical models, omics techniques, isolated microbes, and enzyme assays.}, }
@article {pmid29405134, year = {2017}, author = {Desikan, P}, title = {Our microbial signatures.}, journal = {Indian journal of medical microbiology}, volume = {35}, number = {4}, pages = {443-444}, doi = {10.4103/ijmm.IJMM_17_250}, pmid = {29405134}, issn = {1998-3646}, mesh = {Biological Variation, Individual ; *Dysbiosis ; Healthy Volunteers ; Humans ; Metagenomics ; *Microbiota ; }, }
@article {pmid29108974, year = {2018}, author = {Yasir, M}, title = {Analysis of bacterial communities and characterization of antimicrobial strains from cave microbiota.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {49}, number = {2}, pages = {248-257}, doi = {10.1016/j.bjm.2017.08.005}, pmid = {29108974}, issn = {1678-4405}, mesh = {*Antibiosis ; Bacteria/*classification/genetics/growth & development/*isolation & purification ; *Biota ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Environmental Microbiology ; Euryarchaeota/classification/genetics/growth & development/isolation & purification ; Metagenomics ; Pakistan ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {In this study for the first-time microbial communities in the caves located in the mountain range of Hindu Kush were evaluated. The samples were analyzed using culture-independent (16S rRNA gene amplicon sequencing) and culture-dependent methods. The amplicon sequencing results revealed a broad taxonomic diversity, including 21 phyla and 20 candidate phyla. Proteobacteria were dominant in both caves, followed by Bacteroidetes, Actinobacteria, Firmicutes, Verrucomicrobia, Planctomycetes, and the archaeal phylum Euryarchaeota. Representative operational taxonomic units from Koat Maqbari Ghaar and Smasse-Rawo Ghaar were grouped into 235 and 445 different genera, respectively. Comparative analysis of the cultured bacterial isolates revealed distinct bacterial taxonomic profiles in the studied caves dominated by Proteobacteria in Koat Maqbari Ghaar and Firmicutes in Smasse-Rawo Ghaar. Majority of those isolates were associated with the genera Pseudomonas and Bacillus. Thirty strains among the identified isolates from both caves showed antimicrobial activity. Overall, the present study gave insight into the great bacterial taxonomic diversity and antimicrobial potential of the isolates from the previously uncharacterized caves located in the world's highest mountains range in the Indian sub-continent.}, }
@article {pmid28336973, year = {2017}, author = {Wang, R and Zhang, H and Sun, L and Qi, G and Chen, S and Zhao, X}, title = {Microbial community composition is related to soil biological and chemical properties and bacterial wilt outbreak.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {343}, doi = {10.1038/s41598-017-00472-6}, pmid = {28336973}, issn = {2045-2322}, mesh = {Bacteria/classification/genetics/*isolation & purification ; *Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fungi/classification/genetics/*isolation & purification ; Hydrogen-Ion Concentration ; Metagenomics ; Phosphorus/analysis ; Phylogeny ; Plant Diseases/*microbiology ; Potassium/analysis ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Soil microbes play important roles in plant growth and health. Little is known about the differences of soil microbes between healthy and bacterial wilt infected soils with Ralstonia solanacearum. By Illumina-MiSeq sequencing of 16S rRNA and 18S rRNA gene amplicons, we found the soil microbial composition and diversity were distinct between healthy and bacterial wilt infected soils. Soil microbial community varied at different plant growth stages due to changes of root exudates composition and soil pH. Healthy soils exhibited higher microbial diversity than the bacterial wilt infected soils. More abundant beneficial microbes including Bacillus, Agromyces, Micromonospora, Pseudonocardia, Acremonium, Lysobacter, Mesorhizobium, Microvirga, Bradyrhizobium, Acremonium and Chaetomium were found in the healthy soils rather than the bacterial wilt infected soils. Compared to bacterial wilt infected soils, the activities of catalase, invertase and urease, as well as soil pH, available phosphorous and potassium content, were all significantly increased in the healthy soils. In a conclusion, the higher abundance of beneficial microbes are positively related the higher soil quality, including better plant growth, lower disease incidence, and higher nutrient contents, soil enzyme activities and soil pH.}, }
@article {pmid29380873, year = {2018}, author = {Bapatla, KG and Singh, A and Yeddula, S and Patil, RH}, title = {Annotation of gut bacterial taxonomic and functional diversity in Spodoptera litura and Spilosoma obliqua.}, journal = {Journal of basic microbiology}, volume = {58}, number = {3}, pages = {217-226}, doi = {10.1002/jobm.201700462}, pmid = {29380873}, issn = {1521-4028}, mesh = {Animals ; Bacteria/*classification/*genetics ; *Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Gastrointestinal Tract/microbiology ; Helianthus/parasitology ; High-Throughput Nucleotide Sequencing ; Lepidoptera/*microbiology ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soybeans/parasitology ; }, abstract = {The insect gut has been the house of many taxonomically and physiologically diverse groups of microbial colonizers as symbionts and commensals, which are evolving to support the physiological requirement of insects. Lepidoptera is one of the important family of class hexapoda, comprising agriculture insect pest Spodoptera litura and Spilosoma obliqua. Information on gut microbiota and their functional role in these insects was meager to elucidate the wide-ranging survivalist mechanisms. In this context, we analyzed the composition, diversity and functional role of gut bacteria in S. litura and S. obliqua collected from soybean and sunflower crops, respectively, using Next Generation Sequencing of 16S rRNA. A total of 3427 and 206 Operation Taxonomic Units (OTUs) were identified in S. litura and S. obliqua gut metagenome, respectively. Highest number of sequences were annotated to unclassified bacteria (34%), followed by Proteobacteria (27%), and Chlorobi (14%) in S. litura, while S. obliqua has significant representation of Firmicutes (48%), followed by Bacteroidetes (20%), and unclassified bacteria (11%). Functionality of both metagenomes revealed, high abundance of ammonia oxidizers (20.1 58.0%) followed by relative abundance of detoxifying processes - dehalogenation (17.4-41.2%) and aromatic hydrocarbons degradation (1.1-3.1%). This study highlights the significance of the inherent microbiome of two defoliators in shaping the metagenome for nutrition and detoxifying the chemical molecules, and opens an avenue for exploring role of insect gut bacteria in host selection, metabolic endurance of insecticides and synergistic or agonistic mechanisms inside gut of insects feeding on insect-resistant biotech crops.}, }
@article {pmid29129355, year = {2018}, author = {Li, J and Fu, R and Yang, Y and Horz, HP and Guan, Y and Lu, Y and Lou, H and Tian, L and Zheng, S and Liu, H and Shi, M and Tang, K and Wang, S and Xu, S}, title = {A metagenomic approach to dissect the genetic composition of enterotypes in Han Chinese and two Muslim groups.}, journal = {Systematic and applied microbiology}, volume = {41}, number = {1}, pages = {1-12}, doi = {10.1016/j.syapm.2017.09.006}, pmid = {29129355}, issn = {1618-0984}, mesh = {Asian Continental Ancestry Group ; Bacteria/*classification/*genetics ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Ethnic Groups ; *Gastrointestinal Microbiome ; Genetic Association Studies ; Healthy Volunteers ; Humans ; Islam ; Lysophospholipase/genetics ; *Metagenomics ; *Microbiota ; Phylogeny ; Polymorphism, Single Nucleotide ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Distinct enterotypes have been observed in the human gut but little is known about the genetic basis of the microbiome. Moreover, it is not clear how many genetic differences exist between enterotypes within or between populations. In this study, both the 16S rRNA gene and the metagenomes of the gut microbiota were sequenced from 48 Han Chinese, 48 Kazaks, and 96 Uyghurs, and taxonomies were assigned after de novo assembly. Single nucleotide polymorphisms were also identified by referring to data from the Human Microbiome Project. Systematic analysis of the gut communities in terms of their abundance and genetic composition was also performed, together with a genome-wide association study of the host genomes. The gut microbiota of 192 subjects was clearly classified into two enterotypes (Bacteroides and Prevotella). Interestingly, both enterotypes showed a clear genetic differentiation in terms of their functional catalogue of genes, especially for genes involved in amino acid and carbohydrate metabolism. In addition, several differentiated genera and genes were found among the three populations. Notably, one human variant (rs878394) was identified that showed significant association with the abundance of Prevotella, which is linked to LYPLAL1, a gene associated with body fat distribution, the waist-hip ratio and insulin sensitivity. Taken together, considerable differentiation was observed in gut microbes between enterotypes and among populations that was reflected in both the taxonomic composition and the genetic makeup of their functional genes, which could have been influenced by a variety of factors, such as diet and host genetic variation.}, }
@article {pmid29415902, year = {2018}, author = {Kishida, S and Kato-Mori, Y and Hagiwara, K}, title = {Influence of changes in the intestinal microflora on the immune function in mice.}, journal = {The Journal of veterinary medical science}, volume = {80}, number = {3}, pages = {440-446}, doi = {10.1292/jvms.17-0485}, pmid = {29415902}, issn = {1347-7439}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Concanavalin A/metabolism ; Cytokines/metabolism ; Flow Cytometry ; Gastrointestinal Microbiome/drug effects/*immunology ; Immunity/immunology/*physiology ; Mice/immunology/microbiology ; Mice, Inbred BALB C/immunology/microbiology ; RNA, Ribosomal, 16S ; Real-Time Polymerase Chain Reaction ; Spleen/cytology ; T-Lymphocyte Subsets/immunology/physiology ; }, abstract = {The composition of the intestinal microbiota is related to the health and immune function of the host. Administration of antibiotics affects the composition of the intestinal microbiota. However, the effects of immune function on the composition of the intestinal microbiota are still unclear. In this study, we investigated the lymphocyte composition and determined the relationships between lymphocyte function and the intestinal microbiota following antibiotic treatment in mice. To change the composition of the intestinal microbiota, mice were treated with or without antibiotics. Analysis of intestinal microbiota was performed by metagenomic analysis targeting 16S rRNA. Lymphocyte subsets of splenocytes were measured by flow cytometry. For functional analysis of T cells, splenocytes were stimulated with concanavalin (Con A), and cytokine gene expression was measured by real-time polymerase chain reaction. Firmicutes were predominant in the control group, whereas Bacteroidetes predominated in the antibiotic-treated group, as determined by metagenomic analysis. The diversity of the microbiota decreased in the antibiotic-treated group. Analysis of lymphocyte subsets showed that CD3+ cells decreased, whereas CD19+ cells increased in the antibiotic-treated group. All cytokine genes in splenocytes treated with Con A were downregulated in the antibiotic-treated group; in particular, genes encoding interferon-γ, interleukin (IL)-6, and IL-13 significantly decreased. Taken together, these results revealed that changes in the composition of the intestinal microbiota by antibiotic treatment influenced the population of lymphocytes in splenocytes and affected the immune response.}, }
@article {pmid28640714, year = {2017}, author = {Wen, SW and Wong, CHY}, title = {An unexplored brain-gut microbiota axis in stroke.}, journal = {Gut microbes}, volume = {8}, number = {6}, pages = {601-606}, doi = {10.1080/19490976.2017.1344809}, pmid = {28640714}, issn = {1949-0984}, mesh = {Animals ; Bacteria/classification ; *Bacterial Physiological Phenomena ; Bacterial Translocation ; *Disease Models, Animal ; Dysbiosis/etiology/*microbiology ; Escherichia coli/physiology ; Gastrointestinal Tract/microbiology ; *Host-Pathogen Interactions ; Humans ; Lung/microbiology ; Mice ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Specific Pathogen-Free Organisms ; Stroke/complications/*microbiology ; }, abstract = {Microbiota research, in particular that of the gut, has recently gained much attention in medical research owing to technological advances in metagenomics and metabolomics. Despite this, much of the research direction has focused on long-term or chronic effects of microbiota manipulation on health and disease. In this addendum, we reflect on our recent publication that reported findings addressing a rather unconventional hypothesis. Bacterial pneumonia is highly prevalent and is one of the leading contributors to stroke morbidity and mortality worldwide. However, microbiological cultures of samples taken from stroke patient with a suspected case of pneumonia often return with a negative result. Therefore, we proposed that post-stroke infection may be due to the presence of anaerobic bacteria, possibly those originated from the host gut microbiota. Supporting this, we showed that stroke promotes intestinal barrier breakdown and robust microbiota changes, and the subsequent translocation of selective bacterial strain from the host gut microbiota to peripheral tissues (i.e. lung) induces post-stroke infections. Our findings were further supported by various elegant studies published in the past 12 months. Here, we discuss and provide an overview of our key findings, supporting studies, and the implications for future advances in stroke research.}, }
@article {pmid27352007, year = {2016}, author = {Jangi, S and Gandhi, R and Cox, LM and Li, N and von Glehn, F and Yan, R and Patel, B and Mazzola, MA and Liu, S and Glanz, BL and Cook, S and Tankou, S and Stuart, F and Melo, K and Nejad, P and Smith, K and Topçuolu, BD and Holden, J and Kivisäkk, P and Chitnis, T and De Jager, PL and Quintana, FJ and Gerber, GK and Bry, L and Weiner, HL}, title = {Alterations of the human gut microbiome in multiple sclerosis.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {12015}, doi = {10.1038/ncomms12015}, pmid = {27352007}, issn = {2041-1723}, support = {P30 DK034854/DK/NIDDK NIH HHS/United States ; R01 AI126880/AI/NIAID NIH HHS/United States ; R01 NS087226/NS/NINDS NIH HHS/United States ; R21 NS087867/NS/NINDS NIH HHS/United States ; }, mesh = {Adult ; Breath Tests ; Case-Control Studies ; Female ; *Gastrointestinal Microbiome ; Genes, Bacterial ; Humans ; Immunomodulation ; Male ; Methane/analysis ; Middle Aged ; Monocytes/metabolism ; Multiple Sclerosis, Relapsing-Remitting/immunology/*microbiology/therapy ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; T-Lymphocytes/metabolism ; }, abstract = {The gut microbiome plays an important role in immune function and has been implicated in several autoimmune disorders. Here we use 16S rRNA sequencing to investigate the gut microbiome in subjects with multiple sclerosis (MS, n=60) and healthy controls (n=43). Microbiome alterations in MS include increases in Methanobrevibacter and Akkermansia and decreases in Butyricimonas, and correlate with variations in the expression of genes involved in dendritic cell maturation, interferon signalling and NF-kB signalling pathways in circulating T cells and monocytes. Patients on disease-modifying treatment show increased abundances of Prevotella and Sutterella, and decreased Sarcina, compared with untreated patients. MS patients of a second cohort show elevated breath methane compared with controls, consistent with our observation of increased gut Methanobrevibacter in MS in the first cohort. Further study is required to assess whether the observed alterations in the gut microbiome play a role in, or are a consequence of, MS pathogenesis.}, }
@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}, doi = {10.3389/fmicb.2018.01687}, 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 {pmid29169222, year = {2018}, author = {Kim, D and Hong, S and Kim, YT and Ryu, S and Kim, HB and Lee, JH}, title = {Metagenomic Approach to Identifying Foodborne Pathogens on Chinese Cabbage.}, journal = {Journal of microbiology and biotechnology}, volume = {28}, number = {2}, pages = {227-235}, doi = {10.4014/jmb.1710.10021}, pmid = {29169222}, issn = {1738-8872}, mesh = {Bacteria/*classification/genetics/*isolation & purification ; Biodiversity ; Brassica/*microbiology ; DNA, Bacterial/genetics ; Foodborne Diseases/*microbiology ; *Metagenomics ; Microbial Consortia ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, DNA ; }, abstract = {Foodborne illness represents a major threat to public health and is frequently attributed to pathogenic microorganisms on fresh produce. Recurrent outbreaks often come from vegetables that are grown close to or within the ground. Therefore, the first step to understanding the public health risk of microorganisms on fresh vegetables is to identify and describe microbial communities. We investigated the phyllospheres on Chinese cabbage (Brassica rapa subsp. pekinensis, N = 54). 16S rRNA gene amplicon sequencing targeting the V5-V6 region of 16S rRNA genes was conducted by employing the Illumina MiSeq system. Sequence quality was assessed, and phylogenetic assessments were performed using the RDP classifier implemented in QIIME with a bootstrap cutoff of 80%. Principal coordinate analysis was performed using a weighted Fast UniFrac matrix. The average number of sequence reads generated per sample was 34,584. At the phylum level, bacterial communities were composed primarily of Proteobacteria and Bacteroidetes. The most abundant genera on Chinese cabbages were Chryseobacterium, Aurantimonadaceae_g, Sphingomonas, and Pseudomonas. Diverse potential pathogens, such as Pantoea, Erwinia, Klebsiella, Yersinia, Bacillus, Staphylococcus, Salmonella, and Clostridium were also detected from the samples. Although further epidemiological studies will be required to determine whether the detected potential pathogens are associated with foodborne illness, our results imply that a metagenomic approach can be used to detect pathogenic bacteria on fresh vegetables.}, }
@article {pmid28766918, year = {2018}, author = {Sherwani, MA and Tufail, S and Muzaffar, AF and Yusuf, N}, title = {The skin microbiome and immune system: Potential target for chemoprevention?.}, journal = {Photodermatology, photoimmunology & photomedicine}, volume = {34}, number = {1}, pages = {25-34}, doi = {10.1111/phpp.12334}, pmid = {28766918}, issn = {1600-0781}, mesh = {Animals ; Gastrointestinal Microbiome ; Humans ; *Microbiota/radiation effects ; Prebiotics ; Probiotics/pharmacology ; Skin/*immunology/*microbiology ; Skin Neoplasms/immunology/*microbiology/*prevention & control ; Ultraviolet Rays ; Virus Diseases/complications ; Vitamin D/analogs & derivatives/metabolism ; }, abstract = {There has been increasing interest in understanding the role of the human microbiome in skin diseases. Microbiome studies are being utilized in skin cancer research in numerous ways. Commensal bacteria are being studied as a potential tool to judge the biggest environmental risk of skin cancer, ultraviolet (UV) radiation. Owing to the recognized link of skin microbes in the process of inflammation, there have been theories linking commensal bacteria to skin cancer. Viral metagenomics has also provided insight into virus linked forms of skin cancers. Speculations can be drawn for skin microbiome that in a manner similar to gut microbiome, they can be involved in chemoprevention of skin cancer. Nonetheless, there are definitely huge gaps in our knowledge of the relationship of microbiome and skin cancers, especially in relation to chemoprevention. The utilization of microbiome in skin cancer research seems to be a promising field and may help yield novel skin cancer prevention and treatment options. This review focuses on recent utilization of the microbiome in skin cancer research, and it explores the potential of utilizing the microbiome in prevention, earlier diagnosis, and treatment of skin cancers.}, }
@article {pmid30117250, year = {2018}, author = {Cabello-Yeves, PJ and Picazo, A and Camacho, A and Callieri, C and Rosselli, R and Roda-Garcia, JJ and Coutinho, FH and Rodriguez-Valera, F}, title = {Ecological and genomic features of two widespread freshwater picocyanobacteria.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14377}, pmid = {30117250}, issn = {1462-2920}, }
@article {pmid27571981, year = {2016}, author = {Schimel, J}, title = {Microbial ecology: Linking omics to biogeochemistry.}, journal = {Nature microbiology}, volume = {1}, number = {}, pages = {15028}, doi = {10.1038/nmicrobiol.2015.28}, pmid = {27571981}, issn = {2058-5276}, mesh = {*Ecology ; *Ecosystem ; Metagenomics ; Microbial Consortia ; Proteomics ; }, }
@article {pmid29878736, year = {2016}, author = {Lin, Z and Zu, XP and Xie, HS and Jin, HZ and Yang, N and Liu, XR and Zhang, WD}, title = {[Research progress in mechanism of intestinal microorganisms in human diseases].}, journal = {Yao xue xue bao = Acta pharmaceutica Sinica}, volume = {51}, number = {6}, pages = {843-852}, pmid = {29878736}, issn = {0513-4870}, mesh = {*Gastrointestinal Microbiome ; Humans ; Intestines/*microbiology ; *Metagenomics ; Symbiosis ; }, abstract = {The international cooperated research projects of the Human Microbiome Project (HMP) and Metagenomics of The Human Intestinal Tract (MetaHIT) were officially launched in 2007, which indicated the era of metagenomics research of microorganisms in human gastrointestinal tract had been coming. Each human body is a superorganism which is composed of 90% commensal microorganisms, especially the intestinal microorganisms. The intestinal microorganisms play an important role on health maintenance since they are involved in the absorption and metabolism of nutrients in the human bodies. Herein, we review the research progress in the mechanism of intestinal microorganisms in human diseases. Our purpose is to provide novel ideas on human health and therapeutic targets of diseases.}, }
@article {pmid28390093, year = {2018}, author = {Aw, W and Fukuda, S}, title = {Understanding the role of the gut ecosystem in diabetes mellitus.}, journal = {Journal of diabetes investigation}, volume = {9}, number = {1}, pages = {5-12}, doi = {10.1111/jdi.12673}, pmid = {28390093}, issn = {2040-1124}, mesh = {Animals ; Diabetes Mellitus, Type 1/metabolism/*microbiology ; Diabetes Mellitus, Type 2/metabolism/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Metabolome ; Metabolomics ; Metagenome ; }, abstract = {Diabetes mellitus is a type of metabolic disorder whereby patients are unable to regulate glycemia. It is currently a worldwide public health issue, and is a burden to society because of its disabling and common complications. Diabetes is multifactorial, and also induces the onset of other diseases. In the present report, we review the labyrinth encompassing the gut microbiota and gut microbiota-derived metabolites in type 1 diabetes and type 2 diabetes pathogenesis. There have been exceptional improvements in deoxyribonucleic acid sequencing and mass spectrometry technologies throughout these past years, and these have allowed the comprehensive collection of information on our unique gut ecosystem. We would like to advocate incorporating metagenome and metabolome information for a comprehensive perspective of the complex interrelationships between the gut environment, host metabolism and diabetes pathogenesis. We hope that with this improved understanding we would be able to provide exciting novel therapeutic approaches to engineer an ideal gut ecosystem for optimal health.}, }
@article {pmid29748902, year = {2018}, author = {Escudero, L and Oetiker, N and Gallardo, K and Tebes-Cayo, C and Guajardo, M and Nuñez, C and Davis-Belmar, C and Pueyo, JJ and Chong Díaz, G and Demergasso, C}, title = {A thiotrophic microbial community in an acidic brine lake in Northern Chile.}, journal = {Antonie van Leeuwenhoek}, volume = {111}, number = {8}, pages = {1403-1419}, doi = {10.1007/s10482-018-1087-8}, pmid = {29748902}, issn = {1572-9699}, support = {1100795//Fondecyt/ ; 32002137//BHP Minerals Americas/ ; }, mesh = {Bacteria/*classification/metabolism ; Biodiversity ; Carbon Cycle ; Chile ; DNA, Bacterial/genetics ; Energy Metabolism ; Geologic Sediments/microbiology ; Lakes/*microbiology ; Metagenomics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Salts ; Sulfur/*metabolism ; }, abstract = {The endorheic basins of the Northern Chilean Altiplano contain saline lakes and salt flats. Two of the salt flats, Gorbea and Ignorado, have high acidic brines. The causes of the local acidity have been attributed to the occurrence of volcanic native sulfur, the release of sulfuric acid by oxidation, and the low buffering capacity of the rocks in the area. Understanding the microbial community composition and available energy in this pristine ecosystem is relevant in determining the origin of the acidity and in supporting the rationale of conservation policies. Besides, a comparison between similar systems in Australia highlights key microbial components and specific ones associated with geological settings and environmental conditions. Sediment and water samples from the Salar de Gorbea were collected, physicochemical parameters measured and geochemical and molecular biological analyses performed. A low diversity microbial community was observed in brines and sediments dominated by Actinobacteria, Algae, Firmicutes and Proteobacteria. Most of the constituent genera have been reported to be either sulfur oxidizing microorganisms or ones having the potential for sulfur oxidation given available genomic data and information drawn from the literature on cultured relatives. In addition, a link between sulfur oxidation and carbon fixation was observed. In contrast, to acid mine drainage communities, Gorbea microbial diversity is mainly supported by chemolithoheterotrophic, facultative chemolithoautotrophic and oligotrophic sulfur oxidizing populations indicating that microbial activity should also be considered as a causative agent of local acidity.}, }
@article {pmid29721711, year = {2018}, author = {Goodfellow, M and Nouioui, I and Sanderson, R and Xie, F and Bull, AT}, title = {Rare taxa and dark microbial matter: novel bioactive actinobacteria abound in Atacama Desert soils.}, journal = {Antonie van Leeuwenhoek}, volume = {111}, number = {8}, pages = {1315-1332}, doi = {10.1007/s10482-018-1088-7}, pmid = {29721711}, issn = {1572-9699}, mesh = {Actinobacteria/*classification/genetics/isolation & purification/metabolism ; Altitude ; Anti-Bacterial Agents/isolation & purification ; *Biodiversity ; Chile ; *Desert Climate ; Ecosystem ; Metagenomics ; *Phylogeny ; *Soil Microbiology ; Species Specificity ; }, abstract = {An "in house" taxonomic approach to drug discovery led to the isolation of diverse actinobacteria from hyper-arid, extreme hyper-arid and very high altitude Atacama Desert soils. A high proportion of the isolates were assigned to novel taxa, with many showing activity in standard antimicrobial plug assays. The application of more advanced taxonomic and screening strategies showed that strains classified as novel species of Lentzea and Streptomyces synthesised new specialised metabolites thereby underpinning the premise that the extreme abiotic conditions in the Atacama Desert favour the development of a unique actinobacterial diversity which is the basis of novel chemistry. Complementary metagenomic analyses showed that the soils encompassed an astonishing degree of actinobacterial 'dark matter', while rank-abundance analyses showed them to be highly diverse habitats mainly composed of rare taxa that have not been recovered using culture-dependent methods. The implications of these pioneering studies on future bioprospecting campaigns are discussed.}, }
@article {pmid29396587, year = {2018}, author = {Mahony, J and Lugli, GA and van Sinderen, D and Ventura, M}, title = {Impact of gut-associated bifidobacteria and their phages on health: two sides of the same coin?.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {5}, pages = {2091-2099}, doi = {10.1007/s00253-018-8795-x}, pmid = {29396587}, issn = {1432-0614}, mesh = {Animals ; Bacteriophages/classification/genetics/isolation & purification/*physiology ; Bifidobacterium/classification/genetics/*physiology/virology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology/*virology ; Humans ; }, abstract = {Bifidobacteria are among the first microbial colonisers of the human infant gut post-partum. Their early appearance and dominance in the human infant gut and the reported health-promoting or probiotic status of several bifidobacterial strains has culminated in intensive research efforts that focus on their activities as part of the gut microbiota and the concomitant implications for human health. In this mini-review, we evaluate current knowledge on the genomics of this diverse bacterial genus, and on the genetic and functional adaptations that have underpinned the success of bifidobacteria in colonising the infant gut. The growing interest in functional genomics of bifidobacteria has also created interest in the interactions of bifidobacteria and their (bacterio)phages. While virulent phages of bifidobacteria have yet to be isolated, the incidence of integrated (pro)phages in bifidobacterial genomes are widely reported and this mini-review considers the role of these so-called bifidoprophages in modulating bifidobacterial populations in the human gastrointestinal tract and the implications for existing and future development of probiotic therapies.}, }
@article {pmid29136413, year = {2017}, author = {Degois, J and Clerc, F and Simon, X and Bontemps, C and Leblond, P and Duquenne, P}, title = {First Metagenomic Survey of the Microbial Diversity in Bioaerosols Emitted in Waste Sorting Plants.}, journal = {Annals of work exposures and health}, volume = {61}, number = {9}, pages = {1076-1086}, doi = {10.1093/annweh/wxx075}, pmid = {29136413}, issn = {2398-7316}, mesh = {Aerosols/*analysis ; *Air Microbiology ; Bacteria/genetics/*isolation & purification ; Biodiversity ; DNA, Ribosomal/analysis ; Environmental Monitoring/*methods ; Feasibility Studies ; Fungi/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/*methods ; Occupational Exposure/analysis ; Proteobacteria/isolation & purification ; Reproducibility of Results ; }, abstract = {Waste sorting activities are source of occupational bioaerosol exposures that are associated with several health disorders. New analytical tools, based on next-generation sequencing (NGS) technologies, provide powerful methods to assess the microbial composition of bioaerosols. The objectives of the study were (i) to assess the feasibility and the repeatability of NGS-based biodiversity measurements and (ii) to study the microbial biodiversity using NGS in bioaerosols emitted in a waste sorting plant (WSP). Three stationary parallel samples were collected in a sorting cabin using closed-face cassettes equipped with polycarbonate membranes. Bacterial and fungal diversity was assessed by sequencing 16S and 18S rDNA genes using either Illumina sequencing or 454 pyrosequencing methods. At sampling point, airborne bacteria were dominated by Proteobacteria, Firmicutes, and Actinobacteria with prevailing genera assigned to unclassified Enterobacteriaceae, Staphylococcus, Acinetobacter, Leuconostoc, Pseudomonas, and Lactobacillus. Airborne fungi were dominated by Ascomycota with prevailing genera assigned to Penicillium, Aspergillus, Rhizopus, Wallemia, and Hemicarpenteles. The NGS biodiversity measurements revealed a higher biodiversity bioaerosols that previously reported for WSP in studies carried out using culture methods followed by identification of microorganisms. These results provide the first survey about taxonomic biodiversity in bioaerosols from WSPs using high-throughput sequencing.}, }
@article {pmid28000755, year = {2016}, author = {Barnard, E and Shi, B and Kang, D and Craft, N and Li, H}, title = {The balance of metagenomic elements shapes the skin microbiome in acne and health.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {39491}, doi = {10.1038/srep39491}, pmid = {28000755}, issn = {2045-2322}, support = {R01 GM099530/GM/NIGMS NIH HHS/United States ; UH2 AR057503/AR/NIAMS NIH HHS/United States ; }, mesh = {Acne Vulgaris/*microbiology ; Adolescent ; Adult ; Aged ; Bacteriophages/*isolation & purification ; Case-Control Studies ; Cohort Studies ; Healthy Volunteers ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; Middle Aged ; Propionibacterium acnes/*isolation & purification/virology ; Sequence Analysis, DNA ; Skin/*microbiology ; Virulence ; Young Adult ; }, abstract = {Studies have emphasized the importance of disease-associated microorganisms in perturbed communities, however, the protective roles of commensals are largely under recognized and poorly understood. Using acne as a model disease, we investigated the determinants of the overall virulence property of the skin microbiota when disease- and health-associated organisms coexist in the community. By ultra-deep metagenomic shotgun sequencing, we revealed higher relative abundances of propionibacteria and Propionibacterium acnes phage in healthy skin. In acne patients, the microbiome composition at the species level and at P. acnes strain level was more diverse than in healthy individuals, with enriched virulence-associated factors and reduced abundance of metabolic synthesis genes. Based on the abundance profiles of the metagenomic elements, we constructed a quantitative prediction model, which classified the clinical states of the host skin with high accuracy in both our study cohort (85%) and an independent sample set (86%). Our results suggest that the balance between metagenomic elements, not the mere presence of disease-associated strains, shapes the overall virulence property of the skin microbiota. This study provides new insights into the microbial mechanism of acne pathogenesis and suggests probiotic and phage therapies as potential acne treatments to modulate the skin microbiota and to maintain skin health.}, }
@article {pmid29689266, year = {2018}, author = {Nakatsu, G and Zhou, H and Wu, WKK and Wong, SH and Coker, OO and Dai, Z and Li, X and Szeto, CH and Sugimura, N and Lam, TY and Yu, AC and Wang, X and Chen, Z and Wong, MC and Ng, SC and Chan, MTV and Chan, PKS and Chan, FKL and Sung, JJ and Yu, J}, title = {Alterations in Enteric Virome Are Associated With Colorectal Cancer and Survival Outcomes.}, journal = {Gastroenterology}, volume = {155}, number = {2}, pages = {529-541.e5}, doi = {10.1053/j.gastro.2018.04.018}, pmid = {29689266}, issn = {1528-0012}, mesh = {Austria/epidemiology ; Biomarkers, Tumor/*analysis ; Case-Control Studies ; Cohort Studies ; Colonoscopy ; Colorectal Neoplasms/diagnostic imaging/mortality/pathology/*virology ; Cross-Sectional Studies ; Dysbiosis/diagnostic imaging/*virology ; Feces/virology ; Female ; France/epidemiology ; Gastrointestinal Microbiome/*genetics ; Germany/epidemiology ; Hong Kong/epidemiology ; Humans ; Male ; Metagenomics ; Middle Aged ; Sensitivity and Specificity ; Survival Analysis ; Viruses/*genetics ; }, abstract = {BACKGROUND & AIMS: Patients with colorectal cancer (CRC) have a different gut microbiome signature than individuals without CRC. Little is known about the viral component of CRC-associated microbiome. We aimed to identify and validate viral taxonomic markers of CRC that might be used in detection of the disease or predicting outcome.
METHODS: We performed shotgun metagenomic analyses of viromes of fecal samples from 74 patients with CRC (cases) and 92 individuals without CRC (controls) in Hong Kong (discovery cohort). Viral sequences were classified by taxonomic alignment against an integrated microbial reference genome database. Viral markers associated with CRC were validated using fecal samples from 3 separate cohorts: 111 patients with CRC and 112 controls in Hong Kong, 46 patients with CRC and 63 controls in Austria, and 91 patients with CRC and 66 controls in France and Germany. Using abundance profiles of CRC-associated virome genera, we constructed random survival forest models to identify those associated with patient survival times.
RESULTS: The diversity of the gut bacteriophage community was significantly increased in patients with CRC compared with controls. Twenty-two viral taxa discriminated cases from controls with an area under the receiver operating characteristic curve of 0.802 in the discovery cohort. The viral markers were validated in 3 cohorts, with area under the receiver operating characteristic curves of 0.763, 0.736, and 0.715, respectively. Clinical subgroup analysis showed that dysbiosis of the gut virome was associated with early- and late-stage CRC. A combination of 4 taxonomic markers associated with reduced survival of patients with CRC (log-rank test, P = 8.1 × 10-6) independently of tumor stage, lymph node metastases, or clinical parameters. We found altered interactions between bacteriophages and oral bacterial commensals in fecal samples from patients with CRC compared with controls.
CONCLUSIONS: In a metagenomic analysis of fecal samples from patients and controls, we identified virome signatures associated with CRC. These data might be used to develop tools to identify individuals with CRC or predict outcomes.}, }
@article {pmid29438346, year = {2018}, author = {Wang, C and Zaheer, M and Bian, F and Quach, D and Swennes, AG and Britton, RA and Pflugfelder, SC and de Paiva, CS}, title = {Sjögren-Like Lacrimal Keratoconjunctivitis in Germ-Free Mice.}, journal = {International journal of molecular sciences}, volume = {19}, number = {2}, pages = {}, doi = {10.3390/ijms19020565}, pmid = {29438346}, issn = {1422-0067}, support = {P30 CA125123/CA/NCI NIH HHS/United States ; T32 AI053831/AI/NIAID NIH HHS/United States ; P30 AI036211/AI/NIAID NIH HHS/United States ; P30 EY002520/EY/NEI NIH HHS/United States ; S10 RR024574/RR/NCRR NIH HHS/United States ; R01 EY026893/EY/NEI NIH HHS/United States ; }, mesh = {Animals ; CD4-Positive T-Lymphocytes/immunology ; Fecal Microbiota Transplantation ; Female ; Germ-Free Life/*immunology ; Homeodomain Proteins/genetics/metabolism ; Immunity, Innate ; Interferon-gamma/metabolism ; Keratoconjunctivitis/immunology/*microbiology/therapy ; Male ; Mice ; Mice, Inbred C57BL ; Microbiota ; }, abstract = {Commensal bacteria play an important role in the formation of the immune system but their role in the maintenance of immune homeostasis at the ocular surface and lacrimal gland remains poorly understood. This study investigated the eye and lacrimal gland phenotype in germ-free and conventional C57BL/6J mice. Our results showed that germ-free mice had significantly greater corneal barrier disruption, greater goblet cell loss, and greater total inflammatory cell and CD4⁺ T cell infiltration within the lacrimal gland compared to the conventionally housed group. A greater frequency of CD4⁺IFN-γ⁺ cells was observed in germ-free lacrimal glands. Females exhibited a more severe phenotype compared to males. Adoptive transfer of CD4⁺ T cells isolated from female germ-free mice into RAG1KO mice transferred Sjögren-like lacrimal keratoconjunctivitis. Fecal microbiota transplant from conventional mice reverted dry eye phenotype in germ-free mice and decreased CD4⁺IFN-γ⁺ cells to levels similar to conventional C57BL/6J mice. These findings indicate that germ-free mice have a spontaneous lacrimal keratoconjunctivitis similar to that observed in Sjögren syndrome patients and demonstrate that commensal bacteria function in maintaining immune homeostasis on the ocular surface. Thus, manipulation of intestinal commensal bacteria has the potential to become a novel therapeutic approach to treat Sjögren Syndrome.}, }
@article {pmid29191163, year = {2017}, author = {Ignasiak, K and Maxwell, A}, title = {Antibiotic-resistant bacteria in the guts of insects feeding on plants: prospects for discovering plant-derived antibiotics.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {223}, doi = {10.1186/s12866-017-1133-0}, pmid = {29191163}, issn = {1471-2180}, support = {BBS/E/J/00000201//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004561/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Anti-Bacterial Agents/chemistry/isolation & purification/*pharmacology ; Bacteria/*drug effects/isolation & purification ; Chromatography, High Pressure Liquid ; Chromatography, Liquid ; Drug Resistance, Bacterial/*drug effects ; Gastrointestinal Tract/microbiology ; Insecta/*microbiology ; Metagenomics ; Microbial Sensitivity Tests ; Microbiota ; Plant Extracts/chemistry/*pharmacology ; Plants/chemistry ; Symbiosis ; Tandem Mass Spectrometry ; }, abstract = {BACKGROUND: Although plants produce many secondary metabolites, currently none of these are commercial antibiotics. Insects feeding on specific plants can harbour bacterial strains resistant to known antibiotics suggesting that compounds in the plant have stimulated resistance development. We sought to determine whether the occurrence of antibiotic-resistant bacteria in insect guts was a widespread phenomenon, and whether this could be used as a part of a strategy to identify antibacterial compounds from plants.
RESULTS: Six insect/plant pairs were selected and the insect gut bacteria were identified and assessed for antibiotic susceptibilities compared with type strains from culture collections. We found that the gut strains could be more or less susceptible to antibiotics than the type strains, or show no differences. Evidence of antibacterial activity was found in the plant extracts from five of the six plants, and, in one case Catharanthus roseus (Madagascar Periwinkle), compounds with antibacterial activity were identified.
CONCLUSION: Bacterial strains isolated from insect guts show a range of susceptibilities to antibiotics suggesting a complex interplay between species in the insect gut microbiome. Extracts from selected plants can show antibacterial activity but it is not easy to isolate and identify the active components. We found that vindoline, present in Madagascar Periwinkle extracts, possessed moderate antibacterial activity. We suggest that plant-derived antibiotics are a realistic possibility given the advances in genomic and metabolomic methodologies.}, }
@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 = {}, number = {}, pages = {}, doi = {10.1016/j.fct.2018.08.006}, pmid = {30086347}, issn = {1873-6351}, 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 {pmid29768437, year = {2018}, author = {Willmann, C and Mata, X and Hanghoej, K and Tonasso, L and Tisseyre, L and Jeziorski, C and Cabot, E and Chevet, P and Crubézy, E and Orlando, L and Esclassan, R and Thèves, C}, title = {Oral health status in historic population: Macroscopic and metagenomic evidence.}, journal = {PloS one}, volume = {13}, number = {5}, pages = {e0196482}, doi = {10.1371/journal.pone.0196482}, pmid = {29768437}, issn = {1932-6203}, mesh = {DNA, Ancient/isolation & purification ; DNA, Bacterial/genetics/history/isolation & purification ; Dental Caries/history/microbiology/pathology ; Female ; France ; Health Status ; History, 18th Century ; Humans ; Male ; Metagenomics ; Microbiota/genetics ; Oral Health/*history ; Paleodontology ; Periodontitis/history/microbiology/pathology ; Rural Population/history ; }, abstract = {Recent developments in High-Throughput DNA sequencing (HTS) technologies and ancient DNA (aDNA) research have opened access to the characterization of the microbial communities within past populations. Most studies have, however, relied on the analysis of dental calculus as one particular material type particularly prone to the molecular preservation of ancient microbial biofilms and potential of entire teeth for microbial characterization, both of healthy communities and pathogens in ancient individuals, remains overlooked. In this study, we used shotgun sequencing to characterize the bacterial composition from historical subjects showing macroscopic evidence of oral pathologies. We first carried out a macroscopic analysis aimed at identifying carious or periodontal diseases in subjects belonging to a French rural population of the 18th century AD. We next examined radiographically six subjects showing specific, characteristic dental pathologies and applied HTS shotgun sequencing to characterize the microbial communities present in and on the dental material. The presence of Streptococcus mutans and also Rothia dentocariosa, Actinomyces viscosus, Porphyromonas gingivalis, Tannerella forsythia, Pseudoramibacter alactolyticus, Olsenella uli and Parvimonas micra was confirmed through the presence of typical signatures of post-mortem DNA damage at an average depth-of-coverage ranging from 0.5 to 7X, with a minimum of 35% (from 35 to 93%) of the positions in the genome covered at least once. Each sampled tooth showed a specific bacterial signature associated with carious or periodontal pathologies. This work demonstrates that from a healthy independent tooth, without visible macroscopic pathology, we can identify a signature of specific pathogens and deduce the oral health status of an individual.}, }
@article {pmid29680562, year = {2018}, author = {Ribicic, D and Netzer, R and Hazen, TC and Techtmann, SM and Drabløs, F and Brakstad, OG}, title = {Microbial community and metagenome dynamics during biodegradation of dispersed oil reveals potential key-players in cold Norwegian seawater.}, journal = {Marine pollution bulletin}, volume = {129}, number = {1}, pages = {370-378}, doi = {10.1016/j.marpolbul.2018.02.034}, pmid = {29680562}, issn = {1879-3363}, mesh = {Biodegradation, Environmental ; Environmental Monitoring/*methods ; *Metagenome ; Microbial Consortia/*genetics ; Norway ; Petroleum/*analysis ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry/*microbiology ; Water Pollutants, Chemical/*analysis ; }, abstract = {Oil biodegradation as a weathering process has been extensively investigated over the years, especially after the Deepwater Horizon blowout. In this study, we performed microcosm experiments at 5 °C with chemically dispersed oil in non-amended seawater. We link biodegradation processes with microbial community and metagenome dynamics and explain the succession based on substrate specialization. Reconstructed genomes and 16S rRNA gene analysis revealed that Bermanella and Zhongshania were the main contributors to initial n-alkane breakdown, while subsequent abundances of Colwellia and microorganisms closely related to Porticoccaceae were involved in secondary n‑alkane breakdown and beta‑oxidation. Cycloclasticus, Porticoccaceae and Spongiiabcteraceae were associated with degradation of mono- and poly-cyclic aromatics. Successional pattern of genes coding for hydrocarbon degrading enzymes at metagenome level, and reconstructed genomic content, revealed a high differentiation of bacteria involved in hydrocarbon biodegradation. A cooperation among oil degrading microorganisms is thus needed for the complete substrate transformation.}, }
@article {pmid29440402, year = {2018}, author = {Grébert, T and Doré, H and Partensky, F and Farrant, GK and Boss, ES and Picheral, M and Guidi, L and Pesant, S and Scanlan, DJ and Wincker, P and Acinas, SG and Kehoe, DM and Garczarek, L}, title = {Light color acclimation is a key process in the global ocean distribution of Synechococcus cyanobacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {9}, pages = {E2010-E2019}, doi = {10.1073/pnas.1717069115}, pmid = {29440402}, issn = {1091-6490}, mesh = {*Acclimatization ; Chlorophyll/chemistry ; Color ; Computer Simulation ; Cyanobacteria/*genetics ; Ecosystem ; Ecotype ; Light ; Likelihood Functions ; Metagenome ; *Oceans and Seas ; Photosynthesis/physiology ; Phycobilisomes/*physiology ; Phylogeny ; Pigmentation ; Seawater/*microbiology ; Synechococcus/*genetics ; }, abstract = {Marine Synechococcus cyanobacteria are major contributors to global oceanic primary production and exhibit a unique diversity of photosynthetic pigments, allowing them to exploit a wide range of light niches. However, the relationship between pigment content and niche partitioning has remained largely undetermined due to the lack of a single-genetic marker resolving all pigment types (PTs). Here, we developed and employed a robust method based on three distinct marker genes (cpcBA, mpeBA, and mpeW) to estimate the relative abundance of all known Synechococcus PTs from metagenomes. Analysis of the Tara Oceans dataset allowed us to reveal the global distribution of Synechococcus PTs and to define their environmental niches. Green-light specialists (PT 3a) dominated in warm, green equatorial waters, whereas blue-light specialists (PT 3c) were particularly abundant in oligotrophic areas. Type IV chromatic acclimaters (CA4-A/B), which are able to dynamically modify their light absorption properties to maximally absorb green or blue light, were unexpectedly the most abundant PT in our dataset and predominated at depth and high latitudes. We also identified populations in which CA4 might be nonfunctional due to the lack of specific CA4 genes, notably in warm high-nutrient low-chlorophyll areas. Major ecotypes within clades I-IV and CRD1 were preferentially associated with a particular PT, while others exhibited a wide range of PTs. Altogether, this study provides important insights into the ecology of Synechococcus and highlights the complex interactions between vertical phylogeny, pigmentation, and environmental parameters that shape Synechococcus community structure and evolution.}, }
@article {pmid29103940, year = {2017}, author = {Nater, A and Mattle-Greminger, MP and Nurcahyo, A and Nowak, MG and de Manuel, M and Desai, T and Groves, C and Pybus, M and Sonay, TB and Roos, C and Lameira, AR and Wich, SA and Askew, J and Davila-Ross, M and Fredriksson, G and de Valles, G and Casals, F and Prado-Martinez, J and Goossens, B and Verschoor, EJ and Warren, KS and Singleton, I and Marques, DA and Pamungkas, J and Perwitasari-Farajallah, D and Rianti, P and Tuuga, A and Gut, IG and Gut, M and Orozco-terWengel, P and van Schaik, CP and Bertranpetit, J and Anisimova, M and Scally, A and Marques-Bonet, T and Meijaard, E and Krützen, M}, title = {Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species.}, journal = {Current biology : CB}, volume = {27}, number = {22}, pages = {3487-3498.e10}, doi = {10.1016/j.cub.2017.09.047}, pmid = {29103940}, issn = {1879-0445}, mesh = {Animals ; Behavior, Animal/physiology ; Biological Evolution ; Endangered Species ; Gene Flow/genetics ; *Genetic Speciation ; Genetic Variation ; Genome ; Genomics ; Hominidae/genetics ; Metagenomics/methods ; Phylogeny ; Pongo/classification/*genetics/physiology ; Pongo abelii/genetics ; Pongo pygmaeus/genetics ; }, abstract = {Six extant species of non-human great apes are currently recognized: Sumatran and Bornean orangutans, eastern and western gorillas, and chimpanzees and bonobos [1]. However, large gaps remain in our knowledge of fine-scale variation in hominoid morphology, behavior, and genetics, and aspects of great ape taxonomy remain in flux. This is particularly true for orangutans (genus: Pongo), the only Asian great apes and phylogenetically our most distant relatives among extant hominids [1]. Designation of Bornean and Sumatran orangutans, P. pygmaeus (Linnaeus 1760) and P. abelii (Lesson 1827), as distinct species occurred in 2001 [1, 2]. Here, we show that an isolated population from Batang Toru, at the southernmost range limit of extant Sumatran orangutans south of Lake Toba, is distinct from other northern Sumatran and Bornean populations. By comparing cranio-mandibular and dental characters of an orangutan killed in a human-animal conflict to those of 33 adult male orangutans of a similar developmental stage, we found consistent differences between the Batang Toru individual and other extant Ponginae. Our analyses of 37 orangutan genomes provided a second line of evidence. Model-based approaches revealed that the deepest split in the evolutionary history of extant orangutans occurred ∼3.38 mya between the Batang Toru population and those to the north of Lake Toba, whereas both currently recognized species separated much later, about 674 kya. Our combined analyses support a new classification of orangutans into three extant species. The new species, Pongo tapanuliensis, encompasses the Batang Toru population, of which fewer than 800 individuals survive. VIDEO ABSTRACT.}, }
@article {pmid28844808, year = {2017}, author = {Torres-Fuentes, C and Schellekens, H and Dinan, TG and Cryan, JF}, title = {The microbiota-gut-brain axis in obesity.}, journal = {The lancet. Gastroenterology & hepatology}, volume = {2}, number = {10}, pages = {747-756}, doi = {10.1016/S2468-1253(17)30147-4}, pmid = {28844808}, issn = {2468-1253}, mesh = {Affect ; Appetite Regulation ; Brain/*metabolism ; Diet, Reducing ; Energy Metabolism ; Fecal Microbiota Transplantation ; Feeding Behavior/psychology ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; Obesity/*metabolism/psychology/therapy ; Prebiotics ; Probiotics/therapeutic use ; Reward ; }, abstract = {Changes in microbial diversity and composition are increasingly associated with several disease states including obesity and behavioural disorders. Obesity-associated microbiota alter host energy harvesting, insulin resistance, inflammation, and fat deposition. Additionally, intestinal microbiota can regulate metabolism, adiposity, homoeostasis, and energy balance as well as central appetite and food reward signalling, which together have crucial roles in obesity. Moreover, some strains of bacteria and their metabolites might target the brain directly via vagal stimulation or indirectly through immune-neuroendocrine mechanisms. Therefore, the gut microbiota is becoming a target for new anti-obesity therapies. Further investigations are needed to elucidate the intricate gut-microbiota-host relationship and the potential of gut-microbiota-targeted strategies, such as dietary interventions and faecal microbiota transplantation, as promising metabolic therapies that help patients to maintain a healthy weight throughout life.}, }
@article {pmid26807926, year = {2016}, author = {Groah, SL and Pérez-Losada, M and Caldovic, L and Ljungberg, IH and Sprague, BM and Castro-Nallar, E and Chandel, NJ and Hsieh, MH and Pohl, HG}, title = {Redefining Healthy Urine: A Cross-Sectional Exploratory Metagenomic Study of People With and Without Bladder Dysfunction.}, journal = {The Journal of urology}, volume = {196}, number = {2}, pages = {579-587}, doi = {10.1016/j.juro.2016.01.088}, pmid = {26807926}, issn = {1527-3792}, mesh = {Adult ; Biomarkers/urine ; Case-Control Studies ; Cross-Sectional Studies ; Female ; Humans ; Male ; Metagenomics ; *Microbiota ; Middle Aged ; Phenotype ; Urinary Bladder, Neurogenic/diagnosis/*microbiology/physiopathology/urine ; Urine/*microbiology ; }, abstract = {PURPOSE: We used the PathoScope platform to perform species level analyses of publicly available, 16S rRNA pyrosequenced, asymptomatic urine data to determine relationships between microbiomes, and clinical and functional phenotypes.
MATERIALS AND METHODS: We reanalyzed previously reported, cross-sectionally acquired urine samples from 47 asymptomatic subjects, including 23 controls and 24 subjects with neuropathic bladder. Urine was originally collected by the usual method of bladder drainage and analyzed by urinalysis, culture and pyrosequencing. Urinalysis and culture values were stratified as leukocyte esterase (0, or 1 or greater), nitrite (positive or negative), pyuria (fewer than 5, or 5 or greater white blood cells per high power field), cloudy urine (positive or negative) and urine culture bacterial growth (less than 50,000, or 50,000 or greater cfu/ml). PathoScope was used for next generation sequencing alignment, bacterial classification and microbial diversity characterization.
RESULTS: Subjects with neuropathic bladder were significantly more likely to have positive leukocyte esterase and pyuria, cloudy urine and bacterial growth. Of 47 samples 23 showed bacterial growth on culture and in all samples bacteria were identified by pyrosequencing. Nonneuropathic bladder urine microbiomes included greater proportions of Lactobacillus crispatus in females and Staphylococcus haemolyticus in males. The Lactobacillus community differed significantly among females depending on bladder function. Irrespective of gender the subjects with neuropathic bladder had greater proportions of Enterococcus faecalis, Proteus mirabilis and Klebsiella pneumonia. In 4 subjects with neuropathic bladder Actinobaculum sp. was detected by sequencing and by PathoScope but not by cultivation and in all cases it was associated with pyuria.
CONCLUSIONS: Using PathoScope plus 16S pyrosequencing we were able to identify unique, phenotype dependent, species level microbes. Novel findings included absent L. crispatus in the urine of females with neuropathic bladder and the presence of Actinobaculum only in subjects with neuropathic bladder.}, }
@article {pmid30072968, year = {2018}, author = {Dittberner, H and Ohlmann, N and Acquisti, C}, title = {Stoichio-Metagenomics of Ocean Waters: A Molecular Evolution Approach to Trace the Dynamics of Nitrogen Conservation in Natural Communities.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1590}, doi = {10.3389/fmicb.2018.01590}, pmid = {30072968}, issn = {1664-302X}, abstract = {Nitrogen is crucially limiting in ocean surface waters, and its availability varies substantially with coastal regions typically richer in nutrients than open oceans. In a biological stoichiometry framework, a parsimonious strategy of nitrogen allocation predicts nitrogen content of proteins to be lower in communities adapted to open ocean than to coastal regions. To test this hypothesis we have directly interrogated marine microbial communities, using a series of metagenomics datasets with a broad geographical distribution from the Global Ocean Sampling Expedition. Analyzing over 20 million proteins, we document a ubiquitous signal of nitrogen conservation in open ocean communities, both in membrane and non-membrane proteins. Efficient nitrogen allocation is expected to specifically target proteins that are expressed at high rate in response to nitrogen starvation. Furthermore, in order to preserve protein functional efficiency, economic nitrogen allocation is predicted to target primarily the least functionally constrained regions of proteins. Contrasting the NtcA-induced pathway, typically up-regulated in response to nitrogen starvation, with the arginine anabolic pathway, which is instead up-regulated in response to nitrogen abundance, we show how both these predictions are fulfilled. Using evolutionary rates as an informative proxy of functional constraints, we show that variation in nitrogen allocation between open ocean and coastal communities is primarily localized in the least functionally constrained regions of the genes triggered by NtcA. As expected, such a pattern is not detectable in the genes involved in the arginine anabolic pathway. These results directly link environmental nitrogen availability to different adaptive strategies of genome evolution, and emphasize the relevance of the material costs of evolutionary change in natural ecosystems.}, }
@article {pmid29439665, year = {2018}, author = {Feng, G and Xie, T and Wang, X and Bai, J and Tang, L and Zhao, H and Wei, W and Wang, M and Zhao, Y}, title = {Metagenomic analysis of microbial community and function involved in cd-contaminated soil.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {11}, doi = {10.1186/s12866-018-1152-5}, pmid = {29439665}, issn = {1471-2180}, mesh = {Amino Acids/metabolism ; Bacteria/classification/*drug effects/genetics/metabolism ; Biodiversity ; Cadmium/metabolism/*toxicity ; China ; DNA, Bacterial ; Environmental Pollution ; Fatty Acids/metabolism ; Metabolic Networks and Pathways ; *Metagenomics ; Metals, Heavy/metabolism ; Microbial Consortia/*drug effects ; Nucleotides/metabolism ; Open Reading Frames ; Phylogeny ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/metabolism/*toxicity ; }, abstract = {BACKGROUND: Soil contaminated with the heavy metal Cadmium (Cd) is a widespread problem in many parts of the world. Based on metagenomic analysis, we investigated the functional potential and structural diversity of the microbial community in Cd-contaminated and non-contaminated soil samples and we explored the associated metabolic pathway network in cluster of orthologous groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG).
RESULTS: The results showed that microorganisms in these soils were quite abundant, and many of them possessed numerous physiological functions. However, Cd-contamination has the potential to reduce the microbial diversity and further alter the community structure in the soil. Notably, function analysis of the crucial microorganisms (e. g. Proteobacteria, Sulfuricella and Thiobacillus) indicated that these bacteria and their corresponding physiological functions were important for the community to cope with Cd pollution. The COG annotation demonstrated that the predominant category was the microbial metabolism cluster in both soil samples, while the relative abundance of metabolic genes was increased in the Cd-contaminated soil. The KEGG annotation results exhibited that the non-contaminated soil had more genes, pathways, modules, orthologies and enzymes involved in metabolic pathways of microbial communities than the Cd-contaminated soil. The relative abundance of some dominant KEGG pathways increased in the Cd contaminated soil, and they were mostly enriched to the metabolism, biosynthesis and degradation of amino acids, fatty acids and nucleotides, which was related to Cd tolerance of the microorganisms.
CONCLUSIONS: Cd-contamination can decrease the taxonomic species of microbes in soil and change the soil microbial composition. The functional pathways involved in the soil change with microbial structure variation, many of which are related to the heavy metal tolerance of soil microbes. The Cd-contaminated soil microbes is a potential resource for exploring cadmium resistant or tolerant bacteria.}, }
@article {pmid29153320, year = {2017}, author = {Dudek, NK and Sun, CL and Burstein, D and Kantor, RS and Aliaga Goltsman, DS and Bik, EM and Thomas, BC and Banfield, JF and Relman, DA}, title = {Novel Microbial Diversity and Functional Potential in the Marine Mammal Oral Microbiome.}, journal = {Current biology : CB}, volume = {27}, number = {24}, pages = {3752-3762.e6}, doi = {10.1016/j.cub.2017.10.040}, pmid = {29153320}, issn = {1879-0445}, mesh = {Animals ; Archaea/*classification ; Bacteria/*classification ; Bottle-Nosed Dolphin/*microbiology ; Female ; *Genome, Archaeal ; *Genome, Bacterial ; Male ; *Metagenome ; Metagenomics ; *Microbiota ; Mouth/microbiology ; }, abstract = {The vast majority of bacterial diversity lies within phylum-level lineages called "candidate phyla," which lack isolated representatives and are poorly understood. These bacteria are surprisingly abundant in the oral cavity of marine mammals. We employed a genome-resolved metagenomic approach to recover and characterize genomes and functional potential from microbes in the oral gingival sulcus of two bottlenose dolphins (Tursiops truncatus). We detected organisms from 24 known bacterial phyla and one archaeal phylum. We also recovered genomes from two deep-branching, previously uncharacterized phylum-level lineages (here named "Candidatus Delphibacteria" and "Candidatus Fertabacteria"). The Delphibacteria lineage is found in both managed and wild dolphins; its metabolic profile suggests a capacity for denitrification and a possible role in dolphin health. We uncovered a rich diversity of predicted Cas9 proteins, including the two longest predicted Cas9 proteins to date. Notably, we identified the first type II CRISPR-Cas systems encoded by members of the Candidate Phyla Radiation. Using their spacer sequences, we subsequently identified and assembled a complete Saccharibacteria phage genome. These findings underscore the immense microbial diversity and functional potential that await discovery in previously unexplored environments.}, }
@article {pmid30069051, year = {2018}, author = {Bahram, M and Hildebrand, F and Forslund, SK and Anderson, JL and Soudzilovskaia, NA and Bodegom, PM and Bengtsson-Palme, J and Anslan, S and Coelho, LP and Harend, H and Huerta-Cepas, J and Medema, MH and Maltz, MR and Mundra, S and Olsson, PA and Pent, M and Põlme, S and Sunagawa, S and Ryberg, M and Tedersoo, L and Bork, P}, title = {Structure and function of the global topsoil microbiome.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41586-018-0386-6}, pmid = {30069051}, issn = {1476-4687}, abstract = {Soils harbour some of the most diverse microbiomes on Earth and are essential for both nutrient cycling and carbon storage. To understand soil functioning, it is necessary to model the global distribution patterns and functional gene repertoires of soil microorganisms, as well as the biotic and environmental associations between the diversity and structure of both bacterial and fungal soil communities1-4. Here we show, by leveraging metagenomics and metabarcoding of global topsoil samples (189 sites, 7,560 subsamples), that bacterial, but not fungal, genetic diversity is highest in temperate habitats and that microbial gene composition varies more strongly with environmental variables than with geographic distance. We demonstrate that fungi and bacteria show global niche differentiation that is associated with contrasting diversity responses to precipitation and soil pH. Furthermore, we provide evidence for strong bacterial-fungal antagonism, inferred from antibiotic-resistance genes, in topsoil and ocean habitats, indicating the substantial role of biotic interactions in shaping microbial communities. Our results suggest that both competition and environmental filtering affect the abundance, composition and encoded gene functions of bacterial and fungal communities, indicating that the relative contributions of these microorganisms to global nutrient cycling varies spatially.}, }
@article {pmid29382070, year = {2018}, author = {D'Argenio, V}, title = {Human Microbiome Acquisition and Bioinformatic Challenges in Metagenomic Studies.}, journal = {International journal of molecular sciences}, volume = {19}, number = {2}, pages = {}, doi = {10.3390/ijms19020383}, pmid = {29382070}, issn = {1422-0067}, mesh = {*Gastrointestinal Microbiome ; Genomics/*methods/standards ; Humans ; *Metagenome ; Transcriptome ; }, abstract = {The study of the human microbiome has become a very popular topic. Our microbial counterpart, in fact, appears to play an important role in human physiology and health maintenance. Accordingly, microbiome alterations have been reported in an increasing number of human diseases. Despite the huge amount of data produced to date, less is known on how a microbial dysbiosis effectively contributes to a specific pathology. To fill in this gap, other approaches for microbiome study, more comprehensive than 16S rRNA gene sequencing, i.e., shotgun metagenomics and metatranscriptomics, are becoming more widely used. Methods standardization and the development of specific pipelines for data analysis are required to contribute to and increase our understanding of the human microbiome relationship with health and disease status.}, }
@article {pmid29179769, year = {2017}, author = {Ma, L and Li, B and Jiang, XT and Wang, YL and Xia, Y and Li, AD and Zhang, T}, title = {Catalogue of antibiotic resistome and host-tracking in drinking water deciphered by a large scale survey.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {154}, doi = {10.1186/s40168-017-0369-0}, pmid = {29179769}, issn = {2049-2618}, support = {172057/15E//Hong Kong General Research Fund/ ; JCYJ20150831192847649//Shenzhen Knowledge Innovation Program-Basic Research Project/ ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/classification/drug effects/genetics/*isolation & purification ; China ; Drinking Water/*analysis/*microbiology ; Drug Resistance, Microbial/*genetics ; Drug Resistance, Multiple/genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Hong Kong ; Humans ; Metagenomics/methods ; Microbial Consortia/drug effects/genetics ; Public Health ; Surveys and Questionnaires ; United States ; Water Purification ; }, abstract = {BACKGROUND: Excesses of antibiotic resistance genes (ARGs), which are regarded as emerging environmental pollutants, have been observed in various environments. The incidence of ARGs in drinking water causes potential risks to human health and receives more attention from the public. However, ARGs harbored in drinking water remain largely unexplored. In this study, we aimed at establishing an antibiotic resistome catalogue in drinking water samples from a wide range of regions and to explore the potential hosts of ARGs.
RESULTS: A catalogue of antibiotic resistome in drinking water was established, and the host-tracking of ARGs was conducted through a large-scale survey using metagenomic approach. The drinking water samples were collected at the point of use in 25 cities in mainland China, Hong Kong, Macau, Taiwan, South Africa, Singapore and the USA. In total, 181 ARG subtypes belonging to 16 ARG types were detected with an abundance range of 2.8 × 10-2 to 4.2 × 10-1 copies of ARG per cell. The highest abundance was found in northern China (Henan Province). Bacitracin, multidrug, aminoglycoside, sulfonamide, and beta-lactam resistance genes were dominant in drinking water. Of the drinking water samples tested, 84% had a higher ARG abundance than typical environmental ecosystems of sediment and soil. Metagenomic assembly-based host-tracking analysis identified Acidovorax, Acinetobacter, Aeromonas, Methylobacterium, Methyloversatilis, Mycobacterium, Polaromonas, and Pseudomonas as the hosts of ARGs. Moreover, potential horizontal transfer of ARGs in drinking water systems was proposed by network and Procrustes analyses.
CONCLUSIONS: The antibiotic resistome catalogue compiled using a large-scale survey provides a useful reference for future studies on the global surveillance and risk management of ARGs in drinking water. .}, }
@article {pmid29179741, year = {2017}, author = {Anderson, CL and Sullivan, MB and Fernando, SC}, title = {Dietary energy drives the dynamic response of bovine rumen viral communities.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {155}, doi = {10.1186/s40168-017-0374-3}, pmid = {29179741}, issn = {2049-2618}, support = {2016-67011-24783//National Institute of Food and Agriculture/ ; 2012-68002-19823//National Institute of Food and Agriculture/ ; 3790.01//Gordon and Betty Moore Foundation/ ; }, mesh = {Animals ; Bacteriophages/genetics ; Cattle ; Cross-Over Studies ; DNA, Viral/genetics ; *Diet ; Food ; Metagenome ; Metagenomics/methods ; Microbiota/drug effects/*genetics ; Rumen/microbiology/*virology ; Sequence Analysis, DNA ; Viruses/classification/drug effects/*genetics/isolation & purification ; Zinc/pharmacology ; }, abstract = {BACKGROUND: Rumen microbes play a greater role in host energy acquisition than that of gut-associated microbes in monogastric animals. Although genome-enabled advancements are providing access to the vast diversity of uncultivated microbes, our understanding of variables shaping rumen microbial communities is in its infancy. Viruses have been shown to impact microbial populations through a myriad of processes, including cell lysis and reprogramming of host metabolism. However, little is known about the processes shaping the distribution of rumen viruses or how viruses may modulate microbial-driven processes in the rumen. To this end, we investigated how rumen bacterial and viral community structure and function responded in five steers fed four randomized dietary treatments in a crossover design.
RESULTS: Total digestible nutrients (TDN), a measure of dietary energy, best explained the variation in bacterial and viral communities. Additional ecological drivers of viral communities included dietary zinc content and microbial functional diversity. Using partial least squares regression, we demonstrate significant associations between the abundances of 267 viral populations and variables driving the variation in rumen viral communities. While rumen viruses were dynamic, 14 near ubiquitous viral populations were identified, suggesting the presence of a core rumen virome largely comprised of novel viruses. Moreover, analysis of virally encoded auxiliary metabolic genes (AMGs) indicates rumen viruses have glycosidic hydrolases to potentially augment the breakdown of complex carbohydrates to increase energy production. Other AMGs identified have a role in redirecting carbon to the pentose phosphate pathway and one carbon pools by folate to boost viral replication.
CONCLUSIONS: We demonstrate that rumen bacteria and viruses have differing responses and ecological drivers to dietary perturbation. Our results show that rumen viruses have implications for understanding the structuring of the previously identified core rumen microbiota and impacting microbial metabolism through a vast array of AMGs. AMGs in the rumen appear to have consequences for microbial metabolism that are largely in congruence with the current paradigm established in marine systems. This study provides a foundation for future hypotheses regarding the dynamics of viral-mediated processes in the rumen.}, }
@article {pmid29178920, year = {2017}, author = {Nash, AK and Auchtung, TA and Wong, MC and Smith, DP and Gesell, JR and Ross, MC and Stewart, CJ and Metcalf, GA and Muzny, DM and Gibbs, RA and Ajami, NJ and Petrosino, JF}, title = {The gut mycobiome of the Human Microbiome Project healthy cohort.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {153}, doi = {10.1186/s40168-017-0373-4}, pmid = {29178920}, issn = {2049-2618}, support = {U54 HG003273/HG/NHGRI NIH HHS/United States ; 2 U54 HG003273//National Human Genome Research Institute/ ; }, mesh = {Candida/classification/genetics/isolation & purification ; Cohort Studies ; DNA, Ribosomal Spacer/genetics ; Feces/microbiology ; Fungi/classification/genetics/*isolation & purification ; Gastrointestinal Microbiome/*genetics ; Genetic Variation ; *Healthy Volunteers ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Malassezia/classification/genetics/isolation & purification ; Metagenomics/methods ; *Microbiota ; *Mycobiome ; RNA, Ribosomal, 18S/genetics ; Saccharomyces/classification/genetics/isolation & purification ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Most studies describing the human gut microbiome in healthy and diseased states have emphasized the bacterial component, but the fungal microbiome (i.e., the mycobiome) is beginning to gain recognition as a fundamental part of our microbiome. To date, human gut mycobiome studies have primarily been disease centric or in small cohorts of healthy individuals. To contribute to existing knowledge of the human mycobiome, we investigated the gut mycobiome of the Human Microbiome Project (HMP) cohort by sequencing the Internal Transcribed Spacer 2 (ITS2) region as well as the 18S rRNA gene.
RESULTS: Three hundred seventeen HMP stool samples were analyzed by ITS2 sequencing. Fecal fungal diversity was significantly lower in comparison to bacterial diversity. Yeast dominated the samples, comprising eight of the top 15 most abundant genera. Specifically, fungal communities were characterized by a high prevalence of Saccharomyces, Malassezia, and Candida, with S. cerevisiae, M. restricta, and C. albicans operational taxonomic units (OTUs) present in 96.8, 88.3, and 80.8% of samples, respectively. There was a high degree of inter- and intra-volunteer variability in fungal communities. However, S. cerevisiae, M. restricta, and C. albicans OTUs were found in 92.2, 78.3, and 63.6% of volunteers, respectively, in all samples donated over an approximately 1-year period. Metagenomic and 18S rRNA gene sequencing data agreed with ITS2 results; however, ITS2 sequencing provided greater resolution of the relatively low abundance mycobiome constituents.
CONCLUSIONS: Compared to bacterial communities, the human gut mycobiome is low in diversity and dominated by yeast including Saccharomyces, Malassezia, and Candida. Both inter- and intra-volunteer variability in the HMP cohort were high, revealing that unlike bacterial communities, an individual's mycobiome is no more similar to itself over time than to another person's. Nonetheless, several fungal species persisted across a majority of samples, evidence that a core gut mycobiome may exist. ITS2 sequencing data provided greater resolution of the mycobiome membership compared to metagenomic and 18S rRNA gene sequencing data, suggesting that it is a more sensitive method for studying the mycobiome of stool samples.}, }
@article {pmid29083035, year = {2018}, author = {Laskar, F and Das Purkayastha, S and Sen, A and Bhattacharya, MK and Misra, BB}, title = {Diversity of methanogenic archaea in freshwater sediments of lacustrine ecosystems.}, journal = {Journal of basic microbiology}, volume = {58}, number = {2}, pages = {101-119}, doi = {10.1002/jobm.201700341}, pmid = {29083035}, issn = {1521-4028}, mesh = {Archaea/*classification/genetics/growth & development/*metabolism ; *Biodiversity ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fresh Water/*microbiology ; Geologic Sediments/microbiology ; Lakes/microbiology ; Metagenomics/*methods ; Methane/*metabolism ; Microbiological Techniques/*methods ; Oxidoreductases/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {About half of the global methane (CH4) emission is contributed by the methanogenic archaeal communities leading to a significant increase in global warming. This unprecedented situation has increased the ever growing necessity of evaluating the control measures for limiting CH4 emission to the atmosphere. Unfortunately, research endeavors on the diversity and functional interactions of methanogens are not extensive till date. We anticipate that the study of the diversity of methanogenic community is paramount for understanding the metabolic processes in freshwater lake ecosystems. Although there are several disadvantages of conventional culture-based methods for determining the diversity of methanogenic archaeal communities, in order to understand their ecological roles in natural environments it is required to culture the microbes. Recently different molecular techniques have been developed for determining the structure of methanogenic archaeal communities thriving in freshwater lake ecosystem. The two gene based cloning techniques required for this purpose are 16S rRNA and methyl coenzyme M reductase (mcrA) in addition to the recently developed metagenomics approaches and high throughput next generation sequencing efforts. This review discusses the various methods of culture-dependent and -independent measures of determining the diversity of methanogen communities in lake sediments in lieu of the different molecular approaches and inter-relationships of diversity of methanogenic archaea.}, }
@article {pmid28929212, year = {2018}, author = {Parmar, K and Dafale, N and Pal, R and Tikariha, H and Purohit, H}, title = {An Insight into Phage Diversity at Environmental Habitats using Comparative Metagenomics Approach.}, journal = {Current microbiology}, volume = {75}, number = {2}, pages = {132-141}, doi = {10.1007/s00284-017-1357-0}, pmid = {28929212}, issn = {1432-0991}, mesh = {Bacteriophages/*classification/genetics/*isolation & purification ; *Biodiversity ; *Ecosystem ; Metagenomics ; *Water Microbiology ; }, abstract = {Bacteriophages play significant role in driving microbial diversity; however, little is known about the diversity of phages in different ecosystems. A dynamic predator-prey mechanism called "kill the winner" suggests the elimination of most active bacterial populations through phages. Thus, interaction between phage and host has an effect on the composition of microbial communities in ecosystems. In this study, secondary phage metagenome data from aquatic habitats: wastewater treatment plant (WWTP), fresh, marine, and hot water spring habitat were analyzed using MG-RAST and STAMP tools to explore the diversity of the viruses. Differential relative abundance of phage families-Siphoviridae (34%) and Myoviridae (26%) in WWTP, Myoviridae (30%) and Podoviridae (23%) in fresh water, and Myoviridae (41%) and Podoviridae (8%) in marine-was found to be a discriminating factor among four habitats while Rudiviridae (9%), Globuloviridae (8%), and Lipothrixviridae (1%) were exclusively observed in hot water spring. Subsequently, at genera level, Bpp-1-like virus, Chlorovirus, and T4-like virus were found abundant in WWTP, fresh, and marine habitat, respectively. PCA analysis revealed completely disparate composition of phage in hot water spring from other three ecosystems. Similar analysis of relative abundance of functional features corroborated observations from taxa analysis. Functional features corresponding to phage packaging machinery, replication, integration and excision, and gene transfer discriminated among four habitats. The comparative metagenomics approach exhibited genetically distinct phage communities among four habitats. Results revealed that selective distribution of phage communities would help in understanding the role of phages in food chains, nutrient cycling, and microbial ecology. Study of specific phages would also help in controlling environmental pathogens including MDR bacterial populations using phage therapy approach by selective mining and isolation of phages against specific pathogens persisting in a given environment.}, }
@article {pmid28910638, year = {2017}, author = {Verster, AJ and Ross, BD and Radey, MC and Bao, Y and Goodman, AL and Mougous, JD and Borenstein, E}, title = {The Landscape of Type VI Secretion across Human Gut Microbiomes Reveals Its Role in Community Composition.}, journal = {Cell host & microbe}, volume = {22}, number = {3}, pages = {411-419.e4}, doi = {10.1016/j.chom.2017.08.010}, pmid = {28910638}, issn = {1934-6069}, support = {DP2 AT007802/AT/NCCIH NIH HHS/United States ; R35 GM118159/GM/NIGMS NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; //Howard Hughes Medical Institute/United States ; R01 AI080609/AI/NIAID NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Bacteria/classification/genetics/isolation & purification/*metabolism ; Bacterial Proteins/genetics/*metabolism ; Bacteroides/classification/genetics/isolation & purification/metabolism ; Biodiversity ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Male ; Middle Aged ; Phylogeny ; Type VI Secretion Systems/genetics/*metabolism ; Young Adult ; }, abstract = {Although gut microbiome composition is well defined, the mechanisms underlying community assembly remain poorly understood. Bacteroidales possess three genetic architectures (GA1-3) of the type VI secretion system (T6SS), an effector delivery pathway that mediates interbacterial competition. Here we define the distribution and role of GA1-3 in the human gut using metagenomic analysis. We find that adult microbiomes harbor limited effector and cognate immunity genes, suggesting selection for compatibility at the species (GA1 and GA2) and strain (GA3) levels. Bacteroides fragilis GA3 is known to mediate potent inter-strain competition, and we observe GA3 enrichment among strains colonizing infant microbiomes, suggesting competition early in life. Additionally, GA3 is associated with increased Bacteroides abundance, indicating that this system confers an advantage in Bacteroides-rich ecosystems. Collectively, these analyses uncover the prevalence of T6SS-dependent competition and reveal its potential role in shaping human gut microbial composition.}, }
@article {pmid30055354, year = {2018}, author = {Linard, B and Crampton-Platt, A and Moriniere, J and Timmermans, MJTN and Andujar, C and Arribas, P and Miller, KE and Lipecki, J and Favreau, E and Hunter, A and Gómez-Rodríguez, C and Barton, C and Nie, R and Gillett, CPDT and Breeschoten, T and Bocak, L and Vogler, AP}, title = {The contribution of mitochondrial metagenomics to large-scale data mining and phylogenetic analysis of Coleoptera.}, journal = {Molecular phylogenetics and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ympev.2018.07.008}, pmid = {30055354}, issn = {1095-9513}, abstract = {A phylogenetic tree at the species level is still far off for highly diverse insect orders, including the Coleoptera, but the taxonomic breadth of public sequence databases is growing. In addition, new types of data may contribute to increasing taxon coverage, such as metagenomic shotgun sequencing for assembly of mitogenomes from bulk specimen samples. The current study explores the application of these techniques for large-scale efforts to build the tree of Coleoptera. We used shotgun data from 17 different ecological and taxonomic datasets (5 unpublished) to assemble a total of 1942 mitogenome contigs of >3000 bp. These sequences were combined into a single dataset together with all mitochondrial data available at GenBank, in addition to nuclear markers widely used in molecular phylogenetics. The resulting matrix of nearly 16000 species with two or more loci produced trees (RAxML) showing overall congruence with the Linnaean taxonomy at hierarchical levels from suborders to genera. We tested the role of full-length mitogenomes in stabilizing the tree from GenBank data, as mitogenomes might link terminals with non-overlapping gene representation. However, the mitogenome data were only partly useful in this respect, presumably because of the purely automated approach to assembly and gene delimitation, but improvements in future may be possible by using multiple assemblers and manual curation. In conclusion, the combination of data mining and metagenomic sequencing of bulk samples provided the largest phylogenetic tree of Coleoptera to date, which represents a summary of existing phylogenetic knowledge and a defensible tree of great utility, in particular for studies at the intra-familial level, despite some shortcomings for resolving basal nodes.}, }
@article {pmid29664968, year = {2018}, author = {Betiku, OC and Yeoman, CJ and Gaylord, TG and Americus, B and Olivo, S and Duff, GC and Sealey, WM}, title = {Water system is a controlling variable modulating bacterial diversity of gastrointestinal tract and performance in rainbow trout.}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0195967}, doi = {10.1371/journal.pone.0195967}, pmid = {29664968}, issn = {1932-6203}, mesh = {Animal Feed ; Animals ; Bacteria/*classification/genetics ; *Biodiversity ; *Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; Oncorhynchus mykiss/*microbiology ; Vegetable Proteins ; *Water Microbiology ; }, abstract = {A two-phase feeding study evaluating performance of rainbow trout and comparing luminal and mucosal gastrointestinal tract (GIT) bacterial community compositions when fed two alternative protein diets in two rearing systems was conducted. Alternative protein diets (animal protein and plant protein diets) balanced with crystalline amino acids: lysine, methionine and threonine or unbalanced, were fed to rainbow trout in two separate water systems (recirculating (RR) and flow-through (FF)) for a period of 16 weeks. The four diets, each contained 38% digestible protein and 20% fats, were fed to rainbow trout with an average weight of 12.02 ± 0.61 g, and sorted at 30 fish/tank and 12 tanks per dietary treatment. Phase 1 lasted for 8 weeks after which fish from each tank were randomly divided, with one-half moved to new tanks of the opposing system (i.e. from RR to FF and vice versa). The remaining halves were retained in their initial tank and system, and fed their original diets for another 8 weeks (phase 2). After the 16th week, 3 fish/tank were sampled for each of proximate analysis, body indexes and 16S rRNA analysis of GIT microbiota. Fish weight (P = 0.0008, P = 0.0030, P<0.0010) and body fat (P = 0.0008, P = 0.0041, P = 0.0177) were significantly affected by diet, diet quality (balanced or unbalanced) and system, respectively. Feed intake (P = 0.0008) and body energy (P<0.0010) were altered by system. Body indexes were not affected by dietary treatment and water systems. Compositional dissimilarities existed between samples from the rearing water and GIT locations (ANOSIM: (R = 0.29, P = 0.0010), PERMANOVA: R = 0.39, P = 0.0010), but not in dietary samples (ANOSIM: R = 0.004, P = 0.3140, PERMANOVA: R = 0.008, P = 0.4540). Bacteria were predominantly from the phyla Proteobacteria, Firmicutes and Bacteroidetes. Their abundance differed with more dissimilarity in the luminal samples (ANOSIM: R = 0.40, P = 0.0010, PERMANOVA: R = 0.56, P = 0.0010) than those from the mucosal intestine (ANOSIM: R = 0.37, P = 0.0010, PERMANOVA: R = 0.41, P = 0.0010). Bacteria generally associated with carbohydrate and certain amino acids metabolism were observed in the mucosal intestine while rearing water appeared to serve as the main route of colonization of Aeromonas and Acinetobacter in the rainbow trout.}, }
@article {pmid29659617, year = {2018}, author = {Mohamed Ramli, N and Giatsis, C and Md Yusoff, F and Verreth, J and Verdegem, M}, title = {Resistance and resilience of small-scale recirculating aquaculture systems (RAS) with or without algae to pH perturbation.}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0195862}, doi = {10.1371/journal.pone.0195862}, pmid = {29659617}, issn = {1932-6203}, mesh = {Ammonia/chemistry ; *Aquaculture ; Bacteria/classification/genetics ; Biodiversity ; *Chlorophyta ; *Fresh Water ; *Hydrogen-Ion Concentration ; Metagenome ; Metagenomics/methods ; Nitrogen/chemistry ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; Water Quality ; }, abstract = {The experimental set-up of this study mimicked recirculating aquaculture systems (RAS) where water quality parameters such as dissolved oxygen, pH, temperature, and turbidity were controlled and wastes produced by fish and feeding were converted to inorganic forms. A key process in the RAS was the conversion of ammonia to nitrite and nitrite to nitrate through nitrification. It was hypothesized that algae inclusion in RAS would improve the ammonia removal from the water; thereby improving RAS water quality and stability. To test this hypothesis, the stability of the microbiota community composition in a freshwater RAS with (RAS+A) or without algae (RAS-A) was challenged by introducing an acute pH drop (from pH 7 to 4 during three hours) to the system. Stigeoclonium nanum, a periphytic freshwater microalga was used in this study. No significant effect of the algae presence was found on the resistance to the acute pH drop on ammonia conversion to nitrite and nitrite conversion to nitrate. Also the resilience of the ammonia conversion to the pH drop disruption was not affected by the addition of algae. This could be due to the low biomass of algae achieved in the RAS. However, with regard to the conversion step of nitrite to nitrate, RAS+A was significantly more resilient than RAS-A. In terms of overall bacterial communities, the composition and predictive function of the bacterial communities was significantly different between RAS+A and RAS-A.}, }
@article {pmid29187708, year = {2017}, author = {Hirai, M and Nishi, S and Tsuda, M and Sunamura, M and Takaki, Y and Nunoura, T}, title = {Library Construction from Subnanogram DNA for Pelagic Sea Water and Deep-Sea Sediments.}, journal = {Microbes and environments}, volume = {32}, number = {4}, pages = {336-343}, doi = {10.1264/jsme2.ME17132}, pmid = {29187708}, issn = {1347-4405}, mesh = {Base Composition/genetics ; Base Sequence ; Biodiversity ; DNA, Archaeal/analysis/*genetics ; DNA, Bacterial/analysis/*genetics ; DNA, Protozoan/analysis/*genetics ; Gene Library ; Geologic Sediments/*microbiology/*parasitology ; Metagenome/*genetics ; Metagenomics/*methods ; Seawater/microbiology/parasitology ; Sequence Analysis, DNA ; }, abstract = {Shotgun metagenomics is a low biased technology for assessing environmental microbial diversity and function. However, the requirement for a sufficient amount of DNA and the contamination of inhibitors in environmental DNA leads to difficulties in constructing a shotgun metagenomic library. We herein examined metagenomic library construction from subnanogram amounts of input environmental DNA from subarctic surface water and deep-sea sediments using two library construction kits: the KAPA Hyper Prep Kit and Nextera XT DNA Library Preparation Kit, with several modifications. The influence of chemical contaminants associated with these environmental DNA samples on library construction was also investigated. Overall, shotgun metagenomic libraries were constructed from 1 pg to 1 ng of input DNA using both kits without harsh library microbial contamination. However, the libraries constructed from 1 pg of input DNA exhibited larger biases in GC contents, k-mers, or small subunit (SSU) rRNA gene compositions than those constructed from 10 pg to 1 ng DNA. The lower limit of input DNA for low biased library construction in this study was 10 pg. Moreover, we revealed that technology-dependent biases (physical fragmentation and linker ligation vs. tagmentation) were larger than those due to the amount of input DNA.}, }
@article {pmid29490093, year = {2018}, author = {Mulukutla, SN and Hsu, JW and Gaba, R and Bohren, KM and Guthikonda, A and Iyer, D and Ajami, NJ and Petrosino, JF and Hampe, CS and Ram, N and Jahoor, F and Balasubramanyam, A}, title = {Arginine Metabolism Is Altered in Adults with A-β + Ketosis-Prone Diabetes.}, journal = {The Journal of nutrition}, volume = {148}, number = {2}, pages = {185-193}, doi = {10.1093/jn/nxx032}, pmid = {29490093}, issn = {1541-6100}, support = {R01 DK101411/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Arginine/administration & dosage/blood/*metabolism ; Blood Glucose/analysis ; Body Mass Index ; Diabetes Mellitus, Type 1/*metabolism/physiopathology ; Diabetes Mellitus, Type 2/physiopathology ; Female ; Gastrointestinal Microbiome/physiology ; Glucose/administration & dosage ; Glucose Clamp Technique ; Humans ; Hyperglycemia ; Insulin/blood/secretion ; Insulin-Secreting Cells/*physiology ; Kinetics ; Male ; Metabolomics/methods ; Middle Aged ; Nitric Oxide/metabolism ; Ornithine/blood ; }, abstract = {Background: A-β + ketosis-prone diabetes (KPD) is a subset of type 2 diabetes in which patients have severe but reversible β cell dysfunction of unknown etiology. Plasma metabolomic analysis indicates that abnormal arginine metabolism may be involved.
Objective: The objective of this study was to determine the relation between gut microbiome and arginine metabolism and the relation between arginine availability and β cell function in KPD patients compared with control participants.
Methods: Kinetics of arginine and related metabolites were measured with stable isotope tracers, and insulin secretory responses to arginine and glucose were determined under euglycemic and hyperglycemic conditions in 6 KPD patients and 6 age-, gender-, and body mass index-matched control participants. Glucose potentiation of arginine-induced insulin secretion was performed in a different set of 6 KPD and 3 control participants.
Results: Arginine availability was higher in KPD patients during euglycemia [53.5 ± 4.3 (mean ± SEM) compared with 40.3 ± 2.4 μmol · kg lean body mass (LBM)-1 · h-1, P = 0.03] but declined more in response to hyperglycemia (Δ 10.15 ± 2.6 compared with Δ 3.20 ± 1.3 μmol · kg LBM-1 · h-1, P = 0.041). During hyperglycemia, ornithine flux was not different between groups but after an arginine bolus, plasma ornithine AUC trended higher in KPD patients (3360 ± 294 compared with 2584 ± 259 min · μmol · L-1, P = 0.08). In both euglycemia and hyperglycemia, the first-phase insulin responses to glucose stimulation were lower in KPD patients (euglycemic insulin AUC 282 ± 108 compared with 926 ± 257 min · μU · mL-1, P = 0.02; hyperglycemic insulin AUC 358 ± 79 compared with 866 ± 292 min · μU · mL-1, P = 0.05), but exogenous arginine restored first-phase insulin secretion in KPD patients to the level of control participants.
Conclusion: Compared with control participants, KPD patients have increased arginine availability in the euglycemic state, indicating a higher requirement. This is compromised during hyperglycemia, with an inadequate supply of arginine to sustain metabolic functions such as insulin secretion. Exogenous arginine administration restores a normal insulin secretory response.}, }
@article {pmid29189738, year = {2017}, author = {Ticinesi, A and Lauretani, F and Milani, C and Nouvenne, A and Tana, C and Del Rio, D and Maggio, M and Ventura, M and Meschi, T}, title = {Aging Gut Microbiota at the Cross-Road between Nutrition, Physical Frailty, and Sarcopenia: Is There a Gut-Muscle Axis?.}, journal = {Nutrients}, volume = {9}, number = {12}, pages = {}, doi = {10.3390/nu9121303}, pmid = {29189738}, issn = {2072-6643}, mesh = {Aging/*physiology ; *Frailty ; *Gastrointestinal Microbiome ; Humans ; Muscle, Skeletal/*physiology ; *Nutritional Status ; *Sarcopenia ; }, abstract = {Inadequate nutrition and physical inactivity are the mainstays of primary sarcopenia-physiopathology in older individuals. Gut microbiota composition is strongly dependent on both of these elements, and conversely, can also influence the host physiology by modulating systemic inflammation, anabolism, insulin sensitivity, and energy production. The bacterial metabolism of nutrients theoretically influences skeletal muscle cell functionality through producing mediators that drive all of these systemic effects. In this study, we review the scientific literature supporting the concept of the involvement of gut microbiota in primary sarcopenia physiopathology. First, we examine studies associating fecal microbiota alterations with physical frailty, i.e., the loss of muscle performance and normal muscle mass. Then, we consider studies exploring the effects of exercise on gut microbiota composition. Finally, we examine studies demonstrating the possible effects of mediators produced by gut microbiota on skeletal muscle, and intervention studies considering the effects of prebiotic or probiotic administration on muscle function. Even if there is no evidence of a distinct gut microbiota composition in older sarcopenic patients, we conclude that the literature supports the possible presence of a "gut-muscle axis", whereby gut microbiota may act as the mediator of the effects of nutrition on muscle cells.}, }
@article {pmid28973555, year = {2017}, author = {Chi, L and Bian, X and Gao, B and Tu, P and Ru, H and Lu, K}, title = {The Effects of an Environmentally Relevant Level of Arsenic on the Gut Microbiome and Its Functional Metagenome.}, journal = {Toxicological sciences : an official journal of the Society of Toxicology}, volume = {160}, number = {2}, pages = {193-204}, doi = {10.1093/toxsci/kfx174}, pmid = {28973555}, issn = {1096-0929}, support = {P30 ES010126/ES/NIEHS NIH HHS/United States ; R01 ES024950/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Arsenites/*toxicity ; Bacteria/classification/*drug effects/genetics ; Dysbiosis ; Environmental Pollutants/*toxicity ; Female ; Gastrointestinal Microbiome/*drug effects/genetics ; Gene Expression Regulation, Bacterial ; Intestines/*drug effects/microbiology ; Metagenome/*drug effects/genetics ; Mice, Inbred C57BL ; Ribotyping ; Sodium Compounds/*toxicity ; Time Factors ; }, abstract = {Multiple environmental factors induce dysbiosis in the gut microbiome and cause a variety of human diseases. Previously, we have first demonstrated that arsenic alters the composition of the gut microbiome. However, the functional impact of arsenic on the gut microbiome has not been adequately assessed, particularly at environmentally relevant concentrations. In this study, we used 16S rRNA sequencing and metagenomics sequencing to investigate how exposure to 100 ppb arsenic for 13 weeks alters the composition and functional capacity of the gut microbiome in mice. Arsenic exposure altered the alpha and beta diversities as well as the composition profile of the gut microbiota. Metagenomics data revealed that the abundances of genes involved in carbohydrate metabolism, especially pyruvate fermentation, short-chain fatty acid synthesis, and starch utilization, and were significantly changed. Moreover, lipopolysaccharide biosynthesis genes, multiple stress response genes, and DNA repair genes were significantly increased in the gut microbiome of arsenic-exposed mice. The genes involved in the production or processing of multiple vitamins, including folic acid and vitamins B6, B12, and K2, were also enriched in arsenic-treated mice. In, addition, genes involved in multidrug resistance and conjugative transposon proteins were highly increased after treatment with arsenic. In conclusion, we demonstrate that arsenic exposure, at an environmentally relevant dose, not only perturbed the communal composition of the gut microbiome but also profoundly altered a variety of important bacterial functional pathways.}, }
@article {pmid29232848, year = {2017}, author = {Vernocchi, P and Del Chierico, F and Quagliariello, A and Ercolini, D and Lucidi, V and Putignani, L}, title = {A Metagenomic and in Silico Functional Prediction of Gut Microbiota Profiles May Concur in Discovering New Cystic Fibrosis Patient-Targeted Probiotics.}, journal = {Nutrients}, volume = {9}, number = {12}, pages = {}, doi = {10.3390/nu9121342}, pmid = {29232848}, issn = {2072-6643}, mesh = {Bacteria/*genetics ; Case-Control Studies ; Child, Preschool ; Cystic Fibrosis/*microbiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics/*methods ; Phylogeny ; *Probiotics ; RNA, Ribosomal, 16S/analysis ; }, abstract = {Cystic fibrosis (CF) is a life-limiting hereditary disorder that results in aberrant mucosa in the lungs and digestive tract, chronic respiratory infections, chronic inflammation, and the need for repeated antibiotic treatments. Probiotics have been demonstrated to improve the quality of life of CF patients. We investigated the distribution of gut microbiota (GM) bacteria to identify new potential probiotics for CF patients on the basis of GM patterns. Fecal samples of 28 CF patients and 31 healthy controls (HC) were collected and analyzed by 16S rRNA-based pyrosequencing analysis of GM, to produce CF-HC paired maps of the distribution of operational taxonomic units (OTUs), and by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) for Kyoto Encyclopedia of Genes and Genomes (KEGG) biomarker prediction. The maps were scanned to highlight the distribution of bacteria commonly claimed as probiotics, such as bifidobacteria and lactobacilli, and of butyrate-producing colon bacteria, such as Eubacterium spp. and Faecalibacterium prausnitzii. The analyses highlighted 24 OTUs eligible as putative probiotics. Eleven and nine species were prevalently associated with the GM of CF and HC subjects, respectively. Their KEGG prediction provided differential CF and HC pathways, indeed associated with health-promoting biochemical activities in the latter case. GM profiling and KEGG biomarkers concurred in the evaluation of nine bacterial species as novel putative probiotics that could be investigated for the nutritional management of CF patients.}, }
@article {pmid29196353, year = {2017}, author = {Moffatt, MF and Cookson, WO}, title = {The lung microbiome in health and disease.}, journal = {Clinical medicine (London, England)}, volume = {17}, number = {6}, pages = {525-529}, doi = {10.7861/clinmedicine.17-6-525}, pmid = {29196353}, issn = {1473-4893}, mesh = {Asthma/microbiology ; Bronchiectasis/microbiology ; Cystic Fibrosis/microbiology ; Humans ; Lung/*microbiology ; Lung Diseases/*microbiology ; Metagenomics ; *Microbiota/genetics ; Pulmonary Disease, Chronic Obstructive/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The Human Microbiome Project began 10 years ago, leading to a significant growth in understanding of the role the human microbiome plays in health and disease. In this article, we explain with an emphasis on the lung, the origins of microbiome research. We discuss how 16S rRNA gene sequencing became the first major molecular tool to examine the bacterial communities present within the human body. We highlight the pitfalls of molecular-based studies, such as false findings resulting from contamination, and the limitations of 16S rRNA gene sequencing. Knowledge about the lung microbiome has evolved from initial scepticism to the realisation that it might have a significant influence on many illnesses. We also discuss the lung microbiome in the context of disease by giving examples of important respiratory conditions. In addition, we draw attention to the challenges for metagenomic studies of respiratory samples and the importance of systematic bacterial isolation to enable host-microbiome interactions to be understood. We conclude by discussing how knowledge of the lung microbiome impacts current clinical diagnostics.}, }
@article {pmid29301588, year = {2018}, author = {Greay, TL and Gofton, AW and Paparini, A and Ryan, UM and Oskam, CL and Irwin, PJ}, title = {Recent insights into the tick microbiome gained through next-generation sequencing.}, journal = {Parasites & vectors}, volume = {11}, number = {1}, pages = {12}, doi = {10.1186/s13071-017-2550-5}, pmid = {29301588}, issn = {1756-3305}, support = {130100050//Australian Research Council/International ; 130100050//Bayer Australia Ltd/International ; 130100050//Bayer AG (Germany)/International ; }, mesh = {Animals ; High-Throughput Nucleotide Sequencing/*utilization ; Metagenomics/*methods ; *Microbiota ; Ticks/*microbiology ; }, abstract = {The tick microbiome comprises communities of microorganisms, including viruses, bacteria and eukaryotes, and is being elucidated through modern molecular techniques. The advent of next-generation sequencing (NGS) technologies has enabled the genes and genomes within these microbial communities to be explored in a rapid and cost-effective manner. The advantages of using NGS to investigate microbiomes surpass the traditional non-molecular methods that are limited in their sensitivity, and conventional molecular approaches that are limited in their scalability. In recent years the number of studies using NGS to investigate the microbial diversity and composition of ticks has expanded. Here, we provide a review of NGS strategies for tick microbiome studies and discuss the recent findings from tick NGS investigations, including the bacterial diversity and composition, influential factors, and implications of the tick microbiome.}, }
@article {pmid29284535, year = {2017}, author = {Pires, ACAM and Villegas, LEM and Campolina, TB and Orfanó, AS and Pimenta, PFP and Secundino, NFC}, title = {Bacterial diversity of wild-caught Lutzomyia longipalpis (a vector of zoonotic visceral leishmaniasis in Brazil) under distinct physiological conditions by metagenomics analysis.}, journal = {Parasites & vectors}, volume = {10}, number = {1}, pages = {627}, doi = {10.1186/s13071-017-2593-7}, pmid = {29284535}, issn = {1756-3305}, support = {305512/2014-5//Brazilian Council for Scientific and Technological Development- CNPq- Research fellowship/International ; 308849/2015-9//Brazilian Council for Scientific and Technological Development- CNPq (Research fellowship)/International ; 00242-12//Fundação de Amparo à Pesquisa do Estado de Minas Gerais (BR) FAPEMIG/International ; }, mesh = {Animals ; Bacteria/*classification/*genetics ; Brazil ; *Gastrointestinal Microbiome ; Insect Vectors/*microbiology ; Metagenomics ; Psychodidae/*microbiology ; }, abstract = {BACKGROUND: The leishmaniases are a group of diseases caused by protozoans of the genus Leishmania, which are transmitted by the bite of phlebotomine sand flies. In the New World, Lutzomyia longipalpis is the most important vector of visceral leishmaniasis and is a proven vector for Leishmania infantum chagasi in Brazil. During development within the vector, Leishmania can interact with a variety of microorganisms such as fungi and bacteria. The presence of bacteria in the midgut of sand flies can influence the development and survival of the parasite.
RESULTS: The bacteria-targeted metagenomic analysis revealed different community compositions between the distinct physiological stages of those tested. The amplicon-oriented metagenomic profiling revealed 64 bacterial genera and 46 families. By crossing the taxa indices from each experimental condition a core composed of 6 genera was identified (Enterobacter, Serratia, Stenotrophomonas, Enhydrobacter, Pseudomonas and Chryseobacterium).
CONCLUSIONS: The observed dynamic nature of the bacterial community expands the knowledge pertaining to the tripartite host-microbiota-pathogen interactions. Further studies addressing how laboratory and field collected communities differ are critical to successfully develop control strategies based on bacterial symbionts and paratransgenesis, as already tested in other arthropod vectors.}, }
@article {pmid29187243, year = {2017}, author = {Boynton, FDD and Ericsson, AC and Uchihashi, M and Dunbar, ML and Wilkinson, JE}, title = {Doxycycline induces dysbiosis in female C57BL/6NCrl mice.}, journal = {BMC research notes}, volume = {10}, number = {1}, pages = {644}, doi = {10.1186/s13104-017-2960-7}, pmid = {29187243}, issn = {1756-0500}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Disease Models, Animal ; Doxycycline/*pharmacology ; Dysbiosis/*chemically induced ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Mice ; Mice, Inbred C57BL ; RNA, Ribosomal, 16S/genetics ; }, abstract = {OBJECTIVE: This study aims to demonstrate the effect of oral doxycycline on fecal microbiota of mice. Doxycycline is a common effector for control of gene expression using the tet-inducible system in transgenic mice. The effect of oral doxycycline on murine gut microbiota has not been reported. We evaluated the effect of doxycycline treatment by sequencing the V4 hypervariable region of the 16S rRNA gene from fecal samples collected during a 4 week course of treatment at a dose of 2 mg/ml in the drinking water.
RESULTS: The fecal microbiota of treated animals were distinct from control animals; the decreased richness and diversity were characterized primarily by Bacteroides sp. enrichment. These effects persisted when the treatment was temporarily discontinued for 1 week. These data suggest that doxycycline treatment can induce significant dysbiosis, and its effects should be considered when used in animal models that are or maybe sensitive to perturbation of the gut microbiota.}, }
@article {pmid28562180, year = {2018}, author = {Gutleben, J and Chaib De Mares, M and van Elsas, JD and Smidt, H and Overmann, J and Sipkema, D}, title = {The multi-omics promise in context: from sequence to microbial isolate.}, journal = {Critical reviews in microbiology}, volume = {44}, number = {2}, pages = {212-229}, doi = {10.1080/1040841X.2017.1332003}, pmid = {28562180}, issn = {1549-7828}, mesh = {Metabolomics/*methods ; Metagenomics/*methods ; Microbiological Techniques/*methods ; *Microbiota ; Proteomics/*methods ; }, abstract = {The numbers and diversity of microbes in ecosystems within and around us is unmatched, yet most of these microorganisms remain recalcitrant to in vitro cultivation. Various high-throughput molecular techniques, collectively termed multi-omics, provide insights into the genomic structure and metabolic potential as well as activity of complex microbial communities. Nonetheless, pure or defined cultures are needed to (1) decipher microbial physiology and thus test multi-omics-based ecological hypotheses, (2) curate and improve database annotations and (3) realize novel applications in biotechnology. Cultivation thus provides context. In turn, we here argue that multi-omics information awaits integration into the development of novel cultivation strategies. This can build the foundation for a new era of omics information-guided microbial cultivation technology and reduce the inherent trial-and-error search space. This review discusses how information that can be extracted from multi-omics data can be applied for the cultivation of hitherto uncultured microorganisms. Furthermore, we summarize groundbreaking studies that successfully translated information derived from multi-omics into specific media formulations, screening techniques and selective enrichments in order to obtain novel targeted microbial isolates. By integrating these examples, we conclude with a proposed workflow to facilitate future omics-aided cultivation strategies that are inspired by the microbial complexity of the environment.}, }
@article {pmid30018874, year = {2018}, author = {Colabella, C and Corte, L and Roscini, L and Bassetti, M and Tascini, C and Mellor, JC and Meyer, W and Robert, V and Vu, D and Cardinali, G}, title = {NGS barcode sequencing in taxonomy and diagnostics, an application in "Candida" pathogenic yeasts with a metagenomic perspective.}, journal = {IMA fungus}, volume = {9}, number = {1}, pages = {91-105}, doi = {10.5598/imafungus.2018.09.01.07}, pmid = {30018874}, issn = {2210-6340}, abstract = {Species identification of yeasts and other Fungi is currently carried out with Sanger sequences of selected molecular markers, mainly from the ribosomal DNA operon, characterized by hundreds of tandem repeats of the 18S, ITS1, 5.8S, ITS2 and LSU loci. The ITS region has been recently proposed as a primary barcode marker making this region the most used one in taxonomy, phylogeny and diagnostics. The introduction of NGS is providing tools of high efficacy and relatively low cost to amplify two or more markers simultaneously with great sequencing depth. However, the presence of intra-genomic variability between the repeats requires specific analytical procedures and pipelines. In this study, 286 strains belonging to 11 pathogenic yeasts species were analysed with NGS of the region spanning from ITS1 to the D1/D2 domain of the LSU encoding ribosomal DNA. Results showed that relatively high heterogeneity can hamper the use of these sequences for the identification of single strains and even more of complex microbial mixtures. These observations point out that the metagenomics studies could be affected by species inflection at levels higher than currently expected.}, }
@article {pmid30003485, year = {2018}, author = {Li, M and Zhang, X and Yang, H and Li, X and Cui, Z}, title = {Soil sustainable utilization technology: mechanism of flavonols in resistance process of heavy metal.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11356-018-2485-1}, pmid = {30003485}, issn = {1614-7499}, abstract = {The soil ecosystem is critical for agricultural production, affecting many aspects of human health. Soil has more unknown biodiversity and edaphic parameters than any other ecosystem especially when polluted. Metagenomics and metatranscriptomics were applied to research on toxicological characteristics of Pb and resistance mechanism of flavonols. Rhizosphere microorganisms-plants system, a unified system closely related to soil environment was taken as research object. Results emphasize gene expression changes in different test groups. Gene ontology enrichment and eggNOG showed that Pb has a toxic effect on gene and protein function which concentrated on ATPase and ATP-dependent activity. Differentially expressed genes in the flavonols group indicated that flavonols regulate amino acid transport and other transportation process related to Pb stress. Kegg analysis represents that Pb interferences energy production process via not only the upstream like glycolysis and tricarboxylic acid (TCA) circle but also oxidative phosphorylation process, which can also produce reactive oxygen species and impact the eliminating process. Flavonols have shown the ability in alleviating toxic effect of Pb and improving the resistance of plants. Flavonols can recover the electronic transmission and other process in TCA and oxidative phosphorylation via ascorbic acid-glutathione metabolism. Flavonols activated antioxidative process and non-specific immunity via vitamins B2-B6 metabolism.}, }
@article {pmid29976249, year = {2018}, author = {Kayani, MUR and Doyle, SM and Sangwan, N and Wang, G and Gilbert, JA and Christner, BC and Zhu, TF}, title = {Metagenomic analysis of basal ice from an Alaskan glacier.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {123}, doi = {10.1186/s40168-018-0505-5}, pmid = {29976249}, issn = {2049-2618}, support = {2016YFC0206300//Ministry of Science and Technology of the People's Republic of China/ ; }, abstract = {BACKGROUND: Glaciers cover ~ 10% of land but are among the least explored environments on Earth. The basal portion of glaciers often harbors unique aquatic microbial ecosystems in the absence of sunlight, and knowledge on the microbial community structures and their metabolic potential is very limited. Here, we provide insights into the microbial lifestyle present at the base of the Matanuska Glacier, Alaska.
RESULTS: DNA and RNA were extracted from samples of the Matanuska Glacier basal ice. Using Illumina MiSeq and HiSeq sequencing, we investigated the microbial diversity with the metagenomic shotgun reads and 16S ribosomal RNA data. We further assembled 9 partial and draft bacterial genomes from the metagenomic assembly, and identified key metabolic pathways such as sulfur oxidation and nitrification. Collectively, our analyses suggest a prevalence of lithotrophic and heterotrophic metabolisms in the subglacial microbiome.
CONCLUSION: Our results present the first metagenomic assembly and bacterial draft genomes for a subglacial environment. These results extend our understanding of the chemical and biological processes in subglacial environments critically influenced by global climate change.}, }
@article {pmid29964641, year = {2017}, author = {Wang, BQ and Li, CY and Lu, W and Fan, H and Zhang, DZ and Wang, Z and Lü, C and Shen, FD}, title = {[Shift of Microbial Communities During the CO2-Brine-Sandstone Interaction Process].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {38}, number = {7}, pages = {2978-2987}, doi = {10.13227/j.hjkx.201612067}, pmid = {29964641}, issn = {0250-3301}, abstract = {In this study, the dynamic variation of the structure, functionality and biodiversity of indigenous microorganism during the CO2-brine-sandstone interaction process was investigated using MiSeq sequencing techniques. The results indicated that some kinds of indigenous microorganisms could grow well under the extreme condition induced by CO2-injection. After injection of CO2, the species of indigenous microorganisms tended to be single and the relative abundance of Proteobacteria reached up to 99.77% after 6 months. The dominant species varied as follows:Pseudomonas sp., Citrobacter sp. and Brevundimonas sp.. Meanwhile, some special genera such as Bacillus sp., Hydrogenophaga sp. and Rhizobium sp. with functionality of iron-reducing and denitrification were found in this study, which may have a potential effect on the capture and storage of CO2. In addition, the Shannon index decreased from 5.3302 to 1.9465 after injection of CO2, suggesting that the biodiversity reduced significantly. Function and main metabolites analysis of bacteria in the CO2-brine-sandstone interaction process showed that bacteria like Bacillus sp., Citrobacter sp. and Pseudomonas sp. could enhance CO2 solubility-trapping process. Bacteria metabolisms could accelerate the dissolution of feldspar and chlorites, and facilitate the formation of transition-state calcite and siderite. Otherwise, the great variation was mainly attributed to the change of condition driven by CO2-brine-sandstone interactions, such as pH and the chemical composition of brine water(anion and cation), etc.}, }
@article {pmid29915700, year = {2018}, author = {Carew, ME and Coleman, RA and Hoffmann, AA}, title = {Can non-destructive DNA extraction of bulk invertebrate samples be used for metabarcoding?.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e4980}, doi = {10.7717/peerj.4980}, pmid = {29915700}, issn = {2167-8359}, abstract = {Background: High throughput DNA sequencing of bulk invertebrate samples or metabarcoding is becoming increasingly used to provide profiles of biological communities for environmental monitoring. As metabarcoding becomes more widely applied, new reference DNA barcodes linked to individual specimens identified by taxonomists are needed. This can be achieved through using DNA extraction methods that are not only suitable for metabarcoding but also for building reference DNA barcode libraries.
Methods: In this study, we test the suitability of a rapid non-destructive DNA extraction method for metabarcoding of freshwater invertebrate samples.
Results: This method resulted in detection of taxa from many taxonomic groups, comparable to results obtained with two other tissue-based extraction methods. Most taxa could also be successfully used for subsequent individual-based DNA barcoding and taxonomic identification. The method was successfully applied to field-collected invertebrate samples stored for taxonomic studies in 70% ethanol at room temperature, a commonly used storage method for freshwater samples.
Discussion: With further refinement and testing, non-destructive extraction has the potential to rapidly characterise species biodiversity in invertebrate samples, while preserving specimens for taxonomic investigation.}, }
@article {pmid29908593, year = {2018}, author = {Rastrojo, A and Alcamí, A}, title = {Viruses in Polar Lake and Soil Ecosystems.}, journal = {Advances in virus research}, volume = {101}, number = {}, pages = {39-54}, doi = {10.1016/bs.aivir.2018.02.002}, pmid = {29908593}, issn = {1557-8399}, abstract = {Viruses play an important role in the control of microbial communities, and it has been suggested that the influence of viruses in polar ecosystems, with low nutrients and under extreme environmental conditions, may be greater. Viral metagenomics allows the genetic characterization of complex viral communities without the need to isolate and grow viruses. Recent investigations in Antarctica and the Arctic are uncovering a great diversity of DNA viruses, including bacteriophages, circular single-stranded DNA viruses, algal-infecting phycodnaviruses, and virophages, adapted to these extreme environments. The limited sequence similarity between viruses in Antarctica and the Arctic suggests that viral communities in the two polar regions have evolved independently since the formation of the Antarctic continent, estimated to occur 25 million years ago. The community of RNA viruses in Antarctica is dominated by the order Picornavirales and their quasispecies composition suggests that higher genetic variability may correlate with viral adaptation to new environmental conditions.}, }
@article {pmid29874232, year = {2018}, author = {Higashi, K and Suzuki, S and Kurosawa, S and Mori, H and Kurokawa, K}, title = {Latent environment allocation of microbial community data.}, journal = {PLoS computational biology}, volume = {14}, number = {6}, pages = {e1006143}, doi = {10.1371/journal.pcbi.1006143}, pmid = {29874232}, issn = {1553-7358}, mesh = {Computational Biology/*methods ; Databases, Genetic ; Environmental Microbiology ; Humans ; Metagenomics ; *Microbiota/genetics/physiology ; Models, Statistical ; Rivers/microbiology ; }, abstract = {As data for microbial community structures found in various environments has increased, studies have examined the relationship between environmental labels given to retrieved microbial samples and their community structures. However, because environments continuously change over time and space, mixed states of some environments and its effects on community formation should be considered, instead of evaluating effects of discrete environmental categories. Here we applied a hierarchical Bayesian model to paired datasets containing more than 30,000 samples of microbial community structures and sample description documents. From the training results, we extracted latent environmental topics that associate co-occurring microbes with co-occurring word sets among samples. Topics are the core elements of environmental mixtures and the visualization of topic-based samples clarifies the connections of various environments. Based on the model training results, we developed a web application, LEA (Latent Environment Allocation), which provides the way to evaluate typicality and heterogeneity of microbial communities in newly obtained samples without confining environmental categories to be compared. Because topics link words and microbes, LEA also enables to search samples semantically related to the query out of 30,000 microbiome samples.}, }
@article {pmid29800679, year = {2018}, author = {Feranchuk, S and Belkova, N and Potapova, U and Kuzmin, D and Belikov, S}, title = {Evaluating the use of diversity indices to distinguish between microbial communities with different traits.}, journal = {Research in microbiology}, volume = {169}, number = {4-5}, pages = {254-261}, doi = {10.1016/j.resmic.2018.03.004}, pmid = {29800679}, issn = {1769-7123}, abstract = {Several measures of biodiversity are commonly used to describe microbial communities, analyzed using 16S gene sequencing. A wide range of available experiments on 16S gene sequencing allows us to present a framework for a comparison of various diversity indices. The criterion for the comparison is the statistical significance of the difference in index values for microbial communities with different traits, within the same experiment. The results of the evaluation indicate that Shannon diversity is the most effective measure among the commonly used diversity indices. The results also indicate that, within the present framework, the Gini coefficient as a diversity index is comparable to Shannon diversity, despite the fact that the Gini coefficient, as a diversity estimator, is far less popular in microbiology than several other measures.}, }
@article {pmid29758429, year = {2018}, author = {Najar, IN and Sherpa, MT and Das, S and Das, S and Thakur, N}, title = {Microbial ecology of two hot springs of Sikkim: Predominate population and geochemistry.}, journal = {The Science of the total environment}, volume = {637-638}, number = {}, pages = {730-745}, doi = {10.1016/j.scitotenv.2018.05.037}, pmid = {29758429}, issn = {1879-1026}, abstract = {Northeastern regions of India are known for their floral and faunal biodiversity. Especially the state of Sikkim lies in the eastern Himalayan ecological hotspot region. The state harbors many sulfur rich hot springs which have therapeutic and spiritual values. However, these hot springs are yet to be explored for their microbial ecology. The development of neo generation techniques such as metagenomics has provided an opportunity for inclusive study of microbial community of different environment. The present study describes the microbial diversity in two hot springs of Sikkim that is Polok and Borong with the assist of culture dependent and culture independent approaches. The culture independent techniques used in this study were next generation sequencing (NGS) and Phospholipid Fatty Acid Analysis (PLFA). Having relatively distinct geochemistry both the hot springs are thermophilic environments with the temperature range of 50-77 °C and pH range of 5-8. Metagenomic data revealed the dominance of bacteria over archaea. The most abundant phyla were Proteobacteria and Bacteroidetes although other phyla were also present such as Acidobacteria, Nitrospirae, Firmicutes, Proteobacteria, Parcubacteria and Spirochaetes. The PLFA studies have shown the abundance of Gram Positive bacteria followed by Gram negative bacteria. The culture dependent technique was correlative with PLFA studies. Most abundant bacteria as isolated and identified were Gram-positive genus Geobacillus and Anoxybacillus. The genus Geobacillus has been reported for the first time in North-Eastern states of India. The Geobacillus species obtained from the concerned hot springs were Geobacillus toebii, Geobacillus lituanicus, Geobacillus Kaustophillus and the Anoxybacillus species includes Anoxybacillus gonensis and Anoxybacillus Caldiproteolyticus. The distribution of major genera and their statistical correlation analyses with the geochemistry of the springs predicted that the temperature, pH, alkalinity, Ca2+, Mg2+, Cl2+, and sulfur were main environmental variables influencing the microbial community composition and diversity. Also the piper diagram suggested that the water of both the hot springs are Ca-HCO3- type and can be predicted as shallow fresh ground waters. This study has provided an insight into the ecological interaction of the diverse microbial communities and associated physicochemical parameters, which will help in determining the future studies on different biogeochemical pathways in these hot springs.}, }
@article {pmid29750384, year = {2018}, author = {Kosnicki, KL and Penprase, JC and Cintora, P and Torres, PJ and Harris, GL and Brasser, SM and Kelley, ST}, title = {Effects of moderate, voluntary ethanol consumption on the rat and human gut microbiome.}, journal = {Addiction biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/adb.12626}, pmid = {29750384}, issn = {1369-1600}, abstract = {Many alcohol-induced health complications are directly attributable to the toxicity of alcohol or its metabolites, but another potential health impact of alcohol may be on the microbial communities of the human gut. Clear distinctions between healthy and diseased-state gut microbiota have been observed in subjects with metabolic diseases, and recent studies suggest that chronic alcoholism is linked to gut microbiome dysbiosis. Here, we investigated the effects of moderate levels of alcohol consumption on the gut microbiome in both rats and humans. The gut microbiota of rats voluntarily consuming a 20 percent ethanol solution, on alternate days, were compared with a non-exposed control group to identify differential taxonomic and functional profiles. Gut microbial diversity profiles were determined using culture-independent amplification, next-generation sequencing and bioinformatic analysis of bacterial 16S ribosomal RNA gene sequence libraries. Our results showed that, compared with controls, ethanol-consuming rats experienced a significant decline in the biodiversity of their gut microbiomes, a state generally associated with dysbiosis. We also observed significant shifts in the overall diversity of the gut microbial communities and a dramatic change in the relative abundance of particular microbes, such as the Lactobacilli. We also compared our results to human fecal microbiome data collected as part of the citizen science American Gut Project. In contrast to the rat data, human drinkers had significantly higher gut microbial biodiversity than non-drinkers. However, we also observed that microbes that differed among the human subjects displayed similar trends in the rat model, including bacteria implicated in metabolic disease.}, }
@article {pmid29740407, year = {2018}, author = {Nooij, S and Schmitz, D and Vennema, H and Kroneman, A and Koopmans, MPG}, title = {Overview of Virus Metagenomic Classification Methods and Their Biological Applications.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {749}, doi = {10.3389/fmicb.2018.00749}, pmid = {29740407}, issn = {1664-302X}, abstract = {Metagenomics poses opportunities for clinical and public health virology applications by offering a way to assess complete taxonomic composition of a clinical sample in an unbiased way. However, the techniques required are complicated and analysis standards have yet to develop. This, together with the wealth of different tools and workflows that have been proposed, poses a barrier for new users. We evaluated 49 published computational classification workflows for virus metagenomics in a literature review. To this end, we described the methods of existing workflows by breaking them up into five general steps and assessed their ease-of-use and validation experiments. Performance scores of previous benchmarks were summarized and correlations between methods and performance were investigated. We indicate the potential suitability of the different workflows for (1) time-constrained diagnostics, (2) surveillance and outbreak source tracing, (3) detection of remote homologies (discovery), and (4) biodiversity studies. We provide two decision trees for virologists to help select a workflow for medical or biodiversity studies, as well as directions for future developments in clinical viral metagenomics.}, }
@article {pmid29718202, year = {2018}, author = {Wu, L and McCluskey, K and Desmeth, P and Liu, S and Hideaki, S and Yin, Y and Moriya, O and Itoh, T and Kim, CY and Lee, JS and Zhou, Y and Kawasaki, H and Hazbón, MH and Robert, V and Boekhout, T and Lima, N and Evtushenko, L and Boundy-Mills, K and Bunk, B and Moore, ERB and Eurwilaichitr, L and Ingsriswang, S and Shah, H and Yao, S and Jin, T and Huang, J and Shi, W and Sun, Q and Fan, G and Li, W and Li, X and Kurtböke, I and Ma, J}, title = {The global catalogue of microorganisms 10K type strain sequencing project: closing the genomic gaps for the validly published prokaryotic and fungi species.}, journal = {GigaScience}, volume = {7}, number = {5}, pages = {}, doi = {10.1093/gigascience/giy026}, pmid = {29718202}, issn = {2047-217X}, abstract = {Genomic information is essential for taxonomic, phylogenetic, and functional studies to comprehensively decipher the characteristics of microorganisms, to explore microbiomes through metagenomics, and to answer fundamental questions of nature and human life. However, large gaps remain in the available genomic sequencing information published for bacterial and archaeal species, and the gaps are even larger for fungal type strains. The Global Catalogue of Microorganisms (GCM) leads an internationally coordinated effort to sequence type strains and close gaps in the genomic maps of microorganisms. Hence, the GCM aims to promote research by deep-mining genomic data.}, }
@article {pmid29705130, year = {2018}, author = {Kudo, T and Kobiyama, A and Rashid, J and Reza, MS and Yamada, Y and Ikeda, Y and Ikeda, D and Mizusawa, N and Ikeo, K and Sato, S and Ogata, T and Jimbo, M and Kaga, S and Watanabe, S and Naiki, K and Kaga, Y and Segawa, S and Mineta, K and Bajic, V and Gojobori, T and Watabe, S}, title = {Seasonal changes in the abundance of bacterial genes related to dimethylsulfoniopropionate catabolism in seawater from Ofunato Bay revealed by metagenomic analysis.}, journal = {Gene}, volume = {665}, number = {}, pages = {174-184}, doi = {10.1016/j.gene.2018.04.072}, pmid = {29705130}, issn = {1879-0038}, mesh = {Animals ; *Bacteria/genetics/metabolism ; Bays/*microbiology ; *Genes, Bacterial ; Metagenomics/methods ; *Seasons ; Seawater/*microbiology ; Sulfonium Compounds/*metabolism ; *Water Microbiology ; }, abstract = {Ofunato Bay is located in the northeastern Pacific Ocean area of Japan, and it has the highest biodiversity of marine organisms in the world, primarily due to tidal influences from the cold Oyashio and warm Kuroshio Currents. Our previous results from performing shotgun metagenomics indicated that Candidatus Pelagibacter ubique and Planktomarina temperata were the dominant bacteria (Reza et al., 2018a, 2018b). These bacteria are reportedly able to catabolize dimethylsulfoniopropionate (DMSP) produced from phytoplankton into dimethyl sulfide (DMS) or methanethiol (MeSH). This study was focused on seasonal changes in the abundances of bacterial genes (dddP, dmdA) related to DMSP catabolism in the seawater of Ofunato Bay by BLAST+ analysis using shotgun metagenomic datasets. We found seasonal changes among the Candidatus Pelagibacter ubique strains, including those of the HTCC1062 type and the Red Sea type. A good correlation was observed between the chlorophyll a concentrations and the abundances of the catabolic genes, suggesting that the bacteria directly interact with phytoplankton in the marine material cycle system and play important roles in producing DMS and MeSH from DMSP as signaling molecules for the possible formation of the scent of the tidewater or as fish attractants.}, }
@article {pmid29705129, year = {2018}, author = {Reza, MS and Kobiyama, A and Yamada, Y and Ikeda, Y and Ikeda, D and Mizusawa, N and Ikeo, K and Sato, S and Ogata, T and Jimbo, M and Kudo, T and Kaga, S and Watanabe, S and Naiki, K and Kaga, Y and Mineta, K and Bajic, V and Gojobori, T and Watabe, S}, title = {Basin-scale seasonal changes in marine free-living bacterioplankton community in the Ofunato Bay.}, journal = {Gene}, volume = {665}, number = {}, pages = {185-191}, doi = {10.1016/j.gene.2018.04.074}, pmid = {29705129}, issn = {1879-0038}, mesh = {*Archaea/genetics/growth & development ; *Bacteria/genetics/growth & development ; Bays/*microbiology ; Microbial Consortia/*physiology ; *Plankton/genetics/growth & development ; *Seasons ; *Water Microbiology ; }, abstract = {The Ofunato Bay in the northeastern Pacific Ocean area of Japan possesses the highest biodiversity of marine organisms in the world and has attracted much attention due to its economic and environmental importance. We report here a shotgun metagenomic analysis of the year-round variation in free-living bacterioplankton collected across the entire length of the bay. Phylogenetic differences among spring, summer, autumn and winter bacterioplankton suggested that members of Proteobacteria tended to decrease at high water temperatures and increase at low temperatures. It was revealed that Candidatus Pelagibacter varied seasonally, reaching as much as 60% of all sequences at the genus level in the surface waters during winter. This increase was more evident in the deeper waters, where they reached up to 75%. The relative abundance of Planktomarina also rose during winter and fell during summer. A significant component of the winter bacterioplankton community was Archaea (mainly represented by Nitrosopumilus), as their relative abundance was very low during spring and summer but high during winter. In contrast, Actinobacteria and Cyanobacteria appeared to be higher in abundance during high-temperature periods. It was also revealed that Bacteroidetes constituted a significant component of the summer bacterioplankton community, being the second largest bacterial phylum detected in the Ofunato Bay. Its members, notably Polaribacter and Flavobacterium, were found to be high in abundance during spring and summer, particularly in the surface waters. Principal component analysis and hierarchal clustering analyses showed that the bacterial communities in the Ofunato Bay changed seasonally, likely caused by the levels of organic matter, which would be deeply mixed with surface runoff in the winter.}, }
@article {pmid29705124, year = {2018}, author = {Reza, MS and Kobiyama, A and Yamada, Y and Ikeda, Y and Ikeda, D and Mizusawa, N and Ikeo, K and Sato, S and Ogata, T and Jimbo, M and Kudo, T and Kaga, S and Watanabe, S and Naiki, K and Kaga, Y and Mineta, K and Bajic, V and Gojobori, T and Watabe, S}, title = {Taxonomic profiles in metagenomic analyses of free-living microbial communities in the Ofunato Bay.}, journal = {Gene}, volume = {665}, number = {}, pages = {192-200}, doi = {10.1016/j.gene.2018.04.075}, pmid = {29705124}, issn = {1879-0038}, mesh = {*Archaea/classification/genetics/growth & development ; *Bacteria/classification/genetics/growth & development ; Bays/*microbiology ; Metagenomics ; Microbial Consortia/*physiology ; *Seasons ; *Water Microbiology ; }, abstract = {The Ofunato Bay in Iwate Prefecture, Japan is a deep coastal bay located at the center of the Sanriku Rias Coast and considered an economically and environmentally important asset. Here, we describe the first whole genome sequencing (WGS) study on the microbial community of the bay, where surface water samples were collected from three stations along its length to cover the entire bay; we preliminarily sequenced a 0.2 μm filter fraction among sequentially size-fractionated samples of 20.0, 5.0, 0.8 and 0.2 μm filters, targeting the free-living fraction only. From the 0.27-0.34 Gb WGS library, 0.9 × 106-1.2 × 106 reads from three sampling stations revealed 29 bacterial phyla (~80% of assigned reads), 3 archaeal phyla (~4%) and 59 eukaryotic phyla (~15%). Microbial diversity obtained from the WGS approach was compared with 16S rRNA gene results by mining WGS metagenomes, and we found similar estimates. The most frequently recovered bacterial sequences were Proteobacteria, predominantly comprised of 18.0-19.6% Planktomarina (Family Rhodobacteraceae) and 13.7-17.5% Candidatus Pelagibacter (Family Pelagibacterales). Other dominant bacterial genera, including Polaribacter (3.5-6.1%), Flavobacterium (1.8-2.6%), Sphingobacterium (1.4-1.6%) and Cellulophaga (1.4-2.0%), were members of Bacteroidetes and likely associated with the degradation and turnover of organic matter. The Marine Group I Archaea Nitrosopumilus was also detected. Remarkably, eukaryotic green alga Bathycoccus, Ostreococcus and Micromonas accounted for 8.8-15.2%, 3.6-4.9% and 2.1-3.1% of total read counts, respectively, highlighting their potential roles in the phytoplankton bloom after winter mixing.}, }
@article {pmid29694379, year = {2018}, author = {Garris, HW and Baldwin, SA and Taylor, J and Gurr, DB and Denesiuk, DR and Van Hamme, JD and Fraser, LH}, title = {Short-term microbial effects of a large-scale mine-tailing storage facility collapse on the local natural environment.}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0196032}, doi = {10.1371/journal.pone.0196032}, pmid = {29694379}, issn = {1932-6203}, mesh = {Bacteria/*classification/genetics/metabolism ; Biodiversity ; Hydrogen-Ion Concentration ; Metagenomics/*methods ; Mining ; Nitrates/metabolism ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Soil/chemistry ; Water/chemistry ; Wetlands ; }, abstract = {We investigated the impacts of the Mount Polley tailings impoundment failure on chemical, physical, and microbial properties of substrates within the affected watershed, comprised of 70 hectares of riparian wetlands and 40 km of stream and lake shore. We established a biomonitoring network in October of 2014, two months following the disturbance, and evaluated riparian and wetland substrates for microbial community composition and function via 16S and full metagenome sequencing. A total of 234 samples were collected from substrates at 3 depths and 1,650,752 sequences were recorded in a geodatabase framework. These data revealed a wealth of information regarding watershed-scale distribution of microbial community members, as well as community composition, structure, and response to disturbance. Substrates associated with the impact zone were distinct chemically as indicated by elevated pH, nitrate, and sulphate. The microbial community exhibited elevated metabolic capacity for selenate and sulfate reduction and an abundance of chemolithoautotrophs in the Thiobacillus thiophilus/T. denitrificans/T. thioparus clade that may contribute to nitrate attenuation within the affected watershed. The most impacted area (a 6 km stream connecting two lakes) exhibited 30% lower microbial diversity relative to the remaining sites. The tailings impoundment failure at Mount Polley Mine has provided a unique opportunity to evaluate functional and compositional diversity soon after a major catastrophic disturbance to assess metabolic potential for ecosystem recovery.}, }
@article {pmid29694348, year = {2018}, author = {Hoffman, KL and Hutchinson, DS and Fowler, J and Smith, DP and Ajami, NJ and Zhao, H and Scheet, P and Chow, WH and Petrosino, JF and Daniel, CR}, title = {Oral microbiota reveals signs of acculturation in Mexican American women.}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0194100}, doi = {10.1371/journal.pone.0194100}, pmid = {29694348}, issn = {1932-6203}, support = {CA016672/NH/NIH HHS/United States ; R25CA057730/NH/NIH HHS/United States ; }, mesh = {*Acculturation ; Adult ; Aged ; Emigrants and Immigrants ; Female ; Fusobacterium/*isolation & purification ; Humans ; *Mexican Americans ; Microbiota/*physiology ; Middle Aged ; Mouth/*microbiology ; Prevotella/*isolation & purification ; Streptococcus/*isolation & purification ; Young Adult ; }, abstract = {The oral microbiome has been linked to a number of chronic inflammatory conditions, including obesity, diabetes, periodontitis, and cancers of the stomach and liver. These conditions disproportionately affect Mexican American women, yet few studies have examined the oral microbiota in this at-risk group. We characterized the 16S rDNA oral microbiome in 369 non-smoking women enrolled in the MD Anderson Mano a Mano Mexican American Cohort Study. Lower bacterial diversity, a potential indicator of oral health, was associated with increased age and length of US residency among recent immigrants. Grouping women by overarching bacterial community type (e.g., "Streptococcus," "Fusobacterium," and "Prevotella" clusters), we observed differences across a number of acculturation-related variables, including nativity, age at immigration, time in the US, country of longest residence, and a multi-dimensional acculturation scale. Participants in the cluster typified by higher abundance of Streptococcus spp. exhibited the lowest bacterial diversity and appeared the most acculturated as compared to women in the "Prevotella" group. Computationally-predicted functional analysis suggested the Streptococcus-dominated bacterial community had greater potential for carbohydrate metabolism while biosynthesis of essential amino acids and nitrogen metabolism prevailed among the Prevotella-high group. Findings suggest immigration and adaption to life in the US, a well-established mediator of disease risk, is associated with differences in oral microbial profiles in Mexican American women. These results warrant further investigation into the joint and modifying effects of acculturation and oral bacteria on the health of Mexican American women and other immigrant populations. The oral microbiome presents an easily accessible biomarker of disease risk, spanning biological, behavioral, and environmental factors.}, }
@article {pmid29668682, year = {2018}, author = {Hannigan, GD and Duhaime, MB and Koutra, D and Schloss, PD}, title = {Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome.}, journal = {PLoS computational biology}, volume = {14}, number = {4}, pages = {e1006099}, doi = {10.1371/journal.pcbi.1006099}, pmid = {29668682}, issn = {1553-7358}, support = {T32AI007528/NH/NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; P30DK034933/NH/NIH HHS/United States ; U01AI124255/NH/NIH HHS/United States ; U19AI09087/NH/NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; *Bacterial Physiological Phenomena ; Bacteriophages/*genetics/*physiology ; Computational Biology ; Diet ; Humans ; Metagenomics ; Microbial Consortia/genetics/physiology ; Microbiota/*genetics/*physiology ; Models, Biological ; Phylogeography ; Skin/microbiology/virology ; }, abstract = {Viruses and bacteria are critical components of the human microbiome and play important roles in health and disease. Most previous work has relied on studying bacteria and viruses independently, thereby reducing them to two separate communities. Such approaches are unable to capture how these microbial communities interact, such as through processes that maintain community robustness or allow phage-host populations to co-evolve. We implemented a network-based analytical approach to describe phage-bacteria network diversity throughout the human body. We built these community networks using a machine learning algorithm to predict which phages could infect which bacteria in a given microbiome. Our algorithm was applied to paired viral and bacterial metagenomic sequence sets from three previously published human cohorts. We organized the predicted interactions into networks that allowed us to evaluate phage-bacteria connectedness across the human body. We observed evidence that gut and skin network structures were person-specific and not conserved among cohabitating family members. High-fat diets appeared to be associated with less connected networks. Network structure differed between skin sites, with those exposed to the external environment being less connected and likely more susceptible to network degradation by microbial extinction events. This study quantified and contrasted the diversity of virome-microbiome networks across the human body and illustrated how environmental factors may influence phage-bacteria interactive dynamics. This work provides a baseline for future studies to better understand system perturbations, such as disease states, through ecological networks.}, }
@article {pmid29667329, year = {2018}, author = {Bista, I and Carvalho, GR and Tang, M and Walsh, K and Zhou, X and Hajibabaei, M and Shokralla, S and Seymour, M and Bradley, D and Liu, S and Christmas, M and Creer, S}, title = {Performance of amplicon and shotgun sequencing for accurate biomass estimation in invertebrate community samples.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.12888}, pmid = {29667329}, issn = {1755-0998}, abstract = {New applications of DNA and RNA sequencing are expanding the field of biodiversity discovery and ecological monitoring, yet questions remain regarding precision and efficiency. Due to primer bias, the ability of metabarcoding to accurately depict biomass of different taxa from bulk communities remains unclear, while PCR-free whole mitochondrial genome (mitogenome) sequencing may provide a more reliable alternative. Here, we used a set of documented mock communities comprising 13 species of freshwater macroinvertebrates of estimated individual biomass, to compare the detection efficiency of COI metabarcoding (three different amplicons) and shotgun mitogenome sequencing. Additionally, we used individual COI barcoding and de novo mitochondrial genome sequencing, to provide reference sequences for OTU assignment and metagenome mapping (mitogenome skimming), respectively. We found that, even though both methods occasionally failed to recover very low abundance species, metabarcoding was less consistent, by failing to recover some species with higher abundances, probably due to primer bias. Shotgun sequencing results provided highly significant correlations between read number and biomass in all but one species. Conversely, the read-biomass relationships obtained from metabarcoding varied across amplicons. Specifically, we found significant relationships for eight of 13 (amplicons B1FR-450 bp, FF130R-130 bp) or four of 13 (amplicon FFFR, 658 bp) species. Combining the results of all three COI amplicons (multiamplicon approach) improved the read-biomass correlations for some of the species. Overall, mitogenomic sequencing yielded more informative predictions of biomass content from bulk macroinvertebrate communities than metabarcoding. However, for large-scale ecological studies, metabarcoding currently remains the most commonly used approach for diversity assessment.}, }
@article {pmid29665523, year = {2018}, author = {Osimani, A and Milanović, V and Garofalo, C and Cardinali, F and Roncolini, A and Sabbatini, R and De Filippis, F and Ercolini, D and Gabucci, C and Petruzzelli, A and Tonucci, F and Clementi, F and Aquilanti, L}, title = {Revealing the microbiota of marketed edible insects through PCR-DGGE, metagenomic sequencing and real-time PCR.}, journal = {International journal of food microbiology}, volume = {276}, number = {}, pages = {54-62}, doi = {10.1016/j.ijfoodmicro.2018.04.013}, pmid = {29665523}, issn = {1879-3460}, mesh = {Animals ; *Biodiversity ; Denaturing Gradient Gel Electrophoresis ; *Food Microbiology ; High-Throughput Nucleotide Sequencing ; Insecta/*microbiology ; *Metagenomics ; Microbiota/genetics/*physiology ; RNA, Ribosomal, 16S/genetics ; *Real-Time Polymerase Chain Reaction ; Thailand ; }, abstract = {The present study aimed to identify the microbiota present in six species of processed edible insects produced in Thailand and marketed worldwide via the internet, namely, giant water bugs (Belostoma lutarium), black ants (Polyrhachis), winged termites (alates, Termitoidae), rhino beetles (Hyboschema contractum), mole crickets (Gryllotalpidae), and silkworm pupae (Bombyx mori). For each species, two samples of boiled, dried and salted insects were purchased. The microbial DNA was extracted from the insect samples and subjected to polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), high-throughput sequencing and qualitative real-time PCR assays. The microbiota of the analyzed samples were widely characterized by the presence of spore-forming bacteria mainly represented by the genera Bacillus and Clostridium. Moreover, the genera Anaerobacillus, Paenibacillus, Geobacillus, Pseudomonas, Stenotrophomonas, Massilia, Delftia, Lactobacillus, Staphylococcus, Streptococcus, Vagococcus, and Vibrio were also detected. Real-time PCR allowed for ascertainment of the absence of Coxiella burnetii, Shiga toxin-producing E. coli (STEC), and Pseudomonas aeruginosa in all samples. The results of this study confirm the importance of combining different molecular techniques to characterize the biodiversity of complex ecosystems such as edible insects. The presence of potential human pathogens suggests the need for a careful application of good manufacturing practices during insect processing. This study provides further data that will be useful in risk analyses of edible insects as a novel food source.}, }
@article {pmid29625974, year = {2018}, author = {Taboada, B and Isa, P and Gutiérrez-Escolano, AL and Del Ángel, RM and Ludert, JE and Vázquez, N and Tapia-Palacios, MA and Chávez, P and Garrido, E and Espinosa, AC and Eguiarte, LE and López, S and Souza, V and Arias, CF}, title = {The Geographic Structure of Viruses in the Cuatro Ciénegas Basin, a Unique Oasis in Northern Mexico, Reveals a Highly Diverse Population on a Small Geographic Scale.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {11}, pages = {}, doi = {10.1128/AEM.00465-18}, pmid = {29625974}, issn = {1098-5336}, abstract = {The Cuatro Ciénegas Basin (CCB) is located in the Chihuahuan desert in the Mexican state of Coahuila; it has been characterized as a site with high biological diversity despite its extreme oligotrophic conditions. It has the greatest number of endemic species in North America, containing abundant living microbialites (including stromatolites and microbial mats) and diverse microbial communities. With the hypothesis that this high biodiversity and the geographic structure should be reflected in the virome, the viral communities in 11 different locations of three drainage systems, Churince, La Becerra, and Pozas Rojas, and in the intestinal contents of 3 different fish species, were analyzed for both eukaryotic and prokaryotic RNA and DNA viruses using next-generation sequencing methods. Double-stranded DNA (dsDNA) virus families were the most abundant (72.5% of reads), followed by single-stranded DNA (ssDNA) viruses (2.9%) and ssRNA and dsRNA virus families (0.5%). Thirteen families had dsDNA genomes, five had ssDNA, three had dsRNA, and 16 had ssRNA. A highly diverse viral community was found, with an ample range of hosts and a strong geographical structure, with very even distributions and signals of endemicity in the phylogenetic trees from several different virus families. The majority of viruses found were bacteriophages but eukaryotic viruses were also frequent, and the large diversity of viruses related to algae were a surprise, since algae are not evident in the previously analyzed aquatic systems of this ecosystem. Animal viruses were also frequently found, showing the large diversity of aquatic animals in this oasis, where plants, protozoa, and archaea are rare.IMPORTANCE In this study, we tested whether the high biodiversity and geographic structure of CCB is reflected in its virome. CCB is an extraordinarily biodiverse oasis in the Chihuahuan desert, where a previous virome study suggested that viruses had followed the marine ancestry of the marine bacteria and, as a result of their long isolation, became endemic to the site. In this study, which includes a larger sequencing coverage and water samples from other sites within the valley, we confirmed the high virus biodiversity and uniqueness as well as the strong biogeographical diversification of the CCB. In addition, we also analyzed fish intestinal contents, finding that each fish species eats different prey and, as a result, presents different viral compositions even if they coexist in the same pond. These facts highlight the high and novel virus diversity of CCB and its "lost world" status.}, }
@article {pmid29624889, year = {2018}, author = {Michał, B and Gagat, P and Jabłoński, S and Chilimoniuk, J and Gaworski, M and Mackiewicz, P and Marcin, Ł}, title = {PhyMet2 : a database and toolkit for phylogenetic and metabolic analyses of methanogens.}, journal = {Environmental microbiology reports}, volume = {10}, number = {3}, pages = {378-382}, doi = {10.1111/1758-2229.12648}, pmid = {29624889}, issn = {1758-2229}, abstract = {The vast biodiversity of the microbial world and how little is known about it, has already been revealed by extensive metagenomics analyses. Our rudimentary knowledge of microbes stems from difficulties concerning their isolation and culture in laboratory conditions, which is necessary for describing their phenotype, among other things, for biotechnological purposes. An important component of the understudied ecosystems is methanogens, archaea producing a potent greenhouse-effect gas methane. Therefore, we created PhyMet2 , the first database that combines descriptions of methanogens and their culturing conditions with genetic information. The database contains a set of utilities that facilitate interactive data browsing, data comparison, phylogeny exploration and searching for sequence homologues. The most unique feature of the database is the web server MethanoGram, which can be used to significantly reduce the time and cost of searching for the optimal culturing conditions of methanogens by predicting them based on 16S RNA sequences. The database will aid many researchers in exploring the world of methanogens and their applications in biotechnological processes. PhyMet2 with the MethanoGram predictor is available at http://metanogen.biotech.uni.wroc.pl.}, }
@article {pmid29621268, year = {2018}, author = {Peoples, LM and Donaldson, S and Osuntokun, O and Xia, Q and Nelson, A and Blanton, J and Allen, EE and Church, MJ and Bartlett, DH}, title = {Vertically distinct microbial communities in the Mariana and Kermadec trenches.}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0195102}, doi = {10.1371/journal.pone.0195102}, pmid = {29621268}, issn = {1932-6203}, mesh = {Adaptation, Biological ; Biodiversity ; Geologic Sediments/*microbiology ; Hydrostatic Pressure ; Metagenome ; Metagenomics/methods ; *Microbiota ; *Oceans and Seas ; *Water Microbiology ; }, abstract = {Hadal trenches, oceanic locations deeper than 6,000 m, are thought to have distinct microbial communities compared to those at shallower depths due to high hydrostatic pressures, topographical funneling of organic matter, and biogeographical isolation. Here we evaluate the hypothesis that hadal trenches contain unique microbial biodiversity through analyses of the communities present in the bottom waters of the Kermadec and Mariana trenches. Estimates of microbial protein production indicate active populations under in situ hydrostatic pressures and increasing adaptation to pressure with depth. Depth, trench of collection, and size fraction are important drivers of microbial community structure. Many putative hadal bathytypes, such as members related to the Marinimicrobia, Rhodobacteraceae, Rhodospirilliceae, and Aquibacter, are similar to members identified in other trenches. Most of the differences between the two trench microbiomes consists of taxa belonging to the Gammaproteobacteria whose distributions extend throughout the water column. Growth and survival estimates of representative isolates of these taxa under deep-sea conditions suggest that some members may descend from shallower depths and exist as a potentially inactive fraction of the hadal zone. We conclude that the distinct pelagic communities residing in these two trenches, and perhaps by extension other trenches, reflect both cosmopolitan hadal bathytypes and ubiquitous genera found throughout the water column.}, }
@article {pmid29609258, year = {2018}, author = {Shao, DT and Wei, WW}, title = {[Progress in research of human microbiota for upper gastrointestinal tumors and precancerous lesions].}, journal = {Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi}, volume = {39}, number = {3}, pages = {382-386}, pmid = {29609258}, issn = {0254-6450}, mesh = {Esophageal Neoplasms/*microbiology ; *Gastrointestinal Microbiome ; Gastrointestinal Neoplasms/*microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; Lactobacillus ; Metagenomics/methods/trends ; *Microbiota ; Precancerous Conditions/*microbiology ; Prognosis ; Research/*trends ; Risk Factors ; Stomach Neoplasms/microbiology ; }, abstract = {With the widely application of the metagenomics, the relationship between microbiota and disease has become a hot research topic. Understanding the potential association between upper gastrointestinal cancer or precancerous lesions and microbiota may play an important role in the early detection, clinical diagnosis and treatment, and prognostic evaluation of upper gastrointestinal cancer. Therefore, a literature retrieval was conducted by using PubMed, Embase and wanfang databases to summarize the latest research progress in the microbiota of upper gastrointestinal cancer, including oral, esophageal, gastric cancer and precancerous lesions. Lower microbial diversity or richness in esophageal cancer and precancerous lesions and specific prognostic biomarkers for esophageal cancer were found. Lactobacillus richness showed an increase trend during the process from gastritis to gastric cancer. This paper summarizes the progress in the research of potential biological etiology of upper gastrointestinal cancer from the perspective of metagenomics in order to provide evidence on the, prevention and control of upper gastrointestinal cancer.}, }
@article {pmid29596453, year = {2018}, author = {Konstantinou, D and Gerovasileiou, V and Voultsiadou, E and Gkelis, S}, title = {Sponges-Cyanobacteria associations: Global diversity overview and new data from the Eastern Mediterranean.}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0195001}, doi = {10.1371/journal.pone.0195001}, pmid = {29596453}, issn = {1932-6203}, mesh = {Animals ; *Biodiversity ; Cyanobacteria/classification/genetics/*physiology ; Mediterranean Region ; Phylogeny ; Porifera/classification/genetics/*microbiology ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {Sponge-cyanobacteria associations have attracted research interest from an ecological, evolutionary and biotechnological perspective. Current knowledge is, in its majority, "hidden" in metagenomics research studying the entire microbial communities of sponges, while knowledge on these associations is totally missing for certain geographic areas. In this study, we (a) investigated the occurrence of cyanobacteria in 18 sponge species, several of which are studied for the first time for their cyanobionts, from a previously unexplored eastern Mediterranean ecoregion, the Aegean Sea, (b) isolated sponge-associated cyanobacteria, and characterized them based on a polyphasic (morphological-morphometric and molecular phylogenetic analysis) approach, and (c) conducted a meta-analysis on the global diversity of sponge species hosting cyanobacteria, as well as the diversity of cyanobacterial symbionts. Our research provided new records for nine sponge species, previously unknown for this association, while the isolated cyanobacteria were found to form novel clades within Synechococcus, Leptolyngbyaceae, Pseudanabaenaceae, and Schizotrichaceae, whose taxonomic status requires further investigation; this is the first report of a Schizotrichaceae cyanobacterium associated with sponges. The extensive evaluation of the literature along with the new data from the Aegean Sea raised the number of sponge species known for hosting cyanobacteria to 320 and showed that the cyanobacterial diversity reported from sponges is yet underestimated.}, }
@article {pmid29591722, year = {2018}, author = {Wilson, JJ and Brandon-Mong, GJ and Gan, HM and Sing, KW}, title = {High-throughput terrestrial biodiversity assessments: mitochondrial metabarcoding, metagenomics or metatranscriptomics?.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {}, number = {}, pages = {1-8}, doi = {10.1080/24701394.2018.1455189}, pmid = {29591722}, issn = {2470-1408}, abstract = {Consensus on the optimal high-throughput sequencing (HTS) approach to examine biodiversity in mixed terrestrial arthropod samples has not been reached. Metatranscriptomics could increase the proportion of taxonomically informative mitochondrial reads in HTS outputs but has not been investigated for terrestrial arthropod samples. We compared the efficiency of 16S rRNA metabarcoding, metagenomics and metatranscriptomics for detecting species in a mixed terrestrial arthropod sample (pooled DNA/RNA from 38 taxa). 16S rRNA metabarcoding and nuclear rRNA-depleted metatranscriptomics had the highest detection rate with 97% of input species detected. Based on cytochrome c oxidase I, metagenomics had the highest detection rate with 82% of input species detected, but metatranscriptomics produced a larger proportion of reads matching (Sanger) reference sequences. Metatranscriptomics with nuclear rRNA depletion may offer advantages over metabarcoding through reducing the number of spurious operational taxonomic units while retaining high detection rates, and offers natural enrichment of mitochondrial sequences which may enable increased species detection rates compared with metagenomics.}, }
@article {pmid29590046, year = {2018}, author = {Zhao, L and Zhang, F and Ding, X and Wu, G and Lam, YY and Wang, X and Fu, H and Xue, X and Lu, C and Ma, J and Yu, L and Xu, C and Ren, Z and Xu, Y and Xu, S and Shen, H and Zhu, X and Shi, Y and Shen, Q and Dong, W and Liu, R and Ling, Y and Zeng, Y and Wang, X and Zhang, Q and Wang, J and Wang, L and Wu, Y and Zeng, B and Wei, H and Zhang, M and Peng, Y and Zhang, C}, title = {Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes.}, journal = {Science (New York, N.Y.)}, volume = {359}, number = {6380}, pages = {1151-1156}, doi = {10.1126/science.aao5774}, pmid = {29590046}, issn = {1095-9203}, mesh = {Adult ; Aged ; Bacteria/classification/genetics/metabolism ; China ; Diabetes Mellitus, Type 2/*therapy ; Diet ; Dietary Fiber/*metabolism ; Fatty Acids, Volatile/*metabolism ; Feces ; Female ; Fermentation ; *Gastrointestinal Microbiome ; Glucagon-Like Peptide 1/metabolism ; Glycated Hemoglobin A/analysis ; Humans ; Hydrogen Sulfide/metabolism ; Indoles/metabolism ; Male ; Metagenomics ; Middle Aged ; }, abstract = {The gut microbiota benefits humans via short-chain fatty acid (SCFA) production from carbohydrate fermentation, and deficiency in SCFA production is associated with type 2 diabetes mellitus (T2DM). We conducted a randomized clinical study of specifically designed isoenergetic diets, together with fecal shotgun metagenomics, to show that a select group of SCFA-producing strains was promoted by dietary fibers and that most other potential producers were either diminished or unchanged in patients with T2DM. When the fiber-promoted SCFA producers were present in greater diversity and abundance, participants had better improvement in hemoglobin A1c levels, partly via increased glucagon-like peptide-1 production. Promotion of these positive responders diminished producers of metabolically detrimental compounds such as indole and hydrogen sulfide. Targeted restoration of these SCFA producers may present a novel ecological approach for managing T2DM.}, }
@article {pmid29572583, year = {2018}, author = {Verma, D and Garg, PK and Dubey, AK}, title = {Insights into the human oral microbiome.}, journal = {Archives of microbiology}, volume = {200}, number = {4}, pages = {525-540}, doi = {10.1007/s00203-018-1505-3}, pmid = {29572583}, issn = {1432-072X}, support = {SERB/LS-824/2013//Science and Engineering recruitment Board, New Delhi, India/ ; }, mesh = {Bacteria/genetics ; Health ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; Mouth/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Human oral cavity harbors the second most abundant microbiota after the gastrointestinal tract. The expanded Human Oral Microbiome Database (eHOMD) that was last updated on November 22, 2017, contains the information of approximately 772 prokaryotic species, where 70% is cultivable, and 30% belong to the uncultivable class of microorganisms along with whole genome sequences of 482 taxa. Out of 70% culturable species, 57% have already been assigned to their names. The 16S rDNA profiling of the healthy oral cavity categorized the inhabitant bacteria into six broad phyla, viz. Firmicutes, Actinobacteria, Proteobacteria, Fusobacteria, Bacteroidetes and Spirochaetes constituting 96% of total oral bacteria. These hidden oral micro-inhabitants exhibit a direct influence on human health, from host's metabolism to immune responses. Altered oral microflora has been observed in several diseases such as diabetes, bacteremia, endocarditis, cancer, autoimmune disease and preterm births. Therefore, it becomes crucial to understand the oral microbial diversity and how it fluctuates under diseased/perturbed conditions. Advances in metagenomics and next-generation sequencing techniques generate rapid sequences and provide extensive information of inhabitant microorganisms of a niche. Thus, the retrieved information can be utilized for developing microbiome-based biomarkers for their use in early diagnosis of oral and associated diseases. Besides, several apex companies have shown keen interest in oral microbiome for its diagnostic and therapeutic potential indicating a vast market opportunity. This review gives an insight of various associated aspects of the human oral microbiome.}, }
@article {pmid29566905, year = {2017}, author = {Jazayeri, O and Daghighi, SM and Rezaee, F}, title = {Lifestyle alters GUT-bacteria function: Linking immune response and host.}, journal = {Best practice & research. Clinical gastroenterology}, volume = {31}, number = {6}, pages = {625-635}, doi = {10.1016/j.bpg.2017.09.009}, pmid = {29566905}, issn = {1532-1916}, mesh = {Bacteria/*pathogenicity ; Bacterial Physiological Phenomena/*immunology ; Gastrointestinal Microbiome/*immunology ; Humans ; *Life Style ; Microbiota/*immunology ; }, abstract = {Microbiota in human is a "mixture society" of different species (i.e. bacteria, viruses, funguses) populations with a different way of relationship classification to Human. Human GUT serves as the host of the majority of different bacterial populations (GUT flora, more than 500 species), which are with us ("from the beginning") in an innate manner known as the commensal (no harm to each other) and symbiotic (mutual benefit) relationship. A homeostatic balance of host-bacteria relationship is very important and vital for a normal health process. However, this beneficial relationship and delicate homeostatic state can be disrupted by the imbalance of microbiome-composition of gut microbiota, expressing a pathogenic state. A strict homeostatic balance of microbiome-composition strongly depends on several factors; 1- lifestyle, 2- geography, 3- ethnicities, 4- "mom" as prime of the type of bacterial colonization in infant and 5- the disease. With such diversity in individuals combined with huge number of different bacterial species and their interactions, it is wise to perform an in-depth systems biology (e.g. genomics, proteomics, glycomics, and etcetera) analysis of personalized microbiome. Only in this way, we are able to generate a map of complete GUT microbiota and, in turn, to determine its interaction with host and intra-interaction with pathogenic bacteria. A specific microbiome analysis provides us the knowledge to decipher the nature of interactions between the GUT microbiota and the host and its response to the invading bacteria in a pathogenic state. The GUT-bacteria composition is independent of geography and ethnicity but lifestyle well affects GUT-bacteria composition and function. Microbiome knowledge obtained by systems biology also helps us to change the behavior of GUT microbiota in response to the pathogenic microbes as protection. Functional microbiome changes in response to environmental factors will be discussed in this review.}, }
@article {pmid29546438, year = {2018}, author = {Rua, CPJ and de Oliveira, LS and Froes, A and Tschoeke, DA and Soares, AC and Leomil, L and Gregoracci, GB and Coutinho, R and Hajdu, E and Thompson, CC and Berlinck, RGS and Thompson, FL}, title = {Microbial and Functional Biodiversity Patterns in Sponges that Accumulate Bromopyrrole Alkaloids Suggest Horizontal Gene Transfer of Halogenase Genes.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1172-6}, pmid = {29546438}, issn = {1432-184X}, support = {CNE E-26/110.735/2013//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; CIMAR 1986/2014//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; BIOTA/BIOprospecTA grant 2013/50228-8//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2014/17616- 7//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; }, abstract = {Marine sponge holobionts harbor complex microbial communities whose members may be the true producers of secondary metabolites accumulated by sponges. Bromopyrrole alkaloids constitute a typical class of secondary metabolites isolated from sponges that very often display biological activities. Bromine incorporation into secondary metabolites can be catalyzed by either halogenases or haloperoxidases. The diversity of the metagenomes of sponge holobiont species containing bromopyrrole alkaloids (Agelas spp. and Tedania brasiliensis) as well as holobionts devoid of bromopyrrole alkaloids spanning in a vast biogeographic region (approx. Seven thousand km) was studied. The origin and specificity of the detected halogenases was also investigated. The holobionts Agelas spp. and T. brasiliensis did not share microbial halogenases, suggesting a species-specific pattern. Bacteria of diverse phylogenetic origins encoding halogenase genes were found to be more abundant in bromopyrrole-containing sponges. The sponge holobionts (e.g., Agelas spp.) with the greatest number of sequences related to clustered, interspaced, short, palindromic repeats (CRISPRs) exhibited the fewest phage halogenases, suggesting a possible mechanism of protection from phage infection by the sponge host. This study highlights the potential of phages to transport halogenases horizontally across host sponges, particularly in more permissive holobiont hosts, such as Tedania spp.}, }
@article {pmid29544175, year = {2018}, author = {Wang, C and Jiang, K and Zhou, J and Wu, B}, title = {Solidago canadensis invasion affects soil N-fixing bacterial communities in heterogeneous landscapes in urban ecosystems in East China.}, journal = {The Science of the total environment}, volume = {631-632}, number = {}, pages = {702-713}, doi = {10.1016/j.scitotenv.2018.03.061}, pmid = {29544175}, issn = {1879-1026}, mesh = {Biodiversity ; China ; *Ecosystem ; Environmental Monitoring ; *Introduced Species ; Soil/chemistry ; *Soil Microbiology ; Solidago/*growth & development ; }, abstract = {Soil nitrogen-fixing bacterial communities (SNB) can increase the level of available soil N via biological N-fixation to facilitate successful invasion of several invasive plant species (IPS). Meanwhile, landscape heterogeneity can greatly enhance regional invasibility and increase the chances of successful invasion of IPS. Thus, it is important to understand the soil micro-ecological mechanisms driving the successful invasion of IPS in heterogeneous landscapes. This study performed cross-site comparisons, via metagenomics, to comprehensively analyze the effects of Solidago canadensis invasion on SNB in heterogeneous landscapes in urban ecosystems. Rhizospheric soil samples of S. canadensis were obtained from nine urban ecosystems [Three replicate quadrats (including uninvaded sites and invaded sites) for each type of urban ecosystem]. S. canadensis invasion did not significantly affect soil physicochemical properties, the taxonomic diversity of plant communities, or the diversity and richness of SNB. However, some SNB taxa (i.e., f_Micromonosporaceae, f_Oscillatoriaceae, and f_Bacillaceae) changed significantly with S. canadensis invasion. Thus, S. canadensis invasion may alter the community structure, rather than the diversity and richness of SNB, to facilitate its invasion process. Of the nine urban ecosystems, the diversity and richness of SNB was highest in farmland wasteland. Accordingly, the community invasibility of farmland wasteland may be higher than that of the other types of urban ecosystem. In brief, landscape heterogeneity, rather than S. canadensis invasion, was the strongest controlling factor for the diversity and richness of SNB. One possible reason may be the differences in soil electrical conductivity and the taxonomic diversity of plant communities in the nine urban ecosystems, which can cause notable shifts in the diversity and richness of SNB.}, }
@article {pmid29540269, year = {2018}, author = {Villamil, SI and Huerlimann, R and Morianos, C and Sarnyai, Z and Maes, GE}, title = {Adverse effect of early-life high-fat/high-carbohydrate ("Western") diet on bacterial community in the distal bowel of mice.}, journal = {Nutrition research (New York, N.Y.)}, volume = {50}, number = {}, pages = {25-36}, doi = {10.1016/j.nutres.2017.11.008}, pmid = {29540269}, issn = {1879-0739}, abstract = {Obesity and other lifestyle diseases in modern society can be related to historical dietary changes from diets balanced in omega-6 and omega-3 to the unbalanced "Western-type" diet. It is recognized that diet influences the murine and human gut microbiome, and most research indicates that microbial diversity and composition are altered by high-fat diets (HFDs). However, good knowledge about the effects of early exposure to HFD on the maturation and structure of the bacterial community is limited. Using mice as model, we hypothesized that an HFD alters the early dynamic of the gut bacterial community toward an unstable/unhealthy state. By sequencing the V3 and V4 regions of the 16S ribosomal ribonucleic acid gene, we investigated the bacterial community in fecal samples of mice fed a control diet and an HFD at weaning (sampling time 1) and after 8 weeks of dietary intervention (11weeks of age; sampling time 2). Natural temporal microbiome maturation was evidenced by a general increase in microbial diversity and shifts in microbial community between sampling times 1 and 2 toward a mature community. However, the HFD led to significant structural segregation of the microbiome compared with controls; the HFD diet repressed health-enhancing bacteria (eg, Bifidobacterium and Akkermansia) and promoted health-detracting bacteria (ie, those associated with gut disorders, eg, Dorea). We suggest that early-life consumption of HFD negatively impacts the natural gut bacterial community maturation leading toward a potentially persistent unhealthy stage.}, }
@article {pmid29526222, year = {2018}, author = {Andeta, AF and Vandeweyer, D and Woldesenbet, F and Eshetu, F and Hailemicael, A and Woldeyes, F and Crauwels, S and Lievens, B and Ceusters, J and Vancampenhout, K and Van Campenhout, L}, title = {Fermentation of enset (Ensete ventricosum) in the Gamo highlands of Ethiopia: Physicochemical and microbial community dynamics.}, journal = {Food microbiology}, volume = {73}, number = {}, pages = {342-350}, doi = {10.1016/j.fm.2018.02.011}, pmid = {29526222}, issn = {1095-9998}, mesh = {Biodiversity ; Clostridium/classification/genetics/isolation & purification/metabolism ; Ethiopia ; Fermentation ; Hydrogen-Ion Concentration ; Lactobacillales/classification/*isolation & purification/metabolism ; Musaceae/chemistry/metabolism/*microbiology ; Temperature ; }, abstract = {Enset (Ensete ventricosum) provides staple food for 15 million people in Ethiopia after fermentation into kocho. The fermentation process has hardly been investigated and is prone to optimization. The aim of this study was to investigate the physicochemical and microbial dynamics of fermentation practices in the Gamo highlands. These practices show local variation, but two steps were omnipresent: scraping of the pseudostem and fermenting it in a pit or a bamboo basket. Enset plants were fragmented and fermented for two months in order to investigate the physicochemical (temperature, moisture content, pH and titratable acidity) and microbial dynamics (total viable aerobic counts, counts of Enterobacteriaceae, lactic acid bacteria, yeasts and moulds and Clostridium spores counts, and Illumina Miseq sequencing). Samples were taken on days 1, 7, 15, 17, 31 and 60. The pH decreased, whereas the titratable acidity increased during fermentation. Of all counts those of lactic acid bacteria and Clostridium spores increased during fermentation. Leuconostoc mesenteroides initiated the fermentation. Later on, Prevotella paludivivens, Lactobacillus sp. and Bifidobacterium minimum dominated. These three species are potential candidates for the development of a starter culture.}, }
@article {pmid29523545, year = {2018}, author = {Patin, NV and Pratte, ZA and Regensburger, M and Hall, E and Gilde, K and Dove, ADM and Stewart, FJ}, title = {Microbiome Dynamics in a Large Artificial Seawater Aquarium.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {10}, pages = {}, doi = {10.1128/AEM.00179-18}, pmid = {29523545}, issn = {1098-5336}, abstract = {Artificial habitats for animals have high commercial and societal value. Microbial communities (microbiomes) in such habitats may play ecological roles similar to those in nature. However, this hypothesis remains largely untested. Georgia Aquarium's Ocean Voyager (OV) exhibit is a closed-system aquatic habitat that mimics the oligotrophic open ocean and houses thousands of large marine animals, including fish, sea turtles, and whale sharks. We present a 14-month time series characterizing the OV water column microbiome. The composition and stability of the microbiome differed from those of natural marine environments with similar chemical features. The composition shifted dramatically over the span of 2 weeks and was characterized by bloom events featuring members of two heterotrophic bacterial lineages with cosmopolitan distributions in the oceans. The relative abundances of these lineages were inversely correlated, suggesting an overlap in ecological niches. Transcript mapping to metagenome-assembled genomes (MAGs) of these taxa identified unique characteristics, including the presence and activity of genes for the synthesis and degradation of cyanophycin, an amino acid polymer linked to environmental stress and found frequently in cyanobacteria but rarely in heterotrophic bacteria. The dominant MAGs also contained and transcribed plasmid-associated sequences, suggesting a role for conjugation in adaptation to the OV environment. These findings indicate a highly dynamic microbiome despite the stability of the physical and chemical parameters of the water column. Characterizing how such fluctuations affect microbial function may inform our understanding of animal health in closed aquaculture systems.IMPORTANCE Public aquariums play important societal roles, for example, by promoting science education and helping conserve biodiversity. The health of aquarium animals depends on interactions with the surrounding microbiome. However, the extent to which aquariums recreate a stable and natural microbial ecosystem is uncertain. This study describes the taxonomic composition of the water column microbiome over 14 months in a large indoor aquatic habitat, the Ocean Voyager exhibit at the Georgia Aquarium. Despite stable water column conditions, the exhibit experienced blooms in which the abundance of a single bacterial strain increased to over 65% of the community. Genome analysis indicated that the OV's dominant strains share unique adaptations, notably genes for storage polymers associated with environmental stress. These results, interpreted alongside data from natural ocean systems and another artificial seawater aquarium, suggest a highly dynamic aquarium microbiome and raise questions of how microbiome stability may affect the ecological health of the habitat.}, }
@article {pmid29522953, year = {2018}, author = {Cai, L and Chen, TB and Zheng, SW and Liu, HT and Zheng, GD}, title = {Decomposition of lignocellulose and readily degradable carbohydrates during sewage sludge biodrying, insights of the potential role of microorganisms from a metagenomic analysis.}, journal = {Chemosphere}, volume = {201}, number = {}, pages = {127-136}, doi = {10.1016/j.chemosphere.2018.02.177}, pmid = {29522953}, issn = {1879-1298}, mesh = {Carbohydrate Metabolism ; Carbohydrates/*analysis ; Hot Temperature ; Lignin/*analysis ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; Sewage/*chemistry/microbiology ; Waste Disposal, Fluid/*methods ; }, abstract = {Sewage sludge biodrying is a waste treatment method that uses bio-heat generated from organic degradation to remove moisture from sewage sludge. Lignocellulose and carbohydrate decomposition is important when assessing biodrying performance. This study investigated lignocellulose and carbohydrate decomposition, and the potential microbial functions during biodrying. We determined the lignocellulose and carbohydrate contents, assayed related enzyme activity, performed a complete metagenomic study on sewage sludge biodrying material during the thermophilic phase, annotated potential genetic function involved in the decomposition, and summarized the key metabolic pathways. The results indicated that lignocellulose, readily degradable carbohydrates, and starch, significantly decomposed after biodrying. During the thermophilic phase, the majority of lignocellulose and carbohydrate-related enzymes showed significantly higher activity, and glycoside hydrolases and glycosyl transferases showed higher gene counts and reads. Moreover, the top five microorganisms enriched with carbohydrate-active enzyme genes, i.e., Bacillus, Intrasporangium, Tetrasphaera, Rhodobacter, and Streptomyces, were also among the top ten ecologically dominant genera. These findings highlight the crucial phases for biodrying process, reveal the ecologically functional diversity of biodrying-originated microbial consortia, and suggest potential candidates for optimizing biodrying decomposition.}, }
@article {pmid29515540, year = {2018}, author = {Cuadrat, RRC and Ionescu, D and Dávila, AMR and Grossart, HP}, title = {Recovering Genomics Clusters of Secondary Metabolites from Lakes Using Genome-Resolved Metagenomics.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {251}, doi = {10.3389/fmicb.2018.00251}, pmid = {29515540}, issn = {1664-302X}, abstract = {Metagenomic approaches became increasingly popular in the past decades due to decreasing costs of DNA sequencing and bioinformatics development. So far, however, the recovery of long genes coding for secondary metabolites still represents a big challenge. Often, the quality of metagenome assemblies is poor, especially in environments with a high microbial diversity where sequence coverage is low and complexity of natural communities high. Recently, new and improved algorithms for binning environmental reads and contigs have been developed to overcome such limitations. Some of these algorithms use a similarity detection approach to classify the obtained reads into taxonomical units and to assemble draft genomes. This approach, however, is quite limited since it can classify exclusively sequences similar to those available (and well classified) in the databases. In this work, we used draft genomes from Lake Stechlin, north-eastern Germany, recovered by MetaBat, an efficient binning tool that integrates empirical probabilistic distances of genome abundance, and tetranucleotide frequency for accurate metagenome binning. These genomes were screened for secondary metabolism genes, such as polyketide synthases (PKS) and non-ribosomal peptide synthases (NRPS), using the Anti-SMASH and NAPDOS workflows. With this approach we were able to identify 243 secondary metabolite clusters from 121 genomes recovered from our lake samples. A total of 18 NRPS, 19 PKS, and 3 hybrid PKS/NRPS clusters were found. In addition, it was possible to predict the partial structure of several secondary metabolite clusters allowing for taxonomical classifications and phylogenetic inferences. Our approach revealed a high potential to recover and study secondary metabolites genes from any aquatic ecosystem.}, }
@article {pmid29511180, year = {2018}, author = {Hu, Y and Sanders, JG and Łukasik, P and D'Amelio, CL and Millar, JS and Vann, DR and Lan, Y and Newton, JA and Schotanus, M and Kronauer, DJC and Pierce, NE and Moreau, CS and Wertz, JT and Engel, P and Russell, JA}, title = {Herbivorous turtle ants obtain essential nutrients from a conserved nitrogen-recycling gut microbiome.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {964}, doi = {10.1038/s41467-018-03357-y}, pmid = {29511180}, issn = {2041-1723}, mesh = {Amino Acids/metabolism ; Ammonia/metabolism ; Animals ; Ants/*microbiology/*physiology ; Diet ; *Gastrointestinal Microbiome/genetics ; Geography ; Herbivory/*physiology ; Metagenome ; Metagenomics ; Nitrogen/*metabolism ; Nitrogen Fixation/genetics ; Nitrogen Isotopes ; Symbiosis ; Urea/metabolism ; Urease/metabolism ; Uric Acid/metabolism ; }, abstract = {Nitrogen acquisition is a major challenge for herbivorous animals, and the repeated origins of herbivory across the ants have raised expectations that nutritional symbionts have shaped their diversification. Direct evidence for N provisioning by internally housed symbionts is rare in animals; among the ants, it has been documented for just one lineage. In this study we dissect functional contributions by bacteria from a conserved, multi-partite gut symbiosis in herbivorous Cephalotes ants through in vivo experiments, metagenomics, and in vitro assays. Gut bacteria recycle urea, and likely uric acid, using recycled N to synthesize essential amino acids that are acquired by hosts in substantial quantities. Specialized core symbionts of 17 studied Cephalotes species encode the pathways directing these activities, and several recycle N in vitro. These findings point to a highly efficient N economy, and a nutritional mutualism preserved for millions of years through the derived behaviors and gut anatomy of Cephalotes ants.}, }
@article {pmid29498741, year = {2018}, author = {Valeriani, F and Crognale, S and Protano, C and Gianfranceschi, G and Orsini, M and Vitali, M and Spica, VR}, title = {Metagenomic analysis of bacterial community in a travertine depositing hot spring.}, journal = {The new microbiologica}, volume = {41}, number = {2}, pages = {126-135}, pmid = {29498741}, issn = {1121-7138}, mesh = {Bacteria/*genetics/isolation & purification ; Biodiversity ; Computational Biology ; DNA, Bacterial/genetics ; Hot Springs/*microbiology ; Metagenomics/*methods ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; *Water Microbiology ; }, abstract = {Several factors influence bacteria biodiversity in hot springs. The impact of biotic and abiotic pathways on travertine deposition plays a key role in microbial ecology and in the final composition of the waterborne microbiota. The metabolism of some bacterial groups such as photoautotrophs or lithoautotrophs influences water chemistry, favoring carbonate precipitation processes. The role of microbial mats in mineral precipitation processes is not fully clarified. For the first time, a comprehensive metagenomic analysis has been undertaken in the historical Bullicame hot spring. Bacterial biodiversity was characterized and biomineralization activities were assigned to different genera. A higher biodiversity in mat samples compared to water samples was observed: Shannon index of 3.34 and 0.86, respectively. Based on the functional assignment of each Operational Taxonomic Unit, the bacteria involved in biologically- induced mineralization are prevalent in mat and released in the water. According to the principle that each geothermal water specimen has distinctive physic-chemical characteristics, our results suggest new interacting bio-actions within these ecosystems. The saturation index and the chemical composition, as the high concentration of sulfur species and HCO3, can be linked to create a selective environment where pioneer communities are able to live and shape the ecosystem.}, }
@article {pmid29497412, year = {2018}, author = {Garrido-Sanz, D and Manzano, J and Martín, M and Redondo-Nieto, M and Rivilla, R}, title = {Metagenomic Analysis of a Biphenyl-Degrading Soil Bacterial Consortium Reveals the Metabolic Roles of Specific Populations.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {232}, doi = {10.3389/fmicb.2018.00232}, pmid = {29497412}, issn = {1664-302X}, abstract = {Polychlorinated biphenyls (PCBs) are widespread persistent pollutants that cause several adverse health effects. Aerobic bioremediation of PCBs involves the activity of either one bacterial species or a microbial consortium. Using multiple species will enhance the range of PCB congeners co-metabolized since different PCB-degrading microorganisms exhibit different substrate specificity. We have isolated a bacterial consortium by successive enrichment culture using biphenyl (analog of PCBs) as the sole carbon and energy source. This consortium is able to grow on biphenyl, benzoate, and protocatechuate. Whole-community DNA extracted from the consortium was used to analyze biodiversity by Illumina sequencing of a 16S rRNA gene amplicon library and to determine the metagenome by whole-genome shotgun Illumina sequencing. Biodiversity analysis shows that the consortium consists of 24 operational taxonomic units (≥97% identity). The consortium is dominated by strains belonging to the genus Pseudomonas, but also contains betaproteobacteria and Rhodococcus strains. whole-genome shotgun (WGS) analysis resulted in contigs containing 78.3 Mbp of sequenced DNA, representing around 65% of the expected DNA in the consortium. Bioinformatic analysis of this metagenome has identified the genes encoding the enzymes implicated in three pathways for the conversion of biphenyl to benzoate and five pathways from benzoate to tricarboxylic acid (TCA) cycle intermediates, allowing us to model the whole biodegradation network. By genus assignment of coding sequences, we have also been able to determine that the three biphenyl to benzoate pathways are carried out by Rhodococcus strains. In turn, strains belonging to Pseudomonas and Bordetella are the main responsible of three of the benzoate to TCA pathways while the benzoate conversion into TCA cycle intermediates via benzoyl-CoA and the catechol meta-cleavage pathways are carried out by beta proteobacteria belonging to genera such as Achromobacter and Variovorax. We have isolated a Rhodococcus strain WAY2 from the consortium which contains the genes encoding the three biphenyl to benzoate pathways indicating that this strain is responsible for all the biphenyl to benzoate transformations. The presented results show that metagenomic analysis of consortia allows the identification of bacteria active in biodegradation processes and the assignment of specific reactions and pathways to specific bacterial groups.}, }
@article {pmid29494648, year = {2018}, author = {Bhogoju, S and Nahashon, S and Wang, X and Darris, C and Kilonzo-Nthenge, A}, title = {A comparative analysis of microbial profile of Guinea fowl and chicken using metagenomic approach.}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0191029}, doi = {10.1371/journal.pone.0191029}, pmid = {29494648}, issn = {1932-6203}, mesh = {Animal Feed ; Animals ; Galliformes/genetics/*microbiology ; Gastrointestinal Microbiome/*genetics ; *Metagenome ; Metagenomics ; Phylogeny ; Poultry/genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; }, abstract = {Probiotics are live microbial feed supplements that promote growth and health to the host by minimizing non-essential and pathogenic microorganisms in the host's gastrointestinal tract (GIT). The campaign to minimize excessive use of antibiotics in poultry production has necessitated development of probiotics with broad application in multiple poultry species. Design of such probiotics requires understanding of the diversity or similarity in microbial profiles among avian species of economic importance. Therefore, the objective of this research was to establish and compare the microbial profiles of the GIT of Guinea fowl and chicken and to establish the microbial diversity or similarity between the two avian species. A metagenomic approach consisting of the amplification and sequence analysis of the hypervariable regions V1-V9 of the 16S rRNA gene was used to identify the GIT microbes. Collectively, we detected more than 150 microbial families. The total number of microbial species detected in the chicken GIT was higher than that found in the Guinea Fowl GIT. Our studies also revealed phylogenetic diversity among the microbial species found in chicken and guinea fowl. The phylum Firmicutes was most abundant in both avian species whereas Phylum Actinobacteria was most abundant in chickens than Guinea fowls. The diversity of the microbial profiles found in broiler chickens and Guinea fowls suggest that the design of effective avian probiotics would require species specificity.}, }
@article {pmid29486880, year = {2018}, author = {Bodewes, R}, title = {Novel viruses in birds: Flying through the roof or is a cage needed?.}, journal = {Veterinary journal (London, England : 1997)}, volume = {233}, number = {}, pages = {55-62}, doi = {10.1016/j.tvjl.2017.12.023}, pmid = {29486880}, issn = {1532-2971}, mesh = {Animals ; Animals, Domestic/virology ; Animals, Wild/virology ; Bird Diseases/virology ; Birds/*virology ; Chickens/virology ; Columbidae/virology ; Ducks/virology ; Endangered Species ; Virus Diseases/veterinary ; Viruses/isolation & purification/pathogenicity ; }, abstract = {Emerging viral diseases continue to have a major global impact on human beings and animals. To be able to take adequate measures in case of an outbreak of an emerging disease, rapid detection of the causative agent is a crucial first step. In this review, various aspects of virus discovery are discussed, with a special focus on recently discovered viruses in birds. Novel viruses with a potential major impact have been discovered in domestic and wild bird species in recent years using various virus discovery methods. Only a few studies report the detection of novel viruses in endangered bird species, although increased knowledge about viruses circulating in these species is important. Additional studies focusing on the exact role of a novel virus in disease and on the impact of a novel virus on bird populations are often lacking. Intensive collaboration between different disciplines is needed to obtain useful information about the role of these novel viruses.}, }
@article {pmid29474068, year = {2018}, author = {Lu, T and Ke, M and Peijnenburg, WJGM and Zhu, Y and Zhang, M and Sun, L and Fu, Z and Qian, H}, title = {Investigation of Rhizospheric Microbial Communities in Wheat, Barley, and Two Rice Varieties at the Seedling Stage.}, journal = {Journal of agricultural and food chemistry}, volume = {66}, number = {11}, pages = {2645-2653}, doi = {10.1021/acs.jafc.7b06155}, pmid = {29474068}, issn = {1520-5118}, mesh = {Bacteria/classification/genetics/*isolation & purification ; Biodiversity ; Hordeum/*growth & development/microbiology ; Oryza/*growth & development/microbiology ; Rhizosphere ; Seedlings/growth & development/microbiology ; *Soil Microbiology ; Triticum/*growth & development/microbiology ; }, abstract = {The plant rhizosphere microbiota plays multiple roles in plant growth. We investigated the taxonomic and functional variations in the rhizosphere microbial community, examining both prokaryotes and eukaryotes, of four crops at the seedling stage: wheat, barley, and two rice varieties (indica and japonica) seeded in paddy soil. The diversity of rhizosphere communities in these four species was determined. Results showed that wheat and barley had much stronger selection effects than rice for the rhizosphere microbial community. Functional metagenomic profiling indicated that a series of sequences related to glycan, limonene, and pinene degradation pathways as well as some relatively rare functions related to N or S metabolism were enriched in the rhizosphere soil. We conclude that the four tested crops induced the formation of the microbial community with specific features that may influence the plant growth but stochastic processes also appreciably influenced the functional selection.}, }
@article {pmid29472560, year = {2018}, author = {Taş, N and Prestat, E and Wang, S and Wu, Y and Ulrich, C and Kneafsey, T and Tringe, SG and Torn, MS and Hubbard, SS and Jansson, JK}, title = {Landscape topography structures the soil microbiome in arctic polygonal tundra.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {777}, doi = {10.1038/s41467-018-03089-z}, pmid = {29472560}, issn = {2041-1723}, mesh = {Arctic Regions ; Bacteria/classification/genetics/*isolation & purification/metabolism ; Carbon/metabolism ; Climate Change ; Methane/metabolism ; *Microbiota ; Permafrost/*microbiology ; Soil/chemistry ; Soil Microbiology ; Tundra ; }, abstract = {In the Arctic, environmental factors governing microbial degradation of soil carbon (C) in active layer and permafrost are poorly understood. Here we determined the functional potential of soil microbiomes horizontally and vertically across a cryoperturbed polygonal landscape in Alaska. With comparative metagenomics, genome binning of novel microbes, and gas flux measurements we show that microbial greenhouse gas (GHG) production is strongly correlated to landscape topography. Active layer and permafrost harbor contrasting microbiomes, with increasing amounts of Actinobacteria correlating with decreasing soil C in permafrost. While microbial functions such as fermentation and methanogenesis were dominant in wetter polygons, in drier polygons genes for C mineralization and CH4 oxidation were abundant. The active layer microbiome was poised to assimilate N and not to release N2O, reflecting low N2O flux measurements. These results provide mechanistic links of microbial metabolism to GHG fluxes that are needed for the refinement of model predictions.}, }
@article {pmid29463661, year = {2018}, author = {He, Z and Zhang, P and Wu, L and Rocha, AM and Tu, Q and Shi, Z and Wu, B and Qin, Y and Wang, J and Yan, Q and Curtis, D and Ning, D and Van Nostrand, JD and Wu, L and Yang, Y and Elias, DA and Watson, DB and Adams, MWW and Fields, MW and Alm, EJ and Hazen, TC and Adams, PD and Arkin, AP and Zhou, J}, title = {Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning.}, journal = {mBio}, volume = {9}, number = {1}, pages = {}, doi = {10.1128/mBio.02435-17}, pmid = {29463661}, issn = {2150-7511}, abstract = {Contamination from anthropogenic activities has significantly impacted Earth's biosphere. However, knowledge about how environmental contamination affects the biodiversity of groundwater microbiomes and ecosystem functioning remains very limited. Here, we used a comprehensive functional gene array to analyze groundwater microbiomes from 69 wells at the Oak Ridge Field Research Center (Oak Ridge, TN), representing a wide pH range and uranium, nitrate, and other contaminants. We hypothesized that the functional diversity of groundwater microbiomes would decrease as environmental contamination (e.g., uranium or nitrate) increased or at low or high pH, while some specific populations capable of utilizing or resistant to those contaminants would increase, and thus, such key microbial functional genes and/or populations could be used to predict groundwater contamination and ecosystem functioning. Our results indicated that functional richness/diversity decreased as uranium (but not nitrate) increased in groundwater. In addition, about 5.9% of specific key functional populations targeted by a comprehensive functional gene array (GeoChip 5) increased significantly (P < 0.05) as uranium or nitrate increased, and their changes could be used to successfully predict uranium and nitrate contamination and ecosystem functioning. This study indicates great potential for using microbial functional genes to predict environmental contamination and ecosystem functioning.IMPORTANCE Disentangling the relationships between biodiversity and ecosystem functioning is an important but poorly understood topic in ecology. Predicting ecosystem functioning on the basis of biodiversity is even more difficult, particularly with microbial biomarkers. As an exploratory effort, this study used key microbial functional genes as biomarkers to provide predictive understanding of environmental contamination and ecosystem functioning. The results indicated that the overall functional gene richness/diversity decreased as uranium increased in groundwater, while specific key microbial guilds increased significantly as uranium or nitrate increased. These key microbial functional genes could be used to successfully predict environmental contamination and ecosystem functioning. This study represents a significant advance in using functional gene markers to predict the spatial distribution of environmental contaminants and ecosystem functioning toward predictive microbial ecology, which is an ultimate goal of microbial ecology.}, }
@article {pmid29454999, year = {2018}, author = {Wang, J and Tang, L and Zhou, H and Zhou, J and Glenn, TC and Shen, CL and Wang, JS}, title = {Long-term treatment with green tea polyphenols modifies the gut microbiome of female sprague-dawley rats.}, journal = {The Journal of nutritional biochemistry}, volume = {56}, number = {}, pages = {55-64}, doi = {10.1016/j.jnutbio.2018.01.005}, pmid = {29454999}, issn = {1873-4847}, support = {R24 TW009489/TW/FIC NIH HHS/United States ; U01 AT006691/AT/NCCIH NIH HHS/United States ; }, abstract = {Green tea polyphenols (GTP) have been shown to exert a spectrum of health benefits to animals and humans. It is plausible that the beneficial effects of GTP are a result of its interaction with the gut microbiota. This study evaluated the effect of long-term treatment with GTP on the gut microbiota of experimental rats and the potential linkage between changes of the gut microbiota with the beneficial effects of GTP. Six-month-old Sprague-Dawley rats were randomly allocated into three dosing regimens (0, 0.5%, and 1.5% of GTP) and followed for 6 months. At the end of month 3 or month 6, half of the animals from each group were sacrificed and their colon contents were collected for microbiome analysis using 16S ribosomal RNA and shotgun metagenomic community sequencing. GTP treatment significantly decreased the biodiversity and modified the microbial community in a dose-dependent manner; similar patterns were observed at both sampling times. Multiple operational taxonomic units and phylotypes were modified: the phylotypes Bacteroidetes and Oscillospira, previously linked to the lean phenotype in human and animal studies, were enriched; and Peptostreptococcaceae previously linked to colorectal cancer phenotype was depleted in GTP treated groups in a dose-dependent manner. Several microbial gene orthologs were modified, among which genes related to energy production and conversion were consistently enriched in samples from month 6 in a dose-dependent manner. This study showed that long-term treatment with GTP induced a dose-dependent modification of the gut microbiome in experimental rats, which might be linked to beneficial effects of GTP.}, }
@article {pmid29444186, year = {2018}, author = {Donovan, PD and Gonzalez, G and Higgins, DG and Butler, G and Ito, K}, title = {Identification of fungi in shotgun metagenomics datasets.}, journal = {PloS one}, volume = {13}, number = {2}, pages = {e0192898}, doi = {10.1371/journal.pone.0192898}, pmid = {29444186}, issn = {1932-6203}, mesh = {Animals ; Antarctic Regions ; Ascomycota/classification/genetics/isolation & purification ; Candida tropicalis/genetics/pathogenicity ; Databases, Genetic ; Fungi/classification/*genetics/pathogenicity ; Humans ; Metagenome ; *Metagenomics ; Mice ; Microbiota/genetics ; Phylogeny ; Soil Microbiology ; Swine ; Zoonoses/microbiology ; }, abstract = {Metagenomics uses nucleic acid sequencing to characterize species diversity in different niches such as environmental biomes or the human microbiome. Most studies have used 16S rRNA amplicon sequencing to identify bacteria. However, the decreasing cost of sequencing has resulted in a gradual shift away from amplicon analyses and towards shotgun metagenomic sequencing. Shotgun metagenomic data can be used to identify a wide range of species, but have rarely been applied to fungal identification. Here, we develop a sequence classification pipeline, FindFungi, and use it to identify fungal sequences in public metagenome datasets. We focus primarily on animal metagenomes, especially those from pig and mouse microbiomes. We identified fungi in 39 of 70 datasets comprising 71 fungal species. At least 11 pathogenic species with zoonotic potential were identified, including Candida tropicalis. We identified Pseudogymnoascus species from 13 Antarctic soil samples initially analyzed for the presence of bacteria capable of degrading diesel oil. We also show that Candida tropicalis and Candida loboi are likely the same species. In addition, we identify several examples where contaminating DNA was erroneously included in fungal genome assemblies.}, }
@article {pmid29428461, year = {2018}, author = {Perfumo, A and Banat, IM and Marchant, R}, title = {Going Green and Cold: Biosurfactants from Low-Temperature Environments to Biotechnology Applications.}, journal = {Trends in biotechnology}, volume = {36}, number = {3}, pages = {277-289}, doi = {10.1016/j.tibtech.2017.10.016}, pmid = {29428461}, issn = {1879-3096}, abstract = {Approximately 80% of the Earth's biosphere is cold, at an average temperature of 5°C, and is populated by a diversity of microorganisms that are a precious source of molecules with high biotechnological potential. Biosurfactants from cold-adapted organisms can interact with multiple physical phases - water, ice, hydrophobic compounds, and gases - at low and freezing temperatures and be used in sustainable (green) and low-energy-impact (cold) products and processes. We review the biodiversity of microbial biosurfactants produced in cold habitats and provide a perspective on the most promising future applications in environmental and industrial technologies. Finally, we encourage exploring the cryosphere for novel types of biosurfactants via both culture screening and functional metagenomics.}, }
@article {pmid29427960, year = {2018}, author = {Fontana, A and Campanaro, S and Treu, L and Kougias, PG and Cappa, F and Morelli, L and Angelidaki, I}, title = {Performance and genome-centric metagenomics of thermophilic single and two-stage anaerobic digesters treating cheese wastes.}, journal = {Water research}, volume = {134}, number = {}, pages = {181-191}, doi = {10.1016/j.watres.2018.02.001}, pmid = {29427960}, issn = {1879-2448}, abstract = {The present research is the first comprehensive study regarding the thermophilic anaerobic degradation of cheese wastewater, which combines the evaluation of different reactor configurations (i.e. single and two-stage continuous stirred tank reactors) on the process efficiency and the in-depth characterization of the microbial community structure using genome-centric metagenomics. Both reactor configurations showed acidification problems under the tested organic loading rates (OLRs) of 3.6 and 2.4 g COD/L-reactor day and the hydraulic retention time (HRT) of 15 days. However, the two-stage design reached a methane yield equal to 95% of the theoretical value, in contrast with the single stage configuration, which reached a maximum of 33% of the theoretical methane yield. The metagenomic analysis identified 22 new population genomes and revealed that the microbial compositions between the two configurations were remarkably different, demonstrating a higher methanogenic biodiversity in the two-stage configuration. In fact, the acidogenic reactor of the serial configuration was almost solely composed by the lactose degrader Bifidobacterium crudilactis UC0001. The predictive functional analyses of the main population genomes highlighted specific metabolic pathways responsible for the AD process and the mechanisms of main intermediates production. Particularly, the acetate accumulation experienced by the single stage configuration was mainly correlated to the low abundant syntrophic acetate oxidizer Tepidanaerobacter acetatoxydans UC0018 and to the absence of aceticlastic methanogens.}, }
@article {pmid29427518, year = {2018}, author = {Guirro, M and Costa, A and Gual-Grau, A and Mayneris-Perxachs, J and Torrell, H and Herrero, P and Canela, N and Arola, L}, title = {Multi-omics approach to elucidate the gut microbiota activity: Metaproteomics and metagenomics connection.}, journal = {Electrophoresis}, volume = {39}, number = {13}, pages = {1692-1701}, doi = {10.1002/elps.201700476}, pmid = {29427518}, issn = {1522-2683}, abstract = {Over the last few years, the application of high-throughput meta-omics methods has provided great progress in improving the knowledge of the gut ecosystem and linking its biodiversity to host health conditions, offering complementary support to classical microbiology. Gut microbiota plays a crucial role in relevant diseases such as obesity or cardiovascular disease (CVD), and its regulation is closely influenced by several factors, such as dietary composition. In fact, polyphenol-rich diets are the most palatable treatment to prevent hypertension associated with CVD, although the polyphenol-microbiota interactions have not been completely elucidated. For this reason, the aim of this study was to evaluate microbiota effect in obese rats supplemented by hesperidin, after being fed with cafeteria or standard diet, using a multi meta-omics approaches combining strategy of metagenomics and metaproteomics analysis. We reported that cafeteria diet induces obesity, resulting in changes in the microbiota composition, which are related to functional alterations at proteome level. In addition, hesperidin supplementation alters microbiota diversity and also proteins involved in important metabolic pathways. Overall, going deeper into strategies to integrate omics sciences is necessary to understand the complex relationships between the host, gut microbiota, and diet.}, }
@article {pmid29404427, year = {2018}, author = {Hester, ER and Harpenslager, SF and van Diggelen, JMH and Lamers, LL and Jetten, MSM and Lüke, C and Lücker, S and Welte, CU}, title = {Linking Nitrogen Load to the Structure and Function of Wetland Soil and Rhizosphere Microbial Communities.}, journal = {mSystems}, volume = {3}, number = {1}, pages = {}, doi = {10.1128/mSystems.00214-17}, pmid = {29404427}, issn = {2379-5077}, support = {339880//European Research Council/International ; }, abstract = {Wetland ecosystems are important reservoirs of biodiversity and significantly contribute to emissions of the greenhouse gases CO2, N2O, and CH4. High anthropogenic nitrogen (N) inputs from agriculture and fossil fuel combustion have been recognized as a severe threat to biodiversity and ecosystem functioning, such as control of greenhouse gas emissions. Therefore, it is important to understand how increased N input into pristine wetlands affects the composition and activity of microorganisms, especially in interaction with dominant wetland plants. In a series of incubations analyzed over 90 days, we disentangled the effects of N fertilization on the microbial community in bulk soil and the rhizosphere of Juncus acutiflorus, a common and abundant graminoid wetland plant. We observed an increase in greenhouse gas emissions when N is increased in incubations with J. acutiflorus, changing the system from a greenhouse gas sink to a source. Using 16S rRNA gene amplicon sequencing, we determined that the bacterial orders Opitutales, subgroup 6 Acidobacteria, and Sphingobacteriales significantly responded to high N availability. Based on metagenomic data, we hypothesize that these groups are contributing to the increased greenhouse gas emissions. These results indicated that increased N input leads to shifts in microbial activity within the rhizosphere, altering N cycling dynamics. Our study provides a framework for connecting environmental conditions of wetland bulk and rhizosphere soil to the structure and metabolic output of microbial communities. IMPORTANCE Microorganisms living within the rhizospheres of wetland plants significantly contribute to greenhouse gas emissions. Understanding how microbes produce these gases under conditions that have been imposed by human activities (i.e., nitrogen pollution) is important to the development of future management strategies. Our results illustrate that within the rhizosphere of the wetland plant Juncus acutiflorus, physiological differences associated with nitrogen availability can influence microbial activity linked to greenhouse gas production. By pairing taxonomic information and environmental conditions like nitrogen availability with functional outputs of a system such as greenhouse gas fluxes, we present a framework to link certain taxa to both nitrogen load and greenhouse gas production. We view this type of combined information as essential in moving forward in our understanding of complex systems such as rhizosphere microbial communities.}, }
@article {pmid29396619, year = {2018}, author = {Mehetre, G and Shah, M and Dastager, SG and Dharne, MS}, title = {Untapped bacterial diversity and metabolic potential within Unkeshwar hot springs, India.}, journal = {Archives of microbiology}, volume = {200}, number = {5}, pages = {753-770}, doi = {10.1007/s00203-018-1484-4}, pmid = {29396619}, issn = {1432-072X}, support = {EMR/2014/000483//Science and Engineering Research Board/ ; }, mesh = {Amylases/analysis ; Bacteria/enzymology/genetics/isolation & purification ; Bacterial Proteins/analysis ; Biodiversity ; Hot Springs/*microbiology ; India ; Peptide Hydrolases/analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; Xylosidases/analysis ; }, abstract = {Hot springs support diverse and interesting groups of microorganisms adapted to extreme conditions and gaining attention in biotechnological applications. However, due to limitations of cultivation methods, a majority of such extremophiles remain uncultivated and unexplored. The advent of multiple cultivation conditions and specialized culture media could possibly aid to access the unexplored microbial portion of hot springs. In the present study, different media and isolation strategies were applied to isolate hitherto unexplored bacterial taxa in the water samples collected from Unkeshwar hot springs, India. Molecular, phylogenetic and predictive functional characterization of the isolated bacterial population was done using 16S rRNA sequencing coupled with Tax4Fun tools. Furthermore, representative isolates were screened for important enzymes (cellulase, xylanase, amylase, and protease) and heavy metal tolerance (chromium, arsenic) properties. A total of 454 bacterial isolates obtained were mapped into 57 unique bacterial genera and 4 different bacterial phyla. Interestingly, 37 genera not previously isolated from Indian hot springs, were isolated for the first time in the present study. However, most of these genera (23 out of 37) were reported only in metagenomics studies from Indian and global hot springs. Furthermore, around 14 genera not previously cultivated and not detected in metagenomics studies of hot springs are documented here. The metabolic potential was ascertained by determining the abundance of specific genes using in silico based Tax4Fun tool, which identified around 315 metabolic pathways for metabolism of carbohydrates, synthesis of secondary metabolites and degradation of xenobiotic compounds. Bioprospection study revealed that 33 and 25 bacterial genera were positive for enzyme production and resistance to the heavy metals, respectively. The present study revealed the advantages of cultivation methods using a comprehensive multiple isolation approach for exploring untapped and unique bacterial diversity, and also utilities for various biotechnological and environmental applications.}, }
@article {pmid29371626, year = {2018}, author = {Carradec, Q and Pelletier, E and Da Silva, C and Alberti, A and Seeleuthner, Y and Blanc-Mathieu, R and Lima-Mendez, G and Rocha, F and Tirichine, L and Labadie, K and Kirilovsky, A and Bertrand, A and Engelen, S and Madoui, MA and Méheust, R and Poulain, J and Romac, S and Richter, DJ and Yoshikawa, G and Dimier, C and Kandels-Lewis, S and Picheral, M and Searson, S and , and Jaillon, O and Aury, JM and Karsenti, E and Sullivan, MB and Sunagawa, S and Bork, P and Not, F and Hingamp, P and Raes, J and Guidi, L and Ogata, H and de Vargas, C and Iudicone, D and Bowler, C and Wincker, P}, title = {A global ocean atlas of eukaryotic genes.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {373}, doi = {10.1038/s41467-017-02342-1}, pmid = {29371626}, issn = {2041-1723}, support = {294823//European Research Council/International ; }, mesh = {Amino Acid Sequence ; Animals ; *Aquatic Organisms ; Atlases as Topic ; Bacteria/classification/genetics ; Biodiversity ; Ecosystem ; Eukaryota/classification/*genetics ; Eukaryotic Cells/cytology/*metabolism ; *Metagenome ; Metagenomics/methods ; Oceans and Seas ; *Phylogeny ; Phytoplankton/classification/genetics ; Seawater ; Viruses/classification/genetics ; Zooplankton/classification/*genetics ; }, abstract = {While our knowledge about the roles of microbes and viruses in the ocean has increased tremendously due to recent advances in genomics and metagenomics, research on marine microbial eukaryotes and zooplankton has benefited much less from these new technologies because of their larger genomes, their enormous diversity, and largely unexplored physiologies. Here, we use a metatranscriptomics approach to capture expressed genes in open ocean Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster into 116 million unigenes representing the largest reference collection of eukaryotic transcripts from any single biome. The catalog is used to unveil functions expressed by eukaryotic marine plankton, and to assess their functional biogeography. Almost half of the sequences have no similarity with known proteins, and a great number belong to new gene families with a restricted distribution in the ocean. Overall, the resource provides the foundations for exploring the roles of marine eukaryotes in ocean ecology and biogeochemistry.}, }
@article {pmid29361802, year = {2018}, author = {D'Auria, G and Artacho, A and Rojas, RA and Bautista, JS and Méndez, R and Gamboa, MT and Gamboa, JR and Gómez-Cruz, R}, title = {Metagenomics of Bacterial Diversity in Villa Luz Caves with Sulfur Water Springs.}, journal = {Genes}, volume = {9}, number = {1}, pages = {}, doi = {10.3390/genes9010055}, pmid = {29361802}, issn = {2073-4425}, abstract = {New biotechnology applications require in-depth preliminary studies of biodiversity. The methods of massive sequencing using metagenomics and bioinformatics tools offer us sufficient and reliable knowledge to understand environmental diversity, to know new microorganisms, and to take advantage of their functional genes. Villa Luz caves, in the southern Mexican state of Tabasco, are fed by at least 26 groundwater inlets, containing 300-500 mg L-1 H2S and <0.1 mg L-1 O2. We extracted environmental DNA for metagenomic analysis of collected samples in five selected Villa Luz caves sites, with pH values from 2.5 to 7. Foreign organisms found in this underground ecosystem can oxidize H2S to H2SO4. These include: biovermiculites, a bacterial association that can grow on the rock walls; snottites, that are whitish, viscous biofilms hanging from the rock walls, and sacks or bags of phlegm, which live within the aquatic environment of the springs. Through the emergency food assistance program (TEFAP) pyrosequencing, a total of 20,901 readings of amplification products from hypervariable regions V1 and V3 of 16S rRNA bacterial gene in whole and pure metagenomic DNA samples were generated. Seven bacterial phyla were identified. As a result, Proteobacteria was more frequent than Acidobacteria. Finally, acidophilic Proteobacteria was detected in UJAT5 sample.}, }
@article {pmid29355278, year = {2018}, author = {Cheng, M and Zhang, X and Zhu, J and Cheng, L and Cao, J and Wu, Z and Weng, P and Zheng, X}, title = {A metagenomics approach to the intestinal microbiome structure and function in high fat diet-induced obesity mice fed with oolong tea polyphenols.}, journal = {Food & function}, volume = {9}, number = {2}, pages = {1079-1087}, doi = {10.1039/c7fo01570d}, pmid = {29355278}, issn = {2042-650X}, mesh = {Animals ; Bacteria/classification/drug effects/*genetics/isolation & purification ; Camellia sinensis/*chemistry ; Diet, High-Fat/adverse effects ; Disease Models, Animal ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Intestines/metabolism/*microbiology ; Male ; Metagenomics ; Mice ; Mice, Inbred C57BL ; Obesity/*drug therapy/metabolism/microbiology ; Plant Extracts/*administration & dosage ; Polyphenols/*administration & dosage ; Tea/chemistry/metabolism ; }, abstract = {To investigate the modulatory effect of oolong tea polyphenols (OTP) on intestinal microbiota, OTP was prepared by column chromatography and its influence on the gut flora structure was analyzed by high-throughput sequencing with a human flora-associated high fat diet (HFD) induced obesity mouse model. We observed a robust increase in bacterial biodiversity and the abundance of genera known to be butyrate- and acetate-producing bacteria. A large increase in Bacteroidetes with a decrease in Firmicutes was observed after the administration of OTP for 4 weeks, and the corresponding decrease in the Firmicutes/Bacteroidetes ratio reflected the positive modulatory effect of OTP on the intestinal microbiota. In addition, KEGG pathways for the biosynthesis of amino acids, carbon metabolism, and the ribosome were among the most differentially expressed genes after OTP intervention. The current study revealed that OTP rich in tea catechins, especially O-methylated derivatives, may have prebiotic-like activity and can be used as a functional food component with potential therapeutic utility to prevent obesity-related metabolic disorders by manipulating the intestinal microbiota.}, }
@article {pmid29351302, year = {2018}, author = {Bzhalava, Z and Hultin, E and Dillner, J}, title = {Extension of the viral ecology in humans using viral profile hidden Markov models.}, journal = {PloS one}, volume = {13}, number = {1}, pages = {e0190938}, doi = {10.1371/journal.pone.0190938}, pmid = {29351302}, issn = {1932-6203}, mesh = {Algorithms ; Computational Biology ; Contig Mapping/statistics & numerical data ; Databases, Protein/statistics & numerical data ; Humans ; Markov Chains ; Metagenomics/statistics & numerical data ; *Microbiota ; Phylogeny ; Viral Proteins/genetics ; Viruses/classification/*genetics/*isolation & purification ; }, abstract = {When human samples are sequenced, many assembled contigs are "unknown", as conventional alignments find no similarity to known sequences. Hidden Markov models (HMM) exploit the positions of specific nucleotides in protein-encoding codons in various microbes. The algorithm HMMER3 implements HMM using a reference set of sequences encoding viral proteins, "vFam". We used HMMER3 analysis of "unknown" human sample-derived sequences and identified 510 contigs distantly related to viruses (Anelloviridae (n = 1), Baculoviridae (n = 34), Circoviridae (n = 35), Caulimoviridae (n = 3), Closteroviridae (n = 5), Geminiviridae (n = 21), Herpesviridae (n = 10), Iridoviridae (n = 12), Marseillevirus (n = 26), Mimiviridae (n = 80), Phycodnaviridae (n = 165), Poxviridae (n = 23), Retroviridae (n = 6) and 89 contigs related to described viruses not yet assigned to any taxonomic family). In summary, we find that analysis using the HMMER3 algorithm and the "vFam" database greatly extended the detection of viruses in biospecimens from humans.}, }
@article {pmid29334812, year = {2018}, author = {Ding, W and Ma, C and Zhang, W and Chiang, H and Tam, C and Xu, Y and Zhang, G and Qian, PY}, title = {Anti-biofilm effect of a butenolide/polymer coating and metatranscriptomic analyses.}, journal = {Biofouling}, volume = {34}, number = {1}, pages = {111-122}, doi = {10.1080/08927014.2017.1409891}, pmid = {29334812}, issn = {1029-2454}, mesh = {4-Butyrolactone/*analogs & derivatives/pharmacology ; Biofilms/*drug effects ; Biofouling/*prevention & control ; Cell Adhesion ; Metagenomics ; Microbial Consortia/*genetics ; Polyesters/*pharmacology ; Polyurethanes/*pharmacology ; Seawater ; Surface Properties ; Transcriptome ; }, abstract = {Butenolide is an environmentally friendly antifouling natural product, but its efficiency and mechanism in preventing biofilm formation have not been examined. Furthermore, controlling the release of butenolide from paints into seawater is technically challenging. A coating was developed by mixing butenolide with a biodegradable polymer, poly (ε-caprolactone)-based polyurethane, and a one-month in situ anti-biofilm test was conducted in a subtidal area. The constant release of butenolide from the surface suggested that its release was well controlled. Direct observation and confocal microscope investigation indicated that the coating was effective against both biofilm formation and attachment of large fouling organisms. Metatranscriptomic analysis of biofilm samples implied that the coating selectively inhibited the adhesion of microbes from a variety of phyla and targeted particular functional pathways including energy metabolism, drug transport and toxin release. These integrated analyses demonstrated the potential application of this butenolide/polymer coating as an anti-biofilm material.}, }
@article {pmid29330574, year = {2018}, author = {Koizumi, T and Hattori, M and Nara, K}, title = {Ectomycorrhizal fungal communities in alpine relict forests of Pinus pumila on Mt. Norikura, Japan.}, journal = {Mycorrhiza}, volume = {28}, number = {2}, pages = {129-145}, doi = {10.1007/s00572-017-0817-5}, pmid = {29330574}, issn = {1432-1890}, support = {25660115//Japan Society for the Promotion of Science/ ; 16J07343//Japan Society for the Promotion of Science/ ; }, mesh = {Altitude ; *Biodiversity ; DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; *Forests ; Japan ; Mycorrhizae/genetics/*physiology ; Pinus/*microbiology ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Ectomycorrhizal (ECM) symbioses are indispensable for the establishment of host trees, yet available information of ECM symbiosis in alpine forests is scarce. Pinus pumila is a typical ice age relict tree species in Japan and often forms monodominant dwarf vegetation above the tree line in mountains. We studied ECM fungi colonizing P. pumila on Mt. Norikura, Japan, with reference to host developmental stages, i.e., from current-year seedlings to mature trees. ECM fungal species were identified based on rDNA ITS sequences. Ninety-two ECM fungal species were confirmed from a total of 2480 root tips examined. Species in /suillus-rhizopogon and /wilcoxina were dominant in seedling roots. ECM fungal diversity increased with host development, due to the addition of species-rich fungal lineages (/cenococcum, /cortinarius, and /russula-lactarius) in late-successional stages. Such successional pattern of ECM fungi is similar to those in temperate pine systems, suggesting the predominant role of /suillus-rhizopogon in seedling establishment, even in relict alpine habitats fragmented and isolated for a geological time period. Most of the ECM fungi detected were also recorded in Europe or North America, indicating their potential Holarctic distribution and the possibility of their comigration with P. pumila through land bridges during ice ages. In addition, we found significant effects of soil properties on ECM fungal communities, which explained 34.1% of the total variation of the fungal communities. While alpine vegetation is regarded as vulnerable to the ongoing global warming, ECM fungal communities associated with P. pumila could be altered by the edaphic change induced by the warming.}, }
@article {pmid29321767, year = {2017}, author = {Soliman, T and Reimer, JD and Yang, SY and Villar-Briones, A and Roy, MC and Jenke-Kodama, H}, title = {Diversity of Microbial Communities and Quantitative Chemodiversity in Layers of Marine Sediment Cores from a Causeway (Kaichu-Doro) in Okinawa Island, Japan.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2451}, doi = {10.3389/fmicb.2017.02451}, pmid = {29321767}, issn = {1664-302X}, abstract = {Microbial community diversity and chemodiversity were investigated in marine sediments adjacent to the Okinawan "Kaichu-Doro" Causeway, which was constructed 46 years ago to connect a group of four islands (Henza-jima, Miyagi-jima, Ikei-jima, Hamahiga-jima) to the Okinawan main island. This causeway was not built on pilings, but by land reclamation; hence, it now acts as a long, thin peninsula. The construction of this causeway was previously shown to have influenced the surrounding marine ecosystem, causing ecosystem fragmentation and loss of water circulation. In this study, we collected sediment cores (n = 10) from five paired sites in 1 m water depths. Each pair of sites consisted of one site each on the immediate north and south sides of the causeway. Originally the members of each pair were much closer to each other (<150 m) than to other pairs, but now the members of each pair are isolated by the causeway. Each core was 60-80 cm long and was divided into 15-cm layers. We examined the vertical diversity of microbial communities and chemical compounds to determine the correlation between chemodiversity and microbial communities among marine sediment cores and layers. Principal coordinate analyses (PCoA) of detected compounds and of bacterial and archaeal operational taxonomic units (OTUs) revealed that the north and south sides of the causeway are relatively isolated, with each side having unique microbial OTUs. Additionally, some bacterial families (e.g., Acidaminobacteraceae, Rhizobiaceae, and Xanthomonadaceae) were found only on the south side of Kaichu-Doro. Interestingly, we found that the relative abundance of OTUs for some microbial families increased from top to bottom, but this was reversed in some other families. We conclude that the causeway has altered microbial community composition and metabolite profiles in marine sediments.}, }
@article {pmid29312205, year = {2017}, author = {Karimi, E and Ramos, M and Gonçalves, JMS and Xavier, JR and Reis, MP and Costa, R}, title = {Comparative Metagenomics Reveals the Distinctive Adaptive Features of the Spongia officinalis Endosymbiotic Consortium.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2499}, doi = {10.3389/fmicb.2017.02499}, pmid = {29312205}, issn = {1664-302X}, abstract = {Current knowledge of sponge microbiome functioning derives mostly from comparative analyses with bacterioplankton communities. We employed a metagenomics-centered approach to unveil the distinct features of the Spongia officinalis endosymbiotic consortium in the context of its two primary environmental vicinities. Microbial metagenomic DNA samples (n = 10) from sponges, seawater, and sediments were subjected to Hiseq Illumina sequencing (c. 15 million 100 bp reads per sample). Totals of 10,272 InterPro (IPR) predicted protein entries and 784 rRNA gene operational taxonomic units (OTUs, 97% cut-off) were uncovered from all metagenomes. Despite the large divergence in microbial community assembly between the surveyed biotopes, the S. officinalis symbiotic community shared slightly greater similarity (p < 0.05), in terms of both taxonomy and function, to sediment than to seawater communities. The vast majority of the dominant S. officinalis symbionts (i.e., OTUs), representing several, so-far uncultivable lineages in diverse bacterial phyla, displayed higher residual abundances in sediments than in seawater. CRISPR-Cas proteins and restriction endonucleases presented much higher frequencies (accompanied by lower viral abundances) in sponges than in the environment. However, several genomic features sharply enriched in the sponge specimens, including eukaryotic-like repeat motifs (ankyrins, tetratricopeptides, WD-40, and leucine-rich repeats), and genes encoding for plasmids, sulfatases, polyketide synthases, type IV secretion proteins, and terpene/terpenoid synthases presented, to varying degrees, higher frequencies in sediments than in seawater. In contrast, much higher abundances of motility and chemotaxis genes were found in sediments and seawater than in sponges. Higher cell and surface densities, sponge cell shedding and particle uptake, and putative chemical signaling processes favoring symbiont persistence in particulate matrices all may act as mechanisms underlying the observed degrees of taxonomic connectivity and functional convergence between sponges and sediments. The reduced frequency of motility and chemotaxis genes in the sponge microbiome reinforces the notion of a prevalent mutualistic mode of living inside the host. This study highlights the S. officinalis "endosymbiome" as a distinct consortium of uncultured prokaryotes displaying a likely "sit-and-wait" strategy to nutrient foraging coupled to sophisticated anti-viral defenses, unique natural product biosynthesis, nutrient utilization and detoxification capacities, and both microbe-microbe and host-microbe gene transfer amenability.}, }
@article {pmid29304124, year = {2018}, author = {Krehenwinkel, H and Fong, M and Kennedy, S and Huang, EG and Noriyuki, S and Cayetano, L and Gillespie, R}, title = {The effect of DNA degradation bias in passive sampling devices on metabarcoding studies of arthropod communities and their associated microbiota.}, journal = {PloS one}, volume = {13}, number = {1}, pages = {e0189188}, doi = {10.1371/journal.pone.0189188}, pmid = {29304124}, issn = {1932-6203}, mesh = {Animals ; Arthropods/classification/*genetics/*microbiology ; Biodiversity ; DNA/*analysis/*genetics ; DNA Barcoding, Taxonomic/*methods/statistics & numerical data ; DNA Primers ; Ecosystem ; Hawaii ; Metagenome ; Metagenomics/methods/statistics & numerical data ; Microbiota/*genetics ; Polymerase Chain Reaction/methods ; Selection Bias ; }, abstract = {PCR amplification bias is a well-known problem in metagenomic analysis of arthropod communities. In contrast, variation of DNA degradation rates is a largely neglected source of bias. Differential degradation of DNA molecules could cause underrepresentation of taxa in a community sequencing sample. Arthropods are often collected by passive sampling devices, like malaise traps. Specimens in such a trap are exposed to varying periods of suboptimal storage and possibly different rates of DNA degradation. Degradation bias could thus be a significant issue, skewing diversity estimates. Here, we estimate the effect of differential DNA degradation on the recovery of community diversity of Hawaiian arthropods and their associated microbiota. We use a simple DNA size selection protocol to test for degradation bias in mock communities, as well as passively collected samples from actual Malaise traps. We compare the effect of DNA degradation to that of varying PCR conditions, including primer choice, annealing temperature and cycle number. Our results show that DNA degradation does indeed bias community analyses. However, the effect of this bias is of minor importance compared to that induced by changes in PCR conditions. Analyses of the macro and microbiome from passively collected arthropod samples are thus well worth pursuing.}, }
@article {pmid29297295, year = {2017}, author = {Herath, D and Tang, SL and Tandon, K and Ackland, D and Halgamuge, SK}, title = {CoMet: a workflow using contig coverage and composition for binning a metagenomic sample with high precision.}, journal = {BMC bioinformatics}, volume = {18}, number = {Suppl 16}, pages = {571}, doi = {10.1186/s12859-017-1967-3}, pmid = {29297295}, issn = {1471-2105}, abstract = {BACKGROUND: In metagenomics, the separation of nucleotide sequences belonging to an individual or closely matched populations is termed binning. Binning helps the evaluation of underlying microbial population structure as well as the recovery of individual genomes from a sample of uncultivable microbial organisms. Both supervised and unsupervised learning methods have been employed in binning; however, characterizing a metagenomic sample containing multiple strains remains a significant challenge. In this study, we designed and implemented a new workflow, Coverage and composition based binning of Metagenomes (CoMet), for binning contigs in a single metagenomic sample. CoMet utilizes coverage values and the compositional features of metagenomic contigs. The binning strategy in CoMet includes the initial grouping of contigs in guanine-cytosine (GC) content-coverage space and refinement of bins in tetranucleotide frequencies space in a purely unsupervised manner. With CoMet, the clustering algorithm DBSCAN is employed for binning contigs. The performances of CoMet were compared against four existing approaches for binning a single metagenomic sample, including MaxBin, Metawatt, MyCC (default) and MyCC (coverage) using multiple datasets including a sample comprised of multiple strains.
RESULTS: Binning methods based on both compositional features and coverages of contigs had higher performances than the method which is based only on compositional features of contigs. CoMet yielded higher or comparable precision in comparison to the existing binning methods on benchmark datasets of varying complexities. MyCC (coverage) had the highest ranking score in F1-score. However, the performances of CoMet were higher than MyCC (coverage) on the dataset containing multiple strains. Furthermore, CoMet recovered contigs of more species and was 18 - 39% higher in precision than the compared existing methods in discriminating species from the sample of multiple strains. CoMet resulted in higher precision than MyCC (default) and MyCC (coverage) on a real metagenome.
CONCLUSIONS: The approach proposed with CoMet for binning contigs, improves the precision of binning while characterizing more species in a single metagenomic sample and in a sample containing multiple strains. The F1-scores obtained from different binning strategies vary with different datasets; however, CoMet yields the highest F1-score with a sample comprised of multiple strains.}, }
@article {pmid29293631, year = {2018}, author = {Villegas, LEM and Campolina, TB and Barnabe, NR and Orfano, AS and Chaves, BA and Norris, DE and Pimenta, PFP and Secundino, NFC}, title = {Zika virus infection modulates the bacterial diversity associated with Aedes aegypti as revealed by metagenomic analysis.}, journal = {PloS one}, volume = {13}, number = {1}, pages = {e0190352}, doi = {10.1371/journal.pone.0190352}, pmid = {29293631}, issn = {1932-6203}, mesh = {Aedes/*microbiology/virology ; Animals ; Bacteria/*classification/genetics ; *Biodiversity ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; Mosquito Vectors ; RNA, Ribosomal, 16S/genetics ; Zika Virus Infection/*microbiology ; }, abstract = {Zika is a re-emerging infection that has been considered a major threat to global public health. Currently at least 100 countries are at risk of Zika virus (ZIKV) transmission. Aedes aegypti is the main mosquito vector in the Americas. This vector is exposed to, and interacts symbiotically with a variety of microorganisms in its environment, which may result in the formation of a lifetime association. Here, the unknown effect that ZIKV exerts on the dynamic bacterial community harbored by this mosquito vector was investigated using a metagenomic analysis of its microbiota. Groups of Ae. aegypti were experimentally fed on sugar, blood and blood mixed with ZIKV, and held for 3 to 7 days after blood meal and eggs development respectively. The infected groups were processed by qPCR to confirm the presence of ZIKV. All groups were analyzed by metagenomics (Illumina Hiseq Sequencing) and 16S rRNA amplicon sequences were obtained to create bacterial taxonomic profiles. A core microbiota and exclusive bacterial taxa were identified that incorporate 50.5% of the predicted reads from the dataset, with 40 Gram-negative and 9 Gram-positive families. To address how ZIKV invasion may disturb the ecological balance of the Ae. aegypti microbiota, a CCA analysis coupled with an explanatory matrix was performed to support the biological interpretation of shifts in bacterial signatures. Two f-OTUs appeared as potential biomarkers of ZIKV infection: Rhodobacteraceae and Desulfuromonadaceae. Coincidentally, both f-OTUs were exclusively present in the ZIKV- infected blood-fed and ZIKV- infected gravid groups. In conclusion, this study shows that bacterial symbionts act as biomarkers of the insect physiological states and how they respond as a community when ZIKV invades Ae. aegypti. Basic knowledge of local haematophagous vectors and their associated microbiota is relevant when addressing transmission of vector-borne infectious diseases in their regional surroundings.}, }
@article {pmid29292539, year = {2018}, author = {Porter, TM and Hajibabaei, M}, title = {Scaling up: A guide to high-throughput genomic approaches for biodiversity analysis.}, journal = {Molecular ecology}, volume = {27}, number = {2}, pages = {313-338}, doi = {10.1111/mec.14478}, pmid = {29292539}, issn = {1365-294X}, abstract = {The purpose of this review is to present the most common and emerging DNA-based methods used to generate data for biodiversity and biomonitoring studies. As environmental assessment and monitoring programmes may require biodiversity information at multiple levels, we pay particular attention to the DNA metabarcoding method and discuss a number of bioinformatic tools and considerations for producing DNA-based indicators using operational taxonomic units (OTUs), taxa at a variety of ranks and community composition. By developing the capacity to harness the advantages provided by the newest technologies, investigators can "scale up" by increasing the number of samples and replicates processed, the frequency of sampling over time and space, and even the depth of sampling such as by sequencing more reads per sample or more markers per sample. The ability to scale up is made possible by the reduced hands-on time and cost per sample provided by the newest kits, platforms and software tools. Results gleaned from broad-scale monitoring will provide opportunities to address key scientific questions linked to biodiversity and its dynamics across time and space as well as being more relevant for policymakers, enabling science-based decision-making, and provide a greater socio-economic impact. As genomic approaches are continually evolving, we provide this guide to methods used in biodiversity genomics.}, }
@article {pmid29272370, year = {2018}, author = {Laenen, L and Vergote, V and Kafetzopoulou, LE and Wawina, TB and Vassou, D and Cook, JA and Hugot, JP and Deboutte, W and Kang, HJ and Witkowski, PT and Köppen-Rung, P and Krüger, DH and Licková, M and Stang, A and Striešková, L and Szemeš, T and Markowski, J and Hejduk, J and Kafetzopoulos, D and Van Ranst, M and Yanagihara, R and Klempa, B and Maes, P}, title = {A Novel Hantavirus of the European Mole, Bruges Virus, Is Involved in Frequent Nova Virus Coinfections.}, journal = {Genome biology and evolution}, volume = {10}, number = {1}, pages = {45-55}, doi = {10.1093/gbe/evx268}, pmid = {29272370}, issn = {1759-6653}, support = {P20 GM103516/GM/NIGMS NIH HHS/United States ; R01 AI075057/AI/NIAID NIH HHS/United States ; U54 MD007601/MD/NIMHD NIH HHS/United States ; }, abstract = {Hantaviruses are zoonotic viruses with a complex evolutionary history of virus-host coevolution and cross-species transmission. Although hantaviruses have a broad reservoir host range, virus-host relationships were previously thought to be strict, with a single virus species infecting a single host species. Here, we describe Bruges virus, a novel hantavirus harbored by the European mole (Talpa europaea), which is the well-known host of Nova virus. Phylogenetic analyses of all three genomic segments showed tree topology inconsistencies, suggesting that Bruges virus has emerged from cross-species transmission and ancient reassortment events. A high number of coinfections with Bruges and Nova viruses was detected, but no evidence was found for reassortment between these two hantaviruses. These findings highlight the complexity of hantavirus evolution and the importance of further investigation of hantavirus-reservoir relationships.}, }
@article {pmid29261736, year = {2017}, author = {Camacho-Ortiz, A and Gutiérrez-Delgado, EM and Garcia-Mazcorro, JF and Mendoza-Olazarán, S and Martínez-Meléndez, A and Palau-Davila, L and Baines, SD and Maldonado-Garza, H and Garza-González, E}, title = {Randomized clinical trial to evaluate the effect of fecal microbiota transplant for initial Clostridium difficile infection in intestinal microbiome.}, journal = {PloS one}, volume = {12}, number = {12}, pages = {e0189768}, doi = {10.1371/journal.pone.0189768}, pmid = {29261736}, issn = {1932-6203}, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/genetics ; Biodiversity ; Clostridium Infections/drug therapy/*therapy ; Demography ; *Fecal Microbiota Transplantation ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Genotype ; Humans ; Male ; Metagenomics ; Microbial Sensitivity Tests ; Middle Aged ; Phylogeny ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; Tissue Donors ; Vancomycin/therapeutic use ; Young Adult ; }, abstract = {OBJECTIVE: The aim of this study was to evaluate the impact of fecal donor-unrelated donor mix (FMT-FURM) transplantation as first-line therapy for C. difficile infection (CDI) in intestinal microbiome.
METHODS: We designed an open, two-arm pilot study with oral vancomycin (250mg every 6 h for 10-14 days) or FMT-FURM as treatments for the first CDI episode in hospitalized adult patients in Hospital Universitario "Dr. Jose Eleuterio Gonzalez". Patients were randomized by a closed envelope method in a 1: 1 ratio to either oral vancomycin or FMT-FURM. CDI resolution was considered when there was a reduction on the Bristol scale of at least 2 points, a reduction of at least 50% in the number of bowel movements, absence of fever, and resolution of abdominal pain (at least two criteria). From each patient, a fecal sample was obtained at days 0, 3, and 7 after treatment. Specimens were cultured to isolate C. difficile, and isolates were characterized by PCR. Susceptibility testing of isolates was performed using the agar dilution method. Fecal samples and FMT-FURM were analyzed by 16S rRNA sequencing.
RESULTS: We included 19 patients; 10 in the vancomycin arm and 9 in the FMT-FURM arm. However, one of the patients in the vancomycin arm and two patients in the FMT-FURM arm were eliminated. Symptoms resolved in 8/9 patients (88.9%) in the vancomycin group, while symptoms resolved in 4/7 patients (57.1%) after the first FMT-FURM dose (P = 0.26) and in 5/7 patients (71.4%) after the second dose (P = 0.55). During the study, no adverse effects attributable to FMT-FURM were observed in patients. Twelve isolates were recovered, most isolates carried tcdB, tcdA, cdtA, and cdtB, with an 18-bp deletion in tcdC. All isolates were resistant to ciprofloxacin and moxifloxacin but susceptible to metronidazole, linezolid, fidaxomicin, and tetracycline. In the FMT-FURM group, the bacterial composition was dominated by Firmicutes, Bacteroidetes, and Proteobacteria at all-time points and the microbiota were remarkably stable over time. The vancomycin group showed a very different pattern of the microbial composition when comparing to the FMT-FURM group over time.
CONCLUSION: The results of this preliminary study showed that FMT-FURM for initial CDI is associated with specific bacterial communities that do not resemble the donors' sample.}, }
@article {pmid29255014, year = {2018}, author = {Bergauer, K and Fernandez-Guerra, A and Garcia, JAL and Sprenger, RR and Stepanauskas, R and Pachiadaki, MG and Jensen, ON and Herndl, GJ}, title = {Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {3}, pages = {E400-E408}, doi = {10.1073/pnas.1708779115}, pmid = {29255014}, issn = {1091-6490}, support = {268595//European Research Council/International ; }, mesh = {Archaea/genetics/*metabolism ; Archaeal Proteins/*metabolism ; Atlantic Ocean ; Bacteria/genetics/*metabolism ; Bacterial Proteins/*metabolism ; Biodiversity ; Genome, Archaeal ; Genome, Bacterial ; Metagenomics ; Proteomics/*methods ; Seawater ; *Water Microbiology ; }, abstract = {The phylogenetic composition of the heterotrophic microbial community is depth stratified in the oceanic water column down to abyssopelagic layers. In the layers below the euphotic zone, it has been suggested that heterotrophic microbes rely largely on solubilized particulate organic matter as a carbon and energy source rather than on dissolved organic matter. To decipher whether changes in the phylogenetic composition with depth are reflected in changes in the bacterial and archaeal transporter proteins, we generated an extensive metaproteomic and metagenomic dataset of microbial communities collected from 100- to 5,000-m depth in the Atlantic Ocean. By identifying which compounds of the organic matter pool are absorbed, transported, and incorporated into microbial cells, intriguing insights into organic matter transformation in the deep ocean emerged. On average, solute transporters accounted for 23% of identified protein sequences in the lower euphotic and ∼39% in the bathypelagic layer, indicating the central role of heterotrophy in the dark ocean. In the bathypelagic layer, substrate affinities of expressed transporters suggest that, in addition to amino acids, peptides and carbohydrates, carboxylic acids and compatible solutes may be essential substrates for the microbial community. Key players with highest expression of solute transporters were Alphaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria, accounting for 40%, 11%, and 10%, respectively, of relative protein abundances. The in situ expression of solute transporters indicates that the heterotrophic prokaryotic community is geared toward the utilization of similar organic compounds throughout the water column, with yet higher abundances of transporters targeting aromatic compounds in the bathypelagic realm.}, }
@article {pmid29228901, year = {2017}, author = {Forsell, J and Bengtsson-Palme, J and Angelin, M and Johansson, A and Evengård, B and Granlund, M}, title = {The relation between Blastocystis and the intestinal microbiota in Swedish travellers.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {231}, doi = {10.1186/s12866-017-1139-7}, pmid = {29228901}, issn = {1471-2180}, mesh = {Adult ; Biodiversity ; Blastocystis/*classification/physiology ; Blastocystis Infections/epidemiology/*microbiology/*parasitology/transmission ; Feces/microbiology/parasitology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics ; Prevalence ; Sweden/epidemiology ; *Travel ; Young Adult ; }, abstract = {BACKGROUND: Blastocystis sp. is a unicellular eukaryote that is commonly found in the human intestine. Its ability to cause disease is debated and a subject for ongoing research. In this study, faecal samples from 35 Swedish university students were examined through shotgun metagenomics before and after travel to the Indian peninsula or Central Africa. We aimed at assessing the impact of travel on Blastocystis carriage and seek associations between Blastocystis and the bacterial microbiota.
RESULTS: We found a prevalence of Blastocystis of 16/35 (46%) before travel and 15/35 (43%) after travel. The two most commonly Blastocystis subtypes (STs) found were ST3 and ST4, accounting for 20 of the 31 samples positive for Blastocystis. No mixed subtype carriage was detected. All ten individuals with a typable ST before and after travel maintained their initial ST. The composition of the gut bacterial community was not significantly different between Blastocystis-carriers and non-carriers. Interestingly, the presence of Blastocystis was accompanied with higher abundances of the bacterial genera Sporolactobacillus and Candidatus Carsonella. Blastocystis carriage was positively associated with high bacterial genus richness, and negatively correlated to the Bacteroides-driven enterotype. These associations were both largely dependent on ST4 - a subtype commonly described from Europe - while the globally prevalent ST3 did not show such significant relationships.
CONCLUSIONS: The high rate of Blastocystis subtype persistence found during travel indicates that long-term carriage of Blastocystis is common. The associations between Blastocystis and the bacterial microbiota found in this study could imply a link between Blastocystis and a healthy microbiota as well as with diets high in vegetables. Whether the associations between Blastocystis and the microbiota are resulting from the presence of Blastocystis, or are a prerequisite for colonization with Blastocystis, are interesting questions for further studies.}, }
@article {pmid29223543, year = {2018}, author = {Cowart, DA and Murphy, KR and Cheng, CC}, title = {Metagenomic sequencing of environmental DNA reveals marine faunal assemblages from the West Antarctic Peninsula.}, journal = {Marine genomics}, volume = {37}, number = {}, pages = {148-160}, doi = {10.1016/j.margen.2017.11.003}, pmid = {29223543}, issn = {1876-7478}, abstract = {The West Antarctic Peninsula (WAP) is the fastest warming region in Antarctica where climate impact on the cold-adapted marine ecosystem is already visible. To monitor faunal changes in remote vast bodies of Antarctic waters, efficient and informative tools are essential. High-throughput sequencing of environmental DNA (eDNA) has emerged as one such tool for monitoring biodiversity and ecosystems, as it increases detection sensitivity of taxa, and sampling is often simpler and less costly than traditional collection methods. We collected water samples from four WAP shallow (≤300m) shelf regions, recovered the eDNA therein, and performed metagenomic shotgun sequencing and analyses to determine the effectiveness of this method to assess marine benthic faunal diversity; this includes the detection of deep-water predatory king crabs whose potential shoreward expansion to warming shelves has sparked much concern. Using a customized bioinformatics pipeline, we identified abundant signatures of common benthic invertebrate fauna, endemic notothenioid fishes, as well as lithodid king crabs. We also uncovered species richness and diversity comparable to biological inventories compiled by the use of traditional survey methods, supporting the efficacy of the eDNA shotgun sequencing approach. As the rate of eDNA degradation affects faunal detection sensitivity, we also quantified mitochondrial ND2 gene copies in eDNA derived from a WAP icefish and found ND2 copies persisted to at least 20days in the cold WAP water, much longer than values reported for temperate environments. We propose that eDNA metagenomic sequencing complements traditional sampling, and combining both will enable more inclusive biodiversity detection and faunal change monitoring in the vast Southern Ocean.}, }
@article {pmid29222756, year = {2018}, author = {Ye, C and Xu, N and Chen, X and Liu, L}, title = {Metabolic Model Reconstruction and Analysis of an Artificial Microbial Ecosystem.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1716}, number = {}, pages = {219-238}, doi = {10.1007/978-1-4939-7528-0_10}, pmid = {29222756}, issn = {1940-6029}, mesh = {Algorithms ; Metabolomics/*methods ; Metagenomics ; Microbial Consortia ; *Models, Biological ; Phylogeny ; }, abstract = {Microbial communities are widespread in the environment, and to isolate and identify species or to determine relations among microorganisms, some 'omics methods like metagenomics, proteomics, and metabolomics have been used. When combined with various 'omics data, models known as artificial microbial ecosystems (AME) are powerful methods that can make functional predictions about microbial communities. Reconstruction of an AME model is the first step for model analysis. Many techniques have been applied to the construction of AME models, e.g., the compartmentalization approach, community objectives method, and dynamic analysis approach. Of these approaches, species compartmentalization is the most relevant to genetics. Besides, some algorithms have been developed for the analysis of AME models. In this chapter, we present a general protocol for the use of the species compartmentalization method to reconstruct a model of microbial communities. Then, the analysis of an AME is discussed.}, }
@article {pmid29211769, year = {2017}, author = {Dong, X and Shulzhenko, N and Lemaitre, J and Greer, RL and Peremyslova, K and Quamruzzaman, Q and Rahman, M and Hasan, OS and Joya, SA and Golam, M and Christiani, DC and Morgun, A and Kile, ML}, title = {Arsenic exposure and intestinal microbiota in children from Sirajdikhan, Bangladesh.}, journal = {PloS one}, volume = {12}, number = {12}, pages = {e0188487}, doi = {10.1371/journal.pone.0188487}, pmid = {29211769}, issn = {1932-6203}, mesh = {Arsenic/*toxicity ; Bangladesh ; Child, Preschool ; Drinking Water/*chemistry ; Drug Resistance, Microbial ; *Environmental Exposure ; Female ; Humans ; Intestines/*microbiology ; Male ; Microbiota/*drug effects/genetics ; RNA, Ribosomal, 16S/genetics ; Water Pollutants, Chemical/*toxicity ; }, abstract = {BACKGROUND: Arsenic has antimicrobial properties at high doses yet few studies have examined its effect on gut microbiota. This warrants investigation since arsenic exposure increases the risk of many diseases in which gut microbiota have been shown to play a role. We examined the association between arsenic exposure from drinking water and the composition of intestinal microbiota in children exposed to low and high arsenic levels during prenatal development and early life.
RESULTS: 16S rRNA gene sequencing revealed that children with high arsenic exposure had a higher abundance of Proteobacteria in their stool compared to matched controls with low arsenic exposure. Furthermore, whole metagenome shotgun sequencing identified 332 bacterial SEED functions that were enriched in the high exposure group. A separate model showed that these genes, which included genes involved in virulence and multidrug resistance, were positively correlated with arsenic concentration within the group of children in the high arsenic group. We performed reference free genome assembly, and identified strains of E.coli as contributors to the arsenic enriched SEED functions. Further genome annotation of the E.coli genome revealed two strains containing two different arsenic resistance operons that are not present in the gut microbiome of a recently described European human cohort (Metagenomics of the Human Intestinal Tract, MetaHIT). We then performed quantification by qPCR of two arsenic resistant genes (ArsB, ArsC). We observed that the expression of these two operons was higher among the children with high arsenic exposure compared to matched controls.
CONCLUSIONS: This preliminary study indicates that arsenic exposure early in life was associated with altered gut microbiota in Bangladeshi children. The enrichment of E.coli arsenic resistance genes in the high exposure group provides an insight into the possible mechanisms of how this toxic compound could affect gut microbiota.}, }
@article {pmid29192628, year = {2017}, author = {Anukam, KC and Agbakoba, NR}, title = {A comparative study of the oral microbiome compositions of healthy postmenopausal, premenopausal, and prepubertal Nigerian females, using 16s rrna metagenomics methods.}, journal = {Nigerian journal of clinical practice}, volume = {20}, number = {10}, pages = {1250-1258}, doi = {10.4103/njcp.njcp_32_17}, pmid = {29192628}, issn = {1119-3077}, mesh = {Adolescent ; Adult ; Aged ; Bacteria/classification/*genetics ; Child ; Female ; Humans ; Metagenomics/*methods ; *Microbiota ; Middle Aged ; Mouth/*microbiology ; Pilot Projects ; *Postmenopause ; *Premenopause ; RNA, Ribosomal, 16S/*genetics ; Young Adult ; }, abstract = {INTRODUCTION: There is a paucity of information on the oral microbiome compositions of Nigerians, mostly due to lack of appropriate molecular techniques. In this pilot study, we sought to determine and characterize the oral bacterial compositions of "healthy" females.
MATERIALS AND METHODS: Oral samples were collected from three randomly selected females aged 56, 28, and 8 years. DNA was extracted and 16S rRNA V4 region was amplified using custom-barcoded primers before sequencing with Illumina MiSeq platform. Quantitative Insights into Microbial Ecology pipeline was used for 16S rRNA recognition. Distribution of taxonomic categories at different levels of resolution was done using the ribosomal RNA similarities to entries in the REFseq protein database. Diversity score was calculated based on the inverse Simpson's index.
RESULTS: The inverse Simpson's diversity index for the postmenopausal, premenopausal, and prepubertal was 7.74, 6.95, and 7.42 respectively. A total of 12 phyla, 70 genera, and 85 species were detected. Firmicutes followed by Proteobacteria, Actinobacteria, Bacteroidetes, and Fusobacteria dominated the oral microbiome of the subjects. Streptococcus thermophilus (33.19%) was the most abundance species in subject 1, while subject 2 was highly predominated by Haemophilus parainfluenzae (80.65%), and subject 3 was predominated by Haemophilus influenzae (23.05%).
CONCLUSION: The study has revealed that bacteria with varying diversities colonized the subjects and it highlighted the importance of metagenomics in deciphering the oral bacterial compositions from females of different age groups. More studies are needed using metagenomics approach, to appreciate these bacterial organisms that are associated with health and disease in our environment.}, }
@article {pmid29191900, year = {2017}, author = {Coles, VJ and Stukel, MR and Brooks, MT and Burd, A and Crump, BC and Moran, MA and Paul, JH and Satinsky, BM and Yager, PL and Zielinski, BL and Hood, RR}, title = {Ocean biogeochemistry modeled with emergent trait-based genomics.}, journal = {Science (New York, N.Y.)}, volume = {358}, number = {6367}, pages = {1149-1154}, doi = {10.1126/science.aan5712}, pmid = {29191900}, issn = {1095-9203}, mesh = {Atlantic Ocean ; Biochemical Phenomena/genetics ; Metabolic Networks and Pathways/*genetics ; Metagenome ; *Metagenomics ; Microbial Consortia/*genetics ; Models, Biological ; Seawater/*microbiology ; Transcriptome ; }, abstract = {Marine ecosystem models have advanced to incorporate metabolic pathways discovered with genomic sequencing, but direct comparisons between models and "omics" data are lacking. We developed a model that directly simulates metagenomes and metatranscriptomes for comparison with observations. Model microbes were randomly assigned genes for specialized functions, and communities of 68 species were simulated in the Atlantic Ocean. Unfit organisms were replaced, and the model self-organized to develop community genomes and transcriptomes. Emergent communities from simulations that were initialized with different cohorts of randomly generated microbes all produced realistic vertical and horizontal ocean nutrient, genome, and transcriptome gradients. Thus, the library of gene functions available to the community, rather than the distribution of functions among specific organisms, drove community assembly and biogeochemical gradients in the model ocean.}, }
@article {pmid29187204, year = {2017}, author = {Mallick, H and Ma, S and Franzosa, EA and Vatanen, T and Morgan, XC and Huttenhower, C}, title = {Experimental design and quantitative analysis of microbial community multiomics.}, journal = {Genome biology}, volume = {18}, number = {1}, pages = {228}, doi = {10.1186/s13059-017-1359-z}, pmid = {29187204}, issn = {1474-760X}, support = {R01 HG005220/HG/NHGRI NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; U54 DK102557/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Computational Biology/methods ; DNA Barcoding, Taxonomic ; Gene Expression Profiling/methods ; Humans ; *Metabolomics/methods ; *Metagenomics/methods ; *Microbiota ; *Proteomics/methods ; *Research Design ; }, abstract = {Studies of the microbiome have become increasingly sophisticated, and multiple sequence-based, molecular methods as well as culture-based methods exist for population-scale microbiome profiles. To link the resulting host and microbial data types to human health, several experimental design considerations, data analysis challenges, and statistical epidemiological approaches must be addressed. Here, we survey current best practices for experimental design in microbiome molecular epidemiology, including technologies for generating, analyzing, and integrating microbiome multiomics data. We highlight studies that have identified molecular bioactives that influence human health, and we suggest steps for scaling translational microbiome research to high-throughput target discovery across large populations.}, }
@article {pmid29186720, year = {2017}, author = {Pampillón-González, L and Ortiz-Cornejo, NL and Luna-Guido, M and Dendooven, L and Navarro-Noya, YE}, title = {Archaeal and Bacterial Community Structure in an Anaerobic Digestion Reactor (Lagoon Type) Used for Biogas Production at a Pig Farm.}, journal = {Journal of molecular microbiology and biotechnology}, volume = {27}, number = {5}, pages = {306-317}, doi = {10.1159/000479108}, pmid = {29186720}, issn = {1660-2412}, mesh = {Anaerobiosis ; Animals ; Animals, Domestic ; Archaea/*classification/genetics/*metabolism ; Bacteria, Anaerobic/*classification/genetics/*metabolism ; *Biofuels ; *Bioreactors ; Chemical Phenomena ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Farms ; Feces/*microbiology ; *Fermentation ; Metagenome/genetics ; Metagenomics/methods ; Methane/biosynthesis ; Mexico ; Microbial Consortia/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Swine ; Waste Disposal, Fluid ; Waste Water/microbiology ; }, abstract = {Biogas production from animal waste is an economically viable way to reduce environmental pollution and produce valuable products, i.e., methane and a nutrient-rich organic waste product. An anaerobic digestion reactor for biogas production from pig waste was sampled at the entrance, middle (digestion chamber), and exit of a digester, while the bacterial and archaeal community structure was studied by 16S rRNA gene metagenomics. The number of bacterial operational taxonomic units (OTU)-97% was 3-7 times larger than that of archaeal ones. Bacteria and Archaea found in feces of animals (e.g., Clostridiaceae, Lachnospiraceae, Ruminococcaceae, Methanosarcina, Methanolobus, Methanosaeta, and Methanospirillum) dominated the entrance of the digester. The digestion chamber was dominated by anaerobic sugar-fermenting OP9 bacteria and the syntrophic bacteria Candidatus Cloacamonas (Waste Water of Evry 1; WWE1). The methanogens dominant in the digestion chamber were the acetoclastic Methanosaeta and the hydrogenothrophic Methanoculleus and Methanospirillum. Similar bacterial and archaeal groups that dominated in the middle of the digestion chamber were found in the waste that left the digester. Predicted functions associated with degradation of xenobiotic compounds were significantly different between the sampling locations. The microbial community found in an anaerobic digestion reactor loaded with pig manure contained microorganisms with biochemical capacities related to the 4 phases of methane production.}, }
@article {pmid29186317, year = {2017}, author = {Dovrolis, N and Kolios, G and Spyrou, GM and Maroulakou, I}, title = {Computational profiling of the gut-brain axis: microflora dysbiosis insights to neurological disorders.}, journal = {Briefings in bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1093/bib/bbx154}, pmid = {29186317}, issn = {1477-4054}, abstract = {Almost 2500 years after Hippocrates' observations on health and its direct association to the gastrointestinal tract, a paradigm shift has recently occurred, making the gut and its symbionts (bacteria, fungi, archaea and viruses) a point of convergence for studies. It is nowadays well established that the gut microflora's compositional diversity regulates via its genes (the microbiome) the host's health and provides preliminary insights into disease progression and regulation. The microbiome's involvement is evident in immunological and physiological studies that link changes in its biodiversity to its contributions to the host's phenotype but also in neurological investigations, substantiating the aptly named gut-brain axis. The definitive mechanisms of this last bidirectional interaction will be our main focus because it presents researchers with a new conundrum. In this review, we prospect current literature for computational analysis methodologies that accommodate the need for better understanding of the microbiome-gut-brain interactions and neurological disorder onset and progression, through cross-disciplinary systems biology applications. We will present bioinformatics tools used in exploring these synergies that help build and interpret microbial 16S ribosomal RNA data sets, produced by shotgun and high-throughput sequencing of healthy and neurological disorder samples stored in biological databases. These approaches provide alternative means for researchers to form hypotheses to their inquests faster, cheaper and swith precision. The goal of these studies relies on the integration of combined metagenomics and metabolomics assessments. An accurate characterization of the microbiome and its functionality can support new diagnostic, prognostic and therapeutic strategies for neurological disorders, customized for each individual host.}, }
@article {pmid29184025, year = {2017}, author = {Gnanaprakasam, ET and Lloyd, JR and Boothman, C and Ahmed, KM and Choudhury, I and Bostick, BC and van Geen, A and Mailloux, BJ}, title = {Microbial Community Structure and Arsenic Biogeochemistry in Two Arsenic-Impacted Aquifers in Bangladesh.}, journal = {mBio}, volume = {8}, number = {6}, pages = {}, doi = {10.1128/mBio.01326-17}, pmid = {29184025}, issn = {2150-7511}, support = {P42 ES010349/ES/NIEHS NIH HHS/United States ; }, mesh = {Arsenates/analysis ; Arsenic/*metabolism ; Arsenites/analysis ; Bacteria/*classification/*genetics ; Bangladesh ; *Biota ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Geologic Sediments/chemistry ; Groundwater/*microbiology ; Iron/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Long-term exposure to trace levels of arsenic (As) in shallow groundwater used for drinking and irrigation puts millions of people at risk of chronic disease. Although microbial processes are implicated in mobilizing arsenic from aquifer sediments into groundwater, the precise mechanism remains ambiguous. The goal of this work was to target, for the first time, a comprehensive suite of state-of-the-art molecular techniques in order to better constrain the relationship between indigenous microbial communities and the iron and arsenic mineral phases present in sediments at two well-characterized arsenic-impacted aquifers in Bangladesh. At both sites, arsenate [As(V)] was the major species of As present in sediments at depths with low aqueous As concentrations, while most sediment As was arsenite [As(III)] at depths with elevated aqueous As concentrations. This is consistent with a role for the microbial As(V) reduction in mobilizing arsenic. 16S rRNA gene analysis indicates that the arsenic-rich sediments were colonized by diverse bacterial communities implicated in both dissimilatory Fe(III) and As(V) reduction, while the correlation analyses involved phylogenetic groups not normally associated with As mobilization. Findings suggest that direct As redox transformations are central to arsenic fate and transport and that there is a residual reactive pool of both As(V) and Fe(III) in deeper sediments that could be released by microbial respiration in response to hydrologic perturbation, such as increased groundwater pumping that introduces reactive organic carbon to depth.IMPORTANCE The consumption of arsenic in waters collected from tube wells threatens the lives of millions worldwide and is particularly acute in the floodplains and deltas of southern Asia. The cause of arsenic mobilization from natural sediments within these aquifers to groundwater is complex, with recent studies suggesting that sediment-dwelling microorganisms may be the cause. In the absence of oxygen at depth, specialist bacteria are thought able to use metals within the sediments to support their metabolism. Via these processes, arsenic-contaminated iron minerals are transformed, resulting in the release of arsenic into the aquifer waters. Focusing on a field site in Bangladesh, a comprehensive, multidisciplinary study using state-of-the-art geological and microbiological techniques has helped better understand the microbes that are present naturally in a high-arsenic aquifer and how they may transform the chemistry of the sediment to potentially lethal effect.}, }
@article {pmid29184020, year = {2017}, author = {Luo, E and Aylward, FO and Mende, DR and DeLong, EF}, title = {Bacteriophage Distributions and Temporal Variability in the Ocean's Interior.}, journal = {mBio}, volume = {8}, number = {6}, pages = {}, doi = {10.1128/mBio.01903-17}, pmid = {29184020}, issn = {2150-7511}, mesh = {Bacteriophages/*classification/genetics/*isolation & purification ; *Biodiversity ; DNA, Viral/analysis/genetics ; Genotype ; Lysogeny ; Metagenomics ; *Oceans and Seas ; Seawater/*virology ; Spatio-Temporal Analysis ; }, abstract = {Bacteriophages are numerically the most abundant DNA-containing entities in the oligotrophic ocean, yet how specific phage populations vary over time and space remains to be fully explored. Here, we conducted a metagenomic time-series survey of double-stranded DNA phages throughout the water column in the North Pacific Subtropical Gyre, encompassing 1.5 years from depths of 25 to 1,000 m. Viral gene sequences were identified in assembled metagenomic samples, yielding an estimated 172,385 different viral gene families. Viral marker gene distributions suggested that lysogeny was more prevalent at mesopelagic depths than in surface waters, consistent with prior prophage induction studies using mitomycin C. A total of 129 ALOHA viral genomes and genome fragments from 20 to 108 kbp were selected for further study, which represented the most abundant phages in the water column. Phage genotypes displayed discrete population structures. Most phages persisted throughout the time-series and displayed a strong depth structure that mirrored the stratified depth distributions of co-occurring bacterial taxa in the water column. Mesopelagic phages were distinct from surface water phages with respect to diversity, gene content, putative life histories, and temporal persistence, reflecting depth-dependent differences in host genomic architectures and phage reproductive strategies. The spatiotemporal distributions of the most abundant open-ocean bacteriophages that we report here provide new insight into viral temporal persistence, life history, and virus-host-environment interactions throughout the open-ocean water column.IMPORTANCE The North Pacific Subtropical Gyre represents one of the largest biomes on the planet, where microbial communities are central mediators of ecosystem dynamics and global biogeochemical cycles. Critical members of these communities are the viruses of marine bacteria, which can alter microbial metabolism and significantly influence their survival and productivity. To better understand these viral assemblages, we conducted genomic analyses of planktonic viruses over a seasonal cycle to ocean depths of 1,000 m. We identified 172,385 different viral gene families and 129 unique virus genotypes in this open-ocean setting. The spatiotemporal distributions of the most abundant open-ocean viruses that we report here provide new insights into viral temporal variability, life history, and virus-host-environment interactions throughout the water column.}, }
@article {pmid29184019, year = {2017}, author = {Chatzidaki-Livanis, M and Coyne, MJ and Roelofs, KG and Gentyala, RR and Caldwell, JM and Comstock, LE}, title = {Gut Symbiont Bacteroides fragilis Secretes a Eukaryotic-Like Ubiquitin Protein That Mediates Intraspecies Antagonism.}, journal = {mBio}, volume = {8}, number = {6}, pages = {}, doi = {10.1128/mBio.01902-17}, pmid = {29184019}, issn = {2150-7511}, support = {R01 AI093771/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*metabolism ; *Antibiosis ; Bacterial Proteins/genetics/*secretion ; Bacteroides fragilis/growth & development/metabolism/*physiology ; DNA Transposable Elements ; Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Gene Deletion ; Humans ; Metagenomics ; Microbiota ; Mutagenesis, Insertional ; Ubiquitin/genetics/*secretion ; }, abstract = {Human gut Bacteroides species produce different types of toxins that antagonize closely related members of the gut microbiota. Some are toxic effectors delivered by type VI secretion systems, and others are non-contact-dependent secreted antimicrobial proteins. Many strains of Bacteroides fragilis secrete antimicrobial molecules, but only one of these toxins has been described to date (Bacteroidales secreted antimicrobial protein 1 [BSAP-1]). In this study, we describe a novel secreted protein produced by B. fragilis strain 638R that mediated intraspecies antagonism. Using transposon mutagenesis and deletion mutation, we identified a gene encoding a eukaryotic-like ubiquitin protein (BfUbb) necessary for toxin activity against a subset of B. fragilis strains. The addition of ubb into a heterologous background strain conferred toxic activity on that strain. We found this gene to be one of the most highly expressed in the B. fragilis genome. The mature protein is 84% similar to human ubiquitin but has an N-terminal signal peptidase I (SpI) signal sequence and is secreted extracellularly. We found that the mature 76-amino-acid synthetic protein has very potent activity, confirming that BfUbb mediates the activity. Analyses of human gut metagenomic data sets revealed that ubb is present in 12% of the metagenomes that have evidence of B. fragilis As 638R produces both BSAP-1 and BfUbb, we performed a comprehensive analysis of the toxin activity of BSAP-1 and BfUbb against a set of 40 B. fragilis strains, revealing that 75% of B. fragilis strains are targeted by one or the other of these two secreted proteins of strain 638R.IMPORTANCE We are just beginning to understand some of the important interactions that occur between microbes of the human gut microbiota that dictate the composition and abundance of its constituent members. The ability of one member to produce molecules that directly kill a coresident member has been shown among minor gut species and is just starting to be studied in the abundant Bacteroides species. Here, we show that some strains of Bacteroides fragilis have acquired a gene encoding a secreted eukaryotic-like ubiquitin protein with potent inhibitory activity against other B. fragilis stains. This is the first bacterially encoded ubiquitin-like molecule shown to function like a bacterial toxin. This molecule is an example of a gut symbiont acquiring and adapting a eukaryotic molecule likely to increase its competitiveness in the mammalian gut. Understanding antagonistic factors produced by abundant gut symbionts is an important prerequisite to properly engineer strains to colonize the gut for health benefits.}, }
@article {pmid29173869, year = {2018}, author = {Heintz-Buschart, A and Wilmes, P}, title = {Human Gut Microbiome: Function Matters.}, journal = {Trends in microbiology}, volume = {26}, number = {7}, pages = {563-574}, doi = {10.1016/j.tim.2017.11.002}, pmid = {29173869}, issn = {1878-4380}, abstract = {The human gut microbiome represents a complex ecosystem contributing essential functions to its host. Recent large-scale metagenomic studies have provided insights into its structure and functional potential. However, the functional repertoire which is actually contributed to human physiology remains largely unexplored. Here, by leveraging recent omics datasets, we challenge current assumptions regarding key attributes of the functional gut microbiome, in particular with respect to its variability. We further argue that the closing of existing gaps in functional knowledge should be addressed by a most-wanted gene list, the development and application of molecular and cellular high-throughput measurements, the development and sensible use of experimental models, as well as the direct study of observable molecular effects in the human host.}, }
@article {pmid29169786, year = {2018}, author = {Kanokratana, P and Wongwilaiwalin, S and Mhuantong, W and Tangphatsornruang, S and Eurwilaichitr, L and Champreda, V}, title = {Characterization of cellulolytic microbial consortium enriched on Napier grass using metagenomic approaches.}, journal = {Journal of bioscience and bioengineering}, volume = {125}, number = {4}, pages = {439-447}, doi = {10.1016/j.jbiosc.2017.10.014}, pmid = {29169786}, issn = {1347-4421}, mesh = {Anaerobiosis ; Bacteroidetes/genetics/isolation & purification/metabolism ; Biofuels/microbiology ; Cellulose/*metabolism ; Firmicutes/genetics/isolation & purification/metabolism ; Lignin/metabolism ; *Metagenome ; *Metagenomics ; Microbial Consortia/*genetics ; Pennisetum/*metabolism/*microbiology ; Proteobacteria/genetics/isolation & purification/metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Energy grass is a promising substrate for production of biogas by anaerobic digestion. However, the conversion efficiency is limited by the enzymatically recalcitrant nature of cellulosic wastes. In this study, an active, structurally stable mesophilic lignocellulolytic degrading microbial consortium (Np-LMC) was constructed from forest compost soil microbiota by successive subcultivation on Napier grass under facultative anoxic conditions. According to tagged 16S rRNA gene amplicon sequencing, increasing abundance of facultative Proteobacteria was found in the middle of batch cycle which was then subsequently replaced by the cellulose degraders Firmicutes and Bacteroidetes along with decreasing CMCase, xylanase, and β-glucanase activity profiles in the supernatant after 5 days of incubation. Anaerobic/facultative bacteria Dysgonomonas and Sedimentibacter and aerobic bacteria Comamonas were the major genera found in Np-LMC. The consortium was active on degradation of the native and delignified grass. Direct shotgun sequencing of the consortium metagenome revealed relatively high abundance of genes encoding for various lignocellulose degrading enzymes in 23 glycosyl hydrolase (GH) families compared to previously reported cellulolytic microbial communities in mammalian digestive tracts. Enzymes attacking cellulose and hemicellulose were dominated by GH2, 3, 5, 9, 10, 26, 28 and 43 in addition to a variety of carbohydrate esterases (CE) and auxiliary activities (AA), reflecting adaptation of the enzyme systems to the native herbaceous substrate. The consortium identified here represents the microcosm specifically bred on energy grass, with potential for enhancing degradation of fibrous substrates in bioenergy industry.}, }
@article {pmid29169088, year = {2017}, author = {Maier, L and Typas, A}, title = {Systematically investigating the impact of medication on the gut microbiome.}, journal = {Current opinion in microbiology}, volume = {39}, number = {}, pages = {128-135}, doi = {10.1016/j.mib.2017.11.001}, pmid = {29169088}, issn = {1879-0364}, mesh = {Animals ; Gastrointestinal Microbiome/*drug effects ; Humans ; Models, Biological ; Prescription Drugs/*pharmacology ; }, abstract = {In the recent years, there is accumulating evidence for a strong impact of medication on the gut microbiota composition. This evidence comes from metagenomics-based associations and extends beyond classical antibacterials to a handful of human-targeted drugs. To answer whether such effects are direct and explore their consequences in human health, we need to develop experimental platforms that will allow for systematic profiling of drug-microbiota interactions. Here, we discuss approaches, considerations, experimental setups and strategies that can be used to tackle this need, but can be also readily transmitted to related questions in the microbiome field. A comprehensive understanding of how therapeutics interact with gut microbes will open up the path for further mechanistic dissection of such interactions, and ultimately improve not only our understanding of the gut microbiome, but also drug safety and efficacy.}, }
@article {pmid29163419, year = {2017}, author = {Cabello-Yeves, PJ and Ghai, R and Mehrshad, M and Picazo, A and Camacho, A and Rodriguez-Valera, F}, title = {Reconstruction of Diverse Verrucomicrobial Genomes from Metagenome Datasets of Freshwater Reservoirs.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2131}, doi = {10.3389/fmicb.2017.02131}, pmid = {29163419}, issn = {1664-302X}, abstract = {The phylum Verrucomicrobia contains freshwater representatives which remain poorly studied at the genomic, taxonomic, and ecological levels. In this work we present eighteen new reconstructed verrucomicrobial genomes from two freshwater reservoirs located close to each other (Tous and Amadorio, Spain). These metagenome-assembled genomes (MAGs) display a remarkable taxonomic diversity inside the phylum and comprise wide ranges of estimated genome sizes (from 1.8 to 6 Mb). Among all Verrucomicrobia studied we found some of the smallest genomes of the Spartobacteria and Opitutae classes described so far. Some of the Opitutae family MAGs were small, cosmopolitan, with a general heterotrophic metabolism with preference for carbohydrates, and capable of xylan, chitin, or cellulose degradation. Besides, we assembled large copiotroph genomes, which contain a higher number of transporters, polysaccharide degrading pathways and in general more strategies for the uptake of nutrients and carbohydrate-based metabolic pathways in comparison with the representatives with the smaller genomes. The diverse genomes revealed interesting features like green-light absorbing rhodopsins and a complete set of genes involved in nitrogen fixation. The large diversity in genome sizes and physiological properties emphasize the diversity of this clade in freshwaters enlarging even further the already broad eco-physiological range of these microbes.}, }
@article {pmid29161643, year = {2018}, author = {Silbande, A and Adenet, S and Chopin, C and Cornet, J and Smith-Ravin, J and Rochefort, K and Leroi, F}, title = {Effect of vacuum and modified atmosphere packaging on the microbiological, chemical and sensory properties of tropical red drum (Sciaenops ocellatus) fillets stored at 4°C.}, journal = {International journal of food microbiology}, volume = {266}, number = {}, pages = {31-41}, doi = {10.1016/j.ijfoodmicro.2017.10.015}, pmid = {29161643}, issn = {1879-3460}, mesh = {Animals ; Bacteria/isolation & purification ; Biogenic Amines/analysis ; Colony Count, Microbial ; Fishes/*microbiology ; *Food Microbiology ; Food Packaging/*standards ; Metagenomics ; Microbiota ; Nitrogen/analysis ; *Vacuum ; }, abstract = {AIMS: The effect of vacuum (VP - 4°C) and CO2/N2-atmosphere (MAP - 4°C) packaging on the quality of red drum fillets compared with whole gutted iced fish was investigated.
METHODS AND RESULTS: A metagenomic approach, bacterial enumeration and isolation, biochemical and sensory analyses were carried out. The organoleptic rejection of whole fish was observed at day 15 whereas VP and MAP fillets appeared unacceptable only after 29days. At these dates, total mesophilic counts reached 107-108CFU g-1. According to Illumina MiSeq sequencing, Arthrobacter, Chryseobacterium, Brevibacterium, Staphylococcus and Kocuria were the main genera of the fresh red drum fillets. At the sensory rejection time, lactic acid bacteria (LAB), particularly Carnobacterium sp., dominated the microbiota of both types of packaging. The pH value of fresh samples was between 5.96 and 6.37 and did not vary greatly in all trials. Total volatile basic nitrogen (TVBN) and trimethylamine (TMA) concentrations were low and not represent reliable indicators of the spoilage, contrary to some biogenic amines (cadaverine, putrescine and tyramine).
CONCLUSION: Chilled packed fillets of red drum have an extended shelf-life compared to whole gutted iced fish. Overall, few differences in sensory and microbial quality were observed between the VP and MAP samples.
Next-Generation Sequencing (NGS) provided data on the microbiota of a tropical fish.}, }
@article {pmid29155257, year = {2018}, author = {Fonseca, JP and Hoffmann, L and Cabral, BCA and Dias, VHG and Miranda, MR and de Azevedo Martins, AC and Boschiero, C and Bastos, WR and Silva, R}, title = {Contrasting the microbiomes from forest rhizosphere and deeper bulk soil from an Amazon rainforest reserve.}, journal = {Gene}, volume = {642}, number = {}, pages = {389-397}, doi = {10.1016/j.gene.2017.11.039}, pmid = {29155257}, issn = {1879-0038}, mesh = {Archaea/*classification/genetics/isolation & purification ; Bacteria/*classification/genetics/isolation & purification ; Cluster Analysis ; Fungi/*classification/genetics/isolation & purification ; Metagenomics/methods ; Microbiota ; Rainforest ; Rhizosphere ; Sequence Analysis, DNA/methods ; *Soil Microbiology ; }, abstract = {Pristine forest ecosystems provide a unique perspective for the study of plant-associated microbiota since they host a great microbial diversity. Although the Amazon forest is one of the hotspots of biodiversity around the world, few metagenomic studies described its microbial community diversity thus far. Understanding the environmental factors that can cause shifts in microbial profiles is key to improving soil health and biogeochemical cycles. Here we report a taxonomic and functional characterization of the microbiome from the rhizosphere of Brosimum guianense (Snakewood), a native tree, and bulk soil samples from a pristine Brazilian Amazon forest reserve (Cuniã), for the first time by the shotgun approach. We identified several fungi and bacteria taxon significantly enriched in forest rhizosphere compared to bulk soil samples. For archaea, the trend was the opposite, with many archaeal phylum and families being considerably more enriched in bulk soil compared to forest rhizosphere. Several fungal and bacterial decomposers like Postia placenta and Catenulispora acidiphila which help maintain healthy forest ecosystems were found enriched in our samples. Other bacterial species involved in nitrogen (Nitrobacter hamburgensis and Rhodopseudomonas palustris) and carbon cycling (Oligotropha carboxidovorans) were overrepresented in our samples indicating the importance of these metabolic pathways for the Amazon rainforest reserve soil health. Hierarchical clustering based on taxonomic similar microbial profiles grouped the forest rhizosphere samples in a distinct clade separated from bulk soil samples. Principal coordinate analysis of our samples with publicly available metagenomes from the Amazon region showed grouping into specific rhizosphere and bulk soil clusters, further indicating distinct microbial community profiles. In this work, we reported significant shifts in microbial community structure between forest rhizosphere and bulk soil samples from an Amazon forest reserve that are probably caused by more than one environmental factors such as rhizosphere and soil depth.}, }
@article {pmid29146247, year = {2018}, author = {Vepštaitė-Monstavičė, I and Lukša, J and Stanevičienė, R and Strazdaitė-Žielienė, Ž and Yurchenko, V and Serva, S and Servienė, E}, title = {Distribution of apple and blackcurrant microbiota in Lithuania and the Czech Republic.}, journal = {Microbiological research}, volume = {206}, number = {}, pages = {1-8}, doi = {10.1016/j.micres.2017.09.004}, pmid = {29146247}, issn = {1618-0623}, mesh = {Bacteria/classification/genetics/isolation & purification ; Czech Republic ; DNA, Bacterial/isolation & purification ; DNA, Fungal/isolation & purification ; Ecology ; Fruit/microbiology ; Fungi/classification/genetics/isolation & purification ; Lithuania ; Malus/*microbiology ; Metagenomics/methods ; *Microbial Consortia ; *Microbiota/genetics ; Phylogeny ; Ribes/*microbiology ; }, abstract = {The microbial assemblies on the surface of plants correlate with specific climatic features, suggesting a direct link between environmental conditions and microbial inhabitation patterns. At the same time however, microbial communities demonstrate distinct profiles depending on the plant species and region of origin. In this study, we report Next Generation Sequencing-based metagenomic analysis of microbial communities associated with apple and blackcurrant fruits harvested from Lithuania and the Czech Republic. Differences in the taxonomic composition of eukaryotic and prokaryotic microorganisms were observed between plant types. Our results revealed limited geographic differentiation between the bacterial and fungal communities associated with apples. In contrast, blackcurrant berries harvested from different regions demonstrated high diversity in both bacterial and fungal microbiota structures. Among fungal and bacterial microorganisms, we identified both potentially beneficial (Cryptococcus, Hanseniaspora, Massilia, Rhodotorula, Sphingomonas) and phytopathogenic microorganisms (Cladosporium, Pantoea, Phoma, Pseudomonas, Septoria, Taphrina) indicating their important roles in ecological and evolutionary processes.}, }
@article {pmid29138298, year = {2017}, author = {Koskinen, K and Pausan, MR and Perras, AK and Beck, M and Bang, C and Mora, M and Schilhabel, A and Schmitz, R and Moissl-Eichinger, C}, title = {First Insights into the Diverse Human Archaeome: Specific Detection of Archaea in the Gastrointestinal Tract, Lung, and Nose and on Skin.}, journal = {mBio}, volume = {8}, number = {6}, pages = {}, doi = {10.1128/mBio.00824-17}, pmid = {29138298}, issn = {2150-7511}, mesh = {Archaea/*classification/genetics/*isolation & purification ; Gastrointestinal Tract/*microbiology ; Humans ; Lung/*microbiology ; Metagenomics/methods ; *Microbiota ; Nose/*microbiology ; Polymerase Chain Reaction/methods ; Skin/*microbiology ; }, abstract = {Human-associated archaea remain understudied in the field of microbiome research, although in particular methanogenic archaea were found to be regular commensals of the human gut, where they represent keystone species in metabolic processes. Knowledge on the abundance and diversity of human-associated archaea is extremely limited, and little is known about their function(s), their overall role in human health, or their association with parts of the human body other than the gastrointestinal tract and oral cavity. Currently, methodological issues impede the full assessment of the human archaeome, as bacteria-targeting protocols are unsuitable for characterization of the full spectrum of Archaea The goal of this study was to establish conservative protocols based on specifically archaea-targeting, PCR-based methods to retrieve first insights into the archaeomes of the human gastrointestinal tract, lung, nose, and skin. Detection of Archaea was highly dependent on primer selection and the sequence processing pipeline used. Our results enabled us to retrieve a novel picture of the human archaeome, as we found for the first time Methanobacterium and Woesearchaeota (DPANN superphylum) to be associated with the human gastrointestinal tract and the human lung, respectively. Similar to bacteria, human-associated archaeal communities were found to group biogeographically, forming (i) the thaumarchaeal skin landscape, (ii) the (methano)euryarchaeal gastrointestinal tract, (iii) a mixed skin-gastrointestinal tract landscape for the nose, and (iv) a woesearchaeal lung landscape. On the basis of the protocols we used, we were able to detect unexpectedly high diversity of archaea associated with different body parts.IMPORTANCE In summary, our study highlights the importance of the primers and data processing pipeline used to study the human archaeome. We were able to establish protocols that revealed the presence of previously undetected Archaea in all of the tissue samples investigated and to detect biogeographic patterns of the human archaeome in the gastrointestinal tract and on the skin and for the first time in the respiratory tract, i.e., the nose and lungs. Our results are a solid basis for further investigation of the human archaeome and, in the long term, discovery of the potential role of archaea in human health and disease.}, }
@article {pmid29128292, year = {2017}, author = {Herzog, B and Dötsch, A and Lemmer, H and Horn, H and Müller, E}, title = {Profiling 5-tolyltriazole biodegrading sludge communities using next-generation sequencing and denaturing gradient gel electrophoresis.}, journal = {Systematic and applied microbiology}, volume = {40}, number = {8}, pages = {508-515}, doi = {10.1016/j.syapm.2017.09.007}, pmid = {29128292}, issn = {1618-0984}, mesh = {Betaproteobacteria/classification/isolation & purification/metabolism ; Biodegradation, Environmental ; Bioreactors/*microbiology ; Comamonadaceae/isolation & purification/metabolism ; Denaturing Gradient Gel Electrophoresis/methods ; Flavobacterium/isolation & purification/metabolism ; High-Throughput Nucleotide Sequencing ; Phyllobacteriaceae/classification/isolation & purification/metabolism ; Pseudomonas/isolation & purification/metabolism ; Sewage/*microbiology ; Triazoles/analysis/*metabolism ; Water Pollutants, Chemical/analysis/*metabolism ; }, abstract = {Efficient biodegradation of 5-tolyltriazole (5-TTri) in wastewater treatment would minimize its potential detrimental effects on aquatic systems. Therefore, in order to profile 5-TTri biodegrading activated sludge communities (ASC) by DGGE and NGS, acclimation experiments with (i) easily degradable substrates, and (ii) various complex substrates mimicking wastewater conditions were performed. DGGE revealed four genera: Aminobacter (family Phyllobacteriaceae), Flavobacterium (family Flavobacteriaceae), Pseudomonas (family Pseudomonaceae), and Hydrogenophaga (family Comamonadaceae). Metagenomics (DNA) revealed the dominant families Alcaligenaceae, Pseudomonadaceae and Comamonadaceae that also represented the most active families at the RNA level (metatranscriptomics), which might indicate their importance for 5-TTri biodegradation. ASC acclimation and the composition of the substrate significantly affected 5-TTri biodegradation and the development of biodegrading communities. Using acetate only, a moderate 5-TTri degrading community was detected with a very low biodiversity and Pseudomonas spp. as dominant organisms. In contrast, setups fed 'sludge supernatant' (a complex substrate) efficiently biodegraded 5-TTri and formed a more diverse microbial community but with Hydrogenophaga spp. as the dominant group. Finally, a hypothetical 5-TTri biodegradation pathway was constructed based exclusively on the detected, biodegradation-related, Hydrogenophaga spp. genes.}, }
@article {pmid29126267, year = {2017}, author = {Mancabelli, L and Milani, C and Lugli, GA and Turroni, F and Cocconi, D and van Sinderen, D and Ventura, M}, title = {Identification of universal gut microbial biomarkers of common human intestinal diseases by meta-analysis.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {12}, pages = {}, doi = {10.1093/femsec/fix153}, pmid = {29126267}, issn = {1574-6941}, mesh = {Bacteria/*classification/genetics/*isolation & purification ; Biodiversity ; Biomarkers ; Colitis, Ulcerative/*microbiology ; Crohn Disease/*microbiology ; Enterocolitis, Pseudomembranous/*microbiology ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Intestines/microbiology/pathology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Intestinal diseases, such as Crohn's disease (CD), ulcerative colitis (UC) and pseudomembranous colitis (CDI), are among the most common diseases in humans and may lead to more serious pathologies, e.g. colorectal cancer (CRC). Next generation sequencing has in recent years allowed the identification of correlations between intestinal bacteria and diseases, although the formulation of universal gut microbial biomarkers for such diseases is only in its infancy. In the current study, we selected and reanalyzed a total of 3048 public datasets obtained from 16S rRNA profiling of individuals affected by CD, UC, CDI and CRC. This meta-analysis revealed possible biases in the reconstruction of the gut microbiota composition due to the use of different primer pairs employed for PCR of 16S rRNA gene fragments. Notably, this approach also identified common features of individuals affected by gut diseases (DS), including lower biodiversity compared to control subjects. Moreover, potential universal intestinal disease microbial biomarkers were identified through cross-disease comparisons. In detail, CTRL showed high abundance of the genera Barnesiella, Ruminococcaceae UCG-005, Alistipes, Christensenellaceae R-7 group and unclassified member of Lachnospiraceae family, while DS exhibited high abundance of Lactobacillus, unclassified member of Erysipelotrichaceae family and Streptococcus genera.}, }
@article {pmid29126050, year = {2018}, author = {Abia, ALK and Alisoltani, A and Keshri, J and Ubomba-Jaswa, E}, title = {Metagenomic analysis of the bacterial communities and their functional profiles in water and sediments of the Apies River, South Africa, as a function of land use.}, journal = {The Science of the total environment}, volume = {616-617}, number = {}, pages = {326-334}, doi = {10.1016/j.scitotenv.2017.10.322}, pmid = {29126050}, issn = {1879-1026}, mesh = {Bacteria/classification ; Biodiversity ; DNA, Bacterial/isolation & purification ; Geologic Sediments/*microbiology ; *Metagenomics ; RNA, Ribosomal, 16S ; Rivers/*microbiology ; South Africa ; *Water Microbiology ; }, abstract = {Water quality is an important public health issue given that the presence of pathogenic organisms in such waters can adversely affect human and animal health. Despite the numerous studies conducted to assess the quality of environmental waters in many countries, limited efforts have been put on investigating the microbial quality of the sediments in developing countries and how this relates to different land uses. The present study evaluated the bacterial diversity in water and sediments in a highly used South African river to find out how the different land uses influenced the bacterial diversity, and to verify the human diseases functional classes of the bacterial populations. Samples were collected on river stretches influenced by an informal, a peri-urban and a rural settlement. Genomic DNA was extracted from water and sediment samples and sequenced on an Illumina® MiSeq platform targeting the 16S rRNA gene variable region V3-V4 from the genomic DNA. Metagenomic data analysis revealed that there was a great diversity in the microbial populations associated with the different land uses, with the informal settlement having the most considerable influence on the bacterial diversity in the water and sediments of the Apies River. The Proteobacteria (69.8%), Cyanobacteria (4.3%), Bacteroidetes (2.7%), and Actinobacteria (2.7%) were the most abundant phyla; the Alphaproteobacteria, Betaproteobacteria and Anaerolineae were the most recorded classes. Also, the sediments had a greater diversity and abundance in bacterial population than the water column. The functional profiles of the bacterial populations revealed an association with many human diseases including cancer pathways. Further studies that would isolate these potentially pathogenic organisms in the aquatic environment are therefore needed as this would help in protecting the lives of communities using such rivers, especially against emerging bacterial pathogens.}, }
@article {pmid29124770, year = {2018}, author = {Dulski, T and Zakęś, Z and Ciesielski, S}, title = {Characterization of the gut microbiota in early life stages of pikeperch Sander lucioperca.}, journal = {Journal of fish biology}, volume = {92}, number = {1}, pages = {94-104}, doi = {10.1111/jfb.13496}, pmid = {29124770}, issn = {1095-8649}, mesh = {Animals ; Aquaculture ; DNA, Bacterial/chemistry ; *Gastrointestinal Microbiome ; Metagenomics ; Perches/genetics/growth & development/*microbiology ; Proteobacteria ; RNA, Ribosomal, 16S/genetics ; }, abstract = {This study characterized the gastrointestinal microbiome of nine juvenile farmed pikeperch Sander lucioperca using a metagenomics approach based on bacterial 16S rRNA gene sequencing. Potential changes in the gut microbiota during 2 months of S. lucioperca juvenile life were investigated. Results revealed that gut microbiota was dominated by Proteobacteria (95-92%), while other phyla Firmicutes (1-1·5%) and Actinobacteria (0·9-1·5%) were less abundant. At the family level, fish-gut microbiota were dominated by Enterobacteriaceae, which constituted c. 83% of all DNA sequence reads. Such a situation was present in all of the examined fish except one, which showed a different proportion of particular microbial taxa than the other fish. In this fish, a higher relative abundance (%) of Fusobacteria (21·0%), Bacteroidetes (9·5%) and Firmicutes (7·5%) was observed. There were no significant differences in the gut microbiome structure at different stages of development in the examined fish. This may indicate that Proteobacteria inhabiting the gut microbiota at an early stage of life are a necessary component of the pikeperch microbiome that may support proper nutrition of the fish. The information obtained on the gut microbiome could be useful in determining juvenile S. lucioperca health and improving rearing conditions by welfare monitoring in aquaculture.}, }
@article {pmid29120486, year = {2017}, author = {Miossec, MJ and Valenzuela, SL and Mendez, KN and Castro-Nallar, E}, title = {Computational Methods for Human Microbiome Analysis.}, journal = {Current protocols in microbiology}, volume = {47}, number = {}, pages = {1E.14.1-1E.14.17}, doi = {10.1002/cpmc.41}, pmid = {29120486}, issn = {1934-8533}, mesh = {Computational Biology/*methods ; Humans ; Metagenomics/*methods ; *Microbiota ; }, abstract = {As the field of microbiomics advances, the burden of computational work that scientists need to perform in order to extract biological insight has grown accordingly. Likewise, while human microbiome analyses are increasingly shifting toward a greater integration of various high-throughput data types, a core number of methods form the basis of nearly every study. In this unit, we present step-by-step protocols for five core stages of human microbiome research. The protocols presented in this unit provide a base case for human microbiome analysis, complete with sufficient detail for researchers to tailor certain aspects of the protocols to the specificities of their data. © 2017 by John Wiley & Sons, Inc.}, }
@article {pmid29118049, year = {2017}, author = {Milani, C and Duranti, S and Bottacini, F and Casey, E and Turroni, F and Mahony, J and Belzer, C and Delgado Palacio, S and Arboleya Montes, S and Mancabelli, L and Lugli, GA and Rodriguez, JM and Bode, L and de Vos, W and Gueimonde, M and Margolles, A and van Sinderen, D and Ventura, M}, title = {The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {81}, number = {4}, pages = {}, doi = {10.1128/MMBR.00036-17}, pmid = {29118049}, issn = {1098-5557}, mesh = {Biomarkers/analysis ; Breast Feeding ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Gastrointestinal Tract/*microbiology ; Humans ; Immune System/*microbiology ; Infant ; *Infant Health ; Intestinal Diseases/microbiology ; *Maternal-Fetal Exchange ; Milk, Human/chemistry ; Pregnancy ; Probiotics/therapeutic use ; Symbiosis ; Whole Genome Sequencing ; }, abstract = {The human gut microbiota is engaged in multiple interactions affecting host health during the host's entire life span. Microbes colonize the neonatal gut immediately following birth. The establishment and interactive development of this early gut microbiota are believed to be (at least partially) driven and modulated by specific compounds present in human milk. It has been shown that certain genomes of infant gut commensals, in particular those of bifidobacterial species, are genetically adapted to utilize specific glycans of this human secretory fluid, thus representing a very intriguing example of host-microbe coevolution, where both partners are believed to benefit. In recent years, various metagenomic studies have tried to dissect the composition and functionality of the infant gut microbiome and to explore the distribution across the different ecological niches of the infant gut biogeography of the corresponding microbial consortia, including those corresponding to bacteria and viruses, in healthy and ill subjects. Such analyses have linked certain features of the microbiota/microbiome, such as reduced diversity or aberrant composition, to intestinal illnesses in infants or disease states that are manifested at later stages of life, including asthma, inflammatory bowel disease, and metabolic disorders. Thus, a growing number of studies have reported on how the early human gut microbiota composition/development may affect risk factors related to adult health conditions. This concept has fueled the development of strategies to shape the infant microbiota composition based on various functional food products. In this review, we describe the infant microbiota, the mechanisms that drive its establishment and composition, and how microbial consortia may be molded by natural or artificial interventions. Finally, we discuss the relevance of key microbial players of the infant gut microbiota, in particular bifidobacteria, with respect to their role in health and disease.}, }
@article {pmid29117585, year = {2018}, author = {Zainun, MY and Simarani, K}, title = {Metagenomics profiling for assessing microbial diversity in both active and closed landfills.}, journal = {The Science of the total environment}, volume = {616-617}, number = {}, pages = {269-278}, doi = {10.1016/j.scitotenv.2017.10.266}, pmid = {29117585}, issn = {1879-1026}, mesh = {Archaea/classification ; Bacteria/classification ; Biodiversity ; DNA, Archaeal/isolation & purification ; DNA, Bacterial/isolation & purification ; Malaysia ; *Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/isolation & purification ; *Soil Microbiology ; *Waste Disposal Facilities ; }, abstract = {The municipal landfill is an example of human-made environment that harbours some complex diversity of microorganism communities. To evaluate this complexity, the structures of bacterial communities in active (operational) and closed (non-operational) landfills in Malaysia were analysed with culture independent metagenomics approaches. Several points of soil samples were collected from 0 to 20cm depth and were subjected to physicochemical test, such as temperature, pH, and moisture content. In addition, the heavy metal contamination was determined by using ICPMS. The bacterial enumeration was examined on nutrient agar (NA) plates aerobically at 30°C. The soil DNA was extracted, purified and amplified prior to sequence the 16S rRNA gene for statistical and bioinformatics analyses. As a result, the average of bacteria for the closed landfill was higher compared to that for the active landfill at 9.16×107 and 1.50×107, respectively. The higher bacterial OTUs sequenced was also recorded in closed landfills compared to active landfill i.e. 6625 and 4552 OTUs respectively. The data from both landfills showed that the predominant phyla belonged to Proteobacteria (55.7%). On average, Bacteroidetes was the second highest phylum followed by Firmicutes for the active landfill. While the phyla for communities in closed landfill were dominated by phyla from Acidobacteria and Actinobacteria. There was also Euryarchaeota (Archaea) which became a minor phylum that was detected in active landfill, but almost completely absent in closed landfill. As such, the composition of bacterial communities suggests some variances between the bacterial communities found in active and closed landfills. Thus, this study offers new clues pertaining to bacterial diversity pattern between the varied types of landfills studied.}, }
@article {pmid29115413, year = {2018}, author = {Meng, F and Chen, T and Wang, X and Wang, X and Wei, H and Tian, P and Wang, H and Zhao, X and Shen, L and Xin, H}, title = {Evaluation of the accuracy and sensitivity of high‑throughput sequencing technology using known microbiota.}, journal = {Molecular medicine reports}, volume = {17}, number = {1}, pages = {408-413}, doi = {10.3892/mmr.2017.7849}, pmid = {29115413}, issn = {1791-3004}, mesh = {Biodiversity ; Computational Biology/methods ; Genome, Bacterial ; Genomics/methods ; *High-Throughput Nucleotide Sequencing/methods/standards ; *Metagenome ; *Metagenomics/methods/standards ; *Microbiota ; }, abstract = {Next generation sequencing provides an excellent platform to explore microbiota in any given environment, and little work is required to evaluate the accuracy and sensitivity of high‑throughput sequencing technology. In the present study, a known microbiota containing Escherichia coli, Lactobacillus plantarum, Streptococcus thermophilus, Bifidobacterium bifidum, Bacillus subtilis, Enterococcus faecalis and Salmonella typhimurium was used to evaluate the high‑throughput sequencing technology. The results suggested that there were 122.7 operational taxonomic units (OTUs) in all groups, which is 17.5‑fold (the whole OTU number/the actual bacterial number) greater compared with the actual microbial number in each group, and the Venn method indicated that only 46.38% (64/138), 58.70% (81/138), 86.13% (118/137), 83.57% (117/140) and 89.29% (125/140) of the common OTUs were identified in groups A, B, C, D and E, of which the majority of OTUs did not belong to known bacteria. In addition, the DNA extraction and amplification efficiency failed to identify bacteria at the phylum, class, order, family, genus and species levels, which may further increase false information of microbial analysis. In conclusion, the present study provided basic datato investigate the potential drawbacks of high‑throughput sequencing technology, which will help researchers to avoid exaggerating the bacterial number when this technology is applied to study microbiota in particular environments.}, }
@article {pmid29113561, year = {2017}, author = {Rahman, MA and LaPierre, N and Rangwala, H and Barbara, D}, title = {Metagenome sequence clustering with hash-based canopies.}, journal = {Journal of bioinformatics and computational biology}, volume = {15}, number = {6}, pages = {1740006}, doi = {10.1142/S0219720017400066}, pmid = {29113561}, issn = {1757-6334}, abstract = {Metagenomics is the collective sequencing of co-existing microbial communities which are ubiquitous across various clinical and ecological environments. Due to the large volume and random short sequences (reads) obtained from community sequences, analysis of diversity, abundance and functions of different organisms within these communities are challenging tasks. We present a fast and scalable clustering algorithm for analyzing large-scale metagenome sequence data. Our approach achieves efficiency by partitioning the large number of sequence reads into groups (called canopies) using hashing. These canopies are then refined by using state-of-the-art sequence clustering algorithms. This canopy-clustering (CC) algorithm can be used as a pre-processing phase for computationally expensive clustering algorithms. We use and compare three hashing schemes for canopy construction with five popular and state-of-the-art sequence clustering methods. We evaluate our clustering algorithm on synthetic and real-world 16S and whole metagenome benchmarks. We demonstrate the ability of our proposed approach to determine meaningful Operational Taxonomic Units (OTU) and observe significant speedup with regards to run time when compared to different clustering algorithms. We also make our source code publicly available on Github. a.}, }
@article {pmid29107912, year = {2018}, author = {Oh, S and Hammes, F and Liu, WT}, title = {Metagenomic characterization of biofilter microbial communities in a full-scale drinking water treatment plant.}, journal = {Water research}, volume = {128}, number = {}, pages = {278-285}, doi = {10.1016/j.watres.2017.10.054}, pmid = {29107912}, issn = {1879-2448}, mesh = {Bacteria/genetics ; Biofilms ; Charcoal ; Drinking Water ; Filtration ; *Metagenome ; Metagenomics ; *Microbial Consortia ; Phylogeny ; Silicon Dioxide ; *Water Microbiology ; *Water Purification ; }, abstract = {Microorganisms inhabiting filtration media of a drinking water treatment plant can be beneficial, because they metabolize biodegradable organic matter from source waters and those formed during disinfection processes, leading to the production of biologically stable drinking water. However, which microbial consortia colonize filters and what metabolic capacity they possess remain to be investigated. To gain insights into these issues, we performed metagenome sequencing and analysis of microbial communities in three different filters of a full-scale drinking water treatment plant (DWTP). Filter communities were sampled from a rapid sand filter (RSF), granular activated carbon filter (GAC), and slow sand filter (SSF), and from the Schmutzdecke (SCM, a biologically active scum layer accumulated on top of SSF), respectively. Analysis of community phylogenetic structure revealed that the filter bacterial communities significantly differed from those in the source water and final effluent communities, respectively. Network analysis identified a filter-specific colonization pattern of bacterial groups. Bradyrhizobiaceae were abundant in GAC, whereas Nitrospira were enriched in the sand-associated filters (RSF, SCM, and SSF). The GAC community was enriched with functions associated with aromatics degradation, many of which were encoded by Rhizobiales (∼30% of the total GAC community). Predicting minimum generation time (MGT) of prokaryotic communities suggested that the GAC community potentially select fast-growers (<15 h of MGT) among the four filter communities, consistent with the highest dissolved organic matter removal rate by GAC. Our findings provide new insights into the community phylogenetic structure, colonization pattern, and metabolic capacity that potentially contributes to organic matter removal achieved in the biofiltration stages of the full-scale DWTP.}, }
@article {pmid29101651, year = {2017}, author = {Quach, D and Britton, RA}, title = {Gut Microbiota and Bone Health.}, journal = {Advances in experimental medicine and biology}, volume = {1033}, number = {}, pages = {47-58}, doi = {10.1007/978-3-319-66653-2_4}, pmid = {29101651}, issn = {0065-2598}, mesh = {Animals ; Bone Remodeling/*physiology ; Bone and Bones/*physiology ; Brain/physiology ; Gastrointestinal Microbiome/drug effects/*physiology ; Gastrointestinal Tract/microbiology/*physiology ; Humans ; Prebiotics/administration & dosage ; Probiotics/administration & dosage ; Signal Transduction/drug effects ; }, abstract = {The past decade has seen an explosion of research in the area of how the bacteria that inhabit the human body impact health and disease. One of the more surprising concepts to emerge from this work is the ability of the intestinal microbiota to impact virtually all systems in the body. Recently, the role of gut bacteria in bone health and disease has received more significant attention. In this chapter, we review what has been learned about how the gut microbiome impacts bone health and discuss possible mechanisms of how the gut-bone axis may be connected. We also discuss the use of therapeutic microbes in the modulation of bone health. Finally, we propose an emerging field of the gut-brain-bone axis, in which the gut drives bone physiology via regulation of key hormones that are originally synthesized in the brain.}, }
@article {pmid29097494, year = {2018}, author = {Routy, B and Le Chatelier, E and Derosa, L and Duong, CPM and Alou, MT and Daillère, R and Fluckiger, A and Messaoudene, M and Rauber, C and Roberti, MP and Fidelle, M and Flament, C and Poirier-Colame, V and Opolon, P and Klein, C and Iribarren, K and Mondragón, L and Jacquelot, N and Qu, B and Ferrere, G and Clémenson, C and Mezquita, L and Masip, JR and Naltet, C and Brosseau, S and Kaderbhai, C and Richard, C and Rizvi, H and Levenez, F and Galleron, N and Quinquis, B and Pons, N and Ryffel, B and Minard-Colin, V and Gonin, P and Soria, JC and Deutsch, E and Loriot, Y and Ghiringhelli, F and Zalcman, G and Goldwasser, F and Escudier, B and Hellmann, MD and Eggermont, A and Raoult, D and Albiges, L and Kroemer, G and Zitvogel, L}, title = {Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors.}, journal = {Science (New York, N.Y.)}, volume = {359}, number = {6371}, pages = {91-97}, doi = {10.1126/science.aan3706}, pmid = {29097494}, issn = {1095-9203}, mesh = {Animals ; Anti-Bacterial Agents/therapeutic use ; Antibodies, Monoclonal/therapeutic use ; CD4 Antigens/immunology ; *Fecal Microbiota Transplantation ; Feces/microbiology ; Gastrointestinal Microbiome/genetics/*immunology ; Humans ; Immunotherapy/*methods ; Interleukin-12/immunology ; Metagenome/genetics ; Mice ; Neoplasms/*therapy ; Programmed Cell Death 1 Receptor/*antagonists & inhibitors ; Receptors, CCR/immunology ; Receptors, CXCR3/immunology ; T-Lymphocytes/immunology ; Verrucomicrobia/genetics/immunology ; }, abstract = {Immune checkpoint inhibitors (ICIs) targeting the PD-1/PD-L1 axis induce sustained clinical responses in a sizable minority of cancer patients. We found that primary resistance to ICIs can be attributed to abnormal gut microbiome composition. Antibiotics inhibited the clinical benefit of ICIs in patients with advanced cancer. Fecal microbiota transplantation (FMT) from cancer patients who responded to ICIs into germ-free or antibiotic-treated mice ameliorated the antitumor effects of PD-1 blockade, whereas FMT from nonresponding patients failed to do so. Metagenomics of patient stool samples at diagnosis revealed correlations between clinical responses to ICIs and the relative abundance of Akkermansia muciniphila Oral supplementation with A. muciniphila after FMT with nonresponder feces restored the efficacy of PD-1 blockade in an interleukin-12-dependent manner by increasing the recruitment of CCR9+CXCR3+CD4+ T lymphocytes into mouse tumor beds.}, }
@article {pmid29096601, year = {2017}, author = {Alcon-Giner, C and Caim, S and Mitra, S and Ketskemety, J and Wegmann, U and Wain, J and Belteki, G and Clarke, P and Hall, LJ}, title = {Optimisation of 16S rRNA gut microbiota profiling of extremely low birth weight infants.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {841}, doi = {10.1186/s12864-017-4229-x}, pmid = {29096601}, issn = {1471-2164}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Bifidobacterium/drug effects/genetics/isolation & purification/physiology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/drug effects/*genetics ; Genomics/*methods ; Humans ; Infant ; *Infant, Extremely Low Birth Weight ; Lactobacillus/drug effects/genetics/isolation & purification/physiology ; Male ; Probiotics/pharmacology ; RNA, Ribosomal, 16S/*genetics ; Risk ; Sequence Analysis, RNA/*methods ; }, abstract = {BACKGROUND: Infants born prematurely, particularly extremely low birth weight infants (ELBW) have altered gut microbial communities. Factors such as maternal health, gut immaturity, delivery mode, and antibiotic treatments are associated with microbiota disturbances, and are linked to an increased risk of certain diseases such as necrotising enterocolitis. Therefore, there is a requirement to optimally characterise microbial profiles in this at-risk cohort, via standardisation of methods, particularly for studying the influence of microbiota therapies (e.g. probiotic supplementation) on community profiles and health outcomes. Profiling of faecal samples using the 16S rRNA gene is a cost-efficient method for large-scale clinical studies to gain insights into the gut microbiota and additionally allows characterisation of cohorts were sample quantities are compromised (e.g. ELBW infants). However, DNA extraction method, and the 16S rRNA region targeted can significantly change bacterial community profiles obtained, and so confound comparisons between studies. Thus, we sought to optimise a 16S rRNA profiling protocol to allow standardisation for studying ELBW infant faecal samples, with or without probiotic supplementation.
METHODS: Using ELBW faecal samples, we compared three different DNA extraction methods, and subsequently PCR amplified and sequenced three hypervariable regions of the 16S rRNA gene (V1 + V2 + V3), (V4 + V5) and (V6 + V7 + V8), and compared two bioinformatics approaches to analyse results (OTU and paired end). Paired shotgun metagenomics was used as a 'gold-standard'.
RESULTS: Results indicated a longer bead-beating step was required for optimal bacterial DNA extraction and that sequencing regions (V1 + V2 + V3) and (V6 + V7 + V8) provided the most representative taxonomic profiles, which was confirmed via shotgun analysis. Samples sequenced using the (V4 + V5) region were found to be underrepresented in specific taxa including Bifidobacterium, and had altered diversity profiles. Both bioinformatics 16S rRNA pipelines used in this study (OTU and paired end) presented similar taxonomic profiles at genus level.
CONCLUSIONS: We determined that DNA extraction from ELBW faecal samples, particularly those infants receiving probiotic supplementation, should include a prolonged beat-beating step. Furthermore, use of the 16S rRNA (V1 + V2 + V3) and (V6 + V7 + V8) regions provides reliable representation of ELBW microbiota profiles, while inclusion of the (V4 + V5) region may not be appropriate for studies where Bifidobacterium constitutes a resident microbiota member.}, }
@article {pmid29091761, year = {2017}, author = {Nakamoto, N and Amiya, T and Aoki, R and Taniki, N and Koda, Y and Miyamoto, K and Teratani, T and Suzuki, T and Chiba, S and Chu, PS and Hayashi, A and Yamaguchi, A and Shiba, S and Miyake, R and Katayama, T and Suda, W and Mikami, Y and Kamada, N and Ebinuma, H and Saito, H and Hattori, M and Kanai, T}, title = {Commensal Lactobacillus Controls Immune Tolerance during Acute Liver Injury in Mice.}, journal = {Cell reports}, volume = {21}, number = {5}, pages = {1215-1226}, doi = {10.1016/j.celrep.2017.10.022}, pmid = {29091761}, issn = {2211-1247}, mesh = {Alanine Transaminase/blood ; Animals ; Chemical and Drug Induced Liver Injury/*immunology/pathology ; Dendritic Cells/cytology/metabolism ; Gastrointestinal Microbiome ; Histocompatibility Antigens Class II/metabolism ; *Immune Tolerance ; Immunity, Innate ; Interferon-gamma/metabolism ; Interleukin-10/metabolism ; Interleukins/metabolism ; Intestines/immunology/metabolism/microbiology ; Lactobacillus/*immunology/physiology ; Liver/immunology/metabolism/pathology ; Male ; Mice ; Mice, Inbred C57BL ; T-Lymphocytes, Regulatory/cytology/immunology/metabolism ; Toll-Like Receptor 9/metabolism ; Transforming Growth Factor beta/metabolism ; }, abstract = {Gut-derived microbial antigens trigger the innate immune system during acute liver injury. During recovery, regulatory immunity plays a role in suppressing inflammation; however, the precise mechanism underlying this process remains obscure. Here, we find that recruitment of immune-regulatory classical dendritic cells (cDCs) is crucial for liver tolerance in concanavalin A-induced acute liver injury. Acute liver injury resulted in enrichment of commensal Lactobacillus in the gut. Notably, Lactobacillus activated IL-22 production by gut innate lymphoid cells and raised systemic IL-22 levels. Gut-derived IL-22 enhanced mucosal barrier function and promoted the recruitment of regulatory cDCs to the liver. These cDCs produced IL-10 and TGF-β through TLR9 activation, preventing further liver inflammation. Collectively, our results indicate that beneficial gut microbes influence tolerogenic immune responses in the liver. Therefore, modulation of the gut microbiota might be a potential option to regulate liver tolerance.}, }
@article {pmid29088131, year = {2017}, author = {Woyke, T and Doud, DFR and Schulz, F}, title = {The trajectory of microbial single-cell sequencing.}, journal = {Nature methods}, volume = {14}, number = {11}, pages = {1045-1054}, doi = {10.1038/nmeth.4469}, pmid = {29088131}, issn = {1548-7105}, mesh = {Metagenomics ; Microbiota/genetics ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; *Single-Cell Analysis ; }, abstract = {Over the past decade, it has become nearly routine to sequence genomes of individual microbial cells directly isolated from environmental samples ranging from deep-sea hydrothermal vents to insect guts, providing a powerful complement to shotgun metagenomics in microbial community studies. In this review, we address the technical aspects and challenges of single-cell genome sequencing and discuss some of the scientific endeavors that it has enabled. Specifically, we highlight newly added leaves and branches in the genomic tree of bacterial and archaeal life and illustrate the unique and exciting advantages that single-cell genomics offers over metagenomics, both now and in the near future.}, }
@article {pmid29085573, year = {2017}, author = {Herath, D and Jayasundara, D and Ackland, D and Saeed, I and Tang, SL and Halgamuge, S}, title = {Assessing Species Diversity Using Metavirome Data: Methods and Challenges.}, journal = {Computational and structural biotechnology journal}, volume = {15}, number = {}, pages = {447-455}, doi = {10.1016/j.csbj.2017.09.001}, pmid = {29085573}, issn = {2001-0370}, abstract = {Assessing biodiversity is an important step in the study of microbial ecology associated with a given environment. Multiple indices have been used to quantify species diversity, which is a key biodiversity measure. Measuring species diversity of viruses in different environments remains a challenge relative to measuring the diversity of other microbial communities. Metagenomics has played an important role in elucidating viral diversity by conducting metavirome studies; however, metavirome data are of high complexity requiring robust data preprocessing and analysis methods. In this review, existing bioinformatics methods for measuring species diversity using metavirome data are categorised broadly as either sequence similarity-dependent methods or sequence similarity-independent methods. The former includes a comparison of DNA fragments or assemblies generated in the experiment against reference databases for quantifying species diversity, whereas estimates from the latter are independent of the knowledge of existing sequence data. Current methods and tools are discussed in detail, including their applications and limitations. Drawbacks of the state-of-the-art method are demonstrated through results from a simulation. In addition, alternative approaches are proposed to overcome the challenges in estimating species diversity measures using metavirome data.}, }
@article {pmid29069412, year = {2017}, author = {De Anda, V and Zapata-Peñasco, I and Poot-Hernandez, AC and Eguiarte, LE and Contreras-Moreira, B and Souza, V}, title = {MEBS, a software platform to evaluate large (meta)genomic collections according to their metabolic machinery: unraveling the sulfur cycle.}, journal = {GigaScience}, volume = {6}, number = {11}, pages = {1-17}, doi = {10.1093/gigascience/gix096}, pmid = {29069412}, issn = {2047-217X}, mesh = {Animals ; *Gastrointestinal Microbiome ; Humans ; Metabolic Networks and Pathways/genetics ; *Metagenome ; Sequence Analysis, DNA/*methods ; *Software ; Sulfur/*metabolism ; }, abstract = {The increasing number of metagenomic and genomic sequences has dramatically improved our understanding of microbial diversity, yet our ability to infer metabolic capabilities in such datasets remains challenging. We describe the Multigenomic Entropy Based Score pipeline (MEBS), a software platform designed to evaluate, compare, and infer complex metabolic pathways in large "omic" datasets, including entire biogeochemical cycles. MEBS is open source and available through https://github.com/eead-csic-compbio/metagenome_Pfam_score. To demonstrate its use, we modeled the sulfur cycle by exhaustively curating the molecular and ecological elements involved (compounds, genes, metabolic pathways, and microbial taxa). This information was reduced to a collection of 112 characteristic Pfam protein domains and a list of complete-sequenced sulfur genomes. Using the mathematical framework of relative entropy (H΄), we quantitatively measured the enrichment of these domains among sulfur genomes. The entropy of each domain was used both to build up a final score that indicates whether a (meta)genomic sample contains the metabolic machinery of interest and to propose marker domains in metagenomic sequences such as DsrC (PF04358). MEBS was benchmarked with a dataset of 2107 non-redundant microbial genomes from RefSeq and 935 metagenomes from MG-RAST. Its performance, reproducibility, and robustness were evaluated using several approaches, including random sampling, linear regression models, receiver operator characteristic plots, and the area under the curve metric (AUC). Our results support the broad applicability of this algorithm to accurately classify (AUC = 0.985) hard-to-culture genomes (e.g., Candidatus Desulforudis audaxviator), previously characterized ones, and metagenomic environments such as hydrothermal vents, or deep-sea sediment. Our benchmark indicates that an entropy-based score can capture the metabolic machinery of interest and can be used to efficiently classify large genomic and metagenomic datasets, including uncultivated/unexplored taxa.}, }
@article {pmid29065967, year = {2017}, author = {Park, SJ and Kim, JH and Song, MY and Sung, YC and Lee, SW and Park, Y}, title = {PD-1 deficiency protects experimental colitis via alteration of gut microbiota.}, journal = {BMB reports}, volume = {50}, number = {11}, pages = {578-583}, pmid = {29065967}, issn = {1976-670X}, mesh = {Animals ; Bacteria/genetics ; Colitis/chemically induced/*metabolism/pathology/*prevention & control ; Colon/pathology ; Cytokines/metabolism ; Disease Models, Animal ; Gastrointestinal Microbiome/physiology ; Inflammatory Bowel Diseases/metabolism ; Metagenomics/methods ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Programmed Cell Death 1 Ligand 2 Protein/genetics/*metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Programmed cell death-1 (PD-1) is a coinhibitory molecule and plays a pivotal role in immune regulation. Here, we demonstrate a role for PD-1 in pathogenesis of inflammatory bowel disease (IBD). Wild-type (WT) mice had severe wasting disease during experimentally induced colitis, while mice deficient for PD-1 (PD-1-/-) did not develop colon inflammation. Interestingly, PD-1-/- mice cohoused with WT mice became susceptible to colitis, suggesting that resistance of PD-1-/- mice to colitis is dependent on their gut microbiota. 16S rRNA gene-pyrosequencing analysis showed that PD-1-/- mice had altered composition of gut microbiota with significant reduction in Rikenellaceae family. These altered colon bacteria of PD-1-/- mice induced less amount of inflammatory mediators from colon epithelial cells, including interleukin (IL)-6, and inflammatory chemokines. Taken together, our study indicates that PD-1 expression is involved in the resistance to experimental colitis through altered bacterial communities of colon. [BMB Reports 2017; 50(11): 578-583].}, }
@article {pmid29061202, year = {2017}, author = {Volokhov, DV and Becker, DJ and Bergner, LM and Camus, MS and Orton, RJ and Chizhikov, VE and Altizer, SM and Streicker, DG}, title = {Novel hemotropic mycoplasmas are widespread and genetically diverse in vampire bats.}, journal = {Epidemiology and infection}, volume = {145}, number = {15}, pages = {3154-3167}, doi = {10.1017/S095026881700231X}, pmid = {29061202}, issn = {1469-4409}, support = {G0801822//Medical Research Council/United Kingdom ; 102507/Z/13/Z//Wellcome Trust/United Kingdom ; MC_UU_12014/12//Medical Research Council/United Kingdom ; }, mesh = {Animals ; Belize ; Chiroptera/*microbiology ; DNA, Bacterial/genetics ; Disease Reservoirs/microbiology ; Genetic Variation/genetics ; Mycoplasma/*genetics ; Mycoplasma Infections/microbiology/transmission/*veterinary ; Peru ; Phylogeny ; Polymerase Chain Reaction/veterinary ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Bats (Order: Chiroptera) have been widely studied as reservoir hosts for viruses of concern for human and animal health. However, whether bats are equally competent hosts of non-viral pathogens such as bacteria remains an important open question. Here, we surveyed blood and saliva samples of vampire bats from Peru and Belize for hemotropic Mycoplasma spp. (hemoplasmas), bacteria that can cause inapparent infection or anemia in hosts. 16S rRNA gene amplification of blood showed 67% (150/223) of common vampire bats (Desmodus rotundus) were infected by hemoplasmas. Sequencing of the 16S rRNA gene amplicons revealed three novel genotypes that were phylogenetically related but not identical to hemoplasmas described from other (non-vampire) bat species, rodents, humans, and non-human primates. Hemoplasma prevalence in vampire bats was highest in non-reproductive and young individuals, did not differ by country, and was relatively stable over time (i.e., endemic). Metagenomics from pooled D. rotundus saliva from Peru detected non-hemotropic Mycoplasma species and hemoplasma genotypes phylogenetically similar to those identified in blood, providing indirect evidence for potential direct transmission of hemoplasmas through biting or social contacts. This study demonstrates vampire bats host several novel hemoplasmas and sheds light on risk factors for infection and basic transmission routes. Given the high frequency of direct contacts that arise when vampire bats feed on humans, domestic animals, and wildlife, the potential of these bacteria to be transmitted between species should be investigated in future work.}, }
@article {pmid29056339, year = {2017}, author = {Rosshart, SP and Vassallo, BG and Angeletti, D and Hutchinson, DS and Morgan, AP and Takeda, K and Hickman, HD and McCulloch, JA and Badger, JH and Ajami, NJ and Trinchieri, G and Pardo-Manuel de Villena, F and Yewdell, JW and Rehermann, B}, title = {Wild Mouse Gut Microbiota Promotes Host Fitness and Improves Disease Resistance.}, journal = {Cell}, volume = {171}, number = {5}, pages = {1015-1028.e13}, doi = {10.1016/j.cell.2017.09.016}, pmid = {29056339}, issn = {1097-4172}, mesh = {Animals ; Animals, Laboratory ; Animals, Wild ; Carcinogenesis/immunology ; Disease Resistance ; Female ; *Gastrointestinal Microbiome ; Male ; Maryland ; Mice/*classification/immunology/*microbiology ; Mice, Inbred C57BL ; Peromyscus ; Virus Diseases/immunology ; }, abstract = {Laboratory mice, while paramount for understanding basic biological phenomena, are limited in modeling complex diseases of humans and other free-living mammals. Because the microbiome is a major factor in mammalian physiology, we aimed to identify a naturally evolved reference microbiome to better recapitulate physiological phenomena relevant in the natural world outside the laboratory. Among 21 distinct mouse populations worldwide, we identified a closely related wild relative to standard laboratory mouse strains. Its bacterial gut microbiome differed significantly from its laboratory mouse counterpart and was transferred to and maintained in laboratory mice over several generations. Laboratory mice reconstituted with natural microbiota exhibited reduced inflammation and increased survival following influenza virus infection and improved resistance against mutagen/inflammation-induced colorectal tumorigenesis. By demonstrating the host fitness-promoting traits of natural microbiota, our findings should enable the discovery of protective mechanisms relevant in the natural world and improve the modeling of complex diseases of free-living mammals. VIDEO ABSTRACT.}, }
@article {pmid29053686, year = {2017}, author = {Steffan, SA and Dharampal, PS and Diaz-Garcia, L and Currie, CR and Zalapa, J and Hittinger, CT}, title = {Empirical, Metagenomic, and Computational Techniques Illuminate the Mechanisms by which Fungicides Compromise Bee Health.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {128}, pages = {}, doi = {10.3791/54631}, pmid = {29053686}, issn = {1940-087X}, mesh = {Animals ; Bees/*physiology ; Fungicides, Industrial/*adverse effects ; Metagenomics/*methods ; Microbiota ; Pollen ; Yeasts ; }, abstract = {Growers often use fungicide sprays during bloom to protect crops against disease, which exposes bees to fungicide residues. Although considered "bee-safe," there is mounting evidence that fungicide residues in pollen are associated with bee declines (for both honey and bumble bee species). While the mechanisms remain relatively unknown, researchers have speculated that bee-microbe symbioses are involved. Microbes play a pivotal role in the preservation and/or processing of pollen, which serves as nutrition for larval bees. By altering the microbial community, it is likely that fungicides disrupt these microbe-mediated services, and thereby compromise bee health. This manuscript describes the protocols used to investigate the indirect mechanism(s) by which fungicides may be causing colony decline. Cage experiments exposing bees to fungicide-treated flowers have already provided the first evidence that fungicides cause profound colony losses in a native bumble bee (Bombus impatiens). Using field-relevant doses of fungicides, a series of experiments have been developed to provide a finer description of microbial community dynamics of fungicide-exposed pollen. Shifts in the structural composition of fungal and bacterial assemblages within the pollen microbiome are investigated by next-generation sequencing and metagenomic analysis. Experiments developed herein have been designed to provide a mechanistic understanding of how fungicides affect the microbiome of pollen-provisions. Ultimately, these findings should shed light on the indirect pathway through which fungicides may be causing colony declines.}, }
@article {pmid29053145, year = {2018}, author = {Bernardo, P and Charles-Dominique, T and Barakat, M and Ortet, P and Fernandez, E and Filloux, D and Hartnady, P and Rebelo, TA and Cousins, SR and Mesleard, F and Cohez, D and Yavercovski, N and Varsani, A and Harkins, GW and Peterschmitt, M and Malmstrom, CM and Martin, DP and Roumagnac, P}, title = {Geometagenomics illuminates the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scale.}, journal = {The ISME journal}, volume = {12}, number = {1}, pages = {173-184}, doi = {10.1038/ismej.2017.155}, pmid = {29053145}, issn = {1751-7370}, mesh = {*Agriculture ; Biodiversity ; Climate ; Ecosystem ; France ; Metagenomics ; Plant Viruses/classification/genetics/*isolation & purification ; Plants/virology ; South Africa ; }, abstract = {Disease emergence events regularly result from human activities such as agriculture, which frequently brings large populations of genetically uniform hosts into contact with potential pathogens. Although viruses cause nearly 50% of emerging plant diseases, there is little systematic information about virus distribution across agro-ecological interfaces and large gaps in understanding of virus diversity in nature. Here we applied a novel landscape-scale geometagenomics approach to examine relationships between agricultural land use and distributions of plant-associated viruses in two Mediterranean-climate biodiversity hotspots (Western Cape region of South Africa and Rhône river delta region of France). In total, we analysed 1725 geo-referenced plant samples collected over two years from 4.5 × 4.5 km2 grids spanning farmlands and adjacent uncultivated vegetation. We found substantial virus prevalence (25.8-35.7%) in all ecosystems, but prevalence and identified family-level virus diversity were greatest in cultivated areas, with some virus families displaying strong agricultural associations. Our survey revealed 94 previously unknown virus species, primarily from uncultivated plants. This is the first effort to systematically evaluate plant-associated viromes across broad agro-ecological interfaces. Our findings indicate that agriculture substantially influences plant virus distributions and highlight the extent of current ignorance about the diversity and roles of viruses in nature.}, }
@article {pmid29050881, year = {2017}, author = {Kvas, S and Rahn, J and Engel, K and Neufeld, JD and Villeneuve, PJ and Trevors, JT and Lee, H and Scroggins, RP and Beaudette, LA}, title = {Development of a microbial test suite and data integration method for assessing microbial health of contaminated soil.}, journal = {Journal of microbiological methods}, volume = {143}, number = {}, pages = {66-77}, doi = {10.1016/j.mimet.2017.10.004}, pmid = {29050881}, issn = {1872-8359}, mesh = {Biota/*drug effects ; Canada ; *Data Interpretation, Statistical ; *Environmental Pollution ; Forests ; Metagenomics/methods ; Microbiological Techniques/*methods ; Petroleum/analysis ; *Soil Microbiology ; Soil Pollutants/analysis ; }, abstract = {There is no standard methodology or guideline for assessing soil microbial health for the purposes of contaminant risk assessments. Here we propose a laboratory-based test suite and novel data integration method for evaluating soil microbial health using site-specific contaminated and reference soil. The test suite encompasses experiments for evaluating microbial biomass, activity, and diversity. The results from the tests are then integrated so that a Soil Microbial Health Score (SMHS) may be assigned. This test suite and data integration method was tested on soils from 3 different contaminated sites in Canada. The soil microbial health of a petroleum hydrocarbon (PHC) contaminated site was found to be 'Mildly Impacted' and 'Moderately Impacted' for two soil horizons at a boreal forest site. The soil microbial health of the mixed metal/PHC and mixed metal sites were both found to be 'Not Impacted'. Continued use of this test suite and data integration method will help create guidelines for assessing soil microbial health in ecological risk assessments.}, }
@article {pmid29049378, year = {2017}, author = {Oh, S and Yap, GC and Hong, PY and Huang, CH and Aw, MM and Shek, LP and Liu, WT and Lee, BW}, title = {Immune-modulatory genomic properties differentiate gut microbiota of infants with and without eczema.}, journal = {PloS one}, volume = {12}, number = {10}, pages = {e0184955}, doi = {10.1371/journal.pone.0184955}, pmid = {29049378}, issn = {1932-6203}, mesh = {Case-Control Studies ; Eczema/*genetics/*immunology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Male ; Phylogeny ; Placebos ; }, abstract = {Gut microbiota play an important role in human immunological processes, potentially affecting allergic diseases such as eczema. The diversity and structure of gut microbiota in infants with eczema have been previously documented. This study aims to evaluate by comparative metagenomics differences in genetic content in gut microbiota of infants with eczema and their matched controls. Stools were collected at the age of one month old from twelve infants from an at risk birth cohort in a case control manner. Clinical follow up for atopic outcomes were carried out at the age of 12 and 24 months. Microbial genomic DNA were extracted from stool samples and used for shotgun sequencing. Comparative metagenomic analysis showed that immune-regulatory TCAAGCTTGA motifs were significantly enriched in the six healthy controls (C) communities compared to the six eczema subjects (E), with many encoded by Bifidobacterium (38% of the total motifs in the C communities). Draft genomes of five Bifidobacterium species populations (B. longum, B. bifidum, B. breve, B. dentium, and B. pseudocatenulatum) were recovered from metagenomic datasets. The B. longum BFN-121-2 genome encoded more TCAAGCTTGA motifs (4.2 copies per one million genome sequence) than other Bifidobacterium genomes. Additionally, the communities in the stool of controls (C) were also significantly enriched in functions associated with tetrapyrrole biosynthesis compared to those of eczema (E). Our results show distinct immune-modulatory genomic properties of gut microbiota in infants associated with eczema and provide new insights into potential role of gut microbiota in affecting human immune homeostasis.}, }
@article {pmid29041989, year = {2017}, author = {Dubinkina, VB and Tyakht, AV and Odintsova, VY and Yarygin, KS and Kovarsky, BA and Pavlenko, AV and Ischenko, DS and Popenko, AS and Alexeev, DG and Taraskina, AY and Nasyrova, RF and Krupitsky, EM and Shalikiani, NV and Bakulin, IG and Shcherbakov, PL and Skorodumova, LO and Larin, AK and Kostryukova, ES and Abdulkhakov, RA and Abdulkhakov, SR and Malanin, SY and Ismagilova, RK and Grigoryeva, TV and Ilina, EN and Govorun, VM}, title = {Links of gut microbiota composition with alcohol dependence syndrome and alcoholic liver disease.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {141}, doi = {10.1186/s40168-017-0359-2}, pmid = {29041989}, issn = {2049-2618}, mesh = {Adult ; Alcoholism/*microbiology/physiopathology ; Bifidobacterium/isolation & purification/pathogenicity/physiology ; Dysbiosis ; Enterobacteriaceae/isolation & purification/physiology ; Ethanol/adverse effects/metabolism ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/genetics/physiology ; Humans ; Inflammation ; Lactobacillus/isolation & purification/pathogenicity/physiology ; Liver/physiopathology ; Liver Cirrhosis/*microbiology/physiopathology ; Liver Diseases, Alcoholic/*microbiology/physiopathology/therapy ; Male ; Metagenomics/methods ; Middle Aged ; Probiotics/therapeutic use ; Symbiosis ; Virulence Factors ; Young Adult ; }, abstract = {BACKGROUND: Alcohol abuse has deleterious effects on human health by disrupting the functions of many organs and systems. Gut microbiota has been implicated in the pathogenesis of alcohol-related liver diseases, with its composition manifesting expressed dysbiosis in patients suffering from alcoholic dependence. Due to its inherent plasticity, gut microbiota is an important target for prevention and treatment of these diseases. Identification of the impact of alcohol abuse with associated psychiatric symptoms on the gut community structure is confounded by the liver dysfunction. In order to differentiate the effects of these two factors, we conducted a comparative "shotgun" metagenomic survey of 99 patients with the alcohol dependence syndrome represented by two cohorts-with and without liver cirrhosis. The taxonomic and functional composition of the gut microbiota was subjected to a multifactor analysis including comparison with the external control group.
RESULTS: Alcoholic dependence and liver cirrhosis were associated with profound shifts in gut community structures and metabolic potential across the patients. The specific effects on species-level community composition were remarkably different between cohorts with and without liver cirrhosis. In both cases, the commensal microbiota was found to be depleted. Alcoholic dependence was inversely associated with the levels of butyrate-producing species from the Clostridiales order, while the cirrhosis-with multiple members of the Bacteroidales order. The opportunist pathogens linked to alcoholic dependence included pro-inflammatory Enterobacteriaceae, while the hallmarks of cirrhosis included an increase of oral microbes in the gut and more frequent occurrence of abnormal community structures. Interestingly, each of the two factors was associated with the expressed enrichment in many Bifidobacterium and Lactobacillus-but the exact set of the species was different between alcoholic dependence and liver cirrhosis. At the level of functional potential, the patients showed different patterns of increase in functions related to alcohol metabolism and virulence factors, as well as pathways related to inflammation.
CONCLUSIONS: Multiple shifts in the community structure and metabolic potential suggest strong negative influence of alcohol dependence and associated liver dysfunction on gut microbiota. The identified differences in patterns of impact between these two factors are important for planning of personalized treatment and prevention of these pathologies via microbiota modulation. Particularly, the expansion of Bifidobacterium and Lactobacillus suggests that probiotic interventions for patients with alcohol-related disorders using representatives of the same taxa should be considered with caution. Taxonomic and functional analysis shows an increased propensity of the gut microbiota to synthesis of the toxic acetaldehyde, suggesting higher risk of colorectal cancer and other pathologies in alcoholics.}, }
@article {pmid29041965, year = {2017}, author = {Noyes, NR and Weinroth, ME and Parker, JK and Dean, CJ and Lakin, SM and Raymond, RA and Rovira, P and Doster, E and Abdo, Z and Martin, JN and Jones, KL and Ruiz, J and Boucher, CA and Belk, KE and Morley, PS}, title = {Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {142}, doi = {10.1186/s40168-017-0361-8}, pmid = {29041965}, issn = {2049-2618}, mesh = {Drug Resistance, Microbial/*genetics ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Virulence/genetics ; Whole Genome Sequencing/methods ; }, abstract = {BACKGROUND: Shotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of this method for environmental surveillance of antimicrobial resistance and pathogenic microorganisms is also increasing. In published metagenomic datasets, the total of all resistance- and virulence-related sequences accounts for < 1% of all sequenced DNA, leading to limitations in detection of low-abundance resistome-virulome elements. This study describes the extent and composition of the low-abundance portion of the resistome-virulome, using a bait-capture and enrichment system that incorporates unique molecular indices to count DNA molecules and correct for enrichment bias.
RESULTS: The use of the bait-capture and enrichment system significantly increased on-target sequencing of the resistome-virulome, enabling detection of an additional 1441 gene accessions and revealing a low-abundance portion of the resistome-virulome that was more diverse and compositionally different than that detected by more traditional metagenomic assays. The low-abundance portion of the resistome-virulome also contained resistance genes with public health importance, such as extended-spectrum betalactamases, that were not detected using traditional shotgun metagenomic sequencing. In addition, the use of the bait-capture and enrichment system enabled identification of rare resistance gene haplotypes that were used to discriminate between sample origins.
CONCLUSIONS: These results demonstrate that the rare resistome-virulome contains valuable and unique information that can be utilized for both surveillance and population genetic investigations of resistance. Access to the rare resistome-virulome using the bait-capture and enrichment system validated in this study can greatly advance our understanding of microbiome-resistome dynamics.}, }
@article {pmid29037173, year = {2017}, author = {Beisser, D and Graupner, N and Grossmann, L and Timm, H and Boenigk, J and Rahmann, S}, title = {TaxMapper: an analysis tool, reference database and workflow for metatranscriptome analysis of eukaryotic microorganisms.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {787}, doi = {10.1186/s12864-017-4168-6}, pmid = {29037173}, issn = {1471-2164}, mesh = {*Databases, Genetic ; Eukaryota/*genetics ; High-Throughput Nucleotide Sequencing ; Metagenomics/*standards ; Reference Standards ; Software ; }, abstract = {BACKGROUND: High-throughput sequencing (HTS) technologies are increasingly applied to analyse complex microbial ecosystems by mRNA sequencing of whole communities, also known as metatranscriptome sequencing. This approach is at the moment largely limited to prokaryotic communities and communities of few eukaryotic species with sequenced genomes. For eukaryotes the analysis is hindered mainly by a low and fragmented coverage of the reference databases to infer the community composition, but also by lack of automated workflows for the task.
RESULTS: From the databases of the National Center for Biotechnology Information and Marine Microbial Eukaryote Transcriptome Sequencing Project, 142 references were selected in such a way that the taxa represent the main lineages within each of the seven supergroups of eukaryotes and possess predominantly complete transcriptomes or genomes. From these references, we created an annotated microeukaryotic reference database. We developed a tool called TaxMapper for a reliably mapping of sequencing reads against this database and filtering of unreliable assignments. For filtering, a classifier was trained and tested on each of the following: sequences of taxa in the database, sequences of taxa related to those in the database, and random sequences. Additionally, TaxMapper is part of a metatranscriptomic Snakemake workflow developed to perform quality assessment, functional and taxonomic annotation and (multivariate) statistical analysis including environmental data. The workflow is provided and described in detail to empower researchers to apply it for metatranscriptome analysis of any environmental sample.
CONCLUSIONS: TaxMapper shows superior performance compared to standard approaches, resulting in a higher number of true positive taxonomic assignments. Both the TaxMapper tool and the workflow are available as open-source code at Bitbucket under the MIT license: https://bitbucket.org/dbeisser/taxmapper and as a Bioconda package: https://bioconda.github.io/recipes/taxmapper/README.html .}, }
@article {pmid29029060, year = {2017}, author = {Berini, F and Casciello, C and Marcone, GL and Marinelli, F}, title = {Metagenomics: novel enzymes from non-culturable microbes.}, journal = {FEMS microbiology letters}, volume = {364}, number = {21}, pages = {}, doi = {10.1093/femsle/fnx211}, pmid = {29029060}, issn = {1574-6968}, mesh = {Bacteria/*enzymology ; *Bacterial Proteins/chemistry/classification/genetics ; Biocatalysis ; Environmental Microbiology ; *Enzymes/chemistry/classification/genetics ; Industrial Microbiology ; Metagenomics/*methods ; *Microbiota ; }, abstract = {In the transition to the post-petroleum economy, there is a growing demand for novel enzymes with high process performances to replace traditional chemistry with a more 'green' approach. To date, microorganisms encompass the richest source of industrial biocatalysts, but the Earth-living microbiota remains largely untapped by using traditional isolation and cultivation methods. Metagenomics, which is culture independent, represents a powerful tool for discovering novel enzymes from unculturable microorganisms. Herein, we summarize the variety of approaches adopted for mining environmental DNA and, based on a systematic literature review, we provide a comprehensive list of 332 industrially relevant enzymes discovered from metagenomes within the last three years.}, }
@article {pmid29027998, year = {2018}, author = {Arkhipova, K and Skvortsov, T and Quinn, JP and McGrath, JW and Allen, CC and Dutilh, BE and McElarney, Y and Kulakov, LA}, title = {Temporal dynamics of uncultured viruses: a new dimension in viral diversity.}, journal = {The ISME journal}, volume = {12}, number = {1}, pages = {199-211}, doi = {10.1038/ismej.2017.157}, pmid = {29027998}, issn = {1751-7370}, mesh = {Bacteria/isolation & purification ; Bacteriophages/genetics/isolation & purification ; Biodiversity ; Ecosystem ; *Genome, Viral ; Lakes/microbiology/virology ; Metagenomics ; Viruses/*genetics/isolation & purification ; }, abstract = {Recent work has vastly expanded the known viral genomic sequence space, but the seasonal dynamics of viral populations at the genome level remain unexplored. Here we followed the viral community in a freshwater lake for 1 year using genome-resolved viral metagenomics, combined with detailed analyses of the viral community structure, associated bacterial populations and environmental variables. We reconstructed 8950 complete and partial viral genomes, the majority of which were not persistent in the lake throughout the year, but instead continuously succeeded each other. Temporal analysis of 732 viral genus-level clusters demonstrated that one-fifth were undetectable at specific periods of the year. Based on host predictions for a subset of reconstructed viral genomes, we for the first time reveal three distinct patterns of host-pathogen dynamics, where the viruses may peak before, during or after the peak in their host's abundance, providing new possibilities for modelling of their interactions. Time series metagenomics opens up a new dimension in viral profiling, which is essential to understand the full scale of viral diversity and evolution, and the ecological roles of these important factors in the global ecosystem.}, }
@article {pmid29019934, year = {2017}, author = {Kakuta, M and Suzuki, S and Izawa, K and Ishida, T and Akiyama, Y}, title = {A Massively Parallel Sequence Similarity Search for Metagenomic Sequencing Data.}, journal = {International journal of molecular sciences}, volume = {18}, number = {10}, pages = {}, doi = {10.3390/ijms18102124}, pmid = {29019934}, issn = {1422-0067}, mesh = {Algorithms ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Mouth/*microbiology ; Sequence Analysis, DNA/*methods ; *Sequence Homology, Nucleic Acid ; *Software ; }, abstract = {Sequence similarity searches have been widely used in the analyses of metagenomic sequencing data. Finding homologous sequences in a reference database enables the estimation of taxonomic and functional characteristics of each query sequence. Because current metagenomic sequencing data consist of a large number of nucleotide sequences, the time required for sequence similarity searches account for a large proportion of the total time. This time-consuming step makes it difficult to perform large-scale analyses. To analyze large-scale metagenomic data, such as those found in the human oral microbiome, we developed GHOST-MP (Genome-wide HOmology Search Tool on Massively Parallel system), a parallel sequence similarity search tool for massively parallel computing systems. This tool uses a fast search algorithm based on suffix arrays of query and database sequences and a hierarchical parallel search to accelerate the large-scale sequence similarity search of metagenomic sequencing data. The parallel computing efficiency and the search speed of this tool were evaluated. GHOST-MP was shown to be scalable over 10,000 CPU (Central Processing Unit) cores, and achieved over 80-fold acceleration compared with mpiBLAST using the same computational resources. We applied this tool to human oral metagenomic data, and the results indicate that the oral cavity, the oral vestibule, and plaque have different characteristics based on the functional gene category.}, }
@article {pmid29018189, year = {2017}, author = {Jie, Z and Xia, H and Zhong, SL and Feng, Q and Li, S and Liang, S and Zhong, H and Liu, Z and Gao, Y and Zhao, H and Zhang, D and Su, Z and Fang, Z and Lan, Z and Li, J and Xiao, L and Li, J and Li, R and Li, X and Li, F and Ren, H and Huang, Y and Peng, Y and Li, G and Wen, B and Dong, B and Chen, JY and Geng, QS and Zhang, ZW and Yang, H and Wang, J and Wang, J and Zhang, X and Madsen, L and Brix, S and Ning, G and Xu, X and Liu, X and Hou, Y and Jia, H and He, K and Kristiansen, K}, title = {The gut microbiome in atherosclerotic cardiovascular disease.}, journal = {Nature communications}, volume = {8}, number = {1}, pages = {845}, doi = {10.1038/s41467-017-00900-1}, pmid = {29018189}, issn = {2041-1723}, mesh = {Atherosclerosis/*microbiology ; Case-Control Studies ; Fermentation ; *Gastrointestinal Microbiome/drug effects ; Genome-Wide Association Study ; Humans ; Inflammation/microbiology ; Liver Cirrhosis/microbiology ; *Metagenome ; Metagenomics ; }, abstract = {The gut microbiota has been linked to cardiovascular diseases. However, the composition and functional capacity of the gut microbiome in relation to cardiovascular diseases have not been systematically examined. Here, we perform a metagenome-wide association study on stools from 218 individuals with atherosclerotic cardiovascular disease (ACVD) and 187 healthy controls. The ACVD gut microbiome deviates from the healthy status by increased abundance of Enterobacteriaceae and Streptococcus spp. and, functionally, in the potential for metabolism or transport of several molecules important for cardiovascular health. Although drug treatment represents a confounding factor, ACVD status, and not current drug use, is the major distinguishing feature in this cohort. We identify common themes by comparison with gut microbiome data associated with other cardiometabolic diseases (obesity and type 2 diabetes), with liver cirrhosis, and rheumatoid arthritis. Our data represent a comprehensive resource for further investigations on the role of the gut microbiome in promoting or preventing ACVD as well as other related diseases.The gut microbiota may play a role in cardiovascular diseases. Here, the authors perform a metagenome-wide association study on stools from individuals with atherosclerotic cardiovascular disease and healthy controls, identifying microbial strains and functions associated with the disease.}, }
@article {pmid28978331, year = {2017}, author = {Shamarina, D and Stoyantcheva, I and Mason, CE and Bibby, K and Elhaik, E}, title = {Communicating the promise, risks, and ethics of large-scale, open space microbiome and metagenome research.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {132}, doi = {10.1186/s40168-017-0349-4}, pmid = {28978331}, issn = {2049-2618}, support = {R25 EB020393/EB/NIBIB NIH HHS/United States ; R01 ES021006/ES/NIEHS NIH HHS/United States ; }, mesh = {Environment Design ; *Ethics, Research ; Humans ; *Metagenome ; Metagenomics ; *Microbiota ; Public Opinion ; *Public Relations ; *Research ; }, abstract = {The public commonly associates microorganisms with pathogens. This suspicion of microorganisms is understandable, as historically microorganisms have killed more humans than any other agent while remaining largely unknown until the late seventeenth century with the works of van Leeuwenhoek and Kircher. Despite our improved understanding regarding microorganisms, the general public are apt to think of diseases rather than of the majority of harmless or beneficial species that inhabit our bodies and the built and natural environment. As long as microbiome research was confined to labs, the public's exposure to microbiology was limited. The recent launch of global microbiome surveys, such as the Earth Microbiome Project and MetaSUB (Metagenomics and Metadesign of Subways and Urban Biomes) project, has raised ethical, financial, feasibility, and sustainability concerns as to the public's level of understanding and potential reaction to the findings, which, done improperly, risk negative implications for ongoing and future investigations, but done correctly, can facilitate a new vision of "smart cities." To facilitate improved future research, we describe here the major concerns that our discussions with ethics committees, community leaders, and government officials have raised, and we expound on how to address them. We further discuss ethical considerations of microbiome surveys and provide practical recommendations for public engagement.}, }
@article {pmid28976007, year = {2017}, author = {Rosen, CE and Palm, NW}, title = {Functional Classification of the Gut Microbiota: The Key to Cracking the Microbiota Composition Code: Functional classifications of the gut microbiota reveal previously hidden contributions of indigenous gut bacteria to human health and disease.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {39}, number = {12}, pages = {}, doi = {10.1002/bies.201700032}, pmid = {28976007}, issn = {1521-1878}, mesh = {Dysbiosis/genetics/*immunology/microbiology ; Gastrointestinal Microbiome/*immunology ; Gastrointestinal Tract/immunology/*microbiology ; Humans ; *Immunity, Innate ; Immunoglobulin A/genetics ; Metabolome/immunology ; Metagenome/*immunology ; Microbial Consortia/immunology ; Terminology as Topic ; }, abstract = {The last decade has seen an explosion of research on the gut microbiota-the trillions of microorganisms that colonize the human gut. It is now clear that interindividual diversity in microbiota composition plays an important role in determining susceptibility to a wide variety of diseases. However, identifying the precise changes in microbiota composition that play causal roles has remained a largely unrealized goal. Here, we propose that functional classifications of microbes based on their interactions with and effects on the host-particularly the host immune system-will illuminate the role of the microbiota in shaping human physiology. We outline the benefits of "functional" classification compared to phylogenetic classifications, and review current efforts at functional classification of the microbiota. Finally, we outline a theoretical framework for classifying host-microbiota interactions. Future advances enabling broader functional classifications of the microbiota promise to revolutionize our understanding of the role of gut microbes in health and disease.}, }
@article {pmid28974215, year = {2017}, author = {Lalremruata, A and Jeyaraj, S and Engleitner, T and Joanny, F and Lang, A and Bélard, S and Mombo-Ngoma, G and Ramharter, M and Kremsner, PG and Mordmüller, B and Held, J}, title = {Species and genotype diversity of Plasmodium in malaria patients from Gabon analysed by next generation sequencing.}, journal = {Malaria journal}, volume = {16}, number = {1}, pages = {398}, doi = {10.1186/s12936-017-2044-0}, pmid = {28974215}, issn = {1475-2875}, mesh = {*Biodiversity ; Gabon ; Genetic Variation ; *Genotype ; High-Throughput Nucleotide Sequencing ; Humans ; Malaria/diagnosis/parasitology ; Plasmodium/genetics/*physiology ; RNA, Protozoan/genetics ; RNA, Ribosomal, 18S/genetics ; }, abstract = {BACKGROUND: Six Plasmodium species are known to naturally infect humans. Mixed species infections occur regularly but morphological discrimination by microscopy is difficult and multiplicity of infection (MOI) can only be evaluated by molecular methods. This study investigated the complexity of Plasmodium infections in patients treated for microscopically detected non-falciparum or mixed species malaria in Gabon.
METHODS: Ultra-deep sequencing of nucleus (18S rRNA), mitochondrion, and apicoplast encoded genes was used to evaluate Plasmodium species diversity and MOI in 46 symptomatic Gabonese patients with microscopically diagnosed non-falciparum or mixed species malaria.
RESULTS: Deep sequencing revealed a large complexity of confections in patients with uncomplicated malaria, both on species and genotype levels. Mixed infections involved up to four parasite species (Plasmodium falciparum, Plasmodium malariae, Plasmodium ovale curtisi, and P. ovale wallikeri). Multiple genotypes from each species were determined from the asexual 18S rRNA gene. 17 of 46 samples (37%) harboured multiple genotypes of at least one Plasmodium species. The number of genotypes per sample (MOI) was highest in P. malariae (n = 4), followed by P. ovale curtisi (n = 3), P. ovale wallikeri (n = 3), and P. falciparum (n = 2). The highest combined genotype complexity in samples that contained mixed-species infections was seven.
CONCLUSIONS: Ultra-deep sequencing showed an unexpected breadth of Plasmodium species and within species diversity in clinical samples. MOI of P. ovale curtisi, P. ovale wallikeri and P. malariae infections were higher than anticipated and contribute significantly to the burden of malaria in Gabon.}, }
@article {pmid28973392, year = {2017}, author = {Chen, YC and Greenbaum, J and Shen, H and Deng, HW}, title = {Association Between Gut Microbiota and Bone Health: Potential Mechanisms and Prospective.}, journal = {The Journal of clinical endocrinology and metabolism}, volume = {102}, number = {10}, pages = {3635-3646}, doi = {10.1210/jc.2017-00513}, pmid = {28973392}, issn = {1945-7197}, support = {R01 AR059781/AR/NIAMS NIH HHS/United States ; R01 AR069055/AR/NIAMS NIH HHS/United States ; D43 TW009107/TW/FIC NIH HHS/United States ; R01 GM109068/GM/NIGMS NIH HHS/United States ; R01 AR057049/AR/NIAMS NIH HHS/United States ; U19 AG055373/AG/NIA NIH HHS/United States ; P50 AR055081/AR/NIAMS NIH HHS/United States ; P20 GM109036/GM/NIGMS NIH HHS/United States ; R01 MH104680/MH/NIMH NIH HHS/United States ; R01 MH107354/MH/NIMH NIH HHS/United States ; }, mesh = {Animals ; Animals, Laboratory ; Anti-Bacterial Agents/pharmacology ; Bone Resorption/microbiology ; Bone and Bones/drug effects/*metabolism ; Gastrointestinal Microbiome/*physiology ; Germ-Free Life ; Health ; Humans ; Prebiotics ; Probiotics/pharmacology ; }, abstract = {Context: It has been well established that the human gut microbiome plays a critical role in the regulation of important biological processes and the mechanisms underlying numerous complex diseases. Although researchers have only recently begun to study the relationship between the gut microbiota and bone metabolism, early efforts have provided increased evidence to suggest an important association.
Evidence Acquisition: In this study, we attempt to comprehensively summarize the relationship between the gut microbiota and bone metabolism by detailing the regulatory effects of the microbiome on various biological processes, including nutrient absorption and the intestinal mucosal barrier, immune system functionality, the gut-brain axis, and excretion of functional byproducts. In this review, we incorporate evidence from various types of studies, including observational, in vitro and in vivo animal experiments, as well as small efficacy clinic trails.
Evidence Synthesis: We review the various potential mechanisms of influence for the gut microbiota on the regulation of bone metabolism and discuss the importance of further examining the potential effects of the gut microbiota on the risk of osteoporosis in humans. Furthermore, we outline some useful tools/approaches for metagenomics research and present some prominent examples of metagenomics association studies in humans.
Conclusion: Current research efforts, although limited, clearly indicate that the gut microbiota may be implicated in bone metabolism, and therefore, further exploration of this relationship is a promising area of focus in bone health and osteoporosis research. Although most existing studies investigate this relationship using animal models, human studies are both needed and on the horizon.}, }
@article {pmid28970223, year = {2017}, author = {Xiao, C and Lu, ZM and Zhang, XJ and Wang, ST and Ao, L and Shen, CH and Shi, JS and Xu, ZH}, title = {Bio-Heat Is a Key Environmental Driver Shaping the Microbial Community of Medium-Temperature Daqu.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {23}, pages = {}, doi = {10.1128/AEM.01550-17}, pmid = {28970223}, issn = {1098-5336}, mesh = {Bacteria/classification/genetics/isolation & purification/*metabolism ; Biodiversity ; China ; Edible Grain/microbiology ; *Microbiota ; Temperature ; Wine/analysis/*microbiology ; }, abstract = {"Daqu" is a saccharifying and fermenting agent commonly used in the traditional solid-state fermentation industry (e.g., baijiu and vinegar). The patterns of microbial community succession and flavor formation are highly similar among batches, yet the mechanisms promoting temporal succession in the Daqu microbial ecology remain unclear. Here, we first correlated temporal profiles of microbial community succession with environmental variables (temperature, moisture, and titratable acidity) in medium temperature Daqu (MT-Daqu) throughout fermentation. Temperature dynamics significantly correlated (P < 0.05) with the quick succession of MT-Daqu microbiota in the first 12 d of fermentation, while the community structure was relatively stable after 12 d. Then, we explored the effect of temperature on the MT-Daqu community assembly. In the first 4 d of fermentation, the rapid propagation of most bacterial taxa and several fungal taxa, including Candida, Wickerhamomyces, and unclassified Dipodascaceae and Saccharomycetales species, significantly increased MT-Daqu temperature to 55°C. Subsequently, sustained bio-heat generated by microbial metabolism (53 to 56°C) within MT-Daqu inhibited the growth of most microbes from day 4 to day 12, while thermotolerant taxa, including Bacillus, unclassified Streptophyta, Weissella, Thermoactinomyces, Thermoascus, and Thermomyces survived or kept on growing. Furthermore, temperature as a major driving force on the shaping of MT-Daqu microbiota was validated. Lowering the fermentation temperature by placing the MT-Daqu in a 37°C incubator resulted in decreased relative abundances of thermotolerant taxa, including Bacillus, Thermoactinomyces, and Thermoascus, in the MT-Daqu microbiota. This study revealed that bio-heat functioned as a primary endogenous driver promoting the formation of functional MT-Daqu microbiota.IMPORTANCE Humans have mastered the Daqu preparation technique of cultivating functional microbiota on starchy grains over thousands of years, and it is well known that the metabolic activity of these microbes is key to the flavor production of Chinese baijiu. The pattern of microbial community succession and flavor formation remains highly similar between batches, yet mechanistic insight into these patterns and into microbial population fidelity to specific environmental conditions remains unclear. Our study revealed that bio-heat was generated within Daqu bricks in the first 4 d of fermentation, concomitant with rapid microbial propagation and metabolism. The sustained bio-heat may then function as a major endogenous driving force promoting the formation of the MT-Daqu microbiota from day 4 to day 12. The bio-heat-driven growth of thermotolerant microorganisms might contribute to the formation of flavor metabolites. This study provides useful information for the temperature-based modulation of microbiota function during the fermentation of Daqu.}, }
@article {pmid28969605, year = {2017}, author = {Zhai, P and Yang, L and Guo, X and Wang, Z and Guo, J and Wang, X and Zhu, H}, title = {MetaComp: comprehensive analysis software for comparative meta-omics including comparative metagenomics.}, journal = {BMC bioinformatics}, volume = {18}, number = {1}, pages = {434}, doi = {10.1186/s12859-017-1849-8}, pmid = {28969605}, issn = {1471-2105}, mesh = {Data Interpretation, Statistical ; Gene Expression Profiling/methods ; Genes, Microbial ; Humans ; Metabolomics/methods ; Metagenomics/*methods ; Microbiota/genetics ; Proteomics/methods ; *Software ; }, abstract = {BACKGROUND: During the past decade, the development of high throughput nucleic sequencing and mass spectrometry analysis techniques have enabled the characterization of microbial communities through metagenomics, metatranscriptomics, metaproteomics and metabolomics data. To reveal the diversity of microbial communities and interactions between living conditions and microbes, it is necessary to introduce comparative analysis based upon integration of all four types of data mentioned above. Comparative meta-omics, especially comparative metageomics, has been established as a routine process to highlight the significant differences in taxon composition and functional gene abundance among microbiota samples. Meanwhile, biologists are increasingly concerning about the correlations between meta-omics features and environmental factors, which may further decipher the adaptation strategy of a microbial community.
RESULTS: We developed a graphical comprehensive analysis software named MetaComp comprising a series of statistical analysis approaches with visualized results for metagenomics and other meta-omics data comparison. This software is capable to read files generated by a variety of upstream programs. After data loading, analyses such as multivariate statistics, hypothesis testing of two-sample, multi-sample as well as two-group sample and a novel function-regression analysis of environmental factors are offered. Here, regression analysis regards meta-omic features as independent variable and environmental factors as dependent variables. Moreover, MetaComp is capable to automatically choose an appropriate two-group sample test based upon the traits of input abundance profiles. We further evaluate the performance of its choice, and exhibit applications for metagenomics, metaproteomics and metabolomics samples.
CONCLUSION: MetaComp, an integrative software capable for applying to all meta-omics data, originally distills the influence of living environment on microbial community by regression analysis. Moreover, since the automatically chosen two-group sample test is verified to be outperformed, MetaComp is friendly to users without adequate statistical training. These improvements are aiming to overcome the new challenges under big data era for all meta-omics data. MetaComp is available at: http://cqb.pku.edu.cn/ZhuLab/MetaComp/ and https://github.com/pzhaipku/MetaComp/ .}, }
@article {pmid28967204, year = {2017}, author = {Ferrario, C and Alessandri, G and Mancabelli, L and Gering, E and Mangifesta, M and Milani, C and Lugli, GA and Viappiani, A and Duranti, S and Turroni, F and Ossiprandi, MC and Hiyashi, R and Mackie, R and van Sinderen, D and Ventura, M}, title = {Untangling the cecal microbiota of feral chickens by culturomic and metagenomic analyses.}, journal = {Environmental microbiology}, volume = {19}, number = {11}, pages = {4771-4783}, doi = {10.1111/1462-2920.13943}, pmid = {28967204}, issn = {1462-2920}, mesh = {Animals ; Bacteria/*classification/genetics/*isolation & purification ; Cecum/*microbiology ; Chickens/*microbiology ; Diet ; Gastrointestinal Microbiome/*genetics ; Geography ; Humans ; Metagenomics ; }, abstract = {Different factors may modulate the gut microbiota of animals. In any particular environment, diet, genetic factors and human influences can shape the bacterial communities residing in the gastrointestinal tract. Metagenomic approaches have significantly expanded our knowledge on microbiota dynamics inside hosts, yet cultivation and isolation of bacterial members of these complex ecosystems may still be necessary to fully understand interactions between bacterial communities and their host. A dual approach, involving culture-independent and -dependent techniques, was used here to decipher the microbiota communities that inhabit the gastro intestinal tract of free-range, broiler and feral chickens. In silico analysis revealed the presence of a core microbiota that is typical of those animals that live in different geographical areas and that have limited contact with humans. Anthropic influences guide the metabolic potential and the presence of antibiotic resistance genes of these different bacterial communities. Culturomics attempts, based on different cultivation conditions, were applied to reconstruct in vitro the microbiota of feral chickens. A unique strain collection representing members of the four major phyla of the poultry microbiota was assembled, including bacterial strains that are not typically retrieved from the chicken gut.}, }
@article {pmid28961809, year = {2017}, author = {Goss-Souza, D and Mendes, LW and Borges, CD and Baretta, D and Tsai, SM and Rodrigues, JLM}, title = {Soil microbial community dynamics and assembly under long-term land use change.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {10}, pages = {}, doi = {10.1093/femsec/fix109}, pmid = {28961809}, issn = {1574-6941}, mesh = {Archaea/classification/isolation & purification ; Bacteria/classification/isolation & purification ; Biodiversity ; Conservation of Natural Resources ; *Forests ; Grassland ; Metagenome ; *Soil Microbiology ; }, abstract = {We evaluated the bacterial and archaeal community dynamics and assembly in soils under forest, grassland and no-till cropping, using a high-throughput shotgun metagenomics approach. No significant alterations in alpha diversity were observed among different land uses, but beta diversity in grassland was lower than that observed in forest and no-till soils. Grassland communities showed assembly that predominantly followed the neutral model, i.e. high homogenizing selection with moderate dispersion, leading to biotic homogenization. Both no-till and forest soil communities were found to have assembly that predominantly followed a niche model, i.e. low rates of dispersal and weak homogenizing selection, resulting in maintenance of higher beta diversity relative to grasslands, indicating niche specialization or variable selection. Taken together, our results indicate that the patterns of assembly and their governing processes are dependent on the land use employed after deforestation, with consequences for taxa turnover and microbial functional potential.}, }
@article {pmid28961409, year = {2017}, author = {Williamson, KE and Fuhrmann, JJ and Wommack, KE and Radosevich, M}, title = {Viruses in Soil Ecosystems: An Unknown Quantity Within an Unexplored Territory.}, journal = {Annual review of virology}, volume = {4}, number = {1}, pages = {201-219}, doi = {10.1146/annurev-virology-101416-041639}, pmid = {28961409}, issn = {2327-0578}, mesh = {*Biodiversity ; DNA, Single-Stranded/isolation & purification ; *Ecosystem ; Food Chain ; Gene Transfer, Horizontal ; Genome, Viral ; Humans ; Metagenomics ; *Soil Microbiology ; Virus Physiological Phenomena ; Viruses/*genetics ; }, abstract = {Viral abundance in soils can range from below detection limits in hot deserts to over 1 billion per gram in wetlands. Abundance appears to be strongly influenced by water availability and temperature, but a lack of informational standards creates difficulties for cross-study analysis. Soil viral diversity is severely underestimated and undersampled, although current measures of viral richness are higher for soils than for aquatic ecosystems. Both morphometric and metagenomic analyses have raised questions about the prevalence of nontailed, ssDNA viruses in soils. Soil is complex and critically important to terrestrial biodiversity and human civilization, but impacts of viral activities on soil ecosystem services are poorly understood. While information from aquatic systems and medical microbiology suggests the potential for viral influences on nutrient cycles, food web interactions, gene transfer, and other key processes in soils, very few empirical data are available. To understand the soil virome, much work remains.}, }
@article {pmid28955471, year = {2017}, author = {van Nieuwenhuijzen, EJ and Houbraken, JAMP and Punt, PJ and Roeselers, G and Adan, OCG and Samson, RA}, title = {The fungal composition of natural biofinishes on oil-treated wood.}, journal = {Fungal biology and biotechnology}, volume = {4}, number = {}, pages = {2}, doi = {10.1186/s40694-017-0030-5}, pmid = {28955471}, issn = {2054-3085}, abstract = {BACKGROUND: Biofinished wood is considered to be a decorative and protective material for outdoor constructions, showing advantages compared to traditional treated wood in terms of sustainability and self-repair. Natural dark wood staining fungi are essential to biofinish formation on wood. Although all sorts of outdoor situated timber are subjected to fungal staining, the homogenous dark staining called biofinish has only been detected on specific vegetable oil-treated substrates. Revealing the fungal composition of various natural biofinishes on wood is a first step to understand and control biofinish formation for industrial application.
RESULTS: A culture-based survey of fungi in natural biofinishes on oil-treated wood samples showed the common wood stain fungus Aureobasidium and the recently described genus Superstratomyces to be predominant constituents. A culture-independent approach, based on amplification of the internal transcribed spacer regions, cloning and Sanger sequencing, resulted in clone libraries of two types of biofinishes. Aureobasidium was present in both biofinish types, but was only predominant in biofinishes on pine sapwood treated with raw linseed oil. Most cloned sequences of the other biofinish type (pine sapwood treated with olive oil) could not be identified. In addition, a more in-depth overview of the fungal composition of biofinishes was obtained with Illumina amplicon sequencing that targeted the internal transcribed spacer region 1. All investigated samples, that varied in wood species, (oil) treatments and exposure times, contained Aureobasidium and this genus was predominant in the biofinishes on pine sapwood treated with raw linseed oil. Lapidomyces was the predominant genus in most of the other biofinishes and present in all other samples. Surprisingly, Superstratomyces, which was predominantly detected by the cultivation-based approach, could not be found with the Illumina sequencing approach, while Lapidomyces was not detected in the culture-based approach.
CONCLUSIONS: Overall, the culture-based approach and two culture-independent methods that were used in this study revealed that natural biofinishes were composed of multiple fungal genera always containing the common wood staining mould Aureobasidium. Besides Aureobasidium, the use of other fungal genera for the production of biofinished wood has to be considered.}, }
@article {pmid28955177, year = {2017}, author = {Ericsson, AC and Montonye, DR and Smith, CR and Franklin, CL}, title = {Modeling a Superorganism - Considerations Regarding the Use of "Dirty" Mice in Biomedical Research
.}, journal = {The Yale journal of biology and medicine}, volume = {90}, number = {3}, pages = {361-371}, pmid = {28955177}, issn = {1551-4056}, support = {U42 OD010918/OD/NIH HHS/United States ; }, mesh = {Animals ; Biomedical Research ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Microbiota/genetics/physiology ; T-Lymphocytes/metabolism/physiology ; }, abstract = {An ever-expanding body of evidence in both humans and animal models demonstrates the influence of the resident gut microbiota on host health and disease susceptibility. However, as unwanted bacterial, viral, protozoal, and parasitic agents have gradually been eliminated from colonies of purpose-bred laboratory mice, the resident microbiota has lost richness and complexity. Recent studies have shown that the ultra-hygienic environment of traditional laboratory mice and lack of antigenic exposure during development results in mice with an immune system more akin to that of a neonate than an adult human. In contrast, wild mice or mice purchased from pet stores are exposed to much greater antigen burdens and their immune system reflects this with significantly greater numbers of memory T cells and more robust vaccine responses. The current review explores the use of alternative sources for research rodents, with an emphasis on the differences in resident gut microbiota and pathogen burden between wild mice, pet store-origin mice, and traditional laboratory mice. Specifically, the literature is compared and contrasted to our own data reflecting the endogenous gut microbiota and pathogen load of wild and pet store mice, as well as the changes in both during and after procedures intended to eliminate certain zoonotic agents present in pet store mice. These data demonstrate that, while alternative sources of research rodents will likely provide models that are more translatable to the human condition, there are also several real-world considerations for scientists including contamination of research facilities and human health risks such as zoonotic diseases.}, }
@article {pmid28954247, year = {2018}, author = {Grohmann, A and Fehrmann, S and Vainshtein, Y and Haag, NL and Wiese, F and Stevens, P and Naegele, HJ and Oechsner, H and Hartsch, T and Sohn, K and Grumaz, C}, title = {Microbiome dynamics and adaptation of expression signatures during methane production failure and process recovery.}, journal = {Bioresource technology}, volume = {247}, number = {}, pages = {347-356}, doi = {10.1016/j.biortech.2017.08.214}, pmid = {28954247}, issn = {1873-2976}, mesh = {Acclimatization ; Anaerobiosis ; Archaea ; Biofuels ; *Bioreactors ; *Methane ; Microbiota ; }, abstract = {This study aimed to uncover microbial dynamics and transcriptional adaptations during mesophilic AD of maize silage and slurry. While one digester performed under optimal conditions, the investigations also evaluated the microbiome during a temperature drop mediated process failure accompanied by acidification and how it contributed to a process recovery. Composition and pathway activities were analyzed by whole genome shotgun (WGS) and metatranscriptome sequencing, respectively. A biodiversity of 112 species was observed with noticeable shifts over process time. Although four distinct groups of microbes could be identified with a correlating versatility according to substrate and to process disturbance, also tremendous effects on gene expression were monitored especially of the archaeal methane metabolism. Particularly, the expression of acetogenotrophic methanogenesis related genes was identified to be relevant for process regeneration.}, }
@article {pmid28950879, year = {2017}, author = {Valseth, K and Nesbø, CL and Easterday, WR and Turner, WC and Olsen, JS and Stenseth, NC and Haverkamp, THA}, title = {Temporal dynamics in microbial soil communities at anthrax carcass sites.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {206}, doi = {10.1186/s12866-017-1111-6}, pmid = {28950879}, issn = {1471-2180}, mesh = {Animals ; Anthrax/*microbiology/*veterinary ; Bacillus anthracis/classification/genetics/isolation & purification/*physiology ; Biodiversity ; Cadaver ; DNA, Bacterial/analysis ; Ecology ; Equidae/microbiology ; Genes, rRNA ; Metagenomics ; Namibia ; Soil ; *Soil Microbiology ; Spores, Bacterial/genetics ; }, abstract = {BACKGROUND: Anthrax is a globally distributed disease affecting primarily herbivorous mammals. It is caused by the soil-dwelling and spore-forming bacterium Bacillus anthracis. The dormant B. anthracis spores become vegetative after ingestion by grazing mammals. After killing the host, B. anthracis cells return to the soil where they sporulate, completing the lifecycle of the bacterium. Here we present the first study describing temporal microbial soil community changes in Etosha National Park, Namibia, after decomposition of two plains zebra (Equus quagga) anthrax carcasses. To circumvent state-associated-challenges (i.e. vegetative cells/spores) we monitored B. anthracis throughout the period using cultivation, qPCR and shotgun metagenomic sequencing.
RESULTS: The combined results suggest that abundance estimation of spore-forming bacteria in their natural habitat by DNA-based approaches alone is insufficient due to poor recovery of DNA from spores. However, our combined approached allowed us to follow B. anthracis population dynamics (vegetative cells and spores) in the soil, along with closely related organisms from the B. cereus group, despite their high sequence similarity. Vegetative B. anthracis abundance peaked early in the time-series and then dropped when cells either sporulated or died. The time-series revealed that after carcass deposition, the typical semi-arid soil community (e.g. Frankiales and Rhizobiales species) becomes temporarily dominated by the orders Bacillales and Pseudomonadales, known to contain plant growth-promoting species.
CONCLUSION: Our work indicates that complementing DNA based approaches with cultivation may give a more complete picture of the ecology of spore forming pathogens. Furthermore, the results suggests that the increased vegetation biomass production found at carcass sites is due to both added nutrients and the proliferation of microbial taxa that can be beneficial for plant growth. Thus, future B. anthracis transmission events at carcass sites may be indirectly facilitated by the recruitment of plant-beneficial bacteria.}, }
@article {pmid28941534, year = {2017}, author = {Mourani, PM and Sontag, MK}, title = {Ventilator-Associated Pneumonia in Critically Ill Children: A New Paradigm.}, journal = {Pediatric clinics of North America}, volume = {64}, number = {5}, pages = {1039-1056}, doi = {10.1016/j.pcl.2017.06.005}, pmid = {28941534}, issn = {1557-8240}, mesh = {Child ; Critical Care/methods ; Critical Illness ; Humans ; Lung/microbiology ; Metagenomics ; Microbiota ; *Pneumonia, Ventilator-Associated/diagnosis/etiology/therapy ; Proteomics ; Risk Factors ; }, abstract = {Ventilator-associated pneumonia (VAP) is a serious complication of critical illness. Surveillance definitions have undergone revisions for more objective and consistent reporting. The 1 organism-1 disease paradigm for microbial involvement may not adequately apply to many cases of VAP, in which pathogens are introduced to a pre-existing and often complex microbial community that facilitates or hinders the potential pathogen, consequently determining whether progression to VAP occurs. As omics technology is applied to VAP, a paradigm is emerging incorporating simultaneous assessments of microbial populations and their activity, as well as the host response, to personalize prevention and treatment.}, }
@article {pmid28938903, year = {2017}, author = {O'Hara, NB and Reed, HJ and Afshinnekoo, E and Harvin, D and Caplan, N and Rosen, G and Frye, B and Woloszynek, S and Ounit, R and Levy, S and Butler, E and Mason, CE}, title = {Metagenomic characterization of ambulances across the USA.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {125}, doi = {10.1186/s40168-017-0339-6}, pmid = {28938903}, issn = {2049-2618}, support = {R01 AI125416/AI/NIAID NIH HHS/United States ; }, mesh = {*Ambulances ; Bacteria/classification/genetics/*isolation & purification/pathogenicity ; Cross Infection/microbiology ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Hospitals ; Humans ; *Metagenome ; *Metagenomics ; *Microbial Consortia/genetics ; *Microbiota/genetics ; United States ; }, abstract = {BACKGROUND: Microbial communities in our built environments have great influence on human health and disease. A variety of built environments have been characterized using a metagenomics-based approach, including some healthcare settings. However, there has been no study to date that has used this approach in pre-hospital settings, such as ambulances, an important first point-of-contact between patients and hospitals.
RESULTS: We sequenced 398 samples from 137 ambulances across the USA using shotgun sequencing. We analyzed these data to explore the microbial ecology of ambulances including characterizing microbial community composition, nosocomial pathogens, patterns of diversity, presence of functional pathways and antimicrobial resistance, and potential spatial and environmental factors that may contribute to community composition. We found that the top 10 most abundant species are either common built environment microbes, microbes associated with the human microbiome (e.g., skin), or are species associated with nosocomial infections. We also found widespread evidence of antimicrobial resistance markers (hits ~ 90% samples). We identified six factors that may influence the microbial ecology of ambulances including ambulance surfaces, geographical-related factors (including region, longitude, and latitude), and weather-related factors (including temperature and precipitation).
CONCLUSIONS: While the vast majority of microbial species classified were beneficial, we also found widespread evidence of species associated with nosocomial infections and antimicrobial resistance markers. This study indicates that metagenomics may be useful to characterize the microbial ecology of pre-hospital ambulance settings and that more rigorous testing and cleaning of ambulances may be warranted.}, }
@article {pmid28936948, year = {2017}, author = {Collins, J and Auchtung, JM}, title = {Control of Clostridium difficile Infection by Defined Microbial Communities.}, journal = {Microbiology spectrum}, volume = {5}, number = {5}, pages = {}, doi = {10.1128/microbiolspec.BAD-0009-2016}, pmid = {28936948}, issn = {2165-0497}, support = {R21 AI121522/AI/NIAID NIH HHS/United States ; R33 AI121522/AI/NIAID NIH HHS/United States ; U01 AI124290/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Clostridium Infections/*microbiology/*therapy ; Clostridium difficile/genetics/isolation & purification/*physiology ; *Fecal Microbiota Transplantation ; Feces/microbiology ; Gastrointestinal Microbiome ; Humans ; }, abstract = {Each year in the United States, billions of dollars are spent combating almost half a million Clostridium difficile infections (CDIs) and trying to reduce the ∼29,000 patient deaths in which C. difficile has an attributed role. In Europe, disease prevalence varies by country and level of surveillance, though yearly costs are estimated at €3 billion. One factor contributing to the significant health care burden of C. difficile is the relatively high frequency of recurrent CDIs. Recurrent CDI, i.e., a second episode of symptomatic CDI occurring within 8 weeks of successful initial CDI treatment, occurs in ∼25% of patients, with 35 to 65% of these patients experiencing multiple episodes of recurrent disease. Using microbial communities to treat recurrent CDI, either as whole fecal transplants or as defined consortia of bacterial isolates, has shown great success (in the case of fecal transplants) or potential promise (in the case of defined consortia of isolates). This review will briefly summarize the epidemiology and physiology of C. difficile infection, describe our current understanding of how fecal microbiota transplants treat recurrent CDI, and outline potential ways that knowledge can be used to rationally design and test alternative microbe-based therapeutics.}, }
@article {pmid28934964, year = {2017}, author = {McIntyre, ABR and Ounit, R and Afshinnekoo, E and Prill, RJ and Hénaff, E and Alexander, N and Minot, SS and Danko, D and Foox, J and Ahsanuddin, S and Tighe, S and Hasan, NA and Subramanian, P and Moffat, K and Levy, S and Lonardi, S and Greenfield, N and Colwell, RR and Rosen, GL and Mason, CE}, title = {Comprehensive benchmarking and ensemble approaches for metagenomic classifiers.}, journal = {Genome biology}, volume = {18}, number = {1}, pages = {182}, doi = {10.1186/s13059-017-1299-7}, pmid = {28934964}, issn = {1474-760X}, support = {R01 AI125416/AI/NIAID NIH HHS/United States ; R01 ES021006/ES/NIEHS NIH HHS/United States ; R25 EB020393/EB/NIBIB NIH HHS/United States ; }, mesh = {Benchmarking/*methods/standards ; Contig Mapping/*methods/standards ; DNA Barcoding, Taxonomic/*methods/standards ; Humans ; *Metagenome ; Microbiota ; Phylogeny ; Sequence Analysis, DNA/*methods/standards ; *Software ; }, abstract = {BACKGROUND: One of the main challenges in metagenomics is the identification of microorganisms in clinical and environmental samples. While an extensive and heterogeneous set of computational tools is available to classify microorganisms using whole-genome shotgun sequencing data, comprehensive comparisons of these methods are limited.
RESULTS: In this study, we use the largest-to-date set of laboratory-generated and simulated controls across 846 species to evaluate the performance of 11 metagenomic classifiers. Tools were characterized on the basis of their ability to identify taxa at the genus, species, and strain levels, quantify relative abundances of taxa, and classify individual reads to the species level. Strikingly, the number of species identified by the 11 tools can differ by over three orders of magnitude on the same datasets. Various strategies can ameliorate taxonomic misclassification, including abundance filtering, ensemble approaches, and tool intersection. Nevertheless, these strategies were often insufficient to completely eliminate false positives from environmental samples, which are especially important where they concern medically relevant species. Overall, pairing tools with different classification strategies (k-mer, alignment, marker) can combine their respective advantages.
CONCLUSIONS: This study provides positive and negative controls, titrated standards, and a guide for selecting tools for metagenomic analyses by comparing ranges of precision, accuracy, and recall. We show that proper experimental design and analysis parameters can reduce false positives, provide greater resolution of species in complex metagenomic samples, and improve the interpretation of results.}, }
@article {pmid28934322, year = {2017}, author = {Moussa, TAA and Al-Zahrani, HS and Almaghrabi, OA and Abdelmoneim, TS and Fuller, MP}, title = {Comparative metagenomics approaches to characterize the soil fungal communities of western coastal region, Saudi Arabia.}, journal = {PloS one}, volume = {12}, number = {9}, pages = {e0185096}, doi = {10.1371/journal.pone.0185096}, pmid = {28934322}, issn = {1932-6203}, mesh = {Biodiversity ; Classification ; Fungi/*genetics ; *Metagenomics ; Oceans and Seas ; Phylogeny ; Polymerase Chain Reaction ; Saudi Arabia ; Sequence Analysis, DNA ; Soil ; *Soil Microbiology ; }, abstract = {A total of 145007 reads were obtained from pyrosequencing for all the 4 samples. The total count ranged from 11,301,014 (Mecca old road) to 23,503,512 bp (Thuwal). A total of 460 fungal species belonging to 133 genera, 58 families, 33 orders, 13 classes and 4 phyla was identified across the four sites. The most abundant phylum at all four sites was Ascomycota followed by Basidiomycota. Four phyla (Ascomycota-99.31%, Basidiomycota-0.59%, Chytridiomycota-0.04%, Glomeromycota-0.03%) were detected in Khulais. Except for Glomeromycota, all phyla were detected at Mecca old road (Ascomycota-74.26%, Basidiomycota-25.71%, Chytridiomycota-0.01%) and Thuwal (Ascomycota-99.59%, Basidiomycota-0.40%, Chytridiomycota-0.002%); while only Ascomycota-90.98% and Basidiomycota-9.01% were detected in Asfan road. At the class level, Sordariomycetes was predominantly observed at Asfan road-59.88%, Khulais-68.26% and Thuwal-94.84%; while Pezizomycetes was dominant at Mecca old road-56.01%, was absent at Asfan road. Agaricomycetes was present only at Mecca old road-25.73%; while Tremellomycetes-5.77%, Malasseizomycetes-2.13% and Microbotryomycetes-1.10% were found only at Asfan road. The phylogenetic trees revealed that clear genus level differences are visible across all the four sites, with an overall predominance of Thielavia followed by Madurella, Aspergillus, and Gelasinospora. Chaetomium sp., Aspergillus caespitosus and Aspergillus sp. were found in moderate (Mecca old road and Thuwal) to abundant (Asfan road and Khulais) quantities. Thielavia sp., Thielavia hyalocarpa and Madurella sp. are found in moderate quantities at Khulais and Mecca old road, while in abundant levels at Asfan road and Thuwal. Fusarium equisati and F. oxysporum were detected at Thuwal and Khulais. Sordaria araneosa was present at Khulais, while Malasseiza globosa species was detected in moderate quantities across all sites except Khulais.}, }
@article {pmid28927227, year = {2017}, author = {Cannon, K and Byrne, B and Happe, J and Wu, K and Ward, L and Chesnel, L and Louie, T}, title = {Enteric microbiome profiles during a randomized Phase 2 clinical trial of surotomycin versus vancomycin for the treatment of Clostridium difficile infection.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {72}, number = {12}, pages = {3453-3461}, doi = {10.1093/jac/dkx318}, pmid = {28927227}, issn = {1460-2091}, mesh = {Administration, Oral ; Adolescent ; Adult ; Aged ; Aged, 80 and over ; Anti-Bacterial Agents/administration & dosage/*adverse effects ; Bacteria/classification/*isolation & purification ; Bacterial Load ; Bacteriological Techniques ; Clostridium Infections/*drug therapy ; Double-Blind Method ; Dysbiosis/*chemically induced ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Lipopeptides/administration & dosage/*adverse effects ; Male ; Metagenomics ; Middle Aged ; Peptides, Cyclic/administration & dosage/*adverse effects ; Real-Time Polymerase Chain Reaction ; Time Factors ; Vancomycin/administration & dosage/*adverse effects ; Young Adult ; }, abstract = {Objectives: The effects of surotomycin (CB-183,315, MK-4261), a bactericidal cyclic lipopeptide, and vancomycin, the current standard-of-care for Clostridium difficile infection (CDI), on intestinal pathogens and microbiota were evaluated parallel to a Phase 2 randomized, double-blind clinical trial.
Methods: The single-centre cohort included 26 patients receiving surotomycin [125 or 250 mg twice daily (n = 9 each)] or oral vancomycin [125 mg four times daily (n = 8)] for 10 days. Faecal samples were collected at days 0-42 to quantify both C. difficile by conventional culture and the major components of the microbiome by quantitative PCR.
Results: Surotomycin 250 mg twice daily or vancomycin 125 mg four times daily reduced faecal C. difficile counts from ∼105-107 log10 cfu/g at baseline to ≤ 102 cfu/g by days 4-10 of treatment. Day 10 counts of C. difficile in 3/9 patients receiving surotomycin 125 mg twice daily remained detectable, including one patient who failed to achieve clinical cure. Bacteroidetes and Prevotella mean counts increased 0.7 log10 or remained unchanged with surotomycin 125 and 250 mg twice daily, respectively, whereas vancomycin reduced counts by 2.5-3.2 log10 (P < 0.02). Vancomycin reduced Firmicutes counts by 2.5-2.8 log10; surotomycin moderately suppressed these microbes in a dose-dependent manner.
Conclusions: In this Phase 2 trial substudy, compared with vancomycin 125 mg four times daily, surotomycin 250 mg twice daily is as active in vivo against C. difficile, but was more sparing of microbiota. Surotomycin is no longer in development due to failed Phase 3 efficacy results.}, }
@article {pmid28923537, year = {2017}, author = {Frankel, AE and Coughlin, LA and Kim, J and Froehlich, TW and Xie, Y and Frenkel, EP and Koh, AY}, title = {Metagenomic Shotgun Sequencing and Unbiased Metabolomic Profiling Identify Specific Human Gut Microbiota and Metabolites Associated with Immune Checkpoint Therapy Efficacy in Melanoma Patients.}, journal = {Neoplasia (New York, N.Y.)}, volume = {19}, number = {10}, pages = {848-855}, doi = {10.1016/j.neo.2017.08.004}, pmid = {28923537}, issn = {1476-5586}, support = {P30 CA142543/CA/NCI NIH HHS/United States ; R01 CA152301/CA/NCI NIH HHS/United States ; R01 CA172211/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Antineoplastic Agents, Immunological/pharmacology/therapeutic use ; Biomarkers, Tumor ; Chromatography, High Pressure Liquid ; Cluster Analysis ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Melanoma/drug therapy/*etiology/*metabolism/pathology ; *Metabolomics/methods ; *Metagenome ; *Metagenomics/methods ; Middle Aged ; Molecular Targeted Therapy ; Neoplasm Metastasis ; Neoplasm Staging ; Prognosis ; Tandem Mass Spectrometry ; Treatment Outcome ; }, abstract = {This is the first prospective study of the effects of human gut microbiota and metabolites on immune checkpoint inhibitor (ICT) response in metastatic melanoma patients. Whereas many melanoma patients exhibit profound response to ICT, there are fewer options for patients failing ICT-particularly with BRAF-wild-type disease. In preclinical studies, specific gut microbiota promotes regression of melanoma in mice. We therefore conducted a study of the effects of pretreatment gut microbiota and metabolites on ICT Response Evaluation Criteria in Solid Tumors response in 39 metastatic melanoma patients treated with ipilimumab, nivolumab, ipilimumab plus nivolumab (IN), or pembrolizumab (P). IN yielded 67% responses and 8% stable disease; P achieved 23% responses and 23% stable disease. ICT responders for all types of therapies were enriched for Bacteroides caccae. Among IN responders, the gut microbiome was enriched for Faecalibacterium prausnitzii, Bacteroides thetaiotamicron, and Holdemania filiformis. Among P responders, the microbiome was enriched for Dorea formicogenerans. Unbiased shotgun metabolomics revealed high levels of anacardic acid in ICT responders. Based on these pilot studies, both additional confirmatory clinical studies and preclinical testing of these bacterial species and metabolites are warranted to confirm their ICT enhancing activity.}, }
@article {pmid28915922, year = {2017}, author = {Winglee, K and Howard, AG and Sha, W and Gharaibeh, RZ and Liu, J and Jin, D and Fodor, AA and Gordon-Larsen, P}, title = {Recent urbanization in China is correlated with a Westernized microbiome encoding increased virulence and antibiotic resistance genes.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {121}, doi = {10.1186/s40168-017-0338-7}, pmid = {28915922}, issn = {2049-2618}, support = {UL1 TR001111/TR/NCATS NIH HHS/United States ; P30 ES010126/ES/NIEHS NIH HHS/United States ; R01 DK104371/DK/NIDDK NIH HHS/United States ; R01 HL108427/HL/NHLBI NIH HHS/United States ; R24 HD050924/HD/NICHD NIH HHS/United States ; }, mesh = {Aged ; Bacteria/*genetics/pathogenicity ; China ; *Diet, Western ; Drug Resistance, Microbial/*genetics ; Escherichia coli/genetics/pathogenicity ; Feeding Behavior ; Female ; *Gastrointestinal Microbiome/genetics ; Genetic Variation ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Metabolome ; Metagenomics ; Middle Aged ; Shigella/genetics/pathogenicity ; *Urbanization ; Virulence/genetics ; }, abstract = {BACKGROUND: Urbanization is associated with an increased risk for a number of diseases, including obesity, diabetes, and cancer, which all also show associations with the microbiome. While microbial community composition has been shown to vary across continents and in traditional versus Westernized societies, few studies have examined urban-rural differences in neighboring communities within a single country undergoing rapid urbanization. In this study, we compared the gut microbiome, plasma metabolome, dietary habits, and health biomarkers of rural and urban people from a single Chinese province.
RESULTS: We identified significant differences in the microbiota and microbiota-related plasma metabolites in rural versus recently urban subjects from the Hunan province of China. Microbes with higher relative abundance in Chinese urban samples have been associated with disease in other studies and were substantially more prevalent in the Human Microbiome Project cohort of American subjects. Furthermore, using whole metagenome sequencing, we found that urbanization was associated with a loss of microbial diversity and changes in the relative abundances of Viruses, Archaea, and Bacteria. Gene diversity, however, increased with urbanization, along with the proportion of reads associated with antibiotic resistance and virulence, which were strongly correlated with the presence of Escherichia and Shigella.
CONCLUSIONS: Our data suggest that urbanization has produced convergent evolution of the gut microbial composition in American and urban Chinese populations, resulting in similar compositional patterns of abundant microbes through similar lifestyles on different continents, including a loss of potentially beneficial bacteria and an increase in potentially harmful genes via increased relative abundance of Escherichia and Shigella.}, }
@article {pmid28904137, year = {2017}, author = {Wu, Q and Wang, X and Ding, Y and Hu, Y and Nie, Y and Wei, W and Ma, S and Yan, L and Zhu, L and Wei, F}, title = {Seasonal variation in nutrient utilization shapes gut microbiome structure and function in wild giant pandas.}, journal = {Proceedings. Biological sciences}, volume = {284}, number = {1862}, pages = {}, doi = {10.1098/rspb.2017.0955}, pmid = {28904137}, issn = {1471-2954}, mesh = {Animals ; Diet/*veterinary ; Food ; *Gastrointestinal Microbiome ; Metagenomics ; Plant Leaves ; Plant Shoots ; *Seasons ; Ursidae/*microbiology ; }, abstract = {Wild giant pandas use different parts of bamboo (shoots, leaves and stems) and different bamboo species at different times of the year. Their usage of bamboo can be classified temporally into a distinct leaf stage, shoot stage and transition stage. An association between this usage pattern and variation in the giant panda gut microbiome remains unknown. Here, we found associations using a gut metagenomic approach and nutritional analyses whereby diversity of the gut microbial community in the leaf and shoot stages was significantly different. Functional metagenomic analysis showed that in the leaf stage, bacteria species over-represented genes involved in raw fibre utilization and cell cycle control. Thus, raw fibre utilization by the gut microbiome was guaranteed during the nutrient-deficient leaf stage by reinforcing gut microbiome robustness. During the protein-abundant shoot stage, the functional capacity of the gut microbiome expanded to include prokaryotic secretion and signal transduction activity, suggesting active interactions between the gut microbiome and host. These results illustrate that seasonal nutrient variation in wild giant pandas substantially influences gut microbiome composition and function. Nutritional interactions between gut microbiomes and hosts appear to be complex and further work is needed.}, }
@article {pmid28899105, year = {2017}, author = {Williams, B and Ghosh, M and Boucher, CAB and Bushman, F and Carrington-Lawrence, S and Collman, RG and Dandekar, S and Dang, Q and Malaspina, A and Paredes, R and Wilson, CC and Nowak, P and Klatt, NR and Lagenaur, L and Landay, AL}, title = {A Summary of the Second Annual HIV Microbiome Workshop.}, journal = {AIDS research and human retroviruses}, volume = {33}, number = {12}, pages = {1258-1264}, doi = {10.1089/aid.2017.0137}, pmid = {28899105}, issn = {1931-8405}, support = {P51 OD010425/OD/NIH HHS/United States ; }, mesh = {Bacteria/classification/*isolation & purification ; Fungi/classification/*isolation & purification ; HIV Infections/*pathology/*transmission/virology ; Humans ; Microbial Interactions/*physiology ; Microbiota/*physiology ; Symbiosis/physiology ; }, abstract = {Commensal organisms appear to play significant roles in normal homeostasis as well as in the pathogenesis of HIV infection in a number of different organ systems. On November 17th and 18th, 2016, leading researchers from around the world met to discuss their insights on advances in our understanding of HIV and the microbiome at the National Institutes of Health (NIH) in Bethesda. Dr. Elhanan Borenstein of the University of Washington gave a keynote address where he discussed new developments in systems biology which hold the promise of illuminating the pathways by which these organisms interact with human physiology. He suggested that we need to get past correlations in microbiome research by using models and informatics which incorporate metagenomics to predict functional changes in the microbiome.}, }
@article {pmid28898777, year = {2017}, author = {Liu, P and Jia, S and He, X and Zhang, X and Ye, L}, title = {Different impacts of manure and chemical fertilizers on bacterial community structure and antibiotic resistance genes in arable soils.}, journal = {Chemosphere}, volume = {188}, number = {}, pages = {455-464}, doi = {10.1016/j.chemosphere.2017.08.162}, pmid = {28898777}, issn = {1879-1298}, mesh = {Agriculture/methods ; China ; Drug Resistance, Microbial/*genetics ; *Fertilizers ; Genes, Bacterial ; High-Throughput Screening Assays ; *Manure ; Metagenomics ; Microbiota/*drug effects/genetics ; Soil/*chemistry ; Soil Microbiology/*standards ; }, abstract = {Both manure and chemical fertilizers are widely used in modern agriculture. However, the impacts of different fertilizers on bacterial community structure and antibiotic resistance genes (ARGs) in arable soils still remain unclear. In this study, high-throughput sequencing and quantitative PCR were employed to investigate the bacterial community structure, ARGs and mobile genetic elements (MGEs) influenced by the application of different fertilizers, including chemical fertilizers, piggery manure and straw ash. The results showed that the application of fertilizers could significantly change the soil bacterial community and the abundance of Gaiella under phylum Actinobacteria was significantly reduced from 12.9% in unfertilized soil to 4.1%-7.4% in fertilized soil (P < 0.05). It was also found that the application of manure could cause a transient effect on soil resistome composition and the relative abundance of ARGs increased from 7.37 ppm to 32.10 ppm. The abundance of aminoglycoside, sulfonamide and tetracycline resistance genes greatly increased after manure fertilization and then gradually returned to normal levels with the decay of some intestinal bacteria carrying ARGs. In contrast, the application of chemical fertilizers and straw ash significantly changed the bacterial community structure but exerted little effect on soil resistome. Overall, the results of this study illustrated the different effects of different fertilizers on the soil resistome and revealed that the changes of soil resistome induced by manure application mainly resulted from alteration of bacteria community rather than the horizontal gene transfer.}, }
@article {pmid28898292, year = {2017}, author = {Elderman, M and Sovran, B and Hugenholtz, F and Graversen, K and Huijskes, M and Houtsma, E and Belzer, C and Boekschoten, M and de Vos, P and Dekker, J and Wells, J and Faas, M}, title = {The effect of age on the intestinal mucus thickness, microbiota composition and immunity in relation to sex in mice.}, journal = {PloS one}, volume = {12}, number = {9}, pages = {e0184274}, doi = {10.1371/journal.pone.0184274}, pmid = {28898292}, issn = {1932-6203}, mesh = {Age Factors ; Aging/immunology/metabolism ; Animals ; Biodiversity ; Cell Differentiation/genetics/immunology ; Colon/cytology/immunology/metabolism/microbiology ; Dendritic Cells/cytology/immunology/metabolism ; Female ; Gastrointestinal Microbiome/*immunology ; Gene Expression Profiling ; Gene Expression Regulation ; *Immunity, Mucosal ; Intestinal Mucosa/*cytology/*immunology/metabolism ; Male ; Metagenome ; Metagenomics/methods ; Mice ; Mucus/metabolism ; Peyer's Patches/immunology/metabolism ; Sex Factors ; Signal Transduction ; Spleen/immunology/metabolism ; T-Lymphocytes/cytology/metabolism ; Transcriptome ; }, abstract = {A mucus layer covers and protects the intestinal epithelial cells from direct contact with microbes. This mucus layer not only prevents inflammation but also plays an essential role in microbiota colonization, indicating the complex interplay between mucus composition-microbiota and intestinal health. However, it is unknown whether the mucus layer is influenced by age or sex and whether this contributes to reported differences in intestinal diseases in males and females or with ageing. Therefore, in this study we investigated the effect of age on mucus thickness, intestinal microbiota composition and immune composition in relation to sex. The ageing induced shrinkage of the colonic mucus layer was associated with bacterial penetration and direct contact of bacteria with the epithelium in both sexes. Additionally, several genes involved in the biosynthesis of mucus were downregulated in old mice, especially in males, and this was accompanied by a decrease in abundances of various Lactobacillus species and unclassified Clostridiales type IV and XIV and increase in abundance of the potential pathobiont Bacteroides vulgatus. The changes in mucus and microbiota in old mice were associated with enhanced activation of the immune system as illustrated by a higher percentage of effector T cells in old mice. Our data contribute to a better understanding of the interplay between mucus-microbiota-and immune responses and ultimately may lead to more tailored design of strategies to modulate mucus production in targeted groups.}, }
@article {pmid28898207, year = {2017}, author = {Quince, C and Walker, AW and Simpson, JT and Loman, NJ and Segata, N}, title = {Shotgun metagenomics, from sampling to analysis.}, journal = {Nature biotechnology}, volume = {35}, number = {9}, pages = {833-844}, doi = {10.1038/nbt.3935}, pmid = {28898207}, issn = {1546-1696}, support = {MR/M50161X/1//Medical Research Council/United Kingdom ; MR/M501621/1//Medical Research Council/United Kingdom ; }, mesh = {Animals ; Biomedical Research ; *High-Throughput Nucleotide Sequencing ; Humans ; *Metagenomics ; *Microbiota/genetics/physiology ; }, abstract = {Diverse microbial communities of bacteria, archaea, viruses and single-celled eukaryotes have crucial roles in the environment and in human health. However, microbes are frequently difficult to culture in the laboratory, which can confound cataloging of members and understanding of how communities function. High-throughput sequencing technologies and a suite of computational pipelines have been combined into shotgun metagenomics methods that have transformed microbiology. Still, computational approaches to overcome the challenges that affect both assembly-based and mapping-based metagenomic profiling, particularly of high-complexity samples or environments containing organisms with limited similarity to sequenced genomes, are needed. Understanding the functions and characterizing specific strains of these communities offers biotechnological promise in therapeutic discovery and innovative ways to synthesize products using microbial factories and can pinpoint the contributions of microorganisms to planetary, animal and human health.}, }
@article {pmid28893994, year = {2017}, author = {Berer, K and Gerdes, LA and Cekanaviciute, E and Jia, X and Xiao, L and Xia, Z and Liu, C and Klotz, L and Stauffer, U and Baranzini, SE and Kümpfel, T and Hohlfeld, R and Krishnamoorthy, G and Wekerle, H}, title = {Gut microbiota from multiple sclerosis patients enables spontaneous autoimmune encephalomyelitis in mice.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {40}, pages = {10719-10724}, doi = {10.1073/pnas.1711233114}, pmid = {28893994}, issn = {1091-6490}, support = {K12 GM081266/GM/NIGMS NIH HHS/United States ; R25 NS070680/NS/NINDS NIH HHS/United States ; }, mesh = {Adult ; Aged ; Animals ; Brain/*immunology/microbiology/pathology ; Cohort Studies ; *Disease Models, Animal ; Encephalomyelitis, Autoimmune, Experimental/*immunology/microbiology/pathology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics ; Mice ; Middle Aged ; Multiple Sclerosis/*immunology/microbiology/pathology ; T-Lymphocytes, Regulatory/*immunology ; Young Adult ; }, abstract = {There is emerging evidence that the commensal microbiota has a role in the pathogenesis of multiple sclerosis (MS), a putative autoimmune disease of the CNS. Here, we compared the gut microbial composition of 34 monozygotic twin pairs discordant for MS. While there were no major differences in the overall microbial profiles, we found a significant increase in some taxa such as Akkermansia in untreated MS twins. Furthermore, most notably, when transplanted to a transgenic mouse model of spontaneous brain autoimmunity, MS twin-derived microbiota induced a significantly higher incidence of autoimmunity than the healthy twin-derived microbiota. The microbial profiles of the colonized mice showed a high intraindividual and remarkable temporal stability with several differences, including Sutterella, an organism shown to induce a protective immunoregulatory profile in vitro. Immune cells from mouse recipients of MS-twin samples produced less IL-10 than immune cells from mice colonized with healthy-twin samples. IL-10 may have a regulatory role in spontaneous CNS autoimmunity, as neutralization of the cytokine in mice colonized with healthy-twin fecal samples increased disease incidence. These findings provide evidence that MS-derived microbiota contain factors that precipitate an MS-like autoimmune disease in a transgenic mouse model. They hence encourage the detailed search for protective and pathogenic microbial components in human MS.}, }
@article {pmid28893308, year = {2017}, author = {Michas, A and Vestergaard, G and Trautwein, K and Avramidis, P and Hatzinikolaou, DG and Vorgias, CE and Wilkes, H and Rabus, R and Schloter, M and Schöler, A}, title = {More than 2500 years of oil exposure shape sediment microbiomes with the potential for syntrophic degradation of hydrocarbons linked to methanogenesis.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {118}, doi = {10.1186/s40168-017-0337-8}, pmid = {28893308}, issn = {2049-2618}, mesh = {Anaerobiosis ; *Biodegradation, Environmental ; Chemoautotrophic Growth ; Geologic Sediments/*microbiology ; High-Throughput Nucleotide Sequencing ; Hydrocarbons/*metabolism ; Lakes/microbiology ; *Metagenome ; Metagenomics/methods ; Methane/*metabolism ; Microbial Interactions ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfates/metabolism ; Time Factors ; }, abstract = {BACKGROUND: Natural oil seeps offer the opportunity to study the adaptation of ecosystems and the associated microbiota to long-term oil exposure. In the current study, we investigated a land-to-sea transition ecosystem called "Keri Lake" in Zakynthos Island, Greece. This ecosystem is unique due to asphalt oil springs found at several sites, a phenomenon already reported 2500 years ago. Sediment microbiomes at Keri Lake were studied, and their structure and functional potential were compared to other ecosystems with oil exposure histories of various time periods.
RESULTS: Replicate sediment cores (up to 3-m depth) were retrieved from one site exposed to oil as well as a non-exposed control site. Samples from three different depths were subjected to chemical analysis and metagenomic shotgun sequencing. At the oil-exposed site, we observed high amounts of asphalt oil compounds and a depletion of sulfate compared to the non-exposed control site. The numbers of reads assigned to genes involved in the anaerobic degradation of hydrocarbons were similar between the two sites. The numbers of denitrifiers and sulfate reducers were clearly lower in the samples from the oil-exposed site, while a higher abundance of methanogens was detected compared to the non-exposed site. Higher abundances of the genes of methanogenesis were also observed in the metagenomes from other ecosystems with a long history of oil exposure, compared to short-term exposed environments.
CONCLUSIONS: The analysis of Keri Lake metagenomes revealed that microbiomes in the oil-exposed sediment have a higher potential for methanogenesis over denitrification/sulfate reduction, compared to those in the non-exposed site. Comparison with metagenomes from various oil-impacted environments suggests that syntrophic interactions of hydrocarbon degraders with methanogens are favored in the ecosystems with a long-term presence of oil.}, }
@article {pmid28892512, year = {2017}, author = {Mezzasalma, V and Sandionigi, A and Bruni, I and Bruno, A and Lovicu, G and Casiraghi, M and Labra, M}, title = {Grape microbiome as a reliable and persistent signature of field origin and environmental conditions in Cannonau wine production.}, journal = {PloS one}, volume = {12}, number = {9}, pages = {e0184615}, doi = {10.1371/journal.pone.0184615}, pmid = {28892512}, issn = {1932-6203}, mesh = {Agriculture ; Bacteria/classification/genetics ; Biodiversity ; Cluster Analysis ; DNA Barcoding, Taxonomic ; *Environment ; Fungi/classification/genetics ; Geography ; Metagenome ; Metagenomics/methods ; *Microbiota ; Vitis/*microbiology ; *Wine ; }, abstract = {Grape berries harbor a wide range of microbes originating from the vineyard environment, many of which are recognized for their role in the must fermentation process shaping wine quality. To better clarify the contribution of the microbiome of grape fruits during wine fermentation, we used high-throughput sequencing to identify bacterial and fungi communities associated with berries and musts of Cannonau. This is the most important cultivar-wine of Sardinia (Italy) where most vineyards are cultivated without phytochemical treatments. Results suggested that microbiomes of berries collected at four different localities share a core composition characterized by Enterobacteriales, Pseudomonadales, Bacillales, and Rhodospirillales. However, any area seems to enrich berries microbiome with peculiar microbial traits. For example, berries belonging to the biodynamic vineyards of Mamoiada were rich in Bacillales typical of manure (i.e. Lysinibacillus, Bacillus, and Sporosarcina), whereas in the Santadi locality, berries showed soil bacteria such as Pasteurellales and Bacteroidales as well as Rhodospirillales and Lactobacillales which are commonly involved in wine fermentation. In the case of fungi, the most abundant taxa were Dothioraceae, Pleosporaceae, and Saccharomycodaceae, and although the proportion of these families varied among localities, they occurred ubiquitously in all vineyards. During vinification processes performed at the same wine cellar under controlled conditions and without using any yeast starter, more than 50% of bacteria groups of berries reached musts, and each locality had its own private bacteria signature, even if Saccharomyces cerevisiae represented the most abundant fungal species. This work suggests that natural berries microbiome could be influenced by pedoclimatic and anthropologic conditions (e.g., farming management), and the fruits' microorganisms persist during the fermentation process. For these reasons, a reliable wine genotyping should include the entire holobiont (plant and all its symbionts), and bioprospecting activities on grape microbiota could lead to improved viticulture yields and wine quality.}, }
@article {pmid28892494, year = {2017}, author = {Jenkins, TP and Rathnayaka, Y and Perera, PK and Peachey, LE and Nolan, MJ and Krause, L and Rajakaruna, RS and Cantacessi, C}, title = {Infections by human gastrointestinal helminths are associated with changes in faecal microbiota diversity and composition.}, journal = {PloS one}, volume = {12}, number = {9}, pages = {e0184719}, doi = {10.1371/journal.pone.0184719}, pmid = {28892494}, issn = {1932-6203}, mesh = {Analysis of Variance ; Animals ; *Biodiversity ; Computational Biology/methods ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Helminthiasis/*microbiology/*parasitology ; *Helminths ; Humans ; Intestinal Diseases, Parasitic/*microbiology ; Metagenome ; Metagenomics/methods ; Sri Lanka ; }, abstract = {Investigations of the impact that patent infections by soil-transmitted gastrointestinal nematode parasites exert on the composition of the host gut commensal flora are attracting growing interest by the scientific community. However, information collected to date varies across experiments, and further studies are needed to identify consistent relationships between parasites and commensal microbial species. Here, we explore the qualitative and quantitative differences between the microbial community profiles of cohorts of human volunteers from Sri Lanka with patent infection by one or more parasitic nematode species (H+), as well as that of uninfected subjects (H-) and of volunteers who had been subjected to regular prophylactic anthelmintic treatment (Ht). High-throughput sequencing of the bacterial 16S rRNA gene, followed by bioinformatics and biostatistical analyses of sequence data revealed no significant differences in alpha diversity (Shannon) and richness between groups (P = 0.65, P = 0.13 respectively); however, beta diversity was significantly increased in H+ and Ht when individually compared to H-volunteers (P = 0.04). Among others, bacteria of the families Verrucomicrobiaceae and Enterobacteriaceae showed a trend towards increased abundance in H+, whereas the Leuconostocaceae and Bacteroidaceae showed a relative increase in H- and Ht respectively. Our findings add valuable knowledge to the vast, and yet little explored, research field of parasite-microbiota interactions and will provide a basis for the elucidation of the role such interactions play in pathogenic and immune-modulatory properties of parasitic nematodes in both human and animal hosts.}, }
@article {pmid28887679, year = {2018}, author = {Poddar, A and Das, SK}, title = {Microbiological studies of hot springs in India: a review.}, journal = {Archives of microbiology}, volume = {200}, number = {1}, pages = {1-18}, doi = {10.1007/s00203-017-1429-3}, pmid = {28887679}, issn = {1432-072X}, mesh = {Bacteria/classification/genetics/*isolation & purification ; Hot Springs/chemistry/*microbiology ; India ; Microbiota ; Phylogeny ; }, abstract = {The earliest microbiological studies on hot springs in India date from 2003, a much later date compared to global attention in this striking field of study. As of today, 28 out of 400 geothermal springs have been explored following both culturable and non-culturable approaches. The temperatures and pH of the springs are 37-99 °C and 6.8-10, respectively. Several studies have been performed on the description of novel genera and species, characterization of different bio-resources, metagenomics of hot spring microbiome and whole genome analysis of few isolates. 17 strains representing novel species and many thermostable enzymes, including lipase, protease, chitinase, amylase, etc. with potential biotechnological applications have been reported by several authors. Influence of physico-chemical conditions, especially that of temperature, on shaping the hot spring microbiome has been established by metagenomic investigations. Bacteria are the predominant life forms in all the springs with an abundance of phyla Firmicutes, Proteobacteria, Actinobacteria, Thermi, Bacteroidetes, Deinococcus-Thermus and Chloroflexi. In this review, we have discussed the findings on all microbiological studies that have been carried out to date, on the 28 hot springs. Further, the possibilities of extrapolating these studies for practical applications and environmental impact assessment towards protection of natural ecosystem of hot springs have also been discussed.}, }
@article {pmid28886166, year = {2017}, author = {Festa, S and Coppotelli, BM and Madueño, L and Loviso, CL and Macchi, M and Neme Tauil, RM and Valacco, MP and Morelli, IS}, title = {Assigning ecological roles to the populations belonging to a phenanthrene-degrading bacterial consortium using omic approaches.}, journal = {PloS one}, volume = {12}, number = {9}, pages = {e0184505}, doi = {10.1371/journal.pone.0184505}, pmid = {28886166}, issn = {1932-6203}, mesh = {Bacteria/*classification/genetics/*metabolism ; *Biodegradation, Environmental ; DNA, Bacterial/genetics ; Gene Order ; Genes, Bacterial ; Metagenome ; Metagenomics/methods ; *Microbial Consortia ; Phenanthrenes/*metabolism ; Phylogeny ; Proteomics/methods ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {The present study describes the behavior of a natural phenanthrene-degrading consortium (CON), a synthetic consortium (constructed with isolated strains from CON) and an isolated strain form CON (Sphingobium sp. AM) in phenanthrene cultures to understand the interactions among the microorganisms present in the natural consortium during phenanthrene degradation as a sole carbon and energy source in liquid cultures. In the contaminant degradation assay, the defined consortium not only achieved a major phenanthrene degradation percentage (> 95%) but also showed a more efficient elimination of the intermediate metabolite. The opposite behavior occurred in the CON culture where the lowest phenanthrene degradation and the highest HNA accumulation were observed, which suggests the presence of positive and also negative interaction in CON. To consider the uncultured bacteria present in CON, a metagenomic library was constructed with total CON DNA. One of the resulting scaffolds (S1P3) was affiliated with the Betaproteobacteria class and resulted in a significant similarity with a genome fragment from Burkholderia sp. HB1 chromosome 1. A complete gene cluster, which is related to one of the lower pathways (meta-cleavage of catechol) involved in PAH degradation (ORF 31-43), mobile genetic elements and associated proteins, was found. These results suggest the presence of at least one other microorganism in CON besides Sphingobium sp. AM, which is capable of degrading PAH through the meta-cleavage pathway. Burkholderiales order was further found, along with Sphingomonadales order, by a metaproteomic approach, which indicated that both orders were metabolically active in CON. Our results show the presence of negative interactions between bacterial populations found in a natural consortium selected by enrichment techniques; moreover, the synthetic syntrophic processing chain with only one microorganism with the capability of degrading phenanthrene was more efficient in contaminant and intermediate metabolite degradation than a generalist strain (Sphingobium sp. AM).}, }
@article {pmid28878025, year = {2017}, author = {Sarashina-Kida, H and Negishi, H and Nishio, J and Suda, W and Nakajima, Y and Yasui-Kato, M and Iwaisako, K and Kang, S and Endo, N and Yanai, H and Asagiri, M and Kida, H and Hattori, M and Kumanogoh, A and Taniguchi, T}, title = {Gallbladder-derived surfactant protein D regulates gut commensal bacteria for maintaining intestinal homeostasis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {38}, pages = {10178-10183}, doi = {10.1073/pnas.1712837114}, pmid = {28878025}, issn = {1091-6490}, mesh = {Animals ; Colitis/*metabolism/microbiology ; Forkhead Transcription Factors/metabolism ; Gallbladder/*metabolism ; *Gastrointestinal Microbiome ; Glucocorticoids/biosynthesis ; Homeostasis ; Intestinal Mucosa/immunology ; Liver/metabolism ; Mice, Inbred C57BL ; Pulmonary Surfactant-Associated Protein D/*metabolism ; Symbiosis ; T-Lymphocytes, Regulatory/metabolism ; }, abstract = {The commensal microbiota within the gastrointestinal tract is essential in maintaining homeostasis. Indeed, dysregulation in the repertoire of microbiota can result in the development of intestinal immune-inflammatory diseases. Further, this immune regulation by gut microbiota is important systemically, impacting health and disease of organ systems beyond the local environment of the gut. What has not been explored is how distant organs might in turn shape the microbiota via microbe-targeted molecules. Here, we provide evidence that surfactant protein D (SP-D) synthesized in the gallbladder and delivered into intestinal lumen binds selectively to species of gut commensal bacteria. SP-D-deficient mice manifest intestinal dysbiosis and show a susceptibility to dextran sulfate sodium-induced colitis. Further, fecal transfer from SP-D-deficient mice to wild-type, germ-free mice conveyed colitis susceptibility. Interestingly, colitis caused a notable increase in Sftpd gene expression in the gallbladder, but not in the lung, via the activity of glucocorticoids produced in the liver. These findings describe a unique mechanism of interorgan regulation of intestinal immune homeostasis by SP-D with potential clinical implications such as cholecystectomy.}, }
@article {pmid28873967, year = {2017}, author = {Kuang, YS and Lu, JH and Li, SH and Li, JH and Yuan, MY and He, JR and Chen, NN and Xiao, WQ and Shen, SY and Qiu, L and Wu, YF and Hu, CY and Wu, YY and Li, WD and Chen, QZ and Deng, HW and Papasian, CJ and Xia, HM and Qiu, X}, title = {Connections between the human gut microbiome and gestational diabetes mellitus.}, journal = {GigaScience}, volume = {6}, number = {8}, pages = {1-12}, doi = {10.1093/gigascience/gix058}, pmid = {28873967}, issn = {2047-217X}, support = {R01 AR069055/AR/NIAMS NIH HHS/United States ; }, mesh = {Biomarkers ; Blood Glucose ; Cluster Analysis ; Diabetes, Gestational/*etiology ; Female ; *Gastrointestinal Microbiome ; Humans ; *Metagenome ; *Metagenomics/methods ; Models, Biological ; Pregnancy ; ROC Curve ; }, abstract = {The human gut microbiome can modulate metabolic health and affect insulin resistance, and it may play an important role in the etiology of gestational diabetes mellitus (GDM). Here, we compared the gut microbial composition of 43 GDM patients and 81 healthy pregnant women via whole-metagenome shotgun sequencing of their fecal samples, collected at 21-29 weeks, to explore associations between GDM and the composition of microbial taxonomic units and functional genes. A metagenome-wide association study identified 154 837 genes, which clustered into 129 metagenome linkage groups (MLGs) for species description, with significant relative abundance differences between the 2 cohorts. Parabacteroides distasonis, Klebsiella variicola, etc., were enriched in GDM patients, whereas Methanobrevibacter smithii, Alistipes spp., Bifidobacterium spp., and Eubacterium spp. were enriched in controls. The ratios of the gross abundances of GDM-enriched MLGs to control-enriched MLGs were positively correlated with blood glucose levels. A random forest model shows that fecal MLGs have excellent discriminatory power to predict GDM status. Our study discovered novel relationships between the gut microbiome and GDM status and suggests that changes in microbial composition may potentially be used to identify individuals at risk for GDM.}, }
@article {pmid28870713, year = {2017}, author = {Zhang, S and Yang, J and Henning, SM and Lee, R and Hsu, M and Grojean, E and Pisegna, R and Ly, A and Heber, D and Li, Z}, title = {Dietary pomegranate extract and inulin affect gut microbiome differentially in mice fed an obesogenic diet.}, journal = {Anaerobe}, volume = {48}, number = {}, pages = {184-193}, doi = {10.1016/j.anaerobe.2017.08.017}, pmid = {28870713}, issn = {1095-8274}, mesh = {*Animal Feed ; Animals ; Biodiversity ; Biomarkers ; Chemokine CCL2/metabolism ; *Dietary Supplements ; Disease Models, Animal ; Gastrointestinal Microbiome/*drug effects ; *Inulin/administration & dosage ; Male ; Metagenome ; Metagenomics/methods ; Mice ; Obesity/etiology/metabolism ; *Plant Extracts/administration & dosage ; Punicaceae/*chemistry ; }, abstract = {Growing evidence suggests that dysbiosis of gut microbiota is associated with pathogenesis of a variety of human diseases. Using dietary intervention to shape the composition and metabolism of the gut microbiota is increasingly recognized. In the present study, we investigated the effects of polysaccharide inulin and polyphenol-rich pomegranate extract (PomX) alone or in combination on the cecal microbiota composition and function in a diet induced obesity mouse model. Male C57BL/6 mice were randomly divided into four experimental groups and consumed either high-fat/high-sucrose [HF/HS (32% energy from fat, 25% energy from sucrose, 17% energy from protein)] diet, HF/HS diet supplemented with PomX (0.25%), or inulin (9%) or PomX and inulin in combination for 4 weeks. In mice fed the PomX-diet the proportion of Turicibacteraceae and Ruminococcaceae was significantly increased compared to the control HF/HS diet. Supplementation with inulin alone and inulin + PomX combination significantly increased the proportion of Verrucomicrobiaceae (A. muciniphila) and decreased Clostridiaceae. Only mice fed the inulin diet experienced an increase in serum lipopolysaccharide (LPS) and monocyte chemoattractant protein 1 (MCP-1), which was reversed when feeding the inulin + PomX diet. Feeding the inulin + PomX diet was associated with a significant increase in Bifidobacteriaceae and Rikenellaceae, which may have contributed to the reduction of endotoxemia markers. Inulin supplementation showed lower species richness of gut microbiota compared to mice fed with HF/HS or HF/HS/PomX, and the reduction was reversed by the addition of PomX. Inulin alone and in combination with PomX had distinct microbial clusters determined by both weighted and unweighted UniFrac Beta-Diversity principle coordinate analysis. A total of 19 KEGG biological pathways were significantly regulated in the gut microbiota with PomX and inulin alone or combined treatment. Inulin significantly enhanced KEGG infectious disease-related pathway associated with increase of serum LPS and MCP-1. No changes in gene expression of ileal proinflammatory cytokine and tight junction genes were observed in mice treated with PomX and inulin. Our results demonstrated that the gut microbiota and their biological pathways were differentially effected by dietary PomX and inulin fed combined or alone. It is therefore very important to consider the interaction among bioactive components of food when evaluating potential prebiotic effects.}, }
@article {pmid28869283, year = {2017}, author = {Carding, SR and Davis, N and Hoyles, L}, title = {Review article: the human intestinal virome in health and disease.}, journal = {Alimentary pharmacology & therapeutics}, volume = {46}, number = {9}, pages = {800-815}, doi = {10.1111/apt.14280}, pmid = {28869283}, issn = {1365-2036}, support = {MR/L01632X/1//Medical Research Council/United Kingdom ; }, mesh = {Animals ; Anti-Bacterial Agents/therapeutic use ; Bacteriophages/isolation & purification ; Feces/virology ; *Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/virology ; Intestines/*virology ; Metagenomics ; Viruses/isolation & purification ; }, abstract = {BACKGROUND: The human virome consists of animal-cell viruses causing transient infections, bacteriophage (phage) predators of bacteria and archaea, endogenous retroviruses and viruses causing persistent and latent infections. High-throughput, inexpensive, sensitive sequencing methods and metagenomics now make it possible to study the contribution dsDNA, ssDNA and RNA virus-like particles make to the human virome, and in particular the intestinal virome.
AIM: To review and evaluate the pioneering studies that have attempted to characterise the human virome and generated an increased interest in understanding how the intestinal virome might contribute to maintaining health, and the pathogenesis of chronic diseases.
METHODS: Relevant virome-related articles were selected for review following extensive language- and date-unrestricted, electronic searches of the literature.
RESULTS: The human intestinal virome is personalised and stable, and dominated by phages. It develops soon after birth in parallel with prokaryotic communities of the microbiota, becoming established during the first few years of life. By infecting specific populations of bacteria, phages can alter microbiota structure by killing host cells or altering their phenotype, enabling phages to contribute to maintaining intestinal homeostasis or microbial imbalance (dysbiosis), and the development of chronic infectious and autoimmune diseases including HIV infection and Crohn's disease, respectively.
CONCLUSIONS: Our understanding of the intestinal virome is fragmented and requires standardised methods for virus isolation and sequencing to provide a more complete picture of the virome, which is key to explaining the basis of virome-disease associations, and how enteric viruses can contribute to disease aetiologies and be rationalised as targets for interventions.}, }
@article {pmid28867788, year = {2017}, author = {Dong, B and Yi, Y and Liang, L and Shi, Q}, title = {High Throughput Identification of Antimicrobial Peptides from Fish Gastrointestinal Microbiota.}, journal = {Toxins}, volume = {9}, number = {9}, pages = {}, doi = {10.3390/toxins9090266}, pmid = {28867788}, issn = {2072-6651}, mesh = {Animals ; Antimicrobial Cationic Peptides/*metabolism ; Bacteria/genetics/isolation & purification/metabolism ; Bacterial Proteins/*metabolism ; Carps/*microbiology ; *Gastrointestinal Microbiome ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; }, abstract = {Antimicrobial peptides (AMPs) are a group of small peptides, which are secreted by almost all creatures in nature. They have been explored in therapeutic and agricultural aspects as they are toxic to many bacteria. A considerable amount of work has been conducted in analyzing 16S and metagenomics of the gastrointestinal (GI) microbiome of grass carp (Ctenopharyngodon idellus). However, these datasets are still untapped resources. In this present study, a homologous search was performed to predict AMPs from our newly generated metagenome of grass carp. We identified five AMPs with high similarities to previously reported bacterial toxins, such as lantibiotic and class II bacteriocins. In addition, we observed that the top abundant genus in the GI microbiota of the grass carp was generally consistent with the putative AMP-producing strains, which are mainly from Lactobacillales. Furthermore, we constructed the phylogenetic relationship of these putative AMP-producing bacteria existing in the GI of grass carp and some popular commercial probiotics (commonly used for microecologics), demonstrating that they are closely related. Thus, these strains have the potential to be developed into novel microecologics. In a word, we provide a high-throughput way to discover AMPs from fish GI microbiota, which can be developed as alternative pathogen antagonists (toxins) for microecologics or probiotic supplements.}, }
@article {pmid28859695, year = {2017}, author = {Cai, Y and Gu, H and Kenney, T}, title = {Learning Microbial Community Structures with Supervised and Unsupervised Non-negative Matrix Factorization.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {110}, doi = {10.1186/s40168-017-0323-1}, pmid = {28859695}, issn = {2049-2618}, support = {250043//European Research Council/International ; }, mesh = {Algorithms ; Gastrointestinal Microbiome/*genetics ; Humans ; *Metagenome ; Metagenomics/*methods ; *Microbial Consortia ; Supervised Machine Learning ; Unsupervised Machine Learning ; }, abstract = {BACKGROUND: Learning the structure of microbial communities is critical in understanding the different community structures and functions of microbes in distinct individuals. We view microbial communities as consisting of many subcommunities which are formed by certain groups of microbes functionally dependent on each other. The focus of this paper is on methods for extracting the subcommunities from the data, in particular Non-Negative Matrix Factorization (NMF). Our methods can be applied to both OTU data and functional metagenomic data. We apply the existing unsupervised NMF method and also develop a new supervised NMF method for extracting interpretable information from classification problems.
RESULTS: The relevance of the subcommunities identified by NMF is demonstrated by their excellent performance for classification. Through three data examples, we demonstrate how to interpret the features identified by NMF to draw meaningful biological conclusions and discover hitherto unidentified patterns in the data. Comparing whole metagenomes of various mammals, (Muegge et al., Science 332:970-974, 2011), the biosynthesis of macrolides pathway is found in hindgut-fermenting herbivores, but not carnivores. This is consistent with results in veterinary science that macrolides should not be given to non-ruminant herbivores. For time series microbiome data from various body sites (Caporaso et al., Genome Biol 12:50, 2011), a shift in the microbial communities is identified for one individual. The shift occurs at around the same time in the tongue and gut microbiomes, indicating that the shift is a genuine biological trait, rather than an artefact of the method. For whole metagenome data from IBD patients and healthy controls (Qin et al., Nature 464:59-65, 2010), we identify differences in a number of pathways (some known, others new).
CONCLUSIONS: NMF is a powerful tool for identifying the key features of microbial communities. These identified features can not only be used to perform difficult classification problems with a high degree of accuracy, they are also very interpretable and can lead to important biological insights into the structure of the communities. In addition, NMF is a dimension-reduction method (similar to PCA) in that it reduces the extremely complex microbial data into a low-dimensional representation, allowing a number of analyses to be performed more easily-for example, searching for temporal patterns in the microbiome. When we are interested in the differences between the structures of two groups of communities, supervised NMF provides a better way to do this, while retaining all the advantages of NMF-e.g. interpretability and a simple biological intuition.}, }
@article {pmid28855895, year = {2017}, author = {Novello, G and Gamalero, E and Bona, E and Boatti, L and Mignone, F and Massa, N and Cesaro, P and Lingua, G and Berta, G}, title = {The Rhizosphere Bacterial Microbiota of Vitis vinifera cv. Pinot Noir in an Integrated Pest Management Vineyard.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1528}, doi = {10.3389/fmicb.2017.01528}, pmid = {28855895}, issn = {1664-302X}, abstract = {Microorganisms associated with Vitis vinifera (grapevine) can affect its growth, health and grape quality. The aim of this study was to unravel the biodiversity of the bacterial rhizosphere microbiota of grapevine in an integrated pest management vineyard located in Piedmont, Italy. Comparison between the microbial community structure in the bulk and rhizosphere soil (variable: space) were performed. Moreover, the possible shifts of the bulk and rhizosphere soil microbiota according to two phenological stages such as flowering and early fruit development (variable: time) were characterized. The grapevine microbiota was identified using metagenomics and next-generation sequencing. Biodiversity was higher in the rhizosphere than in the bulk soil, independent of the phenological stage. Actinobacteria were the dominant class with frequencies ≥ 50% in all the soil samples, followed by Proteobacteria, Gemmatimonadetes, and Bacteroidetes. While Actinobacteria and Proteobacteria are well-known as being dominant in soil, this is the first time the presence of Gemmatimonadetes has been observed in vineyard soils. Gaiella was the dominant genus of Actinobacteria in all the samples. Finally, the microbiota associated with grapevine differed from the bulk soil microbiota and these variations were independent of the phenological stage of the plant.}, }
@article {pmid28852824, year = {2017}, author = {Bai, Y and Huo, Y and Liao, K and Qu, J}, title = {Influence of microbial community diversity and function on pollutant removal in ecological wastewater treatment.}, journal = {Applied microbiology and biotechnology}, volume = {101}, number = {19}, pages = {7293-7302}, doi = {10.1007/s00253-017-8464-5}, pmid = {28852824}, issn = {1432-0614}, support = {51578537//National Natural Science Foundation of China/ ; 51420105012//National Natural Science Foundation of China/ ; ZDRW-ZS-2016-5-6//Chinese Academy of Sciences/ ; }, mesh = {Biodegradation, Environmental ; Biomass ; Comamonadaceae/genetics/isolation & purification ; Metagenomics ; *Microbial Consortia ; Nerium/microbiology ; Poaceae/microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Waste Disposal, Fluid ; Waste Water/*microbiology ; *Water Purification ; }, abstract = {Traditional wastewater treatments based on activated sludge often encounter the problems of bulking and foaming, as well as malodor. To solve these problems, new treatment technologies have emerged in recent decades, including the ecological wastewater treatment process, which introduces selected local plants into the treatment system. With a focus on the underlying mechanisms of the ecological treatment process, we explored the microbial community biomass, composition, and function in the treatment system to understand the microbial growth in this system and its role in pollutant removal. Flow cytometry analysis revealed that ecological treatment significantly decreased influent bacterial quantity, with around 80% removal. 16S rRNA gene sequencing showed that the ecological treatment also altered the bacterial community structure of the wastewater, leading to a significant change in Comamonadaceae in the effluent. In the internal ecological system, because most of microbes aggregate in the plant rhizosphere and the sludge under plant roots, we selected two plant species (Nerium oleander and Arundo donax) to study the characteristics of rhizosphere and sludge microbes. Metagenomic results showed that the microbial community composition and function differed between the two species, and the microbial communities of A. donax were more sensitive to seasonal effects. Combined with their greater biomass and abundance of metabolic genes, microbes associated with N. oleander showed a greater contribution to pollutant removal. Further, the biodegradation pathways of some micropollutants, e.g., atrazine, were estimated.}, }
@article {pmid28849048, year = {2017}, author = {Chen, H and Xia, Y and Zhu, S and Yang, J and Yao, J and Di, J and Liang, Y and Gao, R and Wu, W and Yang, Y and Shi, C and Hu, D and Qin, H and Wang, Z}, title = {Lactobacillus plantarum LP‑Onlly alters the gut flora and attenuates colitis by inducing microbiome alteration in interleukin‑10 knockout mice.}, journal = {Molecular medicine reports}, volume = {16}, number = {5}, pages = {5979-5985}, doi = {10.3892/mmr.2017.7351}, pmid = {28849048}, issn = {1791-3004}, mesh = {Actinobacteria/classification/genetics/isolation & purification ; Animals ; Bacteroidetes/classification/genetics/isolation & purification ; Colitis/immunology/microbiology/pathology/*therapy ; DNA, Bacterial/*genetics ; Disease Models, Animal ; Female ; Firmicutes/classification/genetics/isolation & purification ; Gastrointestinal Microbiome/*genetics ; Gene Deletion ; High-Throughput Nucleotide Sequencing ; Homozygote ; Interleukin-10/*deficiency/genetics ; Lactobacillus plantarum/*physiology ; Mice ; Mice, Knockout ; Probiotics/*pharmacology ; Proteobacteria/classification/genetics/isolation & purification ; }, abstract = {The association between inflammatory bowel disease (IBD) and gut microbes has been widely investigated. Our previous study demonstrated that Lactobacillus plantarum LP‑Onlly (LP) applied as a probiotic altered the gut flora and attenuated colitis in interleukin (IL)‑10 knockout (IL‑10‑/‑) mice. In the present study, metagenome sequencing was performed to investigate the gut microbiome in IL‑10‑/‑mice and the influence of oral administration of LP on microbial composition. Metagenomics sequencing was performed to investigate the influence of IBD on the gut microbiome with and without LP treatment. The alteration of the abundances of various taxonomic and functional groups were investigated across these gut microbiomes. The present study demonstrates that Akkermansia muciniphila was significantly enriched in IL‑10‑/‑ mice, and bacteroides were significantly increased following LP administration. In addition, the phylum Bacteroidetes and Firmicutes were significantly influenced by LP administration. Further characterization of functional capacity revealed that in the gut metagenomes of IL‑10‑/‑mice, genes encoding cell cycle control, replication, recombination, repair and cell envelope biogenesis were decreased, but intracellular trafficking, secretion, and vesicular transport were increased. The present findings indicate that the gut metagenome is associated with IBD, and oral administration of LP contributes to prevention of gut inflammation, providing insight into the treatment of IBD.}, }
@article {pmid28849032, year = {2017}, author = {Ji, W and Zhu, Y and Kan, P and Cai, Y and Wang, Z and Wu, Z and Yang, P}, title = {Analysis of intestinal microbial communities of cerebral infarction and ischemia patients based on high throughput sequencing technology and glucose and lipid metabolism.}, journal = {Molecular medicine reports}, volume = {16}, number = {4}, pages = {5413-5417}, doi = {10.3892/mmr.2017.7227}, pmid = {28849032}, issn = {1791-3004}, mesh = {Aged ; Aged, 80 and over ; Blood Glucose ; Brain Ischemia/etiology/*metabolism ; Cerebral Infarction/etiology/*metabolism ; Cluster Analysis ; Female ; *Gastrointestinal Microbiome ; Humans ; *Lipid Metabolism ; Lipids/blood ; Male ; *Metagenome ; *Metagenomics/methods ; Middle Aged ; }, abstract = {Currently, cerebral infarction (CI) is the leading cause of disability and the second leading cause of mortality in China, seriously affecting patient quality of life. Ischemia (IS) is considered to be the early stage of CI. The present study aims to investigate the variation of intestinal microbial communities in patients with CI and IS using high throughput sequencing technology, and then analyze the results to identify a novel potential pathogenic mechanism of CI and IS. In total, 8 patients with CI, 2 patients with IS and 10 healthy volunteers as a control were selected. Throughput sequencing technology was used to analyze the character and microbial population of the gut. The abundance of Escherichia, Bacteroides, Megamonas, Parabacteroides, Akkermansia, Prevotella, Faecalibacterium, Dialister, Bifidobacterium and Ruminococcus was the significant difference in the intestinal microbial communities of the CI and IS patients compared with the healthy group. It was also observed that CI and IS were closely associated with internal glucose metabolism. The intestinal gut disturbance of CI patients may be one of the causes inducing CI by glucose metabolism and maybe considered as a potential method to predict the disease.}, }
@article {pmid28841911, year = {2017}, author = {Jeon, SJ and Cunha, F and Vieira-Neto, A and Bicalho, RC and Lima, S and Bicalho, ML and Galvão, KN}, title = {Blood as a route of transmission of uterine pathogens from the gut to the uterus in cows.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {109}, doi = {10.1186/s40168-017-0328-9}, pmid = {28841911}, issn = {2049-2618}, mesh = {Animals ; Bacteria/classification/*genetics/*isolation & purification/pathogenicity ; Bacteroides/physiology ; Blood/*microbiology ; Cattle/*microbiology ; Feces/*microbiology ; Female ; Gene Regulatory Networks ; Metagenomics ; Microbial Interactions ; *Microbiota ; Polymerase Chain Reaction ; Porphyromonas/physiology ; *Postpartum Period ; Uterus/*microbiology ; Vagina/microbiology ; }, abstract = {BACKGROUND: Metritis is an inflammatory disease of the uterus caused by bacterial infection, particularly Bacteroides, Porphyromonas, and Fusobacterium. Bacteria from the environment, feces, or vagina are believed to be the only sources of uterine contamination. Blood seeps into the uterus after calving; therefore, we hypothesized that blood could also be a seeding source of uterine bacteria. Herein, we compared bacterial communities from blood, feces, and uterine samples from the same cows at 0 and 2 days postpartum using deep sequencing and qPCR. The vaginal microbiome 7 days before calving was also compared.
RESULTS: There was a unique structure of bacterial communities by sample type. Principal coordinate analysis revealed two distinct clusters for blood and feces, whereas vaginal and uterine bacterial communities were more scattered, indicating greater variability. Cluster analysis indicated that uterine bacterial communities were more similar to fecal bacterial communities than vaginal and blood bacterial communities. Nonetheless, there were core genera shared by all blood, feces, vaginal, and uterine samples. Major uterine pathogens such as Bacteroides, Porphyromonas, and Fusobacterium were part of the core genera in blood, feces, and vagina. Other uterine pathogens such as Prevotella and Helcococcus were not part of the core genera in vaginal samples. In addition, uterine pathogens showed a strong and significant interaction with each other in the network of blood microbiota, but not in feces or vagina. These microbial interactions in blood may be an important component of disease etiology. The copy number of total bacteria in blood and uterus was correlated; the same did not occur in other sites. Bacteroides heparinolyticus was more abundant in the uterus on day 0, and both B. heparinolyticus and Fusobacterium necrophorum were more abundant in the uterus than in the blood and feces on day 2. This indicates that B. heparinolyticus has a tropism for the uterus, whereas both pathogens thrive in the uterine environment early postpartum.
CONCLUSIONS: Blood harbored a unique microbiome that contained the main uterine pathogens such as Bacteroides, Porphyromonas, and Fusobacterium. The presence of these pathogens in blood shortly after calving shows the feasibility of hematogenous spread of uterine pathogens in cows.}, }
@article {pmid28835538, year = {2017}, author = {Ngugi, DK and Miyake, S and Cahill, M and Vinu, M and Hackmann, TJ and Blom, J and Tietbohl, MD and Berumen, ML and Stingl, U}, title = {Genomic diversification of giant enteric symbionts reflects host dietary lifestyles.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {36}, pages = {E7592-E7601}, doi = {10.1073/pnas.1703070114}, pmid = {28835538}, issn = {1091-6490}, mesh = {Animals ; Bacteria/metabolism ; Biomass ; Diet ; Ecology ; Fishes/metabolism/microbiology/physiology ; Genomics/methods ; Herbivory/physiology ; Host-Pathogen Interactions/*physiology ; Life Style ; Metagenomics/methods ; Microbiota/physiology ; Phaeophyta/metabolism/microbiology/physiology ; Phylogeny ; Polysaccharides/metabolism ; Rhodophyta/metabolism/microbiology/physiology ; Symbiosis/*physiology ; }, abstract = {Herbivorous surgeonfishes are an ecologically successful group of reef fish that rely on marine algae as their principal food source. Here, we elucidated the significance of giant enteric symbionts colonizing these fishes regarding their roles in the digestive processes of hosts feeding predominantly on polysiphonous red algae and brown Turbinaria algae, which contain different polysaccharide constituents. Using metagenomics, single-cell genomics, and metatranscriptomic analyses, we provide evidence of metabolic diversification of enteric microbiota involved in the degradation of algal biomass in these fishes. The enteric microbiota is also phylogenetically and functionally simple relative to the complex lignocellulose-degrading microbiota of terrestrial herbivores. Over 90% of the enzymes for deconstructing algal polysaccharides emanate from members of a single bacterial lineage, "Candidatus Epulopiscium" and related giant bacteria. These symbionts lack cellulases but encode a distinctive and lineage-specific array of mostly intracellular carbohydrases concurrent with the unique and tractable dietary resources of their hosts. Importantly, enzymes initiating the breakdown of the abundant and complex algal polysaccharides also originate from these symbionts. These are also highly transcribed and peak according to the diel lifestyle of their host, further supporting their importance and host-symbiont cospeciation. Because of their distinctive genomic blueprint, we propose the classification of these giant bacteria into three candidate genera. Collectively, our findings show that the acquisition of metabolically distinct "Epulopiscium" symbionts in hosts feeding on compositionally varied algal diets is a key niche-partitioning driver in the nutritional ecology of herbivorous surgeonfishes.}, }
@article {pmid28835260, year = {2017}, author = {Dombrowski, N and Seitz, KW and Teske, AP and Baker, BJ}, title = {Genomic insights into potential interdependencies in microbial hydrocarbon and nutrient cycling in hydrothermal sediments.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {106}, doi = {10.1186/s40168-017-0322-2}, pmid = {28835260}, issn = {2049-2618}, mesh = {Archaea/classification/*genetics/*metabolism/physiology ; Bacteria/*genetics/*metabolism ; Biodiversity ; DNA, Bacterial/genetics ; Deltaproteobacteria/classification/genetics/metabolism ; Genomics ; Hydrocarbons/*metabolism ; Hydrothermal Vents/*microbiology ; Metagenome ; Metagenomics ; Methane/metabolism ; *Microbiota ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Deep-sea hydrothermal vents are hotspots for productivity and biodiversity. Thermal pyrolysis and circulation produce fluids rich in hydrocarbons and reduced compounds that stimulate microbial activity in surrounding sediments. Several studies have characterized the diversity of Guaymas Basin (Gulf of California) sediment-inhabiting microorganisms; however, many of the identified taxa lack cultures or genomic representations. Here, we resolved the metabolic potential and community-level interactions of these diverse communities by reconstructing and analyzing microbial genomes from metagenomic sequencing data.
RESULTS: We reconstructed 115 microbial metagenome-assembled genomes comprising 27 distinct archaeal and bacterial phyla. The archaea included members of the DPANN and TACK superphyla, Bathyarchaeota, novel Methanosarcinales (GoM-Arc1), and anaerobic methane-oxidizing lineages (ANME-1). Among the bacterial phyla, members of the Bacteroidetes, Chloroflexi, and Deltaproteobacteria were metabolically versatile and harbored potential pathways for hydrocarbon and lipid degradation and a variety of respiratory processes. Genes encoding enzymes that activate anaerobic hydrocarbons for degradation were detected in Bacteroidetes, Chloroflexi, Latescibacteria, and KSB1 phyla, while the reconstructed genomes for most candidate bacteria phyla (Aminicenantes, Atribacteria, Omnitrophica, and Stahlbacteria) indicated a fermentative metabolism. Newly obtained GoM-Arc1 archaeal genomes encoded novel pathways for short-chain hydrocarbon oxidation by alkyl-coenzyme M formation. We propose metabolic linkages among different functional groups, such as fermentative community members sharing substrate-level interdependencies with sulfur- and nitrogen-cycling microbes.
CONCLUSIONS: Overall, inferring the physiologies of archaea and bacteria from metagenome-assembled genomes in hydrothermal deep-sea sediments has revealed potential mechanisms of carbon cycling in deep-sea sediments. Our results further suggest a network of biogeochemical interdependencies in organic matter utilization, hydrocarbon degradation, and respiratory sulfur cycling among deep-sea-inhabiting microbial communities.}, }
@article {pmid28835202, year = {2017}, author = {Bond, SL and Timsit, E and Workentine, M and Alexander, T and Léguillette, R}, title = {Upper and lower respiratory tract microbiota in horses: bacterial communities associated with health and mild asthma (inflammatory airway disease) and effects of dexamethasone.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {184}, doi = {10.1186/s12866-017-1092-5}, pmid = {28835202}, issn = {1471-2180}, mesh = {Animals ; Asthma/drug therapy/*microbiology/veterinary ; Bacteria/classification/*drug effects/isolation & purification/pathogenicity ; Biodiversity ; Bronchoalveolar Lavage Fluid/immunology/microbiology ; DNA, Bacterial ; Dexamethasone/*pharmacology ; Horse Diseases/drug therapy/immunology/*microbiology ; Horses/*microbiology ; Inflammation/drug therapy/microbiology ; Metagenomics ; Microbial Consortia/drug effects ; Microbiota/*drug effects ; Respiratory System/immunology/*microbiology ; }, abstract = {BACKGROUND: The microbial composition of the equine respiratory tract, and differences due to mild equine asthma (also called Inflammatory Airway Disease (IAD)) have not been reported. The primary treatment for control of IAD in horses are corticosteroids. The objectives were to characterize the upper and lower respiratory tract microbiota associated with respiratory health and IAD, and to investigate the effects of dexamethasone on these bacterial communities using high throughput sequencing.
RESULTS: The respiratory microbiota of horses was dominated by four major phyla, Proteobacteria (43.85%), Actinobacteria (21.63%), Firmicutes (16.82%), and Bacteroidetes (13.24%). Fifty genera had a relative abundance > 0.1%, with Sphingomonas and Pantoea being the most abundant. The upper and lower respiratory tract microbiota differed in healthy horses, with a decrease in richness in the lower airways, and 2 OTUs that differed in abundance. There was a separation between bacterial communities in the lower respiratory tract of healthy and IAD horses; 6 OTUs in the tracheal community had different abundance with disease status, with Streptococcus being increased in IAD horses. Treatment with dexamethasone had an effect on the lower respiratory tract microbiota of both heathy and IAD horses, with 8 OTUs increasing in abundance (including Streptococcus) and 1 OTU decreasing.
CONCLUSIONS: The lower respiratory tract microbiota differed between healthy and IAD horses. Further research on the role of Streptococcus in IAD is warranted. Dexamethasone treatment affected the lower respiratory tract microbiota, which suggests that control of bacterial overgrowth in IAD horses treated with dexamethasone could be part of the treatment strategy.}, }
@article {pmid28834331, year = {2017}, author = {O' Donnell, MM and Harris, HMB and Ross, RP and O'Toole, PW}, title = {Core fecal microbiota of domesticated herbivorous ruminant, hindgut fermenters, and monogastric animals.}, journal = {MicrobiologyOpen}, volume = {6}, number = {5}, pages = {}, doi = {10.1002/mbo3.509}, pmid = {28834331}, issn = {2045-8827}, mesh = {Animals ; *Animals, Domestic ; Biodiversity ; Cluster Analysis ; Feces/*microbiology ; Gastrointestinal Microbiome ; *Herbivory ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/methods ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; *Ruminants ; }, abstract = {In this pilot study, we determined the core fecal microbiota composition and overall microbiota diversity of domesticated herbivorous animals of three digestion types: hindgut fermenters, ruminants, and monogastrics. The 42 animals representing 10 animal species were housed on a single farm in Ireland and all the large herbivores consumed similar feed, harmonizing two of the environmental factors that influence the microbiota. Similar to other mammals, the fecal microbiota of all these animals was dominated by the Firmicutes and Bacteroidetes phyla. The fecal microbiota spanning all digestion types comprised 42% of the genera identified. Host phylogeny and, to a lesser extent, digestion type determined the microbiota diversity in these domesticated herbivores. This pilot study forms a platform for future studies into the microbiota of nonbovine and nonequine domesticated herbivorous animals.}, }
@article {pmid28833934, year = {2017}, author = {do Vale Pereira, G and da Cunha, DG and Pedreira Mourino, JL and Rodiles, A and Jaramillo-Torres, A and Merrifield, DL}, title = {Characterization of microbiota in Arapaima gigas intestine and isolation of potential probiotic bacteria.}, journal = {Journal of applied microbiology}, volume = {123}, number = {5}, pages = {1298-1311}, doi = {10.1111/jam.13572}, pmid = {28833934}, issn = {1365-2672}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics/metabolism ; Fishes/*microbiology ; *Gastrointestinal Microbiome ; Intestines/*microbiology ; Lactobacillales/classification/drug effects/genetics/*isolation & purification ; Probiotics/*isolation & purification ; }, abstract = {AIMS: The aim of this study was to determine the intestinal microbiota of pirarucu (Arapaima gigas) in different growth stages (adult and fingerlings) and to isolate and identify potential probiotic bacteria.
METHODS AND RESULTS: High-throughput sequencing analysis of the intestinal contents revealed that the majority of sequences belonged to the Proteobacteria, Fusobacteria and Firmicutes phyla. At the genus level, the greatest number of sequences belonged to Bradyrhizobium in adult fish, while Cetobacterium was the most abundant in juvenile fish. Twenty-three lactic-acid bacteria (LABs) were isolated on MRS agar from healthy juvenile fish. The isolates were tested in vitro for probiotic properties. Two isolates (identified as strains of Lactococcus lactis subsp. lactis and Enterococcus faecium) displayed antagonism against all 10 pathogens tested, were nonhaemolytic and maintained good viability for at least 3 weeks when supplemented to fish diets. The presence of a number of antibiotic resistance genes (ARGs), conferring resistance to erythromycin, tetracycline and chloramphenicol, was investigated by PCR.
CONCLUSIONS: The absence of ARGs investigated the potential to antagonize pathogens, and favourable growth and survival characteristics indicate that these autochthonous isolates have the potential to be considered probiotics, which will be studied in future in vivo experiments.
This study has demonstrated, for the first time, the normal microbiota in the A. gigas intestine during different life stages and the presence of LAB strains. It also demonstrated LAB antibiotic resistance and antagonistic behaviour against pathogens isolated from the same fish.}, }
@article {pmid28831604, year = {2018}, author = {Mendes, LW and Tsai, SM}, title = {Distinct taxonomic and functional composition of soil microbiomes along the gradient forest-restinga-mangrove in southeastern Brazil.}, journal = {Antonie van Leeuwenhoek}, volume = {111}, number = {1}, pages = {101-114}, doi = {10.1007/s10482-017-0931-6}, pmid = {28831604}, issn = {1572-9699}, support = {2007/01859-4//FAPESP/ ; }, mesh = {Biodiversity ; Brazil ; *Forests ; Geography ; *Metagenome ; *Metagenomics/methods ; *Soil Microbiology ; *Wetlands ; }, abstract = {Soil microorganisms play crucial roles in ecosystem functioning, and the central goal in microbial ecology studies is to elucidate which factors shape community structure. A better understanding of the relationship between microbial diversity, functions and environmental parameters would increase our ability to set conservation priorities. Here, the bacterial and archaeal community structure in Atlantic Forest, restinga and mangrove soils was described and compared based on shotgun metagenomics. We hypothesized that each distinct site would harbor a distinct taxonomic and functional soil community, which is influenced by environmental parameters. Our data showed that the microbiome is shaped by soil properties, with pH, base saturation, boron and iron content significantly correlated to overall community structure. When data of specific phyla were correlated to specific soil properties, we demonstrated that parameters such as boron, copper, sulfur, potassium and aluminum presented significant correlation with the most number of bacterial groups. Mangrove soil was the most distinct site and presented the highest taxonomic and functional diversity in comparison with forest and restinga soils. From the total 34 microbial phyla identified, 14 were overrepresented in mangrove soils, including several archaeal groups. Mangrove soils hosted a high abundance of sequences related to replication, survival and adaptation; forest soils included high numbers of sequences related to the metabolism of nutrients and other composts; while restinga soils included abundant genes related to the metabolism of carbohydrates. Overall, our finds show that the microbial community structure and functional potential were clearly different across the environmental gradient, followed by functional adaptation and both were related to the soil properties.}, }
@article {pmid28830999, year = {2017}, author = {Kowarsky, M and Camunas-Soler, J and Kertesz, M and De Vlaminck, I and Koh, W and Pan, W and Martin, L and Neff, NF and Okamoto, J and Wong, RJ and Kharbanda, S and El-Sayed, Y and Blumenfeld, Y and Stevenson, DK and Shaw, GM and Wolfe, ND and Quake, SR}, title = {Numerous uncharacterized and highly divergent microbes which colonize humans are revealed by circulating cell-free DNA.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {36}, pages = {9623-9628}, doi = {10.1073/pnas.1707009114}, pmid = {28830999}, issn = {1091-6490}, mesh = {Cell-Free Nucleic Acids/*blood/*genetics ; DNA, Bacterial/*blood/*genetics ; DNA, Viral/*blood/*genetics ; Genetic Variation ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/methods ; Microbiota/*genetics ; Phylogeny ; }, abstract = {Blood circulates throughout the human body and contains molecules drawn from virtually every tissue, including the microbes and viruses which colonize the body. Through massive shotgun sequencing of circulating cell-free DNA from the blood, we identified hundreds of new bacteria and viruses which represent previously unidentified members of the human microbiome. Analyzing cumulative sequence data from 1,351 blood samples collected from 188 patients enabled us to assemble 7,190 contiguous regions (contigs) larger than 1 kbp, of which 3,761 are novel with little or no sequence homology in any existing databases. The vast majority of these novel contigs possess coding sequences, and we have validated their existence both by finding their presence in independent experiments and by performing direct PCR amplification. When their nearest neighbors are located in the tree of life, many of the organisms represent entirely novel taxa, showing that microbial diversity within the human body is substantially broader than previously appreciated.}, }
@article {pmid28828756, year = {2017}, author = {Suhaimi, NSM and Goh, SY and Ajam, N and Othman, RY and Chan, KG and Thong, KL}, title = {Diversity of microbiota associated with symptomatic and non-symptomatic bacterial wilt-diseased banana plants determined using 16S rRNA metagenome sequencing.}, journal = {World journal of microbiology & biotechnology}, volume = {33}, number = {9}, pages = {168}, doi = {10.1007/s11274-017-2336-0}, pmid = {28828756}, issn = {1573-0972}, mesh = {Bacteria/*classification/genetics/isolation & purification ; Cyanobacteria/classification/genetics/isolation & purification ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Fusarium ; High-Throughput Nucleotide Sequencing/methods ; Malaysia ; Metagenomics/*methods ; Musa/*microbiology ; Phylogeny ; Plant Diseases/*microbiology ; Proteobacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Banana is one of the most important fruits cultivated in Malaysia, and it provides many health benefits. However, bacterial wilt disease, which attacks bananas, inflicts major losses on the banana industry in Malaysia. To understand the complex interactions of the microbiota of bacterial wilt-diseased banana plants, we first determined the bacterial communities residing in the pseudostems of infected (symptomatic) and diseased-free (non-symptomatic) banana plants. We characterized the associated microorganisms using the targeted 16S rRNA metagenomics sequencing on the Illumina MiSeq platform. Taxonomic classifications revealed 17 and nine known bacterial phyla in the tissues of non-symptomatic and symptomatic plants, respectively. Cyanobacteria and Proteobacteria (accounted for more than 99% of the 16S rRNA gene fragments) were the two most abundant phyla in both plants. The five major genera found in both plant samples were Ralstonia, Sphingomonas, Methylobacterium, Flavobacterium, and Pseudomonas. Ralstonia was more abundant in symptomatic plant (59% out of the entire genera) as compared to those in the non-symptomatic plant (only 36%). Our data revealed that 102 bacterial genera were only assigned to the non-symptomatic plant. Overall, this study indicated that more diverse and abundant microbiota were associated with the non-symptomatic bacterial wilt-diseased banana plant as compared to the symptomatic plant. The higher diversity of endophytic microbiota in the non-symptomatic banana plant could be an indication of pathogen suppression which delayed or prevented the disease expression. This comparative study of the microbiota in the two plant conditions might provide caveats for potential biological control strategies.}, }
@article {pmid28828247, year = {2017}, author = {Tomczyk-Żak, K and Szczesny, P and Gromadka, R and Zielenkiewicz, U}, title = {Taxonomic and chemical assessment of exceptionally abundant rock mine biofilm.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e3635}, doi = {10.7717/peerj.3635}, pmid = {28828247}, issn = {2167-8359}, abstract = {BACKGROUND: An exceptionally thick biofilm covers walls of ancient gold and arsenic Złoty Stok mine (Poland) in the apparent absence of organic sources of energy.
METHODS AND RESULTS: We have characterized this microbial community using culture-dependent and independent methods. We sequenced amplicons of the 16S rRNA gene obtained using generic primers and additional primers targeted at Archaea and Actinobacteria separately. Also, we have cultured numerous isolates from the biofilm on different media under aerobic and anaerobic conditions. We discovered very high biodiversity, and no single taxonomic group was dominant. The majority of almost 4,000 OTUs were classified above genus level indicating presence of novel species. Elemental analysis, performed using SEM-EDS and X-ray, of biofilm samples showed that carbon, sulphur and oxygen were not evenly distributed in the biofilm and that their presence is highly correlated. However, the distribution of arsenic and iron was more flat, and numerous intrusions of elemental silver and platinum were noted, indicating that microorganisms play a key role in releasing these elements from the rock.
CONCLUSIONS: Altogether, the picture obtained throughout this study shows a very rich, complex and interdependent system of rock biofilm. The chemical heterogeneity of biofilm is a likely explanation as to why this oligotrophic environment is capable of supporting such high microbial diversity.}, }
@article {pmid28821976, year = {2017}, author = {Gao, R and Kong, C and Li, H and Huang, L and Qu, X and Qin, N and Qin, H}, title = {Dysbiosis signature of mycobiota in colon polyp and colorectal cancer.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {36}, number = {12}, pages = {2457-2468}, doi = {10.1007/s10096-017-3085-6}, pmid = {28821976}, issn = {1435-4373}, support = {No. 81230057//National Natural Science Foundation of China/ ; No. 81472262//National Natural Science Foundation of China/ ; 81372615//National Natural Science Foundation of China/ ; 81200264//National Natural Science Foundation of China/ ; No.SHDC12012106//Shen Kang Hospital Development Center of Shanghai/ ; No.162385//Tongji University Subject Pilot Program/ ; }, mesh = {Aged ; Biodiversity ; Colonic Polyps/*microbiology/pathology ; Colorectal Neoplasms/*etiology/pathology ; Disease Susceptibility ; *Dysbiosis ; Feces/microbiology ; Female ; *Fungi/classification ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; Neoplasm Staging ; Tumor Burden ; }, abstract = {Microbiota refers to a colony of microorganisms, and they are found in all multicellular organisms. This colony plays a major role in both the physiology and disease of the organism it inhabits. Much attention has been paid to host-microbiota interactions, but there has been little investigation on its role in carcinogenesis. In this study, we characterized a fecal mycobiota, also known as fungal signature, for the first time with 131 subjects, comprising polyp and colorectal cancer (CRC) patients, as well as a healthy control population. The data obtained were analyzed to assess the biodiversity and composition of the fungi. The impacts of anatomic position and tumor stage on the mycobiota were also evaluated. Correlations between fungi were investigated using the Spearman test. We observed fungal dysbiosis in colon polyps and CRC, including decreased diversity in polyp patients, an increased Ascomycota/Basidiomycota ratio, and an increased proportion of opportunistic fungi Trichosporon and Malassezia, which might favor the progression of CRC. Subsequent analysis with regard to tumor stage demonstrated a lower diversity and significant mycobiota alteration in early-stage tumors. Finally, the fungal correlation showed a close relationship within the community and concomitantly revealed a dramatically structured discrepancy in each clinical phenotype. In conclusion, our study has uncovered a distinct fungal dysbiosis and an alteration in the fungal network, which could play important roles in polyp and CRC pathogenesis.}, }
@article {pmid28821012, year = {2017}, author = {Fukuyama, J and Rumker, L and Sankaran, K and Jeganathan, P and Dethlefsen, L and Relman, DA and Holmes, SP}, title = {Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment.}, journal = {PLoS computational biology}, volume = {13}, number = {8}, pages = {e1005706}, doi = {10.1371/journal.pcbi.1005706}, pmid = {28821012}, issn = {1553-7358}, mesh = {Adult ; DNA, Bacterial/analysis/genetics ; Diarrhea ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Longitudinal Studies ; Male ; Metagenome/*genetics ; Metagenomics/*methods ; Middle Aged ; *Models, Biological ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {Our work focuses on the stability, resilience, and response to perturbation of the bacterial communities in the human gut. Informative flash flood-like disturbances that eliminate most gastrointestinal biomass can be induced using a clinically-relevant iso-osmotic agent. We designed and executed such a disturbance in human volunteers using a dense longitudinal sampling scheme extending before and after induced diarrhea. This experiment has enabled a careful multidomain analysis of a controlled perturbation of the human gut microbiota with a new level of resolution. These new longitudinal multidomain data were analyzed using recently developed statistical methods that demonstrate improvements over current practices. By imposing sparsity constraints we have enhanced the interpretability of the analyses and by employing a new adaptive generalized principal components analysis, incorporated modulated phylogenetic information and enhanced interpretation through scoring of the portions of the tree most influenced by the perturbation. Our analyses leverage the taxa-sample duality in the data to show how the gut microbiota recovers following this perturbation. Through a holistic approach that integrates phylogenetic, metagenomic and abundance information, we elucidate patterns of taxonomic and functional change that characterize the community recovery process across individuals. We provide complete code and illustrations of new sparse statistical methods for high-dimensional, longitudinal multidomain data that provide greater interpretability than existing methods.}, }
@article {pmid28815328, year = {2018}, author = {Mardanov, AV and Gumerov, VM and Beletsky, AV and Ravin, NV}, title = {Microbial diversity in acidic thermal pools in the Uzon Caldera, Kamchatka.}, journal = {Antonie van Leeuwenhoek}, volume = {111}, number = {1}, pages = {35-43}, doi = {10.1007/s10482-017-0924-5}, pmid = {28815328}, issn = {1572-9699}, support = {11-04-00671//Russian Foundation for Basic Research/ ; 14-14-01016//Russian Science Foundation/ ; }, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; *Biodiversity ; Hot Springs/*chemistry/*microbiology ; Hydrogen-Ion Concentration ; *Metagenome ; *Metagenomics/methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {Microbial communities of four acidic thermal pools in the Uzon Caldera, Kamchatka, Russia, were studied using amplification and pyrosequencing of 16S rRNA gene fragments. The sites differed in temperature and pH: 1805 (60 °C, pH 3.7), 1810 (90 °C, pH 4.1), 1818 (80 °C, pH 3.5), and 1807 (86 °C, pH 5.6). Archaea of the order Sulfolobales were present among the dominant groups in all four pools. Acidilobales dominated in pool 1818 but were a minor fraction at the higher temperature in pool 1810. Uncultivated Archaea of the Hot Thaumarchaeota-related clade were present in significant quantities in pools 1805 and 1807, but they were not abundant in pools 1810 and 1818, where high temperatures were combined with low pH. Nanoarchaeota were present in all pools, but were more abundant in pools 1810 and 1818. A similar abundance pattern was observed for Halobacteriales. Thermophilic Bacteria were less diverse and were mostly represented by aerobic hydrogen- and sulfur-oxidizers of the phylum Aquificae and sulfur-oxidising Proteobacteria of the genus Acidithiobacillus. Thus we showed that extremely acidic hot pools contain diverse microbial communities comprising different metabolic groups of prokaryotes, including putative lithoautotrophs using energy sources of volcanic origin, and various facultative and obligate heterotrophs.}, }
@article {pmid28814344, year = {2017}, author = {Wang, C and Dong, D and Strong, PJ and Zhu, W and Ma, Z and Qin, Y and Wu, W}, title = {Microbial phylogeny determines transcriptional response of resistome to dynamic composting processes.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {103}, doi = {10.1186/s40168-017-0324-0}, pmid = {28814344}, issn = {2049-2618}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteriophages/genetics ; *Composting ; Drug Resistance, Microbial/*genetics ; Genes, Bacterial ; Livestock/microbiology ; Manure/*microbiology ; Metagenomics ; *Microbiota/drug effects/genetics ; *Phylogeny ; RNA Viruses/genetics ; *Soil Microbiology ; Tetracycline Resistance/genetics ; *Transcription, Genetic ; }, abstract = {BACKGROUND: Animal manure is a reservoir of antibiotic resistance genes (ARGs) that pose a potential health risk globally, especially for resistance to the antibiotics commonly used in livestock production (such as tetracycline, sulfonamide, and fluoroquinolone). Currently, the effects of biological treatment (composting) on the transcriptional response of manure ARGs and their microbial hosts are not well characterized. Composting is a dynamic process that consists of four distinct phases that are distinguished by the temperature resulting from microbial activity, namely the mesophilic, thermophilic, cooling, and maturing phases. In this study, changes of resistome expression were determined and related to active microbiome profiles during the dynamic composting process. This was achieved by integrating metagenomic and time series metatranscriptomic data for the evolving microbial community during composting.
RESULTS: Composting noticeably reduced the aggregated expression level of the manure resistome, which primarily consisted of genes encoding for tetracycline, vancomycin, fluoroquinolone, beta-lactam, and aminoglycoside resistance, as well as efflux pumps. Furthermore, a varied transcriptional response of resistome to composting at the ARG levels was highlighted. The expression of tetracycline resistance genes (tetM-tetW-tetO-tetS) decreased during composting, where distinctive shifts in the four phases of composting were related to variations in antibiotic concentration. Composting had no effect on the expression of sulfonamide and fluoroquinolone resistance genes, which increased slightly during the thermophilic phase and then decreased to initial levels. As indigenous populations switched greatly throughout the dynamic composting, the core resistome persisted and their reservoir hosts' composition was significantly correlated with dynamic active microbial phylogenetic structure. Hosts for sulfonamide and fuoroquinolone resistance genes changed notably in phylognetic structure and underwent an initial increase and then a decrease in abundance. By contrast, hosts for tetracycline resistance genes (tetM-tetW-tetO-tetS) exhibited a constant decline through time.
CONCLUSIONS: The transcriptional patterns of a core resistome over the course of composting were identified, and microbial phylogeny was the key determinant in defining the varied transcriptional response of resistome to this dynamic biological process. This research demonstrated the benefits of composting for manure treatment. It reduced the risk of emerging environmental contaminants such as tetracyclines, tetracycline resistance genes, and clinically relevant pathogens carrying ARGs, as well as RNA viruses and bacteriophages.}, }
@article {pmid28813529, year = {2017}, author = {Abecia, L and Jiménez, E and Martínez-Fernandez, G and Martín-García, AI and Ramos-Morales, E and Pinloche, E and Denman, SE and Newbold, CJ and Yáñez-Ruiz, DR}, title = {Natural and artificial feeding management before weaning promote different rumen microbial colonization but not differences in gene expression levels at the rumen epithelium of newborn goats.}, journal = {PloS one}, volume = {12}, number = {8}, pages = {e0182235}, doi = {10.1371/journal.pone.0182235}, pmid = {28813529}, issn = {1932-6203}, mesh = {*Animal Feed ; Animals ; Biodiversity ; Biomarkers ; DNA Barcoding, Taxonomic ; Female ; Gastric Mucosa/immunology/*metabolism/*microbiology ; *Gastrointestinal Microbiome ; *Gene Expression ; Goats ; Immunoglobulin A/blood/immunology ; Immunoglobulin G/blood/immunology ; Metagenome ; Metagenomics/methods ; *Nutritional Support ; Pregnancy ; Rumen/immunology/*microbiology ; *Weaning ; }, abstract = {The aim of this work was to evaluate the effect of feeding management during the first month of life (natural with the mother, NAT, or artificial with milk replacer, ART) on the rumen microbial colonization and the host innate immune response. Thirty pregnant goats carrying two fetuses were used. At birth one kid was taken immediately away from the doe and fed milk replacer (ART) while the other remained with the mother (NAT). Kids from groups received colostrum during first 2 days of life. Groups of four kids (from ART and NAT experimental groups) were slaughtered at 1, 3, 7, 14, 21 and 28 days of life. On the sampling day, after slaughtering, the rumen content was sampled and epithelial rumen tissue was collected. Pyrosequencing analyses of the bacterial community structure on samples collected at 3, 7, 14 and 28 days showed that both systems promoted significantly different colonization patterns (P = 0.001). Diversity indices increased with age and were higher in NAT feeding system. Lower mRNA abundance was detected in TLR2, TLR8 and TLR10 in days 3 and 5 compared to the other days (7, 14, 21 and 28). Only TLR5 showed a significantly different level of expression according to the feeding system, presenting higher mRNA abundances in ART kids. PGLYRP1 showed significantly higher abundance levels in days 3, 5 and 7, and then experienced a decline independently of the feeding system. These observations confirmed a highly diverse microbial colonisation from the first day of life in the undeveloped rumen, and show that the colonization pattern substantially differs between pre-ruminants reared under natural or artificial milk feeding systems. However, the rumen epithelial immune development does not differentially respond to distinct microbial colonization patterns.}, }
@article {pmid28813450, year = {2017}, author = {Chen, H and Peng, S and Dai, L and Zou, Q and Yi, B and Yang, X and Ma, ZS}, title = {Oral microbial community assembly under the influence of periodontitis.}, journal = {PloS one}, volume = {12}, number = {8}, pages = {e0182259}, doi = {10.1371/journal.pone.0182259}, pmid = {28813450}, issn = {1932-6203}, mesh = {Algorithms ; *Biodiversity ; Case-Control Studies ; Datasets as Topic ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; Models, Theoretical ; Mouth Mucosa/*microbiology ; Periodontitis/*microbiology ; }, abstract = {Several ecological hypotheses (e.g., specific plaque, non-specific plaque and keystone pathogen) regarding the etiology of periodontitis have been proposed since the 1990s, most of which have been centered on the concept of dysbiosis associated with periodontitis. Nevertheless, none of the existing hypotheses have presented mechanistic interpretations on how and why dysbiosis actually occurs. Hubbell's neutral theory of biodiversity offers a powerful null model to test hypothesis regarding the mechanism of community assembly and diversity maintenance from the metagenomic sequencing data, which can help to understand the forces that shape the community dynamics such as dysbiosis. Here we reanalyze the dataset from Abusleme et al.'s comparative study of the oral microbial communities from periodontitis patients and healthy individuals. Our study demonstrates that 14 out of 61 communities (23%) passed the neutrality test, a percentage significantly higher than the previous reported neutrality rate of 1% in human microbiome (Li & Ma 2016, Scientific Reports). This suggests that, while the niche selection may play a predominant role in the assembly and diversity maintenance in oral microbiome, the effect of neutral dynamics may not be ignored. However, no statistically significant differences in the neutrality passing rates were detected between the periodontitis and healthy treatments with Fisher's exact probability test and multiple testing corrections, suggesting that the mechanism of community assembly is robust against disturbances such as periodontitis. In addition, our study confirmed previous finding that periodontitis patients exhibited higher biodiversity. These findings suggest that while periodontitis may significantly change the community composition measured by diversity (i.e., the exhibition or 'phenotype' of community assembly), it does not seem to cause the 'mutation' of the 'genotype" (mechanism) of community assembly. We argue that the 'phenotypic' changes explain the observed link (not necessarily causal) between periodontitis and community dysbiosis, which is certainly worthy of further investigation.}, }
@article {pmid28813445, year = {2017}, author = {Masuoka, H and Shimada, K and Kiyosue-Yasuda, T and Kiyosue, M and Oishi, Y and Kimura, S and Ohashi, Y and Fujisawa, T and Hotta, K and Yamada, A and Hirayama, K}, title = {Transition of the intestinal microbiota of cats with age.}, journal = {PloS one}, volume = {12}, number = {8}, pages = {e0181739}, doi = {10.1371/journal.pone.0181739}, pmid = {28813445}, issn = {1932-6203}, mesh = {Age Factors ; Animals ; Bifidobacterium/classification/genetics ; *Biodiversity ; Cats ; DNA, Bacterial/genetics ; Feces/microbiology ; *Gastrointestinal Microbiome ; Lactobacillus/classification/genetics ; Metagenome ; Metagenomics/methods ; }, abstract = {The transition of intestinal microbiota with age has been well described in humans. However, the age-related changes in intestinal microbiota of cats have not been well studied. In the present study, we investigated the composition of intestinal microbiota of cats in 5 different age groups (pre-weanling, weanling, young, aged, senile) with a culture-based method. For lactobacilli and bifidobacteria, we also quantified with molecular-based method, real-time PCR. The results suggested that the composition of the feline intestinal microbiota changes with age, while the changes were different from those of humans and dogs. Bifidobacteria which are predominant in human intestine or lactobacilli which are predominant in dog intestine, did not appear to be important in cat intestines. Enterococci, instead, seem to be major lactic acid producing bacteria in cats. We also identified lactobacilli and bifidobacteria at the species level based on 16S rRNA gene sequences and found that the species composition of Lactobacillus also changed with age.}, }
@article {pmid28810907, year = {2017}, author = {Emerson, JB and Adams, RI and Román, CMB and Brooks, B and Coil, DA and Dahlhausen, K and Ganz, HH and Hartmann, EM and Hsu, T and Justice, NB and Paulino-Lima, IG and Luongo, JC and Lymperopoulou, DS and Gomez-Silvan, C and Rothschild-Mancinelli, B and Balk, M and Huttenhower, C and Nocker, A and Vaishampayan, P and Rothschild, LJ}, title = {Schrödinger's microbes: Tools for distinguishing the living from the dead in microbial ecosystems.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {86}, doi = {10.1186/s40168-017-0285-3}, pmid = {28810907}, issn = {2049-2618}, mesh = {Bacteria/*isolation & purification ; *Bacterial Physiological Phenomena ; Biomass ; *Ecosystem ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/methods ; Microbial Consortia ; *Microbial Viability ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {While often obvious for macroscopic organisms, determining whether a microbe is dead or alive is fraught with complications. Fields such as microbial ecology, environmental health, and medical microbiology each determine how best to assess which members of the microbial community are alive, according to their respective scientific and/or regulatory needs. Many of these fields have gone from studying communities on a bulk level to the fine-scale resolution of microbial populations within consortia. For example, advances in nucleic acid sequencing technologies and downstream bioinformatic analyses have allowed for high-resolution insight into microbial community composition and metabolic potential, yet we know very little about whether such community DNA sequences represent viable microorganisms. In this review, we describe a number of techniques, from microscopy- to molecular-based, that have been used to test for viability (live/dead determination) and/or activity in various contexts, including newer techniques that are compatible with or complementary to downstream nucleic acid sequencing. We describe the compatibility of these viability assessments with high-throughput quantification techniques, including flow cytometry and quantitative PCR (qPCR). Although bacterial viability-linked community characterizations are now feasible in many environments and thus are the focus of this critical review, further methods development is needed for complex environmental samples and to more fully capture the diversity of microbes (e.g., eukaryotic microbes and viruses) and metabolic states (e.g., spores) of microbes in natural environments.}, }
@article {pmid28799713, year = {2017}, author = {Dunthorn, M and Kauserud, H and Bass, D and Mayor, J and Mahé, F}, title = {Yeasts dominate soil fungal communities in three lowland Neotropical rainforests.}, journal = {Environmental microbiology reports}, volume = {9}, number = {5}, pages = {668-675}, doi = {10.1111/1758-2229.12575}, pmid = {28799713}, issn = {1758-2229}, mesh = {*Biodiversity ; Fungi/*classification/*genetics ; Metagenome ; Metagenomics/methods ; Phylogeography ; *Rainforest ; *Soil Microbiology ; *Tropical Climate ; }, abstract = {Forest soils typically harbour a vast diversity of fungi, but are usually dominated by filamentous (hyphae-forming) taxa. Compared to temperate and boreal forests, though, we have limited knowledge about the fungal diversity in tropical rainforest soils. Here we show, by environmental metabarcoding of soil samples collected in three Neotropical rainforests, that Yeasts dominate the fungal communities in terms of the number of sequencing reads and OTUs. These unicellular forms are commonly found in aquatic environments, and their hyperdiversity may be the result of frequent inundation combined with numerous aquatic microenvironments in these rainforests. Other fungi that are frequent in aquatic environments, such as the abundant Chytridiomycotina, were also detected. While there was low similarity in OTU composition within and between the three rainforests, the fungal communities in Central America were more similar to each other than the communities in South America, reflecting a general biogeographic pattern also seen in animals, plants and protists.}, }
@article {pmid28799297, year = {2017}, author = {Hussein, EI and Jacob, JH and Shakhatreh, MAK and Abd Al-Razaq, MA and Juhmani, AF and Cornelison, CT}, title = {Exploring the microbial diversity in Jordanian hot springs by comparative metagenomic analysis.}, journal = {MicrobiologyOpen}, volume = {6}, number = {6}, pages = {}, doi = {10.1002/mbo3.521}, pmid = {28799297}, issn = {2045-8827}, mesh = {Archaea/classification/genetics/*isolation & purification ; Bacteria/classification/genetics/*isolation & purification ; *Biodiversity ; Hot Springs/chemistry/*microbiology ; Hydrogen-Ion Concentration ; Jordan ; Metagenome ; Metagenomics ; Phylogeny ; }, abstract = {A culture-independent approach was utilized in this study to reveal the microbial diversity in Jordanian hot springs represented by Ma'in and Afra hot springs. Water samples from Ma'in and Afra hot springs were collected in June 2015. The in situ temperature of water samples range was 38-59°C and the pH range was 7.4-8.4. The metagenome was extracted and analyzed using the next generation technology (bTEFAP®). A total of 314,310 sequences were parsed and 288,452 were then clustered. The sequences were predominated by bacteria (>84%) and the relative abundance of archaea in each sample was <1%. Eukaryotic microorganisms were detected but with varying abundances (0.6%-15%). Because most of the detected sequences were found to belong to the domain of bacteria (196,936 sequences out 288,452), the bacterial sequences were utilized for further microbial analyses. With respect to alpha and beta diversity, samples were rarefied to 30,000 sequences and bootstrapped at 10,000 sequences. The Shannon-Wiener Index curve plot reaches a plateau at approximately 3,000 sequences indicating that sequencing depth was sufficient to capture the full scope of microbial diversity. By examining the relative abundance of phyla detected in each sample, it appears that the biota of both Jordanian hot springs sampled are compositionally similar, with over 50% of the microbial community of each sample being comprised of the phylum Proteobacteria. The second most abundant phylum was the phylum Bacteroidetes which represents more than 13% in each sample. The phylum Firmicutes was also detected with a significant abundance. However, lower abundance of Deinococcus, Verrucomicrobia, Planctomycetes, and Chloroflexi was detected. A principal coordinate analysis plot was generated based upon the weighted UniFrac distance matrix. By utilizing Monte Carlo simulations, we were able to determine that there were no significant differences in the microbial diversity between each sample.}, }
@article {pmid28798873, year = {2017}, author = {Aswad, A and Katzourakis, A}, title = {A novel viral lineage distantly related to herpesviruses discovered within fish genome sequence data.}, journal = {Virus evolution}, volume = {3}, number = {2}, pages = {vex016}, doi = {10.1093/ve/vex016}, pmid = {28798873}, issn = {2057-1577}, abstract = {Pathogenic viruses represent a small fraction of viral diversity, and emerging diseases are frequently the result of cross-species transmissions. Therefore, we need to develop high-throughput techniques to investigate a broader range of viral biodiversity across a greater number of species. This is especially important in the context of new practices in agriculture that have arisen to tackle the challenges of global food security, including the rising number of marine and freshwater species that are used in aquaculture. In this study, we demonstrate the utility of combining evolutionary approaches with bioinformatics to mine non-viral genome data for viruses, by adapting methods from paleovirology. We report the discovery of a new lineage of dsDNA viruses that are associated with at least fifteen different species of fish. This approach also enabled us to simultaneously identify sequences that likely represent endogenous viral elements, which we experimentally confirmed in commercial salmon samples. Moreover, genomic analysis revealed that the endogenous sequences have co-opted PiggyBac-like transposable elements, possibly as a mechanism of intragenomic proliferation. The identification of novel viruses from genome data shows that our approach has applications in genomics, virology, and the development of best practices for aquaculture and farming.}, }
@article {pmid28797298, year = {2017}, author = {Petersen, LM and Bautista, EJ and Nguyen, H and Hanson, BM and Chen, L and Lek, SH and Sodergren, E and Weinstock, GM}, title = {Community characteristics of the gut microbiomes of competitive cyclists.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {98}, doi = {10.1186/s40168-017-0320-4}, pmid = {28797298}, issn = {2049-2618}, support = {P30 CA034196/CA/NCI NIH HHS/United States ; U54 DE023789/DE/NIDCR NIH HHS/United States ; U54 HG004968/HG/NHGRI NIH HHS/United States ; }, mesh = {Adult ; *Athletes ; Bacteria/classification/*genetics/*isolation & purification ; Bacteroides/genetics/isolation & purification ; *Bicycling ; Carbohydrate Metabolism/genetics ; Diet ; Exercise ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Gene Expression Profiling ; High-Throughput Nucleotide Sequencing ; Humans ; Life Style ; Male ; Metabolic Networks and Pathways/genetics ; Metagenome ; Metagenomics ; Methane/*metabolism ; Middle Aged ; Pilot Projects ; Prevotella/genetics/isolation & purification ; }, abstract = {BACKGROUND: Changes in diet and exercise can alter the gut microbiome of humans and mice; however, few studies to date have assessed the microbiomes of highly fit athletes. In this pilot study, we used metagenomic whole genome shotgun (mWGS) and metatranscriptomic (RNA-Seq) sequencing to show what organisms are both present and active in the gut microbiomes of both professional and amateur level competitive cyclists and to determine if any significant differences exist between these two groups.
RESULTS: Using mWGS sequencing data, we showed that the gut microbiomes of 33 cyclists split into three taxonomic clusters, characterized by either high Prevotella, high Bacteroides or a mix of many genera including Bacteroides, Prevotella, Eubacterium, Ruminococcus, and Akkermansia. While no significant correlations could be found between taxonomic cluster and being either a professional or amateur level cyclist, high abundance of the genus Prevotella (≥2.5%) was significantly correlated with time reported exercising during an average week. Increased abundance of Prevotella was correlated with a number of amino acid and carbohydrate metabolism pathways, including branched chain amino acid metabolism. Further analysis of the metatranscriptome revealed significant taxonomic differences when compared to the metagenome. There was increased abundance of Methanobrevibacter smithii transcripts in a number of professional cyclists in comparison to amateur cyclists and this archaeon had upregulation of genes involved in the production of methane. Furthermore, when methane metabolism was upregulated, there was similar upregulation of energy and carbohydrate metabolism pathways.
CONCLUSIONS: These results provide a framework for common constituents of the gut community in individuals who follow an exercise-rich lifestyle. These data also suggest how certain organisms such as M. smithii may beneficially influence the metabolic efficiency of the gut community in professional cyclists due to synergistic metabolic cross-feeding events.}, }
@article {pmid28797279, year = {2017}, author = {Zhang, Y and Xu, J and Riera, N and Jin, T and Li, J and Wang, N}, title = {Huanglongbing impairs the rhizosphere-to-rhizoplane enrichment process of the citrus root-associated microbiome.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {97}, doi = {10.1186/s40168-017-0304-4}, pmid = {28797279}, issn = {2049-2618}, mesh = {Bacteria/genetics ; Burkholderia/physiology ; Citrus/*microbiology ; Gene Expression Profiling/methods ; Host-Pathogen Interactions/genetics ; Metagenomics/methods ; Microbiota/*genetics ; Phylogeny ; Plant Diseases/*microbiology ; Plant Roots/*microbiology ; RNA, Ribosomal, 16S/genetics ; Rhizobiaceae/genetics ; Rhizosphere ; *Soil Microbiology ; }, abstract = {BACKGROUND: Roots are the primary site for plant-microbe interactions. Among the three root-associated layers (i.e., rhizosphere, rhizoplane, and endorhiza), the rhizoplane is a key component serving a critical gating role that controls microbial entry into plant roots. The microbial communities colonizing the three layers are believed to be gradually enriched from the bulk soil inoculum. However, it is unknown how this enrichment process, particularly the rhizosphere to rhizoplane step, is affected by biotic stresses, such as disease. In this study, we address this question using the citrus root-associated microbiome as a model.
RESULTS: We identified the rhizosphere-to-rhizoplane-enriched taxonomic and functional properties of the citrus root-associated microbiome and determined how they were affected by Huanglongbing (HLB), a severe systemic disease caused by Candidatus Liberibacter asiaticus, using metagenomic and metatranscriptomic approaches. Multiple rhizoplane-enriched genera were identified, with Bradyrhizobium and Burkholderia being the most dominant. Plant-derived carbon sources are an important driving force for the enrichment process. The enrichment of functional attributes, such as motility, chemotaxis, secretion systems, and lipopolysaccharide (LPS) synthesis, demonstrated more active microbe-plant interactions on the rhizoplane than the rhizosphere. We observed that HLB impaired the rhizosphere-to-rhizoplane enrichment process of the citrus root-associated microbiome in three ways: (1) by decreasing the relative abundance of most rhizoplane-enriched genera; (2) by reducing the relative abundance and/or expression activity of the functional attributes involved in microbe-plant interactions; and (3) by recruiting more functional features involved in autotrophic life cycle adaptation, such as carbon fixation and nitrogen nitrification in the HLB rhizoplane microbiome. Finally, our data showed that inoculation of Burkholderia strains isolated from the healthy citrus root-associated microbiome could trigger the expression of genes involved in induced systemic resistance in inoculated plants.
CONCLUSIONS: HLB causes decreased relative abundance and/or expression activity of rhizoplane-enriched taxonomic and functional properties, collectively resulting in impaired plant host-microbiome interactions. Manipulation of the citrus root-associated microbiome, for instance, by inoculating citrus roots with beneficial Burkholderia strains, has potential to promote plant health. Our results provide novel insights for understanding the contributions of the community enrichment process of the root-associated microbiome to the plant hosts.}, }
@article {pmid28793929, year = {2017}, author = {Broman, E and Sjöstedt, J and Pinhassi, J and Dopson, M}, title = {Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {96}, doi = {10.1186/s40168-017-0311-5}, pmid = {28793929}, issn = {2049-2618}, mesh = {Bacteria/classification/*genetics/isolation & purification/*metabolism ; Bacterial Physiological Phenomena/genetics ; Baltic States ; Gene Expression Profiling ; Geologic Sediments/*chemistry/*microbiology ; Hydrogen Sulfide/metabolism ; Metagenomics ; Methane/metabolism ; Microbial Consortia/*genetics/physiology ; Oceans and Seas ; Oxidation-Reduction ; Oxygen/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: A key characteristic of eutrophication in coastal seas is the expansion of hypoxic bottom waters, often referred to as 'dead zones'. One proposed remediation strategy for coastal dead zones in the Baltic Sea is to mix the water column using pump stations, circulating oxygenated water to the sea bottom. Although microbial metabolism in the sediment surface is recognized as key in regulating bulk chemical fluxes, it remains unknown how the microbial community and its metabolic processes are influenced by shifts in oxygen availability. Here, coastal Baltic Sea sediments sampled from oxic and anoxic sites, plus an intermediate area subjected to episodic oxygenation, were experimentally exposed to oxygen shifts. Chemical, 16S rRNA gene, metagenomic, and metatranscriptomic analyses were conducted to investigate changes in chemistry fluxes, microbial community structure, and metabolic functions in the sediment surface.
RESULTS: Compared to anoxic controls, oxygenation of anoxic sediment resulted in a proliferation of bacterial populations in the facultative anaerobic genus Sulfurovum that are capable of oxidizing toxic sulfide. Furthermore, the oxygenated sediment had higher amounts of RNA transcripts annotated as sqr, fccB, and dsrA involved in sulfide oxidation. In addition, the importance of cryptic sulfur cycling was highlighted by the oxidative genes listed above as well as dsvA, ttrB, dmsA, and ddhAB that encode reductive processes being identified in anoxic and intermediate sediments turned oxic. In particular, the intermediate site sediments responded differently upon oxygenation compared to the anoxic and oxic site sediments. This included a microbial community composition with more habitat generalists, lower amounts of RNA transcripts attributed to methane oxidation, and a reduced rate of organic matter degradation.
CONCLUSIONS: These novel data emphasize that genetic expression analyses has the power to identify key molecular mechanisms that regulate microbial community responses upon oxygenation of dead zones. Moreover, these results highlight that microbial responses, and therefore ultimately remediation efforts, depend largely on the oxygenation history of sites. Furthermore, it was shown that re-oxygenation efforts to remediate dead zones could ultimately be facilitated by in situ microbial molecular mechanisms involved in removal of toxic H2S and the potent greenhouse gas methane.}, }
@article {pmid28790452, year = {2017}, author = {Claesson, MJ and Clooney, AG and O'Toole, PW}, title = {A clinician's guide to microbiome analysis.}, journal = {Nature reviews. Gastroenterology & hepatology}, volume = {14}, number = {10}, pages = {585-595}, doi = {10.1038/nrgastro.2017.97}, pmid = {28790452}, issn = {1759-5053}, mesh = {Computational Biology/*methods ; *Gastrointestinal Microbiome ; Genetic Techniques ; Humans ; Metagenomics/*methods ; Research Design ; }, abstract = {Microbiome analysis involves determining the composition and function of a community of microorganisms in a particular location. For the gastroenterologist, this technology opens up a rapidly evolving set of challenges and opportunities for generating novel insights into the health of patients on the basis of microbiota characterizations from intestinal, hepatic or extraintestinal samples. Alterations in gut microbiota composition correlate with intestinal and extraintestinal disease and, although only a few mechanisms are known, the microbiota are still an attractive target for developing biomarkers for disease detection and management as well as potential therapeutic applications. In this Review, we summarize the major decision points confronting new entrants to the field or for those designing new projects in microbiome research. We provide recommendations based on current technology options and our experience of sequencing platform choices. We also offer perspectives on future applications of microbiome research, which we hope convey the promise of this technology for clinical applications.}, }
@article {pmid28786955, year = {2017}, author = {Arafat, Y and Wei, X and Jiang, Y and Chen, T and Saqib, HSA and Lin, S and Lin, W}, title = {Spatial Distribution Patterns of Root-Associated Bacterial Communities Mediated by Root Exudates in Different Aged Ratooning Tea Monoculture Systems.}, journal = {International journal of molecular sciences}, volume = {18}, number = {8}, pages = {}, doi = {10.3390/ijms18081727}, pmid = {28786955}, issn = {1422-0067}, mesh = {Bacteria/*classification/genetics ; Biodiversity ; Chromatography, High Pressure Liquid ; Cluster Analysis ; Computational Biology/methods ; *Exudates and Transudates ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/methods ; Plant Roots/*chemistry/*microbiology ; *Rhizosphere ; Soil/chemistry ; Soil Microbiology ; Spectrometry, Mass, Electrospray Ionization ; *Tea ; }, abstract = {Positive plant-soil feedback depends on beneficial interactions between roots and microbes for nutrient acquisition; growth promotion; and disease suppression. Recent pyrosequencing approaches have provided insight into the rhizosphere bacterial communities in various cropping systems. However; there is a scarcity of information about the influence of root exudates on the composition of root-associated bacterial communities in ratooning tea monocropping systems of different ages. In Southeastern China; tea cropping systems provide the unique natural experimental environment to compare the distribution of bacterial communities in different rhizo-compartments. High performance liquid chromatography-electrospray ionization-mass spectrometry (HPLC-ESI-MS) was performed to identify and quantify the allelochemicals in root exudates. A high-throughput sequence was used to determine the structural dynamics of the root-associated bacterial communities. Although soil physiochemical properties showed no significant differences in nutrients; long-term tea cultivation resulted in the accumulation of catechin-containing compounds in the rhizosphere and a lowering of pH. Moreover; distinct distribution patterns of bacterial taxa were observed in all three rhizo-compartments of two-year and 30-year monoculture tea; mediated strongly by soil pH and catechin-containing compounds. These results will help to explore the reasons why soil quality and fertility are disturbed in continuous ratooning tea monocropping systems; and to clarify the associated problems.}, }
@article {pmid28783248, year = {2017}, author = {Cui, J and Xiao, M and Liu, M and Wang, Z and Liu, F and Guo, L and Meng, H and Zhang, H and Yang, J and Deng, D and Huang, S and Ma, Y and Liu, C}, title = {Coupling metagenomics with cultivation to select host-specific probiotic micro-organisms for subtropical aquaculture.}, journal = {Journal of applied microbiology}, volume = {123}, number = {5}, pages = {1274-1285}, doi = {10.1111/jam.13555}, pmid = {28783248}, issn = {1365-2672}, mesh = {Animals ; Aquaculture/methods ; Fishes/*microbiology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Lactobacillales/classification/*genetics/*isolation & purification ; Metagenomics ; Probiotics/classification/*isolation & purification ; Shellfish/*microbiology ; Species Specificity ; }, abstract = {AIMS: To demonstrate a nonempirical workflow to select host-specific probiotics for aquaculture industry.
METHODS AND RESULTS: Using both culture-dependent and culture-independent methods, we have systematically investigated, for the first time, the gut microbiota of twelve subtropical aquatic animal species. We found that the diversity, abundance and distribution of gut micro-organisms of these animals were host-specific and that lactic acid bacteria (LAB) were predominant among the indigenous probiotic microbes. Using culturing method, we isolated and characterized ninety-eight LAB strains; however, only a few strains was representative of the dominant LAB OTUs recovered by culture-independent analysis.
CONCLUSIONS: Two cultured LAB strains, Enterococcus faecalis LS1-2 and Enterococcus faecium Z1-2, capturing the major LAB OTUs in the sequencing data set of the most animal samples and showing significant antimicrobial activities against shrimp pathogens, were suggested to be the candidates of shrimp probiotics.
Disease outbreak and the consequential abuse of antibiotics have been the constraints to the aquaculture industry. However, the selection of probiotic bacteria is currently still an empirical process due to our limited knowledge on the gastrointestinal microbiota of aquatic organisms. Our study points to a nonempirical selection process by which host-specific probiotics can be developed.}, }
@article {pmid28774270, year = {2017}, author = {Galia, W and Leriche, F and Cruveiller, S and Garnier, C and Navratil, V and Dubost, A and Blanquet-Diot, S and Thevenot-Sergentet, D}, title = {Strand-specific transcriptomes of Enterohemorrhagic Escherichia coli in response to interactions with ground beef microbiota: interactions between microorganisms in raw meat.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {574}, doi = {10.1186/s12864-017-3957-2}, pmid = {28774270}, issn = {1471-2164}, mesh = {Amino Acids/biosynthesis/metabolism ; Biological Transport/genetics ; Cell Membrane/metabolism ; Cell Wall/metabolism ; Down-Regulation ; Enterohemorrhagic Escherichia coli/cytology/*genetics/metabolism/*physiology ; *Gene Expression Profiling ; Microbiota/*genetics ; Nitrates/metabolism ; Nitrites/metabolism ; Red Meat/*microbiology ; Species Specificity ; }, abstract = {BACKGROUND: Enterohemorrhagic Escherichia coli (EHEC) are zoonotic agents associated with outbreaks worldwide. Growth of EHEC strains in ground beef could be inhibited by background microbiota that is present initially at levels greater than that of the pathogen E. coli. However, how the microbiota outcompetes the pathogenic bacteria is unknown. Our objective was to identify metabolic pathways of EHEC that were altered by natural microbiota in order to improve our understanding of the mechanisms controlling the growth and survival of EHECs in ground beef.
RESULTS: Based on 16S metagenomics analysis, we identified the microbial community structure in our beef samples which was an essential preliminary for subtractively analyzing the gene expression of the EHEC strains. Then, we applied strand-specific RNA-seq to investigate the effects of this microbiota on the global gene expression of EHEC O2621765 and O157EDL933 strains by comparison with their behavior in beef meat without microbiota. In strain O2621765, the expression of genes connected with nitrate metabolism and nitrite detoxification, DNA repair, iron and nickel acquisition and carbohydrate metabolism, and numerous genes involved in amino acid metabolism were down-regulated. Further, the observed repression of ftsL and murF, involved respectively in building the cytokinetic ring apparatus and in synthesizing the cytoplasmic precursor of cell wall peptidoglycan, might help to explain the microbiota's inhibitory effect on EHECs. For strain O157EDL933, the induced expression of the genes implicated in detoxification and the general stress response and the repressed expression of the peR gene, a gene negatively associated with the virulence phenotype, might be linked to the survival and virulence of O157:H7 in ground beef with microbiota.
CONCLUSION: In the present study, we show how RNA-Seq coupled with a 16S metagenomics analysis can be used to identify the effects of a complex microbial community on relevant functions of an individual microbe within it. These findings add to our understanding of the behavior of EHECs in ground beef. By measuring transcriptional responses of EHEC, we could identify putative targets which may be useful to develop new strategies to limit their shedding in ground meat thus reducing the risk of human illnesses.}, }
@article {pmid28771471, year = {2017}, author = {Deck, J and Gaither, MR and Ewing, R and Bird, CE and Davies, N and Meyer, C and Riginos, C and Toonen, RJ and Crandall, ED}, title = {The Genomic Observatories Metadatabase (GeOMe): A new repository for field and sampling event metadata associated with genetic samples.}, journal = {PLoS biology}, volume = {15}, number = {8}, pages = {e2002925}, doi = {10.1371/journal.pbio.2002925}, pmid = {28771471}, issn = {1545-7885}, mesh = {*Biodiversity ; *Databases, Nucleic Acid ; *Metadata ; *Metagenomics ; }, abstract = {The Genomic Observatories Metadatabase (GeOMe, http://www.geome-db.org/) is an open access repository for geographic and ecological metadata associated with biosamples and genetic data. Whereas public databases have served as vital repositories for nucleotide sequences, they do not accession all the metadata required for ecological or evolutionary analyses. GeOMe fills this need, providing a user-friendly, web-based interface for both data contributors and data recipients. The interface allows data contributors to create a customized yet standard-compliant spreadsheet that captures the temporal and geospatial context of each biosample. These metadata are then validated and permanently linked to archived genetic data stored in the National Center for Biotechnology Information's (NCBI's) Sequence Read Archive (SRA) via unique persistent identifiers. By linking ecologically and evolutionarily relevant metadata with publicly archived sequence data in a structured manner, GeOMe sets a gold standard for data management in biodiversity science.}, }
@article {pmid28770172, year = {2017}, author = {Filardo, S and Di Pietro, M and Porpora, MG and Recine, N and Farcomeni, A and Latino, MA and Sessa, R}, title = {Diversity of Cervical Microbiota in Asymptomatic Chlamydia trachomatis Genital Infection: A Pilot Study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {7}, number = {}, pages = {321}, doi = {10.3389/fcimb.2017.00321}, pmid = {28770172}, issn = {2235-2988}, mesh = {*Asymptomatic Diseases ; Cervix Uteri/*microbiology ; Chlamydia Infections/*microbiology ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Female ; Humans ; Metagenomics ; *Microbiota ; Phylogeny ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; Reproductive Tract Infections/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Chlamydia trachomatis genital infection continues to be an important public health problem worldwide due to its increasing incidence. C. trachomatis infection can lead to severe sequelae, such as pelvic inflammatory disease, obstructive infertility, and preterm birth. Recently, it has been suggested that the cervico-vaginal microbiota may be an important defense factor toward C. trachomatis infection as well as the development of chronic sequelae. Therefore, the investigation of microbial profiles associated to chlamydial infection is of the utmost importance. Here we present a pilot study aiming to characterize, through the metagenomic analysis of sequenced 16s rRNA gene amplicons, the cervical microbiota from reproductive age women positive to C. trachomatis infection. The main finding of our study showed a marked increase in bacterial diversity in asymptomatic C. trachomatis positive women as compared to healthy controls in terms of Shannon's diversity and Shannon's evenness (P = 0.031 and P = 0.026, respectively). More importantly, the cervical microbiota from C. trachomatis positive women and from healthy controls significantly separated into two clusters in the weighted UniFrac analysis (P = 0.0027), suggesting that differences between the two groups depended entirely on the relative abundance of bacterial taxa rather than on the types of bacterial taxa present. Furthermore, C. trachomatis positive women showed an overall decrease in Lactobacillus spp. and an increase in anaerobes. These findings are part of an ongoing larger epidemiological study that will evaluate the potential role of distinct bacterial communities of the cervical microbiota in C. trachomatis infection.}, }
@article {pmid28761980, year = {2017}, author = {Jin, W and Xue, C and Liu, J and Yin, Y and Zhu, W and Mao, S}, title = {Effects of Disodium Fumarate on In Vitro Rumen Fermentation, The Production of Lipopolysaccharide and Biogenic Amines, and The Rumen Bacterial Community.}, journal = {Current microbiology}, volume = {74}, number = {11}, pages = {1337-1342}, doi = {10.1007/s00284-017-1322-y}, pmid = {28761980}, issn = {1432-0991}, mesh = {Animals ; Bacteria/classification/genetics/*metabolism ; Biogenic Amines/*biosynthesis ; Cattle ; Cluster Analysis ; Fermentation/*drug effects ; Fumarates/*pharmacology ; Lipopolysaccharides/*biosynthesis ; Metagenome ; Metagenomics/methods ; Microbiota/*drug effects ; Rumen/*microbiology ; }, abstract = {The effect of disodium fumarate (DF) on the ruminal fermentation profiles, the accumulation of lipopolysaccharide (LPS) and bioamines, and the composition of the ruminal bacterial community was investigated by in vitro rumen fermentation. The addition of DF increased the total gas production; the concentrations of propionate, valerate, total volatile fatty acids, and ammonia-nitrogen; and the rumen pH after a 24 h fermentation. By contrast, DF addition decreased the ratio of acetate to propionate and the concentrations of lactate, lipopolysaccharide, methylamine, tryptamine, putrescine, histamine, and tyramine (P < 0.05). Principal coordinates analysis and molecular variance analysis showed that DF altered the ruminal bacterial community (P < 0.05). At the phylum level, DF decreased the proportion of Proteobacteria, and increased the proportions of Spirochaetae and Elusimicrobia (P < 0.05). At the genus level, DF decreased the percentage of Ruminobacter, while increasing the percentage of Succinivibrio and Treponema (P < 0.05). Overall, the results indicate that DF modified rumen fermentation and mitigated the production of several toxic compounds. Thus, DF has great potential for preventing subacute rumen acidosis in dairy cows and for improving the health of ruminants.}, }
@article {pmid28760934, year = {2017}, author = {Spinler, JK and Auchtung, J and Brown, A and Boonma, P and Oezguen, N and Ross, CL and Luna, RA and Runge, J and Versalovic, J and Peniche, A and Dann, SM and Britton, RA and Haag, A and Savidge, TC}, title = {Next-Generation Probiotics Targeting Clostridium difficile through Precursor-Directed Antimicrobial Biosynthesis.}, journal = {Infection and immunity}, volume = {85}, number = {10}, pages = {}, doi = {10.1128/IAI.00303-17}, pmid = {28760934}, issn = {1098-5522}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; U01 AI124290/AI/NIAID NIH HHS/United States ; U19 AI090872/AI/NIAID NIH HHS/United States ; UL1 TR000071/TR/NCATS NIH HHS/United States ; R21 DK096323/DK/NIDDK NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*biosynthesis/pharmacology/therapeutic use ; Bacterial Proteins/genetics ; Clostridium Infections/immunology/*prevention & control/therapy ; Clostridium difficile/drug effects/*growth & development ; Drug Discovery/methods ; Drug Resistance, Bacterial ; Feces/microbiology ; Fermentation ; Gastrointestinal Microbiome ; Glyceraldehyde/*analogs & derivatives/metabolism/pharmacology/therapeutic use ; Glycerol/*administration & dosage/immunology/metabolism ; Humans ; Lactobacillus reuteri/*metabolism ; Metabolomics ; *Probiotics ; Propane/*metabolism/pharmacology/therapeutic use ; Vancomycin/pharmacology ; }, abstract = {Integration of antibiotic and probiotic therapy has the potential to lessen the public health burden of antimicrobial-associated diseases. Clostridium difficile infection (CDI) represents an important example where the rational design of next-generation probiotics is being actively pursued to prevent disease recurrence. Because intrinsic resistance to clinically relevant antibiotics used to treat CDI (vancomycin, metronidazole, and fidaxomicin) is a desired trait in such probiotic species, we screened several bacteria and identified Lactobacillus reuteri to be a promising candidate for adjunct therapy. Human-derived L. reuteri bacteria convert glycerol to the broad-spectrum antimicrobial compound reuterin. When supplemented with glycerol, strains carrying the pocR gene locus were potent reuterin producers, with L. reuteri 17938 inhibiting C. difficile growth at a level on par with the level of growth inhibition by vancomycin. Targeted pocR mutations and complementation studies identified reuterin to be the precursor-induced antimicrobial agent. Pathophysiological relevance was demonstrated when the codelivery of L. reuteri with glycerol was effective against C. difficile colonization in complex human fecal microbial communities, whereas treatment with either glycerol or L. reuteri alone was ineffective. A global unbiased microbiome and metabolomics analysis independently confirmed that glycerol precursor delivery with L. reuteri elicited changes in the composition and function of the human microbial community that preferentially targets C. difficile outgrowth and toxicity, a finding consistent with glycerol fermentation and reuterin production. Antimicrobial resistance has thus been successfully exploited in the natural design of human microbiome evasion of C. difficile, and this method may provide a prototypic precursor-directed probiotic approach. Antibiotic resistance and substrate bioavailability may therefore represent critical new determinants of probiotic efficacy in clinical trials.}, }
@article {pmid28759053, year = {2017}, author = {Legoff, J and Resche-Rigon, M and Bouquet, J and Robin, M and Naccache, SN and Mercier-Delarue, S and Federman, S and Samayoa, E and Rousseau, C and Piron, P and Kapel, N and Simon, F and Socié, G and Chiu, CY}, title = {The eukaryotic gut virome in hematopoietic stem cell transplantation: new clues in enteric graft-versus-host disease.}, journal = {Nature medicine}, volume = {23}, number = {9}, pages = {1080-1085}, doi = {10.1038/nm.4380}, pmid = {28759053}, issn = {1546-170X}, mesh = {Adolescent ; Adult ; Aged ; Anelloviridae/genetics/immunology ; DNA, Viral/*analysis ; Feces/chemistry ; Female ; Gastrointestinal Microbiome/genetics/*immunology ; Graft vs Host Disease/*immunology ; *Hematopoietic Stem Cell Transplantation ; Herpesviridae/genetics/immunology ; Humans ; Intestinal Diseases/*immunology ; Intestines/*virology ; Leukocyte L1 Antigen Complex/metabolism ; Male ; Metagenomics ; Middle Aged ; Papillomaviridae/genetics/immunology ; Picobirnavirus/genetics/immunology ; Polyomaviridae/genetics/immunology ; Proportional Hazards Models ; Risk Factors ; Severity of Illness Index ; Transplantation, Homologous ; Young Adult ; alpha 1-Antitrypsin/metabolism ; }, abstract = {Much attention has been focused on the role of the bacterial microbiome in human health, but the virome is understudied. Although previously investigated in individuals with inflammatory bowel diseases or solid-organ transplants, virome dynamics in allogeneic hematopoietic stem cell transplantation (HSCT) and enteric graft-versus-host disease (GVHD) remain unexplored. Here we characterize the longitudinal gut virome in 44 recipients of HSCT using metagenomics. A viral 'bloom' was identified, and significant increases were demonstrated in the overall proportion of vertebrate viral sequences following transplantation (P = 0.02). Increases in both the rates of detection (P < 0.0001) and number of sequences (P = 0.047) of persistent DNA viruses (anelloviruses, herpesviruses, papillomaviruses and polyomaviruses) over time were observed in individuals with enteric GVHD relative to those without, a finding accompanied by a reduced phage richness (P = 0.01). Picobirnaviruses were detected in 18 individuals (40.9%), more frequently before or within a week after transplant than at later time points (P = 0.008). In a time-dependent Cox proportional-hazards model, picobirnaviruses were predictive of the occurrence of severe enteric GVHD (hazard ratio, 2.66; 95% confidence interval (CI) = 1.46-4.86; P = 0.001), and correlated with higher fecal levels of two GVHD severity markers, calprotectin and α1-antitrypsin. These results reveal a progressive expansion of vertebrate viral infections over time following HSCT, and they suggest an unexpected association of picobirnaviruses with early post-transplant GVHD.}, }
@article {pmid28758937, year = {2017}, author = {Bacci, G and Mengoni, A and Fiscarelli, E and Segata, N and Taccetti, G and Dolce, D and Paganin, P and Morelli, P and Tuccio, V and De Alessandri, A and Lucidi, V and Bevivino, A}, title = {A Different Microbiome Gene Repertoire in the Airways of Cystic Fibrosis Patients with Severe Lung Disease.}, journal = {International journal of molecular sciences}, volume = {18}, number = {8}, pages = {}, doi = {10.3390/ijms18081654}, pmid = {28758937}, issn = {1422-0067}, mesh = {Adolescent ; Adult ; Bacteria/*genetics ; *Cystic Fibrosis/genetics/microbiology ; Drug Resistance, Multiple, Bacterial/*genetics ; Female ; *Genes, Bacterial ; Humans ; Lung/microbiology/pathology ; Male ; Microbiota/*genetics ; Middle Aged ; Severity of Illness Index ; Virulence Factors/*genetics ; }, abstract = {In recent years, next-generation sequencing (NGS) was employed to decipher the structure and composition of the microbiota of the airways in cystic fibrosis (CF) patients. However, little is still known about the overall gene functions harbored by the resident microbial populations and which specific genes are associated with various stages of CF lung disease. In the present study, we aimed to identify the microbial gene repertoire of CF microbiota in twelve patients with severe and normal/mild lung disease by performing sputum shotgun metagenome sequencing. The abundance of metabolic pathways encoded by microbes inhabiting CF airways was reconstructed from the metagenome. We identified a set of metabolic pathways differently distributed in patients with different pulmonary function; namely, pathways related to bacterial chemotaxis and flagellar assembly, as well as genes encoding efflux-mediated antibiotic resistance mechanisms and virulence-related genes. The results indicated that the microbiome of CF patients with low pulmonary function is enriched in virulence-related genes and in genes encoding efflux-mediated antibiotic resistance mechanisms. Overall, the microbiome of severely affected adults with CF seems to encode different mechanisms for the facilitation of microbial colonization and persistence in the lung, consistent with the characteristics of multidrug-resistant microbial communities that are commonly observed in patients with severe lung disease.}, }
@article {pmid28758342, year = {2017}, author = {Rodgers, TW and Xu, CCY and Giacalone, J and Kapheim, KM and Saltonstall, K and Vargas, M and Yu, DW and Somervuo, P and McMillan, WO and Jansen, PA}, title = {Carrion fly-derived DNA metabarcoding is an effective tool for mammal surveys: Evidence from a known tropical mammal community.}, journal = {Molecular ecology resources}, volume = {17}, number = {6}, pages = {e133-e145}, doi = {10.1111/1755-0998.12701}, pmid = {28758342}, issn = {1755-0998}, mesh = {Animal Feed/*analysis ; Animals ; Biodiversity ; DNA/*genetics/isolation & purification ; DNA Barcoding, Taxonomic/*methods ; Diptera/*physiology ; *Feeding Behavior ; Mammals/*classification/genetics ; Metagenomics/*methods ; Panama ; }, abstract = {Metabarcoding of vertebrate DNA derived from carrion flies has been proposed as a promising tool for biodiversity monitoring. To evaluate its efficacy, we conducted metabarcoding surveys of carrion flies on Barro Colorado Island (BCI), Panama, which has a well-known mammal community, and compared our results against diurnal transect counts and camera trapping. We collected 1,084 flies in 29 sampling days, conducted metabarcoding with mammal-specific (16S) and vertebrate-specific (12S) primers, and sequenced amplicons on Illumina MiSeq. For taxonomic assignment, we compared blast with the new program protax, and we found that protax improved species identifications. We detected 20 mammal, four bird, and one lizard species from carrion fly metabarcoding, all but one of which are known from BCI. Fly metabarcoding detected more mammal species than concurrent transect counts (29 sampling days, 13 species) and concurrent camera trapping (84 sampling days, 17 species), and detected 67% of the number of mammal species documented by 8 years of transect counts and camera trapping combined, although fly metabarcoding missed several abundant species. This study demonstrates that carrion fly metabarcoding is a powerful tool for mammal biodiversity surveys and has the potential to detect a broader range of species than more commonly used methods.}, }
@article {pmid28754704, year = {2017}, author = {Muhammed, MK and Kot, W and Neve, H and Mahony, J and Castro-Mejía, JL and Krych, L and Hansen, LH and Nielsen, DS and Sørensen, SJ and Heller, KJ and van Sinderen, D and Vogensen, FK}, title = {Metagenomic Analysis of Dairy Bacteriophages: Extraction Method and Pilot Study on Whey Samples Derived from Using Undefined and Defined Mesophilic Starter Cultures.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {19}, pages = {}, doi = {10.1128/AEM.00888-17}, pmid = {28754704}, issn = {1098-5336}, mesh = {Animals ; Bacteriophages/classification/genetics/*isolation & purification/ultrastructure ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Milk/*virology ; Pilot Projects ; Siphoviridae/classification/genetics/*isolation & purification/ultrastructure ; Whey/*virology ; }, abstract = {Despite being potentially highly useful for characterizing the biodiversity of phages, metagenomic studies are currently not available for dairy bacteriophages, partly due to the lack of a standard procedure for phage extraction. We optimized an extraction method that allows the removal of the bulk protein from whey and milk samples with losses of less than 50% of spiked phages. The protocol was applied to extract phages from whey in order to test the notion that members of Lactococcus lactis 936 (now Sk1virus), P335, c2 (now C2virus) and Leuconostoc phage groups are the most frequently encountered in the dairy environment. The relative abundance and diversity of phages in eight and four whey mixtures from dairies using undefined mesophilic mixed-strain cultures containing Lactococcus lactis subsp. lactis biovar diacetylactis and Leuconostoc species (i.e., DL starter cultures) and defined cultures, respectively, were assessed. Results obtained from transmission electron microscopy and high-throughput sequence analyses revealed the dominance of Lc. lactis 936 phages (order Caudovirales, family Siphoviridae) in dairies using undefined DL starter cultures and Lc. lactis c2 phages (order Caudovirales, family Siphoviridae) in dairies using defined cultures. The 936 and Leuconostoc phages demonstrated limited diversity. Possible coinduction of temperate P335 prophages and satellite phages in one of the whey mixtures was also observed.IMPORTANCE The method optimized in this study could provide an important basis for understanding the dynamics of the phage community (abundance, development, diversity, evolution, etc.) in dairies with different sizes, locations, and production strategies. It may also enable the discovery of previously unknown phages, which is crucial for the development of rapid molecular biology-based methods for phage burden surveillance systems. The dominance of only a few phage groups in the dairy environment signifies the depth of knowledge gained over the past decades, which served as the basis for designing current phage control strategies. The presence of a correlation between phages and the type of starter cultures being used in dairies might help to improve the selection and/or design of suitable, custom, and cost-efficient phage control strategies.}, }
@article {pmid28750650, year = {2017}, author = {Wen, C and Zheng, Z and Shao, T and Liu, L and Xie, Z and Le Chatelier, E and He, Z and Zhong, W and Fan, Y and Zhang, L and Li, H and Wu, C and Hu, C and Xu, Q and Zhou, J and Cai, S and Wang, D and Huang, Y and Breban, M and Qin, N and Ehrlich, SD}, title = {Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis.}, journal = {Genome biology}, volume = {18}, number = {1}, pages = {142}, doi = {10.1186/s13059-017-1271-6}, pmid = {28750650}, issn = {1474-760X}, mesh = {Adolescent ; Adult ; Aged ; Autoimmune Diseases/immunology/*microbiology/pathology ; Bacteroides/classification/genetics/isolation & purification ; Bifidobacterium/classification/genetics/isolation & purification ; Biomarkers/metabolism ; Case-Control Studies ; Dysbiosis/immunology/*microbiology/pathology ; Female ; Gastrointestinal Microbiome/*genetics ; *Genes, Bacterial ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenomics/*methods ; Middle Aged ; Phylogeny ; Prevotella/classification/genetics/isolation & purification ; Spondylitis, Ankylosing/immunology/*microbiology/pathology ; }, abstract = {BACKGROUND: The assessment and characterization of the gut microbiome has become a focus of research in the area of human autoimmune diseases. Ankylosing spondylitis is an inflammatory autoimmune disease and evidence showed that ankylosing spondylitis may be a microbiome-driven disease.
RESULTS: To investigate the relationship between the gut microbiome and ankylosing spondylitis, a quantitative metagenomics study based on deep shotgun sequencing was performed, using gut microbial DNA from 211 Chinese individuals. A total of 23,709 genes and 12 metagenomic species were shown to be differentially abundant between ankylosing spondylitis patients and healthy controls. Patients were characterized by a form of gut microbial dysbiosis that is more prominent than previously reported cases with inflammatory bowel disease. Specifically, the ankylosing spondylitis patients demonstrated increases in the abundance of Prevotella melaninogenica, Prevotella copri, and Prevotella sp. C561 and decreases in Bacteroides spp. It is noteworthy that the Bifidobacterium genus, which is commonly used in probiotics, accumulated in the ankylosing spondylitis patients. Diagnostic algorithms were established using a subset of these gut microbial biomarkers.
CONCLUSIONS: Alterations of the gut microbiome are associated with development of ankylosing spondylitis. Our data suggest biomarkers identified in this study might participate in the pathogenesis or development process of ankylosing spondylitis, providing new leads for the development of new diagnostic tools and potential treatments.}, }
@article {pmid28750626, year = {2017}, author = {Oliveira, JS and Araújo, WJ and Figueiredo, RM and Silva-Portela, RCB and de Brito Guerra, A and da Silva Araújo, SC and Minnicelli, C and Carlos, AC and de Vasconcelos, ATR and Freitas, AT and Agnez-Lima, LF}, title = {Biogeographical distribution analysis of hydrocarbon degrading and biosurfactant producing genes suggests that near-equatorial biomes have higher abundance of genes with potential for bioremediation.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {168}, doi = {10.1186/s12866-017-1077-4}, pmid = {28750626}, issn = {1471-2180}, mesh = {Bacteria/classification/*genetics/isolation & purification/*metabolism ; Bacterial Proteins/*genetics/metabolism ; Biodegradation, Environmental ; Ecosystem ; Hydrocarbons/*metabolism ; Metagenomics ; Microbial Consortia ; Petroleum/*microbiology ; Phylogeny ; Surface-Active Agents/*metabolism ; }, abstract = {BACKGROUND: Bacterial and Archaeal communities have a complex, symbiotic role in crude oil bioremediation. Their biosurfactants and degradation enzymes have been in the spotlight, mainly due to the awareness of ecosystem pollution caused by crude oil accidents and their use. Initially, the scientific community studied the role of individual microbial species by characterizing and optimizing their biosurfactant and oil degradation genes, studying their individual distribution. However, with the advances in genomics, in particular with the use of New-Generation-Sequencing and Metagenomics, it is now possible to have a macro view of the complex pathways related to the symbiotic degradation of hydrocarbons and surfactant production. It is now possible, although more challenging, to obtain the DNA information of an entire microbial community before automatically characterizing it. By characterizing and understanding the interconnected role of microorganisms and the role of degradation and biosurfactant genes in an ecosystem, it becomes possible to develop new biotechnological approaches for bioremediation use. This paper analyzes 46 different metagenome samples, spanning 20 biomes from different geographies obtained from different research projects.
RESULTS: A metagenomics bioinformatics pipeline, focused on the biodegradation and biosurfactant-production pathways, genes and organisms, was applied. Our main results show that: (1) surfactation and degradation are correlated events, and therefore should be studied together; (2) terrestrial biomes present more degradation genes, especially cyclic compounds, and less surfactation genes, when compared to water biomes; and (3) latitude has a significant influence on the diversity of genes involved in biodegradation and biosurfactant production. This suggests that microbiomes found near the equator are richer in genes that have a role in these processes and thus have a higher biotechnological potential.
CONCLUSION: In this work we have focused on the biogeographical distribution of hydrocarbon degrading and biosurfactant producing genes. Our principle results can be seen as an important step forward in the application of bioremediation techniques, by considering the biostimulation, optimization or manipulation of a starting microbial consortia from the areas with higher degradation and biosurfactant producing genetic diversity.}, }
@article {pmid28748273, year = {2017}, author = {She, R and Li, TT and Luo, D and Li, JB and Yin, LY and Li, H and Liu, YM and Li, XZ and Yan, QG}, title = {Changes in the Intestinal Microbiota of Gibel Carp (Carassius gibelio) Associated with Cyprinid herpesvirus 2 (CyHV-2) Infection.}, journal = {Current microbiology}, volume = {74}, number = {10}, pages = {1130-1136}, doi = {10.1007/s00284-017-1294-y}, pmid = {28748273}, issn = {1432-0991}, support = {IRT0848//the Program for Changjiang Scholars and Innovative Research Team in University, China/ ; }, mesh = {Animals ; Biodiversity ; Fish Diseases/*microbiology/*virology ; *Gastrointestinal Microbiome ; *Herpesviridae ; Herpesviridae Infections/*veterinary ; *Host-Pathogen Interactions ; Metagenome ; Metagenomics/methods ; RNA, Ribosomal, 16S ; ROC Curve ; }, abstract = {Gut microbiota are integral to the host, and have received increased attention in recent years. However, information regarding the intestinal microbiota of many aquaculture animals is insufficient; elucidating the dynamics of the intestinal microbiota can be beneficial for nutrition, immunity, and disease control. In this study, we used 16S rRNA sequencing to observe changes in the intestinal microbiota of gibel carp (Carassius auratus gibelio) associated with cyprinid herpesvirus 2 (CyHV-2) infection. Our results indicate that the diversity of the intestinal microbiota was strongly reduced, and the composition was dramatically altered following CyHV-2 infection. The most dominant species in healthy fish were Cetobacterium, Rhodobacter, and Crenothrix; meanwhile, Cetobacterium, Plesiomonas, Bacteroides, and Flavobacterium were the most abundant species in sick fish. Plesiomonas was highly abundant in infected samples, and could be used as a microbial biomarker for CyHV-2 infection. Chemical properties of the aquaculture water were significantly correlated with the microbial community structure; however, it is difficult to determine whether these changes are a cause or consequence of infection. However, it may be possible to use probiotics or prebiotics to restore the richness of the host intestinal microbiota in infected animals to maintain host health.}, }
@article {pmid28747215, year = {2017}, author = {Hasegawa, K and Stewart, CJ and Mansbach, JM and Linnemann, RW and Ajami, NJ and Petrosino, JF and Camargo, CA}, title = {Sphingolipid metabolism potential in fecal microbiome and bronchiolitis in infants: a case-control study.}, journal = {BMC research notes}, volume = {10}, number = {1}, pages = {325}, doi = {10.1186/s13104-017-2659-9}, pmid = {28747215}, issn = {1756-0500}, support = {R01 AI127507/AI/NIAID NIH HHS/United States ; R01 AI108588/AI/NIAID NIH HHS/United States ; U01 AI087881/AI/NIAID NIH HHS/United States ; R21 HL129909/HL/NHLBI NIH HHS/United States ; R01 AI114552/AI/NIAID NIH HHS/United States ; UG3 OD023253/OD/NIH HHS/United States ; }, mesh = {Bronchiolitis/*microbiology ; Case-Control Studies ; *Feces ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Male ; *Metabolic Networks and Pathways ; Sphingolipids/*metabolism ; }, abstract = {OBJECTIVE: Emerging evidence demonstrated that the structure of fecal microbiome is associated with the likelihood of bronchiolitis in infants. However, no study has examined functional profiles of fecal microbiome in infants with bronchiolitis. In this context, we conducted a case-control study. As a part of multicenter prospective study, we collected stool samples from 40 infants hospitalized with bronchiolitis (cases). We concurrently enrolled 115 age-matched healthy controls.
RESULTS: First, by applying 16S rRNA gene sequencing to these 155 fecal samples, we identified the taxonomic profiles of fecal microbiome. Next, based on the taxonomy data, we inferred the functional capabilities of fecal microbiome and tested for differences in the functional capabilities between cases and controls. Overall, the median age was 3 months and 45% were female. Among 274 metabolic pathways surveyed, there were significant differences between bronchiolitis cases and healthy controls for 37 pathways, including lipid metabolic pathways (false discovery rate [FDR] <0.05). Particularly, the fecal microbiome of bronchiolitis cases had consistently higher abundances of gene function related to the sphingolipid metabolic pathways compared to that of controls (FDR <0.05). These pathways were more abundant in infants with Bacteroides-dominant microbiome profile compared to the others (FDR <0.001). On the basis of the predicted metagenome in this case-control study, we found significant differences in the functional potential of fecal microbiome between infants with bronchiolitis and healthy controls. Although causal inferences remain premature, our data suggest a potential link between the bacteria-derived metabolites, modulations of host immune response, and development of bronchiolitis.}, }
@article {pmid28742928, year = {2017}, author = {Choo, LQ and Crampton-Platt, A and Vogler, AP}, title = {Shotgun mitogenomics across body size classes in a local assemblage of tropical Diptera: Phylogeny, species diversity and mitochondrial abundance spectrum.}, journal = {Molecular ecology}, volume = {26}, number = {19}, pages = {5086-5098}, doi = {10.1111/mec.14258}, pmid = {28742928}, issn = {1365-294X}, mesh = {Animals ; *Body Size ; Borneo ; Contig Mapping ; DNA, Mitochondrial/genetics ; Diptera/anatomy & histology/*classification ; *Genome, Mitochondrial ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Mitochondrial genomes can be assembled readily from shotgun-sequenced DNA mixtures of mass-trapped arthropods ("mitochondrial metagenomics"), speeding up the taxonomic characterization. Bulk sequencing was conducted on some 800 individuals of Diptera obtained by canopy fogging of a single tree in Borneo dominated by small (<1.5 mm) individuals. Specimens were split into five body size classes for DNA extraction, to equalize read numbers across specimens and to study how body size, a key ecological trait, interacts with species and phylogenetic diversity. Genome assembly produced 304 orthologous mitochondrial contigs presumed to each represent a different species. The small-bodied fraction was the by far most species-rich (187 contigs). Identification of contigs was through phylogenetic analysis together with 56 reference mitogenomes, which placed most of the Bornean community into seven clades of small-bodied species, indicating phylogenetic conservation of body size. Mapping of shotgun reads against the mitogenomes showed wide ranges of read abundances within each size class. Ranked read abundance plots were largely log-linear, indicating a uniformly filled abundance spectrum, especially for small-bodied species. Small-bodied species differed greatly from other size classes in neutral metacommunity parameters, exhibiting greater levels of immigration, besides greater total community size. We suggest that the established uses of mitochondrial metagenomics for analysis of species and phylogenetic diversity can be extended to parameterize recent theories of community ecology and biodiversity, and by focusing on the number mitochondria, rather than individuals, a new theoretical framework for analysis of mitochondrial abundance spectra can be developed that incorporates metabolic activity approximated by the count of mitochondria.}, }
@article {pmid28732171, year = {2017}, author = {Eaton, WD and Shokralla, S and McGee, KM and Hajibabaei, M}, title = {Using metagenomics to show the efficacy of forest restoration in the New Jersey Pine Barrens.}, journal = {Genome}, volume = {60}, number = {10}, pages = {825-836}, doi = {10.1139/gen-2015-0199}, pmid = {28732171}, issn = {1480-3321}, mesh = {Animals ; Biomass ; Carbon/metabolism ; Chamaecyparis ; Ecosystem ; Environmental Restoration and Remediation/*methods ; *Forests ; High-Throughput Nucleotide Sequencing ; Invertebrates/genetics ; Metagenomics/*methods ; Mycorrhizae/genetics ; New Jersey ; *Soil Microbiology ; Vaccinium macrocarpon ; Wetlands ; }, abstract = {The Franklin Parker Preserve within the New Jersey Pine Barrens contains 5000 acres of wetlands habitat, including old-growth Atlantic white cedar (or AWC; Chamaecyparis thyoides) swamps, cranberry bogs, and former cranberry bogs undergoing restoration into AWC forests. This study showed that the C-use efficiency was greater in the old-growth AWC soils than in soils from 8-year-old mid-stage restored AWC stands, which were greater than found in soil from 4-year-old AWC stands-the latter two stands being restored from long-term cranberry bogs. A metagenomic analysis of eDNA extracted from these soils showed that the C-cycle trends were associated with increases in the relative numbers of DNA sequences from several copiotrophic bacterial groups (Bacteroidetes and Proteobacteria), complex C-decomposing fungal groups (Sordiomycetes, Mortierellales, and Thelephorales), and collembolan and formicid invertebrates. All groups are indicators of successionally more advanced soils, and critical for soil C-cycle activities. These data suggest that the restoration activities studied are enhancing critical guilds of soil biota, and increasing C-use efficiency in the soils of restored habitats, and that the use of metagenomic analysis of soil eDNA can be used in the development of assessment models for soil recovery of wetlands following restoration.}, }
@article {pmid28731475, year = {2017}, author = {Suzuki, S and Ishii, S and Hoshino, T and Rietze, A and Tenney, A and Morrill, PL and Inagaki, F and Kuenen, JG and Nealson, KH}, title = {Unusual metabolic diversity of hyperalkaliphilic microbial communities associated with subterranean serpentinization at The Cedars.}, journal = {The ISME journal}, volume = {11}, number = {11}, pages = {2584-2598}, doi = {10.1038/ismej.2017.111}, pmid = {28731475}, issn = {1751-7370}, mesh = {Alkalies/*metabolism ; Archaea/classification/genetics/*isolation & purification/*metabolism ; Bacteria/classification/genetics/*isolation & purification/*metabolism ; Biodiversity ; Metagenomics ; Natural Springs/analysis/*microbiology ; Phylogeny ; }, abstract = {Water from The Cedars springs that discharge from serpentinized ultramafic rocks feature highly basic (pH=~12), highly reducing (Eh<-550 mV) conditions with low ionic concentrations. These conditions make the springs exceptionally challenging for life. Here, we report the metagenomic data and recovered draft genomes from two different springs, GPS1 and BS5. GPS1, which was fed solely by a deep groundwater source within the serpentinizing system, was dominated by several bacterial taxa from the phyla OD1 ('Parcubacteria') and Chloroflexi. Members of the GPS1 community had, for the most part, the smallest genomes reported for their respective taxa, and encoded only archaeal (A-type) ATP synthases or no ATP synthases at all. Furthermore, none of the members encoded respiration-related genes and some of the members also did not encode key biosynthesis-related genes. In contrast, BS5, fed by shallow water, appears to have a community driven by hydrogen metabolism and was dominated by a diverse group of Proteobacteria similar to those seen in many terrestrial serpentinization sites. Our findings indicated that the harsh ultrabasic geological setting supported unexpectedly diverse microbial metabolic strategies and that the deep-water-fed springs supported a community that was remarkable in its unusual metagenomic and genomic constitution.}, }
@article {pmid28731473, year = {2017}, author = {Svartström, O and Alneberg, J and Terrapon, N and Lombard, V and de Bruijn, I and Malmsten, J and Dalin, AM and El Muller, E and Shah, P and Wilmes, P and Henrissat, B and Aspeborg, H and Andersson, AF}, title = {Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation.}, journal = {The ISME journal}, volume = {11}, number = {11}, pages = {2538-2551}, doi = {10.1038/ismej.2017.108}, pmid = {28731473}, issn = {1751-7370}, support = {322820//European Research Council/International ; }, mesh = {Animal Feed/analysis ; Animals ; Bacteria/classification/*genetics/*isolation & purification/metabolism ; Biomass ; Deer/metabolism/*microbiology ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Lignin/metabolism ; Metagenome ; Metagenomics ; Phylogeny ; Poaceae/metabolism ; Rumen/metabolism/*microbiology ; }, abstract = {The moose (Alces alces) is a ruminant that harvests energy from fiber-rich lignocellulose material through carbohydrate-active enzymes (CAZymes) produced by its rumen microbes. We applied shotgun metagenomics to rumen contents from six moose to obtain insights into this microbiome. Following binning, 99 metagenome-assembled genomes (MAGs) belonging to 11 prokaryotic phyla were reconstructed and characterized based on phylogeny and CAZyme profile. The taxonomy of these MAGs reflected the overall composition of the metagenome, with dominance of the phyla Bacteroidetes and Firmicutes. Unlike in other ruminants, Spirochaetes constituted a significant proportion of the community and our analyses indicate that the corresponding strains are primarily pectin digesters. Pectin-degrading genes were also common in MAGs of Ruminococcus, Fibrobacteres and Bacteroidetes and were overall overrepresented in the moose microbiome compared with other ruminants. Phylogenomic analyses revealed several clades within the Bacteriodetes without previously characterized genomes. Several of these MAGs encoded a large numbers of dockerins, a module usually associated with cellulosomes. The Bacteroidetes dockerins were often linked to CAZymes and sometimes encoded inside polysaccharide utilization loci, which has never been reported before. The almost 100 CAZyme-annotated genomes reconstructed in this study provide an in-depth view of an efficient lignocellulose-degrading microbiome and prospects for developing enzyme technology for biorefineries.}, }
@article {pmid28724443, year = {2017}, author = {Su, JQ and An, XL and Li, B and Chen, QL and Gillings, MR and Chen, H and Zhang, T and Zhu, YG}, title = {Metagenomics of urban sewage identifies an extensively shared antibiotic resistome in China.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {84}, doi = {10.1186/s40168-017-0298-y}, pmid = {28724443}, issn = {2049-2618}, mesh = {Anti-Bacterial Agents/pharmacology ; Antimicrobial Stewardship ; Bacteria/classification/*drug effects/*genetics/isolation & purification ; China ; Drug Resistance, Bacterial/*genetics ; Gastrointestinal Microbiome/genetics ; *Genes, Bacterial ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; Urban Renewal ; }, abstract = {BACKGROUND: Antibiotic-resistant pathogens are challenging treatment of infections worldwide. Urban sewage is potentially a major conduit for dissemination of antibiotic resistance genes into various environmental compartments. However, the diversity and abundance of such genes in wastewater are not well known.
METHODS: Here, seasonal and geographical distributions of antibiotic resistance genes and their host bacterial communities from Chinese urban sewage were characterized, using metagenomic analyses and 16S rRNA gene-based Illumina sequencing, respectively.
RESULTS: In total, 381 different resistance genes were detected, and these genes were extensively shared across China, with no geographical clustering. Seasonal variation in abundance of resistance genes was observed, with average concentrations of 3.27 × 1011 and 1.79 × 1012 copies/L in summer and winter, respectively. Bacterial communities did not exhibit geographical clusters, but did show a significant distance-decay relationship (P < 0.01). The core, shared resistome accounted for 57.7% of the total resistance genes, and was significantly associated with the core microbial community (P < 0.01). The core human gut microbiota was also strongly associated with the shared resistome, demonstrating the potential contribution of human gut microbiota to the dissemination of resistance elements via sewage disposal.
CONCLUSIONS: This study provides a baseline for investigating environmental dissemination of resistance elements and raises the possibility of using the abundance of resistance genes in sewage as a tool for antibiotic stewardship.}, }
@article {pmid28724401, year = {2017}, author = {Cernava, T and Erlacher, A and Aschenbrenner, IA and Krug, L and Lassek, C and Riedel, K and Grube, M and Berg, G}, title = {Deciphering functional diversification within the lichen microbiota by meta-omics.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {82}, doi = {10.1186/s40168-017-0303-5}, pmid = {28724401}, issn = {2049-2618}, mesh = {Alphaproteobacteria/genetics ; Ascomycota/genetics ; Bacteria/classification/genetics ; Chlorophyta/genetics ; Gene Expression Profiling ; Lichens/genetics/metabolism/*microbiology ; *Metagenomics ; Microbial Consortia/genetics/physiology ; *Microbiota ; Phylogeny ; *Proteomics ; *Symbiosis ; }, abstract = {BACKGROUND: Recent evidence of specific bacterial communities extended the traditional concept of fungal-algal lichen symbioses by a further organismal kingdom. Although functional roles were already assigned to dominant members of the highly diversified microbiota, a substantial fraction of the ubiquitous colonizers remained unexplored. We employed a multi-omics approach to further characterize functional guilds in an unconventional model system.
RESULTS: The general community structure of the lichen-associated microbiota was shown to be highly similar irrespective of the employed omics approach. Five highly abundant bacterial orders-Sphingomonadales, Rhodospirillales, Myxococcales, Chthoniobacterales, and Sphingobacteriales-harbor functions that are of substantial importance for the holobiome. Identified functions range from the provision of vitamins and cofactors to the degradation of phenolic compounds like phenylpropanoid, xylenols, and cresols.
CONCLUSIONS: Functions that facilitate the persistence of Lobaria pulmonaria under unfavorable conditions were present in previously overlooked fractions of the microbiota. So far, unrecognized groups like Chthoniobacterales (Verrucomicrobia) emerged as functional protectors in the lichen microbiome. By combining multi-omics and imaging techniques, we highlight previously overlooked participants in the complex microenvironment of the lichens.}, }
@article {pmid28721658, year = {2017}, author = {Vieira, AS and Ramalho, MO and Martins, C and Martins, VG and Bueno, OC}, title = {Microbial Communities in Different Tissues of Atta sexdens rubropilosa Leaf-cutting Ants.}, journal = {Current microbiology}, volume = {74}, number = {10}, pages = {1216-1225}, doi = {10.1007/s00284-017-1307-x}, pmid = {28721658}, issn = {1432-0991}, support = {157837/2015-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 306910/2011-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 007343/2014-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 2012/12541-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; }, mesh = {Animals ; Ants/*microbiology ; Biodiversity ; Metagenome ; Metagenomics ; *Microbiota ; Organ Specificity ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Bacterial endosymbionts are common in all insects, and symbiosis has played an integral role in ant evolution. Atta sexdens rubropilosa leaf-cutting ants cultivate their symbiotic fungus using fresh leaves. They need to defend themselves and their brood against diseases, but they also need to defend their obligate fungus gardens, their primary food source, from infection, parasitism, and usurpation by competitors. This study aimed to characterize the microbial communities in whole workers and different tissues of A. sexdens rubropilosa queens using Ion Torrent NGS. Our results showed that the microbial community in the midgut differs in abundance and diversity from the communities in the postpharyngeal gland of the queen and in whole workers. The main microbial orders in whole workers were Lactobacillales, Clostridiales, Enterobacteriales, Actinomycetales, Burkholderiales, and Bacillales. In the tissues of the queens, the main orders were Burkholderiales, Clostridiales, Syntrophobacterales, Lactobacillales, Bacillales, and Actinomycetales (midgut) and Entomoplasmatales, unclassified γ-proteobacteria, and Actinomycetales (postpharyngeal glands). The high abundance of Entomoplasmatales in the postpharyngeal glands (77%) of the queens was an unprecedented finding. We discuss the role of microbial communities in different tissues and castes. Bacteria are likely to play a role in nutrition and immune defense as well as helping antimicrobial defense in this ant species.}, }
@article {pmid28716113, year = {2017}, author = {Be, NA and Avila-Herrera, A and Allen, JE and Singh, N and Checinska Sielaff, A and Jaing, C and Venkateswaran, K}, title = {Whole metagenome profiles of particulates collected from the International Space Station.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {81}, doi = {10.1186/s40168-017-0292-4}, pmid = {28716113}, issn = {2049-2618}, mesh = {Archaea/classification/*genetics/isolation & purification ; Astronauts ; Bacteria/classification/*genetics/isolation & purification ; Dust/*analysis ; Environment Design ; Environment, Controlled ; High-Throughput Nucleotide Sequencing ; Humans ; International Agencies ; *Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Phylogeny ; Space Flight ; *Spacecraft ; Weightlessness ; }, abstract = {BACKGROUND: The built environment of the International Space Station (ISS) is a highly specialized space in terms of both physical characteristics and habitation requirements. It is unique with respect to conditions of microgravity, exposure to space radiation, and increased carbon dioxide concentrations. Additionally, astronauts inhabit a large proportion of this environment. The microbial composition of ISS particulates has been reported; however, its functional genomics, which are pertinent due to potential impact of its constituents on human health and operational mission success, are not yet characterized.
METHODS: This study examined the whole metagenome of ISS microbes at both species- and gene-level resolution. Air filter and dust samples from the ISS were analyzed and compared to samples collected in a terrestrial cleanroom environment. Furthermore, metagenome mining was carried out to characterize dominant, virulent, and novel microorganisms. The whole genome sequences of select cultivable strains isolated from these samples were extracted from the metagenome and compared.
RESULTS: Species-level composition in the ISS was found to be largely dominated by Corynebacterium ihumii GD7, with overall microbial diversity being lower in the ISS relative to the cleanroom samples. When examining detection of microbial genes relevant to human health such as antimicrobial resistance and virulence genes, it was found that a larger number of relevant gene categories were observed in the ISS relative to the cleanroom. Strain-level cross-sample comparisons were made for Corynebacterium, Bacillus, and Aspergillus showing possible distinctions in the dominant strain between samples.
CONCLUSION: Species-level analyses demonstrated distinct differences between the ISS and cleanroom samples, indicating that the cleanroom population is not necessarily reflective of space habitation environments. The overall population of viable microorganisms and the functional diversity inherent to this unique closed environment are of critical interest with respect to future space habitation. Observations and studies such as these will be important to evaluating the conditions required for long-term health of human occupants in such environments.}, }
@article {pmid28716079, year = {2017}, author = {Sundin, OH and Mendoza-Ladd, A and Zeng, M and Diaz-Arévalo, D and Morales, E and Fagan, BM and Ordoñez, J and Velez, P and Antony, N and McCallum, RW}, title = {The human jejunum has an endogenous microbiota that differs from those in the oral cavity and colon.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {160}, doi = {10.1186/s12866-017-1059-6}, pmid = {28716079}, issn = {1471-2180}, mesh = {Adult ; Aged ; Bacteria/classification/genetics/growth & development/*isolation & purification ; Colon/*microbiology ; Female ; Humans ; Jejunum/*microbiology ; Male ; *Microbiota ; Middle Aged ; Mouth/*microbiology ; }, abstract = {BACKGROUND: The upper half of the human small intestine, known as the jejunum, is the primary site for absorption of nutrient-derived carbohydrates, amino acids, small peptides, and vitamins. In contrast to the colon, which contains 1011-1012 colony forming units of bacteria per ml (CFU/ml), the normal jejunum generally ranges from 103 to 105 CFU per ml. Because invasive procedures are required to access the jejunum, much less is known about its bacterial microbiota. Bacteria inhabiting the jejunal lumen have been investigated by classical culture techniques, but not by culture-independent metagenomics.
RESULTS: The lumen of the upper jejunum was sampled during enteroscopy of 20 research subjects. Culture on aerobic and anaerobic media gave live bacterial counts ranging from 5.8 × 103 CFU/ml to 8.0 × 106 CFU/ml. DNA from the same samples was analyzed by 16S rRNA gene-specific quantitative PCR, yielding values from 1.5 × 105 to 3.1 × 107 bacterial genomes per ml. When calculated for each sample, estimated bacterial viability ranged from effectively 100% to a low of 0.3%. 16S rRNA metagenomic analysis of uncultured bacteria by Illumina MiSeq sequencing gave detailed microbial composition by phylum, genus and species. The genera Streptococcus, Prevotella, Veillonella and Fusobacterium, were especially abundant, as well as non-oral genera including Escherichia, Klebsiella, and Citrobacter. The jejunum was devoid of the genera Alistipes, Ruminococcus, Faecalibacterium, and other extreme anaerobes abundant in the colon. In patients with higher bacterial loads, there was no significant change in microbial species composition.
CONCLUSIONS: The jejunal lumen contains a distinctive bacterial population consisting primarily of facultative anaerobes and oxygen-tolerant obligate anaerobes similar to those found in the oral cavity. However, the frequent abundance of Enterobacteriaceae represents a major difference from oral microbiota. Although a few genera are shared with the colon, we found no evidence for retrograde movement of the most abundant colonic microbes to the jejunum. Some individuals had much higher bacterial loads, but this was not correlated with decreases in bacterial species diversity or other evidence of dysbiosis.}, }
@article {pmid28715458, year = {2017}, author = {Hirai, J and Nagai, S and Hidaka, K}, title = {Evaluation of metagenetic community analysis of planktonic copepods using Illumina MiSeq: Comparisons with morphological classification and metagenetic analysis using Roche 454.}, journal = {PloS one}, volume = {12}, number = {7}, pages = {e0181452}, doi = {10.1371/journal.pone.0181452}, pmid = {28715458}, issn = {1932-6203}, mesh = {Animals ; Biodiversity ; Classification ; Computational Biology ; Copepoda/*genetics ; High-Throughput Nucleotide Sequencing/*instrumentation ; Metagenome/*genetics ; Metagenomics/*instrumentation ; Oceans and Seas ; Plankton/*genetics ; }, abstract = {Metagenetics is a rapid and taxonomically comprehensive method for revealing community structures within environmental samples, based on large amounts of sequence data produced by high-throughput sequencers. Because community structures of planktonic copepods are important in the ocean owing to their high diversity and abundance, a metagenetic analysis of the 28S D2 region using Roche 454 was previously developed. However, the Illumina MiSeq platform with a high sequence output is being used more frequently in metagenetics, and non-calanoid copepods have not previously been fully evaluated. Here, we evaluated an Illumina MiSeq-based metagenetic analysis using a mock community and field-collected samples that were examined in a previous study using Roche 454, and the community structure, including non-calanoid copepods, was compared among morphological and metagenetic analyses. We removed a singleton read and applied an appropriate abundance threshold to remove erroneous Molecular Operational Taxonomic Units (MOTUs) with low-abundance sequences in the MiSeq-based analysis. Results showed that the copepod community was successfully characterized using Illumina MiSeq. Higher-quality sequences were obtained using MiSeq than by Roche 454, which reduced the overestimation of diversity, especially at a strict 99% similarity threshold for MOTU clustering. Taxonomic compositions in terms of both biomass and presence/absence of species, including non-calanoids, were more appropriately represented in the MiSeq- than in Roche 454-based analysis. Our data showed that metagenetic analysis using Illumina MiSeq is more useful for revealing copepod communities than Roche 454, owing to the lower cost and higher quality.}, }
@article {pmid28714286, year = {2017}, author = {Bozic, J and Capone, A and Pediconi, D and Mensah, P and Cappelli, A and Valzano, M and Mancini, MV and Scuppa, P and Martin, E and Epis, S and Rossi, P and Favia, G and Ricci, I}, title = {Mosquitoes can harbour yeasts of clinical significance and contribute to their environmental dissemination.}, journal = {Environmental microbiology reports}, volume = {9}, number = {5}, pages = {642-648}, doi = {10.1111/1758-2229.12569}, pmid = {28714286}, issn = {1758-2229}, mesh = {Animals ; Culicidae/*microbiology ; *Environment ; Female ; *Host-Pathogen Interactions ; Male ; Metagenome ; Metagenomics/methods ; Microbiota ; Polymerase Chain Reaction ; *Yeasts/classification/genetics/isolation & purification ; }, abstract = {There is still a lack of studies on fungal microbiota in mosquitoes, compared with the number available on bacterial microbiota. This study reports the identification of yeasts of clinical significance in laboratory mosquito species: Anopheles gambiae, Anopheles stephensi, Culex quinquefasciatus, Aedes albopictus and Aedes aegypti. Among the yeasts isolated, they focused on the opportunistic pathogen Candida parapsilosis, since there is a need to better understand breakthrough candidaemia with resistance to the usual antifungals, which requires careful consideration in the broad-spectrum therapy, as documented in many clinical reports. C. parapsilosis occurs widely and has been isolated from diverse sources, including insects, which may contribute to its dissemination. In this study, it was isolated from the gut of An. gambiae and its presence in developmental stages and organs of different mosquito species was studied. Our results indicated that there was a stable association between C. parapsilosis and reared mosquitoes during the entire life cycle, and in adult male and female gut and gonads. A wide occurrence of C. parapsilosis was also documented in several populations of wild mosquitoes. Based on these findings, it can be said that mosquitoes might participate in the spreading of this opportunistic pathogen, not only as a carrier.}, }
@article {pmid28711820, year = {2017}, author = {Chen, Z and Zheng, Y and Ding, C and Ren, X and Yuan, J and Sun, F and Li, Y}, title = {Integrated metagenomics and molecular ecological network analysis of bacterial community composition during the phytoremediation of cadmium-contaminated soils by bioenergy crops.}, journal = {Ecotoxicology and environmental safety}, volume = {145}, number = {}, pages = {111-118}, doi = {10.1016/j.ecoenv.2017.07.019}, pmid = {28711820}, issn = {1090-2414}, mesh = {Biodegradation, Environmental ; *Biofuels ; Cadmium/*analysis/metabolism ; *Metagenomics ; Microbial Consortia/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Soil Microbiology/standards ; Soil Pollutants/*analysis/metabolism ; Soybeans/*growth & development/metabolism ; Zea mays/*growth & development/metabolism ; }, abstract = {Two energy crops (maize and soybean) were used in the remediation of cadmium-contaminated soils. These crops were used because they are fast growing, have a large biomass and are good sources for bioenergy production. The total accumulation of cadmium in maize and soybean plants was 393.01 and 263.24μg pot-1, respectively. The rhizosphere bacterial community composition was studied by MiSeq sequencing. Phylogenetic analysis was performed using 16S rRNA gene sequences. The rhizosphere bacteria were divided into 33 major phylogenetic groups according to phyla. The dominant phylogenetic groups included Proteobacteria, Acidobacteria, Actinobacteria, Gemmatimonadetes, and Bacteroidetes. Based on principal component analysis (PCA) and unweighted pair group with arithmetic mean (UPGMA) analysis, we found that the bacterial community was influenced by cadmium addition and bioenergy cropping. Three molecular ecological networks were constructed for the unplanted, soybean- and maize-planted bacterial communities grown in 50mgkg-1 cadmium-contaminated soils. The results indicated that bioenergy cropping increased the complexity of the bacterial community network as evidenced by a higher total number of nodes, the average geodesic distance (GD), the modularity and a shorter geodesic distance. Proteobacteria and Acidobacteria were the keystone bacteria connecting different co-expressed operational taxonomic units (OTUs). The results showed that bioenergy cropping altered the topological roles of individual OTUs and keystone populations. This is the first study to reveal the effects of bioenergy cropping on microbial interactions in the phytoremediation of cadmium-contaminated soils by network reconstruction. This method can greatly enhance our understanding of the mechanisms of plant-microbe-metal interactions in metal-polluted ecosystems.}, }
@article {pmid28710513, year = {2017}, author = {Zhao, H and Sun, W and Wang, Z and Zhang, T and Fan, Y and Gu, H and Li, G}, title = {Mink (Mustela vison) Gut Microbial Communities from Northeast China and Its Internal Relationship with Gender and Food Additives.}, journal = {Current microbiology}, volume = {74}, number = {10}, pages = {1169-1177}, doi = {10.1007/s00284-017-1301-3}, pmid = {28710513}, issn = {1432-0991}, support = {No. 20150101112JC//Natural Science Foundation of Science and Technology Department of Jilin Province, China/ ; }, mesh = {Animals ; Biodiversity ; Computational Biology ; Evolution, Molecular ; Female ; Food Additives ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Male ; *Metagenome ; *Metagenomics/methods ; Mink/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sex Factors ; }, abstract = {It is well documented that the microbial interactions and biodiversity play an important role in health and disease in mammalian species. There is a rare study about gut microbiota of Mustelidae family. In this study, 40 male and female minks from Northeast China were divided into three groups and fed until they reached maturity. The V3 region of 16S rRNA genes was amplified and sequenced using NGS. There were 526 OTUs principally concentrated among five bacterial phyla. Two points about mink's body weight gaining were observed: (1) the weight of male individuals increased more rapidly than female individuals; (2) the weight of individuals whose feed was supplemented with Chinese herb additives increased more rapidly than individuals without giving food additives. The differences of microorganism abundance were shown in two points: (1) two genera which had ≥2-fold change difference were found between male and female minks. (2) Ten genera which had a ≥2-fold change difference were found among minks with and without Chinese herb additive. Findings from this study provide new and fundamental knowledge on the gut microbiota composition of minks farmed in Northeast China, which can contribute to the general well-being of minks worldwide.}, }
@article {pmid28709472, year = {2017}, author = {Tanca, A and Abbondio, M and Palomba, A and Fraumene, C and Manghina, V and Cucca, F and Fiorillo, E and Uzzau, S}, title = {Potential and active functions in the gut microbiota of a healthy human cohort.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {79}, doi = {10.1186/s40168-017-0293-3}, pmid = {28709472}, issn = {2049-2618}, support = {HHSN271201100005C/DA/NIDA NIH HHS/United States ; N01AG12109/AG/NIA NIH HHS/United States ; }, mesh = {Adult ; Bacteria/classification/genetics/isolation & purification/*metabolism ; Biosynthetic Pathways ; Carbohydrate Metabolism ; Cohort Studies ; Faecalibacterium/genetics/isolation & purification/metabolism ; Fatty Acids, Volatile/metabolism ; Female ; Firmicutes/genetics/isolation & purification/metabolism ; *Gastrointestinal Microbiome/genetics/physiology ; Healthy Volunteers ; Homeostasis ; Humans ; Italy ; Male ; Metagenome ; *Metagenomics ; Middle Aged ; *Proteomics ; Young Adult ; }, abstract = {BACKGROUND: The study of the gut microbiota (GM) is rapidly moving towards its functional characterization by means of shotgun meta-omics. In this context, there is still no consensus on which microbial functions are consistently and constitutively expressed in the human gut in physiological conditions. Here, we selected a cohort of 15 healthy subjects from a native and highly monitored Sardinian population and analyzed their GMs using shotgun metaproteomics, with the aim of investigating GM functions actually expressed in a healthy human population. In addition, shotgun metagenomics was employed to reveal GM functional potential and to compare metagenome and metaproteome profiles in a combined taxonomic and functional fashion.
RESULTS: Metagenomic and metaproteomic data concerning the taxonomic structure of the GM under study were globally comparable. On the contrary, a considerable divergence between genetic potential and functional activity of the human healthy GM was observed, with the metaproteome displaying a higher plasticity, compared to the lower inter-individual variability of metagenome profiles. The taxon-specific contribution to functional activities and metabolic tasks was also examined, giving insights into the peculiar role of several GM members in carbohydrate metabolism (including polysaccharide degradation, glycan transport, glycolysis, and short-chain fatty acid production). Noteworthy, Firmicutes-driven butyrogenesis (mainly due to Faecalibacterium spp.) was shown to be the metabolic activity with the highest expression rate and the lowest inter-individual variability in the study cohort, in line with the previously reported importance of the biosynthesis of this microbial product for the gut homeostasis.
CONCLUSIONS: Our results provide detailed and taxon-specific information regarding functions and pathways actively working in a healthy GM. The reported discrepancy between expressed functions and functional potential suggests that caution should be used before drawing functional conclusions from metagenomic data, further supporting metaproteomics as a fundamental approach to characterize the human GM metabolic functions and activities.}, }
@article {pmid28704437, year = {2017}, author = {Lai, PS and Allen, JG and Hutchinson, DS and Ajami, NJ and Petrosino, JF and Winters, T and Hug, C and Wartenberg, GR and Vallarino, J and Christiani, DC}, title = {Impact of environmental microbiota on human microbiota of workers in academic mouse research facilities: An observational study.}, journal = {PloS one}, volume = {12}, number = {7}, pages = {e0180969}, doi = {10.1371/journal.pone.0180969}, pmid = {28704437}, issn = {1932-6203}, support = {K23 ES023700/ES/NIEHS NIH HHS/United States ; P30 ES000002/ES/NIEHS NIH HHS/United States ; T32 ES007069/ES/NIEHS NIH HHS/United States ; }, mesh = {Air Pollutants, Occupational/analysis ; Animal Technicians ; Animals ; Bacteria/*classification/genetics ; DNA, Bacterial/genetics ; Endotoxins/*genetics ; Humans ; Medical Laboratory Personnel ; Mice ; *Microbiota ; Mouth/microbiology ; Nose/microbiology ; Occupational Exposure/*classification ; RNA, Ribosomal, 16S/*genetics ; Skin/microbiology ; }, abstract = {OBJECTIVES: To characterize the microbial environment of workers in academic mouse research facilities using endotoxin, 16S qPCR, and 16S amplicon sequencing. To determine whether the work microbiome contributes to the human microbiome of workers.
METHODS: We performed area air sampling from the animal rooms, dirty, middle, and setup cage wash locations in four academic mouse research facilities. 10 workers in the dirty cage wash area underwent personal air sampling as well as repeated collection of nasal, oral, and skin samples before and after the work shift. Environmental samples underwent measurement of endotoxin, mouse allergen, bacteria copy number via 16S qPCR, and microbial identification via 16S rDNA sequencing. 16S rDNA sequencing was also performed on human samples before and after the work shift. SourceTracker was used to identify the contribution of the work microbiome to the human microbiome.
RESULTS: Median endotoxin levels ranged from undetectable to 1.0 EU/m3. Significant differences in mouse allergen levels, bacterial copy number, microbial richness, and microbial community structure were identified between animal, dirty, middle, and setup cage wash locations. Endotoxin levels had only a moderate correlation with microbial composition. Location within a facility was a stronger predictor of microbial community composition (R2 = 0.41, p = 0.002) than facility. The contribution of the work microbiome to the pre-shift human microbiome of workers was estimated to be 0.1 ± 0.1% for the oral microbiome; 3.1 ± 1.9% for the nasal microbiome; and 3.0 ± 1.5% for the skin microbiome.
CONCLUSIONS: The microbial environment of academic animal care facilities varies significantly by location rather than facility. Endotoxin is not a proxy for assessment of environmental microbial exposures using 16S qPCR or 16S rDNA sequencing. The work microbiome contributes to the composition of the nasal and skin microbiome of workers; the clinical implications of this observation should be further studied.}, }
@article {pmid28703874, year = {2017}, author = {Tao, Y and Wang, X and Li, X and Wei, N and Jin, H and Xu, Z and Tang, Q and Zhu, X}, title = {The functional potential and active populations of the pit mud microbiome for the production of Chinese strong-flavour liquor.}, journal = {Microbial biotechnology}, volume = {10}, number = {6}, pages = {1603-1615}, doi = {10.1111/1751-7915.12729}, pmid = {28703874}, issn = {1751-7915}, mesh = {Alcoholic Beverages/analysis/*microbiology ; Aluminum Silicates/*chemistry ; Bacteria/classification/genetics/isolation & purification/*metabolism ; Caproates/analysis/metabolism ; China ; Fermentation ; Flavoring Agents/analysis/*metabolism ; *Microbiota ; }, abstract = {The popular distilled Chinese strong-flavour liquor (CSFL) is produced by solid fermentation in the ground pit. Microbes inhabiting in the pit mud (PM) on the walls of the fermentation pit are responsible for the production of caproic acid (CA) that determines the quality of CSFL to a large degree. However, little is known about the active microbial populations and metabolic potential of the PM microbiome. Here, we investigated the overall metabolic features of the PM microbiome and its active microbial components by combining metagenomics and MiSeq-sequencing analyses of the 16S rRNA genes from DNA and RNA (cDNA). Results showed that prokaryotes were predominant populations in the PM microbiome, accounting for 95.3% of total metagenomic reads, while eukaryotic abundance was only 1.8%. The dominant prokaryotic phyla were Firmicutes, Euryarchaeota, Bacteroidetes, Actinobacteria and Proteobacteria, accounting for 48.0%, 19.0%, 13.5%, 2.5% and 2.1% of total metagenomic reads respectively. Most genes encoding putative metabolic pathways responsible for the putative CA production via chain elongation pathway were detected. This indicated that the PM microbiome owned functional potential for synthesizing CA from ethanol or lactate. Some key genes encoding enzymes involved in hydrogenotrophic and acetoclastic methanogenesis pathways were detected in the PM metagenome, suggesting the possible occurrence of interspecies hydrogen transfer between CA-producing bacteria and methanogens. The 16S rDNA and 16S rRNA profiles showed that the Clostridial cluster IV, Lactobacillus, Caloramator, Clostridium, Sedimentibacter, Bacteroides and Porphyromonas were active populations in situ, in which Clostridial cluster IV and Clostridium were likely involved in the CA production. This study improved our understandings on the active populations and metabolic pathways of the PM microbiome involved in the CA synthesis in the CSFL fermentation.}, }
@article {pmid28701177, year = {2017}, author = {Stewart, CJ and Embleton, ND and Marrs, ECL and Smith, DP and Fofanova, T and Nelson, A and Skeath, T and Perry, JD and Petrosino, JF and Berrington, JE and Cummings, SP}, title = {Longitudinal development of the gut microbiome and metabolome in preterm neonates with late onset sepsis and healthy controls.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {75}, doi = {10.1186/s40168-017-0295-1}, pmid = {28701177}, issn = {2049-2618}, mesh = {Acetic Acid/metabolism ; Bacterial Translocation ; Bifidobacterium/isolation & purification/physiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology/*physiology ; Humans ; Infant ; Infant, Newborn ; Infant, Premature ; Infant, Premature, Diseases/diagnosis/*microbiology ; *Metabolome ; Metabolomics/methods ; Neonatal Sepsis/diagnosis/*microbiology ; Raffinose/metabolism ; Sucrose/metabolism ; }, abstract = {BACKGROUND: Late onset sepsis (LOS) in preterm infants is associated with considerable morbidity and mortality. While studies have implicated gut bacteria in the aetiology of the disease, functional analysis and mechanistic insights are generally lacking. We performed temporal bacterial (n = 613) and metabolomic (n = 63) profiling on extensively sampled stool from 7 infants with LOS and 28 matched healthy (no LOS or NEC) controls.
RESULTS: The bacteria isolated in diagnostic blood culture usually corresponded to the dominant bacterial genera in the gut microbiome. Longitudinal changes were monitored based on preterm gut community types (PGCTs), where control infants had an increased number of PGCTs compared to LOS infants (P = 0.011). PGCT 6, characterised by Bifidobacteria dominance, was only present in control infants. Metabolite profiles differed between LOS and control infants at diagnosis and 7 days later, but not 7 days prior to diagnosis. Bifidobacteria was positively correlated with control metabolites, including raffinose, sucrose, and acetic acid.
CONCLUSIONS: Using multi-omic analysis, we show that the gut microbiome is involved in the pathogenesis of LOS. While the causative agent of LOS varies, it is usually abundant in the gut. Bifidobacteria dominance was associated with control infants, and the presence of this organism may directly protect, or act as a marker for protection, against gut epithelial translocation. While the metabolomic data is preliminary, the findings support that gut development and protection in preterm infants is associated with increased in prebiotic oligosaccharides (e.g. raffinose) and the growth of beneficial bacteria (e.g. Bifidobacterium).}, }
@article {pmid28700218, year = {2017}, author = {Sun, W and Xiao, E and Xiao, T and Krumins, V and Wang, Q and Häggblom, M and Dong, Y and Tang, S and Hu, M and Li, B and Xia, B and Liu, W}, title = {Response of Soil Microbial Communities to Elevated Antimony and Arsenic Contamination Indicates the Relationship between the Innate Microbiota and Contaminant Fractions.}, journal = {Environmental science & technology}, volume = {51}, number = {16}, pages = {9165-9175}, doi = {10.1021/acs.est.7b00294}, pmid = {28700218}, issn = {1520-5851}, mesh = {*Antimony ; *Arsenic ; China ; Environmental Monitoring ; Humans ; Microbiota ; RNA, Ribosomal, 16S ; Soil ; *Soil Microbiology ; *Soil Pollutants ; }, abstract = {Mining of sulfide ore deposits containing metalloids, such as antimony and arsenic, has introduced serious soil contamination around the world, posing severe threats to food safety and human health. Hence, it is important to understand the behavior and composition of the microbial communities that control the mobilization or sequestration of these metal(loid)s. Here, we selected two sites in Southwest China with different levels of Sb and As contamination to study interactions among various Sb and As fractions and the soil microbiota, with a focus on the microbial response to metalloid contamination. Comprehensive geochemical analyses and 16S rRNA gene amplicon sequencing demonstrated distinct soil taxonomic inventories depending on Sb and As contamination levels. Stochastic gradient boosting indicated that citric acid extractable Sb(V) and As(V) contributed 5% and 15%, respectively, to influencing the community diversity. Random forest predicted that low concentrations of Sb(V) and As(V) could enhance the community diversity but generally, the Sb and As contamination impairs microbial diversity. Co-occurrence network analysis indicated a strong correlation between the indigenous microbial communities and various Sb and As fractions. A number of taxa were identified as core genera due to their elevated abundances and positive correlation with contaminant fractions (total Sb and As concentrations, bioavailable Sb and As extractable fractions, and Sb and As redox species). Shotgun metagenomics indicated that Sb and As biogeochemical redox reactions may exist in contaminated soils. All these observations suggest the potential for bioremediation of Sb- and As-contaminated soils.}, }
@article {pmid28699116, year = {2017}, author = {Thomas, P and Sekhar, AC and Shaik, SP}, title = {High taxonomic diversity of cultivation-recalcitrant endophytic bacteria in grapevine field shoots, their in vitro introduction, and unsuspected persistence.}, journal = {Planta}, volume = {246}, number = {5}, pages = {879-898}, doi = {10.1007/s00425-017-2733-5}, pmid = {28699116}, issn = {1432-2048}, support = {AMASS project//National Bureau of Agriculturally Important Microorganisms/ ; }, mesh = {Bacteria/classification/*genetics/isolation & purification ; Biodiversity ; Endophytes ; *Metagenomics ; Plant Shoots/microbiology ; Polymerase Chain Reaction ; Tissue Culture Techniques ; Vitis/*microbiology ; }, abstract = {MAIN CONCLUSION: Molecular and microscopic analyses reveal enormous non-cultivable endophytic bacteria in grapevine field shoots with functional significance. Diverse bacteria enter tissue cultures through surface-sterilized tissues and survive surreptitiously with varying taxonomic realignments. The study was envisaged to assess the extent of endophytic bacterial association with field shoot tissues of grapevine and the likelihood of introduction of such internally colonizing bacteria in vitro adopting molecular techniques targeting the non-cultivable bacterial community. PowerFood®-kit derived DNA from surface-sterilized field shoot tips of grapevine Flame Seedless was employed in a preliminary bacterial class-specific PCR screening proving positive for major prokaryotic taxa including Archaea. Taxonomic and functional diversity were analyzed through whole metagenome profiling (WMG) which revealed predominantly phylum Actinobacteria, Proteobacteria, and minor shares of Firmicutes, Bacteroidetes, and Deinococcus-Thermus with varying functional roles ascribable to the whole bacterial community. Field shoot tip tissues and callus derived from stem segments were further employed in 16S rRNA V3-V4 amplicon taxonomic profiling. This revealed elevated taxonomic diversity in field shoots over WMG, predominantly Proteobacteria succeeded by Actinobacteria, Firmicutes, Bacteroidetes, and 15 other phyla including several candidate phyla (135 families, 179 genera). Callus stocks also displayed broad bacterial diversity (16 phyla; 96 families; 141 genera) bearing resemblance to field tissues with Proteobacterial dominance but a reduction in its share, enrichment of Actinobacteria and Firmicutes, disappearance of some field-associated phyla and detection of a few additional taxonomic groups over field community. Similar results were documented during 16S V3-V4 amplicon taxonomic profiling on Thompson Seedless field shoot tip and callus tissues. Video microscopy on tissue homogenates corroborated enormous endophytic bacteria. This study elucidates a vast diversity of cultivation-recalcitrant endophytic bacteria prevailing in grapevine field shoots, their in vitro introduction, and unsuspecting sustenance with possible silent participation in tissue culture processes.}, }
@article {pmid28698277, year = {2017}, author = {He, T and Li, H and Zhang, X}, title = {Deep-Sea Hydrothermal Vent Viruses Compensate for Microbial Metabolism in Virus-Host Interactions.}, journal = {mBio}, volume = {8}, number = {4}, pages = {}, doi = {10.1128/mBio.00893-17}, pmid = {28698277}, issn = {2150-7511}, mesh = {Archaea/genetics/*metabolism/virology ; Bacteria/genetics/*metabolism/virology ; Bacteriophages/genetics/*metabolism ; Ecosystem ; Hydrothermal Vents/*microbiology/*virology ; Metagenomics ; *Microbial Interactions ; Microbiota/genetics ; Oceans and Seas ; Phylogeny ; Seawater/*microbiology ; Symbiosis ; }, abstract = {Viruses are believed to be responsible for the mortality of host organisms. However, some recent investigations reveal that viruses may be essential for host survival. To date, it remains unclear whether viruses are beneficial or harmful to their hosts. To reveal the roles of viruses in the virus-host interactions, viromes and microbiomes of sediment samples from three deep-sea hydrothermal vents were explored in this study. To exclude the influence of exogenous DNAs on viromes, the virus particles were purified with nuclease (DNase I and RNase A) treatments and cesium chloride density gradient centrifugation. The metagenomic analysis of viromes without exogenous DNA contamination and microbiomes of vent samples indicated that viruses had compensation effects on the metabolisms of their host microorganisms. Viral genes not only participated in most of the microbial metabolic pathways but also formed branched pathways in microbial metabolisms, including pyrimidine metabolism; alanine, aspartate, and glutamate metabolism; nitrogen metabolism and assimilation pathways of the two-component system; selenocompound metabolism; aminoacyl-tRNA biosynthesis; and amino sugar and nucleotide sugar metabolism. As is well known, deep-sea hydrothermal vent ecosystems exist in relatively isolated environments which are barely influenced by other ecosystems. The metabolic compensation of hosts mediated by viruses might represent a very important aspect of virus-host interactions.IMPORTANCE Viruses are the most abundant biological entities in the oceans and have very important roles in regulating microbial community structure and biogeochemical cycles. The relationship between virus and host microbes is broadly thought to be that of predator and prey. Viruses can lyse host cells to control microbial population sizes and affect community structures of hosts by killing specific microbes. However, viruses also influence their hosts through manipulation of bacterial metabolism. We found that viral genes not only participated in most microbial metabolic pathways but also formed branched pathways in microbial metabolisms. The metabolic compensation of hosts mediated by viruses may help hosts to adapt to extreme environments and may be essential for host survival.}, }
@article {pmid28696422, year = {2017}, author = {Slaby, BM and Hackl, T and Horn, H and Bayer, K and Hentschel, U}, title = {Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization.}, journal = {The ISME journal}, volume = {11}, number = {11}, pages = {2465-2478}, doi = {10.1038/ismej.2017.101}, pmid = {28696422}, issn = {1751-7370}, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; Bacterial Physiological Phenomena ; Metagenomics ; Microbiota ; Phylogeny ; Porifera/*microbiology/physiology ; Symbiosis ; }, abstract = {Marine sponges are ancient metazoans that are populated by distinct and highly diverse microbial communities. In order to obtain deeper insights into the functional gene repertoire of the Mediterranean sponge Aplysina aerophoba, we combined Illumina short-read and PacBio long-read sequencing followed by un-targeted metagenomic binning. We identified a total of 37 high-quality bins representing 11 bacterial phyla and two candidate phyla. Statistical comparison of symbiont genomes with selected reference genomes revealed a significant enrichment of genes related to bacterial defense (restriction-modification systems, toxin-antitoxin systems) as well as genes involved in host colonization and extracellular matrix utilization in sponge symbionts. A within-symbionts genome comparison revealed a nutritional specialization of at least two symbiont guilds, where one appears to metabolize carnitine and the other sulfated polysaccharides, both of which are abundant molecules in the sponge extracellular matrix. A third guild of symbionts may be viewed as nutritional generalists that perform largely the same metabolic pathways but lack such extraordinary numbers of the relevant genes. This study characterizes the genomic repertoire of sponge symbionts at an unprecedented resolution and it provides greater insights into the molecular mechanisms underlying microbial-sponge symbiosis.}, }
@article {pmid28695665, year = {2017}, author = {Auer, L and Mariadassou, M and O'Donohue, M and Klopp, C and Hernandez-Raquet, G}, title = {Analysis of large 16S rRNA Illumina data sets: Impact of singleton read filtering on microbial community description.}, journal = {Molecular ecology resources}, volume = {17}, number = {6}, pages = {e122-e132}, doi = {10.1111/1755-0998.12700}, pmid = {28695665}, issn = {1755-0998}, mesh = {Cluster Analysis ; Computational Biology/*methods ; DNA, Ribosomal/chemistry/genetics ; Metagenomics/*methods ; *Microbiota ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Next-generation sequencing technologies give access to large sets of data, which are extremely useful in the study of microbial diversity based on 16S rRNA gene. However, the production of such large data sets is not only marred by technical biases and sequencing noise but also increases computation time and disc space use. To improve the accuracy of OTU predictions and overcome both computations, storage and noise issues, recent studies and tools suggested removing all single reads and low abundant OTUs, considering them as noise. Although the effect of applying an OTU abundance threshold on α- and β-diversity has been well documented, the consequences of removing single reads have been poorly studied. Here, we test the effect of singleton read filtering (SRF) on microbial community composition using in silico simulated data sets as well as sequencing data from synthetic and real communities displaying different levels of diversity and abundance profiles. Scalability to large data sets is also assessed using a complete MiSeq run. We show that SRF drastically reduces the chimera content and computational time, enabling the analysis of a complete MiSeq run in just a few minutes. Moreover, SRF accurately determines the actual community diversity: the differences in α- and β-community diversity obtained with SRF and standard procedures are much smaller than the intrinsic variability of technical and biological replicates.}, }
@article {pmid28693612, year = {2017}, author = {Xiong, W and Brown, CT and Morowitz, MJ and Banfield, JF and Hettich, RL}, title = {Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {72}, doi = {10.1186/s40168-017-0290-6}, pmid = {28693612}, issn = {2049-2618}, support = {R01 GM103600/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acids/metabolism ; Bacterial Proteins/classification/genetics/isolation & purification/metabolism ; Carbohydrate Metabolism ; Fatty Acids, Volatile/biosynthesis ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics/physiology ; Humans ; Infant, Newborn ; *Infant, Premature ; Lipid Metabolism ; Metagenomics ; Proteome ; *Proteomics ; Species Specificity ; }, abstract = {BACKGROUND: Establishment of the human gut microbiota begins at birth. This early-life microbiota development can impact host physiology during infancy and even across an entire life span. However, the functional stability and population structure of the gut microbiota during initial colonization remain poorly understood. Metaproteomics is an emerging technology for the large-scale characterization of metabolic functions in complex microbial communities (gut microbiota).
RESULTS: We applied a metagenome-informed metaproteomic approach to study the temporal and inter-individual differences of metabolic functions during microbial colonization of preterm human infants' gut. By analyzing 30 individual fecal samples, we identified up to 12,568 protein groups for each of four infants, including both human and microbial proteins. With genome-resolved matched metagenomics, proteins were confidently identified at the species/strain level. The maximum percentage of the proteome detected for the abundant organisms was ~45%. A time-dependent increase in the relative abundance of microbial versus human proteins suggested increasing microbial colonization during the first few weeks of early life. We observed remarkable variations and temporal shifts in the relative protein abundances of each organism in these preterm gut communities. Given the dissimilarity of the communities, only 81 microbial EggNOG orthologous groups and 57 human proteins were observed across all samples. These conserved microbial proteins were involved in carbohydrate, energy, amino acid and nucleotide metabolism while conserved human proteins were related to immune response and mucosal maturation. We identified seven proteome clusters for the communities and showed infant gut proteome profiles were unstable across time and not individual-specific. Applying a gut-specific metabolic module (GMM) analysis, we found that gut communities varied primarily in the contribution of nutrient (carbohydrates, lipids, and amino acids) utilization and short-chain fatty acid production.
CONCLUSIONS: Overall, this study reports species-specific proteome profiles and metabolic functions of human gut microbiota during early colonization. In particular, our work contributes to reveal microbiota-associated shifts and variations in the metabolism of three major nutrient sources and short-chain fatty acid during colonization of preterm infant gut.}, }
@article {pmid28692666, year = {2017}, author = {Sui, S and Yang, Y and Sun, Y and Wang, X and Wang, G and Shan, G and Wang, J and Yu, J}, title = {On the core bacterial flora of Ixodes persulcatus (Taiga tick).}, journal = {PloS one}, volume = {12}, number = {7}, pages = {e0180150}, doi = {10.1371/journal.pone.0180150}, pmid = {28692666}, issn = {1932-6203}, mesh = {Animals ; Bacteria/classification/genetics ; Female ; Ixodes/*microbiology ; *Microbiota ; Phylogeny ; Sequence Analysis, DNA ; *Taiga ; }, abstract = {Ixodes persulcatus is a predominant hard tick species that transmits a wide range of human and animal pathogens. Since bacterial flora of the tick dwelling in the wild always vary according to their hosts and the environment, it is highly desirable that species-associated microbiomes are fully determined by using next-generation sequencing and based on comparative metagenomics. Here, we examine such metagenomic changes of I. persulcatus starting with samples collected from the wild ticks and followed by the reared animals under pathogen-free laboratory conditions over multiple generations. Based on high-coverage genomic sequences from three experimental groups-wild, reared for a single generation or R1, and reared for eight generations or R8 -we identify the core bacterial flora of I. persulcatus, which contains 70 species that belong to 69 genera of 8 phyla; such a core is from the R8 group, which is reduced from 4625 species belonging to 1153 genera of 29 phyla in the wild group. Our study provides a novel example of tick core bacterial flora acquired based on wild-to-reared comparison, which paves a way for future research on tick metagenomics and tick-borne disease pandemics.}, }
@article {pmid28689814, year = {2017}, author = {Song, YH and Lee, KT and Baek, JY and Kim, MJ and Kwon, MR and Kim, YJ and Park, MR and Ko, H and Lee, JS and Kim, KS}, title = {Isolation and characterization of a novel endo-β-1,4-glucanase from a metagenomic library of the black-goat rumen.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {48}, number = {4}, pages = {801-808}, doi = {10.1016/j.bjm.2017.03.006}, pmid = {28689814}, issn = {1678-4405}, mesh = {Animals ; Bacteria/classification/*enzymology/genetics/isolation & purification ; Bacterial Proteins/*chemistry/*genetics/metabolism ; Cellulase/*chemistry/*genetics/metabolism ; Cloning, Molecular ; Enzyme Stability ; Gastrointestinal Microbiome ; Goats ; Hydrogen-Ion Concentration ; Metagenome ; Metagenomics ; Rumen/*microbiology ; }, abstract = {The various types of lignocellulosic biomass found in plants comprise the most abundant renewable bioresources on Earth. In this study, the ruminal microbial ecosystem of black goats was explored because of their strong ability to digest lignocellulosic forage. A metagenomic fosmid library containing 115,200 clones was prepared from the black-goat rumen and screened for a novel cellulolytic enzyme. The KG35 gene, containing a novel glycosyl hydrolase family 5 cellulase domain, was isolated and functionally characterized. The novel glycosyl hydrolase family 5 cellulase gene is composed of a 963-bp open reading frame encoding a protein of 320 amino acid residues (35.1kDa). The deduced amino acid sequence showed the highest sequence identity (58%) for sequences from the glycosyl hydrolase family 5 cellulases. The novel glycosyl hydrolase family 5 cellulase gene was overexpressed in Escherichia coli. Substrate specificity analysis revealed that this recombinant glycosyl hydrolase family 5 cellulase functions as an endo-β-1,4-glucanase. The recombinant KG35 endo-β-1,4-glucanase showed optimal activity within the range of 30-50°C at a pH of 6-7. The thermostability was retained and the pH was stable in the range of 30-50°C at a pH of 5-7.}, }
@article {pmid28686659, year = {2017}, author = {Williams, KE and Huyvaert, KP and Piaggio, AJ}, title = {Clearing muddied waters: Capture of environmental DNA from turbid waters.}, journal = {PloS one}, volume = {12}, number = {7}, pages = {e0179282}, doi = {10.1371/journal.pone.0179282}, pmid = {28686659}, issn = {1932-6203}, mesh = {Animals ; DNA/chemistry/genetics/*isolation & purification ; *Ecosystem ; Endangered Species ; Introduced Species ; Metagenomics/*methods ; Swine/*genetics ; Water/chemistry ; }, abstract = {Understanding the differences in efficiencies of various methods to concentrate, extract, and amplify environmental DNA (eDNA) is vital for best performance of eDNA detection. Aquatic systems vary in characteristics such as turbidity, eDNA concentration, and inhibitor load, thus affecting eDNA capture efficiency. Application of eDNA techniques to the detection of terrestrial invasive or endangered species may require sampling at intermittent water sources that are used for drinking and cooling; these water bodies may often be stagnant and turbid. We present our best practices technique for the detection of wild pig eDNA in water samples, a protocol that will have wide applicability to the detection of elusive vertebrate species. We determined the best practice for eDNA capture in a turbid water system was to concentrate DNA from a 15 mL water sample via centrifugation, purify DNA with the DNeasy mericon Food kit, and remove inhibitors with Zymo Inhibitor Removal Technology columns. Further, we compared the sensitivity of conventional PCR to quantitative PCR and found that quantitative PCR was more sensitive in detecting lower concentrations of eDNA. We show significant differences in efficiencies among methods in each step of eDNA capture, emphasizing the importance of optimizing best practices for the system of interest.}, }
@article {pmid28686570, year = {2017}, author = {Mendes, LW and Braga, LPP and Navarrete, AA and Souza, DG and Silva, GGZ and Tsai, SM}, title = {Using Metagenomics to Connect Microbial Community Biodiversity and Functions.}, journal = {Current issues in molecular biology}, volume = {24}, number = {}, pages = {103-118}, doi = {10.21775/cimb.024.103}, pmid = {28686570}, issn = {1467-3045}, abstract = {Microbes constitute about a third of the Earth's biomass and are composed by an enormous genetic diversity. In a majority of environments the microbial communities play crucial roles for the ecosystem functioning, where a drastic biodiversity alteration or loss could lead to negative effects on the environment and sustainability. A central goal in microbiome studies is to elucidate the relation between microbial diversity to functions. A better understanding of the relation diversity-function would increase the ability to manipulate that diversity to improve plant and animal health and also setting conservation priorities. The recent advances in genomic methodologies in microbial ecology have provide means to assess highly complex communities in detail, making possible the link between diversity and the functions performed by the microbes. In this work we first explore some advances in bioinformatics tools to connect the microbial community biodiversity to their potential metabolism and after present some examples of how this information can be useful for a better understanding of the microbial role in the environment.}, }
@article {pmid28683828, year = {2017}, author = {Ren, J and Ahlgren, NA and Lu, YY and Fuhrman, JA and Sun, F}, title = {VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {69}, doi = {10.1186/s40168-017-0283-5}, pmid = {28683828}, issn = {2049-2618}, support = {R01 GM120624/GM/NIGMS NIH HHS/United States ; }, mesh = {Computational Biology/methods ; DNA, Viral/*genetics ; Gastrointestinal Microbiome ; *Genome, Viral ; Humans ; Liver Cirrhosis/virology ; Machine Learning ; Metagenome ; Metagenomics/*methods ; Phylogeny ; Sequence Analysis, DNA ; *Software ; }, abstract = {BACKGROUND: Identifying viral sequences in mixed metagenomes containing both viral and host contigs is a critical first step in analyzing the viral component of samples. Current tools for distinguishing prokaryotic virus and host contigs primarily use gene-based similarity approaches. Such approaches can significantly limit results especially for short contigs that have few predicted proteins or lack proteins with similarity to previously known viruses.
METHODS: We have developed VirFinder, the first k-mer frequency based, machine learning method for virus contig identification that entirely avoids gene-based similarity searches. VirFinder instead identifies viral sequences based on our empirical observation that viruses and hosts have discernibly different k-mer signatures. VirFinder's performance in correctly identifying viral sequences was tested by training its machine learning model on sequences from host and viral genomes sequenced before 1 January 2014 and evaluating on sequences obtained after 1 January 2014.
RESULTS: VirFinder had significantly better rates of identifying true viral contigs (true positive rates (TPRs)) than VirSorter, the current state-of-the-art gene-based virus classification tool, when evaluated with either contigs subsampled from complete genomes or assembled from a simulated human gut metagenome. For example, for contigs subsampled from complete genomes, VirFinder had 78-, 2.4-, and 1.8-fold higher TPRs than VirSorter for 1, 3, and 5 kb contigs, respectively, at the same false positive rates as VirSorter (0, 0.003, and 0.006, respectively), thus VirFinder works considerably better for small contigs than VirSorter. VirFinder furthermore identified several recently sequenced virus genomes (after 1 January 2014) that VirSorter did not and that have no nucleotide similarity to previously sequenced viruses, demonstrating VirFinder's potential advantage in identifying novel viral sequences. Application of VirFinder to a set of human gut metagenomes from healthy and liver cirrhosis patients reveals higher viral diversity in healthy individuals than cirrhosis patients. We also identified contig bins containing crAssphage-like contigs with higher abundance in healthy patients and a putative Veillonella genus prophage associated with cirrhosis patients.
CONCLUSIONS: This innovative k-mer based tool complements gene-based approaches and will significantly improve prokaryotic viral sequence identification, especially for metagenomic-based studies of viral ecology.}, }
@article {pmid28680419, year = {2017}, author = {Cabello-Yeves, PJ and Haro-Moreno, JM and Martin-Cuadrado, AB and Ghai, R and Picazo, A and Camacho, A and Rodriguez-Valera, F}, title = {Novel Synechococcus Genomes Reconstructed from Freshwater Reservoirs.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1151}, doi = {10.3389/fmicb.2017.01151}, pmid = {28680419}, issn = {1664-302X}, abstract = {Freshwater picocyanobacteria including Synechococcus remain poorly studied at the genomic level, compared to their marine representatives. Here, using a metagenomic assembly approach we discovered two novel Synechococcus sp. genomes from two freshwater reservoirs Tous and Lake Lanier, both sharing 96% average nucleotide identity and displaying high abundance levels in these two lakes located at similar altitudes and temperate latitudes. These new genomes have the smallest estimated size (2.2 Mb) and average intergenic spacer length (20 bp) of any previously sequenced freshwater Synechococcus, which may contribute to their success in oligotrophic freshwater systems. Fluorescent in situ hybridization confirmed that Synechococcus sp. Tous comprises small cells (0.987 ± 0.139 μm length, 0.723 ± 0.119 μm width) that amount to 90% of the picocyanobacteria in Tous. They appear together in a phylogenomic tree with Synechococcus sp. RCC307 strain, the main representative of sub-cluster 5.3 that has itself one of the smallest marine Synechococcus genomes. We detected a type II phycobilisome (PBS) gene cluster in both genomes, which suggests that they belong to a phycoerythrin-rich pink low-light ecotype. The decrease of acidic proteins and the higher content of basic transporters and membrane proteins in the novel Synechococcus genomes, compared to marine representatives, support their freshwater specialization. A sulfate Cys transporter which is absent in marine but has been identified in many freshwater cyanobacteria was also detected in Synechococcus sp. Tous. The RuBisCo subunits from this microbe are phylogenetically close to the freshwater amoeba Paulinella chromatophora symbiont, hinting to a freshwater origin of the carboxysome operon of this protist. The novel genomes enlarge the known diversity of freshwater Synechococcus and improve the overall knowledge of the relationships among members of this genus at large.}, }
@article {pmid28679747, year = {2017}, author = {Malik, AA and Thomson, BC and Whiteley, AS and Bailey, M and Griffiths, RI}, title = {Bacterial Physiological Adaptations to Contrasting Edaphic Conditions Identified Using Landscape Scale Metagenomics.}, journal = {mBio}, volume = {8}, number = {4}, pages = {}, doi = {10.1128/mBio.00799-17}, pmid = {28679747}, issn = {2150-7511}, mesh = {*Adaptation, Physiological ; Bacteria/*genetics ; *Bacterial Physiological Phenomena ; Biodiversity ; Ecosystem ; Genome, Bacterial ; Hydrogen-Ion Concentration ; Metagenomics/*methods ; Phylogeny ; Soil/chemistry ; *Soil Microbiology ; United Kingdom ; }, abstract = {Environmental factors relating to soil pH are important regulators of bacterial taxonomic biodiversity, yet it remains unclear if such drivers affect community functional potential. To address this, we applied whole-genome metagenomics to eight geographically distributed soils at opposing ends of a landscape soil pH gradient (where "low-pH" is ~pH 4.3 and "high-pH" is ~pH 8.3) and evaluated functional differences with respect to functionally annotated genes. First, differences in taxonomic and functional diversity between the two pH categories were assessed with respect to alpha diversity (mean sample richness) and gamma diversity (total richness pooled for each pH category). Low-pH soils, also exhibiting higher organic matter and moisture, consistently had lower taxonomic alpha and gamma diversity, but this was not apparent in assessments of functional alpha and gamma diversity. However, coherent changes in the relative abundances of annotated genes between low- and high-pH soils were identified; with strong multivariate clustering of samples according to pH independent of geography. Assessment of indicator genes revealed that the acidic organic-rich soils possessed a greater abundance of cation efflux pumps, C and N direct fixation systems, and fermentation pathways, indicating adaptations to both acidity and anaerobiosis. Conversely, high-pH soils possessed more direct transporter-mediated mechanisms for organic C and N substrate acquisition. These findings highlight the distinctive physiological adaptations required for bacteria to survive in soils of various nutrient availability and edaphic conditions and more generally indicate that bacterial functional versatility with respect to functional gene annotations may not be constrained by taxonomy.IMPORTANCE Over a set of soil samples spanning Britain, the widely reported reductions in bacterial taxonomic richness at low pH were found not to be accompanied by significant reductions in the richness of functional genes. However, consistent changes in the abundance of related functional genes were observed, characteristic of differential ecological and nutrient acquisition strategies between high-pH mineral soils and low-pH organic anaerobic soils. Our assessment at opposing ends of a soil gradient encapsulates the limits of functional diversity in temperate climates and identifies key pathways that may serve as indicators for soil element cycling and C storage processes in other soil systems. To this end, we make available a data set identifying functional indicators of the different soils; as well as raw sequences, which given the geographic scale of our sampling should be of value in future studies assessing novel genetic diversity of a wide range of soil functional attributes.}, }
@article {pmid28677677, year = {2017}, author = {Coutinho, FH and Silveira, CB and Gregoracci, GB and Thompson, CC and Edwards, RA and Brussaard, CPD and Dutilh, BE and Thompson, FL}, title = {Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans.}, journal = {Nature communications}, volume = {8}, number = {}, pages = {15955}, doi = {10.1038/ncomms15955}, pmid = {28677677}, issn = {2041-1723}, abstract = {Marine viruses are key drivers of host diversity, population dynamics and biogeochemical cycling and contribute to the daily flux of billions of tons of organic matter. Despite recent advancements in metagenomics, much of their biodiversity remains uncharacterized. Here we report a data set of 27,346 marine virome contigs that includes 44 complete genomes. These outnumber all currently known phage genomes in marine habitats and include members of previously uncharacterized lineages. We designed a new method for host prediction based on co-occurrence associations that reveals these viruses infect dominant members of the marine microbiome such as Prochlorococcus and Pelagibacter. A negative association between host abundance and the virus-to-host ratio supports the recently proposed Piggyback-the-Winner model of reduced phage lysis at higher host densities. An analysis of the abundance patterns of viruses throughout the oceans revealed how marine viral communities adapt to various seasonal, temperature and photic regimes according to targeted hosts and the diversity of auxiliary metabolic genes.}, }
@article {pmid28677326, year = {2017}, author = {Jacob, JH and Hussein, EI and Shakhatreh, MAK and Cornelison, CT}, title = {Microbial community analysis of the hypersaline water of the Dead Sea using high-throughput amplicon sequencing.}, journal = {MicrobiologyOpen}, volume = {6}, number = {5}, pages = {}, doi = {10.1002/mbo3.500}, pmid = {28677326}, issn = {2045-8827}, mesh = {Bacteria/classification/genetics ; Biodiversity ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; *Salinity ; Seawater/*chemistry/*microbiology ; *Water Microbiology ; }, abstract = {Amplicon sequencing using next-generation technology (bTEFAP®) has been utilized in describing the diversity of Dead Sea microbiota. The investigated area is a well-known salt lake in the western part of Jordan found in the lowest geographical location in the world (more than 420 m below sea level) and characterized by extreme salinity (approximately, 34%) in addition to other extreme conditions (low pH, unique ionic composition different from sea water). DNA was extracted from Dead Sea water. A total of 314,310 small subunit RNA (SSU rRNA) sequences were parsed, and 288,452 sequences were then clustered. For alpha diversity analysis, sample was rarefied to 3,000 sequences. The Shannon-Wiener index curve plot reached a plateau at approximately 3,000 sequences indicating that sequencing depth was sufficient to capture the full scope of microbial diversity. Archaea was found to be dominating the sequences (52%), whereas Bacteria constitute 45% of the sequences. Altogether, prokaryotic sequences (which constitute 97% of all sequences) were found to predominate. The findings expand on previous studies by using high-throughput amplicon sequencing to describe the microbial community in an environment which in recent years has been shown to hide some interesting diversity.}, }
@article {pmid28677262, year = {2017}, author = {Mikaelyan, A and Thompson, CL and Meuser, K and Zheng, H and Rani, P and Plarre, R and Brune, A}, title = {High-resolution phylogenetic analysis of Endomicrobia reveals multiple acquisitions of endosymbiotic lineages by termite gut flagellates.}, journal = {Environmental microbiology reports}, volume = {9}, number = {5}, pages = {477-483}, doi = {10.1111/1758-2229.12565}, pmid = {28677262}, issn = {1758-2229}, mesh = {Animals ; Bacteria/classification/genetics ; DNA, Intergenic ; *Gastrointestinal Microbiome ; Insecta/microbiology ; *Metagenome ; *Metagenomics/methods ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; *Symbiosis ; }, abstract = {Bacteria of the class Endomicrobia form a deep-branching clade in the Elusimicrobia phylum. They are found almost exclusively in the intestinal tract of animals and are particularly abundant in many termites, where they reside as intracellular symbionts in the cellulolytic gut flagellates. Although small populations of putatively free-living lineages have been detected in faunated and flagellate-free hosts, the evolutionary origin of the endosymbionts is obscured by the limited amount of phylogenetic information provided by the 16S rRNA gene fragment amplified with Endomicrobia-specific primers. Here, we present a robust phylogenetic framework based on the near-full-length 16S-23S rRNA gene region of a diverse set of Endomicrobia from termites and cockroaches, which also allowed us to classify the shorter reads from previous studies. Our data revealed that endosymbionts arose independently at least four times from different free-living lineages, which were already present in ancestral cockroaches but became associated with their respective hosts long after the digestive symbiosis between termites and flagellates had been established. Pyrotag sequencing revealed that the proportion of putatively free-living lineages increased, when all flagellates and their symbionts were removed from the gut of lower termites by starvation, starch feeding or hyperbaric oxygen, but results varied between different methods.}, }
@article {pmid28676106, year = {2017}, author = {Yun, Y and Kim, HN and Kim, SE and Heo, SG and Chang, Y and Ryu, S and Shin, H and Kim, HL}, title = {Comparative analysis of gut microbiota associated with body mass index in a large Korean cohort.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {151}, doi = {10.1186/s12866-017-1052-0}, pmid = {28676106}, issn = {1471-2180}, mesh = {Adult ; Bacteria/*classification/genetics ; Body Mass Index ; Cross-Sectional Studies ; DNA, Bacterial/genetics ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics ; Middle Aged ; Obesity/*microbiology ; Overweight/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Gut microbiota plays an important role in the harvesting, storage, and expenditure of energy obtained from one's diet. Our cross-sectional study aimed to identify differences in gut microbiota according to body mass index (BMI) in a Korean population. 16S rRNA gene sequence data from 1463 subjects were categorized by BMI into normal, overweight, and obese groups. Fecal microbiotas were compared to determine differences in diversity and functional inference analysis related with BMI. The correlation between genus-level microbiota and BMI was tested using zero-inflated Gaussian mixture models, with or without covariate adjustment of nutrient intake.
RESULTS: We confirmed differences between 16Sr RNA gene sequencing data of each BMI group, with decreasing diversity in the obese compared with the normal group. According to analysis of inferred metagenomic functional content using PICRUSt algorithm, a highly significant discrepancy in metabolism and immune functions (P < 0.0001) was predicted in the obese group. Differential taxonomic components in each BMI group were greatly affected by nutrient adjustment, whereas signature bacteria were not influenced by nutrients in the obese compared with the overweight group.
CONCLUSIONS: We found highly significant statistical differences between normal, overweight and obese groups using a large sample size with or without diet confounding factors. Our informative dataset sheds light on the epidemiological study on population microbiome.}, }
@article {pmid28673401, year = {2017}, author = {Renz, H and Holt, PG and Inouye, M and Logan, AC and Prescott, SL and Sly, PD}, title = {An exposome perspective: Early-life events and immune development in a changing world.}, journal = {The Journal of allergy and clinical immunology}, volume = {140}, number = {1}, pages = {24-40}, doi = {10.1016/j.jaci.2017.05.015}, pmid = {28673401}, issn = {1097-6825}, mesh = {Animals ; Diet ; *Environmental Exposure ; Gastrointestinal Tract/microbiology ; Humans ; Immune System/*growth & development ; Microbiota ; }, abstract = {Advances in metagenomics, proteomics, metabolomics, and systems biology are providing a new emphasis in research; interdisciplinary work suggests that personalized medicine is on the horizon. These advances are illuminating sophisticated interactions between human-associated microbes and the immune system. The result is a transformed view of future prevention and treatment of chronic noncommunicable diseases, including allergy. Paradigm-shifting gains in scientific knowledge are occurring at a time of rapid global environmental change, urbanization, and biodiversity losses. Multifactorial and multigenerational implications of total environmental exposures, the exposome, require coordinated interdisciplinary efforts. It is clear that the genome alone cannot provide answers to urgent questions. Here we review the historical origins of exposome research and define a new concept, the metaexposome, which considers the bidirectional effect of the environment on human subjects and the human influence on all living systems and their genomes. The latter is essential for human health. We place the metaexposome in the context of early-life immune functioning and describe how various aspects of a changing environment, especially through microbiota exposures, can influence health and disease over the life course.}, }
@article {pmid28673041, year = {2017}, author = {Bengtsson-Palme, J and Larsson, DGJ and Kristiansson, E}, title = {Using metagenomics to investigate human and environmental resistomes.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {72}, number = {10}, pages = {2690-2703}, doi = {10.1093/jac/dkx199}, pmid = {28673041}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/*pharmacology ; Chromosome Mapping/methods ; Data Interpretation, Statistical ; Databases, Genetic ; Drug Resistance, Bacterial/*genetics ; Gastrointestinal Microbiome/genetics ; Genes, Bacterial/drug effects ; Geologic Sediments/microbiology ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Lakes/microbiology ; Metagenomics/*methods ; Microbiota/*genetics ; }, abstract = {Antibiotic resistance is a global health concern declared by the WHO as one of the largest threats to modern healthcare. In recent years, metagenomic DNA sequencing has started to be applied as a tool to study antibiotic resistance in different environments, including the human microbiota. However, a multitude of methods exist for metagenomic data analysis, and not all methods are suitable for the investigation of resistance genes, particularly if the desired outcome is an assessment of risks to human health. In this review, we outline the current state of methods for sequence handling, mapping to databases of resistance genes, statistical analysis and metagenomic assembly. In addition, we provide an overview of important considerations related to the analysis of resistance genes, and recommend some of the currently used tools and methods that are best equipped to inform research and clinical practice related to antibiotic resistance.}, }
@article {pmid28673033, year = {2017}, author = {Corcoll, N and Österlund, T and Sinclair, L and Eiler, A and Kristiansson, E and Backhaus, T and Eriksson, KM}, title = {Comparison of four DNA extraction methods for comprehensive assessment of 16S rRNA bacterial diversity in marine biofilms using high-throughput sequencing.}, journal = {FEMS microbiology letters}, volume = {364}, number = {14}, pages = {}, doi = {10.1093/femsle/fnx139}, pmid = {28673033}, issn = {1574-6968}, mesh = {Bacteria/*genetics ; Biodiversity ; *Biofilms ; DNA, Bacterial/analysis/genetics/*isolation & purification ; DNA, Ribosomal/analysis/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Molecular Biology/*methods ; Periphyton/*genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {High-throughput DNA sequencing technologies are increasingly used for the metagenomic characterisation of microbial biodiversity. However, basic issues, such as the choice of an appropriate DNA extraction method, are still not resolved for non-model microbial communities. This study evaluates four commonly used DNA extraction methods for marine periphyton biofilms in terms of DNA yield, efficiency, purity, integrity and resulting 16S rRNA bacterial diversity. Among the tested methods, the Plant DNAzol® Reagent (PlantDNAzol) and the FastDNA® SPIN Kit for Soil (FastDNA Soil) methods were best suited to extract high quantities of DNA (77-130 μg g wet wt-1). Lower amounts of DNA were obtained (<37 μg g wet wt-1) with the Power Plant® Pro DNA Isolation Kit (PowerPlant) and the Power Biofilm® DNA Isolation Kit (PowerBiofilm) methods, but integrity and purity of the extracted DNA were higher. Results from 16S rRNA amplicon sequencing demonstrate that the choice of a DNA extraction method significantly influences the bacterial community profiles generated. A higher number of bacterial OTUs were detected when DNA was extracted with the PowerBiofilm and the PlantDNAzol methods. Overall, this study demonstrates the potential bias in metagenomic diversity estimates associated with different DNA extraction methods.}, }
@article {pmid28671295, year = {2017}, author = {Xu, L and Zhu, Y and Ren, L and Xu, B and Liu, C and Xie, Z and Shen, K}, title = {Characterization of the nasopharyngeal viral microbiome from children with community-acquired pneumonia but negative for Luminex xTAG respiratory viral panel assay detection.}, journal = {Journal of medical virology}, volume = {89}, number = {12}, pages = {2098-2107}, doi = {10.1002/jmv.24895}, pmid = {28671295}, issn = {1096-9071}, mesh = {Child, Preschool ; Community-Acquired Infections/*virology ; Female ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Infant ; Male ; Metagenomics/methods ; Microbiota/*genetics ; Molecular Diagnostic Techniques ; Nasopharynx/*virology ; Parainfluenza Virus 3, Human/genetics/isolation & purification ; Pneumonia/diagnosis/*virology ; Respiratory System/virology ; Respiratory Tract Infections/virology ; Sensitivity and Specificity ; Viruses/classification/genetics/*isolation & purification ; }, abstract = {In the present study, 50 nasopharyngeal swabs from children with community-acquired pneumonia (CAP) but negative for 18 common respiratory viruses, as measured by the Luminex xTAG Respiratory Viral Panel Assay, were subjected to multiplex metagenomic analyses using a next-generation sequencing platform. Taxonomic analysis showed that all sequence reads could be assigned to a specific species. An average of 95.13% were assigned to the Bacteria kingdom, whereas, only 0.72% were potentially virus derived. This snapshot of the respiratory tract virome revealed most viral reads to be respiratory tract related, classified into four known virus families: Paramyxoviridae, Herpesviridae, Anelloviridae, and Polyomaviridae. Importantly, we detected a novel human parainfluenza virus 3 (HPIV 3) strain with a 32-bp insertion in the haemagglutinin-neuraminidase (HN) gene that produced a negative result in the Luminex assay, highlighting the strength of virome metagenomic analysis to identify not only novel viruses but also viruses likely to be missed by ordinary clinical tests. Thus, virome metagenomic analysis could become a viable clinical diagnostic method.}, }
@article {pmid28669650, year = {2017}, author = {Malone, M and Johani, K and Jensen, SO and Gosbell, IB and Dickson, HG and Hu, H and Vickery, K}, title = {Next Generation DNA Sequencing of Tissues from Infected Diabetic Foot Ulcers.}, journal = {EBioMedicine}, volume = {21}, number = {}, pages = {142-149}, doi = {10.1016/j.ebiom.2017.06.026}, pmid = {28669650}, issn = {2352-3964}, mesh = {Aged ; Biodiversity ; Diabetic Foot/diagnosis/*microbiology ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Severity of Illness Index ; }, abstract = {We used next generation DNA sequencing to profile the microbiome of infected Diabetic Foot Ulcers (DFUs). The microbiota was correlated to clinical parameters and treatment outcomes to determine if directed antimicrobial therapy based on conventional microbiological cultures are relevant based on genomic analysis. Patients≥18years presenting with a new Diabetic Foot Infection (DFI) who had not received topical or oral antimicrobials in the two weeks prior to presentation, were eligible for enrolment. Tissue punch biopsies were obtained from infected DFUs for analysis. Demographics, clinical and laboratory data were collected and correlated against microbiota data. Thirty-nine patients with infected DFUs were recruited over twelve-months. Shorter duration DFUs (
OBJECTIVE: To compare the relative amounts of Akkermansia muciniphila, Clostridium leptum, Faecalibacterium prausnitzii, and Enterobacteriaceae as members of gut microbiota among patients with chronic urticaria (CU) and healthy controls.
METHODS: A total of 20 patients with CU and 20 healthy individuals matched by age and sex participated in the study. Fresh fecal samples were collected, and DNA extracted from stool samples was analyzed by real-time polymerase chain reaction for the qualitative and quantitative assays of the so-called bacteria.
RESULTS: The frequencies of A muciniphila, C leptum, and F prausnitzii in healthy controls' stool samples were significantly more than those of patients with CU (P < .001, P < .01, and P < .05, respectively), whereas the Enterobacteriaceae family was detected in all patients and healthy controls' stool samples. The relative amounts of A muciniphila in healthy control positive samples were significantly higher than those of samples from patients with CU (P < .001). Furthermore, there was a corresponding increase of relative amounts of C leptum and F prausnitzii in healthy control positive samples compared with those of patients with CU (P = .09 and P = .08, respectively). The mean of the relative amounts of Enterobacteriaceae family in the stool samples from patients with CU was more than that of healthy controls; however, the difference was nearly significant (P = .12).
CONCLUSION: The results reveal a change of frequency and relative amounts of A muciniphila, C leptum, and F prausnitzii in patients with CU compared with healthy controls. This is the first study, to our knowledge, to show the change of microbiota composition in patients with CU.}, }
@article {pmid28665922, year = {2017}, author = {Ravi, A and Estensmo, ELF and Abée-Lund, TML and Foley, SL and Allgaier, B and Martin, CR and Claud, EC and Rudi, K}, title = {Association of the gut microbiota mobilome with hospital location and birth weight in preterm infants.}, journal = {Pediatric research}, volume = {82}, number = {5}, pages = {829-838}, doi = {10.1038/pr.2017.146}, pmid = {28665922}, issn = {1530-0447}, mesh = {*Birth Weight ; Case-Control Studies ; Computational Biology ; DNA, Bacterial/*genetics ; Databases, Genetic ; Enterocolitis, Necrotizing/diagnosis/epidemiology/*microbiology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Genome, Bacterial ; Gestational Age ; Humans ; Infant, Newborn ; *Infant, Premature ; *Infant, Very Low Birth Weight ; *Interspersed Repetitive Sequences ; Male ; Metagenome ; Metagenomics/methods ; Premature Birth/diagnosis/epidemiology/*microbiology ; Ribotyping ; United States/epidemiology ; }, abstract = {BackgroundThe preterm infant gut microbiota is vulnerable to different biotic and abiotic factors. Although the development of this microbiota has been extensively studied, the mobilome-i.e. the mobile genetic elements (MGEs) in the gut microbiota-has not been considered. Therefore, the aim of this study was to investigate the association of the mobilome with birth weight and hospital location in the preterm infant gut microbiota.MethodsThe data set consists of fecal samples from 62 preterm infants with and without necrotizing enterocolitis (NEC) from three different hospitals. We analyzed the gut microbiome by using 16S rRNA amplicon sequencing, shot-gun metagenome sequencing, and quantitative PCR. Predictive models and other data analyses were performed using MATLAB and QIIME.ResultSThe microbiota composition was significantly different between NEC-positive and NEC-negative infants and significantly different between hospitals. An operational taxanomic unit (OTU) showed strong positive and negative correlation with NEC and birth weight, respectively, whereas none showed significance for mode of delivery. Metagenome analyses revealed high levels of conjugative plasmids with MGEs and virulence genes. Results from quantitative PCR showed that the plasmid signature genes were significantly different between hospitals and in NEC-positive infants.ConclusionOur results point toward an association of the mobilome with hospital location in preterm infants.}, }
@article {pmid28663049, year = {2017}, author = {Heyer, R and Schallert, K and Zoun, R and Becher, B and Saake, G and Benndorf, D}, title = {Challenges and perspectives of metaproteomic data analysis.}, journal = {Journal of biotechnology}, volume = {261}, number = {}, pages = {24-36}, doi = {10.1016/j.jbiotec.2017.06.1201}, pmid = {28663049}, issn = {1873-4863}, mesh = {Environmental Microbiology ; Mass Spectrometry ; *Metagenomics ; *Microbial Consortia ; *Proteomics ; Software ; }, abstract = {In nature microorganisms live in complex microbial communities. Comprehensive taxonomic and functional knowledge about microbial communities supports medical and technical application such as fecal diagnostics as well as operation of biogas plants or waste water treatment plants. Furthermore, microbial communities are crucial for the global carbon and nitrogen cycle in soil and in the ocean. Among the methods available for investigation of microbial communities, metaproteomics can approximate the activity of microorganisms by investigating the protein content of a sample. Although metaproteomics is a very powerful method, issues within the bioinformatic evaluation impede its success. In particular, construction of databases for protein identification, grouping of redundant proteins as well as taxonomic and functional annotation pose big challenges. Furthermore, growing amounts of data within a metaproteomics study require dedicated algorithms and software. This review summarizes recent metaproteomics software and addresses the introduced issues in detail.}, }
@article {pmid28660691, year = {2017}, author = {Sambles, C and Moore, K and Lux, TM and Jones, K and Littlejohn, GR and Gouveia, JD and Aves, SJ and Studholme, DJ and Lee, R and Love, J}, title = {Metagenomic analysis of the complex microbial consortium associated with cultures of the oil-rich alga Botryococcus braunii.}, journal = {MicrobiologyOpen}, volume = {6}, number = {4}, pages = {}, doi = {10.1002/mbo3.482}, pmid = {28660691}, issn = {2045-8827}, support = {//Wellcome Trust/United Kingdom ; BB/K003240/2//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/K003240/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/M008924/1//Medical Research Council/United Kingdom ; WT097835MF//Wellcome Trust/United Kingdom ; WT101650MA//Wellcome Trust/United Kingdom ; }, mesh = {Bacteria/*classification/genetics/growth & development/*isolation & purification ; Chlorophyta/*growth & development ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Metagenomics ; *Microbial Consortia ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Microalgae are widely viewed as a promising and sustainable source of renewable chemicals and biofuels. Botryococcus braunii synthesizes and secretes significant amounts of long-chain (C30 -C40) hydrocarbons that can be subsequently converted into gasoline, diesel, and aviation fuel. B. braunii cultures are not axenic and the effects of co-cultured microorganisms on B. braunii growth and hydrocarbon yield are important, but sometimes contradictory. To understand the composition of the B. braunii microbial consortium, we used high throughput Illumina sequencing of metagenomic DNA to profile the microbiota within a well established, stable B. braunii culture and characterized the demographic changes in the microcosm following modification to the culture conditions. DNA sequences attributed to B. braunii were present in equal quantities in all treatments, whereas sequences assigned to the associated microbial community were dramatically altered. Bacterial species least affected by treatments, and more robustly associated with the algal cells, included members of Rhizobiales, comprising Bradyrhizobium and Methylobacterium, and representatives of Dyadobacter, Achromobacter and Asticcacaulis. The presence of bacterial species identified by metagenomics was confirmed by additional 16S rDNA analysis of bacterial isolates. Our study demonstrates the advantages of high throughput sequencing and robust metagenomic analyses to define microcosms and further our understanding of microbial ecology.}, }
@article {pmid28655556, year = {2017}, author = {Koo, H and Hakim, JA and Morrow, CD and Eipers, PG and Davila, A and Andersen, DT and Bej, AK}, title = {Comparison of two bioinformatics tools used to characterize the microbial diversity and predictive functional attributes of microbial mats from Lake Obersee, Antarctica.}, journal = {Journal of microbiological methods}, volume = {140}, number = {}, pages = {15-22}, doi = {10.1016/j.mimet.2017.06.017}, pmid = {28655556}, issn = {1872-8359}, support = {UL1 TR001417/TR/NCATS NIH HHS/United States ; P30 AR050948/AR/NIAMS NIH HHS/United States ; P30 AI027767/AI/NIAID NIH HHS/United States ; }, mesh = {Antarctic Regions ; Computational Biology/*methods ; Cyanobacteria/genetics ; Databases, Factual ; *Genetic Variation ; High-Throughput Nucleotide Sequencing ; Lakes/*microbiology ; Metagenome ; Metagenomics/methods ; Microbial Consortia/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In this study, using NextGen sequencing of the collective 16S rRNA genes obtained from two sets of samples collected from Lake Obersee, Antarctica, we compared and contrasted two bioinformatics tools, PICRUSt and Tax4Fun. We then developed an R script to assess the taxonomic and predictive functional profiles of the microbial communities within the samples. Taxa such as Pseudoxanthomonas, Planctomycetaceae, Cyanobacteria Subsection III, Nitrosomonadaceae, Leptothrix, and Rhodobacter were exclusively identified by Tax4Fun that uses SILVA database; whereas PICRUSt that uses Greengenes database uniquely identified Pirellulaceae, Gemmatimonadetes A1-B1, Pseudanabaena, Salinibacterium and Sinobacteraceae. Predictive functional profiling of the microbial communities using Tax4Fun and PICRUSt separately revealed common metabolic capabilities, while also showing specific functional IDs not shared between the two approaches. Combining these functional predictions using a customized R script revealed a more inclusive metabolic profile, such as hydrolases, oxidoreductases, transferases; enzymes involved in carbohydrate and amino acid metabolisms; and membrane transport proteins known for nutrient uptake from the surrounding environment. Our results present the first molecular-phylogenetic characterization and predictive functional profiles of the microbial mat communities in Lake Obersee, while demonstrating the efficacy of combining both the taxonomic assignment information and functional IDs using the R script created in this study for a more streamlined evaluation of predictive functional profiles of microbial communities.}, }
@article {pmid28655159, year = {2017}, author = {He, Q and Gao, Y and Jie, Z and Yu, X and Laursen, JM and Xiao, L and Li, Y and Li, L and Zhang, F and Feng, Q and Li, X and Yu, J and Liu, C and Lan, P and Yan, T and Liu, X and Xu, X and Yang, H and Wang, J and Madsen, L and Brix, S and Wang, J and Kristiansen, K and Jia, H}, title = {Two distinct metacommunities characterize the gut microbiota in Crohn's disease patients.}, journal = {GigaScience}, volume = {6}, number = {7}, pages = {1-11}, doi = {10.1093/gigascience/gix050}, pmid = {28655159}, issn = {2047-217X}, mesh = {Adolescent ; Adult ; Case-Control Studies ; Crohn Disease/diet therapy/*microbiology ; Enteral Nutrition/adverse effects/methods ; Fatty Acids/metabolism ; Female ; *Gastrointestinal Microbiome ; Humans ; Lipopolysaccharides/metabolism ; Male ; Metagenome ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The inflammatory intestinal disorder Crohn's disease (CD) has become a health challenge worldwide. The gut microbiota closely interacts with the host immune system, but its functional impact in CD is unclear. Except for studies on a small number of CD patients, analyses of the gut microbiota in CD have used 16S rDNA amplicon sequencing. Here we employed metagenomic shotgun sequencing to provide a detailed characterization of the compositional and functional features of the CD microbiota, comprising also unannotated bacteria, and investigated its modulation by exclusive enteral nutrition. Based on signature taxa, CD microbiotas clustered into 2 distinct metacommunities, indicating individual variability in CD microbiome structure. Metacommunity-specific functional shifts in CD showed enrichment in producers of the pro-inflammatory hexa-acylated lipopolysaccharide variant and a reduction in the potential to synthesize short-chain fatty acids. Disruption of ecological networks was evident in CD, coupled with reduction in growth rates of many bacterial species. Short-term exclusive enteral nutrition elicited limited impact on the overall composition of the CD microbiota, although functional changes occurred following treatment. The microbiotas in CD patients can be stratified into 2 distinct metacommunities, with the most severely perturbed metacommunity exhibiting functional potentials that deviate markedly from that of the healthy individuals, with possible implication in relation to CD pathogenesis.}, }
@article {pmid28654183, year = {2017}, author = {Zhang, Y and Oh, S and Liu, WT}, title = {Impact of drinking water treatment and distribution on the microbiome continuum: an ecological disturbance's perspective.}, journal = {Environmental microbiology}, volume = {19}, number = {8}, pages = {3163-3174}, doi = {10.1111/1462-2920.13800}, pmid = {28654183}, issn = {1462-2920}, mesh = {Bacteria/classification/genetics/growth & development/*isolation & purification ; Disinfection ; Drinking Water/*microbiology ; Groundwater/microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Water Purification/*methods ; }, abstract = {While microbes are known to be present at different stages of a drinking water system, their potential functions and ability to grow in such systems are poorly understood. In this study, we demonstrated that treatment and distribution processes could be viewed as ecological disturbances exhibited over space on the microbiome continuum in a groundwater-derived system. Results from 16S rRNA gene amplicon analysis and metagenomics suggested that disturbances in the system were intense as the community diversity was substantially reduced during the treatment steps. Specifically, syntrophs and methanogens dominant in raw water (RW) disappeared after water abstraction, accompanied by a substantial decrease in both the abundance and number of functional genes related to methanogenesis. The softening effluent was dominated by an Exiguobacterium-related population, likely due to its ability to use the phosphotransferase system (PTS) as regulatory machinery to control the energy conditions of the cell. After disinfection and entering the distribution system, community-level functionality remained relatively stable, whereas the community structure differed from those taken in the treatment steps. The diversity and high abundance of some eukaryotic groups in the system suggested that predation could be a disturbance to the bacterial microbiome, which could further drive the diversification of the bacterial community.}, }
@article {pmid28654083, year = {2017}, author = {Siegwald, L and Audebert, C and Even, G and Viscogliosi, E and Caboche, S and Chabé, M}, title = {Targeted metagenomic sequencing data of human gut microbiota associated with Blastocystis colonization.}, journal = {Scientific data}, volume = {4}, number = {}, pages = {170081}, doi = {10.1038/sdata.2017.81}, pmid = {28654083}, issn = {2052-4463}, mesh = {*Blastocystis ; Gastrointestinal Microbiome/*genetics ; Humans ; *Metagenomics ; Sequence Analysis ; }, abstract = {In the past decade, metagenomics studies have become widespread due to the arrival of second-generation sequencing platforms characterized by low costs, high throughput and short read lengths. Today, although benchtop sequencers are considered to be accurate platforms to deliver data for targeted metagenomics studies, the limiting factor has become the analysis of these data. In a previous paper, we performed an Ion Torrent PGM 16S rDNA gene sequencing of faecal DNAs from 48 Blastocystis-colonized patients and 48 Blastocystis-negative subjects, in order to decipher the impact of this widespread protist on gut microbiota composition and diversity. We report here on the Ion Torrent targeted metagenomic sequencing and analysis of these 96 human faecal samples, and the complete datasets from raw to analysed data. We also provide the key steps of the bioinformatic analyses, from library preparation to data filtering and OTUs tables generation. This data represents a valuable resource for the scientific community, enabling re-processing of these targeted metagenomic datasets through various pipelines and a comparative evaluation of microbiota analysis methods.}, }
@article {pmid28651652, year = {2017}, author = {Andersen, VD and DE Knegt, LV and Munk, P and Jensen, MS and Agersø, Y and Aarestrup, FM and Vigre, H}, title = {The association between measurements of antimicrobial use and resistance in the faeces microbiota of finisher batches.}, journal = {Epidemiology and infection}, volume = {145}, number = {13}, pages = {2827-2837}, doi = {10.1017/S0950268817001285}, pmid = {28651652}, issn = {1469-4409}, mesh = {Animals ; Anti-Infective Agents/administration & dosage/*pharmacology ; Denmark ; *Drug Resistance, Microbial ; Feces/*microbiology ; Microbial Sensitivity Tests/veterinary ; Microbiota/*drug effects ; Sus scrofa/*microbiology ; }, abstract = {The objectives were to present three approaches for calculating antimicrobial (AM) use in pigs that take into account the rearing period and rearing site, and to study the association between these measurements and phenotypical resistance and abundance of resistance genes in faeces samples from 10 finisher batches. The AM use was calculated relative to the rearing period of the batches as (i) 'Finisher Unit Exposure' at unit level, (ii) 'Lifetime Exposure' at batch level and (iii) 'Herd Exposure' at herd level. A significant effect on the occurrence of tetracycline resistance measured by cultivation was identified for Lifetime Exposure for the AM class: tetracycline. Furthermore, for Lifetime Exposure for the AM classes: macrolide, broad-spectrum penicillin, sulfonamide and tetracycline use as well as Herd Unit Exposure for the AM classes: aminoglycoside, lincosamide and tetracycline use, a significant effect was observed on the occurrence of genes coding for the AM resistance classes: aminoglycoside, lincosamide, macrolide, β-lactam, sulfonamide and tetracycline. No effect was observed for Finisher Unit Exposure. Overall, the study shows that Lifetime Exposure is an efficient measurement of AM use in finisher batches, and has a significant effect on the occurrence of resistance, measured either by cultivation or metagenomics.}, }
@article {pmid28646502, year = {2018}, author = {Yip, LY and Aw, CC and Lee, SH and Hong, YS and Ku, HC and Xu, WH and Chan, JMX and Cheong, EJY and Chng, KR and Ng, AHQ and Nagarajan, N and Mahendran, R and Lee, YK and Browne, ER and Chan, ECY}, title = {The liver-gut microbiota axis modulates hepatotoxicity of tacrine in the rat.}, journal = {Hepatology (Baltimore, Md.)}, volume = {67}, number = {1}, pages = {282-295}, doi = {10.1002/hep.29327}, pmid = {28646502}, issn = {1527-3350}, mesh = {Animals ; Biopsy, Needle ; Chemical and Drug Induced Liver Injury/*etiology/pathology ; Disease Models, Animal ; Dose-Response Relationship, Drug ; Gastrointestinal Microbiome/*drug effects ; Immunohistochemistry ; Liver Function Tests ; Male ; Random Allocation ; Rats ; Rats, Inbred Strains ; Reference Values ; Severity of Illness Index ; Tacrine/pharmacokinetics/pharmacology/*toxicity ; }, abstract = {The gut microbiota possesses diverse metabolic activities, but its contribution toward heterogeneous toxicological responses is poorly understood. In this study, we investigated the role of the liver-gut microbiota axis in underpinning the hepatotoxicity of tacrine. We employed an integrated strategy combining pharmacokinetics, toxicology, metabonomics, genomics, and metagenomics to elucidate and validate the mechanism of tacrine-induced hepatotoxicity in Lister hooded rats. Pharmacokinetic studies in rats demonstrated 3.3-fold higher systemic exposure to tacrine in strong responders that experienced transaminitis, revealing enhanced enterohepatic recycling of deglucuronidated tacrine in this subgroup, not attributable to variation in hepatic disposition gene expression. Metabonomic studies implicated variations in gut microbial activities that mapped onto tacrine-induced transaminitis. Metagenomics delineated greater deglucuronidation capabilities in strong responders, based on differential gut microbial composition (e.g., Lactobacillus, Bacteroides, and Enterobacteriaceae) and approximately 9% higher β-glucuronidase gene abundance compared with nonresponders. In the validation study, coadministration with oral β-glucuronidase derived from Escherichia coli and pretreatment with vancomycin and imipenem significantly modulated the susceptibility to tacrine-induced transaminitis in vivo.
CONCLUSION: This study establishes pertinent gut microbial influences in modifying the hepatotoxicity of tacrine, providing insights for personalized medicine initiatives. (Hepatology 2018;67:282-295).}, }
@article {pmid28632934, year = {2018}, author = {Savage, JH and Lee-Sarwar, KA and Sordillo, J and Bunyavanich, S and Zhou, Y and O'Connor, G and Sandel, M and Bacharier, LB and Zeiger, R and Sodergren, E and Weinstock, GM and Gold, DR and Weiss, ST and Litonjua, AA}, title = {A prospective microbiome-wide association study of food sensitization and food allergy in early childhood.}, journal = {Allergy}, volume = {73}, number = {1}, pages = {145-152}, doi = {10.1111/all.13232}, pmid = {28632934}, issn = {1398-9995}, support = {R01 HL091528/HL/NHLBI NIH HHS/United States ; R01 HL108818/HL/NHLBI NIH HHS/United States ; T32 AI007306/AI/NIAID NIH HHS/United States ; R01 AI118833/AI/NIAID NIH HHS/United States ; K23 AI110522/AI/NIAID NIH HHS/United States ; }, mesh = {Allergens/immunology ; Biodiversity ; Child, Preschool ; Female ; Food Hypersensitivity/*epidemiology/*immunology ; Gastrointestinal Microbiome ; Humans ; *Immunization ; Immunoglobulin E/immunology ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota/immunology ; }, abstract = {BACKGROUND: Alterations in the intestinal microbiome are prospectively associated with the development of asthma; less is known regarding the role of microbiome alterations in food allergy development.
METHODS: Intestinal microbiome samples were collected at age 3-6 months in children participating in the follow-up phase of an interventional trial of high-dose vitamin D given during pregnancy. At age 3, sensitization to foods (milk, egg, peanut, soy, wheat, walnut) was assessed. Food allergy was defined as caretaker report of healthcare provider-diagnosed allergy to the above foods prior to age 3 with evidence of IgE sensitization. Analysis was performed using Phyloseq and DESeq2; P-values were adjusted for multiple comparisons.
RESULTS: Complete data were available for 225 children; there were 87 cases of food sensitization and 14 cases of food allergy. Microbial diversity measures did not differ between food sensitization and food allergy cases and controls. The genera Haemophilus (log2 fold change -2.15, P=.003), Dialister (log2 fold change -2.22, P=.009), Dorea (log2 fold change -1.65, P=.02), and Clostridium (log2 fold change -1.47, P=.002) were underrepresented among subjects with food sensitization. The genera Citrobacter (log2 fold change -3.41, P=.03), Oscillospira (log2 fold change -2.80, P=.03), Lactococcus (log2 fold change -3.19, P=.05), and Dorea (log2 fold change -3.00, P=.05) were underrepresented among subjects with food allergy.
CONCLUSIONS: The temporal association between bacterial colonization and food sensitization and allergy suggests that the microbiome may have a causal role in the development of food allergy. Our findings have therapeutic implications for the prevention and treatment of food allergy.}, }
@article {pmid28631400, year = {2017}, author = {Sutcliffe, B and Chariton, AA and Harford, AJ and Hose, GC and Greenfield, P and Elbourne, LDH and Oytam, Y and Stephenson, S and Midgley, DJ and Paulsen, IT}, title = {Effects of uranium concentration on microbial community structure and functional potential.}, journal = {Environmental microbiology}, volume = {19}, number = {8}, pages = {3323-3341}, doi = {10.1111/1462-2920.13839}, pmid = {28631400}, issn = {1462-2920}, mesh = {ATP-Binding Cassette Transporters/genetics ; Australia ; Bacteria/classification/*genetics/metabolism ; Base Sequence ; Carbon/metabolism ; Carbon Cycle/*genetics ; Ecosystem ; Geologic Sediments/*chemistry/microbiology ; Metagenomics ; Methane/metabolism ; Microbial Consortia/*drug effects ; Mining ; Nitrogen/metabolism ; Nitrogen Cycle/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Uranium/metabolism/pharmacology ; }, abstract = {Located in the Northern Territory of Australia, Ranger uranium mine is directly adjacent to the UNESCO World Heritage listed Kakadu National Park, with rehabilitation targets needed to ensure the site can be incorporated into the park following the mine's closure in 2026. This study aimed to understand the impact of uranium concentration on microbial communities, in order to identify and describe potential breakpoints in microbial ecosystem services. This is the first study to report in situ deployment of uranium-spiked sediments along a concentration gradient (0-4000 mg U kg-1), with the study design maximising the advantages of both field surveys and laboratory manipulative studies. Changes to microbial communities were characterised through the use of amplicon and shotgun metagenomic next-generation sequencing. Significant changes to taxonomic and functional community assembly occurred at a concentration of 1500 mg U kg-1 sediment and above. At uranium concentrations of ≥ 1500 mg U kg-1 , genes associated with methanogenic consortia and processes increased in relative abundance, while numerous significant changes were also seen in the relative abundances of genes involved in nitrogen cycling. Such alterations in carbon and nitrogen cycling pathways suggest that taxonomic and functional changes to microbial communities may result in changes in ecosystem processes and resilience.}, }
@article {pmid28625159, year = {2017}, author = {Marotz, C and Amir, A and Humphrey, G and Gaffney, J and Gogul, G and Knight, R}, title = {DNA extraction for streamlined metagenomics of diverse environmental samples.}, journal = {BioTechniques}, volume = {62}, number = {6}, pages = {290-293}, doi = {10.2144/000114559}, pmid = {28625159}, issn = {1940-9818}, mesh = {Bacteria/*genetics/isolation & purification ; DNA, Bacterial/genetics/*isolation & purification ; Feces/microbiology ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/*methods ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; Sequence Analysis, DNA/methods ; Skin/microbiology ; Soil Microbiology ; Water Microbiology ; }, abstract = {A major bottleneck for metagenomic sequencing is rapid and efficient DNA extraction. Here, we compare the extraction efficiencies of three magnetic bead-based platforms (KingFisher, epMotion, and Tecan) to a standardized column-based extraction platform across a variety of sample types, including feces, oral, skin, soil, and water. Replicate sample plates were extracted and prepared for 16S rRNA gene amplicon sequencing in parallel to assess extraction bias and DNA quality. The data demonstrate that any effect of extraction method on sequencing results was small compared with the variability across samples; however, the KingFisher platform produced the largest number of high-quality reads in the shortest amount of time. Based on these results, we have identified an extraction pipeline that dramatically reduces sample processing time without sacrificing bacterial taxonomic or abundance information.}, }
@article {pmid28624689, year = {2017}, author = {Clavel, T and Lagkouvardos, I and Stecher, B}, title = {From complex gut communities to minimal microbiomes via cultivation.}, journal = {Current opinion in microbiology}, volume = {38}, number = {}, pages = {148-155}, doi = {10.1016/j.mib.2017.05.013}, pmid = {28624689}, issn = {1879-0364}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Mammals ; Metagenomics/*methods ; Microbiological Techniques/*methods ; }, abstract = {The mammalian gut microbiota is dominated by populations of bacteria, mostly strict anaerobes. Because these bacteria can influence the health of their host, it is important to investigate their diversity and functions, which can be done via culture-based or molecular approaches. In recent years, microbiologists have very often preferred the use of molecular techniques, as they do not limit the analysis to the fraction of communities that can be grown in the laboratory. In reality, cultivation and molecular methods are complementary, and we are now witnessing a period of unification. Obtaining strains that can be grown in vitro is currently indispensable for the description of novel diversity and eventually the improvement of taxonomic and sequence databases. Moreover, cultivation allows using host-specific minimal consortia of microbes that are helpful for detailed and standardized studies of gut microbial communities and microbe-host interactions. Molecular techniques are helpful because they can provide insights into strain-level diversity and the functional potential of organisms. Furthermore, genomic and metagenomic data allow inferring growth conditions for uncultured bacteria and also enable detailed genetic studies. In the present manuscript, we highlight recent work on culture-based investigation of mammalian gut bacteria and microbe-host interactions and give our opinions on challenges and perspectives in the field.}, }
@article {pmid28623024, year = {2017}, author = {Weisse, T}, title = {Functional diversity of aquatic ciliates.}, journal = {European journal of protistology}, volume = {61}, number = {Pt B}, pages = {331-358}, doi = {10.1016/j.ejop.2017.04.001}, pmid = {28623024}, issn = {1618-0429}, mesh = {*Biodiversity ; Ciliophora/*classification/*physiology ; Fresh Water ; }, abstract = {This paper first reviews the concept of functional diversity in general terms and then applies it to free-living aquatic ciliates. Ciliates are extremely versatile organisms and display an enormous functional diversity as key elements of pelagic food webs, acting as predators of bacteria, algae, other protists and even some metazoans. Planktonic ciliates are important food for zooplankton, and mixotrophic and functionally autotrophic species may significantly contribute to primary production in the ocean and in lakes. The co-occurrence of many ciliate species in seemingly homogenous environments indicates a wide range of their ecological niches. Variation in space and time may foster co-occurrence and prevent violating the competitive exclusion principle among ciliates using the same resources. Considering that many ciliates may be dormant and/or rare in many habitats, ciliate species diversity must be higher than can be deduced from simple sampling techniques; molecular methods of identification clearly point to this hidden diversity. From a functional point of view, the question is how much of this diversity represents redundancy. A key challenge for future research is to link the ecophysiological performance of naturally co-occurring ciliates to their functional genes. To this end, more experimental research is needed with with functionally different species.}, }
@article {pmid28610994, year = {2017}, author = {Chi, L and Gao, B and Bian, X and Tu, P and Ru, H and Lu, K}, title = {Manganese-induced sex-specific gut microbiome perturbations in C57BL/6 mice.}, journal = {Toxicology and applied pharmacology}, volume = {331}, number = {}, pages = {142-153}, doi = {10.1016/j.taap.2017.06.008}, pmid = {28610994}, issn = {1096-0333}, support = {P30 ES010126/ES/NIEHS NIH HHS/United States ; R01 ES024950/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Female ; Gastrointestinal Microbiome/*drug effects/physiology ; Gastrointestinal Tract/drug effects/physiology ; Male ; Manganese/*administration & dosage/*toxicity ; Mice ; Mice, Inbred C57BL ; *Sex Characteristics ; }, abstract = {Overexposure to manganese (Mn) leads to toxic effects, such as promoting the development of Parkinson's-like neurological disorders. The gut microbiome is deeply involved in immune development, host metabolism, and xenobiotics biotransformation, and significantly influences central nervous system (CNS) via the gut-brain axis, i.e. the biochemical signaling between the gastrointestinal tract and the CNS. However, it remains unclear whether Mn can affect the gut microbiome and its metabolic functions, particularly those linked to neurotoxicity. In addition, sex-specific effects of Mn have been reported, with no mechanism being identified yet. Recently, we have shown that the gut microbiome is largely different between males and females, raising the possibility that differential gut microbiome responses may contribute to sex-selective toxicity of Mn. Here, we applied high-throughput sequencing and gas chromatography-mass spectrometry (GC-MS) metabolomics to explore how Mn2+ exposure affects the gut microbiome and its metabolism in C57BL/6 mice. Mn2+ exposure perturbed the gut bacterial compositions, functional genes and fecal metabolomes in a highly sex-specific manner. In particular, bacterial genes and/or key metabolites of neurotransmitter synthesis and pro-inflammatory mediators are significantly altered by Mn2+ exposure, which can potentially affect chemical signaling of gut-brain interactions. Likewise, functional genes involved in iron homeostasis, flagellar motility, quorum sensing, and Mn transportation/oxidation are also widely changed by Mn2+ exposure. Taken together, this study has demonstrated that Mn2+ exposure perturbs the gut microbiome and its metabolic functions, which highlights the potential role of the gut microbiome in Mn2+ toxicity, particularly its sex-specific toxic effects.}, }
@article {pmid28609785, year = {2017}, author = {Philips, A and Stolarek, I and Kuczkowska, B and Juras, A and Handschuh, L and Piontek, J and Kozlowski, P and Figlerowicz, M}, title = {Comprehensive analysis of microorganisms accompanying human archaeological remains.}, journal = {GigaScience}, volume = {6}, number = {7}, pages = {1-13}, doi = {10.1093/gigascience/gix044}, pmid = {28609785}, issn = {2047-217X}, mesh = {Archaeology/*methods ; Bone and Bones/microbiology ; *DNA, Ancient ; Fossils/microbiology ; Humans ; Metagenome ; *Microbiota ; Sequence Analysis, DNA/methods ; }, abstract = {Metagenome analysis has become a common source of information about microbial communities that occupy a wide range of niches, including archaeological specimens. It has been shown that the vast majority of DNA extracted from ancient samples come from bacteria (presumably modern contaminants). However, characterization of microbial DNA accompanying human remains has never been done systematically for a wide range of different samples. We used metagenomic approaches to perform comparative analyses of microorganism communities present in 161 archaeological human remains. DNA samples were isolated from the teeth of human skeletons dated from 100 AD to 1200 AD. The skeletons were collected from 7 archaeological sites in Central Europe and stored under different conditions. The majority of identified microbes were ubiquitous environmental bacteria that most likely contaminated the host remains not long ago. We observed that the composition of microbial communities was sample-specific and not correlated with its temporal or geographical origin. Additionally, traces of bacteria and archaea typical for human oral/gut flora, as well as potential pathogens, were identified in two-thirds of the samples. The genetic material of human-related species, in contrast to the environmental species that accounted for the majority of identified bacteria, displayed DNA damage patterns comparable with endogenous human ancient DNA, which suggested that these microbes might have accompanied the individual before death. Our study showed that the microbiome observed in an individual sample is not reliant on the method or duration of sample storage. Moreover, shallow sequencing of DNA extracted from ancient specimens and subsequent bioinformatics analysis allowed both the identification of ancient microbial species, including potential pathogens, and their differentiation from contemporary species that colonized human remains more recently.}, }
@article {pmid28606169, year = {2017}, author = {Gao, B and Tu, P and Bian, X and Chi, L and Ru, H and Lu, K}, title = {Profound perturbation induced by triclosan exposure in mouse gut microbiome: a less resilient microbial community with elevated antibiotic and metal resistomes.}, journal = {BMC pharmacology & toxicology}, volume = {18}, number = {1}, pages = {46}, doi = {10.1186/s40360-017-0150-9}, pmid = {28606169}, issn = {2050-6511}, support = {P30 ES010126/ES/NIEHS NIH HHS/United States ; R01 ES024950/ES/NIEHS NIH HHS/United States ; }, mesh = {Administration, Oral ; Animals ; Anti-Infective Agents, Local/*pharmacology ; Drinking Water ; Drug Resistance, Microbial/genetics ; Gastrointestinal Microbiome/*drug effects/genetics ; Metagenomics ; Metals, Heavy/toxicity ; Mice, Inbred C57BL ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Triclosan/*pharmacology ; }, abstract = {BACKGROUND: Environmental chemical-induced perturbations of gut microbiome are associated with a series of adverse health outcomes. The effects of triclosan on human health have been controversial in recent years. The purpose of this study is to investigate the functional impact of triclosan on the mouse gut microbiome and the link between triclosan exposure and resistomes in gut bacteria.
METHODS: We combined 16S rRNA gene sequencing and shotgun metagenomics sequencing to examine the compositional and functional impact of triclosan exposure on the gut microbiota of C57BL/6 mice.
RESULTS: 16S rRNA sequencing results revealed that 13-week triclosan exposure in drinking water induced significant perturbations in mouse gut bacterial assemblages with distinct trajectories compared to controls. Metagenomics sequencing results indicated a remarkable enrichment of gut bacterial genes related to triclosan resistance, stress response, antibiotic resistance and heavy metal resistance.
CONCLUSIONS: Triclosan exposure has a profound impact on the mouse gut microbiome by inducing perturbations at both compositional and functional levels. To our best knowledge, this is the first evidence regarding the functional alterations of gut microbiome induced by triclosan exposure, which may provide novel mechanistic insights into triclosan exposure and associated diseases.}, }
@article {pmid28605130, year = {2017}, author = {Martín-Peláez, S and Camps-Bossacoma, M and Massot-Cladera, M and Rigo-Adrover, M and Franch, À and Pérez-Cano, FJ and Castell, M}, title = {Effect of cocoa's theobromine on intestinal microbiota of rats.}, journal = {Molecular nutrition & food research}, volume = {61}, number = {10}, pages = {}, doi = {10.1002/mnfr.201700238}, pmid = {28605130}, issn = {1613-4133}, mesh = {Animals ; Bifidobacterium/drug effects/isolation & purification ; Butyric Acid/metabolism ; Cacao/*chemistry ; Clostridium histolyticum/drug effects/isolation & purification ; Colony Count, Microbial ; DNA, Bacterial/genetics ; Diet ; Escherichia coli/drug effects/isolation & purification ; Fatty Acids, Volatile/metabolism ; Feces/microbiology ; Fermentation ; Gastrointestinal Microbiome/*drug effects ; Immunoglobulin A/metabolism ; In Situ Hybridization, Fluorescence ; Lactic Acid/metabolism ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Inbred Lew ; Streptococcus/drug effects/isolation & purification ; Theobromine/*pharmacology ; }, abstract = {SCOPE: To establish the role of cocoa theobromine on gut microbiota composition and fermentation products after cocoa consumption in rats.
METHODS AND RESULTS: Lewis rats were fed either a standard diet (RF diet), a diet containing 10% cocoa (CC diet) or a diet including 0.25% theobromine (TB diet) for 15 days. Gut microbiota (fluorescence in situ hybridization coupled to flow cytometry and metagenomics analysis), SCFA and IgA-coated bacteria were analyzed in fecal samples. CC and TB diets induced lower counts of E. coli whereas TB diet led to lower counts of Bifidobacterium spp., Streptococcus spp. and Clostridium histolyticum-C. perfingens group compared to RF diet. Metagenomics analysis also revealed a different microbiota pattern among the studied groups. The SCFA content was higher after both CC and TB diets, which was mainly due to enhanced butyric acid production. Furthermore, both diets decreased the proportion of IgA-coated bacteria.
CONCLUSION: Cocoa's theobromine plays a relevant role in some effects related to cocoa intake, such as the lower proportion of IgA-coated bacteria. Moreover, theobromine modifies gut microbiota although other cocoa compounds could also act on intestinal bacteria, attenuating or enhancing the theobromine effects.}, }
@article {pmid28603873, year = {2017}, author = {Ushio, M and Fukuda, H and Inoue, T and Makoto, K and Kishida, O and Sato, K and Murata, K and Nikaido, M and Sado, T and Sato, Y and Takeshita, M and Iwasaki, W and Yamanaka, H and Kondoh, M and Miya, M}, title = {Environmental DNA enables detection of terrestrial mammals from forest pond water.}, journal = {Molecular ecology resources}, volume = {17}, number = {6}, pages = {e63-e75}, doi = {10.1111/1755-0998.12690}, pmid = {28603873}, issn = {1755-0998}, mesh = {Animals ; DNA/genetics/*isolation & purification ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; *Forests ; Japan ; Mammals/*classification/genetics ; Metagenomics/*methods ; *Ponds ; Water/*analysis ; }, abstract = {Terrestrial animals must have frequent contact with water to survive, implying that environmental DNA (eDNA) originating from those animals should be detectable from places containing water in terrestrial ecosystems. Aiming to detect the presence of terrestrial mammals using forest water samples, we applied a set of universal PCR primers (MiMammal, a modified version of fish universal primers) for metabarcoding mammalian eDNA. The versatility of MiMammal primers was tested in silico and by amplifying DNAs extracted from tissues. The results suggested that MiMammal primers are capable of amplifying and distinguishing a diverse group of mammalian species. In addition, analyses of water samples from zoo cages of mammals with known species composition suggested that MiMammal primers could successfully detect mammalian species from water samples in the field. Then, we performed an experiment to detect mammals from natural ecosystems by collecting five 500-ml water samples from ponds in two cool-temperate forests in Hokkaido, northern Japan. MiMammal amplicon libraries were constructed using eDNA extracted from water samples, and sequences generated by Illumina MiSeq were subjected to data processing and taxonomic assignment. We thereby detected multiple species of mammals common to the sampling areas, including deer (Cervus nippon), mouse (Mus musculus), vole (Myodes rufocanus), raccoon (Procyon lotor), rat (Rattus norvegicus) and shrew (Sorex unguiculatus). Many previous applications of the eDNA metabarcoding approach have been limited to aquatic/semiaquatic systems, but the results presented here show that the approach is also promising even for forest mammal biodiversity surveys.}, }
@article {pmid28602995, year = {2017}, author = {Wang, H and Zheng, H and Browne, F and Roehe, R and Dewhurst, RJ and Engel, F and Hemmje, M and Lu, X and Walsh, P}, title = {Integrated metagenomic analysis of the rumen microbiome of cattle reveals key biological mechanisms associated with methane traits.}, journal = {Methods (San Diego, Calif.)}, volume = {124}, number = {}, pages = {108-119}, doi = {10.1016/j.ymeth.2017.05.029}, pmid = {28602995}, issn = {1095-9130}, mesh = {Animals ; Archaeal Proteins/classification/*genetics/metabolism ; Bacterial Proteins/classification/*genetics/metabolism ; Cattle ; Fungal Proteins/classification/*genetics/metabolism ; Gastrointestinal Microbiome/*genetics ; Gene Ontology ; Metabolic Networks and Pathways/genetics ; *Metagenome ; Metagenomics/methods ; Methane/*biosynthesis ; Molecular Sequence Annotation ; Oxidoreductases/classification/genetics/metabolism ; Protozoan Proteins/classification/*genetics/metabolism ; Rumen/microbiology ; }, abstract = {Methane is one of the major contributors to global warming. The rumen microbiota is directly involved in methane production in cattle. The link between variation in rumen microbial communities and host genetics has important applications and implications in bioscience. Having the potential to reveal the full extent of microbial gene diversity and complex microbial interactions, integrated metagenomics and network analysis holds great promise in this endeavour. This study investigates the rumen microbial community in cattle through the integration of metagenomic and network-based approaches. Based on the relative abundance of 1570 microbial genes identified in a metagenomics analysis, the co-abundance network was constructed and functional modules of microbial genes were identified. One of the main contributions is to develop a random matrix theory-based approach to automatically determining the correlation threshold used to construct the co-abundance network. The resulting network, consisting of 549 microbial genes and 3349 connections, exhibits a clear modular structure with certain trait-specific genes highly over-represented in modules. More specifically, all the 20 genes previously identified to be associated with methane emissions are found in a module (hypergeometric test, p<10-11). One third of genes are involved in methane metabolism pathways. The further examination of abundance profiles across 8 samples of genes highlights that the revealed pattern of metagenomics abundance has a strong association with methane emissions. Furthermore, the module is significantly enriched with microbial genes encoding enzymes that are directly involved in methanogenesis (hypergeometric test, p<10-9).}, }
@article {pmid28595639, year = {2017}, author = {Wolff, SM and Ellison, MJ and Hao, Y and Cockrum, RR and Austin, KJ and Baraboo, M and Burch, K and Lee, HJ and Maurer, T and Patil, R and Ravelo, A and Taxis, TM and Truong, H and Lamberson, WR and Cammack, KM and Conant, GC}, title = {Diet shifts provoke complex and variable changes in the metabolic networks of the ruminal microbiome.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {60}, doi = {10.1186/s40168-017-0274-6}, pmid = {28595639}, issn = {2049-2618}, mesh = {Animal Feed/analysis ; Animals ; *Diet ; Digestion/physiology ; Edible Grain ; Feeding Behavior ; Gastrointestinal Microbiome/*physiology ; *Metabolic Networks and Pathways ; *Metagenomics ; Rumen/*microbiology/physiology ; Sheep/*microbiology/physiology ; }, abstract = {BACKGROUND: Grazing mammals rely on their ruminal microbial symbionts to convert plant structural biomass into metabolites they can assimilate. To explore how this complex metabolic system adapts to the host animal's diet, we inferred a microbiome-level metabolic network from shotgun metagenomic data.
RESULTS: Using comparative genomics, we then linked this microbial network to that of the host animal using a set of interface metabolites likely to be transferred to the host. When the host sheep were fed a grain-based diet, the induced microbial metabolic network showed several critical differences from those seen on the evolved forage-based diet. Grain-based (e.g., concentrate) diets tend to be dominated by a smaller set of reactions that employ metabolites that are nearer in network space to the host's metabolism. In addition, these reactions are more central in the network and employ substrates with shorter carbon backbones. Despite this apparent lower complexity, the concentrate-associated metabolic networks are actually more dissimilar from each other than are those of forage-fed animals. Because both groups of animals were initially fed on a forage diet, we propose that the diet switch drove the appearance of a number of different microbial networks, including a degenerate network characterized by an inefficient use of dietary nutrients. We used network simulations to show that such disparate networks are not an unexpected result of a diet shift.
CONCLUSION: We argue that network approaches, particularly those that link the microbial network with that of the host, illuminate aspects of the structure of the microbiome not seen from a strictly taxonomic perspective. In particular, different diets induce predictable and significant differences in the enzymes used by the microbiome. Nonetheless, there are clearly a number of microbiomes of differing structure that show similar functional properties. Changes such as a diet shift uncover more of this type of diversity.}, }
@article {pmid28593475, year = {2017}, author = {Ottoni, JR and Cabral, L and de Sousa, STP and Júnior, GVL and Domingos, DF and Soares Junior, FL and da Silva, MCP and Marcon, J and Dias, ACF and de Melo, IS and de Souza, AP and Andreote, FD and de Oliveira, VM}, title = {Functional metagenomics of oil-impacted mangrove sediments reveals high abundance of hydrolases of biotechnological interest.}, journal = {World journal of microbiology & biotechnology}, volume = {33}, number = {7}, pages = {141}, doi = {10.1007/s11274-017-2307-5}, pmid = {28593475}, issn = {1573-0972}, mesh = {Bacteria/*classification/enzymology/genetics/isolation & purification ; Bacterial Proteins/genetics ; Biodiversity ; Brazil ; Genomic Library ; Geologic Sediments/*microbiology ; High-Throughput Nucleotide Sequencing ; Hydrolases/*genetics ; Metagenomics/*methods ; Petroleum Pollution/adverse effects ; Phylogeny ; Sequence Analysis, DNA ; Soil Microbiology ; Wetlands ; }, abstract = {Mangroves are located in coastal wetlands and are susceptible to the consequences of oil spills, what may threaten the diversity of microorganisms responsible for the nutrient cycling and the consequent ecosystem functioning. Previous reports show that high concentration of oil favors the incidence of epoxide hydrolases and haloalkane dehalogenases in mangroves. This finding has guided the goals of this study in an attempt to broaden the analysis to other hydrolases and thereby verify whether oil contamination interferes with the prevalence of particular hydrolases and their assigned microorganisms. For this, an in-depth survey of the taxonomic and functional microbial diversity recovered in a fosmid library (Library_Oil Mgv) constructed from oil-impacted Brazilian mangrove sediment was carried out. Fosmid DNA of the whole library was extracted and submitted to Illumina HiSeq sequencing. The resulting Library Oil_Mgv dataset was further compared with those obtained by direct sequencing of environmental DNA from Brazilian mangroves (from distinct regions and affected by distinct sources of contamination), focusing on hydrolases with potential use in biotechnological processes. The most abundant hydrolases found were proteases, esterases and amylases, with similar occurrence profile in all datasets. The main microbial groups harboring such hydrolase-encoding genes were distinct in each mangrove, and in the fosmid library these enzymes were mainly assigned to Chloroflexaceae (for amylases), Planctomycetaceae (for esterases) and Bradyrhizobiaceae (for proteases). Assembly and analysis of Library_Oil Mgv reads revealed three potentially novel enzymes, one epoxide hydrolase, one xylanase and one amylase, to be further investigated via heterologous expression assays.}, }
@article {pmid28586542, year = {2017}, author = {Andújar, C and Arribas, P and Vogler, AP}, title = {Terra incognita of soil biodiversity: unseen invasions under our feet.}, journal = {Molecular ecology}, volume = {26}, number = {12}, pages = {3087-3089}, doi = {10.1111/mec.14112}, pmid = {28586542}, issn = {1365-294X}, abstract = {Whilst cartographers of the 19th century endeavoured to chart the last unknown lands, the great challenge for biologists in the 21st century is to fill the gaps on the biodiversity map of the Earth. And one of the largest gaps concerns the biodiversity of soils, a terra incognita right under our feet. The study of soil biodiversity, and particularly the complex communities of small invertebrates, has suffered from a severe 'taxonomic impediment' (Decaëns) leading to great uncertainties about total species richness, phylogenetic diversity, geographical structure, temporal dynamics of soil organisms, and consequently about their role on ecosystem function (Bardgett & van der Putten). However, the revolution in high-throughput sequencing is now revealing the hidden biodiversity of the soil with unprecedented detail (e.g. Arribas et al.). In a noteworthy from the Cover article in this issue of Molecular Ecology, Cicconardi et al. () apply these new tools to study soil communities of Collembola in three distant oceanic islands of volcanic origin, obtaining a striking result: only 38 of 70 species (54%) are exclusively found in a single island, with the remaining shared among islands or with other distant regions, suggesting a massive recent introduction of soil species, whose impact is entirely unknown.}, }
@article {pmid28585938, year = {2017}, author = {Borrel, G and McCann, A and Deane, J and Neto, MC and Lynch, DB and Brugère, JF and O'Toole, PW}, title = {Genomics and metagenomics of trimethylamine-utilizing Archaea in the human gut microbiome.}, journal = {The ISME journal}, volume = {11}, number = {9}, pages = {2059-2074}, doi = {10.1038/ismej.2017.72}, pmid = {28585938}, issn = {1751-7370}, mesh = {Aged ; Aged, 80 and over ; Animals ; Archaea/classification/*genetics/isolation & purification/*metabolism ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Genomics ; Humans ; Male ; Metagenome ; Metagenomics ; Methylamines/*metabolism ; Microbiota ; Phylogeny ; }, abstract = {The biological significance of Archaea in the human gut microbiota is largely unclear. We recently reported genomic and biochemical analyses of the Methanomassiliicoccales, a novel order of methanogenic Archaea dwelling in soil and the animal digestive tract. We now show that these Methanomassiliicoccales are present in published microbiome data sets from eight countries. They are represented by five Operational Taxonomic Units present in at least four cohorts and phylogenetically distributed into two clades. Genes for utilizing trimethylamine (TMA), a bacterial precursor to an atherosclerogenic human metabolite, were present in four of the six novel Methanomassiliicoccales genomes assembled from ELDERMET metagenomes. In addition to increased microbiota TMA production capacity in long-term residential care subjects, abundance of TMA-utilizing Methanomassiliicoccales correlated positively with bacterial gene count for TMA production and negatively with fecal TMA concentrations. The two large Methanomassiliicoccales clades have opposite correlations with host health status in the ELDERMET cohort and putative distinct genomic signatures for gut adaptation.}, }
@article {pmid28576763, year = {2017}, author = {Gill, AS and Lee, A and McGuire, KL}, title = {Phylogenetic and Functional Diversity of Total (DNA) and Expressed (RNA) Bacterial Communities in Urban Green Infrastructure Bioswale Soils.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {16}, pages = {}, doi = {10.1128/AEM.00287-17}, pmid = {28576763}, issn = {1098-5336}, mesh = {Bacteria/classification/genetics/*isolation & purification/metabolism ; Biodiversity ; DNA, Bacterial/genetics ; Hydrocarbons/metabolism ; New York City ; *Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Urban Renewal ; }, abstract = {New York City (NYC) is pioneering green infrastructure with the use of bioswales and other engineered soil-based habitats to provide stormwater infiltration and other ecosystem functions. In addition to avoiding the environmental and financial costs of expanding traditional built infrastructure, green infrastructure is thought to generate cobenefits in the form of diverse ecological processes performed by its plant and microbial communities. Yet, although plant communities in these habitats are closely managed, we lack basic knowledge about how engineered ecosystems impact the distribution and functioning of soil bacteria. We sequenced amplicons of the 16S ribosomal subunit, as well as seven genes associated with functional pathways, generated from both total (DNA-based) and expressed (RNA) soil communities in the Bronx, NYC, NY, in order to test whether bioswale soils host characteristic bacterial communities with evidence for enriched microbial functioning, compared to nonengineered soils in park lawns and tree pits. Bioswales had distinct, phylogenetically diverse bacterial communities, including taxa associated with nutrient cycling and metabolism of hydrocarbons and other pollutants. Bioswale soils also had a significantly greater diversity of genes involved in several functional pathways, including carbon fixation (cbbL-R [cbbL gene, red-like subunit] and apsA), nitrogen cycling (noxZ and amoA), and contaminant degradation (bphA); conversely, no functional genes were significantly more abundant in nonengineered soils. These results provide preliminary evidence that urban land management can shape the diversity and activity of soil communities, with positive consequences for genetic resources underlying valuable ecological functions, including biogeochemical cycling and degradation of common urban pollutants.IMPORTANCE Management of urban soil biodiversity by favoring taxa associated with decontamination or other microbial metabolic processes is a powerful prospect, but it first requires an understanding of how engineered soil habitats shape patterns of microbial diversity. This research adds to our understanding of urban microbial biogeography by providing data on soil bacteria in bioswales, which had relatively diverse and compositionally distinct communities compared to park and tree pit soils. Bioswales also contained comparatively diverse pools of genes related to carbon sequestration, nitrogen cycling, and contaminant degradation, suggesting that engineered soils may serve as effective reservoirs of functional microbial biodiversity. We also examined both total (DNA-based) and expressed (RNA) communities, revealing that total bacterial communities (the exclusive targets in the vast majority of soil studies) were poor predictors of expressed community diversity, pointing to the value of quantifying RNA, especially when ecological functioning is considered.}, }
@article {pmid28576366, year = {2017}, author = {Lee, M and Song, JH and Jung, MY and Lee, SH and Chang, JY}, title = {Large-scale targeted metagenomics analysis of bacterial ecological changes in 88 kimchi samples during fermentation.}, journal = {Food microbiology}, volume = {66}, number = {}, pages = {173-183}, doi = {10.1016/j.fm.2017.05.002}, pmid = {28576366}, issn = {1095-9998}, mesh = {Bacteria/classification/genetics/isolation & purification/*metabolism ; *Biodiversity ; Brassica/metabolism/*microbiology ; Fermentation ; Metagenomics ; Vegetables/metabolism/*microbiology ; }, abstract = {The microbial communities in kimchi vary widely, but the precise effects of differences in region of origin, ingredients, and preparation method on the microbiota are unclear. We analyzed the bacterial community composition of household (n = 69) and commercial (n = 19) kimchi samples obtained from six Korean provinces between April and August 2015. Samples were analyzed by barcoded pyrosequencing targeting the V1-V3 region of the 16S ribosomal RNA gene. The initial pH of the kimchi samples was 5.00-6.39, and the salt concentration was 1.72-4.42%. Except for sampling locality, all categorical variables, i.e., salt concentration, major ingredient, fermentation period, sampling time, and manufacturing process, influenced the bacterial community composition. Particularly, samples were highly clustered by sampling time and salt concentration in non-metric multidimensional scaling plots and an analysis of similarity. These results indicated that the microbial community differed according to fermentation conditions such as salt concentration, major ingredient, fermentation period, and sampling time. Furthermore, fermentation properties, including pH, acidity, salt concentration, and microbial abundance differed between kimchi samples from household and commercial sources. Analyses of changes in bacterial ecology during fermentation will improve our understanding of the biological properties of kimchi, as well as the relationships between these properties and the microbiota of kimchi.}, }
@article {pmid28576115, year = {2017}, author = {Esmaeili Taheri, A and Chatterton, S and Gossen, BD and McLaren, DL}, title = {Metagenomic analysis of oomycete communities from the rhizosphere of field pea on the Canadian prairies.}, journal = {Canadian journal of microbiology}, volume = {63}, number = {9}, pages = {758-768}, doi = {10.1139/cjm-2017-0099}, pmid = {28576115}, issn = {1480-3275}, mesh = {Biodiversity ; Canada ; Grassland ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Oomycetes/classification/*genetics/*isolation & purification ; Peas/growth & development/*parasitology ; Plant Roots/parasitology ; Rhizosphere ; Soil/*parasitology ; }, abstract = {Oomycetes are a diverse group of microorganisms; however, little is known about their composition and biodiversity in agroecosystems. Illumina MiSeq was used to determine the type and abundance of oomycetes associated with pea root rot in the Canadian prairies. Additional objectives of the study were to identify differences in oomycete communities associated with pea root health and compare oomycete communities among the 3 prairie provinces, where field peas are commonly cultivated. Samples of soil from the rhizosphere of field pea (Pisum sativum L.) were collected from patches of asymptomatic or diseased plants from 26 commercial fields in 2013 and 2014. Oomycete communities were characterized using metagenomic analysis of the ITS1 region on Illumina MiSeq. From 105 identified operational taxonomic units (OTUs), 45 and 16 oomycete OTUs were identified at species and genus levels, respectively. Pythium was the most prevalent genus and Pythium heterothallicum the most prevalent species in all 3 provinces in both 2013 and 2014. Aphanomyces euteiches, a very important pea root rot pathogen in regions of the prairies, was detected in 57% of sites but at very low abundance (<0.2%). Multivariate analysis revealed differences in the relative abundance of species in oomycete communities between asymptomatic and diseased sites, and among years and provinces. This study demonstrated that deep amplicon sequencing can provide information on the composition and diversity of oomycete communities in agricultural soils.}, }
@article {pmid28571671, year = {2017}, author = {Millar, M and Seale, J and Greenland, M and Hardy, P and Juszczak, E and Wilks, M and Panton, N and Costeloe, K and Wade, WG}, title = {The Microbiome of Infants Recruited to a Randomised Placebo-controlled Probiotic Trial (PiPS Trial).}, journal = {EBioMedicine}, volume = {20}, number = {}, pages = {255-262}, doi = {10.1016/j.ebiom.2017.05.019}, pmid = {28571671}, issn = {2352-3964}, mesh = {Bifidobacterium ; Dysbiosis ; Enterocolitis, Necrotizing/etiology/*prevention & control ; Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; Infant, Premature ; Metagenome ; Metagenomics ; *Microbiota ; Odds Ratio ; Outcome Assessment (Health Care) ; Probiotics/*administration & dosage ; RNA, Ribosomal, 16S ; Time-to-Treatment ; }, abstract = {The microbial dysbiosis associated with necrotizing enterocolitis (NEC) in preterm infants suggests that early exposure to probiotics may decrease and antibiotics may increase NEC risk. However, administration of Bifidobacterium breve strain BBG-001 to preterm infants did not affect NEC incidence in a multicenter randomised controlled phase 3 trial (PiPS trial). Using a subset of these subjects we compared the fecal microbiome of probiotic and placebo groups and assessed the impact of early antibiotic treatment. Extracted DNA from 103 fecal samples collected at 36weeks post-menstrual age underwent PCR amplification of a fragment of the 16S rRNA gene. Heatmaps were constructed showing the proportions of sequences from bacterial families present at >1% of the community. Stepwise logistic regression assessed the association between early antibiotic exposure and microbiome group. There was no difference in the microbial richness and diversity of the microbiome of preterm infants following treatment with probiotic or a placebo. Conversely, early antimicrobial exposure was associated with different patterns of colonisation, specifically a relative abundance of Proteobacteria. These findings highlight that the potential influence of probiotics on the microbiome of preterm infants remains unclear whereas the modulatory effect of antibiotic exposure on microbial colonisation requires further research.}, }
@article {pmid28545131, year = {2017}, author = {Gontang, EA and Aylward, FO and Carlos, C and Glavina Del Rio, T and Chovatia, M and Fern, A and Lo, CC and Malfatti, SA and Tringe, SG and Currie, CR and Kolter, R}, title = {Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach.}, journal = {PloS one}, volume = {12}, number = {5}, pages = {e0177189}, doi = {10.1371/journal.pone.0177189}, pmid = {28545131}, issn = {1932-6203}, support = {F32 GM087941/GM/NIGMS NIH HHS/United States ; R01 GM082137/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Ants/microbiology ; Biodiversity ; Cockroaches/*microbiology ; Gastrointestinal Microbiome/genetics/*physiology ; Gastrointestinal Tract/*microbiology ; *Metagenome ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {Investigations of gut microbiomes have shed light on the diversity and genetic content of these communities, and helped shape our understanding of how host-associated microorganisms influence host physiology, behavior, and health. Despite the importance of gut microbes to metazoans, our understanding of the changes in diversity and composition across the alimentary tract, and the source of the resident community are limited. Here, using community metagenomics and 16S rRNA gene sequencing, we assess microbial community diversity and coding potential in the foregut, midgut, and hindgut of a juvenile Panchlora cockroach, which resides in the refuse piles of the leaf-cutter ant species Atta colombica. We found a significant shift in the microbial community structure and coding potential throughout the three gut sections of Panchlora sp., and through comparison with previously generated metagenomes of the cockroach's food source and niche, we reveal that this shift in microbial community composition is influenced by the ecosystems in which Panchlora sp. occurs. While the foregut is composed of microbes that likely originate from the symbiotic fungus gardens of the ants, the midgut and hindgut are composed of a microbial community that is likely cockroach-specific. Analogous to mammalian systems, the midgut and hindgut appear to be dominated by Firmicutes and Bacteroidetes with the capacity for polysaccharide degradation, suggesting they may assist in the degradation of dietary plant material. Our work underscores the prominence of community changes throughout gut microbiomes and highlights ecological factors that underpin the structure and function of the symbiotic microbial communities of metazoans.}, }
@article {pmid28544522, year = {2017}, author = {Rasigraf, O and Schmitt, J and Jetten, MSM and Lüke, C}, title = {Metagenomic potential for and diversity of N-cycle driving microorganisms in the Bothnian Sea sediment.}, journal = {MicrobiologyOpen}, volume = {6}, number = {4}, pages = {}, doi = {10.1002/mbo3.475}, pmid = {28544522}, issn = {2045-8827}, mesh = {Aerobiosis ; Anaerobiosis ; Archaea/classification/*enzymology/genetics ; Bacteria/classification/*enzymology/genetics ; *Biota ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Geologic Sediments/*microbiology ; Metagenome ; Nitrogen/*metabolism ; *Nitrogen Cycle ; Oceans and Seas ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The biological nitrogen cycle is driven by a plethora of reactions transforming nitrogen compounds between various redox states. Here, we investigated the metagenomic potential for nitrogen cycle of the in situ microbial community in an oligotrophic, brackish environment of the Bothnian Sea sediment. Total DNA from three sediment depths was isolated and sequenced. The characterization of the total community was performed based on 16S rRNA gene inventory using SILVA database as reference. The diversity of diagnostic functional genes coding for nitrate reductases (napA;narG), nitrite:nitrate oxidoreductase (nxrA), nitrite reductases (nirK;nirS;nrfA), nitric oxide reductase (nor), nitrous oxide reductase (nosZ), hydrazine synthase (hzsA), ammonia monooxygenase (amoA), hydroxylamine oxidoreductase (hao), and nitrogenase (nifH) was analyzed by blastx against curated reference databases. In addition, Polymerase chain reaction (PCR)-based amplification was performed on the hzsA gene of anammox bacteria. Our results reveal high genomic potential for full denitrification to N2 , but minor importance of anaerobic ammonium oxidation and dissimilatory nitrite reduction to ammonium. Genomic potential for aerobic ammonia oxidation was dominated by Thaumarchaeota. A higher diversity of anammox bacteria was detected in metagenomes than with PCR-based technique. The results reveal the importance of various N-cycle driving processes and highlight the advantage of metagenomics in detection of novel microbial key players.}, }
@article {pmid28543439, year = {2017}, author = {Iliev, I and Yahubyan, G and Marhova, M and Apostolova, E and Gozmanova, M and Gecheva, G and Kostadinova, S and Ivanova, A and Baev, V}, title = {Metagenomic profiling of the microbial freshwater communities in two Bulgarian reservoirs.}, journal = {Journal of basic microbiology}, volume = {57}, number = {8}, pages = {669-679}, doi = {10.1002/jobm.201700137}, pmid = {28543439}, issn = {1521-4028}, mesh = {Actinobacteria/classification/genetics ; Bacteria/classification/*genetics ; Bacteroidetes/classification/genetics ; Biodiversity ; Bulgaria ; Ecosystem ; Fresh Water/*microbiology ; High-Throughput Nucleotide Sequencing ; Lakes/microbiology ; *Metagenomics ; *Microbial Consortia ; Phylogeny ; Plankton/classification/*genetics ; Proteobacteria/classification/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Microorganisms inhabiting freshwater environments are an integral part of the aquatic ecosystems. Very few data are available regarding the profiles of the microbial communities in the reservoirs in Bulgaria, despite their key role in the biogeochemical processes. In the present study, we provide the first comprehensive metagenomic analysis on the planktonic bacterial diversity of two large and economically important Bulgarian reservoirs (Batak and Tsankov Kamak) using next-generation sequencing of 16S ribosomal RNA gene (16S rRNA). Analysis of the metagenomic amplicon datasets, including quality filtering, clustering of Operational Taxonomic Units and taxonomy assignment revealed that 78.45% of the microbial communities between the two reservoirs were overlapping. The diversity (H) and Pielou's evenness (J) indices declined along the longitudinal axis of both reservoirs. The estimated values for the Shannon diversity index are typically observed in oligotrophic lakes. The microbial communities of both reservoirs were dominated by Proteobacteria, followed by Actinobacteria and Bacteroidetes all comprised over 95% of the relative abundance, regardless of the reservoir's large hydrogeological differences. The bacterioplankton was characterized by high phylogenetic heterogeneity in the taxonomic structure, being distributed among 211 genera. The genera Limnohabitans and Rhodoferax held the absolute predominance, implying their significance in the aquatic food webs. The obtained data can contribute to the better systematic understanding of the microbial diversity of freshwater environments.}, }
@article {pmid28543188, year = {2017}, author = {Chitrala, KN and Guan, H and Singh, NP and Busbee, B and Gandy, A and Mehrpouya-Bahrami, P and Ganewatta, MS and Tang, C and Chatterjee, S and Nagarkatti, P and Nagarkatti, M}, title = {CD44 deletion leading to attenuation of experimental autoimmune encephalomyelitis results from alterations in gut microbiome in mice.}, journal = {European journal of immunology}, volume = {47}, number = {7}, pages = {1188-1199}, doi = {10.1002/eji.201646792}, pmid = {28543188}, issn = {1521-4141}, support = {R01 AI129788/AI/NIAID NIH HHS/United States ; R01 MH094755/MH/NIMH NIH HHS/United States ; R01 ES019313/ES/NIEHS NIH HHS/United States ; P20 GM103641/GM/NIGMS NIH HHS/United States ; P01 AT003961/AT/NCCIH NIH HHS/United States ; R01 AT006888/AT/NCCIH NIH HHS/United States ; R01 AI123947/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteroidetes/genetics/immunology/isolation & purification ; Disease Models, Animal ; Dysbiosis ; Encephalomyelitis, Autoimmune, Experimental/*immunology/physiopathology ; Fatty Acids, Volatile/immunology ; Fecal Microbiota Transplantation ; Feces/microbiology ; Firmicutes/genetics/immunology/isolation & purification ; Gastrointestinal Microbiome/genetics/*immunology ; Gene Deletion ; Hyaluronan Receptors/*genetics/*immunology ; Metagenomics ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Propionates/metabolism ; RNA, Ribosomal, 16S ; }, abstract = {Dysbiosis in gut microbiome has been shown to be associated with inflammatory and autoimmune diseases. Previous studies from our laboratory demonstrated the pivotal role played by CD44 in the regulation of EAE, a murine model of multiple sclerosis. In the current study, we determined whether these effects resulted from an alteration in gut microbiota and the short-chain fatty acid (SCFA) production in CD44 knockout (CD44KO) mice. Fecal transfer from naïve CD44KO but not C57BL/6 wild type (CD44WT) mice, into EAE-induced CD44WT mice, led to significant amelioration of EAE. High-throughput bacterial 16S rRNA gene sequencing, followed by clustering sequences into operational taxonomic units (OTUs) and biochemical analysis, revealed that EAE-induced CD44KO mice showed significant diversity, richness, and evenness when compared to EAE-induced CD44WT mice at the phylum level, with dominant Bacteroidetes (68.5%) and low Firmicutes (26.8%). Further, data showed a significant change in the abundance of SCFAs, propionic acid, and i-butyric acid in EAE-CD44KO compared to EAE-CD44WT mice. In conclusion, our results demonstrate that the attenuation of EAE seen following CD44 gene deletion in mice may result from alterations in the gut microbiota and SCFAs. Furthermore, our studies also demonstrate that the phenotype of gene knock-out animals may be shaped by gut microbiota.}, }
@article {pmid28542523, year = {2017}, author = {Zaza, G and Dalla Gassa, A and Felis, G and Granata, S and Torriani, S and Lupo, A}, title = {Impact of maintenance immunosuppressive therapy on the fecal microbiome of renal transplant recipients: Comparison between an everolimus- and a standard tacrolimus-based regimen.}, journal = {PloS one}, volume = {12}, number = {5}, pages = {e0178228}, doi = {10.1371/journal.pone.0178228}, pmid = {28542523}, issn = {1932-6203}, mesh = {Adult ; Aged ; Everolimus/adverse effects/*therapeutic use ; Female ; Gastrointestinal Microbiome/*drug effects/genetics ; Humans ; Immunosuppressive Agents/adverse effects/*therapeutic use ; *Kidney Transplantation ; Maintenance Chemotherapy/adverse effects ; Male ; Metagenomics ; Middle Aged ; Mycophenolic Acid/therapeutic use ; Tacrolimus/adverse effects/*therapeutic use ; }, abstract = {BACKGROUND: The gut microbiome is the full set of microbes living in the gastrointestinal tract and is emerging as an important dynamic/fluid system that, if altered by environmental, dietetic or pharmacological factors, could considerably influence drug response. However, the immunosuppressive drug-induced modifications of this system are still poorly defined.
METHODS: We employed an innovative bioinformatics approach to assess differences in the whole-gut microbial metagenomic profile of 20 renal transplant recipients undergoing maintenance treatment with two different immunosuppressive protocols. Nine patients were treated with everolimus plus mycophenolate mofetil (EVE+MMF group), and 11 patients were treated with a standard therapy with tacrolimus plus mycophenolate mofetil (TAC+MMF group).
RESULTS: A statistical analysis of comparative high-throughput data demonstrated that although similar according to the degree of Shannon diversity (alpha diversity) at the taxonomic level, three functional genes clearly discriminated EVE+MMF versus TAC+MMF (cutoff: log2 fold change≥1, FDR≤0.05). Flagellar motor switch protein (fliNY) and type IV pilus assembly protein pilM (pilM) were significantly enriched in TAC+MMF-treated patients, while macrolide transport system mrsA (msrA) was more abundant in patients treated with EVE+MMF. Finally, PERMANOVA revealed that among the variables analyzed and included in our model, only the consumption of sugar significantly influenced beta diversity.
CONCLUSIONS: Our study, although performed on a relatively small number of patients, showed, for the first time, specific immunosuppressive-related effects on fecal microbiome of renal transplant recipients and it suggested that the analysis of the gut microbes community could represent a new tool to better understand the effects of drugs currently employed in organ transplantations. However, multicenter studies including healthy controls should be undertaken to better address this objective.}, }
@article {pmid28542458, year = {2017}, author = {Cameron, SJS and Lewis, KE and Huws, SA and Hegarty, MJ and Lewis, PD and Pachebat, JA and Mur, LAJ}, title = {A pilot study using metagenomic sequencing of the sputum microbiome suggests potential bacterial biomarkers for lung cancer.}, journal = {PloS one}, volume = {12}, number = {5}, pages = {e0177062}, doi = {10.1371/journal.pone.0177062}, pmid = {28542458}, issn = {1932-6203}, mesh = {Aged ; Bacteria/*genetics ; Biomarkers, Tumor/*genetics ; Female ; Humans ; Lung Neoplasms/*microbiology ; Male ; Metagenomics/methods ; Microbiota/*genetics ; Middle Aged ; Pilot Projects ; Sputum/*microbiology ; }, abstract = {Lung cancer (LC) is the most prevalent cancer worldwide, and responsible for over 1.3 million deaths each year. Currently, LC has a low five year survival rates relative to other cancers, and thus, novel methods to screen for and diagnose malignancies are necessary to improve patient outcomes. Here, we report on a pilot-sized study to evaluate the potential of the sputum microbiome as a source of non-invasive bacterial biomarkers for lung cancer status and stage. Spontaneous sputum samples were collected from ten patients referred with possible LC, of which four were eventually diagnosed with LC (LC+), and six had no LC after one year (LC-). Of the seven bacterial species found in all samples, Streptococcus viridans was significantly higher in LC+ samples. Seven further bacterial species were found only in LC-, and 16 were found only in samples from LC+. Additional taxonomic differences were identified in regards to significant fold changes between LC+ and LC-cases, with five species having significantly higher abundances in LC+, with Granulicatella adiacens showing the highest level of abundance change. Functional differences, evident through significant fold changes, included polyamine metabolism and iron siderophore receptors. G. adiacens abundance was correlated with six other bacterial species, namely Enterococcus sp. 130, Streptococcus intermedius, Escherichia coli, S. viridans, Acinetobacter junii, and Streptococcus sp. 6, in LC+ samples only, which could also be related to LC stage. Spontaneous sputum appears to be a viable source of bacterial biomarkers which may have utility as biomarkers for LC status and stage.}, }
@article {pmid28539477, year = {2017}, author = {Lax, S and Sangwan, N and Smith, D and Larsen, P and Handley, KM and Richardson, M and Guyton, K and Krezalek, M and Shogan, BD and Defazio, J and Flemming, I and Shakhsheer, B and Weber, S and Landon, E and Garcia-Houchins, S and Siegel, J and Alverdy, J and Knight, R and Stephens, B and Gilbert, JA}, title = {Bacterial colonization and succession in a newly opened hospital.}, journal = {Science translational medicine}, volume = {9}, number = {391}, pages = {}, doi = {10.1126/scitranslmed.aah6500}, pmid = {28539477}, issn = {1946-6242}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/genetics/*isolation & purification ; Bayes Theorem ; *Hospitals ; Humans ; Microbiota ; Propionibacterium/genetics/isolation & purification ; Staphylococcus/genetics/isolation & purification ; }, abstract = {The microorganisms that inhabit hospitals may influence patient recovery and outcome, although the complexity and diversity of these bacterial communities can confound our ability to focus on potential pathogens in isolation. To develop a community-level understanding of how microorganisms colonize and move through the hospital environment, we characterized the bacterial dynamics among hospital surfaces, patients, and staff over the course of 1 year as a new hospital became operational. The bacteria in patient rooms, particularly on bedrails, consistently resembled the skin microbiota of the patient occupying the room. Bacterial communities on patients and room surfaces became increasingly similar over the course of a patient's stay. Temporal correlations in community structure demonstrated that patients initially acquired room-associated taxa that predated their stay but that their own microbial signatures began to influence the room community structure over time. The α- and β-diversity of patient skin samples were only weakly or nonsignificantly associated with clinical factors such as chemotherapy, antibiotic usage, and surgical recovery, and no factor except for ambulatory status affected microbial similarity between the microbiotas of a patient and their room. Metagenomic analyses revealed that genes conferring antimicrobial resistance were consistently more abundant on room surfaces than on the skin of the patients inhabiting those rooms. In addition, persistent unique genotypes of Staphylococcus and Propionibacterium were identified. Dynamic Bayesian network analysis suggested that hospital staff were more likely to be a source of bacteria on the skin of patients than the reverse but that there were no universal patterns of transmission across patient rooms.}, }
@article {pmid28535299, year = {2017}, author = {Escobedo-Hinojosa, W and Pardo-López, L}, title = {Analysis of bacterial metagenomes from the Southwestern Gulf of Mexico for pathogens detection.}, journal = {Pathogens and disease}, volume = {75}, number = {5}, pages = {}, doi = {10.1093/femspd/ftx058}, pmid = {28535299}, issn = {2049-632X}, mesh = {Bacteria/*classification/*genetics/isolation & purification ; *Biota ; Gulf of Mexico ; *Metagenome ; Seawater/*microbiology ; }, abstract = {Little is known about the diversity of bacteria in the Southwestern Gulf of Mexico. The aim of the study illustrated in this perspective was to search for the presence of bacterial pathogens in this ecosystem, using metagenomic data recently generated by the Mexican research group known as the Gulf of Mexico Research Consortium. Several genera of bacteria annotated as pathogens were detected in water and sediment marine samples. As expected, native and ubiquitous pathogenic bacteria genera such as Burkolderia, Halomonas, Pseudomonas, Shewanella and Vibrio were highly represented. Surprisingly, non-native genera of public health concern were also detected, including Borrelia, Ehrlichia, Leptospira, Mycobacterium, Mycoplasma, Salmonella, Staphylococcus, Streptococcus and Treponema. While there are no previous metagenomics studies of this environment, the potential influences of natural, anthropogenic and ecological factors on the diversity of putative pathogenic bacteria found in it are reviewed. The taxonomic annotation herein reported provides a starting point for an improved understanding of bacterial biodiversity in the Southwestern Gulf of Mexico. It also represents a useful tool in public health as it may help identify infectious diseases associated with exposure to marine water and ingestion of fish or shellfish, and thus may be useful in predicting and preventing waterborne disease outbreaks.}, }
@article {pmid28534987, year = {2017}, author = {Chen, T and Shi, Y and Wang, X and Wang, X and Meng, F and Yang, S and Yang, J and Xin, H}, title = {High‑throughput sequencing analyses of oral microbial diversity in healthy people and patients with dental caries and periodontal disease.}, journal = {Molecular medicine reports}, volume = {16}, number = {1}, pages = {127-132}, doi = {10.3892/mmr.2017.6593}, pmid = {28534987}, issn = {1791-3004}, mesh = {Adolescent ; Adult ; Biodiversity ; Child ; Computational Biology/methods ; Dental Caries/*microbiology ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Middle Aged ; Mouth/*microbiology ; Periodontal Diseases/*microbiology ; Young Adult ; }, abstract = {Recurrence of oral diseases caused by antibiotics has brought about an urgent requirement to explore the oral microbial diversity in the human oral cavity. In the present study, the high‑throughput sequencing method was adopted to compare the microbial diversity of healthy people and oral patients and sequence analysis was performed by UPARSE software package. The Venn results indicated that a mean of 315 operational taxonomic units (OTUs) was obtained, and 73, 64, 53, 19 and 18 common OTUs belonging to Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria and Fusobacteria, respectively, were identified in healthy people. Moreover, the reduction of Firmicutes and the increase of Proteobacteria in the children group, and the increase of Firmicutes and the reduction of Proteobacteria in the youth and adult groups, indicated that the age bracket and oral disease had largely influenced the tooth development and microbial development in the oral cavity. In addition, the traditional 'pathogenic bacteria' of Firmicutes, Proteobacteria and Bacteroidetes (accounted for >95% of the total sequencing number in each group) indicated that the 'harmful' bacteria may exert beneficial effects on oral health. Therefore, the data will provide certain clues for curing some oral diseases by the strategy of adjusting the disturbed microbial compositions in oral disease to healthy level.}, }
@article {pmid28530702, year = {2017}, author = {Wu, H and Esteve, E and Tremaroli, V and Khan, MT and Caesar, R and Mannerås-Holm, L and Ståhlman, M and Olsson, LM and Serino, M and Planas-Fèlix, M and Xifra, G and Mercader, JM and Torrents, D and Burcelin, R and Ricart, W and Perkins, R and Fernàndez-Real, JM and Bäckhed, F}, title = {Metformin alters the gut microbiome of individuals with treatment-naive type 2 diabetes, contributing to the therapeutic effects of the drug.}, journal = {Nature medicine}, volume = {23}, number = {7}, pages = {850-858}, doi = {10.1038/nm.4345}, pmid = {28530702}, issn = {1546-170X}, mesh = {Animals ; Bile Acids and Salts/metabolism ; DNA, Bacterial/*analysis ; Diabetes Mellitus, Type 2/*drug therapy/microbiology ; Double-Blind Method ; Fatty Acids, Volatile/metabolism ; Fecal Microbiota Transplantation ; Feces/chemistry/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Germ-Free Life ; Glucose Tolerance Test ; Humans ; Hypoglycemic Agents/*therapeutic use ; In Vitro Techniques ; Male ; Metagenomics ; Metformin/*therapeutic use ; Mice ; Middle Aged ; }, abstract = {Metformin is widely used in the treatment of type 2 diabetes (T2D), but its mechanism of action is poorly defined. Recent evidence implicates the gut microbiota as a site of metformin action. In a double-blind study, we randomized individuals with treatment-naive T2D to placebo or metformin for 4 months and showed that metformin had strong effects on the gut microbiome. These results were verified in a subset of the placebo group that switched to metformin 6 months after the start of the trial. Transfer of fecal samples (obtained before and 4 months after treatment) from metformin-treated donors to germ-free mice showed that glucose tolerance was improved in mice that received metformin-altered microbiota. By directly investigating metformin-microbiota interactions in a gut simulator, we showed that metformin affected pathways with common biological functions in species from two different phyla, and many of the metformin-regulated genes in these species encoded metalloproteins or metal transporters. Our findings provide support for the notion that altered gut microbiota mediates some of metformin's antidiabetic effects.}, }
@article {pmid28530140, year = {2017}, author = {Stewart, CJ and Mansbach, JM and Wong, MC and Ajami, NJ and Petrosino, JF and Camargo, CA and Hasegawa, K}, title = {Associations of Nasopharyngeal Metabolome and Microbiome with Severity among Infants with Bronchiolitis. A Multiomic Analysis.}, journal = {American journal of respiratory and critical care medicine}, volume = {196}, number = {7}, pages = {882-891}, doi = {10.1164/rccm.201701-0071OC}, pmid = {28530140}, issn = {1535-4970}, support = {R01 AI127507/AI/NIAID NIH HHS/United States ; R01 AI108588/AI/NIAID NIH HHS/United States ; U01 AI087881/AI/NIAID NIH HHS/United States ; R21 HL129909/HL/NHLBI NIH HHS/United States ; R01 AI114552/AI/NIAID NIH HHS/United States ; UG3 OD023253/OD/NIH HHS/United States ; }, mesh = {Bronchiolitis/*metabolism/*microbiology/therapy ; Cohort Studies ; Continuous Positive Airway Pressure/statistics & numerical data ; Female ; Humans ; Infant ; Male ; Metabolome/*physiology ; Microbiota/*physiology ; Nasopharynx/*metabolism/*microbiology ; Prospective Studies ; Severity of Illness Index ; }, abstract = {RATIONALE: Bronchiolitis is the most common lower respiratory infection in infants; however, it remains unclear which infants with bronchiolitis will develop severe illness. In addition, although emerging evidence indicates associations of the upper-airway microbiome with bronchiolitis severity, little is known about the mechanisms linking airway microbes and host response to disease severity.
OBJECTIVES: To determine the relations among the nasopharyngeal airway metabolome profiles, microbiome profiles, and severity in infants with bronchiolitis.
METHODS: We conducted a multicenter prospective cohort study of infants (age <1 yr) hospitalized with bronchiolitis. By applying metabolomic and metagenomic (16S ribosomal RNA gene and whole-genome shotgun sequencing) approaches to 144 nasopharyngeal airway samples collected within 24 hours of hospitalization, we determined metabolome and microbiome profiles and their association with higher severity, defined by the use of positive pressure ventilation (i.e., continuous positive airway pressure and/or intubation).
MEASUREMENTS AND MAIN RESULTS: Nasopharyngeal airway metabolome profiles significantly differed by bronchiolitis severity (P < 0.001). Among 254 metabolites identified, a panel of 25 metabolites showed high sensitivity (84%) and specificity (86%) in predicting the use of positive pressure ventilation. The intensity of these metabolites was correlated with relative abundance of Streptococcus pneumoniae. In the pathway analysis, sphingolipid metabolism was the most significantly enriched subpathway in infants with positive pressure ventilation use compared with those without (P < 0.001). Enrichment of sphingolipid metabolites was positively correlated with the relative abundance of S. pneumoniae.
CONCLUSIONS: Although further validation is needed, our multiomic analyses demonstrate the potential of metabolomics to predict bronchiolitis severity and better understand microbe-host interaction.}, }
@article {pmid28528426, year = {2017}, author = {Nielsen, J and Archer, J and Essack, M and Bajic, VB and Gojobori, T and Mijakovic, I}, title = {Building a bio-based industry in the Middle East through harnessing the potential of the Red Sea biodiversity.}, journal = {Applied microbiology and biotechnology}, volume = {101}, number = {12}, pages = {4837-4851}, doi = {10.1007/s00253-017-8310-9}, pmid = {28528426}, issn = {1432-0614}, mesh = {Bacillus/physiology ; *Biodiversity ; *Bioelectric Energy Sources ; Cyanobacteria/physiology ; Indian Ocean ; Metabolic Engineering/economics/methods/utilization ; Metagenomics/economics/methods ; Middle East ; Synthetic Biology/economics/methods ; }, abstract = {The incentive for developing microbial cell factories for production of fuels and chemicals comes from the ability of microbes to deliver these valuable compounds at a reduced cost and with a smaller environmental impact compared to the analogous chemical synthesis. Another crucial advantage of microbes is their great biological diversity, which offers a much larger "catalog" of molecules than the one obtainable by chemical synthesis. Adaptation to different environments is one of the important drives behind microbial diversity. We argue that the Red Sea, which is a rather unique marine niche, represents a remarkable source of biodiversity that can be geared towards economical and sustainable bioproduction processes in the local area and can be competitive in the international bio-based economy. Recent bioprospecting studies, conducted by the King Abdullah University of Science and Technology, have established important leads on the Red Sea biological potential, with newly isolated strains of Bacilli and Cyanobacteria. We argue that these two groups of local organisms are currently most promising in terms of developing cell factories, due to their ability to operate in saline conditions, thus reducing the cost of desalination and sterilization. The ability of Cyanobacteria to perform photosynthesis can be fully exploited in this particular environment with one of the highest levels of irradiation on the planet. We highlight the importance of new experimental and in silico methodologies needed to overcome the hurdles of developing efficient cell factories from the Red Sea isolates.}, }
@article {pmid28527760, year = {2017}, author = {Shi, Y and Zhai, Q and Li, D and Mao, B and Liu, X and Zhao, J and Zhang, H and Chen, W}, title = {Restoration of cefixime-induced gut microbiota changes by Lactobacillus cocktails and fructooligosaccharides in a mouse model.}, journal = {Microbiological research}, volume = {200}, number = {}, pages = {14-24}, doi = {10.1016/j.micres.2017.04.001}, pmid = {28527760}, issn = {1618-0623}, mesh = {Animals ; Blood Chemical Analysis ; Cecum/chemistry/microbiology/pathology ; Cefixime/administration & dosage/*pharmacology ; Cell Adhesion/drug effects ; Colon/microbiology/pathology ; DNA, Bacterial/genetics ; Disease Models, Animal ; Fatty Acids, Volatile/analysis ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects ; Gastrointestinal Tract/drug effects/microbiology ; HT29 Cells ; Humans ; Ileum/microbiology/pathology ; Intestines ; Lactobacillus/classification/isolation & purification/metabolism/*physiology ; Male ; Metagenomics ; Mice ; Mice, Inbred C57BL ; Microbial Consortia/*drug effects ; Oligosaccharides/*pharmacology ; Probiotics/pharmacology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Probiotics have been used to rebuild the antibiotic-induced dysfunction in gut microbiota, but whether the different strains of probiotics result in similar or reverse effects remains unclear. In this study, the different recovery effects of two cocktails (each contains four strains) of Lactobacillus and fructooligosaccharide against cefixime-induced change of gut microbiota were evaluated in C57BL/6J mice. The results show that the use of cefixime caused a reduction in the diversities of the microbial community and led to significantly decreasing to one preponderant Firmicutes phylum, which was difficult to restore naturally in the short term. The gut microbiota compositions of the groups treated with the probiotic cocktails were much more diverse than those of the natural recovery group. The effects of Lactobacillus cocktails against the cefixime-induced gut microbiota change may mainly be due to the beneficial SCFAs production in vivo and also be related to the good cell adhesion properties performed in vitro. Meanwhile, the restoration of the cefixime-induced gut microbiota was significantly different between two Lactobacillus groups since the Lactobacillus strains with high levels of fructooligosaccharide use and better cell adhesion properties performed considerably better than the Lactobacillus strains with high survival rates in the gastrointestinal tract. The contents of short-chain fatty acids in ceca were increased to 26.483±1.925 and 25.609±2.782μmol/g in the two probiotic cocktail groups respectively compared to 15.791±0.833μmol/g (P<0.05) in control group. Moreover, intestinal inflammation was alleviated by administration of the Lactobacillus cocktails. However, fructooligasaccharide administration showed certain effects on gut microbiota restoration (such as an increase of Akkermansia), although its effect on the entire microbiome structure is not so obvious.}, }
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