@article {pmid31602443, year = {2019}, author = {Li, Q and Chen, H and Zhang, M and Wu, T and Liu, R}, title = {Altered short chain fatty acid profiles induced by dietary fiber intervention regulate AMPK levels and intestinal homeostasis.}, journal = {Food & function}, volume = {10}, number = {11}, pages = {7174-7187}, doi = {10.1039/c9fo01465a}, pmid = {31602443}, issn = {2042-650X}, mesh = {AMP-Activated Protein Kinases/genetics/*metabolism ; Animals ; Bacteria/classification/genetics/isolation & purification/*metabolism ; Dietary Fiber/*metabolism ; Fatty Acids, Volatile/chemistry/*metabolism ; Female ; *Gastrointestinal Microbiome ; Homeostasis ; Intestinal Mucosa/enzymology/*metabolism/microbiology ; Male ; Methylamines/blood ; Mice, Inbred C57BL ; Triglycerides/blood ; }, abstract = {The objective of this study was to investigate the effects of dietary intervention on intestinal microbiota-mediated change in short chain fatty acid (SCFA) profile and intestinal homeostasis. Sequencing of the 16S rDNA of gut bacteria, metagenomics, intestinal epithelial transcriptomics, and metabonomics were conducted. Results showed that the dietary interventions altered the microbiota composition of cecal digesta, microbiota-mediated metabolism, and the gene expression profile in intestinal epithelial cells. Compared with red meat-diet-fed mice, fiber-diet-fed mice presented a shift in the gut microbiome toward increased production of butanoate, which was accompanied by up-regulation of microbiota- and AMP-activated protein kinase (AMPK)-dependent gene expression and decrease in serum concentrations of trimethylamine N-oxide (TMAO), triglyceride (TG) and glucose (GLU). The results suggested a new regulatory mechanism via which butanoate and AMPK activation contributed to intestinal integrity and homeostasis by affecting metabolism, intestinal barrier function and transporter expression.}, }
@article {pmid30658982, year = {2019}, author = {Jiao, S and Chen, W and Wei, G}, title = {Resilience and Assemblage of Soil Microbiome in Response to Chemical Contamination Combined with Plant Growth.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {6}, pages = {}, doi = {10.1128/AEM.02523-18}, pmid = {30658982}, issn = {1098-5336}, mesh = {Bacteria/classification/genetics/*isolation & purification/metabolism ; Biodiversity ; Fabaceae/*growth & development/*microbiology ; Metagenomics ; Metals/analysis/metabolism ; *Microbiota ; Phylogeny ; Soil/chemistry ; Soil Microbiology ; Soil Pollutants/analysis/*metabolism ; }, abstract = {A lack of knowledge of the microbial responses to environmental change at the species and functional levels hinders our ability to understand the intrinsic mechanisms underlying the maintenance of microbial ecosystems. Here, we present results from temporal microcosms that introduced inorganic and organic contaminants into agro-soils for 90 days, with three common legume plants. Temporal dynamics and assemblage of soil microbial communities and functions in response to contamination under the influence of growth of different plants were explored via sequencing of the 16S rRNA amplicon and by shotgun metagenomics. Soil microbial alpha diversity and structure at the taxonomic and functional levels exhibited resilience patterns. Functional profiles showed greater resilience than did taxonomic ones. Different legume plants imposed stronger selection on taxonomic profiles than on functional ones. Network and random forest analyses revealed that the functional potential of soil microbial communities was fostered by various taxonomic groups. Betaproteobacteria were important predictors of key functional traits such as amino acid metabolism, nucleic acid metabolism, and hydrocarbon degradation. Our study reveals the strong resilience of the soil microbiome to chemical contamination and sensitive responses of taxonomic rather than functional profiles to selection processes induced by different legume plants. This is pivotal to develop approaches and policies for the protection of soil microbial diversity and functions in agro-ecosystems with different response strategies from global environmental drivers, such as soil contamination and plant invasion.IMPORTANCE Exploring the microbial responses to environmental disturbances is a central issue in microbial ecology. Understanding the dynamic responses of soil microbial communities to chemical contamination and the microbe-soil-plant interactions is essential for forecasting the long-term changes in soil ecosystems. Nevertheless, few studies have applied multi-omics approaches to assess the microbial responses to soil contamination and the microbe-soil-plant interactions at the taxonomic and functional levels simultaneously. Our study reveals clear succession and resilience patterns of soil microbial diversity and structure in response to chemical contamination. Different legume plants exerted stronger selection processes on taxonomic than on functional profiles in contaminated soils, which could benefit plant growth and fitness as well as foster the potential abilities of hydrocarbon degradation and metal tolerance. These results provide new insight into the resilience and assemblage of soil microbiome in response to environmental disturbances in agro-ecosystems at the species and functional levels.}, }
@article {pmid30658973, year = {2019}, author = {Malmuthuge, N and Liang, G and Griebel, PJ and Guan, LL}, title = {Taxonomic and Functional Compositions of the Small Intestinal Microbiome in Neonatal Calves Provide a Framework for Understanding Early Life Gut Health.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {6}, pages = {}, doi = {10.1128/AEM.02534-18}, pmid = {30658973}, issn = {1098-5336}, support = {//Canadian Institute for Health Research/International ; }, mesh = {Animals ; Animals, Newborn/*microbiology ; Bacteria/*classification/genetics/*isolation & purification ; Cattle ; DNA, Bacterial/genetics ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Intestine, Small/*microbiology ; Male ; Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {A lack of information on the intestinal microbiome of neonatal calves prevents the use of microbial intervention strategies to improve calf gut health. This study profiled the taxonomic and functional composition of the small intestinal luminal microbiome of neonatal calves using whole-genome sequencing of the metagenome, aiming to understand the dynamics of microbial establishment during early life. Despite highly individualized microbial communities, we identified two distinct taxonomy-based clusters from the collective luminal microbiomes comprising a high level of either Lactobacillus or Bacteroides Among the clustered microbiomes, Lactobacillus-dominant ileal microbiomes had significantly lower abundances of Bacteroides, Prevotella, Roseburia, Ruminococcus, and Veillonella compared to the Bacteroides-dominated ileal microbiomes. In addition, the upregulated ileal genes of the Lactobacillus-dominant calves were related to leukocyte and lymphocyte chemotaxis, the cytokine/chemokine-mediated signaling pathway, and inflammatory responses, while the upregulated ileal genes of the Bacteroides-dominant calves were related to cell adhesion, response to stimulus, cell communication and regulation of mitogen-activated protein kinase cascades. The functional profiles of the luminal microbiomes also revealed two distinct clusters consisting of functions related to either high protein metabolism or sulfur metabolism. A lower abundance of Bifidobacterium and a higher abundance of sulfur-reducing bacteria (SRB) were observed in the sulfur metabolism-dominant cluster (0.2% ± 0.1%) compared to the protein metabolism-dominant cluster (12.6% ± 5.7%), suggesting an antagonistic relationship between SRB and Bifidobacterium, which both compete for cysteine. These distinct taxonomic and functional clusters may provide a framework to further analyze interactions between the intestinal microbiome and the immune function and health of neonatal calves.IMPORTANCE Dietary interventions to manipulate neonatal gut microbiota have been proposed to generate long-term impacts on hosts. Currently, our understanding of the early gut microbiome of neonatal calves is limited to 16S rRNA gene amplicon based microbial profiling, which is a barrier to developing dietary interventions to improve calf gut health. The use of a metagenome sequencing-based approach in the present study revealed high individual animal variation in taxonomic and functional abundance of intestinal microbiome and potential impacts of early microbiome on mucosal immune responses during the preweaning period. During this developmental period, age- and diet-related changes in microbial diversity, richness, density, and the abundance of taxa and functions were observed. A correlation-based approach to further explore the individual animal variation revealed potential enterotypes that can be linked to calf gut health, which may pave the way to developing strategies to manipulate the microbiome and improve calf health.}, }
@article {pmid30582346, year = {2020}, author = {Rizo, J and Guillén, D and Farrés, A and Díaz-Ruiz, G and Sánchez, S and Wacher, C and Rodríguez-Sanoja, R}, title = {Omics in traditional vegetable fermented foods and beverages.}, journal = {Critical reviews in food science and nutrition}, volume = {60}, number = {5}, pages = {791-809}, doi = {10.1080/10408398.2018.1551189}, pmid = {30582346}, issn = {1549-7852}, mesh = {Beverages/*microbiology ; Fermentation ; Fermented Foods and Beverages/*microbiology ; *Food Analysis ; *Microbiota ; Vegetables/*microbiology ; }, abstract = {For a long time, food microbiota has been studied using traditional microbiological techniques. With the arrival of molecular or culture-independent techniques, a strong understanding of microbiota dynamics has been achieved. However, analyzing the functional role of microbial communities is not an easy task. The application of omics sciences to the study of fermented foods would provide the metabolic and functional understanding of the microbial communities and their impact on the fermented product, including the molecules that define its aroma and flavor, as well as its nutritional properties. Until now, most omics studies have focused on commercial fermented products, such as cheese, wine, bread and beer, but traditional fermented foods have been neglected. Therefore, the information that allows to relate the present microbiota in the food and its properties remains limited. In this review, reports on the applications of omics in the study of traditional fermented foods and beverages are reviewed to propose new ways to analyze the fermentation phenomena.}, }
@article {pmid30485448, year = {2019}, author = {Chang, Y and Desirò, A and Na, H and Sandor, L and Lipzen, A and Clum, A and Barry, K and Grigoriev, IV and Martin, FM and Stajich, JE and Smith, ME and Bonito, G and Spatafora, JW}, title = {Phylogenomics of Endogonaceae and evolution of mycorrhizas within Mucoromycota.}, journal = {The New phytologist}, volume = {222}, number = {1}, pages = {511-525}, doi = {10.1111/nph.15613}, pmid = {30485448}, issn = {1469-8137}, support = {DEB-1441604//National Science Foundation/International ; DEB-1441715//National Science Foundation/International ; DEB-1441677//National Science Foundation/International ; DEB 1737898//National Science Foundation/International ; MICL02416//United States Department of Agriculture NIFA/International ; ANR-11-LABX-0002-01//French National Research Agency through the Laboratory of Excellence ARBRE/International ; DE-AC02-05CH11231//Office of Science of the US Department of Energy/International ; }, mesh = {*Biological Evolution ; Genome, Fungal ; Metagenomics ; Microbiota/genetics ; Molecular Sequence Annotation ; Mucorales/*genetics ; Mycoplasma/genetics ; Mycorrhizae/*physiology ; *Phylogeny ; Repetitive Sequences, Nucleic Acid/genetics ; }, abstract = {Endogonales (Mucoromycotina), composed of Endogonaceae and Densosporaceae, is the only known non-Dikarya order with ectomycorrhizal members. They also form mycorrhizal-like association with some nonspermatophyte plants. It has been recently proposed that Endogonales were among the earliest mycorrhizal partners with land plants. It remains unknown whether Endogonales possess genomes with mycorrhizal-lifestyle signatures and whether Endogonales originated around the same time as land plants did. We sampled sporocarp tissue from four Endogonaceae collections and performed shotgun genome sequencing. After binning the metagenome data, we assembled and annotated the Endogonaceae genomes. We performed comparative analysis on plant-cell-wall-degrading enzymes (PCWDEs) and small secreted proteins (SSPs). We inferred phylogenetic placement of Endogonaceae and estimated the ages of Endogonaceae and Endogonales with expanded taxon sampling. Endogonaceae have large genomes with high repeat content, low diversity of PCWDEs, but without elevated SSP/secretome ratios. Dating analysis estimated that Endogonaceae originated in the Permian-Triassic boundary and Endogonales originated in the mid-late Silurian. Mycoplasma-related endobacterium sequences were identified in three Endogonaceae genomes. Endogonaceae genomes possess typical signatures of mycorrhizal lifestyle. The early origin of Endogonales suggests that the mycorrhizal association between Endogonales and plants might have played an important role during the colonization of land by plants.}, }
@article {pmid31948613, year = {2020}, author = {Knight, SJ and Karon, O and Goddard, MR}, title = {Small scale fungal community differentiation in a vineyard system.}, journal = {Food microbiology}, volume = {87}, number = {}, pages = {103358}, doi = {10.1016/j.fm.2019.103358}, pmid = {31948613}, issn = {1095-9998}, mesh = {Discriminant Analysis ; Fermentation ; Fruit/microbiology ; Fungi/classification/genetics/*isolation & purification ; *Mycobiome ; New Zealand ; Vitis/*microbiology ; Wine/*analysis/microbiology ; }, abstract = {Microbes influence the quality of agricultural commodities and contribute to their distinctive sensorial attributes. Increasingly studies have demonstrated not only differential geographic patterns in microbial communities and populations, but that these contribute to valuable regionally distinct agricultural product identities, the most well-known example being wine. However, little is understood about microbial geographic patterns at scales of less than 100 km. For wine, single vineyards are the smallest (and most valuable) scale at which wine is asserted to differ; however, it is unknown whether microbes play any role in agricultural produce differentiation at this scale. Here we investigate whether vineyard fungal communities and yeast populations driving the spontaneous fermentation of fruit from these same vineyards are differentiated using metagenomics and population genetics. Significant differentiation of fungal communities was revealed between four Central Otago (New Zealand) Pinot Noir vineyard sites. However, there was no vineyard demarcation between fermenting populations of S. cerevisiae. Overall, this provides evidence that vineyard microbiomes potentially contribute to vineyard specific attributes in wine. Understanding the scale at which microbial communities are differentiated, and how these communities influence food product attributes has direct economic implications for industry and could inform sustainable management practices that maintain and enhance microbial diversity.}, }
@article {pmid31831198, year = {2020}, author = {Royo-Llonch, M and Sánchez, P and González, JM and Pedrós-Alió, C and Acinas, SG}, title = {Ecological and functional capabilities of an uncultured Kordia sp.}, journal = {Systematic and applied microbiology}, volume = {43}, number = {1}, pages = {126045}, doi = {10.1016/j.syapm.2019.126045}, pmid = {31831198}, issn = {1618-0984}, mesh = {Bacterial Proteins/genetics ; DNA, Bacterial/genetics ; Ecosystem ; Flavobacteriaceae/*classification/*genetics ; Genome, Bacterial/genetics ; Indian Ocean ; Metagenomics ; Microbiota/genetics ; Nucleic Acid Hybridization ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhodopsins, Microbial/genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; }, abstract = {Cultivable bacteria represent only a fraction of the diversity in microbial communities. However, the official procedures for classification and characterization of a novel prokaryotic species still rely on isolates. Nevertheless, due to single cell genomics, it is possible to retrieve genomes from environmental samples by sequencing them individually, and to assign specific genes to a specific taxon, regardless of their ability to grow in culture. In this study, a complete description was performed for uncultured Kordia sp. TARA_039_SRF, a proposed novel species within the genus Kordia, using culture-independent techniques. The type material was a high-quality draft genome (94.97% complete, 4.65% gene redundancy) co-assembled using ten nearly identical single amplified genomes (SAGs) from surface seawater in the North Indian Ocean during the Tara Oceans Expedition. The assembly process was optimized to obtain the best possible assembly metrics and a less fragmented genome. The closest relative of the species was Kordia periserrulae, which shared 97.56% similarity of the 16S rRNA gene, 75% orthologs and 89.13% average nucleotide identity. The functional potential of the proposed novel species included proteorhodopsin, the ability to incorporate nitrate, cytochrome oxidases with high affinity for oxygen, and CAZymes that were unique features within the genus. Its abundance at different depths and size fractions was also evaluated together with its functional annotation, revealing that its putative ecological niche could be particles of phytoplanktonic origin. It could putatively attach to these particles and consume them while sinking to the deeper and oxygen depleted layers of the North Indian Ocean.}, }
@article {pmid31367746, year = {2019}, author = {Dai, W and Wang, H and Zhou, Q and Li, D and Feng, X and Yang, Z and Wang, W and Qiu, C and Lu, Z and Xu, X and Lyu, M and Xie, G and Li, Y and Bao, Y and Liu, Y and Shen, K and Yao, K and Feng, X and Yang, Y and Zhou, K and Li, S and Zheng, Y}, title = {An integrated respiratory microbial gene catalogue to better understand the microbial aetiology of Mycoplasma pneumoniae pneumonia.}, journal = {GigaScience}, volume = {8}, number = {8}, pages = {}, doi = {10.1093/gigascience/giz093}, pmid = {31367746}, issn = {2047-217X}, mesh = {Case-Control Studies ; Child ; Child, Preschool ; Female ; Genes, Microbial ; Humans ; Infant ; Male ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Mycoplasma pneumoniae/*classification/*genetics ; Pneumonia, Mycoplasma/*microbiology ; }, abstract = {BACKGROUND: The imbalanced respiratory microbiota observed in pneumonia causes high morbidity and mortality in childhood. Respiratory metagenomic analysis demands a comprehensive microbial gene catalogue, which will significantly advance our understanding of host-microorganism interactions.<br><br>RESULTS: We collected 334 respiratory microbial samples from 171 healthy children and 76 children with pneumonia. The respiratory microbial gene catalogue we established comprised 2.25 million non-redundant microbial genes, covering 90.52% of prevalent genes. The major oropharyngeal microbial species found in healthy children were Prevotella and Streptococcus. In children with Mycoplasma pneumoniae pneumonia (MPP), oropharyngeal microbial diversity and associated gene numbers decreased compared with those of healthy children. The concurrence network of oropharyngeal microorganisms in patients predominantly featured Staphylococcus spp. and M. pneumoniae. Functional orthologues, which are associated with the metabolism of various lipids, membrane transport, and signal transduction, accumulated in the oropharyngeal microbiome of children with pneumonia. Several antibiotic resistance genes and virulence factor genes were identified in the genomes of M. pneumoniae and 13 other microorganisms reconstructed via metagenomic data. Although the common macrolide/β-lactam resistance genes were not identified in the assembled M. pneumoniae genome, a single-nucleotide polymorphism (A2063G) related to macrolide resistance was identified in a 23S ribosomal RNA gene.<br><br>CONCLUSIONS: The results of this study will facilitate exploration of unknown microbial components and host-microorganism interactions in studies of the respiratory microbiome. They will also yield further insights into the microbial aetiology of MPP.}, }
@article {pmid31339905, year = {2019}, author = {Sheahan, T and Hakstol, R and Kailasam, S and Glaister, GD and Hudson, AJ and Wieden, HJ}, title = {Rapid metagenomics analysis of EMS vehicles for monitoring pathogen load using nanopore DNA sequencing.}, journal = {PloS one}, volume = {14}, number = {7}, pages = {e0219961}, doi = {10.1371/journal.pone.0219961}, pmid = {31339905}, issn = {1932-6203}, mesh = {Ambulances/*standards ; Biological Monitoring/*methods ; Clostridium/genetics/isolation &amp; purification ; Cross Infection/microbiology/prevention &amp; control ; DNA, Bacterial/chemistry/genetics ; Metagenomics/*methods ; *Microbiota ; Nanopore Sequencing/*methods ; Staphylococcus/genetics/isolation &amp; purification ; }, abstract = {Pathogen monitoring, detection and removal are essential to public health and outbreak management. Systems are in place for monitoring the microbial load of hospitals and public health facilities with strategies to mitigate pathogen spread. However, no such strategies are in place for ambulances, which are tasked with transporting at-risk individuals in immunocompromised states. As standard culturing techniques require a laboratory setting, and are time consuming and labour intensive, our approach was designed to be portable, inexpensive and easy to use based on the MinION third-generation sequencing platform from Oxford Nanopore Technologies. We developed a transferable sampling-to-analysis pipeline to characterize the microbial community in emergency medical service vehicles. Our approach identified over sixty-eight organisms in ambulances to the genera level, with a proportion of these being connected with health-care associated infections, such as Clostridium spp. and Staphylococcus spp. We also monitored the microbiome of different locations across three ambulances over time, and examined the dynamic community of microorganisms found in emergency medical service vehicles. Observed differences identified hot spots, which may require heightened monitoring and extensive cleaning. Through metagenomics analysis it is also possible to identify how microorganisms spread between patients and colonize an ambulance over time. The sequencing results aid in the development of practices to mitigate disease spread, while also providing a useful tool for outbreak prediction through ongoing analysis of the ambulance microbiome to identify new and emerging pathogens. Overall, this pipeline allows for the tracking and monitoring of pathogenic microorganisms of epidemiological interest, including those related to health-care associated infections.}, }
@article {pmid31025063, year = {2019}, author = {Negi, A and Sarethy, IP}, title = {Microbial Biodeterioration of Cultural Heritage: Events, Colonization, and Analyses.}, journal = {Microbial ecology}, volume = {78}, number = {4}, pages = {1014-1029}, pmid = {31025063}, issn = {1432-184X}, mesh = {Architecture ; *Bacterial Physiological Phenomena ; Biofilms/*growth &amp; development ; Construction Materials/*microbiology ; Microbiota/*physiology ; }, abstract = {Geochemical cycles result in the chemical, physical, and mineralogical modification of rocks, eventually leading to formation of soil. However, when the stones and rocks are a part of historic buildings and monuments, the effects are deleterious. In addition, microorganisms also colonize these monuments over a period of time, resulting in formation of biofilms; their metabolites lead to physical weakening and discoloration of stone eventually. This process, known as biodeterioration, leads to a significant loss of cultural heritage. For formulating effective conservation strategies to prevent biodeterioration and restore monuments, it is important to know which microorganisms are colonizing the substrate and the different energy sources they consume to sustain themselves. With this view in scope, this review focuses on studies that have attempted to understand the process of biodeterioration, the mechanisms by which they colonize and affect the monuments, the techniques used for assessment of biodeterioration, and conservation strategies that aim to preserve the original integrity of the monuments. This review also includes the &quot;omics&quot; technologies that have started playing a large role in elucidating the nature of microorganisms, and how they can play a role in hastening the formulation of effective conservation strategies.}, }
@article {pmid30994187, year = {2019}, author = {Wang, T and Yang, C and Zhao, H}, title = {Prediction analysis for microbiome sequencing data.}, journal = {Biometrics}, volume = {75}, number = {3}, pages = {875-884}, doi = {10.1111/biom.13061}, pmid = {30994187}, issn = {1541-0420}, mesh = {Algorithms ; Bacteria/genetics ; Humans ; Likelihood Functions ; Microbiota/*genetics ; Monte Carlo Method ; Regression Analysis ; *Sequence Analysis ; }, abstract = {One goal of human microbiome studies is to relate host traits with human microbiome compositions. The analysis of microbial community sequencing data presents great statistical challenges, especially when the samples have different library sizes and the data are overdispersed with many zeros. To address these challenges, we introduce a new statistical framework, called predictive analysis in metagenomics via inverse regression (PAMIR), to analyze microbiome sequencing data. Within this framework, an inverse regression model is developed for overdispersed microbiota counts given the trait, and then a prediction rule is constructed by taking advantage of the dimension-reduction structure in the model. An efficient Monte Carlo expectation-maximization algorithm is proposed for maximum likelihood estimation. The method is further generalized to accommodate other types of covariates. We demonstrate the advantages of PAMIR through simulations and two real data examples.}, }
@article {pmid30875036, year = {2019}, author = {Al-Masaudi, S and El Kaoutari, A and Drula, E and Redwan, EM and Lombard, V and Henrissat, B}, title = {A metagenomics investigation of carbohydrate-active enzymes along the goat and camel intestinal tract.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {22}, number = {4}, pages = {429-435}, doi = {10.1007/s10123-019-00068-2}, pmid = {30875036}, issn = {1618-1905}, support = {67/130/35-HiCi//Deanship of Scientific Research, King Abdulaziz University, Jeddah/ ; }, mesh = {Animals ; Bacteria/classification/*enzymology/genetics/isolation &amp; purification ; Bacterial Proteins/*genetics/metabolism ; Camelus/metabolism/*microbiology ; *Carbohydrate Metabolism ; *Gastrointestinal Microbiome ; Goats/metabolism/*microbiology ; Intestines/microbiology ; Metagenomics ; Rumen/metabolism/microbiology ; Sheep ; }, abstract = {Studies of the digestive microbiota of ruminant animals most often focus on the bacterial diversity in the rumen or the feces of the animals, but little is known about the diversity and functions of their distal intestine. Here, the bacterial microbiota of the distal intestinal tract of two goats and two camels was investigated by metagenomics techniques. The bacterial taxonomic diversity and carbohydrate-active enzyme profile were estimated for samples taken from the small intestine, the large intestine, and the rectum of each animal. The bacterial diversity and abundance in the small intestine were lower than in the rectal and large intestinal samples. Analysis of the carbohydrate-active enzyme profiles at each site revealed a comparatively low abundance of enzymes targeting xylan and cellulose in all animals examined, similar to what has been reported earlier for sheep and therefore suggesting that plant cell wall digestion probably takes place elsewhere, such as in the rumen.}, }
@article {pmid30871675, year = {2019}, author = {Ni, YH}, title = {Bugs to debug? The exploration of gut microbiome in human health and diseases.}, journal = {Journal of the Formosan Medical Association = Taiwan yi zhi}, volume = {118 Suppl 1}, number = {}, pages = {S1-S2}, doi = {10.1016/j.jfma.2019.01.017}, pmid = {30871675}, issn = {0929-6646}, mesh = {*Disease ; Environment ; Gastrointestinal Microbiome/*physiology ; *Health ; Host Microbial Interactions/*physiology ; Humans ; Metagenomics ; }, }
@article {pmid30774010, year = {2019}, author = {Umiker, B and Lee, HH and Cope, J and Ajami, NJ and Laine, JP and Fregeau, C and Ferguson, H and Alves, SE and Sciammetta, N and Kleinschek, M and Salmon, M}, title = {The NLRP3 inflammasome mediates DSS-induced intestinal inflammation in Nod2 knockout mice.}, journal = {Innate immunity}, volume = {25}, number = {2}, pages = {132-143}, pmid = {30774010}, issn = {1753-4267}, mesh = {Animals ; Colitis/chemically induced/*immunology ; Crohn Disease/*immunology ; Dextran Sulfate ; Disease Models, Animal ; Furans/administration &amp; dosage/pharmacology ; Gastrointestinal Microbiome/*immunology ; Humans ; Inflammasomes/*metabolism ; Interleukin-1beta/metabolism ; Intestinal Mucosa/*immunology ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; NLR Family, Pyrin Domain-Containing 3 Protein/antagonists &amp; inhibitors/*metabolism ; Nod2 Signaling Adaptor Protein/*genetics ; Signal Transduction ; Sulfonamides/administration &amp; dosage/pharmacology ; }, abstract = {Crohn's disease (CD) is a chronic disorder of the gastrointestinal tract characterized by inflammation and intestinal epithelial injury. Loss of function mutations in the intracellular bacterial sensor NOD2 are major risk factors for the development of CD. In the absence of robust bacterial recognition by NOD2 an inflammatory cascade is initiated through alternative PRRs leading to CD. In the present study, MCC950, a specific small molecule inhibitor of NLR pyrin domain-containing protein 3 (NLRP3), abrogated dextran sodium sulfate (DSS)-induced intestinal inflammation in Nod2-/- mice. NLRP3 inflammasome formation was observed at a higher rate in NOD2-deficient small intestinal lamina propria cells after insult by DSS. NLRP3 complex formation led to an increase in IL-1β secretion in both the small intestine and colon of Nod2ko mice. This increase in IL-1β secretion in the intestine was attenuated by MCC950 leading to decreased disease severity in Nod2ko mice. Our work suggests that NLRP3 inflammasome activation may be a key driver of intestinal inflammation in the absence of functional NOD2. NLRP3 pathway inhibition can prevent intestinal inflammation in the absence of robust NOD2 signaling.}, }
@article {pmid30392727, year = {2019}, author = {Wang, L and Ravichandran, V and Yin, Y and Yin, J and Zhang, Y}, title = {Natural Products from Mammalian Gut Microbiota.}, journal = {Trends in biotechnology}, volume = {37}, number = {5}, pages = {492-504}, doi = {10.1016/j.tibtech.2018.10.003}, pmid = {30392727}, issn = {1879-3096}, mesh = {Animals ; *Bacteria/chemistry/genetics/metabolism ; *Biological Products ; Drug Discovery ; *Gastrointestinal Microbiome ; Genomics ; Humans ; Mammals/*microbiology ; }, abstract = {The mammalian gut has a remarkable abundance of microbes. These microbes have strong potential to biosynthesize distinct metabolites that are promising drugs, and many more bioactive compounds have yet to be explored as potential drug candidates. These small bioactive molecules often mediate important host-microbe and microbe-microbe interactions. In this review, we provide perspectives on and challenges associated with three mining strategies - culture-based, (meta)genomics-based, and metabolomics-based mining approaches - for discovering natural products derived from biosynthetic gene clusters (BGCs) in mammalian gut microbiota. In addition, we comprehensively summarize the structures, biological functions, and BGCs of these compounds. Improving these techniques, including by using combinatorial approaches, may accelerate drug discovery from gut microbes.}, }
@article {pmid31194675, year = {2019}, author = {Bernstein, DB and Dewhirst, FE and Segrè, D}, title = {Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, doi = {10.7554/eLife.39733}, pmid = {31194675}, issn = {2050-084X}, support = {T32GM008764/GM/NIGMS NIH HHS/United States ; T32 GM008764/GM/NIGMS NIH HHS/United States ; R01 DE024468/DE/NIDCR NIH HHS/United States ; R01 GM121950/GM/NIGMS NIH HHS/United States ; DE-SC0012627//Biological and Environmental Research/International ; RGP0020/2016//Human Frontier Science Program/International ; NSFOCE-BSF 1635070//National Science Foundation/International ; HR0011-15-C-0091//Defense Advanced Research Projects Agency/International ; R37DE016937/DE/NIDCR NIH HHS/United States ; R37 DE016937/DE/NIDCR NIH HHS/United States ; R01GM121950/GM/NIGMS NIH HHS/United States ; R01DE024468/DE/NIDCR NIH HHS/United States ; 1457695//National Science Foundation/International ; }, mesh = {Computational Biology ; Humans ; *Metabolic Networks and Pathways ; Metagenomics ; *Microbial Interactions ; *Microbiota ; Mouth/*microbiology ; }, abstract = {The biosynthetic capabilities of microbes underlie their growth and interactions, playing a prominent role in microbial community structure. For large, diverse microbial communities, prediction of these capabilities is limited by uncertainty about metabolic functions and environmental conditions. To address this challenge, we propose a probabilistic method, inspired by percolation theory, to computationally quantify how robustly a genome-derived metabolic network produces a given set of metabolites under an ensemble of variable environments. We used this method to compile an atlas of predicted biosynthetic capabilities for 97 metabolites across 456 human oral microbes. This atlas captures taxonomically-related trends in biomass composition, and makes it possible to estimate inter-microbial metabolic distances that correlate with microbial co-occurrences. We also found a distinct cluster of fastidious/uncultivated taxa, including several Saccharibacteria (TM7) species, characterized by their abundant metabolic deficiencies. By embracing uncertainty, our approach can be broadly applied to understanding metabolic interactions in complex microbial ecosystems.}, }
@article {pmid31703868, year = {2020}, author = {Chen, SH and Fegan, N and Kocharunchitt, C and Bowman, JP and Duffy, LL}, title = {Changes of the bacterial community diversity on chicken carcasses through an Australian poultry processing line.}, journal = {Food microbiology}, volume = {86}, number = {}, pages = {103350}, doi = {10.1016/j.fm.2019.103350}, pmid = {31703868}, issn = {1095-9998}, mesh = {Animals ; Australia ; Bacteria/classification/genetics/*growth &amp; development/isolation &amp; purification ; *Biodiversity ; Chickens/*microbiology ; Colony Count, Microbial ; Food Contamination/analysis ; Food Handling ; Poultry Products/analysis/*microbiology ; }, abstract = {Understanding the bacterial community profile through poultry processing could help the industry to produce better poultry products. In this study, 10 chicken carcasses were randomly sampled from before and after scalding, before and after immersion chilling, and after air chilling each through a modern commercial processing line, along with the contents of 10 caeca. The sampled processing line effectively reduced the bacterial counts by > 4.6 Log10 CFU/ml for each of Total Viable Counts, Escherichia coli and Campylobacter. However, the metagenomics results suggested that Lactobacillus, Staphylococcus and unclassified Lachnospiraceae persisted at all sampling stages. Pseudomonas, Paeniglutamicibacter, Chryseobacterium and Pseudarthrobacter comprised 47.2% in the bacterial community on samples after air chilling compared to 0.3% on samples after immersion chilling, whereas TVCs were the same. Overall, the current interventions of the investigated poultry processing line were unable to eliminate persistence of certain foodborne pathogens, despite a significant reduction of the overall bacterial counts. Chilling is an important controlling point in contamination/cross-contamination, particularly extended air chilling. Lastly, the large presence of Pseudomonas on chickens after air chilling may lead to downstream spoilage related issues, which needs more investigation to explore quantitatively the effect on the shelf life of poultry products.}, }
@article {pmid31462412, year = {2019}, author = {Stewart, DB and Wright, JR and Fowler, M and McLimans, CJ and Tokarev, V and Amaniera, I and Baker, O and Wong, HT and Brabec, J and Drucker, R and Lamendella, R}, title = {Integrated Meta-omics Reveals a Fungus-Associated Bacteriome and Distinct Functional Pathways in Clostridioides difficile Infection.}, journal = {mSphere}, volume = {4}, number = {4}, pages = {}, doi = {10.1128/mSphere.00454-19}, pmid = {31462412}, issn = {2379-5042}, mesh = {Adult ; Aged ; Aged, 80 and over ; Biofilms ; Clostridium Infections/*microbiology ; Clostridium difficile/*genetics ; Diarrhea/microbiology ; Feces/microbiology ; Fungi/*genetics ; *Gastrointestinal Microbiome ; Humans ; Metabolic Networks and Pathways ; *Metagenomics ; Middle Aged ; Sequence Analysis, DNA ; *Transcriptome ; }, abstract = {There has been no prior application of matched metagenomics and metatranscriptomics in Clostridioides difficile infection (CDI) evaluating the role of fungi in CDI or identifying community functions that contribute to the development of this disease. We collected diarrheal stools from 49 inpatients (18 of whom tested positive for CDI) under stringent inclusion criteria. We utilized a tiered sequencing approach to identify enriched bacterial and fungal taxa, using 16S and internal transcribed spacer (ITS) rRNA gene amplicon sequencing, with matched metagenomics and metatranscriptomics performed on a subset of the population. Distinct bacterial and fungal compositions distinguished CDI-positive and -negative patients, with the greatest differentiation between the cohorts observed based on bacterial metatranscriptomics. Bipartite network analyses demonstrated that Aspergillus and Penicillium taxa shared a strong positive relationship in CDI patients and together formed negative cooccurring relationships with several bacterial taxa, including the Oscillospira, Comamonadaceae, Microbacteriaceae, and Cytophagaceae Metatranscriptomics revealed enriched pathways in CDI patients associated with biofilm production primarily driven by Escherichia coli and Pseudomonas, quorum-sensing proteins, and two-component systems related to functions such as osmotic regulation, linoleic acid metabolism, and flagellar assembly. Differential expression of functional pathways unveiled a mechanism by which the causal dysbiosis of CDI may self-perpetuate, potentially contributing to treatment failures. We propose that CDI has a distinct fungus-associated bacteriome, and this first description of metatranscriptomics in human subjects with CDI demonstrates that inflammation, osmotic changes, and biofilm production are key elements of CDI pathophysiology.IMPORTANCE Our data suggest a potential role for fungi in the most common nosocomial bacterial infection in the United States, introducing the concept of a transkingdom interaction between bacteria and fungi in this disease. We also provide the first direct measure of microbial community function in Clostridioides difficile infection using patient-derived tissue samples, revealing antibiotic-independent mechanisms by which C. difficile infection may resist a return to a healthy gut microbiome.}, }
@article {pmid31429790, year = {2019}, author = {Yue, S and He, T and Li, B and Qu, Y and Peng, H and Chen, J and Lei, M and Chen, C and Wu, W}, title = {Effectiveness of Yi-Zhi-An-Shen granules on cognition and sleep quality in older adults with amnestic mild cognitive impairment: protocol for a randomized, double-blind, placebo-controlled trial.}, journal = {Trials}, volume = {20}, number = {1}, pages = {518}, doi = {10.1186/s13063-019-3607-x}, pmid = {31429790}, issn = {1745-6215}, support = {JDZX2015298//State Administration of Traditional Chinese Medicine of the People's Republic of China/ ; JDZX2015298//Chengdu Science and Technology Bureau/ ; 2018-504//Cadres Health Care Research Program of Sichuan Province (CN)/ ; 2017-501//Cadres Health Care Research Program of Sichuan Province (CN)/ ; }, mesh = {Aged ; Aged, 80 and over ; Amnesia/diagnosis/*drug therapy/physiopathology/psychology ; Biomarkers/blood ; China ; Cognition/*drug effects ; Cognitive Dysfunction/diagnosis/*drug therapy/physiopathology/psychology ; Double-Blind Method ; Drugs, Chinese Herbal/adverse effects/therapeutic use ; Female ; Gastrointestinal Microbiome/drug effects ; Humans ; Hypnotics and Sedatives/adverse effects/*therapeutic use ; Inflammation Mediators/blood ; Male ; Memory/*drug effects ; Middle Aged ; Nootropic Agents/adverse effects/*therapeutic use ; Randomized Controlled Trials as Topic ; Sleep/*drug effects ; Time Factors ; Treatment Outcome ; }, abstract = {BACKGROUND: Amnestic mild cognitive impairment (aMCI) is a syndrome characterized by significant forgetfulness that does not meet the criteria of dementia. Individuals with aMCI are at greater risk of progressing to dementia. Current studies suggest that good sleep quality is linked with preserved cognition in the elderly, and sleep complaints are common among the elderly with amnesia. Therefore, improving their sleep may be helpful for maintaining and improving their cognitive capacity. According to the theory of traditional Chinese medicine, Yi-Zhi-An-Shen is an herbal compound which may ameliorate forgetfulness and sleep disorders. As growing evidence indicates that the gut microbiome is associated with major mental symptoms, a hypothesis was proposed that Yi-Zhi-An-Shen granules (YZASG) might work by alternating microbial abundance and diversity. In this study, the investigators intend to assess the efficacy of YZASG on global cognition in the elderly suffering from aMCI and evaluate its safety as well as its potential mechanisms via sleep quality, fecal microbial 16S ribosomal DNA and metagenomics analyses, and serum markers.<br><br>METHODS/DESIGN: This study is a randomized, double-blind, placebo-controlled clinical trial. A total of 80 patients (aged 60-85 years) will be recruited and allocated randomly to a treatment group and a placebo group in a 1:1 ratio and will then be administered YZASG or isodose placebo three times a day. The intervention course is 16 weeks, with an 18 months follow-up. The primary outcome is the Alzheimer's Disease Assessment Scale-Cognitive Subscale. Secondary outcome measures are the Mini-Mental State Examination, Montreal Cognitive Assessment, Pittsburgh Sleep Quality Index, serum concentrations of immunological factors and inflammatory cytokines, and fecal microbiota. Fecal microbiota will only be collected at the baseline and endpoint of the intervention.<br><br>DISCUSSION: The results of this trial will be conducive to assessing the safety and effectiveness on cognition of YZASG in intervening aMCI among the elderly and determining if it takes effect via the improvement of sleep quality, regulation of gut microbiota, and concentration of certain serum markers.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov, NCT03601000 . Registered on 26 July 2018.}, }
@article {pmid31292233, year = {2019}, author = {Moeller, AH and Gomes-Neto, JC and Mantz, S and Kittana, H and Segura Munoz, RR and Schmaltz, RJ and Ramer-Tait, AE and Nachman, MW}, title = {Experimental Evidence for Adaptation to Species-Specific Gut Microbiota in House Mice.}, journal = {mSphere}, volume = {4}, number = {4}, pages = {}, doi = {10.1128/mSphere.00387-19}, pmid = {31292233}, issn = {2379-5042}, support = {R01 GM074245/GM/NIGMS NIH HHS/United States ; R01 GM127468/GM/NIGMS NIH HHS/United States ; }, mesh = {*Adaptation, Physiological ; Animals ; Bacteria/*classification ; Female ; *Gastrointestinal Microbiome ; Germ-Free Life ; *Host Microbial Interactions ; *Host Specificity ; Male ; Metagenome ; Mice ; Mice, Inbred C57BL ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; }, abstract = {The gut microbial communities of mammals have codiversified with host species, and changes in the gut microbiota can have profound effects on host fitness. Therefore, the gut microbiota may drive adaptation in mammalian species, but this possibility is underexplored. Here, we show that the gut microbiota has codiversified with mice in the genus Mus over the past ∼6 million years, and we present experimental evidence that the gut microbiota has driven adaptive evolution of the house mouse, Mus musculusdomesticus Phylogenetic analyses of metagenome-assembled bacterial genomic sequences revealed that gut bacterial lineages have been retained within and diversified alongside Mus species over evolutionary time. Transplantation of gut microbiotas from various Mus species into germfree M. m. domesticus showed that foreign gut microbiotas slowed growth rate and upregulated macrophage inflammatory protein in hosts. These results suggest adaptation by M. m. domesticus to its gut microbiota since it diverged from other Mus species.IMPORTANCE The communities of bacteria that reside within mammalian guts are deeply integrated with their hosts, but the impact of this gut microbiota on mammalian evolution remains poorly understood. Experimental transplantation of the gut microbiota between mouse species revealed that foreign gut microbiotas lowered the host growth rate and upregulated the expression of an immunomodulating cytokine. In addition, foreign gut microbiotas increased host liver sizes and attenuated sex-specific differences in host muscle and fat content. These results suggest that the house mouse has adapted to its species-specific gut microbiota.}, }
@article {pmid31601001, year = {2019}, author = {Ali, NABM and Mac Aogáin, M and Morales, RF and Tiew, PY and Chotirmall, SH}, title = {Optimisation and Benchmarking of Targeted Amplicon Sequencing for Mycobiome Analysis of Respiratory Specimens.}, journal = {International journal of molecular sciences}, volume = {20}, number = {20}, pages = {}, pmid = {31601001}, issn = {1422-0067}, support = {Clinician-Scientist Individual Research Grant (MOH-000141)//Singapore Ministry of Health's National Medical Research Council/ ; Research Training Fellowship (NMRC/Fellowship/0049/2017)//Singapore Ministry of Health's National Medical Research Council/ ; Singapore Ministry of Education Academic Research Fund Tier 1 (2016-T1-001-050)//Singapore Ministry of Education/ ; NTU Integrated Medical, Biological and Environmental Life Sciences (NIMBELS) [NIM/03/2018]//Nanyang Technological University/ ; }, mesh = {Benchmarking ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Fungi/genetics ; Humans ; *Metagenome ; *Metagenomics/methods ; *Mycobiome ; Respiratory Mucosa/*microbiology ; }, abstract = {(1) Background: Firm consensus has yet to be established in relation to taxonomic classification and primer choice in targeted amplicon sequencing of the mycobiome. While the nuclear ribosomal internal transcribed spacer (ITS) region are recognized as the formal fungal taxonomic barcode, appraisal of different ITS sub-regions and the influence of DNA extraction methods have not been comprehensively undertaken using human respiratory specimens. (2) Methods: We performed ITS analysis of respiratory (sputum) samples by assessing (a) the effect of alternate DNA extraction techniques and (b) an evaluation of four different ITS primer pairs (ITS1F and ITS2; ITS1-30F and ITS1-217R; gITS7ngs and ITS4ng; and Fseq and Rseq) on the mycobiome profiles generated for mock fungal communities and their respective clinical (airway) specimens. (3) Results: Primer pairs varied in their resulting ITS mycobiome profiles, suggesting that particular pairs may be more relevant for analysis of respiratory samples compared to others. Assessment of DNA extraction methods highlighted lower final DNA concentrations achieved by mechanical disruption compared to enzymatic lysis. However, despite lower yields, DNA liberated by mechanical lysis more readily yielded ITS bands with highest success in combination with the Fseq and Rseq primers. (4) Conclusion: Choice of extraction method, primers used, and sequencing approach are all important considerations in sequencing the mycobiome and should be tailored to sample type. A standardization of approach to mycobiome studies using respiratory specimens will permit more reliable comparisons between studies and improve our understanding of the role of fungi in the human airway.}, }
@article {pmid31502536, year = {2019}, author = {McLaren, MR and Willis, AD and Callahan, BJ}, title = {Consistent and correctable bias in metagenomic sequencing experiments.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, doi = {10.7554/eLife.46923}, pmid = {31502536}, issn = {2050-084X}, mesh = {Bacteria/classification/genetics ; *Bias ; Biota ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Metagenomics/*methods ; *Models, Theoretical ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Marker-gene and metagenomic sequencing have profoundly expanded our ability to measure biological communities. But the measurements they provide differ from the truth, often dramatically, because these experiments are biased toward detecting some taxa over others. This experimental bias makes the taxon or gene abundances measured by different protocols quantitatively incomparable and can lead to spurious biological conclusions. We propose a mathematical model for how bias distorts community measurements based on the properties of real experiments. We validate this model with 16S rRNA gene and shotgun metagenomics data from defined bacterial communities. Our model better fits the experimental data despite being simpler than previous models. We illustrate how our model can be used to evaluate protocols, to understand the effect of bias on downstream statistical analyses, and to measure and correct bias given suitable calibration controls. These results illuminate new avenues toward truly quantitative and reproducible metagenomics measurements.}, }
@article {pmid31502535, year = {2019}, author = {Forsberg, KJ and Bhatt, IV and Schmidtke, DT and Javanmardi, K and Dillard, KE and Stoddard, BL and Finkelstein, IJ and Kaiser, BK and Malik, HS}, title = {Functional metagenomics-guided discovery of potent Cas9 inhibitors in the human microbiome.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, doi = {10.7554/eLife.46540}, pmid = {31502535}, issn = {2050-084X}, support = {R01 GM105691/GM/NIGMS NIH HHS/United States ; F31 GM125201/GM/NIGMS NIH HHS/United States ; R01 GM124131/GM/NIGMS NIH HHS/United States ; F-1808//Welch Foundation/International ; }, mesh = {Bacterial Proteins/genetics/isolation &amp; purification/*metabolism ; CRISPR-Associated Protein 9/*antagonists &amp; inhibitors ; Enzyme Inhibitors/isolation &amp; purification/*metabolism ; Feces/microbiology/virology ; Humans ; Metagenomics ; *Microbiota ; Mouth/microbiology/virology ; Viral Proteins/genetics/isolation &amp; purification/*metabolism ; }, abstract = {CRISPR-Cas systems protect bacteria and archaea from phages and other mobile genetic elements, which use small anti-CRISPR (Acr) proteins to overcome CRISPR-Cas immunity. Because Acrs are challenging to identify, their natural diversity and impact on microbial ecosystems are underappreciated. To overcome this discovery bottleneck, we developed a high-throughput functional selection to isolate ten DNA fragments from human oral and fecal metagenomes that inhibit Streptococcus pyogenes Cas9 (SpyCas9) in Escherichia coli. The most potent Acr from this set, AcrIIA11, was recovered from a Lachnospiraceae phage. We found that AcrIIA11 inhibits SpyCas9 in bacteria and in human cells. AcrIIA11 homologs are distributed across diverse bacteria; many distantly-related homologs inhibit both SpyCas9 and a divergent Cas9 from Treponema denticola. We find that AcrIIA11 antagonizes SpyCas9 using a different mechanism than other previously characterized Type II-A Acrs. Our study highlights the power of functional selection to uncover widespread Cas9 inhibitors within diverse microbiomes.}, }
@article {pmid31293986, year = {2019}, author = {Zhou, P and Li, Z and Xu, D and Wang, Y and Bai, Q and Feng, Y and Su, G and Chen, P and Wang, Y and Liu, H and Wang, X and Zhang, R and Wang, Y}, title = {Cepharanthine Hydrochloride Improves Cisplatin Chemotherapy and Enhances Immunity by Regulating Intestinal Microbes in Mice.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {225}, doi = {10.3389/fcimb.2019.00225}, pmid = {31293986}, issn = {2235-2988}, mesh = {Animals ; Antineoplastic Agents/pharmacology ; Apoptosis/drug effects ; Bacteria/classification/drug effects ; Benzylisoquinolines/*pharmacology ; Cell Line, Tumor ; Cisplatin/*pharmacology ; DNA, Ribosomal/genetics ; Disease Models, Animal ; Drug Synergism ; Drug Therapy/*methods ; Esophageal Neoplasms/drug therapy/pathology ; Esophageal Squamous Cell Carcinoma/drug therapy/pathology ; Female ; Gastrointestinal Microbiome/*drug effects/physiology ; Humans ; Immunity/*drug effects ; Immunity, Innate/drug effects ; Intestinal Mucosa/*drug effects/immunology/microbiology ; Metagenomics ; Mice ; Mice, Inbred BALB C ; Mice, Nude ; Myeloid Differentiation Factor 88/metabolism ; Signal Transduction/drug effects ; Toll-Like Receptor 4/metabolism ; Xenograft Model Antitumor Assays ; }, abstract = {Chemotherapy is one of the major treatment strategies for esophageal squamous cell carcinoma (ESCC). Unfortunately, most chemotherapeutic drugs have significant impacts on the intestinal microbes, resulting in side effects and reduced efficiency. Therefore, new strategies capable of overcoming these disadvantages of current chemotherapies are in urgent need. The natural product, Cepharanthine hydrochloride (CEH), is known for its anticancer and immunoregulatory properties. By sequencing the V4 region of 16S rDNA, we characterized the microbes of tumor-bearing mice treated with different chemotherapy strategies, including with CEH. We found that CEH improved the therapeutic effect of CDDP by manipulating the gut microbiota. Through metagenomic analyses of the microbes community, we identified a severe compositional and functional imbalance in the gut microbes community after CDDP treatment. However, CEH improved the effect of chemotherapy and ameliorated CDDP treatment-induced imbalance in the intestinal microbes. Mechanically, CEH activated TLR4 and MYD88 innate immune signaling, which is advantageous for the activation of the host's innate immunity to exert a balanced intestinal environment as well as to trigger a better chemotherapeutic response to esophageal cancer. In addition, TNFR death receptors were activated to induce apoptosis. In summary, our findings suggest that chemotherapy of CDDP combined with CEH increased the effect of chemotherapy and reduced the side effects on the microbes and intestinal mucosal immunity. We believe that these findings provide a theoretical basis for new clinical treatment strategies.}, }
@article {pmid32065891, year = {2020}, author = {Santos, SS and Schöler, A and Nielsen, TK and Hansen, LH and Schloter, M and Winding, A}, title = {Land use as a driver for protist community structure in soils under agricultural use across Europe.}, journal = {The Science of the total environment}, volume = {717}, number = {}, pages = {137228}, doi = {10.1016/j.scitotenv.2020.137228}, pmid = {32065891}, issn = {1879-1026}, abstract = {Soil biodiversity is threatened by intensification of land use. The consequences of different land use on belowground biodiversity remain insufficiently explored for soil protists. Alongside being abundant and extremely diverse in soil, protists provide many ecosystem services: key players in the microbial loop, turnover of organic matter and stimulation of plant growth-promoting rhizobacteria. However, we lack knowledge of effects of site, land use intensity and management on diversity of soil protists. Here we assessed protist communities in four European arable sites with contrasting land use intensities at each site: Lusignan, France; Moskanjci, Slovenia; Castro Verde, Portugal and Scheyern, Germany as well as two grassland sites: Hainich, Germany and Lancaster, UK. Each site has consistent agricultural management history of low and high land use intensities quantified in terms of land use index (LUI). We employed high-throughput sequencing of environmental DNA, targeting the V4 region of the 18S rRNA gene. By assigning the protist composition to trophic groups, we inspected for effects of management, and other biotic and abiotic variables. While overall protist richness was unaffected by LUI within sites, specific trophic groups such as plant pathogens and saprotrophs were affected. Effects on protist biome across land uses and sites were also observed. LUI sensitive taxa were taxonomically diverse in each plot, and their trophic groups responded in specific patterns to specific practices. The most abundant trophic group was phagotrophs (73%), followed by photoautotrophs (16%), plant pathogens (4%), animal parasites (2%) and saprotrophs (1%). Community compositions and factors affecting the structure of individual trophic groups differed between land uses and management systems. The agricultural management selected for distinct protist populations as well as specific functional traits, and the protist community and diversity were indeed affected by site, LUI and management, which indicates the ecological significance of protists in the soil food web.}, }
@article {pmid32065512, year = {2020}, author = {van der Heyde, M and Bunce, M and Wardell-Johnson, G and Fernandes, K and White, NE and Nevill, P}, title = {Testing multiple substrates for terrestrial biodiversity monitoring using environmental DNA (eDNA) metabarcoding.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13148}, pmid = {32065512}, issn = {1755-0998}, abstract = {Biological surveys based on visual identification of the biota are challenging, expensive, and time consuming, yet crucial for effective biomonitoring. DNA metabarcoding is a rapidly developing technology that can also facilitate biological surveys. This method involves the use of next generation sequencing technology to determine the community composition of a sample. However, it is uncertain as to what biological substrate should be the primary focus of metabarcoding surveys. This study aims to test multiple sample substrates (soil, scat, plant material and bulk arthropods) to determine what organisms can be detected from each and where they overlap. Samples (n = 200) were collected in the Pilbara (hot desert climate) and Swan Coastal Plain (hot mediterranean climate) regions of Western Australia. Soil samples yielded little plant or animal DNA, especially in the Pilbara, likely due to conditions not conducive to long-term preservation. In contrast, scat samples contained the highest overall diversity with 131 plant, vertebrate, and invertebrate families detected. Invertebrate and plant sequences were detected in the plant (86 families), pitfall (127 families), and vane trap (126 families) samples. In total 278 families were recovered from the survey, 217 in the Swan Coastal Plain and 156 in the Pilbara. Aside from soil, 22-43% of the families detected were unique to the particular substrate and community composition varied significantly between substrates. These results demonstrate the importance of selecting appropriate metabarcoding substrates when undertaking terrestrial surveys. If the aim is to broadly capture all biota then multiple substrates will be required.}, }
@article {pmid31111267, year = {2019}, author = {Jadeja, NB and Purohit, HJ and Kapley, A}, title = {Decoding microbial community intelligence through metagenomics for efficient wastewater treatment.}, journal = {Functional &amp; integrative genomics}, volume = {19}, number = {6}, pages = {839-851}, pmid = {31111267}, issn = {1438-7948}, mesh = {Biodegradation, Environmental ; Chlorobenzoates/analysis/metabolism ; Cresols/analysis/metabolism ; *Metagenome ; Metagenomics/*methods ; *Microbiota ; Waste Water/chemistry/*microbiology ; }, abstract = {Activated sludge, a microbial ecosystem at industrial wastewater treatment plants, is an active collection of diverse gene pool that creates the intelligence required for coexistence at the cost of pollutants. This study has analyzed one such ecosystem from a site treating wastewater pooled from over 200 different industries. The metagenomics approach used could predict the degradative pathways of more than 30 dominating molecules commonly found in wastewater. Results were extended to design a bioremediation strategy using 4-methylphenol, 2-chlorobenzoate, and 4-chlorobenzoate as target compounds. Catabolic potential required to degrade four aromatic families, namely benzoate family, PAH family, phenol family, and PCB family, was mapped. Results demonstrated a network of diverse genera, where a few phylotypes were seen to contain diverse catabolic capacities and were seen to be present in multiple networks. The study highlights the importance of looking more closely at the microbial community of activated sludge to harness its latent potential. Conventionally treated as a black box, the activated biomass does not perform at its full potential. Metagenomics allows a clearer insight into the complex pathways operating at the site and the detailed documentation of genes allows the activated biomass to be used as a bioresource.}, }
@article {pmid32058299, year = {2020}, author = {Khachatryan, L and de Leeuw, RH and Kraakman, MEM and Pappas, N and Te Raa, M and Mei, H and de Knijff, P and Laros, JFJ}, title = {Taxonomic classification and abundance estimation using 16S and WGS-A comparison using controlled reference samples.}, journal = {Forensic science international. Genetics}, volume = {46}, number = {}, pages = {102257}, doi = {10.1016/j.fsigen.2020.102257}, pmid = {32058299}, issn = {1878-0326}, abstract = {The assessment of microbiome biodiversity is the most common application of metagenomics. While 16S sequencing remains standard procedure for taxonomic profiling of metagenomic data, a growing number of studies have clearly demonstrated biases associated with this method. By using Whole Genome Shotgun sequencing (WGS) metagenomics, most of the known restrictions associated with 16S data are alleviated. However, due to the computationally intensive data analyses and higher sequencing costs, WGS based metagenomics remains a less popular option. Selecting the experiment type that provides a comprehensive, yet manageable amount of information is a challenge encountered in many metagenomics studies. In this work, we created a series of artificial bacterial mixes, each with a different distribution of skin-associated microbial species. These mixes were used to estimate the resolution of two different metagenomic experiments - 16S and WGS - and to evaluate several different bioinformatics approaches for taxonomic read classification. In all test cases, WGS approaches provide much more accurate results, in terms of taxa prediction and abundance estimation, in comparison to those of 16S. Furthermore, we demonstrate that a 16S dataset, analysed using different state of the art techniques and reference databases, can produce widely different results. In light of the fact that most forensic metagenomic analysis are still performed using 16S data, our results are especially important.}, }
@article {pmid31756192, year = {2019}, author = {Watts, GS and Thornton, JE and Youens-Clark, K and Ponsero, AJ and Slepian, MJ and Menashi, E and Hu, C and Deng, W and Armstrong, DG and Reed, S and Cranmer, LD and Hurwitz, BL}, title = {Identification and quantitation of clinically relevant microbes in patient samples: Comparison of three k-mer based classifiers for speed, accuracy, and sensitivity.}, journal = {PLoS computational biology}, volume = {15}, number = {11}, pages = {e1006863}, pmid = {31756192}, issn = {1553-7358}, mesh = {Algorithms ; Bacteria/*genetics/*isolation &amp; purification ; DNA Barcoding, Taxonomic/methods ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Metagenomics/*methods ; Microbiota/genetics ; Sensitivity and Specificity ; Sequence Analysis, DNA/methods ; }, abstract = {Infections are a serious health concern worldwide, particularly in vulnerable populations such as the immunocompromised, elderly, and young. Advances in metagenomic sequencing availability, speed, and decreased cost offer the opportunity to supplement or even replace culture-based identification of pathogens with DNA sequence-based diagnostics. Adopting metagenomic analysis for clinical use requires that all aspects of the workflow are optimized and tested, including data analysis and computational time and resources. We tested the accuracy, sensitivity, and resource requirements of three top metagenomic taxonomic classifiers that use fast k-mer based algorithms: Centrifuge, CLARK, and KrakenUniq. Binary mixtures of bacteria showed all three reliably identified organisms down to 1% relative abundance, while only the relative abundance estimates of Centrifuge and CLARK were accurate. All three classifiers identified the organisms present in their default databases from a mock bacterial community of 20 organisms, but only Centrifuge had no false positives. In addition, Centrifuge required far less computational resources and time for analysis. Centrifuge analysis of metagenomes obtained from samples of VAP, infected DFUs, and FN showed Centrifuge identified pathogenic bacteria and one virus that were corroborated by culture or a clinical PCR assay. Importantly, in both diabetic foot ulcer patients, metagenomic sequencing identified pathogens 4-6 weeks before culture. Finally, we show that Centrifuge results were minimally affected by elimination of time-consuming read quality control and host screening steps.}, }
@article {pmid31585122, year = {2020}, author = {Gu, S and Zaidi, S and Hassan, MI and Mohammad, T and Malta, TM and Noushmehr, H and Nguyen, B and Crandall, KA and Srivastav, J and Obias, V and Lin, P and Nguyen, BN and Yao, M and Yao, R and King, CH and Mazumder, R and Mishra, B and Rao, S and Mishra, L}, title = {Mutated CEACAMs Disrupt Transforming Growth Factor Beta Signaling and Alter the Intestinal Microbiome to Promote Colorectal Carcinogenesis.}, journal = {Gastroenterology}, volume = {158}, number = {1}, pages = {238-252}, doi = {10.1053/j.gastro.2019.09.023}, pmid = {31585122}, issn = {1528-0012}, support = {R01 AA023146/AA/NIAAA NIH HHS/United States ; R01 CA236591/CA/NCI NIH HHS/United States ; U01 CA230690/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics/isolation &amp; purification ; Carcinoembryonic Antigen/*genetics/metabolism ; Carcinogenesis/*genetics ; Colorectal Neoplasms/*genetics/microbiology/mortality ; Disease Models, Animal ; Feces/microbiology ; GPI-Linked Proteins/genetics/metabolism ; Gain of Function Mutation ; Gastrointestinal Microbiome/*physiology ; Gene Expression Regulation, Neoplastic ; HCT116 Cells ; Humans ; Metagenomics ; Mice ; Mice, Transgenic ; Protein Domains/genetics ; Receptor, Transforming Growth Factor-beta Type I/metabolism ; Signal Transduction/*genetics ; Smad4 Protein/genetics/metabolism ; Spheroids, Cellular ; Survival Analysis ; Transforming Growth Factor beta/metabolism ; }, abstract = {BACKGROUND &amp; AIMS: We studied interactions among proteins of the carcinoembryonic antigen-related cell adhesion molecule (CEACAM) family, which interact with microbes, and transforming growth factor beta (TGFB) signaling pathway, which is often altered in colorectal cancer cells. We investigated mechanisms by which CEACAM proteins inhibit TGFB signaling and alter the intestinal microbiome to promote colorectal carcinogenesis.<br><br>METHODS: We collected data on DNA sequences, messenger RNA expression levels, and patient survival times from 456 colorectal adenocarcinoma cases, and a separate set of 594 samples of colorectal adenocarcinomas, in The Cancer Genome Atlas. We performed shotgun metagenomic sequencing analyses of feces from wild-type mice and mice with defects in TGFB signaling (Sptbn1+/- and Smad4+/-/Sptbn1+/-) to identify changes in microbiota composition before development of colon tumors. CEACAM protein and its mutants were overexpressed in SW480 and HCT116 colorectal cancer cell lines, which were analyzed by immunoblotting and proliferation and colony formation assays.<br><br>RESULTS: In colorectal adenocarcinomas, high expression levels of genes encoding CEACAM proteins, especially CEACAM5, were associated with reduced survival times of patients. There was an inverse correlation between expression of CEACAM genes and expression of TGFB pathway genes (TGFBR1, TGFBR2, and SMAD3). In colorectal adenocarcinomas, we also found an inverse correlation between expression of genes in the TGFB signaling pathway and genes that regulate stem cell features of cells. We found mutations encoding L640I and A643T in the B3 domain of human CEACAM5 in colorectal adenocarcinomas; structural studies indicated that these mutations would alter the interaction between CEACAM5 and TGFBR1. Overexpression of these mutants in SW480 and HCT116 colorectal cancer cell lines increased their anchorage-independent growth and inhibited TGFB signaling to a greater extent than overexpression of wild-type CEACAM5, indicating that they are gain-of-function mutations. Compared with feces from wild-type mice, feces from mice with defects in TGFB signaling had increased abundance of bacterial species that have been associated with the development of colon tumors, including Clostridium septicum, and decreased amounts of beneficial bacteria, such as Bacteroides vulgatus and Parabacteroides distasonis.<br><br>CONCLUSION: We found expression of CEACAMs and genes that regulate stem cell features of cells to be increased in colorectal adenocarcinomas and inversely correlated with expression of TGFB pathway genes. We found colorectal adenocarcinomas to express mutant forms of CEACAM5 that inhibit TGFB signaling and increase proliferation and colony formation. We propose that CEACAM proteins disrupt TGFB signaling, which alters the composition of the intestinal microbiome to promote colorectal carcinogenesis.}, }
@article {pmid31022704, year = {2019}, author = {Benic, GZ and Farella, M and Morgan, XC and Viswam, J and Heng, NC and Cannon, RD and Mei, L}, title = {Oral probiotics reduce halitosis in patients wearing orthodontic braces: a randomized, triple-blind, placebo-controlled trial.}, journal = {Journal of breath research}, volume = {13}, number = {3}, pages = {036010}, doi = {10.1088/1752-7163/ab1c81}, pmid = {31022704}, issn = {1752-7163}, mesh = {Administration, Oral ; Adolescent ; Adult ; Breath Tests ; Child ; Dental Plaque Index ; Double-Blind Method ; Female ; Halitosis/*microbiology/*therapy ; Humans ; Male ; Metagenomics ; Microbiota/genetics ; *Orthodontic Brackets ; Periodontal Index ; Placebos ; Probiotics/*administration &amp; dosage/*therapeutic use ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Sulfur Compounds/analysis ; Young Adult ; }, abstract = {Orthodontic braces can impede oral hygiene and promote halitosis. The aim of the study was to investigate the effect of the oral probiotic Streptococcus salivarius M18 on oral hygiene indices and halitosis in patients wearing orthodontic braces. The study was a prospective, randomized, triple-blind, placebo-controlled trial. Patients undergoing fixed orthodontic treatment were randomly allocated to a probiotic group (n = 32) and a placebo group (n = 32). Patients consumed 2 lozenges d-1 for one month. Assessments were taken at baseline, at the end of the intervention, and at a 3 month follow-up. The outcome measures were plaque index (PI), gingival index (GI) and halitosis-causing volatile sulfur compound (VSC) levels. The dental biofilms before and after the intervention were analyzed utilizing next-generation sequencing of bacterial 16S rRNA genes. PI and GI scores were not significantly influenced by the probiotic intervention (intervention × time: p > 0.05). The level of VSCs decreased significantly in both the probiotic group (VSC reduction = -8.5%, 95%CI = -7.4% to -9.1%, p = 0.015) and the placebo group (-6.5%, 95%CI = -6.0% to -7.4%, p = 0.039) after 1 month intervention. However, at the 3 month follow-up, the VSC levels in the placebo group returned to baseline levels whereas those in the probiotic group decreased further (-10.8%, 95%CI = -10.5% to -12.9%, p = 0.005). Time, but not treatment, was associated with the decrease in microbial community alpha diversity and a modest effect on beta diversity. Oral probiotic S. salivarius M18 reduced the level of halitosis in patients with orthodontic braces, but had minimal effects on PI, GI and dental biofilm microflora.}, }
@article {pmid31896192, year = {2020}, author = {Li, W and Tan, Q and Zhou, W and Chen, J and Li, Y and Wang, F and Zhang, J}, title = {Impact of substrate material and chlorine/chloramine on the composition and function of a young biofilm microbial community as revealed by high-throughput 16S rRNA sequencing.}, journal = {Chemosphere}, volume = {242}, number = {}, pages = {125310}, doi = {10.1016/j.chemosphere.2019.125310}, pmid = {31896192}, issn = {1879-1298}, mesh = {Biofilms/*drug effects ; Chloramines/*pharmacology ; Chlorine/*pharmacology ; Construction Materials/microbiology ; Disinfectants/*pharmacology ; Disinfection/methods ; Drinking Water/chemistry/*microbiology ; Iron ; Microbiota/*drug effects/genetics ; RNA, Ribosomal, 16S/genetics ; Stainless Steel ; Water Microbiology/standards ; }, abstract = {The bacterial composition of biofilms in drinking water distribution systems is significantly impacted by the disinfection regime and substrate material. However, studies that have addressed the changes in the biofilm community during the early stage of formation (less than 10 weeks) were not yet adequate. Here, we explore the effects of the substrate materials (cast iron, stainless steel, copper, polyvinyl chloride, and high density polyethylene) and different disinfectants (chlorine and chloramine) on the community composition and function of young biofilm by using 16S rDNA sequencing. The results showed that Alphaproteobacteria (39.14%-80.87%) and Actinobacteria (5.90%-40.03%) were the dominant classes in chlorine-disinfection samples, while Alphaproteobacteria (17.46%-74.18%) and Betaproteobacteria (3.79%-68.50%) became dominant in a chloraminated group. The infrequently discussed genus Phreatobacter became predominant in the chlorinated samples, but it was inhibited by chloramine and copper ions. The key driver of the community composition was indicated as different disinfectants according to principle coordination analysis (PCoA) and Permutational multivariate analysis of variance (Adonis test), and the bacterial community changed significantly over time. Communities of biofilms grown on cast iron showed a great distance from the other materials according to Bray-Curtis dissimilarity, and they had a unique dominant genus, Dechloromonas. A metagenomics prediction based on 16S rDNA was used to detect the functional pathways of antibiotic biosynthesis and beta-lactam resistance, and it revealed that several pathways were significantly different in terms of their chlorinated and chloraminated groups.}, }
@article {pmid31877275, year = {2020}, author = {Fuentes-Valencia, MA and Fajer-Ávila, EJ and Chávez-Sánchez, MC and Martínez-Palacios, CA and Martínez-Chávez, CC and Junqueira-Machado, G and Lara, HH and Raggi, L and Gómez-Gil, B and Pestryakov, AA and Bogdanchikova, N}, title = {Silver nanoparticles are lethal to the ciliate model Tetrahymena and safe to the pike silverside Chirostoma estor.}, journal = {Experimental parasitology}, volume = {209}, number = {}, pages = {107825}, doi = {10.1016/j.exppara.2019.107825}, pmid = {31877275}, issn = {1090-2449}, mesh = {Animals ; Aquaculture ; Ectoparasitic Infestations/drug therapy/parasitology/*veterinary ; Fish Diseases/*drug therapy/parasitology ; Fishes ; Fresh Water ; Gastrointestinal Microbiome ; Humans ; Lethal Dose 50 ; Metagenomics ; Metal Nanoparticles/chemistry/*toxicity ; Microscopy, Electron, Scanning/veterinary ; Silver/chemistry/*pharmacology/toxicity ; Tetrahymena/*drug effects/ultrastructure ; }, abstract = {Ciliate ectoparasites are one of the most important groups of pathogens in fish culture, and the traditional treatments are sometimes harmful to the fish and the environment. Thus, the search for novel compounds that are effective at low concentrations and safe for fish are necessary to optimise treatments in aquaculture. The antiprotozoal capacity of silver nanoparticles (AgNPs) against the ciliate Tetrahymena has been documented; however, their toxicity may vary with the synthesis methodology and nanoparticle size. The objectives of this study were a) to evaluate the acute toxicity in vitro of two AgNPs (Argovit™ and UTSA) on Tetrahymena sp., a biological model for ciliated ectoparasites of fish and b) to test the safety of lethal and higher doses of UTSA AgNPs for ciliates on the fish C. estor. Light microscopy and scanning electron microscopy (SEM) were used to determine whether AgNPs affected the structure of the cell surface of Tetrahymena. The mortality, histopathological alterations and metagenomics of the fish were used to determine the major effects of UTSA AgNPs. In Tetrahymena, the median lethal concentration (LC50) for Argovit™ was 2501 ± 1717 ng/L at 15 min and 796 ± 510 ng/L at 60 min, while the LC50 for UTSA AgNPs was 4 ± 2 and 1 ± 0.6 ng/L at 15 min and 60 min, respectively. A concentration of 3300 ng/L Argovit™ and 10.6 ng/L UTSA AgNPs for 15 and 60 min, respectively, was 100% effective against Tetrahymena. After 60 min of exposure to 0.25 and 0.50 ng/L UTSA AgNPs, the number of cilia significantly reduced, there were small holes on the cell surface, and the cellular membrane was ruptured. In fish exposed to lethal (10.6 ng/L) and higher (31.8 and 95.4 ng/L) doses of UTSA, the AgNPs did not affect fish survival after 96 h, and there were no signs of histopathological damage or gut microbial changes. This study is the first report on microscopic and ultrastructural changes in Tetrahymena after exposure to significantly low concentrations of UTSA AgNPs with antiprotozoal efficacy without evidence of harmful effects on fish. These results provide the basis for further studies of both pet aquarium and commercial fish that may validate these findings at a larger experimental scale, taking into account AgNPs bioaccumulation, safety for human consumption and environmental impact.}, }
@article {pmid31450818, year = {2019}, author = {Enagbonma, BJ and Aremu, BR and Babalola, OO}, title = {Profiling the Functional Diversity of Termite Mound Soil Bacteria as Revealed by Shotgun Sequencing.}, journal = {Genes}, volume = {10}, number = {9}, pages = {}, pmid = {31450818}, issn = {2073-4425}, mesh = {Animals ; Genes, Bacterial ; Isoptera/pathogenicity/*physiology ; *Metagenome ; Metagenomics/methods ; *Microbiota ; Sequence Analysis, DNA/methods ; Soil/chemistry/*parasitology ; *Soil Microbiology ; }, abstract = {Profiling the metabolic processes performed by bacteria is vital both for understanding and for manipulating ecosystems for industrial or research purposes. In this study we aim to assess the bacterial functional diversity in termite mound soils with the assumption that significant differences will be observed in the functional diversity of bacteria between the termite mound soils and their surrounding soils and that each environment has a distinguishing metabolic profile. Here, metagenomic DNA extracted from termite mound soils and their corresponding surrounding soils, which are 10 m apart, were sequenced using a shotgun sequencing approach. Our results revealed that the relative abundances of 16 functional categories differed significantly between both habitats. The α diversity analysis indicated no significant difference in bacterial functional categories within the habitats while the β diversity showed that the bacterial functional categories varied significantly between the termite mound soils and the surrounding soil samples. The variations in soil physical and chemical properties existing between the two environments were held accountable for the differences in bacterial functional structure. With the high relative abundance of functional categories with unknown function reported in this study, this could signify the likelihood of getting novel genes from termite mound soils, which are needed for research and commercial applications.}, }
@article {pmid31096909, year = {2019}, author = {Zhang, J and Lacroix, C and Wortmann, E and Ruscheweyh, HJ and Sunagawa, S and Sturla, SJ and Schwab, C}, title = {Gut microbial beta-glucuronidase and glycerol/diol dehydratase activity contribute to dietary heterocyclic amine biotransformation.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {99}, doi = {10.1186/s12866-019-1483-x}, pmid = {31096909}, issn = {1471-2180}, mesh = {Bacteria/*enzymology/genetics ; Bacteroidetes/enzymology/genetics ; Biotransformation ; Carcinogens/metabolism ; Colorectal Neoplasms ; *Diet ; Feces/chemistry/microbiology ; Firmicutes/enzymology/genetics ; *Gastrointestinal Microbiome ; Glucuronidase/*metabolism ; Glucuronides/*metabolism ; Glycerol/chemistry ; Humans ; Imidazoles/metabolism ; Meat/analysis ; Metagenomics ; Propanediol Dehydratase/*metabolism ; Proteobacteria/enzymology/genetics ; }, abstract = {BACKGROUND: Consuming red and processed meat has been associated with an increased risk of colorectal cancer (CRC), which is partly attributed to exposure to carcinogens such as heterocyclic amines (HCA) formed during cooking and preservation processes. The interaction of gut microbes and HCA can result in altered bioactivities and it has been shown previously that human gut microbiota can transform mutagenic HCA to a glycerol conjugate with reduced mutagenic potential. However, the major form of HCA in the colon are glucuronides (HCA-G) and it is not known whether these metabolites, via stepwise microbial hydrolysis and acrolein conjugation, are viable precursors for glycerol conjugated metabolites. We hypothesized that such a process could be concurrently catalyzed by bacterial beta-glucuronidase (B-GUS) and glycerol/diol dehydratase (GDH) activity. We therefore investigated how the HCA-G PhIP-N2-β-D-glucuronide (PhIP-G), a representative liver metabolite of PhIP (2-Amino-1-methyl-6-phenylimidazo [4,5-b] pyridine), which is the most abundant carcinogenic HCA in well-cooked meat, is transformed by enzymatic activity of human gut microbial representatives of the phyla Firmicutes, Bacteroidetes, and Proteobacteria.<br><br>RESULTS: We employed a combination of growth and enzymatic assays, and a bioanalysis approach combined with metagenomics. B-GUS of Faecalibacterium prausnitzii converted PhIP-G to PhIP and GDH of Flavonifractor plautii, Blautia obeum, Eubacterium hallii, and Lactobacillus reuteri converted PhIP to PhIP-M1 in the presence of glycerol. In addition, B-GUS- and GDH-positive bacteria cooperatively converted PhIP-G to PhIP-M1. A screen of genes encoding B-GUS and GDH was performed for fecal microbiome data from healthy individuals (n = 103) and from CRC patients (n = 53), which revealed a decrease in abundance of taxa with confirmed GDH and HCA transformation activity in CRC patients.<br><br>CONCLUSIONS: This study for the first time demonstrates that gut microbes mediate the stepwise transformation of PhIP-G to PhIP-M1 via the intermediate production of PhIP. Findings from this study suggest that targeted manipulation with gut microbes bearing specific functions, or dietary glycerol supplementation might modify gut microbial activity to reduce HCA-induced CRC risk.}, }
@article {pmid30961521, year = {2019}, author = {Dos Santos, HRM and Argolo, CS and Argôlo-Filho, RC and Loguercio, LL}, title = {A 16S rDNA PCR-based theoretical to actual delta approach on culturable mock communities revealed severe losses of diversity information.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {74}, doi = {10.1186/s12866-019-1446-2}, pmid = {30961521}, issn = {1471-2180}, mesh = {Bacteria/classification/growth &amp; development ; Cacao/microbiology ; DNA Fingerprinting ; DNA Primers ; DNA, Bacterial/genetics ; DNA, Ribosomal/*genetics ; Endophytes/*classification ; *Genetic Variation ; *Microbiota ; *Models, Theoretical ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Stem Cells ; }, abstract = {BACKGROUND: Subunits of ribosomal RNA genes (rDNAs) characterized by PCR-based protocols have been the proxy for studies in microbial taxonomy, phylogenetics, evolution and ecology. However, relevant factors have shown to interfere in the experimental outputs in a variety of systems. In this work, a 'theoretical' to 'actual' delta approach was applied to data on culturable mock bacterial communities (MBCs) to study the levels of losses in operational taxonomic units (OTUs) detectability. Computational and lab-bench strategies based on 16S rDNA amplification by 799F and U1492R primers were employed, using a fingerprinting method with highly improved detectability of fragments as a case-study tool. MBCs were of two major types: in silico MBCs, assembled with database-retrieved sequences, and in vitro MBCs, with AluI digestions of PCR data generated from culturable endophytes isolated from cacao trees.<br><br>RESULTS: Interfering factors for the 16 s rDNA amplifications, such as the type of template, direct and nested PCR, proportion of chloroplast DNA from a tropical plant source (Virola officinalis), and biased-amplification by the primers resulted in altered bacterial 16S rDNA amplification, both on MBCs and V. officinalis leaf-extracted DNA. For the theoretical data, the maximum number of fragments for in silico and in vitro cuts were not significantly different from each other. Primers' preferences for certain sequences were detected, depending on the MBCs' composition prior to PCR. The results indicated overall losses from 2.3 up to 8.2 times in the number of OTUs detected from actual AluI digestions of MBCs when compared to in silico and in vitro theoretical data.<br><br>CONCLUSIONS: Due to all those effects, the final amplification profile of the bacterial community assembled was remarkably simplified when compared to the expected number of detectable fragments known to be present in the MBC. From these findings, the scope of hypotheses generation and conclusions from experiments based on PCR amplifications of bacterial communities was discussed.}, }
@article {pmid30832576, year = {2019}, author = {Stewart, CJ and Fatemizadeh, R and Parsons, P and Lamb, CA and Shady, DA and Petrosino, JF and Hair, AB}, title = {Using formalin fixed paraffin embedded tissue to characterize the preterm gut microbiota in necrotising enterocolitis and spontaneous isolated perforation using marginal and diseased tissue.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {52}, doi = {10.1186/s12866-019-1426-6}, pmid = {30832576}, issn = {1471-2180}, mesh = {Bacteroidetes/classification ; DNA, Bacterial/isolation &amp; purification ; Enterocolitis, Necrotizing/*microbiology ; Female ; *Formaldehyde ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; Infant, Premature ; *Intestinal Perforation ; Intestines/microbiology ; Male ; *Paraffin Embedding ; Proteobacteria/classification ; RNA, Ribosomal, 16S/genetics ; Rupture, Spontaneous ; }, abstract = {BACKGROUND: Necrotising enterocolitis (NEC) is a common cause of death in preterm infants and is closely linked to the gut microbiota. Spontaneous intestinal perforation (SIP) also occurs in preterm neonates, but results in lower mortality and less adverse neonatal outcomes than NEC. Existing studies are largely limited to non-invasive stool samples, which may not be reflective of the anatomical site of disease. Therefore, we analysed historical formalin-fixed paraffin-embedded (FFPE) tissue from NEC and SIP preterm infants. A total of 13 NEC and 16 SIP infants were included. Extracted DNA from FFPE tissue blocks underwent 16S rRNA gene sequencing. For a subset of infants, diseased tissue and marginal healthy tissue from the same infant were compared.<br><br>RESULTS: Xylene provided a cost and time effective means of deparaffinization. Tissue from the site of disease was highly comparable to adjacent healthier tissue. Comparing only diseased tissue from all infants showed significantly lower Shannon diversity in NEC (P = 0.026). The overall bacterial communities were also significantly different in NEC samples compared to SIP (P = 0.038), and large variability within NEC infants was observed. While no single OTU or genus was significantly associated with NEC or SIP, at the phylum level Proteobacteria (P = 0.045) and Bacteroidetes (P = 0.024) were significantly higher in NEC and SIP infants, respectively.<br><br>CONCLUSIONS: Existing banks of intestinal FFPE blocks provide a robust and specific sample for profiling the microbiota at the site of disease. We showed preterm infants with NEC have lower diversity and different bacterial communities when compared to SIP controls.}, }
@article {pmid31592756, year = {2019}, author = {Millán-Aguiñaga, N and Soldatou, S and Brozio, S and Munnoch, JT and Howe, J and Hoskisson, PA and Duncan, KR}, title = {Awakening ancient polar Actinobacteria: diversity, evolution and specialized metabolite potential.}, journal = {Microbiology (Reading, England)}, volume = {165}, number = {11}, pages = {1169-1180}, doi = {10.1099/mic.0.000845}, pmid = {31592756}, issn = {1465-2080}, mesh = {Actinobacteria/classification/*genetics/isolation &amp; purification/*metabolism ; Antarctic Regions ; Arctic Regions ; Biodiversity ; Biological Products/classification/metabolism ; DNA, Bacterial/genetics ; Evolution, Molecular ; Geologic Sediments/microbiology ; Metagenomics ; Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/chemistry ; }, abstract = {Polar and subpolar ecosystems are highly vulnerable to global climate change with consequences for biodiversity and community composition. Bacteria are directly impacted by future environmental change and it is therefore essential to have a better understanding of microbial communities in fluctuating ecosystems. Exploration of Polar environments, specifically sediments, represents an exciting opportunity to uncover bacterial and chemical diversity and link this to ecosystem and evolutionary parameters. In terms of specialized metabolite production, the bacterial order Actinomycetales, within the phylum Actinobacteria are unsurpassed, producing 10 000 specialized metabolites accounting for over 45 % of all bioactive microbial metabolites. A selective isolation approach focused on spore-forming Actinobacteria of 12 sediment cores from the Antarctic and sub-Arctic generated a culture collection of 50 strains. This consisted of 39 strains belonging to rare Actinomycetales genera including Microbacterium, Rhodococcus and Pseudonocardia. This study used a combination of nanopore sequencing and molecular networking to explore the community composition, culturable bacterial diversity, evolutionary relatedness and specialized metabolite potential of these strains. Metagenomic analyses using MinION sequencing was able to detect the phylum Actinobacteria across polar sediment cores at an average of 13 % of the total bacterial reads. The resulting molecular network consisted of 1652 parent ions and the lack of known metabolite identification supports the argument that Polar bacteria are likely to produce previously unreported chemistry.}, }
@article {pmid31450270, year = {2019}, author = {Sandhu, SS and Pourang, A and Sivamani, RK}, title = {A review of next generation sequencing technologies used in the evaluation of the skin microbiome: what a time to be alive.}, journal = {Dermatology online journal}, volume = {25}, number = {7}, pages = {}, pmid = {31450270}, issn = {1087-2108}, mesh = {*High-Throughput Nucleotide Sequencing ; Humans ; Metabolomics/methods ; Metagenomics/*methods ; *Microbiota ; Proteomics/methods ; Skin/*microbiology ; }, abstract = {The role of the microbiome in healthy and disease states of the human body is progressively being found to extend beyond the gastrointestinal tract and into other organ systems such as the skin. Researching the microbiome thus has become paramount to understanding additional physiological and pathophysiological mechanisms that may be at play between microbes and their hosts. Cell cultures have traditionally been used to study the microbiome, but in our current day and age, advanced metagenomic techniques - such as 16S rRNA amplicon sequencing and whole metagenomic shotgun sequencing - are better able to classify the microorganisms making up the microbiome. Utilizing metagenomics alone, however, does not allow for the study of the more complex effects of the microbiome, such as changes in gene expression and metabolic byproducts. Thus, incorporation of other modalities such as metatranscriptomics, metaproteomics, and metabolomics are needed to further elucidate the extensive intricacies of the skin microbiome.}, }
@article {pmid31245304, year = {2019}, author = {Mattei, V and Murugesan, S and Al Hashmi, M and Mathew, R and James, N and Singh, P and Kumar, M and Lakshmanan, AP and Terranegra, A and Al Khodor, S and Tomei, S}, title = {Evaluation of Methods for the Extraction of Microbial DNA From Vaginal Swabs Used for Microbiome Studies.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {197}, doi = {10.3389/fcimb.2019.00197}, pmid = {31245304}, issn = {2235-2988}, mesh = {Adult ; Biodiversity ; DNA, Bacterial/*isolation &amp; purification ; DNA, Ribosomal/genetics ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Vagina/*microbiology ; }, abstract = {Background: The composition of the microbiome in human body sites plays an important role in health. The vaginal environment is colonized by several species of bacteria that have a major influence on reproductive health. The advancement of sequencing technologies has made the assessment of the composition of the microbiota possible through microbial DNA extraction and sequencing. Therefore, it is of a paramount importance to select a sensitive and reproducible DNA extraction method, that facilitates isolation of microbial DNA with a sufficient quantity and purity, from microbial species living in the vaginal environment. Here, we have evaluated four different DNA extraction protocols from self-collected vaginal swabs. Methods: Five healthy female volunteers were enrolled in the study. Each donor was asked to self-collect 4 samples using Copan ESwab. DNA was extracted using Qiagen DNeasy kit and three modified protocols of the MoBio PowerSoil kit (&quot;DNeasy PowerSoil&quot; after acquisition from Qiagen). DNA quantity and integrity was checked through Nanodrop and LabChip GX. DNA was further tested through quantitative real-time PCR (qPCR) and 16S sequencing. Vaginal microbiota diversities were determined using MiSeq-Illumina high-throughput sequencing of bacterial 16S rDNA V1-V3 fingerprint. Sequencing data were analyzed using QIIME pipeline. Results: Qiagen DNeasy protocol resulted in the highest DNA yield as compared to the modified protocols of MoBio Powersoil kit. The size of the DNA extracted using each protocol was ~40 kb. Qiagen DNeasy protocol gave the highest Genomic Quality Score (average ± standard deviation: 4.24 ± 0.36), followed by the different MoBio Powersoil protocols. A substantial variability in microbial DNA abundance was found across the protocols. The vaginal microbiota of the healthy volunteers was dominated by Lactobacillus species. MoBio Powersoil kit provided a significantly higher alpha diversity as compared to the Qiagen DNeasy kit, while beta diversity measures did not reveal any significant cluster changes, except when the Bray-Curtis method was applied. Conclusion: We were able to isolate microbial DNA from the vaginal swabs. Qiagen DNeasy method gave the highest DNA yield and quality but was not optimal in detecting microbial diversity. The modified MoBio PowerSoil protocols showed higher microbial diversities as compared to the standard protocol.}, }
@article {pmid31138751, year = {2019}, author = {Wang, S and El-Fahmawi, A and Christian, DA and Fang, Q and Radaelli, E and Chen, L and Sullivan, MC and Misic, AM and Ellringer, JA and Zhu, XQ and Winter, SE and Hunter, CA and Beiting, DP}, title = {Infection-Induced Intestinal Dysbiosis Is Mediated by Macrophage Activation and Nitrate Production.}, journal = {mBio}, volume = {10}, number = {3}, pages = {}, doi = {10.1128/mBio.00935-19}, pmid = {31138751}, issn = {2150-7511}, support = {R21 AI126042/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Cytokines/analysis ; Dysbiosis/*immunology ; Enterobacteriaceae/classification ; Female ; *Gastrointestinal Microbiome ; Inflammation ; Interferon-gamma/immunology ; Intestine, Small/*immunology/microbiology/parasitology/*pathology ; *Macrophage Activation ; Mice ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; Nitrates/*metabolism ; Nitric Oxide Synthase Type II/immunology ; Toxoplasma/pathogenicity ; Toxoplasmosis, Animal/*immunology/microbiology ; }, abstract = {Oral infection of C57BL/6J mice with Toxoplasma gondii results in a marked bacterial dysbiosis and the development of severe pathology in the distal small intestine that is dependent on CD4+ T cells and interferon gamma (IFN-γ). This dysbiosis and bacterial translocation contribute to the development of ileal pathology, but the factors that support the bloom of bacterial pathobionts are unclear. The use of microbial community profiling and shotgun metagenomics revealed that Toxoplasma infection induces a dysbiosis dominated by Enterobacteriaceae and an increased potential for nitrate respiration. In vivo experiments using bacterial metabolic mutants revealed that during this infection, host-derived nitrate supports the expansion of Enterobacteriaceae in the ileum via nitrate respiration. Additional experiments with infected mice indicate that the IFN-γ/STAT1/iNOS axis, while essential for parasite control, also supplies a pool of nitrate that serves as a source for anaerobic respiration and supports overgrowth of Enterobacteriaceae Together, these data reveal a trade-off in intestinal immunity after oral infection of C57BL/6J mice with T. gondii, in which inducible nitric oxide synthase (iNOS) is required for parasite control, while this host enzyme is responsible for specific modification of the composition of the microbiome that contributes to pathology.IMPORTANCEToxoplasma gondii is a protozoan parasite and a leading cause of foodborne illness. Infection is initiated when the parasite invades the intestinal epithelium, and in many host species, this leads to intense inflammation and a dramatic disruption of the normal microbial ecosystem that resides in the healthy gut (the so-called microbiome). One characteristic change in the microbiome during infection with Toxoplasma-as well as numerous other pathogens-is the overgrowth of Escherichia coli or similar bacteria and a breakdown of commensal containment leading to seeding of peripheral organs with gut bacteria and subsequent sepsis. Our findings provide one clear explanation for how this process is regulated, thereby improving our understanding of the relationship between parasite infection, inflammation, and disease. Furthermore, our results could serve as the basis for the development of novel therapeutics to reduce the potential for harmful bacteria to bloom in the gut during infection.}, }
@article {pmid30994437, year = {2019}, author = {Carrasco, J and Tello, ML and de Toro, M and Tkacz, A and Poole, P and Pérez-Clavijo, M and Preston, G}, title = {Casing microbiome dynamics during button mushroom cultivation: implications for dry and wet bubble diseases.}, journal = {Microbiology (Reading, England)}, volume = {165}, number = {6}, pages = {611-624}, doi = {10.1099/mic.0.000792}, pmid = {30994437}, issn = {1465-2080}, mesh = {Agaricus/*growth &amp; development ; Bacteria/classification/genetics/growth &amp; development/isolation &amp; purification ; Culture Media/chemistry ; Hypocreales/growth &amp; development/isolation &amp; purification ; Microbial Interactions ; Microbiota/*physiology ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {The casing material required in mushroom cultivation presents a very rich ecological niche, which is inhabited by a diverse population of bacteria and fungi. In this work three different casing materials, blonde peat, black peat and a 50 : 50 mixture of both, were compared for their capacity to show a natural suppressive response against dry bubble, Lecanicillium fungicola (Preuss) Zare and Gams, and wet bubble, Mycogone perniciosa (Magnus) Delacroix. The highest mushroom production was collected from crops cultivated using the mixed casing and black peat, which were not significantly different in yield. However, artificial infection with mycoparasites resulted in similar yield losses irrespective of the material used, indicating that the casing materials do not confer advantages in disease suppression. The composition of the microbiome of the 50 : 50 casing mixture along the crop cycle and the compost and basidiomes was evaluated through next-generation sequencing (NGS) of the V3-V4 region of the bacterial 16S rRNA gene and the fungal ITS2 region. Once colonized by Agaricus bisporus, the bacterial diversity of the casing microbiome increased and the fungal diversity drastically decreased. From then on, the composition of the casing microbiome remained relatively stable. Analysis of the composition of the bacterial microbiome in basidiomes indicated that it is highly influenced by the casing microbiota. Notably, L. fungicola was consistently detected in uninoculated control samples of compost and casing using NGS, even in asymptomatic crops. This suggests that the naturally established casing microbiota was able to help to suppress disease development when inoculum levels were low, but was not effective in suppressing high pressure from artificially introduced fungal inoculum. Determination of the composition of the casing microbiome paves the way for the development of synthetic casing communities that can be used to investigate the role of specific components of the casing microbiota in mushroom production and disease control.}, }
@article {pmid30942859, year = {2019}, author = {Paul, VJ and Freeman, CJ and Agarwal, V}, title = {Chemical Ecology of Marine Sponges: New Opportunities through &quot;-Omics&quot;.}, journal = {Integrative and comparative biology}, volume = {59}, number = {4}, pages = {765-776}, pmid = {30942859}, issn = {1557-7023}, support = {R00 ES026620/ES/NIEHS NIH HHS/United States ; R01 CA172310/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Aquatic Organisms/genetics/physiology ; Genome/*physiology ; *Host Microbial Interactions ; Microbiota ; Porifera/genetics/microbiology/*physiology ; Transcriptome/*physiology ; }, abstract = {The chemical ecology and chemical defenses of sponges have been investigated for decades; consequently, sponges are among the best understood marine organisms in terms of their chemical ecology, from the level of molecules to ecosystems. Thousands of natural products have been isolated and characterized from sponges, and although relatively few of these compounds have been studied for their ecological functions, some are known to serve as chemical defenses against predators, microorganisms, fouling organisms, and other competitors. Sponges are hosts to an exceptional diversity of microorganisms, with almost 40 microbial phyla found in these associations to date. Microbial community composition and abundance are highly variable across host taxa, with a continuum from diverse assemblages of many microbial taxa to those that are dominated by a single microbial group. Microbial communities expand the nutritional repertoire of their hosts by providing access to inorganic and dissolved sources of nutrients. Not only does this continuum of microorganism-sponge associations lead to divergent nutritional characteristics in sponges, these associated microorganisms and symbionts have long been suspected, and are now known, to biosynthesize some of the natural products found in sponges. Modern &quot;omics&quot; tools provide ways to study these sponge-microbe associations that would have been difficult even a decade ago. Metabolomics facilitate comparisons of sponge compounds produced within and among taxa, and metagenomics and metatranscriptomics provide tools to understand the biology of host-microbe associations and the biosynthesis of ecologically relevant natural products. These combinations of ecological, microbiological, metabolomic and genomics tools, and techniques provide unprecedented opportunities to advance sponge biology and chemical ecology across many marine ecosystems.}, }
@article {pmid30928605, year = {2019}, author = {Kraberger, S and Cook, CN and Schmidlin, K and Fontenele, RS and Bautista, J and Smith, B and Varsani, A}, title = {Diverse single-stranded DNA viruses associated with honey bees (Apis mellifera).}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {71}, number = {}, pages = {179-188}, doi = {10.1016/j.meegid.2019.03.024}, pmid = {30928605}, issn = {1567-7257}, mesh = {Animals ; Bees/*virology ; DNA Viruses/*genetics ; Metagenomics ; Microbiota/genetics ; Microviridae/genetics ; }, abstract = {Honey bees (Apis mellifera) research has increased in light of their progressive global decline over the last decade and the important role they play in pollination. One expanding area of honey bee research is analysis of their microbial community including viruses. Several RNA viruses have been characterized but little is known about DNA viruses associated with bees. Here, using a metagenomics based approach, we reveal the presence of a broad range of novel single-stranded DNA viruses from the hemolymph and brain of nurse and forager (worker divisions of labour) bees belonging to two honey bees subspecies, Italian (Apis mellifera linguistica) and New World Carniolan (Apis mellifera carnica). Genomes of 100 diverse viruses were identified, designated into three groupings; genomoviruses (family Genomoviridae) (n = 4), unclassified replication associated protein encoding single-stranded DNA viruses (n = 28), and microviruses (family Microviridae; subfamily Gokushovirinae) (n = 70). Amongst the viruses identified, it appears that nurses harbour a higher diversity of these viruses comparative to the foragers. Between subspecies, the most striking outcome was the extremely high number of diverse microviruses identified in the Italian bees comparative to the New World Carniolan, likely indicating an association to the diversity of the bacterial community associated with these subspecies.}, }
@article {pmid30894059, year = {2019}, author = {Bjørkhaug, ST and Aanes, H and Neupane, SP and Bramness, JG and Malvik, S and Henriksen, C and Skar, V and Medhus, AW and Valeur, J}, title = {Characterization of gut microbiota composition and functions in patients with chronic alcohol overconsumption.}, journal = {Gut microbes}, volume = {10}, number = {6}, pages = {663-675}, pmid = {30894059}, issn = {1949-0984}, mesh = {Adult ; Aged ; Aged, 80 and over ; Alcoholism/blood/*microbiology/physiopathology ; Ascorbic Acid/blood ; Bacteria/classification/genetics/isolation &amp; purification ; Bacterial Proteins/genetics ; Fatty Acids, Volatile/analysis ; Feces/chemistry/microbiology ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Hand Strength ; Humans ; Male ; Metagenomics ; Middle Aged ; Nutrition Assessment ; RNA, Ribosomal, 16S/genetics ; Vitamins/blood ; }, abstract = {Excessive alcohol intake can alter the gut microbiota, which may underlie the pathophysiology of alcohol-related diseases. We examined gut microbiota composition and functions in patients with alcohol overconsumption for >10 years, compared to a control group of patients with a history of no or low alcohol intake. Faecal microbiota composition was assessed by 16S rRNA sequencing. Gut microbiota functions were evaluated by quantification of short-chain fatty acids (SCFAs) and predictive metagenome profiling (PICRUSt). Twenty-four patients, mean age 64.8 years (19 males), with alcohol overconsumption, and 18 control patients, mean age 58.2 years (14 males) were included. The two groups were comparable regarding basic clinical variables. Nutritional assessment revealed lower total score on the screening tool Mini Nutritional Assessment, lower muscle mass as assessed by handgrip strength, and lower plasma vitamin C levels in the alcohol overconsumption group. Bacteria from phylum Proteobacteria were found in higher relative abundance, while bacteria from genus Faecalibacterium were found in lower relative abundance in the group of alcohol overconsumers. The group also had higher levels of the genera Sutterella, Holdemania and Clostridium, and lower concentration and percentage of butyric acid. When applying PICRUSt to predict the metagenomic composition, we found that genes related to invasion of epithelial cells were more common in the group of alcohol overconsumers. We conclude that gut microbiota composition and functions in patients with alcohol overconsumption differ from patients with low consumption of alcohol, and seem to be skewed into a putative pro-inflammatory direction.}, }
@article {pmid30866714, year = {2019}, author = {Park, H and Laffin, MR and Jovel, J and Millan, B and Hyun, JE and Hotte, N and Kao, D and Madsen, KL}, title = {The success of fecal microbial transplantation in Clostridium difficile infection correlates with bacteriophage relative abundance in the donor: a retrospective cohort study.}, journal = {Gut microbes}, volume = {10}, number = {6}, pages = {676-687}, pmid = {30866714}, issn = {1949-0984}, support = {//CIHR/Canada ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/classification/genetics/isolation &amp; purification ; Bacteriophages/*classification/genetics ; Clostridium Infections/microbiology/*therapy/*virology ; Clostridium difficile/physiology ; Cohort Studies ; *Fecal Microbiota Transplantation ; Feces/microbiology/virology ; Female ; Gastrointestinal Microbiome/genetics ; Humans ; Male ; Middle Aged ; Recurrence ; Retrospective Studies ; *Tissue Donors ; Treatment Outcome ; }, abstract = {Background: Fecal microbial transplantation (FMT) is used in the treatment of relapsing Clostridium difficile infection (rCDI). Failure rate for FMT is as high as 10% but the mechanisms contributing to a failed FMT are not understood. We utilized metagenomic data to identify the role of bacteria and bacteriophages on FMT success.Results: Subjects with rCDI (n = 19) received FMT from volunteer donors (n = 7) via colonoscopy. Twelve patients fully recovered after a single FMT, while seven patients required a subsequent FMT. DNA was extracted from patient and donor stool samples for shotgun metagenomic analysis. Metagenomics libraries were analyzed focusing on bacterial taxonomy and bacteriophage sequences. Gammaproteobacteria were dominant in rCDI patients prior to FMT largely due to elevated levels of Klebsiella and Escherichia. A successful FMT led to increased levels of Clostridia and Bacteroidia and a reduction in Gammaproteobacteria. In contrast, a failed FMT led to no significant changes in bacterial composition. Bacteriophages were classified during whole metagenomic analysis of each sample and were markedly different between rCDI patients, donors, and a healthy control cohort (n = 96). Bacteriophage sequence reads were increased in CDI patients compared with donors and healthy controls. Successful FMT donors had higher bacteriophage α-diversity and lower relative abundance compared to the donors of a failed initial FMT.Conclusions: In this retrospective analysis, FMTs with increased bacteriophage α-diversity were more likely to successfully treat rCDI. In addition, the relative number of bacteriophage reads was lower in donations leading to a successful FMT. These results suggest that bacteriophage abundance may have some role in determining the relative success of FMT.}, }
@article {pmid30836173, year = {2019}, author = {Ruppé, E and Schrenzel, J}, title = {Messages from the third International Conference on Clinical Metagenomics (ICCMg3).}, journal = {Microbes and infection}, volume = {21}, number = {7}, pages = {273-277}, doi = {10.1016/j.micinf.2019.02.004}, pmid = {30836173}, issn = {1769-714X}, mesh = {*Clinical Laboratory Techniques/standards/trends ; Communicable Diseases/*diagnosis/microbiology ; Computational Biology/standards/trends ; High-Throughput Nucleotide Sequencing/standards/trends ; Humans ; Metagenome/genetics ; *Metagenomics/standards/statistics &amp; numerical data ; Microbiota/genetics ; }, abstract = {Clinical metagenomics (CMg), referring to as the application of metagenomic sequencing of clinical samples in order to recover clinically-relevant information, has been rapidly evolving these last years. Following this trend, we held the third International Conference on Clinical Metagenomics (ICCMg3) in Geneva in October 2018. During the two days of the conference, several aspects of CMg were addressed, which we propose to summarize in the present manuscript. During this ICCMg3, we kept on following the progresses achieved worldwide on clinical metagenomics, but also this year in clinical genomics. Besides, the use of metagenomics in cancer diagnostic and management was addressed. Some new challenges have also been raised such as the way to report clinical (meta)genomics output to clinicians and the pivotal place of ethics in this expanding field.}, }
@article {pmid30649166, year = {2019}, author = {Schiffer, L and Azhar, R and Shepherd, L and Ramos, M and Geistlinger, L and Huttenhower, C and Dowd, JB and Segata, N and Waldron, L}, title = {HMP16SData: Efficient Access to the Human Microbiome Project Through Bioconductor.}, journal = {American journal of epidemiology}, volume = {188}, number = {6}, pages = {1023-1026}, doi = {10.1093/aje/kwz006}, pmid = {30649166}, issn = {1476-6256}, support = {R01 HG005220/HG/NHGRI NIH HHS/United States ; R21 AI121784/AI/NIAID NIH HHS/United States ; U24 CA180996/CA/NCI NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Computational Biology ; Databases, Genetic/*statistics &amp; numerical data ; Female ; Humans ; Male ; Microbiota/*physiology ; RNA, Ribosomal, 16S/*metabolism ; Young Adult ; }, abstract = {Phase 1 of the Human Microbiome Project (HMP) investigated 18 body subsites of 242 healthy American adults to produce the first comprehensive reference for the composition and variation of the &quot;healthy&quot; human microbiome. Publicly available data sets from amplicon sequencing of two 16S ribosomal RNA variable regions, with extensive controlled-access participant data, provide a reference for ongoing microbiome studies. However, utilization of these data sets can be hindered by the complex bioinformatic steps required to access, import, decrypt, and merge the various components in formats suitable for ecological and statistical analysis. The HMP16SData package provides count data for both 16S ribosomal RNA variable regions, integrated with phylogeny, taxonomy, public participant data, and controlled participant data for authorized researchers, using standard integrative Bioconductor data objects. By removing bioinformatic hurdles of data access and management, HMP16SData enables epidemiologists with only basic R skills to quickly analyze HMP data.}, }
@article {pmid31468349, year = {2019}, author = {Giannattasio-Ferraz, S and Laguardia-Nascimento, M and Gasparini, MR and Leite, LR and Araujo, FMG and de Matos Salim, AC and de Oliveira, AP and Nicoli, JR and de Oliveira, GC and da Fonseca, FG and Barbosa-Stancioli, EF}, title = {A common vaginal microbiota composition among breeds of Bos taurus indicus (Gyr and Nellore).}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {50}, number = {4}, pages = {1115-1124}, pmid = {31468349}, issn = {1678-4405}, support = {473879/2013-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, mesh = {Animals ; Archaea/classification/genetics/*isolation &amp; purification ; Bacteria/classification/genetics/*isolation &amp; purification ; Breeding ; Cattle/genetics/*microbiology ; Female ; Fungi/classification/genetics/*isolation &amp; purification ; Metagenomics ; *Microbiota ; Phylogeny ; Rumen/microbiology ; Vagina/*microbiology ; }, abstract = {Describing the bovine vaginal microbiota is essential to better understand its physiology and its impact on health maintenance. Despite the economic importance of reproduction of these animals, bovine vaginal microbial community is still poorly described in comparison with rumen microbiome. Previous studies of our group described the vaginal microbiota of Nellore, an important Bos taurus indicus breed, using metagenomics. In order to better understand this microbiota, the present work aims to investigate another important breed, Gyr. Results have shown bacterial dominance over Archaea and Fungi was observed, with the most abundant bacterial phylum (Firmicutes) representing 40-50% of bacterial population, followed by Bacteroidetes, Proteobacteria, and Actinobacteria. The Fungi kingdom had the Mycosphaerella genus as its main representative, followed by Cladosporium. Archaea were observed at a very low abundance in all animals, with a high relative abundance of Methanobrevibacter genus. These results demonstrate a high microbial diversity on vaginal tract of Gyr, as demonstrated for Nellore and different from the previously described for other species. Our results indicate a great similarity between vaginal microbiota of Nellore and Gyr despite the differences in animal handling and genetic improvement. As observed for both breeds, individual variation is the largest source of microbial diversity between animals.}, }
@article {pmid31787070, year = {2019}, author = {Kang, JB and Siranosian, BA and Moss, EL and Banaei, N and Andermann, TM and Bhatt, AS}, title = {Intestinal microbiota domination under extreme selective pressures characterized by metagenomic read cloud sequencing and assembly.}, journal = {BMC bioinformatics}, volume = {20}, number = {Suppl 16}, pages = {585}, pmid = {31787070}, issn = {1471-2105}, mesh = {Base Sequence ; Biodiversity ; Drug Resistance, Microbial/genetics ; Escherichia coli/genetics ; *Gastrointestinal Microbiome/genetics ; Genes, Bacterial ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenome/genetics ; Metagenomics/*methods ; Microbiota/genetics ; Principal Component Analysis ; *Selection, Genetic ; Synteny/genetics ; }, abstract = {BACKGROUND: Low diversity of the gut microbiome, often progressing to the point of intestinal domination by a single species, has been linked to poor outcomes in patients undergoing hematopoietic cell transplantation (HCT). Our ability to understand how certain organisms attain intestinal domination over others has been restricted in part by current metagenomic sequencing technologies that are typically unable to reconstruct complete genomes for individual organisms present within a sequenced microbial community. We recently developed a metagenomic read cloud sequencing and assembly approach that generates improved draft genomes for individual organisms compared to conventional short-read sequencing and assembly methods. Herein, we applied metagenomic read cloud sequencing to four stool samples collected longitudinally from an HCT patient preceding treatment and over the course of heavy antibiotic exposure.<br><br>RESULTS: Characterization of microbiome composition by taxonomic classification of reads reveals that that upon antibiotic exposure, the subject's gut microbiome experienced a marked decrease in diversity and became dominated by Escherichia coli. While diversity is restored at the final time point, this occurs without recovery of the original species and strain-level composition. Draft genomes for individual organisms within each sample were generated using both read cloud and conventional assembly. Read clouds were found to improve the completeness and contiguity of genome assemblies compared to conventional assembly. Moreover, read clouds enabled the placement of antibiotic resistance genes present in multiple copies both within a single draft genome and across multiple organisms. The occurrence of resistance genes associates with the timing of antibiotics administered to the patient, and comparative genomic analysis of the various intestinal E. coli strains across time points as well as the bloodstream isolate showed that the subject's E. coli bloodstream infection likely originated from the intestine. The E. coli genome from the initial pre-transplant stool sample harbors 46 known antimicrobial resistance genes, while all other species from the pre-transplant sample each contain at most 5 genes, consistent with a model of heavy antibiotic exposure resulting in selective outgrowth of the highly antibiotic-resistant E. coli.<br><br>CONCLUSION: This study demonstrates the application and utility of metagenomic read cloud sequencing and assembly to study the underlying strain-level genomic factors influencing gut microbiome dynamics under extreme selective pressures in the clinical context of HCT.}, }
@article {pmid31676016, year = {2019}, author = {Wang, Y and Shi, Q and Yang, P and Zhang, C and Mortuza, SM and Xue, Z and Ning, K and Zhang, Y}, title = {Fueling ab initio folding with marine metagenomics enables structure and function predictions of new protein families.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {229}, pmid = {31676016}, issn = {1474-760X}, support = {GM083107/GM/NIGMS NIH HHS/United States ; GM116960/GM/NIGMS NIH HHS/United States ; AI134678//National Institute of Allergy and Infectious Diseases/International ; }, mesh = {Aquatic Organisms ; Deep Learning ; Metagenomics/*methods ; Microbiota ; *Models, Chemical ; Multigene Family ; Proteins/chemistry/*genetics ; *Structure-Activity Relationship ; }, abstract = {INTRODUCTION: The ocean microbiome represents one of the largest microbiomes and produces nearly half of the primary energy on the planet through photosynthesis or chemosynthesis. Using recent advances in marine genomics, we explore new applications of oceanic metagenomes for protein structure and function prediction.<br><br>RESULTS: By processing 1.3 TB of high-quality reads from the Tara Oceans data, we obtain 97 million non-redundant genes. Of the 5721 Pfam families that lack experimental structures, 2801 have at least one member associated with the oceanic metagenomics dataset. We apply C-QUARK, a deep-learning contact-guided ab initio structure prediction pipeline, to model 27 families, where 20 are predicted to have a reliable fold with estimated template modeling score (TM-score) at least 0.5. Detailed analyses reveal that the abundance of microbial genera in the ocean is highly correlated to the frequency of occurrence in the modeled Pfam families, suggesting the significant role of the Tara Oceans genomes in the contact-map prediction and subsequent ab initio folding simulations. Of interesting note, PF15461, which has a majority of members coming from ocean-related bacteria, is identified as an important photosynthetic protein by structure-based function annotations. The pipeline is extended to a set of 417 Pfam families, built on the combination of Tara with other metagenomics datasets, which results in 235 families with an estimated TM-score over 0.5.<br><br>CONCLUSIONS: These results demonstrate a new avenue to improve the capacity of protein structure and function modeling through marine metagenomics, especially for difficult proteins with few homologous sequences.}, }
@article {pmid31672156, year = {2019}, author = {Sanders, JG and Nurk, S and Salido, RA and Minich, J and Xu, ZZ and Zhu, Q and Martino, C and Fedarko, M and Arthur, TD and Chen, F and Boland, BS and Humphrey, GC and Brennan, C and Sanders, K and Gaffney, J and Jepsen, K and Khosroheidari, M and Green, C and Liyanage, M and Dang, JW and Phelan, VV and Quinn, RA and Bankevich, A and Chang, JT and Rana, TM and Conrad, DJ and Sandborn, WJ and Smarr, L and Dorrestein, PC and Pevzner, PA and Knight, R}, title = {Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {226}, pmid = {31672156}, issn = {1474-760X}, support = {T32GM8806/NH/NIH HHS/United States ; DA046171/DA/NIDA NIH HHS/United States ; DA039562/DA/NIDA NIH HHS/United States ; }, mesh = {Animals ; Benchmarking ; Gastrointestinal Microbiome ; *Genomic Library ; *High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/*methods ; Mice ; }, abstract = {As metagenomic studies move to increasing numbers of samples, communities like the human gut may benefit more from the assembly of abundant microbes in many samples, rather than the exhaustive assembly of fewer samples. We term this approach leaderboard metagenome sequencing. To explore protocol optimization for leaderboard metagenomics in real samples, we introduce a benchmark of library prep and sequencing using internal references generated by synthetic long-read technology, allowing us to evaluate high-throughput library preparation methods against gold-standard reference genomes derived from the samples themselves. We introduce a low-cost protocol for high-throughput library preparation and sequencing.}, }
@article {pmid31604942, year = {2019}, author = {Kaehler, BD and Bokulich, NA and McDonald, D and Knight, R and Caporaso, JG and Huttley, GA}, title = {Species abundance information improves sequence taxonomy classification accuracy.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {4643}, pmid = {31604942}, issn = {2041-1723}, support = {P30 MH062512/MH/NIMH NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Classification/methods ; Computational Biology ; Metagenomics/methods ; Microbiota/*genetics ; *Phylogeny ; Population Density ; Software ; }, abstract = {Popular naive Bayes taxonomic classifiers for amplicon sequences assume that all species in the reference database are equally likely to be observed. We demonstrate that classification accuracy degrades linearly with the degree to which that assumption is violated, and in practice it is always violated. By incorporating environment-specific taxonomic abundance information, we demonstrate a significant increase in the species-level classification accuracy across common sample types. At the species level, overall average error rates decline from 25% to 14%, which is favourably comparable to the error rates that existing classifiers achieve at the genus level (16%). Our findings indicate that for most practical purposes, the assumption that reference species are equally likely to be observed is untenable. q2-clawback provides a straightforward alternative for samples from common environments.}, }
@article {pmid31597208, year = {2020}, author = {Berman, HL and McLaren, MR and Callahan, BJ}, title = {Understanding and interpreting community sequencing measurements of the vaginal microbiome.}, journal = {BJOG : an international journal of obstetrics and gynaecology}, volume = {127}, number = {2}, pages = {139-146}, doi = {10.1111/1471-0528.15978}, pmid = {31597208}, issn = {1471-0528}, mesh = {Female ; Humans ; Microbiota/*genetics ; RNA, Ribosomal, 16S ; Reproducibility of Results ; Sequence Analysis, DNA ; Vagina/*microbiology ; }, abstract = {Community-wide high-throughput sequencing has transformed the study of the vaginal microbiome, and clinical applications are on the horizon. Here we outline the three main community sequencing methods: (1) amplicon sequencing, (2) shotgun metagenomic sequencing, and (3) metatranscriptomic sequencing. We discuss the advantages and limitations of community sequencing generally, and the unique strengths and weaknesses of each method. We briefly review the contributions of community sequencing to vaginal microbiome research and practice. We develop suggestions for critically interpreting research results and potential clinical applications based on community sequencing of the vaginal microbiome. TWEETABLE ABSTRACT: We review the advantages and limitations of amplicon sequencing, metagenomics, and metatranscriptomics methods for the study of the vaginal microbiome.}, }
@article {pmid31587490, year = {2020}, author = {O'Callaghan, JL and Turner, R and Dekker Nitert, M and Barrett, HL and Clifton, V and Pelzer, ES}, title = {Re-assessing microbiomes in the low-biomass reproductive niche.}, journal = {BJOG : an international journal of obstetrics and gynaecology}, volume = {127}, number = {2}, pages = {147-158}, doi = {10.1111/1471-0528.15974}, pmid = {31587490}, issn = {1471-0528}, support = {//National Health and Medical Research Council Early Career Research fellowship/ ; //Mater Foundation/ ; }, mesh = {*Biomass ; Female ; Gastrointestinal Microbiome/genetics/immunology/*physiology ; Humans ; Metagenomics ; Placenta/immunology/*microbiology ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; *Reproductive Health ; Reproductive Tract Infections/*microbiology ; Sequence Analysis, DNA ; Vagina/immunology/*microbiology ; }, abstract = {The female reproductive tract represents a continuum between the vagina and the upper genital tract. New evidence from cultivation-independent studies suggests that the female upper genital tract is not sterile; however, the significance of this for reproductive health and disease remains to be elucidated fully. Further, diagnosis and treatment of infectious reproductive tract pathologies using cultivation-independent technologies represents a largely unchartered area of modern medical science. The challenge now is to design well-controlled experiments to account for the ease of contamination known to confound molecular-based studies of low-biomass niches, including the uterus and placenta. This will support robust assessment of the potential function of microorganisms, microbial metabolites, and cell-free bacterial DNA on reproductive function in health and disease. TWEETABLE ABSTRACT: Molecular microbial studies of low-biomass niches require stringent experimental controls to reveal causal relations in reproductive health and disease.}, }
@article {pmid31563776, year = {2019}, author = {Torres, GG and Figueroa-Galvis, I and Muñoz-García, A and Polanía, J and Vanegas, J}, title = {Potential bacterial bioindicators of urban pollution in mangroves.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {255}, number = {Pt 2}, pages = {113293}, doi = {10.1016/j.envpol.2019.113293}, pmid = {31563776}, issn = {1873-6424}, mesh = {Colombia ; Environmental Biomarkers/*genetics ; Environmental Pollution/*adverse effects ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Soil Microbiology/*standards ; *Wetlands ; }, abstract = {Despite their ecological and socioeconomic importance, mangroves are among the most threatened tropical environments in the world. In the past two decades, the world's mangrove degradation and loss were estimated to lie between an 35% and >80%. However, appropriate bioindicators for assessing the impact of external factors, and for differentiating polluted from unpolluted areas are still scarce. Here, we determine the physicochemical profiles of the soils of two mangroves, one exposed to and one not exposed to anthropogenic factors. By metagenomic analysis based on 16S rRNA, we generated the bacterial diversity profiles of the soils and estimated their functional profiles. Our results showed that the two examined mangrove forests differed significantly in the physicochemical properties of the soils, especially regarding organic carbon, phosphorus and metal content, as well as in their microbial communities, which was likely caused by anthropogenic pollution. The physicochemical differences between the soils explained 76% of the differential bacterial composition, and 64% depended solely on gradients of phosphorus, metal ions and potassium. We found two genera JL-ETNP-Z39 and TA06 exclusively in polluted and non-polluted mangroves, respectively. Additionally, the polluted mangrove was enriched in Gemmatimonadetes, Cyanobacteria, Chloroflexi, Firmicutes, Acidobacteria, and Nitrospirae. A total of 77 genera were affected by anthropic contamination, of which we propose 33 as bioindicators; 26 enriched, and 7 depleted upon pollution.}, }
@article {pmid31561965, year = {2019}, author = {Jahn, MT and Arkhipova, K and Markert, SM and Stigloher, C and Lachnit, T and Pita, L and Kupczok, A and Ribes, M and Stengel, ST and Rosenstiel, P and Dutilh, BE and Hentschel, U}, title = {A Phage Protein Aids Bacterial Symbionts in Eukaryote Immune Evasion.}, journal = {Cell host &amp; microbe}, volume = {26}, number = {4}, pages = {542-550.e5}, doi = {10.1016/j.chom.2019.08.019}, pmid = {31561965}, issn = {1934-6069}, mesh = {Animals ; Ankyrins/*metabolism ; Bacteria/genetics/*immunology/virology ; Bacteriophages/classification/*genetics ; Cell Line ; Female ; Immune Evasion/*immunology ; Mice ; Mice, Inbred C57BL ; Microbiota/physiology ; Porifera/*immunology/*virology ; Symbiosis/physiology ; }, abstract = {Phages are increasingly recognized as important members of host-associated microbiomes, with a vast genomic diversity. The new frontier is to understand how phages may affect higher order processes, such as in the context of host-microbe interactions. Here, we use marine sponges as a model to investigate the interplay between phages, bacterial symbionts, and eukaryotic hosts. Using viral metagenomics, we find that sponges, although massively filtering seawater, harbor species-specific and even individually unique viral signatures that are taxonomically distinct from other environments. We further discover a symbiont phage-encoded ankyrin-domain-containing protein, which is widely spread in phages of many host-associated contexts including human. We confirm in macrophage infection assays that the ankyrin protein (ANKp) modulates the eukaryotic host immune response against bacteria. We predict that the role of ANKp in nature is to facilitate coexistence in the tripartite interplay between phages, symbionts, and sponges and possibly many other host-microbe associations.}, }
@article {pmid31545807, year = {2019}, author = {Planes, S and Allemand, D and Agostini, S and Banaigs, B and Boissin, E and Boss, E and Bourdin, G and Bowler, C and Douville, E and Flores, JM and Forcioli, D and Furla, P and Galand, PE and Ghiglione, JF and Gilson, E and Lombard, F and Moulin, C and Pesant, S and Poulain, J and Reynaud, S and Romac, S and Sullivan, MB and Sunagawa, S and Thomas, OP and Troublé, R and de Vargas, C and Vega Thurber, R and Voolstra, CR and Wincker, P and Zoccola, D and , }, title = {The Tara Pacific expedition-A pan-ecosystemic approach of the &quot;-omics&quot; complexity of coral reef holobionts across the Pacific Ocean.}, journal = {PLoS biology}, volume = {17}, number = {9}, pages = {e3000483}, pmid = {31545807}, issn = {1545-7885}, mesh = {Animals ; Anthozoa/*microbiology ; *Coral Reefs ; *Expeditions ; Metabolomics ; Metagenomics ; *Microbiota ; Pacific Ocean ; Symbiosis ; }, abstract = {Coral reefs are the most diverse habitats in the marine realm. Their productivity, structural complexity, and biodiversity critically depend on ecosystem services provided by corals that are threatened because of climate change effects-in particular, ocean warming and acidification. The coral holobiont is composed of the coral animal host, endosymbiotic dinoflagellates, associated viruses, bacteria, and other microeukaryotes. In particular, the mandatory photosymbiosis with microalgae of the family Symbiodiniaceae and its consequences on the evolution, physiology, and stress resilience of the coral holobiont have yet to be fully elucidated. The functioning of the holobiont as a whole is largely unknown, although bacteria and viruses are presumed to play roles in metabolic interactions, immunity, and stress tolerance. In the context of climate change and anthropogenic threats on coral reef ecosystems, the Tara Pacific project aims to provide a baseline of the &quot;-omics&quot; complexity of the coral holobiont and its ecosystem across the Pacific Ocean and for various oceanographically distinct defined areas. Inspired by the previous Tara Oceans expeditions, the Tara Pacific expedition (2016-2018) has applied a pan-ecosystemic approach on coral reefs throughout the Pacific Ocean, drawing an east-west transect from Panama to Papua New Guinea and a south-north transect from Australia to Japan, sampling corals throughout 32 island systems with local replicates. Tara Pacific has developed and applied state-of-the-art technologies in very-high-throughput genetic sequencing and molecular analysis to reveal the entire microbial and chemical diversity as well as functional traits associated with coral holobionts, together with various measures on environmental forcing. This ambitious project aims at revealing a massive amount of novel biodiversity, shedding light on the complex links between genomes, transcriptomes, metabolomes, organisms, and ecosystem functions in coral reefs and providing a reference of the biological state of modern coral reefs in the Anthropocene.}, }
@article {pmid31492563, year = {2019}, author = {Zhong, H and Ren, H and Lu, Y and Fang, C and Hou, G and Yang, Z and Chen, B and Yang, F and Zhao, Y and Shi, Z and Zhou, B and Wu, J and Zou, H and Zi, J and Chen, J and Bao, X and Hu, Y and Gao, Y and Zhang, J and Xu, X and Hou, Y and Yang, H and Wang, J and Liu, S and Jia, H and Madsen, L and Brix, S and Kristiansen, K and Liu, F and Li, J}, title = {Distinct gut metagenomics and metaproteomics signatures in prediabetics and treatment-naïve type 2 diabetics.}, journal = {EBioMedicine}, volume = {47}, number = {}, pages = {373-383}, pmid = {31492563}, issn = {2352-3964}, mesh = {Chromatography, Liquid ; Diabetes Mellitus, Type 2/*etiology/*metabolism/therapy ; Feces/virology ; *Gastrointestinal Microbiome ; Humans ; *Metagenome ; *Metagenomics/methods ; *Proteomics/methods ; Tandem Mass Spectrometry ; }, abstract = {BACKGROUND: The gut microbiota plays important roles in modulating host metabolism. Previous studies have demonstrated differences in the gut microbiome of T2D and prediabetic individuals compared to healthy individuals, with distinct disease-related microbial profiles being reported in groups of different age and ethnicity. However, confounding factors such as anti-diabetic medication hamper identification of the gut microbial changes in disease development.<br><br>METHOD: We used a combination of in-depth metagenomics and metaproteomics analyses of faecal samples from treatment-naïve type 2 diabetic (TN-T2D, n = 77), pre-diabetic (Pre-DM, n = 80), and normal glucose tolerant (NGT, n = 97) individuals to investigate compositional and functional changes of the gut microbiota and the faecal content of microbial and host proteins in Pre-DM and treatment-naïve T2D individuals to elucidate possible host-microbial interplays characterizing different disease stages.<br><br>FINDINGS: We observed distinct differences characterizing the gut microbiota of these three groups and validated several key features in an independent TN-T2D cohort. We also demonstrated that the content of several human antimicrobial peptides and pancreatic enzymes differed in faecal samples between three groups.<br><br>INTERPRETATION: Our findings suggest a complex, disease stage-dependent interplay between the gut microbiota and the host and point to the value of metaproteomics to gain further insight into interplays between the gut microbiota and the host. FUND: The study was supported by the National Natural Science Foundation of China (No. 31601073), the National Key Research and Development Program of China (No. 2017YFC0909703) and the Shenzhen Municipal Government of China (No. JCYJ20170817145809215). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.}, }
@article {pmid31408742, year = {2019}, author = {Ari, O and Karabudak, S and Kalcioglu, MT and Gunduz, AY and Durmaz, R}, title = {The bacteriome of otitis media with effusion: Does it originate from the adenoid?.}, journal = {International journal of pediatric otorhinolaryngology}, volume = {126}, number = {}, pages = {109624}, doi = {10.1016/j.ijporl.2019.109624}, pmid = {31408742}, issn = {1872-8464}, mesh = {Adenoids/*microbiology ; Child ; Child, Preschool ; Ear, Middle/*microbiology ; Female ; Humans ; Infant ; Male ; Metagenomics ; *Microbiota ; Otitis Media with Effusion/*microbiology ; RNA, Ribosomal, 16S/analysis ; }, abstract = {OBJECTIVE: The aim of this study was to evaluate the composition and the diversity of bacteriome in middle ear effusion (MEE) and adenoid specimens of pediatric patients having otitis media with effusion (OME).<br><br>MATERIALS AND METHODS: Sample collection from children with OME followed by next generation sequencing. Seventeen adenoid and 43 middle ear effusion specimens from 25 children having OME were evaluated. Microbiome analysis was performed via Ion 16S rRNA metagenomics kit.<br><br>RESULTS: Twenty-two different bacterial species were identified from all of the samples analyzed. There were variations in the prevalence and relative abundance of the bacteriome observed between adenoid and MEE samples. MEE microbiome was significantly dominated by Alloicoccus otitis (44%), Turicella otitidis (6%), and Staphylococcus auricularis (3%). Whereas, Rothia mucilaginosa (39%), R. dentocariosa (11%), S. aureus (5%), Veillonella rogosae (2%), Granulicatella elegans (2%), Granulicatella adiacens (2%), Eikenella corrodens (1%), and Prevotella nanceiensis (1%) had significantly higher relative abundance in adenoid samples. Overall, there was no statistically significant difference in alpha diversity of MEE and adenoid samples, whereas adenoid samples constituted a cluster in the beta diversity graph.<br><br>CONCLUSION: Bacteriome of MEE is mostly dominated by A. otitis yet accompanied by other bacteria with lower relative abundances suggests that OME is likely to be a polymicrobial process. Despite similarities, significant differences in relative abundances of several predominant species between bacteriome in the MEE and adenoid put the theory that OME in children is originated from the adenoids under question.}, }
@article {pmid31376240, year = {2020}, author = {Kuperman, AA and Zimmerman, A and Hamadia, S and Ziv, O and Gurevich, V and Fichtman, B and Gavert, N and Straussman, R and Rechnitzer, H and Barzilay, M and Shvalb, S and Bornstein, J and Ben-Shachar, I and Yagel, S and Haviv, I and Koren, O}, title = {Deep microbial analysis of multiple placentas shows no evidence for a placental microbiome.}, journal = {BJOG : an international journal of obstetrics and gynaecology}, volume = {127}, number = {2}, pages = {159-169}, doi = {10.1111/1471-0528.15896}, pmid = {31376240}, issn = {1471-0528}, support = {FP7-PEOPLE-2013-CIG-630956//The Marie Curie International Reintegration Grant/International ; 3-0000-10451//The Israeli Ministry of Health/International ; }, mesh = {Amniotic Fluid/immunology/*microbiology ; Animals ; Female ; Gastrointestinal Microbiome/immunology/*physiology ; Humans ; Immunohistochemistry ; Metagenomics ; Mice ; Microbiota/*genetics ; Placenta/immunology/*microbiology ; Pregnancy ; RNA, Ribosomal, 16S/genetics/*physiology ; Sequence Analysis, DNA ; }, abstract = {OBJECTIVES: To resolve the controversy regarding the presence of a microbiota in the placenta.<br><br>DESIGN: Classical and molecular microbiological study.<br><br>SETTING: All samples were collected during caesarean section.<br><br>POPULATION: A total of 28 human placentas and six murine placentas.<br><br>METHODS: All 28 human placentas were checked for 16S rRNA gene amplification products. Three locations from four selected human placentas and three 'environmental controls' for each placenta were placed in seven culture media. The four selected human placentas were further analysed using Gram stain, immunohistochemistry for bacteria, electron microscopy, and TaqMan RT-qPCR. Six placentas from three SPF mice were cut into four pieces each, and further analysed for 16S rRNA gene amplification.<br><br>MAIN OUTCOME MEASURES: Microbiological and molecular evidence of bacteria.<br><br>RESULTS: None of the placental cultures used for the full analysis, or their environmental cultures, was positive for bacterial growth. None of the other methods showed any evidence of bacteria. Immunohistochemistry showed negligible bacterial counts. None of the murine placentas showed evidence of 16S rRNA gene amplification.<br><br>CONCLUSIONS: Our results support that the fetal environment in the womb is sterile. Based on the immunohistochemistry and the limit of detection of the other methods used, if a placental microbiome exists, it is of extreme low biomass, and thus its effect on clinical phenotypes is probably minor, if it exists at all.<br><br>TWEETABLE ABSTRACT: Using several microbiological and molecular methods in parallel, we found no compelling evidence of bacteria in human and mouse placentas.}, }
@article {pmid31188837, year = {2019}, author = {Williams, GM and Leary, SD and Ajami, NJ and Chipper Keating, S and Petrosin, JF and Hamilton-Shield, JP and Gillespie, KM}, title = {Gut microbiome analysis by post: Evaluation of the optimal method to collect stool samples from infants within a national cohort study.}, journal = {PloS one}, volume = {14}, number = {6}, pages = {e0216557}, doi = {10.1371/journal.pone.0216557}, pmid = {31188837}, issn = {1932-6203}, support = {/DH_/Department of Health/United Kingdom ; }, mesh = {Bacteria/*classification/genetics ; Cohort Studies ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome ; Humans ; Infant ; Male ; Parents ; RNA, Ribosomal, 16S/genetics ; Specimen Handling/*methods ; }, abstract = {BACKGROUND: Understanding the role of the gut microbiome is pivotal for the future development of therapies for the prevention and management of autoimmune conditions such as type 1 diabetes when sampling during early life may be particularly important. The current standard methods for collecting gut microbiome samples for research is to extract fresh samples or freeze samples immediately after collection. This is often impractical however for population-based studies. The aim of this study was to determine the optimal method for the stabilization of stool bacterial DNA obtained from nappies and transported by post in ambient conditions to the research centre for a national birth cohort study.<br><br>METHODS: Four methods to collect samples were compared to immediate freezing of samples: 1) collecting faeces onto a swab which was immediately frozen, 2) using a commercially available kit with stabilisation solution (OMNIgene•GUT kit) at ambient temperature, 3) collecting onto a swab and 4) collecting into a sterile plain tube. Samples 3) and 4) were returned to the laboratory by post at ambient temperatures. A Bland Altman analysis was used to assess the agreement between the different methods and the frozen standard.<br><br>RESULTS: Stool samples were collected by parents. For samples transported in ambient conditions, the limits of agreement showed that the OMNIgene•GUT kit had the narrowest 95% limits of agreement with the frozen standard as measured by the number of operational taxonomic units and the Shannon diversity index.<br><br>CONCLUSIONS: All methods assessed for preserving samples collected from nappies at a distance and delivered by post for gut microbiome analysis showed variation / disagreement from the frozen standard. Overall, the OMNIgene•GUT kit preserved the samples with minimal changes compared to other methods and was practical for parents to use.}, }
@article {pmid31149718, year = {2019}, author = {Zuo, K and Li, J and Li, K and Hu, C and Gao, Y and Chen, M and Hu, R and Liu, Y and Chi, H and Wang, H and Qin, Y and Liu, X and Li, S and Cai, J and Zhong, J and Yang, X}, title = {Disordered gut microbiota and alterations in metabolic patterns are associated with atrial fibrillation.}, journal = {GigaScience}, volume = {8}, number = {6}, pages = {}, doi = {10.1093/gigascience/giz058}, pmid = {31149718}, issn = {2047-217X}, mesh = {Aged ; Asian Continental Ancestry Group ; Atrial Fibrillation/*etiology/microbiology ; Bacteria/*genetics/metabolism ; Feces/chemistry/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; Metabolomics ; Metagenomics ; Middle Aged ; Serum/chemistry ; }, abstract = {BACKGROUND: With the establishment of the heart-gut axis concept, accumulating studies suggest that the gut microbiome plays an important role in the pathogenesis of cardiovascular diseases. Yet, little evidence has been reported in characterizing the gut microbiota shift in atrial fibrillation.<br><br>METHODS: We include the result of the global alterations that occur in the intestinal microbiota in a cohort of 50 patients with atrial fibrillation and 50 matched controls based on a strategy of metagenomic and metabolomic analyses.<br><br>RESULTS: The alterations include a dramatic elevation in microbial diversity and a specific perturbation of gut microbiota composition. Overgrowth of Ruminococcus, Streptococcus, and Enterococcus, as well as reduction of Faecalibacterium, Alistipes, Oscillibacter, and Bilophila were detected in patients with atrial fibrillation. A gut microbial function imbalance and correlated metabolic pattern changes were observed with atrial fibrillation in both fecal and serum samples. The differential gut microbiome signatures could be used to identify patients with atrial fibrillation.<br><br>CONCLUSIONS: Our findings characterize the disordered gut microbiota and microbial metabolite profiles in atrial fibrillation. Further research could determine whether intervention strategies targeting intestinal microbiome composition might be useful to counteract the progression of atrial fibrillation.}, }
@article {pmid31136592, year = {2019}, author = {Czech, L and Stamatakis, A}, title = {Scalable methods for analyzing and visualizing phylogenetic placement of metagenomic samples.}, journal = {PloS one}, volume = {14}, number = {5}, pages = {e0217050}, doi = {10.1371/journal.pone.0217050}, pmid = {31136592}, issn = {1932-6203}, mesh = {Algorithms ; Animals ; Cluster Analysis ; Computational Biology ; Computers ; Databases, Genetic ; Diatoms/classification ; Female ; Gastrointestinal Microbiome/*genetics ; Geography ; Humans ; *Metagenome ; Metagenomics/*methods ; *Oceans and Seas ; *Phylogeny ; Software ; Vaginosis, Bacterial/*microbiology ; }, abstract = {BACKGROUND: The exponential decrease in molecular sequencing cost generates unprecedented amounts of data. Hence, scalable methods to analyze these data are required. Phylogenetic (or Evolutionary) Placement methods identify the evolutionary provenance of anonymous sequences with respect to a given reference phylogeny. This increasingly popular method is deployed for scrutinizing metagenomic samples from environments such as water, soil, or the human gut.<br><br>NOVEL METHODS: Here, we present novel and, more importantly, highly scalable methods for analyzing phylogenetic placements of metagenomic samples. More specifically, we introduce methods for (a) visualizing differences between samples and their correlation with associated meta-data on the reference phylogeny, (b) clustering similar samples using a variant of the k-means method, and (c) finding phylogenetic factors using an adaptation of the Phylofactorization method. These methods enable to interpret metagenomic data in a phylogenetic context, to find patterns in the data, and to identify branches of the phylogeny that are driving these patterns.<br><br>RESULTS: To demonstrate the scalability and utility of our methods, as well as to provide exemplary interpretations of our methods, we applied them to 3 publicly available datasets comprising 9782 samples with a total of approximately 168 million sequences. The results indicate that new biological insights can be attained via our methods.}, }
@article {pmid31006170, year = {2020}, author = {Coker, MO and Hoen, AG and Dade, E and Lundgren, S and Li, Z and Wong, AD and Zens, MS and Palys, TJ and Morrison, HG and Sogin, ML and Baker, ER and Karagas, MR and Madan, JC}, title = {Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study.}, journal = {BJOG : an international journal of obstetrics and gynaecology}, volume = {127}, number = {2}, pages = {217-227}, pmid = {31006170}, issn = {1471-0528}, support = {NIGMS P20GM104416/NH/NIH HHS/United States ; RD83544201//U.S. Environmental Protection Agency/International ; 1P20ES018175-02/NH/NIH HHS/United States ; UH3 OD023275/OD/NIH HHS/United States ; R01 GM123014/GM/NIGMS NIH HHS/United States ; RD83459901//U.S. Environmental Protection Agency/International ; R01 LM012723/LM/NLM NIH HHS/United States ; K01 LM011985/LM/NLM NIH HHS/United States ; NIEHS P01ES022832/NH/NIH HHS/United States ; P20 ES018175/ES/NIEHS NIH HHS/United States ; NIEHS P20ES018175/NH/NIH HHS/United States ; P01 ES022832/ES/NIEHS NIH HHS/United States ; NLM K01LM011985/NH/NIH HHS/United States ; P20 GM104416/GM/NIGMS NIH HHS/United States ; }, mesh = {*Antibiotic Prophylaxis ; Bacteroides/growth &amp; development ; Bacteroidetes ; Bifidobacterium ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Infant, Newborn ; Lactobacillus ; Maternal Exposure ; Mothers ; Pregnancy ; Prospective Studies ; RNA, Ribosomal, 16S ; Sequence Analysis, RNA ; Term Birth ; Vagina/*microbiology ; beta-Lactamases ; }, abstract = {OBJECTIVE: To evaluate the potential impact of intrapartum antibiotics, and their specific classes, on the infant gut microbiota in the first year of life.<br><br>DESIGN: Prospective study of infants in the New Hampshire Birth Cohort Study (NHBCS).<br><br>SETTINGS: Rural New Hampshire, USA.<br><br>POPULATION OR SAMPLE: Two hundred and sixty-six full-term infants from the NHBCS.<br><br>METHODS: Intrapartum antibiotic use during labour and delivery was abstracted from medical records. Faecal samples collected at 6 weeks and 1 year of age were characterised by 16S rRNA sequencing, and metagenomics analysis in a subset of samples.<br><br>EXPOSURES: Maternal exposure to antibiotics during labour and delivery.<br><br>MAIN OUTCOME MEASURE: Taxonomic and functional profiles of faecal samples.<br><br>RESULTS: Infant exposure to intrapartum antibiotics, particularly to two or more antibiotic classes, was independently associated with lower microbial diversity scores as well as a unique bacterial community at 6 weeks (GUnifrac, P = 0.02). At 1 year, infants in the penicillin-only group had significantly lower α diversity scores than infants not exposed to intrapartum antibiotics. Within the first year of life, intrapartum exposure to penicillins was related to a significantly lower increase in several taxa including Bacteroides, use of cephalosporins was associated with a significantly lower rise over time in Bifidobacterium and infants in the multi-class group experienced a significantly higher increase in Veillonella dispar.<br><br>CONCLUSIONS: Our findings suggest that intrapartum antibiotics alter the developmental trajectory of the infant gut microbiome, and specific antibiotic types may impact community composition, diversity and keystone immune training taxa.<br><br>TWEETABLE ABSTRACT: Class of intrapartum antibiotics administered during delivery relates to maturation of infant gut microbiota.}, }
@article {pmid29777234, year = {2019}, author = {Hjorth, MF and Blædel, T and Bendtsen, LQ and Lorenzen, JK and Holm, JB and Kiilerich, P and Roager, HM and Kristiansen, K and Larsen, LH and Astrup, A}, title = {Prevotella-to-Bacteroides ratio predicts body weight and fat loss success on 24-week diets varying in macronutrient composition and dietary fiber: results from a post-hoc analysis.}, journal = {International journal of obesity (2005)}, volume = {43}, number = {1}, pages = {149-157}, doi = {10.1038/s41366-018-0093-2}, pmid = {29777234}, issn = {1476-5497}, mesh = {Adult ; Bacteroides/*physiology ; Diet, Reducing ; Dietary Fiber/administration &amp; dosage ; Energy Intake ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Male ; Middle Aged ; Nutrients/*administration &amp; dosage ; Overweight/*diet therapy/metabolism/microbiology ; Prevotella/*physiology ; RNA, Ribosomal, 16S ; Retrospective Studies ; Weight Loss/*physiology ; }, abstract = {BACKGROUND/OBJECTIVES: Individuals with high pre-treatment bacterial Prevotella-to-Bacteroides (P/B) ratio have been reported to lose more body weight on diets high in fiber than subjects with a low P/B ratio. Therefore, the aim of the present study was to examine potential differences in dietary weight loss responses between participants with low and high P/B.<br><br>SUBJECTS/METHODS: Eighty overweight participants were randomized (52 completed) to a 500 kcal/d energy deficit diet with a macronutrient composition of 30 energy percentage (E%) fat, 52 E% carbohydrate and 18 E% protein either high (≈1500 mg calcium/day) or low (≤ 600 mg calcium/day) in dairy products for 24 weeks. Body weight, body fat, and dietary intake (by 7-day dietary records) were determined. Individuals were dichotomized according to their pre-treatment P/B ratio derived from 16S rRNA gene sequencing of collected fecal samples to test the potential modification of dietary effects using linear mixed models.<br><br>RESULTS: Independent of the randomized diets, individuals with high P/B lost 3.8 kg (95%CI, 1.8,5.8; P < 0.001) more body weight and 3.8 kg (95% CI, 1.1, 6.5; P = 0.005) more body fat compared to individuals with low P/B. After adjustment for multiple covariates, individuals with high P/B ratio lost 8.3 kg (95% CI, 5.8;10.9, P < 0.001) more body weight when consuming above compared to below 30 g fiber/10MJ whereas this weight loss was 3.2 kg (95% CI, 0.8;5.5, P = 0.008) among individuals with low P/B ratio [Mean difference: 5.1 kg (95% CI, 1.7;8.6, P = 0.003)]. Partial correlation coefficients between fiber intake and weight change was 0.90 (P < 0.001) among individuals with high P/B ratio and 0.25 (P = 0.29) among individuals with low P/B ratio.<br><br>CONCLUSIONS: Individuals with high P/B lost more body weight and body fat compared to individuals with low P/B, confirming that individuals with a high P/B are more susceptible to weight loss on a diet rich in fiber.}, }
@article {pmid32005134, year = {2020}, author = {Krotman, Y and Yergaliyev, TM and Alexander Shani, R and Avrahami, Y and Szitenberg, A}, title = {Dissecting the factors shaping fish skin microbiomes in a heterogeneous inland water system.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {9}, doi = {10.1186/s40168-020-0784-5}, pmid = {32005134}, issn = {2049-2618}, support = {03-16-06a//ICA in Israel/ ; }, abstract = {BACKGROUND: Fish skin microbiomes are rarely studied in inland water systems, in spite of their importance for fish health and ecology. This is mainly because fish species distribution often covaries with other biotic and abiotic factors, complicating the study design. We tackled this issue in the northern part of the Jordan River system, in which a few fish species geographically overlap, across steep gradients of water temperature and salinity.<br><br>RESULTS: Using 16S rRNA metabarcoding, we studied the water properties that shape the skin bacterial communities, and their interaction with fish taxonomy. To better characterise the indigenous skin community, we excluded bacteria that were equally abundant in the skin samples and in the water samples, from our analysis of the skin samples. With this in mind, we found alpha diversity of the skin communities to be stable across sites, but higher in benthic loaches, compared to other fish. Beta diversity was found to be different among sites and to weakly covary with the dissolved oxygen, when treated skin communities were considered. In contrast, water temperature and conductivity were strong factors explaining beta diversity in the untreated skin communities. Beta diversity differences between co-occurring fish species emerged only for the treated skin communities. Metagenomics predictions highlighted the microbiome functional implications of excluding the water community contamination from the fish skin communities. Finally, we found that human-induced eutrophication promotes dysbiosis of the fish skin community, with signatures relating to fish health.<br><br>CONCLUSIONS: Consideration of the background water microbiome when studying fish skin microbiomes, across varying fish species and water properties, exposes patterns otherwise undetected and highlight among-fish-species differences. We suggest that sporadic nutrient pollution events, otherwise undetected, drive fish skin communities to dysbiosis. This finding is in line with a recent study, showing that biofilms capture sporadic pollution events, undetectable by interspersed water monitoring. Video abstract.}, }
@article {pmid31563955, year = {2019}, author = {Weinroth, MD and Martin, JN and Doster, E and Geornaras, I and Parker, JK and Carlson, CR and Metcalf, JL and Morley, PS and Belk, KE}, title = {Investigation of tylosin in feed of feedlot cattle and effects on liver abscess prevalence, and fecal and soil microbiomes and resistomes1.}, journal = {Journal of animal science}, volume = {97}, number = {11}, pages = {4567-4578}, pmid = {31563955}, issn = {1525-3163}, mesh = {Animal Feed/analysis ; Animals ; Anti-Bacterial Agents/*administration &amp; dosage ; Cattle ; Cattle Diseases/epidemiology/microbiology/*prevention &amp; control ; Dietary Supplements/*analysis ; Drug Resistance, Bacterial ; Feces/microbiology ; Female ; Geography ; Liver Abscess/epidemiology/microbiology/prevention &amp; control/*veterinary ; Male ; Metagenomics ; Microbiota/*drug effects/genetics ; Models, Statistical ; Prevalence ; Soil Microbiology ; Tylosin/*administration &amp; dosage ; }, abstract = {Liver abscesses in feedlot cattle are detrimental to animal performance and economic return. Tylosin, a macrolide antibiotic, is used to reduce prevalence of liver abscesses, though there is variable efficacy among different groups of cattle. There is an increased importance in better understanding the etiology and pathogenesis of this condition because of growing concern over antibiotic resistance and increased scrutiny regarding use of antibiotics in food animal production. The objective of this study was to compare the microbiomes and antimicrobial resistance genes (resistomes) of feces of feedlot cattle administered or not administered tylosin and in their pen soil in 3 geographical regions with differing liver abscess prevalences. Cattle (total of 2,256) from 3 geographical regions were selected for inclusion based on dietary supplementation with tylosin (yes/no). Feces and pen soil samples were collected before harvest, and liver abscesses were identified at harvest. Shotgun and 16S rRNA amplicon sequencing were used to evaluate the soil and feces. Microbiome and resistome composition of feces (as compared by UniFrac distances and Euclidian distances, respectively) did not differ (P > 0.05) among tylosin or no tylosin-administered cattle. However, feedlot location was associated with differences (P ≤ 0.05) of resistomes and microbiomes. Using LASSO, a statistical model identified both fecal and soil microbial communities as predictive of liver abscess prevalence in pens. This model explained 75% of the variation in liver abscess prevalence, though a larger sample size would be needed to increase robustness of the model. These data suggest that tylosin exposure does not have a large impact on cattle resistomes or microbiomes, but instead, location of cattle production may be a stronger driver of both the resistome and microbiome composition of feces.}, }
@article {pmid31451112, year = {2019}, author = {Ghurye, J and Treangen, T and Fedarko, M and Hervey, WJ and Pop, M}, title = {MetaCarvel: linking assembly graph motifs to biological variants.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {174}, doi = {10.1186/s13059-019-1791-3}, pmid = {31451112}, issn = {1474-760X}, support = {R01AI100947//National Institute of Allergy and Infectious Diseases/International ; }, mesh = {Acinetobacter/genetics ; *Algorithms ; Base Sequence ; Databases, Genetic ; Feces/microbiology ; *Genetic Variation ; Humans ; Metagenomics/*methods ; Microbiota/genetics ; Mutation/genetics ; Repetitive Sequences, Nucleic Acid/genetics ; Sequence Analysis, DNA ; }, abstract = {Reconstructing genomic segments from metagenomics data is a highly complex task. In addition to general challenges, such as repeats and sequencing errors, metagenomic assembly needs to tolerate the uneven depth of coverage among organisms in a community and differences between nearly identical strains. Previous methods have addressed these issues by smoothing genomic variants. We present a variant-aware metagenomic scaffolder called MetaCarvel, which combines new strategies for repeat detection with graph analytics for the discovery of variants. We show that MetaCarvel can accurately reconstruct genomic segments from complex microbial mixtures and correctly identify and characterize several classes of common genomic variants.}, }
@article {pmid31451108, year = {2019}, author = {Rhoades, N and Barr, T and Hendrickson, S and Prongay, K and Haertel, A and Gill, L and Garzel, L and Whiteson, K and Slifka, M and Messaoudi, I}, title = {Maturation of the infant rhesus macaque gut microbiome and its role in the development of diarrheal disease.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {173}, doi = {10.1186/s13059-019-1789-x}, pmid = {31451108}, issn = {1474-760X}, support = {P51 OD011092/OD/NIH HHS/United States ; }, mesh = {Aging ; Animals ; Animals, Newborn ; Anti-Bacterial Agents/therapeutic use ; Bacteria/genetics ; Biomarkers/metabolism ; Carrier State/microbiology ; Child ; Child, Preschool ; Developed Countries ; Developing Countries ; Diarrhea/drug therapy/*microbiology ; Disease Susceptibility ; Female ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Humans ; Infant ; Macaca mulatta ; Male ; Metagenomics ; Phylogeny ; }, abstract = {BACKGROUND: Diarrhea is the second leading cause of death in children under 5 years of age. Enhanced understanding of causal pathways, pathogenesis, and sequelae of diarrhea is urgently needed. Although the gut microbiota is believed to play a role in susceptibility to diarrheal diseases, our understanding of this association remains incomplete. Infant rhesus macaques (Macaca mulatta) are susceptible to diarrhea making them an ideal model to address this question.<br><br>RESULTS: The maturation of the infant rhesus macaque gut microbiome throughout the first 8 months of life occurs in a similar pattern as that described for human infants. Moreover, the microbiome of the captive reared infant rhesus macaque more closely resembles that of human infants in the developing world than in the western world. Importantly, prior to disease onset, the gut microbiome of infants that later develop diarrhea is enriched in pathways of immunomodulatory metabolite synthesis, while those of infants that remain asymptomatic are enriched in pathways for short-chain fatty acid production. We identify Prevotella strains that are more abundant at 1 month in infants that later develop diarrhea. At 8 months, the microbiomes of animals that experience diarrhea show increased abundance of Campylobacter and a reduction in Helicobacter macacae.<br><br>CONCLUSION: The composition of the microbial community could provide a phenotypic marker of an infant's susceptibility to diarrheal disease. Given the significant physiological and immunological similarities between human and nonhuman primates, these findings provide potential markers of susceptibility to diarrhea that could be modulated to improve infant health, especially in the developing world.}, }
@article {pmid31443695, year = {2019}, author = {Malmuthuge, N and Liang, G and Guan, LL}, title = {Regulation of rumen development in neonatal ruminants through microbial metagenomes and host transcriptomes.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {172}, doi = {10.1186/s13059-019-1786-0}, pmid = {31443695}, issn = {1474-760X}, mesh = {Animals ; Animals, Newborn ; Bacteria/*genetics ; Cattle ; Epithelium/growth &amp; development ; Fatty Acids, Volatile/metabolism ; Gene Regulatory Networks ; Metabolome/genetics ; Metagenome/*genetics ; MicroRNAs/genetics/metabolism ; Microbiota/*genetics ; Rumen/*microbiology ; Ruminants/*genetics/*growth &amp; development/microbiology ; Transcriptome/*genetics ; Weaning ; }, abstract = {BACKGROUND: In ruminants, early rumen development is vital for efficient fermentation that converts plant materials to human edible food such as milk and meat. Here, we investigate the extent and functional basis of host-microbial interactions regulating rumen development during the first 6 weeks of life.<br><br>RESULTS: The use of microbial metagenomics, together with quantification of volatile fatty acids (VFAs) and qPCR, reveals the colonization of an active bacterial community in the rumen at birth. Colonization of active complex carbohydrate fermenters and archaea with methyl-coenzyme M reductase activity was also observed from the first week of life in the absence of a solid diet. Integrating microbial metagenomics and host transcriptomics reveals only 26.3% of mRNA transcripts, and 46.4% of miRNAs were responsive to VFAs, while others were ontogenic. Among these, one host gene module was positively associated with VFAs, while two other host gene modules and one miRNA module were negatively associated with VFAs. Eight host genes and five miRNAs involved in zinc ion binding-related transcriptional regulation were associated with a rumen bacterial cluster consisting of Prevotella, Bacteroides, and Ruminococcus.<br><br>CONCLUSION: This three-way interaction suggests a potential role of bacteria-driven transcriptional regulation in early rumen development via miRNAs. Our results reveal a highly active early microbiome that regulates rumen development of neonatal calves at the cellular level, and miRNAs may coordinate these host-microbial interactions.}, }
@article {pmid31407040, year = {2019}, author = {Evangelista, DE and de Oliveira Arnoldi Pellegrini, V and Santo, ME and McQueen-Mason, S and Bruce, NC and Polikarpov, I}, title = {Biochemical characterization and low-resolution SAXS shape of a novel GH11 exo-1,4-β-xylanase identified in a microbial consortium.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {19}, pages = {8035-8049}, doi = {10.1007/s00253-019-10033-8}, pmid = {31407040}, issn = {1432-0614}, support = {10/52362-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 11/20505-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 11/21608-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 15/13684-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 405191/2015-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 303988/2016-9//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 440977/2016-9//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 151963/2018-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; BB/I018492/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Disaccharides/metabolism ; Endo-1,4-beta Xylanases/*chemistry/isolation &amp; purification/*metabolism ; Enzyme Stability ; Gene Expression Profiling ; Hydrogen-Ion Concentration ; Metagenomics ; *Microbial Consortia ; Protein Conformation ; Recombinant Proteins/chemistry/isolation &amp; purification/metabolism ; Scattering, Small Angle ; Temperature ; Xylans/metabolism ; }, abstract = {Biotechnologies that aim to produce renewable fuels, chemicals, and bioproducts from residual ligno(hemi)cellulosic biomass mostly rely on enzymatic depolymerization of plant cell walls (PCW). This process requires an arsenal of diverse enzymes, including xylanases, which synergistically act on the hemicellulose, reducing the long and complex xylan chains to oligomers and simple sugars. Thus, xylanases play a crucial role in PCW depolymerization. Until recently, the largest xylanase family, glycoside hydrolase family 11 (GH11) has been exclusively represented by endo-catalytic β-1,4- and β-1,3-xylanases. Analysis of a metatranscriptome library from a microbial lignocellulose community resulted in the identification of an unusual exo-acting GH11 β-1,4-xylanase (MetXyn11). Detailed characterization has been performed on recombinant MetXyn11 including determination of its low-resolution small-angle X-ray scattering (SAXS) molecular envelope in solution. Our results reveal that MetXyn11 is a monomeric globular enzyme that liberates xylobiose from heteroxylans as the only product. MetXyn11 has an optimal activity in a pH range from 6 to 9 and an optimal temperature of 50 °C. The enzyme maintained above 65% of its original activity in the pH range 5 to 6 after being incubated for 72 h at 50 °C. Addition of the enzyme to a commercial enzymatic cocktail (CelicCtec3) promoted a significant increase of enzymatic hydrolysis yields of hydrothermally pretreated sugarcane bagasse (16% after 24 h of hydrolysis).}, }
@article {pmid31401751, year = {2019}, author = {Chen, J and Yu, B and Chen, D and Zheng, P and Luo, Y and Huang, Z and Luo, J and Mao, X and Yu, J and He, J}, title = {Changes of porcine gut microbiota in response to dietary chlorogenic acid supplementation.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {19}, pages = {8157-8168}, doi = {10.1007/s00253-019-10025-8}, pmid = {31401751}, issn = {1432-0614}, support = {2016TD0028//the Youth Innovation teams of animal Feed Biotechnology of Sichuan Province/ ; 2018NZDZX0005//the key Research and Development program of Sichuan Province/ ; }, mesh = {Animals ; Anti-Infective Agents/*administration &amp; dosage ; Bacteria/classification/*drug effects/genetics ; Chlorogenic Acid/*administration &amp; dosage ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Gastrointestinal Contents/chemistry ; Gastrointestinal Microbiome/*drug effects ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Swine ; }, abstract = {Chlorogenic acids (CGA), the most abundant natural polyphenol present in human diet and plants, have attracted considerable research interest because of their broad bioactivities including the antimicrobial activity. However, little is known about their influences on intestinal bacterial communities. Here, we described a response in intestinal microbiome to CGA using a porcine model. Twenty-four weaned pigs were allotted to two groups and fed with a basal diet or a basal diet containing 1000 mg/kg CGA. Results showed that CGA significantly increased the length of the small intestine (P < 0.05) and enhanced the activity of diamine oxidase (DAO) and the concentration of MHC-II in the jejunal and ileal mucosa (P < 0.05). Moreover, the acetate concentration in ileum and cecum digesta, and the propionate and butyrate concentrations in the cecum digesta, were significantly elevated by CGA (P < 0.05). Interestingly, CGA significantly increased the total 16S rRNA gene copies and bacterial alpha diversity in the cecum (P < 0.05). The relative abundance of bacteria from phyla Firmicutes and Bacteroidetes was increased in the cecum digesta (P < 0.05), whereas the abundance of bacteria from phylum Protebacteria was decreased by CGA (P < 0.05). Importantly, pigs on CGA-containing diet had higher abundance of Lactobacillus spp., Prevotella spp., Anaerovibrio spp., and Alloprevotella spp. in the cecum (P < 0.05). Not only did our study suggest a synergic response of intestinal barrier function and microbiota to the CGA, but the result will also contribute to understanding of the mechanisms behind the CGA-modulated gut health.}, }
@article {pmid31187446, year = {2019}, author = {Gupta, SK and Raza, S and Unno, T}, title = {Comparison of de-novo assembly tools for plasmid metagenome analysis.}, journal = {Genes &amp; genomics}, volume = {41}, number = {9}, pages = {1077-1083}, doi = {10.1007/s13258-019-00839-1}, pmid = {31187446}, issn = {2092-9293}, mesh = {Contig Mapping/*methods ; Metagenome ; Metagenomics/*methods ; Microbiota/genetics ; Plasmids/genetics ; Sequence Analysis, DNA/*methods ; *Software ; Water Microbiology ; }, abstract = {BACKGROUND: With the advent of next-generation sequencing techniques, culture-independent metagenome approaches have now made it possible to predict possible presence of genes in the environmental bacteria most of which may be non-cultivable. Short reads obtained from the deep sequencing can be assembled into long contigs some of which include plasmids. Plasmids are the circular double stranded DNA in bacteria and known as one of the major carriers of antibiotic resistance genes.<br><br>OBJECTIVE: Metagenomic analyses, especially focused on plasmids, could help us predict dissemination mechanisms of antibiotic resistance genes in the environment. However, with the availability of a myriad of metagenomic assemblers, the selection of the most appropriate metagenome assembler for the plasmid metagenome study might be challenging. Therefore, in this study, we compared five open source assemblers to suggest most effective way of plasmid metagenome analysis.<br><br>METHODS: IDBA-UD, MEGAHIT, SPAdes, SOAPdenovo2, and Velvet are compared for conducting plasmid metagenome analyses using two water samples.<br><br>RESULTS: Our results clearly showed that abundance and types of antibiotic resistance genes on plasmids varied depending on the selection of assembly tools. IDBA-UD and MEGAHIT demonstrated the overall best assembly statistics with high N50 values with higher portion of longer contigs.<br><br>CONCLUSION: These two assemblers also detected more diverse plasmids. Among the two, MEGAHIT showed more memory efficient assembly, therefore we suggest that the use of MEGAHIT for plasmid metagenome analysis may offer more diverse plasmids with less computer resource required. Here, we also summarized a fundamental plasmid metagenome work flow, especially for antibiotic resistance gene investigation.}, }
@article {pmid31704413, year = {2020}, author = {Rehman, ZU and Fortunato, L and Cheng, T and Leiknes, T}, title = {Metagenomic analysis of sludge and early-stage biofilm communities of a submerged membrane bioreactor.}, journal = {The Science of the total environment}, volume = {701}, number = {}, pages = {134682}, doi = {10.1016/j.scitotenv.2019.134682}, pmid = {31704413}, issn = {1879-1026}, mesh = {*Biofilms ; Biofouling ; Bioreactors/*microbiology ; Membranes, Artificial ; Metagenome ; *Microbiota ; Sewage/microbiology ; *Waste Disposal, Fluid ; }, abstract = {Biofilm formation on membranes in activated sludge membrane bioreactors (MBR), commonly identified as biofouling, is a significant problem for MBR operations. A better understanding of microbial species involved in the biofilm formation is needed to develop anti-biofilm measures. A read-based and genome-resolved shotgun metagenomic approach was applied to characterize the composition and functional potential of the sludge and early stage biofilm microbial communities in an MBR process. Read-based analysis revealed that the prevalence of different phyla are relatively similar in both the sludge and biofilm samples, with Proteobacteria as the most dominant, followed by Chloroflexi, Bacteroidetes and Planctomycetes. However, the relative abundance of these phyla slightly varies between the sludge and biofilm. Phyla such as Actinobacteria, bacterial candidate phyla, Chlamydiae, Cyanobacteria/Melainabacteria and Firmicutes are 2 to 4 times more abundant in the biofilm than in the sludge. At the genus level, genera belonging to Proteobacteria (Legionella, Caulobacter, Sphingomonas, Acinetobacter and Rhizobium), Cyanobacteria (Hassallia), and Spirochaetes (Turneriella) are at least twice more abundant in the biofilm. These genera, especially those belonging to Phylum Proteobacteria, are known to play an important role in the formation of biofilms on surfaces. The Alpha diversity is found slightly higher in the biofilm, compared with sludge samples. Functional classification of reads through the SEED subsystem shows that functional classes such as those involved in the metabolism of various molecules are significantly different in the biofilm and sludge. A phylogenomic analysis of the six extracted metagenome assembled genomes (MAGs) shows that three MAGs belong to Proteobacteria, and one MAG belong to each of Chloroflexi, Bacteroidetes and Planctomycetes. The relative abundance of the MAG belonging to Alphaproteobacteria is higher in the biofilm. A functional potential analysis of the MAGs reveals their potential to metabolize carbon and nitrogen sources, as well as the prevalence of antibiotic resistance genes.}, }
@article {pmid31248008, year = {2019}, author = {Steury, RA and Currey, MC and Cresko, WA and Bohannan, BJM}, title = {Population Genetic Divergence and Environment Influence the Gut Microbiome in Oregon Threespine Stickleback.}, journal = {Genes}, volume = {10}, number = {7}, pages = {}, doi = {10.3390/genes10070484}, pmid = {31248008}, issn = {2073-4425}, support = {P50GM098911/NH/NIH HHS/United States ; R24RR032670/NH/NIH HHS/United States ; }, mesh = {Animals ; Environment ; Gastrointestinal Microbiome/*genetics ; *Genetic Variation ; Genetics, Population ; Geography ; Host Microbial Interactions ; Metagenomics ; Microbiota ; Oregon ; Smegmamorpha/genetics/*microbiology ; }, abstract = {Much of animal-associated microbiome research has been conducted in&amp;nbsp;species&amp;nbsp;for which little is known of their natural ecology and evolution.&amp;nbsp;Microbiome studies that combine population genetic, environment, and geographic data for wild organisms can be very informative, especially in situations where host genetic variation and the environment both influence microbiome variation.&amp;nbsp;The few studies that have&amp;nbsp;related&amp;nbsp;population genetic&amp;nbsp;and microbiome variation in wild populations&amp;nbsp;have been constrained by observation-based kinship data or&amp;nbsp;incomplete genomic information. Here we&amp;nbsp;integrate population genomic&amp;nbsp;and microbiome analyses&amp;nbsp;in wild threespine stickleback fish distributed throughout western Oregon, USA. We found that gut microbiome diversity and composition partitioned more among than within wild host populations and was better explained by host population genetic divergence than&amp;nbsp;by environment and geography. We also identified gut microbial taxa that were most differentially abundant across environments and across genetically divergent populations. Our findings highlight the benefits of studies that investigate host-associated microbiomes in wild organisms.}, }
@article {pmid31164469, year = {2019}, author = {Namasivayam, S and Kauffman, KD and McCulloch, JA and Yuan, W and Thovarai, V and Mittereder, LR and Trinchieri, G and Barber, DL and Sher, A}, title = {Correlation between Disease Severity and the Intestinal Microbiome in Mycobacterium tuberculosis-Infected Rhesus Macaques.}, journal = {mBio}, volume = {10}, number = {3}, pages = {}, doi = {10.1128/mBio.01018-19}, pmid = {31164469}, issn = {2150-7511}, mesh = {Animals ; Disease Susceptibility/*microbiology ; Dysbiosis/microbiology ; Female ; *Gastrointestinal Microbiome ; Macaca mulatta/microbiology ; Male ; Metagenomics ; Mycobacterium tuberculosis/pathogenicity ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Tuberculosis/*microbiology ; }, abstract = {The factors that determine host susceptibility to tuberculosis (TB) are poorly defined. The microbiota has been identified as a key influence on the nutritional, metabolic, and immunological status of the host, although its role in the pathogenesis of TB is currently unclear. Here, we investigated the influence of Mycobacterium tuberculosis exposure on the microbiome and conversely the impact of the intestinal microbiome on the outcome of M. tuberculosis exposure in a rhesus macaque model of tuberculosis. Animals were infected with different strains and doses of M. tuberculosis in three independent experiments, resulting in a range of disease severities. The compositions of the microbiotas were then assessed using a combination of 16S rRNA and metagenomic sequencing in fecal samples collected pre- and postinfection. Clustering analyses of the microbiota compositions revealed that alterations in the microbiome after M. tuberculosis infection were of much lower magnitude than the variability seen between individual monkeys. However, the microbiomes of macaques that developed severe disease were noticeably distinct from those of the animals with less severe disease as well as from each other. In particular, the bacterial families Lachnospiraceae and Clostridiaceae were enriched in monkeys that were more susceptible to infection, while numbers of Streptococcaceae were decreased. These findings in infected nonhuman primates reveal that certain baseline microbiome communities may strongly associate with the development of severe tuberculosis following infection and can be more important disease correlates than alterations to the microbiota following M. tuberculosis infection itself.IMPORTANCE Why some but not all individuals infected with Mycobacterium tuberculosis develop disease is poorly understood. Previous studies have revealed an important influence of the microbiota on host resistance to infection with a number of different disease agents. Here, we investigated the possible role of the individual's microbiome in impacting the outcome of M. tuberculosis infection in rhesus monkeys experimentally exposed to this important human pathogen. Although M. tuberculosis infection itself caused only minor alterations in the composition of the gut microbiota in these animals, we observed a significant correlation between an individual monkey's microbiome and the severity of pulmonary disease. More importantly, this correlation between microbiota structure and disease outcome was evident even prior to infection. Taken together, our findings suggest that the composition of the microbiome may be a useful predictor of tuberculosis progression in infected individuals either directly because of the microbiome's direct influence on host resistance or indirectly because of its association with other host factors that have this influence. This calls for exploration of the potential of the microbiota composition as a predictive biomarker through carefully designed prospective studies.}, }
@article {pmid30788772, year = {2019}, author = {Federici, M}, title = {Gut microbiome and microbial metabolites: a new system affecting metabolic disorders.}, journal = {Journal of endocrinological investigation}, volume = {42}, number = {9}, pages = {1011-1018}, doi = {10.1007/s40618-019-01022-9}, pmid = {30788772}, issn = {1720-8386}, mesh = {*Gastrointestinal Microbiome ; Humans ; Metabolic Diseases/*etiology/metabolism/pathology ; *Metabolome ; }, abstract = {INTRODUCTION: The gut microbiome is emerging as an important player in the field of metabolic disorders.<br><br>MATERIALS AND METHODS: Currently, several studies are ongoing to determine whether the effect of gut microbiome on obesity, type 2 diabetes, non-alcoholic fatty liver disease, and other metabolic diseases is determined by singular species or rather by a functional role of bacterial metabolism at higher taxonomical level. Deciphering if a single or more species are responsible for metabolic traits or rather microbial metabolic pathways are responsible for effects on host metabolism may help to identify appropriate dietary interventions to support microbial functions according to the prevalent host disease. Furthermore, the combination of metagenomics and metabolomics-based signature might be applied in the future to improve the risk prediction in healthy subjects.<br><br>CONCLUSION: In this review, I will summarize the current findings regarding the role of gut microbiome and metabolites in metabolic disorders to argue whether the current achievements may be translated into clinical practice.}, }
@article {pmid30282116, year = {2019}, author = {Taylor, SL and O'Farrell, HE and Simpson, JL and Yang, IA and Rogers, GB}, title = {The contribution of respiratory microbiome analysis to a treatable traits model of care.}, journal = {Respirology (Carlton, Vic.)}, volume = {24}, number = {1}, pages = {19-28}, doi = {10.1111/resp.13411}, pmid = {30282116}, issn = {1440-1843}, mesh = {Airway Management/*methods ; Humans ; Metagenomics/methods ; Microbiological Phenomena ; *Microbiota/drug effects/physiology ; Models, Organizational ; Patient Care Management/*organization &amp; administration ; *Pulmonary Disease, Chronic Obstructive/immunology/microbiology/physiopathology/therapy ; Respiratory System/*microbiology ; }, abstract = {The composition of the airway microbiome in patients with chronic airway diseases, such as severe asthma, chronic obstructive pulmonary disease (COPD), bronchiectasis and cystic fibrosis (CF), has the potential to inform a precision model of clinical care. Patients with these conditions share overlapping disease characteristics, including airway inflammation and airflow limitation. The clinical management of chronic respiratory conditions is increasingly moving away from a one-size-fits-all model based on primary diagnosis, towards care targeting individual disease traits, and is particularly useful for subgroups of patients who respond poorly to conventional therapies. Respiratory microbiome analysis is an important potential contributor to such a 'treatable traits' approach, providing insight into both microbial drivers of airways disease, and the selective characteristics of the changing lower airway environment. We explore the potential to integrate respiratory microbiome analysis into a treatable traits model of clinical care and provide a practical guide to the application and clinical interpretation of respiratory microbiome analysis.}, }
@article {pmid31965701, year = {2020}, author = {Muñoz-Arenas, LC and Fusaro, C and Hernández-Guzmán, M and Dendooven, L and Estrada-Torres, A and Navarro-Noya, YE}, title = {Soil microbial diversity drops with land use change in a high mountain temperate forest: a metagenomics survey.}, journal = {Environmental microbiology reports}, volume = {}, number = {}, pages = {}, doi = {10.1111/1758-2229.12822}, pmid = {31965701}, issn = {1758-2229}, abstract = {Land-use change has been identified as the most severe threat to biodiversity. Soils are important biodiversity reservoirs, but to what extent conversion of high altitude temperate forest to arable land affects taxonomic and functional soil biodiversity is still largely unknown. Shotgun metagenomics was used to determine the taxonomic and functional diversity of Bacteria, Archaea and DNA Virus in terms of effective number of species in high altitude temperate Oak and Pine-oak forest and arable soils from Mexico. Generally, the soil ecosystem maintained its microbial species richness notwithstanding land-use change. Archaea diversity was not affected by land-use change, but the bacterial diversity decreased with 45-55% when the oak forest was converted to arable land and 65-75% when the pine-oak forest was. Loss in bacterial diversity as a result of land-use change was positively correlated (R2 = 0.41) with the 10 to 25% loss in functional diversity. The archaeal communities were evener than the bacterial ones, which might explain their different response to land-use change. We expected a decrease in DNA viral communities as the bacterial diversity decreased, i.e. their potential hosts. However, a higher viral diversity was found in the arable than in the forest soils. It was found that converting high altitude oak and pine-oak forests to arable land more than halved the bacterial diversity, but did not affect the archaeal and even increased the viral diversity. This article is protected by copyright. All rights reserved.}, }
@article {pmid31824656, year = {2019}, author = {Barton, W and O'Sullivan, O and Cotter, PD}, title = {Metabolic phenotyping of the human microbiome.}, journal = {F1000Research}, volume = {8}, number = {}, pages = {}, pmid = {31824656}, issn = {2046-1402}, mesh = {Humans ; Metabolomics ; *Microbiota ; }, abstract = {The human microbiome has been identified as having a key role in health and numerous diseases. Trillions of microbial cells and viral particles comprise the microbiome, each representing modifiable working elements of an intricate bioactive ecosystem. The significance of the human microbiome as it relates to human biology has progressed through culture-dependent (for example, media-based methods) and, more recently, molecular (for example, genetic sequencing and metabolomic analysis) techniques. The latter have become increasingly popular and evolved from being used for taxonomic identification of microbiota to elucidation of functional capacity (sequencing) and metabolic activity (metabolomics). This review summarises key elements of the human microbiome and its metabolic capabilities within the context of health and disease.}, }
@article {pmid31629904, year = {2019}, author = {Almeida, AR and Alves, M and Domingues, I and Henriques, I}, title = {The impact of antibiotic exposure in water and zebrafish gut microbiomes: A 16S rRNA gene-based metagenomic analysis.}, journal = {Ecotoxicology and environmental safety}, volume = {186}, number = {}, pages = {109771}, doi = {10.1016/j.ecoenv.2019.109771}, pmid = {31629904}, issn = {1090-2414}, mesh = {Animals ; Anti-Bacterial Agents/*toxicity ; Aquaculture ; Gastrointestinal Microbiome/*drug effects/genetics ; Humans ; Metagenome/*drug effects/genetics ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Water Pollutants, Chemical/*toxicity ; Zebrafish/genetics/*microbiology ; }, abstract = {In order to supply human demand for food, the aquaculture industry has been growing fast in the last years, being fish usually cultivated in overcrowded conditions. Hence, to prevent the rapidly disease spreading, antibiotics may be applied to both sick and healthy animals. Due to its broad spectrum, oxytetracycline (OTC) is one of the most used antibiotics in food-production. Yet, although useful to prevent infections, antibiotics may reshape aquatic animals' microbiome, disturbing hosts' welfare. However, the impact of this exposure to the organism microbiome and its surrounding environment is poorly understood. Then, the objective of this study was to analyze in detail the long-term effect of OTC in both zebrafish gut and water microbiomes. Zebrafish adults were exposed, via water, for two months to three concentrations of OTC (0, 10 and 10000 μg/L). Total DNA was extracted from gut and water samples and the V3-V4 region of the bacterial 16 S rRNA gene was sequenced using Illumina technology. Results of alpha and beta-diversity analyses revealed that long-term exposure to OTC impacted both zebrafish gut and water microbiomes. In water samples, effects were observed even at the lowest (10 μg/L) OTC concentration tested resulting in an increase in Deltaproteobacteria, namely the Myxococcales and Bdellovibrionales orders. On the other hand, effects on zebrafish gut were only observed at the highest concentration with the selection of Alphaproteobacteria and Actinobacteria classes. Although these classes are common in fish gut, the increase of Actinobacteria may represent a health problem since some genera like Gordonia are linked to some human infection disease. Nevertheless, in both gut and water, it was observed a decrease in Gamaproteobacteria, probably due to OTC mode of action. In silico functional metagenomic analysis revealed that OTC exposure selected general detoxification mechanisms. In addition, the abundance of functional genes involved in Quorum Sensing (QS) increased under OTC exposure suggesting that QS may help bacteria to survive OTC stress. Thus, future studies should consider post-exposure scenarios for a deeper analysis of the water and zebrafish gut resistome, since bacteria may react differently after exposure ceased.}, }
@article {pmid31454888, year = {2019}, author = {Borghi, E and Vignoli, A}, title = {Rett Syndrome and Other Neurodevelopmental Disorders Share Common Changes in Gut Microbial Community: A Descriptive Review.}, journal = {International journal of molecular sciences}, volume = {20}, number = {17}, pages = {}, doi = {10.3390/ijms20174160}, pmid = {31454888}, issn = {1422-0067}, mesh = {Animals ; Biodiversity ; Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; Metagenomics/methods ; Neurodevelopmental Disorders/diagnosis/*etiology ; Phenotype ; Rett Syndrome/diagnosis/*etiology ; }, abstract = {In this narrative review, we summarize recent pieces of evidence of the role of microbiota alterations in Rett syndrome (RTT). Neurological problems are prominent features of the syndrome, but the pathogenic mechanisms modulating its severity are still poorly understood. Gut microbiota was recently demonstrated to be altered both in animal models and humans with different neurodevelopmental disorders and/or epilepsy. By investigating gut microbiota in RTT cohorts, a less rich microbial community was identified which was associated with alterations of fecal microbial short-chain fatty acids. These changes were positively correlated with severe clinical outcomes. Indeed, microbial metabolites can play a crucial role both locally and systemically, having dynamic effects on host metabolism and gene expression in many organs. Similar alterations were found in patients with autism and down syndrome as well, suggesting a potential common pathway of gut microbiota involvement in neurodevelopmental disorders.}, }
@article {pmid31450659, year = {2019}, author = {Aarnoutse, R and Ziemons, J and Penders, J and Rensen, SS and de Vos-Geelen, J and Smidt, ML}, title = {The Clinical Link between Human Intestinal Microbiota and Systemic Cancer Therapy.}, journal = {International journal of molecular sciences}, volume = {20}, number = {17}, pages = {}, doi = {10.3390/ijms20174145}, pmid = {31450659}, issn = {1422-0067}, mesh = {Combined Modality Therapy/adverse effects/methods ; Disease Management ; *Gastrointestinal Microbiome/drug effects/radiation effects ; Humans ; Metagenome ; Metagenomics/methods ; Neoplasms/complications/mortality/*therapy ; Prognosis ; Treatment Outcome ; }, abstract = {Clinical interest in the human intestinal microbiota has increased considerably. However, an overview of clinical studies investigating the link between the human intestinal microbiota and systemic cancer therapy is lacking. This systematic review summarizes all clinical studies describing the association between baseline intestinal microbiota and systemic cancer therapy outcome as well as therapy-related changes in intestinal microbiota composition. A systematic literature search was performed and provided 23 articles. There were strong indications for a close association between the intestinal microbiota and outcome of immunotherapy. Furthermore, the development of chemotherapy-induced infectious complications seemed to be associated with the baseline microbiota profile. Both chemotherapy and immunotherapy induced drastic changes in gut microbiota composition with possible consequences for treatment efficacy. Evidence in the field of hormonal therapy was very limited. Large heterogeneity concerning study design, study population, and methods used for analysis limited comparability and generalization of results. For the future, longitudinal studies investigating the predictive ability of baseline intestinal microbiota concerning treatment outcome and complications as well as the potential use of microbiota-modulating strategies in cancer patients are required. More knowledge in this field is likely to be of clinical benefit since modulation of the microbiota might support cancer therapy in the future.}, }
@article {pmid31119104, year = {2019}, author = {Govender, Y and Gabriel, I and Minassian, V and Fichorova, R}, title = {The Current Evidence on the Association Between the Urinary Microbiome and Urinary Incontinence in Women.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {133}, doi = {10.3389/fcimb.2019.00133}, pmid = {31119104}, issn = {2235-2988}, mesh = {Female ; *Host Microbial Interactions ; Humans ; *Microbiota ; Prevalence ; Risk Factors ; Urinary Incontinence/*epidemiology/*physiopathology ; Urinary Tract/*microbiology ; }, abstract = {Urinary incontinence (UI) is a burdensome condition with high prevalence in middle-aged to older women and an unclear etiology. Advances in our understanding of host-microbe interactions in the urogenital tract have stimulated interest in the urinary microbiome. DNA sequencing and enhanced urine culture suggest that similarly to other mucosal sites, the urinary bladder of healthy individuals harbors resident microbial communities that may play distinct roles in bladder function. This review focused on the urobiome (expanded quantitative urine culture-based or genomic sequencing-based urinary microbiome) associated with different subtypes of UI, including stress, urgency and mixed urinary incontinence, and related syndromes, such as interstitial cystitis and overactive bladder in women, contrasted to urinary tract infections. Furthermore, we examined clinical evidence for the association of the urinary microbiome with responses to pharmacotherapy for amelioration of UI symptoms. Although published studies are still relatively limited in number, study design and sample size, cumulative evidence suggests that certain Lactobacillus species may play a role in maintaining a healthy bladder milieu. Higher bacterial diversity in the absence of Lactobacillus dominance was associated with urgency UI and resistance to anticholinergic treatment for this condition. UI may also facilitate the persistence of uropathogens following antibiotic treatment, which in turn can alter the commensal/potentially beneficial microbial communities. Risk factors of UI, including age, menopausal status, sex steroid hormones, and body mass index may also impact the urinary microbiome. However, it is yet unclear whether the effects of these risks factors on UI are mediated by urinary host-microbe interactions and a mechanistic link with the female urogenital microbiome is still to be established. Strategies for future research are suggested.}, }
@article {pmid31053982, year = {2019}, author = {Van Dexter, S and Oubre, C and Boopathy, R}, title = {Carbon ecology of termite gut and phenol degradation by a bacterium isolated from the gut of termite.}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {46}, number = {9-10}, pages = {1265-1271}, pmid = {31053982}, issn = {1476-5535}, mesh = {Animals ; Bacteria/isolation &amp; purification/*metabolism ; Carbon/*metabolism ; Cellobiose/metabolism ; Ecosystem ; Gastrointestinal Microbiome ; Isoptera/*microbiology ; Metagenomics ; Phenols/*metabolism ; }, abstract = {Metagenomics and transcriptomics have had some success analyzing community and functional ecology of the termite gut, but carbon utilization ecology and the effect of diet on the gut community are not well understood. This study was done to determine the effect of three hardwood tree types, oak (Quercus spp.), red maple (Acer rubrum), and tupelo (Nyssa aquatica) on the termite species, Reticulitermes flavipes in the family Rhinotermitidae. Termite abdomen homogenates were incubated on agar plates containing three common carbon sources in the termite gut, namely, acetate, cellobiose, and phenol under aerobic and anaerobic conditions. Bacterial growth was higher on cellobiose than any other carbon source. Higher bacterial growth on cellobiose was observed from termite colonies feeding on oak than on phenol from the other two wood types. The difference between aerobic and anaerobic conditions was not significant. A bacterium, Acinetobacter tandoii isolated and identified from our previous study was subjected to high concentrations of phenol as the sole carbon source and this bacterium was able to degrade phenol concentration up to 600 mg/L.}, }
@article {pmid31521989, year = {2019}, author = {Breton-Deval, L and Sanchez-Flores, A and Juárez, K and Vera-Estrella, R}, title = {Integrative study of microbial community dynamics and water quality along The Apatlaco River.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {255}, number = {Pt 1}, pages = {113158}, doi = {10.1016/j.envpol.2019.113158}, pmid = {31521989}, issn = {1873-6424}, mesh = {Bacteria/classification/*isolation &amp; purification ; Biological Oxygen Demand Analysis ; Environmental Monitoring/*methods ; Humans ; Mexico ; Microbiota ; Nitrogen/analysis ; Oxygen/analysis ; Phosphorus/analysis ; Rivers/chemistry/*microbiology ; Urbanization ; Water Pollutants, Chemical/*analysis ; Water Pollution/*analysis ; Water Quality ; }, abstract = {The increasing demand for clean water resources for human consumption, is raising concerning about the sustainable worldwide provisioning. In Mexico, rivers near to high-density urbanizations are subject to irrational exploitation where polluted water is a risk for human health. Therefore, the aims of this study are to analyze water quality parameters and bacterial community dynamics to understand the relation between them, in the Apatlaco river, which presents a clear environmental perturbance. Parameters such as total coliforms, chemical oxygen demand, harness, ammonium, nitrite, nitrate, total Kjeldahl nitrogen, dissolved oxygen, total phosphorus, total dissolved solids, and temperature were analyzed in 17 sampling points along the river. The high pollution level was registered in the sampling point 10 with 480 mg/L chemical oxygen demand, 7 mg/L nitrite, 34 mg/L nitrate, 2 mg/L dissolved oxygen, and 299 mg/L of total dissolved solids. From these sites, we selected four samples for DNA extraction and performed a metagenomic analysis using a whole metagenome shotgun approach, to compare the microbial communities between polluted and non-polluted sites. In general, Proteobacteria was the most representative phylum in all sites. However, the clean water reference point was enriched with microorganism from the Limnohabitans genus, a planktonic bacterium widespread in freshwater ecosystems. Nevertheless, in the polluted sampled sites, we found a high abundance of potential opportunistic pathogen genera such as Acinetobacter, Arcobacter, and Myroides, among others. This suggests that in addition to water contamination, an imminent human health risk due to pathogenic bacteria can potentially affect a population of ∼1.6 million people dwelling nearby. These results will contribute to the knowledge regarding anthropogenic pollution on the microbial population dynamic and how they affect human health and life quality.}, }
@article {pmid31110364, year = {2019}, author = {Diamond, S and Andeer, PF and Li, Z and Crits-Christoph, A and Burstein, D and Anantharaman, K and Lane, KR and Thomas, BC and Pan, C and Northen, TR and Banfield, JF}, title = {Mediterranean grassland soil C-N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms.}, journal = {Nature microbiology}, volume = {4}, number = {8}, pages = {1356-1367}, pmid = {31110364}, issn = {2058-5276}, mesh = {Bacteria/classification/*genetics/metabolism ; Biodiversity ; California ; Carbon/*metabolism ; Carbon Cycle ; Ecology ; Ecosystem ; *Genomics ; *Grassland ; Metagenomics ; Nitrogen/*metabolism ; Nitrogen Cycle ; Proteomics ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Soil microbial activity drives the carbon and nitrogen cycles and is an important determinant of atmospheric trace gas turnover, yet most soils are dominated by microorganisms with unknown metabolic capacities. Even Acidobacteria, among the most abundant bacteria in soil, remain poorly characterized, and functions across groups such as Verrucomicrobia, Gemmatimonadetes, Chloroflexi and Rokubacteria are understudied. Here, we have resolved 60 metagenomic and 20 proteomic data sets from a Mediterranean grassland soil ecosystem and recovered 793 near-complete microbial genomes from 18 phyla, representing around one-third of all microorganisms detected. Importantly, this enabled extensive genomics-based metabolic predictions for these communities. Acidobacteria from multiple previously unstudied classes have genomes that encode large enzyme complements for complex carbohydrate degradation. Alternatively, most microorganisms encode carbohydrate esterases that strip readily accessible methyl and acetyl groups from polymers like pectin and xylan, forming methanol and acetate, the availability of which could explain the high prevalence of C1 metabolism and acetate utilization in genomes. Microorganism abundances among samples collected at three soil depths and under natural and amended rainfall regimes indicate statistically higher associations of inorganic nitrogen metabolism and carbon degradation in deep and shallow soils, respectively. This partitioning decreased in samples under extended spring rainfall, indicating that long-term climate alteration can affect both carbon and nitrogen cycling. Overall, by leveraging natural and experimental gradients with genome-resolved metabolic profiles, we link microorganisms lacking prior genomic characterization to specific roles in complex carbon, C1, nitrate and ammonia transformations, and constrain factors that impact their distributions in soil.}, }
@article {pmid31055031, year = {2019}, author = {Seferovic, MD and Pace, RM and Carroll, M and Belfort, B and Major, AM and Chu, DM and Racusin, DA and Castro, ECC and Muldrew, KL and Versalovic, J and Aagaard, KM}, title = {Visualization of microbes by 16S in situ hybridization in term and preterm placentas without intraamniotic infection.}, journal = {American journal of obstetrics and gynecology}, volume = {221}, number = {2}, pages = {146.e1-146.e23}, doi = {10.1016/j.ajog.2019.04.036}, pmid = {31055031}, issn = {1097-6868}, mesh = {Adult ; DNA Barcoding, Taxonomic ; Female ; Humans ; In Situ Hybridization ; Metagenomics ; Microbiota ; Placenta/*microbiology ; Pregnancy ; Premature Birth ; RNA, Bacterial/analysis ; *RNA, Ribosomal, 16S ; Sequence Analysis, RNA ; Term Birth ; }, abstract = {BACKGROUND: Numerous reports have documented bacteria in the placental membranes and basal plate decidua in the absence of immunopathology using histologic techniques. Similarly, independent metagenomic characterizations have identified an altered taxonomic makeup in association with spontaneous preterm birth. Here we sought to corroborate these findings by localizing presumptive intact bacteria using molecular histology within the placental microanatomy.<br><br>OBJECTIVE: Here we examined for microbes in term and preterm gestations using a signal-amplified 16S universal in situ hybridization probe set for bacterial rRNA, alongside traditional histologic methods of Warthin-Starry and Gram stains, as well as clinical culture methodologies. We further sought to differentiate accompanying 16S gene sequencing taxonomic profiles from germ-free (gnotobiotic) mouse and extraction and amplicon contamination controls.<br><br>STUDY DESIGN: Placentas were collected from a total of 53 subjects, composed of term labored (n = 4) and unlabored cesarean deliveries (n = 22) and preterm vaginal (n = 18) and cesarean deliveries (n = 8); a placenta from a single subject with clinical and histologic evident choriomanionitis was employed as a positive control (n = 1). The preterm cohort included spontaneous preterm birth with (n = 6) and without (n = 10) preterm premature rupture of membranes, as well as medically indicated preterm births (n = 10). Placental microbes were visualized using an in situ hybridization probe set designed against highly conserved regions of the bacterial 16S ribosome, which produces an amplified stable signal using branched DNA probes. Extracted bacterial nucleic acids from these same samples were subjected to 16S rRNA metagenomic sequencing (Illumina, V4) for course taxonomic analysis, alongside environmental and kit contaminant controls. A subset of unlabored, cesarean-delivered term pregnancies were also assessed with clinical culture for readily cultivatable pathogenic microbes.<br><br>RESULTS: Molecular in situ hybridization of bacterial rRNA enabled visualization and localization of low-abundance microbes after systematic high-power scanning. Despite the absence of clinical or histologic chorioamnionitis in 52 of 53 subjects, instances of 16S rRNA signal were confidently observed in 13 of 16 spontaneous preterm birth placentas, which was not significantly different from term unlabored cesarean specimens (18 of 22; P > .05). 16S rRNA signal was largely localized to the villous parenchyma and/or syncytiotrophoblast, and less commonly the chorion and the maternal intervillous space. In all term and unlabored cesarean deliveries, visualization of evident placental microbes by in situ hybridization occurred in the absence of clinical or histologic detection using conventional clinical cultivation, hematoxylin-eosin, and Gram staining. In 1 subject, appreciable villous bacteria localized to an infarction, where 16S microbial detection was confirmed by Warthin-Starry stain. In all instances, parallel sample principle coordinate analysis using Bray-Cutis distances of 16S rRNA gene sequencing data demonstrated consistent taxonomic distinction from all negative or potential contamination controls (P = .024, PERMANOVA). Classification from contaminant filtered data identified a distinct taxonomic makeup among term and preterm cohorts when compared with contaminant controls (false discovery rate <0.05).<br><br>CONCLUSION: Presumptively intact placental microbes are visualized as low-abundance, low-biomass and sparse populations within the placenta regardless of gestational age and mode of delivery. Their taxonomic makeup is distinct from contamination controls. These findings further support several previously published findings, including our own, which have used metagenomics to characterize low-abundance and low-biomass microbial communities in the placenta.}, }
@article {pmid31289831, year = {2019}, author = {Youens-Clark, K and Bomhoff, M and Ponsero, AJ and Wood-Charlson, EM and Lynch, J and Choi, I and Hartman, JH and Hurwitz, BL}, title = {iMicrobe: Tools and data-dreaiven discovery platform for the microbiome sciences.}, journal = {GigaScience}, volume = {8}, number = {7}, pages = {}, doi = {10.1093/gigascience/giz083}, pmid = {31289831}, issn = {2047-217X}, mesh = {Big Data ; Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; *Software ; }, abstract = {BACKGROUND: Scientists have amassed a wealth of microbiome datasets, making it possible to study microbes in biotic and abiotic systems on a population or planetary scale; however, this potential has not been fully realized given that the tools, datasets, and computation are available in diverse repositories and locations. To address this challenge, we developed iMicrobe.us, a community-driven microbiome data marketplace and tool exchange for users to integrate their own data and tools with those from the broader community.<br><br>FINDINGS: The iMicrobe platform brings together analysis tools and microbiome datasets by leveraging National Science Foundation-supported cyberinfrastructure and computing resources from CyVerse, Agave, and XSEDE. The primary purpose of iMicrobe is to provide users with a freely available, web-based platform to (1) maintain and share project data, metadata, and analysis products, (2) search for related public datasets, and (3) use and publish bioinformatics tools that run on highly scalable computing resources. Analysis tools are implemented in containers that encapsulate complex software dependencies and run on freely available XSEDE resources via the Agave API, which can retrieve datasets from the CyVerse Data Store or any web-accessible location (e.g., FTP, HTTP).<br><br>CONCLUSIONS: iMicrobe promotes data integration, sharing, and community-driven tool development by making open source data and tools accessible to the research community in a web-based platform.}, }
@article {pmid31232514, year = {2019}, author = {Matesanz, S and Pescador, DS and Pías, B and Sánchez, AM and Chacón-Labella, J and Illuminati, A and de la Cruz, M and López-Angulo, J and Marí-Mena, N and Vizcaíno, A and Escudero, A}, title = {Estimating belowground plant abundance with DNA metabarcoding.}, journal = {Molecular ecology resources}, volume = {19}, number = {5}, pages = {1265-1277}, doi = {10.1111/1755-0998.13049}, pmid = {31232514}, issn = {1755-0998}, support = {CGL2015-66809-P//Secretaría de Estado de Investigación, Desarrollo e Innovación/ ; }, mesh = {*Biota ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/genetics ; Metagenomics/*methods ; Plant Roots/classification/genetics ; Plants/*classification/*genetics ; }, abstract = {Most work on plant community ecology has been performed above ground, neglecting the processes that occur in the soil. DNA metabarcoding, in which multiple species are computationally identified in bulk samples, can help to overcome the logistical limitations involved in sampling plant communities belowground. However, a major limitation of this methodology is the quantification of species' abundances based on the percentage of sequences assigned to each taxon. Using root tissues of five dominant species in a semi-arid Mediterranean shrubland (Bupleurum fruticescens, Helianthemum cinereum, Linum suffruticosum, Stipa pennata and Thymus vulgaris), we built pairwise mixtures of relative abundance (20%, 50% and 80% biomass), and implemented two methods (linear model fits and correction indices) to improve estimates of root biomass. We validated both methods with multispecies mixtures that simulate field-collected samples. For all species, we found a positive and highly significant relationship between the percentage of sequences and biomass in the mixtures (R2 = .44-.66), but the equations for each species (slope and intercept) differed among them, and two species were consistently over- and under-estimated. The correction indices greatly improved the estimates of biomass percentage for all five species in the multispecies mixtures, and reduced the overall error from 17% to 6%. Our results show that, through the use of post-sequencing quantification methods on mock communities, DNA metabarcoding can be effectively used to determine not only species' presence but also their relative abundance in field samples of root mixtures. Importantly, knowledge of these aspects will allow us to study key, yet poorly understood, belowground processes.}, }
@article {pmid31353293, year = {2019}, author = {Powell, EA and Fontanella, S and Boakes, E and Belgrave, D and Shaw, AG and Cornwell, E and Fernandez-Crespo, R and Fink, CG and Custovic, A and Kroll, JS}, title = {Temporal association of the development of oropharyngeal microbiota with early life wheeze in a population-based birth cohort.}, journal = {EBioMedicine}, volume = {46}, number = {}, pages = {486-498}, doi = {10.1016/j.ebiom.2019.07.034}, pmid = {31353293}, issn = {2352-3964}, mesh = {Age Factors ; Biodiversity ; Cohort Studies ; Female ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Oropharynx/*microbiology ; Population Surveillance ; Respiratory Sounds/*etiology ; United Kingdom/epidemiology ; }, abstract = {BACKGROUND: A critical window in infancy has been proposed, during which the microbiota may affect subsequent health. The longitudinal development of the oropharyngeal microbiota is under-studied and may be associated with early-life wheeze. We aimed to investigate the temporal association of the development of the oropharyngeal microbiota with early-life wheeze.<br><br>METHODS: A population-based birth cohort based in London, UK was followed for 24 months. We collected oropharyngeal swabs at six time-points. Microbiota was determined using sequencing of the V3-V5 region of the 16S rRNA-encoding gene. Medical records were reviewed for the outcome of doctor diagnosed wheeze. We used a time-varying model to investigate the temporal association between the development of microbiota and doctor-diagnosed wheeze.<br><br>FINDINGS: 159 participants completed the study to 24 months and for 98 there was complete sequencing data at all timepoints and outcome data. Of these, 26 had doctor-diagnosed wheeze. We observed significant increase in the abundance of Neisseria between 9 and 24 months in children who developed wheeze (p = 0∙003), while in those without wheezing there was a significant increment in the abundance of Granulicatella (p = 0∙012) between 9 and 12 months, and of Prevotella (p = 0∙018) after 18 months.<br><br>INTERPRETATION: A temporal association between the respiratory commensal Granulicatella and also Prevotella with wheeze (negative), and between Neisseria and wheeze (positive) was identified in infants prior to one year of age. This adds to evidence for the proposed role of the microbiota in the development of wheeze. FUND: Research funding from the Winnicott Foundation, Meningitis Now and Micropathology Ltd.}, }
@article {pmid31327695, year = {2019}, author = {Clos-Garcia, M and Andrés-Marin, N and Fernández-Eulate, G and Abecia, L and Lavín, JL and van Liempd, S and Cabrera, D and Royo, F and Valero, A and Errazquin, N and Vega, MCG and Govillard, L and Tackett, MR and Tejada, G and Gónzalez, E and Anguita, J and Bujanda, L and Orcasitas, AMC and Aransay, AM and Maíz, O and López de Munain, A and Falcón-Pérez, JM}, title = {Gut microbiome and serum metabolome analyses identify molecular biomarkers and altered glutamate metabolism in fibromyalgia.}, journal = {EBioMedicine}, volume = {46}, number = {}, pages = {499-511}, doi = {10.1016/j.ebiom.2019.07.031}, pmid = {31327695}, issn = {2352-3964}, mesh = {Adult ; Aged ; Biomarkers ; Chromatography, High Pressure Liquid ; Computational Biology/methods ; Cytokines/metabolism ; Female ; Fibromyalgia/*etiology/*metabolism ; *Gastrointestinal Microbiome ; Glutamates/*metabolism ; Humans ; Male ; *Metabolome ; *Metabolomics/methods ; Metagenome ; Metagenomics/methods ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; ROC Curve ; Tandem Mass Spectrometry ; }, abstract = {BACKGROUND: Fibromyalgia is a complex, relatively unknown disease characterised by chronic, widespread musculoskeletal pain. The gut-brain axis connects the gut microbiome with the brain through the enteric nervous system (ENS); its disruption has been associated with psychiatric and gastrointestinal disorders. To gain an insight into the pathogenesis of fibromyalgia and identify diagnostic biomarkers, we combined different omics techniques to analyse microbiome and serum composition.<br><br>METHODS: We collected faeces and blood samples to study the microbiome, the serum metabolome and circulating cytokines and miRNAs from a cohort of 105 fibromyalgia patients and 54 age- and environment-matched healthy individuals. We sequenced the V3 and V4 regions of the 16S rDNA gene from faeces samples. UPLC-MS metabolomics and custom multiplex cytokine and miRNA analysis (FirePlex™ technology) were used to examine sera samples. Finally, we combined the different data types to search for potential biomarkers.<br><br>RESULTS: We found that the diversity of bacteria is reduced in fibromyalgia patients. The abundance of the Bifidobacterium and Eubacterium genera (bacteria participating in the metabolism of neurotransmitters in the host) in these patients was significantly reduced. The serum metabolome analysis revealed altered levels of glutamate and serine, suggesting changes in neurotransmitter metabolism. The combined serum metabolomics and gut microbiome datasets showed a certain degree of correlation, reflecting the effect of the microbiome on metabolic activity. We also examined the microbiome and serum metabolites, cytokines and miRNAs as potential sources of molecular biomarkers of fibromyalgia.<br><br>CONCLUSIONS: Our results show that the microbiome analysis provides more significant biomarkers than the other techniques employed in the work. Gut microbiome analysis combined with serum metabolomics can shed new light onto the pathogenesis of fibromyalgia. We provide a list of bacteria whose abundance changes in this disease and propose several molecules as potential biomarkers that can be used to evaluate the current diagnostic criteria.}, }
@article {pmid31021803, year = {2019}, author = {Wassan, JT and Wang, H and Browne, F and Zheng, H}, title = {Phy-PMRFI: Phylogeny-Aware Prediction of Metagenomic Functions Using Random Forest Feature Importance.}, journal = {IEEE transactions on nanobioscience}, volume = {18}, number = {3}, pages = {273-282}, doi = {10.1109/TNB.2019.2912824}, pmid = {31021803}, issn = {1558-2639}, mesh = {Algorithms ; Databases, Genetic ; *Decision Trees ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome/*genetics ; *Metagenomics/classification/methods ; Microbiota/genetics ; Pharynx/microbiology ; Phylogeny ; *Support Vector Machine ; }, abstract = {High-throughput sequencing techniques have accelerated functional metagenomics studies through the generation of large volumes of omics data. The integration of these data using computational approaches is potentially useful for predicting metagenomic functions. Machine learning (ML) models can be trained using microbial features which are then used to classify microbial data into different functional classes. For example, ML analyses over the human microbiome data has been linked to the prediction of important biological states. For analysing omics data, integrating abundance count of taxonomical features with their biological relationships is important. These relationships can potentially be uncovered from the phylogenetic tree of microbial taxa. In this paper, we propose a novel integrative framework Phy-PMRFI. This framework is driven by the phylogeny-based modeling of omics data to predict metagenomic functions using important features selected by a random forest importance (RFI) strategy. The proposed framework integrates the underlying phylogenetic tree information with abundance measures of microbial species (features) by creating a novel phylogeny and abundance aware matrix structure (PAAM). Phy-PMRFI progresses by ranking the microbial features using an RFI measure. This is then used as input for microbiome classification. The resultant feature set enhances the performance of the state-of-art methods such as support vector machines. Our proposed integrative framework also outperforms the state-of-the-art pipeline of phylogenetic isometric log-ratio transform (PhILR) and MetaPhyl. Prediction accuracy of 90 % is obtained with Phy-PMRFI over human throat microbiome in comparison to other approaches of PhILR with 53% and MetaPhyl with 71% accuracy.}, }
@article {pmid30853704, year = {2019}, author = {Watahiki, S and Kimura, N and Yamazoe, A and Miura, T and Sekiguchi, Y and Noda, N and Matsukura, S and Kasai, D and Takahata, Y and Nojiri, H and Fukuda, M}, title = {Ecological impact assessment of a bioaugmentation site on remediation of chlorinated ethylenes by multi-omics analysis.}, journal = {The Journal of general and applied microbiology}, volume = {65}, number = {5}, pages = {225-233}, doi = {10.2323/jgam.2018.10.003}, pmid = {30853704}, issn = {1349-8037}, abstract = {Bioremediation may affect the ecological system around bioremediation sites. However, little is known about how microbial community structures change over time after the initial injection of degraders. In this study, we have assessed the ecological impact of bioaugmentation using metagenomic and metatranscriptomic approaches to remove trichlorinated ethylene/cis-dichloroethylene (TCE/cDCE) by Rhodococcus jostii strain RHA1 as an aerobic chemical compound degrader. Metagenomic analysis showed that the number of organisms belonging to the genus Rhodococcus, including strain RHA1, increased from 0.1% to 76.6% of the total microbial community on day 0 at the injection site. Subsequently, the populations of strain RHA1 and other TCE/cDCE-degrading bacteria gradually decreased over time, whereas the populations of the anaerobic dechlorinators Geobacter and Dehalococcoides increased at later stages. Metatranscriptomic analysis revealed a high expression of aromatic compound-degrading genes (bphA1-A4) in strain RHA1 after RHA1 injection. From these results, we concluded that the key dechlorinators of TCE/cDCE were mainly aerobic bacteria, such as RHA1, until day 1, after which the key dechlorinators changed to anaerobic bacteria, such as Geobacter and Dehalococcocides, after day 6 at the injection well. Based on the α-diversity, the richness levels of the microbial community were increased after injection of strain RHA1, and the microbial community composition had not been restored to that of the original composition during the 19 days after treatment. These results provide insights into the assessment of the ecological impact and bioaugmentation process of RHA1 at bioremediation sites.}, }
@article {pmid30809227, year = {2019}, author = {Schwarzer, M and Hermanova, P and Srutkova, D and Golias, J and Hudcovic, T and Zwicker, C and Sinkora, M and Akgün, J and Wiedermann, U and Tuckova, L and Kozakova, H and Schabussova, I}, title = {Germ-Free Mice Exhibit Mast Cells With Impaired Functionality and Gut Homing and Do Not Develop Food Allergy.}, journal = {Frontiers in immunology}, volume = {10}, number = {}, pages = {205}, doi = {10.3389/fimmu.2019.00205}, pmid = {30809227}, issn = {1664-3224}, abstract = {Background: Mucosal mast cells (MC) are key players in IgE-mediated food allergy (FA). The evidence on the interaction between gut microbiota, MC and susceptibility to FA is contradictory. Objective: We tested the hypothesis that commensal bacteria are essential for MC migration to the gut and their maturation impacting the susceptibility to FA. Methods: The development and severity of FA symptoms was studied in sensitized germ-free (GF), conventional (CV), and mice mono-colonized with L. plantarum WCFS1 or co-housed with CV mice. MC were phenotypically and functionally characterized. Results: Systemic sensitization and oral challenge of GF mice with ovalbumin led to increased levels of specific IgE in serum compared to CV mice. Remarkably, despite the high levels of sensitization, GF mice did not develop diarrhea or anaphylactic hypothermia, common symptoms of FA. In the gut, GF mice expressed low levels of the MC tissue-homing markers CXCL1 and CXCL2, and harbored fewer MC which exhibited lower levels of MC protease-1 after challenge. Additionally, MC in GF mice were less mature as confirmed by flow-cytometry and their functionality was impaired as shown by reduced edema formation after injection of degranulation-provoking compound 48/80. Co-housing of GF mice with CV mice fully restored their susceptibility to develop FA. However, this did not occur when mice were mono-colonized with L. plantarum. Conclusion: Our results demonstrate that microbiota-induced maturation and gut-homing of MC is a critical step for the development of symptoms of experimental FA. This new mechanistic insight into microbiota-MC-FA axis can be exploited in the prevention and treatment of FA in humans.}, }
@article {pmid31267543, year = {2020}, author = {Zhang, L and Li, YY and Tang, X and Zhao, X}, title = {Faecal microbial dysbiosis in children with Wiskott-Aldrich syndrome.}, journal = {Scandinavian journal of immunology}, volume = {91}, number = {1}, pages = {e12805}, doi = {10.1111/sji.12805}, pmid = {31267543}, issn = {1365-3083}, mesh = {Animals ; Biodiversity ; Biomarkers ; Case-Control Studies ; Child, Preschool ; Disease Models, Animal ; *Dysbiosis ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Inflammatory Bowel Diseases/etiology ; Male ; Metagenome ; Metagenomics/methods ; Mice ; Mice, Knockout ; Mutation ; RNA, Ribosomal, 16S/genetics ; Wiskott-Aldrich Syndrome/diagnosis/*etiology ; Wiskott-Aldrich Syndrome Protein/deficiency ; }, abstract = {Wiskott-Aldrich syndrome (WAS) is an X-linked primary immunodeficiency disease caused by a mutation in the WAS gene that encodes the WAS protein (WASp); up to 5-10% of these patients develop inflammatory bowel disease (IBD). The mechanisms by which WASp deficiency causes IBD are unclear. Intestinal microbial dysbiosis and imbalances in host immune responses play important roles in the pathogenesis of polygenetic IBD; however, few studies have conducted detailed examination of the microbial alterations and their relationship with IBD in WAS. Here, we collected faecal samples from 19 children (all less than 2 years old) with WAS and samples from WASp-KO mice with IBD and subjected them to 16S ribosomal RNA sequencing. We found that microbial community richness and structure in WAS children were different from those in controls; WAS children revealed reduced microbial community richness and diversity. Relative abundance of Bacteroidetes and Verrucomicrobiain in WAS children was significantly lower, while that of Proteobacteria was markedly higher. WASp-KO mice revealed a significantly decreased abundance of Firmicutes. Faecal microbial dysbiosis caused by WASp deficiency is similar to that observed for polygenetic IBD, suggesting that WASp may play crucial function in microbial homoeostasis and that microbial dysbiosis may contribute to IBD in WAS. These microbial alterations may be useful targets for monitoring and therapeutically managing intestinal inflammation in WAS.}, }
@article {pmid31083685, year = {2019}, author = {Grant, ET and Kyes, RC and Kyes, P and Trinh, P and Ramirez, V and Tanee, T and Pinlaor, P and Dangtakot, R and Rabinowitz, PM}, title = {Fecal microbiota dysbiosis in macaques and humans within a shared environment.}, journal = {PloS one}, volume = {14}, number = {5}, pages = {e0210679}, doi = {10.1371/journal.pone.0210679}, pmid = {31083685}, issn = {1932-6203}, support = {P51 OD010425/OD/NIH HHS/United States ; T42 OH008433/OH/NIOSH CDC HHS/United States ; }, mesh = {Animals ; Biodiversity ; Cross-Sectional Studies ; *Environment ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Macaca fascicularis ; Metagenome ; Metagenomics/methods ; Thailand ; }, abstract = {Traditional zoonotic disease research focuses on detection of recognized pathogens and may miss opportunities to understand broader microbial transmission dynamics between humans, animals, and the environment. We studied human-macaque microbiome overlap in Kosum Phisai District, Maha Sarakham Province, Thailand, where a growing population of long-tailed macaques (Macaca fascicularis) in Kosumpee Forest Park interact with humans from an adjacent village. We surveyed workers in or near the park with elevated exposure to macaques to characterize tasks resulting in exposure to macaque feces in addition to dietary and lifestyle factors that influence gut microbiome composition. Fecal samples were collected from 12 exposed workers and 6 controls without macaque exposure, as well as 8 macaques from Kosumpee Forest Park and 4 from an isolated forest patch with minimal human contact. The V4 region of the 16S rRNA gene from fecal sample extracted DNA was amplified and sequenced using Illumina MiSeq to characterize the microbial community. A permuted betadisper test on the weighted UniFrac distances revealed significant differences in the dispersion patterns of gut microbiota from exposed and control macaques (p = 0.03). The high variance in gut microbiota composition of macaques in contact with humans has potential implications for gut microbiome stability and susceptibility to disease, described by the Anna Karenina principle (AKP). Human samples had homogenous variance in beta diversity but different spatial medians between groups (p = 0.02), indicating a shift in microbial composition that may be explained by fundamental lifestyle differences between the groups unrelated to exposure status. SourceTracker was used to estimate the percent of gut taxa in exposed humans that was contributed by macaques. While one worker showed evidence of elevated contribution, the overall trend was not significant. Task observations among workers revealed opportunities to employ protective measures or training to reduce exposure to occupational hazards. These results suggest the potential for hygiene measures to mitigate negative aspects of contact between humans and macaques in order to optimize the health of both populations.}, }
@article {pmid31562300, year = {2019}, author = {Liu, J and Taft, DH and Maldonado-Gomez, MX and Johnson, D and Treiber, ML and Lemay, DG and DePeters, EJ and Mills, DA}, title = {The fecal resistome of dairy cattle is associated with diet during nursing.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {4406}, doi = {10.1038/s41467-019-12111-x}, pmid = {31562300}, issn = {2041-1723}, support = {R01 AT007079/AT/NCCIH NIH HHS/United States ; R01 AT008759/AT/NCCIH NIH HHS/United States ; S10 RR027303/RR/NCRR NIH HHS/United States ; S10 RR029668/RR/NCRR NIH HHS/United States ; }, mesh = {Animal Feed/*analysis ; Animals ; Animals, Newborn ; Anti-Bacterial Agents/pharmacology ; Cattle ; Colostrum/microbiology ; Dairying ; *Diet ; Drug Resistance, Multiple, Bacterial/drug effects/*genetics ; Feces/*microbiology ; Gastrointestinal Microbiome/drug effects/genetics ; *Gene Regulatory Networks ; Genes, Bacterial/*genetics ; Manure/microbiology ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; }, abstract = {Antimicrobial resistance is a global public health concern, and livestock play a significant role in selecting for resistance and maintaining such reservoirs. Here we study the succession of dairy cattle resistome during early life using metagenomic sequencing, as well as the relationship between resistome, gut microbiota, and diet. In our dataset, the gut of dairy calves serves as a reservoir of 329 antimicrobial resistance genes (ARGs) presumably conferring resistance to 17 classes of antibiotics, and the abundance of ARGs declines gradually during nursing. ARGs appear to co-occur with antibacterial biocide or metal resistance genes. Colostrum is a potential source of ARGs observed in calves at day 2. The dynamic changes in the resistome are likely a result of gut microbiota assembly, which is closely associated with diet transition in dairy calves. Modifications in the resistome may be possible via early-life dietary interventions to reduce overall antimicrobial resistance.}, }
@article {pmid31554820, year = {2019}, author = {Riva, A and Kuzyk, O and Forsberg, E and Siuzdak, G and Pfann, C and Herbold, C and Daims, H and Loy, A and Warth, B and Berry, D}, title = {A fiber-deprived diet disturbs the fine-scale spatial architecture of the murine colon microbiome.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {4366}, doi = {10.1038/s41467-019-12413-0}, pmid = {31554820}, issn = {2041-1723}, mesh = {Animals ; Colon/*microbiology ; *Diet ; Dietary Fiber/*deficiency ; Gastrointestinal Microbiome/genetics/*physiology ; Intestinal Mucosa/microbiology ; Metagenomics/methods ; Mice, Inbred C57BL ; Microbiota/genetics/*physiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Compartmentalization of the gut microbiota is thought to be important to system function, but the extent of spatial organization in the gut ecosystem remains poorly understood. Here, we profile the murine colonic microbiota along longitudinal and lateral axes using laser capture microdissection. We found fine-scale spatial structuring of the microbiota marked by gradients in composition and diversity along the length of the colon. Privation of fiber reduces the diversity of the microbiota and disrupts longitudinal and lateral gradients in microbiota composition. Both mucus-adjacent and luminal communities are influenced by the absence of dietary fiber, with the loss of a characteristic distal colon microbiota and a reduction in the mucosa-adjacent community, concomitant with depletion of the mucus layer. These results indicate that diet has not only global but also local effects on the composition of the gut microbiota, which may affect function and resilience differently depending on location.}, }
@article {pmid31437154, year = {2019}, author = {Pichler, V and Kotsakiozi, P and Caputo, B and Serini, P and Caccone, A and Della Torre, A}, title = {Complex interplay of evolutionary forces shaping population genomic structure of invasive Aedes albopictus in southern Europe.}, journal = {PLoS neglected tropical diseases}, volume = {13}, number = {8}, pages = {e0007554}, doi = {10.1371/journal.pntd.0007554}, pmid = {31437154}, issn = {1935-2735}, support = {R01 AI132409/AI/NIAID NIH HHS/United States ; }, mesh = {Aedes/classification/*genetics ; Albania ; Animal Migration ; Animals ; *Biological Evolution ; Europe ; Gene Flow ; Genetic Variation ; Greece ; Insect Vectors/classification/*genetics ; Introduced Species ; Italy ; *Metagenomics ; Phylogeny ; Polymorphism, Single Nucleotide ; }, abstract = {BACKGROUND: In the last four decades, the Asian tiger mosquito, Aedes albopictus, vector of several human arboviruses, has spread from its native range in South-East Asia to all over the world, largely through the transportation of its eggs via the international trade in used tires. Albania was the first country invaded in Europe in 1979, followed by Italy in 1990 and other Mediterranean countries after 2000.<br><br>METHODS/PRINCIPAL FINDINGS: We here inferred the invasion history and migration patterns of Ae. albopictus in Italy (today the most heavily-infested country in Europe), Greece and Albania, by analyzing a panel of >100,000 single nucleotide polymorphisms (SNPs) obtained by sequencing of double-digest Restriction site-Associated DNA (ddRADseq). The obtained dataset was combined with samples previously analyzed from both the native and invasive range worldwide to interpret the results using a broader spatial and historical context. The emerging evolutionary scenario complements the results of other studies in showing that the extraordinary worldwide expansion of Ae. albopictus has occurred thanks to multiple independent invasions by large numbers of colonists from multiple geographic locations in both native and previously invaded areas, consistently with the role of used tires shipments to move large numbers of eggs worldwide. By analyzing mosquitoes from nine sites across ~1,000-km transect in Italy, we were able to detect a complex interplay of drift, isolation by distance mediated divergence, and gene flow in shaping the species very recent invasion and range expansion, suggesting overall high connectivity, likely due to passive transportation of adults via ground transportation, as well as specific adaptations to local conditions.<br><br>CONCLUSIONS/SIGNIFICANCE: Results contribute to characterize one of the most successful histories of animal invasion, and could be used as a baseline for future studies to track epidemiologically relevant characters (e.g. insecticide resistance).}, }
@article {pmid31926407, year = {2019}, author = {Edge, TA and Baird, DJ and Bilodeau, G and Gagné, N and Greer, C and Konkin, D and Newton, G and Séguin, A and Beaudette, L and Bilkhu, S and Bush, A and Chen, W and Comte, J and Condie, J and Crevecoeur, S and El-Kayssi, N and Emilson, EJS and Fancy, DL and Kandalaft, I and Khan, IUH and King, I and Kreutzweiser, D and Lapen, D and Lawrence, J and Lowe, C and Lung, O and Martineau, C and Meier, M and Ogden, N and Paré, D and Phillips, L and Porter, TM and Sachs, J and Staley, Z and Steeves, R and Venier, L and Veres, T and Watson, C and Watson, S and Macklin, J}, title = {The Ecobiomics project: Advancing metagenomics assessment of soil health and freshwater quality in Canada.}, journal = {The Science of the total environment}, volume = {710}, number = {}, pages = {135906}, doi = {10.1016/j.scitotenv.2019.135906}, pmid = {31926407}, issn = {1879-1026}, abstract = {Transformative advances in metagenomics are providing an unprecedented ability to characterize the enormous diversity of microorganisms and invertebrates sustaining soil health and water quality. These advances are enabling a better recognition of the ecological linkages between soil and water, and the biodiversity exchanges between these two reservoirs. They are also providing new perspectives for understanding microorganisms and invertebrates as part of interacting communities (i.e. microbiomes and zoobiomes), and considering plants, animals, and humans as holobionts comprised of their own cells as well as diverse microorganisms and invertebrates often acquired from soil and water. The Government of Canada's Genomics Research and Development Initiative (GRDI) launched the Ecobiomics Project to coordinate metagenomics capacity building across federal departments, and to apply metagenomics to better characterize microbial and invertebrate biodiversity for advancing environmental assessment, monitoring, and remediation activities. The Project has adopted standard methods for soil, water, and invertebrate sampling, collection and provenance of metadata, and nucleic acid extraction. High-throughput sequencing is located at a centralized sequencing facility. A centralized Bioinformatics Platform was established to enable a novel government-wide approach to harmonize metagenomics data collection, storage and bioinformatics analyses. Sixteen research projects were initiated under Soil Microbiome, Aquatic Microbiome, and Invertebrate Zoobiome Themes. Genomic observatories were established at long-term environmental monitoring sites for providing more comprehensive biodiversity reference points to assess environmental change.}, }
@article {pmid31757198, year = {2019}, author = {Qian, J and Comin, M}, title = {MetaCon: unsupervised clustering of metagenomic contigs with probabilistic k-mers statistics and coverage.}, journal = {BMC bioinformatics}, volume = {20}, number = {Suppl 9}, pages = {367}, pmid = {31757198}, issn = {1471-2105}, mesh = {*Algorithms ; Cluster Analysis ; *Contig Mapping ; Databases, Genetic ; *Metagenome ; *Metagenomics ; Microbiota/genetics ; *Probability ; *Statistics as Topic ; }, abstract = {MOTIVATION: Sequencing technologies allow the sequencing of microbial communities directly from the environment without prior culturing. Because assembly typically produces only genome fragments, also known as contigs, it is crucial to group them into putative species for further taxonomic profiling and down-streaming functional analysis. Taxonomic analysis of microbial communities requires contig clustering, a process referred to as binning, that is still one of the most challenging tasks when analyzing metagenomic data. The major problems are the lack of taxonomically related genomes in existing reference databases, the uneven abundance ratio of species, sequencing errors, and the limitations due to binning contig of different lengths.<br><br>RESULTS: In this context we present MetaCon a novel tool for unsupervised metagenomic contig binning based on probabilistic k-mers statistics and coverage. MetaCon uses a signature based on k-mers statistics that accounts for the different probability of appearance of a k-mer in different species, also contigs of different length are clustered in two separate phases. The effectiveness of MetaCon is demonstrated in both simulated and real datasets in comparison with state-of-art binning approaches such as CONCOCT, MaxBin and MetaBAT.}, }
@article {pmid31524629, year = {2020}, author = {Lo, KH and Lu, CW and Lin, WH and Chien, CC and Chen, SC and Kao, CM}, title = {Enhanced reductive dechlorination of trichloroethene with immobilized Clostridium butyricum in silica gel.}, journal = {Chemosphere}, volume = {238}, number = {}, pages = {124596}, doi = {10.1016/j.chemosphere.2019.124596}, pmid = {31524629}, issn = {1879-1298}, mesh = {Biodegradation, Environmental ; Chloroflexi/growth &amp; development/*metabolism ; Clostridium butyricum/*metabolism ; Groundwater/*chemistry ; Halogenation ; Metagenomics ; Microbiota/physiology ; Silica Gel ; Trichloroethylene/*metabolism ; }, abstract = {Deteriorated environmental conditions during the bioremediation of trichloroethene (TCE)-polluted groundwater cause decreased treatment efficiencies. This study assessed the effect of applying immobilized Clostridium butyricum (a hydrogen-producing bacterium) in silica gel on enhancing the reductive dechlorination efficiency of TCE with the slow polycolloid-releasing substrate (SPRS) supplement in groundwater. The responses of microbial communities with the immobilized system (immobilized Clostridium butyricum and SPRS amendments) were also characterized by the metagenomics assay. A complete TCE removal in microcosms was obtained within 30 days with the application of this immobilized system via reductive dechlorination processes. An increase in the population of Dehalococcoides spp. was observed using the quantitative polymerase chain reaction (qPCR) analysis. Results of metagenomics assay reveal that the microbial communities in the immobilized system were distinct from those in systems with SPRS only. Bacterial communities associated with TCE biodegradation also increased in microcosms treated with the immobilized system. The immobilized system shows a great potential to promote the TCE dechlorination efficiency, and the metagenomics-based approach provides detailed insights into dechlorinating microbial community dynamics. The results would be helpful in designing an in situ immobilized system to enhance the bioremediation efficiency of TCE-contaminated groundwater.}, }
@article {pmid31500705, year = {2020}, author = {Dugat-Bony, E and Lossouarn, J and De Paepe, M and Sarthou, AS and Fedala, Y and Petit, MA and Chaillou, S}, title = {Viral metagenomic analysis of the cheese surface: A comparative study of rapid procedures for extracting viral particles.}, journal = {Food microbiology}, volume = {85}, number = {}, pages = {103278}, doi = {10.1016/j.fm.2019.103278}, pmid = {31500705}, issn = {1095-9998}, mesh = {Bacteriophages/genetics ; Cheese/*virology ; *Metagenome ; Metagenomics/*methods ; Microbiota ; Virion/*genetics ; Virology/methods ; }, abstract = {The structure and functioning of microbial communities from fermented foods, including cheese, have been extensively studied during the past decade. However, there is still a lack of information about both the occurrence and the role of viruses in modulating the function of this type of spatially structured and solid ecosystems. Viral metagenomics was recently applied to a wide variety of environmental samples and standardized procedures for recovering viral particles from different type of materials has emerged. In this study, we adapted a procedure originally developed to extract viruses from fecal samples, in order to enable efficient virome analysis of cheese surface. We tested and validated the positive impact of both addition of a filtration step prior to virus concentration and substitution of purification by density gradient ultracentrifugation by a simple chloroform treatment to eliminate membrane vesicles. Viral DNA extracted from the several procedures, as well as a vesicle sample, were sequenced using Illumina paired-end MiSeq technology and the subsequent clusters assembled from the virome were analyzed to assess those belonging to putative phages, plasmid-derived DNA, or even from bacterial chromosomal DNA. The best procedure was then chosen, and used to describe the first cheese surface virome, using Epoisses cheese as example. This study provides the basis of future investigations regarding the ecological importance of viruses in cheese microbial ecosystems.}, }
@article {pmid31500701, year = {2020}, author = {Li, Z and Dong, L and Zhao, C and Zhu, Y}, title = {Metagenomic insights into the changes in microbial community and antimicrobial resistance genes associated with different salt content of red pepper (Capsicum annuum L.) sauce.}, journal = {Food microbiology}, volume = {85}, number = {}, pages = {103295}, doi = {10.1016/j.fm.2019.103295}, pmid = {31500701}, issn = {1095-9998}, mesh = {Capsicum/*chemistry ; Drug Resistance, Bacterial/*genetics ; Enterobacteriaceae/*genetics/growth &amp; development ; Fermentation ; Genes, Bacterial ; Lactobacillaceae/*genetics/growth &amp; development ; *Metagenome ; Metagenomics ; *Microbiota ; Osmotic Pressure ; Sodium Chloride/*chemistry ; }, abstract = {Fermented red pepper (FRP) sauce has been eaten in worldwide for many years. The salt content and resident microbial community influences the quality of the FRP sauce and may confer health (e.g., probiotics) or harm (e.g., antibiotic resistance genes) to the consumers in some circumstances; however, the salt-mediated alteration of microbial community and antibiotic resistance genes are little known. In this study, a combination of whole genome sequencing and amplicon analysis was used to investigate the changes in microbial community and antimicrobial resistance genes in response to different salt content during red pepper fermentation. While the family Enterobacteriaceae dominated in high-salt (15-25%) samples, Lactobacillaceae quickly became the dominant population in place of Enterobacteriaceae after 24 days in 10% salt samples. Compared to 0.05 antibiotic resistance genes (ARGs) per cell number on average in 10% salt sample, 16.6 ARGs were present in high-salt samples, wherein the bacterial hosts were major assigned to Enterobacteriaceae including genera Enterobacter, Citrobacter, Escherichia, Salmonella and Klebsiella. Multidrug resistance genes were the predominant ARG type. Functional profiling showed that histidine kinase functions were of much higher abundance in high-salt samples and included several osmotic stress-related two-component systems that simultaneously encoded ARGs. These results give first metagenomic insights into the salt-mediated changes in microbial community composition and a broad view of associated antibiotic resistance genes in the process of food fermentation.}, }
@article {pmid31366182, year = {2019}, author = {Deshpande, SV and Reed, TM and Sullivan, RF and Kerkhof, LJ and Beigel, KM and Wade, MM}, title = {Offline Next Generation Metagenomics Sequence Analysis Using MinION Detection Software (MINDS).}, journal = {Genes}, volume = {10}, number = {8}, pages = {}, doi = {10.3390/genes10080578}, pmid = {31366182}, issn = {2073-4425}, mesh = {DNA Barcoding, Taxonomic/methods ; High-Throughput Nucleotide Sequencing/*methods ; Metagenome ; Metagenomics/*methods ; Microbiota ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {Field laboratories interested in using the MinION often need the internet to perform sample analysis. Thus, the lack of internet connectivity in resource-limited or remote locations renders downstream analysis problematic, resulting in a lack of sample identification in the field. Due to this dependency, field samples are generally transported back to the lab for analysis where internet availability for downstream analysis is available. These logistics problems and the time lost in sample characterization and identification, pose a significant problem for field scientists. To address this limitation, we have developed a stand-alone data analysis packet using open source tools developed by the Nanopore community that does not depend on internet availability. Like Oxford Nanopore Technologies' (ONT) cloud-based What's In My Pot (WIMP) software, we developed the offline MinION Detection Software (MINDS) based on the Centrifuge classification engine for rapid species identification. Several online bioinformatics applications have been developed surrounding ONT's framework for analysis of long reads. We have developed and evaluated an offline real time classification application pipeline using open source tools developed by the Nanopore community that does not depend on internet availability. Our application has been tested on ATCC's 20 strain even mix whole cell (ATCC MSA-2002) sample. Using the Rapid Sequencing Kit (SQK-RAD004), we were able to identify all 20 organisms at species level. The analysis was performed in 15 min using a Dell Precision 7720 laptop. Our offline downstream bioinformatics application provides a cost-effective option as well as quick turn-around time when analyzing samples in the field, thus enabling researchers to fully utilize ONT's MinION portability, ease-of-use, and identification capability in remote locations.}, }
@article {pmid31278679, year = {2019}, author = {Mitra, S}, title = {Multiple Data Analyses and Statistical Approaches for Analyzing Data from Metagenomic Studies and Clinical Trials.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1910}, number = {}, pages = {605-634}, doi = {10.1007/978-1-4939-9074-0_20}, pmid = {31278679}, issn = {1940-6029}, mesh = {Algorithms ; Biodiversity ; *Computational Biology/methods ; Data Interpretation, Statistical ; *Data Mining/methods ; Evolution, Molecular ; Fatty Acids, Omega-3/pharmacology ; Gastrointestinal Microbiome/drug effects ; Humans ; *Metagenome ; *Metagenomics/methods ; Microbiota ; Molecular Sequence Annotation ; Plaque, Atherosclerotic/etiology ; Workflow ; }, abstract = {Metagenomics, also known as environmental genomics, is the study of the genomic content of a sample of organisms (microbes) obtained from a common habitat. Metagenomics and other &quot;omics&quot; disciplines have captured the attention of researchers for several decades. The effect of microbes in our body is a relevant concern for health studies. There are plenty of studies using metagenomics which examine microorganisms that inhabit niches in the human body, sometimes causing disease, and are often correlated with multiple treatment conditions. No matter from which environment it comes, the analyses are often aimed at determining either the presence or absence of specific species of interest in a given metagenome or comparing the biological diversity and the functional activity of a wider range of microorganisms within their communities. The importance increases for comparison within different environments such as multiple patients with different conditions, multiple drugs, and multiple time points of same treatment or same patient. Thus, no matter how many hypotheses we have, we need a good understanding of genomics, bioinformatics, and statistics to work together to analyze and interpret these datasets in a meaningful way. This chapter provides an overview of different data analyses and statistical approaches (with example scenarios) to analyze metagenomics samples from different medical projects or clinical trials.}, }
@article {pmid31278668, year = {2019}, author = {Watson, AK and Lannes, R and Pathmanathan, JS and Méheust, R and Karkar, S and Colson, P and Corel, E and Lopez, P and Bapteste, E}, title = {The Methodology Behind Network Thinking: Graphs to Analyze Microbial Complexity and Evolution.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1910}, number = {}, pages = {271-308}, doi = {10.1007/978-1-4939-9074-0_9}, pmid = {31278668}, issn = {1940-6029}, mesh = {Biodiversity ; Biological Evolution ; Computational Biology/methods ; Ecosystem ; Evolution, Molecular ; Gene Ontology ; Gene Regulatory Networks ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics/methods ; Microbiota ; Molecular Sequence Annotation ; Multigene Family ; }, abstract = {In the post genomic era, large and complex molecular datasets from genome and metagenome sequencing projects expand the limits of what is possible for bioinformatic analyses. Network-based methods are increasingly used to complement phylogenetic analysis in studies in molecular evolution, including comparative genomics, classification, and ecological studies. Using network methods, the vertical and horizontal relationships between all genes or genomes, whether they are from cellular chromosomes or mobile genetic elements, can be explored in a single expandable graph. In recent years, development of new methods for the construction and analysis of networks has helped to broaden the availability of these approaches from programmers to a diversity of users. This chapter introduces the different kinds of networks based on sequence similarity that are already available to tackle a wide range of biological questions, including sequence similarity networks, gene-sharing networks and bipartite graphs, and a guide for their construction and analyses.}, }
@article {pmid31154531, year = {2019}, author = {Tutuncu, HE and Balci, N and Tuter, M and Karaguler, NG}, title = {Recombinant production and characterization of a novel esterase from a hypersaline lake, Acıgöl, by metagenomic approach.}, journal = {Extremophiles : life under extreme conditions}, volume = {23}, number = {5}, pages = {507-520}, doi = {10.1007/s00792-019-01103-w}, pmid = {31154531}, issn = {1433-4909}, mesh = {Bacterial Proteins/chemistry/*genetics/metabolism ; Enzyme Stability ; Esterases/chemistry/*genetics/metabolism ; Halomonas/enzymology/genetics ; Lakes/microbiology ; *Metagenome ; Microbiota ; Salinity ; *Salt Tolerance ; Substrate Specificity ; }, abstract = {The aim of this study was to isolate a novel esterase from a hypersaline lake by sequence-based metagenomics. The metagenomic DNA was isolated from the enriched hypersaline lake sediment. Degenerate primers targeting the conserved regions of lipolytic enzymes of halophilic microorganisms were used for polymerase chain reaction (PCR) and a whole gene was identified by genome walking. The gene was composed of 783 bp, which corresponds to 260 amino acids with a molecular weight of 28.2 kDa. The deduced amino acid sequence best matched with the esterase from Halomonas gudaonensis with an identity of 91%. Recombinantly expressed enzyme exhibited maximum activity towards pNP-hexanoate with a kcat value of 12.30 s-1. The optimum pH and temperature of the enzyme were found as 9 and 30 °C, respectively. The effects of NaCl, solvents, metal ions, detergents and enzyme inhibitors were also studied. In conclusion, a novel enzyme, named as hypersaline lake &quot;Acıgöl&quot; esterase (hAGEst), was identified by sequence-based metagenomics. The high expression level, the ability to maintain activity at cold temperatures and tolerance to DMSO and metal ions are the most outstanding properties of the hAGEst.}, }
@article {pmid31039168, year = {2019}, author = {De La Torre, U and Henderson, JD and Furtado, KL and Pedroja, M and Elenamarie, O and Mora, A and Pechanec, MY and Maga, EA and Mienaltowski, MJ}, title = {Utilizing the fecal microbiota to understand foal gut transitions from birth to weaning.}, journal = {PloS one}, volume = {14}, number = {4}, pages = {e0216211}, doi = {10.1371/journal.pone.0216211}, pmid = {31039168}, issn = {1932-6203}, mesh = {Animals ; Animals, Newborn ; Bacteria/growth &amp; development ; Biodiversity ; Feces/*microbiology ; Gastrointestinal Tract/*microbiology ; Horses/*microbiology ; Metagenomics ; *Microbiota ; Phylogeny ; Principal Component Analysis ; *Weaning ; }, abstract = {A healthy gastrointestinal (GI) tract with a properly established microbiota is necessary for a foal to develop into a healthy weanling. A foal's health can be critically impacted by aberrations in the microbiome such as with diarrhea which can cause great morbidity and mortality in foals. In this study, we hypothesized that gut establishment in the foal transitioning from a diet of milk to a diet of grain, forage, and pasture would be detectable through analyses of the fecal microbiotas. Fecal samples from 37 sets of foals and mares were collected at multiple time points ranging from birth to weaning. Bacterial DNA was isolated from the samples, and the V4 domain of bacterial 16S rRNA genes were amplified via polymerase chain reaction. Next generation sequencing was then performed on the resulting amplicons, and analyses were performed to characterize the microbiome as well as the relative abundance of microbiota present. We found that bacterial population compositions followed a pattern throughout the early life of the foal in an age-dependent manner. As foals transitioned from milk consumption to a forage and grain diet, there were recognizable changes in fecal microbial compositions from initial populations predominant in the ability to metabolize milk to populations capable of utilizing fibrous plant material. We were also able to recognize differences in microbial populations amongst diarrheic foals as well as microbial population differences associated with differences in management styles between facilities. Future efforts will gauge the effects of lesser abundant bacterial populations that could also be essential to GI health, as well as to determine how associations between microbial population profiles and animal management practices can be used to inform strategies for improving upon the health and growth of horses overall.}, }
@article {pmid31854766, year = {2019}, author = {Hu, WC and Zhao, C and Wang, QJ and Liu, RP and Bai, YH}, title = {[Metabolic Functional Analysis of Dominant Microbial Communities in the Rapid Sand Filters for Drinking Water].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {40}, number = {8}, pages = {3604-3611}, doi = {10.13227/j.hjkx.201901167}, pmid = {31854766}, issn = {0250-3301}, mesh = {Denitrification ; *Drinking Water ; *Microbiota ; Nitrogen ; Oxidation-Reduction ; Sand ; Water Microbiology ; *Water Purification ; }, abstract = {Rapid sand filter (RSF) is widely used in drinking water treatment plants. Rapid filtration is always considered a physicochemical process, but the effect of the microorganisms that attach to the filter media remain inadequately investigated. In order to understand the composition and functional characteristics of microbial communities in RSFs, influent water, effluent water, and filter materials from eleven RSFs in eight Chinese cities were sampled and analyzed. After filtration, dissolved organic carbon (DOC) showed a slight but significant removal due to the growth of heterotrophic microbes. The activity of ammonia-oxidizing microbes and nitrite-oxidizing microbes promoted a significant decrease in ammonia nitrogen (NH4+-N) and a significant increase in nitrate nitrogen (NO3--N) in water. No significant changes in total nitrogen (TN) were observed, indicating that denitrification and anammox were weak in the RSFs. The composition and function of the microbial communities of RSFs were assessed using metagenomic methods. Genera in the top 10% with respect to relative abundance (14 genera in total) were identified as the dominant genera, including the two ammonia-oxidizing bacteria Nitrospira and Nitrosomonas. Functional gene information for the dominant genera was also extracted for analysis. The dominant genera exhibited higher relative abundances of carbohydrate, nitrogen, sulfur, and xenobiotic metabolic pathways. Aeromonas had the highest relative abundance of carbohydrate metabolic genes, and Bradyrhizobium had the highest relative abundance of nitrogen, sulfur, and xenobiotics metabolic genes, indicating that these two genera play an important role in the transformation of substances in drinking water. Finally, the metabolic potential of the dominant genera on xenobiotics was evaluated, and the results showed that Bradyrhizobium, Sphingomonas, Methyloglobulus, Sphingopyxis, and Klebsiella were the key bacterial genera for the removal of micropollutants in RSFs.}, }
@article {pmid31673867, year = {2019}, author = {Puri, RR and Adachi, F and Omichi, M and Saeki, Y and Yamamoto, A and Hayashi, S and Ali, MA and Itoh, K}, title = {Metagenomic study of endophytic bacterial community of sweet potato (Ipomoea batatas) cultivated in different soil and climatic conditions.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {35}, number = {11}, pages = {176}, pmid = {31673867}, issn = {1573-0972}, support = {16KT0032//Japan Society for the Promotion of Science/ ; }, mesh = {Bacteria/*classification/genetics/*metabolism ; Base Sequence ; Biodiversity ; *Climate ; DNA, Bacterial/analysis ; DNA, Mitochondrial/analysis ; Endophytes/*classification/genetics ; Ipomoea batatas/*microbiology ; *Metagenome ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; Soil Microbiology ; }, abstract = {The aim of this study was to clarify effects of soil and climatic conditions on community structure of sweet potato bacterial endophytes by applying locked nucleic acid oligonucleotide-PCR clamping technique and metagenomic analysis. For this purpose, the soil samples in three locations were transferred each other and sweet potato nursery plants from the same farm were cultivated for ca. 3 months. After removal of plastid, mitochondria and undefined sequences, the averaged numbers of retained sequences and operational taxonomic units per sample were 20,891 and 846, respectively. Proteobacteria (85.0%), Bacteroidetes (6.6%) and Actinobacteria (6.3%) were the three most dominant phyla, accounting for 97.9% of the reads, and γ-Proteobacteria (66.3%) being the most abundant. Top 10 genera represented 81.2% of the overall reads in which Pseudomonas (31.9-45.0%) being the most predominant. The overall endophytic bacterial communities were similar among the samples which indicated that the soil and the climatic conditions did not considerably affect the entire endophytic community. The original endophytic bacterial community might be kept during the cultivation period.}, }
@article {pmid31492655, year = {2019}, author = {Soto-Perez, P and Bisanz, JE and Berry, JD and Lam, KN and Bondy-Denomy, J and Turnbaugh, PJ}, title = {CRISPR-Cas System of a Prevalent Human Gut Bacterium Reveals Hyper-targeting against Phages in a Human Virome Catalog.}, journal = {Cell host &amp; microbe}, volume = {26}, number = {3}, pages = {325-335.e5}, pmid = {31492655}, issn = {1934-6069}, support = {DP5 OD021344/OD/NIH HHS/United States ; R01 HL122593/HL/NHLBI NIH HHS/United States ; }, mesh = {Actinobacteria/virology ; Bacteria/genetics/*virology ; Bacteriophages/*genetics ; Base Sequence ; *CRISPR-Cas Systems ; DNA, Bacterial/analysis ; DNA, Viral/analysis ; Databases, Genetic ; Gastrointestinal Tract/*microbiology ; Genome, Bacterial ; Genome, Viral ; Humans ; Metagenomics ; Microbiota/genetics ; Sequence Analysis, DNA ; }, abstract = {Bacteriophages are abundant within the human gastrointestinal tract, yet their interactions with gut bacteria remain poorly understood, particularly with respect to CRISPR-Cas immunity. Here, we show that the type I-C CRISPR-Cas system in the prevalent gut Actinobacterium Eggerthella lenta is transcribed and sufficient for specific targeting of foreign and chromosomal DNA. Comparative analyses of E. lenta CRISPR-Cas systems across (meta)genomes revealed 2 distinct clades according to cas sequence similarity and spacer content. We assembled a human virome database (HuVirDB), encompassing 1,831 samples enriched for viral DNA, to identify protospacers. This revealed matches for a majority of spacers, a marked increase over other databases, and uncovered &quot;hyper-targeted&quot; phage sequences containing multiple protospacers targeted by several E. lenta strains. Finally, we determined the positional mismatch tolerance of observed spacer-protospacer pairs. This work emphasizes the utility of merging computational and experimental approaches for determining the function and targets of CRISPR-Cas systems.}, }
@article {pmid31488812, year = {2019}, author = {Mora, M and Wink, L and Kögler, I and Mahnert, A and Rettberg, P and Schwendner, P and Demets, R and Cockell, C and Alekhova, T and Klingl, A and Krause, R and Zolotariof, A and Alexandrova, A and Moissl-Eichinger, C}, title = {Space Station conditions are selective but do not alter microbial characteristics relevant to human health.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {3990}, doi = {10.1038/s41467-019-11682-z}, pmid = {31488812}, issn = {2041-1723}, mesh = {Archaea/*classification/genetics/isolation &amp; purification ; Bacteria/*classification/genetics/isolation &amp; purification ; Biodiversity ; Biofilms/growth &amp; development ; Extremophiles ; Fungi/*classification/genetics/isolation &amp; purification ; *Health ; Host Microbial Interactions ; Humans ; Metagenomics ; Microbiota/genetics/*physiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Space Flight ; }, abstract = {The International Space Station (ISS) is a unique habitat for humans and microorganisms. Here, we report the results of the ISS experiment EXTREMOPHILES, including the analysis of microbial communities from several areas aboard at three time points. We assess microbial diversity, distribution, functional capacity and resistance profile using a combination of cultivation-independent analyses (amplicon and shot-gun sequencing) and cultivation-dependent analyses (physiological and genetic characterization of microbial isolates, antibiotic resistance tests, co-incubation experiments). We show that the ISS microbial communities are highly similar to those present in ground-based confined indoor environments and are subject to fluctuations, although a core microbiome persists over time and locations. The genomic and physiological features selected by ISS conditions do not appear to be directly relevant to human health, although adaptations towards biofilm formation and surface interactions were observed. Our results do not raise direct reason for concern with respect to crew health, but indicate a potential threat towards material integrity in moist areas.}, }
@article {pmid31311146, year = {2019}, author = {Vamanu, E and Pelinescu, D and Gatea, F and Sârbu, I}, title = {Altered in Vitro Metabolomic Response of the Human Microbiota to Sweeteners.}, journal = {Genes}, volume = {10}, number = {7}, pages = {}, doi = {10.3390/genes10070535}, pmid = {31311146}, issn = {2073-4425}, mesh = {Ammonia/metabolism ; Diterpenes, Kaurane/metabolism ; Dysbiosis ; Fatty Acids/metabolism ; Gastrointestinal Microbiome/drug effects ; Humans ; *Metabolome ; *Metabolomics/methods ; Metagenome ; Metagenomics/methods ; Microbiota/*drug effects ; Sweetening Agents/*pharmacology ; }, abstract = {Non-nutritive sweeteners represent an ingredient class that directly affects human health, via the development of inflammatory processes that promote chronic diseases related to microbiota dysbiosis. Several in vitro tests were conducted in the static GIS1 simulator. The aim of the study was to highlight the effect of sweeteners on the microbiota pattern of healthy individuals, associated with any alteration in the metabolomic response, through the production of organic acids and ammonium. The immediate effect of the in vitro treatment and the influence of the specific sweetener type on the occurrence of dysbiosis were evaluated by determining the biomarkers of the microbiota response. The presence of the steviol reduced the ammonium level (minimum of 410 mg/L), while the addition of cyclamate and saccharin caused a decrease in the number of microorganisms, in addition to lowering the total quantity of synthesized short-chain fatty acids (SCFAs). The bifidobacteria appeared to decrease below 102 genomes/mL in all the analyzed samples at the end of the in vitro simulation period. Barring the in vitro treatment of steviol, all the sweeteners tested exerted a negative influence on the fermentative profile, resulting in a decline in the fermentative processes, a rise in the colonic pH, and uniformity of the SCFA ratio.}, }
@article {pmid31197613, year = {2019}, author = {Debédat, J and Clément, K and Aron-Wisnewsky, J}, title = {Gut Microbiota Dysbiosis in Human Obesity: Impact of Bariatric Surgery.}, journal = {Current obesity reports}, volume = {8}, number = {3}, pages = {229-242}, doi = {10.1007/s13679-019-00351-3}, pmid = {31197613}, issn = {2162-4968}, mesh = {Animals ; Bacteria ; Bariatric Surgery/*methods ; Diabetes Mellitus, Type 2/complications ; Dysbiosis/*complications/*therapy ; Gastrectomy ; Gastrointestinal Microbiome/*physiology ; Humans ; Inflammation ; Obesity/*complications/*surgery ; Obesity, Morbid/complications/surgery ; Postoperative Period ; Treatment Outcome ; Weight Gain ; Weight Loss ; }, abstract = {PURPOSE OF REVIEW: In this review, we summarize what is currently described in terms of gut microbiota (GM) dysbiosis modification post-bariatric surgery (BS) and their link with BS-induced clinical improvement. We also discuss how the major inter-individual variability in terms of GM changes could impact the clinical improvements seen in patients.<br><br>RECENT FINDINGS: The persisting increase in severe obesity prevalence has led to the subsequent burst in BS number. Indeed, it is to date the best treatment option to induce major and sustainable weight loss and metabolic improvement in these patients. During obesity, the gut microbiota displays distinctive features such as low microbial gene richness and compositional and functional alterations (termed dysbiosis) which have been associated with low-grade inflammation, increased body weight and fat mass, as well as type-2 diabetes. Interestingly, GM changes post-BS is currently being proposed as one the many mechanism explaining BS beneficial clinical outcomes. BS enables partial rescue of GM dysbiosis observed during obesity. Some of the GM characteristics modified post-BS (composition in terms of bacteria and functions) are linked to BS beneficial outcomes such as weight loss or metabolic improvements. Nevertheless, the changes in GM post-BS display major variability from one patient to the other. As such, further large sample size studies associated with GM transfer studies in animals are still needed to completely decipher the role of GM in the clinical improvements observed post-surgery.}, }
@article {pmid31153098, year = {2019}, author = {Farina, R and Severi, M and Carrieri, A and Miotto, E and Sabbioni, S and Trombelli, L and Scapoli, C}, title = {Whole metagenomic shotgun sequencing of the subgingival microbiome of diabetics and non-diabetics with different periodontal conditions.}, journal = {Archives of oral biology}, volume = {104}, number = {}, pages = {13-23}, doi = {10.1016/j.archoralbio.2019.05.025}, pmid = {31153098}, issn = {1879-1506}, mesh = {*Dental Plaque ; *Diabetes Mellitus, Type 2/complications/microbiology ; Gingiva ; Humans ; *Metagenomics ; *Microbiota ; *Mouth/microbiology ; *Periodontitis/complications/microbiology ; }, abstract = {OBJECTIVE: The aim of this study was to use high-resolution whole metagenomic shotgun sequencing to characterize the subgingival microbiome of patients with/without type 2 Diabetes Mellitus and with/without periodontitis.<br><br>DESIGN: Twelve subjects, falling into one of the four study groups based on the presence/absence of poorly controlled type 2 Diabetes Mellitus and moderate-severe periodontitis, were selected. For each eligible subject, subgingival plaque samples were collected at 4 sites, all representative of the periodontal condition of the individual (i.e., non-bleeding sulci in subjects without a history of periodontitis, bleeding pockets in patients with moderate-severe periodontitis). The subgingival microbiome was evaluated using high-resolution whole metagenomic shotgun sequencing.<br><br>RESULTS: The results showed that: (i) the presence of type 2 Diabetes Mellitus and/or periodontitis were associated with a tendency of the subgingival microbiome to decrease in richness and diversity; (ii) the presence of type 2 Diabetes Mellitus was not associated with significant differences in the relative abundance of one or more species in patients either with or without periodontitis; (iii) the presence of periodontitis was associated with a significantly higher relative abundance of Anaerolineaceae bacterium oral taxon 439 in type 2 Diabetes Mellitus patients.<br><br>CONCLUSIONS: Whole metagenomic shotgun sequencing of the subgingival microbiome was extremely effective in the detection of low-abundant taxon. Our results point out a significantly higher relative abundance of Anaerolineaceae bacterium oral taxon 439 in patients with moderate to severe periodontitis vs patients without history of periodontitis, which was maintained when the comparison was restricted to type 2 diabetics.}, }
@article {pmid30599936, year = {2019}, author = {Danneskiold-Samsøe, NB and Dias de Freitas Queiroz Barros, H and Santos, R and Bicas, JL and Cazarin, CBB and Madsen, L and Kristiansen, K and Pastore, GM and Brix, S and Maróstica Júnior, MR}, title = {Interplay between food and gut microbiota in health and disease.}, journal = {Food research international (Ottawa, Ont.)}, volume = {115}, number = {}, pages = {23-31}, doi = {10.1016/j.foodres.2018.07.043}, pmid = {30599936}, issn = {1873-7145}, mesh = {*Diet ; Dietary Fiber/metabolism ; Dietary Proteins/metabolism ; Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Lipid Metabolism ; Polyphenols/metabolism ; Prebiotics/analysis ; }, abstract = {Numerous microorganisms colonize the human gastrointestinal tract playing pivotal roles in relation to digestion and absorption of dietary components. They biotransform food components and produce metabolites, which in combination with food components shape and modulate the host immune system and metabolic responses. Reciprocally, the diet modulates the composition and functional capacity of the gut microbiota, which subsequently influence host biochemical processes establishing a system of mutual interaction and inter-dependency. Macronutrients, fibers, as well as polyphenols and prebiotics are strong drivers shaping the composition of the gut microbiota. Especially, short-chain fatty acids produced from ingested fibers and tryptophan metabolites are key in modulating host immune responses. Since reciprocal interactions between diet, host, and microbiota are personal, understanding this complex network of interactions calls for novel use of large datasets and the implementation of machine learning algorithms and artificial intelligence. In this review, we aim to provide a base for future investigations of how interactions between food components and gut microbiota may influence or even determine human health and disease.}, }
@article {pmid30592383, year = {2019}, author = {van Dijkhuizen, EHP and Del Chierico, F and Malattia, C and Russo, A and Pires Marafon, D and Ter Haar, NM and Magni-Manzoni, S and Vastert, SJ and Dallapiccola, B and Prakken, B and Martini, A and De Benedetti, F and Putignani, L and , }, title = {Microbiome Analytics of the Gut Microbiota in Patients With Juvenile Idiopathic Arthritis: A Longitudinal Observational Cohort Study.}, journal = {Arthritis &amp; rheumatology (Hoboken, N.J.)}, volume = {71}, number = {6}, pages = {1000-1010}, doi = {10.1002/art.40827}, pmid = {30592383}, issn = {2326-5205}, mesh = {Arthritis, Juvenile/epidemiology/*microbiology ; Case-Control Studies ; Child ; Child, Preschool ; Cohort Studies ; Comorbidity ; Dysbiosis/*epidemiology ; Faecalibacterium prausnitzii ; Female ; Firmicutes ; Gastrointestinal Microbiome/*genetics ; Humans ; Italy/epidemiology ; Logistic Models ; Longitudinal Studies ; Male ; Metagenomics ; Netherlands/epidemiology ; RNA, Ribosomal, 16S ; Severity of Illness Index ; }, abstract = {OBJECTIVE: To assess the composition of gut microbiota in Italian and Dutch patients with juvenile idiopathic arthritis (JIA) at baseline, with inactive disease, and with persistent activity compared to healthy controls.<br><br>METHODS: In a multicenter, prospective, observational cohort study, fecal samples were collected at baseline from 78 Italian and 21 Dutch treatment-naive JIA patients with <6 months of disease duration and compared to 107 geographically matched samples from healthy children. Forty-four follow-up samples from patients with inactive disease and 25 follow-up samples from patients with persistent activity were analyzed. Gut microbiota composition was determined by 16S ribosomal RNA-based metagenomics. Alpha- and β-diversity were computed, and log ratios of relative abundance were compared between patients and healthy controls using random forest models and logistic regression.<br><br>RESULTS: Baseline samples from Italian patients showed reduced richness compared to healthy controls (P < 0.001). Random forest models distinguished between Italian patient baseline samples and healthy controls and suggested differences between Dutch patient samples and healthy controls (areas under the curve >0.99 and 0.71, respectively). The operational taxonomic units (OTUs) of Erysipelotrichaceae (increased in patients), Allobaculum (decreased in patients), and Faecalibacterium prausnitzii (increased in patients) showed different relative abundance in Italian patient baseline samples compared to controls after controlling for multiple comparisons. Some OTUs differed between Dutch patient samples and healthy controls, but no evidence remained after controlling for multiple comparisons. No differences were found in paired analysis between Italian patient baseline and inactive disease samples.<br><br>CONCLUSION: Our findings show evidence for dysbiosis in JIA patients. Only patient/control status, age, and geographic origin appear to be drivers of the microbiota profiles, regardless of disease activity stage, inflammation, and markers of autoimmunity.}, }
@article {pmid31373310, year = {2019}, author = {Peric, A and Weiss, J and Vulliemoz, N and Baud, D and Stojanov, M}, title = {Bacterial Colonization of the Female Upper Genital Tract.}, journal = {International journal of molecular sciences}, volume = {20}, number = {14}, pages = {}, doi = {10.3390/ijms20143405}, pmid = {31373310}, issn = {1422-0067}, mesh = {Bacteroidetes/genetics/isolation &amp; purification ; Fallopian Tubes/*microbiology ; Female ; Humans ; Lactobacillus/genetics/*isolation &amp; purification ; Microbiota/physiology ; Ovary/*microbiology ; Placenta/*microbiology ; Pregnancy ; Proteobacteria/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Uterus/*microbiology ; }, abstract = {Bacteria colonize most of the human body, and the female genital tract is not an exception. While the existence of a vaginal microbiota has been well established, the upper genital tract has been considered a sterile environment, with a general assumption that bacterial presence is associated with adverse clinical manifestation. However, recent metagenomic studies identified specific patterns of microbiota colonizing the uterus, fallopian tubes, ovaries, and placenta. These results need confirmation and further investigations since the data are only scarce. Bacterial colonization of these sites appears different from the vaginal one, despite evidence that vaginal bacteria could ascend to the upper genital tract through the cervix. Are these bacteria only commensal or do they play a role in the physiology of the female upper genital tract? Which are the genera that may have a negative and a positive impact on the female reproductive function? The aim of this review is to critically present all available data on upper genital tract microbiota and discuss its role in human reproduction, ranging from the technical aspects of these types of analyses to the description of specific bacterial genera. Although still very limited, research focusing on genital colonization of bacteria other than the vaginal milieu might bring novel insights into physiopathology of human reproduction.}, }
@article {pmid31021333, year = {2019}, author = {Xu, H and Zhao, F and Hou, Q and Huang, W and Liu, Y and Zhang, H and Sun, Z}, title = {Metagenomic analysis revealed beneficial effects of probiotics in improving the composition and function of the gut microbiota in dogs with diarrhoea.}, journal = {Food &amp; function}, volume = {10}, number = {5}, pages = {2618-2629}, doi = {10.1039/c9fo00087a}, pmid = {31021333}, issn = {2042-650X}, mesh = {Animals ; Bacteria/classification/drug effects/*genetics/isolation &amp; purification ; Diarrhea/drug therapy/microbiology/*veterinary ; Dog Diseases/*drug therapy/microbiology ; Dogs ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects ; Metagenomics ; Phylogeny ; Probiotics/*administration &amp; dosage ; }, abstract = {The aim of the present study was to evaluate the effects of probiotics on the composition and function of the gut microbiota in dogs with diarrhoea. Forty dogs with diarrhoea were randomly allocated to the treatment group or control group. Probiotics, containing Lactobacillus casei Zhang, Lactobacillus plantarum P-8, and Bifidobacterium animalis subsp. lactis V9, were only fed to 20 treated dogs for 60 days. The faecal samples of all dogs at day 0 and day 60 were analyzed using a metagenomic approach. The results showed a significantly higher microbial diversity and an obvious change in the structure of the gut microbiota in the treatment group. There was also an increase in the abundance of some beneficial bacteria in differently aged dogs, such as Lactobacillus johnsonii (P < 0.05), Lactobacillus reuteri (P < 0.01), Lactobacillus acidophilus (P < 0.05) and Butyricicoccus pullicaecorum (P < 0.05), and a reduction in the abundance of many opportunistic pathogenic bacteria such as Clostridium perfringens (P < 0.05) and Stenotrophomonas maltophilia (P < 0.05) with the supplementation of probiotics. Intriguingly, the correlated networks among some pathogenic bacteria decreased following the administration of probiotics. Additionally, metagenomic analysis revealed the upregulation of pathways involved in the metabolism of amino acids and biosynthesis of secondary metabolites, accompanied by the downregulation of pathways associated with virulence of pathogenic bacteria and cell signaling, suggesting that probiotics could improve the health of dogs with diarrhoea through regulation of the gut microbiota. Our research provides new information relevant to the treatment of diarrhoea in animals and humans.}, }
@article {pmid30810996, year = {2019}, author = {Pérez-Fernández, CA and Iriarte, M and Rivera-Pérez, J and Tremblay, RL and Toranzos, GA}, title = {Microbiota dispersion in the Uyuni salt flat (Bolivia) as determined by community structure analyses.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {22}, number = {3}, pages = {325-336}, doi = {10.1007/s10123-018-00052-2}, pmid = {30810996}, issn = {1618-1905}, support = {5R25GM061151-12, -13//Research Initiative for Scientific Enhancement Program/ ; }, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; *Biota ; Bolivia ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Soil microbial communities are an important component of biological diversity and terrestrial ecosystems which is responsible for processes such as decomposition, mineralization of nutrients, and accumulation of organic matter. One of the factors that provide information on the mechanisms regulating biodiversity is spatial scaling. We characterized the microbial communities using 16S rRNA gene sequences from DNA isolated from halite at various locations and correlated these to geographic distance in the Uyuni salt flat (Bolivia). Sequences from each site were analyzed to determine any spatial patterns of diversity, as well as to describe the microbial communities. Results suggest that different taxa are able to disperse over Uyuni's surface crust regardless of distance. As expected, ubiquitous taxa included members of Halobacteriaceae such as Haloarcula, Halorubrum, Halorhabdus, Halolamina, and halophilic bacteria Salinibacter, Halorhodospira, and unclassified members of the Gammaproteobacteria. Archaeal communities were homogeneous across the salt flat. In contrast, bacterial communities present strong local variations which could be attributed to external factors. Likely sources for these variations are the Rio Grande river influent in the south shore and the Tunupa volcano influencing the northern area.}, }
@article {pmid30738924, year = {2019}, author = {Wang, Y and Liu, F and Urban, JF and Paerewijck, O and Geldhof, P and Li, RW}, title = {Ascaris suum infection was associated with a worm-independent reduction in microbial diversity and altered metabolic potential in the porcine gut microbiome.}, journal = {International journal for parasitology}, volume = {49}, number = {3-4}, pages = {247-256}, doi = {10.1016/j.ijpara.2018.10.007}, pmid = {30738924}, issn = {1879-0135}, mesh = {Animals ; Ascariasis/complications/epidemiology/*veterinary ; Ascaris suum/*isolation &amp; purification ; Cluster Analysis ; Colon/microbiology ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Dysbiosis/epidemiology/*veterinary ; Fatty Acids, Volatile/analysis ; Feces/chemistry/microbiology ; *Gastrointestinal Microbiome ; Metabolomics ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Swine ; Swine Diseases/*epidemiology ; }, abstract = {The effect of infection of pigs with Ascaris suum on the microbial composition in the proximal colon and fecal matter was investigated using 16S rRNA gene sequencing. The infection significantly decreased various microbial diversity indices including Chao1 richness, but the effect on Chao1 in the colon luminal contents was worm burden-independent. The abundance of 49 genera present in colon contents, such as Prevotella and Faecalibacterium, and 179 operational taxonomic units was significantly changed as a result of infection. Notably, infection was also associated with a significant shift in the metabolic potential of the proximal colon microbiome, where the relative abundance of at least 30 metabolic pathways including carbohydrate metabolism and amino acid metabolism was reduced, while the abundance of 28 pathways was increased by infection. Furthermore, the microbial co-occurrence network in infected pigs was highly modular. Two of 52 modules or subnetworks were negatively correlated with fecal butyrate concentrations (r < -0.7; P < 0.05) while one module with 18 members was negatively correlated with fecal acetate, propionate and total short-chain fatty acids. A partial Mantel test identified a strong positive correlation between node connectivity of the operational taxonomic units assigned to β-Proteobacteria (especially the family Alcaligenaceae) and fecal acetate and propionate levels (r = 0.82 and 0.74, respectively), while that of the family Porphyromonadaceae was positively correlated with fecal egg counts. Overall, Ascaris infection was associated with a profound change in the gut microbiome, especially in the proximity of the initial site of larval infection, and should facilitate our understanding of the pathophysiological consequence of gastrointestinal nematode infections.}, }
@article {pmid31892895, year = {2019}, author = {Vinas, N and Thrash, A and Ii, MA and Jones, R and Douglas, T and Perkins, E}, title = {Keanu: A Novel Visualization Tool to Explore Biodiversity in Metagenomes.}, journal = {Journal of biomolecular techniques : JBT}, volume = {30}, number = {Suppl}, pages = {S24}, pmid = {31892895}, issn = {1943-4731}, abstract = {One of the main challenges when analyzing complex metagenomics data is the fact that large amounts of information need to be presented in a comprehensive and easy-to-navigate way. Here, we describe development and application of a command-line tool for exploring sample content in metagenomics data. Keanu, a tool for exploring sequence content, allows a user to understand what organisms are present in a sample and their abundance by analyzing alignments against a BLAST database and displaying them in an interactive web page. The content of a sample can be presented as a collapsible tree, with node sizes indicating abundance, or a bilevel partition graph, with arc size indicating abundance.Here, we show how we used Keanu to explore shotgun metagenomics data from a sample collected from a bluff that contained paleosols in an alpine site in interior Alaska. The site contained a krotovina, which is an ancient nest of unknown origin. Keanu allowed us to explore the potential origin of the krotovina by visualizing the number of hits related to different taxonomic categories. In summary, Keanu provides a facile means by which researchers can explore and visualize species present in sequence data generated from complex communities and environments. Keanu is written in Python and is freely available at https://github.com/IGBB/keanu.}, }
@article {pmid31734392, year = {2020}, author = {Li, W and Zhuang, JL and Zhou, YY and Meng, FG and Kang, D and Zheng, P and Shapleigh, JP and Liu, YD}, title = {Metagenomics reveals microbial community differences lead to differential nitrate production in anammox reactors with differing nitrogen loading rates.}, journal = {Water research}, volume = {169}, number = {}, pages = {115279}, doi = {10.1016/j.watres.2019.115279}, pmid = {31734392}, issn = {1879-2448}, mesh = {Bioreactors ; Denitrification ; Metagenomics ; *Microbiota ; *Nitrogen ; Oxidation-Reduction ; }, abstract = {Nitrate production during anammox can decrease total nitrogen removal efficiency, which will negatively impact its usefulness for the removal of nitrogen from waste streams. However, neither the performance characteristics nor physiological shifts associated with nitrate accumulation in anammox reactors under different nitrogen loading rates (NLRs) is well understood. Consequently, these parameters were studied in a lower NLR anammox reactor, termed R1, producing higher than expected levels of nitrate and compared with a higher NLR reactor, termed R2, showing no excess nitrate production. While both reactors showed high NH4+-N removal efficiencies (>90%), the total nitrogen removal efficiency (<60%) was much lower in R1 due to higher nitrate production. Metagenomic analysis found that the number of reads derived from anammox bacteria were significantly higher in R2. Another notable trend in reads occurrence was the relatively higher levels of reads from genes predicted to be nitrite oxidoreductases (nxr) in R1. Binning yielded 27 high quality draft genomes from the two reactors. Analysis of bin occurrence found that R1 showing both a decrease in anammox bacteria and an unexpected increase in nxr. In-situ assays confirmed that R1 had higher rates of nitrite oxidation to nitrate and suggested that it was not solely due to obligate NOB, but other nxr-containing bacteria are important contributors as well. Our results demonstrate that nitrate accumulation can be a serious operational concern for the application of anammox technology to low-strength wastewater treatment and provide insight into the community changes leading to this outcome.}, }
@article {pmid31226275, year = {2019}, author = {Assié, A and Samuel, BS}, title = {The Devil Is in the Microbial Genetic Details.}, journal = {Molecular cell}, volume = {74}, number = {6}, pages = {1108-1109}, doi = {10.1016/j.molcel.2019.06.003}, pmid = {31226275}, issn = {1097-4164}, mesh = {*Gastrointestinal Microbiome ; Genetics, Microbial ; Humans ; }, abstract = {The work of Zeevi et al. (2019) in a recent issue of Nature shows that variations in gene content and organization between different strains of the same microbial species are widespread in the human gut microbiota and could be linked to many measures of health.}, }
@article {pmid31884983, year = {2019}, author = {Traoré, SI and Bilen, M and Cadoret, F and Khelaifia, S and Million, M and Raoult, D and Lagier, JC}, title = {Study of Human Gastrointestinal Microbiota by Culturomics in Africa.}, journal = {Medecine et sante tropicales}, volume = {29}, number = {4}, pages = {366-370}, doi = {10.1684/mst.2019.0943}, pmid = {31884983}, issn = {2261-2211}, abstract = {The interest in studying gut microbiota has been rekindled with the advent of molecular techniques, in particular, metagenomics. Culturomics (high throughput microbial culture with identification of the colonies by Maldi-TOF) has demonstrated its complementarity with metagenomics for comprehensive study of the microbiota. The main metagenomic studies have revealed an increase in biodiversity, with in particular an increase of Spirochaetes and Prevotella in subjects of African origin compared with Western subjects. Studies on malnutrition have shown a reduction of all bacteria and in particular of anaerobic bacteria and methanogenic archaea. Of the 1,162 bacteria isolated by culturomics studies, 476 were isolated only from non-African samples, 445 were isolated in African and non-African groups, and 241 bacteria were isolated from samples of African origin including 68 new species. Further studies of African microbiota by culturomics and metagenomics will make it possible to assess whether some bacteria have particular specificities and if these might play a role in certain pathologies such as malnutrition.}, }
@article {pmid31884971, year = {2019}, author = {Coutinho, FH and Edwards, RA and Rodríguez-Valera, F}, title = {Charting the diversity of uncultured viruses of Archaea and Bacteria.}, journal = {BMC biology}, volume = {17}, number = {1}, pages = {109}, doi = {10.1186/s12915-019-0723-8}, pmid = {31884971}, issn = {1741-7007}, support = {APOSTD/2018/186//Conselleria d'Educació, Investigació, Cultura i Esport/ ; GL2016-76273-P//Ministerio de Economía y Competitividad/ ; CGL2015-71523-REDC//Ministerio de Economía y Competitividad/ ; }, abstract = {BACKGROUND: Viruses of Archaea and Bacteria are among the most abundant and diverse biological entities on Earth. Unraveling their biodiversity has been challenging due to methodological limitations. Recent advances in culture-independent techniques, such as metagenomics, shed light on the unknown viral diversity, revealing thousands of new viral nucleotide sequences at an unprecedented scale. However, these novel sequences have not been properly classified and the evolutionary associations between them were not resolved.<br><br>RESULTS: Here, we performed phylogenomic analysis of nearly 200,000 viral nucleotide sequences to establish GL-UVAB: Genomic Lineages of Uncultured Viruses of Archaea and Bacteria. The pan-genome content of the identified lineages shed light on some of their infection strategies, potential to modulate host physiology, and mechanisms to escape host resistance systems. Furthermore, using GL-UVAB as a reference database for annotating metagenomes revealed elusive habitat distribution patterns of viral lineages and environmental drivers of community composition.<br><br>CONCLUSIONS: These findings provide insights about the genomic diversity and ecology of viruses of prokaryotes. The source code used in these analyses is freely available at https://sourceforge.net/projects/gluvab/.}, }
@article {pmid31181638, year = {2019}, author = {Astó, E and Méndez, I and Rodríguez-Prado, M and Cuñé, J and Espadaler, J and Farran-Codina, A}, title = {Effect of the Degree of Polymerization of Fructans on Ex Vivo Fermented Human Gut Microbiome.}, journal = {Nutrients}, volume = {11}, number = {6}, pages = {}, doi = {10.3390/nu11061293}, pmid = {31181638}, issn = {2072-6643}, mesh = {Adult ; Bacteria/*drug effects/growth &amp; development ; Bacterial Typing Techniques/methods ; Colon/microbiology ; Female ; Fermentation ; Fructans/chemistry/*pharmacology ; Gastrointestinal Microbiome/*drug effects ; Humans ; Inulin/chemistry/pharmacology ; Male ; Oligosaccharides/chemistry/*pharmacology ; *Polymerization ; *Prebiotics ; }, abstract = {Prebiotic supplements are used to promote gastrointestinal health by stimulating beneficial bacteria. The aim of this study was to compare the potential prebiotic effects of fructans with increasing degrees of polymerization, namely fructooligosaccharides (FOS) and inulins with a low and high polymerization degree (LPDI and HPDI, respectively), using an ex vivo fermentation system to simulate the colonic environment. The system was inoculated with pooled feces from three healthy donors with the same baseline enterotype. Changes in microbiota composition were measured by 16S metagenomic sequencing after 2, 7, and 14 days of fermentation, and acid production was measured throughout the experiment. Alpha-diversity decreased upon inoculation of the ex vivo fermentation under all treatments. Composition changed significantly across both treatments and time (ANOSIM p < 0.005 for both factors). HPDI and LPDI seemed to be similar to each other regarding composition and acidification activity, but different from the control and FOS. FOS differed from the control in terms of composition but not acidification. HDPI restored alpha-diversity on day 14 as compared to the control (Bonferroni p < 0.05). In conclusion, the prebiotic activity of fructans appears to depend on the degree of polymerization, with LPDI and especially HPDI having a greater effect than FOS.}, }
@article {pmid30832245, year = {2019}, author = {Cortes-Rodriguez, N and Campana, MG and Berry, L and Faegre, S and Derrickson, SR and Ha, RR and Dikow, RB and Rutz, C and Fleischer, RC}, title = {Population Genomics and Structure of the Critically Endangered Mariana Crow (Corvus kubaryi).}, journal = {Genes}, volume = {10}, number = {3}, pages = {}, doi = {10.3390/genes10030187}, pmid = {30832245}, issn = {2073-4425}, support = {BB/G023913/2//Biotechnology and Biological Sciences Research Council (BBSRC) David Phillips Fellowship/International ; }, mesh = {Animals ; Conservation of Natural Resources ; Crows/*classification/genetics ; Endangered Species ; Evolution, Molecular ; Female ; Guam ; High-Throughput Nucleotide Sequencing ; Male ; Metagenomics/*methods ; Phylogeography ; Polymorphism, Single Nucleotide ; Whole Genome Sequencing/*methods ; }, abstract = {The Mariana Crow, or Åga (Corvus kubaryi), is a critically endangered species (IUCN -International Union for Conservation of Nature), endemic to the islands of Guam and Rota in the Mariana Archipelago. It is locally extinct on Guam, and numbers have declined dramatically on Rota to a historical low of less than 55 breeding pairs throughout the island in 2013. Because of its extirpation on Guam and population decline on Rota, it is of critical importance to assess the genetic variation among individuals to assist ongoing recovery efforts. We conducted a population genomics analysis comparing the Guam and Rota populations and studied the genetic structure of the Rota population. We used blood samples from five birds from Guam and 78 birds from Rota. We identified 145,552 candidate single nucleotide variants (SNVs) from a genome sequence of an individual from Rota and selected a subset of these to develop an oligonucleotide in-solution capture assay. The Guam and Rota populations were genetically differentiated from each other. Crow populations sampled broadly across their range on Rota showed significant genetic structuring ⁻ a surprising result given the small size of this island and the good flight capabilities of the species. Knowledge of its genetic structure will help improve management strategies to help with its recovery.}, }
@article {pmid29572891, year = {2018}, author = {Caussy, C and Hsu, C and Lo, MT and Liu, A and Bettencourt, R and Ajmera, VH and Bassirian, S and Hooker, J and Sy, E and Richards, L and Schork, N and Schnabl, B and Brenner, DA and Sirlin, CB and Chen, CH and Loomba, R and , }, title = {Link between gut-microbiome derived metabolite and shared gene-effects with hepatic steatosis and fibrosis in NAFLD.}, journal = {Hepatology (Baltimore, Md.)}, volume = {68}, number = {3}, pages = {918-932}, pmid = {29572891}, issn = {1527-3350}, support = {//American Gastroenterological Association (AGA) Foundation- Sucampo - ASP Designated Research Award in Geriatric Gastroenterology/International ; //T. Franklin Williams Scholarship Award/International ; //Atlantic Philanthropies, Inc/International ; //John A. Hartford Foundation/International ; //OM/International ; //Association of Specialty Professors/International ; K23-DK090303//American Gastroenterological Association/International ; R01-DK106419//American Gastroenterological Association/International ; //Société Francophone du Diabète (SFD)/International ; //Philippe Foundation and Monahan Foundation/International ; //Fulbright program/International ; K23 DK090303/DK/NIDDK NIH HHS/United States ; KL2 RR031978/RR/NCRR NIH HHS/United States ; P42 ES010337/ES/NIEHS NIH HHS/United States ; R01 DK106419/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Aged ; Cross-Sectional Studies ; Female ; *Gastrointestinal Microbiome ; Humans ; Liver Cirrhosis/*blood/microbiology ; Male ; Metformin ; Middle Aged ; Non-alcoholic Fatty Liver Disease/*blood/microbiology ; Phenylpropionates/*blood ; Proof of Concept Study ; }, abstract = {Previous studies have shown that gut-microbiome is associated with nonalcoholic fatty liver disease (NAFLD). We aimed to examine if serum metabolites, especially those derived from the gut-microbiome, have a shared gene-effect with hepatic steatosis and fibrosis. This is a cross-sectional analysis of a prospective discovery cohort including 156 well-characterized twins and families with untargeted metabolome profiling assessment. Hepatic steatosis was assessed using magnetic-resonance-imaging proton-density-fat-fraction (MRI-PDFF) and fibrosis using MR-elastography (MRE). A twin additive genetics and unique environment effects (AE) model was used to estimate the shared gene-effect between metabolites and hepatic steatosis and fibrosis. The findings were validated in an independent prospective validation cohort of 156 participants with biopsy-proven NAFLD including shotgun metagenomics sequencing assessment in a subgroup of the cohort. In the discovery cohort, 56 metabolites including 6 microbial metabolites had a significant shared gene-effect with both hepatic steatosis and fibrosis after adjustment for age, sex and ethnicity. In the validation cohort, 6 metabolites were associated with advanced fibrosis. Among them, only one microbial metabolite, 3-(4-hydroxyphenyl)lactate, remained consistent and statistically significantly associated with liver fibrosis in the discovery and validation cohort (fold-change of higher-MRE versus lower-MRE: 1.78, P < 0.001 and of advanced versus no advanced fibrosis: 1.26, P = 0.037, respectively). The share genetic determination of 3-(4-hydroxyphenyl)lactate with hepatic steatosis was RG :0.57,95%CI:0.27-0.80, P < 0.001 and with fibrosis was RG :0.54,95%CI:0.036-1, P = 0.036. Pathway reconstruction linked 3-(4-hydroxyphenyl)lactate to several human gut-microbiome species. In the validation cohort, 3-(4-hydroxyphenyl)lactate was significantly correlated with the abundance of several gut-microbiome species, belonging only to Firmicutes, Bacteroidetes and Proteobacteria phyla, previously reported as associated with advanced fibrosis. Conclusion: This proof of concept study provides evidence of a link between the gut-microbiome and 3-(4-hydroxyphenyl)lactate that shares gene-effect with hepatic steatosis and fibrosis. (Hepatology 2018).}, }
@article {pmid31159288, year = {2019}, author = {Couto-Rodríguez, RL and Montalvo-Rodríguez, R}, title = {Temporal Analysis of the Microbial Community from the Crystallizer Ponds in Cabo Rojo, Puerto Rico, Using Metagenomics.}, journal = {Genes}, volume = {10}, number = {6}, pages = {}, doi = {10.3390/genes10060422}, pmid = {31159288}, issn = {2073-4425}, support = {52007566/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Bacteroidetes/genetics ; Euryarchaeota/genetics ; Metagenome/*genetics ; *Metagenomics ; Microbiota/*genetics ; *Phylogeny ; Ponds/microbiology ; Proteobacteria/genetics ; Puerto Rico ; Tropical Climate ; Water Microbiology ; }, abstract = {The Cabo Rojo solar salterns are a hypersaline environment located in a tropical climate, where conditions remain stable throughout the year. These conditions can favor the establishment of steady microbial communities. Little is known about the microbial composition that thrives in hypersaline environments in the tropics. The main goal of this study was to assess the microbial diversity present in the crystallizer ponds of Cabo Rojo, in terms of structure and metabolic processes across time using metagenomic techniques. Three samplings (December 2014, March and July 2016) were carried out, where water samples (50 L each) were filtered through a Millipore pressurized filtering system. DNA was subsequently extracted using physical-chemical methods and sequenced using paired end Illumina technologies. The sequencing effort produced three paired end libraries with a total of 111,816,040 reads, that were subsequently assembled into three metagenomes. Out of the phyla detected, the microbial diversity was dominated in all three samples by Euryarchaeota, followed by Bacteroidetes and Proteobacteria. However, sample MFF1 (for Muestreo Final Fraternidad) exhibited a higher diversity, with 12 prokaryotic phyla detected at 34% NaCl (w/v), when compared to samples MFF2 and MFF3, which only exhibited three phyla. Precipitation events might be one of the contributing factors to the change in the microbial community composition through time. Diversity at genus level revealed a more stable community structure, with an overwhelming dominance of the square archaeon Haloquadratum in the three metagenomes. Furthermore, functional annotation was carried out in order to detect genes related to metabolic processes, such as carbon, nitrogen, and sulfur cycles. The presence of gene sequences related to nitrogen fixation, ammonia oxidation, sulfate reduction, sulfur oxidation, and phosphate solubilization were detected. Through binning methods, four putative novel genomes were obtained, including a possible novel genus belonging to the Bacteroidetes and possible new species for the genera Natronomonas, Halomicrobium, and Haloquadratum. Using a metagenomic approach, a 3-year study has been performed in a Caribbean hypersaline environment. When compared to other salterns around the world, the Cabo Rojo salterns harbor a similar community composition, which is stable through time. Moreover, an analysis of gene composition highlights the importance of the microbial community in the biogeochemical cycles at hypersaline environments.}, }
@article {pmid31035394, year = {2019}, author = {Jaswal, R and Pathak, A and Edwards, B and Lewis, R and Seaman, JC and Stothard, P and Krivushin, K and Blom, J and Rupp, O and Chauhan, A}, title = {Metagenomics-Guided Survey, Isolation, and Characterization of Uranium Resistant Microbiota from the Savannah River Site, USA.}, journal = {Genes}, volume = {10}, number = {5}, pages = {}, doi = {10.3390/genes10050325}, pmid = {31035394}, issn = {2073-4425}, mesh = {Ascomycota/genetics/radiation effects ; Biodegradation, Environmental ; Burkholderia/genetics/radiation effects ; Ecosystem ; Grassland ; Humans ; Metagenomics ; Microbiota/*genetics/radiation effects ; Penicillium/genetics/radiation effects ; Rivers ; *Soil Microbiology ; United States ; Uranium/*toxicity ; }, abstract = {Despite the recent advancements in culturomics, isolation of the majority of environmental microbiota performing critical ecosystem services, such as bioremediation of contaminants, remains elusive. Towards this end, we conducted a metagenomics-guided comparative assessment of soil microbial diversity and functions present in uraniferous soils relative to those that grew in diffusion chambers (DC) or microbial traps (MT), followed by isolation of uranium (U) resistant microbiota. Shotgun metagenomic analysis performed on the soils used to establish the DC/MT chambers revealed Proteobacterial phyla and Burkholderia genus to be the most abundant among bacteria. The chamber-associated growth conditions further increased their abundances relative to the soils. Ascomycota was the most abundant fungal phylum in the chambers relative to the soils, with Penicillium as the most dominant genus. Metagenomics-based taxonomic findings completely mirrored the taxonomic composition of the retrieved isolates such that the U-resistant bacteria and fungi mainly belonged to Burkholderia and Penicillium species, thus confirming that the chambers facilitated proliferation and subsequent isolation of specific microbiota with environmentally relevant functions. Furthermore, shotgun metagenomic analysis also revealed that the gene classes for carbohydrate metabolism, virulence, and respiration predominated with functions related to stress response, membrane transport, and metabolism of aromatic compounds were also identified, albeit at lower levels. Of major note was the successful isolation of a potentially novel Penicillium species using the MT approach, as evidenced by whole genome sequence analysis and comparative genomic analysis, thus enhancing our overall understanding on the uranium cycling microbiota within the tested uraniferous soils.}, }
@article {pmid31207997, year = {2019}, author = {Garrido-Sanz, D and Redondo-Nieto, M and Guirado, M and Pindado Jiménez, O and Millán, R and Martin, M and Rivilla, R}, title = {Metagenomic Insights into the Bacterial Functions of a Diesel-Degrading Consortium for the Rhizoremediation of Diesel-Polluted Soil.}, journal = {Genes}, volume = {10}, number = {6}, pages = {}, doi = {10.3390/genes10060456}, pmid = {31207997}, issn = {2073-4425}, mesh = {*Biodegradation, Environmental ; Biodiversity ; Chryseobacterium/classification/genetics ; Metagenome/*genetics ; Microbiota/*genetics ; Petroleum/*metabolism ; Phylogeny ; Polycyclic Aromatic Hydrocarbons/metabolism/toxicity ; Pseudomonas/classification/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Soil Pollutants/metabolism/toxicity ; }, abstract = {Diesel is a complex pollutant composed of a mixture of aliphatic and aromatic hydrocarbons. Because of this complexity, diesel bioremediation requires multiple microorganisms, which harbor the catabolic pathways to degrade the mixture. By enrichment cultivation of rhizospheric soil from a diesel-polluted site, we have isolated a bacterial consortium that can grow aerobically with diesel and different alkanes and polycyclic aromatic hydrocarbons (PAHs) as the sole carbon and energy source. Microbiome diversity analyses based on 16S rRNA gene showed that the diesel-degrading consortium consists of 76 amplicon sequence variants (ASVs) and it is dominated by Pseudomonas, Aquabacterium, Chryseobacterium, and Sphingomonadaceae. Changes in microbiome composition were observed when growing on specific hydrocarbons, reflecting that different populations degrade different hydrocarbons. Shotgun metagenome sequence analysis of the consortium growing on diesel has identified redundant genes encoding enzymes implicated in the initial oxidation of alkanes (AlkB, LadA, CYP450) and a variety of hydroxylating and ring-cleavage dioxygenases involved in aromatic and polyaromatic hydrocarbon degradation. The phylogenetic assignment of these enzymes to specific genera allowed us to model the role of specific populations in the diesel-degrading consortium. Rhizoremediation of diesel-polluted soil microcosms using the consortium, resulted in an important enhancement in the reduction of total petroleum hydrocarbons (TPHs), making it suited for rhizoremediation applications.}, }
@article {pmid30624643, year = {2019}, author = {Baldrian, P}, title = {The known and the unknown in soil microbial ecology.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {2}, pages = {}, doi = {10.1093/femsec/fiz005}, pmid = {30624643}, issn = {1574-6941}, mesh = {Bacteria/*classification/enzymology/genetics ; Ecology ; Ecosystem ; Fungi/*classification/enzymology/genetics ; Metabolomics ; Metagenomics ; Microbiota/*genetics ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {The methodical developments in the fields of molecular biology and analytical chemistry significantly increased the level of detail that we achieve when exploring soils and their microbial inhabitants. High-resolution description of microbial communities, detection of taxa with minor abundances, screening of gene expression or the detailed characterization of metabolomes are nowadays technically feasible. Despite all of this, our understanding of soil is limited in many ways. The imperfect tools to describe microbial communities and limited possibilities to assign traits to community members make it difficult to link microbes to functions. Also the analysis of processes exemplified by enzyme activity measurements is still imperfect. In the future, it is important to look at soil at a finer detail to obtain a better picture on the properties of individual microbes, their in situ interactions, metabolic rates and activity at a scale relevant to individual microbes. Scaling up is needed as well to get answers at ecosystem or biome levels and to enable global modelling. The recent development of novel tools including metabolomics, identification of genomes in metagenomics sequencing datasets or collection of trait data have the potential to bring soil ecology further. It will, however, always remain a highly demanding scientific discipline.}, }
@article {pmid31873124, year = {2019}, author = {Ottoni, C and Guellil, M and Ozga, AT and Stone, AC and Kersten, O and Bramanti, B and Porcier, S and Van Neer, W}, title = {Metagenomic analysis of dental calculus in ancient Egyptian baboons.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {19637}, doi = {10.1038/s41598-019-56074-x}, pmid = {31873124}, issn = {2045-2322}, abstract = {Dental calculus, or mineralized plaque, represents a record of ancient biomolecules and food residues. Recently, ancient metagenomics made it possible to unlock the wealth of microbial and dietary information of dental calculus to reconstruct oral microbiomes and lifestyle of humans from the past. Although most studies have so far focused on ancient humans, dental calculus is known to form in a wide range of animals, potentially informing on how human-animal interactions changed the animals' oral ecology. Here, we characterise the oral microbiome of six ancient Egyptian baboons held in captivity during the late Pharaonic era (9th-6th centuries BC) and of two historical baboons from a zoo via shotgun metagenomics. We demonstrate that these captive baboons possessed a distinctive oral microbiome when compared to ancient and modern humans, Neanderthals and a wild chimpanzee. These results may reflect the omnivorous dietary behaviour of baboons, even though health, food provisioning and other factors associated with human management, may have changed the baboons' oral microbiome. We anticipate our study to be a starting point for more extensive studies on ancient animal oral microbiomes to examine the extent to which domestication and human management in the past affected the diet, health and lifestyle of target animals.}, }
@article {pmid31316056, year = {2019}, author = {Mallick, H and Franzosa, EA and Mclver, LJ and Banerjee, S and Sirota-Madi, A and Kostic, AD and Clish, CB and Vlamakis, H and Xavier, RJ and Huttenhower, C}, title = {Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {3136}, doi = {10.1038/s41467-019-10927-1}, pmid = {31316056}, issn = {2041-1723}, support = {P30 DK036836/DK/NIDDK NIH HHS/United States ; P30 DK040561/DK/NIDDK NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; }, mesh = {Algorithms ; Colitis, Ulcerative/microbiology ; Crohn Disease/microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; *Metabolomics ; Metagenomics ; Microbiota/*genetics ; *Models, Genetic ; }, abstract = {Microbial community metabolomics, particularly in the human gut, are beginning to provide a new route to identify functions and ecology disrupted in disease. However, these data can be costly and difficult to obtain at scale, while amplicon or shotgun metagenomic sequencing data are readily available for populations of many thousands. Here, we describe a computational approach to predict potentially unobserved metabolites in new microbial communities, given a model trained on paired metabolomes and metagenomes from the environment of interest. Focusing on two independent human gut microbiome datasets, we demonstrate that our framework successfully recovers community metabolic trends for more than 50% of associated metabolites. Similar accuracy is maintained using amplicon profiles of coral-associated, murine gut, and human vaginal microbiomes. We also provide an expected performance score to guide application of the model in new samples. Our results thus demonstrate that this 'predictive metabolomic' approach can aid in experimental design and provide useful insights into the thousands of community profiles for which only metagenomes are currently available.}, }
@article {pmid31211676, year = {2019}, author = {Langelier, C and Graves, M and Kalantar, K and Caldera, S and Durrant, R and Fisher, M and Backman, R and Tanner, W and DeRisi, JL and Leung, DT}, title = {Microbiome and Antimicrobial Resistance Gene Dynamics in International Travelers.}, journal = {Emerging infectious diseases}, volume = {25}, number = {7}, pages = {1380-1383}, doi = {10.3201/eid2507.181492}, pmid = {31211676}, issn = {1080-6059}, support = {K23 HL138461/HL/NHLBI NIH HHS/United States ; }, mesh = {Biodiversity ; Communicable Diseases/*epidemiology/*microbiology ; Computational Biology/methods ; Databases, Genetic ; *Drug Resistance, Microbial ; Gene Transfer, Horizontal ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; *Metagenomics/methods ; *Microbiota/drug effects/genetics ; *Travel ; *Travel-Related Illness ; }, abstract = {We used metagenomic next-generation sequencing to longitudinally assess the gut microbiota and antimicrobial resistomes of international travelers to clarify global exchange of resistant organisms. Travel resulted in an increase in antimicrobial resistance genes and a greater proportion of Escherichia species within gut microbial communities without impacting diversity.}, }
@article {pmid31194939, year = {2019}, author = {Johnson, AJ and Vangay, P and Al-Ghalith, GA and Hillmann, BM and Ward, TL and Shields-Cutler, RR and Kim, AD and Shmagel, AK and Syed, AN and ,  and Walter, J and Menon, R and Koecher, K and Knights, D}, title = {Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans.}, journal = {Cell host &amp; microbe}, volume = {25}, number = {6}, pages = {789-802.e5}, doi = {10.1016/j.chom.2019.05.005}, pmid = {31194939}, issn = {1934-6069}, mesh = {Adult ; *Diet ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Longitudinal Studies ; Male ; Metagenomics ; *Microbiota ; Middle Aged ; Young Adult ; }, abstract = {Diet is a key determinant of human gut microbiome variation. However, the fine-scale relationships between daily food choices and human gut microbiome composition remain unexplored. Here, we used multivariate methods to integrate 24-h food records and fecal shotgun metagenomes from 34 healthy human subjects collected daily over 17 days. Microbiome composition depended on multiple days of dietary history and was more strongly associated with food choices than with conventional nutrient profiles, and daily microbial responses to diet were highly personalized. Data from two subjects consuming only meal replacement beverages suggest that a monotonous diet does not induce microbiome stability in humans, and instead, overall dietary diversity associates with microbiome stability. Our work provides key methodological insights for future diet-microbiome studies and suggests that food-based interventions seeking to modulate the gut microbiota may need to be tailored to the individual microbiome. Trial Registration: ClinicalTrials.gov: NCT03610477.}, }
@article {pmid31089679, year = {2019}, author = {Nicholls, SM and Quick, JC and Tang, S and Loman, NJ}, title = {Ultra-deep, long-read nanopore sequencing of mock microbial community standards.}, journal = {GigaScience}, volume = {8}, number = {5}, pages = {}, doi = {10.1093/gigascience/giz043}, pmid = {31089679}, issn = {2047-217X}, support = {//Medical Research Council/United Kingdom ; //Department of Health/United Kingdom ; }, mesh = {*Metagenome ; Metagenomics/*methods/standards ; Microbiota/*genetics ; Nanopore Sequencing/*methods/standards ; Reference Standards ; }, abstract = {BACKGROUND: Long sequencing reads are information-rich: aiding de novo assembly and reference mapping, and consequently have great potential for the study of microbial communities. However, the best approaches for analysis of long-read metagenomic data are unknown. Additionally, rigorous evaluation of bioinformatics tools is hindered by a lack of long-read data from validated samples with known composition.<br><br>FINDINGS: We sequenced 2 commercially available mock communities containing 10 microbial species (ZymoBIOMICS Microbial Community Standards) with Oxford Nanopore GridION and PromethION. Both communities and the 10 individual species isolates were also sequenced with Illumina technology. We generated 14 and 16 gigabase pairs from 2 GridION flowcells and 150 and 153 gigabase pairs from 2 PromethION flowcells for the evenly distributed and log-distributed communities, respectively. Read length N50 ranged between 5.3 and 5.4 kilobase pairs over the 4 sequencing runs. Basecalls and corresponding signal data are made available (4.2 TB in total). Alignment to Illumina-sequenced isolates demonstrated the expected microbial species at anticipated abundances, with the limit of detection for the lowest abundance species below 50 cells (GridION). De novo assembly of metagenomes recovered long contiguous sequences without the need for pre-processing techniques such as binning.<br><br>CONCLUSIONS: We present ultra-deep, long-read nanopore datasets from a well-defined mock community. These datasets will be useful for those developing bioinformatics methods for long-read metagenomics and for the validation and comparison of current laboratory and software pipelines.}, }
@article {pmid30872807, year = {2019}, author = {Thomas, F and Corre, E and Cébron, A}, title = {Stable isotope probing and metagenomics highlight the effect of plants on uncultured phenanthrene-degrading bacterial consortium in polluted soil.}, journal = {The ISME journal}, volume = {13}, number = {7}, pages = {1814-1830}, doi = {10.1038/s41396-019-0394-z}, pmid = {30872807}, issn = {1751-7370}, mesh = {Bacteria/genetics/*isolation &amp; purification/metabolism ; Biodegradation, Environmental ; Carbon Isotopes/analysis ; Lolium/*microbiology ; *Metagenomics ; *Microbial Consortia ; Phenanthrenes/*analysis ; Plant Roots/metabolism ; Polycyclic Aromatic Hydrocarbons/*analysis ; Soil/chemistry ; Soil Microbiology ; Soil Pollutants/*analysis ; Sphingomonadaceae/genetics/isolation &amp; purification/metabolism ; }, abstract = {Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous soil pollutants. The discovery that plants can stimulate microbial degradation of PAHs has promoted research on rhizoremediation strategies. We combined DNA-SIP with metagenomics to assess the influence of plants on the identity and metabolic functions of active PAH-degrading bacteria in contaminated soil, using phenanthrene (PHE) as a model hydrocarbon. 13C-PHE dissipation was 2.5-fold lower in ryegrass-planted conditions than in bare soil. Metabarcoding of 16S rDNA revealed significantly enriched OTUs in 13C-SIP incubations compared to 12C-controls, namely 130 OTUs from bare soil and 73 OTUs from planted soil. Active PHE-degraders were taxonomically diverse (Proteobacteria, Actinobacteria and Firmicutes), with Sphingomonas and Sphingobium dominating in bare and planted soil, respectively. Plant root exudates favored the development of PHE-degraders having specific functional traits at the genome level. Indeed, metagenomes of 13C-enriched DNA fractions contained more genes involved in aromatic compound metabolism in bare soil, whereas carbohydrate catabolism genes were more abundant in planted soil. Functional gene annotation allowed reconstruction of complete pathways with several routes for PHE catabolism. Sphingomonadales were the major taxa performing the first steps of PHE degradation in both conditions, suggesting their critical role to initiate in situ PAH remediation. Active PHE-degraders act in a consortium, whereby complete PHE mineralization is achieved through the combined activity of taxonomically diverse co-occurring bacteria performing successive metabolic steps. Our study reveals hitherto underestimated functional interactions for full microbial detoxification in contaminated soils.}, }
@article {pmid31863999, year = {2019}, author = {Llorens-Marès, T and Catalan, J and Casamayor, EO}, title = {Taxonomy and functional interactions in upper and bottom waters of an oligotrophic high-mountain deep lake (Redon, Pyrenees) unveiled by microbial metagenomics.}, journal = {The Science of the total environment}, volume = {707}, number = {}, pages = {135929}, doi = {10.1016/j.scitotenv.2019.135929}, pmid = {31863999}, issn = {1879-1026}, abstract = {High mountain lakes are, in general, highly sensitive systems to external forcing and good sentinels of global environmental changes. For a better understanding of internal lake processes, we examined microbial biodiversity and potential biogeochemical interactions in the oligotrophic deep high-mountain Lake Redon (Pyrenees, 2240 m altitude) using shotgun metagenomics. We analyzed the two ends of the range of environmental conditions found in Lake Redon, at 2 and 60 m depths. Bacteria were the most abundant component of the metagenomic reads (>90%) and the diversity indices of both taxonomic (16S and 18S rRNA) and functional (carbon-, nitrogen-, sulfur-, and phosphorous-cycling) related genes were higher in the bottom dark layer than in the upper compartment. A marked segregation was observed both in biodiversity and in the dominant energy and biomass generating pathways between the extremes. The aerobic respiration was mainly dominated by heterotrophic Burkholderiales at the top and Actinobacteria and Burkholderiales at the lake bottom. The potential for an active nitrogen cycle (nitrogen fixation, nitrification, nitrite oxidation, and nitrate reduction) was mainly found at 60 m, and potential for methanogenesis, anaerobic ammonia oxidation and dissimilatory sulfur pathways were only observed there. Some unexpected and mostly unseen energy and biomass pathways were found relevant for the biogeochemical cycling in lake Redon, i.e., those related to carbon monoxide oxidation and phosphonates processing. We provide a general scheme of the main biogeochemical processes that may operate in the sentinel deep Lake Redon. This framework may help for a better understanding of the whole lake metabolism.}, }
@article {pmid31856722, year = {2019}, author = {Zupančič, J and Turk, M and Črnigoj, M and Ambrožič Avguštin, J and Gunde-Cimerman, N}, title = {The dishwasher rubber seal acts as a reservoir of bacteria in the home environment.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {300}, doi = {10.1186/s12866-019-1674-5}, pmid = {31856722}, issn = {1471-2180}, support = {382228-1/2013//Ministrstvo za visoko šolstvo, znanost in tehnologijo/ ; P1-0170//Javna Agencija za Raziskovalno Dejavnost RS/ ; }, abstract = {BACKGROUND: In modern lifestyles, people make their everyday tasks easier by using household appliances, for example dishwashers. Previous studies showed massive contamination of dishwasher rubber seals with fungi, thus bacterial community, able to survive under harsh conditions, remain undetermined.<br><br>METHODS: Bacteria that colonise the extreme environment of household dishwasher rubber seals were investigated using cultivation-dependent and metagenomic approaches. All bacterial isolates were tested for resistance to seven selected antibiotics. Same time bacterial diversity of tap water, connected to the dishwashers was investigated.<br><br>RESULTS: All 30 dishwashers investigated were colonised by various bacteria. Cultivation approaches resulted in 632 bacterial isolates in total, belonging to four phyla, eight classes, 40 genera and 74 species. The majority were Gram-positive, as solely Firmicutes (dominated by the Bacillus cereus group) and Actinobacteria. Gammaproteobacteria were primarily represented by Stenotrophomonas maltophilia, Pseudomonas aeruginosa and Escherichia coli. Metagenomic assessment of the bacterial biodiversity of the dishwasher rubber seals confirmed the predominance of Gram-positive bacteria, as primarily Actinobacteria, followed by Proteobacteria dominated by Gammaproteobacteria, and by pathogenic species such as Escherichia sp., Acinetobacter baumannii, Pseudomonas sp., Stenotrophomonas maltophilia, and Enterobacter sp.. Metagenomic assessment of bacterial biodiversity in the tap water connected to dishwashers revealed predominance of Gram-negative bacteria, in particular Proteobacteria, mainly represented by Tepidimonas sp.. Actinobacteria showed low numbers while no Firmicutes were detected in the tap water. The bacterial diversity of tap water was also lower, 23 genera compared to 39 genera on dishwasher rubber seals. Only 13 out of 49 genera identified by metagenomics approach was found in both environments, of those Gordonia was enriched while half of 13 genera were depleted in dishwashers compared to tap water.<br><br>CONCLUSIONS: These data indicate that colonisation of dishwasher rubber seals probably depends primarily on the bacterial input from the dirty vessels, and much less on the bacteria in the tap water. Based on the antibiotic resistance data, the dishwasher rubber seal bacterial isolates do not represent a serious threat for the spread of antibiotic resistance into the household environment. Nevertheless dishwashers cannot be ignored as potential sources of human infections, in particular for immuno-compromised individuals.}, }
@article {pmid31361989, year = {2019}, author = {Abbasi, I and Nasereddin, A and Warburg, A}, title = {Development of a next generation DNA sequencing-based multi detection assay for detecting and identifying Leishmania parasites, blood sources, plant meals and intestinal microbiome in phlebotomine sand flies.}, journal = {Acta tropica}, volume = {199}, number = {}, pages = {105101}, doi = {10.1016/j.actatropica.2019.105101}, pmid = {31361989}, issn = {1873-6254}, mesh = {Animals ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Insect Vectors/*parasitology ; Leishmania/genetics/*isolation &amp; purification ; Leishmaniasis/transmission ; Phlebotomus/*parasitology ; }, abstract = {Leishmaniasis is a disease caused by Leishmania parasites transmitted by phlebotomine sand flies (Diptera: Psychodidae). Human infections with different Leishmania species cause characteristic clinical manifestations; cutaneous or visceral leishmaniasis. Here we describe the development and application of a Miseq Next GenerationSequencing (NGS)-based Multi Detection Assay (MDA) designed to characterize metagenomics parameters pertinent to the sand fly vectors which may affect their vectorial capacity for Leishmania. For this purpose, we developed a MDA by which, DNA fragments were amplified through polymerase chain reactions (PCR) and then sequenced by MiSeq/NGS. PCR amplification was achieved using some published and some new primers designed specifically for identifying Leishmania spp. (ITS1), sand fly spp. (cytochrome oxidase I), vertebrate blood (Cytochrome b), plant DNA ribulose-1,5-bisphosphate carboxylase large subunit gene (rbcL), and prokaryotic micobiome (16 s rRNA). This MDA/NGS analysis was performed on two species of wild-caught sand flies that transmit different Leishmania spp. in two ecologically distinct, but geographically neighboring locations. The results were analyzed to identify, quantitate and correlate the measured parameters in order to assess their putative importance in the transmission dynamics of leishmaniasis.}, }
@article {pmid31426820, year = {2019}, author = {Li, H and Li, H and Wang, J and Guo, L and Fan, H and Zheng, H and Yang, Z and Huang, X and Chu, M and Yang, F and He, Z and Li, N and Yang, J and Wu, Q and Shi, H and Liu, L}, title = {The altered gut virome community in rhesus monkeys is correlated with the gut bacterial microbiome and associated metabolites.}, journal = {Virology journal}, volume = {16}, number = {1}, pages = {105}, doi = {10.1186/s12985-019-1211-z}, pmid = {31426820}, issn = {1743-422X}, mesh = {Animals ; Anti-Bacterial Agents/administration &amp; dosage ; Bacteria/classification/*isolation &amp; purification ; Feces/microbiology/virology ; Gastrointestinal Microbiome/*drug effects ; Longitudinal Studies ; Macaca mulatta/microbiology/virology ; Metabolic Networks and Pathways ; Metabolome ; Metagenomics ; *Microbial Interactions ; Viruses/classification/*isolation &amp; purification ; }, abstract = {BACKGROUND: The gut microbiome is closely associated with the health of the host; although the interaction between the bacterial microbiome and the whole virome has rarely been studied, it is likely of medical importance. Examination of the interactions between the gut bacterial microbiome and virome of rhesus monkey would significantly contribute to revealing the gut microbiome composition.<br><br>METHODS: Here, we conducted a metagenomic analysis of the gut microbiome of rhesus monkeys in a longitudinal cohort treated with an antibiotic cocktail, and we documented the interactions between the bacterial microbiome and virome. The depletion of viral populations was confirmed at the species level by real-time PCR. We also detected changes in the gut metabolome by GC-MS and LC-MS.<br><br>RESULTS: A majority of bacteria were depleted after treatment with antibiotics, and the Shannon diversity index decreased from 2.95 to 0.22. Furthermore, the abundance-based coverage estimator (ACE) decreased from 104.47 to 33.84, and the abundance of eukaryotic viruses also changed substantially. In the annotation, 6 families of DNA viruses and 1 bacteriophage family were present in the normal monkeys but absent after gut bacterial microbiome depletion. Intriguingly, we discovered that changes in the gut bacterial microbiome composition may promote changes in the gut virome composition, and tryptophan, arginine, and quinone may play roles in the interaction between the bacterial microbiome and virome.<br><br>CONCLUSION: Our results indicated that the clearly altered composition of the virome was correlated with depletion in the bacterial community and that metabolites produced by bacteria possibly play important roles in the interaction.}, }
@article {pmid31415755, year = {2019}, author = {Tierney, BT and Yang, Z and Luber, JM and Beaudin, M and Wibowo, MC and Baek, C and Mehlenbacher, E and Patel, CJ and Kostic, AD}, title = {The Landscape of Genetic Content in the Gut and Oral Human Microbiome.}, journal = {Cell host &amp; microbe}, volume = {26}, number = {2}, pages = {283-295.e8}, doi = {10.1016/j.chom.2019.07.008}, pmid = {31415755}, issn = {1934-6069}, support = {R00 ES023504/ES/NIEHS NIH HHS/United States ; R01 AI127250/AI/NIAID NIH HHS/United States ; R21 ES025052/ES/NIEHS NIH HHS/United States ; P30 DK036836/DK/NIDDK NIH HHS/United States ; T32 DK110919/DK/NIDDK NIH HHS/United States ; K99 ES023504/ES/NIEHS NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics ; Biodiversity ; Cluster Analysis ; DNA Fingerprinting ; Databases, Factual ; Gastrointestinal Tract/microbiology ; Genetic Heterogeneity ; Host Microbial Interactions ; Humans ; Metagenome/*genetics ; Metagenomics ; Microbiota/*genetics/*physiology ; Mouth/microbiology ; Multigene Family ; Phenotype ; }, abstract = {Despite substantial interest in the species diversity of the human microbiome and its role in disease, the scale of its genetic diversity, which is fundamental to deciphering human-microbe interactions, has not been quantified. Here, we conducted a cross-study meta-analysis of metagenomes from two human body niches, the mouth and gut, covering 3,655 samples from 13 studies. We found staggering genetic heterogeneity in the dataset, identifying a total of 45,666,334 non-redundant genes (23,961,508 oral and 22,254,436 gut) at the 95% identity level. Fifty percent of all genes were &quot;singletons,&quot; or unique to a single metagenomic sample. Singletons were enriched for different functions (compared with non-singletons) and arose from sub-population-specific microbial strains. Overall, these results provide potential bases for the unexplained heterogeneity observed in microbiome-derived human phenotypes. One the basis of these data, we built a resource, which can be accessed at https://microbial-genes.bio.}, }
@article {pmid31399369, year = {2019}, author = {Thingholm, LB and Rühlemann, MC and Koch, M and Fuqua, B and Laucke, G and Boehm, R and Bang, C and Franzosa, EA and Hübenthal, M and Rahnavard, A and Frost, F and Lloyd-Price, J and Schirmer, M and Lusis, AJ and Vulpe, CD and Lerch, MM and Homuth, G and Kacprowski, T and Schmidt, CO and Nöthlings, U and Karlsen, TH and Lieb, W and Laudes, M and Franke, A and Huttenhower, C}, title = {Obese Individuals with and without Type 2 Diabetes Show Different Gut Microbial Functional Capacity and Composition.}, journal = {Cell host &amp; microbe}, volume = {26}, number = {2}, pages = {252-264.e10}, doi = {10.1016/j.chom.2019.07.004}, pmid = {31399369}, issn = {1934-6069}, support = {T32 HL069766/HL/NHLBI NIH HHS/United States ; P01 HL028481/HL/NHLBI NIH HHS/United States ; R01 HL144651/HL/NHLBI NIH HHS/United States ; R01 GM083198/GM/NIGMS NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; Diabetes Mellitus, Type 2/*complications ; Diet ; Dietary Supplements ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Germany ; Humans ; Iron/metabolism ; Magnesium/metabolism ; Male ; Metabolic Diseases/complications ; Metagenomics ; Mice ; Mice, Inbred C57BL ; Multivariate Analysis ; Nutrition Assessment ; Obesity/*complications/*microbiology ; Serum/metabolism ; }, abstract = {Obesity and type 2 diabetes (T2D) are metabolic disorders that are linked to microbiome alterations. However, their co-occurrence poses challenges in disentangling microbial features unique to each condition. We analyzed gut microbiomes of lean non-diabetic (n = 633), obese non-diabetic (n = 494), and obese individuals with T2D (n = 153) from German population and metabolic disease cohorts. Microbial taxonomic and functional profiles were analyzed along with medical histories, serum metabolomics, biometrics, and dietary data. Obesity was associated with alterations in microbiome composition, individual taxa, and functions with notable changes in Akkermansia, Faecalibacterium, Oscillibacter, and Alistipes, as well as in serum metabolites that correlated with gut microbial patterns. However, microbiome associations were modest for T2D, with nominal increases in Escherichia/Shigella. Medications, including antihypertensives and antidiabetics, along with dietary supplements including iron, were significantly associated with microbiome variation. These results differentiate microbial components of these interrelated metabolic diseases and identify dietary and medication exposures to consider in future studies.}, }
@article {pmid30562162, year = {2018}, author = {Peng, W and Yi, P and Yang, J and Xu, P and Wang, Y and Zhang, Z and Huang, S and Wang, Z and Zhang, C}, title = {Association of gut microbiota composition and function with a senescence-accelerated mouse model of Alzheimer's Disease using 16S rRNA gene and metagenomic sequencing analysis.}, journal = {Aging}, volume = {10}, number = {12}, pages = {4054-4065}, doi = {10.18632/aging.101693}, pmid = {30562162}, issn = {1945-4589}, mesh = {Aging ; Alzheimer Disease ; Animals ; *Disease Models, Animal ; Gastrointestinal Microbiome/*genetics ; Male ; Metagenomics ; Mice ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {Although an intriguing potential association of the gut microbiome with Alzheimer's disease (AD) has attracted recent interest, few studies have directly assessed this relationship or underlying mechanism. Here, we compared the gut microbiota composition and functional differentiation of senescence-accelerated mouse prone 8 (SAMP8) mice with control senescence-accelerated mouse resistant 1 (SAMR1) mice using 16S rRNA gene and metagenomic sequencing analysis, respectively. Specifically, 16S sequencing results showed that the SAMP8 mice displayed a characteristic composition of the gut microbiome that clearly differed from that of the SAMR1 mice. Moreover, network analysis revealed that the gut microbiota of SAMP8 mice had decreased correlation density and clustering of operational taxonomic units. Metagenomic results revealed that the predominant Cluster of Orthologous Groups functional category related to these changes was the metabolism cluster in SAMP8 mice. The Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation further demonstrated enrichment of the relative abundance of some dominant metabolism-related KEGG pathways in the SAMP8 mice, consistent with the suggested pathogenic mechanisms of AD. In conclusion, this study suggests that perturbations of the gut microbiota composition and the functional metagenome may be associated with AD. Further studies are warranted to elucidate the potential new mechanism contributing to AD progression.}, }
@article {pmid30406643, year = {2019}, author = {Gao, B and Chi, L and Tu, P and Gao, N and Lu, K}, title = {The Carbamate Aldicarb Altered the Gut Microbiome, Metabolome, and Lipidome of C57BL/6J Mice.}, journal = {Chemical research in toxicology}, volume = {32}, number = {1}, pages = {67-79}, doi = {10.1021/acs.chemrestox.8b00179}, pmid = {30406643}, issn = {1520-5010}, support = {R01 ES024950/ES/NIEHS NIH HHS/United States ; }, mesh = {Administration, Oral ; Aldicarb/administration &amp; dosage/*pharmacology ; Animals ; DNA Damage ; Gastrointestinal Microbiome/*drug effects ; Insecticides/administration &amp; dosage/*pharmacology ; Lipidomics ; *Lipids ; Male ; Metabolome/*drug effects ; Mice ; Mice, Inbred C57BL ; Molecular Structure ; Oxidative Stress/drug effects ; }, abstract = {The gut microbiome is highly involved in numerous aspects of host physiology, from energy harvest to stress response, and can confer many benefits to the host. The gut microbiome development could be affected by genetic and environmental factors, including pesticides. The carbamate insecticide aldicarb has been extensively used in agriculture, which raises serious public health concerns. However, the impact of aldicarb on the gut microbiome, host metabolome, and lipidome has not been well studied yet. Herein, we use multiomics approaches, including16S rRNA sequencing, shotgun metagenomics sequencing, metabolomics, and lipidomics, to elucidate aldicarb-induced toxicity in the gut microbiome and the host metabolic homeostasis. We demonstrated that aldicarb perturbed the gut microbiome development trajectory, enhanced gut bacterial pathogenicity, altered complex lipid profile, and induced oxidative stress, protein degradation, and DNA damage. The brain metabolism was also disturbed by the aldicarb exposure. These findings may provide a novel understanding of the toxicity of carbamate insecticides.}, }
@article {pmid31849864, year = {2019}, author = {Bains, M and Laney, C and Wolfe, AE and Orr, M and Waschek, JA and Ericsson, AC and Dorsam, GP}, title = {Vasoactive Intestinal Peptide Deficiency Is Associated With Altered Gut Microbiota Communities in Male and Female C57BL/6 Mice.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2689}, doi = {10.3389/fmicb.2019.02689}, pmid = {31849864}, issn = {1664-302X}, abstract = {Vasoactive intestinal peptide (VIP) is crucial for gastrointestinal tract (GIT) health. VIP sustains GIT homeostasis through maintenance of the intestinal epithelial barrier and acts as a potent anti-inflammatory mediator that contributes to gut bacterial tolerance. Based on these biological functions by VIP, we hypothesized that its deficiency would alter gut microbial ecology. To this end, fecal samples from male and female VIP+/+, VIP+/-, and VIP-/- littermates (n = 47) were collected and 16S rRNA sequencing was conducted. Our data revealed significant changes in bacterial composition, biodiversity, and weight loss from VIP-/- mice compared to VIP+/+ and VIP+/- littermates, irrespective of sex. The gut bacteria compositional changes observed in VIP-/- mice was consistent with gut microbial structure changes reported for certain inflammatory and autoimmune disorders. Moreover, predicted functional changes by PICRUSt software suggested an energy surplus within the altered microbiota from VIP-/- mice. These data support that VIP plays an important role in maintaining microbiota balance, biodiversity, and GIT function, and its genetic removal results in significant gut microbiota restructuring and weight loss.}, }
@article {pmid31429791, year = {2019}, author = {Casimiro-Soriguer, CS and Loucera, C and Perez Florido, J and López-López, D and Dopazo, J}, title = {Antibiotic resistance and metabolic profiles as functional biomarkers that accurately predict the geographic origin of city metagenomics samples.}, journal = {Biology direct}, volume = {14}, number = {1}, pages = {15}, doi = {10.1186/s13062-019-0246-9}, pmid = {31429791}, issn = {1745-6150}, mesh = {Biomarkers/*analysis ; Cities ; *Drug Resistance, Microbial ; *Machine Learning ; *Metabolome ; *Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; }, abstract = {BACKGROUND: The availability of hundreds of city microbiome profiles allows the development of increasingly accurate predictors of the origin of a sample based on its microbiota composition. Typical microbiome studies involve the analysis of bacterial abundance profiles.<br><br>RESULTS: Here we use a transformation of the conventional bacterial strain or gene abundance profiles to functional profiles that account for bacterial metabolism and other cell functionalities. These profiles are used as features for city classification in a machine learning algorithm that allows the extraction of the most relevant features for the classification.<br><br>CONCLUSIONS: We demonstrate here that the use of functional profiles not only predict accurately the most likely origin of a sample but also to provide an interesting functional point of view of the biogeography of the microbiota. Interestingly, we show how cities can be classified based on the observed profile of antibiotic resistances.<br><br>REVIEWERS: Open peer review: Reviewed by Jin Zhuang Dou, Jing Zhou, Torsten Semmler and Eran Elhaik.}, }
@article {pmid31420049, year = {2019}, author = {Ryan, FJ}, title = {Application of machine learning techniques for creating urban microbial fingerprints.}, journal = {Biology direct}, volume = {14}, number = {1}, pages = {13}, doi = {10.1186/s13062-019-0245-x}, pmid = {31420049}, issn = {1745-6150}, mesh = {Cities ; DNA Fingerprinting/*methods ; *Machine Learning ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; }, abstract = {BACKGROUND: Research has found that human associated microbial communities play a role in homeostasis and the disruption of these communities may be important in an array of medical conditions. However outside of the human body many of these communities remain poorly studied. The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium is characterizing the microbiomes of urban environments with the aim to improve design of mass transit systems. As part of the CAMDA 2018 MetaSUB Forensics Challenge 311 city microbiome samples were provided to create urban microbial fingerprints, as well as a further 3 mystery datasets for validation.<br><br>RESULTS: MetaSUB samples were clustered using t-SNE in an unsupervised fashion to almost discrete groups, which upon inspection represented city of origin. Based on this clustering, geographically close metropolitan areas appear to display similar microbial profiles such as those of Auckland and Hamilton. Mystery unlabeled samples were provided part of the challenge. A random forest classifier built on the initial dataset of 311 samples was capable of correctly classifying 83.3% of the mystery samples to their city of origin. Random Forest analyses also identified features with the highest discriminatory power, ranking bacterial species such as Campylobacter jejuni and Staphylococcus argenteus as highly predictive of city of origin. The surface from which the sample was collected displayed little detectable impact on the microbial profiles in the data generated here. The proportion of reads classified per sample varied greatly and so de-novo assembly was applied to recover genomic fragments representing organisms not captured in reference databases.<br><br>CONCLUSIONS: Current methods can differentiate urban microbiome profiles from each other with relative ease. De-novo assembly indicated that the MetaSUB metagenomic data contains adequate depth to recover metagenomic assembled genomes and that current databases are not sufficient to fully characterize urban microbiomes. Profiles found here indicate there may be a relationship between geographical distance between areas and the urban microbiome composition although this will need further research. The impact of these different profiles on public health is currently unknown but the MetaSUB consortium is uniquely suited to evaluate these and provide a roadmap for the inclusion of urban microbiome information for city planning and public health policy.<br><br>REVIEWERS: This article was reviewed by Dimitar Vassilev, Eran Elhaik and Chengsheng Zhu.}, }
@article {pmid31400683, year = {2019}, author = {Ceccon, DM and Faoro, H and Lana, PDC and Souza, EM and Pedrosa, FO}, title = {Metataxonomic and metagenomic analysis of mangrove microbiomes reveals community patterns driven by salinity and pH gradients in Paranaguá Bay, Brazil.}, journal = {The Science of the total environment}, volume = {694}, number = {}, pages = {133609}, doi = {10.1016/j.scitotenv.2019.133609}, pmid = {31400683}, issn = {1879-1026}, mesh = {Bays/chemistry/*microbiology ; Brazil ; *Environmental Monitoring ; Hydrogen-Ion Concentration ; *Metagenomics ; *Microbiota ; *Salinity ; }, abstract = {While environmental drivers regulate the structure of mangrove microbial communities, their exact nature and the extent of their influence require further elucidation. By means of 16S rRNA gene-based sequencing, we determined the microbial taxonomic profiles of mangroves in the subtropical Paranaguá Bay, Brazil, considering as potential drivers: salinity, as represented by two sectors in the extremes of a salinity gradient (<5 PSU and >30 PSU); proximity to/absence of the prevailing plants, Avicennia schaueriana, Laguncularia racemosa, Rhizophora mangle, and Spartina alterniflora; and the chemical composition of the sediments. Salinity levels within the estuary had the strongest influence on microbial structure, and pH was important to separate two communities within the high salinity environment. About one fourth of the total variation in community structure resulted from covariation of salinity and the overall chemical composition, which might indicate that the chemical profile was also related to salinity. The most prevalent bacterial phyla associated with the mangrove soils analyzed included Proteobacteria, Actinobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, and Cyanobacteria. Taxonomic and functional comparisons of our results for whole-genome sequencing with available data from other biomes showed that the studied microbiomes cluster first according to biome type, then to matrix type and salinity status. Metabolic functions were more conserved than organisms within mangroves and across all biomes, indicating that core functions are preserved in any of the given conditions regardless of the specific organisms harboring them.}, }
@article {pmid31371723, year = {2019}, author = {Coyne, MJ and Béchon, N and Matano, LM and McEneany, VL and Chatzidaki-Livanis, M and Comstock, LE}, title = {A family of anti-Bacteroidales peptide toxins wide-spread in the human gut microbiota.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {3460}, doi = {10.1038/s41467-019-11494-1}, pmid = {31371723}, issn = {2041-1723}, support = {P30 DK034854/DK/NIDDK NIH HHS/United States ; R01 AI093771/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*biosynthesis/pharmacology ; Bacterial Proteins/biosynthesis/genetics/pharmacology ; Bacterial Toxins/*biosynthesis/genetics/pharmacology ; Bacteriocins/*biosynthesis/*genetics/pharmacology ; Bacteroidetes/drug effects/genetics/*metabolism ; Base Sequence ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Gastrointestinal Tract/microbiology ; Gene Transfer, Horizontal/genetics ; Humans ; Interspersed Repetitive Sequences ; Metagenomics ; Microbial Sensitivity Tests ; Peptides/genetics/*metabolism/pharmacology ; Prevotella/drug effects ; Sequence Analysis, Protein ; Vaginosis, Bacterial ; }, abstract = {Bacteria often produce antimicrobial toxins to compete in microbial communities. Here we identify a family of broad-spectrum peptide toxins, named bacteroidetocins, produced by Bacteroidetes species. We study this toxin family using phenotypic, mutational, bioinformatic, and human metagenomic analyses. Bacteroidetocins are related to class IIa bacteriocins of Gram-positive bacteria and kill members of the Bacteroidetes phylum, including Bacteroides, Parabacteroides, and Prevotella gut species, as well as pathogenic Prevotella species. The bacteroidetocin biosynthesis genes are found in horizontally acquired mobile elements, which likely allow dissemination within the gut microbiota and may explain their wide distribution in human populations. Bacteroidetocins may have potential applications in microbiome engineering and as therapeutics for polymicrobial diseases such as bacterial vaginosis and periodontal disease.}, }
@article {pmid31370905, year = {2019}, author = {Harris, ZN and Dhungel, E and Mosior, M and Ahn, TH}, title = {Massive metagenomic data analysis using abundance-based machine learning.}, journal = {Biology direct}, volume = {14}, number = {1}, pages = {12}, doi = {10.1186/s13062-019-0242-0}, pmid = {31370905}, issn = {1745-6150}, mesh = {*Data Analysis ; *Machine Learning ; *Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; }, abstract = {BACKGROUND: Metagenomics is the application of modern genomic techniques to investigate the members of a microbial community directly in their natural environments and is widely used in many studies to survey the communities of microbial organisms that live in diverse ecosystems. In order to understand the metagenomic profile of one of the densest interaction spaces for millions of people, the public transit system, the MetaSUB international Consortium has collected and sequenced metagenomes from subways of different cities across the world. In collaboration with CAMDA, MetaSUB has made the metagenomic samples from these cities available for an open challenge of data analysis including, but not limited in scope to, the identification of unknown samples.<br><br>RESULTS: To distinguish the metagenomic profiling among different cities and also predict unknown samples precisely based on the profiling, two different approaches are proposed using machine learning techniques; one is a read-based taxonomy profiling of each sample and prediction method, and the other is a reduced representation assembly-based method. Among various machine learning techniques tested, the random forest technique showed promising results as a suitable classifier for both approaches. Random forest models developed from read-based taxonomic profiling could achieve an accuracy of 91% with 95% confidence interval between 80 and 93%. The assembly-based random forest model prediction also reached 90% accuracy. However, both models achieved roughly the same accuracy on the testing test, whereby they both failed to predict the most abundant label.<br><br>CONCLUSION: Our results suggest that both read-based and assembly-based approaches are powerful tools for the analysis of metagenomics data. Moreover, our results suggest that reduced representation assembly-based methods are able to simultaneous provide high-accuracy prediction on available data. Overall, we show that metagenomic samples can be traced back to their location with careful generation of features from the composition of microbes and utilizing existing machine learning algorithms. Proposed approaches show high accuracy of prediction, but require careful inspection before making any decisions due to sample noise or complexity.<br><br>REVIEWERS: This article was reviewed by Eugene V. Koonin, Jing Zhou and Serghei Mangul.}, }
@article {pmid31340852, year = {2019}, author = {Walker, AR and Datta, S}, title = {Identification of city specific important bacterial signature for the MetaSUB CAMDA challenge microbiome data.}, journal = {Biology direct}, volume = {14}, number = {1}, pages = {11}, doi = {10.1186/s13062-019-0243-z}, pmid = {31340852}, issn = {1745-6150}, mesh = {Bacteria/*genetics ; Cities ; High-Throughput Nucleotide Sequencing/*methods ; *Machine Learning ; Metagenomics/*methods ; Microbiota/*genetics ; }, abstract = {BACKGROUND: Metagenomic data of whole genome sequences (WGS) from samples across several cities around the globe may unravel city specific signatures of microbes. Illumina MiSeq sequencing data was provided from 12 cities in 7 different countries as part of the 2018 CAMDA &quot;MetaSUB Forensic Challenge&quot;, including also samples from three mystery sets. We used appropriate machine learning techniques on this massive dataset to effectively identify the geographical provenance of &quot;mystery&quot; samples. Additionally, we pursued compositional data analysis to develop accurate inferential techniques for such microbiome data. It is expected that this current data, which is of higher quality and higher sequence depth compared to the CAMDA 2017 MetaSUB challenge data, along with improved analytical techniques would yield many more interesting, robust and useful results that can be beneficial for forensic analysis.<br><br>RESULTS: A preliminary quality screening of the data revealed a much better dataset in terms of Phred quality score (hereafter Phred score), and larger paired-end MiSeq reads, and a more balanced experimental design, though still not equal number of samples across cities. PCA (Principal Component Analysis) analysis showed interesting clusters of samples and a large amount of the variability in the data was explained by the first three components (~ 70%). The classification analysis proved to be consistent across both the testing mystery sets with a similar percentage of the samples correctly predicted (up to 90%). The analysis of the relative abundance of bacterial &quot;species&quot; showed that some &quot;species&quot; are specific to some regions and can play important roles for predictions. These results were also corroborated by the variable importance given to the &quot;species&quot; during the internal cross validation (CV) run with Random Forest (RF).<br><br>CONCLUSIONS: The unsupervised analysis (PCA and two-way heatmaps) of the log2-cpm normalized data and relative abundance differential analysis seemed to suggest that the bacterial signature of common &quot;species&quot; was distinctive across the cities; which was also supported by the variable importance results. The prediction of the city for mystery sets 1 and 3 showed convincing results with high classification accuracy/consistency. The focus of this work on the current MetaSUB data and the analytical tools utilized here can be of great help in forensic, metagenomics, and other sciences to predict city of provenance of metagenomic samples, as well as in other related fields. Additionally, the pairwise analysis of relative abundance showed that the approach provided consistent and comparable &quot;species&quot; when compared with the classification importance variables.<br><br>REVIEWERS: This article was reviewed by Manuela Oliveira, Dimitar Vassilev, and Patrick Lee.}, }
@article {pmid31332169, year = {2019}, author = {Antunes, KH and Fachi, JL and de Paula, R and da Silva, EF and Pral, LP and Dos Santos, AÁ and Dias, GBM and Vargas, JE and Puga, R and Mayer, FQ and Maito, F and Zárate-Bladés, CR and Ajami, NJ and Sant'Ana, MR and Candreva, T and Rodrigues, HG and Schmiele, M and Silva Clerici, MTP and Proença-Modena, JL and Vieira, AT and Mackay, CR and Mansur, D and Caballero, MT and Marzec, J and Li, J and Wang, X and Bell, D and Polack, FP and Kleeberger, SR and Stein, RT and Vinolo, MAR and de Souza, APD}, title = {Microbiota-derived acetate protects against respiratory syncytial virus infection through a GPR43-type 1 interferon response.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {3273}, doi = {10.1038/s41467-019-11152-6}, pmid = {31332169}, issn = {2041-1723}, mesh = {A549 Cells ; Acetates/metabolism/*pharmacology ; Animals ; Cell Line ; Chlorocebus aethiops ; Humans ; Interferon Type I/*metabolism ; Lung/drug effects/metabolism/virology ; Mice, Inbred C57BL ; Mice, Knockout ; *Microbiota ; Polymorphism, Single Nucleotide ; Protective Agents/metabolism/pharmacology ; Receptor, Interferon alpha-beta/genetics ; Receptors, G-Protein-Coupled/genetics/*metabolism ; Respiratory Syncytial Virus Infections/genetics/*prevention &amp; control/virology ; Vero Cells ; Viral Load/drug effects/genetics ; }, abstract = {Severe respiratory syncytial virus (RSV) infection is a major cause of morbidity and mortality in infants <2 years-old. Here we describe that high-fiber diet protects mice from RSV infection. This effect was dependent on intestinal microbiota and production of acetate. Oral administration of acetate mediated interferon-β (IFN-β) response by increasing expression of interferon-stimulated genes in the lung. These effects were associated with reduction of viral load and pulmonary inflammation in RSV-infected mice. Type 1 IFN signaling via the IFN-1 receptor (IFNAR) was essential for acetate antiviral activity in pulmonary epithelial cell lines and for the acetate protective effect in RSV-infected mice. Activation of Gpr43 in pulmonary epithelial cells reduced virus-induced cytotoxicity and promoted antiviral effects through IFN-β response. The effect of acetate on RSV infection was abolished in Gpr43-/- mice. Our findings reveal antiviral effects of acetate involving IFN-β in lung epithelial cells and engagement of GPR43 and IFNAR.}, }
@article {pmid31250899, year = {2019}, author = {Aluthge, ND and Van Sambeek, DM and Carney-Hinkle, EE and Li, YS and Fernando, SC and Burkey, TE}, title = {BOARD INVITED REVIEW: The pig microbiota and the potential for harnessing the power of the microbiome to improve growth and health1.}, journal = {Journal of animal science}, volume = {97}, number = {9}, pages = {3741-3757}, doi = {10.1093/jas/skz208}, pmid = {31250899}, issn = {1525-3163}, mesh = {Animals ; Diet/veterinary ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Metabolomics ; *Prebiotics ; *Probiotics ; Swine/growth &amp; development/*microbiology/physiology ; *Synbiotics ; }, abstract = {A variety of microorganisms inhabit the gastrointestinal tract of animals including bacteria, archaea, fungi, protozoa, and viruses. Pioneers in gut microbiology have stressed the critical importance of diet:microbe interactions and how these interactions may contribute to health status. As scientists have overcome the limitations of culture-based microbiology, the importance of these interactions has become more clear even to the extent that the gut microbiota has emerged as an important immunologic and metabolic organ. Recent advances in metagenomics and metabolomics have helped scientists to demonstrate that interactions among the diet, the gut microbiota, and the host to have profound effects on animal health and disease. However, although scientists have now accumulated a great deal of data with respect to what organisms comprise the gastrointestinal landscape, there is a need to look more closely at causative effects of the microbiome. The objective of this review is intended to provide: 1) a review of what is currently known with respect to the dynamics of microbial colonization of the porcine gastrointestinal tract; 2) a review of the impact of nutrient:microbe effects on growth and health; 3) examples of the therapeutic potential of prebiotics, probiotics, and synbiotics; and 4) a discussion about what the future holds with respect to microbiome research opportunities and challenges. Taken together, by considering what is currently known in the four aforementioned areas, our overarching goal is to set the stage for narrowing the path towards discovering how the porcine gut microbiota (individually and collectively) may affect specific host phenotypes.}, }
@article {pmid31247969, year = {2019}, author = {Yu, JC and Hale, VL and Khodadadi, H and Baban, B}, title = {Whole Body Vibration-Induced Omental Macrophage Polarization and Fecal Microbiome Modification in a Murine Model.}, journal = {International journal of molecular sciences}, volume = {20}, number = {13}, pages = {}, doi = {10.3390/ijms20133125}, pmid = {31247969}, issn = {1422-0067}, mesh = {Animals ; Biodiversity ; Biomarkers ; Diabetes Mellitus, Type 2 ; Disease Models, Animal ; Feces/microbiology ; *Gastrointestinal Microbiome ; Immunophenotyping ; Macrophage Activation/*immunology ; Macrophages/*immunology/metabolism ; Metagenome ; Metagenomics/methods ; Mice ; Omentum/*immunology ; *Vibration ; }, abstract = {Human nutrient metabolism, developed millions of years ago, is anachronistic. Adaptive features that offered survival advantages are now great liabilities. The current dietary pattern, coupled with massively reduced physical activities, causes an epidemic of obesity and chronic metabolic diseases, such as type 2 diabetes mellitus. Chronic inflammation is a major contributing factor to the initiation and progression of most metabolic and cardiovascular diseases. Among all components of an innate immune system, due to their dual roles as phagocytic as well as antigen-presenting cells, macrophages play an important role in the regulation of inflammatory responses, affecting the body's microenvironment and homeostasis. Earlier studies have established the beneficial, anti-inflammatory effects of whole body vibration (WBV) as a partial exercise mimetic, including reversing the effects of glucose intolerance and hepatic steatosis. Here for the first time, we describe potential mechanisms by which WBV may improve metabolic status and ameliorate the adverse consequences through macrophage polarization and altering the fecal microbiome.}, }
@article {pmid31242612, year = {2019}, author = {Rampelotto, PH and Sereia, AFR and de Oliveira, LFV and Margis, R}, title = {Exploring the Hospital Microbiome by High-Resolution 16S rRNA Profiling.}, journal = {International journal of molecular sciences}, volume = {20}, number = {12}, pages = {}, doi = {10.3390/ijms20123099}, pmid = {31242612}, issn = {1422-0067}, mesh = {Bacteria/classification/genetics ; Biodiversity ; *Environmental Microbiology ; *Hospitals ; *Metagenomics/methods ; Microbiota/*genetics ; Models, Theoretical ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {The aim of this work was to analyze and compare the bacterial communities of 663 samples from a Brazilian hospital by using high-throughput sequencing of the 16S rRNA gene. To increase taxonomic profiling and specificity of 16S-based identification, a strict sequence quality filtering process was applied for the accurate identification of clinically relevant bacterial taxa. Our results indicate that the hospital environment is predominantly inhabited by closely related species. A massive dominance of a few taxa in all taxonomic levels down to the genera was observed, where the ten most abundant genera in each facility represented 64.4% of all observed taxa, with a major predominance of Acinetobacter and Pseudomonas. The presence of several nosocomial pathogens was revealed. Co-occurrence analysis indicated that the present hospital microbial network had low connectedness, forming a clustered topology, but not structured among groups of nodes (i.e., modules). Furthermore, we were able to detect ecologically relevant relationships between specific microbial taxa, in particular, potential competition between pathogens and non-pathogens. Overall, these results provide new insight into different aspects of a hospital microbiome and indicate that 16S rRNA sequencing may serve as a robust one-step tool for microbiological identification and characterization of a wide range of clinically relevant bacterial taxa in hospital settings with a high resolution.}, }
@article {pmid31240226, year = {2019}, author = {Yu, H and Qin, L and Hu, H and Wang, Z}, title = {Alteration of the Gut Microbiota and Its Effect on AMPK/NADPH Oxidase Signaling Pathway in 2K1C Rats.}, journal = {BioMed research international}, volume = {2019}, number = {}, pages = {8250619}, doi = {10.1155/2019/8250619}, pmid = {31240226}, issn = {2314-6141}, mesh = {AMP-Activated Protein Kinases/*metabolism ; Acetyl-CoA Carboxylase/metabolism ; Animals ; Bacteria/classification/metabolism ; Fatty Acids, Volatile/blood ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Kidney/*metabolism ; Male ; Metagenomics ; Models, Animal ; NADPH Oxidases/*metabolism ; Nitrates/blood ; Nitrites/blood ; Phosphorylation ; Rats ; Rats, Wistar ; Signal Transduction/*physiology ; Superoxide Dismutase/metabolism ; }, abstract = {Background: The purpose of this study was to evaluate the alteration of the gut microbiota and its effect on adenosine monophosphate-activated protein kinase (AMPK)/nicotinamide adenine dinucleotide phosphate oxidase (NADPH oxidase) signaling pathway in two-kidney one-clip (2K1C) rats.<br><br>Methods: The 2K1C rat models were established. The rats were randomly divided into the following 2 groups: 2K1C group and sham group. Alterations of the gut microbiota were analyzed based on the high throughput sequencing method. Plasma concentrations of short chain fatty acids (SCFAs) were measured by chromatography. The protein expression of phosphorylated AMPK and acetyl-CoA carboxylase (ACC) was determined by western blotting. NADPH oxidase activity was measured by a luminometer.<br><br>Results: Microbial community analyses revealed that the structure and composition of the gut microbiota were significantly disrupted in 2K1C rats when compared to sham rats. This disruption was associated with the drastic increase in relative abundance of the genera Prevotella and the decrease in SCFA-producing bacterial population. We further confirm that SCFAs produced by the gut microbiota influence NADPH oxidase activity through AMPK.<br><br>Conclusions: Our data implicated the important role of gut microbiota in the regulation of AMPK/NADPH oxidase signaling pathway.}, }
@article {pmid31221587, year = {2019}, author = {Aho, VTE and Pereira, PAB and Voutilainen, S and Paulin, L and Pekkonen, E and Auvinen, P and Scheperjans, F}, title = {Gut microbiota in Parkinson's disease: Temporal stability and relations to disease progression.}, journal = {EBioMedicine}, volume = {44}, number = {}, pages = {691-707}, doi = {10.1016/j.ebiom.2019.05.064}, pmid = {31221587}, issn = {2352-3964}, mesh = {Aged ; Biodiversity ; Case-Control Studies ; Disease Progression ; *Disease Susceptibility ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenomics/methods ; Middle Aged ; Parkinson Disease/*etiology/*metabolism/pathology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Several publications have described differences in cross-sectional comparisons of gut microbiota between patients with Parkinson's disease and control subjects, with considerable variability of the reported differentially abundant taxa. The temporal stability of such microbiota alterations and their relationship to disease progression have not been previously studied with a high-throughput sequencing based approach.<br><br>METHODS: We collected clinical data and stool samples from 64 Parkinson's patients and 64 control subjects twice, on average 2·25 years apart. Disease progression was evaluated based on changes in Unified Parkinson's Disease Rating Scale and Levodopa Equivalent Dose, and microbiota were characterized with 16S rRNA gene amplicon sequencing.<br><br>FINDINGS: We compared patients to controls, and patients with stable disease to those with faster progression. There were significant differences between microbial communities of patients and controls when corrected for confounders, but not between timepoints. Specific bacterial taxa that differed between patients and controls at both timepoints included several previously reported ones, such as Roseburia, Prevotella and Bifidobacterium. In progression comparisons, differentially abundant taxa were inconsistent across methods and timepoints, but there was some support for a different distribution of enterotypes and a decreased abundance of Prevotella in faster-progressing patients.<br><br>INTERPRETATION: The previously detected gut microbiota differences between Parkinson's patients and controls persisted after 2 years. While we found some evidence for a connection between microbiota and disease progression, a longer follow-up period is required to confirm these findings.}, }
@article {pmid31172250, year = {2019}, author = {Ali, N and Gong, H and Giwa, AS and Yuan, Q and Wang, K}, title = {Metagenomic analysis and characterization of acidogenic microbiome and effect of pH on organic acid production.}, journal = {Archives of microbiology}, volume = {201}, number = {9}, pages = {1163-1171}, doi = {10.1007/s00203-019-01676-2}, pmid = {31172250}, issn = {1432-072X}, support = {21206084//National Natural Science Foundation of China/ ; }, mesh = {Acetates/*metabolism ; Bifidobacterium/classification/*genetics/metabolism ; Bioreactors/*microbiology ; Carbohydrate Metabolism ; Fermentation/genetics ; High-Throughput Nucleotide Sequencing ; Hydrogen-Ion Concentration ; Hydrolysis ; Lactic Acid/*metabolism ; Lactobacillus/classification/*genetics/metabolism ; Metagenomics ; Microbiota/*genetics ; }, abstract = {Organic acid production including lactate and acetate is an economically attractive technology that has gained momentum worldwide over the past years. These series of action need to be performed by an esoteric and complex microbial community, in which different members have distinct roles in the establishment of a collective organization. In this study, we analyzed the bioma from bioreactors with various pH conditions of 4.0, 5.0 and 6.0 (R1, R2 and R3), respectively, involved in acidogenic digestion for stable production of various organic acids by means of high-throughput Illumina sequencing, disclosing thousands of genes and extracting more than 53 microbial genomes. At pH 5.0, the hydrolysis reaction was enhanced and thus the lactic acid fermentation was stably improved to 45.96 mm/L and acetic acid to 73.77 mm/L. R2 was found with the most suitable pH condition for stable organic acids production as Lactobacilli and Bifidobacteria were the major members. Both the members have the key roles in heterofermentation and produce higher transcripts of key encoding enzymes involved in the dominant heterofermentation pathways.}, }
@article {pmid31160269, year = {2019}, author = {Dahlin, M and Prast-Nielsen, S}, title = {The gut microbiome and epilepsy.}, journal = {EBioMedicine}, volume = {44}, number = {}, pages = {741-746}, doi = {10.1016/j.ebiom.2019.05.024}, pmid = {31160269}, issn = {2352-3964}, mesh = {Animals ; Anticonvulsants/therapeutic use ; Diet Therapy ; Diet, Ketogenic ; Disease Models, Animal ; Dysbiosis ; Epilepsy/*etiology/therapy ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; Nervous System Diseases/etiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Recently, evidence from both animal studies and human cases has emerged that a dysbiosis in the gut may be associated with certain forms of epilepsy. The ketogenic diet is an alternative treatment of drug-resistant epilepsy, although its precise mechanism of action has been unclear. It has now been shown that the ketogenic diet changes the composition and function of the gut microbiome in epilepsy patients. Studies in mice have demonstrated that the gut microbiota was necessary for the therapeutic effect of the diet and a mechanism of action has been proposed, providing new potential strategies for treatment. Further studies are needed to confirm the clinical relevance of this discovery. Below, we will discuss the scientific evidence of the role of the microbiome in seizure disorders, the impact of the ketogenic diet on the intestinal microbiota as well as the interactions described between commonly used antiepileptic drugs and intestinal microbial communities. We also discuss the potential of modulators of the gut microbiota as possible future anti-seizure therapeutics.}, }
@article {pmid31101528, year = {2019}, author = {Hagihara, M and Yamashita, R and Matsumoto, A and Mori, T and Inagaki, T and Nonogaki, T and Kuroki, Y and Higashi, S and Oka, K and Takahashi, M and Mikamo, H}, title = {The impact of probiotic Clostridium butyricum MIYAIRI 588 on murine gut metabolic alterations.}, journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy}, volume = {25}, number = {8}, pages = {571-577}, doi = {10.1016/j.jiac.2019.02.008}, pmid = {31101528}, issn = {1437-7780}, mesh = {Animals ; Clindamycin/adverse effects ; Clostridium butyricum/*growth &amp; development ; Feces/microbiology ; Female ; Firmicutes/drug effects ; Gastrointestinal Microbiome/*drug effects ; Japan ; Metabolic Networks and Pathways/drug effects ; Metagenomics/methods ; Mice ; Mice, Inbred ICR ; Probiotics/*pharmacology ; }, abstract = {INTRODUCTION: Clostridium butyricum MIYAIRI 588 (CBM 588) is a probiotic bacterium used in antidiarrheal medicine in Japan. A few studies analyzed the changes in gut microbiome in patients treated with antimicrobials based on metagenomics sequencing. However, the impact of CBM 588 on gut metabolic alterations has not been fully elucidated. This study was to reveal the impact of CBM 588 on gut metabolic alterations.<br><br>MATERIAL AND METHODS: In this in vivo study, mice were divided into four groups and CBM 588, clindamycin (CLDM), and normal saline (control) was orally administered (1. CLDM, 2. CBM 588, 3. CBM 588 + CLDM, 4. water) for 4 days. Fecal samples were collected to extract DNA for metagenomics analysis. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was used to obtain relative Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway abundance information derived from metagenomics data.<br><br>RESULTS: CLDM treatment resulted in a dramatic increase in Firmicutes phylum compared to non-CLDM-treated groups (control and CBM 588-treated group). Then, the CBM 588 + CLDM-treated group showed a trend similar in many metabolic pathways to the CLDM-treated group. On the other hand, the CBM 588 + CLDM-treated group showed higher relative abundance compared to the CLDM-treated group especially in starch and sucrose metabolism.<br><br>DISCUSSION: We concluded that CBM 588 caused a gut microbiome functional shift toward increased carbohydrate metabolism. These results support the hypothesis that CBM 588 treatment modulates gut microbiome under dysbiosis conditions due to antimicrobials.}, }
@article {pmid31065547, year = {2019}, author = {Zhuang, H and Cheng, L and Wang, Y and Zhang, YK and Zhao, MF and Liang, GD and Zhang, MC and Li, YG and Zhao, JB and Gao, YN and Zhou, YJ and Liu, SL}, title = {Dysbiosis of the Gut Microbiome in Lung Cancer.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {112}, doi = {10.3389/fcimb.2019.00112}, pmid = {31065547}, issn = {2235-2988}, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/*classification/*genetics ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Dysbiosis ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Lung Neoplasms/*complications ; Male ; Metagenomics ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {Lung cancer (LC) is one of the most serious malignant tumors, which has the fastest growing morbidity and mortality worldwide. A role of the lung microbiota in LC pathogenesis has been analyzed, but a comparable role of the gut microbiota has not yet been investigated. In this study, the gut microbiota of 30 LC patients and 30 healthy controls were examined via next-generation sequencing of 16S rRNA and analyzed for diversity and biomarkers. We found that there was no decrease in significant microbial diversity (alpha diversity) in LC patients compared to controls (P observed = 0.1422), while the composition (beta diversity) differed significantly between patients and controls (phylum [stress = 0.153], class [stress = 0.16], order [stress = 0.146], family [stress = 0.153]). Controls had a higher abundance of the bacterial phylum Actinobacteria and genus Bifidobacterium, while patients with LC showed elevated levels of Enterococcus. These bacteria were found as possible biomarkers for LC. A decline of normal function of the gut microbiome in LC patients was also observed. These results provide the basic guidance for a systematic, multilayered assessment of the role of the gut microbiome in LC, which has a promising potential for early prevention and targeted intervention.}, }
@article {pmid31024861, year = {2019}, author = {Meriwether, KV and Lei, Z and Singh, R and Gaskins, J and Hobson, DTG and Jala, V}, title = {The Vaginal and Urinary Microbiomes in Premenopausal Women With Interstitial Cystitis/Bladder Pain Syndrome as Compared to Unaffected Controls: A Pilot Cross-Sectional Study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {92}, doi = {10.3389/fcimb.2019.00092}, pmid = {31024861}, issn = {2235-2988}, mesh = {Adult ; Cross-Sectional Studies ; Cystitis, Interstitial/*microbiology ; Female ; Humans ; Metagenomics ; *Microbiota ; *Premenopause ; Surveys and Questionnaires ; Urine/*microbiology ; Vagina/*microbiology ; Young Adult ; }, abstract = {Interstitial cystitis/bladder pain syndrome (ICBPS) may be related to an altered genitourinary microbiome. Our aim was to compare the vaginal and urinary microbiomes between premenopausal women with ICBPS and unaffected controls. This cross-sectional study screened premenopausal women with an O'Leary-Sant questionnaire (ICBPS if score ≥6 on either index; controls <6 on both). Women completed questionnaires on health characteristics, pelvic floor symptoms (OABq, PFDI-20), body image (mBIS), and sexual function (PISQ-IR). Bacterial genomic DNA was isolated from vaginal and clean-catch urinary specimens; the bacterial 16 rRNA gene was sequenced and analyzed using the QIIME pipeline. We performed UniFrac analysis (β-diversity) and generated Chao1 estimator (richness) and Simpson index (richness and evenness) values. We analyzed 23 ICBPS and 18 non-ICBPS patients. ICBPS patients had increased vaginal deliveries, BMI, and public insurance as well as worsened OAB-q, PFDI-20, mBIS, and PISQ-IR domain scores. Lactobacilli was the most abundant genus in both cohorts, and anaerobic or fastidious predominance was similar between groups (p = 0.99). For both the urine and vagina specimens, Chao1 and Simpson indices were similar between ICBPS and unaffected women. Weighted and unweighted UniFrac analyses showed no differences between groups. A significant correlation existed between the urinary and vaginal Simpson indices in ICBPS women, but not in unaffected women. Premenopausal women with ICBPS, despite worsened socioeconomic indicators and pelvic floor function, were not found to have significantly different urinary and vaginal microbiomes compared to women without ICBPS.}, }
@article {pmid31001490, year = {2019}, author = {Hu, Y and Feng, Y and Wu, J and Liu, F and Zhang, Z and Hao, Y and Liang, S and Li, B and Li, J and Lv, N and Xu, Y and Zhu, B and Sun, Z}, title = {The Gut Microbiome Signatures Discriminate Healthy From Pulmonary Tuberculosis Patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {90}, doi = {10.3389/fcimb.2019.00090}, pmid = {31001490}, issn = {2235-2988}, mesh = {Bacteria/classification/genetics/metabolism ; *Dysbiosis ; Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; *Microbiota ; Tuberculosis, Pulmonary/*complications ; }, abstract = {Cross talk occurs between the human gut and the lung through a gut-lung axis involving the gut microbiota. However, the signatures of the human gut microbiota after active Mycobacterium tuberculosis infection have not been fully understood. Here, we investigated changes in the gut microbiota in tuberculosis (TB) patients by shotgun sequencing the gut microbiomes of 31 healthy controls and 46 patients. We observed a dramatic changes in gut microbiota in tuberculosis patients as reflected by significant decreases in species number and microbial diversity. The gut microbiota of TB patients were mostly featured by the striking decrease of short-chain fatty acids (SCFAs)-producingbacteria as well as associated metabolic pathways. A classification model based on the abundance of three species, Haemophilus parainfluenzae, Roseburia inulinivorans, and Roseburia hominis, performed well for discriminating between healthy and diseased patients. Additionally, the healthy and diseased states can be distinguished by SNPs in the species of B. vulgatus. We present a comprehensive profile of changes in the microbiota in clinical TB patients. Our findings will shed light on the design of future diagnoses and treatments for M. tuberculosis infections.}, }
@article {pmid30942867, year = {2019}, author = {Brown, SM and Chen, H and Hao, Y and Laungani, BP and Ali, TA and Dong, C and Lijeron, C and Kim, B and Wultsch, C and Pei, Z and Krampis, K}, title = {MGS-Fast: Metagenomic shotgun data fast annotation using microbial gene catalogs.}, journal = {GigaScience}, volume = {8}, number = {4}, pages = {}, doi = {10.1093/gigascience/giz020}, pmid = {30942867}, issn = {2047-217X}, support = {UH3 CA140233/CA/NCI NIH HHS/United States ; UL1 TR000457/TR/NCATS NIH HHS/United States ; G12 MD007599/MD/NIMHD NIH HHS/United States ; R01 AI110372/AI/NIAID NIH HHS/United States ; U54 CA221705/CA/NCI NIH HHS/United States ; R01 CA159036/CA/NCI NIH HHS/United States ; R21 DE025352/DE/NIDCR NIH HHS/United States ; U01 CA182370/CA/NCI NIH HHS/United States ; }, mesh = {Algorithms ; Cloud Computing ; Computational Biology/*methods ; Humans ; Metagenome ; Metagenomics/*methods ; Microbiology ; Microbiota ; Molecular Sequence Annotation ; Reproducibility of Results ; *Software ; Workflow ; }, abstract = {BACKGROUND: Current methods used for annotating metagenomics shotgun sequencing (MGS) data rely on a computationally intensive and low-stringency approach of mapping each read to a generic database of proteins or reference microbial genomes.<br><br>RESULTS: We developed MGS-Fast, an analysis approach for shotgun whole-genome metagenomic data utilizing Bowtie2 DNA-DNA alignment of reads that is an alternative to using the integrated catalog of reference genes database of well-annotated genes compiled from human microbiome data. This method is rapid and provides high-stringency matches (>90% DNA sequence identity) of the metagenomics reads to genes with annotated functions. We demonstrate the use of this method with data from a study of liver disease and synthetic reads, and Human Microbiome Project shotgun data, to detect differentially abundant Kyoto Encyclopedia of Genes and Genomes gene functions in these experiments. This rapid annotation method is freely available as a Galaxy workflow within a Docker image.<br><br>CONCLUSIONS: MGS-Fast can confidently transfer functional annotations from gene databases to metagenomic reads, with speed and accuracy.}, }
@article {pmid30922964, year = {2019}, author = {Liao, X and Song, L and Zeng, B and Liu, B and Qiu, Y and Qu, H and Zheng, Y and Long, M and Zhou, H and Wang, Y and Du, Y and Xu, J and Shen, R and Tong, Q and Cai, L and Li, X and Guo, S and Yang, G and Zhu, Z and Pu, X and Wei, H and Zheng, H}, title = {Alteration of gut microbiota induced by DPP-4i treatment improves glucose homeostasis.}, journal = {EBioMedicine}, volume = {44}, number = {}, pages = {665-674}, doi = {10.1016/j.ebiom.2019.03.057}, pmid = {30922964}, issn = {2352-3964}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Blood Glucose ; Diabetes Mellitus, Type 2/metabolism ; Diet, High-Fat ; Dipeptidyl-Peptidase IV Inhibitors/*pharmacology ; Disease Models, Animal ; Gastrointestinal Microbiome/*drug effects ; Glucose/*metabolism ; Glucose Tolerance Test ; Homeostasis/*drug effects ; Humans ; Insulin/metabolism ; Male ; Metagenome ; Metagenomics/methods ; Mice ; }, abstract = {BACKGROUND: Increasing evidence indicates that the gut microbiota contributes to the occurrence and development of metabolic diseases. However, little is known about the effects of commonly used antidiabetic agents on the gut microbiota. In this study, we investigated the roles of dipeptidyl peptidase-4 inhibitors (DPP-4i) and α-glucosidase inhibitor in modulating the gut microbiota.<br><br>METHODS: 16S-rDNA sequencing was performed to analyse the effects of DPP-4i and acarbose on the gut microbiota in mice fed a high-fat diet (HFD). Fecal microbiota transplantation (FMT) from type 2 diabetes patients to germ-free mice was performed to investigate the contribution of the altered microbiome to antidiabetic effects of the drugs. Fecal metabolomics was also analysed by untargeted and targeted GC-MS systems.<br><br>FINDINGS: Although DPP-4i and α-glucosidase inhibitor both altered the gut microbial composition, only the microbiome modulation of DPP-4i contributed to its hypoglycemic effect. Specifically, the changes of 68.6% genera induced by HFD were rescued by DPP-4i. FMT showed that the DPP-4i-altered microbiome improved glucose tolerance in colonized mice, while acarbose did not. Moreover, DPP-4i increased the abundance of Bacteroidetes, and also promoted a functional shift in the gut microbiome, especially increasing the production of succinate.<br><br>INTERPRETATION: Our findings demonstrate an important effect of DPP-4i on the gut microbiota, revealing a new hypoglycemic mechanism and an additional benefit of it. Furthermore, modulating the microbial composition, and the functional shift arising from changes in the microbiome, might be a potential strategy for improving glucose homeostasis. FUND: This work was supported by grants from the National Natural Science Foundation of China (No. 81700757, No. 81471039, No. 81700714 and No. 81770434), the National Key R&amp;D Program of China (No. 2017YFC1309602, No. 2016YFC1101100, No. 2017YFD0500503 and No. 2017YFD0501001), and the Natural Science Foundation of Chongqing (No. cstc2014jcyjjq10006, No. cstc2016jcyjA0093 and No. cstc2016jcyjA0518).}, }
@article {pmid30898652, year = {2019}, author = {O'Connor, KM and Lucking, EF and Golubeva, AV and Strain, CR and Fouhy, F and Cenit, MC and Dhaliwal, P and Bastiaanssen, TFS and Burns, DP and Stanton, C and Clarke, G and Cryan, JF and O'Halloran, KD}, title = {Manipulation of gut microbiota blunts the ventilatory response to hypercapnia in adult rats.}, journal = {EBioMedicine}, volume = {44}, number = {}, pages = {618-638}, doi = {10.1016/j.ebiom.2019.03.029}, pmid = {30898652}, issn = {2352-3964}, mesh = {Animals ; Anti-Bacterial Agents/administration &amp; dosage/adverse effects ; Biomarkers ; Blood Gas Analysis ; Brain Stem/metabolism/physiopathology ; Breath Tests ; Cell Membrane Permeability ; Disease Models, Animal ; Fecal Microbiota Transplantation ; Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; Heart Function Tests ; Heart Rate ; Hypercapnia/blood/*etiology/*physiopathology ; Hypoxia/metabolism ; Intestinal Mucosa/metabolism ; Male ; Metagenome ; Metagenomics/methods ; Rats ; Receptors, Serotonin, 5-HT3/metabolism ; *Respiration ; }, abstract = {BACKGROUND: It is increasingly evident that perturbations to the diversity and composition of the gut microbiota have significant consequences for the regulation of integrative physiological systems. There is growing interest in the potential contribution of microbiota-gut-brain signalling to cardiorespiratory control in health and disease.<br><br>METHODS: In adult male rats, we sought to determine the cardiorespiratory effects of manipulation of the gut microbiota following a 4-week administration of a cocktail of antibiotics. We subsequently explored the effects of administration of faecal microbiota from pooled control (vehicle) rat faeces, given by gavage to vehicle- and antibiotic-treated rats.<br><br>FINDINGS: Antibiotic intervention depressed the ventilatory response to hypercapnic stress in conscious animals, owing to a reduction in the respiratory frequency response to carbon dioxide. Baseline frequency, respiratory timing variability, and the expression of apnoeas and sighs were normal. Microbiota-depleted rats had decreased systolic blood pressure. Faecal microbiota transfer to vehicle- and antibiotic-treated animals also disrupted the gut microbiota composition, associated with depressed ventilatory responsiveness to hypercapnia. Chronic antibiotic intervention or faecal microbiota transfer both caused significant disruptions to brainstem monoamine neurochemistry, with increased homovanillic acid:dopamine ratio indicative of increased dopamine turnover, which correlated with the abundance of several bacteria of six different phyla.<br><br>INTERPRETATION: Chronic antibiotic administration and faecal microbiota transfer disrupt gut microbiota, brainstem monoamine concentrations and the ventilatory response to hypercapnia. We suggest that aberrant microbiota-gut-brain axis signalling has a modulatory influence on respiratory behaviour during hypercapnic stress. FUND: Department of Physiology and APC Microbiome Ireland, University College Cork, Ireland.}, }
@article {pmid30856229, year = {2019}, author = {Salgado-Flores, A and Tveit, AT and Wright, AD and Pope, PB and Sundset, MA}, title = {Characterization of the cecum microbiome from wild and captive rock ptarmigans indigenous to Arctic Norway.}, journal = {PloS one}, volume = {14}, number = {3}, pages = {e0213503}, doi = {10.1371/journal.pone.0213503}, pmid = {30856229}, issn = {1932-6203}, mesh = {Animals ; Animals, Wild/metabolism/microbiology ; Archaea/genetics/isolation &amp; purification/metabolism ; Arctic Regions ; Bacteria/genetics/isolation &amp; purification/metabolism ; Cecum/metabolism/*microbiology ; Galliformes/metabolism/*microbiology ; Metagenome ; Methane/metabolism ; Microbiota ; Norway ; Svalbard ; }, abstract = {Rock ptarmigans (Lagopus muta) are gallinaceous birds inhabiting arctic and sub-arctic environments. Their diet varies by season, including plants or plant parts of high nutritional value, but also toxic plant secondary metabolites (PSMs). Little is known about the microbes driving organic matter decomposition in the cecum of ptarmigans, especially the last steps leading to methanogenesis. The cecum microbiome in wild rock ptarmigans from Arctic Norway was characterized to unveil their functional potential for PSM detoxification, methanogenesis and polysaccharides degradation. Cecal samples were collected from wild ptarmigans from Svalbard (L. m. hyperborea) and northern Norway (L. m. muta) during autumn/winter (Sept-Dec). Samples from captive Svalbard ptarmigans fed commercial pelleted feed were included to investigate the effect of diet on microbial composition and function. Abundances of methanogens and bacteria were determined by qRT-PCR, while microbial community composition and functional potential were studied using 16S rRNA gene sequencing and shotgun metagenomics. Abundances of bacteria and methanogenic Archaea were higher in wild ptarmigans compared to captive birds. The ceca of wild ptarmigans housed bacterial groups involved in PSM-degradation, and genes mediating the conversion of phenol compounds to pyruvate. Methanomassiliicoccaceae was the major archaeal family in wild ptarmigans, carrying the genes for methanogenesis from methanol. It might be related to increased methanol production from pectin degradation in wild birds due to a diet consisting of primarily fresh pectin-rich plants. Both wild and captive ptarmigans possessed a broad suite of genes for the depolymerization of hemicellulose and non-cellulosic polysaccharides (e.g. starch). In conclusion, there were no physiological and phenotypical dissimilarities in the microbiota found in the cecum of wild ptarmigans on mainland Norway and Svalbard. While substantial differences in the functional potential for PSM degradation and methanogenesis in wild and captive birds seem to be a direct consequence of their dissimilar diets.}, }
@article {pmid30817265, year = {2019}, author = {Touyz, RM and Camargo, LL}, title = {Microglia, the Missing Link in the Brain-Gut-Hypertension Axis.}, journal = {Circulation research}, volume = {124}, number = {5}, pages = {671-673}, doi = {10.1161/CIRCRESAHA.119.314718}, pmid = {30817265}, issn = {1524-4571}, support = {CH/4/29762/BHF_/British Heart Foundation/United Kingdom ; }, mesh = {Angiotensin II ; Brain ; *Gastrointestinal Microbiome ; Humans ; *Hypertension ; Microglia ; }, }
@article {pmid30809010, year = {2019}, author = {Jones, DS and Walker, GM and Johnson, NW and Mitchell, CPJ and Coleman Wasik, JK and Bailey, JV}, title = {Molecular evidence for novel mercury methylating microorganisms in sulfate-impacted lakes.}, journal = {The ISME journal}, volume = {13}, number = {7}, pages = {1659-1675}, doi = {10.1038/s41396-019-0376-1}, pmid = {30809010}, issn = {1751-7370}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification/metabolism ; Bacterial Proteins/genetics/metabolism ; Lakes/analysis/*microbiology ; Mercury/analysis/*metabolism ; Methylation ; Methylmercury Compounds/analysis/metabolism ; Microbiota ; Sulfates/analysis/*metabolism ; Sulfides/analysis/metabolism ; }, abstract = {Methylmercury (MeHg) is a bioaccumulative neurotoxin that is produced by certain anaerobic microorganisms, but the abundance and importance of different methylating populations in the environment is not well understood. We combined mercury geochemistry, hgcA gene cloning, rRNA methods, and metagenomics to compare microbial communities associated with MeHg production in two sulfate-impacted lakes on Minnesota's Mesabi Iron Range. The two lakes represent regional endmembers among sulfate-impacted sites in terms of their dissolved sulfide concentrations and MeHg production potential. rRNA amplicon sequencing indicates that sediments and anoxic bottom waters from both lakes contained diverse communities with multiple clades of sulfate reducing Deltaproteobacteria and Clostridia. In hgcA gene clone libraries, however, hgcA sequences were from taxa associated with methanogenesis and iron reduction in addition to sulfate reduction, and the most abundant clones were from unknown groups. We therefore applied metagenomics to identify the unknown populations in the lakes with the capability to methylate mercury, and reconstructed 27 genomic bins with hgcA. Some of the most abundant potential methylating populations were from phyla that are not typically associated with MeHg production, including a relative of the Aminicenantes (formerly candidate phylum OP8) and members of the Kiritimatiellaeota (PVC superphylum) and Spirochaetes that, together, were more than 50% of the potential methylators in some samples. These populations do not have genes for sulfate reduction, and likely degrade organic compounds by fermentation or other anaerobic processes. Our results indicate that previously unrecognized populations with hgcAB are abundant and may be important for MeHg production in some freshwater ecosystems.}, }
@article {pmid30717674, year = {2019}, author = {Lei, Z and Zhang, K and Li, C and Jiao, T and Wu, J and Wei, Y and Tian, K and Li, C and Tang, D and Davis, DI and Casper, DP and Jiang, H and Wang, X and Wang, J}, title = {Ruminal metagenomic analyses of goat data reveals potential functional microbiota by supplementation with essential oil-cobalt complexes.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {30}, doi = {10.1186/s12866-019-1400-3}, pmid = {30717674}, issn = {1471-2180}, mesh = {Animal Feed/analysis ; Animals ; Cobalt/*administration &amp; dosage ; *Dietary Supplements ; Digestion ; Fatty Acids, Volatile/metabolism ; Fermentation ; Goats ; Male ; *Metagenomics ; Methane/metabolism ; Microbiota/*drug effects ; Oils, Volatile/*administration &amp; dosage ; Rumen/*microbiology ; }, abstract = {BACKGROUND: Essential Oils (EO) are complex mixtures of plant secondary metabolites that have been proposed as promising feed additives for mitigating methane and ammonia emissions. We have previously demonstrated that Essential Oil-Cobalt (EOC) supplementation resulted in increased average daily gain and improved phenotypes (cashmere fiber traits, carcass weight, and meat quality) when cashmere goats received supplementation at approximately 2 mg/kg of body weight. However, the ruminal microbiological effects of EO remain poorly understood with regard to the extent to which ruminal populations can adapt to EO presence as feed ingredients. The effects of varying levels of EO require additional study.<br><br>RESULTS: In this study, we conducted metagenomic analyses using ruminal fluid samples from three groups (addition of 0, 52, and 91 mg) to evaluate the influence of dietary EOC supplementation on goat rumen bacterial community dynamics. EOC addition resulted in changes of ruminal fermentation types and the EOC dose strongly impacted the stability of ruminal microbiota. The Bacteroides sp. and Succinivibrio sp. type bacterial community was positively associated with improved volatile fatty acid production when the diet was supplemented with EOC.<br><br>CONCLUSIONS: A clear pattern was found that reflected rapid fermentative improvement in the rumen, subsequent to butyrate metabolism and EOC based feed additives may affect rumen microbes to further improve feed conversion. This observation indicates that EOC can be safely used to enhance animal productivity and to reduce ammonia and waste gas emissions, thus positively impacting the environment.}, }
@article {pmid30717284, year = {2019}, author = {Ai, D and Pan, H and Han, R and Li, X and Liu, G and Xia, LC}, title = {Using Decision Tree Aggregation with Random Forest Model to Identify Gut Microbes Associated with Colorectal Cancer.}, journal = {Genes}, volume = {10}, number = {2}, pages = {}, doi = {10.3390/genes10020112}, pmid = {30717284}, issn = {2073-4425}, support = {HG006137-07//Foundation for the National Institutes of Health/International ; }, mesh = {*Algorithms ; Colorectal Neoplasms/*microbiology ; Firmicutes/genetics/isolation &amp; purification ; Fusobacterium/genetics/isolation &amp; purification ; *Gastrointestinal Microbiome ; Humans ; *Metagenome ; Porphyromonas/genetics/isolation &amp; purification ; Sequence Analysis, DNA/methods ; }, abstract = {The imbalance of human gut microbiota has been associated with colorectal cancer. In recent years, metagenomics research has provided a large amount of scientific data enabling us to study the dedicated roles of gut microbes in the onset and progression of cancer. We removed unrelated and redundant features during feature selection by mutual information. We then trained a random forest classifier on a large metagenomics dataset of colorectal cancer patients and healthy people assembled from published reports and extracted and analysed the information from the learned decision trees. We identified key microbial species associated with colorectal cancers. These microbes included Porphyromonasasaccharolytica, Peptostreptococcusstomatis, Fusobacterium,Parvimonas sp., Streptococcusvestibularis and Flavonifractorplautii. We obtained the optimal splitting abundance thresholds for these species to distinguish between healthy and colorectal cancer samples. This extracted consensus decision tree may be applied to the diagnosis of colorectal cancers.}, }
@article {pmid30709012, year = {2019}, author = {Dang, Z and McLenachan, PA and Lockhart, PJ and Waipara, N and Er, O and Reynolds, C and Blanchon, D}, title = {Metagenome Profiling Identifies Potential Biocontrol Agents for Selaginella kraussiana in New Zealand.}, journal = {Genes}, volume = {10}, number = {2}, pages = {}, doi = {10.3390/genes10020106}, pmid = {30709012}, issn = {2073-4425}, mesh = {Introduced Species ; *Metagenome ; Pseudomonas syringae/pathogenicity ; Selaginellaceae/*genetics/microbiology ; Weed Control/methods ; Xanthomonas/pathogenicity ; }, abstract = {Metagenomics can be used to identify potential biocontrol agents for invasive species and was used here to identify candidate species for biocontrol of an invasive club moss in New Zealand. Profiles were obtained for Selaginella kraussiana collected from nine geographically disjunct locations in Northern New Zealand. These profiles were distinct from those obtained for the exotic club moss Selaginella moellendorffii and the native club mosses Lycopodium deuterodensum and Lycopodium volubile also collected in Northern New Zealand. Fungi and bacteria implicated elsewhere in causing plant disease were identified on plants of Selaginella that exhibited signs of necrosis. Most notably, high densities of sequence reads from Xanthomonas translucens and Pseudomonas syringae were associated with some populations of Selaginella but not Lycopodium. Since these bacteria are already in use as biocontrol agents elsewhere, further investigation into their potential as biocontrol of Selaginella in New Zealand is suggested.}, }
@article {pmid30700057, year = {2019}, author = {Castillo Villamizar, GA and Nacke, H and Griese, L and Tabernero, L and Funkner, K and Daniel, R}, title = {Characteristics of the First Protein Tyrosine Phosphatase with Phytase Activity from a Soil Metagenome.}, journal = {Genes}, volume = {10}, number = {2}, pages = {}, doi = {10.3390/genes10020101}, pmid = {30700057}, issn = {2073-4425}, support = {G0701233//Medical Research Council/United Kingdom ; }, mesh = {6-Phytase/chemistry/*genetics/metabolism ; Amino Acid Motifs ; Bacterial Proteins/chemistry/*genetics/metabolism ; Cloning, Molecular ; *Metagenome ; Microbiota ; Mycobacterium tuberculosis/enzymology ; Phytic Acid/metabolism ; Protein Tyrosine Phosphatases/chemistry/*genetics/metabolism ; *Soil Microbiology ; }, abstract = {Protein tyrosine phosphatases (PTPs) fulfil multiple key regulatory functions. Within the group of PTPs, the atypical lipid phosphatases (ALPs) are known for their role as virulence factors associated with human pathogens. Another group of PTPs, which is capable of using inositol-hexakisphosphate (InsP₆) as substrate, are known as phytases. Phytases play major roles in the environmental phosphorus cycle, biotechnology, and pathogenesis. So far, all functionally characterized PTPs, including ALPs and PTP-phytases, have been derived exclusively from isolated microorganisms. In this study, screening of a soil-derived metagenomic library resulted in identification of a gene (pho16B), encoding a PTP, which shares structural characteristics with the ALPs. In addition, the characterization of the gene product (Pho16B) revealed the capability of the protein to use InsP₆ as substrate, and the potential of soil as a source of phytases with so far unknown characteristics. Thus, Pho16B represents the first functional environmentally derived PTP-phytase. The enzyme has a molecular mass of 38 kDa. The enzyme is promiscuous, showing highest activity and affinity toward naphthyl phosphate (Km 0.966 mM). Pho16B contains the HCXXGKDR[TA]G submotif of PTP-ALPs, and it is structurally related to PtpB of Mycobacterium tuberculosis. This study demonstrates the presence and functionality of an environmental gene codifying a PTP-phytase homologous to enzymes closely associated to bacterial pathogenicity.}, }
@article {pmid30632609, year = {2019}, author = {Hamada, T and Nowak, JA and Milner, DA and Song, M and Ogino, S}, title = {Integration of microbiology, molecular pathology, and epidemiology: a new paradigm to explore the pathogenesis of microbiome-driven neoplasms.}, journal = {The Journal of pathology}, volume = {247}, number = {5}, pages = {615-628}, doi = {10.1002/path.5236}, pmid = {30632609}, issn = {1096-9896}, support = {R35 CA197735/CA/NCI NIH HHS/United States ; K99 CA215314/CA/NCI NIH HHS/United States ; R00 CA215314/CA/NCI NIH HHS/United States ; }, mesh = {Carcinogenesis/pathology ; Forecasting ; Humans ; Microbiota/*physiology ; Neoplasms/epidemiology/*microbiology/therapy ; Precision Medicine/methods ; }, abstract = {Molecular pathological epidemiology (MPE) is an integrative transdisciplinary field that addresses heterogeneous effects of exogenous and endogenous factors (collectively termed 'exposures'), including microorganisms, on disease occurrence and consequences, utilising molecular pathological signatures of the disease. In parallel with the paradigm of precision medicine, findings from MPE research can provide aetiological insights into tailored strategies of disease prevention and treatment. Due to the availability of molecular pathological tests on tumours, the MPE approach has been utilised predominantly in research on cancers including breast, lung, prostate, and colorectal carcinomas. Mounting evidence indicates that the microbiome (inclusive of viruses, bacteria, fungi, and parasites) plays an important role in a variety of human diseases including neoplasms. An alteration of the microbiome may be not only a cause of neoplasia but also an informative biomarker that indicates or mediates the association of an epidemiological exposure with health conditions and outcomes. To adequately educate and train investigators in this emerging area, we herein propose the integration of microbiology into the MPE model (termed 'microbiology-MPE'), which could improve our understanding of the complex interactions of environment, tumour cells, the immune system, and microbes in the tumour microenvironment during the carcinogenic process. Using this approach, we can examine how lifestyle factors, dietary patterns, medications, environmental exposures, and germline genetics influence cancer development and progression through impacting the microbial communities in the human body. Further integration of other disciplines (e.g. pharmacology, immunology, nutrition) into microbiology-MPE would expand this developing research frontier. With the advent of high-throughput next-generation sequencing technologies, researchers now have increasing access to large-scale metagenomics as well as other omics data (e.g. genomics, epigenomics, proteomics, and metabolomics) in population-based research. The integrative field of microbiology-MPE will open new opportunities for personalised medicine and public health. Copyright © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley &amp; Sons, Ltd.}, }
@article {pmid30561396, year = {2018}, author = {Ticinesi, A and Nouvenne, A and Tana, C and Prati, B and Cerundolo, N and Miraglia, C and De' Angelis, GL and Di Mario, F and Meschi, T}, title = {The impact of intestinal microbiota on bio-medical research: definitions, techniques and physiology of a &quot;new frontier&quot;.}, journal = {Acta bio-medica : Atenei Parmensis}, volume = {89}, number = {9-S}, pages = {52-59}, doi = {10.23750/abm.v89i9-S.7906}, pmid = {30561396}, issn = {2531-6745}, mesh = {Adult ; Aged ; Aging ; Bacteria/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; Diet ; Exercise ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics/physiology ; High-Throughput Nucleotide Sequencing ; Homeostasis ; Humans ; *Metagenomics/trends ; Research ; Ribotyping ; }, abstract = {In recent years the metagenomics techniques have allowed to study composition and function of the intestinal microbiota. The microbiota is a new frontier of biomedical research to be explored and there is growing evidence of its fundamental health-promoting activity. The present review gives a synthetic overview on the characteristics and the role of the microbiota in the adult with particular reference to physiology, pathophysiology and relationships with the host and the environment.}, }
@article {pmid30504850, year = {2018}, author = {Letuma, P and Arafat, Y and Waqas, M and Lin, F and Lin, W and Zhang, Y and Masita, M and Fan, K and Li, Z and Lin, W}, title = {Gene mutation associated with esl mediates shifts on fungal community composition in rhizosphere soil of rice at grain-filling stage.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {17521}, pmid = {30504850}, issn = {2045-2322}, support = {31701329//National Natural Science Foundation of China (National Science Foundation of China)/International ; 2015M580560//China Postdoctoral Science Foundation/International ; 2016J01100//Natural Science Foundation of Fujian Province (Fujian Provincial Natural Science Foundation)/International ; }, mesh = {Biomass ; *Edible Grain ; Fungi/classification/genetics/*isolation &amp; purification ; *Genes, Fungal ; Metagenomics ; *Mutation ; *Mycobiome ; Oryza/*genetics ; Plant Leaves/metabolism ; RNA, Ribosomal, 18S/genetics ; *Rhizosphere ; *Soil Microbiology ; }, abstract = {Generally, plant roots shape the rhizosphere fungal community but how individual plant genes involved in senescence affect this shaping is less studied. We used an early senescence leaf (esl) mutant rice and compared it with its isogenic wild type variety to evaluate the effect of the vacuolar H+-ATPase (VHA-A1) gene mutation on the rhizosphere fungal community structure and composition using a metagenomic pyrosequencing approach. The most predominate fungal phyla identified for both isogenic lines belonged to Ascomycota, Basidiomycota and Glomeromycota, where Ascomycota were more prevalent in the esl mutant than the wild type variety. Real-time quantitative PCR analysis confirmed a significant rise in the richness of Cladosporium cladosporioides in esl mutant rice than the wild type variety. Correlation analysis revealed four most abundant genera identified for the esl mutant and their close association with yield and biomass decline, lipid peroxidation, lower root vitality, chlorophyll degradation and limited VHA activity. Higher K+ efflux, H+ and a lower Ca2+ influx was also observed in the esl mutant which could be the reason for abnormal functioning of mutant plants. These results illustrate that besides the well-known effect of senescence on plant physiology and yield decline, it can further shape the rhizosphere fungal community.}, }
@article {pmid30497919, year = {2019}, author = {Eisenhofer, R and Minich, JJ and Marotz, C and Cooper, A and Knight, R and Weyrich, LS}, title = {Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations.}, journal = {Trends in microbiology}, volume = {27}, number = {2}, pages = {105-117}, doi = {10.1016/j.tim.2018.11.003}, pmid = {30497919}, issn = {1878-4380}, mesh = {*Biomass ; *DNA Contamination ; DNA, Bacterial/analysis/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; Microbiological Techniques/methods/standards ; Microbiota/*genetics ; Reproducibility of Results ; Specimen Handling ; }, abstract = {Next-generation sequencing approaches in microbiome research have allowed surveys of microbial communities, their genomes, and their functions with higher sensitivity than ever before. However, this sensitivity is a double-edged sword because these tools also efficiently detect contaminant DNA and cross-contamination, which can confound the interpretation of microbiome data. Therefore, there is an urgent need to integrate key controls into microbiome research to improve the integrity of microbiome studies. Here, we review how contaminant DNA and cross-contamination arise within microbiome studies and discuss their negative impacts, especially during the analysis of low microbial biomass samples. We then identify several key measures that researchers can implement to reduce the impact of contaminant DNA and cross-contamination during microbiome research. We put forward a set of minimal experimental criteria, the 'RIDE' checklist, to improve the validity of future low microbial biomass research.}, }
@article {pmid30413731, year = {2018}, author = {Suryavanshi, MV and Bhute, SS and Gune, RP and Shouche, YS}, title = {Functional eubacteria species along with trans-domain gut inhabitants favour dysgenic diversity in oxalate stone disease.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {16598}, pmid = {30413731}, issn = {2045-2322}, mesh = {Bacteria/classification/*genetics ; Calcium Oxalate/*adverse effects/chemistry ; Case-Control Studies ; Dysbiosis/*classification/etiology/*pathology ; Gastrointestinal Microbiome/*physiology ; Humans ; Kidney Calculi/*complications ; *Metagenomics ; }, abstract = {Analyses across all three domains of life are necessary to advance our understanding of taxonomic dysbiosis in human diseases. In the present study, we assessed gut microbiota (eubacteria, archaea, and eukaryotes) of recurrent oxalate kidney stone suffers to explore the extent of trans-domain and functional species dysbiosis inside the gut. Trans-domain taxonomic composition, active oxalate metabolizer and butyrate-producing diversity were explored by utilizing frc-, but-, and buk- functional gene amplicon analysis. Operational taxonomic units (OTUs) level analyses confound with the observation that dysbiosis in gut microbiota is not just limited to eubacteria species, but also to other domains like archaea and eukaryotes. We found that some of healthy eubacterial population retained together with Oxalobacter formigenes and Lactobacillus plantarum colonization in disease condition (p < 0.001 &amp; FDR = 0.05). Interestingly, trans-domain species diversity has been less shared and dysgenic taxa augmentation was found to be higher. Oxalate metabolizing bacterial species (OMBS) and butyrate-producing eubacteria species were found to be decreased in Oxalobacter non-colonizers; and Prevotella and Ruminococcus species which may contribute to oxalate metabolism and butyrate synthesis as well. Our study underscores fact that microbial dysbiosis is not limited to eubacteria only hence suggest the necessity of the trans-domain surveillance in metabolic diseases for intervention studies.}, }
@article {pmid30067975, year = {2018}, author = {Kang, K and Ni, Y and Li, J and Imamovic, L and Sarkar, C and Kobler, MD and Heshiki, Y and Zheng, T and Kumari, S and Wong, JCY and Archna, A and Wong, CWM and Dingle, C and Denizen, S and Baker, DM and Sommer, MOA and Webster, CJ and Panagiotou, G}, title = {The Environmental Exposures and Inner- and Intercity Traffic Flows of the Metro System May Contribute to the Skin Microbiome and Resistome.}, journal = {Cell reports}, volume = {24}, number = {5}, pages = {1190-1202.e5}, doi = {10.1016/j.celrep.2018.06.109}, pmid = {30067975}, issn = {2211-1247}, mesh = {Drug Resistance, Bacterial/genetics ; *Environmental Exposure ; Hong Kong ; Humans ; Metagenome ; *Microbiota ; *Railroads ; Skin/*microbiology ; }, abstract = {The skin functions as the primary interface between the human body and the external environment. To understand how the microbiome varies within urban mass transit and influences the skin microbiota, we profiled the human palm microbiome after contact with handrails within the Hong Kong Mass Transit Railway (MTR) system. Intraday sampling time was identified as the primary determinant of the variation and recurrence of the community composition, whereas human-associated species and clinically important antibiotic resistance genes (ARGs) were captured as p.m. signatures. Line-specific signatures were notably correlated with line-specific environmental exposures and city characteristics. The sole cross-border line appeared as an outlier in most analyses and showed high relative abundance and a significant intraday increment of clinically important ARGs (24.1%), suggesting potential cross-border ARG transmission, especially for tetracycline and vancomycin resistance. Our study provides an important reference for future public health strategies to mitigate intracity and cross-border pathogen and ARG transmission.}, }
@article {pmid30039859, year = {2019}, author = {Lu, J and Shi, P and Li, H}, title = {Generalized linear models with linear constraints for microbiome compositional data.}, journal = {Biometrics}, volume = {75}, number = {1}, pages = {235-244}, doi = {10.1111/biom.12956}, pmid = {30039859}, issn = {1541-0420}, mesh = {Bacteria/*isolation &amp; purification ; Computer Simulation ; Confidence Intervals ; Feces/microbiology ; Humans ; Inflammatory Bowel Diseases/microbiology ; Likelihood Functions ; *Linear Models ; *Microbiota ; Regression Analysis ; }, abstract = {Motivated by regression analysis for microbiome compositional data, this article considers generalized linear regression analysis with compositional covariates, where a group of linear constraints on regression coefficients are imposed to account for the compositional nature of the data and to achieve subcompositional coherence. A penalized likelihood estimation procedure using a generalized accelerated proximal gradient method is developed to efficiently estimate the regression coefficients. A de-biased procedure is developed to obtain asymptotically unbiased and normally distributed estimates, which leads to valid confidence intervals of the regression coefficients. Simulations results show the correctness of the coverage probability of the confidence intervals and smaller variances of the estimates when the appropriate linear constraints are imposed. The methods are illustrated by a microbiome study in order to identify bacterial species that are associated with inflammatory bowel disease (IBD) and to predict IBD using fecal microbiome.}, }
@article {pmid29633335, year = {2018}, author = {Gautam, A and Kumar, R and Chakraborty, N and Muhie, S and Hoke, A and Hammamieh, R and Jett, M}, title = {Altered fecal microbiota composition in all male aggressor-exposed rodent model simulating features of post-traumatic stress disorder.}, journal = {Journal of neuroscience research}, volume = {96}, number = {7}, pages = {1311-1323}, doi = {10.1002/jnr.24229}, pmid = {29633335}, issn = {1097-4547}, mesh = {Animals ; Bacteroidetes/isolation &amp; purification ; Feces/*microbiology ; Firmicutes/isolation &amp; purification ; *Gastrointestinal Microbiome ; Male ; Mice ; Mice, Inbred C57BL ; Models, Animal ; Proteobacteria/isolation &amp; purification ; Stress Disorders, Post-Traumatic/*microbiology ; }, abstract = {The bidirectional role of gut-brain axis that integrates the gut and central nervous system activities has recently been investigated. We studied &quot;cage-within-cage resident-intruder&quot; all-male model, where subject male mice (C57BL/6J) are exposed to aggressor mice (SJL albino), and gut microbiota-derived metabolites were identified in plasma after 10 days of exposure. We assessed 16S ribosomal RNA gene from fecal samples collected daily from these mice during the 10-day study. Alpha diversity using Chao indices indicated no change in diversity in aggressor-exposed samples. The abundance profile showed the top phyla were Firmicutes and Bacteroidetes, Tenericutes, Verrucomicrobia, Actinobacteria and Proteobacteria, respectively. The phyla Firmicutes and Bacteroidetes are vulnerable to PTSD-eliciting stress and the Firmicutes/Bacteroidetes ratio increases with stress. Principal coordinate analysis showed the control and aggressor-exposed samples cluster separately where samples from early time points (day 1-3) clustered together and were distinct from late time points (day 4-9). The genus-based analysis revealed all control time points clustered together and aggressor-exposed samples had multiple clusters. The decrease in proportion of Firmicutes after aggressor exposure persisted throughout the study. The proportion of Verrucomicrobia immediately decreased and was significantly shifted at most of the later time points. The genus Oscillospira, Lactobacillus, Akkermansia and Anaeroplasma are the top four genera that differed between control and stressor-exposed mice. The data showed immediate effect on microbiome composition during a 10 day time period of stress exposure. Studying the longitudinal effects of a stressor is an important step toward an improved mechanistic understanding of the microbiome dynamics.}, }
@article {pmid31835740, year = {2019}, author = {Truchado, DA and Diaz-Piqueras, JM and Gomez-Lucia, E and Doménech, A and Milá, B and Pérez-Tris, J and Schmidt-Chanasit, J and Cadar, D and Benítez, L}, title = {A Novel and Divergent Gyrovirus with Unusual Genomic Features Detected in Wild Passerine Birds from a Remote Rainforest in French Guiana.}, journal = {Viruses}, volume = {11}, number = {12}, pages = {}, doi = {10.3390/v11121148}, pmid = {31835740}, issn = {1999-4915}, support = {CGL2017-82117-P//Spanish National Research Agency/ ; CGL2013-41642-P/BOS//Spanish National Research Agency/ ; CEBA:ANR-10-LABX-25-01//Agence Nationale de la Recherche (ANR)/ ; CT27/16-CT28/16//UCM/ ; }, abstract = {Sequence-independent amplification techniques have become important tools for virus discovery, metagenomics, and exploration of viral diversity at the global scale, especially in remote areas. Here, we describe the detection and genetic characterization of a novel gyrovirus, named GyV11, present in cloacal, oral, and blood samples from neotropical wild birds in French Guiana. The molecular epidemiology revealed the presence of GyV11 only in passerine birds from three different species at a low prevalence (0.73%). This is the first characterization and prevalence study of a gyrovirus carried out in resident wild bird populations in a remote region, and provides evidence of the fecal-oral route transmission and local circulation of the virus. The molecular phylogeny of gyroviruses reveals the existence of two distinct gyrovirus lineages in which GyV11 is phylogenetically distinct from previously reported gyroviruses. Furthermore, GyV11 is placed basal in the gyrovirus phylogeny, likely owing to its ancestral origin and marked divergence. This study also provides important insights into the ecology, epidemiology, and genomic features of gyroviruses in a remote neotropical rainforest. The pathogenesis of this virus in avian species or whether GyV11 can infect humans and/or chickens needs to be further investigated.}, }
@article {pmid31795935, year = {2019}, author = {Raj, G and Shadab, M and Deka, S and Das, M and Baruah, J and Bharali, R and Talukdar, NC}, title = {Seed interior microbiome of rice genotypes indigenous to three agroecosystems of Indo-Burma biodiversity hotspot.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {924}, doi = {10.1186/s12864-019-6334-5}, pmid = {31795935}, issn = {1471-2164}, abstract = {BACKGROUND: Seeds of plants are a confirmation of their next generation and come associated with a unique microbia community. Vertical transmission of this microbiota signifies the importance of these organisms for a healthy seedling and thus a healthier next generation for both symbionts. Seed endophytic bacterial community composition is guided by plant genotype and many environmental factors. In north-east India, within a narrow geographical region, several indigenous rice genotypes are cultivated across broad agroecosystems having standing water in fields ranging from 0-2 m during their peak growth stage. Here we tried to trap the effect of rice genotypes and agroecosystems where they are cultivated on the rice seed microbiota. We used culturable and metagenomics approaches to explore the seed endophytic bacterial diversity of seven rice genotypes (8 replicate hills) grown across three agroecosystems.<br><br>RESULTS: From seven growth media, 16 different species of culturable EB were isolated. A predictive metabolic pathway analysis of the EB showed the presence of many plant growth promoting traits such as siroheme synthesis, nitrate reduction, phosphate acquisition, etc. Vitamin B12 biosynthesis restricted to bacteria and archaea; pathways were also detected in the EB of two landraces. Analysis of 522,134 filtered metagenomic sequencing reads obtained from seed samples (n=56) gave 4061 OTUs. Alpha diversity indices showed significant differences in observed OTU richness (P≤0.05) across genotypes. Significant differences were also found between the individual hills of a rice genotype. PCoA analysis exhibited three separate clusters and revealed the clusters separated based on genotype, while agroecosystem showed a minimal effect on the variation of seed microbiota (adonis, R2=0.07, P=0.024). Interestingly, animal gut resident bacteria such as Bifidobacterium, Faecalibacterium, Lactobacillus, etc. were found in abundance as members of the seed microbiota.<br><br>CONCLUSION: Overall, our study demonstrates, indigenous rice genotypes of north-east India have a unique blend of endophytic bacteria in their mature seeds. While there are notable variations among plants of the same genotype, we found similarities among genotypes cultivated in completely different environmental conditions. The beta diversity variations across the seven rice genotypes were significantly shaped by their genotype rather than their agroecosystems.}, }
@article {pmid31574349, year = {2019}, author = {Chen, H and Bai, X and Li, Y and Jing, L and Chen, R and Teng, Y}, title = {Source identification of antibiotic resistance genes in a peri-urban river using novel crAssphage marker genes and metagenomic signatures.}, journal = {Water research}, volume = {167}, number = {}, pages = {115098}, doi = {10.1016/j.watres.2019.115098}, pmid = {31574349}, issn = {1879-2448}, mesh = {Animals ; Anti-Bacterial Agents ; Drug Resistance, Microbial ; Genes, Bacterial ; Humans ; Metagenomics ; *Microbiota ; *Rivers ; Swine ; }, abstract = {Antimicrobial resistance is a growing public health concern, and environment is regarded as an important reservoir and dissemination route for antibiotic resistance genes (ARGs). To prevent and control ARG pollution, it is essential to correctly disentangle source-sink relationship of ARGs in the environment. However, accurately apportioning sources of ARGs is still a big challenge due to the complex interaction of multiple sources and contaminants in the environment with changing dynamics. In this study, we addressed this problem and focused on identifying the potential sources of ARGs in a peri-urban river by jointly utilizing two novel microbial source tracking methods. To attain the objective, sediment/water samples were collected from the peri-urban river and four ARG-associated ecotypes including effluents of sewage treatment plants (STPs), STP influent, chicken manures and pig manures. The high-throughput profilings of ARGs and microbial taxa in the river sediments and the four ecotypes were comprehensively characterized in combination of shotgun sequencing and metagenomic assembly analysis. CrAssphage, a recently-discovered DNA bacteriophage, was employed to track the impact of human fecal pollution on ARGs in the river sediments. Further, SourceTracker, a machine-learning classification tool, was used for quantifying the contributions of potential sources to ARGs in the river sediments based on the metagenomic signatures of ARGs and microbial taxa. In total, 888 ARG subtypes belonging to 29 ARG types were detected across all samples, including mcr-1 and a range of carbapenemases types. Statistical analyses suggested different ecotypes generally had distinct profiles of both ARGs and microbial taxa, while the ARG compositions were significantly correlated with the microbial community. Source tracking with crAssphage showed the presence of ARGs in the river sediments might be largely impacted by the extent of human fecal pollution, which was also confirmed by the analyses of SourceTracker that the discharge from STPs was the largest contributor of ARGs (81.6-92.1%) and microbes (49.3-68.1%) in the river sediments. Results of the study can help us to better understand the characterization of ARGs in the peri-urban ecosystem and to design effective prevention and control strategies for reducing ARG dissemination.}, }
@article {pmid31500892, year = {2019}, author = {Sims, TT and Colbert, LE and Zheng, J and Delgado Medrano, AY and Hoffman, KL and Ramondetta, L and Jazaeri, A and Jhingran, A and Schmeler, KM and Daniel, CR and Klopp, A}, title = {Gut microbial diversity and genus-level differences identified in cervical cancer patients versus healthy controls.}, journal = {Gynecologic oncology}, volume = {155}, number = {2}, pages = {237-244}, pmid = {31500892}, issn = {1095-6859}, support = {T32 CA101642/CA/NCI NIH HHS/United States ; P30 CA016672/CA/NCI NIH HHS/United States ; }, mesh = {Aged ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Lymphatic Metastasis ; Middle Aged ; Neoplasm Staging ; Prospective Studies ; Uterine Cervical Neoplasms/genetics/*microbiology/pathology ; }, abstract = {OBJECTIVES: The aim of this study was to characterize variation in the gut microbiome of women with locally advanced cervical cancer and compare it to healthy controls.<br><br>METHODS: We characterized the 16S rDNA fecal microbiome in 42 cervical cancer patients and 46 healthy female controls. Shannon diversity index (SDI) was used to evaluate alpha (within sample) diversity. Beta (between sample) diversity was examined using principle coordinate analysis (PCoA) of unweighted Unifrac distances. Relative abundance of microbial taxa was compared between samples using Linear Discriminant Analysis Effect Size (LEfSe).<br><br>RESULTS: Within cervical cancer patients, bacterial alpha diversity was positively correlated with age (p = 0.22) but exhibited an inverse relationship in control subjects (p < 0.01). Alpha diversity was significantly higher in cervical cancer patients as compared to controls (p < 0.05), though stratification by age suggested this relationship was restricted to older women (>50 years; p < 0.01). Beta diversity (unweighted Unifrac; p < 0.01) also significantly differed between cervical cancer patients and controls. Based on age- and race-adjusted LEfSe analysis, multiple taxa significantly differed between cervical cancer patients and controls. Prevotella, Porphyromonas, and Dialister were significantly enriched in cervical cancer patients, while Bacteroides, Alistipes and members of the Lachnospiracea family were significantly enriched in healthy subjects.<br><br>CONCLUSION: Our study suggests differences in gut microbiota diversity and composition between cervical cancer patients and controls. Associations within the gut microbiome by age may reflect etiologic/clinical differences. These findings provide rationale for further study of the gut microbiome in cervical cancer.}, }
@article {pmid31027194, year = {2019}, author = {Teigen, LM and Geng, Z and Sadowsky, MJ and Vaughn, BP and Hamilton, MJ and Khoruts, A}, title = {Dietary Factors in Sulfur Metabolism and Pathogenesis of Ulcerative Colitis.}, journal = {Nutrients}, volume = {11}, number = {4}, pages = {}, doi = {10.3390/nu11040931}, pmid = {31027194}, issn = {2072-6643}, support = {2017-2019//Allen Foundation/ ; 2017-2019//Healthy Foods, Healthy Lives Institute, University of Minnesota/ ; }, mesh = {Bacteria/metabolism ; Colitis, Ulcerative/*metabolism/*microbiology/pathology ; *Diet ; Gastrointestinal Microbiome ; Humans ; Sulfur/*metabolism ; }, abstract = {The biogeography of inflammation in ulcerative colitis (UC) suggests a proximal to distal concentration gradient of a toxin. Hydrogen sulfide (H2S) has long been considered one such toxin candidate, and dietary sulfur along with the abundance of sulfate reducing bacteria (SRB) were considered the primary determinants of H2S production and clinical course of UC. The metabolic milieu in the lumen of the colon, however, is the result of a multitude of factors beyond dietary sulfur intake and SRB abundance. Here we present an updated formulation of the H2S toxin hypothesis for UC pathogenesis, which strives to incorporate the interdependency of diet composition and the metabolic activity of the entire colon microbial community. Specifically, we suggest that the increasing severity of inflammation along the proximal-to-distal axis in UC is due to the dilution of beneficial factors, concentration of toxic factors, and changing detoxification capacity of the host, all of which are intimately linked to the nutrient flow from the diet.}, }
@article {pmid30176961, year = {2018}, author = {Xu, H and Li, X and Zheng, X and Xia, Y and Fu, Y and Li, X and Qian, Y and Zou, J and Zhao, A and Guan, J and Gu, M and Yi, H and Jia, W and Yin, S}, title = {Pediatric Obstructive Sleep Apnea is Associated With Changes in the Oral Microbiome and Urinary Metabolomics Profile: A Pilot Study.}, journal = {Journal of clinical sleep medicine : JCSM : official publication of the American Academy of Sleep Medicine}, volume = {14}, number = {9}, pages = {1559-1567}, pmid = {30176961}, issn = {1550-9397}, mesh = {Child ; Child, Preschool ; China ; Chromatography, Liquid ; Female ; Humans ; Male ; Mass Spectrometry ; Metabolome/*physiology ; Metabolomics/*methods ; Microbiota/*physiology ; Mouth/*microbiology ; Pilot Projects ; Sleep Apnea, Obstructive/*microbiology/*urine ; }, abstract = {STUDY OBJECTIVES: Several cross-sectional studies have reported associations between oral diseases and obstructive sleep apnea (OSA). However, there have been no reports regarding the structure and composition of the oral microbiota with simultaneous evaluation of potential associations with perturbed metabolic profiles in pediatric OSA.<br><br>METHODS: An integrated approach, combining metagenomics based on high-throughput 16S rRNA gene sequencing, and metabolomics based on ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry and gas chromatography coupled with time-of-flight mass spectrometry, was used to evaluate the oral microbiome and the urinary metabolome.<br><br>RESULTS: 16S rRNA gene sequencing indicated that the oral microbiome composition was significantly perturbed in pediatric OSA compared with normal controls, especially with regard to Firmicutes, Proteobacteria, Bacteroidetes, Fusobacteria, and Actinobacteria. Moreover, metabolomics profiling indicated that 57 metabolites, 5 of which were metabolites related to the microflora of the digestive tract, were differentially present in the urine of pediatric patients with OSA and controls. Co-inertia and correlation analyses revealed that several oral microbiome changes were correlated with urinary metabolite perturbations in pediatric OSA. However, this correlation relationship does not imply causality.<br><br>CONCLUSIONS: High-throughput sequencing revealed that the oral microbiome composition and function were significantly altered in pediatric OSA. Further studies are needed to confirm and determine the mechanisms underlying these findings.}, }
@article {pmid30951921, year = {2019}, author = {De Jode, A and David, R and Haguenauer, A and Cahill, AE and Erga, Z and Guillemain, D and Sartoretto, S and Rocher, C and Selva, M and Le Gall, L and Féral, JP and Chenuil, A}, title = {From seascape ecology to population genomics and back. Spatial and ecological differentiation among cryptic species of the red algae Lithophyllum stictiforme/L. cabiochiae, main bioconstructors of coralligenous habitats.}, journal = {Molecular phylogenetics and evolution}, volume = {137}, number = {}, pages = {104-113}, doi = {10.1016/j.ympev.2019.04.005}, pmid = {30951921}, issn = {1095-9513}, mesh = {Animals ; Anthozoa/*physiology ; Biodiversity ; *Ecosystem ; Genetic Variation ; Genetics, Population ; Haplotypes/genetics ; Mediterranean Sea ; *Metagenomics ; Phylogeny ; Principal Component Analysis ; Rhodophyta/*genetics ; Species Specificity ; }, abstract = {Ecosystem engineering species alter the physical structure of their environment and can create or modify habitats, having a massive impact on local biodiversity. Coralligenous reefs are highly diverse habitats endemic to the Mediterranean Sea built by calcareous benthic organisms among which Crustose Coralline Algae are the main engineering species. We analyzed the diversity of Lithophyllum stictiforme or L. cabiochiae in coralligenous habitats combining a multiple barcode and a population genomics approach with seascape features. Population genomics allowed disentangling pure spatial effects from environmental effects. We found that these taxa form a complex of eight highly divergent cryptic species that are easily identifiable using classic barcode markers (psbA, LSU, COI). Three factors have a significant effect on the relative abundances of these cryptic species: the location along the French Mediterranean coast, depth and Photosynthetic Active Radiation (PAR). The analysis of around 5000 SNPs for the most abundant species revealed genetic differentiation among localities in the Bay of Marseille but no differentiation between depths within locality. Thus, the effect of depth and PAR on cryptic species communities is not a consequence of restricted connectivity but rather due to differential settlement or survival among cryptic species. This differential is more likely driven by irradiance levels rather than by pressure or temperature. Both the genetic and species diversity patterns are congruent with the main patterns of currents in the Bay. Ecological differentiation among these engineering cryptic species, sensitive to ocean warming and acidification, could have important consequences on the diversity and structure of the coralligenous communities.}, }
@article {pmid30915280, year = {2019}, author = {Wei, Y and Shi, M and Zhen, M and Wang, C and Hu, W and Nie, Y and Wu, X}, title = {Comparison of Subgingival and Buccal Mucosa Microbiome in Chronic and Aggressive Periodontitis: A Pilot Study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {53}, doi = {10.3389/fcimb.2019.00053}, pmid = {30915280}, issn = {2235-2988}, mesh = {Adult ; Aggressive Periodontitis/*microbiology ; Chronic Disease ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Female ; Gingiva/*microbiology ; Humans ; Male ; Metagenomics ; *Microbiota ; Mouth Mucosa/*microbiology ; Phylogeny ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {Periodontal microorganisms not only colonize subgingival pockets, but also are detected on various mucous membranes in patients with periodontitis. The object of this pilot study was, using the next-generation sequencing of 16S RNA gene, to characterize the microbiota in two oral habitats (buccal mucosas and subgingival pockets) in patients with different forms of periodontitis. Thirty-two buccal swab samples and 113 subgingival samples were obtained from eleven subjects with chronic periodontitis (ChP), twelve subjects with aggressive periodontitis (AgP), and nine periodontally healthy individuals (HP). Using Miseq Sequencing of 16S rRNA gene, we found that the subgingival and buccal mucosa microbiome of ChP and AgP patients both differed from HP. Meanwhile, Veillonella, Treponema, Filifactor, Fretibacterium, Peptostreptococcaceae_[XI][G-6], Peptostreptococcaceae_[XI][G-5], Bacteroidetes_[G-5], Bacteroidetes_[G-3], Peptostreptococcaceae_[XI][G-4], Peptostreptococcaceae_[XI][G-2] significantly increased both in buccal and subgingival plaque samples in periodontitis subjects (ChP and AgP) compared with HP. Moreover, the results based on the Unweighted UniFrac distance showed that buccal and subgingival plaque samples from the same individuals show higher community divergence than same habitats from different subject samples. This study demonstrated that the microbiome of buccal mucosa can be influenced by periodontitis. However, subgingival and buccal mucosa microbiome seem to be characterized by species-specific colonization patterns. This pilot study provides a glimpse at the changes of subgingival and buccal mucosa associated with periodontitis from a holistic view. Further studies should be taken to illuminate the interplay between these detected changes and periodontitis development.}, }
@article {pmid30881924, year = {2019}, author = {Tribble, GD and Angelov, N and Weltman, R and Wang, BY and Eswaran, SV and Gay, IC and Parthasarathy, K and Dao, DV and Richardson, KN and Ismail, NM and Sharina, IG and Hyde, ER and Ajami, NJ and Petrosino, JF and Bryan, NS}, title = {Frequency of Tongue Cleaning Impacts the Human Tongue Microbiome Composition and Enterosalivary Circulation of Nitrate.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {39}, doi = {10.3389/fcimb.2019.00039}, pmid = {30881924}, issn = {2235-2988}, mesh = {Anti-Bacterial Agents/*administration &amp; dosage ; Blood Pressure/drug effects ; Chlorhexidine/*administration &amp; dosage ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Healthy Volunteers ; Humans ; Microbiota/*drug effects ; Mouthwashes/administration &amp; dosage ; Nitrates/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Tongue/*microbiology ; }, abstract = {The oral microbiome has the potential to provide an important symbiotic function in human blood pressure physiology by contributing to the generation of nitric oxide (NO), an essential cardiovascular signaling molecule. NO is produced by the human body via conversion of arginine to NO by endogenous nitric oxide synthase (eNOS) but eNOS activity varies by subject. Oral microbial communities are proposed to supplement host NO production by reducing dietary nitrate to nitrite via bacterial nitrate reductases. Unreduced dietary nitrate is delivered to the oral cavity in saliva, a physiological process termed the enterosalivary circulation of nitrate. Previous studies demonstrated that disruption of enterosalivary circulation via use of oral antiseptics resulted in increases in systolic blood pressure. These previous studies did not include detailed information on the oral health of enrolled subjects. Using 16S rRNA gene sequencing and analysis, we determined whether introduction of chlorhexidine antiseptic mouthwash for 1 week was associated with changes in tongue bacterial communities and resting systolic blood pressure in healthy normotensive individuals with documented oral hygiene behaviors and free of oral disease. Tongue cleaning frequency was a predictor of chlorhexidine-induced changes in systolic blood pressure and tongue microbiome composition. Twice-daily chlorhexidine usage was associated with a significant increase in systolic blood pressure after 1 week of use and recovery from use resulted in an enrichment in nitrate-reducing bacteria on the tongue. Individuals with relatively high levels of bacterial nitrite reductases had lower resting systolic blood pressure. These results further support the concept of a symbiotic oral microbiome contributing to human health via the enterosalivary nitrate-nitrite-NO pathway. These data suggest that management of the tongue microbiome by regular cleaning together with adequate dietary intake of nitrate provide an opportunity for the improvement of resting systolic blood pressure.}, }
@article {pmid30838178, year = {2019}, author = {Nearing, JT and Connors, J and Whitehouse, S and Van Limbergen, J and Macdonald, T and Kulkarni, K and Langille, MGI}, title = {Infectious Complications Are Associated With Alterations in the Gut Microbiome in Pediatric Patients With Acute Lymphoblastic Leukemia.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {28}, doi = {10.3389/fcimb.2019.00028}, pmid = {30838178}, issn = {2235-2988}, mesh = {Child ; Child, Preschool ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Dysbiosis/*complications ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Male ; Metagenomics ; *Microbiota ; Opportunistic Infections/*microbiology ; Phylogeny ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/*complications ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Acute lymphoblastic leukemia is the most common pediatric cancer. Fortunately, survival rates exceed 90%, however, infectious complications remain a significant issue that can cause reductions in the quality of life and prognosis of patients. Recently, numerous studies have linked shifts in the gut microbiome composition to infection events in various hematological malignances including acute lymphoblastic leukemia (ALL). These studies have been limited to observing broad taxonomic changes using 16S rRNA gene profiling, while missing possible differences within microbial functions encoded by individual species. In this study we present the first combined 16S rRNA gene and metagenomic shotgun sequencing study on the gut microbiome of an independent pediatric ALL cohort during treatment. In this study we found distinctive differences in alpha diversity and beta diversity in samples from patients with infectious complications in the first 6 months of therapy. We were also able to find specific species and functional pathways that were significantly different in relative abundance between samples that came from patients with infectious complications. Finally, machine learning models based on patient metadata and bacterial species were able to classify samples with high accuracy (84.09%), with bacterial species being the most important classifying features. This study strengthens our understanding of the association between infection and pediatric acute lymphoblastic leukemia treatment and warrants further investigation in the future.}, }
@article {pmid30189365, year = {2018}, author = {Zhou, J and Tang, L and Shen, CL and Wang, JS}, title = {Green tea polyphenols modify gut-microbiota dependent metabolisms of energy, bile constituents and micronutrients in female Sprague-Dawley rats.}, journal = {The Journal of nutritional biochemistry}, volume = {61}, number = {}, pages = {68-81}, doi = {10.1016/j.jnutbio.2018.07.018}, pmid = {30189365}, issn = {1873-4847}, support = {R24 TW009489/TW/FIC NIH HHS/United States ; U01 AT006691/AT/NCCIH NIH HHS/United States ; }, mesh = {Animals ; Bile/drug effects/metabolism ; Dose-Response Relationship, Drug ; Energy Metabolism/*drug effects ; Female ; Gastrointestinal Contents/chemistry ; Gastrointestinal Microbiome/*drug effects/genetics/physiology ; Micronutrients/metabolism ; Polyphenols/administration &amp; dosage/*pharmacology ; Rats, Sprague-Dawley ; Tea/*chemistry ; }, abstract = {Our recent metagenomics analysis has uncovered remarkable modifying effects of green tea polyphenols (GTP) on gut-microbiota community structure and energy conversion related gene orthologs in rats. How these genomic changes could further influence host health is still unclear. In this work, the alterations of gut-microbiota dependent metabolites were studied in the GTP-treated rats. Six groups of female SD rats (n=12/group) were administered drinking water containing 0%, 0.5%, and 1.5% GTP (wt/vol). Their gut contents were collected at 3 and 6 months and were analyzed via high performance liquid chromatography (HPLC) and gas chromatography (GC)-mass spectrometry (MS). GC-MS based metabolomics analysis captured 2668 feature, and 57 metabolites were imputatively from top 200 differential features identified via NIST fragmentation database. A group of key metabolites were quantitated using standard calibration methods. Compared with control, the elevated components in the GTP-treated groups include niacin (8.61-fold), 3-phenyllactic acid (2.20-fold), galactose (3.13-fold), mannose (2.05-fold), pentadecanoic acid (2.15-fold), lactic acid (2.70-fold), and proline (2.15-fold); the reduced components include cholesterol (0.29-fold), cholic acid (0.62-fold), deoxycholic acid (0.41-fold), trehalose (0.14-fold), glucose (0.46-fold), fructose (0.12-fold), and alanine (0.61-fold). These results were in line with the genomic alterations of gut-microbiome previously discovered by metagenomics analysis. The alterations of these metabolites suggested the reduction of calorific carbohydrates, elevation of vitamin production, decreases of bile constituents, and modified metabolic pattern of amino acids in the GTP-treated animals. Changes in gut-microbiota associated metabolism may be a major contributor to the anti-obesity function of GTP.}, }
@article {pmid31413226, year = {2019}, author = {Ward, LM and Idei, A and Nakagawa, M and Ueno, Y and Fischer, WW and McGlynn, SE}, title = {Geochemical and Metagenomic Characterization of Jinata Onsen, a Proterozoic-Analog Hot Spring, Reveals Novel Microbial Diversity including Iron-Tolerant Phototrophs and Thermophilic Lithotrophs.}, journal = {Microbes and environments}, volume = {34}, number = {3}, pages = {278-292}, pmid = {31413226}, issn = {1347-4405}, mesh = {Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; *Biodiversity ; Biomass ; Chemoautotrophic Growth ; Geography ; Hot Springs/*chemistry/*microbiology ; Iron/analysis/*metabolism ; Metagenomics ; Microbiota/genetics ; Oxygen/analysis/metabolism ; Phototrophic Processes ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Temperature ; }, abstract = {Hydrothermal systems, including terrestrial hot springs, contain diverse geochemical conditions that vary over short spatial scales due to progressive interactions between reducing hydrothermal fluids, the oxygenated atmosphere, and, in some cases, seawater. At Jinata Onsen on Shikinejima Island, Japan, an intertidal, anoxic, iron-rich hot spring mixes with the oxygenated atmosphere and seawater over short spatial scales, creating diverse chemical potentials and redox pairs over a distance of ~10 m. We characterized geochemical conditions along the outflow of Jinata Onsen as well as the microbial communities present in biofilms, mats, and mineral crusts along its traverse using 16S rRNA gene amplicon and genome-resolved shotgun metagenomic sequencing. Microbial communities significantly changed downstream as temperatures and dissolved iron concentrations decreased and dissolved oxygen increased. Biomass was more limited near the spring source than downstream, and primary productivity appeared to be fueled by the oxidation of ferrous iron and molecular hydrogen by members of Zetaproteobacteria and Aquificae. The microbial community downstream was dominated by oxygenic Cyanobacteria. Cyanobacteria are abundant and active even at ferrous iron concentrations of ~150 μM, which challenges the idea that iron toxicity limited cyanobacterial expansion in Precambrian oceans. Several novel lineages of Bacteria are also present at Jinata Onsen, including previously uncharacterized members of the phyla Chloroflexi and Calditrichaeota, positioning Jinata Onsen as a valuable site for the future characterization of these clades.}, }
@article {pmid30636326, year = {2019}, author = {Lucek, K and Gompert, Z and Nosil, P}, title = {The role of structural genomic variants in population differentiation and ecotype formation in Timema cristinae walking sticks.}, journal = {Molecular ecology}, volume = {28}, number = {6}, pages = {1224-1237}, doi = {10.1111/mec.15016}, pmid = {30636326}, issn = {1365-294X}, support = {R/129639//H2020 European Research Council/International ; P2BEP3_152103//Swiss National Science Foundation/Switzerland ; }, mesh = {Adaptation, Biological/genetics ; Animals ; *Ecotype ; Genetic Drift ; Genetics, Population ; Genome/*genetics ; Genomic Structural Variation/*genetics ; Genomics ; Metagenomics/methods ; Neoptera/*genetics ; Selection, Genetic ; }, abstract = {Theory predicts that structural genomic variants such as inversions can promote adaptive diversification and speciation. Despite increasing empirical evidence that adaptive divergence can be triggered by one or a few large inversions, the degree to which widespread genomic regions under divergent selection are associated with structural variants remains unclear. Here we test for an association between structural variants and genomic regions that underlie parallel host-plant-associated ecotype formation in Timema cristinae stick insects. Using mate-pair resequencing of 20 new whole genomes we find that moderately sized structural variants such as inversions, deletions and duplications are widespread across the genome, being retained as standing variation within and among populations. Using 160 previously published, standard-orientation whole genome sequences we find little to no evidence that the DNA sequences within inversions exhibit accentuated differentiation between ecotypes. In contrast, a formerly described large region of reduced recombination that harbours genes controlling colour-pattern exhibits evidence for accentuated differentiation between ecotypes, which is consistent with differences in the frequency of colour-pattern morphs between host-associated ecotypes. Our results suggest that some types of structural variants (e.g., large inversions) are more likely to underlie adaptive divergence than others, and that structural variants are not required for subtle yet genome-wide genetic differentiation with gene flow.}, }
@article {pmid31766550, year = {2019}, author = {Jonge, PA and Meijenfeldt, FABV and Rooijen, LEV and Brouns, SJJ and Dutilh, BE}, title = {Evolution of BACON Domain Tandem Repeats in crAssphage and Novel Gut Bacteriophage Lineages.}, journal = {Viruses}, volume = {11}, number = {12}, pages = {}, doi = {10.3390/v11121085}, pmid = {31766550}, issn = {1999-4915}, support = {864.14.004//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 016.160.63//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 639707/ERC_/European Research Council/International ; 864.11.005//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; }, abstract = {The human gut contains an expanse of largely unstudied bacteriophages. Among the most common are crAss-like phages, which were predicted to infect Bacteriodetes hosts. CrAssphage, the first crAss-like phage to be discovered, contains a protein encoding a Bacteroides-associated carbohydrate-binding often N-terminal (BACON) domain tandem repeat. Because protein domain tandem repeats are often hotspots of evolution, BACON domains may provide insight into the evolution of crAss-like phages. Here, we studied the biodiversity and evolution of BACON domains in bacteriophages by analysing over 2 million viral contigs. We found a high biodiversity of BACON in seven gut phage lineages, including five known crAss-like phage lineages and two novel gut phage lineages that are distantly related to crAss-like phages. In three BACON-containing phage lineages, we found that BACON domain tandem repeats were associated with phage tail proteins, suggestive of a possible role of these repeats in host binding. In contrast, individual BACON domains that did not occur in tandem were not found in the proximity of tail proteins. In two lineages, tail-associated BACON domain tandem repeats evolved largely through horizontal transfer of separate domains. In the third lineage that includes the prototypical crAssphage, the tandem repeats arose from several sequential domain duplications, resulting in a characteristic tandem array that is distinct from bacterial BACON domains. We conclude that phage tail-associated BACON domain tandem repeats have evolved in at least two independent cases in gut bacteriophages, including in the widespread gut phage crAssphage.}, }
@article {pmid31234773, year = {2019}, author = {Das, P and Marcišauskas, S and Ji, B and Nielsen, J}, title = {Metagenomic analysis of bile salt biotransformation in the human gut microbiome.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {517}, doi = {10.1186/s12864-019-5899-3}, pmid = {31234773}, issn = {1471-2164}, support = {HEALTH-F4-2012-305312//METACARDIS/ ; }, mesh = {Bacteria/classification/genetics/*metabolism ; Bacterial Proteins/genetics ; Bile Acids and Salts/*metabolism ; Biotransformation/genetics ; Dysbiosis/metabolism/microbiology ; Firmicutes/genetics/metabolism ; Gastrointestinal Microbiome/*genetics ; Humans ; Inflammatory Bowel Diseases/metabolism/microbiology ; Metagenomics ; }, abstract = {BACKGROUND: In the biochemical milieu of human colon, bile acids act as signaling mediators between the host and its gut microbiota. Biotransformation of primary to secondary bile acids have been known to be involved in the immune regulation of human physiology. Several 16S amplicon-based studies with inflammatory bowel disease (IBD) subjects were found to have an association with the level of fecal bile acids. However, a detailed investigation of all the bile salt biotransformation genes in the gut microbiome of healthy and IBD subjects has not been performed.<br><br>RESULTS: Here, we report a comprehensive analysis of the bile salt biotransformation genes and their distribution at the phyla level. Based on the analysis of shotgun metagenomes, we found that the IBD subjects harbored a significantly lower abundance of these genes compared to the healthy controls. Majority of these genes originated from Firmicutes in comparison to other phyla. From metabolomics data, we found that the IBD subjects were measured with a significantly low level of secondary bile acids and high levels of primary bile acids compared to that of the healthy controls.<br><br>CONCLUSIONS: Our bioinformatics-driven approach of identifying bile salt biotransformation genes predicts the bile salt biotransformation potential in the gut microbiota of IBD subjects. The functional level of dysbiosis likely contributes to the variation in the bile acid pool. This study sets the stage to envisage potential solutions to modulate the gut microbiome with the objective to restore the bile acid pool in the gut.}, }
@article {pmid30953072, year = {2019}, author = {De Cesare, A and Faria do Valle, Ì and Sala, C and Sirri, F and Astolfi, A and Castellani, G and Manfreda, G}, title = {Effect of a low protein diet on chicken ceca microbiome and productive performances.}, journal = {Poultry science}, volume = {98}, number = {9}, pages = {3963-3976}, doi = {10.3382/ps/pez132}, pmid = {30953072}, issn = {1525-3171}, mesh = {Animal Feed/analysis ; Animals ; Bacteria/classification/*genetics ; Bacterial Physiological Phenomena ; Cecum/microbiology ; Chickens/*microbiology ; Diet/veterinary ; Diet, Protein-Restricted/*veterinary ; Gastrointestinal Microbiome/drug effects/genetics/*physiology ; Male ; *Metagenome ; Time Factors ; }, abstract = {The aim of this study was to investigate the impact of supplementation of a low protein diet on ceca microbiome and productive performances of broiler chickens. A total of 1,170 one-day-old male chicks (Ross 308) were divided in 2 diet groups and reared in the same conditions up to 42 D. Birds belonging to the control group were fed a basal diet. Birds belonging to the low protein group the basal diet with a reduced level of crude protein (-7%). Cecum contents from randomly selected birds were collected at 14 and 42 D within each diet group, submitted to DNA extraction and then tested by shotgun metagenomic sequencing. Abundances of species belonging to Actinobacteria and Proteobacteria were mainly affected by the diet as well as interaction between diet and time, while species belonging to Firmicutes and Cyanobacteria changed mainly according to the age of the birds. At family level, Lactobacillaceae significantly decreased in the low protein group up to 14 D. However, at the end of the rearing period the same family was significantly higher in the low protein group. The most abundant functional genes, represented by cystine desulfurase, alpha-galactosidase, and serine hydroxymethyltransferase, displayed comparable abundances in both diet groups, although significative differences were identified for less abundant functional genes at both sampling times. Birds fed control and low protein diets showed similar productive performances. However, in the finisher phase, feed conversion rate was significantly better in chickens fed the low protein diet. Overall, this study showed that a reduced intake of crude protein in broilers increases the abundance of Lactobacillaceae in the ceca over time and this seems to be linked to a better feed conversion rate between 36 and 42 D. A reduced intake of crude protein in chicken production can help to improve exploitation of edible resources, while reducing the emission of nitrogen pollutants in the environment.}, }
@article {pmid30661755, year = {2019}, author = {Pasolli, E and Asnicar, F and Manara, S and Zolfo, M and Karcher, N and Armanini, F and Beghini, F and Manghi, P and Tett, A and Ghensi, P and Collado, MC and Rice, BL and DuLong, C and Morgan, XC and Golden, CD and Quince, C and Huttenhower, C and Segata, N}, title = {Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle.}, journal = {Cell}, volume = {176}, number = {3}, pages = {649-662.e20}, doi = {10.1016/j.cell.2019.01.001}, pmid = {30661755}, issn = {1097-4172}, support = {MR/L015080/1//Medical Research Council/United Kingdom ; U54 DE023798/DE/NIDCR NIH HHS/United States ; R01 HG005220/HG/NHGRI NIH HHS/United States ; MR/M50161X/1//Medical Research Council/United Kingdom ; R24 DK110499/DK/NIDDK NIH HHS/United States ; }, mesh = {Big Data ; Genetic Variation/genetics ; Geography ; Humans ; Life Style ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {The body-wide human microbiome plays a role in health, but its full diversity remains uncharacterized, particularly outside of the gut and in international populations. We leveraged 9,428 metagenomes to reconstruct 154,723 microbial genomes (45% of high quality) spanning body sites, ages, countries, and lifestyles. We recapitulated 4,930 species-level genome bins (SGBs), 77% without genomes in public repositories (unknown SGBs [uSGBs]). uSGBs are prevalent (in 93% of well-assembled samples), expand underrepresented phyla, and are enriched in non-Westernized populations (40% of the total SGBs). We annotated 2.85 M genes in SGBs, many associated with conditions including infant development (94,000) or Westernization (106,000). SGBs and uSGBs permit deeper microbiome analyses and increase the average mappability of metagenomic reads from 67.76% to 87.51% in the gut (median 94.26%) and 65.14% to 82.34% in the mouth. We thus identify thousands of microbial genomes from yet-to-be-named species, expand the pangenomes of human-associated microbes, and allow better exploitation of metagenomic technologies.}, }
@article {pmid30292825, year = {2018}, author = {Minty, M and Canceill, T and Lê, S and Dubois, P and Amestoy, O and Loubieres, P and Christensen, JE and Champion, C and Azalbert, V and Grasset, E and Hardy, S and Loubes, JM and Mallet, JP and Tercé, F and Vergnes, JN and Burcelin, R and Serino, M and Diemer, F and Blasco-Baque, V}, title = {Oral health and microbiota status in professional rugby players: A case-control study.}, journal = {Journal of dentistry}, volume = {79}, number = {}, pages = {53-60}, doi = {10.1016/j.jdent.2018.10.001}, pmid = {30292825}, issn = {1879-176X}, mesh = {*Athletes ; Case-Control Studies ; Football ; Humans ; *Microbiota ; *Oral Health ; Sports ; }, abstract = {OBJECTIVE: Elite athletes are prone to develop oral diseases, which could increase the risk for injuries. The aim of this study was to evaluate the oral health and the composition of oral microbiota of elite rugby players compared to the general population.<br><br>METHODS: We set up a case-control study by screening 24 professional rugby players (PRG) and 22 control patients (CG) for dental and gingival examinations and performed a taxonomic analysis and a predicted functional analysis of oral microbiota.<br><br>RESULTS: The Decay, Missing and Filled (DMF) teeth index (5.54 ± 6.18 versus 2.14 ± 3.01; p = 0.01) and the frequency of gingivitis (58,33% versus 13.63%) were significantly increased in PRG compared to CG. PRG were characterized by a dysbiotic oral microbiota (Shannon Index: 3.32 ± 0.62 in PRG versus 3.79 ± 0.68 in CG; p = 0.03) with an increase of Streptococcus (58.43 ± 16.84 versus 42.60 ± 17.45; p = 0.005), the main genus implicated in caries. Predicted metagenomics of oral microbiota in rugby players was suggestive of a cariogenic metagenome favourable to the development of caries.<br><br>CONCLUSIONS: Our study shows that the oral health of PRG was poorer than the general population. PRG are characterized by a dysbiotic oral microbiota with an increase of the relative abundance of Streptococcus genus, positively correlated to the weight and negatively correlated to the diversity of oral microbiota.<br><br>CLINICAL SIGNIFICANCE: Dental screening should be included in the medical follow-up of professional rugby players as a part of their health management. New strategies such as using probiotics like Lactobacillus could help to control the dysbiosis of oral microbiota.}, }
@article {pmid31465907, year = {2019}, author = {Nnadozie, CF and Odume, ON}, title = {Freshwater environments as reservoirs of antibiotic resistant bacteria and their role in the dissemination of antibiotic resistance genes.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {254}, number = {Pt B}, pages = {113067}, doi = {10.1016/j.envpol.2019.113067}, pmid = {31465907}, issn = {1873-6424}, mesh = {Anti-Bacterial Agents ; Bacteria/genetics ; Drug Resistance, Bacterial/*genetics ; Fresh Water/*microbiology ; *Genes, Bacterial ; Humans ; Lakes ; Metagenomics ; Methicillin-Resistant Staphylococcus aureus/genetics ; Microbiota ; Polymerase Chain Reaction ; Rivers ; Sewage ; Water Microbiology ; }, abstract = {Freshwater environments are susceptible to possible contamination by residual antibiotics that are released through different sources, such as agricultural runoffs, sewage discharges and leaching from nearby farms. Freshwater environment can thus become reservoirs where an antibiotic impact microorganisms, and is an important public health concern. Degradation and dilution processes are fundamental for predicting the actual risk of antibiotic resistance dissemination from freshwater reservoirs. This study reviews major approaches for detecting and quantifying antibiotic resistance bacteria (ARBs) and genes (ARGs) in freshwater and their prevalence in these environments. Finally, the role of dilution, degradation, transmission and the persistence and fate of ARB/ARG in these environments are also reviewed. Culture-based single strain approaches and molecular techniques that include polymerase chain reaction (PCR), quantitative polymerase chain reaction (qPCR) and metagenomics are techniques for quantifying ARB and ARGs in freshwater environments. The level of ARBs is extremely high in most of the river systems (up to 98% of the total detected bacteria), followed by lakes (up to 77% of the total detected bacteria), compared to dam, pond, and spring (<1%). Of most concern is the occurrence of extended-spectrum β-lactamase producing Enterobacteriaceae, methicillin resistant Staphylococcus aureus (MRSA) and vancomycin resistant Enterococcus (VRE), which cause highly epidemic infections. Dilution and natural degradation do not completely eradicate ARBs and ARGs in the freshwater environment. Even if the ARBs in freshwater are effectively inactivated by sunlight, their ARG-containing DNA can still be intact and capable of transferring resistance to non-resistant strains. Antibiotic resistance persists and is preserved in freshwater bodies polluted with high concentrations of antibiotics. Direct transmission of indigenous freshwater ARBs to humans as well as their transitory insertion in the microbiota can occur. These findings are disturbing especially for people that rely on freshwater resources for drinking, crop irrigation, and food in form of fish.}, }
@article {pmid31300992, year = {2019}, author = {Sonthiphand, P and Ruangroengkulrith, S and Mhuantong, W and Charoensawan, V and Chotpantarat, S and Boonkaewwan, S}, title = {Metagenomic insights into microbial diversity in a groundwater basin impacted by a variety of anthropogenic activities.}, journal = {Environmental science and pollution research international}, volume = {26}, number = {26}, pages = {26765-26781}, doi = {10.1007/s11356-019-05905-5}, pmid = {31300992}, issn = {1614-7499}, support = {New Researcher Grant//Mahidol University/ ; MRG6080235//Thailand Research Fund (TRF) Grant/ ; }, mesh = {Anaerobiosis ; Arsenic/metabolism ; Bacteria/genetics ; Biodiversity ; Groundwater/*chemistry/*microbiology ; Metagenomics ; Methane/metabolism ; Microbiota/genetics/*physiology ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Thailand ; Water Pollutants, Chemical/analysis ; }, abstract = {Microbial communities in groundwater are diverse and each may respond differently to environmental change. The goal of this study was to investigate the diversity, abundance, and dynamics of microbial communities in impacted groundwater and correlate them to the corresponding land use and groundwater geochemistry, using an Illumina MiSeq platform targeting the V3 and V4 regions of the 16S rRNA gene. The resulting MiSeq sequencing revealed the co-occurrence patterns of both abundant and rare microbial taxa within an impacted groundwater basin. Proteobacteria were the most common groundwater-associated bacterial phylum, mainly composed of the classes Gammaproteobacteria, Betaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria. The phyla detected at less abundances were the Firmicutes, Bacteroidetes, Planctomycetes, Actinobacteria, OD1, and Nitrospirae. The members of detected groundwater microorganisms involved in natural biogeochemical processes such as nitrification, anammox, methane oxidation, sulfate reduction, and arsenic transformation. Some of the detected microorganisms were able to perform anaerobic degradation of organic pollutants. The resulting PCA indicates that major land usage within the sampling area seemed to be significantly linked to the groundwater microbial distributions. The distinct microbial pattern was observed in the groundwater collected from a landfill area. This study suggests that the combinations of anthropogenic and natural effects possibly led to a unique pattern of microbial diversity across different locations at the impacted groundwater basin.}, }
@article {pmid31028005, year = {2019}, author = {Zhao, S and Lieberman, TD and Poyet, M and Kauffman, KM and Gibbons, SM and Groussin, M and Xavier, RJ and Alm, EJ}, title = {Adaptive Evolution within Gut Microbiomes of Healthy People.}, journal = {Cell host &amp; microbe}, volume = {25}, number = {5}, pages = {656-667.e8}, doi = {10.1016/j.chom.2019.03.007}, pmid = {31028005}, issn = {1934-6069}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; }, mesh = {*Adaptation, Biological ; Adult ; Bacteroides fragilis/*genetics/*growth &amp; development ; Female ; *Gastrointestinal Microbiome ; Genetics, Population ; Healthy Volunteers ; Humans ; Male ; Metagenomics ; *Microbiota ; Mutation ; Selection, Genetic ; Young Adult ; }, abstract = {Natural selection shapes bacterial evolution in all environments. However, the extent to which commensal bacteria diversify and adapt within the human gut remains unclear. Here, we combine culture-based population genomics and metagenomics to investigate the within-microbiome evolution of Bacteroides fragilis. We find that intra-individual B. fragilis populations contain substantial de novo nucleotide and mobile element diversity, preserving years of within-person history. This history reveals multiple signatures of within-person adaptation, including parallel evolution in sixteen genes. Many of these genes are implicated in cell-envelope biosynthesis and polysaccharide utilization. Tracking evolutionary trajectories using near-daily metagenomic sampling, we find evidence for years-long coexistence in one subject despite adaptive dynamics. We used public metagenomes to investigate one adaptive mutation common in our cohort and found that it emerges frequently in Western, but not Chinese, microbiomes. Collectively, these results demonstrate that B. fragilis adapts within individual microbiomes, pointing to factors that promote long-term gut colonization.}, }
@article {pmid31006638, year = {2019}, author = {Kalan, LR and Meisel, JS and Loesche, MA and Horwinski, J and Soaita, I and Chen, X and Uberoi, A and Gardner, SE and Grice, EA}, title = {Strain- and Species-Level Variation in the Microbiome of Diabetic Wounds Is Associated with Clinical Outcomes and Therapeutic Efficacy.}, journal = {Cell host &amp; microbe}, volume = {25}, number = {5}, pages = {641-655.e5}, doi = {10.1016/j.chom.2019.03.006}, pmid = {31006638}, issn = {1934-6069}, support = {R01 NR009448/NR/NINR NIH HHS/United States ; R01 AR066663/AR/NIAMS NIH HHS/United States ; P30 AR069589/AR/NIAMS NIH HHS/United States ; T32 GM007229/GM/NIGMS NIH HHS/United States ; P20 NR018081/NR/NINR NIH HHS/United States ; R01 NR015639/NR/NINR NIH HHS/United States ; T32 AR007465/AR/NIAMS NIH HHS/United States ; R00 AR060873/AR/NIAMS NIH HHS/United States ; }, mesh = {Animals ; Anti-Infective Agents/*therapeutic use ; Coinfection/*microbiology/therapy ; *Debridement ; Diabetic Foot/*microbiology/therapy ; Disease Models, Animal ; Longitudinal Studies ; Mice ; *Microbiota ; Prospective Studies ; Treatment Outcome ; Wound Healing ; Wound Infection/*microbiology/therapy ; }, abstract = {Chronic wounds are a major complication of diabetes associated with high morbidity and health care expenditures. To investigate the role of colonizing microbiota in diabetic wound healing, clinical outcomes, and response to interventions, we conducted a longitudinal, prospective study of patients with neuropathic diabetic foot ulcers (DFU). Metagenomic shotgun sequencing revealed that strain-level variation of Staphylococcus aureus and genetic signatures of biofilm formation were associated with poor outcomes. Cultured wound isolates of S. aureus elicited differential phenotypes in mouse models that corresponded with patient outcomes, while wound &quot;bystanders&quot; such as Corynebacterium striatum and Alcaligenes faecalis, typically considered commensals or contaminants, also significantly impacted wound severity and healing. Antibiotic resistance genes were widespread, and debridement, rather than antibiotic treatment, significantly shifted the DFU microbiota in patients with more favorable outcomes. These findings suggest that the DFU microbiota may be a marker for clinical outcomes and response to therapeutic interventions.}, }
@article {pmid30937653, year = {2019}, author = {Parvathi, A and Jasna, V and Aswathy, VK and Nathan, VK and Aparna, S and Balachandran, KK}, title = {Microbial diversity in a coastal environment with co-existing upwelling and mud-banks along the south west coast of India.}, journal = {Molecular biology reports}, volume = {46}, number = {3}, pages = {3113-3127}, doi = {10.1007/s11033-019-04766-y}, pmid = {30937653}, issn = {1573-4978}, support = {OLP1709//National Institute of Oceanography, India/ ; }, mesh = {*Biodiversity ; Computational Biology/methods ; *Environmental Microbiology ; Geography ; India ; Metagenome ; Metagenomics/methods ; *Microbiota ; Phylogeny ; Seawater/*microbiology ; *Soil Microbiology ; *Water Microbiology ; }, abstract = {Upwelling and mud banks are two prominent oceanographic features in the coastal waters along the south west coast of India during the southwest monsoon (MON) season. The present study investigates the microbial diversity in the coastal environments of Alappuzha, India, where upwelling and mud banks co-exist. Water samples were collected from three stations, M1, M2, and M3, on a weekly basis to estimate the physico-chemical parameters and microbial abundance (MA). Presence of cold waters (< 26 °C) with high nitrate (6-8 µM) and low dissolved oxygen (5 µM) in the sub surface waters during monsoon (M) confirmed the presence of upwelling at all the three stations. Simultaneously, presence of unusually calm waters was seen at M2 alone during M indicating the formation of mud banks. The microbial diversity was determined from three stations, with distinct oceanographic conditions (M1: coastal reference station with only upwelling, M2: mud banks + upwelling, and M3: offshore reference station with only upwelling). The water samples were collected during two seasons, pre-monsoon (April) and M (July) and analysed using 16S rRNA-based Illumina high-throughput metagenomic sequencing. Proteobacteria was the most dominant phyla, followed by Bacteroidetes, Firmicutes, Cyanobacteria, Actinobacteria, and Verrucomicrobia in order, with variations in their relative abundance spatially and seasonally. Though the MA increased during M at all the stations, the relative abundance of most of the bacterial phyla except Proteobacteria decreased during M season. Interestingly, most of the sequences at M2 during mud banks were unclassified at the class level indicating the presence of unique microbial populations in this station. Prediction of metabolic activity revealed ammonia oxidation, nitrite reduction, sulphate reduction, xylan degradation, dehalogenation, chitin degradation, etc. as important functions. The metabolic activity throws light on the role of microbes in this environment thereby providing a system-scale perspective of microbial community interactions.}, }
@article {pmid30389965, year = {2018}, author = {Ammon, UV and Wood, SA and Laroche, O and Zaiko, A and Tait, L and Lavery, S and Inglis, GJ and Pochon, X}, title = {Combining morpho-taxonomy and metabarcoding enhances the detection of non-indigenous marine pests in biofouling communities.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {16290}, pmid = {30389965}, issn = {2045-2322}, mesh = {Animals ; Aquatic Organisms/genetics/*isolation &amp; purification ; Biodiversity ; *Biofouling ; DNA Barcoding, Taxonomic/methods ; Databases, Genetic/statistics &amp; numerical data ; *Introduced Species ; Metagenome/genetics ; Metagenomics/methods ; Microbiota/*genetics ; New Zealand ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; }, abstract = {Marine infrastructure can favor the spread of non-indigenous marine biofouling species by providing a suitable habitat for them to proliferate. Cryptic organisms or those in early life stages can be difficult to distinguish by conventional morphological taxonomy. Molecular tools, such as metabarcoding, may improve their detection. In this study, the ability of morpho-taxonomy and metabarcoding (18S rRNA and COI) using three reference databases (PR2, BOLD and NCBI) to characterize biodiversity and detect non-indigenous species (NIS) in biofouling was compared on 60 passive samplers deployed over summer and winter in a New Zealand marina. Highest resolution of metazoan taxa was identified using 18S rRNA assigned to PR2. There were higher assignment rates to NCBI reference sequences, but poorer taxonomic identification. Using all methods, 48 potential NIS were identified. Metabarcoding detected the largest proportion of those NIS: 77% via 18S rRNA/PR2 and NCBI and 35% via COI/BOLD and NCBI. Morpho-taxonomy detected an additional 14% of all identified NIS comprising mainly of bryozoan taxa. The data highlight several on-going challenges, including: differential marker resolution, primer biases, incomplete sequence reference databases, and variations in bioinformatic pipelines. Combining morpho-taxonomy and molecular analysis methods will likely enhance the detection of NIS from complex biofouling.}, }
@article {pmid30106217, year = {2019}, author = {Rubin, BER and Kautz, S and Wray, BD and Moreau, CS}, title = {Dietary specialization in mutualistic acacia-ants affects relative abundance but not identity of host-associated bacteria.}, journal = {Molecular ecology}, volume = {28}, number = {4}, pages = {900-916}, doi = {10.1111/mec.14834}, pmid = {30106217}, issn = {1365-294X}, support = {DEB-1311417//National Science Foundation/International ; DEB-1050243//National Science Foundation/International ; DEB-1442316//National Science Foundation/International ; }, mesh = {Acacia/*physiology ; Acetobacteraceae/physiology ; Animals ; Ants/*physiology ; Bartonella/physiology ; Herbivory/physiology ; Metagenomics ; Microbiota/physiology ; Nocardiaceae/physiology ; Symbiosis/genetics/physiology ; }, abstract = {Acacia-ant mutualists in the genus Pseudomyrmex nest obligately in acacia plants and, as we show through stable isotope analysis, feed at a remarkably low trophic level. Insects with diets such as these sometimes depend on bacterial symbionts for nutritional enrichment. We, therefore, examine the bacterial communities associated with acacia-ants in order to determine whether they host bacterial partners likely to contribute to their nutrition. Despite large differences in trophic position, acacia-ants and related species with generalized diets do not host distinct bacterial taxa. However, we find that a small number of previously undescribed bacterial taxa do differ in relative abundance between acacia-ants and generalists, including several Acetobacteraceae and Nocardiaceae lineages related to common insect associates. Comparisons with an herbivorous generalist, a parasite that feeds on acacias and a mutualistic species with a generalized diet show that trophic level is likely responsible for these small differences in bacterial community structure. While we did not experimentally test for a nutritional benefit to hosts of these bacterial lineages, metagenomic analysis reveals a Bartonella relative with an intact nitrogen-recycling pathway widespread across Pseudomyrmex mutualists and generalists. This taxon may be contributing to nitrogen enrichment of its ant hosts through urease activity and, concordant with an obligately host-associated lifestyle, appears to be experiencing genomewide relaxed selection. The lack of distinctiveness in bacterial communities across trophic level in this group of ants shows a remarkable ability to adjust to varied diets, possibly with assistance from these diverse ant-specific bacterial lineages.}, }
@article {pmid30006634, year = {2018}, author = {Kawai, K and Kamochi, R and Oiki, S and Murata, K and Hashimoto, W}, title = {Probiotics in human gut microbiota can degrade host glycosaminoglycans.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {10674}, pmid = {30006634}, issn = {2045-2322}, mesh = {Aldose-Ketose Isomerases/genetics/metabolism ; Bacteria/*enzymology/genetics ; Bacterial Proteins/genetics/isolation &amp; purification/*metabolism ; Caco-2 Cells ; Carbohydrate Dehydrogenases/genetics/metabolism ; Coculture Techniques ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; Glycosaminoglycans/*metabolism ; Humans ; Metagenomics ; Probiotics/*metabolism ; }, abstract = {Glycosaminoglycans (GAGs) (e.g. heparin, chondroitin sulfate, and hyaluronan) show various significant physiological functions as a major component of extracellular matrix in animals. Some bacteria target GAGs for adhesion and/or infection to host cells, although no probiotics have been known to degrade GAGs. Here, we show GAG degradation by probiotics from human gut microbiota and their adhesion to human intestinal cells through a GAG. GAG-degrading bacteria were isolated from human faeces and identified as Enterococcus faecium, and some typical probiotics such as Lactobacillus casei, Lactobacillus rhamnosus and Enterococcus faecalis were also found to degrade heparin. GAG-degrading lactobacilli and enterococci including the isolated E. faecium possessed a genetic cluster encoding GAG-degrading/metabolising enzymes in the bacterial genome. KduI and KduD enzymes encoded in the GAG cluster of L. rhamnosus functioned as 4-deoxy-l-threo-5-hexosulose-uronate ketol-isomerase and 2-keto-3-deoxy-d-gluconate dehydrogenase, respectively, both of which were crucial for GAG metabolism. GAG-degrading L. rhamnosus and E. faecium attached to human intestinal Caco-2 cells via heparin. Some species of Bacteroides, considered to be the next generation probiotics, degraded chondroitin sulfate C and hyaluronan, and genes coding for the Bacteroides GAG-degrading enzyme were frequently detected from human gut microbiota. This is the first report on GAG-degrading probiotics in human gut microbiota.}, }
@article {pmid29844399, year = {2018}, author = {Ghosh, S and Das, AP}, title = {Metagenomic insights into the microbial diversity in manganese-contaminated mine tailings and their role in biogeochemical cycling of manganese.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {8257}, pmid = {29844399}, issn = {2045-2322}, mesh = {Actinobacteria/*physiology ; Biodiversity ; Energy Metabolism/genetics ; Magnesium/metabolism ; Manganese/*metabolism ; Metabolic Networks and Pathways/genetics ; Metagenomics ; Microbial Consortia ; Mining ; Phylogeny ; Proteobacteria/*physiology ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, RNA ; Soil Microbiology ; }, abstract = {To extend the knowledge on the microbial diversity of manganese rich environments, we performed a clone library based study using metagenomic approach. Pyrosequencing based analysis of 16S rRNA genes were carried out on an Illumina platform to gain insights into the bacterial community inhabiting in a manganese mining site and the taxonomic profiles were correlated with the inherent capacities of these strains to solubilise manganese. The application of shot gun sequencing in this study yielded results which revealed the highest prevalence of Proteobacteria (42.47%), followed by Actinobacteria (23.99%) in the area of study. Cluster of orthologous group (COG) functional category has 85,066 predicted functions. Out of which 11% are involved in metabolism of amino acid, 9% are involved in production and conversion of energy while Keto Encyclopedia of Gene and Genomes (KEGG) functional category has 107,388 predicted functions, out of which 55% are involved in cellular metabolism, 15% are environmental and information processing and 12% are genetic information processing in nature. The isolated microbial consortia demonstrated visible growth in presence of high concentrations of Mn. Solubilisation studies resulted in 86% of manganese recovery after 20 days. The result presented in this study has important implications in understanding the microbial diversity in manganese contaminated mine tailings and their role in natural geochemical cycling of Mn.}, }
@article {pmid31549239, year = {2019}, author = {Emmanuel, SA and Sul, WJ and Seong, HJ and Rhee, C and Ekpheghere, KI and Kim, IS and Kim, HG and Koh, SC}, title = {Metagenomic analysis of relationships between the denitrification process and carbon metabolism in a bioaugmented full-scale tannery wastewater treatment plant.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {35}, number = {10}, pages = {149}, doi = {10.1007/s11274-019-2716-8}, pmid = {31549239}, issn = {1573-0972}, support = {2017R1D1A3B03036376//National Research Foundation of Korea/ ; }, mesh = {Bacteria/classification/*genetics/isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biodegradation, Environmental ; Bioreactors/microbiology ; Carbon/*metabolism ; Denitrification ; Ketoglutarate Dehydrogenase Complex/genetics/metabolism ; Metagenomics ; Microbial Consortia ; Nitrates/metabolism ; Sewage/chemistry/microbiology ; Tryptophan Synthase/genetics/metabolism ; Waste Water/*microbiology ; Water Purification/instrumentation/methods ; }, abstract = {The goal of this study was to investigate the relationship between the denitrification process and carbon metabolism in a full-scale tannery wastewater treatment plant bioaugmented with the microbial consortium BM-S-1. The metagenomic analysis of the microbial community showed that Brachymonas denitrificans, a known denitrifier, was present at a high level in the treatment stages of buffering (B), primary aeration (PA), and sludge digestion (SD). The occurrences of the amino acid-degrading enzymes alpha ketoglutarate dehydrogenase (α-KGDH) and tryptophan synthase were highly correlated with the presence of denitrification genes, such as napA, narG, nosZ and norB. The occurrence of glutamate dehydrogenase (GDH) was also highly paralleled with the occurrence of denitrification genes such as napA, narG, and norZ. The denitrification genes (nosZ, narG, napA, norB and nrfA) and amino acid degradation enzymes (tryptophan synthase, α-KGDH and pyridoxal phosphate dependent enzymes) were observed at high levels in B. This indicates that degradation of amino acids and denitrification of nitrate may potentially occur in B. The high concentrations of the fatty acid degradation enzyme groups (enoyl-CoA hydratase, 3-hydroxyacyl-CoA dehydrogenase and β-ketothiolase) were observed together with the denitrification genes, such as napA, narG and nosZ. Phospholipase/carboxylesterase, enoyl-CoA hydratase/isomerase, acyl-CoA dehydrogenase, phenylacetate degradation enzyme and 3-hydroxyacyl-CoA dehydrogenase 2 were also dominant in B. All these results clearly indicate that the denitrification pathways are potentially linked to the degradation pathways of amino acids and fatty acids whose degradation products go through the TCA cycle, generating the NADH that is used as electron donors for denitrification.}, }
@article {pmid30422704, year = {2019}, author = {Yue, SJ and Liu, J and Wang, AT and Meng, XT and Yang, ZR and Peng, C and Guan, HS and Wang, CY and Yan, D}, title = {Berberine alleviates insulin resistance by reducing peripheral branched-chain amino acids.}, journal = {American journal of physiology. Endocrinology and metabolism}, volume = {316}, number = {1}, pages = {E73-E85}, doi = {10.1152/ajpendo.00256.2018}, pmid = {30422704}, issn = {1522-1555}, mesh = {3-Methyl-2-Oxobutanoate Dehydrogenase (Lipoamide)/metabolism ; 3T3-L1 Cells ; Adipocytes/drug effects/metabolism ; Adipose Tissue, White/*drug effects/metabolism ; Adult ; Amino Acids, Branched-Chain/*drug effects/metabolism ; Animals ; Berberine/*pharmacology ; Diabetes Mellitus/metabolism ; Diet, High-Fat ; Dysbiosis/*metabolism ; Fatty Liver ; Female ; Gastrointestinal Microbiome/*drug effects/genetics ; Glucose Intolerance ; Hepatocytes/drug effects/metabolism ; Humans ; *Insulin Resistance ; Liver/*drug effects/metabolism ; Male ; Metagenomics ; Mice ; Middle Aged ; Obesity/*metabolism ; Protein Kinases ; }, abstract = {Increased circulating branched-chain amino acids (BCAAs) have been involved in the pathogenesis of obesity and insulin resistance (IR). However, evidence relating berberine (BBR), gut microbiota, BCAAs, and IR is limited. Here, we showed that BBR could effectively rectify steatohepatitis and glucose intolerance in high-fat diet (HFD)-fed mice. BBR reorganized gut microbiota populations under both the normal chow diet (NCD) and HFD. Particularly, BBR noticeably decreased the relative abundance of BCAA-producing bacteria, including order Clostridiales; families Streptococcaceae, Clostridiaceae, and Prevotellaceae; and genera Streptococcus and Prevotella. Compared with the HFD group, predictive metagenomics indicated a reduction in the proportion of gut microbiota genes involved in BCAA biosynthesis but the enrichment genes for BCAA degradation and transport by BBR treatment. Accordingly, the elevated serum BCAAs of HFD group were significantly decreased by BBR. Furthermore, the Western blotting results implied that BBR could promote the BCAA catabolism in the liver and epididymal white adipose tissues of HFD-fed mice by activation of the multienzyme branched-chain α-ketoacid dehydrogenase complex (BCKDC), whereas by inhibition of the phosphorylation state of BCKDHA (E1α subunit) and branched-chain α-ketoacid dehydrogenase kinase (BCKDK). The ex vivo assay further confirmed that BBR could increase BCAA catabolism in both AML12 hepatocytes and 3T3-L1 adipocytes. Finally, data from healthy subjects and diabetics confirmed that BBR could improve glycemic control and modulate circulating BCAAs. Together, our findings clarified BBR improving IR associated not only with gut microbiota alteration in BCAA biosynthesis but also with BCAA catabolism in liver and adipose tissues.}, }
@article {pmid31713170, year = {2019}, author = {Astudillo-de la Vega, H and Alonso-Luna, O and Ali-Pérez, J and López-Camarillo, C and Ruiz-Garcia, E}, title = {Oncobiome at the Forefront of a Novel Molecular Mechanism to Understand the Microbiome and Cancer.}, journal = {Advances in experimental medicine and biology}, volume = {1168}, number = {}, pages = {147-156}, doi = {10.1007/978-3-030-24100-1_10}, pmid = {31713170}, issn = {0065-2598}, mesh = {Bacteria/genetics ; Dysbiosis ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; *Microbiota/genetics/physiology ; *Neoplasms/microbiology ; }, abstract = {The microbiome comprises all the genetic material within a microbiota, that represents tenfold higher than that of our cells. The microbiota it includes a wide variety of microorganisms such as bacteria, viruses, protozoans, fungi, and archaea, and this ecosystem is personalized in any body space of every individual. Balanced microbial communities can positively contribute to training the immune system and maintaining immune homeostasis. Dysbiosis is a change in the normal microbiome composition that can initiate chronic inflammation, epithelial barrier breaches, and overgrowth of harmful bacteria. The next-generation sequencing methods have revolutionized the study of the microbiome. Bioinformatic tools to manage large volumes of new information, it became possible to assess species diversity and measure dynamic fluctuations in microbial communities. The burden of infections that are associated to human cancer is increasing but is underappreciated by the cancer research community. The rich content in microbes of normal and tumoral tissue reflect could be defining diverse physiological or pathological states. Genomic research has emerged a new focus on the interplay between the human microbiome and carcinogenesis and has been termed the 'oncobiome'. The interactions among the microbiota in all epithelium, induce changes in the host immune interactions and can be a cause of cancer. Microbes have been shown to have systemic effects on the host that influence the efficacy of anticancer drugs. Metagenomics allows to investigate the composition of microbial community. Metatranscriptome analysis applies RNA sequencing to microbial samples to determine which species are present. Cancer can be caused by changes in the microbiome. The roles of individual microbial species in cancer progression have been identified long ago for various tissue types. The identification of microbiomes of drug resistance in the treatment of cancer patients has been the subject of numerous microbiome studies. The complexity of cancer genetic alterations becomes irrelevant in certain cancers to explain the origin, the cause or the oncogenic maintenance by the oncogene addiction theory.}, }
@article {pmid31161391, year = {2019}, author = {Fujimoto, M and Carey, DE and Zitomer, DH and McNamara, PJ}, title = {Syntroph diversity and abundance in anaerobic digestion revealed through a comparative core microbiome approach.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {15}, pages = {6353-6367}, doi = {10.1007/s00253-019-09862-4}, pmid = {31161391}, issn = {1432-0614}, mesh = {Anaerobiosis ; *Biota ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Fatty Acids, Volatile/metabolism ; Hydrogen-Ion Concentration ; Metagenomics ; Methane/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/*microbiology ; *Water Purification ; }, abstract = {Anaerobic digestion is an important biotechnology treatment process for conversion of waste to energy. In this study, a comparative core microbiome approach, i.e., determining taxa that are shared in functioning digesters but not shared in non-functioning digesters, was used to determine microbial taxa that could play key roles for effective anaerobic digestion. Anaerobic digester functions were impaired by adding the broad-spectrum antimicrobial triclosan (TCS) or triclocarban (TCC) at different concentrations, and the core microbiomes in both functioning and non-functioning anaerobic digesters were compared. Digesters treated with high (2500 mg/kg) or medium (450 mg/kg) TCS and high (850 mg/kg) TCC concentrations lost their function, i.e., methane production decreased, effluent volatile fatty acid concentrations increased, and pH decreased. Changes in microbial community diversity and compositions were assessed using 16S rRNA gene amplicon sequencing. Microbial richness decreased significantly in non-functioning digesters (p < 0.001). Microbial community compositions in non-functioning digesters significantly differed from those in functioning digesters (p = 0.001, ANOSIM). Microbes identified as potentially key taxa included previously known fatty acid-degrading syntrophs and amino acid-degrading syntrophs. A diverse group of syntrophs detected in this study had low relative abundance in functioning digesters, suggesting the importance of rare microbes in anaerobic digester operation. The comparative microbiome approach used in this study can be applied to other microbial systems where a community-driven biological phenomena can be observed directly.}, }
@article {pmid31742865, year = {2019}, author = {Geesink, P and Wegner, CE and Probst, AJ and Herrmann, M and Dam, HT and Kaster, AK and Küsel, K}, title = {Genome-inferred spatio-temporal resolution of an uncultivated Roizmanbacterium reveals its ecological preferences in groundwater.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14865}, pmid = {31742865}, issn = {1462-2920}, abstract = {Subsurface ecosystems like groundwater harbor diverse microbial communities, including small-sized, putatively symbiotic organisms of the Candidate Phyla Radiation, yet little is known about their ecological preferences and potential microbial partners. Here, we investigated a member of the superphylum Microgenomates (Cand. Roizmanbacterium ADI133) from oligotrophic groundwater using mini-metagenomics and monitored its spatio-temporal distribution using 16S rRNA gene analyses. A Roizmanbacteria-specific quantitative PCR assay allowed us to track its abundance over the course of one year within eight groundwater wells along a 5.4 km hillslope transect, where Roizmanbacteria reached maximum relative abundances of 2.3 %. In-depth genomic analyses suggested that Cand. Roizmanbacterium ADI133 is a lactic acid fermenter, potentially able to utilize a range of complex carbon substrates, including cellulose We hypothesize that it attaches to host cells using a trimeric autotransporter adhesin and inhibits their cell wall biosynthesis using a toxin-antitoxin system. Network analyses based on correlating Cand. Roizmanbacterium ADI133 abundances with amplicon sequencing derived microbial community profiles suggested one potential host organism, classified as a member of the class Thermodesulfovibrionia (Nitrospirae). By providing lactate as an electron donor Cand. Roizmanbacterium ADI133 potentially mediates the transfer of carbon to other microorganisms and thereby is an important connector in the microbial community. This article is protected by copyright. All rights reserved.}, }
@article {pmid30815250, year = {2018}, author = {Cuscó, A and Catozzi, C and Viñes, J and Sanchez, A and Francino, O}, title = {Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and the 16S-ITS-23S of the rrn operon.}, journal = {F1000Research}, volume = {7}, number = {}, pages = {1755}, doi = {10.12688/f1000research.16817.2}, pmid = {30815250}, issn = {2046-1402}, mesh = {Animals ; Dogs ; Metagenomics ; *Microbiota ; *Nanopores ; Operon ; RNA, Ribosomal, 16S ; }, abstract = {Background: Profiling the microbiome of low-biomass samples is challenging for metagenomics since these samples are prone to contain DNA from other sources (e.g. host or environment). The usual approach is sequencing short regions of the 16S rRNA gene, which fails to assign taxonomy to genus and species level. To achieve an increased taxonomic resolution, we aim to develop long-amplicon PCR-based approaches using Nanopore sequencing. We assessed two different genetic markers: the full-length 16S rRNA (~1,500 bp) and the 16S-ITS-23S region from the rrn operon (4,300 bp). Methods: We sequenced a clinical isolate of Staphylococcus pseudintermedius, two mock communities and two pools of low-biomass samples (dog skin). Nanopore sequencing was performed on MinION™ using the 1D PCR barcoding kit. Sequences were pre-processed, and data were analyzed using EPI2ME or Minimap2 with rrn database. Consensus sequences of the 16S-ITS-23S genetic marker were obtained using canu. Results: The full-length 16S rRNA and the 16S-ITS-23S region of the rrn operon were used to retrieve the microbiota composition of the samples at the genus and species level. For the Staphylococcus pseudintermedius isolate, the amplicons were assigned to the correct bacterial species in ~98% of the cases with the16S-ITS-23S genetic marker, and in ~68%, with the 16S rRNA gene when using EPI2ME. Using mock communities, we found that the full-length 16S rRNA gene represented better the abundances of a microbial community; whereas, 16S-ITS-23S obtained better resolution at the species level. Finally, we characterized low-biomass skin microbiota samples and detected species with an environmental origin. Conclusions: Both full-length 16S rRNA and the 16S-ITS-23S of the rrn operon retrieved the microbiota composition of simple and complex microbial communities, even from the low-biomass samples such as dog skin. For an increased resolution at the species level, targeting the 16S-ITS-23S of the rrn operon would be the best choice.}, }
@article {pmid31351355, year = {2019}, author = {Zhang, F and Zhang, W and Qian, DK and Dai, K and van Loosdrecht, MCM and Zeng, RJ}, title = {Synergetic alginate conversion by a microbial consortium of hydrolytic bacteria and methanogens.}, journal = {Water research}, volume = {163}, number = {}, pages = {114892}, doi = {10.1016/j.watres.2019.114892}, pmid = {31351355}, issn = {1879-2448}, mesh = {Alginates ; Anaerobiosis ; Bacteria ; Bioreactors ; *Euryarchaeota ; Methane ; *Microbial Consortia ; Sewage ; }, abstract = {Sludge, of which alginate-like biomaterial is a major organic component, is an increasing environmental problem. Thus, efficient anaerobic degradation of alginate provides a new method for sludge utilization. In this study, anaerobic alginate hydrolytic bacteria (AHB) were proposed to enrich with methanogens synergetically to reduce the inhibition of intermediate metabolites. The COD of produced methane reached 80.7 ± 1.9% (n = 4) of initial alginate COD. After considering the microbial growth (8%-18% of COD), a good COD balance indicated that alginate was fully consumed and the main final metabolites were methane and CO2. Methanogenesis could promote alginate conversion by AHB. The enriched bacteria for alginate degradation in this study were different from that of former known AHB. The metabolic pathway of alginate degradation was revealed by metagenomics, in which oligo-alginate lyase was detected in twelve bacteria, and typical carbon metabolic pathways to convert alginate to methane were identified. More studies of bacterial isolation and biofuel production are still needed in the future.}, }
@article {pmid30941531, year = {2019}, author = {Qian, W and Ao, W and Jia, C and Li, Z}, title = {Bacterial colonisation of reeds and cottonseed hulls in the rumen of Tarim red deer (Cervus elaphus yarkandensis).}, journal = {Antonie van Leeuwenhoek}, volume = {112}, number = {9}, pages = {1283-1296}, doi = {10.1007/s10482-019-01260-0}, pmid = {30941531}, issn = {1572-9699}, support = {HS201702//Opening Project of Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production &amp; Construction Group/ ; 31460610//National Natural Science Foundation of China/ ; 31660671//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Bacteria/*classification/*genetics/metabolism ; *Biota ; Cellulose/metabolism ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Deer/*microbiology ; Gossypium/*microbiology ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Phylogeny ; Poaceae/*microbiology ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Sequence Analysis, DNA ; }, abstract = {The rumen microbiome contributes greatly to the degradation of plant fibres to volatile fatty acids and microbial products, affecting the health and productivity of ruminants. In this study, we investigated the dynamics of colonisation by bacterial communities attached to reeds and cottonseed hulls in the rumen of Tarim red deer, a native species distributed in the desert of the Tarim Basin. The reed and cottonseed hull samples incubated in nylon bags for 1, 6, 12, and 48 h were collected and used to examine the bacterial communities by next-generation sequencing of the bacterial 16S rRNA gene. Prevotella1 and Rikenellaceae RC9 were the most abundant taxa in both the reed and cottonseed hull groups at various times, indicating a key role of these organisms in rumen fermentation in Tarim red deer. The relative abundances of cellulolytic bacteria, such as members of Fibrobacter, Treponema 2, Ruminococcaceae NK4A214 and Succiniclasticum increased, while that of the genus Prevotella 1 decreased, with increasing incubation time in both reeds and cottonseed hulls. Moreover, the temporal changes in bacterial diversity between reeds and cottonseed hulls were different, as demonstrated by the variations in the taxa Ruminococcaceae UCG 010 and Papillibacter in the reed group and Sphaerochaeta and Erysipelotrichaceae UCG 004 in the cottonseed hull group; the abundances of these bacteria first decreased and then increased. In conclusion, our results reveal the dynamics of bacterial colonisation of reeds and cottonseed hulls in the rumen of Tarim red deer.}, }
@article {pmid30832984, year = {2019}, author = {Theis, KR and Romero, R and Winters, AD and Greenberg, JM and Gomez-Lopez, N and Alhousseini, A and Bieda, J and Maymon, E and Pacora, P and Fettweis, JM and Buck, GA and Jefferson, KK and Strauss, JF and Erez, O and Hassan, SS}, title = {Does the human placenta delivered at term have a microbiota? Results of cultivation, quantitative real-time PCR, 16S rRNA gene sequencing, and metagenomics.}, journal = {American journal of obstetrics and gynecology}, volume = {220}, number = {3}, pages = {267.e1-267.e39}, doi = {10.1016/j.ajog.2018.10.018}, pmid = {30832984}, issn = {1097-6868}, support = {HHSN275201300006C/HD/NICHD NIH HHS/United States ; U54 DE023786/DE/NIDCR NIH HHS/United States ; U54 HD080784/HD/NICHD NIH HHS/United States ; ZIA HD002400-27/ImNIH/Intramural NIH HHS/United States ; R01 HD092415/HD/NICHD NIH HHS/United States ; }, mesh = {Adult ; Cesarean Section ; Cross-Sectional Studies ; DNA Contamination ; DNA, Bacterial/analysis ; Female ; Genetic Markers ; Humans ; Metagenomics ; *Microbiota/genetics ; Placenta/*microbiology ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Term Birth ; }, abstract = {BACKGROUND: The human placenta has been traditionally viewed as sterile, and microbial invasion of this organ has been associated with adverse pregnancy outcomes. Yet, recent studies that utilized sequencing techniques reported that the human placenta at term contains a unique microbiota. These conclusions are largely based on the results derived from the sequencing of placental samples. However, such an approach carries the risk of capturing background-contaminating DNA (from DNA extraction kits, polymerase chain reaction reagents, and laboratory environments) when low microbial biomass samples are studied.<br><br>OBJECTIVE: To determine whether the human placenta delivered at term in patients without labor who undergo cesarean delivery harbors a resident microbiota (&quot;the assemblage of microorganisms present in a defined niche or environment&quot;).<br><br>STUDY DESIGN: This cross-sectional study included placentas from 29 women who had a cesarean delivery without labor at term. The study also included technical controls to account for potential background-contaminating DNA, inclusive in DNA extraction kits, polymerase chain reaction reagents, and laboratory environments. Bacterial profiles of placental tissues and background technical controls were characterized and compared with the use of bacterial culture, quantitative real-time polymerase chain reaction, 16S ribosomal RNA gene sequencing, and metagenomic surveys.<br><br>RESULTS: (1) Twenty-eight of 29 placental tissues had a negative culture for microorganisms. The microorganisms retrieved by culture from the remaining sample were likely contaminants because corresponding 16S ribosomal RNA genes were not detected in the same sample. (2) Quantitative real-time polymerase chain reaction did not indicate greater abundances of bacterial 16S ribosomal RNA genes in placental tissues than in technical controls. Therefore, there was no evidence of the presence of microorganisms above background contamination from reagents in the placentas. (3) 16S ribosomal RNA gene sequencing did not reveal consistent differences in the composition or structure of bacterial profiles between placental samples and background technical controls. (4) Most of the bacterial sequences obtained from metagenomic surveys of placental tissues were from cyanobacteria, aquatic bacteria, or plant pathogens, which are microbes unlikely to populate the human placenta. Coprobacillus, which constituted 30.5% of the bacterial sequences obtained through metagenomic sequencing of placental samples, was not identified in any of the 16S ribosomal RNA gene surveys of these samples. These observations cast doubt as to whether this organism is really present in the placenta of patients at term not in labor.<br><br>CONCLUSION: With the use of multiple modes of microbiologic inquiry, a resident microbiota could not be identified in human placentas delivered at term from women without labor. A consistently significant difference in the abundance and/or presence of a microbiota between placental tissue and background technical controls could not be found. All cultures of placental tissue, except 1, did not yield bacteria. Incorporating technical controls for potential sources of background-contaminating DNA for studies of low microbial biomass samples, such as the placenta, is necessary to derive reliable conclusions.}, }
@article {pmid30462522, year = {2019}, author = {Shi, Z and Fultz, RS and Engevik, MA and Gao, C and Hall, A and Major, A and Mori-Akiyama, Y and Versalovic, J}, title = {Distinct roles of histamine H1- and H2-receptor signaling pathways in inflammation-associated colonic tumorigenesis.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {316}, number = {1}, pages = {G205-G216}, doi = {10.1152/ajpgi.00212.2018}, pmid = {30462522}, issn = {1522-1547}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; U01 CA170930/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Carcinogenesis/drug effects/*metabolism ; Colon/drug effects/metabolism ; Disease Models, Animal ; Gastrointestinal Microbiome/drug effects ; Histamine/metabolism ; Histamine H1 Antagonists/pharmacology ; Inflammation/*metabolism ; Intestinal Mucosa/drug effects/metabolism ; Lipopolysaccharides/pharmacology ; Mice, Transgenic ; Receptors, Histamine H1/drug effects/*metabolism ; Receptors, Histamine H2/drug effects/*metabolism ; Signal Transduction/drug effects ; }, abstract = {Inflammatory bowel disease (IBD) is a well-known risk factor for the development of colorectal cancer. Prior studies have demonstrated that microbial histamine can ameliorate intestinal inflammation in mice. We tested the hypothesis whether microbe-derived luminal histamine suppresses inflammation-associated colon cancer in Apcmin/+ mice. Mice were colonized with the human-derived Lactobacillus reuteri. Chronic inflammation was induced by repeated cycles of low-dose dextran sulfate sodium (DSS). Mice that were given histamine-producing L. reuteri via oral gavage developed fewer colonic tumors, despite the presence of a complex mouse gut microbiome. We further demonstrated that administration of a histamine H1-receptor (H1R) antagonist suppressed tumorigenesis, while administration of histamine H2-receptor (H2R) antagonist significantly increased both tumor number and size. The bimodal functions of histamine include protumorigenic effects through H1R and antitumorigenic effects via H2R, and these results were supported by gene expression profiling studies on tumor specimens of patients with colorectal cancer. Greater ratios of gene expression of H2R (HRH2) vs. H1R (HRH1) were correlated with improved overall survival outcomes in patients with colorectal cancer. Additionally, activation of H2R suppressed phosphorylation of mitogen-activated protein kinases (MAPKs) and inhibited chemokine gene expression induced by H1R activation in colorectal cancer cells. Moreover, the combination of a H1R antagonist and a H2R agonist yielded potent suppression of lipopolysaccharide-induced MAPK signaling in macrophages. Given the impact on intestinal epithelial and immune cells, simultaneous modulation of H1R and H2R signaling pathways may be a promising therapeutic target for the prevention and treatment of inflammation-associated colorectal cancer. NEW &amp; NOTEWORTHY Histamine-producing Lactobacillus reuteri can suppress development of inflammation-associated colon cancer in an established mouse model. The net effects of histamine may depend on the relative activity of H1R and H2R signaling pathways in the intestinal mucosa. Our findings suggest that treatment with H1R or H2R antagonists could yield opposite effects. However, by harnessing the ability to block H1R signaling while stimulating H2R signaling, novel strategies for suppression of intestinal inflammation and colorectal neoplasia could be developed.}, }
@article {pmid30794590, year = {2019}, author = {Saito, K and Koido, S and Odamaki, T and Kajihara, M and Kato, K and Horiuchi, S and Adachi, S and Arakawa, H and Yoshida, S and Akasu, T and Ito, Z and Uchiyama, K and Saruta, M and Xiao, JZ and Sato, N and Ohkusa, T}, title = {Metagenomic analyses of the gut microbiota associated with colorectal adenoma.}, journal = {PloS one}, volume = {14}, number = {2}, pages = {e0212406}, doi = {10.1371/journal.pone.0212406}, pmid = {30794590}, issn = {1932-6203}, mesh = {Adenoma/genetics/*microbiology ; Aged ; Bacteria/*classification/genetics/isolation &amp; purification ; Case-Control Studies ; Colorectal Neoplasms/genetics/*microbiology ; Disease Progression ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; *Metagenomics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Recent studies have suggested an association between certain members of the Fusobacterium genus, especially F. nucleatum, and the progression of advanced colorectal carcinoma (CRC). We assessed such an association of the gut microbiota in Japanese patients with colorectal adenoma (CRA) or intramucosal CRC using colonoscopy aspirates. We analyzed samples from 81 Japanese patients, including 47 CRA and 24 intramucosal CRC patients, and 10 healthy subjects. Metagenomic analysis of the V3-V4 region of the 16S ribosomal RNA gene was performed. The linear discriminant analysis (LDA) effect size (LEfSe) method was used to examine microbial dysbiosis, revealing significant differences in bacterial abundances between the healthy controls and CRA or intramucosal CRC patients. In particular, F. varium was statistically more abundant in patients with CRA and intramucosal CRC than in healthy subjects. Here, we present the metagenomic profile of CRA and intramucosal CRC and demonstrate that F. varium is at least partially involved in the pathogenesis of CRA and intramucosal CRC.}, }
@article {pmid31734483, year = {2019}, author = {Khan, MS and Koizumi, N and Olds, JL}, title = {Biofixation of atmospheric nitrogen in the context of world staple crop production: Policy perspectives.}, journal = {The Science of the total environment}, volume = {701}, number = {}, pages = {134945}, doi = {10.1016/j.scitotenv.2019.134945}, pmid = {31734483}, issn = {1879-1026}, abstract = {The extensive use of nitrogen (N) fertilizers implicates a paradox: while fertilizers ensure the supply of a large amount of food, they cause negative environmental externalities, including reduced biodiversity, and eutrophic streams and lakes. Moreover, such fertilizers may also result in a major public health hazard: increased antibiotic resistance. This article discusses the critical implications of perturbations in N cycle caused by excessive use of fertilizers and resulting policy implications as they relate to ecosystem services. While there are solutions such as cover crops, these solutions are expensive and inconvenient for farmers. We advocate the use of biological fixation (BF) for staple crops-microbiome mediated natural supply of fixed N. This would involve engineering a microbiome that can be grown cheaply and at industrial scale. Fertilizers resulting from such innovation are termed as &quot;biofertilizers&quot; in this article. Following a qualitative cost-benefit analysis broken down by key stakeholders and a quick exploration of policy frameworks as they relate to the advancement of biofertilizers, we propose a practical pathway of where and how research investments should be directed to make such a solution feasible. We make five policy recommendations for decision-makers to facilitate a successful trajectory for this solution: (1) Future agricultural science should seek to understand how BF might be employed as a practical and efficient strategy. This effort would require that industry and the government partner to establish a pre-competitive research laboratory equipped with the latest state-of-the-art technologies that conduct metagenomic experiments to reveal signature microbiomes and form novel symbiotic connections. (2) To have a smooth ride in the market, ag-bio companies should: (i) create awareness among farmers; (ii) impart skills to farmers in testing and using biofertilizers, and (iii) conduct extensive field tests and more research in studying the scalability potential of such fertilizers. (3)The United States Department of Agriculture (USDA) and state governments should provide research and development (R&amp;D) tax credits to biotech companies specifically geared towards R&amp;D investments aimed at increasing the viability of BF and microbiome engineering. (4) To control agricultural pollution in the biosphere, federal governments should consider passing a Clean Agriculture Act (CAA), including a specific clause that regulate the use of chemical fertilizers. (5) Governments and the UN Food and Agriculture Organization (FAO) should coordinate Biological Advanced Research in Agriculture (BARA)-a global agricultural innovation initiative for investments and research in biological fixation and ethical, legal, and social implications of such innovation. While biological fixation will be central in BARA, we envision it to conduct research around other agricultural innovations as well, such as increasing photosynthetic efficiency.}, }
@article {pmid31338542, year = {2019}, author = {Bohra, V and Dafale, NA and Purohit, HJ}, title = {Understanding the alteration in rumen microbiome and CAZymes profile with diet and host through comparative metagenomic approach.}, journal = {Archives of microbiology}, volume = {201}, number = {10}, pages = {1385-1397}, doi = {10.1007/s00203-019-01706-z}, pmid = {31338542}, issn = {1432-072X}, mesh = {Animals ; Bacteria/*classification/*enzymology/genetics ; Bacteroidetes/genetics ; *Buffaloes/microbiology ; *Cattle/microbiology ; Cellulases/metabolism ; *Diet/veterinary ; Dietary Fiber ; Glycoside Hydrolases/metabolism ; Metagenome ; Metagenomics ; Microbial Consortia/genetics ; Microbiota/*physiology ; Phylogeny ; Rumen/*microbiology ; }, abstract = {Rumen microbial community harbors a distinct genetic reservoir of potent carbohydrate-active enzymes (CAZyme) that functions efficiently for the deconstruction of plant biomass. Based on this premise, metagenomics approach was applied to characterize the rumen microbial community and identify carbohydrate-active genes of Bos taurus (cow) and Bubalus bubalis (buffalo) fed on green or dry roughage. Metadata was generated from the samples: green roughage-fed cow (NDC_GR), buffalo (NDB_GR) and dry roughage-fed cow (NDC_DR), buffalo (NDB_DR). Phylogenetic analysis revealed the dominance of Bacteroidetes, Firmicutes, Proteobacteria, Actinobacteria and Fibrobacter in all the four samples, covering 90-96% of the total bacterial population. On finer resolution, higher abundance of bacterial genera Fibrobacter, Bacteroides, Clostridium, Prevotella and Ruminococcus involved in plant biomass hydrolysis was observed in NDB_DR. Functional annotation using dbCAN annotation algorithm identified 28.13%, 8.08% 10.93% and 12.53% of the total contigs as putatively carbohydrate-active against NDC_GR, NDB_GR, NDC_DR and NDB_DR, respectively. Additional profiling of CAZymes revealed an over representation and diversity of putative glycoside hydrolases (GHs) in the animals fed on dry roughage with substantial enrichments of genes encoding GHs from families GH2, GH3, GH13 and GH43. GHs of families GH45, GH12, GH113, GH128, GH54 and GH27 were observed exclusively in NDB_DR metagenome. A higher abundance of cellulases, hemicellulases, debranching and oligosaccharide hydrolyzing enzymes was revealed in NDB_DR metagenome. Accordingly, it can be concluded that buffalo rumen microbiome are more efficient in plant biomass hydrolysis. The present study provides a deep understanding of the shifts in microbial community and plant polysaccharide deconstructing capabilities of rumen microbiome in response to changes in the feed type and host animal. Activity-specific microbial consortia procured from these animals can be used further for efficient plant biomass hydrolysis. The study also establishes the utility of rumen microbiome as a unique resource for mining diverse lignocellulolytic enzymes.}, }
@article {pmid30366990, year = {2019}, author = {Zhang, W and Watanabe, HK and Ding, W and Lan, Y and Tian, RM and Sun, J and Chen, C and Cai, L and Li, Y and Oguri, K and Toyofuku, T and Kitazato, H and Drazen, JC and Bartlett, D and Qian, PY}, title = {Gut Microbial Divergence between Two Populations of the Hadal Amphipod Hirondellea gigas.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {1}, pages = {}, doi = {10.1128/AEM.02032-18}, pmid = {30366990}, issn = {1098-5336}, mesh = {Amphipoda/*microbiology ; Animals ; Archaea/classification/*physiology ; Bacteria/classification ; *Bacterial Physiological Phenomena ; Gastrointestinal Microbiome/*physiology ; Hydrothermal Vents ; }, abstract = {Hadal environments sustain diverse microorganisms. A few studies have investigated hadal microbial communities consisting of free-living or particle-associated bacteria and archaea. However, animal-associated microbial communities in hadal environments remain largely unexplored, and comparative analyses of animal gut microbiota between two isolated hadal environments have never been done so far. In the present study, 228 Gb of gut metagenomes of the giant amphipod Hirondellea gigas from two hadal trenches, the Mariana Trench and Japan Trench, were sequenced and analyzed. Taxonomic analysis identified 49 microbial genera commonly shared by the gut microbiota of the two H. gigas populations. However, the results of statistical analysis, in congruency with the alpha and beta diversity analyses, revealed significant differences in gut microbial composition across the two trenches. Abundance variation of Psychromonas, Propionibacterium, and Pseudoalteromonas species was observed. Microbial cooccurrence was demonstrated for microbes that were overrepresented in the Mariana trench. Comparison of functional potential showed that the percentage of carbohydrate metabolic genes among the total microbial genes was significantly higher in the guts of H. gigas specimens from the Mariana Trench. Integrating carbon input information and geological characters of the two hadal trenches, we propose that the differences in the community structure might be due to several selective factors, such as environmental variations and microbial interactions.IMPORTANCE The taxonomic composition and functional potential of animal gut microbiota in deep-sea environments remain largely unknown. Here, by performing comparative metagenomics, we suggest that the gut microbial compositions of two Hirondellea gigas populations from the Mariana Trench and the Japan Trench have undergone significant divergence. Through analyses of functional potentials and microbe-microbe correlations, our findings shed light on the contributions of animal gut microbiota to host adaptation to hadal environments.}, }
@article {pmid31250091, year = {2019}, author = {Llacsa, LX and Solis-Castro, RL and Mialhe, E and García-Seminario, R}, title = {Metagenomic Analysis of the Bacterial and Fungal Community Associated to the Rhizosphere of Tabebuia chrysantha and T. billbergii.}, journal = {Current microbiology}, volume = {76}, number = {9}, pages = {1073-1080}, doi = {10.1007/s00284-019-01725-5}, pmid = {31250091}, issn = {1432-0991}, support = {Resolución Nº 0543-2014/UNT-R).//Canon Universidad Nacional de Tumbes/ ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Fungi/classification/genetics/*isolation &amp; purification ; Metagenomics ; Phylogeny ; Rhizosphere ; *Soil Microbiology ; Tabebuia/*microbiology ; }, abstract = {The rhizosphere of plants contains a diversity of microorganisms, some of which play an important role in the growth and development of the host plant. In this work, the diversity of fungi and bacteria associated to the rhizosphere of Tabebuia chrysantha and T. billbergii plants was analyzed. The molecular identification was performed by sequencing the ITS and 16S rDNA for fungi and bacteria, respectively. The analysis of the rDNA sequences of the rhizosphere of T. billergii showed that for domain Eukaria, the most abundant phyla were Glomeromycota (56%) and Ascomycota (39%), and for domain Bacteria, the phylum Firmicutes (19.17%) was the most abundant followed by Actinobacteria (14.90%) and Proteobacteria (8.94%). In the rhizosphere of T. chrysantha the most abundant phylum of Eukaria was Ascomycota (98%), and for Bacteria the most representative phyla were Proteobacteria (18.61%) and Actinobacteria (11.93%). A diversity of genera and species of fungi and bacteria was observed, to be more significant in T. chrysantha than T. billbergii. The taxonomic assignment of metagenomic sequences revealed a homology associated with genomic sequences of 546 bacteria and 147 fungi in T. chrysantha and 154 bacteria and 122 fungi in T. billbergii.}, }
@article {pmid31235964, year = {2019}, author = {Scheiman, J and Luber, JM and Chavkin, TA and MacDonald, T and Tung, A and Pham, LD and Wibowo, MC and Wurth, RC and Punthambaker, S and Tierney, BT and Yang, Z and Hattab, MW and Avila-Pacheco, J and Clish, CB and Lessard, S and Church, GM and Kostic, AD}, title = {Meta-omics analysis of elite athletes identifies a performance-enhancing microbe that functions via lactate metabolism.}, journal = {Nature medicine}, volume = {25}, number = {7}, pages = {1104-1109}, doi = {10.1038/s41591-019-0485-4}, pmid = {31235964}, issn = {1546-170X}, mesh = {Animals ; *Athletes ; Exercise ; *Gastrointestinal Microbiome ; Humans ; Lactic Acid/*metabolism ; *Metagenomics ; Mice ; Mice, Inbred C57BL ; Propionates/metabolism ; *Running ; Veillonella/*metabolism ; }, abstract = {The human gut microbiome is linked to many states of human health and disease1. The metabolic repertoire of the gut microbiome is vast, but the health implications of these bacterial pathways are poorly understood. In this study, we identify a link between members of the genus Veillonella and exercise performance. We observed an increase in Veillonella relative abundance in marathon runners postmarathon and isolated a strain of Veillonella atypica from stool samples. Inoculation of this strain into mice significantly increased exhaustive treadmill run time. Veillonella utilize lactate as their sole carbon source, which prompted us to perform a shotgun metagenomic analysis in a cohort of elite athletes, finding that every gene in a major pathway metabolizing lactate to propionate is at higher relative abundance postexercise. Using 13C3-labeled lactate in mice, we demonstrate that serum lactate crosses the epithelial barrier into the lumen of the gut. We also show that intrarectal instillation of propionate is sufficient to reproduce the increased treadmill run time performance observed with V. atypica gavage. Taken together, these studies reveal that V. atypica improves run time via its metabolic conversion of exercise-induced lactate into propionate, thereby identifying a natural, microbiome-encoded enzymatic process that enhances athletic performance.}, }
@article {pmid30228361, year = {2018}, author = {Mangifesta, M and Mancabelli, L and Milani, C and Gaiani, F and de'Angelis, N and de'Angelis, GL and van Sinderen, D and Ventura, M and Turroni, F}, title = {Mucosal microbiota of intestinal polyps reveals putative biomarkers of colorectal cancer.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {13974}, pmid = {30228361}, issn = {2045-2322}, mesh = {Adenomatous Polyps/*diagnosis/genetics/microbiology ; Aged ; Bacteria/*classification/genetics/isolation &amp; purification ; Biomarkers/*analysis ; Colorectal Neoplasms/*diagnosis/genetics/microbiology ; Female ; Gastrointestinal Microbiome ; Humans ; Intestinal Polyps/*diagnosis/genetics/microbiology ; Male ; Metagenomics ; Microbiota/*genetics ; Mucous Membrane/*metabolism/microbiology ; Pilot Projects ; Prognosis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The human intestine retains a complex microbial ecosystem, which performs crucial functions that impact on host health. Several studies have indicated that intestinal dysbiosis may impact on the establishment of life-threatening intestinal diseases such as colorectal cancer. An adenomatous polyp is the result of abnormal tissue growth, which is benign but is considered to be associated with a high risk of developing colorectal cancer, based on its grade of dysplasia. Development of diagnostic tools that are based on surveying the gut microbiota and are aimed at early detection of colorectal cancer represent highly desirable target. For this purpose, we performed a pilot study in which we applied a metataxonomic analysis based on 16S rRNA gene sequencing approach to unveil the composition of microbial communities of intestinal polyps. Moreover, we performed a meta-analysis involving the reconstructed microbiota composition of adenomatous polyps and publicly available metagenomics datasets of colorectal cancer. These analyses allowed the identification of microbial taxa such as Faecalibacterium, Bacteroides and Romboutsia, which appear to be depleted in cancerogenic mucosa as well as in adenomatous polyps, thus representing novel microbial biomarkers associated with early tumor formation. Furthermore, an absolute quantification of Fusubacterium nucleatum in polyps further compounded the important role of this microorganism as a valuable putative microbial biomarker for early diagnosis of colorectal cancer.}, }
@article {pmid31406349, year = {2019}, author = {Doan, T and Hinterwirth, A and Worden, L and Arzika, AM and Maliki, R and Abdou, A and Kane, S and Zhong, L and Cummings, SL and Sakar, S and Chen, C and Cook, C and Lebas, E and Chow, ED and Nachamkin, I and Porco, TC and Keenan, JD and Lietman, TM}, title = {Gut microbiome alteration in MORDOR I: a community-randomized trial of mass azithromycin distribution.}, journal = {Nature medicine}, volume = {25}, number = {9}, pages = {1370-1376}, doi = {10.1038/s41591-019-0533-0}, pmid = {31406349}, issn = {1546-170X}, mesh = {Azithromycin/*administration &amp; dosage ; Campylobacter/drug effects/pathogenicity ; Campylobacter Infections/*drug therapy/genetics/mortality ; Child ; Child Mortality ; Child, Preschool ; Drug Resistance, Bacterial/drug effects/genetics ; Gastrointestinal Microbiome/*drug effects ; Gene Expression Regulation, Bacterial/drug effects ; Humans ; Macrolides/administration &amp; dosage ; Male ; *Metagenomics ; Nigeria/epidemiology ; Sequence Analysis, RNA ; }, abstract = {The MORDOR I trial1, conducted in Niger, Malawi and Tanzania, demonstrated that mass azithromycin distribution to preschool children reduced childhood mortality1. However, the large but simple trial design precluded determination of the mechanisms involved. Here we examined the gut microbiome of preschool children from 30 Nigerien communities randomized to either biannual azithromycin or placebo. Gut microbiome γ-diversity was not significantly altered (P = 0.08), but the relative abundances of two Campylobacter species, along with another 33 gut bacteria, were significantly reduced in children treated with azithromycin at the 24-month follow-up. Metagenomic analysis revealed functional differences in gut bacteria between treatment groups. Resistome analysis showed an increase in macrolide resistance gene expression in gut microbiota in communities treated with azithromycin (P = 0.004). These results suggest that prolonged mass azithromycin distribution to reduce childhood mortality reduces certain gut bacteria, including known pathogens, while selecting for antibiotic resistance.}, }
@article {pmid30187987, year = {2019}, author = {Hooper, R and Brealey, JC and van der Valk, T and Alberdi, A and Durban, JW and Fearnbach, H and Robertson, KM and Baird, RW and Bradley Hanson, M and Wade, P and Gilbert, MTP and Morin, PA and Wolf, JBW and Foote, AD and Guschanski, K}, title = {Host-derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin.}, journal = {Molecular ecology}, volume = {28}, number = {2}, pages = {484-502}, doi = {10.1111/mec.14860}, pmid = {30187987}, issn = {1365-294X}, support = {//Lindblad Expeditions/National Geographic Conservation Fund/International ; ERCStG-336536//European Research Council/International ; DNRF94//Danish National Research Foundation/International ; //Antarctic Science Bursary/International ; //Welsh Government and Higher Education Funding Council for Wales through the Sêr Cymru National Research Network for Low Carbon, Energy and Environment/International ; 663830//European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie/International ; SR17/1227//British Ecological Society/International ; 2016-00835//FORMAS/International ; 5051-00033//Danish Council for Independent Research-DFF/International ; R250-2017-1351//Lundbeckfonden/International ; }, mesh = {Animals ; Antarctic Regions ; Diatoms/genetics ; Geography ; *Metagenomics ; Microbiota/*genetics ; Skin/*microbiology ; Whale, Killer/*microbiology/parasitology ; }, abstract = {Recent exploration into the interactions and relationship between hosts and their microbiota has revealed a connection between many aspects of the host's biology, health and associated micro-organisms. Whereas amplicon sequencing has traditionally been used to characterize the microbiome, the increasing number of published population genomics data sets offers an underexploited opportunity to study microbial profiles from the host shotgun sequencing data. Here, we use sequence data originally generated from killer whale Orcinus orca skin biopsies for population genomics, to characterize the skin microbiome and investigate how host social and geographical factors influence the microbial community composition. Having identified 845 microbial taxa from 2.4 million reads that did not map to the killer whale reference genome, we found that both ecotypic and geographical factors influence community composition of killer whale skin microbiomes. Furthermore, we uncovered key taxa that drive the microbiome community composition and showed that they are embedded in unique networks, one of which is tentatively linked to diatom presence and poor skin condition. Community composition differed between Antarctic killer whales with and without diatom coverage, suggesting that the previously reported episodic migrations of Antarctic killer whales to warmer waters associated with skin turnover may control the effects of potentially pathogenic bacteria such as Tenacibaculum dicentrarchi. Our work demonstrates the feasibility of microbiome studies from host shotgun sequencing data and highlights the importance of metagenomics in understanding the relationship between host and microbial ecology.}, }
@article {pmid31076501, year = {2019}, author = {Toivonen, L and Hasegawa, K and Waris, M and Ajami, NJ and Petrosino, JF and Camargo, CA and Peltola, V}, title = {Early nasal microbiota and acute respiratory infections during the first years of life.}, journal = {Thorax}, volume = {74}, number = {6}, pages = {592-599}, doi = {10.1136/thoraxjnl-2018-212629}, pmid = {31076501}, issn = {1468-3296}, mesh = {Acute Disease ; Corynebacterium/isolation &amp; purification ; Disease Susceptibility ; Female ; Finland/epidemiology ; Gram-Positive Bacteria/isolation &amp; purification ; Humans ; Incidence ; Infant ; Infant, Newborn ; Male ; *Microbiota ; Moraxella/isolation &amp; purification ; Nasal Cavity/*microbiology ; Prospective Studies ; Respiratory Tract Infections/epidemiology/*microbiology ; Staphylococcus/isolation &amp; purification ; Streptococcus/isolation &amp; purification ; }, abstract = {BACKGROUND: Emerging evidence shows that airway microbiota may modulate local immune responses, thereby contributing to the susceptibility and severity of acute respiratory infections (ARIs). However, there are little data on the longitudinal relationships between airway microbiota and susceptibility to ARIs in children.<br><br>OBJECTIVE: We aimed to investigate the association of early nasal microbiota and the subsequent risk of ARIs during the first years of life.<br><br>METHODS: In this prospective population-based birth-cohort study in Finland, we followed 839 healthy infants for ARIs from birth to age 24 months. Nasal microbiota was tested using 16S rRNA gene sequencing at age 2 months. We applied an unsupervised clustering approach to identify early nasal microbiota profiles, and examined the association of profiles with the rate of ARIs during age 2-24 months.<br><br>RESULTS: We identified five nasal microbiota profiles dominated by Moraxella, Streptococcus, Dolosigranulum, Staphylococcus and Corynebacteriaceae, respectively. Incidence rate of ARIs was highest in children with an early Moraxella-dominant profile and lowest in those with a Corynebacteriaceae-dominant profile (738 vs 552/100 children years; unadjusted incidence rate ratio (IRR), 1.34; 95% CI 1.16 to 1.54; p < 0.001). After adjusting for nine potential confounders, the Moraxella-dominant profile-ARI association persisted (adjusted IRR (aIRR), 1.19; 95% CI 1.04 to 1.37; p = 0.01). Similarly, the incidence rate of lower respiratory tract infections (a subset of all ARIs) was significantly higher in children with an early Moraxella-dominant profile (aIRR, 2.79; 95% CI 1.04 to 8.09; p = 0.04).<br><br>CONCLUSION: Moraxella-dominant nasal microbiota profile in early infancy was associated with an increased rate of ARIs during the first 2 years of life.}, }
@article {pmid31308552, year = {2019}, author = {Ji, BW and Sheth, RU and Dixit, PD and Huang, Y and Kaufman, A and Wang, HH and Vitkup, D}, title = {Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling.}, journal = {Nature methods}, volume = {16}, number = {8}, pages = {731-736}, doi = {10.1038/s41592-019-0467-y}, pmid = {31308552}, issn = {1548-7105}, support = {R01 AI132403/AI/NIAID NIH HHS/United States ; R01 DK118044/DK/NIDDK NIH HHS/United States ; }, mesh = {*Algorithms ; Bacteria/classification/*genetics ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Metagenomics/*methods ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; *Soil Microbiology ; *Spatio-Temporal Analysis ; Specimen Handling ; }, abstract = {Metagenomic sequencing has enabled detailed investigation of diverse microbial communities, but understanding their spatiotemporal variability remains an important challenge. Here, we present decomposition of variance using replicate sampling (DIVERS), a method based on replicate sampling and spike-in sequencing. The method quantifies the contributions of temporal dynamics, spatial sampling variability, and technical noise to the variances and covariances of absolute bacterial abundances. We applied DIVERS to investigate a high-resolution time series of the human gut microbiome and a spatial survey of a soil bacterial community in Manhattan's Central Park. Our analysis showed that in the gut, technical noise dominated the abundance variability for nearly half of the detected taxa. DIVERS also revealed substantial spatial heterogeneity of gut microbiota, and high temporal covariances of taxa within the Bacteroidetes phylum. In the soil community, spatial variability primarily contributed to abundance fluctuations at short time scales (weeks), while temporal variability dominated at longer time scales (several months).}, }
@article {pmid31189463, year = {2019}, author = {Thomas, AM and Segata, N}, title = {Multiple levels of the unknown in microbiome research.}, journal = {BMC biology}, volume = {17}, number = {1}, pages = {48}, doi = {10.1186/s12915-019-0667-z}, pmid = {31189463}, issn = {1741-7007}, mesh = {Archaea/classification/physiology ; Bacteria/classification ; Bacterial Physiological Phenomena ; *Metagenome ; *Metagenomics ; *Microbiota/genetics ; }, abstract = {Metagenomics allows exploration of aspects of a microbial community that were inaccessible by cultivation-based approaches targeting single microbes. Many new microbial taxa and genes have been discovered using metagenomics, but different kinds of &quot;unknowns&quot; still remain in a microbiome experiment. We discuss here whether and how it is possible to deal with them.}, }
@article {pmid30799264, year = {2019}, author = {De Filippis, F and Pasolli, E and Tett, A and Tarallo, S and Naccarati, A and De Angelis, M and Neviani, E and Cocolin, L and Gobbetti, M and Segata, N and Ercolini, D}, title = {Distinct Genetic and Functional Traits of Human Intestinal Prevotella copri Strains Are Associated with Different Habitual Diets.}, journal = {Cell host &amp; microbe}, volume = {25}, number = {3}, pages = {444-453.e3}, doi = {10.1016/j.chom.2019.01.004}, pmid = {30799264}, issn = {1934-6069}, mesh = {Diet/*methods ; *Feeding Behavior ; Female ; Gastrointestinal Microbiome ; Genome, Bacterial ; Genotype ; Healthy Volunteers ; Humans ; Italy ; Male ; *Microbiota ; Phenotype ; Prevalence ; Prevotella/*classification/genetics/*isolation &amp; purification/physiology ; }, abstract = {The role of intestinal Prevotella species in human health is controversial, with both positive and negative associations. Strain-level diversity may contribute to discrepancies in genus and species associations with health and disease. We dissected the gut metagenomes of Italians with varying dietary habits, investigating the presence of distinct Prevotella copri strains. Fiber-rich diets were linked to P. copri types with enhanced potential for carbohydrate catabolism. P. copri strains associated with an omnivore diet had a higher prevalence of the leuB gene-involved in branched-chain amino acid biosynthesis-a risk factor for glucose intolerance and type 2 diabetes. These P. copri pangenomes were compared to existing cohorts, providing evidence of distinct gene repertoires characterizing different P. copri populations, with drug metabolism and complex carbohydrate degradation significantly associated with Western and non-Western individuals, respectively. Strain-level P. copri diversity in gut microbiomes is affected by diet and should be considered when examining host-microbe associations.}, }
@article {pmid30667580, year = {2019}, author = {Chen, T and Liu, AB and Sun, S and Ajami, NJ and Ross, MC and Wang, H and Zhang, L and Reuhl, K and Kobayashi, K and Onishi, JC and Zhao, L and Yang, CS}, title = {Green Tea Polyphenols Modify the Gut Microbiome in db/db Mice as Co-Abundance Groups Correlating with the Blood Glucose Lowering Effect.}, journal = {Molecular nutrition &amp; food research}, volume = {63}, number = {8}, pages = {e1801064}, doi = {10.1002/mnfr.201801064}, pmid = {30667580}, issn = {1613-4133}, support = {P30 ES005022/ES/NIEHS NIH HHS/United States ; P30 ES023512/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Biflavonoids/pharmacology ; Blood Glucose/*metabolism ; Body Weight/drug effects ; Catechin/analogs &amp; derivatives/pharmacology ; Female ; Gastrointestinal Microbiome/*drug effects/genetics/physiology ; Hypoglycemic Agents/pharmacology ; Insulin/blood ; Insulin-Secreting Cells/drug effects/pathology ; Mice, Mutant Strains ; Organ Size/drug effects ; Polyphenols/*pharmacology ; RNA, Ribosomal, 16S ; Tea/*chemistry ; }, abstract = {SCOPE: The effects of green tea polyphenols, Polyphenon E (PPE), and black tea polyphenols, theaflavins (TFs), on gut microbiota and development of diabetes in db/db mice are investigated and compared.<br><br>METHODS AND RESULTS: Supplementation of PPE (0.1%) in the diet of female db/db mice for 7 weeks decreases fasting blood glucose levels and mesenteric fat while increasing the serum level of insulin, possibly through protection against β-cell damage. However, TFs are less or not effective. Microbiome analysis through 16S rRNA gene sequencing shows that PPE and TFs treatments significantly alter the bacterial community structure in the cecum and colon, but not in the ileum. The key bacterial phylotypes responding to the treatments are then clustered into 11 co-abundance groups (CAGs). CAGs 6 and 7, significantly increased by PPE but not by TFs, are negatively associated with blood glucose levels. The operational taxonomic units in these CAGs are from two different phyla, Firmicutes and Bacteroidetes. CAG 10, decreased by PPE and TFs, is positively associated with blood glucose levels.<br><br>CONCLUSION: Gut microbiota respond to tea polyphenol treatments as CAGs instead of taxa. Some of the CAGs associated with the blood glucose lowering effect are enriched by PPE, but not TFs.}, }
@article {pmid31605831, year = {2020}, author = {Yang, Y and Pan, J and Zhou, Z and Wu, J and Liu, Y and Lin, JG and Hong, Y and Li, X and Li, M and Gu, JD}, title = {Complex microbial nitrogen-cycling networks in three distinct anammox-inoculated wastewater treatment systems.}, journal = {Water research}, volume = {168}, number = {}, pages = {115142}, doi = {10.1016/j.watres.2019.115142}, pmid = {31605831}, issn = {1879-2448}, mesh = {Ammonia ; Bioreactors ; Microbial Consortia ; *Nitrification ; Nitrites ; Nitrogen ; Nitrogen Cycle ; Oxidation-Reduction ; *Waste Water ; }, abstract = {Microbial nitrogen removal mediated by anaerobic ammonium oxidation (anammox) are cost-effective, yet it is time-consuming to accumulate the slow-growing anammox bacteria in conventional wastewater treatment plants (WWTPs). Inoculation of anammox enriched pellets is an effective way to establish anammox and achieve shortcut nitrogen removal in full-scale WWTPs. However, little is known about the complex microbial nitrogen-cycling networks in these anammox-inoculated WWTPs. Here, we applied metagenomic and metatranscriptomic tools to study the microbial nitrogen removal in three conventional WWTPs, which have been inoculated exogenous anammox pellets, representing partial-nitrification anammox (PNA) and nitrification-denitrification nitrogen removal processes. In the PNA system of Bali (BL), ammonia was partially oxidized by ammonia-oxidizing bacteria (AOB) Nitrosomonas and the oxidized nitrite and the remaining ammonium were directly converted to N2 by anammox bacteria Ca. Brocadia and Ca. Kuenenia. In the nitrification-denitrification system of Wenshan (WS), ammonia-oxidizing archaea (AOA) Thaumarchaeota unexpectedly dominated the nitrifying community in the presence of AOB Nitrosomonas. Meanwhile, the biomass yield of Ca. Brocadia was likely inhibited by the high biodegradable organic compound input and limited by substrate competitions from AOA, AOB, complete ammonia oxidizers (comammox) Nitrospira, nitrite-oxidizing bacteria (NOB) Nitrospira, and heterotrophic denitrifiers. Unexpectedly, comammox Nitrospira was the predominant nitrifier in the presence of AOB Nitrosomonas in the organic carbon-rich nitrification-denitrification system of Linkou (LK). These results clearly showed that distinct active groups were working in concert for an effective nitrogen removal in different WWTPs. This study confirmed the feasibility of anammox application in ammonium-rich systems by direct inoculation of the exogenous anammox pellets and improved our understanding of microbial nitrogen cycling in anammox-driven conventional WWTPs from both physiochemical and omics perspectives.}, }
@article {pmid31359005, year = {2019}, author = {Bertrand, D and Shaw, J and Kalathiyappan, M and Ng, AHQ and Kumar, MS and Li, C and Dvornicic, M and Soldo, JP and Koh, JY and Tong, C and Ng, OT and Barkham, T and Young, B and Marimuthu, K and Chng, KR and Sikic, M and Nagarajan, N}, title = {Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes.}, journal = {Nature biotechnology}, volume = {37}, number = {8}, pages = {937-944}, doi = {10.1038/s41587-019-0191-2}, pmid = {31359005}, issn = {1546-1696}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/*drug effects/*genetics ; Drug Resistance, Bacterial ; Feces/microbiology ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome ; Metagenomics/*methods ; Microbiota/*drug effects ; Nanopores ; Sequence Analysis, DNA/*methods ; Software ; }, abstract = {Characterization of microbiomes has been enabled by high-throughput metagenomic sequencing. However, existing methods are not designed to combine reads from short- and long-read technologies. We present a hybrid metagenomic assembler named OPERA-MS that integrates assembly-based metagenome clustering with repeat-aware, exact scaffolding to accurately assemble complex communities. Evaluation using defined in vitro and virtual gut microbiomes revealed that OPERA-MS assembles metagenomes with greater base pair accuracy than long-read (>5×; Canu), higher contiguity than short-read (~10× NGA50; MEGAHIT, IDBA-UD, metaSPAdes) and fewer assembly errors than non-metagenomic hybrid assemblers (2×; hybridSPAdes). OPERA-MS provides strain-resolved assembly in the presence of multiple genomes of the same species, high-quality reference genomes for rare species (<1%) with ~9× long-read coverage and near-complete genomes with higher coverage. We used OPERA-MS to assemble 28 gut metagenomes of antibiotic-treated patients, and showed that the inclusion of long nanopore reads produces more contiguous assemblies (200× improvement over short-read assemblies), including more than 80 closed plasmid or phage sequences and a new 263 kbp jumbo phage. High-quality hybrid assemblies enable an exquisitely detailed view of the gut resistome in human patients.}, }
@article {pmid31332325, year = {2019}, author = {Sheth, RU and Li, M and Jiang, W and Sims, PA and Leong, KW and Wang, HH}, title = {Spatial metagenomic characterization of microbial biogeography in the gut.}, journal = {Nature biotechnology}, volume = {37}, number = {8}, pages = {877-883}, doi = {10.1038/s41587-019-0183-2}, pmid = {31332325}, issn = {1546-1696}, support = {R01 AI132403/AI/NIAID NIH HHS/United States ; R01 DK118044/DK/NIDDK NIH HHS/United States ; T32 GM008224/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA Barcoding, Taxonomic ; DNA, Bacterial/genetics ; *Gastrointestinal Microbiome ; *Genome, Bacterial ; Metagenome ; Metagenomics/*methods ; Mice ; Microfluidic Analytical Techniques ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA/methods ; }, abstract = {Spatial structuring is important for the maintenance of natural ecological systems1,2. Many microbial communities, including the gut microbiome, display intricate spatial organization3-9. Mapping the biogeography of bacteria can shed light on interactions that underlie community functions10-12, but existing methods cannot accommodate the hundreds of species that are found in natural microbiomes13-17. Here we describe metagenomic plot sampling by sequencing (MaPS-seq), a culture-independent method to characterize the spatial organization of a microbiome at micrometer-scale resolution. Intact microbiome samples are immobilized in a gel matrix and cryofractured into particles. Neighboring microbial taxa in the particles are then identified by droplet-based encapsulation, barcoded 16S rRNA amplification and deep sequencing. Analysis of three regions of the mouse intestine revealed heterogeneous microbial distributions with positive and negative co-associations between specific taxa. We identified robust associations between Bacteroidales taxa in all gut compartments and showed that phylogenetically clustered local regions of bacteria were associated with a dietary perturbation. Spatial metagenomics could be used to study microbial biogeography in complex habitats.}, }
@article {pmid31185914, year = {2019}, author = {Tran, HT and Wang, HC and Hsu, TW and Sarkar, R and Huang, CL and Chiang, TY}, title = {Revegetation on abandoned salt ponds relieves the seasonal fluctuation of soil microbiomes.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {478}, doi = {10.1186/s12864-019-5875-y}, pmid = {31185914}, issn = {1471-2164}, support = {Aim for the Top University Project//National Cheng Kung University/ ; }, mesh = {Ecosystem ; Environmental Restoration and Remediation ; Metabolic Networks and Pathways ; *Microbiota ; *Plant Development ; Ponds/*chemistry/*microbiology ; *Salts ; *Seasons ; *Soil Microbiology ; }, abstract = {BACKGROUND: Salt pond restoration aims to recover the environmental damages that accumulated over the long history of salt production. Of the restoration strategies, phytoremediation that utilizes salt-tolerant plants and soil microorganisms to reduce the salt concentrations is believed to be environmentally-friendly. However, little is known about the change of bacterial community during salt pond restoration in the context of phytoremediation. In the present study, we used 16S metagenomics to compare seasonal changes of bacterial communities between the revegetated and barren salterns at Sicao, Taiwan.<br><br>RESULTS: In both saltern types, Proteobacteria, Planctomycetes, Chloroflexi, and Bacteroidetes were predominant at the phylum level. In the revegetated salterns, the soil microbiomes displayed high species diversities and underwent a stepwise transition across seasons. In the barren salterns, the soil microbiomes fluctuated greatly, indicating that mangroves tended to stabilize the soil microorganism communities over the succession. Bacteria in the order Halanaerobiaceae and archaea in the family Halobacteriaceae that were adapted to high salinity exclusively occurred in the barren salterns. Among the 441 persistent operational taxonomic units detected in the revegetated salterns, 387 (87.5%) were present as transient species in the barren salterns. Only 32 persistent bacteria were exclusively detected in the revegetated salterns. Possibly, salt-tolerant plants provided shelters for those new colonizers.<br><br>CONCLUSIONS: The collective data indicate that revegetation tended to stabilize the microbiome across seasons and enriched the microbial diversity in the salterns, especially species of Planctomycetes and Acidobacteria.}, }
@article {pmid31167634, year = {2019}, author = {LaPierre, N and Mangul, S and Alser, M and Mandric, I and Wu, NC and Koslicki, D and Eskin, E}, title = {MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples.}, journal = {BMC genomics}, volume = {20}, number = {Suppl 5}, pages = {423}, doi = {10.1186/s12864-019-5699-9}, pmid = {31167634}, issn = {1471-2164}, support = {R01 ES021801/ES/NIEHS NIH HHS/United States ; R01 MH101782/MH/NIMH NIH HHS/United States ; K25 HL080079/HL/NHLBI NIH HHS/United States ; P01 HL028481/HL/NHLBI NIH HHS/United States ; U01 DA024417/DA/NIDA NIH HHS/United States ; T32 EB016640/EB/NIBIB NIH HHS/United States ; R01 ES022282/ES/NIEHS NIH HHS/United States ; P01 HL030568/HL/NHLBI NIH HHS/United States ; R01 GM083198/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Computational Biology/*methods ; Fungi/classification/*genetics ; *Genetic Markers ; Genome, Fungal ; Genome, Viral ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/*methods ; *Microbiota ; Sequence Analysis, DNA/*methods ; Viruses/classification/*genetics ; }, abstract = {BACKGROUND: High throughput sequencing has spurred the development of metagenomics, which involves the direct analysis of microbial communities in various environments such as soil, ocean water, and the human body. Many existing methods based on marker genes or k-mers have limited sensitivity or are too computationally demanding for many users. Additionally, most work in metagenomics has focused on bacteria and archaea, neglecting to study other key microbes such as viruses and eukaryotes.<br><br>RESULTS: Here we present a method, MiCoP (Microbiome Community Profiling), that uses fast-mapping of reads to build a comprehensive reference database of full genomes from viruses and eukaryotes to achieve maximum read usage and enable the analysis of the virome and eukaryome in each sample. We demonstrate that mapping of metagenomic reads is feasible for the smaller viral and eukaryotic reference databases. We show that our method is accurate on simulated and mock community data and identifies many more viral and fungal species than previously-reported results on real data from the Human Microbiome Project.<br><br>CONCLUSIONS: MiCoP is a mapping-based method that proves more effective than existing methods at abundance profiling of viruses and eukaryotes in metagenomic samples. MiCoP can be used to detect the full diversity of these communities. The code, data, and documentation are publicly available on GitHub at: https://github.com/smangul1/MiCoP .}, }
@article {pmid30959166, year = {2019}, author = {Marón, CF and Kohl, KD and Chirife, A and Di Martino, M and Fons, MP and Navarro, MA and Beingesser, J and McAloose, D and Uzal, FA and Dearing, MD and Rowntree, VJ and Uhart, M}, title = {Symbiotic microbes and potential pathogens in the intestine of dead southern right whale (Eubalaena australis) calves.}, journal = {Anaerobe}, volume = {57}, number = {}, pages = {107-114}, doi = {10.1016/j.anaerobe.2019.04.003}, pmid = {30959166}, issn = {1095-8274}, mesh = {Animals ; Animals, Newborn ; Argentina ; Bacteria/*classification/*isolation &amp; purification ; Bacteriological Techniques ; *Cadaver ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Metagenomics ; Whales/*microbiology ; }, abstract = {Between 2003 and 2017, at least 706 southern right whale (Eubalaena australis) calves died at the Península Valdés calving ground in Argentina. Pathogenic microbes are often suggested to be the cause of stranding events in cetaceans; however, to date there is no evidence supporting bacterial infections as a leading cause of right whale calf deaths in Argentina. We used high-throughput sequencing and culture methods to characterize the bacterial communities and to detect potential pathogens from the intestine of stranded calves. We analyzed small and large intestinal contents from 44 dead calves that stranded at Península Valdés from 2005 to 2010 and found 108 bacterial genera, most identified as Firmicutes or Bacteroidetes, and 9 genera that have been previously implicated in diseases of marine mammals. Only one operational taxonomic unit was present in all samples and identified as Clostridium perfringens type A. PCR results showed that all C. perfringens isolates (n = 38) were positive for alpha, 50% for beta 2 (n = 19) and 47% for enterotoxin (CPE) genes (n = 18). The latter is associated with food-poisoning and gastrointestinal diseases in humans and possibly other animals. The prevalence of the cpe gene found in the Valdés' calves is unusually high compared with other mammals. However, insufficient histologic evidence of gastrointestinal inflammation or necrosis (the latter possibly masked by autolysis) in the gut of stranded calves, and absence of enterotoxin detection precludes conclusions about the role of C. perfringens in calf deaths. Further work is required to determine whether C. perfringens or other pathogens detected in this study are causative agents of calf deaths at Península Valdés.}, }
@article {pmid30832983, year = {2019}, author = {Bushman, FD}, title = {De-Discovery of the Placenta Microbiome.}, journal = {American journal of obstetrics and gynecology}, volume = {220}, number = {3}, pages = {213-214}, doi = {10.1016/j.ajog.2018.11.1093}, pmid = {30832983}, issn = {1097-6868}, mesh = {Female ; Humans ; *Metagenomics ; *Microbiota ; Placenta ; Pregnancy ; RNA, Ribosomal, 16S ; Real-Time Polymerase Chain Reaction ; }, }
@article {pmid31680056, year = {2019}, author = {Heinrichs, L and Aytur, SA and Bucci, JP}, title = {Whole metagenomic sequencing to characterize the sediment microbial community within the Stellwagen Bank National Marine Sanctuary and preliminary biosynthetic gene cluster screening of Streptomyces scabrisporus.}, journal = {Marine genomics}, volume = {}, number = {}, pages = {100718}, doi = {10.1016/j.margen.2019.100718}, pmid = {31680056}, issn = {1876-7478}, abstract = {Understanding the marine sediment microbial community structure is of increasing importance to microbiologists since little is known of the diverse taxonomy that exists within this environment. Quantifying microbial species distribution patterns within marine sanctuaries is necessary to address conservation requirements. The objectives of this study were to characterize the relative abundance and biodiversity of metagenome samples of the sediment microbial community in the Stellwagen Bank National Marine Sanctuary (SBNMS). Related to the need for a comprehensive assessment of the microbial habitat within marine sanctuaries is the increased threat of antibiotic-resistant pathogens, coupled with multi-resistant bacterial strains. This has necessitated a renewed search for bioactive compounds in marine benthic habitat. An additional aim was to initiate quantification of biosynthetic gene clusters in species that have potential for natural product and drug discovery relevant to human health. Surficial sediment from 18 samples was collected in the summer and fall of 2017 from three benthic sites in the SBNMS. Microbial DNA was extracted from samples, and sequencing libraries were prepared for taxonomic analysis. Whole metagenome sequencing (WMGS) in combination with a bioinformatics pipeline was employed to delineate the taxa of bacteria present in each sample. Among all sampling sites, biodiversity was higher for summer compared to fall for class (p = 0.0013; F = 4.5) and genus (p = 0.0219; F = 4.4). Actinobacteria was the fifth most abundant class in both seasons (7.81%). Streptomyces was observed to be the fourth most abundant genus in both seasons with significantly higher prevalence in summer compared to fall samples. In summer, site 3 had the highest percentage of Streptomyces (1.71%) compared to sites 2 (1.62%) and 1 (1.37%). The results enabled preliminary quantification of the sequenced hits from the SBNMS sites with the highest potential for harboring secondary metabolite biosynthetic gene clusters for Streptomyces scabrisporus strain (NF3) genomic regions. This study is one of the first to use a whole metagenomics approach to characterize sediment microbial biodiversity in partnership with the SBNMS and demonstrates the potential for future ecological and biomedical research.}, }
@article {pmid31337187, year = {2019}, author = {Zhang, C and Xu, B and Lu, T and Huang, Z}, title = {Metagenomic Analysis of the Fecal Microbiomes of Wild Asian Elephants Reveals Microflora and Enzymes that Mainly Digest Hemicellulose.}, journal = {Journal of microbiology and biotechnology}, volume = {29}, number = {8}, pages = {1255-1265}, doi = {10.4014/jmb.1904.04033}, pmid = {31337187}, issn = {1738-8872}, mesh = {Animals ; Bacteria/classification/enzymology/genetics ; Biodiversity ; Cellulose/metabolism ; China ; Elephants/*microbiology ; Enzymes/*classification ; Feces/*microbiology ; Firmicutes/genetics ; Gastrointestinal Microbiome/genetics/*physiology ; Gastrointestinal Tract/*microbiology ; Lignin/metabolism ; *Metagenomics ; Phylogeny ; Polysaccharides/*metabolism ; }, abstract = {To investigate the diversity of gastrointestinal microflora and lignocellulose-degrading enzymes in wild Asian elephants, three of these animals living in the same group were selected for study from the Wild Elephant Valley in the Xishuangbanna Nature Reserve of Yunnan Province, China. Fresh fecal samples from the three wild Asian elephants were analyzed by metagenomic sequencing to study the diversity of their gastrointestinal microbes and cellulolytic enzymes. There were a high abundance of Firmicutes and a higher abundance of hemicellulose-degrading hydrolases than cellulose-degrading hydrolases in the wild Asian elephants. Furthermore, there were a high abundance and a rich diversity of carbohydrate active enzymes (CAZymes) obtained from the gene set annotation of the three samples, with the majority of them showing low identity with the CAZy database entry. About half of the CAZymes had no species source at the phylum or genus level. These indicated that the wild Asian elephants might possess greater ability to digest hemicellulose than cellulose to provide energy, and moreover, the gastrointestinal tracts of these pachyderms might be a potential source of novel efficient lignocellulose-degrading enzymes. Therefore, the exploitation and utilization of these enzyme resources could help us to alleviate the current energy crisis and ensure food security.}, }
@article {pmid31022528, year = {2019}, author = {Watts, MP and Spurr, LP and Lê Cao, KA and Wick, R and Banfield, JF and Moreau, JW}, title = {Genome-resolved metagenomics of an autotrophic thiocyanate-remediating microbial bioreactor consortium.}, journal = {Water research}, volume = {158}, number = {}, pages = {106-117}, doi = {10.1016/j.watres.2019.02.058}, pmid = {31022528}, issn = {1879-2448}, mesh = {Autotrophic Processes ; Bioreactors ; *Metagenomics ; Microbial Consortia ; *Thiocyanates ; }, abstract = {Industrial thiocyanate (SCN-) waste streams from gold mining and coal coking have polluted environments worldwide. Modern SCN- bioremediation involves use of complex engineered heterotrophic microbiomes; little attention has been given to the ability of a simple environmental autotrophic microbiome to biodegrade SCN-. Here we present results from a bioreactor experiment inoculated with SCN- -loaded mine tailings, incubated autotrophically, and subjected to a range of environmentally relevant conditions. Genome-resolved metagenomics revealed that SCN- hydrolase-encoding, sulphur-oxidizing autotrophic bacteria mediated SCN- degradation. These microbes supported metabolically-dependent non-SCN--degrading sulphur-oxidizing autotrophs and non-sulphur oxidizing heterotrophs, and &quot;niche&quot; microbiomes developed spatially (planktonic versus sessile) and temporally (across changing environmental parameters). Bioreactor microbiome structures changed significantly with increasing temperature, shifting from Thiobacilli to a novel SCN- hydrolase-encoding gammaproteobacteria. Transformation of carbonyl sulphide (COS), a key intermediate in global biogeochemical sulphur cycling, was mediated by plasmid-hosted CS2 and COS hydrolase genes associated with Thiobacillus, revealing a potential for horizontal transfer of this function. Our work shows that simple native autotrophic microbiomes from mine tailings can be employed for SCN- bioremediation, thus improving the recycling of ore processing waters and reducing the hydrological footprint of mining.}, }
@article {pmid30464240, year = {2018}, author = {Wood, JR and Díaz, FP and Latorre, C and Wilmshurst, JM and Burge, OR and Gutiérrez, RA}, title = {Plant pathogen responses to Late Pleistocene and Holocene climate change in the central Atacama Desert, Chile.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {17208}, pmid = {30464240}, issn = {2045-2322}, support = {Core funding for Crown Research Institutes//Ministry of Business, Innovation and Employment (MBIE)/International ; Core funding to Crown Research Institutes//Ministry for Business Innovation and Employment (MBIE)/International ; }, mesh = {Animals ; Chile ; *Climate Change ; DNA, Ancient/*isolation &amp; purification ; DNA, Fungal/*isolation &amp; purification ; Desert Climate ; Feces/chemistry ; *Fossils ; Fungi/*classification/*genetics ; Metagenomics/methods ; Plant Diseases/*microbiology ; RNA, Ribosomal, 18S/genetics ; Rodentia ; }, abstract = {Future climate change has the potential to alter the distribution and prevalence of plant pathogens, which may have significant implications for both agricultural crops and natural plant communities. However, there are few long-term datasets against which modelled predictions of pathogen responses to climate change can be tested. Here, we use 18S metabarcoding of 28 rodent middens (solidified deposits of rodent coprolites and nesting material) from the Central Atacama, spanning the last ca. 49 ka, to provide the first long-term late Quaternary record of change in plant pathogen communities in response to changing climate. Plant pathogen richness was significantly greater in middens deposited during the Central Andean Pluvial Event (CAPE); a period of increased precipitation between 17.5-8.5 ka. Moreover, the occurrence frequency of Pucciniaceae (rust fungi) was significantly greater during the CAPE, and the highest relative abundances for five additional potentially pathogenic taxa also occurred during this period. The results demonstrate the promising potential for ancient DNA analysis of late Quaternary samples to reveal insights into how plant pathogens responded to past climatic and environmental change, which could help predict how pathogens may responded to future change.}, }
@article {pmid29718124, year = {2018}, author = {Inoue, T and Nakayama, J and Moriya, K and Kawaratani, H and Momoda, R and Ito, K and Iio, E and Nojiri, S and Fujiwara, K and Yoneda, M and Yoshiji, H and Tanaka, Y}, title = {Gut Dysbiosis Associated With Hepatitis C Virus Infection.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {67}, number = {6}, pages = {869-877}, doi = {10.1093/cid/ciy205}, pmid = {29718124}, issn = {1537-6591}, mesh = {Aged ; Aged, 80 and over ; Alanine Transaminase/blood ; Bacteria/classification/*isolation &amp; purification ; Case-Control Studies ; DNA, Bacterial/genetics ; Disease Progression ; Dysbiosis/*virology ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Hepacivirus/isolation &amp; purification ; Hepatitis C, Chronic/*complications ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenomics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Background: Little is known about the effect of hepatitis C virus (HCV) infection on gut microbiota and the relationship between alteration of gut microbiota and chronic hepatitis C (CHC) progression. We performed a comparative study of gut microbiota composition between CHC patients and healthy individuals.<br><br>Methods: Fecal samples from 166 CHC patients were compared with those from 23 healthy individuals; the gut microbiota community was analyzed using 16S ribosomal RNA gene sequencing. CHC patients were diagnosed with persistently normal serum alanine aminotransferase without evidence of liver cirrhosis (LC) (PNALT, n = 18), chronic hepatitis (CH, n = 84), LC (n = 40), and hepatocellular carcinoma in LC (n = 24).<br><br>Results: Compared with healthy individuals, bacterial diversity was lower in persons with HCV infection, with a decrease in the order Clostridiales and an increase in Streptococcus and Lactobacillus. Microbiota dysbiosis already appeared in the PNALT stage with the transient increase in Bacteroides and Enterobacteriaceae. Predicted metagenomics of microbial communities showed an increase in the urease gene mainly encoded by viridans streptococci during CHC progression, consistent with a significantly higher fecal pH in CH and LC patients than in healthy individuals or those in the PNALT stage.<br><br>Conclusions: HCV infection is associated with gut dysbiosis, even in patients with mild liver disease. Additionally, overgrowth of viridans streptococci can account for hyperammonemia in CH and LC. Further studies would help to propose a novel treatment strategy because the gut microbiome can be therapeutically altered, potentially reducing the complications of chronic liver disease.}, }
@article {pmid31670799, year = {2019}, author = {Arribas, P and Andújar, C and Moraza, ML and Linard, B and Emerson, BC and Vogler, AP}, title = {Mitochondrial metagenomics reveals the ancient origin and phylodiversity of soil mites and provides a phylogeny of the Acari.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msz255}, pmid = {31670799}, issn = {1537-1719}, abstract = {High-throughput DNA methods hold great promise for phylogenetic analysis of lineages that are difficult to study with conventional molecular and morphological approaches. The mites (Acari), and in particular the highly diverse soil-dwelling lineages, are among the least known branches of the metazoan Tree-of-Life. We extracted numerous minute mites from soils in an area of mixed forest and grassland in southern Iberia. Selected specimens representing the full morphological diversity were shotgun sequenced in bulk, followed by genome assembly of short reads from the mixture, which produced >100 mitochondrial genomes representing diverse acarine lineages. Phylogenetic analyses in combination with taxonomically limited mitogenomes available publicly resulted in plausible trees defining basal relationships of the Acari. Several critical nodes were supported by ancestral-state reconstructions of mitochondrial gene rearrangements. Molecular calibration placed the minimum age for the common ancestor of the superorder Acariformes, which includes most soil-dwelling mites, to the Cambrian-Ordovician (likely within 455-552 Mya), while the origin of the superorder Parasitiformes was placed later in the Carboniferous-Permian. Most family-level taxa within the Acariformes were dated to the Jurassic and Triassic. The ancient origin of Acariformes and the early diversification of major extant lineages linked to the soil are consistent with a pioneering role for mites in building the earliest terrestrial ecosystems.}, }
@article {pmid31306822, year = {2019}, author = {Han, L and Cai, L and Zhang, H and Long, Z and Yu, Y and Fang, H}, title = {Development of antibiotic resistance genes in soils with ten successive treatments of chlortetracycline and ciprofloxacin.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {253}, number = {}, pages = {152-160}, doi = {10.1016/j.envpol.2019.07.031}, pmid = {31306822}, issn = {1873-6424}, mesh = {Agriculture ; Anti-Bacterial Agents/*toxicity ; Chlortetracycline/analysis/*toxicity ; Ciprofloxacin/*toxicity ; Drug Resistance, Microbial/*genetics ; Manure/analysis ; Metagenomics ; Microbiota/drug effects ; Soil ; *Soil Microbiology ; Tetracycline/pharmacology ; Tetracycline Resistance ; }, abstract = {Antibiotic contamination caused by the long-term use of organic manure (OM) in greenhouse agricultural soils poses potential detrimental effects to the soil environment. By applying OM containing chlortetracycline (CTC) and/or ciprofloxacin (CIP) ten times in soil under laboratory conditions, we investigated the dissipation and accumulation characteristics of CTC and CIP in the soil, the changes in the microbial pollution-induced community tolerance (PICT), and the diversity and abundance of antibiotic resistance genes (ARGs) in the soil microbiome. The dissipation of CTC was rapid while CIP was accumulated in repeatedly treated soils; further, CIP could inhibit the dissipation of CTC. Meanwhile, the PICT to CTC and/or CIP significantly increased up to 15.0-fold after ten successive treatments compared to that in the first treatment. As the treatment frequency increased, significant upward trends in the abundances of tetracycline resistance genes tetA(G), tetX2, tetX, tetG, tetA(33), tetA, tetW, and tetA(P), fluoroquinolone resistance gene qnrA6, and multiple resistance gene mexF were revealed by both metagenomic and qPCR analyses. The findings demonstrated that repeated treatments with CTC and/or CIP can alter the dissipation rate, promote an increase in PICT to CTC and/or CIP, and increase the ARGs abundance in steps.}, }
@article {pmid31117952, year = {2019}, author = {Moore, SG and Ericsson, AC and Behura, SK and Lamberson, WR and Evans, TJ and McCabe, MS and Poock, SE and Lucy, MC}, title = {Concurrent and long-term associations between the endometrial microbiota and endometrial transcriptome in postpartum dairy cows.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {405}, doi = {10.1186/s12864-019-5797-8}, pmid = {31117952}, issn = {1471-2164}, mesh = {Animals ; Cattle ; Endometrium/*metabolism/*microbiology ; *Estrous Cycle ; Female ; Lactation ; Metabolome ; *Microbiota ; *Postpartum Period ; RNA, Ribosomal, 16S/genetics ; *Transcriptome ; }, abstract = {BACKGROUND: Fertility in dairy cows depends on ovarian cyclicity and on uterine involution. Ovarian cyclicity and uterine involution are delayed when there is uterine dysbiosis (overgrowth of pathogenic bacteria). Fertility in dairy cows may involve a mechanism through which the uterine microbiota affects ovarian cyclicity as well as the transcriptome of the endometrium within the involuting uterus. The hypothesis was that the transcriptome of the endometrium in postpartum cows would be associated with the cyclicity status of the cow as well as the microbiota during uterine involution. The endometrium of first lactation dairy cows was sampled at 1, 5, and 9 weeks postpartum. All cows were allowed to return to cyclicity without intervention until week 5 and treated with an ovulation synchronization protocol so that sampling at week 9 was on day 13 of the estrous cycle. The endometrial microbiota was measured by 16S rRNA gene sequencing and principal component analysis. The endometrial transcriptome was measured by mRNA sequencing, differential gene expression analysis, and Ingenuity Pathway Analysis.<br><br>RESULTS: The endometrial microbiota changed from week 1 to week 5 but the week 5 and week 9 microbiota were similar. The endometrial transcriptome differed for cows that were either cycling or not cycling at week 5 and cyclicity status depended in part on the endometrial microbiota. Compared with cows cycling at week 5, there were large changes in the transcriptome of cows that progressed from non-cycling at week 5 to cycling at week 9. There was evidence for concurrent and longer-term associations between the endometrial microbiota and transcriptome. The week 1 endometrial microbiota had the greatest effect on the subsequent endometrial transcriptome and this effect was greatest at week 5 and diminished by week 9.<br><br>CONCLUSIONS: The cumulative response of the endometrial transcriptome to the microbiota represented the combination of past microbial exposure and current microbial exposure. The endometrial transcriptome in postpartum cows, therefore, depended on the immediate and longer-term effects of the uterine microbiota that acted directly on the uterus. There may also be an indirect mechanism through which the microbiome affects the transcriptome through the restoration of ovarian cyclicity postpartum.}, }
@article {pmid30989782, year = {2019}, author = {Guo, MY and Hou, CJ and Bian, MH and Shen, CH and Zhang, SY and Huo, DQ and Ma, Y}, title = {Characterization of microbial community profiles associated with quality of Chinese strong-aromatic liquor through metagenomics.}, journal = {Journal of applied microbiology}, volume = {127}, number = {3}, pages = {750-762}, doi = {10.1111/jam.14279}, pmid = {30989782}, issn = {1365-2672}, support = {31171684//National Natural Science Foundation of China (NSFC)/ ; 2010NZ0093//Science and Technology Support Program of Sichuan Province (STSP-SC)/ ; 2013FZ0043//Science and Technology Support Program of Sichuan Province (STSP-SC)/ ; GY2015-01//Workstation in Sichuan Province/ ; }, mesh = {Alcoholic Beverages/*microbiology ; Bacteria/*classification/genetics ; China ; *Fermentation ; Metagenomics ; Microbiota/*genetics ; Sequence Analysis, DNA ; }, abstract = {AIMS: Microorganisms in fermentation pits (FPs) play key roles for Chinese-strong-aromatic-liquor (CSAL) production. However, the microbial community in the FPs is still poorly understood. Here, the aim of this study was to reveal the diversity and potential functions of microbiota in FPs.<br><br>METHODS AND RESULTS: Sequencing-by-synthesis-based metagenomic sequencing and annotation results revealed that the microbiota of FPs was primarily composed of Firmicutes (54·6%), Euryarchaeota (15·3%), Bacteroidetes (10·1%), Gammaproteobacteria (5·8%), Opisthokonta (5·7%) and Unclassified_Bacteria (2·3%). And 133 genera were identified as the dominant genera of this fermentative food. Lactobacillus, Sedimentibacter, Syntrophomonas, Methanoculleus, Methanobacterium, Bacillus, Clostridium, Galactomyces, Candida, Pichia, Penicillium and Aspergillus were defined as active populations for biosynthesizing the characteristic volatile compounds of CSAL. The study also revealed that the microbial community structures changed significantly with different cellar ages and over different geographical regions. (i) The presence of Bacteroidetes was the most distinctive feature that characterized the different FPs ages. (ii) Distinct contents of Gammaproteobacteria and Euryarchaeota were observed at different positions in the FPs. (iii) Euryarchaeota markedly contributed to the generation of the character of the liquors with distinct geographical associations.<br><br>CONCLUSIONS: This study demonstrated that the changes of microbial communities determined the different quality characteristics of CSAL.<br><br>This research contributes to a deeper understanding of the FPs microbial composition and shows a new microbial resource for biotechnological applications.}, }
@article {pmid30843322, year = {2019}, author = {More, KD and Giosan, L and Grice, K and Coolen, MJL}, title = {Holocene paleodepositional changes reflected in the sedimentary microbiome of the Black Sea.}, journal = {Geobiology}, volume = {17}, number = {4}, pages = {436-448}, doi = {10.1111/gbi.12338}, pmid = {30843322}, issn = {1472-4669}, mesh = {Bacteria/classification/genetics ; *Bacterial Physiological Phenomena ; Black Sea ; Bulgaria ; Fossils ; Geologic Sediments/*microbiology ; *Metagenome ; *Microbiota ; }, abstract = {Subsurface microbial communities are generally thought to be structured through in situ environmental conditions such as the availability of electron acceptors and donors and porosity, but recent studies suggest that the vertical distribution of a subset of subseafloor microbial taxa, which were present at the time of deposition, were selected by the paleodepositional environment. However, additional highly resolved temporal records of subsurface microbiomes and paired paleoenvironmental reconstructions are needed to justify this claim. Here, we performed a highly resolved shotgun metagenomics survey to study the taxonomic and functional diversity of the subsurface microbiome in Holocene sediments underlying the permanently stratified and anoxic Black Sea. Obligate aerobic bacteria made the largest contribution to the observed shifts in microbial communities associated with known Holocene climate stages and transitions. This suggests that the aerobic fraction of the subseafloor microbiome was seeded from the water column and did not undergo post-depositional selection. In contrast, obligate and facultative anaerobic bacteria showed the most significant response to the establishment of modern-day environmental conditions 5.2 ka ago that led to a major shift in planktonic communities and in the type of sequestered organic matter available for microbial degradation. No significant shift in the subseafloor microbiome was observed as a result of environmental changes that occurred shortly after the marine reconnection, 9 ka ago. This supports the general view that the marine reconnection was a gradual process. We conclude that a high-resolution analysis of downcore changes in the subseafloor microbiome can provide detailed insights into paleoenvironmental conditions and biogeochemical processes that occurred at the time of deposition.}, }
@article {pmid30826613, year = {2019}, author = {Zeng, J and Pan, Y and Yang, J and Hou, M and Zeng, Z and Xiong, W}, title = {Metagenomic insights into the distribution of antibiotic resistome between the gut-associated environments and the pristine environments.}, journal = {Environment international}, volume = {126}, number = {}, pages = {346-354}, doi = {10.1016/j.envint.2019.02.052}, pmid = {30826613}, issn = {1873-6750}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics ; Chickens ; Drug Resistance, Microbial/*genetics ; Environmental Monitoring ; Environmental Pollutants/*analysis ; Feces/*microbiology ; Gastrointestinal Microbiome/*genetics ; *Genes, Bacterial ; Humans ; Metagenomics ; Seawater/*microbiology ; *Soil Microbiology ; Swine ; }, abstract = {Antibiotic resistance genes (ARGs) in the environment are promoted by anthropogenic activities, which cause potential risks to human health. However, large-scale quantitative data on antibiotic resistome from the pristine and anthropogenic environments remains largely unexplored. Here, we used metagenome-wide analysis to investigate the share and divergence in ARG profiles and their potential bacterial hosts between the pristine and gut-associated environments. We found that the abundance of total ARGs in gut-associated environments was significantly higher than the pristine environments (P < 0.001). The mcr-1 and tetX, the genes resistant to the last resort antibiotics (colistin and tigecycline, respectively), were in high abundance (4.57 copies/Gb and 3.39 copies/Gb, respectively) in gut-associated environments, suggesting the ARG pollution caused by anthropogenic antibiotics. Metagenomic assembly-based host-tracking analysis identified Escherichia, Bacteroides, and Clostridium as the predominant bacterial hosts of ARGs in gut-associated environments, while Alteromonas, Vibrio, and Proteobacteria as the predominant bacterial hosts of ARGs in pristine environments. We first described the broad diversity of ARG hosts in different environments using metagenome-wide analysis. Our results revealed the heterogeneous distribution of ARGs and their hosts among different microbial niches in gut-associated environments and the pristine environments.}, }
@article {pmid30405146, year = {2018}, author = {Lloyd, MM and Pespeni, MH}, title = {Microbiome shifts with onset and progression of Sea Star Wasting Disease revealed through time course sampling.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {16476}, pmid = {30405146}, issn = {2045-2322}, mesh = {Animal Diseases/*microbiology ; Animals ; Disease Progression ; Metagenomics/methods ; *Microbiota ; Starfish/*microbiology ; Time Factors ; }, abstract = {The recent outbreak of Sea Star Wasting Disease (SSWD) is one of the largest marine epizootics in history, but the host-associated microbial community changes specific to disease progression have not been characterized. Here, we sampled the microbiomes of ochre sea stars, Pisaster ochraceus, through time as animals stayed healthy or became sick and died with SSWD. We found community-wide differences in the microbiomes of sick and healthy sea stars, changes in microbial community composition through disease progression, and a decrease in species richness of the microbiome in late stages of SSWD. Known beneficial taxa (Pseudoalteromonas spp.) decreased in abundance at symptom onset and through disease progression, while known pathogenic (Tenacibaculum spp.) and putatively opportunistic bacteria (Polaribacter spp. and Phaeobacter spp.) increased in abundance in early and late disease stages. Functional profiling revealed microbes more abundant in healthy animals performed functions that inhibit growth of other microbes, including pathogen detection, biosynthesis of secondary metabolites, and degradation of xenobiotics. Changes in microbial composition with disease onset and progression suggest that a microbial imbalance of the host could lead to SSWD or be a consequence of infection by another pathogen. This work highlights the importance of the microbiome in SSWD and also suggests that a healthy microbiome may help confer resistance to SSWD.}, }
@article {pmid30310127, year = {2018}, author = {Cuer, CA and Rodrigues, RAR and Balieiro, FC and Jesus, J and Silva, EP and Alves, BJR and Rachid, CTCC}, title = {Short-term effect of Eucalyptus plantations on soil microbial communities and soil-atmosphere methane and nitrous oxide exchange.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {15133}, pmid = {30310127}, issn = {2045-2322}, mesh = {Atmosphere/*chemistry ; Brazil ; Environmental Monitoring ; *Eucalyptus ; Forests ; Metagenomics/methods ; Methane/*analysis ; Microbiota ; Nitrous Oxide/*analysis ; RNA, Ribosomal, 16S ; Soil/*chemistry ; *Soil Microbiology ; Time Factors ; }, abstract = {Soil greenhouse gas (GHG) emissions are a significant environmental problem resulting from microbially-mediated nitrogen (N) and carbon (C) cycling. This study aimed to investigate the impact of Eucalyptus plantations on the structure and function of a soil microbial community, and how resulting alterations may be linked to GHG fluxes. We sampled and monitored two adjacent Eucalyptus plantations-a recently logged site that harbored new seedlings and an adult plantation-and compared them to a site hosting native vegetation. We used 16S rRNA gene sequencing and qPCR amplifications of key nitrogen and methane cycle genes to characterize microbial structure and functional gene abundance and compared our data with soil parameters and GHG fluxes. Both microbial community attributes were significantly affected by land use and logging of Eucalyptus plantations. The genes nosZ and archaeal amoA were significantly more abundant in native forest than in either young or old Eucalyptus plantations. Statistical analyses suggest that land use type has a greater impact on microbial community structure and functional gene abundance than Eucalyptus rotation. There was no correlation between GHG fluxes and shifts in microbial community, suggesting that microbial community structure and functional gene abundance are not the main drivers of GHG fluxes in this system.}, }
@article {pmid30133062, year = {2018}, author = {Bracewell-Milnes, T and Saso, S and Nikolaou, D and Norman-Taylor, J and Johnson, M and Thum, MY}, title = {Investigating the effect of an abnormal cervico-vaginal and endometrial microbiome on assisted reproductive technologies: A systematic review.}, journal = {American journal of reproductive immunology (New York, N.Y. : 1989)}, volume = {80}, number = {5}, pages = {e13037}, doi = {10.1111/aji.13037}, pmid = {30133062}, issn = {1600-0897}, mesh = {Animals ; Cervix Uteri/*microbiology ; Endometrium/*microbiology ; Female ; Humans ; Infertility/*microbiology/therapy ; Metagenomics ; Microbiota/*physiology ; Reproductive Techniques, Assisted ; Vagina/*microbiology ; }, abstract = {The female reproductive tract has an active microbiome, and it is suggested that these microbes could influence the outcome of assisted reproductive technologies (ART). This systematic review aimed to assess the vaginal/uterine microbiome, specifically with regard to improving the outcome of ART. English peer-reviewed journals were searched for studies investigating the vaginal/uterine micriobiome and female reproductive tract, using PRISMA guidelines. Twenty-six studies were included, 19 studying the vaginal and seven investigating the uterine microbiome. Studies using culture-based technologies found an abnormal vaginal microbiome AVM was not associated with ART outcome. However, studies using sequence-based technologies found an abnormal vaginal microbiome had a negative effect on ART. An abnormal uterine microbiome impacted ART outcome in all of the studies which used culture-based methods and the most extensive of the two studies using metagenomic sequencing. This review has revealed a lack of translational data relating an abnormal vaginal/uterine microbiome to ART outcomes, with inconsistencies between the results of the different studies. Therefore the nature of the relationship between the vaginal/uterine microbiome and fertility remains unknown. As we better characterize this relationship using modern metagenomic techniques, the potential to manipulate the female reproductive tract microbiome to improve ART could be a reality.}, }
@article {pmid30108275, year = {2018}, author = {Shin, JH and Eom, H and Song, WJ and Rho, M}, title = {Integrative metagenomic and biochemical studies on rifamycin ADP-ribosyltransferases discovered in the sediment microbiome.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {12143}, pmid = {30108275}, issn = {2045-2322}, mesh = {ADP Ribose Transferases/chemistry/*genetics ; Amino Acid Sequence/genetics ; Bacterial Proteins/chemistry/*genetics ; Drug Resistance, Microbial/*genetics ; Enzyme Assays ; Escherichia coli/drug effects/genetics ; Genes, Bacterial/genetics ; Geologic Sediments/microbiology ; Metagenomics ; Microbial Sensitivity Tests ; Microbiota/*genetics ; Mutation ; Phylogeny ; Recombinant Proteins/chemistry/genetics ; Rifampin/*pharmacology ; Sequence Alignment ; Soil Microbiology ; Transformation, Bacterial ; }, abstract = {Antibiotic resistance is a serious and growing threat to human health. The environmental microbiome is a rich reservoir of resistomes, offering opportunities to discover new antibiotic resistance genes. Here we demonstrate an integrative approach of utilizing gene sequence and protein structural information to characterize unidentified genes that are responsible for the resistance to the action of rifamycin antibiotic rifampin, a first-line antimicrobial agent to treat tuberculosis. Biochemical characterization of four environmental metagenomic proteins indicates that they are adenosine diphosphate (ADP)-ribosyltransferases and effective in the development of resistance to FDA-approved rifamycins. Our analysis suggests that even a single residue with low sequence conservation plays an important role in regulating the degrees of antibiotic resistance. In addition to advancing our understanding of antibiotic resistomes, this work demonstrates the importance of an integrative approach to discover new metagenomic genes and decipher their biochemical functions.}, }
@article {pmid30108256, year = {2018}, author = {Stefanni, S and Stanković, D and Borme, D and de Olazabal, A and Juretić, T and Pallavicini, A and Tirelli, V}, title = {Multi-marker metabarcoding approach to study mesozooplankton at basin scale.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {12085}, pmid = {30108256}, issn = {2045-2322}, mesh = {Animals ; *Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Ecological Parameter Monitoring/*methods ; High-Throughput Nucleotide Sequencing/methods ; Introduced Species ; Marine Biology/methods ; Metagenome/genetics ; Metagenomics/*methods ; Oceans and Seas ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA/methods ; Zooplankton/classification/*genetics ; }, abstract = {Zooplankton plays a pivotal role in marine ecosystems and the characterisation of its biodiversity still represents a challenge for marine ecologists. In this study, mesozooplankton composition from 46 samples collected in summer along the western Adriatic Sea, was retrieved by DNA metabarcoding analysis. For the first time, the highly variable fragments of the mtDNA COI and the V9 region of 18S rRNA genes were used in a combined matrix to compile an inventory of mesozooplankton at basin scale. The number of sequences retrieved after quality filtering were 824,148 and 223,273 for COI and 18S (V9), respectively. The taxonomical assignment against reference sequences, using 95% (for COI) and 97% (for 18S) similarity thresholds, recovered 234 taxa. NMDS plots and cluster analysis divided coastal from offshore samples and the most representative species of these clusters were distributed according to the dominant surface current pattern of the Adriatic for the summer period. For selected sampling sites, mesozooplankton species were also identified under a stereo microscope providing insights on the strength and weakness of the two approaches. In addition, DNA metabarcoding was shown to be helpful for the monitoring of non-indigenous marine metazoans and spawning areas of commercial fish species. We defined pros and cons of applying this approach at basin scale and the benefits of combining the datasets from two genetic markers.}, }
@article {pmid30104612, year = {2018}, author = {Jenkins, TP and Peachey, LE and Ajami, NJ and MacDonald, AS and Hsieh, MH and Brindley, PJ and Cantacessi, C and Rinaldi, G}, title = {Schistosoma mansoni infection is associated with quantitative and qualitative modifications of the mammalian intestinal microbiota.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {12072}, pmid = {30104612}, issn = {2045-2322}, support = {R01 AI072773/AI/NIAID NIH HHS/United States ; R21 AI109532/AI/NIAID NIH HHS/United States ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //HHSN272201000005I/International ; }, mesh = {Animals ; Bacteroides/genetics/immunology/isolation &amp; purification ; DNA, Bacterial/isolation &amp; purification ; Disease Models, Animal ; Female ; Gastrointestinal Microbiome/genetics/*immunology ; Humans ; Intestines/*microbiology/pathology ; Lactobacillus/genetics/immunology/isolation &amp; purification ; Mice ; RNA, Ribosomal, 16S/genetics ; Schistosoma mansoni/immunology/*pathogenicity ; Schistosomiasis mansoni/*immunology/microbiology/parasitology/pathology ; Verrucomicrobia/genetics/immunology/isolation &amp; purification ; }, abstract = {In spite of the extensive contribution of intestinal pathology to the pathophysiology of schistosomiasis, little is known of the impact of schistosome infection on the composition of the gut microbiota of its mammalian host. Here, we characterised the fluctuations in the composition of the gut microbial flora of the small and large intestine, as well as the changes in abundance of individual microbial species, of mice experimentally infected with Schistosoma mansoni with the goal of identifying microbial taxa with potential roles in the pathophysiology of infection and disease. Bioinformatic analyses of bacterial 16S rRNA gene data revealed an overall reduction in gut microbial alpha diversity, alongside a significant increase in microbial beta diversity characterised by expanded populations of Akkermansia muciniphila (phylum Verrucomicrobia) and lactobacilli, in the gut microbiota of S. mansoni-infected mice when compared to uninfected control animals. These data support a role of the mammalian gut microbiota in the pathogenesis of hepato-intestinal schistosomiasis and serves as a foundation for the design of mechanistic studies to unravel the complex relationships amongst parasitic helminths, gut microbiota, pathophysiology of infection and host immunity.}, }
@article {pmid30002438, year = {2018}, author = {Hart, EH and Creevey, CJ and Hitch, T and Kingston-Smith, AH}, title = {Meta-proteomics of rumen microbiota indicates niche compartmentalisation and functional dominance in a limited number of metabolic pathways between abundant bacteria.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {10504}, pmid = {30002438}, issn = {2045-2322}, support = {BB/E/W/10964A01//Biotechnology and Biological Sciences Research Council (BBSRC)/International ; }, mesh = {Animal Feed ; Animals ; Bacteria/genetics/isolation &amp; purification/*metabolism ; Bacterial Proteins/*metabolism ; Cattle ; DNA, Bacterial/isolation &amp; purification ; Female ; Fermentation/physiology ; Gastrointestinal Microbiome/*physiology ; Gene Expression Profiling ; Metabolic Networks and Pathways/physiology ; Proteome/*metabolism ; Proteomics/methods ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; }, abstract = {The rumen is a complex ecosystem. It is the primary site for microbial fermentation of ingested feed allowing conversion of a low nutritional feed source into high quality meat and milk products. However, digestive inefficiencies lead to production of high amounts of environmental pollutants; methane and nitrogenous waste. These inefficiencies could be overcome by development of forages which better match the requirements of the rumen microbial population. Although challenging, the application of meta-proteomics has potential for a more complete understanding of the rumen ecosystem than sequencing approaches alone. Here, we have implemented a meta-proteomic approach to determine the association between taxonomies of microbial sources of the most abundant proteins in the rumens of forage-fed dairy cows, with taxonomic abundances typical of those previously described by metagenomics. Reproducible proteome profiles were generated from rumen samples. The most highly abundant taxonomic phyla in the proteome were Bacteriodetes, Firmicutes and Proteobacteria, which corresponded with the most abundant taxonomic phyla determined from 16S rRNA studies. Meta-proteome data indicated differentiation between metabolic pathways of the most abundant phyla, which is in agreement with the concept of diversified niches within the rumen microbiota.}, }
@article {pmid29844325, year = {2018}, author = {Iebba, V and Guerrieri, F and Di Gregorio, V and Levrero, M and Gagliardi, A and Santangelo, F and Sobolev, AP and Circi, S and Giannelli, V and Mannina, L and Schippa, S and Merli, M}, title = {Combining amplicon sequencing and metabolomics in cirrhotic patients highlights distinctive microbiota features involved in bacterial translocation, systemic inflammation and hepatic encephalopathy.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {8210}, pmid = {29844325}, issn = {2045-2322}, mesh = {*Bacterial Translocation ; Carbon/metabolism ; Fatty Acids/metabolism ; Feces/microbiology ; *Gene Amplification ; Hepatic Encephalopathy/*metabolism/microbiology ; Humans ; Inflammation/*metabolism ; Liver Cirrhosis/*metabolism/microbiology ; *Metabolomics ; Metagenomics ; Methane/metabolism ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In liver cirrhosis (LC), impaired intestinal functions lead to dysbiosis and possible bacterial translocation (BT). Bacteria or their byproducts within the bloodstream can thus play a role in systemic inflammation and hepatic encephalopathy (HE). We combined 16S sequencing, NMR metabolomics and network analysis to describe the interrelationships of members of the microbiota in LC biopsies, faeces, peripheral/portal blood and faecal metabolites with clinical parameters. LC faeces and biopsies showed marked dysbiosis with a heightened proportion of Enterobacteriaceae. Our approach showed impaired faecal bacterial metabolism of short-chain fatty acids (SCFAs) and carbon/methane sources in LC, along with an enhanced stress-related response. Sixteen species, mainly belonging to the Proteobacteria phylum, were shared between LC peripheral and portal blood and were functionally linked to iron metabolism. Faecal Enterobacteriaceae and trimethylamine were positively correlated with blood proinflammatory cytokines, while Ruminococcaceae and SCFAs played a protective role. Within the peripheral blood and faeces, certain species (Stenotrophomonas pavanii, Methylobacterium extorquens) and metabolites (methanol, threonine) were positively related to HE. Cirrhotic patients thus harbour a 'functional dysbiosis' in the faeces and peripheral/portal blood, with specific keystone species and metabolites related to clinical markers of systemic inflammation and HE.}, }
@article {pmid29497066, year = {2018}, author = {Meale, SJ and Auffret, MD and Watson, M and Morgavi, DP and Cantalapiedra-Hijar, G and Duthie, CA and Roehe, R and Dewhurst, RJ}, title = {Fat accretion measurements strengthen the relationship between feed conversion efficiency and Nitrogen isotopic discrimination while rumen microbial genes contribute little.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {3854}, pmid = {29497066}, issn = {2045-2322}, mesh = {Adipose Tissue/metabolism ; Animal Feed/analysis ; Animal Husbandry/methods ; Animal Nutritional Physiological Phenomena ; Animals ; Body Weight ; Breeding ; Cattle ; Diet ; Gastrointestinal Microbiome/*genetics ; Genes, Microbial/genetics ; Metagenomics/methods ; Nitrogen/*metabolism ; Nitrogen Isotopes/metabolism ; Poaceae/metabolism ; Red Meat ; Rumen/microbiology/*physiology ; Silage/analysis ; Zea mays/metabolism ; }, abstract = {The use of biomarkers for feed conversion efficiency (FCE), such as Nitrogen isotopic discrimination (Δ15N), facilitates easier measurement and may be useful in breeding strategies. However, we need to better understand the relationship between FCE and Δ15N, particularly the effects of differences in the composition of liveweight gain and rumen N metabolism. Alongside measurements of FCE and Δ15N, we estimated changes in body composition and used dietary treatments with and without nitrates, and rumen metagenomics to explore these effects. Nitrate fed steers had reduced FCE and higher Δ15N in plasma compared to steers offered non-nitrate containing diets. The negative relationship between FCE and Δ15N was strengthened with the inclusion of fat depth change at the 3rd lumbar vertebrae, but not with average daily gain. We identified 1,700 microbial genes with a relative abundance >0.01% of which, 26 were associated with Δ15N. These genes explained 69% of variation in Δ15N and showed clustering in two distinct functional networks. However, there was no clear relationship between their relative abundances and Δ15N, suggesting that rumen microbial genes contribute little to Δ15N. Conversely, we show that changes in the composition of gain (fat accretion) provide additional strength to the relationship between FCE and Δ15N.}, }
@article {pmid29350561, year = {2018}, author = {De Filippis, F and Parente, E and Ercolini, D}, title = {Recent Past, Present, and Future of the Food Microbiome.}, journal = {Annual review of food science and technology}, volume = {9}, number = {}, pages = {589-608}, doi = {10.1146/annurev-food-030117-012312}, pmid = {29350561}, issn = {1941-1413}, mesh = {Computational Biology ; Fermentation ; *Food Microbiology ; Food Safety ; Food Technology/*methods ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics ; Microbiota/*genetics ; }, abstract = {Sequencing technologies have deeply changed our approach to the study of food microbial communities. This review describes recent exploitations of high-throughput sequencing applications to improve our knowledge of food microbial consortia. In the past 10 years, target amplicon sequencing has become routinely used in many food microbiology laboratories, providing a detailed picture of food-associated microbiota. Metagenomics and metatranscriptomics approaches are still underexploited in food microbial ecology, despite their potential to uncover the functionality of complex communities. In a near future, sequencing technologies will surely advance our understanding of how to effectively use the invaluable microbial resources to improve food quality and safety.}, }
@article {pmid31649656, year = {2019}, author = {Epp Schmidt, DJ and Kotze, DJ and Hornung, E and Setälä, H and Yesilonis, I and Szlavecz, K and Dombos, M and Pouyat, R and Cilliers, S and Tóth, Z and Yarwood, S}, title = {Metagenomics Reveals Bacterial and Archaeal Adaptation to Urban Land-Use: N Catabolism, Methanogenesis, and Nutrient Acquisition.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2330}, doi = {10.3389/fmicb.2019.02330}, pmid = {31649656}, issn = {1664-302X}, abstract = {Urbanization results in the systemic conversion of land-use, driving habitat and biodiversity loss. The &quot;urban convergence hypothesis&quot; posits that urbanization represents a merging of habitat characteristics, in turn driving physiological and functional responses within the biotic community. To test this hypothesis, we sampled five cities (Baltimore, MD, United States; Helsinki and Lahti, Finland; Budapest, Hungary; Potchefstroom, South Africa) across four different biomes. Within each city, we sampled four land-use categories that represented a gradient of increasing disturbance and management (from least intervention to highest disturbance: reference, remnant, turf/lawn, and ruderal). Previously, we used amplicon sequencing that targeted bacteria/archaea (16S rRNA) and fungi (ITS) and reported convergence in the archaeal community. Here, we applied shotgun metagenomic sequencing and QPCR of functional genes to the same soil DNA extracts to test convergence in microbial function. Our results suggest that urban land-use drives changes in gene abundance related to both the soil N and C metabolism. Our updated analysis found taxonomic convergence in both the archaeal and bacterial community (16S amplicon data). Convergence of the archaea was driven by increased abundance of ammonia oxidizing archaea and genes for ammonia oxidation (QPCR and shotgun metagenomics). The proliferation of ammonia-oxidizers under turf and ruderal land-use likely also contributes to the previously documented convergence of soil mineral N pools. We also found a higher relative abundance of methanogens (amplicon sequencing), a higher relative abundance of gene sequences putatively identified as Ni-Fe hydrogenase and nickel uptake (shotgun metagenomics) under urban land-use; and a convergence of gene sequences putatively identified as contributing to the nickel transport function under urban turf sites. High levels of disturbance lead to a higher relative abundance of gene sequences putatively identified as multiple antibiotic resistance protein marA and multidrug efflux pump mexD, but did not lead to an overall convergence in antibiotic resistance gene sequences.}, }
@article {pmid31387630, year = {2019}, author = {Zhu, Z and Ren, J and Michail, S and Sun, F}, title = {MicroPro: using metagenomic unmapped reads to provide insights into human microbiota and disease associations.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {154}, doi = {10.1186/s13059-019-1773-5}, pmid = {31387630}, issn = {1474-760X}, support = {R01GM120624/NH/NIH HHS/United States ; R01HD081197/NH/NIH HHS/United States ; R01 GM131407/GM/NIGMS NIH HHS/United States ; }, mesh = {Colorectal Neoplasms/virology ; Diabetes Mellitus, Type 2/virology ; *Disease ; High-Throughput Nucleotide Sequencing ; Humans ; Liver Cirrhosis/virology ; Metagenomics/*methods ; Microbiota/*genetics ; *Software ; *Virus Physiological Phenomena ; }, abstract = {We develop a metagenomic data analysis pipeline, MicroPro, that takes into account all reads from known and unknown microbial organisms and associates viruses with complex diseases. We utilize MicroPro to analyze four metagenomic datasets relating to colorectal cancer, type 2 diabetes, and liver cirrhosis and show that including reads from unknown organisms significantly increases the prediction accuracy of the disease status for three of the four datasets. We identify new microbial organisms associated with these diseases and show viruses play important prediction roles in colorectal cancer and liver cirrhosis, but not in type 2 diabetes. MicroPro is freely available at https://github.com/zifanzhu/MicroPro .}, }
@article {pmid31375138, year = {2019}, author = {Bickhart, DM and Watson, M and Koren, S and Panke-Buisse, K and Cersosimo, LM and Press, MO and Van Tassell, CP and Van Kessel, JAS and Haley, BJ and Kim, SW and Heiner, C and Suen, G and Bakshy, K and Liachko, I and Sullivan, ST and Myer, PR and Ghurye, J and Pop, M and Weimer, PJ and Phillippy, AM and Smith, TPL}, title = {Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {153}, doi = {10.1186/s13059-019-1760-x}, pmid = {31375138}, issn = {1474-760X}, support = {R44AI122654-02A1//National Institute of Allergy and Infectious Diseases (US)/International ; }, mesh = {Animals ; Cattle ; Clustered Regularly Interspaced Short Palindromic Repeats ; Drug Resistance, Microbial/*genetics ; Gene Transfer, Horizontal ; Genes, Microbial ; Metagenomics/*methods ; Microbiota/*genetics ; Open Reading Frames ; Prophages/genetics ; Rumen/microbiology/virology ; Sequence Analysis, DNA/*methods ; Viruses/*genetics/isolation &amp; purification ; }, abstract = {We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. Long-read alignments and Hi-C linkage between contigs support the identification of 188 novel virus-host associations and the determination of phage life cycle states in the rumen microbial community. The long-read assembly also identifies 94 antimicrobial resistance genes, compared to only seven alleles in the short-read assembly. We demonstrate novel techniques that work synergistically to improve characterization of biological features in a highly complex rumen microbial community.}, }
@article {pmid31296857, year = {2019}, author = {Dilthey, AT and Jain, C and Koren, S and Phillippy, AM}, title = {Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {3066}, doi = {10.1038/s41467-019-10934-2}, pmid = {31296857}, issn = {2041-1723}, mesh = {Algorithms ; Computational Biology/*methods ; *Data Analysis ; Datasets as Topic ; High-Throughput Nucleotide Sequencing/methods ; Metagenome/genetics ; Metagenomics/*methods ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; Software ; }, abstract = {Metagenomic sequence classification should be fast, accurate and information-rich. Emerging long-read sequencing technologies promise to improve the balance between these factors but most existing methods were designed for short reads. MetaMaps is a new method, specifically developed for long reads, capable of mapping a long-read metagenome to a comprehensive RefSeq database with >12,000 genomes in <16 GB or RAM on a laptop computer. Integrating approximate mapping with probabilistic scoring and EM-based estimation of sample composition, MetaMaps achieves >94% accuracy for species-level read assignment and r2 > 0.97 for the estimation of sample composition on both simulated and real data when the sample genomes or close relatives are present in the classification database. To address novel species and genera, which are comparatively harder to predict, MetaMaps outputs mapping locations and qualities for all classified reads, enabling functional studies (e.g. gene presence/absence) and detection of incongruities between sample and reference genomes.}, }
@article {pmid30405201, year = {2018}, author = {Wankhade, UD and Zhong, Y and Kang, P and Alfaro, M and Chintapalli, SV and Piccolo, BD and Mercer, KE and Andres, A and Thakali, KM and Shankar, K}, title = {Maternal High-Fat Diet Programs Offspring Liver Steatosis in a Sexually Dimorphic Manner in Association with Changes in Gut Microbial Ecology in Mice.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {16502}, pmid = {30405201}, issn = {2045-2322}, mesh = {Animals ; Bile Acids and Salts/metabolism ; Biodiversity ; Biomarkers ; Diet, High-Fat/*adverse effects ; Fatty Liver/*etiology/*metabolism/pathology ; Female ; *Gastrointestinal Microbiome ; Lipid Metabolism ; Male ; Maternal Exposure/*adverse effects ; Metabolic Networks and Pathways ; Metagenome ; Metagenomics/methods ; Mice ; Phylogeny ; Sex Characteristics ; Weight Gain ; }, abstract = {The contributions of maternal diet and obesity in shaping offspring microbiome remain unclear. Here we employed a mouse model of maternal diet-induced obesity via high-fat diet feeding (HFD, 45% fat calories) for 12 wk prior to conception on offspring gut microbial ecology. Male and female offspring were provided access to control or HFD from weaning until 17 wk of age. Maternal HFD-associated programming was sexually dimorphic, with male offspring from HFD dams showing hyper-responsive weight gain to postnatal HFD. Likewise, microbiome analysis of offspring cecal contents showed differences in α-diversity, β-diversity and higher Firmicutes in male compared to female mice. Weight gain in offspring was significantly associated with abundance of Lachnospiraceae and Clostridiaceae families and Adlercreutzia, Coprococcus and Lactococcus genera. Sex differences in metagenomic pathways relating to lipid metabolism, bile acid biosynthesis and immune response were also observed. HFD-fed male offspring from HFD dams also showed worse hepatic pathology, increased pro-inflammatory cytokines, altered expression of bile acid regulators (Cyp7a1, Cyp8b1 and Cyp39a1) and serum bile acid concentrations. These findings suggest that maternal HFD alters gut microbiota composition and weight gain of offspring in a sexually dimorphic manner, coincident with fatty liver and a pro-inflammatory state in male offspring.}, }
@article {pmid30375431, year = {2018}, author = {Jasna, V and Parvathi, A and Dash, A}, title = {Genetic and functional diversity of double-stranded DNA viruses in a tropical monsoonal estuary, India.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {16036}, pmid = {30375431}, issn = {2045-2322}, support = {SIP1302//CSIR | National Institute of Oceanography, India (CSIR, National Institute of Oceanography)/International ; }, mesh = {*Biodiversity ; DNA Barcoding, Taxonomic ; DNA Viruses/classification/*genetics ; DNA, Viral ; *Environmental Microbiology ; Environmental Monitoring ; India ; Metagenomics/methods ; Seasons ; *Tropical Climate ; }, abstract = {The present study illustrates the genetic diversity of four uncultured viral communities from the surface waters of Cochin Estuary (CE), India. Viral diversity inferred using Illumina HiSeq paired-end sequencing using a linker-amplified shotgun library (LASL) revealed different double-stranded DNA (dsDNA) viral communities. The water samples were collected from four stations PR1, PR2, PR3, and PR4, during the pre-monsoon (PRM) season. Analysis of virus families indicated that the Myoviridae was the most common viral community in the CE followed by Siphoviridae and Podoviridae. There were significant (p < 0.05) spatial variations in the relative abundance of dominant families in response to the salinity regimes. The relative abundance of Myoviridae and Podoviridae were high in the euryhaline region and Siphoviridae in the mesohaline region of the estuary. The predominant phage type in CE was phages that infected Synechococcus. The viral proteins were found to be involved in major functional activities such as ATP binding, DNA binding, and DNA replication. The study highlights the genetic diversity of dsDNA viral communities and their functional protein predictions from a highly productive estuarine system. Further, the metavirome data generated in this study will enhance the repertoire of publicly available dataset and advance our understanding of estuarine viral ecology.}, }
@article {pmid30086520, year = {2018}, author = {Crampon, M and Bodilis, J and Portet-Koltalo, F}, title = {Linking initial soil bacterial diversity and polycyclic aromatic hydrocarbons (PAHs) degradation potential.}, journal = {Journal of hazardous materials}, volume = {359}, number = {}, pages = {500-509}, doi = {10.1016/j.jhazmat.2018.07.088}, pmid = {30086520}, issn = {1873-3336}, mesh = {Bacteria/genetics/metabolism ; Biodegradation, Environmental ; Microbiota ; Polycyclic Aromatic Hydrocarbons/*metabolism ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Soil Pollutants/*metabolism ; }, abstract = {The aim of this study was to understand the role of indigenous soil microbial communities on the biodegradation of polycyclic aromatic hydrocarbons (PAHs) and to determine whether PAHs degradation potential in soils may be evaluated by analysis of bacterial diversity and potential metabolisms using a metagenomics approach. Five different soils were artificially contaminated with seven selected PAHs and the most abundant bacterial taxa were assessed by sequencing the 16S rRNA gene, and linking them to PAH biodegradation efficiencies. A PICRUSt approach was then led to estimate the degradation potentials by metagenomics inference. Although the role of bacteria in PAHs degradation is not directly established here, the presence of a large number of bacteria belonging to the Betaproteobacteria class correlated to a higher degradation of LMW PAHs. A link with specific bacterial taxa was more difficult to establish concerning HMW PAHs, which seemed to require more complex mechanisms as shown by PICRUSt.}, }
@article {pmid30287908, year = {2018}, author = {Günther, B and Knebelsberger, T and Neumann, H and Laakmann, S and Martínez Arbizu, P}, title = {Metabarcoding of marine environmental DNA based on mitochondrial and nuclear genes.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {14822}, pmid = {30287908}, issn = {2045-2322}, mesh = {Aquatic Organisms/classification/genetics ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/*genetics/*isolation &amp; purification ; DNA, Ribosomal/*genetics/*isolation &amp; purification ; Electron Transport Complex IV/genetics ; Metagenomics/*methods ; North Sea ; RNA, Ribosomal, 18S/genetics ; Seawater/*chemistry ; }, abstract = {We establish the new approach of environmental DNA (eDNA) analyses for the North Sea. Our study uses a multigene approach, including the mitochondrial cytochrome-c-oxidase subunit I (COI) gene for analyzing species composition and the nuclear hypervariable region V8 of 18S rDNA for analyzing supraspecific biodiversity. A new minibarcode primer (124 bp) was created on the basis of a metazoan COI barcode library with 506 species and tested in silico, in vitro, and in situ. We applied high throughput sequencing to filtrates of 23 near-bottom water samples taken at three seasons from 14 stations. The set of COI primers allowed amplification of mitochondrial minibarcodes for diverse metazoan phyla and the differentiation at the species level for more than 99% of the specimens in the dataset. Our results revealed that the number of sequences is not consistent with proportions in the given DNA mixture. Altogether, environmental sequences could be assigned to 114 species and to 12 metazoan phyla. A spatial distribution of taxa recovered by eDNA was congruent with known distributions. Finally, the successful detection of species and biodiversity depends on a comprehensive sequence reference database. Our study offers a powerful tool for future biodiversity research, including the detection of nonnative species.}, }
@article {pmid29959351, year = {2018}, author = {Mann, AE and Sabin, S and Ziesemer, K and Vågene, ÅJ and Schroeder, H and Ozga, AT and Sankaranarayanan, K and Hofman, CA and Fellows Yates, JA and Salazar-García, DC and Frohlich, B and Aldenderfer, M and Hoogland, M and Read, C and Milner, GR and Stone, AC and Lewis, CM and Krause, J and Hofman, C and Bos, KI and Warinner, C}, title = {Differential preservation of endogenous human and microbial DNA in dental calculus and dentin.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {9822}, pmid = {29959351}, issn = {2045-2322}, mesh = {Bacteria/*genetics ; DNA, Bacterial/*analysis/genetics ; Dental Calculus/*genetics/microbiology ; Dentin/*metabolism/microbiology ; Humans ; *Metagenomics ; Microbiota ; Preservation, Biological/*methods ; }, abstract = {Dental calculus (calcified dental plaque) is prevalent in archaeological skeletal collections and is a rich source of oral microbiome and host-derived ancient biomolecules. Recently, it has been proposed that dental calculus may provide a more robust environment for DNA preservation than other skeletal remains, but this has not been systematically tested. In this study, shotgun-sequenced data from paired dental calculus and dentin samples from 48 globally distributed individuals are compared using a metagenomic approach. Overall, we find DNA from dental calculus is consistently more abundant and less contaminated than DNA from dentin. The majority of DNA in dental calculus is microbial and originates from the oral microbiome; however, a small but consistent proportion of DNA (mean 0.08 ± 0.08%, range 0.007-0.47%) derives from the host genome. Host DNA content within dentin is variable (mean 13.70 ± 18.62%, range 0.003-70.14%), and for a subset of dentin samples (15.21%), oral bacteria contribute > 20% of total DNA. Human DNA in dental calculus is highly fragmented, and is consistently shorter than both microbial DNA in dental calculus and human DNA in paired dentin samples. Finally, we find that microbial DNA fragmentation patterns are associated with guanine-cytosine (GC) content, but not aspects of cellular structure.}, }
@article {pmid29705499, year = {2018}, author = {Bielinska, K and Radkowski, M and Grochowska, M and Perlejewski, K and Huc, T and Jaworska, K and Motooka, D and Nakamura, S and Ufnal, M}, title = {High salt intake increases plasma trimethylamine N-oxide (TMAO) concentration and produces gut dysbiosis in rats.}, journal = {Nutrition (Burbank, Los Angeles County, Calif.)}, volume = {54}, number = {}, pages = {33-39}, doi = {10.1016/j.nut.2018.03.004}, pmid = {29705499}, issn = {1873-1244}, mesh = {Animals ; Dysbiosis/*etiology ; Feces/chemistry ; Gastrointestinal Microbiome ; Intestinal Diseases/*etiology ; Male ; Methylamines/*blood ; Rats ; Rats, Sprague-Dawley ; Sodium, Dietary/*adverse effects ; }, abstract = {OBJECTIVE: A high-salt diet is considered a cardiovascular risk factor; however, the mechanisms are not clear. Research suggests that gut bacteria-derived metabolites such as trimethylamine N-oxide (TMAO) are markers of cardiovascular diseases. We evaluated the effect of high salt intake on gut bacteria and their metabolites plasma level.<br><br>METHODS: Sprague Dawley rats ages 12-14 wk were maintained on either water (controls) or 0.9% or 2% sodium chloride (NaCl) water solution (isotonic and hypertonic groups, respectively) for 2 wk. Blood plasma, urine, and stool samples were analyzed for concentrations of trimethylamine (TMA; a TMAO precursor), TMAO, and indoxyl sulfate (indole metabolite). The gut-blood barrier permeability to TMA and TMA liver clearance were assessed at baseline and after TMA intracolonic challenge test. Gut bacterial flora was analyzed with a 16S ribosomal ribonucleic acid (rRNA) gene sequence analysis.<br><br>RESULTS: The isotonic and hypertonic groups showed a significantly higher plasma TMAO and significantly lower 24-hr TMAO urine excretion than the controls. However, the TMA stool level was similar between the groups. There was no significant difference between the groups in gut-blood barrier permeability and TMA liver clearance. Plasma indoxyl concentration and 24-hr urine indoxyl excretion were similar between the groups. There was a significant difference between the groups in gut bacteria composition.<br><br>CONCLUSIONS: High salt intake increases plasma TMAO concentration, which is associated with decreased TMAO urine excretion. Furthermore, high salt intake alters gut bacteria composition. These findings suggest that salt intake affects an interplay between gut bacteria and their host homeostasis.}, }
@article {pmid30424824, year = {2018}, author = {Haney, MM and Ericsson, AC and Lever, TE}, title = {Effects of Intraoperative Vagal Nerve Stimulation on the Gastrointestinal Microbiome in a Mouse Model of Amyotrophic Lateral Sclerosis.}, journal = {Comparative medicine}, volume = {68}, number = {6}, pages = {452-460}, doi = {10.30802/AALAS-CM-18-000039}, pmid = {30424824}, issn = {1532-0820}, support = {K01 OD019924/OD/NIH HHS/United States ; T32 OD011126/OD/NIH HHS/United States ; }, mesh = {Amyotrophic Lateral Sclerosis/*microbiology ; Analysis of Variance ; Animals ; Disease Models, Animal ; *Gastrointestinal Microbiome ; Mice ; Multivariate Analysis ; Signal Transduction ; Vagus Nerve Stimulation/*adverse effects ; }, abstract = {The gastrointestinal microbiota (GM) plays a fundamental role in health and disease and contributes to the bidirectional signaling between the gastrointestinal system and brain. The direct line of communication between these organ systems is through the vagus nerve. Therefore, vagal nerve stimulation (VNS), a commonly used technique for multiple disorders, has potential to modulate the enteric microbiota, enabling investigation and possibly treatment of numerous neurologic disorders in which the microbiota has been linked with disease. Here we investigate the effect of VNS in a mouse model of amyotrophic lateral sclerosis (ALS). B6SJL-Tg(SOD1*G93A)dl 1Gur (SOD1dl) and wildtype mice underwent ventral neck surgery to access the vagus nerve. During surgery, the experimental group received 1 h of VNS, whereas the sham group underwent 1 h of sham treatment. The third (control) group did not undergo any surgical manipulation. Fecal samples were collected before surgery and at 8 d after the initial collection. Microbial DNA was sequenced to determine the GM profiles at both time points. GM profiles did not differ between genotypes at either the initial or end point. In addition, VNS did not alter GM populations, according to the parameters chosen in this study, indicating that this short intraoperative treatment is safe and has no lasting effects on the GM. Future studies are warranted to determine whether different stimulation parameters or chronic use of VNS affect GM profiles.}, }
@article {pmid30056386, year = {2018}, author = {Kushugulova, A and Forslund, SK and Costea, PI and Kozhakhmetov, S and Khassenbekova, Z and Urazova, M and Nurgozhin, T and Zhumadilov, Z and Benberin, V and Driessen, M and Hercog, R and Voigt, AY and Benes, V and Kandels-Lewis, S and Sunagawa, S and Letunic, I and Bork, P}, title = {Metagenomic analysis of gut microbial communities from a Central Asian population.}, journal = {BMJ open}, volume = {8}, number = {7}, pages = {e021682}, pmid = {30056386}, issn = {2044-6055}, mesh = {Adult ; Aged ; Case-Control Studies ; Cohort Studies ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Kazakhstan ; Male ; Metabolic Syndrome/microbiology ; Metagenomics ; Middle Aged ; Probiotics/*administration &amp; dosage ; }, abstract = {OBJECTIVE: Changes in the gut microbiota are increasingly recognised to be involved in many diseases. This ecosystem is known to be shaped by many factors, including climate, geography, host nutrition, lifestyle and medication. Thus, knowledge of varying populations with different habits is important for a better understanding of the microbiome.<br><br>DESIGN: We therefore conducted a metagenomic analysis of intestinal microbiota from Kazakh donors, recruiting 84 subjects, including male and female healthy subjects and metabolic syndrome (MetS) patients aged 25-75 years, from the Kazakh administrative centre, Astana. We characterise and describe these microbiomes, the first deep-sequencing cohort from Central Asia, in comparison with a global dataset (832 individuals from five countries on three continents), and explore correlations between microbiota, clinical and laboratory parameters as well as with nutritional data from Food Frequency Questionnaires.<br><br>RESULTS: We observe that Kazakh microbiomes are relatively different from both European and East Asian counterparts, though similar to other Central Asian microbiomes, with the most striking difference being significantly more samples falling within the Prevotella-rich enterotype, potentially reflecting regional diet and lifestyle. We show that this enterotype designation remains stable within an individual over time in 82% of cases. We further observe gut microbiome features that distinguish MetS patients from controls (eg, significantly reduced Firmicutes to Bacteroidetes ratio, Bifidobacteria and Subdoligranulum, alongside increased Prevotella), though these overlap little with previously published reports and thus may reflect idiosyncrasies of the present cohort.<br><br>CONCLUSION: Taken together, this exploratory study describes gut microbiome data from an understudied population, providing a starting point for further comparative work on biogeography and research on widespread diseases.<br><br>TRIAL REGISTRATION NUMBER: ISRCTN37346212; Post-results.}, }
@article {pmid31207407, year = {2019}, author = {Parente, E and De Filippis, F and Ercolini, D and Ricciardi, A and Zotta, T}, title = {Advancing integration of data on food microbiome studies: FoodMicrobionet 3.1, a major upgrade of the FoodMicrobionet database.}, journal = {International journal of food microbiology}, volume = {305}, number = {}, pages = {108249}, doi = {10.1016/j.ijfoodmicro.2019.108249}, pmid = {31207407}, issn = {1879-3460}, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Databases, Factual ; *Food Microbiology ; Meat/microbiology ; *Microbiota ; Software ; }, abstract = {We present a new version of FoodMicrobionet, a database for the exploration of food bacterial communities. The database, available as an app built with the Shiny package of R, includes data from 44 studies and 2234 samples (food or food environment), covering dairy, meat, fruit and vegetables, cereal based and ready-to-eat foods. The interactive interface allows exploration of data, access to external resources (on line versions of the studies, sequence data on SRA, taxonomic databases), filtering samples on the basis of a number of criteria, aggregation of samples and bacterial taxa and export of data in a variety of formats. FoodMicrobionet is the largest collection of data on food bacterial communities and, due to the structure of sample metadata, largely derived from the European Food Safety Agency FoodEx2 classification, makes comparison and re-analysis of data from published and unpublished studies easy. Data exported from FoodMicrobionet can be readily used for graphical and statistical meta-analyses using open-source software (Gephi, Cytoscape, CoNet, and R packages and apps, such as phyloseq and Shiny-Phyloseq) thus providing scientists, risk assessors and industry with a wealth of information on the structure of food biomes.}, }
@article {pmid30666248, year = {2018}, author = {Malla, MA and Dubey, A and Kumar, A and Yadav, S and Hashem, A and Abd Allah, EF}, title = {Exploring the Human Microbiome: The Potential Future Role of Next-Generation Sequencing in Disease Diagnosis and Treatment.}, journal = {Frontiers in immunology}, volume = {9}, number = {}, pages = {2868}, doi = {10.3389/fimmu.2018.02868}, pmid = {30666248}, issn = {1664-3224}, mesh = {Communicable Diseases/etiology/*microbiology ; Computational Biology/trends ; Dysbiosis/complications ; Forecasting ; High-Throughput Nucleotide Sequencing/instrumentation/*trends ; Host Microbial Interactions/*genetics ; Host-Pathogen Interactions/*genetics ; Humans ; Metagenomics/*trends ; Microbiota/*physiology ; Nanotechnology/methods ; }, abstract = {The interaction between the human microbiome and immune system has an effect on several human metabolic functions and impacts our well-being. Additionally, the interaction between humans and microbes can also play a key role in determining the wellness or disease status of the human body. Dysbiosis is related to a plethora of diseases, including skin, inflammatory, metabolic, and neurological disorders. A better understanding of the host-microbe interaction is essential for determining the diagnosis and appropriate treatment of these ailments. The significance of the microbiome on host health has led to the emergence of new therapeutic approaches focused on the prescribed manipulation of the host microbiome, either by removing harmful taxa or reinstating missing beneficial taxa and the functional roles they perform. Culturing large numbers of microbial taxa in the laboratory is problematic at best, if not impossible. Consequently, this makes it very difficult to comprehensively catalog the individual members comprising a specific microbiome, as well as understanding how microbial communities function and influence host-pathogen interactions. Recent advances in sequencing technologies and computational tools have allowed an increasing number of metagenomic studies to be performed. These studies have provided key insights into the human microbiome and a host of other microbial communities in other environments. In the present review, the role of the microbiome as a therapeutic agent and its significance in human health and disease is discussed. Advances in high-throughput sequencing technologies for surveying host-microbe interactions are also discussed. Additionally, the correlation between the composition of the microbiome and infectious diseases as described in previously reported studies is covered as well. Lastly, recent advances in state-of-the-art bioinformatics software, workflows, and applications for analysing metagenomic data are summarized.}, }
@article {pmid30498254, year = {2018}, author = {Dutta, A and Dutta Gupta, S and Gupta, A and Sarkar, J and Roy, S and Mukherjee, A and Sar, P}, title = {Exploration of deep terrestrial subsurface microbiome in Late Cretaceous Deccan traps and underlying Archean basement, India.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {17459}, pmid = {30498254}, issn = {2045-2322}, support = {MoES/P.O.(Seismo)/1(181)/2013//Ministry of Earth Sciences (MoES)/International ; }, mesh = {Biodiversity ; Computational Biology/methods ; *Environmental Microbiology ; Geologic Sediments/*microbiology ; India ; Metagenome ; Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Scientific deep drilling at Koyna, western India provides a unique opportunity to explore microbial life within deep biosphere hosted by ~65 Myr old Deccan basalt and Archaean granitic basement. Characteristic low organic carbon content, mafic/felsic nature but distinct trend in sulfate and nitrate concentrations demarcates the basaltic and granitic zones as distinct ecological habitats. Quantitative PCR indicates a depth independent distribution of microorganisms predominated by bacteria. Abundance of dsrB and mcrA genes are relatively higher (at least one order of magnitude) in basalt compared to granite. Bacterial communities are dominated by Alpha-, Beta-, Gammaproteobacteria, Actinobacteria and Firmicutes, whereas Euryarchaeota is the major archaeal group. Strong correlation among the abundance of autotrophic and heterotrophic taxa is noted. Bacteria known for nitrite, sulfur and hydrogen oxidation represent the autotrophs. Fermentative, nitrate/sulfate reducing and methane metabolising microorganisms represent the heterotrophs. Lack of shared operational taxonomic units and distinct clustering of major taxa indicate possible community isolation. Shotgun metagenomics corroborate that chemolithoautotrophic assimilation of carbon coupled with fermentation and anaerobic respiration drive this deep biosphere. This first report on the geomicrobiology of the subsurface of Deccan traps provides an unprecedented opportunity to understand microbial composition and function in the terrestrial, igneous rock-hosted, deep biosphere.}, }
@article {pmid30120375, year = {2018}, author = {Goldsmith, DB and Kellogg, CA and Morrison, CL and Gray, MA and Stone, RP and Waller, RG and Brooke, SD and Ross, SW}, title = {Comparison of microbiomes of cold-water corals Primnoa pacifica and Primnoa resedaeformis, with possible link between microbiome composition and host genotype.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {12383}, pmid = {30120375}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*genetics/*microbiology ; Bacteria/classification/genetics ; *Biodiversity ; Computational Biology/methods ; *Genotype ; Metagenome ; Metagenomics/methods ; *Microbiota ; Microsatellite Repeats ; }, abstract = {Cold-water corals provide critical habitats for a multitude of marine species, but are understudied relative to tropical corals. Primnoa pacifica is a cold-water coral prevalent throughout Alaskan waters, while another species in the genus, Primnoa resedaeformis, is widely distributed in the Atlantic Ocean. This study examined the V4-V5 region of the 16S rRNA gene after amplifying and pyrosequencing bacterial DNA from samples of these species. Key differences between the two species' microbiomes included a robust presence of bacteria belonging to the Chlamydiales order in most of the P. pacifica samples, whereas no more than 2% of any microbial community from P. resedaeformis comprised these bacteria. Microbiomes of P. resedaeformis exhibited higher diversity than those of P. pacifica, and the two species largely clustered separately in a principal coordinate analysis. Comparison of P. resedaeformis microbiomes from samples collected in two submarine canyons revealed a significant difference between locations. This finding mirrored significant genetic differences among the P. resedaeformis from the two canyons based upon population genetic analysis of microsatellite loci. This study presents the first report of microbiomes associated with these two coral species.}, }
@article {pmid30046123, year = {2018}, author = {Imchen, M and Kumavath, R and Barh, D and Vaz, A and Góes-Neto, A and Tiwari, S and Ghosh, P and Wattam, AR and Azevedo, V}, title = {Comparative mangrove metagenome reveals global prevalence of heavy metals and antibiotic resistome across different ecosystems.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {11187}, pmid = {30046123}, issn = {2045-2322}, support = {SB-EMEQ-051/2014//DST | Science and Engineering Research Board (SERB)/International ; }, mesh = {Bacteroidetes/genetics ; *Ecosystem ; Firmicutes/genetics ; Geologic Sediments/microbiology ; India ; Metagenome/*genetics ; *Metagenomics ; Microbiota/*genetics ; Proteobacteria/genetics ; Wetlands ; }, abstract = {The mangrove ecosystem harbors a complex microbial community that plays crucial role in biogeochemical cycles. In this study, we analyzed mangrove sediments from India using de novo whole metagenome next generation sequencing (NGS) and compared their taxonomic and functional community structures to mangrove metagenomics samples from Brazil and Saudi Arabia. The most abundant phyla in the mangroves of all three countries was Proteobacteria, followed by Firmicutes and Bacteroidetes. A total of 1,942 genes were found to be common across all the mangrove sediments from each of the three countries. The mangrove resistome consistently showed high resistance to fluoroquinolone and acriflavine. A comparative study of the mangrove resistome with other ecosystems shows a higher frequency of heavy metal resistance in mangrove and terrestrial samples. Ocean samples had a higher abundance of drug resistance genes with fluoroquinolone and methicillin resistance genes being as high as 28.178% ± 3.619 and 10.776% ± 1.823. Genes involved in cobalt-zinc-cadmium resistance were higher in the mangrove (23.495% ± 4.701) and terrestrial (27.479% ± 4.605) ecosystems. Our comparative analysis of samples collected from a variety of habitats shows that genes involved in resistance to both heavy metals and antibiotics are ubiquitous, irrespective of the ecosystem examined.}, }
@article {pmid29941875, year = {2018}, author = {Buendía, E and Zakzuk, J and San-Juan-Vergara, H and Zurek, E and Ajami, NJ and Caraballo, L}, title = {Gut microbiota components are associated with fixed airway obstruction in asthmatic patients living in the tropics.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {9582}, pmid = {29941875}, issn = {2045-2322}, mesh = {Adult ; Asthma/*microbiology/*physiopathology ; Biodiversity ; Female ; *Gastrointestinal Microbiome ; Humans ; Lung/*physiopathology ; Male ; Phenotype ; *Tropical Climate ; }, abstract = {Microbiome composition has been associated to several inflammatory diseases, including asthma. There are few studies exploring the relationships of gut microbiota with airway obstruction pheonotypes in adult asthma, especially those living in the tropics. We sought to evaluate the relationships of gut microbiota with the airway obstruction and other variables of interest in asthmatic patients living in the tropics according to three phenotypes: No Airway Obstruction (NAO), Reversible Airway Obstruction (RAO) or Fixed Airway Obstruction (FAO). We found that Streptococcaceae:Streptococcus and Enterobacteriaceae:Escherichia-Shigella consistently discriminated asthmatic individuals suffering FAO from NAO or RAO, plus Veillonellaceae:Megasphaera when comparing FAO and RAO (p < 0.05; FDR < 0.05). In the FAO, the network showing the genus relations was less complex and interconnected. Several Rumminococcaceae, Lachnospiraceae and Clostridiales were enriched in patients with low specific IgE levels to mites and Ascaris. All patients shared a common exposure framework; control medication usage and smoking habit were uncommon and equally distributed between them. In conclusion, in this tropical asthmatic population, components of human gut microbiota are associated with the presence of a FAO phenotype and lower specific IgE response to mites and Ascaris.}, }
@article {pmid29937540, year = {2018}, author = {Lagier, JC and Dubourg, G and Million, M and Cadoret, F and Bilen, M and Fenollar, F and Levasseur, A and Rolain, JM and Fournier, PE and Raoult, D}, title = {Culturing the human microbiota and culturomics.}, journal = {Nature reviews. Microbiology}, volume = {16}, number = {}, pages = {540-550}, doi = {10.1038/s41579-018-0041-0}, pmid = {29937540}, issn = {1740-1534}, mesh = {Bacteria/*classification/genetics/growth &amp; development/*isolation &amp; purification ; Bacteriological Techniques/*methods/trends ; *Gastrointestinal Microbiome ; Humans ; Metagenomics/methods ; *Microbiota ; }, abstract = {The gut microbiota has an important role in the maintenance of human health and in disease pathogenesis. This importance was realized through the advent of omics technologies and their application to improve our knowledge of the gut microbial ecosystem. In particular, the use of metagenomics has revealed the diversity of the gut microbiota, but it has also highlighted that the majority of bacteria in the gut remain uncultured. Culturomics was developed to culture and identify unknown bacteria that inhabit the human gut as a part of the rebirth of culture techniques in microbiology. Consisting of multiple culture conditions combined with the rapid identification of bacteria, the culturomic approach has enabled the culture of hundreds of new microorganisms that are associated with humans, providing exciting new perspectives on host-bacteria relationships. In this Review, we discuss why and how culturomics was developed. We describe how culturomics has extended our understanding of bacterial diversity and then explore how culturomics can be applied to the study of the human microbiota and the potential implications for human health.}, }
@article {pmid29912385, year = {2018}, author = {Bengtsson-Palme, J and Richardson, RT and Meola, M and Wurzbacher, C and Tremblay, ÉD and Thorell, K and Kanger, K and Eriksson, KM and Bilodeau, GJ and Johnson, RM and Hartmann, M and Nilsson, RH}, title = {Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {23}, pages = {4027-4033}, pmid = {29912385}, issn = {1367-4811}, mesh = {Computational Biology ; *DNA Barcoding, Taxonomic ; *Genetic Markers ; *Metagenomics ; *Phylogeny ; *Software ; }, abstract = {Motivation: Correct taxonomic identification of DNA sequences is central to studies of biodiversity using both shotgun metagenomic and metabarcoding approaches. However, no genetic marker gives sufficient performance across all the biological kingdoms, hampering studies of taxonomic diversity in many groups of organisms. This has led to the adoption of a range of genetic markers for DNA metabarcoding. While many taxonomic classification software tools can be re-trained on these genetic markers, they are often designed with assumptions that impair their utility on genes other than the SSU and LSU rRNA. Here, we present an update to Metaxa2 that enables the use of any genetic marker for taxonomic classification of metagenome and amplicon sequence data.<br><br>Results: We evaluated the Metaxa2 Database Builder on 11 commonly used barcoding regions and found that while there are wide differences in performance between different genetic markers, our software performs satisfactorily provided that the input taxonomy and sequence data are of high quality.<br><br>Freely available on the web as part of the Metaxa2 package at http://microbiology.se/software/metaxa2/.<br><br>Supplementary information: Supplementary data are available at Bioinformatics online.}, }
@article {pmid29531234, year = {2018}, author = {Penington, JS and Penno, MAS and Ngui, KM and Ajami, NJ and Roth-Schulze, AJ and Wilcox, SA and Bandala-Sanchez, E and Wentworth, JM and Barry, SC and Brown, CY and Couper, JJ and Petrosino, JF and Papenfuss, AT and Harrison, LC and , }, title = {Influence of fecal collection conditions and 16S rRNA gene sequencing at two centers on human gut microbiota analysis.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {4386}, pmid = {29531234}, issn = {2045-2322}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; }, mesh = {Australia ; Cryopreservation/methods ; Feces/*microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; Individuality ; RNA, Ribosomal, 16S/*genetics/standards ; Sequence Analysis, DNA ; Specimen Handling/*methods ; United States ; }, abstract = {To optimise fecal sampling for reproducible analysis of the gut microbiome, we compared different methods of sample collection and sequencing of 16S rRNA genes at two centers. Samples collected from six individuals on three consecutive days were placed in commercial collection tubes (OMNIgeneGut OMR-200) or in sterile screw-top tubes in a home fridge or home freezer for 6-24 h, before transfer and storage at -80 °C. Replicate samples were shipped to centers in Australia and the USA for DNA extraction and sequencing by their respective PCR protocols, and analysed with the same bioinformatic pipeline. Variation in gut microbiome was dominated by differences between individuals. Minor differences in the abundance of taxa were found between collection-processing methods and day of collection, and between the two centers. We conclude that collection with storage and transport at 4 °C within 24 h is adequate for 16S rRNA analysis of the gut microbiome. Other factors including differences in PCR and sequencing methods account for relatively minor variation compared to differences between individuals.}, }
@article {pmid29020222, year = {2018}, author = {Leung, V and Vincent, C and Edens, TJ and Miller, M and Manges, AR}, title = {Antimicrobial Resistance Gene Acquisition and Depletion Following Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {66}, number = {3}, pages = {456-457}, pmid = {29020222}, issn = {1537-6591}, mesh = {Anti-Bacterial Agents/pharmacology ; Clostridium Infections/*therapy ; Drug Resistance, Multiple, Bacterial/*genetics ; Fecal Microbiota Transplantation/*adverse effects ; Feces/microbiology ; *Gastrointestinal Microbiome ; Genes, Bacterial ; *Genes, MDR ; High-Throughput Nucleotide Sequencing ; Humans ; Recurrence ; }, abstract = {Fecal microbiota transplantation (FMT) may be a novel approach to eliminate multidrug-resistant bacteria from the gut and to prevent future infections. Using whole metagenome sequencing data from 8 FMT donor-recipient pairs, we identified 37 and 95 antimicrobial resistance genes that were acquired by or removed from FMT recipients, respectively.}, }
@article {pmid31627274, year = {2019}, author = {Maia, LMS and Pinto, AZL and Carvalho, MS and Melo, FL and Ribeiro, BM and Slhessarenko, RD}, title = {Novel Viruses in Mosquitoes from Brazilian Pantanal.}, journal = {Viruses}, volume = {11}, number = {10}, pages = {}, doi = {10.3390/v11100957}, pmid = {31627274}, issn = {1999-4915}, support = {407817/2013-1//Rede Pro-Centro-Oeste of viral biodiversity/ ; }, abstract = {Viruses are ubiquitous and diverse microorganisms arising as a result of interactions within their vertebrate and invertebrate hosts. Here we report the presence of different viruses in the salivary glands of 1657 mosquitoes classified over 28 culicinae species from the North region of the Brazilian Pantanal wetland through metagenomics, viral isolation, and RT-PCR. In total, 12 viruses were found, eight putative novel viruses with relatively low similarity with pre-existing species of viruses within their families, named Pirizal iflavirus, Furrundu phlebovirus, Pixé phlebovirus, Guampa vesiculovirus, Chacororé flavivirus, Rasqueado orbivirus, Uru chuvirus, and Bororo circovirus. We also found the already described Lobeira dielmorhabdovirus, Sabethes flavivirus, Araticum partitivirus, and Murici totivirus. Therefore, these findings underscore the vast diversity of culicinae and novel viruses yet to be explored in Pantanal, the largest wetland on the planet.}, }
@article {pmid30658995, year = {2019}, author = {Hildebrand, F and Moitinho-Silva, L and Blasche, S and Jahn, MT and Gossmann, TI and Huerta-Cepas, J and Hercog, R and Luetge, M and Bahram, M and Pryszlak, A and Alves, RJ and Waszak, SM and Zhu, A and Ye, L and Costea, PI and Aalvink, S and Belzer, C and Forslund, SK and Sunagawa, S and Hentschel, U and Merten, C and Patil, KR and Benes, V and Bork, P}, title = {Antibiotics-induced monodominance of a novel gut bacterial order.}, journal = {Gut}, volume = {68}, number = {10}, pages = {1781-1790}, doi = {10.1136/gutjnl-2018-317715}, pmid = {30658995}, issn = {1468-3288}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/*genetics ; Gastrointestinal Microbiome/*drug effects ; Humans ; Metagenomics/*methods ; Microbiota/drug effects/*genetics ; }, abstract = {OBJECTIVE: The composition of the healthy human adult gut microbiome is relatively stable over prolonged periods, and representatives of the most highly abundant and prevalent species have been cultured and described. However, microbial abundances can change on perturbations, such as antibiotics intake, enabling the identification and characterisation of otherwise low abundant species.<br><br>DESIGN: Analysing gut microbial time-series data, we used shotgun metagenomics to create strain level taxonomic and functional profiles. Community dynamics were modelled postintervention with a focus on conditionally rare taxa and previously unknown bacteria.<br><br>RESULTS: In response to a commonly prescribed cephalosporin (ceftriaxone), we observe a strong compositional shift in one subject, in which a previously unknown species, UBorkfalki ceftriaxensis, was identified, blooming to 92% relative abundance. The genome assembly reveals that this species (1) belongs to a so far undescribed order of Firmicutes, (2) is ubiquitously present at low abundances in at least one third of adults, (3) is opportunistically growing, being ecologically similar to typical probiotic species and (4) is stably associated to healthy hosts as determined by single nucleotide variation analysis. It was the first coloniser after the antibiotic intervention that led to a long-lasting microbial community shift and likely permanent loss of nine commensals.<br><br>CONCLUSION: The bloom of UB. ceftriaxensis and a subsequent one of Parabacteroides distasonis demonstrate the existence of monodominance community states in the gut. Our study points to an undiscovered wealth of low abundant but common taxa in the human gut and calls for more highly resolved longitudinal studies, in particular on ecosystem perturbations.}, }
@article {pmid29624892, year = {2018}, author = {Kaur, K and Saxena, A and Debnath, I and O'Brien, JL and Ajami, NJ and Auchtung, TA and Petrosino, JF and Sougiannis, AJ and Depaep, S and Chumanevich, A and Gummadidala, PM and Omebeyinje, MH and Banerjee, S and Chatzistamou, I and Chakraborty, P and Fayad, R and Berger, FG and Carson, JA and Chanda, A}, title = {Antibiotic-mediated bacteriome depletion in ApcMin/+ mice is associated with reduction in mucus-producing goblet cells and increased colorectal cancer progression.}, journal = {Cancer medicine}, volume = {7}, number = {5}, pages = {2003-2012}, pmid = {29624892}, issn = {2045-7634}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; P30 GM103336/GM/NIGMS NIH HHS/United States ; }, mesh = {Adenomatous Polyposis Coli/*microbiology/*pathology ; Adenomatous Polyposis Coli Protein/genetics ; Animals ; Anti-Bacterial Agents/*adverse effects/*pharmacology ; Colon/pathology ; Disease Models, Animal ; Disease Progression ; Gastrointestinal Microbiome/*drug effects ; Goblet Cells/*cytology ; Intestinal Mucosa/microbiology/*pathology ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; Neomycin/adverse effects/pharmacology ; Streptomycin/adverse effects/pharmacology ; Vancomycin/adverse effects/pharmacology ; }, abstract = {Recent epidemiological evidence suggests that exposure to antibiotics in early-to-middle adulthood is associated with an increased risk of colorectal adenoma. However, mechanistic studies in established preclinical cancer to examine these claims are extremely limited. Therefore, we investigated the effect of long-term exposure of an antibiotic cocktail composed of Vancomycin, Neomycin, and Streptomycin, on tumor development and progression in the ApcMin/+ mouse, an established genetic model for familial adenomatous polyposis. Clinical pathologies related to tumor development as well as intestinal and colon tissue histopathology were studied at ages 8, 12, and 16 weeks of age, which correspond to the approximate ages of development of neoplasia, gut inflammation with polyposis, and cancer progression, respectively, in this animal model. We show that the antibiotics significantly increase the severity of clinical symptoms, including effects on intestinal histology and goblet cell numbers. In addition, they promote small intestinal polyposis. Finally, metagenomic analysis of fecal samples demonstrated that antibiotic exposure is associated with a significant but nonuniform depletion of the animal's natural gut flora. Overall, these findings support the premise that long-term antibiotic exposure mediates the selected depletion of gut microbial communities and the concomitant thinning of the protective mucus layer, resulting in an increase in tumor development.}, }
@article {pmid30065291, year = {2018}, author = {Meier-Kolthoff, JP and Uchiyama, J and Yahara, H and Paez-Espino, D and Yahara, K}, title = {Investigation of recombination-intense viral groups and their genes in the Earth's virome.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {11496}, pmid = {30065291}, issn = {2045-2322}, support = {16H06429//Ministry of Education, Culture, Sports, Science, and Technology (MEXT)/International ; 16K21723//Ministry of Education, Culture, Science, Sports, and Technology (MEXT) of Japan/International ; 17H05826//Ministry of Education, Culture, Science, Sports, and Technology (MEXT) of Japan/International ; }, mesh = {Bacteria/virology ; Bacteriophages/genetics ; Biodiversity ; DNA, Viral/genetics ; Earth (Planet) ; Ecosystem ; Genome, Viral/*genetics ; Host Specificity/genetics ; Humans ; Metagenome/genetics ; Metagenomics/methods ; Mouth/virology ; Recombination, Genetic/*genetics ; Viruses/*genetics ; }, abstract = {Bacteriophages (phages), or bacterial viruses, are the most abundant and diverse biological entities that impact the global ecosystem. Recent advances in metagenomics have revealed their rampant abundance in the biosphere. A fundamental aspect of bacteriophages that remains unexplored in metagenomic data is the process of recombination as a driving force in evolution that occurs among different viruses within the same bacterial host. Here, we systematically examined signatures of recombination in every gene from 211 species-level viral groups in a recently obtained dataset of the Earth's virome that contain corresponding information on the host bacterial species. Our study revealed that signatures of recombination are widespread (84%) among the diverse viral groups. We identified 25 recombination-intense viral groups, widely distributed across the viral taxonomy, and present in bacterial species living in the human oral cavity. We also revealed a significant inverse association between the recombination-intense viral groups and Type II restriction endonucleases, that could be effective in reducing recombination among phages in a cell. Furthermore, we identified recombination-intense genes that are significantly enriched for encoding phage morphogenesis proteins. Changes in the viral genomic sequence by recombination may be important to escape cleavage by the host bacterial immune systems.}, }
@article {pmid29973630, year = {2018}, author = {Hart, ML and Ericsson, AC and Lloyd, KCK and Grimsrud, KN and Rogala, AR and Godfrey, VL and Nielsen, JN and Franklin, CL}, title = {Development of outbred CD1 mouse colonies with distinct standardized gut microbiota profiles for use in complex microbiota targeted studies.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {10107}, pmid = {29973630}, issn = {2045-2322}, support = {T32 OD0112639//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/International ; U42 OD010924/OD/NIH HHS/United States ; T32 OD011126/OD/NIH HHS/United States ; K01 OD019924/OD/NIH HHS/United States ; U42 OD012210/OD/NIH HHS/United States ; U42 OD010918/OD/NIH HHS/United States ; U2C DK092993/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Breeding/*methods ; Embryo Transfer/methods ; Fecal Microbiota Transplantation/*methods ; Female ; *Gastrointestinal Microbiome ; Housing, Animal ; Male ; Mice ; Mice, Inbred C57BL ; Models, Animal ; }, abstract = {Studies indicate that the gut microbiota (GM) can significantly influence both local and systemic host physiologic processes. With rising concern for optimization of experimental reproducibility and translatability, it is essential to consider the GM in study design. However, GM profiles can vary between rodent producers making consistency between models challenging. To circumvent this, we developed outbred CD1 mouse colonies with stable, complex GM profiles that can be used as donors for a variety of GM transfer techniques including rederivation, co-housing, cross-foster, and fecal microbiota transfer (FMT). CD1 embryos were surgically transferred into CD1 or C57BL/6 surrogate dams that varied by GM composition and complexity to establish four separate mouse colonies harboring GM profiles representative of contemporary mouse producers. Using targeted 16S rRNA amplicon sequencing, subsequent female offspring were found to have similar GM profiles to surrogate dams. Furthermore, breeding colonies of CD1 mice with distinct GM profiles were maintained for nine generations, demonstrating GM stability within these colonies. To confirm GM stability, we shipped cohorts of these four colonies to collaborating institutions and found no significant variation in GM composition. These mice are an invaluable experimental resource that can be used to investigate GM effects on mouse model phenotype.}, }
@article {pmid29930350, year = {2018}, author = {Dini-Andreote, F and van Elsas, JD and Olff, H and Salles, JF}, title = {Dispersal-competition tradeoff in microbiomes in the quest for land colonization.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {9451}, pmid = {29930350}, issn = {2045-2322}, mesh = {*Biological Evolution ; *Metagenome ; *Microbiota ; Seawater/microbiology ; *Soil Microbiology ; }, abstract = {Ancestor microbes started colonizing inland habitats approximately 2.7 to 3.5 billion years ago. With some exceptions, the key physiological adaptations of microbiomes associated with marine-to-land transitions have remained elusive. This is essentially caused by the lack of suitable systems that depict changes in microbiomes across sufficiently large time scales. Here, we investigate the adaptive routes taken by microbiomes along a contemporary gradient of land formation. Using functional trait-based metagenomics, we show that a switch from a microbial 'dispersal' to a 'competition' response modus best characterizes the microbial trait changes during this eco-evolutionary trajectory. The 'dispersal' modus prevails in microbiomes at the boundary sites between land and sea. It encompasses traits conferring cell chemosensory and motile behaviors, thus allowing the local microbes to exploit short-lived nutritional patches in high-diffusion microhabitats. A systematic transition towards the 'competition' modus occurs progressively as the soil matures, which is likely due to forces of viscosity or strain that favor traits for competition and chemical defense. Concomitantly, progressive increases in the abundances of genes encoding antibiotic resistance and complex organic substrate degradation were found. Our findings constitute a novel perspective on the ecology and evolution of microbiome traits, tracking back one of the most seminal transitions in the evolutionary history of life.}, }
@article {pmid29700420, year = {2018}, author = {Richardson, JB and Dancy, BCR and Horton, CL and Lee, YS and Madejczyk, MS and Xu, ZZ and Ackermann, G and Humphrey, G and Palacios, G and Knight, R and Lewis, JA}, title = {Exposure to toxic metals triggers unique responses from the rat gut microbiota.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {6578}, pmid = {29700420}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; Disease Models, Animal ; Gastrointestinal Microbiome/*drug effects ; *Heavy Metal Poisoning ; Metagenome ; Metagenomics/methods ; Metals, Heavy/*toxicity ; Rats ; }, abstract = {Our understanding of the interaction between the gut microbiota and host health has recently improved dramatically. However, the effects of toxic metal exposure on the gut microbiota remain poorly characterized. As this microbiota creates a critical interface between the external environment and the host's cells, it may play an important role in host outcomes during exposure. We therefore used 16S ribosomal RNA (rRNA) gene sequencing to track changes in the gut microbiota composition of rats exposed to heavy metals. Rats were exposed daily for five days to arsenic, cadmium, cobalt, chromium, nickel, or a vehicle control. Significant changes to microbiota composition were observed in response to high doses of chromium and cobalt, and significant dose-dependent changes were observed in response to arsenic, cadmium and nickel. Many of these perturbations were not uniform across metals. However, bacteria with higher numbers of iron-importing gene orthologs were overly represented after exposure to arsenic and nickel, suggesting some possibility of a shared response. These findings support the utility of the microbiota as a pre-clinical tool for identifying exposures to specific heavy metals. It is also clear that characterizing changes to the functional capabilities of microbiota is critical to understanding responses to metal exposure.}, }
@article {pmid29891968, year = {2018}, author = {Grey, EK and Bernatchez, L and Cassey, P and Deiner, K and Deveney, M and Howland, KL and Lacoursière-Roussel, A and Leong, SCY and Li, Y and Olds, B and Pfrender, ME and Prowse, TAA and Renshaw, MA and Lodge, DM}, title = {Effects of sampling effort on biodiversity patterns estimated from environmental DNA metabarcoding surveys.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {8843}, pmid = {29891968}, issn = {2045-2322}, mesh = {Animals ; *Biodiversity ; DNA/*genetics/*isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; *Environment ; Metagenomics/*methods ; RNA, Ribosomal, 18S/genetics ; }, abstract = {Environmental DNA (eDNA) metabarcoding can greatly enhance our understanding of global biodiversity and our ability to detect rare or cryptic species. However, sampling effort must be considered when interpreting results from these surveys. We explored how sampling effort influenced biodiversity patterns and nonindigenous species (NIS) detection in an eDNA metabarcoding survey of four commercial ports. Overall, we captured sequences from 18 metazoan phyla with minimal differences in taxonomic coverage between 18 S and COI primer sets. While community dissimilarity patterns were consistent across primers and sampling effort, richness patterns were not, suggesting that richness estimates are extremely sensitive to primer choice and sampling effort. The survey detected 64 potential NIS, with COI identifying more known NIS from port checklists but 18 S identifying more operational taxonomic units shared between three or more ports that represent un-recorded potential NIS. Overall, we conclude that eDNA metabarcoding surveys can reveal global similarity patterns among ports across a broad array of taxa and can also detect potential NIS in these key habitats. However, richness estimates and species assignments require caution. Based on results of this study, we make several recommendations for port eDNA sampling design and suggest several areas for future research.}, }
@article {pmid29872163, year = {2018}, author = {Zhu, Y and Zhang, F and Zhang, C and Yang, L and Fan, G and Xu, Y and Sun, B and Li, X}, title = {Dynamic microbial succession of Shanxi aged vinegar and its correlation with flavor metabolites during different stages of acetic acid fermentation.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {8612}, pmid = {29872163}, issn = {2045-2322}, mesh = {Acetic Acid/*metabolism ; Bacteria/*classification/*metabolism ; *Biota ; Fermentation ; *Food Microbiology ; High-Throughput Nucleotide Sequencing ; Metabolomics ; Metagenomics ; Volatile Organic Compounds/metabolism ; }, abstract = {Shanxi aged vinegar (SAV), one of the famous Chinese vinegars, is produced by multispecies solid-state fermentation in which the acetic acid fermentation stage (AAF) is especially important. However, how bacterial succession and their metabolites change along with the different stages of AAF is still poorly understood. In this study, we investigated the dynamic bacterial succession and flavor formation in three batches of SAV using high-throughput sequencing and metabolomics approaches. It is interesting to find that AAF can be divided into three stages based on its bacterial community succession (early stage, days 0-4; medium stage, days 5-21; and later stage, days 22-26). Pantoea, Pediococcus, Lactococcus and Rhizobium played an important role in the early stage; Lactobacillus was dominant in the medium stage (67.72%); and Acetobacter, Komagataeibacter and Kroppenstedtia were the key bacteria in the later stage. A total of seven organic acids and 42 volatile constituents (esters, alcohol, ketones and aldehydes) were detected during the AAF. Spearman correlation analysis showed a significant correlation between the bacterial community and these flavor metabolites during the AAF of the SAV. This is the first report to explore the relationships between volatile flavor metabolites and bacterial community succession by a three-staged method and provide theoretical support for a flavor formation mechanism in traditional SAV.}, }
@article {pmid29802288, year = {2018}, author = {Waite, DW and Dsouza, M and Sekiguchi, Y and Hugenholtz, P and Taylor, MW}, title = {Network-guided genomic and metagenomic analysis of the faecal microbiota of the critically endangered kakapo.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {8128}, pmid = {29802288}, issn = {2045-2322}, mesh = {Animals ; *Endangered Species ; Feces/*microbiology ; Metagenomics/*methods ; *Microbiota ; Parrots/*genetics/*microbiology ; }, abstract = {The kakapo is a critically endangered, herbivorous parrot endemic to New Zealand. The kakapo hindgut hosts a dense microbial community of low taxonomic diversity, typically dominated by Escherichia fergusonii, and has proven to be a remarkably stable ecosystem, displaying little variation in core membership over years of study. To elucidate mechanisms underlying this robustness, we performed 16S rRNA gene-based co-occurrence network analysis to identify potential interactions between E. fergusonii and the wider bacterial community. Genomic and metagenomic sequencing were employed to facilitate interpretation of potential interactions observed in the network. E. fergusonii maintained very few correlations with other members of the microbiota, and isolates possessed genes for the generation of energy from a wide range of carbohydrate sources, including plant fibres such as cellulose. We surmise that this dominant microorganism is abundant not due to ecological interaction with other members of the microbiota, but its ability to metabolise a wide range of nutrients in the gut. This research represents the first concerted effort to understand the functional roles of the kakapo microbiota, and leverages metagenomic data to contextualise co-occurrence patterns. By combining these two techniques we provide a means for studying the diversity-stability hypothesis in the context of bacterial ecosystems.}, }
@article {pmid29670218, year = {2018}, author = {Jehrke, L and Stewart, FA and Droste, A and Beller, M}, title = {The impact of genome variation and diet on the metabolic phenotype and microbiome composition of Drosophila melanogaster.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {6215}, pmid = {29670218}, issn = {2045-2322}, mesh = {Animals ; Drosophila melanogaster/*genetics/*metabolism/*microbiology ; *Energy Metabolism ; Female ; Genetic Association Studies ; *Genetic Variation ; *Genome ; Genome-Wide Association Study ; Male ; Metabolome ; Metagenome ; Metagenomics/methods ; *Microbiota ; Phenotype ; }, abstract = {The metabolic phenotype of an organism depends on a complex regulatory network, which integrates the plethora of intrinsic and external information and prioritizes the flow of nutrients accordingly. Given the rise of metabolic disorders including obesity, a detailed understanding of this regulatory network is in urgent need. Yet, our level of understanding is far from completeness and complicated by the discovery of additional layers in metabolic regulation, such as the impact of the microbial community present in the gut on the hosts' energy storage levels. Here, we investigate the interplay between genome variation, diet and the gut microbiome in the shaping of a metabolic phenotype. For this purpose, we reared a set of fully sequenced wild type Drosophila melanogaster flies under basal and nutritionally challenged conditions and performed metabolic and microbiome profiling experiments. Our results introduce the fly as a model system to investigate the impact of genome variation on the metabolic response to diet alterations and reveal candidate single nucleotide polymorphisms associated with different metabolic traits, as well as metabolite-metabolite and metabolite-microbe correlations. Intriguingly, the dietary changes affected the microbiome composition less than anticipated. These results challenge the current view of a rapidly changing microbiome in response to environmental fluctuations.}, }
@article {pmid29670191, year = {2018}, author = {Le Bastard, Q and Ward, T and Sidiropoulos, D and Hillmann, BM and Chun, CL and Sadowsky, MJ and Knights, D and Montassier, E}, title = {Fecal microbiota transplantation reverses antibiotic and chemotherapy-induced gut dysbiosis in mice.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {6219}, pmid = {29670191}, issn = {2045-2322}, mesh = {Animals ; Anti-Bacterial Agents/*adverse effects/pharmacology ; Antineoplastic Agents/*adverse effects/pharmacology ; Biodiversity ; Disease Models, Animal ; Dysbiosis/*etiology/*microbiology/therapy ; *Fecal Microbiota Transplantation ; Feces/microbiology ; *Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; Mice ; }, abstract = {Fecal microbiota transplantation (FMT) is now widely used to treat recurrent Clostridium difficile infection, but has been less studied as a means to restore microbiome diversity and composition following antibiotic or chemotherapy treatments. The purpose of our study was to assess the efficacy of FMT to reverse antibiotic- and chemotherapy-induced gut dysbiosis in a mouse model. C57BL/6J mice were treated with ampicillin for 1 week and/or received a single intraperitoneal injection of 5-Fluorouracil. Fresh stool was collected and analyzed using shotgun metagenomics and the Illumina sequencing platform. Ampicillin caused a significant and immediate decrease in bacterial species richness and diversity that persisted for one week. In mice that received FMT, disruption of the intestinal microbiota was reversed immediately. Antibiotic and chemotherapy administration caused significant alteration in species distribution, including a decrease in the relative proportions of Clostridium scindens and Faecalibacterium prausnitzii, and an increase in known pathogenic species. In mice receiving FMT, we observed a significant increase in species known to exhibit anti-inflammatory properties. Moreover, chemotherapy led to a critical decrease in key 'health-promoting' species and to an altered functional profile, especially when chemotherapy was administered in tandem with antibiotics, and that FMT can ameliorate these effects.}, }
@article {pmid29700349, year = {2018}, author = {Lin, Z and Ye, W and Zu, X and Xie, H and Li, H and Li, Y and Zhang, W}, title = {Integrative metabolic and microbial profiling on patients with Spleen-yang-deficiency syndrome.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {6619}, pmid = {29700349}, issn = {2045-2322}, mesh = {Adult ; Aged ; Case-Control Studies ; Computational Biology/methods ; Female ; Gastrointestinal Microbiome ; Humans ; Male ; *Metabolome ; Metabolomics/methods ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Spleen/*immunology/*metabolism ; Syndrome ; Yang Deficiency/diagnosis/*immunology/*metabolism ; Young Adult ; }, abstract = {Gut microbiota is recognized as an indispensable &quot;metabolic organ&quot; that plays crucial roles in maintaining human health or initiating diseases. Spleen-yang-deficiency syndrome (SYDS) is a common syndrome of Traditional Chinese Medicine (TCM) clinic. It is a complex phenotype reflecting the overall changes of metabolism which are mainly caused by digestive disorders. However, little is known about the changes of gut microbiota and metabolism in patients with SYDS, as well as the crosstalk between gut microbiota and host metabolism. In the current study, an integrative metabolic and microbial profiling was performed on plasma, urine and feces from recruited SYDS and healthy individuals by using a LC-QTOFMS-based metabolomic and 16 s rRNA sequencing approaches. Our results showed a potentially significant contribution of gut dysbiosis to the metabolic disorders in SYDS. By integrating the differential gut bacteria with the metabolites, the results revealed some active bacterium of norank_f_CFT112H7, f_lachnospiraceae and bacteroides were closely involved in host mucosal integrity, bile acid metabolism and polysaccharides decomposition. Therefore, our results indicated the probable involvement of gut microbiota in mediating the metabolic changes, which warrants a further investigation on the role of gut microbiota in modulating the pathogenesis of SYDS.}, }
@article {pmid29674332, year = {2018}, author = {Du, F and Hinke, SA and Cavanaugh, C and Polidori, D and Wallace, N and Kirchner, T and Jennis, M and Lang, W and Kuo, GH and Gaul, MD and Lenhard, J and Demarest, K and Ajami, NJ and Liang, Y and Hornby, PJ}, title = {Potent Sodium/Glucose Cotransporter SGLT1/2 Dual Inhibition Improves Glycemic Control Without Marked Gastrointestinal Adaptation or Colonic Microbiota Changes in Rodents.}, journal = {The Journal of pharmacology and experimental therapeutics}, volume = {365}, number = {3}, pages = {676-687}, doi = {10.1124/jpet.118.248575}, pmid = {29674332}, issn = {1521-0103}, mesh = {Animals ; Biodiversity ; Blood Glucose/*metabolism ; Colon/*drug effects/metabolism/*microbiology ; Male ; Mice ; Microbiota/*drug effects ; Rats ; Sodium-Glucose Transporter 1/*antagonists &amp; inhibitors ; Sodium-Glucose Transporter 2/*metabolism ; Sodium-Glucose Transporter 2 Inhibitors/metabolism/*pharmacology ; }, abstract = {The sodium/glucose cotransporters (SGLT1 and SGLT2) transport glucose across the intestinal brush border and kidney tubule. Dual SGLT1/2 inhibition could reduce hyperglycemia more than SGLT2-selective inhibition in patients with type 2 diabetes. However, questions remain about altered gastrointestinal (GI) luminal glucose and tolerability, and this was evaluated in slc5a1-/- mice or with a potent dual inhibitor (compound 8; SGLT1 Ki = 1.5 ± 0.5 nM 100-fold greater potency than phlorizin; SGLT2 Ki = 0.4 ± 0.2 nM). 13C6-glucose uptake was quantified in slc5a1-/- mice and in isolated rat jejunum. Urinary glucose excretion (UGE), blood glucose (Sprague-Dawley rats), glucagon-like peptide 1 (GLP-1), and hemoglobin A1c (HbA1c) levels (Zucker diabetic fatty rats) were measured. Intestinal adaptation and rRNA gene sequencing was analyzed in C57Bl/6 mice. The blood 13C6-glucose area under the curve (AUC) was reduced in the absence of SGLT1 by 75% (245 ± 6 vs. 64 ± 6 mg/dl⋅h in wild-type vs. slc5a1-/- mice) and compound 8 inhibited its transport up to 50% in isolated rat jejunum. Compound 8 reduced glucose excursion more than SGLT2-selective inhibition (e.g., AUC = 129 ± 3 vs. 249 ± 5 mg/dl⋅h for 1 mg/kg compound 8 vs. dapagliflozin) with similar UGE but a lower renal glucose excretion threshold. In Zucker diabetic fatty rats, compound 8 decreased HbA1c and increased total GLP-1 without changes in jejunum SGLT1 expression, mucosal weight, or villus length. Overall, compound 8 (1 mg/kg for 6 days) did not increase cecal glucose concentrations or bacterial diversity in C57BL/6 mice. In conclusion, potent dual SGLT1/2 inhibition lowers blood glucose by reducing intestinal glucose absorption and the renal glucose threshold but minimally impacts the intestinal mucosa or luminal microbiota in chow-fed rodents.}, }
@article {pmid30657979, year = {2019}, author = {Liu, J and Lian, Q and Chen, Y and Qi, J}, title = {Amino acid based de Bruijn graph algorithm for identifying complete coding genes from metagenomic and metatranscriptomic short reads.}, journal = {Nucleic acids research}, volume = {47}, number = {5}, pages = {e30}, doi = {10.1093/nar/gkz017}, pmid = {30657979}, issn = {1362-4962}, mesh = {*Algorithms ; Amino Acids/*genetics ; Datasets as Topic ; Feces/microbiology ; Gastrointestinal Microbiome/genetics ; Genes/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; Microbiota/genetics ; Transcriptome/*genetics ; }, abstract = {Metagenomic studies, greatly promoted by the fast development of next-generation sequencing (NGS) technologies, uncover complex structures of microbial communities and their interactions with environment. As the majority of microbes lack information of genome sequences, it is essential to assemble prokaryotic genomes ab initio aiming to retrieve complete coding genes from various metabolic pathways. The complex nature of microbial composition and the burden of handling a vast amount of metagenomic data, bring great challenges to the development of effective and efficient bioinformatic tools. Here we present a protein assembler (MetaPA), based on de Bruijn graph searching on oligopeptide spaces and can be applied on both metagenomic and metatranscriptomic sequencing data. When public homologous protein sequences are involved to guide the assembling procedures, MetaPA assembles 85% of total proteins in complete sequences with high precision of 83% on real high-throughput sequencing datasets. Application of MetaPA on metatranscriptomic data successfully identifies the majority of actively transcribed genes validated in related studies. The results suggest that MetaPA has a good potential in both metagenomic and metatranscriptomic studies to characterize the composition and abundance of microbiota.}, }
@article {pmid30315079, year = {2018}, author = {Xia, F and Wang, JG and Zhu, T and Zou, B and Rhee, SK and Quan, ZX}, title = {Ubiquity and Diversity of Complete Ammonia Oxidizers (Comammox).}, journal = {Applied and environmental microbiology}, volume = {84}, number = {24}, pages = {}, pmid = {30315079}, issn = {1098-5336}, mesh = {Ammonia/*metabolism ; Archaea/genetics/*metabolism ; Bacteria/genetics/*metabolism ; Geologic Sediments/chemistry ; Metagenomics ; Nitrates/metabolism ; Nitrification ; Nitrites/metabolism ; Nitrogen Cycle ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; Sewage/chemistry ; Soil/chemistry ; Soil Microbiology ; Water/chemistry ; }, abstract = {The discovery of complete ammonia oxidizers (comammox) refutes the century-old paradigm that nitrification requires the activity of two types of microbes. Determining the distribution and abundance of comammox in various environments is important for revealing the ecology of microbial nitrification within the global nitrogen cycle. In this study, the ubiquity and diversity of comammox were analyzed for samples from different types of environments, including soil, sediment, sludge, and water. The results of a two-step PCR using highly degenerate primers (THDP-PCR) and quantitative real-time PCR (qPCR) supported the relatively high abundance of comammox in nearly half of all samples tested, sometimes even outnumbering canonical ammonia-oxidizing bacteria (AOB). In addition, a relatively high proportion of comammox in tap and coastal water samples was confirmed via analysis of metagenomic data sets in public databases. The diversity of comammox was estimated by comammox-specific partial nested PCR amplification of the ammonia monooxygenase subunit A (amoA) gene, and phylogenetic analysis of comammox AmoA clearly showed a split of clade A into clades A.1 and A.2, with the proportions of clades A.1, A.2, and B differing among the various environmental samples. Moreover, compared to the amoA genes of AOB and ammonia-oxidizing archaea (AOA), the comammox amoA gene exhibited higher diversity indices. The ubiquitous distribution and high diversity of comammox indicate that they are likely overlooked contributors to nitrification in various ecosystems.IMPORTANCE The discovery of complete ammonia oxidizers (comammox), which oxidize ammonia to nitrate via nitrite, refutes the century-old paradigm that nitrification requires the activity of two types of microbes and redefines a key process in the biogeochemical nitrogen cycle. Understanding the functional relationships between comammox and other nitrifiers is important for ecological studies on the nitrogen cycle. Therefore, the diversity and contribution of comammox should be considered during ecological analyses of nitrifying microorganisms. In this study, a ubiquitous and highly diverse distribution of comammox was observed in various environmental samples, similar to the distribution of canonical ammonia-oxidizing bacteria. The proportion of comammox was relatively high in coastal water and sediment samples, whereas it was nearly undetectable in open-ocean samples. The ubiquitous distribution and high diversity of comammox indicate that these microorganisms might be important contributors to nitrification.}, }
@article {pmid30054365, year = {2018}, author = {Esteban-Torres, M and Santamaría, L and Cabrera-Rubio, R and Plaza-Vinuesa, L and Crispie, F and de Las Rivas, B and Cotter, P and Muñoz, R}, title = {A Diverse Range of Human Gut Bacteria Have the Potential To Metabolize the Dietary Component Gallic Acid.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {19}, pages = {}, pmid = {30054365}, issn = {1098-5336}, mesh = {Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; DNA, Bacterial/genetics ; Feces/microbiology ; Gallic Acid/*metabolism ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The human gut microbiota contains a broad variety of bacteria that possess functional genes, with resultant metabolites that affect human physiology and therefore health. Dietary gallates are phenolic components that are present in many foods and beverages and are regarded as having health-promoting attributes. However, the potential for metabolism of these phenolic compounds by the human microbiota remains largely unknown. The emergence of high-throughput sequencing (HTS) technologies allows this issue to be addressed. In this study, HTS was used to assess the incidence of gallate-decarboxylating bacteria within the gut microbiota of healthy individuals for whom bacterial diversity was previously determined to be high. This process was facilitated by the design and application of degenerate PCR primers to amplify a region encoding the catalytic C subunit of gallate decarboxylase (LpdC) from total metagenomic DNA extracted from human fecal samples. HTS resulted in the generation of a total of 3,261,967 sequence reads and revealed that the primary gallate-decarboxylating microbial phyla in the intestinal microbiota were Firmicutes (74.6%), Proteobacteria (17.6%), and Actinobacteria (7.8%). These reads corresponded to 53 genera, i.e., 47% of the bacterial genera detected previously in these samples. Among these genera, Anaerostipes and Klebsiella accounted for the majority of reads (40%). The usefulness of the HTS-lpdC method was demonstrated by the production of pyrogallol from gallic acid, as expected for functional gallate decarboxylases, among representative strains belonging to species identified in the human gut microbiota by this method.IMPORTANCE Despite the increasing wealth of sequencing data, the health contributions of many bacteria found in the human gut microbiota have yet to be elucidated. This study applies a novel experimental approach to predict the ability of gut microbes to carry out a specific metabolic activity, i.e., gallate metabolism. The study showed that, while gallate-decarboxylating bacteria represented 47% of the bacterial genera detected previously in the same human fecal samples, no gallate decarboxylase homologs were identified from representatives of Bacteroidetes The presence of functional gallate decarboxylases was demonstrated in representative Proteobacteria and Firmicutes strains from the human microbiota, an observation that could be of considerable relevance to the in vivo production of pyrogallol, a physiologically important bioactive compound.}, }
@article {pmid29898804, year = {2018}, author = {Misic, AM and Miedel, EL and Brice, AK and Cole, S and Zhang, GF and Dyer, CD and Secreto, A and Smith, AL and Danet-Desnoyers, G and Beiting, DP}, title = {Culture-independent Profiling of the Fecal Microbiome to Identify Microbial Species Associated with a Diarrheal Outbreak in Immunocompromised Mice.}, journal = {Comparative medicine}, volume = {68}, number = {4}, pages = {261-268}, pmid = {29898804}, issn = {1532-0820}, mesh = {Animals ; Diarrhea/epidemiology/*microbiology ; Disease Outbreaks ; Feces/*microbiology ; Genetic Variation ; Immunocompromised Host ; Metagenomics ; Mice ; Mice, Inbred NOD ; Mice, SCID ; Microbiota/*genetics ; RNA, Ribosomal, 16S/chemistry ; Sequence Analysis, RNA ; Whole Genome Sequencing ; }, abstract = {Immunocompromised mice are used frequently in biomedical research, in part because they accommodate the engraftment and study of primary human cells within a mouse model; however, these animals are susceptible to opportunistic infections and require special husbandry considerations. In 2015, an outbreak marked by high morbidity but low mortality swept through a colony of immunocompromised mice; this outbreak rapidly affected 75% of the colony and ultimately required complete depopulation of the barrier suite. Conventional microbiologic and molecular diagnostics were unsuccessful in determining the cause; therefore, we explored culture-independent methods to broadly profile the microbial community in the feces of affected animals. This approach identified 4 bacterial taxa- Candidatus Arthromitus, Clostridium celatum, Clostridiales bacterium VE202-01, and Bifidobacterium pseudolongum strain PV8-2- that were significantly enriched in the affected mice. Based on these results, specific changes were made to the animal husbandry procedures for immunocompromised mice. This case report highlights the utility of culture-independent methods in laboratory animal diagnostics.}, }
@article {pmid29872090, year = {2018}, author = {Paul, F and Otte, J and Schmitt, I and Dal Grande, F}, title = {Comparing Sanger sequencing and high-throughput metabarcoding for inferring photobiont diversity in lichens.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {8624}, pmid = {29872090}, issn = {2045-2322}, mesh = {Ascomycota/growth &amp; development ; Chlorophyta/*classification/*genetics/growth &amp; development ; DNA Barcoding, Taxonomic/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Lichens/*growth &amp; development ; Metagenomics/*methods ; Sequence Analysis, DNA/*methods ; Symbiosis ; }, abstract = {The implementation of HTS (high-throughput sequencing) approaches is rapidly changing our understanding of the lichen symbiosis, by uncovering high bacterial and fungal diversity, which is often host-specific. Recently, HTS methods revealed the presence of multiple photobionts inside a single thallus in several lichen species. This differs from Sanger technology, which typically yields a single, unambiguous algal sequence per individual. Here we compared HTS and Sanger methods for estimating the diversity of green algal symbionts within lichen thalli using 240 lichen individuals belonging to two species of lichen-forming fungi. According to HTS data, Sanger technology consistently yielded the most abundant photobiont sequence in the sample. However, if the second most abundant photobiont exceeded 30% of the total HTS reads in a sample, Sanger sequencing generally failed. Our results suggest that most lichen individuals in the two analyzed species, Lasallia hispanica and L. pustulata, indeed contain a single, predominant green algal photobiont. We conclude that Sanger sequencing is a valid approach to detect the dominant photobionts in lichen individuals and populations. We discuss which research areas in lichen ecology and evolution will continue to benefit from Sanger sequencing, and which areas will profit from HTS approaches to assessing symbiont diversity.}, }
@article {pmid29725134, year = {2018}, author = {ElNaker, NA and Elektorowicz, M and Naddeo, V and Hasan, SW and Yousef, AF}, title = {Assessment of Microbial Community Structure and Function in Serially Passaged Wastewater Electro-Bioreactor Sludge: An Approach to Enhance Sludge Settleability.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {7013}, pmid = {29725134}, issn = {2045-2322}, mesh = {Bacteria/classification/genetics ; Biological Oxygen Demand Analysis ; Bioreactors/*microbiology ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Microbiota ; Phosphorus/analysis ; Phylogeny ; Serial Passage ; Sewage/*microbiology ; Water Purification/*methods ; }, abstract = {Several studies have been carried out to understand bulking phenomena and the importance of environmental factors on sludge settling characteristics. The main objective of this study was to carry out functional characterization of microbial community structure of wastewater electro-bioreactor sludge as it undergoes serial passaging in the presence or absence of a current density over 15 days. Illumina MiSeq sequencing and QIIME were used to assess sludge microbial community shifts over time. (α) and (β) diversity analysis were conducted to assess the microbial diversity in electro-bioreactors. A phylogeny-based weighted UniFrac distance analysis was used to compare between bacterial communities while BIO-ENV trend and Spearman's rank correlation analysis were performed to investigate how reactor operational parameters correlated with bacterial community diversity. Results showed that the removal efficiency of soluble chemical oxygen demand (sCOD) ranged from 91-97%, while phosphorous (PO43--P) removal was approximately 99%. Phylogenetic analysis revealed stark differences in the development of sludge microbial communities in the control and treatment reactor. There was no mention of any studies aimed at characterizing functional microbial communities under electric field and the results communicated here are the first, to our knowledge, that address this gap in the literature.}, }
@article {pmid29725059, year = {2018}, author = {Dittmer, J and Bouchon, D}, title = {Feminizing Wolbachia influence microbiota composition in the terrestrial isopod Armadillidium vulgare.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {6998}, pmid = {29725059}, issn = {2045-2322}, mesh = {Animal Structures/*microbiology ; Animals ; Bacteria/classification/genetics ; Isopoda/*microbiology ; Metagenomics ; Microbial Interactions ; *Microbiota ; Wolbachia/*growth &amp; development ; }, abstract = {Wolbachia are widespread heritable endosymbionts of arthropods notorious for their profound effects on host fitness as well as for providing protection against viruses and eukaryotic parasites, indicating that they can interact with other microorganisms sharing the same host environment. Using the terrestrial isopod crustacean Armadillidium vulgare, its highly diverse microbiota (>200 bacterial genera) and its three feminizing Wolbachia strains (wVulC, wVulM, wVulP) as a model system, the present study demonstrates that Wolbachia can even influence the composition of a diverse bacterial community under both laboratory and natural conditions. While host origin is the major determinant of the taxonomic composition of the microbiota in A. vulgare, Wolbachia infection affected both the presence and, more importantly, the abundance of many bacterial taxa within each host population, possibly due to competitive interactions. Moreover, different Wolbachia strains had different impacts on microbiota composition. As such, infection with wVulC affected a higher number of taxa than infection with wVulM, possibly due to intrinsic differences in virulence and titer between these two strains. In conclusion, this study shows that heritable endosymbionts such as Wolbachia can act as biotic factors shaping the microbiota of arthropods, with as yet unknown consequences on host fitness.}, }
@article {pmid31595646, year = {2019}, author = {Strazzulli, A and Cobucci-Ponzano, B and Iacono, R and Giglio, R and Maurelli, L and Curci, N and Schiano-di-Cola, C and Santangelo, A and Contursi, P and Lombard, V and Henrissat, B and Lauro, FM and Fontes, CMGA and Moracci, M}, title = {Discovery of hyperstable carbohydrate-active enzymes through metagenomics of extreme environments.}, journal = {The FEBS journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/febs.15080}, pmid = {31595646}, issn = {1742-4658}, abstract = {The enzymes from hyperthermophilic microorganisms populating volcanic sites represent interesting cases of protein adaptation and biotransformations under conditions where conventional enzymes quickly denature. The difficulties in cultivating extremophiles severely limit access to this class of biocatalysts. To circumvent this problem, we embarked on the exploration of the biodiversity of the solfatara Pisciarelli, Agnano (Naples, Italy) to discover hyperthermophilic carbohydrate-active enzymes (CAZymes) and to characterize the entire set of such enzymes in this environment (CAZome). Here we report the results of the metagenomic analysis of two mud/water pools that greatly differ in both temperature and pH (T=85°C and pH 5.5; T=92°C and pH 1.5, for Pool1 and Pool2, respectively). DNA deep sequencing and following in-silico analysis led to 14,934 and 17,652 complete ORFs in Pool1 and Pool2, respectively. They exclusively belonged to archaeal cells and viruses with great genera variance within the phylum Crenarcheaota, which reflected the difference in temperature and pH of the two Pools. Surprisingly, 30% and 62% of all of the reads obtained from Pool1 and 2, respectively, had no match in nucleotide databanks. Genes associated with carbohydrate metabolism were 15% and 16% of the total in the two Pools, with 278 and 308 putative CAZymes in Pool1 and 2, corresponding to ~2.0% of all ORFs. Biochemical characterization of two CAZymes of a previously unknown archaeon revealed a novel subfamily GH5_19 β-mannanase/β-1,3-glucanase whose hemicellulose specificity correlates with the vegetation surrounding the sampling site, and a novel NAD+ dependent GH109 with a previously unreported β-N-acetylglucosaminide/β-glucoside specificity.}, }
@article {pmid29658784, year = {2018}, author = {Popic, V and Kuleshov, V and Snyder, M and Batzoglou, S}, title = {Fast Metagenomic Binning via Hashing and Bayesian Clustering.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {25}, number = {7}, pages = {677-688}, doi = {10.1089/cmb.2017.0250}, pmid = {29658784}, issn = {1557-8666}, mesh = {*Bayes Theorem ; Cluster Analysis ; Computational Biology/*statistics &amp; numerical data ; Humans ; Metagenome/genetics ; Metagenomics/*statistics &amp; numerical data ; Microbiota/*genetics ; }, abstract = {We introduce GATTACA, a framework for fast unsupervised binning of metagenomic contigs. Similar to recent approaches, GATTACA clusters contigs based on their coverage profiles across a large cohort of metagenomic samples; however, unlike previous methods that rely on read mapping, GATTACA quickly estimates these profiles from kmer counts stored in a compact index. This approach can result in over an order of magnitude speedup, while matching the accuracy of earlier methods on synthetic and real data benchmarks. It also provides a way to index metagenomic samples (e.g., from public repositories such as the Human Microbiome Project) offline once and reuse them across experiments; furthermore, the small size of the sample indices allows them to be easily transferred and stored. Leveraging the MinHash technique, GATTACA also provides an efficient way to identify publicly available metagenomic data that can be incorporated into the set of reference metagenomes to further improve binning accuracy. Thus, enabling easy indexing and reuse of publicly available metagenomic data sets, GATTACA makes accurate metagenomic analyses accessible to a much wider range of researchers.}, }
@article {pmid31564708, year = {2019}, author = {Zheng, A and Yi, H and Li, F and Han, L and Yu, J and Cheng, X and Su, H and Hong, K and Li, J}, title = {Changes in Gut Microbiome Structure and Function of Rats with Isoproterenol-Induced Heart Failure.}, journal = {International heart journal}, volume = {60}, number = {5}, pages = {1176-1183}, doi = {10.1536/ihj.18-194}, pmid = {31564708}, issn = {1349-3299}, mesh = {Animals ; Bacteria/*classification/genetics ; Disease Models, Animal ; Echocardiography ; Gastrointestinal Microbiome/*drug effects ; Heart Failure/chemically induced/diagnostic imaging/*microbiology ; High-Throughput Nucleotide Sequencing ; Injections, Intraperitoneal ; Isoproterenol/*adverse effects/pharmacology ; Male ; Metagenomics/*methods ; Phylogeny ; Rats ; Sequence Analysis, DNA ; }, abstract = {Recently, the potential role of gut microbiome (GM) in cardiovascular diseases has been revealed. Heart failure (HF) is one of the most prevalent cardiovascular diseases worldwide; however, whether GM dysbiosis participates in the development of HF remains largely unknown. This study aimed to investigate the specific changes in GM composition and function in isoproterenol (ISO)-induced HF in rats.The rats were divided into C (control), 4w-HF (ISO, 2.5 mg/kg/day for 4 weeks, intraperitoneally), and 2w-HF (ISO, 2.5 mg/kg/day for 2 weeks, intraperitoneally) groups. The cardiac structure and function in rats were assessed, and metagenomic analyses were then performed. Compared with the healthy control group, we found that the Shannon diversity index and microbial gene count in the 4w-HF and 2w-HF groups was drastically decreased. High-throughput sequencing showed that the three groups differed in intestinal bacterial community composition. Overgrowth of bacteria, such as Prevotella, was observed in the 4w-HF group, with reduced growth of bacteria, such as Roseburia, Lactobacillus, and Butyrivibrio, associated with healthy status compared with the C group on the genus level. Concomitant with the alteration of GM composition, underrepresentation of health-linked microbial function was observed in both the 4w-HF and 2w-HF groups compared with the C group.Iso-induced HF rats showed a significant decrease in the diversity and richness of the intestinal microbiome, with a downregulation of the key intestinal bacterial groups and overgrowth of bacteria considered to be involved in inflammatory responses as well as a decrease in health-linked microbial function. Our data indicated that altered GM may be a potential player in the pathogenesis and progression of HF.}, }
@article {pmid30097447, year = {2018}, author = {Burns, AS and Padilla, CC and Pratte, ZA and Gilde, K and Regensburger, M and Hall, E and Dove, ADM and Stewart, FJ}, title = {Broad Phylogenetic Diversity Associated with Nitrogen Loss through Sulfur Oxidation in a Large Public Marine Aquarium.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {20}, pages = {}, pmid = {30097447}, issn = {1098-5336}, mesh = {Bacteria/*classification/metabolism ; Biodiversity ; Bioreactors/microbiology ; *Denitrification ; *Genetic Variation ; Georgia ; Metagenomics ; Microbiota ; Nitrogen/*metabolism ; Oxidation-Reduction ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sulfur/*metabolism ; Waste Water ; }, abstract = {Denitrification by sulfur-oxidizing bacteria is an effective nitrate removal strategy in engineered aquatic systems. However, the community taxonomic and metabolic diversity of sulfur-driven denitrification (SDN) systems, as well as the relationship between nitrate removal and SDN community structure, remains underexplored. This is particularly true for SDN reactors applied to marine aquaria, despite the increasing use of this technology to supplement filtration. We applied 16S rRNA gene, metagenomic, and metatranscriptomic analyses to explore the microbial basis of SDN reactors operating on Georgia Aquarium's Ocean Voyager, the largest indoor closed-system seawater exhibit in the United States. The exhibit's two SDN systems vary in water retention time and nitrate removal efficiency. The systems also support significantly different microbial communities. These communities contain canonical SDN bacteria, including a strain related to Thiobacillus thioparus that dominates the system with the higher water retention time and nitrate removal but is effectively absent from the other system. Both systems contain a wide diversity of other microbes whose metagenome-assembled genomes contain genes of SDN metabolism. These include hundreds of strains of the epsilonproteobacterium Sulfurimonas, as well as gammaproteobacterial sulfur oxidizers of the Thiotrichales and Chromatiales, and a relative of Sedimenticolathiotaurini with complete denitrification potential. The SDN genes are transcribed and the taxonomic richness of the transcript pool varies markedly among the enzymatic steps, with some steps dominated by transcripts from noncanonical SDN taxa. These results indicate complex and variable SDN communities that may involve chemical dependencies among taxa as well as the potential for altering community structure to optimize nitrate removal.IMPORTANCE Engineered aquatic systems such as aquaria and aquaculture facilities have large societal value. Ensuring the health of animals in these systems requires understanding how microorganisms contribute to chemical cycling and waste removal. Focusing on the largest seawater aquarium in the United States, we explore the microbial communities in specialized reactors designed to remove excess nitrogen through the metabolic activity of sulfur-consuming microbes. We show that the diversity of microbes in these reactors is both high and highly variable, with distinct community types associated with significant differences in nitrogen removal rate. We also show that the genes encoding the metabolic steps of nitrogen removal are distributed broadly throughout community members, suggesting that the chemical transformations in this system are likely a result of microbes relying on other microbes. These results provide a framework for future studies exploring the contributions of different community members, both in waste removal and in structuring microbial biodiversity.}, }
@article {pmid30056005, year = {2018}, author = {Bankevich, A and Pevzner, PA}, title = {Joint Analysis of Long and Short Reads Enables Accurate Estimates of Microbiome Complexity.}, journal = {Cell systems}, volume = {7}, number = {2}, pages = {192-200.e3}, doi = {10.1016/j.cels.2018.06.009}, pmid = {30056005}, issn = {2405-4712}, mesh = {Algorithms ; Bacteria/genetics ; *Gastrointestinal Microbiome ; Genetic Variation ; *Genome, Bacterial ; Humans ; Metagenome ; Metagenomics/*methods ; Sequence Analysis, DNA ; }, abstract = {Reduced microbiome diversity has been linked to several diseases. However, estimating the diversity of bacterial communities-the number and the total length of distinct genomes within a metagenome-remains an open problem in microbial ecology. Here, we describe an algorithm for estimating the microbial diversity in a metagenomic sample based on a joint analysis of short and long reads. Unlike previous approaches, the algorithm does not make any assumptions on the distribution of the frequencies of genomes within a metagenome (as in parametric methods) and does not require a large database that covers the total diversity (as in non-parametric methods). We estimate that genomes comprising a human gut metagenome have total length varying from 1.3 to 3.5 billion nucleotides, with genomes responsible for 50% of total abundance having total length varying from only 25 to 61 million nucleotides. In contrast, genomes comprising an aquifer sediment metagenome have more than two orders of magnitude larger total length (≈840 billion nucleotides).}, }
@article {pmid29884754, year = {2018}, author = {Lugli, GA and Mancino, W and Milani, C and Duranti, S and Turroni, F and van Sinderen, D and Ventura, M}, title = {Reconstruction of the Bifidobacterial Pan-Secretome Reveals the Network of Extracellular Interactions between Bifidobacteria and the Infant Gut.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {16}, pages = {}, pmid = {29884754}, issn = {1098-5336}, mesh = {Bifidobacterium/*genetics/*metabolism ; Bifidobacterium longum/genetics/metabolism ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Glycomics ; Humans ; Infant ; Intestines/*microbiology ; *Metabolome ; Metagenome ; Milk, Human/metabolism ; Oligosaccharides/metabolism ; Proteome ; Symbiosis ; }, abstract = {The repertoire of secreted proteins decoded by a microorganism represents proteins released from or associated with the cell surface. In gut commensals, such as bifidobacteria, these proteins are perceived to be functionally relevant, as they regulate the interaction with the gut environment. In the current study, we screened the predicted proteome of over 300 bifidobacterial strains among the currently recognized bifidobacterial species to generate a comprehensive database encompassing bifidobacterial extracellular proteins. A glycobiome analysis of this predicted bifidobacterial secretome revealed that a correlation exists between particular bifidobacterial species and their capability to hydrolyze human milk oligosaccharides (HMOs) and intestinal glycoconjugates, such as mucin. Furthermore, an exploration of metatranscriptomic data sets of the infant gut microbiota allowed the evaluation of the expression of bifidobacterial genes encoding extracellular proteins, represented by ABC transporter substrate-binding proteins and glycoside hydrolases enzymes involved in the degradation of human milk oligosaccharides and mucin. Overall, this study provides insights into how bifidobacteria interact with their natural yet highly complex environment, the infant gut.IMPORTANCE The ecological success of bifidobacteria relies on the activity of extracellular proteins that are involved in the metabolism of nutrients and the interaction with the environment. To date, information on secreted proteins encoded by bifidobacteria is incomplete and just related to few species. In this study, we reconstructed the bifidobacterial pan-secretome, revealing extracellular proteins that modulate the interaction of bifidobacteria with their natural environment. Furthermore, a survey of the secretion systems between bifidobacterial genomes allowed the identification of a conserved Sec-dependent secretion machinery in all the analyzed genomes and the Tat protein translocation system in the chromosomes of 23 strains belonging to Bifidobacterium longum subsp. longum and Bifidobacterium aesculapii.}, }
@article {pmid29803476, year = {2018}, author = {González-Escobar, JL and Grajales-Lagunes, A and Smoliński, A and Chagolla-López, A and De Léon-Rodríguez, A and Barba de la Rosa, AP}, title = {Microbiota of edible Liometopum apiculatum ant larvae reveals potential functions related to their nutritional value.}, journal = {Food research international (Ottawa, Ont.)}, volume = {109}, number = {}, pages = {497-505}, doi = {10.1016/j.foodres.2018.04.049}, pmid = {29803476}, issn = {1873-7145}, mesh = {Animals ; Ants/*microbiology ; Bacteria/classification/genetics/*isolation &amp; purification ; Female ; Food Analysis/methods ; Host-Pathogen Interactions ; Larva/microbiology ; Male ; Metagenomics ; *Microbiota ; *Nutritive Value ; Ribotyping ; Symbiosis ; }, abstract = {Edible insects, due to their high nutritive value, are currently considered as a potential renewable source for food and feed production. Liometopum apiculatum ants are widely distributed in arid and semi-arid ecosystems and their larvae (escamoles) are considered as a delicacy, however the microbial importance in L. apiculatum nutritional ecology is unknown. The aim of this research was to characterize the microorganisms associated with both L. apiculatum larvae and the reproductive adult ants using the 16S rRNA gene sequencing and culturomics approaches. The obligate endosymbionts were also investigated through microscopic analysis. The most abundant Phylum identified by sequencing in the larvae was Firmicutes while in adult ants was Proteobacteria. Interestingly, the culturomics results showed 15 genera corresponding to the bacteria identified by sequencing analysis. Particularly, it was observed a large population of nitrogen-fixing bacteria, which could be linked with the high protein content in escamoles. Endosymbionts were detected in bacteoriocytes, these bacteria are related with vitamins and essential amino acids biosynthesis, and both compounds contributing to the high nutritional value of escamoles. This is the first report of the microorganisms present in the escamolera ant ensuring their safety as food and opening new areas of nutritional ecological and food processing.}, }
@article {pmid29728382, year = {2018}, author = {Milani, C and Duranti, S and Mangifesta, M and Lugli, GA and Turroni, F and Mancabelli, L and Viappiani, A and Anzalone, R and Alessandri, G and Ossiprandi, MC and van Sinderen, D and Ventura, M}, title = {Phylotype-Level Profiling of Lactobacilli in Highly Complex Environments by Means of an Internal Transcribed Spacer-Based Metagenomic Approach.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {14}, pages = {}, pmid = {29728382}, issn = {1098-5336}, mesh = {Animals ; Cheese/microbiology ; Chickens ; DNA, Bacterial/genetics ; Female ; Gastrointestinal Microbiome ; Gene Expression Profiling ; Host Microbial Interactions ; Humans ; Lactobacillus/classification/*genetics/*metabolism ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; Vagina/microbiology ; }, abstract = {The genus Lactobacillus is a widespread taxon, members of which are highly relevant to functional and fermented foods, while they are also commonly present in host-associated gut and vaginal microbiota. Substantial efforts have been undertaken to disclose the genetic repertoire of all members of the genus Lactobacillus, and yet their species-level profiling in complex matrices is still undeveloped due to the poor phylotype resolution of profiling approaches based on the 16S rRNA gene. To overcome this limitation, an internal transcribed spacer (ITS)-based profiling method was developed to accurately profile lactobacilli at the species level. This approach encompasses a genus-specific primer pair combined with a database of ITS sequences retrieved from all available Lactobacillus genomes and a script for the QIIME software suite that performs all required steps to reconstruct a species-level profile. This methodology was applied to several environments, i.e., human gut and vagina and the ceca of free-range chickens, as well as whey and fresh cheese. Interestingly, the data collected confirmed a relevant role of lactobacilli present in functional and fermented foods in defining the population harbored by the human gut, while, unsurprisingly perhaps, the ceca of free-range chickens were observed to be dominated by lactobacilli characterized in birds living in natural environments. Moreover, vaginal swabs confirmed the existence of previously hypothesized community state types, while analysis of whey and fresh cheese revealed a dominant presence of single Lactobacillus species used as starters for cheese production. Furthermore, application of this ITS profiling method to a mock Lactobacillus community allowed a minimal resolution level of <0.006 ng/μl.IMPORTANCE The genus Lactobacillus is a large and ubiquitous taxon of high scientific and commercial relevance. Despite the fact that the genetic repertoire of Lactobacillus species has been extensively characterized, the ecology of this genus has been explored by metataxonomic techniques that are accurate down to the genus or phylogenetic group level only. Thus, the distribution of lactobacilli in environmental or processed food samples is relatively unexplored. The profiling protocol described here relies on the use of the internal transcribed spacer to perform an accurate classification in a target population of lactobacilli with a <0.006-ng/μl sensitivity. This approach was used to analyze five sample types collected from both human and animal host-associated microbiota, as well as from the cheese production chain. The availability of a tool for species-level profiling of lactobacilli may be highly useful for both academic research and a wide range of industrial applications.}, }
@article {pmid29651035, year = {2018}, author = {Zaheer, R and Noyes, N and Ortega Polo, R and Cook, SR and Marinier, E and Van Domselaar, G and Belk, KE and Morley, PS and McAllister, TA}, title = {Impact of sequencing depth on the characterization of the microbiome and resistome.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {5890}, pmid = {29651035}, issn = {2045-2322}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Archaea/classification/drug effects/*genetics/isolation &amp; purification ; Archaeal Proteins/genetics/metabolism ; Bacteria/classification/drug effects/*genetics/isolation &amp; purification ; Bacterial Proteins/genetics/metabolism ; Cattle ; Drug Resistance/*genetics ; Feces/microbiology ; Fungal Proteins/genetics/metabolism ; Fungi/classification/drug effects/*genetics/isolation &amp; purification ; Gastrointestinal Microbiome/drug effects/*genetics ; Gene Expression ; High-Throughput Nucleotide Sequencing ; Metagenomics/methods ; Phylogeny ; Viral Proteins/genetics/metabolism ; Viruses/classification/drug effects/*genetics/isolation &amp; purification ; }, abstract = {Developments in high-throughput next generation sequencing (NGS) technology have rapidly advanced the understanding of overall microbial ecology as well as occurrence and diversity of specific genes within diverse environments. In the present study, we compared the ability of varying sequencing depths to generate meaningful information about the taxonomic structure and prevalence of antimicrobial resistance genes (ARGs) in the bovine fecal microbial community. Metagenomic sequencing was conducted on eight composite fecal samples originating from four beef cattle feedlots. Metagenomic DNA was sequenced to various depths, D1, D0.5 and D0.25, with average sample read counts of 117, 59 and 26 million, respectively. A comparative analysis of the relative abundance of reads aligning to different phyla and antimicrobial classes indicated that the relative proportions of read assignments remained fairly constant regardless of depth. However, the number of reads being assigned to ARGs as well as to microbial taxa increased significantly with increasing depth. We found a depth of D0.5 was suitable to describe the microbiome and resistome of cattle fecal samples. This study helps define a balance between cost and required sequencing depth to acquire meaningful results.}, }
@article {pmid29593315, year = {2018}, author = {Sun, T and Wang, XQ and Zhao, ZL and Yu, SH and Yang, P and Chen, XM}, title = {A Lethal Fungus Infects the Chinese White Wax Scale Insect and Causes Dramatic Changes in the Host Microbiota.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {5324}, pmid = {29593315}, issn = {2045-2322}, mesh = {Animals ; DNA, Ribosomal Spacer ; Female ; *Fungi/classification/genetics ; Hemiptera/*microbiology ; *Host-Pathogen Interactions ; Metagenome ; Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S ; }, abstract = {The Chinese white wax scale insect (Ericerus pela) is an economically valuable species with an important role in wax production. Recently, in a greenhouse in Kunming, we identified a genus of fungus that infects and kills E. pela females. This study sought to perform the molecular detection of entomopathogens and analyze the changes in the host microbiota after entomopathogen infection. We used library construction, high-throughput sequencing and real-time quantitative polymerase chain reaction (RT-qPCR) to identify the fungi infecting adult E. pela, to understand the changes in the host organism, and to determine the distribution of the entomopathogens. Cladosporium langeronii and C. sphaerospermum were the main pathogenic species that infected the E. pela females, and they were most prevalent in the dorsal cuticle. In vivo, after infection, the proportion of Cladosporium clearly increased. The infection had little influence on the fungal community but had a strong influence on the bacterial community. After infection, Arsenophonus was dominant, and numerous bacterial genera disappeared. However, Rickettsia, instead of Arsenophonus, became dominant in the Cladosporium-infected individuals that had also been infected with Rickettsia. We identified the species that infected E. pela females and determined the influence of infection on the host microorganisms.}, }
@article {pmid29593299, year = {2018}, author = {Wang, X and Wang, Z and Jiang, P and He, Y and Mu, Y and Lv, X and Zhuang, L}, title = {Bacterial diversity and community structure in the rhizosphere of four Ferula species.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {5345}, pmid = {29593299}, issn = {2045-2322}, mesh = {*Bacteria/classification ; *Biodiversity ; Ferula/*microbiology ; Metagenome ; Metagenomics/methods ; *Microbiota ; Phylogeny ; Plant Roots/microbiology ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {The medicinal value of the Ferula L. has been recognized for more than a thousand years. Wild stocks of Ferula have declined dramatically because high economic value has led to overharvesting. The objective of this study was to compare the rhizosphere microbial community of four Ferula species [F. syreitschikowii K.-Pol., F. gracilis (Ledeb.) Ledeb., F. ferulaeoides (Steud.) Korov., and F. lehmannii Boiss.] in the northern part of Xinjiang, China. The 16S rRNA sequences of rhizosphere bacteria were obtained with an Illumina paired-end sequence platform. Analysis was conducted to determine the richness and diversity of the rhizosphere bacterial communities. Two-way ANOVA indicated that plant species and soil depth had no significant effect on the alpha diversity of rhizobacteria. Linear discriminant analysis effect size showed that F. lehmannii followed by F. ferulaeoides had the most biomarkers and the highest taxon level, F. syreitschikowii and F. gracilis the least, while F. syreitschikowii and F. gracilis had the least property. This trend is consistent with reports that the medicinal value of F. lehmannii and F. ferulaeoides is greater than that of F. gracilis and F. syreitschikowii. The results of this study provide information that could be used for the commercial cultivation of Ferula spp.}, }
@article {pmid29293174, year = {2018}, author = {Ikeda, M and Shimizu, K and Ogura, H and Kurakawa, T and Umemoto, E and Motooka, D and Nakamura, S and Ichimaru, N and Takeda, K and Takahara, S and Hirano, SI and Shimazu, T}, title = {Hydrogen-Rich Saline Regulates Intestinal Barrier Dysfunction, Dysbiosis, and Bacterial Translocation in a Murine Model of Sepsis.}, journal = {Shock (Augusta, Ga.)}, volume = {50}, number = {6}, pages = {640-647}, doi = {10.1097/SHK.0000000000001098}, pmid = {29293174}, issn = {1540-0514}, mesh = {Animals ; Bacterial Translocation/drug effects ; Disease Models, Animal ; Dysbiosis/*metabolism ; Enterobacteriaceae/genetics ; Hydrogen/pharmacology ; Intestinal Mucosa/*metabolism ; Male ; Mice ; Mice, Inbred C57BL ; Microbiota/drug effects/genetics ; Oxidative Stress/drug effects/genetics ; RNA, Messenger/genetics ; RNA, Ribosomal, 16S/genetics ; Sepsis ; Tight Junction Proteins/genetics/metabolism ; }, abstract = {Bacterial translocation is a major cause of multiple organ dysfunction syndrome in critical illness, and its management is an important therapeutic strategy. In this study, we focused on the key factors responsible for bacterial translocation including the intestinal microbiome and investigated the impact of molecular hydrogen therapy as a countermeasure against bacterial translocation in a murine model of sepsis. The experimental protocols were divided into the sham, saline treatment (control), and hydrogen treatment (H2) groups. In the H2 group, 15 mL/kg of hydrogen-rich saline (7 ppm) was gavaged daily for 7 days following cecal ligation and puncture (CLP). In the control group, normal saline was gavaged in the same way. In the results, the 7-day survival rate was significantly improved in the H2 group versus the control group (69% vs. 31%, P < 0.05). The incidence of bacterial translocation at 24 h after CLP as assessed by cultivation of mesenteric lymph nodes and blood was significantly decreased in the H2 group versus the control group. Administration of hydrogen-rich saline also prevented the expansion of facultative anaerobic Enterobacteriaceae and ameliorated intestinal hyperpermeability at 24 h after CLP. Intestinal tissue levels of inflammatory mediators such as inducible nitric oxide synthases, tumor necrosis factor α, interleukin (IL)-1β, IL-6, and oxidative stress marker malondialdehyde at 6 h after CLP were down-regulated in the H2 group. These results suggest luminal administration of hydrogen-rich saline, which prevents intestinal dysbiosis, hyperpermeability, and bacterial translocation, could potentially be a new therapeutic strategy in critical illness.}, }
@article {pmid29192012, year = {2018}, author = {Zalewski, S and Stewart, CJ and Embleton, ND and Berrington, JE}, title = {Brief guide to the analysis, interpretation and presentation of microbiota data.}, journal = {Archives of disease in childhood. Education and practice edition}, volume = {103}, number = {6}, pages = {327-330}, doi = {10.1136/archdischild-2017-313838}, pmid = {29192012}, issn = {1743-0593}, mesh = {Computational Biology/*methods ; Humans ; *Microbiota ; }, }
@article {pmid31576426, year = {2019}, author = {Long, Y and Jiang, J and Hu, X and Zhou, J and Hu, J and Zhou, S}, title = {Actinobacterial community in Shuanghe Cave using culture-dependent and -independent approaches.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {35}, number = {10}, pages = {153}, doi = {10.1007/s11274-019-2713-y}, pmid = {31576426}, issn = {1573-0972}, support = {2016YFC0400702//National Key R&amp;D Program of China/ ; }, abstract = {Karst caves, considering to be the &quot;arks&quot; of biodiversity, often contain high levels of endemism. In the present study, the actinobacterial community in Shuanghe Cave, the longest cave in Asia, was analyzed for the first-time using culture-dependent and -independent (16S rRNA amplicon sequencing) approaches. The amplicon sequencing analysis revealed a broad taxonomic diversity in Shuanghe Cave, including 19 phyla (predominantly Actinobacteria) and 264 different genera. While the culture-dependent method got the unrepresentative but supplemental result, a total of 239 actinomycetes were isolated and were identified to seven genera based on culture features and 16S rRNA tests. Among the three habitats (soil, rock soil, and bat guano), the dominant phyla did not differ significantly, while the dominant genus community varied among different habitats, and the richness in soil and rock soil samples was higher than that in bat guano. Furthermore, 16 isolate strains showed antimicrobial activity, especially, the strain S142 (Streptomyces badius) and S761 (Actinoplanes friuliensis) exhibited the most promising activity against various pathogens. Overall, this work showed the abundant bacterial diversity and the antimicrobial potential of the isolates from the Shuanghe Cave.}, }
@article {pmid31561274, year = {2019}, author = {Bergner, LM and Orton, RJ and Benavides, JA and Becker, DJ and Tello, C and Biek, R and Streicker, DG}, title = {Demographic and environmental drivers of metagenomic viral diversity in vampire bats.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.15250}, pmid = {31561274}, issn = {1365-294X}, abstract = {Viruses infect all forms of life and play critical roles as agents of disease, drivers of biochemical cycles and sources of genetic diversity for their hosts. Our understanding of viral diversity derives primarily from comparisons among host species, precluding insight into how intraspecific variation in host ecology affects viral communities or how predictable viral communities are across populations. We test spatial, demographic and environmental hypotheses explaining viral richness and community composition across populations of common vampire bats, which occur in diverse habitats of North, Central and South America. We demonstrate marked variation in viral communities which was not consistently predicted by a null model of declining community similarity with increasing spatial or genetic distances separating populations. We also find no evidence that larger bat colonies host greater viral diversity. Instead, viral diversity follows an elevational gradient, is enriched by juvenile-biased age structure, and declines with local anthropogenic food resources as measured by livestock density. Our results establish the value of linking the modern influx of metagenomic sequence data with comparative ecology, reveal that snapshot views of viral diversity are unlikely to be representative at the species level, and affirm existing ecological theories that link host ecology not only to single pathogen dynamics but also to viral communities.}, }
@article {pmid31546776, year = {2019}, author = {Hickl, O and Heintz-Buschart, A and Trautwein-Schult, A and Hercog, R and Bork, P and Wilmes, P and Becher, D}, title = {Sample Preservation and Storage Significantly Impact Taxonomic and Functional Profiles in Metaproteomics Studies of the Human Gut Microbiome.}, journal = {Microorganisms}, volume = {7}, number = {9}, pages = {}, doi = {10.3390/microorganisms7090367}, pmid = {31546776}, issn = {2076-2607}, support = {C15/BN/10404093//Fonds National de la Recherche Luxembourg/ ; FZT118//Deutsche Forschungsgemeinschaft/ ; }, abstract = {With the technological advances of the last decade, it is now feasible to analyze microbiome samples, such as human stool specimens, using multi-omic techniques. Given the inherent sample complexity, there exists a need for sample methods which preserve as much information as possible about the biological system at the time of sampling. Here, we analyzed human stool samples preserved and stored using different methods, applying metagenomics as well as metaproteomics. Our results demonstrate that sample preservation and storage have a significant effect on the taxonomic composition of identified proteins. The overall identification rates, as well as the proportion of proteins from Actinobacteria were much higher when samples were flash frozen. Preservation in RNAlater overall led to fewer protein identifications and a considerable increase in the share of Bacteroidetes, as well as Proteobacteria. Additionally, a decrease in the share of metabolism-related proteins and an increase of the relative amount of proteins involved in the processing of genetic information was observed for RNAlater-stored samples. This suggests that great care should be taken in choosing methods for the preservation and storage of microbiome samples, as well as in comparing the results of analyses using different sampling and storage methods. Flash freezing and subsequent storage at -80 °C should be chosen wherever possible.}, }
@article {pmid31545802, year = {2019}, author = {Guirro, M and Costa, A and Gual-Grau, A and Herrero, P and Torrell, H and Canela, N and Arola, L}, title = {Effects from diet-induced gut microbiota dysbiosis and obesity can be ameliorated by fecal microbiota transplantation: A multiomics approach.}, journal = {PloS one}, volume = {14}, number = {9}, pages = {e0218143}, doi = {10.1371/journal.pone.0218143}, pmid = {31545802}, issn = {1932-6203}, abstract = {Obesity and its comorbidities are currently considered an epidemic, and the involved pathophysiology is well studied. Hypercaloric diets are tightly related to the obesity etiology and also cause alterations in gut microbiota functionality. Diet and antibiotics are known to play crucial roles in changes in the microbiota ecosystem and the disruption of its balance; therefore, the manipulation of gut microbiota may represent an accurate strategy to understand its relationship with obesity caused by diet. Fecal microbiota transplantation, during which fecal microbiota from a healthy donor is transplanted to an obese subject, has aroused interest as an effective approach for the treatment of obesity. To determine its success, a multiomics approach was used that combined metagenomics and metaproteomics to study microbiota composition and function. To do this, a study was performed in rats that evaluated the effect of a hypercaloric diet on the gut microbiota, and this was combined with antibiotic treatment to deplete the microbiota before fecal microbiota transplantation to verify its effects on gut microbiota-host homeostasis. Our results showed that a high-fat diet induces changes in microbiota biodiversity and alters its function in the host. Moreover, we found that antibiotics depleted the microbiota enough to reduce its bacterial content. Finally, we assessed the use of fecal microbiota transplantation as a complementary obesity therapy, and we found that it reversed the effects of antibiotics and reestablished the microbiota balance, which restored normal functioning and alleviated microbiota disruption. This new approach could be implemented to support the dietary and healthy habits recommended as a first option to maintain the homeostasis of the microbiota.}, }
@article {pmid31539947, year = {2019}, author = {Yadav, S and Kapley, A}, title = {Exploration of activated sludge resistome using metagenomics.}, journal = {The Science of the total environment}, volume = {692}, number = {}, pages = {1155-1164}, doi = {10.1016/j.scitotenv.2019.07.267}, pmid = {31539947}, issn = {1879-1026}, abstract = {Antibiotic resistance is a global problem. In India poor waste management and inadequate sanitary are key factors which encourage the dissemination of antimicrobial resistance. Microbial biodiversity serves as an invaluable source for diverse types of bioactive compounds that encompass most of the pharmaceuticals to date. Therefore, in this study, we used the metagenomic approach for the surveillance of antibiotic resistance genes, drug resistant microbes and mobile-genetic elements in two activated sludge metagenome samples collected from Ankleshwar, Gujarat, India. Proteobacteria were found to be the most abundant bacteria among the metagenome analyzed. Twenty-four genes conferring resistance to antibiotics and heavy metals were found. Multidrug resistant &quot;ESKAPE pathogens&quot; were also abundant in the sludge metagenome. Mobile genetic elements like IncP-1 plasmid pKJK5, IncP-1beta multi resistance plasmid and pB8 were also noticed in the higher abundance. These plasmids play an important role in the spread of antibiotic resistance by the horizontal gene transfer. Statistical analysis of both metagenome using STAMP software confirmed presence of mobile genetic elements such as gene transfer agents, phages, Prophages etc. which also play important role in the dissemination of antibiotic resistant genes.}, }
@article {pmid31507563, year = {2019}, author = {Liang, Y and Wang, L and Wang, Z and Zhao, J and Yang, Q and Wang, M and Yang, K and Zhang, L and Jiao, N and Zhang, Y}, title = {Metagenomic Analysis of the Diversity of DNA Viruses in the Surface and Deep Sea of the South China Sea.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1951}, doi = {10.3389/fmicb.2019.01951}, pmid = {31507563}, issn = {1664-302X}, abstract = {A metagenomic analysis of the viral community from five surface and five deep sea water (>2000 m below the surface, mbs) samples collected from the central basin of the South China Sea and adjacent Northwest Pacific Ocean during July-August 2017 was conducted herein. We builded up a South China Sea DNA virome (SCSV) dataset of 29,967 viral Operational Taxonomic Units (vOTUs), which is comparable to the viral populations from the original Tara Ocean and Malaspina expeditions. The most abundant and widespread viral populations were from the uncultivated viruses annotated from the viral metagenomics. Only 74 and 37 vOTUs have similarity with the reported genomes from the cultivated viruses and the single-virus genomics, respectively. The community structures of deep sea viromes in the SCSV were generally different from the surface viromes. The carbon flux and nutrients (PO4 and NOx) were related to the surface and deep sea viromes in the SCSV, respectively. In the SCSV, the annotated vOTUs could be affiliated to the cultivated viruses mainly including Pelagibacter (SAR11) phage HTVC010P, Prochlorococcus phages (P-GSP1, P-SSM4, and P-TIM68), Cyanophages (MED4-184 and MED4-117) and Mycobacterium phages (Sparky and Squirty). It indicated that phage infection to the SAR11 cluster may occur ubiquitously and has significant impacts on bathypelagic SAR11 communities in the deep sea. Meanwhile, as Prochlorococcus is prominently distributed in the euphotic ocean, the existence of their potential phages in the deep sea suggested the sedimentation mechanism might contribute to the formation of the deep sea viromes. Intriguingly, the presence of Mycobacterium phages only in the deep sea viromes, suggests inhabitance of endemic viral populations in the deep sea viromes in the SCSV. This study provided an insight of the viral community in the South China Sea and for the first time uncovered the deep sea viral diversity in the central basin of the South China Sea.}, }
@article {pmid31465735, year = {2019}, author = {Guadagnini, D and Rocha, GZ and Santos, A and Assalin, HB and Hirabara, SM and Curi, R and Oliveira, AG and Prada, PO and Saad, MJA}, title = {Microbiota determines insulin sensitivity in TLR2-KO mice.}, journal = {Life sciences}, volume = {234}, number = {}, pages = {116793}, doi = {10.1016/j.lfs.2019.116793}, pmid = {31465735}, issn = {1879-0631}, mesh = {Animals ; Endoplasmic Reticulum Stress ; *Gastrointestinal Microbiome ; Gene Deletion ; Glucose Intolerance/genetics/metabolism/microbiology ; Housing, Animal ; Insulin/*metabolism ; *Insulin Resistance/genetics ; Male ; Mice, Inbred C57BL ; Mice, Knockout ; Toll-Like Receptor 2/*genetics/metabolism ; }, abstract = {INTRODUCTION: Environmental factors have a key role in the control of gut microbiota and obesity. TLR2 knockout (TLR2-/-) mice in some housing conditions are protected from diet-induced insulin resistance. However, in our housing conditions these animals are not protected from diet-induced insulin-resistance.<br><br>AIM: The aim of the present study was to investigate the influence of our animal housing conditions on the gut microbiota, glucose tolerance and insulin sensitivity in TLR2-/- mice.<br><br>MATERIAL AND METHODS: The microbiota was investigated by metagenomics, associated with hyperinsulinemic euglycemic clamp and GTT associated with insulin signaling through immunoblotting.<br><br>RESULTS: The results showed that TLR2-/- mice in our housing conditions presented a phenotype of metabolic syndrome characterized by insulin resistance, glucose intolerance and increase in body weight. This phenotype was associated with differences in microbiota in TLR2-/- mice that showed a decrease in the Proteobacteria and Bacteroidetes phyla and an increase in the Firmicutesphylum, associated with and in increase in the Oscillospira and Ruminococcus genera. Furthermore there is also an increase in circulating LPS and subclinical inflammation in TLR2-/-. The molecular mechanism that account for insulin resistance was an activation of TLR4, associated with ER stress and JNK activation. The phenotype and metabolic behavior was reversed by antibiotic treatment and reproduced in WT mice by microbiota transplantation.<br><br>CONCLUSIONS: Our data show, for the first time, that the intestinal microbiota can induce insulin resistance and obesity in an animal model that is genetically protected from these processes.}, }
@article {pmid31464899, year = {2019}, author = {Liang, W and Yang, Y and Wang, H and Wang, H and Yu, X and Lu, Y and Shen, S and Teng, L}, title = {Gut microbiota shifts in patients with gastric cancer in perioperative period.}, journal = {Medicine}, volume = {98}, number = {35}, pages = {e16626}, doi = {10.1097/MD.0000000000016626}, pmid = {31464899}, issn = {1536-5964}, mesh = {Adult ; Bacteria/*classification/genetics/isolation &amp; purification ; China ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Female ; Gastrectomy ; Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged ; Perioperative Period ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; Stomach Neoplasms/microbiology/*surgery ; }, abstract = {Gastric cancer (GC) is one of the common malignant tumors in China, with a high morbidity and mortality. With the development and application of high-throughput sequencing technologies and metagenomics, a great quantity of studies have shown that gastrointestinal microbiota is closely related to digestive system diseases. Although some studies have reported the effect of long-term follow-up after subtotal gastrectomy on intestinal flora changes in patients with GC. However, the features of gut microbiota and their shifts in patients with GC in perioperative period remain unclear.This study was designed to characterize fecal microbiota shifts of the patients with GC before and after the radical distal gastrectomy (RDG) during their hospital staying periods. Furthermore, fecal microbiota was also compared between the GC patients and healthy individuals.Patients who were diagnosed with advanced gastric adenocarcinoma at distal stomach were enrolled in the study. The bacterial burden within fecal samples was determined using quantitative polymerase chain reaction. To analyze the diversity and composition of gut microbiota from fecal DNA of 20 GC patients and 22 healthy controls, amplicons of the 16S rRNA gene from all subjects were pyrosequenced. To study gut microbiota shifts, the fecal microbiota from 6 GC patients before and after RDG was detected and subsequently analyzed. Short-chain fatty acids were also detected by chromatography spectrometer in these 6 GC patients.RDG had a moderate effect on bacterial richness and evenness, but had pronounced effects on the composition of postoperative gut microbiota compared with preoperative group. The relative abundances of genera Akkermansia, Esherichia/Shigella, Lactobacillus, and Dialister were significant changed in perioperative period. Remarkably, higher abundances of Escherichia/Shigella, Veillonella, and Clostridium XVIII and lower abundances of Bacteroides were observed in gut microbiota of overall GC patients compared to healthy controls.This study is the first study to characterize the altered gut microbiota within fecal samples from GC patients during perioperative period, and provide a new insights on such microbial perturbations as a potential effector of perioperative period phenotype. Further research must validate these discoveries and may evaluate targeted microbiota shifts to improve outcomes in GC patients.}, }
@article {pmid31448249, year = {2019}, author = {Pini Prato, A and Bartow-McKenney, C and Hudspeth, K and Mosconi, M and Rossi, V and Avanzini, S and Faticato, MG and Ceccherini, I and Lantieri, F and Mattioli, G and Larson, D and Pavan, W and De Filippo, C and Di Paola, M and Mavilio, D and Cavalieri, D}, title = {A Metagenomics Study on Hirschsprung's Disease Associated Enterocolitis: Biodiversity and Gut Microbial Homeostasis Depend on Resection Length and Patient's Clinical History.}, journal = {Frontiers in pediatrics}, volume = {7}, number = {}, pages = {326}, doi = {10.3389/fped.2019.00326}, pmid = {31448249}, issn = {2296-2360}, abstract = {Objectives: Since 2010, several researches demonstrated that microbiota dynamics correlate and can even predispose to Hirschsprung (HSCR) associated enterocolitis (HAEC). This study aims at assessing the structure of the microbiota of HSCR patients in relation to extent of aganglionosis and HAEC status. Methods: All consecutive HSCR patients admitted to Gaslini Institute (Genova, Italy) between May 2012 and November 2014 were enrolled. Institutional review board (IRB) approval was obtained. Stools were sampled and 16S rDNA V3-V4 regions were sequenced using the Illumina-MiSeq. Taxonomy assignments were performed using QIIME RDP. Alpha diversity indexes were analyzed by Shannon and Simpson Indexes, and Phylogenetic Diversity. Results: We enrolled 20 patients. Male to female ratio was 4:1. Six patients suffered from Total Colonic Aganglionosis (TCSA). Considering sample site (i.e., extent of aganglionosis), we confirmed the known relationship between sample site and both biodiversity and composition of intestinal microbiota. Patients with TCSA showed lower biodiversity and increased Proteobacteria/Bacteroidetes relative abundance ratio. When addressing biodiversity, composition and dynamics of TCSA patients we could not find any significant relationship with regard to HAEC occurrences. Conclusions: The composition of HAEC predisposing microbiota is specific to each patient. We could confirm that total colon resections can change the composition of intestinal microbiota and to dramatically reduce microbial diversity. The subsequent reduction of system robustness could expose TCSA patients to environmental microbes that might not be part of the normal microbiota. Future long-term studies should investigate both patients and their family environment, as well as their disease history.}, }
@article {pmid31448147, year = {2019}, author = {Wu, B and Hussain, M and Zhang, W and Stadler, M and Liu, X and Xiang, M}, title = {Current insights into fungal species diversity and perspective on naming the environmental DNA sequences of fungi.}, journal = {Mycology}, volume = {10}, number = {3}, pages = {127-140}, doi = {10.1080/21501203.2019.1614106}, pmid = {31448147}, issn = {2150-1203}, abstract = {The global bio-diversity of fungi has been extensively investigated and their species number has been estimated. Notably, the development of molecular phylogeny has revealed an unexpected fungal diversity and utilisation of culture-independent approaches including high-throughput amplicon sequencing has dramatically increased number of fungal operational taxonomic units. A number of novel taxa including new divisions, classes, orders and new families have been established in last decade. Many cryptic species were identified by molecular phylogeny. Based on recently generated data from culture-dependent and -independent survey on same samples, the fungal species on the earth were estimated to be 12 (11.7-13.2) million compared to 2.2-3.8 million species recently estimated by a variety of the estimation techniques. Moreover, it has been speculated that the current use of high-throughput sequencing techniques would reveal an even higher diversity than our current estimation. Recently, the formal classification of environmental sequences and permission of DNA sequence data as fungal names' type were proposed but strongly objected by the mycologist community. Surveys on fungi in unusual niches have indicated that many previously regarded &quot;unculturable fungi&quot; could be cultured on certain substrates under specific conditions. Moreover, the high-throughput amplicon sequencing, shotgun metagenomics and a single-cell genomics could be a powerful means to detect novel taxa. Here, we propose to separate the fungal types into physical type based on specimen, genome DNA (gDNA) type based on complete genome sequence of culturable and uncluturable fungal specimen and digital type based on environmental DNA sequence data. The physical and gDNA type should have priority, while the digital type can be temporal supplementary before the physical type and gDNA type being available. The fungal name based on the &quot;digital type&quot; could be assigned as the &quot;clade&quot; name + species name. The &quot;clade&quot; name could be the name of genus, family or order, etc. which the sequence of digital type affiliates to. Facilitating future cultivation efforts should be encouraged. Also, with the advancement in knowledge of fungi inhabiting various environments mostly because of rapid development of new detection technologies, more information should be expected for fungal diversity on our planet.}, }
@article {pmid31444199, year = {2019}, author = {Loit, K and Adamson, K and Bahram, M and Puusepp, R and Anslan, S and Kiiker, R and Drenkhan, R and Tedersoo, L}, title = {Relative Performance of MinION (Oxford Nanopore Technologies) vs. Sequel (Pacific Biosciences) Third-Generation Sequencing Instruments in Identification of Agricultural and Forest Fungal Pathogens.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.01368-19}, pmid = {31444199}, issn = {1098-5336}, abstract = {Culture-based molecular identification methods have revolutionized detection of pathogens, yet these methods are slow and may yield inconclusive results from environmental materials. The second-generation sequencing tools have much improved precision and sensitivity of detection, but these analyses are costly and may take several days to months. Of the third-generation sequencing techniques, the portable MinION device (Oxford Nanopore Technologies) has received much attention because of its small size and possibility of rapid analysis at reasonable cost. Here, we compare the relative performance of two third-generation sequencing instruments, MinION and Sequel (Pacific Biosciences) in identification and diagnostics of fungal and oomycete pathogens from conifer (Pinaceae spp.) needles and potato (Solanum tuberosum) leaves and tubers. We demonstrate that Sequel instrument is efficient for metabarcoding of complex samples, whereas MinION is not suited for this purpose due to the high error rate and multiple biases. However, we find that MinION can be utilized for rapid and accurate identification of dominant pathogenic organisms and other associated organisms from plant tissues following both amplicon-based and PCR-free metagenomics approaches. Using the metagenomics approach with shortened DNA extraction and incubation times, we performed the entire MinION workflow from sample preparation through DNA extraction, sequencing, bioinformatics and interpretation in two and half hours. We advocate the use of MinION for rapid diagnostics of pathogens and potentially other organisms, but care needs to be taken to control or account for multiple potential technical biases.IMPORTANCE Microbial pathogens cause enormous losses to agriculture and forestry, but current combined culturing- and molecular identification-based detection methods are too slow for rapid identification and application of countermeasures. Here we develop new and rapid protocols for Oxford Nanopore MinION-based third-generation diagnostics of plant pathogens that greatly improves the speed of diagnostics. However, due to high error rate and technical biases in MinION, the Pacific BioSciences Sequel platform is more useful for in-depth amplicon-based biodiversity monitoring (metabarcoding) from complex environmental samples.}, }
@article {pmid31438955, year = {2019}, author = {Vavourakis, CD and Mehrshad, M and Balkema, C and van Hall, R and Andrei, AŞ and Ghai, R and Sorokin, DY and Muyzer, G}, title = {Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake.}, journal = {BMC biology}, volume = {17}, number = {1}, pages = {69}, doi = {10.1186/s12915-019-0688-7}, pmid = {31438955}, issn = {1741-7007}, support = {322551/ERC_/European Research Council/International ; 322551/ERC_/European Research Council/International ; 322551/ERC_/European Research Council/International ; L200961651//Czech Academy of Sciences/ ; MSM200961801//Czech Academy of Sciences/ ; 17-04828S//Grant Agency of the Czech Republic/ ; 17-04828S//Grant Agency of the Czech Republic/ ; 24002002//SYAM-Gravitation Program/ ; RFBR 19-04-00401//Russian Foundation for Basic Research/ ; }, abstract = {BACKGROUND: The planetary sulfur cycle is a complex web of chemical reactions that can be microbial-mediated or can occur spontaneously in the environment, depending on the temperature and pH. Inorganic sulfur compounds can serve as energy sources for specialized prokaryotes and are important substrates for microbial growth in general. Here, we investigate dissimilatory sulfur cycling in the brine and sediments of a southwestern Siberian soda lake characterized by an extremely high pH and salinity, combining meta-omics analyses of its uniquely adapted highly diverse prokaryote communities with biogeochemical profiling to identify key microbial players and expand our understanding of sulfur cycling under haloalkaline conditions.<br><br>RESULTS: Peak microbial activity was found in the top 4 cm of the sediments, a layer with a steep drop in oxygen concentration and redox potential. The majority of sulfur was present as sulfate or iron sulfide. Thiosulfate was readily oxidized by microbes in the presence of oxygen, but oxidation was partially inhibited by light. We obtained 1032 metagenome-assembled genomes, including novel population genomes of characterized colorless sulfur-oxidizing bacteria (SOB), anoxygenic purple sulfur bacteria, heterotrophic SOB, and highly active lithoautotrophic sulfate reducers. Surprisingly, we discovered the potential for nitrogen fixation in a new genus of colorless SOB, carbon fixation in a new species of phototrophic Gemmatimonadetes, and elemental sulfur/sulfite reduction in the &quot;Candidatus Woesearchaeota.&quot; Polysulfide/thiosulfate and tetrathionate reductases were actively transcribed by various (facultative) anaerobes.<br><br>CONCLUSIONS: The recovery of over 200 genomes that encoded enzymes capable of catalyzing key reactions in the inorganic sulfur cycle indicates complete cycling between sulfate and sulfide at moderately hypersaline and extreme alkaline conditions. Our results suggest that more taxonomic groups are involved in sulfur dissimilation than previously assumed.}, }
@article {pmid31376000, year = {2019}, author = {Cowan, DA and Hopkins, DW and Jones, BE and Maggs-Kölling, G and Majewska, R and Ramond, JB}, title = {Microbiomics of Namib Desert habitats.}, journal = {Extremophiles : life under extreme conditions}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00792-019-01122-7}, pmid = {31376000}, issn = {1433-4909}, abstract = {The Namib Desert is one of the world's only truly coastal desert ecosystem. Until the end of the 1st decade of the twenty-first century, very little was known of the microbiology of this southwestern African desert, with the few reported studies being based solely on culture-dependent approaches. However, from 2010, an intense research program was undertaken by researchers from the University of the Western Cape Institute for Microbial Biotechnology and Metagenomics, and subsequently the University of Pretoria Centre for Microbial Ecology and Genomics, and their collaborators, led to a more detailed understanding of the ecology of the indigenous microbial communities in many Namib Desert biotopes. Namib Desert soils and the associated specialized niche communities are inhabited by a wide array of prokaryotic, lower eukaryotic and virus/phage taxa. These communities are highly heterogeneous on both small and large spatial scales, with community composition impacted by a range of macro- and micro-environmental factors, from water regime to soil particle size. Community functionality is also surprisingly non-homogeneous, with some taxa retaining functionality even under hyper-arid soil conditions, and with subtle changes in gene expression and phylotype abundances even on diel timescales. Despite the growing understanding of the structure and function of Namib Desert microbiomes, there remain enormous gaps in our knowledge. We have yet to quantify many of the processes in these soil communities, from regional nutrient cycling to community growth rates. Despite the progress that has been made, we still have little knowledge of either the role of phages in microbial community dynamics or inter-species interactions. Furthermore, the intense research efforts of the past decade have highlighted the immense scope for future microbiological research in this dynamic, enigmatic and charismatic region of Africa.}, }
@article {pmid31365065, year = {2019}, author = {Sutela, S and Poimala, A and Vainio, EJ}, title = {Viruses of fungi and oomycetes in the soil environment.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {9}, pages = {}, doi = {10.1093/femsec/fiz119}, pmid = {31365065}, issn = {1574-6941}, abstract = {Soils support a myriad of organisms hosting highly diverse viromes. In this minireview, we focus on viruses hosted by true fungi and oomycetes (members of Stamenopila, Chromalveolata) inhabiting bulk soil, rhizosphere and litter layer, and representing different ecological guilds, including fungal saprotrophs, mycorrhizal fungi, mutualistic endophytes and pathogens. Viruses infecting fungi and oomycetes are characterized by persistent intracellular nonlytic lifestyles and transmission via spores and/or hyphal contacts. Almost all fungal and oomycete viruses have genomes composed of single-stranded or double-stranded RNA, and recent studies have revealed numerous novel viruses representing yet unclassified family-level groups. Depending on the virus-host combination, infections can be asymptomatic, beneficial or detrimental to the host. Thus, mycovirus infections may contribute to the multiplex interactions of hosts, therefore likely affecting the dynamics of fungal communities required for the functioning of soil ecosystems. However, the effects of fungal and oomycete viruses on soil ecological processes are still mostly unknown. Interestingly, new metagenomics data suggest an extensive level of horizontal virus transfer between plants, fungi and insects.}, }
@article {pmid31354669, year = {2019}, author = {Raimondi, S and Amaretti, A and Gozzoli, C and Simone, M and Righini, L and Candeliere, F and Brun, P and Ardizzoni, A and Colombari, B and Paulone, S and Castagliuolo, I and Cavalieri, D and Blasi, E and Rossi, M and Peppoloni, S}, title = {Longitudinal Survey of Fungi in the Human Gut: ITS Profiling, Phenotyping, and Colonization.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1575}, doi = {10.3389/fmicb.2019.01575}, pmid = {31354669}, issn = {1664-302X}, abstract = {The fungal component of the intestinal microbiota of eight healthy subjects was studied over 12 months using metagenome survey and culture-based approaches. Aspergillus, Candida, Debaryomyces, Malassezia, Penicillium, Pichia, and Saccharomyces were the most recurrent and/or dominant fungal genera, according to metagenomic analysis. The biodiversity of fungal communities was lower and characterized by greater unevenness, when compared to bacterial microbiome. The dissimilarities both among subjects and over the time within the same subject suggested that most of the fungi passed through the gastro-intestinal tract (GIT) without becoming stable colonizers. Certain genera, such as Aspergillus and Penicillium, were isolated in a minority of cases, although they recurred abundantly and frequently in the metagenomics survey, likely being environmental or food-borne fungi that do not inhabit the GIT. Candida genus was recurrently detected. Candida albicans isolates dominated among the cultivable mycobiota and longitudinally persisted, likely as commensals inhabiting the intestine or regularly reaching it from Candida-colonized districts, such as the oral cavity. Other putative colonizers belonged to Candida zeylanoides, Geotrichum candidum, and Rhodotorula mucilaginosa, with persisting biotypes being identified. Phenotyping of fungal isolates indicated that C. albicans adhered to human epithelial cells more efficiently and produced greater amounts of biofilm in vitro than non-albicans Candida (NAC) and non-Candida fungi (NCF). The C. albicans isolates also induced the highest release of HBD-2 by human epithelial cells, further differing from NAC and NCF. Nine representative isolates were administered to mice to evaluate the ability to colonize the intestine. Only two out of three C. albicans strains persisted in stools of animals 2 weeks after the end of the oral administration, whereas NAC and NCF did not. These results confirm the allochthonous nature of most the intestinal fungi, while C. albicans appears to be commonly involved in stable colonization. A combination of specific genetic features in the microbe and in the host likely allow colonization from fungi normally present solely as passengers. It remains to be established if other species identified as potential colonizers, in addition to Candida, are true inhabitants of the GIT or rather reach the intestine spreading from other body districts.}, }
@article {pmid31338073, year = {2019}, author = {Praeg, N and Pauli, H and Illmer, P}, title = {Microbial Diversity in Bulk and Rhizosphere Soil of Ranunculus glacialis Along a High-Alpine Altitudinal Gradient.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1429}, doi = {10.3389/fmicb.2019.01429}, pmid = {31338073}, issn = {1664-302X}, abstract = {Serving as &quot;natural laboratories&quot;, altitudinal gradients can be used to study changes in the distribution of microorganisms in response to changing environmental conditions that typically occur over short geographical distances. Besides, rhizosphere zones of plants are known to be hot-spots for microbial diversity and to contain different microbial communities when compared with surrounding bulk soil. To discriminate the effects of altitude and plants, we investigated the microbial communities in the rhizosphere of Ranunculus glacialis and bulk soil along a high-alpine altitudinal gradient (2,600-3,400 m a.s.l.). The research area of this study was Mount (Mt.) &quot;Schrankogel&quot; in the Central Alps of Tyrol (Austria). Our results point to significantly different microbial diversities and community compositions in the different altitudinal belts. In the case of prokaryotes, environmental parameters could explain 41% of the total variation of soil communities, with pH and temperature being the strongest influencing factors. Comparing the effects derived from fraction (bulk vs. rhizosphere soil) and environmental factors, the effects of the roots of R. glacialis accounted for about one third of the explained variation. Fungal communities on the other hand were nearly exclusively influenced by environmental parameters accounting for 37.4% of the total variation. Both, for altitudinal zones as well as for bulk and rhizosphere fractions a couple of very specific biomarker taxa could be identified. Generally, the patterns of abundance of several taxa did not follow a steady increased or decreased trend along the altitudinal gradient but in many cases a maximal or minimal occurrence was established at mid-altitudes (3,000-3,100 m). This mid-altitudinal zone is a transition zone (the so-called alpine-nival ecotone) between the (lower) alpine grassland/tundra zone and the (upper) sparsely vegetated nival zone and was shown to correspond with the summer snow line. Climate change and the associated increase in temperature will shift this transition zone and thus, might also shift the described microbial patterns and biomarkers.}, }
@article {pmid31333598, year = {2019}, author = {Thomas, SC and Tamadonfar, KO and Seymour, CO and Lai, D and Dodsworth, JA and Murugapiran, SK and Eloe-Fadrosh, EA and Dijkstra, P and Hedlund, BP}, title = {Position-Specific Metabolic Probing and Metagenomics of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities at High Temperatures.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1427}, doi = {10.3389/fmicb.2019.01427}, pmid = {31333598}, issn = {1664-302X}, abstract = {Temperature is a primary driver of microbial community composition and taxonomic diversity; however, it is unclear to what extent temperature affects characteristics of central carbon metabolic pathways (CCMPs) at the community level. In this study, 16S rRNA gene amplicon and metagenome sequencing were combined with 13C-labeled metabolite probing of the CCMPs to assess community carbon metabolism along a temperature gradient (60-95°C) in Great Boiling Spring, NV. 16S rRNA gene amplicon diversity was inversely proportional to temperature, and Archaea were dominant at higher temperatures. KO richness and diversity were also inversely proportional to temperature, yet CCMP genes were similarly represented across the temperature gradient and many individual metagenome-assembled genomes had complete pathways. In contrast, genes encoding cellulosomes and many genes involved in plant matter degradation and photosynthesis were absent at higher temperatures. In situ13C-CO2 production from labeled isotopomer pairs of glucose, pyruvate, and acetate suggested lower relative oxidative pentose phosphate pathway activity and/or fermentation at 60°C, and a stable or decreased maintenance energy demand at higher temperatures. Catabolism of 13C-labeled citrate, succinate, L-alanine, L-serine, and L-cysteine was observed at 85°C, demonstrating broad heterotrophic activity and confirming functioning of the TCA cycle. Together, these results suggest that temperature-driven losses in biodiversity and gene content in geothermal systems may not alter CCMP function or maintenance energy demands at a community level.}, }
@article {pmid31307536, year = {2019}, author = {Chen, J and McIlroy, SE and Archana, A and Baker, DM and Panagiotou, G}, title = {A pollution gradient contributes to the taxonomic, functional, and resistome diversity of microbial communities in marine sediments.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {104}, doi = {10.1186/s40168-019-0714-6}, pmid = {31307536}, issn = {2049-2618}, support = {2016-67//Environment and Conservation Fund/ ; }, abstract = {BACKGROUND: Coastal marine environments are one of the most productive ecosystems on Earth. However, anthropogenic impacts exert significant pressure on coastal marine biodiversity, contributing to functional shifts in microbial communities and human health risk factors. However, relatively little is known about the impact of eutrophication-human-derived nutrient pollution-on the marine microbial biosphere.<br><br>RESULTS: Here, we tested the hypothesis that benthic microbial diversity and function varies along a pollution gradient, with a focus on human pathogens and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG annotation revealed that zinc, lead, total volatile solids, and ammonia nitrogen were correlated with microbial diversity and function. We propose several microbes, including Planctomycetes and sulfate-reducing microbes as candidates to reflect pollution concentration. Annotation of antibiotic resistance genes showed that the highest abundance of efflux pumps was found at the most polluted site, corroborating the relationship between pollution and human health risk factors. This result suggests that sediments at polluted sites harbor microbes with a higher capacity to reduce intracellular levels of antibiotics, heavy metals, or other environmental contaminants.<br><br>CONCLUSIONS: Our findings suggest a correlation between pollution and the marine sediment microbiome and provide insight into the role of high-turnover microbial communities as well as potential pathogenic organisms as real-time indicators of water quality, with implications for human health and demonstrate the inner functional shifts contributed by the microcommunities.}, }
@article {pmid31301473, year = {2019}, author = {Bengtsson-Palme, J and Milakovic, M and Švecová, H and Ganjto, M and Jonsson, V and Grabic, R and Udikovic-Kolic, N}, title = {Industrial wastewater treatment plant enriches antibiotic resistance genes and alters the structure of microbial communities.}, journal = {Water research}, volume = {162}, number = {}, pages = {437-445}, doi = {10.1016/j.watres.2019.06.073}, pmid = {31301473}, issn = {1879-2448}, abstract = {Antibiotic resistance is an emerging global health crisis, driven largely by overuse and misuse of antibiotics. However, there are examples in which the production of these antimicrobial agents has polluted the environment with active antibiotic residues, selecting for antibiotic resistant bacteria and the genes they carry. In this work, we have used shotgun metagenomics to investigate the taxonomic structure and resistance gene composition of sludge communities in a treatment plant in Croatia receiving wastewater from production of the macrolide antibiotic azithromycin. We found that the total abundance of antibiotic resistance genes was three times higher in sludge from the treatment plant receiving wastewater from pharmaceutical production than in municipal sludge from a sewage treatment plant in Zagreb. Surprisingly, macrolide resistance genes did not have higher abundances in the industrial sludge, but genes associated with mobile genetic elements such as integrons had. We conclude that at high concentrations of antibiotics, selection may favor taxonomic shifts towards intrinsically resistant species or strains harboring chromosomal resistance mutations rather than acquisition of mobile resistance determinants. Our results underscore the need for regulatory action also within Europe to avoid release of antibiotics into the environment.}, }
@article {pmid31293086, year = {2019}, author = {Ji, Y and Huotari, T and Roslin, T and Schmidt, NM and Wang, J and Yu, DW and Ovaskainen, O}, title = {SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13057}, pmid = {31293086}, issn = {1755-0998}, support = {31400470//National Natural Science Foundation of China/ ; 31500305//National Natural Science Foundation of China/ ; 31670536//National Natural Science Foundation of China/ ; 41661144002//National Natural Science Foundation of China/ ; 276909//Suomen Akatemia/ ; 284601//Suomen Akatemia/ ; 285803//Suomen Akatemia/ ; 309571//Suomen Akatemia/ ; //Jane and Aatos Erkko Foundation Grant/ ; 223257//Research Council of Norway through its Centres of Excellence Funding Scheme/ ; //Danish Environmental Protection Agency/ ; QYZDY-SSW-SMC024//Key Research Program of Frontier Sciences, CAS/ ; GJHZ1754//Bureau of International Cooperation/ ; XDA20050202//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; XDB31000000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2012FY110800//Ministry of Science and Technology of China/ ; GREKF18-04//State Key Laboratory of Genetic Resources and Evolution/ ; //Kunming Institute of Zoology/ ; //University of East Anglia/ ; //University of Chinese Academy of Sciences/ ; }, abstract = {The accurate quantification of eukaryotic species abundances from bulk samples remains a key challenge for community ecology and environmental biomonitoring. We resolve this challenge by combining shotgun sequencing, mapping to reference DNA barcodes or to mitogenomes, and three correction factors: (a) a percent-coverage threshold to filter out false positives, (b) an internal-standard DNA spike-in to correct for stochasticity during sequencing, and (c) technical replicates to correct for stochasticity across sequencing runs. The SPIKEPIPE pipeline achieves a strikingly high accuracy of intraspecific abundance estimates (in terms of DNA mass) from samples of known composition (mapping to barcodes R2 = .93, mitogenomes R2 = .95) and a high repeatability across environmental-sample replicates (barcodes R2 = .94, mitogenomes R2 = .93). As proof of concept, we sequence arthropod samples from the High Arctic, systematically collected over 17 years, detecting changes in species richness, species-specific abundances, and phenology. SPIKEPIPE provides cost-efficient and reliable quantification of eukaryotic communities.}, }
@article {pmid31267680, year = {2019}, author = {Taubert, M and Grob, C and Crombie, A and Howat, AM and Burns, OJ and Weber, M and Lott, C and Kaster, AK and Vollmers, J and Jehmlich, N and von Bergen, M and Chen, Y and Murrell, JC}, title = {Communal metabolism by Methylococcaceae and Methylophilaceae is driving rapid aerobic methane oxidation in sediments of a shallow seep near Elba, Italy.}, journal = {Environmental microbiology}, volume = {21}, number = {10}, pages = {3780-3795}, doi = {10.1111/1462-2920.14728}, pmid = {31267680}, issn = {1462-2920}, support = {GBMF3303//Gordon and Betty Moore Foundation/ ; ECF2016-626//Leverhulme Trust/ ; }, abstract = {The release of abiotic methane from marine seeps into the atmosphere is a major source of this potent greenhouse gas. Methanotrophic microorganisms in methane seeps use methane as carbon and energy source, thus significantly mitigating global methane emissions. Here, we investigated microbial methane oxidation at the sediment-water interface of a shallow marine methane seep. Metagenomics and metaproteomics, combined with 13 C-methane stable isotope probing, demonstrated that various members of the gammaproteobacterial family Methylococcaceae were the key players for methane oxidation, catalysing the first reaction step to methanol. We observed a transfer of carbon to methanol-oxidizing methylotrophs of the betaproteobacterial family Methylophilaceae, suggesting an interaction between methanotrophic and methylotrophic microorganisms that allowed for rapid methane oxidation. From our microcosms, we estimated methane oxidation rates of up to 871 nmol of methane per gram sediment per day. This implies that more than 50% of methane at the seep is removed by microbial oxidation at the sediment-water interface, based on previously reported in situ methane fluxes. The organic carbon produced was further assimilated by different heterotrophic microbes, demonstrating that the methane-oxidizing community supported a complex trophic network. Our results provide valuable eco-physiological insights into this specialized microbial community performing an ecosystem function of global relevance.}, }
@article {pmid31266971, year = {2019}, author = {Fernández-Correa, I and Truchado, DA and Gomez-Lucia, E and Doménech, A and Pérez-Tris, J and Schmidt-Chanasit, J and Cadar, D and Benítez, L}, title = {A novel group of avian astroviruses from Neotropical passerine birds broaden the diversity and host range of Astroviridae.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {9513}, doi = {10.1038/s41598-019-45889-3}, pmid = {31266971}, issn = {2045-2322}, support = {CGL2017-82117-P//Ministry of Economy and Competitiveness | Agencia Estatal de Investigaci&amp;#x00F3;n (Spanish Agencia Estatal de Investigaci&amp;#x00F3;n)/ ; CGL2017-82117-P//Ministry of Economy and Competitiveness | Agencia Estatal de Investigaci&amp;#x00F3;n (Spanish Agencia Estatal de Investigaci&amp;#x00F3;n)/ ; CT27/16-CT28/16//Universidad Complutense de Madrid (Complutense University of Madrid)/ ; }, abstract = {Metagenomics is helping to expand the known diversity of viruses, especially of those with poorly studied hosts in remote areas. The Neotropical region harbors a considerable diversity of avian species that may play a role as both host and short-distance vectors of unknown viruses. Viral metagenomics of cloacal swabs from 50 Neotropical birds collected in French Guiana revealed the presence of four complete astrovirus genomes. They constitute an early diverging novel monophyletic clade within the Avastrovirus phylogeny, representing a putative new astrovirus species (provisionally designated as Avastrovirus 5) according to the International Committee on Taxonomy of Viruses (ICTV) classification criteria. Their genomic organization shares some characteristics with Avastrovirus but also with Mamastrovirus. The pan-astrovirus RT-PCR analysis of the cloacal samples of 406 wild Neotropical birds showed a community-level prevalence of 4.9% (5.1% in passerines, the highest described so far in this order of birds). By screening birds of a remote region, we expanded the known host range of astroviruses to the avian families Cardinalidae, Conopophagidae, Furnariidae, Thamnophilidae, Turdidae and Tyrannidae. Our results provide important first insights into the unexplored viral communities, the ecology, epidemiology and features of host-pathogen interactions that shape the evolution of avastroviruses in a remote Neotropical rainforest.}, }
@article {pmid31264806, year = {2019}, author = {Pereira, O and Hochart, C and Auguet, JC and Debroas, D and Galand, PE}, title = {Genomic ecology of Marine Group II, the most common marine planktonic Archaea across the surface ocean.}, journal = {MicrobiologyOpen}, volume = {8}, number = {9}, pages = {e00852}, doi = {10.1002/mbo3.852}, pmid = {31264806}, issn = {2045-8827}, support = {ANR-14-CE02-0004-01//Agence Nationale de la Recherche/ ; }, abstract = {Planktonic Archaea have been detected in all the world's oceans and are found from surface waters to the deep sea. The two most common Archaea phyla are Thaumarchaeota and Euryarchaeota. Euryarchaeota are generally more common in surface waters, but very little is known about their ecology and their potential metabolisms. In this study, we explore the genomic ecology of the Marine Group II (MGII), the main marine planktonic Euryarchaeota, and test if it is composed of different ecologically relevant units. We re-analyzed Tara Oceans metagenomes from the photic layer and the deep ocean by annotating sequences against a custom MGII database and by mapping gene co-occurrences. Our data provide a global view of the distribution of Euryarchaeota, and more specifically of MGII subgroups, and reveal their association to a number of gene-coding sequences. In particular, we show that MGII proteorhodopsins were detected in both the surface and the deep chlorophyll maximum layer and that different clusters of these light harvesting proteins were present. Our approach helped describing the set of genes found together with specific MGII subgroups. We could thus define genomic environments that could theoretically describe ecologically meaningful units and the ecological niche that they occupy.}, }
@article {pmid31250597, year = {2019}, author = {Wang, L and Li, Z and Liu, R and Li, L and Wang, W}, title = {Bacterial Diversity in Soybean Rhizosphere Soil at Seedling and Mature Stages.}, journal = {Polish journal of microbiology}, volume = {68}, number = {2}, pages = {281-284}, doi = {10.33073/pjm-2019-023}, pmid = {31250597}, issn = {2544-4646}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; *Biota ; Computational Biology ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Rhizosphere ; Seedlings/growth &amp; development/*microbiology ; *Soil Microbiology ; Soybeans/growth &amp; development/*microbiology ; }, abstract = {Changes in the structural diversity of bacterial communities in soybean rhizospheres play important roles in plant growth and crop productivity. However, there are only a few studies on different soybean growth stages. Here, we investigated the changes in the bacterial community of soybean rhizosphere soil at two stages using Illumina high-throughput sequencing. The results showed that the bacterial abundance and diversity in the seeding stage were higher than those in the mature stage and that the diversity changed significantly. Actinobacteria, Acidobacteria, and Proteobacteria were the dominant bacteria in the soybean rhizosphere soil. Additionally, changes in Actinobacteria and Proteobacteria abundances showed opposite trends.<br><br>Changes in the structural diversity of bacterial communities in soybean rhizospheres play important roles in plant growth and crop productivity. However, there are only a few studies on different soybean growth stages. Here, we investigated the changes in the bacterial community of soybean rhizosphere soil at two stages using Illumina high-throughput sequencing. The results showed that the bacterial abundance and diversity in the seeding stage were higher than those in the mature stage and that the diversity changed significantly. Actinobacteria, Acidobacteria, and Proteobacteria were the dominant bacteria in the soybean rhizosphere soil. Additionally, changes in Actinobacteria and Proteobacteria abundances showed opposite trends.}, }
@article {pmid31250077, year = {2019}, author = {Goss-Souza, D and Mendes, LW and Rodrigues, JLM and Tsai, SM}, title = {Ecological Processes Shaping Bulk Soil and Rhizosphere Microbiome Assembly in a Long-Term Amazon Forest-to-Agriculture Conversion.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01401-y}, pmid = {31250077}, issn = {1432-184X}, support = {2008/58114-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2014/50320-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 140317/2014-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico (BR)/ ; 311008/2016-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {Forest-to-agriculture conversion has been identified as a major threat to soil biodiversity and soil processes resilience, although the consequences of long-term land use change to microbial community assembly and ecological processes have been often neglected. Here, we combined metagenomic approach with a large environmental dataset, to (i) identify the microbial assembly patterns and, (ii) to evaluate the ecological processes governing microbial assembly, in bulk soil and soybean rhizosphere, along a long-term forest-to-agriculture conversion chronosequence, in Eastern Amazon. We hypothesized that (i) microbial communities in bulk soil and rhizosphere have different assembly patterns and (ii) the weight of the four ecological processes governing assembly differs between bulk soil and rhizosphere and along the chronosequence in the same fraction. Community assembly in bulk soil fitted most the zero-sum multinomial (ZSM) neutral-based model, regardless of time. Low to intermediate dispersal was observed. Decreasing influence of abiotic factors was counterbalanced by increasing influence of biotic factors, as the chronosequence advanced. Undominated ecological processes of dispersal limitation and variable selection governing community assembly were observed in this soil fraction. For soybean rhizosphere, community assembly fitted most the lognormal niche-based model in all chronosequence areas. High dispersal and an increasing influence of abiotic factors coupled with a decreasing influence of biotic factors were found along the chronosequence. Thus, we found a dominant role of dispersal process governing microbial assembly with a secondary effect of homogeneous selection process, mainly driven by decreasing aluminum and increased cations saturation in soil solution, due to long-term no-till cropping. Together, our results indicate that long-term no-till lead community abundances in bulk soil to be in a transient and conditional state, while for soybean rhizosphere, community abundances reach a periodic and permanent distribution state. Dominant dispersal process in rhizosphere, coupled with homogeneous selection, brings evidences that soybean root system selects microbial taxa via trade-offs in order to keep functional resilience of soil processes.}, }
@article {pmid31243255, year = {2019}, author = {Tamaki, H}, title = {Cultivation Renaissance in the Post-Metagenomics Era: Combining the New and Old.}, journal = {Microbes and environments}, volume = {34}, number = {2}, pages = {117-120}, doi = {10.1264/jsme2.ME3402rh}, pmid = {31243255}, issn = {1347-4405}, mesh = {*Archaea/classification/genetics/growth &amp; development ; *Bacteria/classification/genetics/growth &amp; development ; Biodiversity ; Drug Resistance, Microbial ; *Fungi/classification/genetics/growth &amp; development ; Host Microbial Interactions ; Humans ; *Metagenomics ; Microbiological Techniques/*trends ; Microbiota/genetics ; }, }
@article {pmid31239159, year = {2019}, author = {Costa, M and Weese, JS}, title = {Methods and basic concepts for microbiota assessment.}, journal = {Veterinary journal (London, England : 1997)}, volume = {249}, number = {}, pages = {10-15}, doi = {10.1016/j.tvjl.2019.05.005}, pmid = {31239159}, issn = {1532-2971}, mesh = {Animals ; Bacteria/genetics ; Bacteriological Techniques/*veterinary ; DNA, Bacterial ; Host Microbial Interactions ; *Microbiota ; Sequence Analysis, DNA/veterinary ; }, abstract = {There has been a marked increase in interest regarding complex microbial populations in recent years. The methodology used for microbial assessment has drastically changed over the last two decades and continues to advance at a rapid pace. Culture-based studies have been superseded by those based upon molecular methods, which have been largely used to discover new species and to better characterize complex communities, mainly driven by the advances in DNA sequencing, termed 'next generation sequencing'. These methodologies have allowed for a better understanding of the relationship between hosts and their microbiotas, which have important roles in health maintenance and in the pathophysiology of wide ranging conditions such as obesity, diabetes, allergic diseases and even behavioural changes. While most widely used in humans, these approaches are now commonly used in veterinary research, with increasing interest in direct clinical applications. As these methods provide novel insights that will constitute the basis for the development of new therapeutic and prevention strategies, and as commercial efforts to offer microbiota assessment as a clinical tool expand, it is essential for researchers and clinical veterinarians to understand and have the tools to be able to interpret research performed in this new fascinating field. The objective of this review is to describe some of the most common methods for characterization of microbial communities and to provide an overview of the basic concepts necessary for good interpretation of the research performed in this field.}, }
@article {pmid31236844, year = {2019}, author = {Kunath, BJ and Minniti, G and Skaugen, M and Hagen, LH and Vaaje-Kolstad, G and Eijsink, VGH and Pope, PB and Arntzen, MØ}, title = {Metaproteomics: Sample Preparation and Methodological Considerations.}, journal = {Advances in experimental medicine and biology}, volume = {1073}, number = {}, pages = {187-215}, doi = {10.1007/978-3-030-12298-0_8}, pmid = {31236844}, issn = {0065-2598}, mesh = {*Metagenomics ; *Microbial Consortia ; Proteins ; *Proteomics ; Specimen Handling/*methods ; }, abstract = {Meta-omic techniques have progressed rapidly in the past decade and are frequently used in microbial ecology to study microorganisms in their natural ecosystems independent from culture restrictions. Metaproteomics, in combination with metagenomics, enables quantitative assessment of expressed proteins and pathways from individual members of the consortium. Together, metaproteomics and metagenomics can provide a detailed understanding of which organisms occupy specific metabolic niches, how they interact, and how they utilize nutrients, and these insights can be obtained directly from environmental samples. Here, we outline key aspects of sample preparation, database generation, and other methodological considerations that are required for successful quantitative metaproteomic analyses and we describe case studies on the integration with metagenomics for enhanced functional output.}, }
@article {pmid31236715, year = {2019}, author = {Joishy, TK and Dehingia, M and Khan, MR}, title = {Bacterial diversity and metabolite profiles of curd prepared by natural fermentation of raw milk and back sloping of boiled milk.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {35}, number = {7}, pages = {102}, doi = {10.1007/s11274-019-2677-y}, pmid = {31236715}, issn = {1573-0972}, support = {BT/550/NE/U-Excel/2014//Department of Biotechnology , Ministry of Science and Technology/ ; DST/INSPIRE Fellowship/2015/IF150782//Department of Science and Technology, Ministry of Science and Technology/ ; }, mesh = {Animals ; Bacteria/*isolation &amp; purification/metabolism ; *Biodiversity ; DNA, Bacterial/genetics/isolation &amp; purification ; Enterococcus/isolation &amp; purification/metabolism ; *Fermentation ; Food Handling ; Food Microbiology ; High-Throughput Nucleotide Sequencing ; Lactobacillales ; Lactobacillus/isolation &amp; purification/metabolism ; Lactococcus/isolation &amp; purification/metabolism ; Leuconostoc/isolation &amp; purification/metabolism ; Metagenomics ; Milk/*microbiology ; Multivariate Analysis ; RNA, Ribosomal, 16S/genetics/isolation &amp; purification ; }, abstract = {Preparation of curd vary worldwide due to which its taste, texture and impact on human health also differ. In Assam, curd prepared from raw milk (RMC) is preferred over curd prepared from boiled milk (BMC), a tradition believed to have originated from the Mongoloid customs. Microbial diversity of raw milk (RM), boiled milk (BM), RMC and BMC collected from three farms were investigated by culture dependent and independent techniques. Additionally, metabolite profiles of RMC and BMC were studied by gas chromatography and mass spectroscopy. A total of 59 bacterial isolates were identified from the four different dairy products. In RM, lactic acid bacteria such as Lactococcus, Enterococcus, Lactobacillus and Leuconostoc were obtained along with the environmental bacteria like Bacillus, Staphylococcus, Acetobacter, Chryseobacterium, Streptococcus, Acinetobacter, Kocuria, Klebsiella and Macrococcus. Additionally, Prevotella, Oscillospira, Phascolarctobacterium and Akkermansia were also detected in BM by culture independent technique. In RMC and BMC, Lactococcus, Leuconostoc and Lactobacillus were prevalent. RM and RMC shared Enterococcus, Lactococcus, Streptococcus and Acinetobacter as common bacterial genera. However, no bacterial genus was common in BM and BMC. The correlation analysis revealed that Lactobacillus was negatively correlated to other bacterial genera. Oligotyping analysis revealed that Lactobacillus brevis and L.fermentum were abundant in RMC and BMC, respectively. In metabolomic study, ascorbic acid, dodecanoic acid and hexadecanoic acid were found to be significantly higher in RMC. Presence of different types of probiotics in these curds samples opens a new avenue to understand their effects on human health.}, }
@article {pmid31216991, year = {2019}, author = {Lo, C and Marculescu, R}, title = {MetaNN: accurate classification of host phenotypes from metagenomic data using neural networks.}, journal = {BMC bioinformatics}, volume = {20}, number = {Suppl 12}, pages = {314}, doi = {10.1186/s12859-019-2833-2}, pmid = {31216991}, issn = {1471-2105}, mesh = {*Algorithms ; Area Under Curve ; Databases, Genetic ; Humans ; Machine Learning ; Metagenomics/*methods ; Microbiota/genetics ; Models, Theoretical ; *Neural Networks (Computer) ; Phenotype ; ROC Curve ; Support Vector Machine ; }, abstract = {BACKGROUND: Microbiome profiles in the human body and environment niches have become publicly available due to recent advances in high-throughput sequencing technologies. Indeed, recent studies have already identified different microbiome profiles in healthy and sick individuals for a variety of diseases; this suggests that the microbiome profile can be used as a diagnostic tool in identifying the disease states of an individual. However, the high-dimensional nature of metagenomic data poses a significant challenge to existing machine learning models. Consequently, to enable personalized treatments, an efficient framework that can accurately and robustly differentiate between healthy and sick microbiome profiles is needed.<br><br>RESULTS: In this paper, we propose MetaNN (i.e., classification of host phenotypes from Metagenomic data using Neural Networks), a neural network framework which utilizes a new data augmentation technique to mitigate the effects of data over-fitting.<br><br>CONCLUSIONS: We show that MetaNN outperforms existing state-of-the-art models in terms of classification accuracy for both synthetic and real metagenomic data. These results pave the way towards developing personalized treatments for microbiome related diseases.}, }
@article {pmid31199220, year = {2019}, author = {Karabudak, S and Ari, O and Durmaz, B and Dal, T and Basyigit, T and Kalcioglu, MT and Durmaz, R}, title = {Analysis of the effect of smoking on the buccal microbiome using next-generation sequencing technology.}, journal = {Journal of medical microbiology}, volume = {68}, number = {8}, pages = {1148-1158}, doi = {10.1099/jmm.0.001003}, pmid = {31199220}, issn = {1473-5644}, mesh = {Adult ; Bacteria/classification/genetics ; Female ; Genome, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Microbiota/genetics ; Middle Aged ; Mouth/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Smoking ; Young Adult ; }, abstract = {PURPOSE: This study aimed to investigate the effect of smoking on the buccal microbiome and to analyse the descriptive ability of each of the seven hypervariable regions in their 16S rRNA genes.<br><br>METHODOLOGY: Microbiome compositions of 40 buccal swab samples collected from smokers (n =20) and non-smokers (n =20) were determined using 16S rRNA sequencing. Seven different 16S rRNA hypervariable regions (V2, V3, V4, V6-7, V8 and V9) in each sample were amplified using the Ion Torrent 16S Metagenomics kit and were sequenced on the Ion S5 instrument.<br><br>RESULTS: Seven hypervariable regions in the 16S rRNA gene were successfully sequenced for all samples tested. The data obtained with the V2 region was found to be informative but the consensus data generated according to a number of operational taxonomic unit reads gathered from all seven hypervariable regions gave the most accurate result. At the phylum level, no statistically significant difference was found between smokers and non-smokers whereas relative abundances of Veillonella atypica, Streptococcus australis, Prevotella melaninogenica, Prevotella salivae and Rothia mucilaginosa showed significant increases in the smoker group (P-adj=0.05). Alpha diversity results did not show a significant difference between the two groups; however, beta diversity analysis indicated that samples of smoker and non-smoker groups had a tendency to be clustered within themselves.<br><br>CONCLUSION: The results of the current study indicate that smoking is a factor influencing buccal microbiome composition. In addition, sequencing of all seven hypervariable regions yielded more accurate results than those with any of the single variable regions.}, }
@article {pmid31185897, year = {2019}, author = {Chen, CY and Tang, SL and Chou, ST}, title = {Taxonomy based performance metrics for evaluating taxonomic assignment methods.}, journal = {BMC bioinformatics}, volume = {20}, number = {1}, pages = {310}, doi = {10.1186/s12859-019-2896-0}, pmid = {31185897}, issn = {1471-2105}, support = {105-2410-H-002-101-MY3//The Ministry of Science and Technology of Taiwan/ ; }, mesh = {Bacteria/genetics ; Classification/*methods ; Databases, Genetic ; Metagenomics/*methods ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; }, abstract = {BACKGROUND: Metagenomics experiments often make inferences about microbial communities by sequencing 16S and 18S rRNA, and taxonomic assignment is a fundamental step in such studies. This paper addresses the weaknesses in two types of metrics commonly used by previous studies for measuring the performance of existing taxonomic assignment methods: Sequence count based metrics and Binary error measurement. These metrics made performance evaluation results biased, less informative and mutually incomparable.<br><br>RESULTS: We investigated weaknesses in two types of metrics and proposed new performance metrics including Average Taxonomy Distance (ATD) and ATD_by_Taxa, together with the visualized ATD plot.<br><br>CONCLUSIONS: By comparing the evaluation results from four popular taxonomic assignment methods across three test data sets, we found the new metrics more robust, informative and comparable.}, }
@article {pmid31178526, year = {2019}, author = {Wang, N and Guo, Y and Li, G and Xia, Y and Ma, M and Zang, J and Ma, Y and Yin, X and Han, W and Lv, J and Cao, H}, title = {Geochemical-Compositional-Functional Changes in Arctic Soil Microbiomes Post Land Submergence Revealed by Metagenomics.}, journal = {Microbes and environments}, volume = {34}, number = {2}, pages = {180-190}, doi = {10.1264/jsme2.ME18091}, pmid = {31178526}, issn = {1347-4405}, mesh = {Archaea/classification/genetics ; Archaeal Proteins/genetics/metabolism ; Arctic Regions ; Bacteria/classification/genetics ; Bacterial Proteins/genetics/metabolism ; Biodiversity ; Geologic Sediments/chemistry/*microbiology ; Lakes ; *Metagenomics ; Methane/metabolism ; *Microbiota/genetics ; Nitrogen/metabolism ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Lakes of meltwater in the Artic have become one of the transforming landscape changes under global warming. We herein compared microbial communities between sediments and bank soils at an arctic lake post land submergence using geochemistry, 16S rRNA amplicons, and metagenomes. The results obtained showed that each sample had approximately 2,609 OTUs on average and shared 1,716 OTUs based on the 16S rRNA gene V3-V4 region. Dominant phyla in sediments and soils included Proteobacteria, Acidobacteria, Actinobacteria, Gemmatimonadetes, and Nitrospirae; sediments contained a unique phylum, Euryarchaeota, with the phylum Thaumarchaeota being primarily present in bank soils. Among the top 35 genera across all sites, 17 were more abundant in sediments, while the remaining 18 were more abundant in bank soils; seven out of the top ten genera across all sites were only from sediments. A redundancy analysis separated sediment samples from soil samples based on the components of nitrite and ammonium. Metagenome results supported the role of nitrite because most of the genes for denitrification and methane metabolic genes were more abundant in sediments than in soils, while the abundance of phosphorus-utilizing genes was similar and, thus, was not a significant explanatory factor. We identified several modules from the global networks of OTUs that were closely related to some geochemical factors, such as pH and nitrite. Collectively, the present results showing consistent changes in geochemistry, microbiome compositions, and functional genes suggest an ecological mechanism across molecular and community levels that structures microbiomes post land submergence.}, }
@article {pmid31171880, year = {2019}, author = {Yachida, S and Mizutani, S and Shiroma, H and Shiba, S and Nakajima, T and Sakamoto, T and Watanabe, H and Masuda, K and Nishimoto, Y and Kubo, M and Hosoda, F and Rokutan, H and Matsumoto, M and Takamaru, H and Yamada, M and Matsuda, T and Iwasaki, M and Yamaji, T and Yachida, T and Soga, T and Kurokawa, K and Toyoda, A and Ogura, Y and Hayashi, T and Hatakeyama, M and Nakagama, H and Saito, Y and Fukuda, S and Shibata, T and Yamada, T}, title = {Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer.}, journal = {Nature medicine}, volume = {25}, number = {6}, pages = {968-976}, doi = {10.1038/s41591-019-0458-7}, pmid = {31171880}, issn = {1546-170X}, mesh = {Adult ; Aged ; Case-Control Studies ; Colorectal Neoplasms/genetics/*metabolism/*microbiology ; Disease Progression ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Male ; Metabolomics ; Metagenomics ; Middle Aged ; Neoplasm Staging ; Young Adult ; }, abstract = {In most cases of sporadic colorectal cancers, tumorigenesis is a multistep process, involving genomic alterations in parallel with morphologic changes. In addition, accumulating evidence suggests that the human gut microbiome is linked to the development of colorectal cancer. Here we performed fecal metagenomic and metabolomic studies on samples from a large cohort of 616 participants who underwent colonoscopy to assess taxonomic and functional characteristics of gut microbiota and metabolites. Microbiome and metabolome shifts were apparent in cases of multiple polypoid adenomas and intramucosal carcinomas, in addition to more advanced lesions. We found two distinct patterns of microbiome elevations. First, the relative abundance of Fusobacterium nucleatum spp. was significantly (P < 0.005) elevated continuously from intramucosal carcinoma to more advanced stages. Second, Atopobium parvulum and Actinomyces odontolyticus, which co-occurred in intramucosal carcinomas, were significantly (P < 0.005) increased only in multiple polypoid adenomas and/or intramucosal carcinomas. Metabolome analyses showed that branched-chain amino acids and phenylalanine were significantly (P < 0.005) increased in intramucosal carcinomas and bile acids, including deoxycholate, were significantly (P < 0.005) elevated in multiple polypoid adenomas and/or intramucosal carcinomas. We identified metagenomic and metabolomic markers to discriminate cases of intramucosal carcinoma from the healthy controls. Our large-cohort multi-omics data indicate that shifts in the microbiome and metabolome occur from the very early stages of the development of colorectal cancer, which is of possible etiological and diagnostic importance.}, }
@article {pmid31167633, year = {2019}, author = {Zhong, C and Yang, Y and Yooseph, S}, title = {GRASP2: fast and memory-efficient gene-centric assembly and homolog search for metagenomic sequencing data.}, journal = {BMC bioinformatics}, volume = {20}, number = {Suppl 11}, pages = {276}, doi = {10.1186/s12859-019-2818-1}, pmid = {31167633}, issn = {1471-2105}, mesh = {Algorithms ; Aquatic Organisms/genetics ; *Genes ; Metagenomics/*methods ; Microbiota/genetics ; ROC Curve ; Sequence Analysis, DNA/*methods ; *Sequence Homology, Nucleic Acid ; *Software ; Time Factors ; }, abstract = {BACKGROUND: A crucial task in metagenomic analysis is to annotate the function and taxonomy of the sequencing reads generated from a microbiome sample. In general, the reads can either be assembled into contigs and searched against reference databases, or individually searched without assembly. The first approach may suffer from fragmentary and incomplete assembly, while the second is hampered by the reduced functional signal contained in the short reads. To tackle these issues, we have previously developed GRASP (Guided Reference-based Assembly of Short Peptides), which accepts a reference protein sequence as input and aims to assemble its homologs from a database containing fragmentary protein sequences. In addition to a gene-centric assembly tool, GRASP also serves as a homolog search tool when using the assembled protein sequences as templates to recruit reads. GRASP has significantly improved recall rate (60-80% vs. 30-40%) compared to other homolog search tools such as BLAST. However, GRASP is both time- and space-consuming. Subsequently, we developed GRASPx, which is 30X faster than GRASP. Here, we present a completely redesigned algorithm, GRASP2, for this computational problem.<br><br>RESULTS: GRASP2 utilizes Burrows-Wheeler Transformation (BWT) and FM-index to perform assembly graph generation, and reduces the search space by employing a fast ungapped alignment strategy as a filter. GRASP2 also explicitly generates candidate paths prior to alignment, which effectively uncouples the iterative access of the assembly graph and alignment matrix. This strategy makes the execution of the program more efficient under current computer architecture, and contributes to GRASP2's speedup. GRASP2 is 8-fold faster than GRASPx (and 250-fold faster than GRASP) and uses 8-fold less memory while maintaining the original high recall rate of GRASP. GRASP2 reaches ~ 80% recall rate compared to that of ~ 40% generated by BLAST, both at a high precision level (> 95%). With such a high performance, GRASP2 is only ~3X slower than BLASTP.<br><br>CONCLUSION: GRASP2 is a high-performance gene-centric and homolog search tool with significant speedup compared to its predecessors, which makes GRASP2 a useful tool for metagenomics data analysis, GRASP2 is implemented in C++ and is freely available from http://www.sourceforge.net/projects/grasp2 .}, }
@article {pmid31142849, year = {2019}, author = {Fettweis, JM and Serrano, MG and Brooks, JP and Edwards, DJ and Girerd, PH and Parikh, HI and Huang, B and Arodz, TJ and Edupuganti, L and Glascock, AL and Xu, J and Jimenez, NR and Vivadelli, SC and Fong, SS and Sheth, NU and Jean, S and Lee, V and Bokhari, YA and Lara, AM and Mistry, SD and Duckworth, RA and Bradley, SP and Koparde, VN and Orenda, XV and Milton, SH and Rozycki, SK and Matveyev, AV and Wright, ML and Huzurbazar, SV and Jackson, EM and Smirnova, E and Korlach, J and Tsai, YC and Dickinson, MR and Brooks, JL and Drake, JI and Chaffin, DO and Sexton, AL and Gravett, MG and Rubens, CE and Wijesooriya, NR and Hendricks-Muñoz, KD and Jefferson, KK and Strauss, JF and Buck, GA}, title = {The vaginal microbiome and preterm birth.}, journal = {Nature medicine}, volume = {25}, number = {6}, pages = {1012-1021}, doi = {10.1038/s41591-019-0450-2}, pmid = {31142849}, issn = {1546-170X}, support = {R01 HD092415/HD/NICHD NIH HHS/United States ; UH3 AI083263/AI/NIAID NIH HHS/United States ; U54 DE023786/DE/NIDCR NIH HHS/United States ; R21 HD092965/HD/NICHD NIH HHS/United States ; UH2 AI083263/AI/NIAID NIH HHS/United States ; R25 GM090084/GM/NIGMS NIH HHS/United States ; U54 HD080784/HD/NICHD NIH HHS/United States ; }, mesh = {Adult ; African Americans ; Biodiversity ; Cohort Studies ; Cytokines/metabolism ; Female ; Host Microbial Interactions/immunology ; Humans ; Infant, Newborn ; Inflammation Mediators/metabolism ; Longitudinal Studies ; Metagenomics ; *Microbiota/genetics/immunology ; Premature Birth/etiology/immunology/*microbiology ; Risk Factors ; United States ; Vagina/immunology/*microbiology ; Young Adult ; }, abstract = {The incidence of preterm birth exceeds 10% worldwide. There are significant disparities in the frequency of preterm birth among populations within countries, and women of African ancestry disproportionately bear the burden of risk in the United States. In the present study, we report a community resource that includes 'omics' data from approximately 12,000 samples as part of the integrative Human Microbiome Project. Longitudinal analyses of 16S ribosomal RNA, metagenomic, metatranscriptomic and cytokine profiles from 45 preterm and 90 term birth controls identified harbingers of preterm birth in this cohort of women predominantly of African ancestry. Women who delivered preterm exhibited significantly lower vaginal levels of Lactobacillus crispatus and higher levels of BVAB1, Sneathia amnii, TM7-H1, a group of Prevotella species and nine additional taxa. The first representative genomes of BVAB1 and TM7-H1 are described. Preterm-birth-associated taxa were correlated with proinflammatory cytokines in vaginal fluid. These findings highlight new opportunities for assessment of the risk of preterm birth.}, }
@article {pmid31141902, year = {2019}, author = {Kallies, R and Hölzer, M and Brizola Toscan, R and Nunes da Rocha, U and Anders, J and Marz, M and Chatzinotas, A}, title = {Evaluation of Sequencing Library Preparation Protocols for Viral Metagenomic Analysis from Pristine Aquifer Groundwaters.}, journal = {Viruses}, volume = {11}, number = {6}, pages = {}, doi = {10.3390/v11060484}, pmid = {31141902}, issn = {1999-4915}, support = {CRC 1076//Deutsche Forschungsgemeinschaft/ ; SPP-1596//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Viral ecology of terrestrial habitats is yet-to be extensively explored, in particular the terrestrial subsurface. One problem in obtaining viral sequences from groundwater aquifer samples is the relatively low amount of virus particles. As a result, the amount of extracted DNA may not be sufficient for direct sequencing of such samples. Here we compared three DNA amplification methods to enrich viral DNA from three pristine limestone aquifer assemblages of the Hainich Critical Zone Exploratory to evaluate potential bias created by the different amplification methods as determined by viral metagenomics. Linker amplification shotgun libraries resulted in lowest redundancy among the sequencing reads and showed the highest diversity, while multiple displacement amplification produced the highest number of contigs with the longest average contig size, suggesting a combination of these two methods is suitable for the successful enrichment of viral DNA from pristine groundwater samples. In total, we identified 27,173, 5,886 and 32,613 viral contigs from the three samples from which 11.92 to 18.65% could be assigned to taxonomy using blast. Among these, members of the Caudovirales order were the most abundant group (52.20 to 69.12%) dominated by Myoviridae and Siphoviridae. Those, and the high number of unknown viral sequences, substantially expand the known virosphere.}, }
@article {pmid31129398, year = {2019}, author = {Qi, M and Huang, H and Zhang, Y and Wang, H and Li, H and Lu, Z}, title = {Novel tetrahydrofuran (THF) degradation-associated genes and cooperation patterns of a THF-degrading microbial community as revealed by metagenomic.}, journal = {Chemosphere}, volume = {231}, number = {}, pages = {173-183}, doi = {10.1016/j.chemosphere.2019.05.137}, pmid = {31129398}, issn = {1879-1298}, mesh = {Actinomycetales ; Furans/analysis/*chemistry/metabolism ; Metagenome/*genetics ; Metagenomics ; Microbiota ; Mixed Function Oxygenases/genetics/metabolism ; Open Reading Frames ; }, abstract = {Our understanding of the tetrahydrofuran (THF) degradation in complex environment is limited. The majority of THF degrading genes reported are group V soluble diiron monooxygenases and share greater than 95% homology with one another. In this study, we used sole-carbon-source incubation combined with high-throughput metagenomic sequencing to investigate this contaminant's degradation in environmental samples. We identified as-yet-uncultivated microbe from the genera Pseudonocardia and fungi Scedosporium sp. (Scedosporium sp. was successfully isolated) as THF degraders as containing THF degradation genes, while microbes from the genera Bordetella, Pandoraea and Rhodanobacter functioned as main cooperators by utilizing acidic intermediates and providing anti-acid mechanisms. Furthermore, a 9387-bp THF degradation cluster designated thmX from the as-yet-uncultivated Pseudonocardia (with 6 main ORFs and with 79-93% amino acid sequence identity with previously reported clusters) was discovered. We also found a THF-degrading related cytochrome P450 monooxygenase from the genus Scedosporium and predicted its cognate reductase for the first time. All the genes and clusters mentioned above were successfully amplified from samples and cloned into the suitable expression vectors. This study will provide novel insights for understanding of THF degradation mechanisms under acid stress conditions and mining new THF degradation genes.}, }
@article {pmid31126262, year = {2019}, author = {Ke, S and Fang, S and He, M and Huang, X and Yang, H and Yang, B and Chen, C and Huang, L}, title = {Age-based dynamic changes of phylogenetic composition and interaction networks of health pig gut microbiome feeding in a uniformed condition.}, journal = {BMC veterinary research}, volume = {15}, number = {1}, pages = {172}, doi = {10.1186/s12917-019-1918-5}, pmid = {31126262}, issn = {1746-6148}, support = {31772579//National Natural Science Foundation of China/ ; 31472071//National Natural Science Foundation of China/ ; }, mesh = {*Age Factors ; Animals ; Bacteria/*classification/genetics ; Bacterial Typing Techniques ; Female ; Gastrointestinal Microbiome/*physiology ; Male ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sus scrofa/*microbiology ; }, abstract = {BACKGROUND: The gut microbiota impacts on a range of host biological processes, and the imbalances in its composition are associated with pathology. Though the understanding of contribution of the many factors, e.g. gender, diet and age, in the development of gut microbiota has been well established, the dynamic changes of the phylogenetic composition and the interaction networks along with the age remain unclear in pigs.<br><br>RESULTS: Here we applied 16S ribosomal RNA gene sequencing, enterotype-like clustering (Classification of the gut microbiome into distinct types) and phylogenetic co-occurrence network to explore the dynamic changes of pig gut microbiome following the ages with a successive investigation at four ages in a cohort of 953 pigs. We found that Firmicutes and Bacteroidetes are two predominant phyla throughout the experimental period. The richness of gut microbiota was significantly increased from 25 to 240 days of age. Principal coordinates analysis showed a clear difference in the gut microbial community compositions between pre-weaning piglets and the pigs at the other three age groups. The gut microbiota of pre-weaning piglets was clearly classified into two enterotypes, which were dominated by Fusobacterium and p-75-a5, respectively. However, Prevotella and Treponema were the main drivers of the enterotypes for pigs at the age of 80, 120 and 240 days. Besides the piglets, even some adult pigs switched putative enterotypes between ages. We confirmed that the topological features of phylogenetic co-occurrence networks, including scale, stability and complexity were increased along with the age. The biological significance for modules in the network of piglets were mainly associated with the utilization of simple carbohydrate and lactose, whereas the sub-networks identified at the ages of 80, 120 and 240 days may be involved in the digestion of complex dietary polysaccharide. The modules related to the metabolism of protein and amino acids could be identified in the networks at 120 and 240 days. This dynamic change of the functional capacities of gut microbiome was further supported by functional prediction analysis.<br><br>CONCLUSIONS: The present study provided meaningful biological insights into the age-based dynamic shifts of ecological community of porcine gut microbiota.}, }
@article {pmid31123265, year = {2019}, author = {Li, Y and Fu, X and Ma, J and Zhang, J and Hu, Y and Dong, W and Wan, Z and Li, Q and Kuang, YQ and Lan, K and Jin, X and Wang, JH and Zhang, C}, title = {Altered respiratory virome and serum cytokine profile associated with recurrent respiratory tract infections in children.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {2288}, doi = {10.1038/s41467-019-10294-x}, pmid = {31123265}, issn = {2041-1723}, mesh = {Acute Disease ; Bacteriophages/genetics/*isolation &amp; purification ; Child ; Child, Preschool ; Cytokines/*blood/immunology ; Disease Susceptibility/blood/immunology/microbiology ; Female ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Infant ; Longitudinal Studies ; Male ; Metagenomics/methods ; Microbiota/genetics ; Propionibacterium/virology ; Proteomics/methods ; Recurrence ; Respiratory System/immunology/*virology ; Respiratory Tract Infections/*blood/immunology/microbiology ; Retrospective Studies ; }, abstract = {Recurrent acute respiratory tract infections (ARTIs) affect a large population, yet the specific decisive factors are largely unknown. Here we study a population of 4407 children diagnosed with ARTI, comparing respiratory virome and serum cytokine profiles associated with multiple ARTIs and single ARTI during a six-year period. The relative abundance of Propionibacterium phages is significantly elevated in multiple ARTIs compared to single ARTI group. Serum levels of TIMP-1 and PDGF-BB are markedly increased in multiple ARTIs compared to single-ARTI and non-ARTI controls, making these two cytokines potential predictors for multiple ARTIs. The presence of Propionibacterium phages is associated with higher levels of TIMP-1 and PDGF-BB. Receiver operating characteristic (ROC) curve analyses show that the combination of TIMP-1, PDGF-BB and Propionibacterium phages could be a strong predictor for multiple ARTIs. These findings indicate that respiratory microbe homeostasis and specific cytokines are associated with the onset of multiple ARTIs over time.}, }
@article {pmid31102963, year = {2019}, author = {Liu, S and Chen, Q and Zou, H and Yu, Y and Zhou, Z and Mao, J and Zhang, S}, title = {A metagenomic analysis of the relationship between microorganisms and flavor development in Shaoxing mechanized huangjiu fermentation mashes.}, journal = {International journal of food microbiology}, volume = {303}, number = {}, pages = {9-18}, doi = {10.1016/j.ijfoodmicro.2019.05.001}, pmid = {31102963}, issn = {1879-3460}, mesh = {Chromatography, High Pressure Liquid ; *Fermentation ; Fermented Foods/*microbiology ; Gas Chromatography-Mass Spectrometry ; *Metagenomics ; *Microbiota/genetics ; Taste ; }, abstract = {Complex microbial metabolism is responsible for the unique flavor of Shaoxing mechanized huangjiu. However, the relationship between the microorganisms present during fermentation and the formation of specific flavor components is difficult to understand. In this study, gas chromatography-mass spectrometry and high-performance liquid chromatography were used to identify flavor components, and a metagenomic sequencing approach was used to characterize the taxonomic and functional attributes of the Shaoxing mechanized huangjiu fermentation microbiota. The metagenomic sequencing data were used to predict the relationship between microorganisms and flavor formation. The chromatographic analysis identified amino acids, alcohols, acids, phenols and esters as major flavor components, and six microbial genera (Saccharomyces, Aspergillus, Saccharopolyspora, Staphylococcus, Lactobacillus, and Lactococcus) were most closely related to the production of these flavor components. This study helps clarify the different metabolic roles of microorganisms in flavor formation during Shaoxing huangjiu fermentation.}, }
@article {pmid31102141, year = {2019}, author = {Sahoo, K and Sahoo, RK and Gaur, M and Subudhi, E}, title = {Cellulolytic thermophilic microorganisms in white biotechnology: a review.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, doi = {10.1007/s12223-019-00710-6}, pmid = {31102141}, issn = {1874-9356}, support = {YSS/2014/000413//Science and Engineering Research Board/ ; }, abstract = {Enzymes of microbial origin are of immense importance for organic material decomposition leading to bioremediation of organic waste, bioenergy generation, large-scale industrial bioprocesses, etc. The market demand for microbial cellulase enzyme is growing more rapidly which ultimately becomes the driving force towards research on this biocatalyst, widely used in various industrial activities. The use of novel cellulase genes obtained from various thermophiles through metagenomics and genetic engineering as well as following metabolic engineering pathways would be able to enhance the production of thermophilic cellulase at industrial scale. The present review is mainly focused on thermophilic cellulolytic bacteria, discoveries on cellulase gene, genetically modified cellulase, metabolic engineering, and their various industrial applications. A lot of lacunae are yet to overcome for thermophiles such as metagenome analysis, metabolic pathway modification study, search of heterologous hosts in gene expression system, and improved recombinant strain for better cellulase yield as well as value-added product formation.}, }
@article {pmid31101811, year = {2019}, author = {Sande, CJ and Njunge, JM and Mwongeli Ngoi, J and Mutunga, MN and Chege, T and Gicheru, ET and Gardiner, EM and Gwela, A and Green, CA and Drysdale, SB and Berkley, JA and Nokes, DJ and Pollard, AJ}, title = {Airway response to respiratory syncytial virus has incidental antibacterial effects.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {2218}, doi = {10.1038/s41467-019-10222-z}, pmid = {31101811}, issn = {2041-1723}, support = {//Wellcome Trust/United Kingdom ; WT105882MA//Wellcome Trust (Wellcome)/International ; }, mesh = {Bacterial Infections/*immunology/microbiology ; Cell Degranulation/immunology ; Child, Preschool ; Humans ; Infant ; Infant, Newborn ; Kenya ; Metagenomics/methods ; Microbiota/immunology ; Neutrophils/*immunology ; Proteomics/methods ; Respiratory Mucosa/cytology/*immunology/microbiology ; Respiratory Syncytial Virus Infections/*immunology/virology ; Respiratory Syncytial Virus, Human/*immunology/isolation &amp; purification ; Streptococcus/immunology/isolation &amp; purification ; }, abstract = {RSV infection is typically associated with secondary bacterial infection. We hypothesise that the local airway immune response to RSV has incidental antibacterial effects. Using coordinated proteomics and metagenomics analysis we simultaneously analysed the microbiota and proteomes of the upper airway and determined direct antibacterial activity in airway secretions of RSV-infected children. Here, we report that the airway abundance of Streptococcus was higher in samples collected at the time of RSV infection compared with samples collected one month later. RSV infection is associated with neutrophil influx into the airway and degranulation and is marked by overexpression of proteins with known antibacterial activity including BPI, EPX, MPO and AZU1. Airway secretions of children infected with RSV, have significantly greater antibacterial activity compared to RSV-negative controls. This RSV-associated, neutrophil-mediated antibacterial response in the airway appears to act as a regulatory mechanism that modulates bacterial growth in the airways of RSV-infected children.}, }
@article {pmid31097033, year = {2019}, author = {Lugli, GA and Milani, C and Duranti, S and Alessandri, G and Turroni, F and Mancabelli, L and Tatoni, D and Ossiprandi, MC and van Sinderen, D and Ventura, M}, title = {Isolation of novel gut bifidobacteria using a combination of metagenomic and cultivation approaches.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {96}, doi = {10.1186/s13059-019-1711-6}, pmid = {31097033}, issn = {1474-760X}, mesh = {Animals ; Bifidobacterium/genetics/*isolation &amp; purification ; Callimico ; Callithrix ; Cattle ; Gastrointestinal Microbiome ; Metagenomics ; }, abstract = {Whole metagenome shotgun (WMGS) sequencing is a method that provides insights into the genomic composition and arrangement of complex microbial consortia. Here, we report how WMGS coupled with a cultivation approach allows the isolation of novel bifidobacteria from animal fecal samples. A combination of in silico analyses based on nucleotide and protein sequences facilitate the identification of genetic material belonging to putative novel species. Consequently, the prediction of metabolic properties by in silico analyses permits the identification of specific substrates that are then employed to isolate these species through a cultivation method.}, }
@article {pmid31092601, year = {2019}, author = {Hu, H and da Costa, RR and Pilgaard, B and Schiøtt, M and Lange, L and Poulsen, M}, title = {Fungiculture in Termites Is Associated with a Mycolytic Gut Bacterial Community.}, journal = {mSphere}, volume = {4}, number = {3}, pages = {}, doi = {10.1128/mSphere.00165-19}, pmid = {31092601}, issn = {2379-5042}, mesh = {Animals ; Bacteria/enzymology/genetics ; *Diet ; Fungi/*growth &amp; development ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/enzymology/microbiology ; Isoptera/*enzymology/*microbiology ; Metagenome ; Phylogeny ; Plant Cells/metabolism ; Sequence Analysis, DNA ; Symbiosis ; Wood/metabolism ; }, abstract = {Termites forage on a range of substrates, and it has been suggested that diet shapes the composition and function of termite gut bacterial communities. Through comparative analyses of gut metagenomes in nine termite species with distinct diets, we characterize bacterial community compositions and use peptide-based functional annotation method to determine biomass-degrading enzymes and the bacterial taxa that encode them. We find that fungus-growing termite guts have relatively more fungal cell wall-degrading enzyme genes, while wood-feeding termite gut communities have relatively more plant cell wall-degrading enzyme genes. Interestingly, wood-feeding termite gut bacterial genes code for abundant chitinolytic enzymes, suggesting that fungal biomass within the decaying wood likely contributes to gut bacterial or termite host nutrition. Across diets, the dominant biomass-degrading enzymes are predominantly coded for by the most abundant bacterial taxa, suggesting tight links between diet and gut community composition, with the most marked difference being the communities coding for the mycolytic capacity of the fungus-growing termite gut.IMPORTANCE Understanding functional capacities of gut microbiomes is important to improve our understanding of symbiotic associations. Here, we use peptide-based functional annotation to show that the gut microbiomes of fungus-farming termites code for a wealth of enzymes that likely target the fungal diet the termites eat. Comparisons to other termites showed that fungus-growing termite guts have relatively more fungal cell wall-degrading enzyme genes, whereas wood-feeding termite gut communities have relatively more plant cell wall-degrading enzyme genes. Across termites with different diets, the dominant biomass-degrading enzymes are predominantly coded for by the most abundant bacterial taxa, suggesting tight links between diet and gut community compositions.}, }
@article {pmid31087993, year = {2019}, author = {Liu, ZQ and Zhang, Y and Ma, XS and Zhang, BK and Cao, MJ and Chen, CM}, title = {[Nitrogen Removal Characteristics and Analysis of Microbial Community Structure in an IEM-UF Simultaneous Separation and Denitrification System].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {40}, number = {3}, pages = {1419-1425}, doi = {10.13227/j.hjkx.201808051}, pmid = {31087993}, issn = {0250-3301}, mesh = {Bacteria/classification ; Bioreactors ; *Denitrification ; Ion Exchange ; *Microbiota ; Nitrogen/*isolation &amp; purification ; Ultrafiltration ; Waste Water ; }, abstract = {A system that combines an ion exchange membrane and ultrafiltration membrane (IEM-UF) to form a simultaneous separation and denitrification system was proposed for domestic sewage with a low carbon/nitrogen ratio. The removal of nitrogen and COD in the system was studied under a three phase operating condition. The characteristics of the microbial community in each reactor were analyzed using metagenomics. The results show that, the average rate of ammonia nitrogen enrichment in the separator reached above 116.1% when the current intensity was 0.2 A. When the system was at C/N 2.80 and operating well, the average removal rates of COD and TN reached above 90% and 50%, respectively. The maximum removal rate of TN was above 65.4%. The results of metagenomics showed a genus of phylum Nitrospirae (Nitrospira) and a genus of phylum Proteobacteria (Nitrosomonas), with the proportions of 12.23% and 2.31%, respectively. In the denitrifying reactor, Dechloromonas, Thauera, and Azospira were detected in the proportions 4.57%, 1.76%, and 1.03%, respectively. These proportions were far larger than those of other bacteria in this reactor. Meanwhile, the presence of iron autotrophic denitrifying bacteria increased the denitrification efficiency of the system.}, }
@article {pmid31086312, year = {2019}, author = {Wu, L and Ning, D and Zhang, B and Li, Y and Zhang, P and Shan, X and Zhang, Q and Brown, M and Li, Z and Van Nostrand, JD and Ling, F and Xiao, N and Zhang, Y and Vierheilig, J and Wells, GF and Yang, Y and Deng, Y and Tu, Q and Wang, A and ,  and Zhang, T and He, Z and Keller, J and Nielsen, PH and Alvarez, PJJ and Criddle, CS and Wagner, M and Tiedje, JM and He, Q and Curtis, TP and Stahl, DA and Alvarez-Cohen, L and Rittmann, BE and Wen, X and Zhou, J}, title = {Global diversity and biogeography of bacterial communities in wastewater treatment plants.}, journal = {Nature microbiology}, volume = {4}, number = {7}, pages = {1183-1195}, doi = {10.1038/s41564-019-0426-5}, pmid = {31086312}, issn = {2058-5276}, mesh = {Bacteria/classification/genetics/isolation &amp; purification ; *Biodiversity ; DNA, Bacterial/genetics ; Geography ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/*microbiology ; Water Purification/statistics &amp; numerical data ; }, abstract = {Microorganisms in wastewater treatment plants (WWTPs) are essential for water purification to protect public and environmental health. However, the diversity of microorganisms and the factors that control it are poorly understood. Using a systematic global-sampling effort, we analysed the 16S ribosomal RNA gene sequences from ~1,200 activated sludge samples taken from 269 WWTPs in 23 countries on 6 continents. Our analyses revealed that the global activated sludge bacterial communities contain ~1 billion bacterial phylotypes with a Poisson lognormal diversity distribution. Despite this high diversity, activated sludge has a small, global core bacterial community (n = 28 operational taxonomic units) that is strongly linked to activated sludge performance. Meta-analyses with global datasets associate the activated sludge microbiomes most closely to freshwater populations. In contrast to macroorganism diversity, activated sludge bacterial communities show no latitudinal gradient. Furthermore, their spatial turnover is scale-dependent and appears to be largely driven by stochastic processes (dispersal and drift), although deterministic factors (temperature and organic input) are also important. Our findings enhance our mechanistic understanding of the global diversity and biogeography of activated sludge bacterial communities within a theoretical ecology framework and have important implications for microbial ecology and wastewater treatment processes.}, }
@article {pmid31073898, year = {2019}, author = {Zhao, H and Yan, B and Mo, S and Nie, S and Li, Q and Ou, Q and Wu, B and Jiang, G and Tang, J and Li, N and Jiang, C}, title = {Carbohydrate metabolism genes dominant in a subtropical marine mangrove ecosystem revealed by metagenomics analysis.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {57}, number = {7}, pages = {575-586}, doi = {10.1007/s12275-019-8679-5}, pmid = {31073898}, issn = {1976-3794}, mesh = {*Archaea/classification/genetics/metabolism ; *Bacteria/classification/genetics/metabolism ; Carbohydrate Metabolism/genetics ; China ; Geologic Sediments/*microbiology ; Metagenomics/methods ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Wetlands ; }, abstract = {Mangrove sediment microorganisms play a vital role in the energy transformation and element cycling in marine wetland ecosystems. Using metagenomics analysis strategy, we compared the taxonomic structure and gene profile of the mangrove and non-mangrove sediment samples at the subtropical estuary in Beibu Gulf, South China Sea. Proteobacteria, Bacteroidetes, and Firmicutes were the most abundant bacterial phyla. Archaeal family Methanosarcinaceae and bacterial genera Vibrio and Dehalococcoides were significantly higher in the mangrove sediments than in the nonmangrove sediments. Functional analysis showed that &quot;Carbohydrate metabolism&quot; was the most abundant metabolic category. The feature of carbohydrate-active enzymes (CZs) was analyzed using the Carbohydrate-Active EnZymes Database. The significant differences of CZs between mangrove and non-mangrove sediments, were attributed to the amounts of polyphenol oxidase (EC 1.10.3.-), hexosyltransferase (EC 2.4.1.-), and β-N-acetylhexosaminidase (EC 3.2.1.52), which were higher in the mangrove sediment samples. Principal component analysis indicated that the microbial community and gene profile between mangrove and non-mangrove sediments were distinct. Redundancy analysis showed that total organic carbon is a significant factor that affects the microbial community and gene distribution. The results indicated that the mangrove ecosystem with massive amounts of organic carbon may promote the richness of carbohydrate metabolism genes and enhance the degradation and utilization of carbohydrates in the mangrove sediments.}, }
@article {pmid31064831, year = {2019}, author = {Haran, JP and Bhattarai, SK and Foley, SE and Dutta, P and Ward, DV and Bucci, V and McCormick, BA}, title = {Alzheimer's Disease Microbiome Is Associated with Dysregulation of the Anti-Inflammatory P-Glycoprotein Pathway.}, journal = {mBio}, volume = {10}, number = {3}, pages = {}, doi = {10.1128/mBio.00632-19}, pmid = {31064831}, issn = {2150-7511}, support = {R15 AI112985/AI/NIAID NIH HHS/United States ; R03 AG056356/AG/NIA NIH HHS/United States ; P30 DK034854/DK/NIDDK NIH HHS/United States ; K23 AG057790/AG/NIA NIH HHS/United States ; R01 DK056754/DK/NIDDK NIH HHS/United States ; }, mesh = {ATP Binding Cassette Transporter, Subfamily B/*metabolism ; Aged ; Aged, 80 and over ; Alzheimer Disease/metabolism/*microbiology ; Bacteria/classification/isolation &amp; purification ; Dementia/microbiology ; *Dysbiosis ; Epithelial Cells/metabolism ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Homeostasis ; Humans ; Inflammation/complications ; Intestines/microbiology ; Machine Learning ; Male ; Metabolic Networks and Pathways/immunology ; Metagenomics ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The microbiota-gut-brain axis is a bidirectional communication system that is poorly understood. Alzheimer's disease (AD), the most common cause of dementia, has long been associated with bacterial infections and inflammation-causing immunosenescence. Recent studies examining the intestinal microbiota of AD patients revealed that their microbiome differs from that of subjects without dementia. In this work, we prospectively enrolled 108 nursing home elders and followed each for up to 5 months, collecting longitudinal stool samples from which we performed metagenomic sequencing and in vitro T84 intestinal epithelial cell functional assays for P-glycoprotein (P-gp) expression, a critical mediator of intestinal homeostasis. Our analysis identified clinical parameters as well as numerous microbial taxa and functional genes that act as predictors of AD dementia in comparison to elders without dementia or with other dementia types. We further demonstrate that stool samples from elders with AD can induce lower P-gp expression levels in vitro those samples from elders without dementia or with other dementia types. We also paired functional studies with machine learning approaches to identify bacterial species differentiating the microbiome of AD elders from that of elders without dementia, which in turn are accurate predictors of the loss of dysregulation of the P-gp pathway. We observed that the microbiome of AD elders shows a lower proportion and prevalence of bacteria with the potential to synthesize butyrate, as well as higher abundances of taxa that are known to cause proinflammatory states. Therefore, a potential nexus between the intestinal microbiome and AD is the modulation of intestinal homeostasis by increases in inflammatory, and decreases in anti-inflammatory, microbial metabolism.IMPORTANCE Studies of the intestinal microbiome and AD have demonstrated associations with microbiome composition at the genus level among matched cohorts. We move this body of literature forward by more deeply investigating microbiome composition via metagenomics and by comparing AD patients against those without dementia and with other dementia types. We also exploit machine learning approaches that combine both metagenomic and clinical data. Finally, our functional studies using stool samples from elders demonstrate how the c microbiome of AD elders can affect intestinal health via dysregulation of the P-glycoprotein pathway. P-glycoprotein dysregulation contributes directly to inflammatory disorders of the intestine. Since AD has been long thought to be linked to chronic bacterial infections as a possible etiology, our findings therefore fill a gap in knowledge in the field of AD research by identifying a nexus between the microbiome, loss of intestinal homeostasis, and inflammation that may underlie this neurodegenerative disorder.}, }
@article {pmid31055095, year = {2019}, author = {Hassan, M and Essam, T and Mira, A and Megahed, S}, title = {Biomonitoring detoxification efficiency of an algal-bacterial microcosm system for treatment of coking wastewater: Harmonization between Chlorella vulgaris microalgae and wastewater microbiome.}, journal = {The Science of the total environment}, volume = {677}, number = {}, pages = {120-130}, doi = {10.1016/j.scitotenv.2019.04.304}, pmid = {31055095}, issn = {1879-1026}, mesh = {Bacteria/*metabolism ; Chlorella vulgaris/*metabolism ; Coke ; Egypt ; Environmental Monitoring/*methods ; Environmental Restoration and Remediation/*methods ; Microalgae/metabolism ; Microbiota ; Waste Water/*analysis/*microbiology ; Water Pollutants, Chemical/analysis ; Water Pollution, Chemical/prevention &amp; control ; }, abstract = {Nowadays, due to worldwide water shortage, water utilities are forced to re-evaluate treated wastewater. Consequently, wastewater treatment plants need to conduct biomonitoring. Coking wastewater (CWW) has toxic, mutative and carcinogenic components with threatening effect on the environment. CWW was selected as a model for complex highly toxic industrial wastewater that should be treated. CWW from Egypt was treated in a nine-liter photobioreactor using an algal-bacterial system. The photobioreactor was operated for 154 days changing different parameters (toxic load and light duration) for optimization. Optimized conditions achieved significant reduction (45%) in the operation cost. The algal-bacterial system was monitored using chemical assays (chemical oxygen demand and phenol analysis), bioassays (phytotoxicity, Artemia-toxicity, cytotoxicity, algal-bacterial ratio and settleability) and Illumina-MiSeq sequencing of 16S rRNA gene. The algal-bacterial system detoxified (in terms of phytotoxicity, cytotoxicity and Artemia-toxicity) CWW introduced as influent through all phases. A significant difference was recorded in the microbial diversity between influent and effluent samples. Four phyla dominated influent samples; Proteobacteria (77%), Firmicutes (11%), Bacteroidetes (5%) and Deferribacteres (3%) compared to only two in effluent samples; Proteobacteria (66%) and Bacteroidetes (26%). The significant relative-abundance of versatile aromatic degraders (Comamonadaceae and Pseudomonadaceae families) in influent samples conformed to the nature of CWW. Microbial community shifted and promoted the activity of catabolically versatile and xenobiotics degrading families (Chitinophagaceae and Xanthomonadaceae). Co-culture of microalgae had a positive effect on the biodegrading bacteria that was reflected by enhanced treatment efficiency, significant increase in relative abundance of bacterial genera with cyanide-decomposing potential and negative effect on waterborne pathogens.}, }
@article {pmid31055020, year = {2019}, author = {Xiao Joe, JT and Chiou, PP and Kuo, CY and Jia Lin, JH and Wu, JL and Lu, MW}, title = {The microbiota profile and transcriptome analysis of immune response during metamorphosis stages in orange spotted grouper (Epinephelus coioides).}, journal = {Fish &amp; shellfish immunology}, volume = {90}, number = {}, pages = {141-149}, doi = {10.1016/j.fsi.2019.03.063}, pmid = {31055020}, issn = {1095-9947}, mesh = {Animals ; Bass/*genetics/growth &amp; development/immunology/*microbiology ; Gastrointestinal Microbiome/*physiology ; Gene Expression Profiling ; Gene Expression Regulation/immunology ; Immunity, Innate/*genetics ; Metagenomics ; Metamorphosis, Biological/genetics/immunology ; Transcriptome/*immunology ; }, abstract = {Metamorphosis is a transformation process in larval development associated with changes in morphological and physiological features, including the immune system. The gastrointestinal tract harbors a plethora of bacteria, which might affect the digestion and absorption of nutrients, immunity, and gut-brain crosstalk in the host. In this study, we have performed metagenomic and transcriptomic analyses on the intestines of grouper at the pre-, mid- and post-metamorphosis stages. The sequencing data of 16S rRNA gene showed drastic changes in the microbial communities at different developmental stages. The transcriptomic data revealed that the leukocyte transendothelial migration and the phagosome pathways might play important roles in mediating immunity in grouper at the three developmental stages. This information will increase our understanding of the metamorphosis process in grouper larvae, and shed light on the development of antimicrobial strategy during larval development.}, }
@article {pmid31051396, year = {2019}, author = {Cabral, L and Noronha, MF and de Sousa, STP and Lacerda-Júnior, GV and Richter, L and Fostier, AH and Andreote, FD and Hess, M and Oliveira, VM}, title = {The metagenomic landscape of xenobiotics biodegradation in mangrove sediments.}, journal = {Ecotoxicology and environmental safety}, volume = {179}, number = {}, pages = {232-240}, doi = {10.1016/j.ecoenv.2019.04.044}, pmid = {31051396}, issn = {1090-2414}, mesh = {Biodegradation, Environmental ; Drug Resistance, Microbial/genetics ; Gene Library ; *Geologic Sediments/chemistry/microbiology ; Hydrolases/genetics ; Metagenomics/*methods ; Metals, Heavy/*analysis/toxicity ; Microbiota/drug effects/*genetics ; Petroleum/analysis/toxicity ; *Wetlands ; Xenobiotics/*analysis/toxicity ; }, abstract = {Metagenomics is a powerful approach to study microorganisms present in any given environment and their potential to maintain and improve ecosystem health without the need of cultivating these microorganisms in the laboratory. In this study, we combined a cultivation-independent metagenomics approach with functional assays to identify the detoxification potential of microbial genes evaluating their potential to contribute to xenobiotics resistance in oil-impacted mangrove sediments. A metagenomic fosmid library containing 12,960 clones from highly contaminated mangrove sediment was used in this study. For assessment of metal resistance, clones were grown in culture medium with increasing concentrations of mercury. The analyses metagenomic library sequences revealed the presence of genes related to heavy metals and antibiotics resistance in the oil-impacted mangrove microbiome. The taxonomic profiling of these sequences suggests that at the genus level, Geobacter was the most abundant genus in our dataset. A functional screening assessment of the metagenomic library successfully detected 24 potential heavy metal tolerant clones, six of which were capable of growing with increased concentrations of mercury. The genetic characterization of selected clones allowed the detection of genes related to detoxification processes, such as chromate transport protein ChrA, haloacid dehalogenase-like hydrolase, lipopolysaccharide transport system, and 3-oxoacyl-[acyl-carrier-protein] reductase. Clones were capable of growing in medium containing increased concentrations of metals and antibiotics, but none manifested strong mercury removal from culture medium characteristic of mercuric reductase activity. These results suggest that resistance to xenobiotic stress varies greatly and that additional studies to elucidate the potential of metal biotransformation need to be carried out with the goal of improving bioremediation application.}, }
@article {pmid31043514, year = {2019}, author = {Escudeiro, P and Pothier, J and Dionisio, F and Nogueira, T}, title = {Antibiotic Resistance Gene Diversity and Virulence Gene Diversity Are Correlated in Human Gut and Environmental Microbiomes.}, journal = {mSphere}, volume = {4}, number = {3}, pages = {}, doi = {10.1128/mSphere.00135-19}, pmid = {31043514}, issn = {2379-5042}, mesh = {Adolescent ; Adult ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics ; Child ; Child, Preschool ; Drug Resistance, Microbial/*genetics ; *Environmental Microbiology ; Gastrointestinal Microbiome/*drug effects ; Gastrointestinal Tract/microbiology ; *Genetic Variation ; Humans ; Infant ; Metagenome ; Metagenomics ; Microbiota/*drug effects ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Virulence ; Virulence Factors/genetics ; Young Adult ; }, abstract = {Human beings have used large amounts of antibiotics, not only in medical contexts but also, for example, as growth factors in agriculture and livestock, resulting in the contamination of the environment. Even when pathogenic bacteria are the targets of antibiotics, hundreds of nonpathogenic bacterial species are affected as well. Therefore, both pathogenic and nonpathogenic bacteria have gradually become resistant to antibiotics. We tested whether there is still cooccurrence of resistance and virulence determinants. We performed a comparative study of environmental and human gut metagenomes from different individuals and from distinct human populations across the world. We found a great diversity of antibiotic resistance determinants (AR diversity [ARd]) and virulence factors (VF diversity [VFd]) in metagenomes. Importantly there is a correlation between ARd and VFd, even after correcting for protein family richness. In the human gut, there are less ARd and VFd than in more diversified environments, and yet correlations between the ARd and VFd are stronger. They can vary from very high in Malawi, where antibiotic consumption is unattended, to nonexistent in the uncontacted Amerindian population. We conclude that there is cooccurrence of resistance and virulence determinants in human gut microbiomes, suggesting a possible coselective mechanism.IMPORTANCE Every year, thousands of tons of antibiotics are used, not only in human and animal health but also as growth promoters in livestock. Consequently, during the last 75 years, antibiotic-resistant bacterial strains have been selected in human and environmental microbial communities. This implies that, even when pathogenic bacteria are the targets of antibiotics, hundreds of nonpathogenic bacterial species are also affected. Here, we performed a comparative study of environmental and human gut microbial communities issuing from different individuals and from distinct human populations across the world. We found that antibiotic resistance and pathogenicity are correlated and speculate that, by selecting for resistant bacteria, we may be selecting for more virulent strains as a side effect of antimicrobial therapy.}, }
@article {pmid31036930, year = {2019}, author = {Zhang, J and Liu, YX and Zhang, N and Hu, B and Jin, T and Xu, H and Qin, Y and Yan, P and Zhang, X and Guo, X and Hui, J and Cao, S and Wang, X and Wang, C and Wang, H and Qu, B and Fan, G and Yuan, L and Garrido-Oter, R and Chu, C and Bai, Y}, title = {NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice.}, journal = {Nature biotechnology}, volume = {37}, number = {6}, pages = {676-684}, doi = {10.1038/s41587-019-0104-4}, pmid = {31036930}, issn = {1546-1696}, mesh = {Alleles ; Anion Transport Proteins/chemistry/*genetics ; Bacteria/classification/*genetics ; Genotype ; Metagenomics ; Microbiota/*genetics ; Nitrogen/metabolism ; Oryza/*genetics/growth &amp; development/metabolism/microbiology ; Phylogeny ; Plant Breeding ; Plant Roots/genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Nitrogen-use efficiency of indica varieties of rice is superior to that of japonica varieties. We apply 16S ribosomal RNA gene profiling to characterize root microbiota of 68 indica and 27 japonica varieties grown in the field. We find that indica and japonica recruit distinct root microbiota. Notably, indica-enriched bacterial taxa are more diverse, and contain more genera with nitrogen metabolism functions, than japonica-enriched taxa. Using genetic approaches, we provide evidence that NRT1.1B, a rice nitrate transporter and sensor, is associated with the recruitment of a large proportion of indica-enriched bacteria. Metagenomic sequencing reveals that the ammonification process is less abundant in the root microbiome of the nrt1.1b mutant. We isolated 1,079 pure bacterial isolates from indica and japonica roots and derived synthetic communities (SynComs). Inoculation of IR24, an indica variety, with an indica-enriched SynCom improved rice growth in organic nitrogen conditions compared with a japonica-enriched SynCom. The links between plant genotype and root microbiota membership established in this study will inform breeding strategies to improve nitrogen use in crops.}, }
@article {pmid31036790, year = {2019}, author = {Ghani, MI and Ali, A and Atif, MJ and Ali, M and Amin, B and Anees, M and Khurshid, H and Cheng, Z}, title = {Changes in the Soil Microbiome in Eggplant Monoculture Revealed by High-Throughput Illumina MiSeq Sequencing as Influenced by Raw Garlic Stalk Amendment.}, journal = {International journal of molecular sciences}, volume = {20}, number = {9}, pages = {}, doi = {10.3390/ijms20092125}, pmid = {31036790}, issn = {1422-0067}, support = {2016KTCL02-01//Shaanxi Provincial Sci Tech Innovation Plan/ ; 2016NY-048//Shaanxi provincial Agricultural Sci Tech Innovation and Development Plan/ ; NCI 1501//Xian City Agricultural Sci Tech Innovation Plan P.R China/ ; }, mesh = {Biodiversity ; *Garlic ; *High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/methods ; *Microbiota ; Soil/chemistry ; *Soil Microbiology ; *Solanum melongena ; }, abstract = {The incorporation of plant residues into soil can be considered a keystone sustainability factor in improving soil structure function. However, the effects of plant residue addition on the soil microbial communities involved in biochemical cycles and abiotic stress phenomena are poorly understood. In this study, experiments were conducted to evaluate the role of raw garlic stalk (RGS) amendment in avoiding monoculture-related production constraints by studying the changes in soil chemical properties and microbial community structures. RGS was applied in four different doses, namely the control (RGS0), 1% (RGS1), 3% (RGS2), and 5% (RGS3) per 100 g of soil. The RGS amendment significantly increased soil electrical conductivity (EC), N, P, K, and enzyme activity. The soil pH significantly decreased with RGS application. High-throughput Illumina MiSeq sequencing revealed significant alterations in bacterial community structures in response to RGS application. Among the 23 major taxa detected, Anaerolineaceae, Acidobacteria, and Cyanobacteria exhibited an increased abundance level. RGS2 increased some bacteria reported to be beneficial including Acidobacteria, Bacillus, and Planctomyces (by 42%, 64%, and 1% respectively). Furthermore, internal transcribed spacer (ITS) fungal regions revealed significant diversity among the different treatments, with taxa such as Chaetomium (56.2%), Acremonium (4.3%), Fusarium (4%), Aspergillus (3.4%), Sordariomycetes (3%), and Plectosphaerellaceae (2%) showing much abundance. Interestingly, Coprinellus (14%) was observed only in RGS-amended soil. RGS treatments effectively altered soil fungal community structures and reduced certain known pathogenic fungal genera, i.e., Fusarium and Acremonium. The results of the present study suggest that RGS amendment potentially affects the microbial community structures that probably affect the physiological and morphological attributes of eggplant under a plastic greenhouse vegetable cultivation system (PGVC) in monoculture.}, }
@article {pmid31034867, year = {2019}, author = {Tsiaoussis, J and Antoniou, MN and Koliarakis, I and Mesnage, R and Vardavas, CI and Izotov, BN and Psaroulaki, A and Tsatsakis, A}, title = {Effects of single and combined toxic exposures on the gut microbiome: Current knowledge and future directions.}, journal = {Toxicology letters}, volume = {312}, number = {}, pages = {72-97}, doi = {10.1016/j.toxlet.2019.04.014}, pmid = {31034867}, issn = {1879-3169}, mesh = {Environmental Pollutants/*toxicity ; Gastrointestinal Microbiome/*drug effects ; Hazardous Substances/*toxicity ; Humans ; }, abstract = {Human populations are chronically exposed to mixtures of toxic chemicals. Predicting the health effects of these mixtures require a large amount of information on the mode of action of their components. Xenobiotic metabolism by bacteria inhabiting the gastrointestinal tract has a major influence on human health. Our review aims to explore the literature for studies looking to characterize the different modes of action and outcomes of major chemical pollutants, and some components of cosmetics and food additives, on gut microbial communities in order to facilitate an estimation of their potential mixture effects. We identified good evidence that exposure to heavy metals, pesticides, nanoparticles, polycyclic aromatic hydrocarbons, dioxins, furans, polychlorinated biphenyls, and non-caloric artificial sweeteners affect the gut microbiome and which is associated with the development of metabolic, malignant, inflammatory, or immune diseases. Answering the question 'Who is there?' is not sufficient to define the mode of action of a toxicant in predictive modeling of mixture effects. Therefore, we recommend that new studies focus to simulate real-life exposure to diverse chemicals (toxicants, cosmetic/food additives), including as mixtures, and which combine metagenomics, metatranscriptomics and metabolomic analytical methods achieving in that way a comprehensive evaluation of effects on human health.}, }
@article {pmid31031001, year = {2019}, author = {Gregory, AC and Zayed, AA and Conceição-Neto, N and Temperton, B and Bolduc, B and Alberti, A and Ardyna, M and Arkhipova, K and Carmichael, M and Cruaud, C and Dimier, C and Domínguez-Huerta, G and Ferland, J and Kandels, S and Liu, Y and Marec, C and Pesant, S and Picheral, M and Pisarev, S and Poulain, J and Tremblay, JÉ and Vik, D and ,  and Babin, M and Bowler, C and Culley, AI and de Vargas, C and Dutilh, BE and Iudicone, D and Karp-Boss, L and Roux, S and Sunagawa, S and Wincker, P and Sullivan, MB}, title = {Marine DNA Viral Macro- and Microdiversity from Pole to Pole.}, journal = {Cell}, volume = {177}, number = {5}, pages = {1109-1123.e14}, doi = {10.1016/j.cell.2019.03.040}, pmid = {31031001}, issn = {1097-4172}, support = {T32 AI112542/AI/NIAID NIH HHS/United States ; }, abstract = {Microbes drive most ecosystems and are modulated by viruses that impact their lifespan, gene flow, and metabolic outputs. However, ecosystem-level impacts of viral community diversity remain difficult to assess due to classification issues and few reference genomes. Here, we establish an ∼12-fold expanded global ocean DNA virome dataset of 195,728 viral populations, now including the Arctic Ocean, and validate that these populations form discrete genotypic clusters. Meta-community analyses revealed five ecological zones throughout the global ocean, including two distinct Arctic regions. Across the zones, local and global patterns and drivers in viral community diversity were established for both macrodiversity (inter-population diversity) and microdiversity (intra-population genetic variation). These patterns sometimes, but not always, paralleled those from macro-organisms and revealed temperate and tropical surface waters and the Arctic as biodiversity hotspots and mechanistic hypotheses to explain them. Such further understanding of ocean viruses is critical for broader inclusion in ecosystem models.}, }
@article {pmid31030156, year = {2019}, author = {Darlison, J and Mogren, L and Rosberg, AK and Grudén, M and Minet, A and Liné, C and Mieli, M and Bengtsson, T and Håkansson, Å and Uhlig, E and Becher, PG and Karlsson, M and Alsanius, BW}, title = {Leaf mineral content govern microbial community structure in the phyllosphere of spinach (Spinacia oleracea) and rocket (Diplotaxis tenuifolia).}, journal = {The Science of the total environment}, volume = {675}, number = {}, pages = {501-512}, doi = {10.1016/j.scitotenv.2019.04.254}, pmid = {31030156}, issn = {1879-1026}, mesh = {Biodiversity ; Brassicaceae/chemistry/*microbiology ; *Environmental Monitoring ; Microbiota ; Minerals/*analysis ; Plant Leaves/chemistry/*microbiology ; Spinacia oleracea/chemistry/*microbiology ; }, abstract = {The plant microbiome is an important factor for plant health and productivity. While the impact of nitrogen (N) availability for plant growth and development is well established, its influence on the microbial phyllosphere community structure is unknown. We hypothesize that nitrogen impacts the growth and abundance of several microorganisms on the leaf surface. The bacterial and fungal communities of baby leaf spinach (Spinacia oleracea), and rocket (Diplotaxis tenuifolia) were investigated in a field trial for two years in a commercial setting. Nitrogen fertilizer was tested in four doses (basic nitrogen, basic + suboptimal, basic + commercial, basic + excess) with six replicates in each. Culture-independent (Illumina sequencing) and culture-dependent (viable count and identification of bacterial isolates) community studies were combined with monitoring of plant physiology and site weather conditions. This study found that alpha diversity of bacterial communities decreased in response to increasing nitrogen fertilizer dose, whereas viable counts showed no differences. Correspondingly, fungal communities of the spinach phyllosphere showed a decreasing pattern, whereas the decreasing diversity of fungal communities of rocket was not significant. Plant species and effects of annual variations on microbiome structure were observed for bacterial and fungal communities on both spinach and rocket. This study provides novel insights on the impact of nitrogen fertilizer regime on a nutrient scarce habitat, the phyllosphere.}, }
@article {pmid31027801, year = {2019}, author = {Pangallo, D and Kraková, L and Puškárová, A and Šoltys, K and Bučková, M and Koreňová, J and Budiš, J and Kuchta, T}, title = {Transcription activity of lactic acid bacterial proteolysis-related genes during cheese maturation.}, journal = {Food microbiology}, volume = {82}, number = {}, pages = {416-425}, doi = {10.1016/j.fm.2019.03.015}, pmid = {31027801}, issn = {1095-9998}, mesh = {Animals ; Bacterial Proteins/*genetics/metabolism ; Cheese/*microbiology ; Female ; *Food Microbiology ; Gene Expression Profiling ; Lactobacillales/classification/genetics/isolation &amp; purification/*metabolism ; Metagenomics ; Microbiota/genetics ; Milk/microbiology ; Proteolysis ; RNA, Ribosomal, 16S/genetics ; Sheep ; Transcription, Genetic ; }, abstract = {The catabolism of milk protein in cheese is one way how the microorganisms influence the sensorial characteristics of the final product. In this investigation, we paid attention to four genes [prtP (cell-envelope proteinase gene), pepX (X-prolyl dipeptidyl aminopeptidase gene), pepN (aminopeptidase gene) and bcaT (branched chain aminotransferase gene)] responsible for the production of volatile aroma-active compounds from milk proteins by lactic acid bacteria (LAB). We studied the dynamics of these genes and their corresponding LAB host, during the maturation of a raw ewes' milk-based cheese, using metagenomics and metatranscriptomics approaches. The transcriptome-oriented experiments included the analysis of total RNA (at three stages of cheese maturation) and also the construction of specific cDNA sub-libraries of the abovementioned genes. The proteolytic transcriptome analysis was supported by following the transcription activity of 16S rRNA gene and by metagenomic investigation. The combination of the described methods permitted to screen the dynamics of targeted genes throughout the cheese production. Lactococci were the major players in the LAB group, but the analysis provided also information on the role and properties of members of the genus Lactobacillus, such as Lb. rhamnosus, Lb. helveticus, Lb. pentosus, Lb. curvatus, Lb. parabuchneri, Lb. plantarum, Lb. brevis, Lb. delbrueckii, Lb. paracasei, Lb. fermentum and Lb. heilongjiangensis, proteolysis-related genes of which were active during cheese ripening.}, }
@article {pmid31026582, year = {2019}, author = {Li, J and Rettedal, EA and van der Helm, E and Ellabaan, M and Panagiotou, G and Sommer, MOA}, title = {Antibiotic Treatment Drives the Diversification of the Human Gut Resistome.}, journal = {Genomics, proteomics &amp; bioinformatics}, volume = {17}, number = {1}, pages = {39-51}, doi = {10.1016/j.gpb.2018.12.003}, pmid = {31026582}, issn = {2210-3244}, mesh = {Adult ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/isolation &amp; purification ; Drug Resistance, Bacterial/*genetics ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Metagenomics ; Prospective Studies ; }, abstract = {Despite the documented antibiotic-induced disruption of the gut microbiota, the impact of antibiotic intake on strain-level dynamics, evolution of resistance genes, and factors influencing resistance dissemination potential remains poorly understood. To address this gap we analyzed public metagenomic datasets from 24 antibiotic treated subjects and controls, combined with an in-depth prospective functional study with two subjects investigating the bacterial community dynamics based on cultivation-dependent and independent methods. We observed that short-term antibiotic treatment shifted and diversified the resistome composition, increased the average copy number of antibiotic resistance genes, and altered the dominant strain genotypes in an individual-specific manner. More than 30% of the resistance genes underwent strong differentiation at the single nucleotide level during antibiotic treatment. We found that the increased potential for horizontal gene transfer, due to antibiotic administration, was ∼3-fold stronger in the differentiated resistance genes than the non-differentiated ones. This study highlights how antibiotic treatment has individualized impacts on the resistome and strain level composition, and drives the adaptive evolution of the gut microbiota.}, }
@article {pmid31026577, year = {2019}, author = {Jiang, X and Li, X and Yang, L and Liu, C and Wang, Q and Chi, W and Zhu, H}, title = {How Microbes Shape Their Communities? A Microbial Community Model Based on Functional Genes.}, journal = {Genomics, proteomics &amp; bioinformatics}, volume = {17}, number = {1}, pages = {91-105}, doi = {10.1016/j.gpb.2018.09.003}, pmid = {31026577}, issn = {2210-3244}, mesh = {Gastrointestinal Microbiome/genetics ; *Genes, Microbial ; Humans ; Microbiota/*genetics ; Mining ; Models, Genetic ; Water Pollution ; }, abstract = {Exploring the mechanisms of maintaining microbial community structure is important to understand biofilm development or microbiota dysbiosis. In this paper, we propose a functional gene-based composition prediction (FCP) model to predict the population structure composition within a microbial community. The model predicts the community composition well in both a low-complexity community as acid mine drainage (AMD) microbiota, and a complex community as human gut microbiota. Furthermore, we define community structure shaping (CSS) genes as functional genes crucial for shaping the microbial community. We have identified CSS genes in AMD and human gut microbiota samples with FCP model and find that CSS genes change with the conditions. Compared to essential genes for microbes, CSS genes are significantly enriched in the genes involved in mobile genetic elements, cell motility, and defense mechanisms, indicating that the functions of CSS genes are focused on communication and strategies in response to the environment factors. We further find that it is the minority, rather than the majority, which contributes to maintaining community structure. Compared to health control samples, we find that some functional genes associated with metabolism of amino acids, nucleotides, and lipopolysaccharide are more likely to be CSS genes in the disease group. CSS genes may help us to understand critical cellular processes and be useful in seeking addable gene circuitries to maintain artificial self-sustainable communities. Our study suggests that functional genes are important to the assembly of microbial communities.}, }
@article {pmid31024486, year = {2019}, author = {Sirén, K and Mak, SST and Melkonian, C and Carøe, C and Swiegers, JH and Molenaar, D and Fischer, U and Gilbert, MTP}, title = {Taxonomic and Functional Characterization of the Microbial Community During Spontaneous in vitro Fermentation of Riesling Must.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {697}, doi = {10.3389/fmicb.2019.00697}, pmid = {31024486}, issn = {1664-302X}, abstract = {Although there is an extensive tradition of research into the microbes that underlie the winemaking process, much remains to be learnt. We combined the high-throughput sequencing (HTS) tools of metabarcoding and metagenomics, to characterize how microbial communities of Riesling musts sampled at four different vineyards, and their subsequent spontaneously fermented derivatives, vary. We specifically explored community variation relating to three points: (i) how microbial communities vary by vineyard; (ii) how community biodiversity changes during alcoholic fermentation; and (iii) how microbial community varies between musts that successfully complete alcoholic fermentation and those that become 'stuck' in the process. Our metabarcoding data showed a general influence of microbial composition at the vineyard level. Two of the vineyards (4 and 5) had strikingly a change in the differential abundance of Metschnikowia. We therefore additionally performed shotgun metagenomic sequencing on a subset of the samples to provide preliminary insights into the potential relevance of this observation, and used the data to both investigate functional potential and reconstruct draft genomes (bins). At these two vineyards, we also observed an increase in non-Saccharomycetaceae fungal functions, and a decrease in bacterial functions during the early fermentation stage. The binning results yielded 11 coherent bins, with both vineyards sharing the yeast bins Hanseniaspora and Saccharomyces. Read recruitment and functional analysis of this data revealed that during fermentation, a high abundance of Metschnikowia might serve as a biocontrol agent against bacteria, via a putative iron depletion pathway, and this in turn could help Saccharomyces dominate the fermentation. During alcoholic fermentation, we observed a general decrease in biodiversity in both the metabarcoding and metagenomic data. Unexpected Micrococcus behavior was observed in vineyard 4 according to metagenomic analyses based on reference-based read mapping. Analysis of open reading frames using these data showed an increase of functions assigned to class Actinobacteria in the end of fermentation. Therefore, we hypothesize that bacteria might sit-and-wait until Saccharomyces activity slows down. Complementary approaches to annotation instead of relying a single database provide more coherent information true species. Lastly, our metabarcoding data enabled us to identify a relationship between stuck fermentations and Starmerella abundance. Given that robust chemical analysis indicated that although the stuck samples contained residual glucose, all fructose had been consumed, we hypothesize that this was because fructophilic Starmerella, rather than Saccharomyces, dominated these fermentations. Overall, our results showcase the different ways in which metagenomic analyses can improve our understanding of the wine alcoholic fermentation process.}, }
@article {pmid31023629, year = {2019}, author = {Tokarz, R and Tagliafierro, T and Sameroff, S and Cucura, DM and Oleynik, A and Che, X and Jain, K and Lipkin, WI}, title = {Microbiome analysis of Ixodes scapularis ticks from New York and Connecticut.}, journal = {Ticks and tick-borne diseases}, volume = {10}, number = {4}, pages = {894-900}, doi = {10.1016/j.ttbdis.2019.04.011}, pmid = {31023629}, issn = {1877-9603}, mesh = {Anaplasma phagocytophilum/genetics/isolation &amp; purification ; Animals ; Babesia microti/genetics/isolation &amp; purification ; Bacteria/*genetics/isolation &amp; purification ; Borrelia/genetics/isolation &amp; purification ; Connecticut ; Encephalitis Viruses, Tick-Borne/genetics/isolation &amp; purification ; Female ; High-Throughput Nucleotide Sequencing ; Ixodes/*microbiology/parasitology/virology ; Male ; Metagenomics ; *Microbiota ; Nematoda/genetics/isolation &amp; purification ; New York ; Nymph/microbiology/parasitology/virology ; Rickettsia/genetics/isolation &amp; purification ; Viruses/*genetics/isolation &amp; purification ; }, abstract = {We employed high throughput sequencing to survey the microbiomes of Ixodes scapularis collected in New York and Connecticut. We examined 197 individual I. scapularis adults and pools from 132 adults and 197 nymphs. We detected Borrelia burgdorferi sensu stricto in 56.3% of individual ticks, Anaplasma phagocytophilum in 10.6%, Borrelia miyamotoi in 5%, Babesia microti in 7.6%, and Powassan virus in 3.6%. We did not detect Borrelia mayonii, Ehrlichia muris eauclairensis, Bartonella spp. or pathogenic Babesia species other than B. microti. The most abundant bacterium (65%), and only rickettsial species identified, was the endosymbiont Rickettsia buchneri. A filarial nematode was found in 13.7% of adult ticks. Fourteen viruses were detected including South Bay virus (22%) and blacklegged tick phlebovirus 1 and 2 (73%). This study provides insight into the microbial diversity of I. scapularis in New York State and Connecticut.}, }
@article {pmid31015324, year = {2019}, author = {Easton, AV and Quiñones, M and Vujkovic-Cvijin, I and Oliveira, RG and Kepha, S and Odiere, MR and Anderson, RM and Belkaid, Y and Nutman, TB}, title = {The Impact of Anthelmintic Treatment on Human Gut Microbiota Based on Cross-Sectional and Pre- and Postdeworming Comparisons in Western Kenya.}, journal = {mBio}, volume = {10}, number = {2}, pages = {}, doi = {10.1128/mBio.00519-19}, pmid = {31015324}, issn = {2150-7511}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Anthelmintics/*administration &amp; dosage ; Ascariasis/*drug therapy ; Bacteria/*classification/genetics ; Child ; Child, Preschool ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects ; Humans ; Kenya ; Metagenomics ; Microbiota/*drug effects ; Middle Aged ; Necatoriasis/*drug therapy ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Rural Population ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {Murine studies suggest that the presence of some species of intestinal helminths is associated with changes in host microbiota composition and diversity. However, studies in humans have produced varied conclusions, and the impact appears to vary widely depending on the helminth species present. To demonstrate how molecular approaches to the human gut microbiome can provide insights into the complex interplay among disparate organisms, DNA was extracted from cryopreserved stools collected from residents of 5 rural Kenyan villages prior to and 3 weeks and 3 months following albendazole (ALB) therapy. Samples were analyzed by quantitative PCR (qPCR) for the presence of 8 species of intestinal parasites and by MiSeq 16S rRNA gene sequencing. Based on pretreatment results, the presence of neither Ascaris lumbricoides nor Necator americanus infection significantly altered the overall diversity of the microbiota in comparison with age-matched controls. Following ALB therapy and clearance of soil-transmitted helminths (STH), there were significant increases in the proportion of the microbiota made up by Clostridiales (P = 0.0002; average fold change, 0.57) and reductions in the proportion made up by Enterobacteriales (P = 0.0004; average fold change, -0.58). There was a significant posttreatment decrease in Chao1 richness, even among individuals who were uninfected pretreatment, suggesting that antimicrobial effects must be considered in any posttreatment setting. Nevertheless, the helminth-associated changes in Clostridiales and Enterobacteriales suggest that clearance of STH, and of N. americanus in particular, alters the gut microbiota.IMPORTANCE The gut microbiome is an important factor in human health. It is affected by what we eat, what medicines we take, and what infections we acquire. In turn, it affects the way we absorb nutrients and whether we have excessive intestinal inflammation. Intestinal worms may have an important impact on the composition of the gut microbiome. Without a complete understanding of the impact of mass deworming programs on the microbiome, it is impossible to accurately calculate the cost-effectiveness of such public health interventions and to guard against any possible deleterious side effects. Our research examines this question in a &quot;real-world&quot; setting, using a longitudinal cohort, in which individuals with and without worm infections are treated with deworming medication and followed up at both three weeks and three months posttreatment. We quantify the impact of roundworms and hookworms on gut microbial composition, suggesting that the impact is small, but that treatment of hookworm infection results in significant changes. This work points to the need for follow-up studies to further examine the impact of hookworm on the gut microbiota and determine the health consequences of the observed changes.}, }
@article {pmid31013927, year = {2019}, author = {Laitinen, K and Mokkala, K}, title = {Overall Dietary Quality Relates to Gut Microbiota Diversity and Abundance.}, journal = {International journal of molecular sciences}, volume = {20}, number = {8}, pages = {}, doi = {10.3390/ijms20081835}, pmid = {31013927}, issn = {1422-0067}, support = {#258606//Academy of Finland/ ; -//State research funding for university level health research of the Turku University Hospital Expert Responsibility Area/ ; -//Diabetes Research Foundation/ ; -//Juho Vainio Foundation/ ; }, mesh = {Biodiversity ; *Diet ; Disease Susceptibility ; Female ; *Food Quality ; *Gastrointestinal Microbiome ; Humans ; Metagenomics/methods ; Obesity ; Overweight ; Pregnancy ; Public Health Surveillance ; RNA, Ribosomal, 16S ; }, abstract = {Disturbances in gut microbiota homeostasis may have metabolic consequences with potentially serious clinical manifestations. Diet influences the host's metabolic health in several ways, either directly or indirectly by modulating the composition and function of gut microbiota. This study investigated the extent to which dietary quality is reflected in gut microbiota diversity in overweight and obese pregnant women at risk for metabolic complications. Dietary quality was measured by a validated index of diet quality (IDQ) and microbiota composition was analyzed using 16SrRNA gene sequencing from 84 women pregnant less than 18 weeks. The alpha diversity, measured as Chao1, observed operational taxonomic units (OTUs), phylogenetic diversity, and the Shannon index were calculated. The IDQ score correlated positively with the Shannon index (rho = 0.319, p = 0.003), but not with the other indexes. The women who had the highest dietary quality (highest IDQ quartile) had higher gut microbiota diversity in all the investigated indexes, when compared to the women with the lowest dietary quality (lowest IDQ quartile; p < 0.032). Consequently, a higher dietary quality was reflected in a higher gut microbiota diversity. The presented approach may aid in devising new tools for dietary counseling aiming at holistic health, as well as in microbiome studies, to control for dietary variance.}, }
@article {pmid31012060, year = {2019}, author = {Lorenzi, AS and Chia, MA and Lopes, FAC and Silva, GGZ and Edwards, RA and Bittencourt-Oliveira, MDC}, title = {Cyanobacterial biodiversity of semiarid public drinking water supply reservoirs assessed via next-generation DNA sequencing technology.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {57}, number = {6}, pages = {450-460}, doi = {10.1007/s12275-019-8349-7}, pmid = {31012060}, issn = {1976-3794}, mesh = {Bacterial Toxins/analysis/genetics/isolation &amp; purification ; *Biodiversity ; Brazil ; Cyanobacteria/*classification/genetics/*isolation &amp; purification ; DNA, Bacterial/analysis ; Drinking Water/*microbiology ; Environmental Monitoring/methods ; Genes, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Microcystis/genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Saxitoxin/genetics ; Seasons ; Sequence Analysis, DNA/*methods ; Uracil/analogs &amp; derivatives ; *Water Microbiology ; *Water Supply ; }, abstract = {Next-generation DNA sequencing technology was applied to generate molecular data from semiarid reservoirs during well-defined seasons. Target sequences of 16S-23S rRNA ITS and cpcBA-IGS were used to reveal the taxonomic groups of cyanobacteria present in the samples, and genes coding for cyanotoxins such as microcystins (mcyE), saxitoxins (sxtA), and cylindrospermopsins (cyrJ) were investigated. The presence of saxitoxins in the environmental samples was evaluated using ELISA kit. Taxonomic analyses of high-throughput DNA sequencing data showed the dominance of the genus Microcystis in Mundaú reservoir. Furthermore, it was the most abundant genus in the dry season in Ingazeira reservoir. In the rainy season, 16S-23S rRNA ITS analysis revealed that Cylindrospermopsis raciborskii comprised 46.8% of the cyanobacterial community in Ingazeira reservoir, while the cpcBAIGS region revealed that C. raciborskii (31.8%) was the most abundant taxon followed by Sphaerospermopsis aphanizomenoides (17.3%) and Planktothrix zahidii (16.6%). Despite the presence of other potential toxin-producing genera, the detected sxtA gene belonged to C. raciborskii, while the mcyE gene belonged to Microcystis in both reservoirs. The detected mcyE gene had good correlation with MC content, while the amplification of the sxtA gene was related to the presence of STX. The cyrJ gene was not detected in these samples. Using DNA analyses, our results showed that the cyanobacterial composition of Mundaú reservoir was similar in successive dry seasons, and it varied between seasons in Ingazeira reservoir. In addition, our data suggest that some biases of analysis influenced the cyanobacterial communities seen in the NGS output of Ingazeira reservoir.}, }
@article {pmid31004827, year = {2019}, author = {Sung, CM and Lin, YF and Chen, KF and Ke, HM and Huang, HY and Gong, YN and Tsai, WS and You, JF and Lu, MJ and Cheng, HT and Lin, CY and Kuo, CJ and Tsai, IJ and Hsieh, SY}, title = {Predicting Clinical Outcomes of Cirrhosis Patients With Hepatic Encephalopathy From the Fecal Microbiome.}, journal = {Cellular and molecular gastroenterology and hepatology}, volume = {8}, number = {2}, pages = {301-318.e2}, doi = {10.1016/j.jcmgh.2019.04.008}, pmid = {31004827}, issn = {2352-345X}, abstract = {BACKGROUND &amp; AIMS: Gut dysbiosis plays a role in hepatic encephalopathy (HE), while its relationship at the acute episode of overt HE (AHE), the disease progression and clinical outcomes remains unclear. We aimed to identify AHE-specific microbiome and its association to patients' outcomes.<br><br>METHODS: We profiled fecal microbiome changes for a cohort of 62 patients with cirrhosis and AHE i) before treatment, ii) 2-3 days after medication and iii) 2-3 months after recovery, and three control cohorts i) healthy individuals, patients with ii) compensated or iii) decompensated cirrhosis.<br><br>RESULTS: Comparison of the microbiome shift from compensated, decompensated cirrhosis, AHE to recovery revealed the AHE-specific gut-dysbiosis. The gut microbiome diversity was decreased during AHE, further reduced after medication, and only partially reversed during the recovery. The relative abundance of Bacteroidetes phylum in the microbiome decreased, whereas that of Firmicute, Proteobacteria and Actinobacteria increased in patients during AHE compared with those with compensated cirrhosis. A total of 70 operational taxonomic units (OTUs) were significantly different between AHE and decompensated cirrhosis abundances. Of them, the abundance of Veillonella parvula increased the most during AHE via a metagenomics recovery of the genomes. Moreover, the relative abundances of three (Alistipes, Bacteroides, Phascolarctobacterium) and five OTUs (Clostridium-XI, Bacteroides, Bacteroides, Lactobacillus, Clostridium-sedis) at AHE were respectively associated with HE recurrence and overall survival during the subsequent one-year follow-up.<br><br>CONCLUSIONS: AHE-specific gut OTUs were identified that may be involved in HE development and able to predict clinical outcomes, providing new strategies for the prevention and treatment of HE recurrence in patients with cirrhosis.}, }
@article {pmid31000700, year = {2019}, author = {Dong, X and Greening, C and Rattray, JE and Chakraborty, A and Chuvochina, M and Mayumi, D and Dolfing, J and Li, C and Brooks, JM and Bernard, BB and Groves, RA and Lewis, IA and Hubert, CRJ}, title = {Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1816}, doi = {10.1038/s41467-019-09747-0}, pmid = {31000700}, issn = {2041-1723}, mesh = {Acetates/metabolism ; Archaea/genetics/isolation &amp; purification/*metabolism ; Bacteria/genetics/isolation &amp; purification/*metabolism ; Geologic Sediments/chemistry/*microbiology ; Hydrocarbons/metabolism ; Hydrogen/metabolism ; Metagenome ; Metagenomics/methods ; Mexico ; Microbial Interactions/physiology ; Microbiota/*physiology ; Petroleum/*metabolism ; }, abstract = {The lack of microbial genomes and isolates from the deep seabed means that very little is known about the ecology of this vast habitat. Here, we investigate energy and carbon acquisition strategies of microbial communities from three deep seabed petroleum seeps (3 km water depth) in the Eastern Gulf of Mexico. Shotgun metagenomic analysis reveals that each sediment harbors diverse communities of chemoheterotrophs and chemolithotrophs. We recovered 82 metagenome-assembled genomes affiliated with 21 different archaeal and bacterial phyla. Multiple genomes encode enzymes for anaerobic oxidation of aliphatic and aromatic compounds, including those of candidate phyla Aerophobetes, Aminicenantes, TA06 and Bathyarchaeota. Microbial interactions are predicted to be driven by acetate and molecular hydrogen. These findings are supported by sediment geochemistry, metabolomics, and thermodynamic modelling. Overall, we infer that deep-sea sediments experiencing thermogenic hydrocarbon inputs harbor phylogenetically and functionally diverse communities potentially sustained through anaerobic hydrocarbon, acetate and hydrogen metabolism.}, }
@article {pmid30992350, year = {2019}, author = {Cobián Güemes, AG and Lim, YW and Quinn, RA and Conrad, DJ and Benler, S and Maughan, H and Edwards, R and Brettin, T and Cantú, VA and Cuevas, D and Hamidi, R and Dorrestein, P and Rohwer, F}, title = {Cystic Fibrosis Rapid Response: Translating Multi-omics Data into Clinically Relevant Information.}, journal = {mBio}, volume = {10}, number = {2}, pages = {}, doi = {10.1128/mBio.00431-19}, pmid = {30992350}, issn = {2150-7511}, mesh = {Adult ; Case-Control Studies ; Coinfection/complications ; Cystic Fibrosis/*complications/microbiology ; Disease Management ; *Disease Progression ; Escherichia coli Infections/*diagnosis ; Fatal Outcome ; Gene Expression Profiling ; *Genomics ; Humans ; Lung/*microbiology/physiopathology ; Male ; Metabolome ; *Metabolomics ; Metagenome ; Microbiota ; Shiga Toxin/genetics ; Shiga-Toxigenic Escherichia coli/genetics/pathogenicity ; }, abstract = {Pulmonary exacerbations are the leading cause of death in cystic fibrosis (CF) patients. To track microbial dynamics during acute exacerbations, a CF rapid response (CFRR) strategy was developed. The CFRR relies on viromics, metagenomics, metatranscriptomics, and metabolomics data to rapidly monitor active members of the viral and microbial community during acute CF exacerbations. To highlight CFRR, a case study of a CF patient is presented, in which an abrupt decline in lung function characterized a fatal exacerbation. The microbial community in the patient's lungs was closely monitored through the multi-omics strategy, which led to the identification of pathogenic shigatoxigenic Escherichia coli (STEC) expressing Shiga toxin. This case study illustrates the potential for the CFRR to deconstruct complicated disease dynamics and provide clinicians with alternative treatments to improve the outcomes of pulmonary exacerbations and expand the life spans of individuals with CF.IMPORTANCE Proper management of polymicrobial infections in patients with cystic fibrosis (CF) has extended their life span. Information about the composition and dynamics of each patient's microbial community aids in the selection of appropriate treatment of pulmonary exacerbations. We propose the cystic fibrosis rapid response (CFRR) as a fast approach to determine viral and microbial community composition and activity during CF pulmonary exacerbations. The CFRR potential is illustrated with a case study in which a cystic fibrosis fatal exacerbation was characterized by the presence of shigatoxigenic Escherichia coli The incorporation of the CFRR within the CF clinic could increase the life span and quality of life of CF patients.}, }
@article {pmid30979963, year = {2019}, author = {Singer, GAC and Fahner, NA and Barnes, JG and McCarthy, A and Hajibabaei, M}, title = {Comprehensive biodiversity analysis via ultra-deep patterned flow cell technology: a case study of eDNA metabarcoding seawater.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {5991}, doi = {10.1038/s41598-019-42455-9}, pmid = {30979963}, issn = {2045-2322}, abstract = {The characterization of biodiversity is a crucial element of ecological investigations as well as environmental assessment and monitoring activities. Increasingly, amplicon-based environmental DNA metabarcoding (alternatively, marker gene metagenomics) is used for such studies given its ability to provide biodiversity data from various groups of organisms simply from analysis of bulk environmental samples such as water, soil or sediments. The Illumina MiSeq is currently the most popular tool for carrying out this work, but we set out to determine whether typical studies were reading enough DNA to detect rare organisms (i.e., those that may be of greatest interest such as endangered or invasive species) present in the environment. We collected sea water samples along two transects in Conception Bay, Newfoundland and analyzed them on the MiSeq with a sequencing depth of 100,000 reads per sample (exceeding the 60,000 per sample that is typical of similar studies). We then analyzed these same samples on Illumina's newest high-capacity platform, the NovaSeq, at a depth of 7 million reads per sample. Not surprisingly, the NovaSeq detected many more taxa than the MiSeq thanks to its much greater sequencing depth. However, contrary to our expectations this pattern was true even in depth-for-depth comparisons. In other words, the NovaSeq can detect more DNA sequence diversity within samples than the MiSeq, even at the exact same sequencing depth. Even when samples were reanalyzed on the MiSeq with a sequencing depth of 1 million reads each, the MiSeq's ability to detect new sequences plateaued while the NovaSeq continued to detect new sequence variants. These results have important biological implications. The NovaSeq found 40% more metazoan families in this environment than the MiSeq, including some of interest such as marine mammals and bony fish so the real-world implications of these findings are significant. These results are most likely associated to the advances incorporated in the NovaSeq, especially a patterned flow cell, which prevents similar sequences that are neighbours on the flow cell (common in metabarcoding studies) from being erroneously merged into single spots by the sequencing instrument. This study sets the stage for incorporating eDNA metabarcoding in comprehensive analysis of oceanic samples in a wide range of ecological and environmental investigations.}, }
@article {pmid30978480, year = {2019}, author = {Reddy, B and Pandey, J and Dubey, SK}, title = {Assessment of environmental gene tags linked with carbohydrate metabolism and chemolithotrophy associated microbial community in River Ganga.}, journal = {Gene}, volume = {704}, number = {}, pages = {31-41}, doi = {10.1016/j.gene.2019.04.004}, pmid = {30978480}, issn = {1879-0038}, mesh = {Animals ; Bacteria/classification/genetics/growth &amp; development ; Carbohydrate Metabolism/*genetics ; Chemoautotrophic Growth/*genetics ; DNA Barcoding, Taxonomic ; Environment ; Geologic Sediments/*microbiology ; Humans ; India ; Metabolic Networks and Pathways/genetics ; Metagenome ; *Metagenomics/methods ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; }, abstract = {The microbial community mediated biogeochemical cycles play important role in global C-cycle and display a sensitive response to environmental changes. Limited information is available on microbial composition and functional diversity controlling biogeochemical cycles in the riverine environment. The Ganga River water and sediment samples were studied for environmental gene tags with reference to carbohydrate metabolism, photoheterotrophy and chemolithotrophy using high throughput shotgun metagenomic sequencing and functional annotation. The diversity of environmental gene tags specific microbial community was annotated against reference sequence database using Kaiju taxonomic classifier. The metagenomic analyses revealed that the river harbored a broad range of carbohydrate and energy metabolism genes. The in-depth investigation of metagenomic data revealed that the enzymes associated with reverse TCA cycle, Calvin-Benson cycle enzyme RuBisCO, starch and sucrose metabolism genes were highly abundant. The enzymes associated with sulfur metabolism such as EC:2.7.7.4 (sulfate to ammonium per sulfate), EC:1.8.1.2, EC:1.8.7.1 (sulfite to H2S) were prevalent in both the class of samples. The principal component analysis of the functional profiles revealed that the water and sediment samples were clustered distinctly suggesting that both the sites had variable abundance of functional genes and associated microbiota. The taxonomic classification showed abundance of Proteobacteria, Actinobacteria and Bacteroidetes phyla. Also, the metagenomic study showed the presence of purple sulfur bacteria viz. Thiodictyon, Nitrosococcus and purple non-sulfur bacteria viz. Bradyrhozobium and Rhodobacter. The study demonstrates that the Ganga River microbiome has prevalence of functional genes involved in carbohydrate anabolism and catabolism, and CO2 fixation with great prospects in cellulose and sulfide degrading enzyme production and characterization.}, }
@article {pmid30974142, year = {2019}, author = {Cheng, Y and Sibusiso, L and Hou, L and Jiang, H and Chen, P and Zhang, X and Wu, M and Tong, H}, title = {Sargassum fusiforme fucoidan modifies the gut microbiota during alleviation of streptozotocin-induced hyperglycemia in mice.}, journal = {International journal of biological macromolecules}, volume = {131}, number = {}, pages = {1162-1170}, doi = {10.1016/j.ijbiomac.2019.04.040}, pmid = {30974142}, issn = {1879-0003}, mesh = {Animals ; Blood Glucose/*drug effects ; Chemical Phenomena ; Diabetes Mellitus, Experimental ; Disease Models, Animal ; Gastrointestinal Microbiome/*drug effects ; Gene Expression Profiling ; Hyperglycemia/*blood/drug therapy/*etiology ; Liver/drug effects/metabolism/pathology ; Male ; Metagenome ; Metagenomics/methods ; Mice ; Oxidative Stress/drug effects ; Polysaccharides/*chemistry/*pharmacology ; Sargassum/*chemistry ; Spectrum Analysis ; Streptozocin/adverse effects ; Transcriptome ; }, abstract = {Diabetes is a complicated endocrine and metabolic disorder, which has become an epidemic health issue worldwide. Fucoidan is extensively distributed in the brown algae and several marine invertebrates exhibiting diverse biological activities. In the present study, the physicochemical property of Sargassum fusiforme fucoidan (SFF) and its effects on streptozotocin (STZ)-induced diabetic mice and gut microbiota were investigated. Diabetes mice not only showed abnormal blood glucose, but also accompanied by multiple symptoms, such as gradual emaciation, decreased body weight, increased food and water intake. Compared with diabetic mice after 6-week treatment, administration of SFF significantly decreased the fasting blood glucose, diet and water intake. Furthermore, SFF attenuated the pathological change in the heart and liver, improved the liver function, and suppressed oxidative stress in STZ-induced diabetic mice. Simultaneously, SFF significantly altered the gut microbiota in the faeces of diabetic mice, decreased the relative abundances of the diabetes-related intestinal bacteria, which is a potential mechanism for relieving the symptoms of diabetes. Therefore, SFF might be considered as one of the promising complementary and alternative medicines for the management of diabetes mellitus in future.}, }
@article {pmid30968165, year = {2019}, author = {Rossmassler, K and Snow, CD and Taggart, D and Brown, C and De Long, SK}, title = {Advancing biomarkers for anaerobic o-xylene biodegradation via metagenomic analysis of a methanogenic consortium.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {10}, pages = {4177-4192}, doi = {10.1007/s00253-019-09762-7}, pmid = {30968165}, issn = {1432-0614}, support = {CBET 1438660//National Science Foundation/ ; }, mesh = {Anaerobiosis ; *Biotransformation ; Enzymes/*genetics ; *Genetic Markers ; Metagenomics ; Microbial Consortia/*genetics ; Xylenes/*metabolism ; }, abstract = {Quantifying functional biomarker genes and their transcripts provides critical lines of evidence for contaminant biodegradation; however, accurate quantification depends on qPCR primers that contain no, or minimal, mismatches with the target gene. Developing accurate assays has been particularly challenging for genes encoding fumarate-adding enzymes (FAE) due to the high level of genetic diversity in this gene family. In this study, metagenomics applied to a field-derived, o-xylene-degrading methanogenic consortium revealed genes encoding FAE that would not be accurately quantifiable by any previously available PCR assays. Sequencing indicated that a gene similar to the napthylmethylsuccinate synthase gene (nmsA) was most abundant, although benzylsuccinate synthase genes (bssA) also were present along with genes encoding alkylsuccinate synthase (assA). Upregulation of the nmsA-like gene was observed during o-xylene degradation. Protein homology modeling indicated that mutations in the active site, relative to a BssA that acts on toluene, increase binding site volume and accessibility, potentially to accommodate the relatively larger o-xylene. The new nmsA-like gene was also detected at substantial concentrations at field sites with a history of xylene contamination.}, }
@article {pmid30967110, year = {2019}, author = {Hua, K and Zhang, X}, title = {Estimating the total genome length of a metagenomic sample using k-mers.}, journal = {BMC genomics}, volume = {20}, number = {Suppl 2}, pages = {183}, doi = {10.1186/s12864-019-5467-x}, pmid = {30967110}, issn = {1471-2164}, mesh = {Algorithms ; Datasets as Topic ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA ; *Software ; }, abstract = {BACKGROUND: Metagenomic sequencing is a powerful technology for studying the mixture of microbes or the microbiomes on human and in the environment. One basic task of analyzing metagenomic data is to identify the component genomes in the community. This task is challenging due to the complexity of microbiome composition, limited availability of known reference genomes, and usually insufficient sequencing coverage.<br><br>RESULTS: As an initial step toward understanding the complete composition of a metagenomic sample, we studied the problem of estimating the total length of all distinct component genomes in a metagenomic sample. We showed that this problem can be solved by estimating the total number of distinct k-mers in all the metagenomic sequencing data. We proposed a method for this estimation based on the sequencing coverage distribution of observed k-mers, and introduced a k-mer redundancy index (KRI) to fill in the gap between the count of distinct k-mers and the total genome length. We showed the effectiveness of the proposed method on a set of carefully designed simulation data corresponding to multiple situations of true metagenomic data. Results on real data indicate that the uncaptured genomic information can vary dramatically across metagenomic samples, with the potential to mislead downstream analyses.<br><br>CONCLUSIONS: We proposed the question of how long the total genome length of all different species in a microbial community is and introduced a method to answer it.}, }
@article {pmid30967109, year = {2019}, author = {Abe, K and Hirayama, M and Ohno, K and Shimamura, T}, title = {ENIGMA: an enterotype-like unigram mixture model for microbial association analysis.}, journal = {BMC genomics}, volume = {20}, number = {Suppl 2}, pages = {191}, doi = {10.1186/s12864-019-5476-9}, pmid = {30967109}, issn = {1471-2164}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Case-Control Studies ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; *Microbial Interactions ; Microbiota ; *Models, Biological ; Parkinson Disease/genetics/*microbiology ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: One of the major challenges in microbial studies is detecting associations between microbial communities and a specific disease. A specialized feature of microbiome count data is that intestinal bacterial communities form clusters called as &quot;enterotype&quot;, which are characterized by differences in specific bacterial taxa, making it difficult to analyze these data under health and disease conditions. Traditional probabilistic modeling cannot distinguish between the bacterial differences derived from enterotype and those related to a specific disease.<br><br>RESULTS: We propose a new probabilistic model, named as ENIGMA (Enterotype-like uNIGram mixture model for Microbial Association analysis), which can be used to address these problems. ENIGMA enabled simultaneous estimation of enterotype-like clusters characterized by the abundances of signature bacterial genera and the parameters of environmental effects associated with the disease.<br><br>CONCLUSION: In the simulation study, we evaluated the accuracy of parameter estimation. Furthermore, by analyzing the real-world data, we detected the bacteria related to Parkinson's disease. ENIGMA is implemented in R and is available from GitHub (https://github.com/abikoushi/enigma).}, }
@article {pmid30962514, year = {2019}, author = {Tan, S and Liu, J and Fang, Y and Hedlund, BP and Lian, ZH and Huang, LY and Li, JT and Huang, LN and Li, WJ and Jiang, HC and Dong, HL and Shu, WS}, title = {Insights into ecological role of a new deltaproteobacterial order Candidatus Acidulodesulfobacterales by metagenomics and metatranscriptomics.}, journal = {The ISME journal}, volume = {13}, number = {8}, pages = {2044-2057}, doi = {10.1038/s41396-019-0415-y}, pmid = {30962514}, issn = {1751-7370}, support = {U1501232//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31570506//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41603074//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31600077//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41773132//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41622106//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31570500//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41630103//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2016A030312003//Natural Science Foundation of Guangdong Province (Guangdong Natural Science Foundation)/ ; DEB-1557042//National Science Foundation (NSF)/ ; }, abstract = {Several abundant but yet uncultivated bacterial groups exist in extreme iron- and sulfur-rich environments, and the physiology, biodiversity, and ecological roles of these bacteria remain a mystery. Here we retrieved four metagenome-assembled genomes (MAGs) from an artificial acid mine drainage (AMD) system, and propose they belong to a new deltaproteobacterial order, Candidatus Acidulodesulfobacterales. The distribution pattern of Ca. Acidulodesulfobacterales in AMDs across Southeast China correlated strongly with ferrous iron. Reconstructed metabolic pathways and gene expression profiles showed that they were likely facultatively anaerobic autotrophs capable of nitrogen fixation. In addition to dissimilatory sulfate reduction, encoded by dsrAB, dsrD, dsrL, and dsrEFH genes, these microorganisms might also oxidize sulfide, depending on oxygen concentration and/or oxidation reduction potential. Several genes with homology to those involved in iron metabolism were also identified, suggesting their potential role in iron cycling. In addition, the expression of abundant resistance genes revealed the mechanisms of adaptation and response to the extreme environmental stresses endured by these organisms in the AMD environment. These findings shed light on the distribution, diversity, and potential ecological role of the new order Ca. Acidulodesulfobacterales in nature.}, }
@article {pmid30962029, year = {2019}, author = {Brink, M and Rhode, C and Macey, BM and Christison, KW and Roodt-Wilding, R}, title = {Metagenomic assessment of body surface bacterial communities of the sea urchin, Tripneustes gratilla.}, journal = {Marine genomics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.margen.2019.03.010}, pmid = {30962029}, issn = {1876-7478}, abstract = {Sea urchins, including Tripneustes gratilla, are susceptible to a disease known as bald sea urchin disease, which has the potential to lead to economic losses in this emerging aquaculture industry in South Africa. This disease is characterized by lesions that form on sea urchin exoskeletal surfaces. This study aimed to characterize the body surface bacterial communities associated with T. gratilla, using a 16S rDNA gene metagenomics approach, to provide insight into the bacterial agents associated with this aquaculture species, as well as with this balding disease. Bacterial samples were collected from non-lesioned healthy animals obtained from natural locations along the eastern coast of South Africa, as well as from different cultured cohorts: non-lesioned healthy-, lesioned diseased- and non-lesioned stressed animals. A total of 1,067,515 individual bacterial operational taxonomic units (OTUs) were identified, belonging to 133 family-, 123 genus- and 113 species level OTU groups. Alpha diversity analyses, based on Chao1, Shannon and Simpson indices, showed that there were no statistically significant differences (ANOVA; P > 0.05) between the respective cohorts, as all cohorts displayed a high degree of bacterial diversity. Similarly, beta diversity analyses (Non-metric multidimensional scaling) showed a large degree of overlapping OTUs across the four cohorts. Within each cohort, various OTUs commonly associated with marine environments were found, predominantly belonging to the families Vibrionaceae, Saprospiraceae, Flavobacteriaceae and Sphingomonadaceae. Differential abundance analysis (DESeq2) revealed that OTUs that are differentially abundant across cohorts were likely not responsible for this balding disease, suggesting that complex bacterial agents, rather than a specific pathogenic agent, are likely causing this disease. Furthermore, the putative metabolic functions assigned to the bacterial communities showed that heterotrophic bacteria appear to be responsible for tissue lysis of degrading animal matter. The results from this study, obtained through univariate and multivariate-based approaches, contributes to future management strategies of this emerging aquaculture species by providing insight into the bacterial communities associated with both natural and cultured environments.}, }
@article {pmid30958827, year = {2019}, author = {Martí, JM}, title = {Recentrifuge: Robust comparative analysis and contamination removal for metagenomics.}, journal = {PLoS computational biology}, volume = {15}, number = {4}, pages = {e1006967}, doi = {10.1371/journal.pcbi.1006967}, pmid = {30958827}, issn = {1553-7358}, mesh = {Algorithms ; Big Data ; Computational Biology/methods ; DNA Contamination ; High-Throughput Nucleotide Sequencing ; Humans ; Internet ; Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA/*methods ; Software ; Whole Genome Sequencing/methods ; }, abstract = {Metagenomic sequencing is becoming widespread in biomedical and environmental research, and the pace is increasing even more thanks to nanopore sequencing. With a rising number of samples and data per sample, the challenge of efficiently comparing results within a specimen and between specimens arises. Reagents, laboratory, and host related contaminants complicate such analysis. Contamination is particularly critical in low microbial biomass body sites and environments, where it can comprise most of a sample if not all. Recentrifuge implements a robust method for the removal of negative-control and crossover taxa from the rest of samples. With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications. In addition to contamination-subtracted samples, Recentrifuge provides shared and exclusive taxa per sample, thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics. Regarding the first area, Recentrifuge's novel approach has already demonstrated its benefits showing that microbiomes of Arctic and Antarctic solar panels display similar taxonomic profiles. In the clinical field, to confirm Recentrifuge's ability to analyze complex metagenomes, we challenged it with data coming from a metagenomic investigation of RNA in plasma that suffered from critical contamination to the point of preventing any positive conclusion. Recentrifuge provided results that yielded new biological insight into the problem, supporting the growing evidence of a blood microbiota even in healthy individuals, mostly translocated from the gut, the oral cavity, and the genitourinary tract. We also developed a synthetic dataset carefully designed to rate the robust contamination removal algorithm, which demonstrated a significant improvement in specificity while retaining a high sensitivity even in the presence of cross-contaminants. Recentrifuge's official website is www.recentrifuge.org. The data and source code are anonymously and freely available on GitHub and PyPI. The computing code is licensed under the AGPLv3. The Recentrifuge Wiki is the most extensive and continually-updated source of documentation for Recentrifuge, covering installation, use cases, testing, and other useful topics.}, }
@article {pmid30955771, year = {2019}, author = {Cotta, SR and Cadete, LL and van Elsas, JD and Andreote, FD and Dias, ACF}, title = {Exploring bacterial functionality in mangrove sediments and its capability to overcome anthropogenic activity.}, journal = {Marine pollution bulletin}, volume = {141}, number = {}, pages = {586-594}, doi = {10.1016/j.marpolbul.2019.03.001}, pmid = {30955771}, issn = {1879-3363}, mesh = {Bacteria/genetics/metabolism ; Biodiversity ; Brazil ; Carbon/metabolism ; Ecosystem ; Gene Transfer, Horizontal ; Geologic Sediments/*microbiology ; Metagenomics ; *Microbiota/genetics ; Sulfur/metabolism ; *Wetlands ; }, abstract = {Mangrove forests are highly productive yet vulnerable ecosystems that act as important carbon sinks (&quot;blue carbon&quot;). The objective of this work was to analyze the impact of anthropogenic activities on microbiome structure and functioning. The metagenomic analysis revealed that the taxonomic compositions were grossly similar across all mangrove microbiomes. Remarkably, these microbiomes, along the gradient of anthropogenic impact, showed fluctuations in the relative abundances of bacterial taxa predicted to be involved in sulfur cycling processes. Functions involved in sulfur metabolism, such as APS pathways (associated with sulfate reduction and sulfur oxidation processes) were prevalent across the microbiomes, being sox and dsrAB genes highly expressed on anthropogenically-impacted areas. Apparently, the oil-impacted microbiomes were more affected in taxonomic than in functional terms, as high functional redundancies were noted across them. The microbial gene diversity found was typical for a functional system, even following the previous disturbance.}, }
@article {pmid30955749, year = {2019}, author = {Fernandes, C and Kankonkar, H and Meena, RM and Menezes, G and Shenoy, BD and Khandeparker, R}, title = {Metagenomic analysis of tarball-associated bacteria from Goa, India.}, journal = {Marine pollution bulletin}, volume = {141}, number = {}, pages = {398-403}, doi = {10.1016/j.marpolbul.2019.02.040}, pmid = {30955749}, issn = {1879-3363}, mesh = {Biodegradation, Environmental ; Environmental Monitoring/*methods ; Humans ; India ; Marinobacter/genetics/isolation &amp; purification ; Metagenome/*genetics ; Metagenomics ; Microbiota/*genetics ; Petroleum/*analysis ; Polycyclic Aromatic Hydrocarbons/*analysis ; Proteobacteria/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Water Pollutants, Chemical/*analysis ; }, abstract = {The beaches of Goa state in India are frequently polluted with tarballs, specifically during pre-monsoon and monsoon seasons. Tarballs contain hydrocarbons, including polycyclic aromatic hydrocarbons, which pose significant environmental risks. Microbes associated with tarballs reportedly possess capabilities to degrade toxic hydrocarbons present in tarballs. In this study, bacterial diversity associated with tarballs from Vagator and Morjim beaches of north Goa was analysed based on V3-V4 regions of 16S rRNA gene sequenced using Illumina Miseq Platform. The Proteobacterial members were dominant in both Vagator (≥85.5%) and Morjim (≥94.0%) samples. Many of the identified taxa have been previously reported as hydrocarbon degraders (e.g. Halomonas, Marinobacter) or possible human pathogens (e.g. Acinetobacter, Klebsiella, Rhodococcus, Staphylococcus, Vibrio). This is the first study reported on a metagenomic analysis of bacteria associated with tarballs from Goa.}, }
@article {pmid30953747, year = {2019}, author = {Wei, T and Bao, JY and Yang, HH and Lin, JF and Zheng, QW and Ye, ZW and Zou, Y and Li, X and Jiang, ZL and Guo, LQ}, title = {Musa basjoo regulates the gut microbiota in mice by rebalancing the abundance of probiotic and pathogen.}, journal = {Microbial pathogenesis}, volume = {131}, number = {}, pages = {205-211}, doi = {10.1016/j.micpath.2019.04.003}, pmid = {30953747}, issn = {1096-1208}, mesh = {Animal Feed ; Animals ; Bacteroides/physiology ; Cell Wall/metabolism ; China ; DNA, Ribosomal ; Disease Models, Animal ; Feces/microbiology ; Food Safety ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Lactobacillus casei/physiology ; Lactobacillus plantarum/physiology ; Metagenomics ; Mice/*microbiology ; Mice, Inbred BALB C ; Musa/*chemistry ; *Probiotics/classification/pharmacology ; Specific Pathogen-Free Organisms ; }, abstract = {Musa basjoo is a kind of popular slimming fruit in southern China. However, even though the trophic component and physiological effect are well studied, its internal mechanism in reconstructing gut microbiota remains unclear. In this study, maturity of M. basjoo were divided into four levels. Results indicated that M. basjoo in level Ⅱ (with 35% maturity) represented the greatest increase in the growth in vitro of probiotics, Lactobacillus plantarum FMNP01 and Lactobacillus casei FMNP02. After feeding M. basjoo with the middle dose (2.67 g/kg·BW) to mice for 21 days, gut microbiota from mice feces was isolated and sequenced. Results of 16SrDNA sequencing showed that the scattered genera of gut microbiota were significantly gathered. The amounts of different pathogens were decreased, while probiotics such as genera Bacteroides and Roseburia were significantly increased (p < 0.05). Results of function prediction indicated that the reconstruction of gut microbiota may due to the change in carbohydrate transportation, biosynthesis of cell wall, cell membrane, and cell envelope. This study has drawn a basic mechanism in reconstructing gut microbiota by feeding M. basjoo and lay out a foundation for further reach on the interaction between human as diner and M. basjoo as food.}, }
@article {pmid30953542, year = {2019}, author = {Raymond, F and Boissinot, M and Ouameur, AA and Déraspe, M and Plante, PL and Kpanou, SR and Bérubé, È and Huletsky, A and Roy, PH and Ouellette, M and Bergeron, MG and Corbeil, J}, title = {Culture-enriched human gut microbiomes reveal core and accessory resistance genes.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {56}, doi = {10.1186/s40168-019-0669-7}, pmid = {30953542}, issn = {2049-2618}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/*classification/drug effects/genetics/growth &amp; development ; Bacterial Proteins/genetics ; Bacteriological Techniques/*methods ; *Drug Resistance, Microbial ; Escherichia coli/genetics/growth &amp; development/isolation &amp; purification ; Feces/cytology/microbiology ; Gastrointestinal Microbiome ; Gene Transfer, Horizontal ; Humans ; Metagenomics ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: Low-abundance microorganisms of the gut microbiome are often referred to as a reservoir for antibiotic resistance genes. Unfortunately, these less-abundant bacteria can be overlooked by deep shotgun sequencing. In addition, it is a challenge to associate the presence of resistance genes with their risk of acquisition by pathogens. In this study, we used liquid culture enrichment of stools to assemble the genome of lower-abundance bacteria from fecal samples. We then investigated the gene content recovered from these culture-enriched and culture-independent metagenomes in relation with their taxonomic origin, specifically antibiotic resistance genes. We finally used a pangenome approach to associate resistance genes with the core or accessory genome of Enterobacteriaceae and inferred their propensity to horizontal gene transfer.<br><br>RESULTS: Using culture-enrichment approaches with stools allowed assembly of 187 bacterial species with an assembly size greater than 1 million nucleotides. Of these, 67 were found only in culture-enriched conditions, and 22 only in culture-independent microbiomes. These assembled metagenomes allowed the evaluation of the gene content of specific subcommunities of the gut microbiome. We observed that differentially distributed metabolic enzymes were associated with specific culture conditions and, for the most part, with specific taxa. Gene content differences between microbiomes, for example, antibiotic resistance, were for the most part not associated with metabolic enzymes, but with other functions. We used a pangenome approach to determine if the resistance genes found in Enterobacteriaceae, specifically E. cloacae or E. coli, were part of the core genome or of the accessory genome of this species. In our healthy volunteer cohort, we found that E. cloacae contigs harbored resistance genes that were part of the core genome of the species, while E. coli had a large accessory resistome proximal to mobile elements.<br><br>CONCLUSION: Liquid culture of stools contributed to an improved functional and comparative genomics study of less-abundant gut bacteria, specifically those associated with antibiotic resistance. Defining whether a gene is part of the core genome of a species helped in interpreting the genomes recovered from culture-independent or culture-enriched microbiomes.}, }
@article {pmid30953134, year = {2019}, author = {Grieco, MB and Lopes, FAC and Oliveira, LS and Tschoeke, DA and Popov, CC and Thompson, CC and Gonçalves, LC and Constantino, R and Martins, OB and Kruger, RH and de Souza, W and Thompson, FL}, title = {Metagenomic Analysis of the Whole Gut Microbiota in Brazilian Termitidae Termites Cornitermes cumulans, Cyrilliotermes strictinasus, Syntermes dirus, Nasutitermes jaraguae, Nasutitermes aquilinus, Grigiotermes bequaerti, and Orthognathotermes mirim.}, journal = {Current microbiology}, volume = {76}, number = {6}, pages = {687-697}, doi = {10.1007/s00284-019-01662-3}, pmid = {30953134}, issn = {1432-0991}, support = {563055/2010-3//Conselho Nacional de Desenvolvimento Científico e Tecnológico (BR)/ ; E-26/ 110.634/2014//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; }, mesh = {Animals ; Bacteria/*classification/*genetics ; Biodiversity ; Brazil ; Feeding Behavior ; *Gastrointestinal Microbiome ; Isoptera/*microbiology/physiology ; Metagenomics ; }, abstract = {Although some previous studies have described the microbial diversity of termite in Brazil, the lack of studies about this subject is still evident. In the present study, we described by whole genome sequencing, the gut microbiota of seven species of termites (Termitidae) with different feeding habits from four Brazilian locations. For the litter species, the most abundant bacterial phylum was Firmicutes, where Cornitermes cumulans and Syntermes dirus (Syntermitinae) were identified. For the humus species, the most abundant bacterial phylum was Proteobacteria where three species were studied: Cyrilliotermes strictinasus (Syntermitinae), Grigiotermes bequaerti (Apicotermitinae), and Orthognathotermes mirim (Termitinae). For the wood termites, Firmicutes and Spirochaetes were the most abundant phyla, respectively, where two species were identified: Nasutitermes aquilinus and Nasutitermes jaraguae (Nasutitermitinae). The gut microbiota of all four examined subfamilies shared a conserved functional and carbohydrate-active enzyme profile and specialized in cellulose and chitin degradation. Taken together, these results provide insight into the partnerships between termite and microbes that permit the use of refractory energy sources.}, }
@article {pmid30953119, year = {2019}, author = {Deng, Y and Xu, X and Yin, X and Lu, H and Chen, G and Yu, J and Ruan, Y}, title = {Effect of stock density on the microbial community in biofloc water and Pacific white shrimp (Litopenaeus vannamei) gut microbiota.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {10}, pages = {4241-4252}, doi = {10.1007/s00253-019-09773-4}, pmid = {30953119}, issn = {1432-0614}, mesh = {Animals ; Aquaculture/*methods ; Bacteria/*classification/genetics ; *Gastrointestinal Microbiome ; Metagenomics ; Penaeidae/*microbiology ; *Water Microbiology ; }, abstract = {Biofloc technology is an efficient approach for intensive shrimp culture. However, the extent to which this process can influence the composition of intestinal microbial community is still unknown. Here, we surveyed the shrimp intestinal bacteria as well as the floc water from three biofloc systems with different stock densities. Our study revealed a similar variation trend in phylum taxonomy level between floc bacteria and gut microbiota. Microbial community varied notably in floc water from different stock densities, while a core genus with dominating relative abundance was detected in gut samples. Extensive variation was discovered in gut microbiota, but still clustered into groups according to stock density. Our results indicated that shrimp intestinal microbiota as well as bacteria aggregated in flocs assembled into distinct communities from different stock densities, and the intestinal communities were more similar with the surrounding environment as the increase of stock density and resulting high floc biomass. The high stock density changed the core gut microbiota by reducing the relative abundance of Paracoccus and increasing that of Nocardioides, which may negatively influence shrimp performance. Therefore, this study helps us to understand further bacteria and host interactions in biofloc system.}, }
@article {pmid30947688, year = {2019}, author = {Sevigny, JL and Rothenheber, D and Diaz, KS and Zhang, Y and Agustsson, K and Bergeron, RD and Thomas, WK}, title = {Marker genes as predictors of shared genomic function.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {268}, doi = {10.1186/s12864-019-5641-1}, pmid = {30947688}, issn = {1471-2164}, support = {P20 GM103506/GM/NIGMS NIH HHS/United States ; 16-052: SA 16-18//Gulf of Mexico Research Initiative/ ; 5 P20 GM 10350605//National Institutes of Health: New Hampshire Idea Network of Biological Research Excellence/ ; }, mesh = {Bacteria/*classification/*genetics ; DNA, Bacterial/genetics ; Evolution, Molecular ; Genes, Bacterial/genetics/*physiology ; *Genetic Markers ; *Genome, Bacterial ; *Metagenome ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Although high-throughput marker gene studies provide valuable insight into the diversity and relative abundance of taxa in microbial communities, they do not provide direct measures of their functional capacity. Recently, scientists have shown a general desire to predict functional profiles of microbial communities based on phylogenetic identification inferred from marker genes, and recent tools have been developed to link the two. However, to date, no large-scale examination has quantified the correlation between the marker gene based taxonomic identity and protein coding gene conservation. Here we utilize 4872 representative prokaryotic genomes from NCBI to investigate the relationship between marker gene identity and shared protein coding gene content.<br><br>RESULTS: Even at 99-100% marker gene identity, genomes share on average less than 75% of their protein coding gene content. This occurs regardless of the marker gene(s) used: V4 region of the 16S rRNA, complete 16S rRNA, or single copy orthologs through a multi-locus sequence analysis. An important aspect related to this observation is the intra-organism variation of 16S copies from a single genome. Although the majority of 16S copies were found to have high sequence similarity (> 99%), several genomes contained copies that were highly diverged (< 97% identity).<br><br>CONCLUSIONS: This is the largest comparison between marker gene similarity and shared protein coding gene content to date. The study highlights the limitations of inferring a microbial community's functions based on marker gene phylogeny. The data presented expands upon the results of previous studies that examined one or few bacterial species and supports the hypothesis that 16S rRNA and other marker genes cannot be directly used to fully predict the functional potential of a bacterial community.}, }
@article {pmid30946154, year = {2019}, author = {Sessa, L and Reddel, S and Manno, E and Quagliariello, A and Cotugno, N and Del Chierico, F and Amodio, D and Capponi, C and Leone, F and Bernardi, S and Rossi, P and Putignani, L and Palma, P}, title = {Distinct gut microbiota profile in antiretroviral therapy-treated perinatally HIV-infected patients associated with cardiac and inflammatory biomarkers.}, journal = {AIDS (London, England)}, volume = {33}, number = {6}, pages = {1001-1011}, doi = {10.1097/QAD.0000000000002131}, pmid = {30946154}, issn = {1473-5571}, abstract = {OBJECTIVE: Persistent inflammation and higher risk to develop cardiovascular diseases still represent a major complication for HIV-infected patients despite effective antiretroviral therapy (ART). We investigated the correlation between the gut microbiota profile, markers of inflammation, vascular endothelial activation (VEA) and microbial translocation (MT) in perinatally HIV-infected patients (PHIV) under ART.<br><br>DESIGN: Cross-sectional study including 61 ART-treated PHIV (age range 3-30 years old) and 71 age-matched healthy controls. Blood and stool sample were collected at the same time and analyzed for gut microbiota composition and plasma biomarkers.<br><br>METHODS: Gut microbiota composition was determined by 16S rRNA targeted-metagenomics. Soluble markers of MT, inflammation and VEA were quantified by ELISA or Luminex assay. Markers of immune activation were analyzed by flow cytometry on CD4 and CD8T cells.<br><br>RESULTS: We identified two distinct gut microbiota profiles (groups A and B) among PHIV. No different clinical parameters (age, sex, ethnicity, clinical class), dietary and sexual habits were found between the groups. The group A showed a relative dominance of Akkermansia muciniphila, whereas gut microbiota of group B was characterized by a higher biodiversity. The analysis of soluble markers revealed a significantly higher level of soluble E-selectine (P = 0.0296), intercellular adhesion molecule-1 (P = 0.0028), vascular adhesion molecule-1 (P = 0.0230), IL-6 (P = 0.0247) and soluble CD14 (P = 0.0142) in group A compared with group B.<br><br>CONCLUSION: Distinctive gut microbiota profiles are differently associated with inflammation, microbial translocation and VEA. Future studies are needed to understand the role of A. muciniphila and risk to develop cardiovascular diseases in PHIV.}, }
@article {pmid30942434, year = {2019}, author = {Liu, Z and Kong, Y and Gao, Y and Ren, Y and Zheng, C and Deng, X and Chen, T}, title = {Revealing the interaction between intrauterine adhesion and vaginal microbiota using high‑throughput sequencing.}, journal = {Molecular medicine reports}, volume = {19}, number = {5}, pages = {4167-4174}, doi = {10.3892/mmr.2019.10092}, pmid = {30942434}, issn = {1791-3004}, mesh = {Adolescent ; Adult ; Biodiversity ; Computational Biology/methods ; *Disease Susceptibility ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; Public Health Surveillance ; Tissue Adhesions/diagnosis/epidemiology/*etiology ; Uterine Diseases/diagnosis/epidemiology/*etiology ; Vagina/*microbiology ; Young Adult ; }, abstract = {Intrauterine adhesion (IUA) is one of the most common diseases of the reproductive system. Due to the high postoperative recurrence rate of IUA, it is crucial to identify the possible causes of pathogenesis and recurrence of this disease. In the present study, a high‑throughput sequencing approach was applied to compare the vaginal microbiota between healthy women [healthy vaginal secretion (HVS) group] and patients with IUA [intrauterine adhesion patients' vaginal secretion (IAVS) group]. The results indicated that IUA had little effect on the number of vaginal bacterial species. However, at the phylum level, patients with IUA had a significantly lower percentage of Firmicutes and a higher percentage of Actinobacteria than the HVS group (P<0.05). At the genus level, ~50% of patients with IUA were found to have a marked reduction in probiotic Lactobacillus accompanied by an overgrowth of pathogenic Gardnerella and Prevotella (P<0.05), and the Principal Coordinates Analysis confirmed that 10/20 samples in the IAVS group were scattered far away from the HVS group. Therefore, it was concluded that the interaction between IUA and vaginal microbiota greatly influenced the vaginal diversity of patients with IUA. In order to increase the recovery rate and lower the recurrence rate of IUA, increasing the vaginal Lactobacillus population should be considered.}, }
@article {pmid30936548, year = {2019}, author = {Thomas, AM and Manghi, P and Asnicar, F and Pasolli, E and Armanini, F and Zolfo, M and Beghini, F and Manara, S and Karcher, N and Pozzi, C and Gandini, S and Serrano, D and Tarallo, S and Francavilla, A and Gallo, G and Trompetto, M and Ferrero, G and Mizutani, S and Shiroma, H and Shiba, S and Shibata, T and Yachida, S and Yamada, T and Wirbel, J and Schrotz-King, P and Ulrich, CM and Brenner, H and Arumugam, M and Bork, P and Zeller, G and Cordero, F and Dias-Neto, E and Setubal, JC and Tett, A and Pardini, B and Rescigno, M and Waldron, L and Naccarati, A and Segata, N}, title = {Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation.}, journal = {Nature medicine}, volume = {25}, number = {4}, pages = {667-678}, doi = {10.1038/s41591-019-0405-7}, pmid = {30936548}, issn = {1546-170X}, support = {P30 CA042014/CA/NCI NIH HHS/United States ; R01 CA189184/CA/NCI NIH HHS/United States ; R01 CA207371/CA/NCI NIH HHS/United States ; }, mesh = {Biomarkers, Tumor/metabolism ; Choline/*metabolism ; Cohort Studies ; Colorectal Neoplasms/diagnosis/*metabolism/*microbiology ; Databases, Genetic ; Gastrointestinal Microbiome ; Humans ; Lyases/genetics/metabolism ; *Metagenomics ; Species Specificity ; }, abstract = {Several studies have investigated links between the gut microbiome and colorectal cancer (CRC), but questions remain about the replicability of biomarkers across cohorts and populations. We performed a meta-analysis of five publicly available datasets and two new cohorts and validated the findings on two additional cohorts, considering in total 969 fecal metagenomes. Unlike microbiome shifts associated with gastrointestinal syndromes, the gut microbiome in CRC showed reproducibly higher richness than controls (P < 0.01), partially due to expansions of species typically derived from the oral cavity. Meta-analysis of the microbiome functional potential identified gluconeogenesis and the putrefaction and fermentation pathways as being associated with CRC, whereas the stachyose and starch degradation pathways were associated with controls. Predictive microbiome signatures for CRC trained on multiple datasets showed consistently high accuracy in datasets not considered for model training and independent validation cohorts (average area under the curve, 0.84). Pooled analysis of raw metagenomes showed that the choline trimethylamine-lyase gene was overabundant in CRC (P = 0.001), identifying a relationship between microbiome choline metabolism and CRC. The combined analysis of heterogeneous CRC cohorts thus identified reproducible microbiome biomarkers and accurate disease-predictive models that can form the basis for clinical prognostic tests and hypothesis-driven mechanistic studies.}, }
@article {pmid30927638, year = {2019}, author = {Wei, Z and Yu, S and Huang, Z and Xiao, X and Tang, M and Li, B and Zhang, X}, title = {Simultaneous removal of elemental mercury and NO by mercury induced thermophilic community in membrane biofilm reactor.}, journal = {Ecotoxicology and environmental safety}, volume = {176}, number = {}, pages = {170-177}, doi = {10.1016/j.ecoenv.2019.03.082}, pmid = {30927638}, issn = {1090-2414}, mesh = {Biofilms/*growth &amp; development ; Bioreactors/*microbiology ; Denitrification ; Mercury/*analysis ; Metagenomics ; Microbiota/drug effects/genetics ; Nitric Oxide/*analysis ; Nitrification ; Oxidation-Reduction ; }, abstract = {Thermophilic membrane biofilm reactor (TMBR) for elemental mercury (Hg0) and NO removal in simulated flue gas was investigated at oxygen content of 6% and 60 °C. The performance, the microbial community structures, gene function and the mechanism for Hg0 and NO removal in the TMBR were evaluated. TMBR achieved effective simultaneous Hg0 and NO removal in 210 days of operation, Hg0 and NO removal efficiency were up to 88.9% and 85.3%, respectively. Mercury induced thermophilic community had been formed significantly. Comamonas, Pseudomonas, Desulfomicrobium, Burkholderia and Halomonas were thermophilic mercury resistant bacteria. Brucella, Paracoccus, Tepidiphilus, Proteobacteria, Pseudomonas and Symbiobacterium were nitrifying/denitrifying genera, and had functional genes of mercury and nitrogen metabolism, as shown by16S rDNA and metagenomic sequencing. The biofilm in TMBR was characterized by XPS, HPLC. XPS and HPLC spectra indicate the formation of a mercuric species (Hg2+) from mercury oxidation. TMBR used oxygen as electron acceptor, NO and Hg0 as electron donor in nitrification; O2, NO and NO3- could be used as electron acceptor and Hg0 as electron donor in denitrification.}, }
@article {pmid30927421, year = {2019}, author = {Ding, GC and Bai, M and Han, H and Li, H and Ding, X and Yang, H and Xu, T and Li, J}, title = {Microbial taxonomic, nitrogen cycling and phosphorus recycling community composition during long-term organic greenhouse farming.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {5}, pages = {}, doi = {10.1093/femsec/fiz042}, pmid = {30927421}, issn = {1574-6941}, abstract = {Understanding the interplay between the farming system and soil microbiomes could aid the design of a sustainable and efficient farming system. A comparative greenhouse experiment consisting of organic (ORG), integrated (INT) and conventional (CON) farming systems was established in northern China in 2002. The effects of 12 years of organic farming on soil microbiomes were explored by metagenomic and 16S rRNA gene amplicon sequencing analyses. Long-term ORG shifted the community composition of dominant phyla, especially Acidobacteria, increased the relative abundance of Ignavibacteria and Acidobacteria Gp6 and decreased the relative abundance of Nitrosomonas, Bacillus and Paenibacillus. Metagenomic analysis further revealed that relative abundance of ammonia oxidizing microorganisms (Bacteria and Archaea) and anaerobic ammonium oxidation bacteria decreased during ORG. Conversely, the relative abundance of bacteria-carrying periplasmic nitrate reductases (napA) was slightly higher for ORG. Long-term organic farming also caused significant alterations to the community composition of functional groups associated with ammonia oxidation, denitrification and phosphorus recycling. In summary, this study provides key insights into the composition of soil microbiomes and long-term organic farming under greenhouse conditions.}, }
@article {pmid30926487, year = {2019}, author = {Ji, X and Hou, C and Zhang, X and Han, L and Yin, S and Peng, Q and Wang, M}, title = {Microbiome-metabolomic analysis of the impact of Zizyphus jujuba cv. Muzao polysaccharides consumption on colorectal cancer mice fecal microbiota and metabolites.}, journal = {International journal of biological macromolecules}, volume = {131}, number = {}, pages = {1067-1076}, doi = {10.1016/j.ijbiomac.2019.03.175}, pmid = {30926487}, issn = {1879-0003}, mesh = {Animal Feed ; Animals ; Biomarkers ; Colorectal Neoplasms/etiology/*metabolism/pathology ; Cytokines/metabolism ; Disease Models, Animal ; Fatty Acids, Volatile/metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome ; Inflammation Mediators/metabolism ; Male ; Metabolic Networks and Pathways ; *Metabolome ; *Metabolomics/methods ; Metagenome ; Metagenomics/methods ; Mice ; *Polysaccharides ; RNA, Ribosomal, 16S/genetics ; Ziziphus/*chemistry ; }, abstract = {It is still uncertain whether the consumption of Zizyphus jujuba cv. Muzao polysaccharides (ZMP) alleviates colorectal cancer (CRC) through the gut microbiota. In this study, we investigated the mortality, colon length, inflammatory factors and cecal microbiota, metabolites of healthy and azoxymethane (AOM) and dextran sodium sulfate (DSS) in induced CRC mice, consuming ZMP. Fecal-microbiota composition was examined using 16S rDNA sequencing and fecal-metabolome profiles were evaluated by ultra-high performance liquid chromatograph mass spectrometry (UHPLC-MS). The results showed ZMP consumption prevented CRC mouse colon shortening, decreased their mortality, reduced pro-inflammatory cytokines, increased the concentration of total short-chain fatty acids (SCFAs) and modulated gut microbiota in their feces. ZMP also increased the richness of Bifidobacterium, Bacteroides and Lactobacillus. In addition, among 39 perturbed metabolites, carbohydrate and amino acid production were noticeably altered. Moreover, higher correlations were found between fluctuant gut microbiota and metabolites. These findings provide mechanistic insights into the impact of dietary Zizyphus jujuba cv. Muzao polysaccharides on host health.}, }
@article {pmid30918994, year = {2019}, author = {Klima, CL and Holman, DB and Ralston, BJ and Stanford, K and Zaheer, R and Alexander, TW and McAllister, TA}, title = {Lower Respiratory Tract Microbiome and Resistome of Bovine Respiratory Disease Mortalities.}, journal = {Microbial ecology}, volume = {78}, number = {2}, pages = {446-456}, doi = {10.1007/s00248-019-01361-3}, pmid = {30918994}, issn = {1432-184X}, support = {2015R025R//Alberta Livestock and Meat Agency/ ; 001//Growing Forward II/ ; 001//Genomics Research Initiative/ ; }, mesh = {Alberta ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/classification/drug effects/genetics/*isolation &amp; purification ; Bacterial Infections/microbiology/mortality/*veterinary ; Cattle ; Cattle Diseases/*microbiology/mortality ; *Drug Resistance, Bacterial ; *Microbiota ; Respiratory System/*microbiology ; Respiratory Tract Diseases/microbiology/mortality/*veterinary ; }, abstract = {Bovine respiratory disease (BRD) continues to be a serious health problem in beef cattle production. A multifactorial condition, BRD encompasses several types of pneumonia that are associated with multiple viral and bacterial agents. Comprehensive identification of microbes associated with BRD fatalities could enhance our understanding of the range of pathogens that contribute to the disease and identify new therapeutic targets. This study used metagenomic analysis to describe the lower respiratory tract microbiome and resistome of 15 feedlot cattle BRD and 3 non-BRD mortalities along with any affiliated integrative and conjugative elements (ICEs). Known bacterial pathogens associated with BRD, including Histophilus somni, Mannheimia haemolytica, and Mycoplasma bovis, were relatively abundant (> 5%) in most, but not all samples. Other relatively abundant genera (> 1%) included Acinetobacter, Bacillus, Bacteroides, Clostridium, Enterococcus, and Pseudomonas. Antimicrobial resistance genes (ARGs) comprised up to 0.5% of sequences and many of these genes were associated with ICEs previously described within the Pasteurellaceae family. A total of 20 putative ICEs were detected among 16 samples. These results document the wide diversity of microorganisms in the lower respiratory tract of cattle that have succumbed to BRD. The data also strongly suggest that antimicrobial-resistant Pasteurellaceae strains are prevalent in BRD cases in Alberta and that the resistance observed is associated with ICEs. The presence of ICEs harboring a wide array of ARGs holds significant consequence for the effectiveness of drug therapies for the control of BRD in beef cattle.}, }
@article {pmid30918406, year = {2019}, author = {Zeevi, D and Korem, T and Godneva, A and Bar, N and Kurilshikov, A and Lotan-Pompan, M and Weinberger, A and Fu, J and Wijmenga, C and Zhernakova, A and Segal, E}, title = {Structural variation in the gut microbiome associates with host health.}, journal = {Nature}, volume = {568}, number = {7750}, pages = {43-48}, doi = {10.1038/s41586-019-1065-y}, pmid = {30918406}, issn = {1476-4687}, mesh = {Adaptation, Physiological/genetics ; Bacteria/classification/*genetics/growth &amp; development/metabolism ; Butyrates/metabolism ; Cohort Studies ; Disease Susceptibility/*microbiology ; Ecosystem ; Eubacterium/genetics/metabolism ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics/physiology ; Genes, Bacterial/*genetics ; *Genetic Variation ; *Health ; Host Microbial Interactions/*genetics/physiology ; Humans ; Inositol/metabolism ; Metagenomics ; Microbial Viability/genetics ; Risk Factors ; }, abstract = {Differences in the presence of even a few genes between otherwise identical bacterial strains may result in critical phenotypic differences. Here we systematically identify microbial genomic structural variants (SVs) and find them to be prevalent in the human gut microbiome across phyla and to replicate in different cohorts. SVs are enriched for CRISPR-associated and antibiotic-producing functions and depleted from housekeeping genes, suggesting that they have a role in microbial adaptation. We find multiple associations between SVs and host disease risk factors, many of which replicate in an independent cohort. Exploring genes that are clustered in the same SV, we uncover several possible mechanistic links between the microbiome and its host, including a region in Anaerostipes hadrus that encodes a composite inositol catabolism-butyrate biosynthesis pathway, the presence of which is associated with lower host metabolic disease risk. Overall, our results uncover a nascent layer of variability in the microbiome that is associated with microbial adaptation and host health.}, }
@article {pmid30918057, year = {2019}, author = {Thomas, M and Wongkuna, S and Ghimire, S and Kumar, R and Antony, L and Doerner, KC and Singery, A and Nelson, E and Woyengo, T and Chankhamhaengdecha, S and Janvilisri, T and Scaria, J}, title = {Gut Microbial Dynamics during Conventionalization of Germfree Chicken.}, journal = {mSphere}, volume = {4}, number = {2}, pages = {}, doi = {10.1128/mSphere.00035-19}, pmid = {30918057}, issn = {2379-5042}, mesh = {Animals ; Bacteria/*classification/isolation &amp; purification ; Bacteroidetes/classification/isolation &amp; purification ; Chickens/growth &amp; development ; DNA, Bacterial/genetics ; Firmicutes/classification/isolation &amp; purification ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; *Germ-Free Life ; *Host Microbial Interactions ; Metagenomics ; Phylogeny ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {A gnotobiotic Gallus gallus (chicken) model was developed to study the dynamics of intestinal microflora from hatching to 18 days of age employing metagenomics. Intestinal samples were collected from a local population of feral chickens and administered orally to germfree 3-day-old chicks. Animals were euthanized on days 9 and 18 postinoculation, and intestinal samples were collected and subjected to metagenomic analysis. On day 18, the five most prevalent phyla were Bacteroidetes (43.03 ± 3.19%), Firmicutes (38.51 ± 2.67%), Actinobacteria (6.77 ± 0.7%), Proteobacteria (6.38 ± 0.7%), and Spirochaetes (2.71 ± 0.55%). Principal-coordinate analysis showed that the day 18 variables clustered more closely than the day 9 variables, suggesting that the microbial communities had changed temporally. The Morista-Horn index values ranged from 0.7 to 1, indicating that the communities in the inoculum and in the day 9 and day 18 samples were more similar than dissimilar. The predicted functional profiles of the microbiomes of the inoculum and the day 9 and day 18 samples were also similar (values of 0.98 to 1). These results indicate that the gnotobiotic chicks stably maintained the phylogenetic diversity and predicted metabolic functionality of the inoculum community.IMPORTANCE The domestic chicken is the cornerstone of animal agriculture worldwide, with a flock population exceeding 40 billion birds/year. It serves as an economically valuable source of protein globally. The microbiome of poultry has important effects on chicken growth, feed conversion, immune status, and pathogen resistance. The aim of our research was to develop a gnotobiotic chicken model appropriate for the study chicken gut microbiota function. Our experimental model shows that young germfree chicks are able to colonize diverse sets of gut bacteria. Therefore, besides the use of this model to study mechanisms of gut microbiota interactions in the chicken gut, it could be also used for applied aspects such as determining the safety and efficacy of new probiotic strains derived from chicken gut microbiota.}, }
@article {pmid30915691, year = {2019}, author = {Akyol, Ç and Ozbayram, EG and Demirel, B and Onay, TT and Ince, O and Ince, B}, title = {Linking nano-ZnO contamination to microbial community profiling in sanitary landfill simulations.}, journal = {Environmental science and pollution research international}, volume = {26}, number = {13}, pages = {13580-13591}, doi = {10.1007/s11356-019-04906-8}, pmid = {30915691}, issn = {1614-7499}, support = {112Y322//TUBITAK/ ; 13081//Boğaziçi University Research Fund Project/ ; }, mesh = {Archaea ; Bacteria ; Biofuels ; Bioreactors/*microbiology ; Microbiota ; RNA, Ribosomal, 16S/*chemistry ; Refuse Disposal/methods ; Solid Waste/*analysis ; Waste Disposal Facilities ; Zinc Oxide/*analysis/chemistry ; }, abstract = {Nanomaterials (NMs) commercially used for various activities mostly end up in landfills. Reduced biogas productions reported in landfill reactors create a need for more comprehensive research on these greatly-diverse microbial pools. In order to evaluate the impact of one of the most widely-used NMs, namely nano-zinc oxide (nano-ZnO), simulated bioreactor and conventional landfills were operated using real municipal solid waste (MSW) for 300 days with addition nano-ZnO. Leachate samples were taken at different phases and analyzed by 16S rRNA gene amplicon sequencing. The bacterial communities were distinctly characterized by Cloacamonaceae (phylum WWE1), Rhodocyclaceae (phylum Proteobacteria), Porphyromonadaceae (phylum Bacteroidetes), and Synergistaceae (phylum Synergistetes). The bacterial community in the bioreactors shifted at the end of the operation and was dominated by Rhodocyclaceae. There was not a major change in the bacterial community in the conventional reactors. The methanogenic archaeal diversity highly differed between the bioreactors and conventional reactors. The dominance of Methanomicrobiaceae was observed in the bioreactors during the peak methane-production period; however, their prominence shifted to WSA2 in the nano-ZnO-added bioreactor and to Methanocorpusculaceae in the control bioreactor towards the end. Methanocorpusculaceae was the most abundant family in both conventional control and nano-ZnO-containing reactors.}, }
@article {pmid30914068, year = {2019}, author = {Wang, W and Hu, H and Zijlstra, RT and Zheng, J and Gänzle, MG}, title = {Metagenomic reconstructions of gut microbial metabolism in weanling pigs.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {48}, doi = {10.1186/s40168-019-0662-1}, pmid = {30914068}, issn = {2049-2618}, mesh = {Animals ; Bacteria/*classification/genetics/isolation &amp; purification ; Bacteroidetes/genetics/isolation &amp; purification/metabolism ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Dietary Carbohydrates/*metabolism ; Firmicutes/genetics/isolation &amp; purification/metabolism ; Gastrointestinal Microbiome ; Lactobacillus/genetics/isolation &amp; purification/metabolism ; Male ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; Swine ; }, abstract = {BACKGROUND: The piglets' transition from milk to solid feed induces a succession of bacterial communities, enhancing the hosts' ability to harvest energy from dietary carbohydrates. To reconstruct microbial carbohydrate metabolism in weanling pigs, this study combined 16S rRNA gene sequencing (n = 191) and shotgun metagenomics (n = 72).<br><br>RESULTS: Time and wheat content in feed explained most of the variation of the microbiota as assessed by 16S rRNA gene sequencing in weanling pigs. De novo metagenomic binning reconstructed 360 high-quality genomes that represented 11 prokaryotic and 1 archaeal phylum. Analysis of carbohydrate metabolism in these genomes revealed that starch fermentation is carried out by a consortium of Firmicutes expressing extracellular α-(1 → 4)-glucan branching enzyme (GH13) and Bacteroidetes expressing periplasmic neopullulanase (GH13) and α-glucosidase (GH97). Fructans were degraded by extracellular GH32 enzymes from Bacteriodetes and Lactobacillus. Lactose fermentation by β-galactosidases (GH2 and GH42) was identified in Firmicutes. In conclusion, the assembly of 360 high-quality genomes as the first metagenomic reference for swine intestinal microbiota allowed identification of key microbial contributors to degradation of starch, fructans, and lactose.<br><br>CONCLUSIONS: Microbial consortia that are responsible for degradation of these glycans differ substantially from the microbial consortia that degrade the same glycans in humans. Our study thus enables improvement of feeding models with higher feed efficiency and better pathogen control for weanling pigs.}, }
@article {pmid30906284, year = {2019}, author = {Cycoń, M and Mrozik, A and Piotrowska-Seget, Z}, title = {Antibiotics in the Soil Environment-Degradation and Their Impact on Microbial Activity and Diversity.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {338}, doi = {10.3389/fmicb.2019.00338}, pmid = {30906284}, issn = {1664-302X}, abstract = {Antibiotics play a key role in the management of infectious diseases in humans, animals, livestock, and aquacultures all over the world. The release of increasing amount of antibiotics into waters and soils creates a potential threat to all microorganisms in these environments. This review addresses issues related to the fate and degradation of antibiotics in soils and the impact of antibiotics on the structural, genetic and functional diversity of microbial communities. Due to the emergence of bacterial resistance to antibiotics, which is considered a worldwide public health problem, the abundance and diversity of antibiotic resistance genes (ARGs) in soils are also discussed. When antibiotic residues enter the soil, the main processes determining their persistence are sorption to organic particles and degradation/transformation. The wide range of DT50 values for antibiotic residues in soils shows that the processes governing persistence depend on a number of different factors, e.g., physico-chemical properties of the residue, characteristics of the soil, and climatic factors (temperature, rainfall, and humidity). The results presented in this review show that antibiotics affect soil microorganisms by changing their enzyme activity and ability to metabolize different carbon sources, as well as by altering the overall microbial biomass and the relative abundance of different groups (i.e., Gram-negative bacteria, Gram-positive bacteria, and fungi) in microbial communities. Studies using methods based on analyses of nucleic acids prove that antibiotics alter the biodiversity of microbial communities and the presence of many types of ARGs in soil are affected by agricultural and human activities. It is worth emphasizing that studies on ARGs in soil have resulted in the discovery of new genes and enzymes responsible for bacterial resistance to antibiotics. However, many ambiguous results indicate that precise estimation of the impact of antibiotics on the activity and diversity of soil microbial communities is a great challenge.}, }
@article {pmid30902785, year = {2019}, author = {Kumar, R and Mishra, A and Jha, B}, title = {Bacterial community structure and functional diversity in subsurface seawater from the western coastal ecosystem of the Arabian Sea, India.}, journal = {Gene}, volume = {701}, number = {}, pages = {55-64}, doi = {10.1016/j.gene.2019.02.099}, pmid = {30902785}, issn = {1879-0038}, mesh = {*Bacteria/classification/genetics/growth &amp; development ; *Biodiversity ; India ; Microbial Consortia/*physiology ; Oceans and Seas ; Seawater/*microbiology ; *Water Microbiology ; }, abstract = {The present study revealed the spatial variability of bacteria in relation to physicochemical variations at four different locations (Diu - DIU, Veraval - VER, Porbandar - POR and Okha - OKH) along the Gujarat coast (Arabian Sea, India). The natural habitat was analyzed for temperature, salinity, pH, total dissolved solids, total organic content, total inorganic content, biological oxygen demand, conductivity and total dissolved oxygen. The lowest salinity and conductivity were observed at the VER site, whereas the highest salinity and conductivity were measured with OKH samples. In contrast, the pH was slightly alkaline at all of the sites. The VER site contained the maximum total dissolved solids (TDS), total carbon (TC), total organic carbon (TOC), and total inorganic carbon (TIC), while OKH showed the maximum dissolve oxygen (DO), biological oxygen demand (BOD), pH, temperature, conductivity, and salinity. The physicochemical characteristics showed that the Gujarat coast is alkaline and has a nutrient heterogeneous nature. Average well color development (AWCD) values, calculated using Biolog EcoPlates, showed that the microbial community from VER contained the highest metabolic activities and could metabolize all 31 substrates, followed by DIU > OKH > POR samples. In contrast, the abundance of the bacterial community, determined by qRT-PCR, was maximum in VER samples, followed by OKH > POR > DIU samples. The Shannon and Simpson indices showed that DIU, POR and OKH seawater clone libraries were more diverse. Furthermore, Chao estimator revealed the high diversity of POR and DIU clone libraries. Interestingly, DIU and OKH did not share any common operational taxonomic units (OTUs), and overall, the maximum bacterial diversity was observed with the POR seawater sample. Moreover, these observations were supported by statistical analysis, such as canonical correspondence analysis (CCA) and principal component analysis (PCA). The molecular phylogeny revealed the dominance of Proteobacteria followed by Firmicutes. Within the Proteobacteria phylum, most of the sequences were affiliated with the Gammaproteobacteria class. In total, about 726 OTUs were observed from all four sites which covers 59.79% DIU, 87.5% VER, 50% POR and 98.83% OKH of samples. This study is the first report to describe physicochemical attributes and the bacterial diversity of the coastal area of Gujarat. The study will provide useful insights about bacterial diversity, distribution, and abundance, as well as their relationships with the habitat.}, }
@article {pmid30901843, year = {2019}, author = {Cortes, L and Wopereis, H and Tartiere, A and Piquenot, J and Gouw, JW and Tims, S and Knol, J and Chelsky, D}, title = {Metaproteomic and 16S rRNA Gene Sequencing Analysis of the Infant Fecal Microbiome.}, journal = {International journal of molecular sciences}, volume = {20}, number = {6}, pages = {}, doi = {10.3390/ijms20061430}, pmid = {30901843}, issn = {1422-0067}, mesh = {Anti-Bacterial Agents/pharmacology ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome/drug effects ; Humans ; Infant ; Informatics/methods ; Male ; Metagenome ; *Metagenomics/methods ; Proteome ; *Proteomics/methods ; *RNA, Ribosomal, 16S ; }, abstract = {A metaproteomic analysis was conducted on the fecal microbiome of eight infants to characterize global protein and pathway expression. Although mass spectrometry-based proteomics is now a routine tool, analysis of the microbiome presents specific technical challenges, including the complexity and dynamic range of member taxa, the need for well-annotated metagenomic databases, and high inter-protein sequence redundancy and similarity. In this study, an approach was developed for assessment of biological phenotype and metabolic status, as a functional complement to DNA sequence analysis. Fecal samples were prepared and analysed by tandem mass spectrometry and a homology-based meta-clustering strategy was used to combine peptides from multiple species into representative proteins. In total, 15,250 unique peptides were sequenced and assigned to 2154 metaclusters, which were then assigned to pathways and functional groups. Differences were noted in several pathways, consistent with the dominant genera observed in different subjects. Although this study was not powered to draw conclusions from the comparisons, the results obtained demonstrate the applicability of this approach and provide the methods needed for performing semi-quantitative comparisons of human fecal microbiome composition, physiology and metabolism, as well as a more detailed assessment of microbial composition in comparison to 16S rRNA gene sequencing.}, }
@article {pmid30901128, year = {2019}, author = {Martins, FMS and Galhardo, M and Filipe, AF and Teixeira, A and Pinheiro, P and Paupério, J and Alves, PC and Beja, P}, title = {Have the cake and eat it: Optimizing nondestructive DNA metabarcoding of macroinvertebrate samples for freshwater biomonitoring.}, journal = {Molecular ecology resources}, volume = {19}, number = {4}, pages = {863-876}, doi = {10.1111/1755-0998.13012}, pmid = {30901128}, issn = {1755-0998}, support = {PTDC/AAGMAA/2261/2014-POCI-1-145-FEDER-356016824//Fundação para a Ciência e a Tecnologia/ ; SFRH/BD/104703/2014//Fundação para a Ciência e a Tecnologia/ ; 668981//Horizon 2020 Framework Programme/ ; //EDP-Biodiversity Chair/ ; }, mesh = {Animals ; DNA/*genetics/isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; Ecological Parameter Monitoring/*methods ; Fresh Water/*chemistry ; Invertebrates/classification/genetics ; Metagenomics/*methods ; }, abstract = {DNA metabarcoding can contribute to improving cost-effectiveness and accuracy of biological assessments of aquatic ecosystems, but significant optimization and standardization efforts are still required to mainstream its application into biomonitoring programmes. In assessments based on freshwater macroinvertebrates, a key challenge is that DNA is often extracted from cleaned, sorted and homogenized bulk samples, which is time-consuming and may be incompatible with sample preservation requirements of regulatory agencies. Here, we optimize and evaluate metabarcoding procedures based on DNA recovered from 96% ethanol used to preserve field samples and thus including potential PCR inhibitors and nontarget organisms. We sampled macroinvertebrates at five sites and subsampled the preservative ethanol at 1 to 14 days thereafter. DNA was extracted using column-based enzymatic (TISSUE) or mechanic (SOIL) protocols, or with a new magnetic-based enzymatic protocol (BEAD), and a 313-bp COI fragment was amplified. Metabarcoding detected at least 200 macroinvertebrate taxa, including most taxa detected through morphology and for which there was a reference barcode. Better results were obtained with BEAD than SOIL or TISSUE, and with subsamples taken 7-14 than 1-7 days after sampling, in terms of DNA concentration and integrity, taxa diversity and matching between metabarcoding and morphology. Most variation in community composition was explained by differences among sites, with small but significant contributions of subsampling day and extraction method, and negligible contributions of extraction and PCR replication. Our methods enhance reliability of preservative ethanol as a potential source of DNA for macroinvertebrate metabarcoding, with a strong potential application in freshwater biomonitoring.}, }
@article {pmid30894435, year = {2019}, author = {Majta, J and Odrzywolek, K and Milanovic, B and Hubar, V and Wrobel, S and Strycharz-Angrecka, E and Wojciechowski, S and Milanowska, K}, title = {Identification of Differentiating Metabolic Pathways between Infant Gut Microbiome Populations Reveals Depletion of Function-Level Adaptation to Human Milk in the Finnish Population.}, journal = {mSphere}, volume = {4}, number = {2}, pages = {}, doi = {10.1128/mSphereDirect.00152-19}, pmid = {30894435}, issn = {2379-5042}, mesh = {*Adaptation, Physiological ; Bacteroides/genetics/*metabolism ; Bifidobacterium/genetics/*metabolism ; Feces/microbiology ; Finland ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Genome, Bacterial ; Humans ; Infant ; *Metabolic Networks and Pathways ; Metagenomics ; Milk, Human/*chemistry ; Oligosaccharides/metabolism ; }, abstract = {A variety of autoimmune and allergy events are becoming increasingly common, especially in Western countries. Some pieces of research link such conditions with the composition of microbiota during infancy. In this period, the predominant form of nutrition for gut microbiota is oligosaccharides from human milk (HMO). A number of gut-colonizing strains, such as Bifidobacterium and Bacteroides, are able to utilize HMO, but only some Bifidobacterium strains have evolved to digest the specific composition of human oligosaccharides. Differences in the proportions of the two genera that are able to utilize HMO have already been associated with the frequency of allergies and autoimmune diseases in the Finnish and the Russian populations. Our results show that differences in terms of the taxonomic annotation do not explain the reason for the differences in the Bifidobacterium/Bacteroides ratio between the Finnish and the Russian populations. In this paper, we present the results of function-level analysis. Unlike the typical workflow for gene abundance analysis, BiomeScout technology explains the differences in the Bifidobacterium/Bacteroides ratio. Our research shows the differences in the abundances of the two enzymes that are crucial for the utilization of short type 1 oligosaccharides.IMPORTANCE Knowing the limitations of taxonomy-based research, there is an emerging need for the development of higher-resolution techniques. The significance of this research is demonstrated by the novel method used for the analysis of function-level metagenomes. BiomeScout-the presented technology-utilizes proprietary algorithms for the detection of differences between functionalities present in metagenomic samples.}, }
@article {pmid30890181, year = {2019}, author = {Zheng, T and Li, J and Ni, Y and Kang, K and Misiakou, MA and Imamovic, L and Chow, BKC and Rode, AA and Bytzer, P and Sommer, M and Panagiotou, G}, title = {Mining, analyzing, and integrating viral signals from metagenomic data.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {42}, doi = {10.1186/s40168-019-0657-y}, pmid = {30890181}, issn = {2049-2618}, mesh = {Algorithms ; Anti-Bacterial Agents/*administration &amp; dosage ; Bacteria/*classification/isolation &amp; purification/virology ; Bacteriophages/*genetics ; CRISPR-Cas Systems ; Data Mining/*methods ; Feces/microbiology ; Gastrointestinal Microbiome ; Healthy Volunteers ; Humans ; Metagenomics/*methods ; Random Allocation ; }, abstract = {BACKGROUND: Viruses are important components of microbial communities modulating community structure and function; however, only a couple of tools are currently available for phage identification and analysis from metagenomic sequencing data. Here we employed the random forest algorithm to develop VirMiner, a web-based phage contig prediction tool especially sensitive for high-abundances phage contigs, trained and validated by paired metagenomic and phagenomic sequencing data from the human gut flora.<br><br>RESULTS: VirMiner achieved 41.06% ± 17.51% sensitivity and 81.91% ± 4.04% specificity in the prediction of phage contigs. In particular, for the high-abundance phage contigs, VirMiner outperformed other tools (VirFinder and VirSorter) with much higher sensitivity (65.23% ± 16.94%) than VirFinder (34.63% ± 17.96%) and VirSorter (18.75% ± 15.23%) at almost the same specificity. Moreover, VirMiner provides the most comprehensive phage analysis pipeline which is comprised of metagenomic raw reads processing, functional annotation, phage contig identification, and phage-host relationship prediction (CRISPR-spacer recognition) and supports two-group comparison when the input (metagenomic sequence data) includes different conditions (e.g., case and control). Application of VirMiner to an independent cohort of human gut metagenomes obtained from individuals treated with antibiotics revealed that 122 KEGG orthology and 118 Pfam groups had significantly differential abundance in the pre-treatment samples compared to samples at the end of antibiotic administration, including clustered regularly interspaced short palindromic repeats (CRISPR), multidrug resistance, and protein transport. The VirMiner webserver is available at http://sbb.hku.hk/VirMiner/ .<br><br>CONCLUSIONS: We developed a comprehensive tool for phage prediction and analysis for metagenomic samples. Compared to VirSorter and VirFinder-the most widely used tools-VirMiner is able to capture more high-abundance phage contigs which could play key roles in infecting bacteria and modulating microbial community dynamics.<br><br>TRIAL REGISTRATION: The European Union Clinical Trials Register, EudraCT Number: 2013-003378-28 . Registered on 9 April 2014.}, }
@article {pmid30887686, year = {2019}, author = {Weyrich, LS and Farrer, AG and Eisenhofer, R and Arriola, LA and Young, J and Selway, CA and Handsley-Davis, M and Adler, CJ and Breen, J and Cooper, A}, title = {Laboratory contamination over time during low-biomass sample analysis.}, journal = {Molecular ecology resources}, volume = {19}, number = {4}, pages = {982-996}, doi = {10.1111/1755-0998.13011}, pmid = {30887686}, issn = {1755-0998}, support = {DECRA 150101574//Australian Research Council/ ; }, mesh = {*DNA Contamination ; *Diagnostic Errors ; Metagenomics/*methods ; Molecular Biology/*methods ; }, abstract = {Bacteria are not only ubiquitous on earth but can also be incredibly diverse within clean laboratories and reagents. The presence of both living and dead bacteria in laboratory environments and reagents is especially problematic when examining samples with low endogenous content (e.g., skin swabs, tissue biopsies, ice, water, degraded forensic samples or ancient material), where contaminants can outnumber endogenous microorganisms within samples. The contribution of contaminants within high-throughput studies remains poorly understood because of the relatively low number of contaminant surveys. Here, we examined 144 negative control samples (extraction blank and no-template amplification controls) collected in both typical molecular laboratories and an ultraclean ancient DNA laboratory over 5 years to characterize long-term contaminant diversity. We additionally compared the contaminant content within a home-made silica-based extraction method, commonly used to analyse low endogenous content samples, with a widely used commercial DNA extraction kit. The contaminant taxonomic profile of the ultraclean ancient DNA laboratory was unique compared to modern molecular biology laboratories, and changed over time according to researcher, month and season. The commercial kit also contained higher microbial diversity and several human-associated taxa in comparison to the home-made silica extraction protocol. We recommend a minimum of two strategies to reduce the impacts of laboratory contaminants within low-biomass metagenomic studies: (a) extraction blank controls should be included and sequenced with every batch of extractions and (b) the contributions of laboratory contamination should be assessed and reported in each high-throughput metagenomic study.}, }
@article {pmid30886779, year = {2019}, author = {Eisenhofer, R and Weyrich, LS}, title = {Assessing alignment-based taxonomic classification of ancient microbial DNA.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6594}, doi = {10.7717/peerj.6594}, pmid = {30886779}, issn = {2167-8359}, abstract = {The field of palaeomicrobiology-the study of ancient microorganisms-is rapidly growing due to recent methodological and technological advancements. It is now possible to obtain vast quantities of DNA data from ancient specimens in a high-throughput manner and use this information to investigate the dynamics and evolution of past microbial communities. However, we still know very little about how the characteristics of ancient DNA influence our ability to accurately assign microbial taxonomies (i.e. identify species) within ancient metagenomic samples. Here, we use both simulated and published metagenomic data sets to investigate how ancient DNA characteristics affect alignment-based taxonomic classification. We find that nucleotide-to-nucleotide, rather than nucleotide-to-protein, alignments are preferable when assigning taxonomies to short DNA fragment lengths routinely identified within ancient specimens (<60 bp). We determine that deamination (a form of ancient DNA damage) and random sequence substitutions corresponding to ∼100,000 years of genomic divergence minimally impact alignment-based classification. We also test four different reference databases and find that database choice can significantly bias the results of alignment-based taxonomic classification in ancient metagenomic studies. Finally, we perform a reanalysis of previously published ancient dental calculus data, increasing the number of microbial DNA sequences assigned taxonomically by an average of 64.2-fold and identifying microbial species previously unidentified in the original study. Overall, this study enhances our understanding of how ancient DNA characteristics influence alignment-based taxonomic classification of ancient microorganisms and provides recommendations for future palaeomicrobiological studies.}, }
@article {pmid30885807, year = {2019}, author = {Murray, AK and Zhang, L and Snape, J and Gaze, WH}, title = {Comparing the selective and co-selective effects of different antimicrobials in bacterial communities.}, journal = {International journal of antimicrobial agents}, volume = {53}, number = {6}, pages = {767-773}, doi = {10.1016/j.ijantimicag.2019.03.001}, pmid = {30885807}, issn = {1872-7913}, mesh = {Anti-Infective Agents/*pharmacology ; Bacteria/classification/*drug effects/genetics ; Benzalkonium Compounds/pharmacology ; Biota/*drug effects ; Ciprofloxacin/pharmacology ; *Drug Resistance, Bacterial ; Evolution, Molecular ; Genes, Bacterial ; Metagenomics ; *Selection, Genetic ; Trimethoprim/pharmacology ; Waste Water/*microbiology ; }, abstract = {Bacterial communities are exposed to a cocktail of antimicrobial agents, including antibiotics, heavy metals and biocidal antimicrobials such as quaternary ammonium compounds (QACs). The extent to which these compounds may select or co-select for antimicrobial resistance (AMR) is not fully understood. In this study, human-associated, wastewater-derived bacterial communities were exposed to either benzalkonium chloride (BAC), ciprofloxacin or trimethoprim at sub-point-of-use concentrations for one week to determine selective and co-selective potential. Metagenome analyses were performed to determine effects on bacterial community structure and prevalence of antibiotic resistance genes (ARGs) and metal or biocide resistance genes (MBRGS). Ciprofloxacin had the greatest co-selective potential, significantly enriching for resistance mechanisms to multiple antibiotic classes. Conversely, BAC exposure significantly reduced relative abundance of ARGs and MBRGS, including the well characterised qac efflux genes. However, BAC exposure significantly impacted bacterial community structure. Therefore BAC, and potentially other QACs, did not play as significant a role in co-selection for AMR as antibiotics such as ciprofloxacin at sub-point-of-use concentrations in this study. This approach can be used to identify priority compounds for further study, to better understand evolution of AMR in bacterial communities exposed to sub-point-of-use concentrations of antimicrobials.}, }
@article {pmid30885780, year = {2019}, author = {Zuo, X and Deguchi, Y and Xu, W and Liu, Y and Li, HS and Wei, D and Tian, R and Chen, W and Xu, M and Yang, Y and Gao, S and Jaoude, JC and Liu, F and Chrieki, SP and Moussalli, MJ and Gagea, M and Sebastian, MM and Zheng, X and Tan, D and Broaddus, R and Wang, J and Ajami, NJ and Swennes, AG and Watowich, SS and Shureiqi, I}, title = {PPARD and Interferon Gamma Promote Transformation of Gastric Progenitor Cells and Tumorigenesis in Mice.}, journal = {Gastroenterology}, volume = {157}, number = {1}, pages = {163-178}, doi = {10.1053/j.gastro.2019.03.018}, pmid = {30885780}, issn = {1528-0012}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; R01 CA206539/CA/NCI NIH HHS/United States ; R01 CA195686/CA/NCI NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; R01 CA142969/CA/NCI NIH HHS/United States ; }, mesh = {Adenocarcinoma/genetics/immunology ; Animals ; Carcinogenesis/*genetics/immunology ; Cell Lineage ; Cell Transformation, Neoplastic/*genetics/immunology ; Chemokine CCL20/metabolism ; Chemokine CXCL1/metabolism ; Chemokines ; Cytokines/*immunology ; Feedback, Physiological ; Gastric Mucosa/*metabolism ; Gene Expression Profiling ; Inflammation ; Interferon-gamma/*immunology ; Mice ; Microbiota/immunology ; Microfilament Proteins/genetics ; Receptors, Cytoplasmic and Nuclear/*genetics ; Stem Cells/immunology/*metabolism ; Stomach/*immunology/microbiology ; Stomach Neoplasms/genetics/immunology ; }, abstract = {BACKGROUND &amp; AIMS: The peroxisome proliferator-activated receptor delta (PPARD) regulates cell metabolism, proliferation, and inflammation and has been associated with gastric and other cancers. Villin-positive epithelial cells are a small population of quiescent gastric progenitor cells. We expressed PPARD from a villin promoter to investigate the role of these cells and PPARD in development of gastric cancer.<br><br>METHODS: We analyzed gastric tissues from mice that express the Ppard (PPARD1 and PPARD2 mice) from a villin promoter, and mice that did not carry this transgene (controls), by histology and immunohistochemistry. We performed cell lineage-tracing experiments and analyzed the microbiomes, chemokine and cytokine production, and immune cells and transcriptomes of stomachs of these mice. We also performed immunohistochemical analysis of PPARD levels in 2 sets of human gastric tissue microarrays.<br><br>RESULTS: Thirty-eight percent of PPARD mice developed spontaneous, invasive gastric adenocarcinomas, with severe chronic inflammation. Levels of PPARD were increased in human gastric cancer tissues, compared with nontumor tissues, and associated with gastric cancer stage and grade. We found an inverse correlation between level of PPARD in tumor tissue and patient survival time. Gastric microbiomes from PPARD and control mice did not differ significantly. Lineage-tracing experiments identified villin-expressing gastric progenitor cells (VGPCs) as the origin of gastric tumors in PPARD mice. In these mice, PPARD up-regulated CCL20 and CXCL1, which increased infiltration of the gastric mucosa by immune cells. Immune cell production of inflammatory cytokines promoted chronic gastric inflammation and expansion and transformation of VGPCs, leading to tumorigenesis. We identified a positive-feedback loop between PPARD and interferon gamma signaling that sustained gastric inflammation to induce VGPC transformation and gastric carcinogenesis.<br><br>CONCLUSIONS: We found PPARD overexpression in VPGCs to result in inflammation, dysplasia, and tumor formation. PPARD and VGPCs might be therapeutic targets for stomach cancer.}, }
@article {pmid30885266, year = {2019}, author = {Westreich, ST and Ardeshir, A and Alkan, Z and Kable, ME and Korf, I and Lemay, DG}, title = {Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {41}, doi = {10.1186/s40168-019-0664-z}, pmid = {30885266}, issn = {2049-2618}, support = {P51 OD011107/OD/NIH HHS/United States ; S10 OD010786/OD/NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics ; Diarrhea/*genetics/metabolism/microbiology/parasitology ; Feces/microbiology ; Fucose/*metabolism ; Gastrointestinal Microbiome ; Gene Expression Profiling/*veterinary ; Gene Expression Regulation ; Macaca mulatta ; Metagenomics/*methods ; Mucins/*metabolism ; Proteolysis ; Sequence Analysis, RNA/veterinary ; Trichomonas/classification/genetics ; }, abstract = {BACKGROUND: Idiopathic chronic diarrhea (ICD) is a common cause of morbidity and mortality among juvenile rhesus macaques. Characterized by chronic inflammation of the colon and repeated bouts of diarrhea, ICD is largely unresponsive to medical interventions, including corticosteroid, antiparasitic, and antibiotic treatments. Although ICD is accompanied by large disruptions in the composition of the commensal gut microbiome, no single pathogen has been concretely identified as responsible for the onset and continuation of the disease.<br><br>RESULTS: Fecal samples were collected from 12 ICD-diagnosed macaques and 12 age- and sex-matched controls. RNA was extracted for metatranscriptomic analysis of organisms and functional annotations associated with the gut microbiome. Bacterial, fungal, archaeal, protozoan, and macaque (host) transcripts were simultaneously assessed. ICD-afflicted animals were characterized by increased expression of host-derived genes involved in inflammation and increased transcripts from bacterial pathogens such as Campylobacter and Helicobacter and the protozoan Trichomonas. Transcripts associated with known mucin-degrading organisms and mucin-degrading enzymes were elevated in the fecal microbiomes of ICD-afflicted animals. Assessment of colon sections using immunohistochemistry and of the host transcriptome suggests differential fucosylation of mucins between control and ICD-afflicted animals. Interrogation of the metatranscriptome for fucose utilization genes reveals possible mechanisms by which opportunists persist in ICD. Bacteroides sp. potentially cross-fed fucose to Haemophilus whereas Campylobacter expressed a mucosa-associated transcriptome with increased expression of adherence genes.<br><br>CONCLUSIONS: The simultaneous profiling of bacterial, fungal, archaeal, protozoan, and macaque transcripts from stool samples reveals that ICD of rhesus macaques is associated with increased gene expression by pathogens, increased mucin degradation, and altered fucose utilization. The data suggest that the ICD-afflicted host produces fucosylated mucins that are leveraged by potentially pathogenic microbes as a carbon source or as adhesion sites.}, }
@article {pmid30878035, year = {2019}, author = {Rowe, WP and Carrieri, AP and Alcon-Giner, C and Caim, S and Shaw, A and Sim, K and Kroll, JS and Hall, LJ and Pyzer-Knapp, EO and Winn, MD}, title = {Streaming histogram sketching for rapid microbiome analytics.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {40}, doi = {10.1186/s40168-019-0653-2}, pmid = {30878035}, issn = {2049-2618}, support = {BB/M011216/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; //Wellcome Trust/United Kingdom ; 100/974/C/13/Z//Wellcome Trust/United Kingdom ; BB/R012490/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004529/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Anti-Bacterial Agents/therapeutic use ; Bacteria/*classification ; Bacterial Infections/drug therapy ; Cohort Studies ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; Infant, Premature ; Machine Learning ; Metagenomics/*methods ; Sequence Analysis, DNA ; Software ; }, abstract = {BACKGROUND: The growth in publically available microbiome data in recent years has yielded an invaluable resource for genomic research, allowing for the design of new studies, augmentation of novel datasets and reanalysis of published works. This vast amount of microbiome data, as well as the widespread proliferation of microbiome research and the looming era of clinical metagenomics, means there is an urgent need to develop analytics that can process huge amounts of data in a short amount of time. To address this need, we propose a new method for tyrhe compact representation of microbiome sequencing data using similarity-preserving sketches of streaming k-mer spectra. These sketches allow for dissimilarity estimation, rapid microbiome catalogue searching and classification of microbiome samples in near real time.<br><br>RESULTS: We apply streaming histogram sketching to microbiome samples as a form of dimensionality reduction, creating a compressed 'histosketch' that can efficiently represent microbiome k-mer spectra. Using public microbiome datasets, we show that histosketches can be clustered by sample type using the pairwise Jaccard similarity estimation, consequently allowing for rapid microbiome similarity searches via a locality sensitive hashing indexing scheme. Furthermore, we use a 'real life' example to show that histosketches can train machine learning classifiers to accurately label microbiome samples. Specifically, using a collection of 108 novel microbiome samples from a cohort of premature neonates, we trained and tested a random forest classifier that could accurately predict whether the neonate had received antibiotic treatment (97% accuracy, 96% precision) and could subsequently be used to classify microbiome data streams in less than 3 s.<br><br>CONCLUSIONS: Our method offers a new approach to rapidly process microbiome data streams, allowing samples to be rapidly clustered, indexed and classified. We also provide our implementation, Histosketching Using Little K-mers (HULK), which can histosketch a typical 2 GB microbiome in 50 s on a standard laptop using four cores, with the sketch occupying 3000 bytes of disk space. (https://github.com/will-rowe/hulk).}, }
@article {pmid30876405, year = {2019}, author = {Doyle, SR and Illingworth, CJR and Laing, R and Bartley, DJ and Redman, E and Martinelli, A and Holroyd, N and Morrison, AA and Rezansoff, A and Tracey, A and Devaney, E and Berriman, M and Sargison, N and Cotton, JA and Gilleard, JS}, title = {Population genomic and evolutionary modelling analyses reveal a single major QTL for ivermectin drug resistance in the pathogenic nematode, Haemonchus contortus.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {218}, doi = {10.1186/s12864-019-5592-6}, pmid = {30876405}, issn = {1471-2164}, support = {BB/M003949//Biotechnology and Biological Sciences Research Council/United Kingdom ; 098051 &amp; 206194//Wellcome Trust (GB)/ ; .//Rural and Environment Science and Analytical Services Division (GB)/ ; 101239/Z/13/Z//Wellcome and the Royal Society Sir Henry Dale Fellowship/ ; //Wellcome Trust/United Kingdom ; }, mesh = {Animals ; DNA, Helminth ; *Drug Resistance ; *Evolution, Molecular ; Genetic Variation ; Haemonchus/*drug effects/*genetics ; Insecticides/pharmacology ; Ivermectin/*pharmacology ; *Metagenomics ; *Quantitative Trait Loci ; }, abstract = {BACKGROUND: Infections with helminths cause an enormous disease burden in billions of animals and plants worldwide. Large scale use of anthelmintics has driven the evolution of resistance in a number of species that infect livestock and companion animals, and there are growing concerns regarding the reduced efficacy in some human-infective helminths. Understanding the mechanisms by which resistance evolves is the focus of increasing interest; robust genetic analysis of helminths is challenging, and although many candidate genes have been proposed, the genetic basis of resistance remains poorly resolved.<br><br>RESULTS: Here, we present a genome-wide analysis of two genetic crosses between ivermectin resistant and sensitive isolates of the parasitic nematode Haemonchus contortus, an economically important gastrointestinal parasite of small ruminants and a model for anthelmintic research. Whole genome sequencing of parental populations, and key stages throughout the crosses, identified extensive genomic diversity that differentiates populations, but after backcrossing and selection, a single genomic quantitative trait locus (QTL) localised on chromosome V was revealed to be associated with ivermectin resistance. This QTL was common between the two geographically and genetically divergent resistant populations and did not include any leading candidate genes, suggestive of a previously uncharacterised mechanism and/or driver of resistance. Despite limited resolution due to low recombination in this region, population genetic analyses and novel evolutionary models supported strong selection at this QTL, driven by at least partial dominance of the resistant allele, and that large resistance-associated haplotype blocks were enriched in response to selection.<br><br>CONCLUSIONS: We have described the genetic architecture and mode of ivermectin selection, revealing a major genomic locus associated with ivermectin resistance, the most conclusive evidence to date in any parasitic nematode. This study highlights a novel genome-wide approach to the analysis of a genetic cross in non-model organisms with extreme genetic diversity, and the importance of a high-quality reference genome in interpreting the signals of selection so identified.}, }
@article {pmid30871469, year = {2019}, author = {Perz, AI and Giles, CB and Brown, CA and Porter, H and Roopnarinesingh, X and Wren, JD}, title = {MNEMONIC: MetageNomic Experiment Mining to create an OTU Network of Inhabitant Correlations.}, journal = {BMC bioinformatics}, volume = {20}, number = {Suppl 2}, pages = {96}, doi = {10.1186/s12859-019-2623-x}, pmid = {30871469}, issn = {1471-2105}, support = {P20 GM103636/GM/NIGMS NIH HHS/United States ; P30 AG050911/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; Metagenomics/*methods ; Microbiota/*genetics ; }, abstract = {BACKGROUND: The number of publicly available metagenomic experiments in various environments has been rapidly growing, empowering the potential to identify similar shifts in species abundance between different experiments. This could be a potentially powerful way to interpret new experiments, by identifying common themes and causes behind changes in species abundance.<br><br>RESULTS: We propose a novel framework for comparing microbial shifts between conditions. Using data from one of the largest human metagenome projects to date, the American Gut Project (AGP), we obtain differential abundance vectors for microbes using experimental condition information provided with the AGP metadata, such as patient age, dietary habits, or health status. We show it can be used to identify similar and opposing shifts in microbial species, and infer putative interactions between microbes. Our results show that groups of shifts with similar effects on microbiome can be identified and that similar dietary interventions display similar microbial abundance shifts.<br><br>CONCLUSIONS: Without comparison to prior data, it is difficult for experimentalists to know if their observed changes in species abundance have been observed by others, both in their conditions and in others they would never consider comparable. Yet, this can be a very important contextual factor in interpreting the significance of a shift. We've proposed and tested an algorithmic solution to this problem, which also allows for comparing the metagenomic signature shifts between conditions in the existing body of data.}, }
@article {pmid30871459, year = {2019}, author = {Thrash, A and Arick, M and Barbato, RA and Jones, RM and Douglas, TA and Esdale, J and Perkins, EJ and Garcia-Reyero, N}, title = {Keanu: a novel visualization tool to explore biodiversity in metagenomes.}, journal = {BMC bioinformatics}, volume = {20}, number = {Suppl 2}, pages = {103}, doi = {10.1186/s12859-019-2629-4}, pmid = {30871459}, issn = {1471-2105}, mesh = {Biodiversity ; Metagenomics/*methods ; }, abstract = {BACKGROUND: One of the main challenges when analyzing complex metagenomics data is the fact that large amounts of information need to be presented in a comprehensive and easy-to-navigate way. In the process of analyzing FASTQ sequencing data, visualizing which organisms are present in the data can be useful, especially with metagenomics data or data suspected to be contaminated. Here, we describe the development and application of a command-line tool, Keanu, for visualizing and exploring sample content in metagenomics data. We developed Keanu as an interactive tool to make viewing complex data easier.<br><br>RESULTS: Keanu, a tool for exploring sequence content, helps a user to understand the presence and abundance of organisms in a sample by analyzing alignments against a database that contains taxonomy data and displaying them in an interactive web page. The content of a sample can be presented either as a collapsible tree, with node size indicating abundance, or as a bilevel partition graph, with arc size indicating abundance. Here, we illustrate how Keanu works by exploring shotgun metagenomics data from a sample collected from a bluff that contained paleosols and a krotovina in an alpine site in Ft. Greely, Alaska.<br><br>CONCLUSIONS: Keanu provides a simple means by which researchers can explore and visualize species present in sequence data generated from complex communities and environments. Keanu is written in Python and is freely available at https://github.com/IGBB/keanu .}, }
@article {pmid30871224, year = {2019}, author = {Gurwara, S and Ajami, NJ and Jang, A and Hessel, FC and Chen, L and Plew, S and Wang, Z and Graham, DY and Hair, C and White, DL and Kramer, J and Kourkoumpetis, T and Hoffman, K and Cole, R and Hou, J and Husain, N and Jarbrink-Sehgal, M and Hernaez, R and Kanwal, F and Ketwaroo, G and Shah, R and Velez, M and Natarajan, Y and El-Serag, HB and Petrosino, JF and Jiao, L}, title = {Dietary Nutrients Involved in One-Carbon Metabolism and Colonic Mucosa-Associated Gut Microbiome in Individuals with an Endoscopically Normal Colon.}, journal = {Nutrients}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/nu11030613}, pmid = {30871224}, issn = {2072-6643}, support = {I01 CX001430/CX/CSRD VA/United States ; RP#140767//Cancer Prevention and Research Institute of Texas/ ; 1000//Gillson Longenbaugh Foundation/ ; 0000//Golfers Against Cancer/ ; }, mesh = {Aged ; Bacteria/*metabolism ; Colon/*microbiology ; Cross-Sectional Studies ; *Diet ; Food Analysis ; Gastrointestinal Microbiome/*drug effects/physiology ; Humans ; Intestinal Mucosa/*microbiology ; Male ; Middle Aged ; Prospective Studies ; }, abstract = {One carbon (1C) metabolism nutrients influence epigenetic regulation and they are supplied by diet and synthesized by gut microbiota. We examined the association between dietary consumption of methyl donors (methionine, betaine and choline) and B vitamins (folate, B2, B6, and B12) and the community composition and structure of the colonic mucosa-associated gut microbiota determined by 16S rRNA gene sequencing in 97 colonic biopsies of 35 men. We used the food frequency questionnaire to assess daily consumption of nutrients, and the UPARSE and SILVA databases for operational taxonomic unit classification. The difference in bacterial diversity and taxonomic relative abundance were compared between low versus high consumption of these nutrients. False discover rate (FDR) adjusted p value < 0.05 indicated statistical significance. The bacterial richness and composition differed significantly by the consumption of folate and B vitamins (p < 0.001). Compared with higher consumption, a lower consumption of these nutrients was associated with a lower abundance of Akkermansia (folate), Roseburia (vitamin B2), and Faecalibacterium (vitamins B2, B6, and B12) but a higher abundance of Erysipelatoclostridium (vitamin B2) (FDR p values < 0.05). The community composition and structure of the colonic bacteria differed significantly by dietary consumption of folate and B vitamins.}, }
@article {pmid30868805, year = {2019}, author = {Liu, ZX and Xu, J and Sun, W and Shi, YH and Chen, SL}, title = {[Application of DNA metabarcoding in species identification of Chinese herbal medicines].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {44}, number = {1}, pages = {1-8}, doi = {10.19540/j.cnki.cjcmm.2019.0001}, pmid = {30868805}, issn = {1001-5302}, mesh = {Biodiversity ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Drugs, Chinese Herbal/*analysis ; High-Throughput Nucleotide Sequencing ; Plants, Medicinal/*classification ; }, abstract = {DNA metabarcoding,one rapid and robust method using specific standard DNA fragments,has been widely used for rapid species identification of a bulk sample through high-throughput sequencing technologies.While it has been widely used in the studies of metagenomics,animal and plant biodiversity,it has gradually come to be used as a profitable method in species identification of mixed Chinese herbal medicines.In this paper,we mainly summarize the current studies of the application of DNA metabarcoding in species identification of mixed Chinese herbal medicines.Moreover,high-throughput sequencing technologies adopted in those studies,such as Sanger,the next-generation,and third-generation sequencing technologies,are discussed.It is conducted to provide a theoretical guidance for the application of DNA metabarcoding in species identification of mixed Chinese herbal medicines and in more other biodiversity studies.}, }
@article {pmid30866822, year = {2019}, author = {Lee, Y and Schmidt, H and Collier, TC and Conner, WR and Hanemaaijer, MJ and Slatkin, M and Marshall, JM and Chiu, JC and Smartt, CT and Lanzaro, GC and Mulligan, FS and Cornel, AJ}, title = {Genome-wide divergence among invasive populations of Aedes aegypti in California.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {204}, doi = {10.1186/s12864-019-5586-4}, pmid = {30866822}, issn = {1471-2164}, support = {U01CK000516//ACL HHS/United States ; HR0011-17-2-0047//Defense Sciences Office, DARPA/ ; 1U01CK000516//Centers for Disease Control and Prevention/ ; }, mesh = {Aedes/*classification/genetics ; Animals ; California ; Evolution, Molecular ; Genetic Variation ; Genetics, Population ; Genome Size ; *Genome, Insect ; Introduced Species ; Metagenomics ; Mosquito Vectors/classification/genetics ; Phylogeny ; Phylogeography ; Whole Genome Sequencing/*veterinary ; }, abstract = {BACKGROUND: In the summer of 2013, Aedes aegypti Linnaeus was first detected in three cities in central California (Clovis, Madera and Menlo Park). It has now been detected in multiple locations in central and southern CA as far south as San Diego and Imperial Counties. A number of published reports suggest that CA populations have been established from multiple independent introductions.<br><br>RESULTS: Here we report the first population genomics analyses of Ae. aegypti based on individual, field collected whole genome sequences. We analyzed 46 Ae. aegypti genomes to establish genetic relationships among populations from sites in California, Florida and South Africa. Based on 4.65 million high quality biallelic SNPs, we identified 3 major genetic clusters within California; one that includes all sample sites in the southern part of the state (South of Tehachapi mountain range) plus the town of Exeter in central California and two additional clusters in central California.<br><br>CONCLUSIONS: A lack of concordance between mitochondrial and nuclear genealogies suggests that the three founding populations were polymorphic for two main mitochondrial haplotypes prior to being introduced to California. One of these has been lost in the Clovis populations, possibly by a founder effect. Genome-wide comparisons indicate extensive differentiation between genetic clusters. Our observations support recent introductions of Ae. aegypti into California from multiple, genetically diverged source populations. Our data reveal signs of hybridization among diverged populations within CA. Genetic markers identified in this study will be of great value in pursuing classical population genetic studies which require larger sample sizes.}, }
@article {pmid30866812, year = {2019}, author = {Das, P and Babaei, P and Nielsen, J}, title = {Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {208}, doi = {10.1186/s12864-019-5591-7}, pmid = {30866812}, issn = {1471-2164}, support = {HEALTH-F4-2012-305312//METACARDIS/ ; }, mesh = {Bacteria/*classification/genetics/isolation &amp; purification/metabolism ; Bacterial Proteins/*genetics ; China ; Feces/microbiology ; Gastrointestinal Microbiome ; Gene Expression Profiling ; Humans ; Metagenomics/*methods ; Phylogeny ; Phylogeography ; United States ; Vitamins/*metabolism ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: Human gut microbial communities have been known to produce vitamins, which are subsequently absorbed by the host in the large intestine. However, the relationship between species with vitamin pathway associated functional features or their gene abundance in different states of health and disease is lacking. Here, we analyzed shotgun fecal metagenomes of individuals from four different countries for genes that are involved in vitamin biosynthetic pathways and transport mechanisms and corresponding species' abundance.<br><br>RESULTS: We found that the prevalence of these genes were found to be distributed across the dominant phyla of gut species. The number of positive correlations were high between species harboring genes related to vitamin biosynthetic pathways and transporter mechanisms than that with either alone. Although, the range of total gene abundances remained constant across healthy populations at the global level, species composition and their presence for metabolic pathway related genes determine the abundance and functional genetic content of vitamin metabolism. Based on metatranscriptomics data, the equation between abundance of vitamin-biosynthetic enzymes and vitamin-dependent enzymes suggests that the production and utilization potential of these enzymes seems way more complex usage allocations than just mere direct linear associations.<br><br>CONCLUSIONS: Our findings provide a rationale to examine and disentangle the interrelationship between B-vitamin dosage (dietary or microbe-mediated) on gut microbial members and the host, in the gut microbiota of individuals with under- or overnutrition.}, }
@article {pmid30866521, year = {2019}, author = {François, S and Mutuel, D and Duncan, AB and Rodrigues, LR and Danzelle, C and Lefevre, S and Santos, I and Frayssinet, M and Fernandez, E and Filloux, D and Roumagnac, P and Froissart, R and Ogliastro, M}, title = {A New Prevalent Densovirus Discovered in Acari. Insight from Metagenomics in Viral Communities Associated with Two-Spotted Mite (Tetranychus urticae) Populations.}, journal = {Viruses}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/v11030233}, pmid = {30866521}, issn = {1999-4915}, mesh = {Animals ; Capsid Proteins/genetics ; Densovirus/*genetics/*isolation &amp; purification ; Female ; *Genetic Variation ; Genome, Viral ; Metagenomics ; *Microbiota ; Phylogeny ; Plants/virology ; Prevalence ; Tetranychidae/*virology ; Viral Nonstructural Proteins/genetics ; }, abstract = {Viral metagenomics and high throughput sequence mining have revealed unexpected diversity, and the potential presence, of parvoviruses in animals from all phyla. Among arthropods, this diversity highlights the poor knowledge that we have regarding the evolutionary history of densoviruses. The aim of this study was to explore densovirus diversity in a small arthropod pest belonging to Acari, the two-spotted spider mite Tetranychus urticae, while using viral metagenomics based on virus-enrichment. Here, we present the viromes obtained from T. urticae laboratory populations made of contigs that are attributed to nine new potential viral species, including the complete sequence of a novel densovirus. The genome of this densovirus has an ambisens genomic organization and an unusually compact size with particularly small non-structural proteins and a predicted major capsid protein that lacks the typical PLA2 motif that is common to all ambidensoviruses described so far. In addition, we showed that this new densovirus had a wide prevalence across populations of mite species tested and a genomic diversity that likely correlates with the host phylogeny. In particular, we observed a low densovirus genomic diversity between the laboratory and natural populations, which suggests that virus within-species evolution is probably slower than initially thought. Lastly, we showed that this novel densovirus can be inoculated to the host plant following feeding by infected mites, and circulate through the plant vascular system. These findings offer new insights into densovirus prevalence, evolution, and ecology.}, }
@article {pmid30864326, year = {2019}, author = {Han, W and Ye, Y}, title = {A repository of microbial marker genes related to human health and diseases for host phenotype prediction using microbiome data.}, journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing}, volume = {24}, number = {}, pages = {236-247}, pmid = {30864326}, issn = {2335-6936}, support = {R01 AI108888/AI/NIAID NIH HHS/United States ; R01 AI143254/AI/NIAID NIH HHS/United States ; }, mesh = {Carcinoma, Non-Small-Cell Lung/genetics/microbiology/therapy ; Carcinoma, Renal Cell/genetics/microbiology/therapy ; Computational Biology/methods ; Databases, Genetic ; Diabetes Mellitus, Type 2/genetics/microbiology ; *Genes, Microbial ; Genetic Markers ; Host Microbial Interactions/*genetics ; Humans ; Immunotherapy ; Kidney Neoplasms/genetics/microbiology/therapy ; Liver Cirrhosis/genetics/microbiology ; Lung Neoplasms/genetics/microbiology/therapy ; Machine Learning ; Metagenomics/methods/statistics &amp; numerical data ; Microbiota/*genetics ; Phenotype ; Translational Medical Research ; }, abstract = {The microbiome research is going through an evolutionary transition from focusing on the characterization of reference microbiomes associated with different environments/hosts to the translational applications, including using microbiome for disease diagnosis, improving the effcacy of cancer treatments, and prevention of diseases (e.g., using probiotics). Microbial markers have been identified from microbiome data derived from cohorts of patients with different diseases, treatment responsiveness, etc, and often predictors based on these markers were built for predicting host phenotype given a microbiome dataset (e.g., to predict if a person has type 2 diabetes given his or her microbiome data). Unfortunately, these microbial markers and predictors are often not published so are not reusable by others. In this paper, we report the curation of a repository of microbial marker genes and predictors built from these markers for microbiome-based prediction of host phenotype, and a computational pipeline called Mi2P (from Microbiome to Phenotype) for using the repository. As an initial effort, we focus on microbial marker genes related to two diseases, type 2 diabetes and liver cirrhosis, and immunotherapy efficacy for two types of cancer, non-small-cell lung cancer (NSCLC) and renal cell carcinoma (RCC). We characterized the marker genes from metagenomic data using our recently developed subtractive assembly approach. We showed that predictors built from these microbial marker genes can provide fast and reasonably accurate prediction of host phenotype given microbiome data. As understanding and making use of microbiome data (our second genome) is becoming vital as we move forward in this age of precision health and precision medicine, we believe that such a repository will be useful for enabling translational applications of microbiome data.}, }
@article {pmid30858573, year = {2019}, author = {Kessler, AJ and Chen, YJ and Waite, DW and Hutchinson, T and Koh, S and Popa, ME and Beardall, J and Hugenholtz, P and Cook, PLM and Greening, C}, title = {Bacterial fermentation and respiration processes are uncoupled in anoxic permeable sediments.}, journal = {Nature microbiology}, volume = {4}, number = {6}, pages = {1014-1023}, doi = {10.1038/s41564-019-0391-z}, pmid = {30858573}, issn = {2058-5276}, mesh = {Bacteria/*genetics/*metabolism ; Bacteria, Anaerobic/metabolism ; Carbon Cycle ; *Fermentation ; Gammaproteobacteria/metabolism ; Geologic Sediments/*microbiology ; Hydrogen/metabolism ; Hydrogenase/classification/genetics ; *Hypoxia ; Metagenomics ; Microbiota ; Nitrates/metabolism ; Nitrites/metabolism ; Oceans and Seas ; Oxidation-Reduction ; RNA, Ribosomal, 16S ; Sulfates/metabolism ; }, abstract = {Permeable (sandy) sediments cover half of the continental margin and are major regulators of oceanic carbon cycling. The microbial communities within these highly dynamic sediments frequently shift between oxic and anoxic states, and hence are less stratified than those in cohesive (muddy) sediments. A major question is, therefore, how these communities maintain metabolism during oxic-anoxic transitions. Here, we show that molecular hydrogen (H2) accumulates in silicate sand sediments due to decoupling of bacterial fermentation and respiration processes following anoxia. In situ measurements show that H2 is 250-fold supersaturated in the water column overlying these sediments and has an isotopic composition consistent with fermentative production. Genome-resolved shotgun metagenomic profiling suggests that the sands harbour diverse and specialized microbial communities with a high abundance of [NiFe]-hydrogenase genes. Hydrogenase profiles predict that H2 is primarily produced by facultatively fermentative bacteria, including the dominant gammaproteobacterial family Woeseiaceae, and can be consumed by aerobic respiratory bacteria. Flow-through reactor and slurry experiments consistently demonstrate that H2 is rapidly produced by fermentation following anoxia, immediately consumed by aerobic respiration following reaeration and consumed by sulfate reduction only during prolonged anoxia. Hydrogenotrophic sulfur, nitrate and nitrite reducers were also detected, although contrary to previous hypotheses there was limited capacity for microalgal fermentation. In combination, these experiments confirm that fermentation dominates anoxic carbon mineralization in these permeable sediments and, in contrast to the case in cohesive sediments, is largely uncoupled from anaerobic respiration. Frequent changes in oxygen availability in these sediments may have selected for metabolically flexible bacteria while excluding strict anaerobes.}, }
@article {pmid30853028, year = {2019}, author = {Yason, JA and Liang, YR and Png, CW and Zhang, Y and Tan, KSW}, title = {Interactions between a pathogenic Blastocystis subtype and gut microbiota: in vitro and in vivo studies.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {30}, doi = {10.1186/s40168-019-0644-3}, pmid = {30853028}, issn = {2049-2618}, mesh = {Animals ; Bacterial Proteins/genetics ; Bifidobacterium longum/genetics/growth &amp; development ; Blastocystis/classification/*growth &amp; development/isolation &amp; purification/pathogenicity ; Blastocystis Infections/*microbiology ; Coculture Techniques ; Disease Models, Animal ; Feces/microbiology ; Gastrointestinal Diseases/*microbiology ; *Gastrointestinal Microbiome ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Bacterial ; HT29 Cells ; Humans ; Lactobacillus/genetics/growth &amp; development ; Metagenomics ; Mice ; }, abstract = {BACKGROUND: Blastocystis is a common gut eukaryote detected in humans and animals. It has been associated with gastrointestinal disease in the past although recent metagenomic studies also suggest that it is a member of normal microbiota. This study investigates interactions between pathogenic human isolates belonging to Blastocystis subtype 7 (ST7) and bacterial representatives of the gut microbiota.<br><br>RESULTS: Generally, Blastocystis ST7 exerts a positive effect on the viability of representative gut bacteria except on Bifidobacterium longum. Gene expression analysis and flow cytometry indicate that the bacterium may be undergoing oxidative stress in the presence of Blastocystis. In vitro assays demonstrate that Blastocystis-induced host responses are able to decrease Bifidobacterium counts. Mice infected with Blastocystis also reveal a decrease in beneficial bacteria Bifidobacterium and Lactobacillus.<br><br>CONCLUSIONS: This study shows that particular isolates of Blastocystis ST7 cause changes in microbiota populations and potentially lead to an imbalance of the gut microbiota. This study suggests that certain isolates of Blastocystis exert their pathogenic effects through disruption of the gut microbiota and provides a counterpoint to the increasing reports indicating the commensal nature of this ubiquitous parasite.}, }
@article {pmid30850636, year = {2019}, author = {Hendriksen, RS and Munk, P and Njage, P and van Bunnik, B and McNally, L and Lukjancenko, O and Röder, T and Nieuwenhuijse, D and Pedersen, SK and Kjeldgaard, J and Kaas, RS and Clausen, PTLC and Vogt, JK and Leekitcharoenphon, P and van de Schans, MGM and Zuidema, T and de Roda Husman, AM and Rasmussen, S and Petersen, B and ,  and Amid, C and Cochrane, G and Sicheritz-Ponten, T and Schmitt, H and Alvarez, JRM and Aidara-Kane, A and Pamp, SJ and Lund, O and Hald, T and Woolhouse, M and Koopmans, MP and Vigre, H and Petersen, TN and Aarestrup, FM}, title = {Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1124}, doi = {10.1038/s41467-019-08853-3}, pmid = {30850636}, issn = {2041-1723}, support = {001//World Health Organization/International ; }, mesh = {Africa ; Asia ; Bacteria/classification/*drug effects/genetics/isolation &amp; purification ; Drug Resistance, Multiple, Bacterial/*genetics ; Epidemiological Monitoring ; Europe ; *Genes, Bacterial ; Humans ; *Metagenome ; Metagenomics/methods ; Microbial Consortia/drug effects/genetics ; North America ; Oceania ; Population Health ; Sewage/*microbiology ; Socioeconomic Factors ; South America ; }, abstract = {Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use metagenomic analysis of untreated sewage to characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data and bacterial taxonomy only explains a minor part of the AMR variation that we observe. We find no evidence for cross-selection between antimicrobial classes, or for effect of air travel between sites. However, AMR gene abundance strongly correlates with socio-economic, health and environmental factors, which we use to predict AMR gene abundances in all countries in the world. Our findings suggest that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR. We propose metagenomic analysis of sewage as an ethically acceptable and economically feasible approach for continuous global surveillance and prediction of AMR.}, }
@article {pmid30844070, year = {2019}, author = {Fritz, B and Stavnsbjerg, C and Markvart, M and Damgaard, PB and Nielsen, SH and Bjørndal, L and Qvortrup, K and Bjarnsholt, T}, title = {Shotgun sequencing of clinical biofilm following scanning electron microscopy identifies bacterial community composition.}, journal = {Pathogens and disease}, volume = {77}, number = {1}, pages = {}, doi = {10.1093/femspd/ftz013}, pmid = {30844070}, issn = {2049-632X}, mesh = {Bacteria/*classification/*genetics/ultrastructure ; Biodiversity ; *Biofilms ; Humans ; *Metagenome ; *Metagenomics ; }, abstract = {Bacterial biofilm infections often involve aggregates of bacteria heterogeneously distributed throughout a tissue or on a surface (such as an implanted medical device). Identification of a biofilm infection requires direct visualization via microscopy, followed by characterization of the microbial community by culturing or sequencing-based approaches. A sample, therefore, must be divided prior to analysis, often leading to inconsistent results. We demonstrate a combined approach, using scanning electron microscopy and next-generation shotgun sequencing, to visually identify a biofilm and characterize the microbial community, without dividing the sample. A clinical sample recovered from a patient following a dental root-filling procedure was prepared and visualized by scanning electron microscopy. DNA was then extracted from the sample several years later and analyzed by shotgun sequencing. The method was subsequently validated on in vitro cultures of Pseudomonas aeruginosa biofilm. Between 19 and 21 different genera and species were identified in the clinical sample with an estimated relative abundance greater than 1% by two different estimation approaches. Only eight genera identified were not associated with endodontic infections. This provides a proof-of-concept for a dual, microscopy and sequencing-based approach to identify and characterize bacterial biofilms, which could also easily be implemented in other scientific fields.}, }
@article {pmid30842211, year = {2019}, author = {Zuo, T and Lu, XJ and Zhang, Y and Cheung, CP and Lam, S and Zhang, F and Tang, W and Ching, JYL and Zhao, R and Chan, PKS and Sung, JJY and Yu, J and Chan, FKL and Cao, Q and Sheng, JQ and Ng, SC}, title = {Gut mucosal virome alterations in ulcerative colitis.}, journal = {Gut}, volume = {68}, number = {7}, pages = {1169-1179}, doi = {10.1136/gutjnl-2018-318131}, pmid = {30842211}, issn = {1468-3288}, mesh = {Adult ; Case-Control Studies ; China ; Colitis, Ulcerative/pathology/*virology ; Dysbiosis/pathology/*virology ; Female ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/*virology ; Male ; Rectum/pathology/*virology ; }, abstract = {OBJECTIVE: The pathogenesis of UC relates to gut microbiota dysbiosis. We postulate that alterations in the viral community populating the intestinal mucosa play an important role in UC pathogenesis. This study aims to characterise the mucosal virome and their functions in health and UC.<br><br>DESIGN: Deep metagenomics sequencing of virus-like particle preparations and bacterial 16S rRNA sequencing were performed on the rectal mucosa of 167 subjects from three different geographical regions in China (UC=91; healthy controls=76). Virome and bacteriome alterations in UC mucosa were assessed and correlated with patient metadata. We applied partition around medoids clustering algorithm and classified mucosa viral communities into two clusters, referred to as mucosal virome metacommunities 1 and 2.<br><br>RESULTS: In UC, there was an expansion of mucosa viruses, particularly Caudovirales bacteriophages, and a decrease in mucosa Caudovirales diversity, richness and evenness compared with healthy controls. Altered mucosal virome correlated with intestinal inflammation. Interindividual dissimilarity between mucosal viromes was higher in UC than controls. Escherichia phage and Enterobacteria phage were more abundant in the mucosa of UC than controls. Compared with metacommunity 1, metacommunity 2 was predominated by UC subjects and displa