@article {pmid33463854, year = {2020}, author = {Furey, PC and Lee, SS and Clemans, DL}, title = {Substratum-associated microbiota.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {92}, number = {10}, pages = {1629-1648}, doi = {10.1002/wer.1410}, pmid = {33463854}, issn = {1554-7531}, mesh = {*Cyanobacteria ; Ecology ; Fresh Water ; Metagenomics ; *Microbiota ; }, abstract = {Highlights of new, interesting, and emerging research findings on substratum-associated microbiota covered from a survey of 2019 literature from primarily freshwaters provide insight into research trends of interest to the Water Environment Federation and others interested in benthic, aquatic environments. Coverage of topics on bottom-associated or attached algae and cyanobacteria, though not comprehensive, includes new methods, taxa new-to-science, nutrient dynamics, auto- and heterotrophic interactions, grazers, bioassessment, herbicides and other pollutants, metal contaminants, and nuisance, and bloom-forming and harmful algae. Coverage of bacteria, also not comprehensive, focuses on the ecology of benthic biofilms and microbial communities, along with the ecology of microbes like Caulobacter crescentus, Rhodobacter, and other freshwater microbial species. Bacterial topics covered also include metagenomics and metatranscriptomics, toxins and pollutants, bacterial pathogens and bacteriophages, and bacterial physiology. Readers may use this literature review to learn about or renew their interest in the recent advances and discoveries regarding substratum-associated microbiota. PRACTITIONER POINTS: This review of literature from 2019 on substratum-associated microbiota presents highlights of findings on algae, cyanobacteria, and bacteria from primarily freshwaters. Coverage of algae and cyanobacteria includes findings on new methods, taxa new to science, nutrient dynamics, auto- and heterotrophic interactions, grazers, bioassessment, herbicides and other pollutants, metal contaminants, and nuisance, bloom-forming and harmful algae. Coverage of bacteria includes findings on ecology of benthic biofilms and microbial communities, the ecology of microbes, metagenomics and metatranscriptomics, toxins and pollutants, bacterial pathogens and bacteriophages, and bacterial physiology. Highlights of new, noteworthy and emerging topics build on those from 2018 and will be of relevance to the Water Environment Federation and others interested in benthic, aquatic environments.}, }
@article {pmid33243513, year = {2021}, author = {Calegario, G and Freitas, L and Appolinario, LR and Venas, T and Arruda, T and Otsuki, K and Masi, B and Omachi, C and Moreira, AP and Soares, AC and Rezende, CE and Garcia, G and Tschoeke, D and Thompson, C and Thompson, FL}, title = {Conserved rhodolith microbiomes across environmental gradients of the Great Amazon Reef.}, journal = {The Science of the total environment}, volume = {760}, number = {}, pages = {143411}, doi = {10.1016/j.scitotenv.2020.143411}, pmid = {33243513}, issn = {1879-1026}, mesh = {Coral Reefs ; Metagenome ; *Microbiota ; Photosynthesis ; *Rhodophyta ; Seawater ; }, abstract = {The Great Amazon Reef System (GARS) covers an estimated area of 56,000 km2 off the mouth of the Amazon River. Living rhodolith holobionts are major benthic components of the GARS. However, it is unclear whether environmental conditions modulate the rhodolith microbiomes. Previous studies suggest that environmental parameters such as light, temperature, depth, and nutrients are drivers of rhodolith health. However, it is unclear whether rhodoliths from different sectors (northern, central, and southern) from the GARS have different microbiomes. We analysed metagenomes of rhodoliths (n = 10) and seawater (n = 6), obtained from the three sectors, by illumina shotgun sequencing (total read counts: 25.73 million). Suspended particulate material and isotopic composition of dissolved organic carbon (δ13C) indicated a strong influence of the Amazon river plume over the entire study area. However, photosynthetically active radiation at the bottom (PARb) was higher in the southern sector reefs, ranging from 10.1 to 14.3 E.m-2 day-1. The coralline calcareous red algae (CCA) Corallina caespitosa, Corallina officinalis, Lithophyllum cabiochiae, and Hapalidiales were present in the three sectors and in most rhodolith samples. Rhodolith microbiomes were very homogeneous across the studied area and differed significantly from seawater microbiomes. However, some subtle differences were found when comparing the rhodolith microbiomes from the northern and central sectors to the ones from the southern. Consistent with the higher light availability, two phyla were more abundant in rhodolith microbiomes from southern sites (Bacteroidetes, and Cyanobacteria). In addition, two functional categories were enhanced in southern rhodolith microbiomes (iron acquisition and metabolism, and photosynthesis). Phycobiliprotein-coding genes were also more abundant in southern locations, while the functional categories of respiration and sulfur metabolism were enhanced in northern and central rhodolith microbiomes, consistent with higher nutrient loads. The results confirm the conserved nature of rhodolith microbiomes even under pronounced environmental gradients. Subtle taxonomic and functional differences observed in rhodolith microbiomes may enable rhodoliths to thrive in changing environmental conditions.}, }
@article {pmid33206681, year = {2020}, author = {Gureev, AP and Syromyatnikov, MY and Ignatyeva, DA and Valuyskikh, VV and Solodskikh, SA and Panevina, AV and Gryaznova, MV and Kokina, AV and Popov, VN}, title = {Effect of long-term methylene blue treatment on the composition of mouse gut microbiome and its relationship with the cognitive abilities of mice.}, journal = {PloS one}, volume = {15}, number = {11}, pages = {e0241784}, pmid = {33206681}, issn = {1932-6203}, mesh = {Animals ; Bacteroidetes/genetics/metabolism ; Cognition/drug effects/physiology ; Epsilonproteobacteria/genetics/metabolism ; Gastrointestinal Microbiome/drug effects/genetics ; High-Throughput Nucleotide Sequencing ; Maze Learning ; Methylene Blue/*pharmacology ; Mice ; Mice, Inbred C57BL ; Proteobacteria/genetics/metabolism ; }, abstract = {In recent years, methylene blue (MB) has attracted considerable interest as a potential drug for the treatment of methemoglobinemia and neurodegenerative diseases. MB is active against microorganisms from various taxonomic groups. However, no studies have yet been conducted on the effect of MB on the intestinal microbiome of model animals. The aim of this work was to study the effect of different concentrations of MB on the mouse gut microbiome and its relationship with the cognitive abilities of mice. We showed that a low MB concentration (15 mg/kg/day) did not cause significant changes in the microbiome composition. The Bacteroidetes/Firmicutes ratio decreased relative to the control on the 2nd and 3rd weeks. A slight decrease in the levels Actinobacteria was detected on the 3rd week of the experiment. Changes in the content of Delta, Gamma, and Epsilonproteobacteria have been also observed. We did not find significant alterations in the composition of intestinal microbiome, which could be an indication of the development of dysbiosis or other gut dysfunction. At the same time, a high concentration of MB (50 mg/kg/day) led to pronounced changes, primarily an increase in the levels of Delta, Gamma and Epsilonproteobacteria. Over 4 weeks of therapy, the treatment with high MB concentration has led to an increase in the median content of Proteobacteria to 7.49% vs. 1.61% in the control group. Finally, we found that MB at a concentration of 15 mg/kg/day improved the cognitive abilities of mice, while negative correlation between the content of Deferribacteres and cognitive parameters was revealed. Our data expand the understanding of the relationship between MB, cognitive abilities, and gut microbiome in respect to the antibacterial properties of MB.}, }
@article {pmid32552447, year = {2020}, author = {Hu, Y and Cheng, M and Liu, B and Dong, J and Sun, L and Yang, J and Yang, F and Chen, X and Jin, Q}, title = {Metagenomic analysis of the lung microbiome in pulmonary tuberculosis - a pilot study.}, journal = {Emerging microbes & infections}, volume = {9}, number = {1}, pages = {1444-1452}, pmid = {32552447}, issn = {2222-1751}, mesh = {Bacteria/classification/genetics/isolation & purification ; Bronchoalveolar Lavage Fluid/microbiology ; Humans ; Lung/*microbiology ; Metagenome ; Metagenomics ; *Microbiota ; Mycobacterium tuberculosis/genetics/*physiology ; Pilot Projects ; Tuberculosis, Pulmonary/diagnosis/*microbiology ; }, abstract = {The lung microbiome plays an important role in the pathophysiological processes associated with pulmonary tuberculosis (PTB). However, only a few studies using 16S rDNA amplicon sequencing have been reported, and the interactions between Mycobacterium tuberculosis (MTB) and the lung microbiome remain poorly understood. Patients with respiratory symptoms and imaging abnormalities compatible with tuberculosis (TB) were enrolled. We analyzed the lung microbiome in bronchoalveolar lavage (BAL) samples from 30 MTB-positive (MTB+) subjects and 30 MTB negative (MTB-) subjects by shotgun metagenomic sequencing. Alpha diversity tended to be lower in the MTB+ group than in the MTB- group. There was a significant difference in beta diversity between the MTB+ and MTB- subjects. MTB+ lung samples were dominated by MTB, while MTB- samples were enriched with Streptococcus, Prevotella, Nesseria, Selenomonas and Bifidobacterium, which more closely resemble the microbial composition of a healthy lung. Network analysis suggested that MTB could greatly impact the microbial community structure. MTB+ and MTB- communities showed distinct functional signatures. Fungal communities were also found to be associated with the presence or absence of MTB. Furthermore, it was confirmed that 16S rDNA amplicon sequencing underrepresents Mycobacterium. This pilot study is the first to explore the interplay between MTB and the host microbiome by using metagenomic sequencing. MTB dominates the lung microbiome of MTB+ subjects, while MTB- subjects have a Streptococcus-enriched microbiome. The 16S approach underrepresents Mycobacterium and is not the best way to study the TB-associated microbiome.}, }
@article {pmid32348781, year = {2020}, author = {Bisanz, JE and Soto-Perez, P and Noecker, C and Aksenov, AA and Lam, KN and Kenney, GE and Bess, EN and Haiser, HJ and Kyaw, TS and Yu, FB and Rekdal, VM and Ha, CWY and Devkota, S and Balskus, EP and Dorrestein, PC and Allen-Vercoe, E and Turnbaugh, PJ}, title = {A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria.}, journal = {Cell host & microbe}, volume = {27}, number = {6}, pages = {1001-1013.e9}, pmid = {32348781}, issn = {1934-6069}, support = {R01 AR074500/AR/NIAMS NIH HHS/United States ; R01 HL122593/HL/NHLBI NIH HHS/United States ; R21 CA227232/CA/NCI NIH HHS/United States ; T32 AI060537/AI/NIAID NIH HHS/United States ; }, mesh = {Actinobacteria/classification/drug effects/genetics/isolation & purification ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/classification/drug effects/*genetics/*isolation & purification ; Dissection/*methods ; Gastrointestinal Microbiome/*genetics/physiology ; Gastrointestinal Tract/microbiology ; Genes, Bacterial/genetics ; *Genomics ; Germ-Free Life ; Humans ; Metagenome ; Metagenomics ; Mice ; Microbial Sensitivity Tests ; Multigene Family ; Phenotype ; Polymorphism, Genetic ; }, abstract = {Despite the remarkable microbial diversity found within humans, our ability to link genes to phenotypes is based upon a handful of model microorganisms. We report a comparative genomics platform for Eggerthella lenta and other Coriobacteriia, a neglected taxon broadly relevant to human health and disease. We uncover extensive genetic and metabolic diversity and validate a tool for mapping phenotypes to genes and sequence variants. We also present a tool for the quantification of strains from metagenomic sequencing data, enabling the identification of genes that predict bacterial fitness. Competitive growth is reproducible under laboratory conditions and attributable to intrinsic growth rates and resource utilization. Unique signatures of in vivo competition in gnotobiotic mice include an adhesin enriched in poor colonizers. Together, these computational and experimental resources represent a strong foundation for the continued mechanistic dissection of the Coriobacteriia and a template that can be applied to study other genetically intractable taxa.}, }
@article {pmid32134020, year = {2020}, author = {Agnihotry, S and Sarangi, AN and Aggarwal, R}, title = {Construction &amp; assessment of a unified curated reference database for improving the taxonomic classification of bacteria using 16S rRNA sequence data.}, journal = {The Indian journal of medical research}, volume = {151}, number = {1}, pages = {93-103}, pmid = {32134020}, issn = {0971-5916}, mesh = {Bacteria/classification/*genetics ; *Classification ; Gastrointestinal Microbiome/*genetics ; Humans ; Metagenomics/classification ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {Background &amp; objectives: For bacterial community analysis, 16S rRNA sequences are subjected to taxonomic classification through comparison with one of the three commonly used databases [Greengenes, SILVA and Ribosomal Database Project (RDP)]. It was hypothesized that a unified database containing fully annotated, non-redundant sequences from all the three databases, might provide better taxonomic classification during analysis of 16S rRNA sequence data. Hence, a unified 16S rRNA database was constructed and its performance was assessed by using it with four different taxonomic assignment methods, and for data from various hypervariable regions (HVRs) of 16S rRNA gene.<br><br>Methods: We constructed a unified 16S rRNA database (16S-UDb) by merging non-ambiguous, fully annotated, full-length 16S rRNA sequences from the three databases and compared its performance in taxonomy assignment with that of three original databases. This was done using four different taxonomy assignment methods [mothur Naïve Bayesian Classifier (mothur-nbc), RDP Naïve Bayesian Classifier (rdp-nbc), UCLUST, SortMeRNA] and data from 13 regions of 16S rRNA [seven hypervariable regions (HVR) (V2-V8) and six pairs of adjacent HVRs].<br><br>Results: Our unified 16S rRNA database contained 13,078 full-length, fully annotated 16S rRNA sequences. It could assign genus and species to larger proportions (90.05 and 46.82%, respectively, when used with mothur-nbc classifier and the V2+V3 region) of sequences in the test database than the three original 16S rRNA databases (70.88-87.20% and 10.23-24.28%, respectively, with the same classifier and region).<br><br>Our results indicate that for analysis of bacterial mixtures, sequencing of V2-V3 region of 16S rRNA followed by analysis of the data using the mothur-nbc classifier and our 16S-UDb database may be preferred.}, }
@article {pmid31927795, year = {2020}, author = {Zemb, O and Achard, CS and Hamelin, J and De Almeida, ML and Gabinaud, B and Cauquil, L and Verschuren, LMG and Godon, JJ}, title = {Absolute quantitation of microbes using 16S rRNA gene metabarcoding: A rapid normalization of relative abundances by quantitative PCR targeting a 16S rRNA gene spike-in standard.}, journal = {MicrobiologyOpen}, volume = {9}, number = {3}, pages = {e977}, pmid = {31927795}, issn = {2045-8827}, mesh = {Base Sequence ; Biodiversity ; *DNA Barcoding, Taxonomic/methods ; Environmental Microbiology ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics/methods ; Microbiota/*genetics ; RNA, Ribosomal, 16S/chemistry/*genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {Metabarcoding of the 16S rRNA gene is commonly used to characterize microbial communities, by estimating the relative abundance of microbes. Here, we present a method to retrieve the concentrations of the 16S rRNA gene per gram of any environmental sample using a synthetic standard in minuscule amounts (100 ppm to 1% of the 16S rRNA sequences) that is added to the sample before DNA extraction and quantified by two quantitative polymerase chain reaction (qPCR) reactions. This allows normalizing by the initial microbial density, taking into account the DNA recovery yield. We quantified the internal standard and the total load of 16S rRNA genes by qPCR. The qPCR for the latter uses the exact same primers as those used for Illumina sequencing of the V3-V4 hypervariable regions of the 16S rRNA gene to increase accuracy. We are able to calculate the absolute concentration of the species per gram of sample, taking into account the DNA recovery yield. This is crucial for an accurate estimate as the yield varied between 40% and 84%. This method avoids sacrificing a high proportion of the sequencing effort to quantify the internal standard. If sacrificing a part of the sequencing effort to the internal standard is acceptable, we however recommend that the internal standard accounts for 30% of the environmental 16S rRNA genes to avoid the PCR bias associated with rare phylotypes. The method proposed here was tested on a feces sample but can be applied more broadly on any environmental sample. This method offers a real improvement of metabarcoding of microbial communities since it makes the method quantitative with limited efforts.}, }
@article {pmid31925997, year = {2020}, author = {Niu, KM and Lee, BJ and Kothari, D and Lee, WD and Hur, SW and Lim, SG and Kim, KW and Kim, KD and Kim, NN and Kim, SK}, title = {Dietary effect of low fish meal aquafeed on gut microbiota in olive flounder (Paralichthys olivaceus) at different growth stages.}, journal = {MicrobiologyOpen}, volume = {9}, number = {3}, pages = {e992}, pmid = {31925997}, issn = {2045-8827}, mesh = {*Animal Feed ; Animals ; Biodiversity ; Fishes ; Flounder/*growth &amp; development/*microbiology ; *Gastrointestinal Microbiome ; Metagenomics ; RNA, Ribosomal, 16S ; }, abstract = {This study was conducted to investigate the long-term effect of a low fish meal (FM) diet comprising plant-based protein sources (PPS) on changes of gut microbial diversity in olive flounder (Paralichthys olivaceus) over the course of life. Two experimental diets were prepared to contain 74% FM (control) or 52% FM with 22% PPS (30% FM replacement, FM30). Fish were fed one of the two experimental diets for 8 months, and we collected the midgut contents to analyze the gut bacterial community by Illumina MiSeq based on the metagenomic sequences in the V3-V4 regions of 16S rRNA. We found that there were nine dominant phyla, which in turn presented Proteobacteria, Firmicutes, and Actinobacteria as the three major phyla in the gut microbiota of the flounder. At genus level, the dominant genera were Delftia, Prevotella, and Chthoniobacter at the juvenile stage (below 100 g/fish); Chthoniobacter, Bacillus, and Bradyrhizobium at the grower stage (400 g/fish); Chthoniobacter, Bacillus, and Delftia at the subadult stage (800 g/fish); and Lactobacillus and Prevotella at the adult stage (over 1,000 g/fish). The microbial diversity in olive flounders arched from the juvenile and subadult stage and reached a plateau thereafter. The fish fed the FM30 diet significantly had an increased abundance of Lactobacillus and Photobacterium and had less abundance of Prevotella and Paraprevotella than the control. However, the effect of dietary PPS was not significant on total microbial richness, indicating no negative effect as feed sources on the intestinal microbiota in olive flounder. These results indicate that the life stage of olive flounder is more important in modulating intestinal microbiota than is the diet. It could also be concluded that dietary PPS might be used as a potential fish meal alternative without any compromising effects on microbial diversity of olive flounder for long-term feeding.}, }
@article {pmid31907364, year = {2020}, author = {Sausset, R and Petit, MA and Gaboriau-Routhiau, V and De Paepe, M}, title = {New insights into intestinal phages.}, journal = {Mucosal immunology}, volume = {13}, number = {2}, pages = {205-215}, pmid = {31907364}, issn = {1935-3456}, mesh = {Animals ; *Bacteriophages ; Gastrointestinal Microbiome/*immunology ; Humans ; Immune System/*virology ; Immunity ; Intestines/microbiology/*virology ; Metagenome ; }, abstract = {The intestinal microbiota plays important roles in human health. This last decade, the viral fraction of the intestinal microbiota, composed essentially of phages that infect bacteria, received increasing attention. Numerous novel phage families have been discovered in parallel with the development of viral metagenomics. However, since the discovery of intestinal phages by d'Hérelle in 1917, our understanding of the impact of phages on gut microbiota structure remains scarce. Changes in viral community composition have been observed in several diseases. However, whether these changes reflect a direct involvement of phages in diseases etiology or simply result from modifications in bacterial composition is currently unknown. Here we present an overview of the current knowledge in intestinal phages, their identity, lifestyles, and their possible effects on the gut microbiota. We also gather the main data on phage interactions with the immune system, with a particular emphasis on recent findings.}, }
@article {pmid31902141, year = {2020}, author = {Yu, H and Xue, D and Wang, Y and Zheng, W and Zhang, G and Wang, ZL}, title = {Molecular ecological network analysis of the response of soil microbial communities to depth gradients in farmland soils.}, journal = {MicrobiologyOpen}, volume = {9}, number = {3}, pages = {e983}, pmid = {31902141}, issn = {2045-8827}, mesh = {Biodiversity ; Environment ; *Farms ; Geography ; Metagenome ; Metagenomics/methods ; *Microbiota ; *Soil Microbiology ; }, abstract = {Soil microorganisms are considered to be important indicators of soil fertility and soil quality. Most previous studies have focused solely on surface soil, but there were numerous active cells in deeper soil layers. However, studies regarding microbial communities in deeper soil layers were not comprehensive and sufficient. In this study, phylogenetic molecular ecological networks (pMENs) based on the 16S rRNA Miseq sequencing technique were applied to study the response of soil microbial communities to depth gradients and the changes of key genera along 3 meter depth gradients (0-0.2 m, 0.2-0.4 m 0.4-0.6 m, 0.6-0.8 m, 0.8-1.0 m, 1.0-1.3 m, 1.3-1.6 m, 1.6-2.0 m, 2.0-2.5 m, and 2.5-3.0 m). The results showed that the modularity of microbial communities was consistently high in all soil layers and each layer was similar, which indicated that microbial communities were more resistant to depth changes. The pMENs further demonstrated that microbial community interactions were stable as the depth increased and they cooperated well to adapt to changes in different soil gradients. This was evidenced by similar positive links, average degree, and average clustering coefficient. In addition, key genera were obtained by analyzing module hubs in the pMENs. There may be at least one dominant genus in each layer that adapted to and resisted changes in the soil environment. It seems microbial communities demonstrate a stable and strong adaptability to depth gradients in farmland soils.}, }
@article {pmid31893578, year = {2020}, author = {Zhou, J and Yu, L and Zhang, J and Zhang, X and Xue, Y and Liu, J and Zou, X}, title = {Characterization of the core microbiome in tobacco leaves during aging.}, journal = {MicrobiologyOpen}, volume = {9}, number = {3}, pages = {e984}, pmid = {31893578}, issn = {2045-8827}, mesh = {*Aging ; Bacteria/classification/genetics ; Biodiversity ; Environment ; Humans ; Metagenomics/methods ; Microbiota/genetics ; Plant Leaves/*microbiology ; Tobacco/growth &amp; development/*microbiology ; }, abstract = {Microbiome plays an important role during the tobacco aging process which was an indispensable link in the production and processing of cigarettes. However, the structure and functions of microbiome have not been clarified during the tobacco aging process. In this study, 16S rDNA and ITS amplicon sequencing techniques were used to analyze the core microbiome of 15 tobacco samples from five different aging stages. The whole bacterial microbiome was classified into 29 microbial phyla and 132 orders. Enterobacteriales (63%), Pseudomonadales (16%), Sphingomonadales (8%), Xanthomonadales (4%), Burkholderiales (4%), Rhizobiales (3%), and Bacillales (2%) comprised the core bacterial microbiome. The whole fungal microbiome was classified into five microbial phyla and 52 orders. Incertae_sedis_Eurotiomycetes (27%), Wallemiales (25%), Sporidiobolales (17%), Capnodiales (5%), Eurotiales (2%), an unclassified Ascomycota (12%), and an unidentified Eurotiomycetes (4%) comprised the core fungal microbiome. FAPROTAX function prediction suggested that the core microbiome has a substantial potential for the carbon cycle, nitrate metabolism, aromatic compound degradation, chitinolysis, cellulolysis, and xylanolysis, but simultaneously, the core microbiome is also a source of human pathogens. The dynamics of the bacterial community were primarily determined by the total nitrogen in tobacco leaves during the aging process, while those of the fungal microbiome were primarily determined by total organic carbon. This study indicated that the core microbiome activities may play an important role in regulating the loss of carbon organic compounds and enhancing the secondary metabolites during tobacco leaves aging process.}, }
@article {pmid31884727, year = {2020}, author = {Song, Y and Gyarmati, P}, title = {Microbiota changes in a pediatric acute lymphocytic leukemia mouse model.}, journal = {MicrobiologyOpen}, volume = {9}, number = {3}, pages = {e982}, pmid = {31884727}, issn = {2045-8827}, mesh = {Animals ; Biodiversity ; Feces/microbiology ; Female ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Metagenomics/methods ; Mice ; *Microbiota ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/*microbiology ; RNA, Ribosomal, 16S ; }, abstract = {Hematological malignancies are the most common type of pediatric cancers, and acute lymphocytic leukemia (ALL) is the most frequently occurring hematological malignancy during childhood. A major cause of mortality in leukemia is bloodstream infection (BSI). The aim of the current study was to explore the gut microbiota in ALL and its potential functional alterations. High-throughput sequencing was used to characterize the bacterial and fungal microbiota in feces and their predicted functional characteristics in a xenotransplant pediatric ALL mouse model. Our work shows that gut microbiota significantly changes in leukemia, which may result in functional alterations. This study may provide potential therapeutic or preventive strategies of BSI in ALL.}, }
@article {pmid31880067, year = {2020}, author = {Chen, T and Li, Y and Liang, J and Li, Y and Huang, Z}, title = {Gut microbiota of provisioned and wild rhesus macaques (Macaca mulatta) living in a limestone forest in southwest Guangxi, China.}, journal = {MicrobiologyOpen}, volume = {9}, number = {3}, pages = {e981}, pmid = {31880067}, issn = {2045-8827}, mesh = {Animal Feed ; Animals ; Biodiversity ; *Calcium Carbonate ; China ; *Forests ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; *Macaca mulatta ; Metagenome ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The gut microbiota plays an important role in animal health and is strongly affected by the environment. Captivity and human source food have been shown to influence drastically the gut microbiota composition and function of wild animals. Therefore, in the present study, the gut microbiota of provisioned and wild populations of limestone-living rhesus macaques (Macaca mulatta) were compared using high-throughput 16S rRNA sequencing and bioinformatic analyses. The results indicated that provisioned macaques had a higher microbial richness than wild macaques, but there was no significant difference in the evenness of the gut microbiota between the two populations. Provisioned macaques also showed a higher abundance of Firmicutes and a lower abundance of Bacteroidetes than wild macaques. Functional analysis revealed that wild macaques had enriched microbial pathways involved in glycan biosynthesis and metabolism, transport and catabolism, and the digestive and endocrine systems, while provisioned macaques were richer in pathways associated with signaling molecules and interaction, neurodegenerative diseases. These differences were likely due to modification of the gut microbiota of the provisioned macaques to enable the digestion of new foods.}, }
@article {pmid31840403, year = {2020}, author = {Ahlgren, NA and Belisle, BS and Lee, MD}, title = {Genomic mosaicism underlies the adaptation of marine Synechococcus ecotypes to distinct oceanic iron niches.}, journal = {Environmental microbiology}, volume = {22}, number = {5}, pages = {1801-1815}, doi = {10.1111/1462-2920.14893}, pmid = {31840403}, issn = {1462-2920}, mesh = {Acclimatization/genetics ; Adaptation, Physiological/genetics ; Diatoms/genetics ; Ecosystem ; Ecotype ; Genome, Bacterial/*genetics ; Iron/metabolism ; Metagenomics ; *Mosaicism ; Oceans and Seas ; Phytoplankton ; Prochlorococcus/*genetics/*physiology ; Seawater/microbiology ; Synechococcus/*genetics/*physiology ; }, abstract = {Phytoplankton are limited by iron (Fe) in ~40% of the world's oceans including high-nutrient low-chlorophyll (HNLC) regions. While low-Fe adaptation has been well-studied in large eukaryotic diatoms, less is known for small, prokaryotic marine picocyanobacteria. This study reveals key physiological and genomic differences underlying Fe adaptation in marine picocyanobacteria. HNLC ecotype CRD1 strains have greater physiological tolerance to low Fe congruent with their expanded repertoire of Fe transporter, storage and regulatory genes compared to other ecotypes. From metagenomic analysis, genes encoding ferritin, flavodoxin, Fe transporters and siderophore uptake genes were more abundant in low-Fe waters, mirroring paradigms of low-Fe adaptation in diatoms. Distinct Fe-related gene repertories of HNLC ecotypes CRD1 and CRD2 also highlight how coexisting ecotypes have evolved independent approaches to life in low-Fe habitats. Synechococcus and Prochlorococcus HNLC ecotypes likewise exhibit independent, genome-wide reductions of predicted Fe-requiring genes. HNLC ecotype CRD1 interestingly was most similar to coastal ecotype I in Fe physiology and Fe-related gene content, suggesting populations from these different biomes experience similar Fe-selective conditions. This work supports an improved perspective that phytoplankton are shaped by more nuanced Fe niches in the oceans than previously implied from mostly binary comparisons of low- versus high-Fe habitats and populations.}, }
@article {pmid31808296, year = {2020}, author = {Zhang, Q and Geng, Z and Li, D and Ding, Z}, title = {Characterization and discrimination of microbial community and co-occurrence patterns in fresh and strong flavor style flue-cured tobacco leaves.}, journal = {MicrobiologyOpen}, volume = {9}, number = {2}, pages = {e965}, pmid = {31808296}, issn = {2045-8827}, mesh = {Biodiversity ; Eukaryotic Cells/classification ; *Fermentation ; High-Throughput Nucleotide Sequencing ; Metagenomics/methods ; *Microbiota ; Neural Networks, Computer ; Phylogeny ; Plant Leaves/*microbiology ; Prokaryotic Cells/classification ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; *Tobacco ; }, abstract = {Fermentation, also known as aging, is vital for enhancing the quality of flue-cured tobacco leaves (FTLs). Aged FTLs demonstrate high-quality sensory characteristics, while unaged FTLs do not. Microbes play important roles in the FTL fermentation process. However, the eukaryotic microbial community diversity is poorly understood, as are microbial associations within FTLs. We aimed to characterize and compare the microbiota associated with two important categories, fresh and strong flavor style FTLs, and to reveal correlations between the microbial taxa within them. Based on 16S and 18S rRNA Illumina MiSeq sequencing, the community richness and diversity of prokaryotes were almost as high as that of eukaryotes. The dominant microbes of FTLs belonged to seven genera, including Pseudomonas, Bacillus, Methylobacterium, Acinetobacter, Sphingomonas, Neophaeosphaeria, and Cladosporium, of the Proteobacteria, Firmicutes, and Ascomycota phyla. According to partial least square discriminant analysis (PLS-DA), Xanthomonas, Franconibacter, Massilia, Quadrisphaera, Staphylococcus, Cladosporium, Lodderomyces, Symmetrospora, Golovinomyces, and Dioszegia were significantly positively correlated with fresh flavor style FTLs, while Xenophilus, Fusarium, unclassified Ustilaginaceae, Tilletiopsis, Cryphonectria, Colletotrichum, and Cyanodermella were significantly positively correlated with strong flavor style FTLs. Network analysis identified seven hubs, Aureimonas, Kocuria, Massilia, Brachybacterium, Clostridium, Dietzia, and Vishniacozyma, that may play important roles in FTL ecosystem stability, which may be destroyed by Myrmecridium. FTL microbiota was found to be correlated with flavor style. Species present in lower numbers than the dominant microbes might be used as microbial markers to discriminate different flavor style samples and to stabilize FTL microbial communities. This research advances our understanding of FTL microbiota and describes a means of discriminating between fresh and strong flavor FTLs based on their respective stable microbiota.}, }
@article {pmid31775181, year = {2020}, author = {Rambo, IM and Dombrowski, N and Constant, L and Erdner, D and Baker, BJ}, title = {Metabolic relationships of uncultured bacteria associated with the microalgae Gambierdiscus.}, journal = {Environmental microbiology}, volume = {22}, number = {5}, pages = {1764-1783}, doi = {10.1111/1462-2920.14878}, pmid = {31775181}, issn = {1462-2920}, support = {FG-2016-6301//Alfred P. Sloan Foundation/International ; }, mesh = {Biochemical Phenomena ; Dinoflagellida/*microbiology ; Flavobacteriaceae/*genetics ; Genome, Bacterial/*genetics ; Metagenome ; Metagenomics ; Microalgae/*microbiology ; Microbiota/genetics ; Phylogeny ; Phytoplankton/microbiology ; Rhodobacteraceae/*genetics ; }, abstract = {Microbial communities inhabit algae cell surfaces and produce a variety of compounds that can impact the fitness of the host. These interactions have been studied via culturing, single-gene diversity and metagenomic read survey methods that are limited by culturing biases and fragmented genetic characterizations. Higher-resolution frameworks are needed to resolve the physiological interactions within these algal-bacterial communities. Here, we infer the encoded metabolic capabilities of four uncultured bacterial genomes (reconstructed using metagenomic assembly and binning) associated with the marine dinoflagellates Gambierdiscus carolinianus and G. caribaeus. Phylogenetic analyses revealed that two of the genomes belong to the commonly algae-associated families Rhodobacteraceae and Flavobacteriaceae. The other two genomes belong to the Phycisphaeraceae and include the first algae-associated representative within the uncultured SM1A02 group. Analyses of all four genomes suggest these bacteria are facultative aerobes, with some capable of metabolizing phytoplanktonic organosulfur compounds including dimethylsulfoniopropionate and sulfated polysaccharides. These communities may biosynthesize compounds beneficial to both the algal host and other bacteria, including iron chelators, B vitamins, methionine, lycopene, squalene and polyketides. These findings have implications for marine carbon and nutrient cycling and provide a greater depth of understanding regarding the genetic potential for complex physiological interactions between microalgae and their associated bacteria.}, }
@article {pmid31701637, year = {2020}, author = {Ren, Q and Si, H and Yan, X and Liu, C and Ding, L and Long, R and Li, Z and Qiu, Q}, title = {Bacterial communities in the solid, liquid, dorsal, and ventral epithelium fractions of yak (Bos grunniens) rumen.}, journal = {MicrobiologyOpen}, volume = {9}, number = {2}, pages = {e963}, pmid = {31701637}, issn = {2045-8827}, mesh = {Animals ; Biodiversity ; Cattle ; Computational Biology/methods ; Gastric Mucosa/*microbiology ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Rumen/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Yak (Bos grunniens) is an important and dominant livestock species in the challenging environment of the Qinghai-Tibetan Plateau. Rumen microbiota of the solid, liquid, and epithelium fractions play key roles in nutrient metabolism and contribute to host adaptation in ruminants. However, there is a little knowledge of the microbiota in these rumen fractions of yak. Therefore, we collected samples of solid, liquid, dorsal, and ventral epithelium fractions from five female yaks, then amplified bacterial 16S rRNA gene V4 regions and sequenced them using an Illumina MiSeq platform. Principal coordinates analysis detected significant differences in bacterial communities between the liquid, solid, and epithelium fractions, and between dorsal and ventral epithelium fractions. Rikenellaceae RC9, the families Lachnospiraceae and Ruminococcaceae, and Fibrobacter spp. were the abundant and enriched bacteria in solid fraction, while the genera Prevotella and Prevotellaceae UCG 003 were higher in the liquid fraction. Campylobacter spp., Comamonas spp., Desulfovibrio spp., and Solobacterium spp. were significantly higher in dorsal epithelium, while Howardella spp., Prevotellaceae UCG 001, Ruminococcaceae UCG 005, and Treponema 2 were enriched in the ventral epithelium. Comparison of predictive functional profiles among the solid, liquid, and dorsal, and ventral epithelium fractions also revealed significant differences. Microbiota in the ventral fraction of yak rumen also significantly differ from reported microbiota of cattle. In conclusion, our results improve our knowledge of the taxonomic composition and roles of yak rumen microbiota.}, }
@article {pmid31670480, year = {2020}, author = {Quigley, KM and Alvarez Roa, C and Torda, G and Bourne, DG and Willis, BL}, title = {Co-dynamics of Symbiodiniaceae and bacterial populations during the first year of symbiosis with Acropora tenuis juveniles.}, journal = {MicrobiologyOpen}, volume = {9}, number = {2}, pages = {e959}, pmid = {31670480}, issn = {2045-8827}, mesh = {Age Factors ; Animals ; Anthozoa/*microbiology ; *Bacterial Physiological Phenomena ; Computational Biology/methods ; DNA, Ribosomal Spacer ; Gene Ontology ; Metagenomics/methods ; *Microbiota ; Molecular Typing ; RNA, Ribosomal, 16S/genetics ; *Symbiosis ; }, abstract = {Interactions between corals and their associated microbial communities (Symbiodiniaceae and prokaryotes) are key to understanding corals' potential for and rate of acclimatory and adaptive responses. However, the establishment of microalgal and bacterial communities is poorly understood during coral ontogeny in the wild. We examined the establishment and co-occurrence between multiple microbial communities using 16S rRNA (bacterial) and ITS2 rDNA (Symbiodiniaceae) gene amplicon sequencing in juveniles of the common coral, Acropora tenuis, across the first year of development. Symbiodiniaceae communities in juveniles were dominated by Durusdinium trenchii and glynnii (D1 and D1a), with lower abundances of Cladocopium (C1, C1d, C50, and Cspc). Bacterial communities were more diverse and dominated by taxa within Proteobacteria, Cyanobacteria, and Planctomycetes. Both communities were characterized by significant changes in relative abundance and diversity of taxa throughout the year. D1, D1a, and C1 were significantly correlated with multiple bacterial taxa, including Alpha-, Deltra-, and Gammaproteobacteria, Planctomycetacia, Oxyphotobacteria, Phycisphaerae, and Rhizobiales. Specifically, D1a tended to associate with Oxyphotobacteria and D1 with Alphaproteobacteria, although these associations may represent correlational and not causal relationships. Bioenergetic modeling combined with physiological measurements of coral juveniles (surface area and Symbiodiniaceae cell densities) identified key periods of carbon limitation and nitrogen assimilation, potentially coinciding with shifts in microbial community composition. These results demonstrate that Symbiodiniaceae and bacterial communities are dynamic throughout the first year of ontology and may vary in tandem, with important fitness effects on host juveniles.}, }
@article {pmid33222846, year = {2020}, author = {Wang, J and Bai, X and Peng, C and Yu, Z and Li, B and Zhang, W and Sun, Z and Zhang, H}, title = {Fermented milk containing Lactobacillus casei Zhang and Bifidobacterium animalis ssp. lactis V9 alleviated constipation symptoms through regulation of intestinal microbiota, inflammation, and metabolic pathways.}, journal = {Journal of dairy science}, volume = {103}, number = {12}, pages = {11025-11038}, doi = {10.3168/jds.2020-18639}, pmid = {33222846}, issn = {1525-3198}, mesh = {Adult ; Animals ; Bifidobacterium animalis/*physiology ; Bioreactors ; Constipation/*therapy ; Cultured Milk Products/*microbiology ; Cytokines/blood ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Inflammation/*therapy ; Lactobacillus casei/*physiology ; Male ; Metabolic Networks and Pathways/physiology ; Metabolomics ; Metagenomics ; Probiotics/therapeutic use ; }, abstract = {Studies suggest that probiotics and fermented milk can improve defecation in constipated patients. However, the mechanism of fermented milk containing probiotics on constipation remains poorly understood. Volunteers with chronic constipation symptoms were recruited and given 200 g/d of fermented milk containing Lactobacillus casei Zhang and Bifidobacterium animalis ssp. lactis V9 (PFM) for 4 wk. Clinical symptoms, cytokines, metagenomics, and metabolomics were evaluated in constipated participants before and after PFM intervention. After PFM intervention, we observed significant improvement of constipation symptoms. In the serum samples, the anti-inflammatory cytokine IL-10 increased and the proinflammatory cytokine C-reactive protein and lipopolysaccharides decreased. Metagenomics results showed that the increase of B. animalis was correlated with an increase in defecation frequency. Fatty acid biosynthesis and bile acid biosynthesis in stool samples as well as carnitine shuttle, vitamin E metabolism, and ascorbate and aldarate metabolism were identified as significantly altered metabolic pathways. Acylcarnitine, located on the carnitine shuttle pathway, had a significantly positive correlation with defecation frequency. It was speculated that PFM may contribute to alleviating constipation symptoms through 3 potential mechanisms: fine-tuning gastrointestinal microbiota, fighting inflammation, and regulating metabolic pathways.}, }
@article {pmid32356337, year = {2020}, author = {Shin, NR and Bose, S and Wang, JH and Nam, YD and Song, EJ and Lim, DW and Kim, HB and Lim, YS and Choi, HS and Kim, H}, title = {Chemically or surgically induced thyroid dysfunction altered gut microbiota in rat models.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {34}, number = {6}, pages = {8686-8701}, doi = {10.1096/fj.201903091RR}, pmid = {32356337}, issn = {1530-6860}, mesh = {Animals ; Bacteria/genetics ; Bacteroidetes/genetics ; Disease Models, Animal ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Hypothyroidism/microbiology/pathology ; Male ; Metagenomics/methods ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Sprague-Dawley ; Thyroid Gland/*microbiology/*pathology ; }, abstract = {Thyroid hormones are essential for the regulation of energy homeostasis and metabolic processes. However, the relationship between thyroid function and host gut microbial communities is not properly understood. To determine whether and how gut microbiota is associated with thyroid function, metagenomics analysis of the bacterial population in fecal samples of rat models of hyperthyroidism (induced by levothyroxine) and hypothyroidism (induced by propylthiouracil or thyroidectomy) was conducted through 16S rRNA gene sequencing. Our results revealed that all thyroid dysfunction models were definitely established and gut microbial composition varied according to different thyroid functional status. The relative abundance of Ruminococcus was significantly higher in the hyperthyroidism group (HE) vs both the normal and hypothyroidism groups (HO) while S24-7 was significantly higher in the HO group. The population of Prevotellaceae and Prevotella were significantly lower in the HO group vs the normal. Firmicutes and Oscillospira were significantly higher in the SHO (surgery-induced hypothyroidism) group, while Prevotellaceae and Prevotella showed lower abundance in the SHO group than the SHAM group. Present results suggest that thyroid functions may have the potential to influence the profile of gut microbiota and could be used as foundation to investigate interaction mechanism between thyroid and gut microbiome.}, }
@article {pmid31907101, year = {2020}, author = {Deblais, L and Kathayat, D and Helmy, YA and Closs, G and Rajashekara, G}, title = {Translating 'big data': better understanding of host-pathogen interactions to control bacterial foodborne pathogens in poultry.}, journal = {Animal health research reviews}, volume = {21}, number = {1}, pages = {15-35}, doi = {10.1017/S1466252319000124}, pmid = {31907101}, issn = {1475-2654}, mesh = {Animals ; *Bacteria/genetics ; *Big Data ; *Food Microbiology ; Foodborne Diseases/*microbiology ; Gastrointestinal Microbiome/physiology ; *Host-Pathogen Interactions ; Humans ; Poultry/*microbiology ; Proteomics ; }, abstract = {Recent technological advances has led to the generation, storage, and sharing of colossal sets of information ('big data'), and the expansion of 'omics' in science. To date, genomics/metagenomics, transcriptomics, proteomics, and metabolomics are arguably the most ground breaking approaches in food and public safety. Here we review some of the recent studies of foodborne pathogens (Campylobacter spp., Salmonella spp., and Escherichia coli) in poultry using big data. Genomic/metagenomic approaches have reveal the importance of the gut microbiota in health and disease. They have also been used to identify, monitor, and understand the epidemiology of antibiotic-resistance mechanisms and provide concrete evidence about the role of poultry in human infections. Transcriptomics studies have increased our understanding of the pathophysiology and immunopathology of foodborne pathogens in poultry and have led to the identification of host-resistance mechanisms. Proteomic/metabolomic approaches have aided in identifying biomarkers and the rapid detection of low levels of foodborne pathogens. Overall, 'omics' approaches complement each other and may provide, at least in part, a solution to our current food-safety issues by facilitating the development of new rapid diagnostics, therapeutic drugs, and vaccines to control foodborne pathogens in poultry. However, at this time most 'omics' approaches still remain underutilized due to their high cost and the high level of technical skills required.}, }
@article {pmid32780963, year = {2021}, author = {Wijekoon, C and Quill, Z}, title = {Fungal endophyte diversity in table grapes.}, journal = {Canadian journal of microbiology}, volume = {67}, number = {1}, pages = {29-36}, doi = {10.1139/cjm-2020-0293}, pmid = {32780963}, issn = {1480-3275}, mesh = {Biodiversity ; DNA, Ribosomal Spacer/genetics ; Endophytes/classification/genetics/*isolation &amp; purification ; Fruit/microbiology ; Fungi/classification/genetics/*isolation &amp; purification ; Manitoba ; Microbiota/genetics ; Vitis/*microbiology ; }, abstract = {Plant fungal endophytes are diverse microbial sources that reside inside plants. Grapes (Vitis vinifera) are rich in polyphenols that have beneficial health effects, and recent research has shown that fungal endophytes in grapes may contribute to the production of these polyphenols and may serve as biocontrol agents. In this study, we determined the fungal microbial endophyte diversity in North American table grapes found at a Winnipeg, Manitoba, market. The amplicon internal transcribed spacer (ITS) metagenomics approach was used to profile the fungal communities of the fruit endophyte microbiome of three table grape types. The data supported endophyte diversity in different table grapes, including possible bioactive, saprophytic, and pathogenic fungi. Culturable endophytes were isolated and identified by morphology and ITS amplicon sequencing. The majority of the isolated culturable strains included Alternaria spp. and Cladosporium spp. The results provided evidence of the existence of diverse fungal endophytes isolated and identified from the fruit of the table grapes. These fungal endophytes may have potential in agricultural, industrial, and pharmaceutical applications.}, }
@article {pmid33341726, year = {2021}, author = {Martínez-Gallardo, MR and López, MJ and López-González, JA and Jurado, MM and Suárez-Estrella, F and Pérez-Murcia, MD and Sáez, JA and Moral, R and Moreno, J}, title = {Microbial communities of the olive mill wastewater sludge stored in evaporation ponds: The resource for sustainable bioremediation.}, journal = {Journal of environmental management}, volume = {279}, number = {}, pages = {111810}, doi = {10.1016/j.jenvman.2020.111810}, pmid = {33341726}, issn = {1095-8630}, mesh = {Biodegradation, Environmental ; Industrial Waste/analysis ; *Microbiota ; *Olea ; Olive Oil ; Ponds ; Sewage ; Waste Disposal, Fluid ; Waste Water ; }, abstract = {Olive Mill Wastewater (OMW) is a polluting residue from the olive oil industry. It is usually stored in open-air unprotected evaporation ponds where their sediments accumulate. This study compares the characteristics of OMW sludges stored for long-time in evaporation ponds and assesses their impact on the underlying soil layer. Physicochemical parameters, toxicity bioassays, and full characterization of the microbial community were analyzed. The extension of the polluting effects was assessed by analysis of toxicity, microbial biomass carbon, and respiration. Geostatistics was used to predict their spatial distribution. Organic matter and polyphenol content besides toxicity levels determine variations between OMW sludges and have a high impact on the microbiota they contain. The microbial community was abundant, diverse, and functionally active. However, the biodegradability of the sludges was hindered by the toxicity levels. Toxicity and biomass carbon were higher on the surface of the ponds than in the soil layer revealing a reduced leach flow and depletion of contaminants. The natural microbiota might be biostimulated by means of applying sustainable and feasible biological treatments in order to favor the OMW sludges bioremediation. These results open up the possibility of solving the environmental concern caused by its storage in similar scenarios, which are common in olive oil-producing countries.}, }
@article {pmid33327517, year = {2020}, author = {Menaa, F and Wijesinghe, PAUI and Thiripuranathar, G and Uzair, B and Iqbal, H and Khan, BA and Menaa, B}, title = {Ecological and Industrial Implications of Dynamic Seaweed-Associated Microbiota Interactions.}, journal = {Marine drugs}, volume = {18}, number = {12}, pages = {}, pmid = {33327517}, issn = {1660-3397}, mesh = {Animals ; *Ecology ; Humans ; *Industry ; *Microbiota ; Seaweed/*chemistry ; }, abstract = {Seaweeds are broadly distributed and represent an important source of secondary metabolites (e.g., halogenated compounds, polyphenols) eliciting various pharmacological activities and playing a relevant ecological role in the anti-epibiosis. Importantly, host (as known as basibiont such as algae)-microbe (as known as epibiont such as bacteria) interaction (as known as halobiont) is a driving force for coevolution in the marine environment. Nevertheless, halobionts may be fundamental (harmless) or detrimental (harmful) to the functioning of the host. In addition to biotic factors, abiotic factors (e.g., pH, salinity, temperature, nutrients) regulate halobionts. Spatiotemporal and functional exploration of such dynamic interactions appear crucial. Indeed, environmental stress in a constantly changing ocean may disturb complex mutualistic relations, through mechanisms involving host chemical defense strategies (e.g., secretion of secondary metabolites and antifouling chemicals by quorum sensing). It is worth mentioning that many of bioactive compounds, such as terpenoids, previously attributed to macroalgae are in fact produced or metabolized by their associated microorganisms (e.g., bacteria, fungi, viruses, parasites). Eventually, recent metagenomics analyses suggest that microbes may have acquired seaweed associated genes because of increased seaweed in diets. This article retrospectively reviews pertinent studies on the spatiotemporal and functional seaweed-associated microbiota interactions which can lead to the production of bioactive compounds with high antifouling, theranostic, and biotechnological potential.}, }
@article {pmid33051444, year = {2020}, author = {Moon, K and Kim, S and Kang, I and Cho, JC}, title = {Viral metagenomes of Lake Soyang, the largest freshwater lake in South Korea.}, journal = {Scientific data}, volume = {7}, number = {1}, pages = {349}, pmid = {33051444}, issn = {2052-4463}, support = {NRF-2019R1I1A1A01062072//National Research Foundation of Korea (NRF)/International ; NRF-2019R1I1A1A01063401//National Research Foundation of Korea (NRF)/International ; NRF-2019R1A2B5B02070538//National Research Foundation of Korea (NRF)/International ; }, mesh = {High-Throughput Nucleotide Sequencing ; Lakes/*virology ; *Metagenome ; Metagenomics ; Republic of Korea ; *Virome ; }, abstract = {A high number of viral metagenomes have revealed countless genomes of putative bacteriophages that have not yet been identified due to limitations in bacteriophage cultures. However, most virome studies have been focused on marine or gut environments, thereby leaving the viral community structure of freshwater lakes unclear. Because the lakes located around the globe have independent ecosystems with unique characteristics, viral community structures are also distinctive but comparable. Here, we present data on viral metagenomes that were seasonally collected at a depth of 1 m from Lake Soyang, the largest freshwater reservoir in South Korea. Through shotgun metagenome sequencing using the Illumina MiSeq platform, 3.08 to 5.54-Gbps of reads per virome were obtained. To predict the viral genome sequences within Lake Soyang, contigs were constructed and 648 to 1,004 putative viral contigs were obtained per sample. We expect that both viral metagenome reads and viral contigs would contribute in comparing and understanding of viral communities among different freshwater lakes depending on seasonal changes.}, }
@article {pmid32728075, year = {2020}, author = {Dei-Cas, I and Giliberto, F and Luce, L and Dopazo, H and Penas-Steinhardt, A}, title = {Metagenomic analysis of gut microbiota in non-treated plaque psoriasis patients stratified by disease severity: development of a new Psoriasis-Microbiome Index.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {12754}, pmid = {32728075}, issn = {2045-2322}, mesh = {Adolescent ; Adult ; Bacteroides ; Bacteroidetes ; Biodiversity ; Biomarkers/metabolism ; Clostridiales ; Computational Biology ; Cross-Sectional Studies ; Faecalibacterium ; Female ; Firmicutes ; *Gastrointestinal Microbiome ; Genome, Human ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Metagenomics ; Middle Aged ; Psoriasis/*diagnosis/*microbiology ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {Psoriasis is an immune-mediated skin disorder. Imbalance of gut microbial populations has been implicated in many diseases. We aimed to investigate whether there were differences in gut microbiota in psoriasis patients vs non-psoriasis controls and between psoriasis severity groups. 55 psoriasis patients and 27 controls were included. V3-V4 regions of the 16S rRNA gene of fecal samples were analyzed using Illumina MiSeq. Bioinformatic analysis was performed. We found changes in gut microbiome composition depending on their psoriasis status as determined by weighted unifrac (p < 0.05), in particular an increase in Firmicutes and depletion of Bacteroidetes in psoriasis patients. Additionally, the Faecalibacterium and Blautia genus were higher in psoriasis patients while Bacteroides and Paraprevotella in non-psoriasis controls (p < 0.05, LDA score > 2). Moderate-to-severe psoriasis patients had lower biodiversity than mild psoriatic patients (p = 0.049). No differences for beta-diversity were found. We developed a Psoriasis-Microbiota Index (PMI), which discriminated among psoriasis patients and controls with sensitivity: 0.78 and specificity: 0.79. Furthermore, we performed a meta-analysis with published data to validate this index. We demonstrated gut dysbiosis in psoriasis patients, suggesting a role in psoriasis pathophysiology. Furthermore, we developed a PMI with the potential to discriminate between psoriasis patients and controls across different populations, which could be used as a biomarker in the clinical practice.}, }
@article {pmid32690600, year = {2021}, author = {Zuo, T and Liu, Q and Zhang, F and Lui, GC and Tso, EY and Yeoh, YK and Chen, Z and Boon, SS and Chan, FK and Chan, PK and Ng, SC}, title = {Depicting SARS-CoV-2 faecal viral activity in association with gut microbiota composition in patients with COVID-19.}, journal = {Gut}, volume = {70}, number = {2}, pages = {276-284}, pmid = {32690600}, issn = {1468-3288}, mesh = {Adult ; Aged ; COVID-19/*complications/diagnosis/*microbiology ; Feces/*microbiology/*virology ; Female ; Gastrointestinal Microbiome ; Hospitalization ; Humans ; Longitudinal Studies ; Male ; Middle Aged ; Pilot Projects ; Prospective Studies ; SARS-CoV-2/*isolation &amp; purification ; Young Adult ; }, abstract = {OBJECTIVE: Although severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA was detected in faeces of patients with COVID-19, the activity and infectivity of the virus in the GI tract during disease course is largely unknown. We investigated temporal transcriptional activity of SARS-CoV-2 and its association with longitudinal faecal microbiome alterations in patients with COVID-19.<br><br>DESIGN: We performed RNA shotgun metagenomics sequencing on serial faecal viral extractions from 15 hospitalised patients with COVID-19. Sequencing coverage of the SARS-CoV-2 genome was quantified. We assessed faecal microbiome composition and microbiome functionality in association with signatures of faecal SARS-CoV-2 infectivity.<br><br>RESULTS: Seven (46.7%) of 15 patients with COVID-19 had stool positivity for SARS-CoV-2 by viral RNA metagenomic sequencing. Even in the absence of GI manifestations, all seven patients showed strikingly higher coverage (p=0.0261) and density (p=0.0094) of the 3' vs 5' end of SARS-CoV-2 genome in their faecal viral metagenome profile. Faecal viral metagenome of three patients continued to display active viral infection signature (higher 3' vs 5' end coverage) up to 6 days after clearance of SARS-CoV-2 from respiratory samples. Faecal samples with signature of high SARS-CoV-2 infectivity had higher abundances of bacterial species Collinsella aerofaciens, Collinsella tanakaei, Streptococcus infantis, Morganella morganii, and higher functional capacity for nucleotide de novo biosynthesis, amino acid biosynthesis and glycolysis, whereas faecal samples with signature of low-to-none SARS-CoV-2 infectivity had higher abundances of short-chain fatty acid producing bacteria, Parabacteroides merdae, Bacteroides stercoris, Alistipes onderdonkii and Lachnospiraceae bacterium 1_1_57FAA.<br><br>CONCLUSION: This pilot study provides evidence for active and prolonged 'quiescent' GI infection even in the absence of GI manifestations and after recovery from respiratory infection of SARS-CoV-2. Gut microbiota of patients with active SARS-CoV-2 GI infection was characterised by enrichment of opportunistic pathogens, loss of salutary bacteria and increased functional capacity for nucleotide and amino acid biosynthesis and carbohydrate metabolism.}, }
@article {pmid31897823, year = {2020}, author = {Najar, IN and Sherpa, MT and Das, S and Thakur, N}, title = {Bacterial diversity and functional metagenomics expounding the diversity of xenobiotics, stress, defense and CRISPR gene ontology providing eco-efficiency to Himalayan Hot Springs.}, journal = {Functional &amp; integrative genomics}, volume = {20}, number = {4}, pages = {479-496}, doi = {10.1007/s10142-019-00723-x}, pmid = {31897823}, issn = {1438-7948}, support = {BCIL/NER-BPMC/2016 &amp; BT/20/NE/2011//Department of Biotechnology, Government of India/ ; }, mesh = {Bacterial Proteins/genetics/metabolism ; Endodeoxyribonucleases/genetics/metabolism ; Hot Springs/*microbiology ; Membrane Transport Proteins/genetics/metabolism ; *Metagenome ; *Microbiota ; Stress, Physiological ; Xenobiotics/metabolism ; beta-Lactamases/genetics/metabolism ; }, abstract = {Sikkim is one of the bio-diverse states of India, which harbors diverse alkaline and sulfur rich hot springs in its vicinity. However, there is a dearth of data present in terms of microbial and its functional diversity as only a few hot springs have been studied in this area. Thus, in this regard, microbial and functional diversity of two hot springs by NGS, PLFA, and culture-independent approaches were carried out. PLFA and culture-dependent analysis was complementary as the Gram-positive bacteria were abundant in both the hot springs with the dominance of phylum Firmicutes with Geobacillus. Metagenomic analysis revealed the abundance of Proteobacteria, Actinobacteria, and Firmicutes in both hot springs. Functional metagenomics suggested that both Yumthang and Reshi hot spring possess a diverse set of genes analogous to stress such as genes allied to osmotic, heat shock, and acid stresses; defense analogies such as multidrug resistance efflux pump, multidrug transport system, and β-lactamase; and CRISPR analogues such as related to Cas1, Cas2, Cas3, cmr1-5 proteins, CT1972, and CT1133 gene families. The xenobiotic analogues were found against benzoate, nitrotolune, xylene, DDT, and chlorocyclohexane/chlorobenzene degradation. Thus, these defensive mechanisms against environmental and anthropogenic hiccups and hindrances provide the eco-efficiency to such thermal habitats. The higher enzymatic, degradation, defense, stress potential and the lower percentage identity (< 95%) of isolates encourage the further exploration and exploitation of these habitats for industrial and biotechnological purposes.}, }
@article {pmid31759120, year = {2020}, author = {Kumar, H and Park, W and Lim, D and Srikanth, K and Kim, JM and Jia, XZ and Han, JL and Hanotte, O and Park, JE and Oyola, SO}, title = {Whole metagenome sequencing of cecum microbiomes in Ethiopian indigenous chickens from two different altitudes reveals antibiotic resistance genes.}, journal = {Genomics}, volume = {112}, number = {2}, pages = {1988-1999}, doi = {10.1016/j.ygeno.2019.11.011}, pmid = {31759120}, issn = {1089-8646}, mesh = {Animals ; Bacteroidetes/genetics/pathogenicity ; Cecum/microbiology ; Chickens/*microbiology ; *Drug Resistance, Bacterial ; Ethiopia ; Firmicutes/genetics/pathogenicity ; *Gastrointestinal Microbiome ; *Metagenome ; Metagenomics/methods ; Whole Genome Sequencing/methods ; }, abstract = {We analyzed the whole genomes of cecum microbiomes of Ethiopian indigenous chickens from two distinct geographical zones: Afar (AF) district (Dulecha, 730 m above sea level) and Amhara (AM) district (Menz Gera Midir, 3300 m). Through metagenomic analysis we found that microbial populations were mainly dominated by Bacteroidetes and Firmicutes. We identified 2210 common genes in the two groups. LEfSe showed that the distribution of Coprobacter, Geobacter, Cronobacter, Alloprevotella, and Dysgonomonas were more abundant in AF than AM. Analyses using KEGG, eggNOG, and CAZy databases indicated that the pathways of metabolism, genetic information processing, environmental information processing, and cellular process were significantly enriched. Functional abundance was found to be associated with the nutrient absorption and microbial localization of indigenous chickens. We also investigated antibiotic resistant genes and found antibiotics like LSM, cephalosporin, and tetracycline were significantly more abundant in AF than AM.}, }
@article {pmid33432373, year = {2021}, author = {Malakar, D and Sarathbabu, S and Borah, P and Kumar, NS}, title = {Fish gill microbiome from India's largest Brahmaputra River-a trans-border biodiversity hotspot region.}, journal = {Environmental monitoring and assessment}, volume = {193}, number = {2}, pages = {56}, doi = {10.1007/s10661-021-08847-z}, pmid = {33432373}, issn = {1573-2959}, support = {No. BT/BI/12/060/2012//Department of Biotechnology, Government of India/ ; }, abstract = {In this study, we sequenced the V3-V4 region of 16S rRNA gene amplicon using paired-end Illumina HiSeq to study the bacterial community in the gills of fish from the bank of the trans-border river of Brahmaputra, Northeast India. Metagenome data consisted of 278,784 reads, 248-bp length, and 56.48% GC content with 85% sequence having a Phred score Q = 30. Community metagenomics revealed a total of 631 genera belonging to 22 different phyla, dominated by Proteobacteria (118,222 features), Firmicutes (101,043 features), Actinobacteria (34,189 features), Bacteroidetes (17,977 features), and Cyanobacteria (2730 features). The bacterial community identified was composed of both pathogenic zoonotic and non-harmful groups. The pathway or functional analysis of the fish gill microbiome exhibited 21 different pathways which also included the pathogenic-related functions. Our data detected a wide group of bacterial communities that will be useful in further isolating and characterizing the pathogenic bacteria from the fish and also to understand the bacterial association in highly consumed fish.}, }
@article {pmid33248775, year = {2021}, author = {Centurion, VB and Lacerda-Júnior, GV and Duarte, AWF and Silva, TR and Silva, LJ and Rosa, LH and Oliveira, VM}, title = {Dynamics of microbial stress responses driven by abiotic changes along a temporal gradient in Deception Island, Maritime Antarctica.}, journal = {The Science of the total environment}, volume = {758}, number = {}, pages = {143671}, doi = {10.1016/j.scitotenv.2020.143671}, pmid = {33248775}, issn = {1879-1026}, mesh = {Antarctic Regions ; Islands ; *Microbiota ; }, abstract = {Whalers Bay (WB), Deception Island, is an environment that can drastically change its temperature within a few meters. The main forms of life inhabiting this environment are microorganisms, which, due to the high diversity and their adaptive potential, can survive and thrive under harsh stress conditions. However, the genetic potential and mechanisms to cope with fluctuating adverse conditions as well as what extent environmental variations shape the microbial community over the years it is still unknown in Antarctic environments. In this work, sediments collected in a transect in Whalers Bay, Deception Island, during the Austral Summers of 2014, 2015 and 2017 were analyzed using shotgun metagenomics. Sequence data were further processed with the SqueezeMeta tool for assembly, gene prediction, mapping, taxonomic and functional annotations. Results showed that stress-related functions had the influence of temperatures and solar radiation observed in the years of 2015 and 2017. The most differentiated functions were the ones related to oxidative stress, comparing 2014 vs 2015 and 2014 vs 2017. The genes coding for HSP20 and oxidoreductases (nrdH, grxA, korC and korD), as well as the genes clpE, cspL, and operons mtrAB and vicKR, were differentially enriched between the years, most of them found in gram-positive bacteria. The selective pressures of temperature and radiation may have favored the growth of gram-positive bacteria in 2017, with emphasis on Arthrobacter genus. Data gathered in this work showed that temperature and solar radiation could potentially be the primary driving forces shaping the repertoire of stress-response genes for the maintenance of microbial diversity in WB Antarctic sediments.}, }
@article {pmid32994487, year = {2020}, author = {Alvarez, AS and Tap, J and Chambaud, I and Cools-Portier, S and Quinquis, L and Bourlioux, P and Marteau, P and Guillemard, E and Schrezenmeir, J and Derrien, M}, title = {Safety and functional enrichment of gut microbiome in healthy subjects consuming a multi-strain fermented milk product: a randomised controlled trial.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {15974}, pmid = {32994487}, issn = {2045-2322}, mesh = {Adult ; Bacteria/*classification/genetics/isolation &amp; purification ; Cultured Milk Products/*microbiology ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Double-Blind Method ; Female ; Gastrointestinal Microbiome/*drug effects ; Healthy Volunteers ; Humans ; Lactobacillus/physiology ; Lactobacillus rhamnosus/physiology ; Male ; Middle Aged ; Phylogeny ; Probiotics/*administration &amp; dosage/pharmacology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Vital Signs/drug effects ; Young Adult ; }, abstract = {Many clinical studies have evaluated the effect of probiotics, but only a few have assessed their dose effects on gut microbiota and host. We conducted a randomized, double-blind, controlled intervention clinical trial to assess the safety (primary endpoint) of and gut microbiota response (secondary endpoint) to the daily ingestion for 4 weeks of two doses (1 or 3 bottles/day) of a fermented milk product (Test) in 96 healthy adults. The Test product is a multi-strain fermented milk product, combining yogurt strains and probiotic candidate strains Lactobacillus paracasei subsp. paracasei CNCM I-1518 and CNCM I-3689 and Lactobacillus rhamnosus CNCM I-3690. We assessed the safety of the Test product on the following parameters: adverse events, vital signs, hematological and metabolic profile, hepatic, kidney or thyroid function, inflammatory markers, bowel habits and digestive symptoms. We explored the longitudinal gut microbiota response to product consumption and dose, by 16S rRNA gene sequencing and functional contribution by shotgun metagenomics. Safety results did not show any significant difference between the Test and Control products whatever the parameters assessed, at the two doses ingested daily over a 4-week-period. Probiotic candidate strains were detected only during consumption period, and at a significantly higher level for the three strains in subjects who consumed 3 products bottles/day. The global structure of the gut microbiota as assessed by alpha and beta-diversity, was not altered by consumption of the product for four weeks. A zero-inflated beta regression model with random effects (ZIBR) identified a few bacterial genera with differential responses to test product consumption dose compared to control. Shotgun metagenomics analysis revealed a functional contribution to the gut microbiome of probiotic candidates.}, }
@article {pmid32393180, year = {2020}, author = {Jiang, P and Lai, S and Wu, S and Zhao, XM and Chen, WH}, title = {Host DNA contents in fecal metagenomics as a biomarker for intestinal diseases and effective treatment.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {348}, pmid = {32393180}, issn = {1471-2164}, support = {2018YFC0910502//National Key Research and Development Program of China/ ; 61932008//National Natural Science Foundation of China/ ; 61772368//National Natural Science Foundation of China/ ; 61572363//National Natural Science Foundation of China/ ; 2018YFC0910500//National Key R&amp;D Program of China/ ; 17ZR1445600//Natural Science Foundation of Shanghai/ ; 2018SHZDZX01//Shanghai Municipal Science and Technology Major Project/ ; }, mesh = {Antibodies, Monoclonal/therapeutic use ; Biomarkers/*metabolism ; Colorectal Neoplasms/*diagnosis/genetics/pathology ; Crohn Disease/*diagnosis/drug therapy/genetics/pathology ; DNA/*metabolism ; Dysbiosis ; Feces/*chemistry ; Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/metabolism ; Leukocyte L1 Antigen Complex/metabolism ; Machine Learning ; Metagenomics/methods ; Treatment Outcome ; }, abstract = {BACKGROUND: Compromised intestinal barrier (CIB) has been associated with many enteropathies, including colorectal cancer (CRC) and inflammatory bowel disease (IBD). We hypothesized that CIB could lead to increased host-derived contents including epithelial cells into the gut, change its physio-metabolic properties, and globally alter microbial community and metabolic capacities.<br><br>RESULTS: Consistently, we found host DNA contents (HDCs), calculated as the percentage of metagenomic sequencing reads mapped to the host genome, were significantly elevated in patients of CRC and Crohn's disease (CD). Consistent with our hypothesis, we found that HDC correlated with microbial- and metabolic-biomarkers of these diseases, contributed significantly to machine-learning models for patient stratification and was consequently ranked as a top contributor. CD patients with treatment could partially reverse the changes of many CD-signature species over time, with reduced HDC and fecal calprotectin (FCP) levels. Strikingly, HDC showed stronger correlations with the reversing changes of the CD-related species than FCP, and contributed greatly in classifying treatment responses, suggesting that it was also a biomarker for effective treatment.<br><br>CONCLUSIONS: Together, we revealed that association between HDCs and gut dysbiosis, and identified HDC as a novel biomarker from fecal metagenomics for diagnosis and effective treatment of intestinal diseases; our results also suggested that host-derived contents may have greater impact on gut microbiota than previously anticipated.}, }
@article {pmid32738764, year = {2020}, author = {Luiken, REC and Van Gompel, L and Bossers, A and Munk, P and Joosten, P and Hansen, RB and Knudsen, BE and García-Cobos, S and Dewulf, J and Aarestrup, FM and Wagenaar, JA and Smit, LAM and Mevius, DJ and Heederik, DJJ and Schmitt, H and , }, title = {Farm dust resistomes and bacterial microbiomes in European poultry and pig farms.}, journal = {Environment international}, volume = {143}, number = {}, pages = {105971}, doi = {10.1016/j.envint.2020.105971}, pmid = {32738764}, issn = {1873-6750}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Chickens ; Drug Resistance, Bacterial ; Dust ; Europe ; Farms ; *Microbiota ; *Poultry ; Swine ; }, abstract = {BACKGROUND: Livestock farms are a reservoir of antimicrobial resistant bacteria from feces. Airborne dust-bound bacteria can spread across the barn and to the outdoor environment. Therefore, exposure to farm dust may be of concern for animals, farmers and neighboring residents. Although dust is a potential route of transmission, little is known about the resistome and bacterial microbiome of farm dust.<br><br>OBJECTIVES: We describe the resistome and bacterial microbiome of pig and poultry farm dust and their relation with animal feces resistomes and bacterial microbiomes, and on-farm antimicrobial usage (AMU). In addition, the relation between dust and farmers' stool resistomes was explored.<br><br>METHODS: In the EFFORT-study, resistomes and bacterial microbiomes of indoor farm dust collected on Electrostatic Dust fall Collectors (EDCs), and animal feces of 35 conventional broiler and 44 farrow-to-finish pig farms from nine European countries were determined by shotgun metagenomic analysis. The analysis also included 79 stool samples from farmers working or living at 12 broiler and 19 pig farms and 46 human controls. Relative abundance of and variation in resistome and bacterial composition of farm dust was described and compared to animal feces and farmers' stool.<br><br>RESULTS: The farm dust resistome contained a large variety of antimicrobial resistance genes (ARGs); more than the animal fecal resistome. For both poultry and pigs, composition of dust resistomes finds (partly) its origin in animal feces as dust resistomes correlated significantly with fecal resistomes. The dust bacterial microbiome also correlated significantly with the dust resistome composition. A positive association between AMU in animals on the farm and the total abundance of the dust resistome was found. Occupational exposure to pig farm dust or animal feces may contribute to farmers' resistomes, however no major shifts in farmers resistome towards feces or dust resistomes were found in this study.<br><br>CONCLUSION: Poultry and pig farm dust resistomes are rich and abundant and associated with the fecal resistome of the animals and the dust bacterial microbiome.}, }
@article {pmid32679392, year = {2020}, author = {Van Gompel, L and Luiken, REC and Hansen, RB and Munk, P and Bouwknegt, M and Heres, L and Greve, GD and Scherpenisse, P and Jongerius-Gortemaker, BGM and Tersteeg-Zijderveld, MHG and García-Cobos, S and Dohmen, W and Dorado-García, A and Wagenaar, JA and Urlings, BAP and Aarestrup, FM and Mevius, DJ and Heederik, DJJ and Schmitt, H and Bossers, A and Smit, LAM}, title = {Description and determinants of the faecal resistome and microbiome of farmers and slaughterhouse workers: A metagenome-wide cross-sectional study.}, journal = {Environment international}, volume = {143}, number = {}, pages = {105939}, doi = {10.1016/j.envint.2020.105939}, pmid = {32679392}, issn = {1873-6750}, mesh = {Abattoirs ; Animals ; Anti-Bacterial Agents/pharmacology ; Chickens ; Cross-Sectional Studies ; Drug Resistance, Bacterial ; Farmers ; Humans ; Macrolides ; *Metagenome ; *Microbiota ; Netherlands ; Swine ; }, abstract = {BACKGROUND: By studying the entire human faecal resistome and associated microbiome, the diversity and abundance of faecal antimicrobial resistance genes (ARGs) can be comprehensively characterized. Prior culture-based studies have shown associations between occupational exposure to livestock and carriage of specific antimicrobial resistant bacteria. Using shotgun metagenomics, the present study investigated 194 faecal resistomes and bacteriomes from humans occupationally exposed to ARGs in livestock (i.e. pig and poultry farmers, employees and family members and pig slaughterhouse workers) and a control population (Lifelines cohort) in the Netherlands. In addition, we sought to identify determinants for the human resistome and bacteriome composition by applying a combination of multivariate (NMDS, PERMANOVA, SIMPER and DESeq2 analysis) and multivariable regression analysis techniques.<br><br>RESULTS: Pig slaughterhouse workers and pig farmers carried higher total ARG abundances in their stools compared to broiler farmers and control subjects. Tetracycline, β-lactam and macrolide resistance gene clusters dominated the resistome of all studied groups. No significant resistome alpha diversity differences were found among the four populations. However, the resistome beta diversity showed a separation of the mean resistome composition of pig and pork exposed workers from broiler farmers and controls, independent of their antimicrobial use. We demonstrated differences in resistome composition between slaughter line positions, pig versus poultry exposed workers, as well as differences between farmers and employees versus family members. In addition, we found a significant correlation between the bacteriome and resistome, and significant differences in the bacteriome composition between and within the studied subpopulations. Finally, an in-depth analysis of pig and poultry farms - of which also farm livestock resistomes were analysed - showed positive associations between the number of on-farm working hours and human faecal AMR loads.<br><br>CONCLUSION: We found that the total normalized faecal ARG carriage was larger in persons working in the Dutch pork production chain compared to poultry farmers and controls. Additionally, we showed significant differences in resistome and bacteriome composition of pig and pork exposed workers compared to a control group, as well as within-population (farms, slaughterhouse) compositional differences. The number of on-farm working hours and the farm type (pig or broiler) that persons live or work on are determinants for the human faecal resistome. Overall, our results may suggest direct or indirect livestock contact as a determinant for human ARG carriage. Future studies should further focus on the connection between the human and livestock resistome (i.e. transmission routes) to substantiate the evidence for livestock-associated resistome acquisition.}, }
@article {pmid32572149, year = {2020}, author = {Wutthi-In, M and Cheevadhanarak, S and Yasom, S and Kerdphoo, S and Thiennimitr, P and Phrommintikul, A and Chattipakorn, N and Kittichotirat, W and Chattipakorn, S}, title = {Gut Microbiota Profiles of Treated Metabolic Syndrome Patients and their Relationship with Metabolic Health.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {10085}, pmid = {32572149}, issn = {2045-2322}, mesh = {Aged ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects/*genetics/physiology ; Humans ; Male ; Metabolic Syndrome/classification/*microbiology ; Metagenome ; Metagenomics/methods ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Stress, Physiological/physiology ; Thailand ; }, abstract = {Metabolic syndrome (MetS) has become a worldwide health issue. Recent studies reveal that the human gut microbiota exerts a significant role in the pathogenesis of this disease. While drug treatments may greatly improve metabolic symptoms, little is known about the gut microbiota composition of these treated MetS patients. This study aimed to characterize the gut microbiota composition of treated-MetS patients and analyse the possibility of using gut microbiota as an indicator of metabolic conditions. 16S rRNA metagenomic sequencing approach was used to profile gut microbiota of 111 treated MetS patients from The Cohort of patients at a high Risk of Cardiovascular Events (CORE)-Thailand registry. Our results show that the gut microbiota profiles of MetS patients are diverse across individuals, but can be classified based on their similarity into three groups or enterotypes. We also showed several associations between species abundance and metabolic parameters that are enterotype specific. These findings suggest that information on the gut microbiota can be useful for assessing treatment options for MetS patients. In addition, any correlations between species abundance and human properties are likely specific to each microbial community.}, }
@article {pmid32299221, year = {2020}, author = {Sijbers, AM and Schoemaker, RJW and Nauta, A and Alkema, W}, title = {Revealing new leads for the impact of galacto-oligosaccharides on gut commensals and gut health benefits through text mining.}, journal = {Beneficial microbes}, volume = {11}, number = {3}, pages = {283-302}, doi = {10.3920/BM2019.0105}, pmid = {32299221}, issn = {1876-2891}, mesh = {Bifidobacterium/growth &amp; development/physiology ; *Data Mining ; Feces/microbiology ; Fermentation ; *Galactose ; *Gastrointestinal Microbiome ; Health ; Humans ; Oligosaccharides/*administration &amp; dosage ; Prebiotics/*analysis ; *Symbiosis ; }, abstract = {Galacto-oligosaccharides (GOS) are linked to various health benefits, such as the relief of symptoms of constipation. Part of the beneficial effects of GOS are thought to be the consequence of their bifidogenic effect, stimulating the growth of several Bifidobacterium species in vivo. However, GOS may exert additional effects by directly stimulating other bacterial species or by effects that bifidobacteria may have on other commensals in the gut. To get a better insight into the potential health effects induced by GOS, a good understanding of the gut ecosystem, the role of GOS and bifidobacteria is important. An increasing number of 16S DNA profiling and metagenomics studies have led to an expanding inventory of genera, species and strains that can be found in the human gut. To investigate the potential connection of these commensals with GOS and bifidobacteria, we have undertaken a text-mining study to chart the literature landscape around these commensals. To this end, we created controlled vocabularies describing GOS, a large set of gut commensals and a number of terms related to gut health, which were used to mine the entire MEDLINE database. Co-occurrence text-mining revealed that a large number of commensals found in the gut have a connection with Bifidobacterium species and with gut health effects. Word frequency analysis provided more insight into the functional nature of these relationships. Combined co-occurrence search results pointed to putative novel health benefits indirectly linked to bifidobacteria and GOS. The potential beneficial effects of GOS on the protection of epithelial function and epithelial barrier impairment and appendicitis are interesting novel leads. The text-mining approach reported here revealed a number of novel leads through which GOS could exert health effects and that could be investigated in dedicated studies.}, }
@article {pmid32247371, year = {2020}, author = {Keshavarzian, A and Engen, P and Bonvegna, S and Cilia, R}, title = {The gut microbiome in Parkinson's disease: A culprit or a bystander?.}, journal = {Progress in brain research}, volume = {252}, number = {}, pages = {357-450}, doi = {10.1016/bs.pbr.2020.01.004}, pmid = {32247371}, issn = {1875-7855}, mesh = {Animals ; Dopamine Agents/*pharmacology ; *Dysbiosis/immunology/metabolism/microbiology ; *Gastrointestinal Microbiome/immunology ; Humans ; *Inflammation/immunology/metabolism/microbiology ; *Life Style ; *Parkinson Disease/drug therapy/immunology/metabolism/microbiology ; *alpha-Synuclein/metabolism ; }, abstract = {In recent years, large-scale metagenomics projects such as the Human Microbiome Project placed the gut microbiota under the spotlight of research on its role in health and in the pathogenesis several diseases, as it can be a target for novel therapeutical approaches. The emerging concept of a microbiota modulation of the gut-brain axis in the pathogenesis of neurodegenerative disorders has been explored in several studies in animal models, as well as in human subjects. Particularly, research on changes in the composition of gut microbiota as a potential trigger for alpha-synuclein (α-syn) pathology in Parkinson's disease (PD) has gained increasing interest. In the present review, we first provide the basis to the understanding of the role of gut microbiota in healthy subjects and the molecular basis of the gut-brain interaction, focusing on metabolic and neuroinflammatory factors that could trigger the alpha-synuclein conformational changes and aggregation. Then, we critically explored preclinical and clinical studies reporting on the changes in gut microbiota in PD, as compared to healthy subjects. Furthermore, we examined the relationship between the gut microbiota and PD clinical features, discussing data consistently reported across studies, as well as the potential sources of inconsistencies. As a further step toward understanding the effects of gut microbiota on PD, we discussed the relationship between dysbiosis and response to dopamine replacement therapy, focusing on Levodopa metabolism. We conclude that further studies are needed to determine whether the gut microbiota changes observed so far in PD patients is the cause or, instead, it is merely a consequence of lifestyle changes associated with the disease. Regardless, studies so far strongly suggest that changes in microbiota appears to be impactful in pathogenesis of neuroinflammation. Thus, dysbiotic microbiota in PD could influence the disease course and response to medication, especially Levodopa. Future research will assess the impact of microbiota-directed therapeutic intervention in PD patients.}, }
@article {pmid31954373, year = {2020}, author = {Duan, C and Kuang, L and Xiang, X and Zhang, J and Zhu, Y and Wu, Y and Yan, Q and Liu, L and Li, T}, title = {Activated Drp1-mediated mitochondrial ROS influence the gut microbiome and intestinal barrier after hemorrhagic shock.}, journal = {Aging}, volume = {12}, number = {2}, pages = {1397-1416}, pmid = {31954373}, issn = {1945-4589}, mesh = {Animals ; Biomarkers ; Disease Models, Animal ; Dynamins/*genetics/metabolism ; Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome ; Intestinal Mucosa/*metabolism/*microbiology ; Male ; Metabolomics/methods ; Metagenomics/methods ; Mice ; Mitochondria/*genetics/*metabolism ; Permeability ; RNA, Ribosomal, 16S/genetics ; Reactive Oxygen Species/*metabolism ; Shock, Hemorrhagic/etiology/*metabolism ; }, abstract = {A role of the mitochondrial dynamin-related protein (Drp1) on gut microbiome composition and intestinal barrier function after hemorrhagic shock has not been identified previously and thus addressed in this study. Here, we used a combination of 16S rRNA gene sequencing and mass spectrometry-based metabolomics profiling in WT and Drp1 KO mouse models to examine the functional impact of activated Drp1 on the gut microbiome as well as mitochondrial metabolic regulation after hemorrhagic shock. Our data showed that changes in mitochondrial Drp1 activity participated in the regulation of intestinal barrier function after hemorrhagic shock. Activated Drp1 significantly perturbed gut microbiome composition in the Bacteroidetes phylum. The abundance of short-chain fatty acid (SCFA) producing microbes, such as Bacteroides, Butyricimonas and Odoribacter, was markedly decreased in mice after shock, and was inversely correlated with both the distribution of the tight junction protein ZO1 and intestinal permeability. Together, these data suggest that Drp1 activation perturbs the gut microbiome community and SCFA production in a ROS-specific manner and thereby substantially disturbs tight junctions and intestinal barrier function after hemorrhagic shock. Our findings provide novel insights for targeting Drp1-mediated mitochondrial function as well as the microbiome in the treatment of intestinal barrier dysfunction after shock.}, }
@article {pmid31907339, year = {2020}, author = {Wang, QJ and Shen, YE and Wang, X and Fu, S and Zhang, X and Zhang, YN and Wang, RT}, title = {Concomitant memantine and Lactobacillus plantarum treatment attenuates cognitive impairments in APP/PS1 mice.}, journal = {Aging}, volume = {12}, number = {1}, pages = {628-649}, pmid = {31907339}, issn = {1945-4589}, mesh = {Alzheimer Disease/*complications/etiology/metabolism ; Animals ; Animals, Genetically Modified ; Biomarkers ; Choline/administration &amp; dosage ; Cognitive Dysfunction/*etiology/*therapy ; Dietary Supplements ; Disease Models, Animal ; Gastrointestinal Microbiome ; *Lactobacillus plantarum ; Male ; Memantine/*pharmacology ; Metagenomics/methods ; Mice ; Probiotics ; Pyramidal Cells/metabolism ; }, abstract = {Trimethylamine-N-oxide (TMAO) is a gut microbial metabolite that promotes Alzheimer's disease (AD) progression. Given that probiotics can alleviate AD symptoms by inhibiting the synthesis of TMAO, here we investigated the correlation between TMAO and cognitive deterioration by measuring TMAO levels in the plasma of choline-treated APP/PS1 mice (an AD mouse model) with and without probiotic treatments. We found that declines in L.plantarum in the gut were associated with cognitive impairment. Moreover, 12-weeks of treatment with memantine plus L. plantarum ameliorated cognitive deterioration, decreased Αβ levels in the hippocampus, and protected neuronal integrity and plasticity. These effects were accompanied by reductions in TMAO synthesis and neuroinflammation. These experiments demonstrate that L. plantarum augments the beneficial therapeutic effects of memantine treatment in APP/PS1 mice by remodeling the intestinal microbiota, inhibiting the synthesis of TMAO, and reducing clusterin levels. Our results thus highlight intestinal microbiota as a potential therapeutic target to decrease the risk of AD.}, }
@article {pmid31905172, year = {2020}, author = {Diling, C and Longkai, Q and Yinrui, G and Yadi, L and Xiaocui, T and Xiangxiang, Z and Miao, Z and Ran, L and Ou, S and Dongdong, W and Yizhen, X and Xujiang, Y and Yang, BB and Qingping, W}, title = {CircNF1-419 improves the gut microbiome structure and function in AD-like mice.}, journal = {Aging}, volume = {12}, number = {1}, pages = {260-287}, pmid = {31905172}, issn = {1945-4589}, mesh = {Alzheimer Disease/etiology ; Animals ; Brain/*metabolism ; Disease Models, Animal ; Disease Susceptibility ; *Gastrointestinal Microbiome ; Gene Expression Profiling ; *Homeostasis ; Male ; Metagenomics/methods ; Mice ; Mice, Transgenic ; RNA, Circular/chemistry ; }, abstract = {Our pre-experiments found that the brain circRNA sequence profiles and gut microbiota in AD-like mice were changed, as circNF1-419 could enhance autophagy to ameliorate senile dementia in AD-like mice, so we conclude that there might some connections between circRNA and gut microbiome. Therefore, we use the over-expressed circNF1-419 adeno-associated virus (AAV) animal system with the aim of identifying possible connections. Our results showed that over-expression of circNF1-419 in brain not only influenced the cholinergic system of brain, but also changed the gut microbiota composition as the Candidatus Arthromitus, Lachnospiraceae FCS020 group, Lachnospiraceae UCG-006, and [Eubacterium] xylanophilum group, and the intestinal homeostasis and physiology, and even the gut microbiota trajectory in new born mice. These findings demonstrate a link between circRNA and gut microbiome, enlarge the 'microbiome- transcriptome' linkage library and provide more information on gut-brain axis.}, }
@article {pmid33423396, year = {2021}, author = {Piñol, J}, title = {Genotype by Sequencing: an alternative new method to amplicon metabarcoding and shotgun metagenomics for the assessment of eukaryote biodiversity.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13320}, pmid = {33423396}, issn = {1755-0998}, abstract = {The use of high-throughput DNA-sequencing (HTS) has revolutionised the assessment of biodiversity in plant and animal communities. There are two main approaches to estimate the identity and the relative species abundance (RSA) in complex mixtures using HTS: amplicon metabarcoding and shotgun metagenomics. While amplicon metabarcoding targets one or a few genomic regions, shotgun metagenomics randomly explores the genome of the species. In this issue of Molecular Ecology Resources, Wagemaker et al. (2021) present a new method, multi-species Genotyping by Sequencing (msGBS), as an alternative middle ground between metabarcoding and metagenomics. They apply the technique to mixtures of plant roots and report the remarkable capacity of msGBS to estimate the RSA. If validated in other labs and biological communities, msGBS might become a third method to explore the biodiversity of biological communities, especially of plants, where current techniques are struggling to get sufficient taxonomic resolution.}, }
@article {pmid33422504, year = {2021}, author = {Tan, SM and Ismail, MH and Cao, B}, title = {Biodiversity of Magnetotactic Bacteria in the tropical marine environment of Singapore revealed by metagenomic analysis.}, journal = {Environmental research}, volume = {}, number = {}, pages = {110714}, doi = {10.1016/j.envres.2021.110714}, pmid = {33422504}, issn = {1096-0953}, abstract = {Most studies on the diversity of magnetotactic bacteria (MTB) have been conducted on samples obtained from the Northern or the Southern hemispheres. The diversity of MTB in tropical Asia near the geo-equator, with a close-to-zero geomagnetic inclination, weak magnetic field and constantly high seawater temperature has never been explored. This study aims to decipher the diversity of MTB in the marine environment of Singapore through shotgun metagenomics. Although MTB has been acknowledged to be ubiquitous in aquatic environments, we did not observe magnetotactic behaviour in the samples. However, we detected the presence and determined the diversity of MTB through bioinformatic analyses. Metagenomic analysis suggested majority of the MTB in the seafloor sediments represents novel MTB taxa that cannot be classified at the species level. The relative abundance of MTB (∼0.2-1.69%) in the samples collected from the marine environment of Singapore was found to be substantially lower than studies for other regions. In contrast to other studies, the genera Magnetovibrio and Desulfamplus, but not Magnetococcus, were the dominant MTB. Additionally, we recovered 3 MTB genomic bins that are unclassified at the species level, with Magnetovibrio blakemorei being the closest-associated genome. All the recovered genomic bins contain homologs of at least 5 of the 7 mam genes but lack homologs for mamI, a membrane protein suggested to take part in the magenetosome invagination. This study fills in the knowledge gap of MTB biodiversity in the tropical marine environment near the geo-equator. Our findings will facilitate future research efforts aiming to unravel the ecological roles of MTB in the tropical marine environments as well as to bioprospecting novel MTB that have been adapted to tropical marine environments for biotechnological applications.}, }
@article {pmid33420281, year = {2021}, author = {Wongsaroj, L and Chanabun, R and Tunsakul, N and Prombutara, P and Panha, S and Somboonna, N}, title = {First reported quantitative microbiota in different livestock manures used as organic fertilizers in the Northeast of Thailand.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {102}, pmid = {33420281}, issn = {2045-2322}, support = {GB-A 61 024 23 05//Thai Government Budget Grant/ ; }, abstract = {Northeastern Thailand relies on agriculture as a major economic activity, and has used high levels of agrochemicals due to low facility, and salty sandy soil. To support soil recovery and sustainable agriculture, local farmers have used organic fertilizers from farmed animal feces. However, knowledge about these animal fecal manures remains minimal restricting their optimal use. Specifically, while bacteria are important for soil and plant growth, an abundance and a diversity of bacterial composition in these animal fecal manures have not been reported to allow selection and adjustment for a more effective organic fertilizer. This study thereby utilized metagenomics combined with 16S rRNA gene quantitative PCR (qPCR) and sequencing to analyze quantitative microbiota profiles in association with nutrients (N, P, K), organic matters, and the other physiochemical properties, of the commonly used earthworm manure and other manures from livestock animals (including breed and feeding diet variations) in the region. Unlike the other manures, the earthworm manure demonstrated more favorable nutrient profiles and physiochemical properties for forming fertile soil. Despite low total microbial biomass, the microbiota were enriched with maximal OTUs and Chao richness, and no plant pathogenic bacteria were found based on the VFDB database. The microbial metabolic potentials supported functions to promote crop growth, such as C, N and P cyclings, xenobiotic degradation, and synthesis of bioactive compounds. Pearson's correlation analyses indicated that the quantitative microbiota of the earthworm manure were clustered in the same direction as N, and conductivity, salinity, and water content were essential to control the microbiota of animal manures.}, }
@article {pmid32663709, year = {2020}, author = {Yao, Y and Yan, L and Chen, H and Wu, N and Wang, W and Wang, D}, title = {Cyclocarya paliurus polysaccharides alleviate type 2 diabetic symptoms by modulating gut microbiota and short-chain fatty acids.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {77}, number = {}, pages = {153268}, doi = {10.1016/j.phymed.2020.153268}, pmid = {32663709}, issn = {1618-095X}, mesh = {Adult ; Animals ; Diabetes Mellitus, Experimental/drug therapy/metabolism/microbiology ; Diabetes Mellitus, Type 2/*drug therapy/metabolism/microbiology ; Fatty Acids, Volatile/analysis/biosynthesis ; Feces/chemistry/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects/genetics ; Glucagon-Like Peptide 1/metabolism ; Humans ; Hypoglycemic Agents/*pharmacology ; Juglandaceae/*chemistry/microbiology ; Male ; Metabolomics ; Metagenome ; Plant Leaves/chemistry ; Plants, Medicinal/chemistry ; Polysaccharides/*pharmacology ; Rats, Sprague-Dawley ; }, abstract = {BACKGROUND: Cyclocarya paliurus polysaccharide (CCPP), a primary active component in the leaves of Cyclocarya paliurus (Batal.) Iljinsk (C. paliurus), has the ability to treat type 2 diabetes mellitus (T2DM), but cannot be digested by our digestive system. Therefore, mechanisms of regulating the gut microbiota and intestinal metabolites might exist.<br><br>PURPOSE: To reveal the potential mechanism of CCPP treatment, this study aimed to investigate the alterations of the gut microbiota and intestinal metabolites especially short chain fatty acids (SCFAs) in type 2 diabetic rats.<br><br>STUDY DESIGN AND METHODS: Type 2 diabetic rat models were developed, and the therapeutic effects of CCPP were evaluated. Metagenomics analysis was utilized to analyze the alterations to the gut microbiota, and UHPLC-QTOF/MS-based untargeted metabolomics analysis of colon contents was used to identify the differential intestinal metabolites. GC/MS was used to measure the SCFAs in rat's colon contents and human fecal inoculums. Furthermore, the expression of SCFA receptors including GPR41, GPR43 and GPR109a was verified by qRT-PCR and the concentration of glucagon-like peptide-1(GLP-1) and peptide tyrosinetyrosine (PYY) was measured by Elisa.<br><br>RESULTS: Inhibition of the blood glucose levels and improvements in glucose tolerance and serum lipid parameters were observed after CCPP treatment. Eleven SCFA-producing species including Ruminococcus_bromii, Anaerotruncus_colihominis, Clostridium_methylpentosum, Roseburia_intestinalis, Roseburia_hominis, Clostridium_asparagiforme, Pseudoflavonifractor_capillosus, Intestinimonas_butyriciproducens, Intestinimonas_sp._GD2, Oscillibacter_valericigenes and Oscillibacter_ruminantium were clearly increased in the CCPP group. Furthermore, our study indicated that CCPP increases the production of SCFAs both in vivo and in vitro, and the gut microbiota are the key factor of this process. The SCFA receptors including GPR41, GPR43 and GPR109a, were significantly stimulated in the CCPP treated rats, which was accompanied by the upregulated expression of GLP-1 and PYY.<br><br>CONCLUSION: These results demonstrated that CCPP could alleviate type 2 diabetic symptoms by increasing the SCFA-producing bacteria, promoting the production of SCFAs and upregulating SCFA-GLP1/PYY associated sensory mediators.}, }
@article {pmid32245390, year = {2020}, author = {Levy Karin, E and Mirdita, M and Söding, J}, title = {MetaEuk-sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {48}, pmid = {32245390}, issn = {2049-2618}, mesh = {*Algorithms ; Computational Biology/methods ; Databases, Genetic ; Eukaryota/*genetics ; High-Throughput Screening Assays ; Metagenome ; Metagenomics/instrumentation/*methods ; *Microbiota ; Molecular Sequence Annotation/*methods ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Metagenomics is revolutionizing the study of microorganisms and their involvement in biological, biomedical, and geochemical processes, allowing us to investigate by direct sequencing a tremendous diversity of organisms without the need for prior cultivation. Unicellular eukaryotes play essential roles in most microbial communities as chief predators, decomposers, phototrophs, bacterial hosts, symbionts, and parasites to plants and animals. Investigating their roles is therefore of great interest to ecology, biotechnology, human health, and evolution. However, the generally lower sequencing coverage, their more complex gene and genome architectures, and a lack of eukaryote-specific experimental and computational procedures have kept them on the sidelines of metagenomics.<br><br>RESULTS: MetaEuk is a toolkit for high-throughput, reference-based discovery, and annotation of protein-coding genes in eukaryotic metagenomic contigs. It performs fast searches with 6-frame-translated fragments covering all possible exons and optimally combines matches into multi-exon proteins. We used a benchmark of seven diverse, annotated genomes to show that MetaEuk is highly sensitive even under conditions of low sequence similarity to the reference database. To demonstrate MetaEuk's power to discover novel eukaryotic proteins in large-scale metagenomic data, we assembled contigs from 912 samples of the Tara Oceans project. MetaEuk predicted >12,000,000 protein-coding genes in 8 days on ten 16-core servers. Most of the discovered proteins are highly diverged from known proteins and originate from very sparsely sampled eukaryotic supergroups.<br><br>CONCLUSION: The open-source (GPLv3) MetaEuk software (https://github.com/soedinglab/metaeuk) enables large-scale eukaryotic metagenomics through reference-based, sensitive taxonomic and functional annotation. Video abstract.}, }
@article {pmid32241293, year = {2020}, author = {Sun, S and Jones, RB and Fodor, AA}, title = {Inference-based accuracy of metagenome prediction tools varies across sample types and functional categories.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {46}, pmid = {32241293}, issn = {2049-2618}, mesh = {Animals ; Chickens ; Computational Biology/*methods ; Databases, Factual ; Gorilla gorilla ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Metagenomics/*methods ; Mice ; *Microbiota ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; *Software ; *Soil Microbiology ; }, abstract = {BACKGROUND: Despite recent decreases in the cost of sequencing, shotgun metagenome sequencing remains more expensive compared with 16S rRNA amplicon sequencing. Methods have been developed to predict the functional profiles of microbial communities based on their taxonomic composition. In this study, we evaluated the performance of three commonly used metagenome prediction tools (PICRUSt, PICRUSt2, and Tax4Fun) by comparing the significance of the differential abundance of predicted functional gene profiles to those from shotgun metagenome sequencing across different environments.<br><br>RESULTS: We selected 7 datasets of human, non-human animal, and environmental (soil) samples that have publicly available 16S rRNA and shotgun metagenome sequences. As we would expect based on previous literature, strong Spearman correlations were observed between predicted gene compositions and gene relative abundance measured with shotgun metagenome sequencing. However, these strong correlations were preserved even when the abundance of genes were permuted across samples. This suggests that simple correlation coefficient is a highly unreliable measure for the performance of metagenome prediction tools. As an alternative, we compared the performance of genes predicted with PICRUSt, PICRUSt2, and Tax4Fun to sequenced metagenome genes in inference models associated with metadata within each dataset. With this approach, we found reasonable performance for human datasets, with the metagenome prediction tools performing better for inference on genes related to &quot;housekeeping&quot; functions. However, their performance degraded sharply outside of human datasets when used for inference.<br><br>CONCLUSION: We conclude that the utility of PICRUSt, PICRUSt2, and Tax4Fun for inference with the default database is likely limited outside of human samples and that development of tools for gene prediction specific to different non-human and environmental samples is warranted. Video abstract.}, }
@article {pmid32241287, year = {2020}, author = {Cao, S and Zhang, W and Ding, W and Wang, M and Fan, S and Yang, B and Mcminn, A and Wang, M and Xie, BB and Qin, QL and Chen, XL and He, J and Zhang, YZ}, title = {Structure and function of the Arctic and Antarctic marine microbiota as revealed by metagenomics.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {47}, doi = {10.1186/s40168-020-00826-9}, pmid = {32241287}, issn = {2049-2618}, mesh = {Antarctic Regions ; Arctic Regions ; Bacteria/*classification ; *Metagenomics ; Microbiota/*genetics ; Oceans and Seas ; Phylogeny ; Seawater/*microbiology ; }, abstract = {BACKGROUND: The Arctic and Antarctic are the two most geographically distant bioregions on earth. Recent sampling efforts and following metagenomics have shed light on the global ocean microbial diversity and function, yet the microbiota of polar regions has not been included in such global analyses.<br><br>RESULTS: Here a metagenomic study of seawater samples (n = 60) collected from different depths at 28 locations in the Arctic and Antarctic zones was performed, together with metagenomes from the Tara Oceans. More than 7500 (19%) polar seawater-derived operational taxonomic units could not be identified in the Tara Oceans datasets, and more than 3,900,000 protein-coding gene orthologs had no hits in the Ocean Microbial Reference Gene Catalog. Analysis of 214 metagenome assembled genomes (MAGs) recovered from the polar seawater microbiomes, revealed strains that are prevalent in the polar regions while nearly undetectable in temperate seawater. Metabolic pathway reconstruction for these microbes suggested versatility for saccharide and lipids biosynthesis, nitrate and sulfate reduction, and CO2 fixation. Comparison between the Arctic and Antarctic microbiomes revealed that antibiotic resistance genes were enriched in the Arctic while functions like DNA recombination were enriched in the Antarctic.<br><br>CONCLUSIONS: Our data highlight the occurrence of dominant and locally enriched microbes in the Arctic and Antarctic seawater with unique functional traits for environmental adaption, and provide a foundation for analyzing the global ocean microbiome in a more complete perspective. Video abstract.}, }
@article {pmid32197656, year = {2020}, author = {Dai, Z and Sevillano-Rivera, MC and Calus, ST and Bautista-de Los Santos, QM and Eren, AM and van der Wielen, PWJJ and Ijaz, UZ and Pinto, AJ}, title = {Disinfection exhibits systematic impacts on the drinking water microbiome.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {42}, pmid = {32197656}, issn = {2049-2618}, mesh = {Archaea/classification/drug effects ; Bacteria/classification/drug effects ; Disinfectants/*pharmacology ; *Disinfection ; Drinking Water/analysis/*microbiology ; Eukaryota/classification/drug effects ; Metagenomics ; *Microbiota ; Water Purification ; }, abstract = {Limiting microbial growth during drinking water distribution is achieved either by maintaining a disinfectant residual or through nutrient limitation without using a disinfectant. The impact of these contrasting approaches on the drinking water microbiome is not systematically understood. We use genome-resolved metagenomics to compare the structure, metabolic traits, and population genomes of drinking water microbiome samples from bulk drinking water across multiple full-scale disinfected and non-disinfected drinking water systems. Microbial communities cluster at the structural- and functional potential-level based on the presence/absence of a disinfectant residual. Disinfectant residual alone explained 17 and 6.5% of the variance in structure and functional potential of the drinking water microbiome, respectively, despite including multiple drinking water systems with variable source waters and source water communities and treatment strategies. The drinking water microbiome is structurally and functionally less diverse and variable across disinfected compared to non-disinfected systems. While bacteria were the most abundant domain, archaea and eukaryota were more abundant in non-disinfected and disinfected systems, respectively. Community-level differences in functional potential were driven by enrichment of genes associated with carbon and nitrogen fixation in non-disinfected systems and γ-aminobutyrate metabolism in disinfected systems likely associated with the recycling of amino acids. Genome-level analyses for a subset of phylogenetically-related microorganisms suggests that disinfection selects for microorganisms capable of using fatty acids, presumably from microbial decay products, via the glyoxylate cycle. Overall, we find that disinfection exhibits systematic selective pressures on the drinking water microbiome and may select for microorganisms able to utilize microbial decay products originating from disinfection-inactivated microorganisms. Video abstract.}, }
@article {pmid32197644, year = {2020}, author = {Böhm, ME and Razavi, M and Marathe, NP and Flach, CF and Larsson, DGJ}, title = {Discovery of a novel integron-borne aminoglycoside resistance gene present in clinical pathogens by screening environmental bacterial communities.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {41}, pmid = {32197644}, issn = {2049-2618}, mesh = {Aminoglycosides/*pharmacology ; Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/*drug effects ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/drug effects ; *Integrons ; Metagenomics ; Microbial Sensitivity Tests ; *Microbiota ; Waste Water/*microbiology ; }, abstract = {BACKGROUND: New antibiotic resistance determinants are generally discovered too late, long after they have irreversibly emerged in pathogens and spread widely. Early discovery of resistance genes, before or soon after their transfer to pathogens could allow more effective measures to monitor and reduce spread, and facilitate genetics-based diagnostics.<br><br>RESULTS: We modified a functional metagenomics approach followed by in silico filtering of known resistance genes to discover novel, mobilised resistance genes in class 1 integrons in wastewater-impacted environments. We identified an integron-borne gene cassette encoding a protein that conveys high-level resistance against aminoglycosides with a garosamine moiety when expressed in E. coli. The gene is named gar (garosamine-specific aminoglycoside resistance) after its specificity. It contains none of the functional domains of known aminoglycoside modifying enzymes, but bears characteristics of a kinase. By searching public databases, we found that the gene occurs in three sequenced, multi-resistant clinical isolates (two Pseudomonas aeruginosa and one Luteimonas sp.) from Italy and China, respectively, as well as in two food-borne Salmonella enterica isolates from the USA. In all cases, gar has escaped discovery until now.<br><br>CONCLUSION: To the best of our knowledge, this is the first time a novel resistance gene, present in clinical isolates, has been discovered by exploring the environmental microbiome. The gar gene has spread horizontally to different species on at least three continents, further limiting treatment options for bacterial infections. Its specificity to garosamine-containing aminoglycosides may reduce the usefulness of the newest semisynthetic aminoglycoside plazomicin, which is designed to avoid common aminoglycoside resistance mechanisms. Since the gene appears to be not yet common in the clinics, the data presented here enables early surveillance and maybe even mitigation of its spread.}, }
@article {pmid32138779, year = {2020}, author = {Heshiki, Y and Vazquez-Uribe, R and Li, J and Ni, Y and Quainoo, S and Imamovic, L and Li, J and Sørensen, M and Chow, BKC and Weiss, GJ and Xu, A and Sommer, MOA and Panagiotou, G}, title = {Predictable modulation of cancer treatment outcomes by the gut microbiota.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {28}, pmid = {32138779}, issn = {2049-2618}, mesh = {Adult ; Aged ; Animals ; Bacteria/*classification ; Disease Models, Animal ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Genetic Variation ; Humans ; Longitudinal Studies ; Lung Neoplasms/drug therapy ; Male ; *Metagenomics ; Mice ; Mice, Inbred C57BL ; Middle Aged ; Neoplasms/*drug therapy/*microbiology ; Prognosis ; Treatment Outcome ; }, abstract = {The gut microbiota has the potential to influence the efficacy of cancer therapy. Here, we investigated the contribution of the intestinal microbiome on treatment outcomes in a heterogeneous cohort that included multiple cancer types to identify microbes with a global impact on immune response. Human gut metagenomic analysis revealed that responder patients had significantly higher microbial diversity and different microbiota compositions compared to non-responders. A machine-learning model was developed and validated in an independent cohort to predict treatment outcomes based on gut microbiota composition and functional repertoires of responders and non-responders. Specific species, Bacteroides ovatus and Bacteroides xylanisolvens, were positively correlated with treatment outcomes. Oral gavage of these responder bacteria significantly increased the efficacy of erlotinib and induced the expression of CXCL9 and IFN-γ in a murine lung cancer model. These data suggest a predictable impact of specific constituents of the microbiota on tumor growth and cancer treatment outcomes with implications for both prognosis and therapy.}, }
@article {pmid32061251, year = {2020}, author = {Zhu, X and Campanaro, S and Treu, L and Seshadri, R and Ivanova, N and Kougias, PG and Kyrpides, N and Angelidaki, I}, title = {Metabolic dependencies govern microbial syntrophies during methanogenesis in an anaerobic digestion ecosystem.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {22}, doi = {10.1186/s40168-019-0780-9}, pmid = {32061251}, issn = {2049-2618}, mesh = {Acetates/metabolism ; Anaerobiosis ; Bacteria/classification/*metabolism ; Bioreactors ; Chemoautotrophic Growth ; Ecosystem ; Gene Expression Profiling ; Hydrogen/metabolism ; *Metabolic Networks and Pathways ; Metagenomics ; Methane/*biosynthesis ; Methanosarcina/metabolism ; *Microbiota ; }, abstract = {Methanogenesis, a biological process mediated by complex microbial communities, has attracted great attention due to its contribution to global warming and potential in biotechnological applications. The current study unveiled the core microbial methanogenic metabolisms in anaerobic vessel ecosystems by applying combined genome-centric metagenomics and metatranscriptomics. Here, we demonstrate that an enriched natural system, fueled only with acetate, could support a bacteria-dominated microbiota employing a multi-trophic methanogenic process. Moreover, significant changes, in terms of microbial structure and function, were recorded after the system was supplemented with additional H2. Methanosarcina thermophila, the predominant methanogen prior to H2 addition, simultaneously performed acetoclastic, hydrogenotrophic, and methylotrophic methanogenesis. The methanogenic pattern changed after the addition of H2, which immediately stimulated Methanomicrobia-activity and was followed by a slow enrichment of Methanobacteria members. Interestingly, the essential genes involved in the Wood-Ljungdahl pathway were not expressed in bacterial members. The high expression of a glycine cleavage system indicated the activation of alternative metabolic pathways for acetate metabolism, which were reconstructed in the most abundant bacterial genomes. Moreover, as evidenced by predicted auxotrophies, we propose that specific microbes of the community were forming symbiotic relationships, thus reducing the biosynthetic burden of individual members. These results provide new information that will facilitate future microbial ecology studies of interspecies competition and symbiosis in methanogenic niches. Video abstract.}, }
@article {pmid33398958, year = {2020}, author = {Tan, Y and Hu, H and Li, C and Luo, X and Tan, Y and Dai, L}, title = {[Research progress and applications of strain analysis based on metagenomic data].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {36}, number = {12}, pages = {2610-2621}, doi = {10.13345/j.cjb.200380}, pmid = {33398958}, issn = {1872-2075}, mesh = {Algorithms ; Computational Biology ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; }, abstract = {Strain is the fundamental unit in microbial taxonomy. The functional diversity among strains has great influence on host phenotypes. With the development of microbiome research, knowing the composition and functional capacities of complex microbial communities at the strain level has become increasingly valuable in scientific research and clinical applications. This review introduces the principles of bioinformatics algorithms for strain analysis based on metagenomic data, the applications in microbiome research and directions of future development.}, }
@article {pmid33398955, year = {2020}, author = {Zhang, Y and Cao, J and Zhao, N and Wang, J}, title = {[Virome: the next hotspot in microbiome research].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {36}, number = {12}, pages = {2566-2581}, doi = {10.13345/j.cjb.200372}, pmid = {33398955}, issn = {1872-2075}, mesh = {Animals ; Humans ; Metagenome ; Metagenomics ; *Microbiota/genetics ; Virome ; *Viruses/genetics ; }, abstract = {Virome is the collective term for the viral collection or viral metagenomes that are distributed in various environments. Viruses can be found in bodies of water, glaciers, plants, animals, and even some viruses, which are classified as eukaryotes, prokaryotes and subviruses. Viruses play very important role in maintaining environmental homeostasis and ecosystem balance, and are especially closely related to human health. In recent years, with the advancement of sequencing technology and data analysis, we are able to gain more insights into the virome and explore its potential role in the ecological niche by metagenomic sequencing. A large amount of viral data have been obtained from glaciers, oceans, and various plants and animals, and numerous unknown viruses have been discovered. Virome has been studied mainly through metagenomic data mining, as well as virus-like particles separation and enrichment. To date, several different methods for viral isolation and enrichment exist, and numerous bioinformatic analyses of the virome have been performed. However, there is a lack of specific and complete reviews on the enrichment and data analysis methods for the virome. Thus, our review will summarize viral isolation and enrichment methods and data analysis, and present some of the landmark research conducted by the enrichment method, to provide a reference for researchers of interest and further advance the field of virome research.}, }
@article {pmid33261862, year = {2021}, author = {Liu, D and Legras, JL and Zhang, P and Chen, D and Howell, K}, title = {Diversity and dynamics of fungi during spontaneous fermentations and association with unique aroma profiles in wine.}, journal = {International journal of food microbiology}, volume = {338}, number = {}, pages = {108983}, doi = {10.1016/j.ijfoodmicro.2020.108983}, pmid = {33261862}, issn = {1879-3460}, mesh = {Agriculture ; *Biodiversity ; Farms ; *Fermentation ; Fungi/chemistry/*classification/metabolism ; *Microbiota ; Odorants ; Saccharomyces cerevisiae ; Vitis/microbiology ; Wine/*microbiology ; }, abstract = {Microbial ecology is an integral part of an agricultural ecosystem and influences the quality of agricultural commodities. Microbial activity influences grapevine health and crop production, conversion of sugar to ethanol during fermentation, thus forming wine aroma and flavour. There are regionally differentiated microbial patterns in grapevines and must but how microbial patterns contribute to wine regional distinctiveness (terroir) at small scale (<100 km) is not well defined. Here we characterise fungal communities, yeast populations, and Saccharomyces cerevisiae populations during spontaneous fermentation using metagenomics and population genetics to investigate microbial distribution and fungal contributions to the resultant wine. We found differentiation of fungi, yeasts, and S. cerevisiae between geographic origins (estate/vineyard), with influences from the grape variety. Growth and dominance of S. cerevisiae during fermentation reshaped the fungal community and showed geographic structure at the strain level. Associations between fungal microbiota diversity and wine chemicals suggest that S. cerevisiae plays a primary role in determining wine aroma profiles at a sub-regional scale. The geographic distribution at scales of less than 12 km supports that differential microbial communities, including the dominant fermentative yeast S. cerevisiae can be distinct in a local setting. These findings provide further evidence for microbial contributions to wine terroir, and perspectives for sustainable agricultural practices to maintain microbial diversity and optimise fermentation function to craft beverage quality.}, }
@article {pmid33067398, year = {2020}, author = {Shibl, AA and Isaac, A and Ochsenkühn, MA and Cárdenas, A and Fei, C and Behringer, G and Arnoux, M and Drou, N and Santos, MP and Gunsalus, KC and Voolstra, CR and Amin, SA}, title = {Diatom modulation of select bacteria through use of two unique secondary metabolites.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {44}, pages = {27445-27455}, pmid = {33067398}, issn = {1091-6490}, mesh = {Animals ; Bacteria/genetics/*growth &amp; development ; Cinnamates/metabolism ; Depsides/metabolism ; Diatoms/genetics/*metabolism ; Dicarboxylic Acids/metabolism ; Gene Expression Profiling ; Metabolomics ; Metagenome ; Metagenomics ; Microbiota/*physiology ; Oceans and Seas ; Phytoplankton/genetics/*metabolism ; Secondary Metabolism/physiology ; *Water Microbiology ; }, abstract = {Unicellular eukaryotic phytoplankton, such as diatoms, rely on microbial communities for survival despite lacking specialized compartments to house microbiomes (e.g., animal gut). Microbial communities have been widely shown to benefit from diatom excretions that accumulate within the microenvironment surrounding phytoplankton cells, known as the phycosphere. However, mechanisms that enable diatoms and other unicellular eukaryotes to nurture specific microbiomes by fostering beneficial bacteria and repelling harmful ones are mostly unknown. We hypothesized that diatom exudates may tune microbial communities and employed an integrated multiomics approach using the ubiquitous diatom Asterionellopsis glacialis to reveal how it modulates its naturally associated bacteria. We show that A. glacialis reprograms its transcriptional and metabolic profiles in response to bacteria to secrete a suite of central metabolites and two unusual secondary metabolites, rosmarinic acid and azelaic acid. While central metabolites are utilized by potential bacterial symbionts and opportunists alike, rosmarinic acid promotes attachment of beneficial bacteria to the diatom and simultaneously suppresses the attachment of opportunists. Similarly, azelaic acid enhances growth of beneficial bacteria while simultaneously inhibiting growth of opportunistic ones. We further show that the bacterial response to azelaic acid is numerically rare but globally distributed in the world's oceans and taxonomically restricted to a handful of bacterial genera. Our results demonstrate the innate ability of an important unicellular eukaryotic group to modulate select bacteria in their microbial consortia, similar to higher eukaryotes, using unique secondary metabolites that regulate bacterial growth and behavior inversely across different bacterial populations.}, }
@article {pmid31562947, year = {2020}, author = {Hynönen, U and Zoetendal, EG and Virtala, AK and Shetty, S and Hasan, S and Jakava-Viljanen, M and de Vos, WM and Palva, A}, title = {Molecular ecology of the yet uncultured bacterial Ct85-cluster in the mammalian gut.}, journal = {Anaerobe}, volume = {62}, number = {}, pages = {102104}, doi = {10.1016/j.anaerobe.2019.102104}, pmid = {31562947}, issn = {1095-8274}, mesh = {Animals ; Cluster Analysis ; Databases, Genetic ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Mammals ; *Metagenome ; *Metagenomics/methods ; Molecular Typing ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In our previous studies on irritable bowel syndrome (IBS) -associated microbiota by molecular methods, we demonstrated that a particular 16S rRNA gene amplicon was more abundant in the feces of healthy subjects or mixed type IBS (IBS-M) -sufferers than in the feces of individuals with diarrhea-type IBS (IBS-D). In the current study, we demonstrated that this, so called Ct85-amplicon, consists of a cluster of very heterogeneous 16S rRNA gene sequences, and defined six 16S rRNA gene types, a to f, within this cluster, each representing a novel species-, genus- or family level taxon. We then designed specific PCR primers for these sequence types, mapped the distribution of the Ct85-cluster sequences and that of the newly defined sequence types in several animal species and compared the sequence types present in the feces of healthy individuals and IBS sufferers using two IBS study cohorts, Finnish and Dutch. Various Ct85-cluster sequence types were detected in the fecal samples of several companion and production animal species with remarkably differing prevalences and abundances. The Ct85 sequence type composition of swine closely resembled that of humans. One of the five types (d) shared between humans and swine was not present in any other animals tested, while one sequence type (b) was found only in human samples. In both IBS study cohorts, one type (e) was more prevalent in healthy individuals than in the IBS-M group. By revealing various sequence types in the widespread Ct85-cluster and their distribution, the results improve our understanding of these uncultured bacteria, which is essential for future efforts to cultivate representatives of the Ct85-cluster and reveal their roles in IBS.}, }
@article {pmid33396683, year = {2020}, author = {Kuramae, EE and Dimitrov, MR and da Silva, GHR and Lucheta, AR and Mendes, LW and Luz, RL and Vet, LEM and Fernandes, TV}, title = {On-Site Blackwater Treatment Fosters Microbial Groups and Functions to Efficiently and Robustly Recover Carbon and Nutrients.}, journal = {Microorganisms}, volume = {9}, number = {1}, pages = {}, doi = {10.3390/microorganisms9010075}, pmid = {33396683}, issn = {2076-2607}, support = {729.004.003//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 2013/50351-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 206884/2014-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 99999.008090/2015-07;0622/2014//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, abstract = {Wastewater is considered a renewable resource water and energy. An advantage of decentralized sanitation systems is the separation of the blackwater (BW) stream, contaminated with human pathogens, from the remaining household water. However, the composition and functions of the microbial community in BW are not known. In this study, we used shotgun metagenomics to assess the dynamics of microbial community structure and function throughout a new BW anaerobic digestion system installed at The Netherlands Institute of Ecology. Samples from the influent (BW), primary effluent (anaerobic digested BW), sludge and final effluent of the pilot upflow anaerobic sludge blanket (UASB) reactor and microalgae pilot tubular photobioreactor (PBR) were analyzed. Our results showed a decrease in microbial richness and diversity followed by a decrease in functional complexity and co-occurrence along the different modules of the bioreactor. The microbial diversity and function decrease were reflected both changes in substrate composition and wash conditions. Our wastewater treatment system also decreased microbial functions related to pathogenesis. In summary, the new sanitation system studied here fosters microbial groups and functions that allow the system to efficiently and robustly recover carbon and nutrients while reducing pathogenic groups, ultimately generating a final effluent safe for discharge and reuse.}, }
@article {pmid33395419, year = {2021}, author = {Macher, JN and Prazeres, M and Taudien, S and Jompa, J and Sadekov, A and Renema, W}, title = {Integrating morphology and metagenomics to understand taxonomic variability of Amphisorus (Foraminifera, Miliolida) from Western Australia and Indonesia.}, journal = {PloS one}, volume = {16}, number = {1}, pages = {e0244616}, doi = {10.1371/journal.pone.0244616}, pmid = {33395419}, issn = {1932-6203}, abstract = {Foraminifera are a group of mostly marine protists with high taxonomic diversity. Species identification is often complex, as both morphological and molecular approaches can be challenging due to a lack of unique characters and reference sequences. An integrative approach combining state of the art morphological and molecular tools is therefore promising. In this study, we analysed large benthic Foraminifera of the genus Amphisorus from Western Australia and Indonesia. Based on previous findings on high morphological variability observed in the Soritidae and the discontinuous distribution of Amphisorus along the coast of western Australia, we expected to find multiple morphologically and genetically unique Amphisorus types. In order to gain detailed insights into the diversity of Amphisorus, we applied micro CT scanning and shotgun metagenomic sequencing. We identified four distinct morphotypes of Amphisorus, two each in Australia and Indonesia, and showed that each morphotype is a distinct genotype. Furthermore, metagenomics revealed the presence of three dinoflagellate symbiont clades. The most common symbiont was Fugacium Fr5, and we could show that its genotypes were mostly specific to Amphisorus morphotypes. Finally, we assembled the microbial taxa associated with the two Western Australian morphotypes, and analysed their microbial community composition. Even though each Amphisorus morphotype harboured distinct bacterial communities, sampling location had a stronger influence on bacterial community composition, and we infer that the prokaryotic community is primarily shaped by the microhabitat rather than host identity. The integrated approach combining analyses of host morphology and genetics, dinoflagellate symbionts, and associated microbes leads to the conclusion that we identified distinct, yet undescribed taxa of Amphisorus. We argue that the combination of morphological and molecular methods provides unprecedented insights into the diversity of foraminifera, which paves the way for a deeper understanding of their biodiversity, and facilitates future taxonomic and ecological work.}, }
@article {pmid33277504, year = {2020}, author = {Tian, L and Wang, XW and Wu, AK and Fan, Y and Friedman, J and Dahlin, A and Waldor, MK and Weinstock, GM and Weiss, ST and Liu, YY}, title = {Deciphering functional redundancy in the human microbiome.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {6217}, pmid = {33277504}, issn = {2041-1723}, support = {UH3 OD023268/OD/NIH HHS/United States ; U19 AI095219/AI/NIAID NIH HHS/United States ; U01 HL089856/HL/NHLBI NIH HHS/United States ; R01 AI141529/AI/NIAID NIH HHS/United States ; R01 HD093761/HD/NICHD NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Algorithms ; Bacteria/classification/genetics ; Feces/*microbiology ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Gene Regulatory Networks ; Gene Transfer, Horizontal ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Models, Genetic ; }, abstract = {Although the taxonomic composition of the human microbiome varies tremendously across individuals, its gene composition or functional capacity is highly conserved - implying an ecological property known as functional redundancy. Such functional redundancy has been hypothesized to underlie the stability and resilience of the human microbiome, but this hypothesis has never been quantitatively tested. The origin of functional redundancy is still elusive. Here, we investigate the basis for functional redundancy in the human microbiome by analyzing its genomic content network - a bipartite graph that links microbes to the genes in their genomes. We find that this network exhibits several topological features that favor high functional redundancy. Furthermore, we develop a simple genome evolution model to generate genomic content network, finding that moderate selection pressure and high horizontal gene transfer rate are necessary to generate genomic content networks with key topological features that favor high functional redundancy. Finally, we analyze data from two published studies of fecal microbiota transplantation (FMT), finding that high functional redundancy of the recipient's pre-FMT microbiota raises barriers to donor microbiota engraftment. This work elucidates the potential ecological and evolutionary processes that create and maintain functional redundancy in the human microbiome and contribute to its resilience.}, }
@article {pmid32994464, year = {2020}, author = {Veses, V and González-Torres, P and Carbonetto, B and Del Mar Jovani-Sancho, M and González-Martínez, R and Cortell-Ballester, I and Sheth, CC}, title = {Dental black plaque: metagenomic characterization and comparative analysis with white-plaque.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {15962}, pmid = {32994464}, issn = {2045-2322}, mesh = {Adult ; Cluster Analysis ; Dental Plaque/*genetics ; Dysbiosis/genetics ; Female ; Genes, Bacterial/genetics ; Heme/genetics/metabolism ; Humans ; Male ; Metagenome/genetics ; Metagenomics/methods ; Microbiota/*genetics ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; Spain ; }, abstract = {Extrinsic black dental staining is an external dental discoloration of bacterial origin, considered a special form of dental plaque. Currently, there is no definitive therapeutic option for eliminating black stain. This study employed 16S rRNA metagenomics to analyze black stain and white-plaque samples from 27 adult volunteers. Study objectives were to: describe the microbial diversity of adult black stain samples; characterize their taxonomic profile; compare the microbiomes of black stain versus white-plaque from adult volunteers and propose a functional map of the black stain microbiome using PICRUSt2. The black stain microbiome was poorer in species diversity as compared to white-plaque. The five most abundant genera in black stain were Capnocytophaga, Leptotrichia, Fusobacterium, Corynebacterium and Streptococcus. Functional analysis of microbial species revealed conserved and consistent clustering of functional pathways within and between black stain and white-plaque microbiomes. We describe enrichment of heme biosynthetic pathways in black stain. Our results suggest that the dysbiosis in black stain resembles &quot;orally healthy&quot; communities. The increased abundance of heme biosynthetic pathways suggests that heme-dependent iron sequestration and subsequent metabolism are key for black stain formation. Further research should decipher the regulation of heme biosynthetic genes and characterize the temporal sequence leading to colonization and dysbiosis.}, }
@article {pmid32127018, year = {2020}, author = {Qin, N and Liang, P and Wu, C and Wang, G and Xu, Q and Xiong, X and Wang, T and Zolfo, M and Segata, N and Qin, H and Knight, R and Gilbert, JA and Zhu, TF}, title = {Longitudinal survey of microbiome associated with particulate matter in a megacity.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {55}, pmid = {32127018}, issn = {1474-760X}, mesh = {*Air Pollution ; China ; Cities ; Environmental Monitoring/methods ; *Metagenome ; Metagenomics/methods ; *Microbiota ; *Smog ; }, abstract = {BACKGROUND: While the physical and chemical properties of airborne particulate matter (PM) have been extensively studied, their associated microbiome remains largely unexplored. Here, we performed a longitudinal metagenomic survey of 106 samples of airborne PM2.5 and PM10 in Beijing over a period of 6 months in 2012 and 2013, including those from several historically severe smog events.<br><br>RESULTS: We observed that the microbiome composition and functional potential were conserved between PM2.5 and PM10, although considerable temporal variations existed. Among the airborne microorganisms, Propionibacterium acnes, Escherichia coli, Acinetobacter lwoffii, Lactobacillus amylovorus, and Lactobacillus reuteri dominated, along with several viral species. We further identified an extensive repertoire of genes involved in antibiotic resistance and detoxification, including transporters, transpeptidases, and thioredoxins. Sample stratification based on Air Quality Index (AQI) demonstrated that many microbial species, including those associated with human, dog, and mouse feces, exhibit AQI-dependent incidence dynamics. The phylogenetic and functional diversity of air microbiome is comparable to those of soil and water environments, as its composition likely derives from a wide variety of sources.<br><br>CONCLUSIONS: Airborne particulate matter accommodates rich and dynamic microbial communities, including a range of microbial elements that are associated with potential health consequences.}, }
@article {pmid32093762, year = {2020}, author = {Nazeen, S and Yu, YW and Berger, B}, title = {Carnelian uncovers hidden functional patterns across diverse study populations from whole metagenome sequencing reads.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {47}, pmid = {32093762}, issn = {1474-760X}, support = {T15LM007092//National Institute of Health (NIH)/International ; R01 GM108348/GM/NIGMS NIH HHS/United States ; }, mesh = {Crohn Disease/genetics/microbiology ; Diabetes Mellitus, Type 2/genetics/microbiology ; Gastrointestinal Microbiome/*genetics ; Genome, Human ; Humans ; Metabolic Networks and Pathways ; *Metagenome ; Metagenomics/*methods ; Parkinson Disease/genetics/microbiology ; *Software ; }, abstract = {Microbial populations exhibit functional changes in response to different ambient environments. Although whole metagenome sequencing promises enough raw data to study those changes, existing tools are limited in their ability to directly compare microbial metabolic function across samples and studies. We introduce Carnelian, an end-to-end pipeline for metabolic functional profiling uniquely suited to finding functional trends across diverse datasets. Carnelian is able to find shared metabolic pathways, concordant functional dysbioses, and distinguish Enzyme Commission (EC) terms missed by existing methodologies. We demonstrate Carnelian's effectiveness on type 2 diabetes, Crohn's disease, Parkinson's disease, and industrialized and non-industrialized gut microbiome cohorts.}, }
@article {pmid32673387, year = {2020}, author = {Zhao, F and Zhang, D and Ge, C and Zhang, L and Reinach, PS and Tian, X and Tao, C and Zhao, Z and Zhao, C and Fu, W and Zeng, C and Chen, W}, title = {Metagenomic Profiling of Ocular Surface Microbiome Changes in Meibomian Gland Dysfunction.}, journal = {Investigative ophthalmology &amp; visual science}, volume = {61}, number = {8}, pages = {22}, pmid = {32673387}, issn = {1552-5783}, mesh = {Adult ; *Campylobacter coli/genetics/immunology/pathogenicity ; *Campylobacter jejuni/genetics/immunology/pathogenicity ; Conjunctiva/microbiology ; *Enterococcus faecium/genetics/immunology/pathogenicity ; Eyelids/*microbiology ; Female ; Gene Expression Profiling/methods ; Humans ; Immune Evasion ; Male ; *Meibomian Gland Dysfunction/metabolism/microbiology ; Metagenomics/*methods ; Microbiota/*genetics ; *Tears/metabolism/microbiology ; }, abstract = {Purpose: Ocular surface microbiome changes can affect meibomian gland dysfunction (MGD) development. This study aimed to delineate differences among the microbiome of eyelid skin, conjunctiva, and meibum in healthy controls (HCs) and patients afflicted with MGD.<br><br>Methods: Shotgun metagenomic analysis was used to determine if there are differences between the microbial communities in ocular sites surrounding the meibomian gland in healthy individuals and patients afflicted with MGD.<br><br>Results: The meibum bacterial content of these microbiomes was dissimilar in these two different types of individuals. Almost all of the most significant taxonomic changes in the meibum microbiome of individuals with MGD were also present in their eyelid skin, but not in the conjunctiva. Such site-specific microbe pattern changes accompany increases in the gene expression levels controlling carbohydrate and lipid metabolism. Most of the microbiomes in patients with MGD possess a microbe population capable of metabolizing benzoate. Pathogens known to underlie ocular infection were evident in these individuals. MGD meibum contained an abundance of Campylobacter coli, Campylobacter jejuni, and Enterococcus faecium pathogens, which were almost absent from HCs. Functional annotation indicated that in the microbiomes of MGD meibum their capability to undergo chemotaxis, display immune evasive virulence, and mediate type IV secretion was different than that in the microbiomes of meibum isolated from HCs.<br><br>Conclusions: MGD meibum contains distinct microbiota whose immune evasive virulence is much stronger than that in the HCs. Profiling differences between the meibum microbiome makeup in HCs and patients with MGD characterizes changes of microbial communities associated with the disease status.}, }
@article {pmid32448430, year = {2020}, author = {Pan, S and Chen, R}, title = {Metaproteomic analysis of human gut microbiome in digestive and metabolic diseases.}, journal = {Advances in clinical chemistry}, volume = {97}, number = {}, pages = {1-12}, doi = {10.1016/bs.acc.2019.12.002}, pmid = {32448430}, issn = {2162-9471}, mesh = {Digestive System Diseases/*metabolism ; *Gastrointestinal Microbiome ; Humans ; Metabolic Diseases/*metabolism ; Proteins/*metabolism ; *Proteomics ; }, abstract = {Metaproteomics, as a subfield of proteomics, has quickly emerged as a pivotal tool for global characterization of a microbiome system at a functional level. It has been increasingly applied in studying human digestive and metabolic diseases, and provides information-rich data to identify the dysbiosis of human gut microbiome related to healthy or disease states to elucidate the molecular events underlying host-microbiota interplays. While significant technical challenges still exist, this emerging technology has been demonstrated to provide essential information in interrogating functional changes in the human gut microbiome, complementary to metagenomics and metatranscriptomics. This chapter overviews the overall metaproteomic work flow and its recent applications in studying human gut microbiome relevant to digestive and metabolic diseases.}, }
@article {pmid32679124, year = {2020}, author = {Ibrahim, KS and Craft, JA and Biswas, L and Spencer, J and Shu, X}, title = {Etifoxine reverses weight gain and alters the colonic bacterial community in a mouse model of obesity.}, journal = {Biochemical pharmacology}, volume = {180}, number = {}, pages = {114151}, doi = {10.1016/j.bcp.2020.114151}, pmid = {32679124}, issn = {1873-2968}, mesh = {Animals ; Anti-Anxiety Agents/pharmacology/therapeutic use ; Colon/*drug effects/microbiology/physiology ; Diet, High-Fat/adverse effects ; Disease Models, Animal ; Gastrointestinal Microbiome/*drug effects/physiology ; Male ; Mice ; Mice, Inbred C57BL ; Obesity/*drug therapy/etiology/physiopathology ; Oxazines/*pharmacology/*therapeutic use ; Weight Gain/*drug effects/physiology ; Weight Loss/drug effects/physiology ; }, abstract = {Obesity is intimately associated with diet and dysbiosis of gut microorganisms but anxiolytics, widely used in treatment of psychiatric conditions, frequently result in weight gain and associated metabolic disorders. We are interested in effects of the anxiolytic etifoxine, which has not been studied with respect to weight gain or effects on gut microorganisms. Here we induced obesity in mice by feeding a high-fat diet but found that intraperitoneal administration of etifoxine resulted in weight loss and decreased serum cholesterol and triglycerides. Obese mice had increased hepatic transcripts associated with lipid metabolism (cyp7a1, cyp27a1, abcg1 and LXRα) and inflammatory factors (TNFα and IL18) but these effects were reversed after etifoxine treatment other than cyp7a1. Taxonomic profiles of the organisms from the caecum were generated by 16S rRNA gene sequencing and Obese and etifoxine mice show differences by diversity metrics, Differential Abundance and functional metagenomics. Organisms in genus Oscillospira and genera from Lachnospiraceae family and Clostridiales order are higher in Control than Obese and at intermediate levels with etifoxine treatment. With respect to community metabolic potential, etifoxine mice have characteristics similar to Control and particularly with respect to metabolism of butanoate, sphingolipid, lipid biosynthesis and xenobiotic metabolism. We suggest mechanisms where-by etifoxine influences processes of host, such as on bile acid synthesis, and microbiota, such as signalling from production of butanoate and sphingosine, resulting in decreased cholesterol, lipids and inflammatory factors. We speculate that the indirect effect of etifoxine on microbial composition is mediated by microbial β-glucuronidases that metabolise excreted etifoxine glucuronides.}, }
@article {pmid33202299, year = {2021}, author = {Lu, M and Zhou, W and Ji, F and Wu, J and Nie, Y and Ren, C and Xu, Y}, title = {Profiling prokaryotic community in pit mud of Chinese strong-aroma type liquor by using oligotrophic culturing.}, journal = {International journal of food microbiology}, volume = {337}, number = {}, pages = {108951}, doi = {10.1016/j.ijfoodmicro.2020.108951}, pmid = {33202299}, issn = {1879-3460}, abstract = {Pit mud microbiota plays a key role in flavour production for Chinese strong-aroma type liquor. However, the pit mud microbiota cannot be cultured in laboratory. In this study, an oligotrophic medium with acetate as carbon source was used to enrich pit mud microbiota. The 16S rRNA gene amplicon sequencing was applied to examine the microbial dynamics of the enrichment consortia. Both methanogens and bacteria were simultaneously enriched. Euryarchaeota, Bacteroidetes and Firmicutes were the top 3 enriched phyla, and 31 genera were successfully enriched. More specifically, 11 genera (65%) out of the 17 dominant genera in pit mud were successfully enriched, including Petrimonas, Proteiniphilum, Anaerocella, Hydrogenispora, Methanosarcina, Fermentimonas, LNR_A2-18, Sedimentibacter, Lutispora, Syntrophomonas and Aminobacterium. Furthermore, 20 rare genera in the analyzed pit mud samples were also enriched. Aceticlastic Methanosaeta and Methanosarcina were found to be dominant methanogens in the enrichment consortia. Metagenomic sequencing was then applied to the enriched microbial consortia to explore the metabolic potentials of pit mud microbes. Aceticlastic methanogenesis pathway of Methanosaeta was reconstructed. Furthermore, 26 high-quality metagenome-assembled genomes (MAGs) were obtained based on the metagenomic binning analysis. Moreover, nutrients in pit mud were found to be crucial to sustain the methanogenesis of the enriched microbial consortia. These results suggested that the enrichment approach by using oligotrophic culturing can effectively cultivate the pit mud microbiota. Combined with metagenomics, the oligotrophic culturing will be greatly helpful to decipher the community composition and metabolic potentials of pit mud microbiota.}, }
@article {pmid32844199, year = {2020}, author = {Qian, Y and Yang, X and Xu, S and Huang, P and Li, B and Du, J and He, Y and Su, B and Xu, LM and Wang, L and Huang, R and Chen, S and Xiao, Q}, title = {Gut metagenomics-derived genes as potential biomarkers of Parkinson's disease.}, journal = {Brain : a journal of neurology}, volume = {143}, number = {8}, pages = {2474-2489}, doi = {10.1093/brain/awaa201}, pmid = {32844199}, issn = {1460-2156}, abstract = {Identification of the gut microbiome compositions associated with disease has become a research focus worldwide. Emerging evidence has revealed the presence of gut microbiota dysbiosis in Parkinson's disease. In this study, we aimed to identify the gut microbiome associated with Parkinson's disease and subsequently to screen and to validate potential diagnostic biomarkers of Parkinson's disease. This case-control study investigated gut microbial genes in faeces from 40 volunteer Chinese patients with Parkinson's disease and their healthy spouses using shotgun metagenomic sequencing. Furthermore, the identified specific gut microbial gene markers were validated with real-time PCR in an independent Chinese cohort of 78 Parkinson's disease patients, 75 control subjects, 40 patients with multiple system atrophy and 25 patients with Alzheimer's disease. We developed the first gut microbial gene catalogue associated with Parkinson's disease. Twenty-five gene markers were identified that distinguished Parkinson's disease patients from healthy control subjects, achieving an area under the receiver operating characteristic curve (AUC) of 0.896 (95% confidence interval: 83.1-96.1%). A highly accurate Parkinson's disease index, which was not influenced by disease severity or Parkinson's disease medications, was created. Testing these gene markers using quantitative PCR distinguished Parkinson's disease patients from healthy controls not only in the 40 couples (AUC = 0.922, 95% confidence interval: 86.4-98.0%), but also in an independent group of 78 patients with Parkinson's disease and 75 healthy control subjects (AUC = 0.905, 95% confidence interval: 86.0-95.1%). This classifier also performed a differential diagnosis power in discriminating these 78 patients with Parkinson's disease from a cohort of 40 patients with multiple system atrophy and 25 patients with Alzheimer's disease based on the panel of 25 biomarkers. Based on our results, the identified Parkinson's disease index based on the gene set from the gut microbiome may be a potential diagnostic biomarker of Parkinson's disease.}, }
@article {pmid32081987, year = {2020}, author = {Afshari, R and Pillidge, CJ and Read, E and Rochfort, S and Dias, DA and Osborn, AM and Gill, H}, title = {New insights into cheddar cheese microbiota-metabolome relationships revealed by integrative analysis of multi-omics data.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {3164}, pmid = {32081987}, issn = {2045-2322}, abstract = {Cheese microbiota and metabolites and their inter-relationships that underpin specific cheese quality attributes remain poorly understood. Here we report that multi-omics and integrative data analysis (multiple co-inertia analysis, MCIA) can be used to gain deeper insights into these relationships and identify microbiota and metabolite fingerprints that could be used to monitor product quality and authenticity. Our study into different brands of artisanal and industrial cheddar cheeses showed that Streptococcus, Lactococcus and Lactobacillus were the dominant taxa with overall microbial community structures differing not only between industrial and artisanal cheeses but also among different cheese brands. Metabolome analysis also revealed qualitative and semi-quantitative differences in metabolites between different cheeses. This also included the presence of two compounds (3-hydroxy propanoic acid and O-methoxycatechol-O-sulphate) in artisanal cheese that have not been previously reported in any type of cheese. Integrative analysis of multi-omics datasets revealed that highly similar cheeses, identical in age and appearance, could be distinctively clustered according to cheese type and brand. Furthermore, the analysis detected strong relationships, some previously unknown, which existed between the cheese microbiota and metabolome, and uncovered specific taxa and metabolites that contributed to these relationships. These results highlight the potential of this approach for identifying product specific microbe/metabolite signatures that could be used to monitor and control cheese quality and product authenticity.}, }
@article {pmid32240601, year = {2020}, author = {Yan, Y and Drew, DA and Markowitz, A and Lloyd-Price, J and Abu-Ali, G and Nguyen, LH and Tran, C and Chung, DC and Gilpin, KK and Meixell, D and Parziale, M and Schuck, M and Patel, Z and Richter, JM and Kelsey, PB and Garrett, WS and Chan, AT and Stadler, ZK and Huttenhower, C}, title = {Structure of the Mucosal and Stool Microbiome in Lynch Syndrome.}, journal = {Cell host &amp; microbe}, volume = {27}, number = {4}, pages = {585-600.e4}, pmid = {32240601}, issn = {1934-6069}, support = {R01 CA202704/CA/NCI NIH HHS/United States ; L30 CA209764/CA/NCI NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; R01 CA154426/CA/NCI NIH HHS/United States ; T32 CA009001/CA/NCI NIH HHS/United States ; K01 DK120742/DK/NIDDK NIH HHS/United States ; /CRUK_/Cancer Research UK/United Kingdom ; }, mesh = {Adenoma/microbiology ; Adult ; Aged ; Aged, 80 and over ; Colectomy/adverse effects ; Colonic Neoplasms/diagnosis/*microbiology/pathology ; Colorectal Neoplasms, Hereditary Nonpolyposis/diagnosis/*microbiology/pathology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; Metagenomics ; Middle Aged ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Transcriptome ; Tumor Microenvironment ; }, abstract = {The gut microbiota has been associated with colorectal cancer (CRC), but causal alterations preceding CRC have not been elucidated. To prospectively assess microbiome changes prior to colorectal neoplasia, we investigated samples from 100 Lynch syndrome patients using 16S rRNA gene sequencing of colon biopsies, coupled with metagenomic and metatranscriptomic sequencing of feces. Colectomy and CRC history represented the largest effects on microbiome profiles. A subset of Clostridiaceae were depleted in stool corresponding with baseline adenomas, while Desulfovibrio was enriched both in stool and in mucosal biopsies. A classifier leveraging stool metatranscriptomes resulted in modest power to predict interval development of preneoplastic colonic adenoma. Predictive transcripts corresponded with a shift in flagellin contributors and oxidative metabolic microenvironment, potentially factors in local CRC pathogenesis. This suggests that the effectiveness of prospective microbiome monitoring for adenomas may be limited but supports the potential causality of these consistent, early microbial changes in colonic neoplasia.}, }
@article {pmid32140945, year = {2020}, author = {Leite, GGS and Weitsman, S and Parodi, G and Celly, S and Sedighi, R and Sanchez, M and Morales, W and Villanueva-Millan, MJ and Barlow, GM and Mathur, R and Lo, SK and Jamil, LH and Paski, S and Rezaie, A and Pimentel, M}, title = {Mapping the Segmental Microbiomes in the Human Small Bowel in Comparison with Stool: A REIMAGINE Study.}, journal = {Digestive diseases and sciences}, volume = {65}, number = {9}, pages = {2595-2604}, pmid = {32140945}, issn = {1573-2568}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Bacteria/*classification/genetics ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Intestine, Small/*microbiology ; Male ; Metagenomics ; Middle Aged ; Prospective Studies ; Ribotyping ; Young Adult ; }, abstract = {BACKGROUND: Most gut microbiome studies have been performed using stool samples. However, the small intestine is of central importance to digestion, nutrient absorption, and immune function, and characterizing its microbial populations is essential for elucidating their roles in human health and disease.<br><br>AIMS: To characterize the microbial populations of different small intestinal segments and contrast these to the stool microbiome.<br><br>METHODS: Male and female subjects undergoing esophagogastroduodenoscopy without colon preparation were prospectively recruited. Luminal aspirates were obtained from the duodenum, jejunum, and farthest distance reached. A subset also provided stool samples. 16S rRNA sequencing was performed and analyses were carried out using CLC Genomics Workbench.<br><br>RESULTS: 16S rRNA sequencing identified differences in more than 2000 operational taxonomic units between the small intestinal and stool microbiomes. Firmicutes and Proteobacteria were the most abundant phyla in the small intestine, and Bacteroidetes were less abundant. In the small intestine, phylum Firmicutes was primarily represented by lactic acid bacteria, including families Streptococcaceae, Lactobacillaceae, and Carnobacteriaceae, and Proteobacteria was represented by families Neisseriaceae, Pasteurellaceae, and Enterobacteriaceae. The duodenal and FD microbial signatures were markedly different from each other, but there were overlaps between duodenal and jejunal and between jejunal and FD microbial signatures. In stool, Firmicutes were represented by families Ruminococcaceae, Lachnospiraceae, Christensenellaceae, and Proteobacteria by class Deltaproteobacteria.<br><br>CONCLUSIONS: The small bowel microbiome is markedly different from that in stool and also varies between segments. These findings may be important in determining how compositional changes in small intestinal microbiota contribute to human disease states.}, }
@article {pmid33272203, year = {2020}, author = {Zhang, Q and Dao, T}, title = {A distance based multisample test for high-dimensional compositional data with applications to the human microbiome.}, journal = {BMC bioinformatics}, volume = {21}, number = {Suppl 9}, pages = {205}, pmid = {33272203}, issn = {1471-2105}, mesh = {Aged ; Bayes Theorem ; Computer Simulation ; Humans ; Metagenomics ; *Microbiota ; Middle Aged ; Numerical Analysis, Computer-Assisted ; }, abstract = {BACKGROUND: Compositional data refer to the data that lie on a simplex, which are common in many scientific domains such as genomics, geology and economics. As the components in a composition must sum to one, traditional tests based on unconstrained data become inappropriate, and new statistical methods are needed to analyze this special type of data.<br><br>RESULTS: In this paper, we consider a general problem of testing for the compositional difference between K populations. Motivated by microbiome and metagenomics studies, where the data are often over-dispersed and high-dimensional, we formulate a well-posed hypothesis from a Bayesian point of view and suggest a nonparametric test based on inter-point distance to evaluate statistical significance. Unlike most existing tests for compositional data, our method does not rely on any data transformation, sparsity assumption or regularity conditions on the covariance matrix, but directly analyzes the compositions. Simulated data and two real data sets on the human microbiome are used to illustrate the promise of our method.<br><br>CONCLUSIONS: Our simulation studies and real data applications demonstrate that the proposed test is more sensitive to the compositional difference than the mean-based method, especially when the data are over-dispersed or zero-inflated. The proposed test is easy to implement and computationally efficient, facilitating its application to large-scale datasets.}, }
@article {pmid33216744, year = {2020}, author = {Zhao, C and Ni, H and Zhao, L and Zhou, L and Borrás-Hidalgo, O and Cui, R}, title = {High nitrogen concentration alter microbial community in Allium fistulosum rhizosphere.}, journal = {PloS one}, volume = {15}, number = {11}, pages = {e0241371}, pmid = {33216744}, issn = {1932-6203}, mesh = {Allium/*microbiology/physiology ; Bacteria/isolation &amp; purification ; Biodiversity ; Fungi/isolation &amp; purification ; Metagenomics ; Microbiota/*drug effects ; Nitrogen/*pharmacology ; Phylogeny ; *Rhizosphere ; Soil Microbiology ; Species Specificity ; }, abstract = {Welsh onion (Allium fistulosum L.) constitutes an important plant species cultivated in China due the benefits and applications in different areas. Moreover, nitrogen is an essential nutrient during the growth and development of plant. Here, we present the effects of nitrogen on soil microbiome in welsh onion plants. We used High-throughput sequencing analysis to determine the diversity and abundances of microbes associated to soil rhizosphere in welsh onion under the influence of nitrogen application. Nitrogen application significantly influenced in the diversity of fungal community. The relative abundance of Orbiliomycetes increased with the nitrogen concentration. Nitrogen application did not affect the diversity of bacterial community, whereas the relative abundance of Acidobacteria_Gp2, Verrucomicrobiae and Sphingobacteriia decreased with the nitrogen condition. In this work, we introduced evidences of the effect of nitrogen fertilization on microbial community in welsh onion rhizosphere, and the change of microbial community may interfere the growth and development of welsh onion.}, }
@article {pmid33170893, year = {2020}, author = {Sajulga, R and Easterly, C and Riffle, M and Mesuere, B and Muth, T and Mehta, S and Kumar, P and Johnson, J and Gruening, BA and Schiebenhoefer, H and Kolmeder, CA and Fuchs, S and Nunn, BL and Rudney, J and Griffin, TJ and Jagtap, PD}, title = {Survey of metaproteomics software tools for functional microbiome analysis.}, journal = {PloS one}, volume = {15}, number = {11}, pages = {e0241503}, pmid = {33170893}, issn = {1932-6203}, support = {U24 CA199347/CA/NCI NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Dysbiosis/microbiology ; Gene Ontology ; *Metagenomics ; *Microbiota ; Peptides/analysis/chemistry ; *Proteomics ; *Software ; *Surveys and Questionnaires ; Workflow ; }, abstract = {To gain a thorough appreciation of microbiome dynamics, researchers characterize the functional relevance of expressed microbial genes or proteins. This can be accomplished through metaproteomics, which characterizes the protein expression of microbiomes. Several software tools exist for analyzing microbiomes at the functional level by measuring their combined proteome-level response to environmental perturbations. In this survey, we explore the performance of six available tools, to enable researchers to make informed decisions regarding software choice based on their research goals. Tandem mass spectrometry-based proteomic data obtained from dental caries plaque samples grown with and without sucrose in paired biofilm reactors were used as representative data for this evaluation. Microbial peptides from one sample pair were identified by the X! tandem search algorithm via SearchGUI and subjected to functional analysis using software tools including eggNOG-mapper, MEGAN5, MetaGOmics, MetaProteomeAnalyzer (MPA), ProPHAnE, and Unipept to generate functional annotation through Gene Ontology (GO) terms. Among these software tools, notable differences in functional annotation were detected after comparing differentially expressed protein functional groups. Based on the generated GO terms of these tools we performed a peptide-level comparison to evaluate the quality of their functional annotations. A BLAST analysis against the NCBI non-redundant database revealed that the sensitivity and specificity of functional annotation varied between tools. For example, eggNOG-mapper mapped to the most number of GO terms, while Unipept generated more accurate GO terms. Based on our evaluation, metaproteomics researchers can choose the software according to their analytical needs and developers can use the resulting feedback to further optimize their algorithms. To make more of these tools accessible via scalable metaproteomics workflows, eggNOG-mapper and Unipept 4.0 were incorporated into the Galaxy platform.}, }
@article {pmid32788623, year = {2020}, author = {Latorre-Pérez, A and Villalba-Bermell, P and Pascual, J and Vilanova, C}, title = {Assembly methods for nanopore-based metagenomic sequencing: a comparative study.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {13588}, pmid = {32788623}, issn = {2045-2322}, mesh = {Genome, Bacterial/genetics ; Genomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/genetics ; Nanopore Sequencing/*methods ; *Nanopores ; Reproducibility of Results ; Sequence Analysis, DNA/methods ; }, abstract = {Metagenomic sequencing has allowed for the recovery of previously unexplored microbial genomes. Whereas short-read sequencing platforms often result in highly fragmented metagenomes, nanopore-based sequencers could lead to more contiguous assemblies due to their potential to generate long reads. Nevertheless, there is a lack of updated and systematic studies evaluating the performance of different assembly tools on nanopore data. In this study, we have benchmarked the ability of different assemblers to reconstruct two different commercially-available mock communities that have been sequenced using Oxford Nanopore Technologies platforms. Among the tested tools, only metaFlye, Raven, and Canu performed well in all the datasets. These tools retrieved highly contiguous genomes (or even complete genomes) directly from the metagenomic data. Despite the intrinsic high error of nanopore sequencing, final assemblies reached high accuracy (~ 99.5 to 99.8% of consensus accuracy). Polishing strategies demonstrated to be necessary for reducing the number of indels, and this had an impact on the prediction of biosynthetic gene clusters. Correction with high quality short reads did not always result in higher quality draft assemblies. Overall, nanopore metagenomic sequencing data-adapted to MinION's current output-proved sufficient for assembling and characterizing low-complexity microbial communities.}, }
@article {pmid32519942, year = {2020}, author = {François, S and Pybus, OG}, title = {Towards an understanding of the avian virome.}, journal = {The Journal of general virology}, volume = {101}, number = {8}, pages = {785-790}, pmid = {32519942}, issn = {1465-2099}, support = {BB/T008806/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Animals, Wild/virology ; Birds/*virology ; Genome, Viral/genetics ; Humans ; Poultry Diseases/virology ; Virome/*genetics ; Virus Diseases/virology ; }, abstract = {The last two decades have seen the rise of viromics, the study of viral communities through the detection and characterization of virus genome sequences. Here we systematically review and summarize the scope and limitations of our current understanding of avian viromes, in both domesticated and wild-bird populations. We compare this viromic work to the broader literature on avian prokaryotic microbiomes, and highlight the growing importance of structured sampling and experimental design for testing explanatory hypotheses. We provide a number of recommendations for sample collection and preliminary data analysis to guide the development of avian viromics. Avian viromes have the potential to inform disease surveillance in poultry and improve our understanding of the risk of zoonotic viruses to human health.}, }
@article {pmid32365167, year = {2020}, author = {Hillmann, B and Al-Ghalith, GA and Shields-Cutler, RR and Zhu, Q and Knight, R and Knights, D}, title = {SHOGUN: a modular, accurate and scalable framework for microbiome quantification.}, journal = {Bioinformatics (Oxford, England)}, volume = {36}, number = {13}, pages = {4088-4090}, pmid = {32365167}, issn = {1367-4811}, support = {R01 AI121383/AI/NIAID NIH HHS/United States ; P01 DK078669/DK/NIDDK NIH HHS/United States ; }, mesh = {Bayes Theorem ; Data Analysis ; Metagenomics ; *Microbiota/genetics ; *Software ; }, abstract = {SUMMARY: The software pipeline SHOGUN profiles known taxonomic and gene abundances of short-read shotgun metagenomics sequencing data. The pipeline is scalable, modular and flexible. Data analysis and transformation steps can be run individually or together in an automated workflow. Users can easily create new reference databases and can select one of three DNA alignment tools, ranging from ultra-fast low-RAM k-mer-based database search to fully exhaustive gapped DNA alignment, to best fit their analysis needs and computational resources. The pipeline includes an implementation of a published method for taxonomy assignment disambiguation with empirical Bayesian redistribution. The software is installable via the conda resource management framework, has plugins for the QIIME2 and QIITA packages and produces both taxonomy and gene abundance profile tables with a single command, thus promoting convenient and reproducible metagenomics research.<br><br>https://github.com/knights-lab/SHOGUN.}, }
@article {pmid32245246, year = {2020}, author = {Chandrarathna, HPSU and Liyanage, TD and Edirisinghe, SL and Dananjaya, SHS and Thulshan, EHT and Nikapitiya, C and Oh, C and Kang, DH and De Zoysa, M}, title = {Marine Microalgae, Spirulina maxima-Derived Modified Pectin and Modified Pectin Nanoparticles Modulate the Gut Microbiota and Trigger Immune Responses in Mice.}, journal = {Marine drugs}, volume = {18}, number = {3}, pages = {}, pmid = {32245246}, issn = {1660-3397}, support = {PN68031//National Research Foundation of Korea/ ; PE99621 and PE99722//Korea Institute of Ocean Science and Technology (KIOST)/ ; }, mesh = {Animals ; Antimicrobial Cationic Peptides/analysis/metabolism ; Bacteroidetes/genetics/isolation &amp; purification ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects/genetics ; Immunity, Innate/drug effects ; Immunity, Mucosal/drug effects ; Intestinal Mucosa/drug effects/immunology/metabolism/microbiology ; Male ; Metagenomics ; Mice ; Microalgae/*chemistry ; Models, Animal ; Mucins/analysis/metabolism ; Nanoparticles/*administration &amp; dosage ; Pectins/*administration &amp; dosage/isolation &amp; purification ; Prebiotics/*administration &amp; dosage ; Spirulina/*chemistry ; }, abstract = {This study evaluated the modulation of gut microbiota, immune responses, and gut morphometry in C57BL/6 mice, upon oral administration of S. maxima-derived modified pectin (SmP, 7.5 mg/mL) and pectin nanoparticles (SmPNPs; 7.5 mg/mL). Metagenomics analysis was conducted using fecal samples, and mice duodenum and jejunum were used for analyzing the immune response and gut morphometry, respectively. The results of metagenomics analysis revealed that the abundance of Bacteroidetes in the gut increased in response to both modified SmP and SmPNPs (75%) as compared with that in the control group (66%), while that of Firmicutes decreased in (20%) as compared with that in the control group (30%). The mRNA levels of mucin, antimicrobial peptide, and antiviral and gut permeability-related genes in the duodenum were significantly (p < 0.05) upregulated (> 2-fold) upon modified SmP and SmPNPs feeding. Protein level of intestinal alkaline phosphatase was increased (1.9-fold) in the duodenum of modified SmPNPs feeding, evidenced by significantly increased goblet cell density (0.5 ± 0.03 cells/1000 µm2) and villi height (352 ± 10 µm). Our results suggest that both modified SmP and SmPNPs have the potential to modulate gut microbial community, enhance the expression of immune related genes, and improve gut morphology.}, }
@article {pmid32128982, year = {2020}, author = {Tu, Q}, title = {Random sampling in metagenomic sequencing leads to overestimated spatial scaling of microbial diversity.}, journal = {Environmental microbiology}, volume = {22}, number = {6}, pages = {2140-2149}, doi = {10.1111/1462-2920.14973}, pmid = {32128982}, issn = {1462-2920}, support = {31700427//National Natural Science Foundation of China/International ; 31971446//National Natural Science Foundation of China/International ; LQ17D060002//Zhejiang Provincial Natural Science Foundation of China/International ; kf2016002//Open Project of Key Laboratory of Environmental Biotechnology, CAS/International ; SKYAM002-2016//Open Funding of State Key Laboratory of Applied Microbiology Southern China/International ; 2017C82218//Bureau of Science and Technology of Zhoushan/International ; //Qilu Young Scholarship of Shandong University/International ; }, mesh = {*Biodiversity ; Forests ; Geography ; Metagenome ; Metagenomics ; Microbiota/*genetics ; Random Allocation ; *Soil Microbiology ; }, abstract = {Revealing the spatial scaling patterns of microbial diversity is of special interest in microbial ecology. One critical question is whether the observed spatial turnover rate truly reflect the actual spatial patterns of extremely diverse microbial communities. Using simulated mock communities, this study suggested that the currently observed microbial spatial turnover rates were overestimated by random sampling processes associated with high-throughput metagenomic sequencing. The observed z values were largely contributed by accumulated microbial taxa due to cumulative number of samples. This is a crucial issue because microbial communities already have very low spatial turnover rate due to the small size and potential cosmopolitism nature of microorganisms. Further investigations suggested a linear relationship between the observed and expected z values, which can be applied to remove random sampling noises from the observed z values. Adjustment of z values for data sets from six American forests showed much lower spatial turnover rate than that before adjustment. However, the patterns of z values among these six forests remained unchanged. This study suggested that our current understanding of microbial taxa-area relationships could be inaccurate. Therefore, cautions and efforts should be made for more accurate estimation and interpretation of microbial spatial patterns.}, }
@article {pmid32114693, year = {2020}, author = {Karthikeyan, S and Rodriguez-R, LM and Heritier-Robbins, P and Hatt, JK and Huettel, M and Kostka, JE and Konstantinidis, KT}, title = {Genome repository of oil systems: An interactive and searchable database that expands the catalogued diversity of crude oil-associated microbes.}, journal = {Environmental microbiology}, volume = {22}, number = {6}, pages = {2094-2106}, doi = {10.1111/1462-2920.14966}, pmid = {32114693}, issn = {1462-2920}, support = {No 321611-00//Gulf of Mexico Research Initiative/International ; //Georgia Institute of Technology/International ; }, mesh = {*Biodegradation, Environmental ; *Databases, Genetic ; Gulf of Mexico ; Hydrocarbons/metabolism ; Metagenome/genetics ; Metagenomics ; Microbiota/genetics ; Oil and Gas Fields/*microbiology ; Petroleum/metabolism/*microbiology ; Petroleum Pollution/*analysis ; }, abstract = {Microbial communities ultimately control the fate of petroleum hydrocarbons (PHCs) that enter the natural environment, but the interactions of microbes with PHCs and the environment are highly complex and poorly understood. Genome-resolved metagenomics can help unravel these complex interactions. However, the lack of a comprehensive database that integrates existing genomic/metagenomic data from oil environments with physicochemical parameters known to regulate the fate of PHCs currently limits data analysis and interpretations. Here, we curated a comprehensive, searchable database that documents microbial populations in natural oil ecosystems and oil spills, along with available underlying physicochemical data, geocoded via geographic information system to reveal their geographic distribution patterns. Analysis of the ~2000 metagenome-assembled genomes (MAGs) available in the database revealed strong ecological niche specialization within habitats. Over 95% of the recovered MAGs represented novel taxa underscoring the limited representation of cultured organisms from oil-contaminated and oil reservoir ecosystems. The majority of MAGs linked to oil-contaminated ecosystems were detectable in non-oiled samples from the Gulf of Mexico but not in comparable samples from elsewhere, indicating that the Gulf is primed for oil biodegradation. The repository should facilitate future work toward a predictive understanding of the microbial taxa and their activities that control the fate of oil spills.}, }
@article {pmid32062778, year = {2020}, author = {Nkongolo, KK and Narendrula-Kotha, R}, title = {Advances in monitoring soil microbial community dynamic and function.}, journal = {Journal of applied genetics}, volume = {61}, number = {2}, pages = {249-263}, pmid = {32062778}, issn = {2190-3883}, support = {CRDP-J- 470535-2014//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Bacteria/*genetics/isolation &amp; purification ; *Environmental Monitoring ; High-Throughput Nucleotide Sequencing ; Microbiota/*genetics ; Polymorphism, Restriction Fragment Length/genetics ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {Microorganisms are vital to the overall ecosystem functioning, stability, and sustainability. Soil fertility and health depend on chemical composition and also on the qualitative and quantitative nature of microorganisms inhabiting it. Historically, denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE), single-strand conformation polymorphism, DNA amplification fingerprinting, amplified ribosomal DNA restriction analysis, terminal restriction fragment length polymorphism, length heterogeneity PCR, and ribosomal intergenic spacer analysis were used to assess soil microbial community structure (SMCS), abundance, and diversity. However, these methods had significant shortcomings and limitations for application in land reclamation monitoring. SMCS has been primarily determined by phospholipid fatty acid (PLFA) analysis. This method provides a direct measure of viable biomass in addition to a biochemical profile of the microbial community. PLFA has limitations such as overlap in the composition of microorganisms and the specificity of PLFAs signature. In recent years, high-throughput next-generation sequencing has dramatically increased the resolution and detectable spectrum of diverse microbial phylotypes from environmental samples and it plays a significant role in microbial ecology studies. Next-generation sequencings using 454, Illumina, SOLiD, and Ion Torrent platforms are rapid and flexible. The two methods, PLFA and next-generation sequencing, are useful in detecting changes in microbial community diversity and structure in different ecosystems. Single-molecule real-time (SMRT) and nanopore sequencing technologies represent third-generation sequencing (TGS) platforms that have been developed to address the shortcomings of second-generation sequencing (SGS). Enzymatic and soil respiration analyses are performed to further determine soil quality and microbial activities. Other valuable methods that are being recently applied to microbial function and structures include NanoSIM, GeoChip, and DNA stable staple isotope probing (DNA-SIP) technologies. They are powerful metagenomics tool for analyzing microbial communities, including their structure, metabolic potential, diversity, and their impact on ecosystem functions. This review is a critical analysis of current methods used in monitoring soil microbial community dynamic and functions.}, }
@article {pmid32006353, year = {2020}, author = {Sadan, T and Aravindakshan, TV and Radhika, G and Anand, LF and Ally, K}, title = {Metagenomic analysis exploring taxonomic diversity of rumen microbial communities in Vechur and crossbred cattle of Kerala state, India.}, journal = {Journal of applied genetics}, volume = {61}, number = {2}, pages = {287-297}, pmid = {32006353}, issn = {2190-3883}, support = {CB/51/81/MVM/2016/GT//Kerala Veterinary and Animal Sciences University/ ; }, mesh = {Animals ; Archaea/classification/genetics ; Bacteria/classification/genetics ; Cattle ; Classification ; Genetic Variation/*genetics ; India ; Metagenome/*genetics ; Metagenomics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; }, abstract = {Rumen, one of the most productive diverse microbial habitats plays a vital role in the breakdown of feed to produce energy for maintenance and milk production in cattle. Culture-based procedures could identify only 10% of microbial species present in the rumen. Kerala, one of the southern states of India, owns only one native cattle breed, the Vechur cattle, which is noted for its short stature, disease resistance and adaptability to hot humid climate. Lower population density and decreased milk production potential of Vechur cattle led to the development of crossbred cattle of Kerala, with higher milk yield. A study was conducted to assess the rumen microbial profile of low productive Vechur cattle and high productive crossbred cattle for a better understanding of the relationship between the host and microbial community. DNA isolated from rumen liquor of five cattle each from both genetic groups maintained on standard ration (forage, concentrate ratio of 50:50) was subjected to whole metagenome sequencing. Bioinformatics and statistical analysis revealed that bacteria followed by archaea and eukaryota dominated in the Vechur cattle as well as the crossbred cattle rumen. Bacterial community was dominated by Bacteroidetes and Firmicutes phyla in both genetic groups with a higher Firmicutes to Bacteroidetes ratio of 0.45 in Vechur cattle. Among archaea, Euryarchaeota was more abundant, which constitute methanogens, contributing 98% of total archaeal reads. Prevalent protozoal genus found in the Vechur cattle rumen was Entodinium and in crossbred cattle rumen was Entamoeba. In Vechur and crossbred cattle rumen, 1086 and 1262 microbial species were observed exclusively and 4731 species were shared between habitats. There was a significant difference in total microbial species abundance between the two genetic groups and Vechur cattle displayed significantly higher microbial diversity compared to crossbred. As per literature, this is presumably the first report of rumen metagenome profile of Vechur cattle, a unique short breed of India.}, }
@article {pmid31884359, year = {2020}, author = {Zhang, L and Li, L and Sha, G and Liu, C and Wang, Z and Wang, L}, title = {Aerobic composting as an effective cow manure management strategy for reducing the dissemination of antibiotic resistance genes: An integrated meta-omics study.}, journal = {Journal of hazardous materials}, volume = {386}, number = {}, pages = {121895}, doi = {10.1016/j.jhazmat.2019.121895}, pmid = {31884359}, issn = {1873-3336}, mesh = {Acinetobacter/drug effects/genetics ; Anti-Bacterial Agents/pharmacology ; China ; Composting/*methods ; Drug Resistance, Microbial/*genetics ; Genes, Bacterial/*drug effects ; Manure/*microbiology ; *Metagenomics ; Microbiota/drug effects/*genetics ; Pseudomonas/drug effects/genetics ; Soil/chemistry ; }, abstract = {Livestock manure is considered as an important source for spreading antibiotic resistance genes (ARGs) into the environment, and therefore poses a direct threat to public health. Whereas the effects of reused manure on soil microbial communities and ARGs have been studied extensively, comprehensive characterizations of microbial communities and ARGs of manure produced by different management methods are not well understood. Here, we analyzed the fate of microbial communities and ARGs of cow manure treated by three conventional management strategies: aerobic composting, mechanical drying and precipitation, applying an integrated-omics approach combining metagenomics and metaproteomics. Integrated-omics demonstrated that composted manure contained the lowest diversity of microbial community and ARGs compared with manure treated by other two strategies. Quantitative PCR methods revealed that the abundances of ARGs were reduced by over 83 % after composting for 14 days, regardless of the season. Besides, the potential ARG hosts Acinetobacter and Pseudomonas dominating mechanical drying process were sharply decreased in abundances after composting. The significant co-occurrence networks among bacteria, ARGs and transposase gene tnpA-01 in composting samples indicated the important role of these bacteria in the dissemination of ARGs. These findings offer insight into potential strategies to control the spread of ARGs during livestock manure reuse.}, }
@article {pmid32245128, year = {2020}, author = {Nishiyama, M and Ohtake, N and Kaneko, A and Tsuchiya, N and Imamura, S and Iizuka, S and Ishizawa, S and Nishi, A and Yamamoto, M and Taketomi, A and Kono, T}, title = {Increase of Akkermansia muciniphila by a Diet Containing Japanese Traditional Medicine Bofutsushosan in a Mouse Model of Non-Alcoholic Fatty Liver Disease.}, journal = {Nutrients}, volume = {12}, number = {3}, pages = {}, pmid = {32245128}, issn = {2072-6643}, mesh = {Akkermansia ; *Animal Feed/microbiology ; Animals ; Biodiversity ; Biomarkers ; Biopsy ; Body Weight ; Dietary Supplements ; Disease Models, Animal ; Drugs, Chinese Herbal/*administration &amp; dosage ; Eating ; Gastrointestinal Microbiome ; Humans ; Immunohistochemistry ; Metagenome ; Metagenomics/methods ; Mice ; Mice, Obese ; Non-alcoholic Fatty Liver Disease/*etiology/metabolism/pathology/prevention &amp; control ; }, abstract = {Non-alcoholic fatty liver disease (NAFLD) is considered a worldwide healthcare problem that mirrors the increased prevalence of obesity. Gut microbiota plays a crucial role in the progression and treatment of NAFLD. Bofutsushosan (BTS), a pharmaceutical-grade Japanese traditional medicine, has long been prescribed in Japan for obesity and obesity-related syndrome. Although BTS has been reported to exert an anti-obesity effect in obese patients as well as various obesity-model animals, its effect on gut microbiota is unknown. Here, the effects of BTS on obesity, liver damage, and the gut microbiome in genetically obese mice, ob/ob, were studied. Seven-week-old ob/ob mice were fed a standard diet with (BTS group) or without (CONT group) 5% BTS for 4 weeks. By comparison to the CONT group, the BTS group showed reduced body weight gain and hyperlipidemia as well as improved liver function. Moreover, gut microbiota in the CONT and BTS group formed a significantly different cluster. Specifically, the genera Akkermansia, Bacteroides and an unknown genus of the family Enterobacteriaceae expanded dramatically in the BTS group. Noteworthy, the population of Akkermansia muciniphila, which is reported to elicit an anti-obesity effect and improve various metabolic abnormalities, was markedly increased (93-fold) compared with the CONT group. These results imply that BTS may be a promising agent for treating NAFLD.}, }
@article {pmid33008816, year = {2020}, author = {Hammer, TJ and Dickerson, JC and McMillan, WO and Fierer, N}, title = {Heliconius Butterflies Host Characteristic and Phylogenetically Structured Adult-Stage Microbiomes.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {24}, pages = {}, pmid = {33008816}, issn = {1098-5336}, mesh = {Animals ; Bacteria/*isolation &amp; purification ; *Bacterial Physiological Phenomena ; Butterflies/*microbiology ; Host Microbial Interactions ; *Microbiota ; Phylogeny ; Sequence Analysis, RNA/*methods ; Species Specificity ; }, abstract = {Lepidoptera (butterflies and moths) are diverse and ecologically important, yet we know little about how they interact with microbes as adults. Due to metamorphosis, the form and function of their adult-stage microbiomes might be very different from those of microbiomes in the larval stage (caterpillars). We studied adult-stage microbiomes of Heliconius and closely related passion-vine butterflies (Heliconiini), which are an important model system in evolutionary biology. To characterize the structure and dynamics of heliconiine microbiomes, we used field collections of wild butterflies, 16S rRNA gene sequencing, quantitative PCR, and shotgun metagenomics. We found that Heliconius butterflies harbor simple and abundant bacterial communities that are moderately consistent among conspecific individuals and over time. Heliconiine microbiomes also exhibited a strong signal of the host phylogeny, with a major distinction between Heliconius and other butterflies. These patterns were largely driven by differing relative abundances of bacterial phylotypes shared among host species and genera, as opposed to the presence or absence of host-specific phylotypes. We suggest that the phylogenetic structure in heliconiine microbiomes arises from conserved host traits that differentially filter microbes from the environment. While the relative importance of different traits remains unclear, our data indicate that pollen feeding (unique to Heliconius) is not a primary driver. Using shotgun metagenomics, we also discovered trypanosomatids and microsporidia to be prevalent in butterfly guts, raising the possibility of antagonistic interactions between eukaryotic parasites and colocalized gut bacteria. Our discovery of characteristic and phylogenetically structured microbiomes provides a foundation for tests of adult-stage microbiome function, a poorly understood aspect of lepidopteran biology.IMPORTANCE Many insects host microbiomes with important ecological functions. However, the prevalence of this phenomenon is unclear because in many insect taxa, microbiomes have been studied in only part of the life cycle, if at all. A prominent example is butterflies and moths, in which the composition and functional role of adult-stage microbiomes are largely unknown. We comprehensively characterized microbiomes in adult passion-vine butterflies. Butterfly-associated bacterial communities are generally abundant in guts, consistent within populations, and composed of taxa widely shared among hosts. More closely related butterflies harbor more similar microbiomes, with the most dramatic shift in microbiome composition occurring in tandem with a suite of ecological and life history traits unique to the genus Heliconius Butterflies are also frequently infected with previously undescribed eukaryotic parasites, which may interact with bacteria in important ways. These findings advance our understanding of butterfly biology and insect-microbe interactions generally.}, }
@article {pmid32704056, year = {2020}, author = {Song, CH and Kim, N and Nam, RH and Choi, SI and Lee, HN and Surh, YJ}, title = {17β-Estradiol supplementation changes gut microbiota diversity in intact and colorectal cancer-induced ICR male mice.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {12283}, pmid = {32704056}, issn = {2045-2322}, mesh = {Animals ; *Biodiversity ; Cell Transformation, Neoplastic ; Colorectal Neoplasms/*etiology/metabolism/pathology ; *Dietary Supplements ; Disease Models, Animal ; Disease Susceptibility ; Estradiol/*administration &amp; dosage ; Female ; Gastrointestinal Microbiome/*drug effects ; Male ; Metagenome ; Metagenomics/methods ; Mice ; RNA, Ribosomal, 16S ; }, abstract = {The composition of the gut microbiota is influenced by sex hormones and colorectal cancer (CRC). Previously, we reported that 17β-estradiol (E2) inhibits azoxymethane/dextran sulfate sodium (AOM/DSS)-induced tumorigenesis in male mice. Here, we investigated whether the composition of the gut microbiota is different between male and female, and is regulated by estrogen as a secondary outcome of previous studies. We established four groups of mice based on the sex and estrogen status [ovariectomized (OVX) female and E2-treated male]. Additionally, three groups of males were established by treating them with AOM/DSS, and E2, after subjecting them to AOM/DSS treatment. The mice were sacrificed at 21 weeks old. The composition of the gut microbiota was analyzed using 16S rRNA metagenomics sequencing. We observed a significant increase in the microbial diversity (Chao1 index) in females, males supplemented with E2, and males treated with AOM/DSS/E2 compared with normal males. In normal physiological condition, sex difference and E2 treatment did not affect the ratio of Firmicutes/Bacteroidetes (F/B). However, in AOM/DSS-treated male mice, E2 supplementation showed significantly lower level of the F/B ratio. The ratio of commensal bacteria to opportunistic pathogens was higher in females and E2-treated males compared to normal males and females subjected to OVX. Unexpectedly, this ratio was higher in the AOM/DSS group than that determined in other males and the AOM/DSS/E2 group. Our findings suggest that estrogen alters the gut microbiota in ICR (CrljOri:CD1) mice, particularly AOM/DSS-treated males, by decreasing the F/B ratio and changing Shannon and Simpson index by supply of estrogen. This highlights another possibility that estrogen could cause changes in the gut microbiota, thereby reducing the risk of developing CRC.}, }
@article {pmid32690954, year = {2020}, author = {Wolf, YI and Silas, S and Wang, Y and Wu, S and Bocek, M and Kazlauskas, D and Krupovic, M and Fire, A and Dolja, VV and Koonin, EV}, title = {Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome.}, journal = {Nature microbiology}, volume = {5}, number = {10}, pages = {1262-1270}, pmid = {32690954}, issn = {2058-5276}, support = {R01 GM037706/GM/NIGMS NIH HHS/United States ; R35 GM130366/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Biodiversity ; China ; Computational Biology/methods ; Evolution, Molecular ; Gene Order ; *Genome, Viral ; *Metagenome ; *Metagenomics/methods ; Phylogeny ; RNA Viruses/*classification/*genetics ; Viral Proteins/chemistry/genetics ; Water Microbiology ; }, abstract = {RNA viruses in aquatic environments remain poorly studied. Here, we analysed the RNA virome from approximately 10 l water from Yangshan Deep-Water Harbour near the Yangtze River estuary in China and identified more than 4,500 distinct RNA viruses, doubling the previously known set of viruses. Phylogenomic analysis identified several major lineages, roughly, at the taxonomic ranks of class, order and family. The 719-member-strong Yangshan virus assemblage is the sister clade to the expansive class Alsuviricetes and consists of viruses with simple genomes that typically encode only RNA-dependent RNA polymerase (RdRP), capping enzyme and capsid protein. Several clades within the Yangshan assemblage independently evolved domain permutation in the RdRP. Another previously unknown clade shares ancestry with Potyviridae, the largest known plant virus family. The 'Aquatic picorna-like viruses/Marnaviridae' clade was greatly expanded, with more than 800 added viruses. Several RdRP-linked protein domains not previously detected in any RNA viruses were identified, such as the small ubiquitin-like modifier (SUMO) domain, phospholipase A2 and PrsW-family protease domain. Multiple viruses utilize alternative genetic codes implying protist (especially ciliate) hosts. The results reveal a vast RNA virome that includes many previously unknown groups. However, phylogenetic analysis of the RdRPs supports the previously established five-branch structure of the RNA virus evolutionary tree, with no additional phyla.}, }
@article {pmid32580805, year = {2020}, author = {Garber, A and Hastie, PM and Farci, V and McGuinness, D and Bulmer, L and Alzahal, O and Murray, JMD}, title = {The effect of supplementing pony diets with yeast on 2. The faecal microbiome.}, journal = {Animal : an international journal of animal bioscience}, volume = {14}, number = {12}, pages = {2493-2502}, doi = {10.1017/S1751731120001512}, pmid = {32580805}, issn = {1751-732X}, mesh = {Animal Feed/analysis ; Animals ; Diet/veterinary ; Feces ; Horses ; Male ; *Microbiota ; *Saccharomyces cerevisiae ; }, abstract = {There is a need to develop feeding strategies to prevent the adverse effect of concentrate feeding in high-performance horses fed energy-dense diets aiming to maintain their health and welfare. The objective of this study is to determine the effect of a VistaEQ product containing 4% live yeast Saccharomyces cerevisiae (S. cerevisiae), with activity 5 × 108 colony-forming unit/g and fed 2 g/pony per day, on faecal microbial populations when supplemented with high-starch and high-fibre diets using Illumina next generation sequencing of the V3-V4 region of the 16S ribosomal RNA gene. The four treatments were allocated to eight mature Welsh section A pony geldings enrolled in a 4-period × 8 animal crossover design. Each 19-day experimental period consisted of an 18-day adaptation phase and a single collection day, followed by a 7-day wash out period. After DNA extraction from faeces and library preparation, α-diversity and linear discriminant analysis effect size were performed using 16S metagenomics pipeline in Quantitative Insights Into Microbial Ecology (QIIME™) and Galaxy/Hutlab. Differences between the groups were considered significant when linear discriminant analysis score was >2 corresponding to P < 0.05. The present study showed that S. cerevisiae used was able to induce positive changes in the equine microbiota when supplemented to a high-fibre diet: it increased relative abundance (RA) of Lachnospiraceae and Dehalobacteriaceae family members associated with a healthy core microbiome. Yeast supplementation also increased the RA of fibrolytic bacteria (Ruminococcus) when fed with a high-fibre diet and reduced the RA of lactate producing bacteria (Streptococcus) when a high-starch diet was fed. In addition, yeast increased the RA of acetic, succinic acid producing bacterial family (Succinivibrionaceae) and butyrate producing bacterial genus (Roseburia) when fed with high-starch and high-fibre diets, respectively. VistaEQ supplementation to equine diets can be potentially used to prevent acidosis and increase fibre digestibility. It may help to meet the energy requirements of performance horses while maintaining gut health.}, }
@article {pmid32332864, year = {2020}, author = {Spasov, E and Tsuji, JM and Hug, LA and Doxey, AC and Sauder, LA and Parker, WJ and Neufeld, JD}, title = {High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant.}, journal = {The ISME journal}, volume = {14}, number = {7}, pages = {1857-1872}, pmid = {32332864}, issn = {1751-7370}, mesh = {Ammonia ; Archaea/genetics ; Bacteria/genetics ; *Biological Products ; Canada ; *Microbiota ; Nitrification ; Nitrites ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; *Water Purification ; }, abstract = {Nitrification, the oxidation of ammonia to nitrate via nitrite, is an important process in municipal wastewater treatment plants (WWTPs). Members of the Nitrospira genus that contribute to complete ammonia oxidation (comammox) have only recently been discovered and their relevance to engineered water treatment systems is poorly understood. This study investigated distributions of Nitrospira, ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) in biofilm samples collected from tertiary rotating biological contactors (RBCs) of a municipal WWTP in Guelph, Ontario, Canada. Using quantitative PCR (qPCR), 16S rRNA gene sequencing, and metagenomics, our results demonstrate that Nitrospira species strongly dominate RBC biofilm samples and that comammox Nitrospira outnumber all other nitrifiers. Genome bins recovered from assembled metagenomes reveal multiple populations of comammox Nitrospira with distinct spatial and temporal distributions, including several taxa that are distinct from previously characterized Nitrospira members. Diverse functional profiles imply a high level of niche heterogeneity among comammox Nitrospira, in contrast to the sole detected AOA representative that was previously cultivated and characterized from the same RBC biofilm. Our metagenome bins also reveal two cyanase-encoding populations of comammox Nitrospira, suggesting an ability to degrade cyanate, which has only been shown previously for several Nitrospira representatives that are strict nitrite oxidizers. This study demonstrates the importance of RBCs as model systems for continued investigation of environmental factors that control the distributions and activities of AOB, AOA, comammox Nitrospira, and other nitrite oxidizers.}, }
@article {pmid32228448, year = {2020}, author = {Xu, L and Surathu, A and Raplee, I and Chockalingam, A and Stewart, S and Walker, L and Sacks, L and Patel, V and Li, Z and Rouse, R}, title = {The effect of antibiotics on the gut microbiome: a metagenomics analysis of microbial shift and gut antibiotic resistance in antibiotic treated mice.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {263}, pmid = {32228448}, issn = {1471-2164}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Microbial/genetics ; Gastrointestinal Microbiome/drug effects/genetics ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; Mice ; Mice, Inbred BALB C ; }, abstract = {BACKGROUND: Emergence of antibiotic resistance is a global public health concern. The relationships between antibiotic use, the gut community composition, normal physiology and metabolism, and individual and public health are still being defined. Shifts in composition of bacteria, antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) after antibiotic treatment are not well-understood.<br><br>METHODS: This project used next-generation sequencing, custom-built metagenomics pipeline and differential abundance analysis to study the effect of antibiotic monotherapy on resistome and taxonomic composition in the gut of Balb/c mice infected with E. coli via transurethral catheterization to investigate the evolution and emergence of antibiotic resistance.<br><br>RESULTS: There is a longitudinal decrease of gut microbiota diversity after antibiotic treatment. Various ARGs are enriched within the gut microbiota despite an overall reduction of the diversity and total amount of bacteria after antibiotic treatment. Sometimes treatment with a specific class of antibiotics selected for ARGs that resist antibiotics of a completely different class (e.g. treatment of ciprofloxacin or fosfomycin selected for cepA that resists ampicillin). Relative abundance of some MGEs increased substantially after antibiotic treatment (e.g. transposases in the ciprofloxacin group).<br><br>CONCLUSIONS: Antibiotic treatment caused a remarkable reduction in diversity of gut bacterial microbiota but enrichment of certain types of ARGs and MGEs. These results demonstrate an emergence of cross-resistance as well as a profound change in the gut resistome following oral treatment of antibiotics.}, }
@article {pmid32060494, year = {2020}, author = {Louca, P and Menni, C and Padmanabhan, S}, title = {Genomic Determinants of Hypertension With a Focus on Metabolomics and the Gut Microbiome.}, journal = {American journal of hypertension}, volume = {33}, number = {6}, pages = {473-481}, pmid = {32060494}, issn = {1941-7225}, support = {MR/M016560/1/MRC_/Medical Research Council/United Kingdom ; CS/16/1/31878/BHF_/British Heart Foundation/United Kingdom ; RE/18/6/34217/BHF_/British Heart Foundation/United Kingdom ; }, mesh = {Animals ; Bacteria/*metabolism ; *Blood Pressure ; Diet ; Essential Hypertension/*genetics/*microbiology/physiopathology ; *Gastrointestinal Microbiome ; Gene-Environment Interaction ; Genetic Predisposition to Disease ; *Genetic Variation ; Humans ; *Metabolomics ; Risk Factors ; }, abstract = {Epidemiologic and genomic studies have progressively improved our understanding of the causation of hypertension and the complex relationship with diet and environment. The majority of Mendelian forms of syndromic hypotension and hypertension (HTN) have all been linked to mutations in genes whose encoded proteins regulate salt-water balance in the kidney, supporting the primacy of the kidneys in blood pressure regulation. There are more than 1,477 single nucleotide polymorphisms associated with blood pressure and hypertension and the challenge is establishing a causal role for these variants. Hypertension is a complex multifactorial phenotype and it is likely to be influenced by multiple factors including interactions between diet and lifestyle factors, microbiome, and epigenetics. Given the finite genetic variability that is possible in humans, it is likely that incremental gains from single marker analyses have now plateaued and a greater leap in our understanding of the genetic basis of disease will come from integration of other omics and the interacting environmental factors. In this review, we focus on emerging results from the microbiome and metabolomics and discuss how leveraging these findings may facilitate a deeper understanding of the interrelationships between genomics, diet, and microbial ecology in humans in the causation of essential hypertension.}, }
@article {pmid32937228, year = {2021}, author = {Zhao, Z}, title = {Comparison of microbial communities and the antibiotic resistome between prawn mono- and poly-culture systems.}, journal = {Ecotoxicology and environmental safety}, volume = {207}, number = {}, pages = {111310}, doi = {10.1016/j.ecoenv.2020.111310}, pmid = {32937228}, issn = {1090-2414}, mesh = {*Aquaculture ; Bacteria/drug effects ; Bacteriophages/drug effects/genetics ; China ; Culture ; Drug Resistance, Microbial/*genetics ; Genes, Bacterial/drug effects ; Humans ; Metagenomics ; Microbiota/drug effects/*physiology ; }, abstract = {Antibiotic resistance genes (ARGs) in mariculture sediments pose a potential risk to public health due to their ability to transfer from environmental bacteria to human pathogens. Long term, this may reduce pathogen susceptibility to antibiotics in medical settings. In recent years, the poly-culture of multiple species has become a popular mariculture approach in China, thanks to its environmental and economic benefits. However, differences in microbial communities and antibiotic resistome between mono- and poly-culture systems are still unclear. In this study, microbial community composition and profiles of entire (microbial DNA) and mobile (plasmid and phage) ARGs in prawn mono- and poly-culture systems were investigated using metagenomics. The abundance of several viruses and human pathogens were enhanced in prawn poly-culture ponds, when compared to monoculture systems. In contrast, sediments from poly-culture systems had a lower diversity and ARG abundance when compared to mono-culture approaches. These ARG variations were predominantly related to mobile genetic elements. Prawn mariculture activities exerted a unique selectivity for ARGs in plasmids, and this selectivity was not influenced by culture methods. The findings of this study have important implications for the selection of mariculture systems in preventing pollution with ARGs.}, }
@article {pmid32958861, year = {2020}, author = {Tan, SK and Granados, AC and Bouquet, J and Hoy-Schulz, YE and Green, L and Federman, S and Stryke, D and Haggerty, TD and Ley, C and Yeh, MT and Jannat, K and Maldonado, YA and Andino, R and Parsonnet, J and Chiu, CY}, title = {Metagenomic sequencing of stool samples in Bangladeshi infants: virome association with poliovirus shedding after oral poliovirus vaccination.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {15392}, pmid = {32958861}, issn = {2045-2322}, support = {R01 HD088837/HD/NICHD NIH HHS/United States ; R01501HD063142/NH/NIH HHS/United States ; R01-HD008837/NH/NIH HHS/United States ; UL1 RR025744/RR/NCRR NIH HHS/United States ; TL1 TR001084/TR/NCATS NIH HHS/United States ; }, mesh = {Antibodies, Neutralizing/immunology ; Antibodies, Viral/blood ; Bangladesh/epidemiology ; Feces/virology ; Female ; Humans ; Immunization Schedule ; Infant ; Male ; Metagenome/genetics ; Metagenomics/methods ; Poliomyelitis/virology ; Poliovirus/*genetics/immunology ; Poliovirus Vaccine, Inactivated/immunology ; Poliovirus Vaccine, Oral/*immunology ; Vaccination ; Virome/genetics ; Virus Shedding/*genetics ; }, abstract = {The potential role of enteric viral infections and the developing infant virome in affecting immune responses to the oral poliovirus vaccine (OPV) is unknown. Here we performed viral metagenomic sequencing on 3 serially collected stool samples from 30 Bangladeshi infants following OPV vaccination and compared findings to stool samples from 16 age-matched infants in the United States (US). In 14 Bangladeshi infants, available post-vaccination serum samples were tested for polio-neutralizing antibodies. The abundance (p = 0.006) and richness (p = 0.013) of the eukaryotic virome increased with age and were higher than seen in age-matched US infants (p < 0.001). In contrast, phage diversity metrics remained stable and were similar to those in US infants. Non-poliovirus eukaryotic virus abundance (3.68 log10 vs. 2.25 log10, p = 0.002), particularly from potential viral pathogens (2.78log10 vs. 0.83log10, p = 0.002), and richness (p = 0.016) were inversely associated with poliovirus shedding. Following vaccination, 28.6% of 14 infants tested developed neutralizing antibodies to all three Sabin types and also exhibited higher rates of poliovirus shedding (p = 0.020). No vaccine-derived poliovirus variants were detected. These results reveal an inverse association between eukaryotic virome abundance and poliovirus shedding. Overall gut virome ecology and concurrent viral infections may impact oral vaccine responsiveness in Bangladeshi infants.}, }
@article {pmid32958844, year = {2020}, author = {Dalzochio, MS and Périco, E and Dametto, N and Sahlén, G}, title = {Rapid functional traits turnover in boreal dragonfly communities (Odonata).}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {15411}, pmid = {32958844}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; *Biological Evolution ; Climate Change ; Ecosystem ; *Environment ; Longitudinal Studies ; Metagenomics/methods ; Odonata/*genetics/metabolism ; Phenotype ; Sweden ; }, abstract = {All natural populations show fluctuations in space or time. This is fundamental for the maintenance of biodiversity, as it allows species to coexist. Long-term ecological studies are rare, mainly due to logistics, but studies like the one presented below recognize the dimensionality of temporal change and the ecological processes that lead to shifts in community composition over time. Here, we used three sampling occasions from a dataset spanning 20 years where dragonflies in central Sweden were monitored. Our aim was to investigate how the prevalence of ecological and biological species traits varied over time measured as Community-level Weighted Means of trait values (CWM). Most CWM values varied significantly between years. Most of the traits changed between the second and the last sampling occasion, but not between the two first ones. These changes could be linked to major changes in species abundance. Our work indicates that fundamental shifts in community structure can occur over a short time, providing environmental drivers act on species turnover. In our case, Climate change and pH levels in lakes are most likely the most important factors.}, }
@article {pmid32694705, year = {2020}, author = {Willis, KA and Postnikoff, CK and Freeman, A and Rezonzew, G and Nichols, K and Gaggar, A and Lal, CV}, title = {The closed eye harbours a unique microbiome in dry eye disease.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {12035}, pmid = {32694705}, issn = {2045-2322}, support = {P30 AI027767/AI/NIAID NIH HHS/United States ; K08HL141652/NH/NIH HHS/United States ; UL1 TR000165/TR/NCATS NIH HHS/United States ; R01 HL102371/HL/NHLBI NIH HHS/United States ; R01HL102371/NH/NIH HHS/United States ; P30 AR050948/AR/NIAMS NIH HHS/United States ; 17SDG32720009/AHA/American Heart Association-American Stroke Association/United States ; K08 HL141652/HL/NHLBI NIH HHS/United States ; }, mesh = {Adult ; Case-Control Studies ; Dry Eye Syndromes/diagnosis/*etiology ; Female ; Humans ; Machine Learning ; Male ; Metagenomics/methods ; *Microbiota ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Tears/microbiology ; Trauma Severity Indices ; }, abstract = {Dry eye affects millions of individuals. In experimental models, dry eye disease is associated with T helper cell 17-mediated inflammation of the ocular surface that may cause persistent damage to the corneal epithelium. However, the initiating and perpetuating factors associated with chronic inflammation of the ocular surface remain unclear. The ocular microbiota alters ocular surface inflammation and may influence dry eye disease development and progression. Here, we collected serial samples of tears on awakening from sleep, closed eye tears, during a randomized clinical trial of a non-pharmaceutical dry eye therapy and used 16S rRNA metabarcoding to characterize the microbiome. We show the closed dry eye microbiome is distinct from the healthy closed eye microbiome, and that the microbiome remains distinct despite daily saline eye wash upon awakening. The ocular microbiome was described only recently, and this report implicates a distinct microbiome in ocular disease development. Our findings suggest an interplay between microbial commensals and inflammation on the ocular surface. This information may inform future studies of the pathophysiological mechanisms of dry eye disease.}, }
@article {pmid32209031, year = {2020}, author = {Sarma, SJ and Lei, Z and Rosenfeld, CS and Ericsson, A and Sumner, LW}, title = {Nontargeted fecal metabolomics: an emerging tool to probe the role of the gut microbiome in host health.}, journal = {Bioanalysis}, volume = {12}, number = {6}, pages = {351-353}, doi = {10.4155/bio-2020-0010}, pmid = {32209031}, issn = {1757-6199}, support = {R01 ES025547/ES/NIEHS NIH HHS/United States ; }, mesh = {Feces/*chemistry ; Gastrointestinal Microbiome/*physiology ; Humans ; Metabolomics/*methods ; }, }
@article {pmid32014483, year = {2020}, author = {Li, M and Yue, H and Wang, Y and Guo, C and Du, Z and Jin, C and Ding, K}, title = {Intestinal microbes derived butyrate is related to the immunomodulatory activities of Dendrobium officinale polysaccharide.}, journal = {International journal of biological macromolecules}, volume = {149}, number = {}, pages = {717-723}, doi = {10.1016/j.ijbiomac.2020.01.305}, pmid = {32014483}, issn = {1879-0003}, mesh = {Animals ; Bacteria/classification/drug effects/genetics ; Butyrates/*metabolism/*pharmacology ; Colon/microbiology/pathology ; Dendrobium/*chemistry ; Dietary Carbohydrates ; Fatty Acids, Volatile/analysis ; Female ; Gastrointestinal Microbiome/drug effects ; Glucose ; Glucuronic Acid ; Immunity ; Immunoglobulin M ; Immunologic Factors/*metabolism ; Interleukin-10 ; Intestines/immunology/*microbiology/pathology ; Metagenomics ; Mice ; Mice, Inbred C57BL ; Molecular Weight ; Monosaccharides ; Plant Extracts/chemistry/*pharmacology ; Polysaccharides/*chemistry/isolation &amp; purification/*pharmacology ; Tumor Necrosis Factor-alpha ; }, abstract = {Although immunomodulatory activities of Dendrobium officinale polysaccharide has been investigated for many years, yet the potential contribution of its metabolite derived from intestinal microbes on immunoregulation effect has not been reported. In this study, polysaccharide DOW-5B with average molecular weight of 39.4 kDa was isolated from the stem of Dendrobium officinale Kimura et Migo. The carbohydrate content was 91.97% and no protein was detected. The monosaccharide analysis showed this polysaccharide was composed of glucuronic acid and glucose at a molar ratio (M/G) of 1.2:19.4. Animal test indicated DOW-5B increased the diversity of gut microbiota on mice. Beneficial microbes such as Ruminococcus, Eubacterium, Clostridium, Bifidobacterium, Parabacteroides and Akkermansiamuciniphila increased while harmful bacteria in Proteobacteria decreased. Surprisingly, DOW-5B promoted gut microbes to generate more butyrate and mainly produced by Parabacteroides_sp_HGS0025. Further, we found the health of large intestine as well as immunity response of mice was improved. In addition, Parabacteroides_sp_HGS0025 positively correlated with butyrate, IgM, IL-10, and TNF-α products in intestine and mice blood, respectively. The data suggested that Dendrobium officinale polysaccharide has function on immunity may be mediated by butyrate. It adds new evidence to support the basis of how herbal polysaccharides affect immunity.}, }
@article {pmid32992082, year = {2020}, author = {Lee, JE and Lee, SM and Jung, J}, title = {Integrated omics analysis unraveled the microbiome-mediated effects of Yijin-Tang on hepatosteatosis and insulin resistance in obese mouse.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {79}, number = {}, pages = {153354}, doi = {10.1016/j.phymed.2020.153354}, pmid = {32992082}, issn = {1618-095X}, mesh = {Animals ; Anti-Obesity Agents/*pharmacology ; Bacteroides/drug effects ; Cholesterol/adverse effects ; Diet, High-Fat/adverse effects ; Firmicutes/drug effects ; Gastrointestinal Microbiome/*drug effects/genetics/physiology ; *Insulin Resistance ; Male ; Mice, Inbred C57BL ; Non-alcoholic Fatty Liver Disease/*drug therapy/metabolism/microbiology ; Obesity/*drug therapy/etiology ; Phosphatidylglycerols/metabolism ; Plant Extracts/chemistry/*pharmacology ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Gut microbiota play important roles in insulin homeostasis and the pathogenesis of non-alcoholic fatty liver diseases (NAFLD). Yijin-Tang (YJT), a traditional Korean and Chinese medicine, is used in the treatment of gastrointestinal diseases and obesity-related disorders such as insulin resistance (IR) and NAFLD.<br><br>PURPOSE: Our aim was to identify the microbiome-mediated effects of YJT on IR and associated NAFLD by integrating metagenomics and hepatic lipid profile.<br><br>METHODS: C57BL/6J mice were fed a normal chow diet (NC) or high-fat/high-cholesterol (HFHC) diet with or without YJT treatment. Hepatic lipid profiles were analyzed using liquid chromatography/mass spectrometry, and the composition of gut microbiota was investigated using 16S rRNA sequencing. Then, hepatic lipid profiles, gut microbiome, and inflammatory marker data were integrated using multivariate analysis and bioinformatics tools.<br><br>RESULTS: YJT improved NAFLD, and 39 hepatic lipid metabolites were altered by YJT in a dose-dependent manner. YJT also altered the gut microbiome composition in HFHC-fed mice. In particular, Faecalibaculum rodentium and Bacteroides acidifaciens were altered by YJT in a dose-dependent manner. Also, we found significant correlation among hepatic phosphatidylglycerol metabolites, F. rodentium, and γδ-T cells. Moreover, interleukin (IL)-17, which is secreted by the γδ-T cell when it recognizes lipid antigens, were elevated in HFHC mice and decreased by YJT treatment. In addition, YJT increased the relative abundance of B. acidifaciens in NC or HFHC-fed mice, which is a gut microbiota that mediates anti-obesity and anti-diabetic effects by modulating the gut environment. We also confirmed that YJT ameliorated the gut tight junctions and increased short chain fatty acid (SCFA) levels in the intestine, which resulted in improved IR.<br><br>CONCLUSION: These data demonstrated that gut microbiome and hepatic lipid profiles are regulated by YJT, which improved the IR and NAFLD in mice with diet-induced obesity.}, }
@article {pmid32792677, year = {2020}, author = {Nieuwenhuijse, DF and Oude Munnink, BB and Phan, MVT and ,  and Munk, P and Venkatakrishnan, S and Aarestrup, FM and Cotten, M and Koopmans, MPG}, title = {Setting a baseline for global urban virome surveillance in sewage.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {13748}, pmid = {32792677}, issn = {2045-2322}, mesh = {Cross-Sectional Studies ; Disease Outbreaks ; Environmental Monitoring/*methods ; Food Contamination ; Humans ; Metagenome/genetics ; Metagenomics/methods ; Pilot Projects ; Sewage/*virology ; Vegetables/virology ; Virome/*genetics ; Viruses/*classification/genetics/*isolation &amp; purification ; }, abstract = {The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks. Early detection of unusual disease emergence and spread should therefore include such cities as part of risk-based surveillance. A catch-all metagenomic sequencing approach of urban sewage could potentially provide an unbiased insight into the dynamics of viral pathogens circulating in a community irrespective of access to care, a potential which already has been proven for the surveillance of poliovirus. Here, we present a detailed characterization of sewage viromes from a snapshot of 81 high density urban areas across the globe, including in-depth assessment of potential biases, as a proof of concept for catch-all viral pathogen surveillance. We show the ability to detect a wide range of viruses and geographical and seasonal differences for specific viral groups. Our findings offer a cross-sectional baseline for further research in viral surveillance from urban sewage samples and place previous studies in a global perspective.}, }
@article {pmid33318221, year = {2020}, author = {Gao, Q and Wang, G and Xue, K and Yang, Y and Xie, J and Yu, H and Bai, S and Liu, F and He, Z and Ning, D and Hobbie, SE and Reich, PB and Zhou, J}, title = {Stimulation of soil respiration by elevated CO2 is enhanced under nitrogen limitation in a decade-long grassland study.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {}, number = {}, pages = {}, doi = {10.1073/pnas.2002780117}, pmid = {33318221}, issn = {1091-6490}, abstract = {Whether and how CO2 and nitrogen (N) availability interact to influence carbon (C) cycling processes such as soil respiration remains a question of considerable uncertainty in projecting future C-climate feedbacks, which are strongly influenced by multiple global change drivers, including elevated atmospheric CO2 concentrations (eCO2) and increased N deposition. However, because decades of research on the responses of ecosystems to eCO2 and N enrichment have been done largely independently, their interactive effects on soil respiratory CO2 efflux remain unresolved. Here, we show that in a multifactor free-air CO2 enrichment experiment, BioCON (Biodiversity, CO2, and N deposition) in Minnesota, the positive response of soil respiration to eCO2 gradually strengthened at ambient (low) N supply but not enriched (high) N supply for the 12-y experimental period from 1998 to 2009. In contrast to earlier years, eCO2 stimulated soil respiration twice as much at low than at high N supply from 2006 to 2009. In parallel, microbial C degradation genes were significantly boosted by eCO2 at low but not high N supply. Incorporating those functional genes into a coupled C-N ecosystem model reduced model parameter uncertainty and improved the projections of the effects of different CO2 and N levels on soil respiration. If our observed results generalize to other ecosystems, they imply widely positive effects of eCO2 on soil respiration even in infertile systems.}, }
@article {pmid31819139, year = {2019}, author = {Rosa, UA and Ribeiro, GO and Villanova, F and Luchs, A and Milagres, FAP and Komninakis, SV and Tahmasebi, R and Lobato, MCABS and Brustulin, R and Chagas, RTD and Abrão, MFNDS and Soares, CVDA and Tinker, RJ and Pandey, RP and Raj, VS and Sabino, EC and Deng, X and Delwart, E and Costa, ACD and Leal, É}, title = {First identification of mammalian orthoreovirus type 3 by gut virome analysis in diarrheic child in Brazil.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {18599}, doi = {10.1038/s41598-019-55216-5}, pmid = {31819139}, issn = {2045-2322}, mesh = {Animals ; Brazil/epidemiology ; Cattle ; Child, Preschool ; Chiroptera ; Diarrhea/*virology ; Gastroenteritis/*virology ; Gastrointestinal Microbiome ; Genome, Viral ; Geography ; Humans ; Infant ; Intestines/*virology ; Mammalian orthoreovirus 3/*classification/isolation &amp; purification ; Metagenomics ; Phylogeny ; Rural Population ; Swine ; }, abstract = {Diarrhea remains one of the most common causes of deaths in children. Although many studies have investigated the prevalence of enteric pathogens around the globe some diarrheal episodes remain unexplained. It is possible that some yet-unidentified viral agents could be related to these cases of gastroenteritis. By using viral metagenomics techniques, we screened 251 fecal samples of children between 0.5 to 2.5-year-old with acute diarrhea not associated with common pathogens. These children live in rural areas and have different levels of contact with animals such as pigs, cows and bats. Here we report a complete genome of one mammalian orthoreovirus (MRV) type 3, denoted TO-151/BR, detected in a female child in the state of Tocantins (north of Brazil). Brazilian TO-151/BR strain was classified as MRV-3 based on S1 phylogeny and was closely related to porcine Asian strains. Phylogenetic analyses showed that other segments were more similar to MRV-3s of different geographic locations and hosts, including human and bats, highlighting genome reassortment and lack of host-specific barriers. This is the first report of MRV-3 in South America and a hypothesis of a silent long-term circulation of this virus in Brazil has been raised.}, }
@article {pmid33219095, year = {2020}, author = {Mostafa, HH and Fissel, JA and Fanelli, B and Bergman, Y and Gniazdowski, V and Dadlani, M and Carroll, KC and Colwell, RR and Simner, PJ}, title = {Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients.}, journal = {mBio}, volume = {11}, number = {6}, pages = {}, pmid = {33219095}, issn = {2150-7511}, mesh = {Bacteria/classification ; COVID-19/microbiology/*virology ; Coinfection/microbiology/virology ; Computational Biology ; *High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; *Metagenomics ; Microbiota ; Nasopharynx/*virology ; RNA, Viral/genetics ; SARS-CoV-2/*genetics ; Specimen Handling ; }, abstract = {Metagenomic next-generation sequencing (mNGS) offers an agnostic approach for emerging pathogen detection directly from clinical specimens. In contrast to targeted methods, mNGS also provides valuable information on the composition of the microbiome and might uncover coinfections that may associate with disease progression and impact prognosis. To evaluate the use of mNGS for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and/or other infecting pathogens, we applied direct Oxford Nanopore long-read third-generation metatranscriptomic and metagenomic sequencing. Nasopharyngeal (NP) swab specimens from 50 patients under investigation for CoV disease 2019 (COVID-19) were sequenced, and the data were analyzed by the CosmosID bioinformatics platform. Further, we characterized coinfections and the microbiome associated with a four-point severity index. SARS-CoV-2 was identified in 77.5% (31/40) of samples positive by RT-PCR, correlating with lower cycle threshold (Ct) values and fewer days from symptom onset. At the time of sampling, possible bacterial or viral coinfections were detected in 12.5% of SARS-CoV-2-positive specimens. A decrease in microbial diversity was observed among COVID-19-confirmed patients (Shannon diversity index, P = 0.0082; Chao richness estimate, P = 0.0097; Simpson diversity index, P = 0.018), and differences in microbial communities were linked to disease severity (P = 0.022). Furthermore, statistically significant shifts in the microbiome were identified among SARS-CoV-2-positive and -negative patients, in the latter of whom a higher abundance of Propionibacteriaceae (P = 0.028) and a reduction in the abundance of Corynebacterium accolens (P = 0.025) were observed. Our study corroborates the growing evidence that increased SARS-CoV-2 RNA detection from NP swabs is associated with the early stages rather than the severity of COVID-19. Further, we demonstrate that SARS-CoV-2 causes a significant change in the respiratory microbiome. This work illustrates the utility of mNGS for the detection of SARS-CoV-2, for diagnosing coinfections without viral target enrichment or amplification, and for the analysis of the respiratory microbiome.IMPORTANCE SARS-CoV-2 has presented a rapidly accelerating global public health crisis. The ability to detect and analyze viral RNA from minimally invasive patient specimens is critical to the public health response. Metagenomic next-generation sequencing (mNGS) offers an opportunity to detect SARS-CoV-2 from nasopharyngeal (NP) swabs. This approach also provides information on the composition of the respiratory microbiome and its relationship to coinfections or the presence of other organisms that may impact SARS-CoV-2 disease progression and prognosis. Here, using direct Oxford Nanopore long-read third-generation metatranscriptomic and metagenomic sequencing of NP swab specimens from 50 patients under investigation for COVID-19, we detected SARS-CoV-2 sequences by applying the CosmosID bioinformatics platform. Further, we characterized coinfections and detected a decrease in the diversity of the microbiomes in these patients. Statistically significant shifts in the microbiome were identified among COVID-19-positive and -negative patients, in the latter of whom a higher abundance of Propionibacteriaceae and a reduction in the abundance of Corynebacterium accolens were observed. Our study also corroborates the growing evidence that increased SARS-CoV-2 RNA detection from NP swabs is associated with the early stages of disease rather than with severity of disease. This work illustrates the utility of mNGS for the detection and analysis of SARS-CoV-2 from NP swabs without viral target enrichment or amplification and for the analysis of the respiratory microbiome.}, }
@article {pmid33152096, year = {2020}, author = {Qiu, H and Gu, L and Sun, B and Zhang, J and Zhang, M and He, S and An, S and Leng, X}, title = {Metagenomic Analysis Revealed that the Terrestrial Pollutants Override the Effects of Seasonal Variation on Microbiome in River Sediments.}, journal = {Bulletin of environmental contamination and toxicology}, volume = {105}, number = {6}, pages = {892-898}, doi = {10.1007/s00128-020-03033-2}, pmid = {33152096}, issn = {1432-0800}, support = {2017ZX07602-002//Major Science and Technology Program for Water Pollution Control and Treatment/ ; }, mesh = {Environmental Monitoring/*methods ; Environmental Pollutants ; Geologic Sediments/chemistry/*microbiology ; Microbiota/*genetics ; Rivers/chemistry ; Seasons ; Water Pollutants, Chemical/*analysis ; }, abstract = {Researching the structure and function of sediment microbiome contribute to understanding the response of microbiome to external disturbances. However, seasonal changes in sediment microbiome with different terrestrial pollutants input have not yet been clearly understood. Metagenomic sequencing was used to evaluate the effects of seasonal variations and different land use types on sediment microbiome. Results showed that the differences in structure and functions of sediment microbiome among different land use types were obviously greater than different seasons. This indicated that the terrestrial pollutants weakened the effects of seasonal variations on shaping the sediment microbiome. The significant differences in sediment properties under the input of different terrestrial pollutants was observed, but no obvious differences between seasons, which may be the reason why terrestrial pollutants override the effects of seasonal variation on the sediment microbiome. Overall, the results extended our understanding of the impacts of seasonal variation and terrestrial pollutants on river sediment microbiome.}, }
@article {pmid33057402, year = {2020}, author = {Eriksen, AMH and Nielsen, TK and Matthiesen, H and Carøe, C and Hansen, LH and Gregory, DJ and Turner-Walker, G and Collins, MJ and Gilbert, MTP}, title = {Bone biodeterioration-The effect of marine and terrestrial depositional environments on early diagenesis and bone bacterial community.}, journal = {PloS one}, volume = {15}, number = {10}, pages = {e0240512}, pmid = {33057402}, issn = {1932-6203}, mesh = {Animals ; Bacteria/classification/genetics/*growth &amp; development ; Bone and Bones/metabolism/*microbiology/*pathology ; Environmental Exposure/*analysis ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Swine ; }, abstract = {Bacteria play an important role in the degradation of bone material. However, much remains to be learnt about the structure of their communities in degrading bone, and how the depositional environment influences their diversity throughout the exposure period. We genetically profiled the bacterial community in an experimental series of pig bone fragments (femur and humeri) deposited at different well-defined environments in Denmark. The bacterial community in the bone fragments and surrounding depositional environment were studied over one year, and correlated with the bioerosion damage patterns observed microscopically in the bones. We observed that the bacterial communities within the bones were heavily influenced by the local microbial community, and that the general bone microbial diversity increases with time after exposure. We found the presence of several known collagenase producing bacterial groups, and also observed increases in the relative abundance of several of these in bones with tunneling. We anticipate that future analyses using shotgun metagenomics on this and similar datasets will be able to provide insights into mechanisms of microbiome driven bone degradation.}, }
@article {pmid32917913, year = {2020}, author = {Vaga, S and Lee, S and Ji, B and Andreasson, A and Talley, NJ and Agréus, L and Bidkhori, G and Kovatcheva-Datchary, P and Park, J and Lee, D and Proctor, G and Ehrlich, SD and Nielsen, J and Engstrand, L and Shoaie, S}, title = {Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {14977}, pmid = {32917913}, issn = {2045-2322}, support = {project EP/ S001301/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Bacteroides/classification/genetics/metabolism ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Ileum/*microbiology ; Intestinal Mucosa/*microbiology ; Intestine, Large/*microbiology ; Male ; }, abstract = {Gut mucosal microbes evolved closest to the host, developing specialized local communities. There is, however, insufficient knowledge of these communities as most studies have employed sequencing technologies to investigate faecal microbiota only. This work used shotgun metagenomics of mucosal biopsies to explore the microbial communities' compositions of terminal ileum and large intestine in 5 healthy individuals. Functional annotations and genome-scale metabolic modelling of selected species were then employed to identify local functional enrichments. While faecal metagenomics provided a good approximation of the average gut mucosal microbiome composition, mucosal biopsies allowed detecting the subtle variations of local microbial communities. Given their significant enrichment in the mucosal microbiota, we highlight the roles of Bacteroides species and describe the antimicrobial resistance biogeography along the intestine. We also detail which species, at which locations, are involved with the tryptophan/indole pathway, whose malfunctioning has been linked to pathologies including inflammatory bowel disease. Our study thus provides invaluable resources for investigating mechanisms connecting gut microbiota and host pathophysiology.}, }
@article {pmid32917751, year = {2020}, author = {Park, SJ and Andrei, AŞ and Bulzu, PA and Kavagutti, VS and Ghai, R and Mosier, AC}, title = {Expanded Diversity and Metabolic Versatility of Marine Nitrite-Oxidizing Bacteria Revealed by Cultivation- and Genomics-Based Approaches.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {22}, pages = {}, pmid = {32917751}, issn = {1098-5336}, mesh = {Bacteria/*classification/isolation &amp; purification/*metabolism ; Geologic Sediments/microbiology ; Metabolic Networks and Pathways ; *Microbiota ; Nitrites/*metabolism ; Oxidation-Reduction ; Republic of Korea ; Seawater/microbiology ; }, abstract = {Nitrite-oxidizing bacteria (NOB) are ubiquitous and abundant microorganisms that play key roles in global nitrogen and carbon biogeochemical cycling. Despite recent advances in understanding NOB physiology and taxonomy, currently very few cultured NOB or representative NOB genome sequences from marine environments exist. In this study, we employed enrichment culturing and genomic approaches to shed light on the phylogeny and metabolic capacity of marine NOB. We successfully enriched two marine NOB (designated MSP and DJ) and obtained a high-quality metagenome-assembled genome (MAG) from each organism. The maximum nitrite oxidation rates of the MSP and DJ enrichment cultures were 13.8 and 30.0 μM nitrite per day, respectively, with these optimum rates occurring at 0.1 mM and 0.3 mM nitrite, respectively. Each enrichment culture exhibited a different tolerance to various nitrite and salt concentrations. Based on phylogenomic position and overall genome relatedness indices, both NOB MAGs were proposed as novel taxa within the Nitrospinota and Nitrospirota phyla. Functional predictions indicated that both NOB MAGs shared many highly conserved metabolic features with other NOB. Both NOB MAGs encoded proteins for hydrogen and organic compound metabolism and defense mechanisms for oxidative stress. Additionally, these organisms may have the genetic potential to produce cobalamin (an essential enzyme cofactor that is limiting in many environments) and, thus, may play an important role in recycling cobalamin in marine sediment. Overall, this study appreciably expands our understanding of the Nitrospinota and Nitrospirota phyla and suggests that these NOB play important biogeochemical roles in marine habitats.IMPORTANCE Nitrification is a key process in the biogeochemical and global nitrogen cycle. Nitrite-oxidizing bacteria (NOB) perform the second step of aerobic nitrification (converting nitrite to nitrate), which is critical for transferring nitrogen to other organisms for assimilation or energy. Despite their ecological importance, there are few cultured or genomic representatives from marine systems. Here, we obtained two NOB (designated MSP and DJ) enriched from marine sediments and estimated the physiological and genomic traits of these marine microbes. Both NOB enrichment cultures exhibit distinct responses to various nitrite and salt concentrations. Genomic analyses suggest that these NOB are metabolically flexible (similar to other previously described NOB) yet also have individual genomic differences that likely support distinct niche distribution. In conclusion, this study provides more insights into the ecological roles of NOB in marine environments.}, }
@article {pmid32755308, year = {2020}, author = {Edwards, PT and Kashyap, PC and Preidis, GA}, title = {Microbiota on biotics: probiotics, prebiotics, and synbiotics to optimize growth and metabolism.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {319}, number = {3}, pages = {G382-G390}, pmid = {32755308}, issn = {1522-1547}, support = {R01 DK114007/DK/NIDDK NIH HHS/United States ; K08 DK113114/DK/NIDDK NIH HHS/United States ; T32 DK007664/DK/NIDDK NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; }, mesh = {Digestive System Physiological Phenomena/*genetics ; Gastrointestinal Diseases/prevention &amp; control ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/growth &amp; development/*physiology ; Genomics ; Humans ; *Prebiotics ; Probiotics/*therapeutic use ; *Synbiotics ; }, abstract = {The early stages of the metagenomics era produced countless observational studies linking various human diseases to alterations in the gut microbiota. Only recently have we begun to decipher the causal roles that gut microbes play in many of these conditions. Despite an incomplete understanding of how gut microbes influence pathophysiology, clinical trials have tested empirically numerous microbiota-targeting therapies to prevent or treat disease. Unsurprisingly, these trials have yielded mixed results. Nonetheless, the consumer market for probiotics, prebiotics, and synbiotics continues to grow. This theme paper highlights recent discoveries of mechanisms underlying diet-microbial-host interactions as they pertain to growth and metabolism and discusses current and future applications of microbiota-targeting therapies in the context of child malnutrition as well as obesity and its metabolic comorbidities, including nonalcoholic fatty liver disease and cardiovascular disease. We also highlight current challenges and identify future directions to facilitate a more efficient and direct path to clinical impact.}, }
@article {pmid32612216, year = {2020}, author = {Hofmeyr, S and Egan, R and Georganas, E and Copeland, AC and Riley, R and Clum, A and Eloe-Fadrosh, E and Roux, S and Goltsman, E and Buluç, A and Rokhsar, D and Oliker, L and Yelick, K}, title = {Terabase-scale metagenome coassembly with MetaHipMer.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {10689}, pmid = {32612216}, issn = {2045-2322}, mesh = {Algorithms ; Computational Biology/*methods ; Computers ; Genome, Bacterial/*genetics ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/genetics ; Pseudoalteromonas/genetics/isolation &amp; purification ; Sequence Analysis, DNA/methods ; }, abstract = {Metagenome sequence datasets can contain terabytes of reads, too many to be coassembled together on a single shared-memory computer; consequently, they have only been assembled sample by sample (multiassembly) and combining the results is challenging. We can now perform coassembly of the largest datasets using MetaHipMer, a metagenome assembler designed to run on supercomputers and large clusters of compute nodes. We have reported on the implementation of MetaHipMer previously; in this paper we focus on analyzing the impact of very large coassembly. In particular, we show that coassembly recovers a larger genome fraction than multiassembly and enables the discovery of more complete genomes, with lower error rates, whereas multiassembly recovers more dominant strain variation. Being able to coassemble a large dataset does not preclude one from multiassembly; rather, having a fast, scalable metagenome assembler enables a user to more easily perform coassembly and multiassembly, and assemble both abundant, high strain variation genomes, and low-abundance, rare genomes. We present several assemblies of terabyte datasets that could never be coassembled before, demonstrating MetaHipMer's scaling power. MetaHipMer is available for public use under an open source license and all datasets used in the paper are available for public download.}, }
@article {pmid32541790, year = {2020}, author = {Diakite, A and Dubourg, G and Dione, N and Afouda, P and Bellali, S and Ngom, II and Valles, C and Tall, ML and Lagier, JC and Raoult, D}, title = {Optimization and standardization of the culturomics technique for human microbiome exploration.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {9674}, pmid = {32541790}, issn = {2045-2322}, mesh = {Bacteria/*classification/*growth &amp; development/isolation &amp; purification ; Bacteriological Techniques/methods/*standards ; Culture Media/chemistry ; Feces/*microbiology ; Humans ; Microbiota ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Workflow ; }, abstract = {Culturomics is a high-throughput culture approach that has dramatically contributed to the recent renewal of culture. While metagenomics enabled substantial advances in exploring the microbiota, culturomics significantly expanded our knowledge regarding the bacterial gut repertoire through the discovery and the description of hundreds of new taxa. While this approach relies on the variation of culture conditions and media, we have tested so far more than 300 conditions since the beginning of culturomics studies. In this context, we aimed herein to identify the most profitable conditions for optimizing culturomics approach. For this purpose, we have analysed a set of 58 culturomics conditions that were previously applied to 8 faecal specimens, enabling the isolation of 497 bacterial species. As a result, we were able to reduce the number of conditions used to isolate these 497 of more than a half (i.e. to 25 culture conditions). We have also established a list of the 16 conditions that allowed to capture 98% of the total number of species previously isolated. These data constitute a methodological starting point for culture-based microbiota studies by improving the culturomics workflow without any loss of captured bacterial diversity.}, }
@article {pmid32518251, year = {2020}, author = {Bovo, S and Utzeri, VJ and Ribani, A and Cabbri, R and Fontanesi, L}, title = {Shotgun sequencing of honey DNA can describe honey bee derived environmental signatures and the honey bee hologenome complexity.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {9279}, doi = {10.1038/s41598-020-66127-1}, pmid = {32518251}, issn = {2045-2322}, mesh = {Animals ; Bacteria/genetics ; Bees ; Environmental DNA/*analysis/genetics ; Gastrointestinal Microbiome/genetics ; Genome, Bacterial/genetics ; Genome, Fungal/genetics ; Genome, Plant/genetics ; Genome, Protozoan/genetics ; Genome, Viral/genetics ; Honey/*analysis ; *Metagenomics ; Sequence Analysis, DNA ; }, abstract = {Honey bees are large-scale monitoring tools due to their extensive environmental exploration. In their activities and from the hive ecosystem complex, they get in close contact with many organisms whose traces can be transferred into the honey, which can represent an interesting reservoir of environmental DNA (eDNA) signatures and information useful to analyse the honey bee hologenome complexity. In this study, we tested a deep shotgun sequencing approach of honey DNA coupled with a specifically adapted bioinformatic pipeline. This methodology was applied to a few honey samples pointing out DNA sequences from 191 organisms spanning different kingdoms or phyla (viruses, bacteria, plants, fungi, protozoans, arthropods, mammals). Bacteria included the largest number of species. These multi-kingdom signatures listed common hive and honey bee gut microorganisms, honey bee pathogens, parasites and pests, which resembled a complex interplay that might provide a general picture of the honey bee pathosphere. Based on the Apis mellifera filamentous virus genome diversity (the most abundant detected DNA source) we obtained information that could define the origin of the honey at the apiary level. Mining Apis mellifera sequences made it possible to identify the honey bee subspecies both at the mitochondrial and nuclear genome levels.}, }
@article {pmid32433519, year = {2020}, author = {Mahnic, A and Auchtung, JM and Poklar Ulrih, N and Britton, RA and Rupnik, M}, title = {Microbiota in vitro modulated with polyphenols shows decreased colonization resistance against Clostridioides difficile but can neutralize cytotoxicity.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {8358}, doi = {10.1038/s41598-020-65253-0}, pmid = {32433519}, issn = {2045-2322}, mesh = {Actinobacteria/immunology ; Bacterial Toxins/metabolism/*toxicity ; Biological Assay ; Bioreactors/microbiology ; Clindamycin/adverse effects ; Clostridioides difficile/growth &amp; development/metabolism ; Clostridium/immunology ; Clostridium Infections/immunology/microbiology/*prevention &amp; control ; Disease Resistance/*drug effects/immunology ; Feces/microbiology ; Gastrointestinal Microbiome/drug effects/*immunology ; Humans ; Polyphenols/*pharmacology ; }, abstract = {While the knowledge on gut microbiota - C. difficile interactions has improved over the years, the understanding of the underlying mechanisms providing colonization resistance as well as preventative measures against the infection remain incomplete. In this study the antibiotic clindamycin and polyphenol extracts from pomegranate and blueberries were used individually and in combination to modulate fecal microbial communities in minibioreactor arrays (MBRA). Modulated communities were inoculated with C. difficile (ribotype 027). Subsequent 7-day periodical monitoring included evaluation of C. difficile growth and activity of toxins TcdA and TcdB as well as analysis of MBRA bacterial community structure (V3V4 16 S metagenomics). Polyphenols affected multiple commensal bacterial groups and showed different synergistic and antagonistic effects in combination with clindamycin. Exposure to either clindamycin or polyphenols led to the loss of colonization resistance against C. difficile. The successful growth of C. difficile was most significantly correlated with the decrease in Collinsella and Lachnospiraceae. Additionally, we demonstrated that Clostridium sporogenes decreased the activity of both C. difficile toxins TcdA and TcdB. The feature was shown to be common among distinct C. sporogenes strains and could potentially be applicable as a non-antibiotic agent for the alleviation of C. difficile infection.}, }
@article {pmid32250964, year = {2020}, author = {Byrd, DA and Sinha, R and Hoffman, KL and Chen, J and Hua, X and Shi, J and Chia, N and Petrosino, J and Vogtmann, E}, title = {Comparison of Methods To Collect Fecal Samples for Microbiome Studies Using Whole-Genome Shotgun Metagenomic Sequencing.}, journal = {mSphere}, volume = {5}, number = {1}, pages = {}, pmid = {32250964}, issn = {2379-5042}, support = {R01 CA179243/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; DNA, Bacterial ; Ethanol ; Feces/*microbiology ; Female ; Freezing ; Gastrointestinal Microbiome/*genetics ; Healthy Volunteers ; Humans ; Male ; *Metagenome ; Metagenomics/*methods ; Middle Aged ; Preservation, Biological/methods ; RNA, Ribosomal, 16S/genetics ; Specimen Handling/*methods ; Temperature ; *Whole Genome Sequencing ; }, abstract = {Few previous studies have assessed stability and &quot;gold-standard&quot; concordance of fecal sample collection methods for whole-genome shotgun metagenomic sequencing (WGSS), an increasingly popular method for studying the gut microbiome. We used WGSS data to investigate ambient temperature stability and putative gold-standard concordance of microbial profiles in fecal samples collected and stored using fecal occult blood test (FOBT) cards, fecal immunochemical test (FIT) tubes, 95% ethanol, or RNAlater. Among 15 Mayo Clinic employees, for each collection method, we calculated intraclass correlation coefficients (ICCs) to estimate stability of fecal microbial profiles after storage for 4 days at ambient temperature and concordance with immediately frozen, no-solution samples (i.e., the putative gold standard). ICCs were estimated for multiple metrics, including relative abundances of select phyla, species, KEGG k-genes (representing any coding sequence that had >70% identity and >70% query coverage with respect to a known KEGG ortholog), KEGG modules, and KEGG pathways; species and k-gene alpha diversity; and Bray-Curtis and Jaccard species beta diversity. ICCs for microbial profile stability were excellent (≥90%) for fecal samples collected via most of the collection methods, except those preserved in 95% ethanol. Concordance with the immediately frozen, no-solution samples varied for all collection methods, but the number of observed species and the beta diversity metrics tended to have higher concordance than other metrics. Our findings, taken together with previous studies and feasibility considerations, indicated that FOBT cards, FIT tubes, and RNAlater are acceptable choices for fecal sample collection methods in future WGSS studies.IMPORTANCE A major direction for future microbiome research is implementation of fecal sample collections in large-scale, prospective epidemiologic studies. Studying microbiome-disease associations likely requires microbial data to be pooled from multiple studies. Our findings suggest collection methods that are most optimal to be used standardly across future WGSS microbiome studies.}, }
@article {pmid32235279, year = {2020}, author = {Lundy, SD and Vij, SC and Rezk, AH and Cohen, JA and Bajic, P and Ramasamy, R}, title = {The microbiome of the infertile male.}, journal = {Current opinion in urology}, volume = {30}, number = {3}, pages = {355-362}, doi = {10.1097/MOU.0000000000000742}, pmid = {32235279}, issn = {1473-6586}, mesh = {Humans ; Infertility, Male/*microbiology ; Male ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S ; Semen/*microbiology ; Semen Analysis ; }, abstract = {PURPOSE OF REVIEW: Contrary to historic dogma, many tissues and organs in the human body contain a resident population of bacteria, fungi, and viruses collectively known as the microbiome. The microbiome plays a role in both homeostatic symbiosis and also pathogenic dysbiosis in a wide array of diseases. Our understanding of the relationship between the microbiome and male factor infertility is in its infancy but is slowly evolving.<br><br>RECENT FINDINGS: Recent literature indicates that semen (and likely the testis) is not sterile and contains a distinct microbiome, and these changes in its composition are associated with alterations in semen quality and fertility status. Preliminary investigation indicates that manipulating the human microbiome may have implications in improving semen parameters and fertility.<br><br>SUMMARY: In this review, we describe relationships between the microbiome and the genitourinary system, discuss the prior work on the relationship among bacteriospermia, leukocytospermia and male factor infertility, and summarize the current literature utilizing 16s rRNA-based next-generation sequencing on the seminal and testicular microbiome. We explore the specific microbial taxa implicated in various aspects of spermatic dysfunction and introduce preliminary evidence for therapeutic approaches to alter the microbiome and improve fertility status.}, }
@article {pmid32227463, year = {2020}, author = {Lu, X and Wang, K and Sun, S and Mou, X}, title = {Metatranscriptomic identification of polyamine-transforming bacterioplankton in the Gulf of Mexico.}, journal = {Environmental microbiology reports}, volume = {12}, number = {3}, pages = {258-266}, doi = {10.1111/1758-2229.12841}, pmid = {32227463}, issn = {1758-2229}, support = {OCE1029697//National Science Foundation/International ; }, mesh = {Actinobacteria/classification/genetics/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification ; Bacteroidetes/classification/genetics/isolation &amp; purification ; Cyanobacteria/classification/genetics/isolation &amp; purification ; Gulf of Mexico ; Metagenomics ; Microbiota ; Nitrogen/metabolism ; Phylogeny ; Planctomycetales/classification/genetics/isolation &amp; purification ; *Plankton/metabolism/microbiology ; Polyamines/*metabolism ; Proteobacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry/*microbiology ; Transcriptome ; }, abstract = {The importance of short-chained aliphatic polyamines (PAs) to bacterioplankton-mediated carbon and nitrogen cycles has been repeatedly proposed. However, bacterial taxa and genes involved in the transformations of different PA compounds and their potential spatial variations remain unclear. This study collected surface bacterioplankton from nearshore, offshore, and open ocean stations in the Gulf of Mexico and examined how metatranscriptomes responded to additions of three single PA model compounds (i.e. putrescine, spermidine, or spermine). Our data showed an overrepresentation of genes affiliated with γ-glutamylation and spermidine cleavage pathways in metatranscriptomes received PA amendments and the expression level of each pathway varied among different PA compounds and sampling locations. PA-transforming taxa were affiliated with Actinobacteria, Bacteroidetes, Cyanobacteria, Planctomycetes, and Proteobacteria and their relative importance was also compound and location specific. These findings suggest that PAs are transformed via multiple pathways and by a diversity of marine bacterioplankton in the Gulf of Mexico. The relative importance of different PA transforming pathways and composition of functional microbial communities may be regulated by nutrient status of local environments.}, }
@article {pmid32216046, year = {2020}, author = {Sandoz, FA and Bindschedler, S and Dauphin, B and Farinelli, L and Grant, JR and Hervé, V}, title = {Biotic and abiotic factors shape arbuscular mycorrhizal fungal communities associated with the roots of the widespread fern Botrychium lunaria (Ophioglossaceae).}, journal = {Environmental microbiology reports}, volume = {12}, number = {3}, pages = {342-354}, doi = {10.1111/1758-2229.12840}, pmid = {32216046}, issn = {1758-2229}, support = {//Fonds Wuthrich Mathey-Dupraz/International ; 31003A_156456//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/International ; CR32I2-149853/1//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/International ; CR32I2-149853/1 31003A_156456/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {Ferns/*microbiology ; Genes, Fungal ; Glomeromycota/classification/genetics/isolation &amp; purification ; Grassland ; Metagenomics ; Microbial Interactions ; Microbiota ; Mycobiome/*genetics ; Mycorrhizae/*genetics ; Phylogeny ; Plant Roots/microbiology ; Soil Microbiology ; Switzerland ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) play central roles in terrestrial ecosystems by interacting with both above and belowground communities as well as by influencing edaphic properties. The AMF communities associated with the roots of the fern Botrychium lunaria (Ophioglossaceae) were sampled in four transects at 2400 m a.s.l. in the Swiss Alps and analyzed using metabarcoding. Members of five Glomeromycota genera were identified across the 71 samples. Our analyses revealed the existence of a core microbiome composed of four abundant Glomus operational taxonomic units (OTUs), as well as a low OTU turnover between samples. The AMF communities were not spatially structured, which contrasts with most studies on AMF associated with angiosperms. pH, microbial connectivity and humus cover significantly shaped AMF beta diversity but only explained a minor fraction of variation in beta diversity. AMF OTUs associations were found to be significant by both cohesion and co-occurrence analyses, suggesting a role for fungus-fungus interactions in AMF community assembly. In particular, OTU co-occurrences were more frequent between different genera than among the same genus, rising the hypothesis of functional complementarity among the AMF associated to B. lunaria. Altogether, our results provide new insights into the ecology of fern symbionts in alpine grasslands.}, }
@article {pmid32206831, year = {2020}, author = {Mehta, O and Ghosh, TS and Kothidar, A and Gowtham, MR and Mitra, R and Kshetrapal, P and Wadhwa, N and Thiruvengadam, R and ,  and Nair, GB and Bhatnagar, S and Das, B}, title = {Vaginal Microbiome of Pregnant Indian Women: Insights into the Genome of Dominant Lactobacillus Species.}, journal = {Microbial ecology}, volume = {80}, number = {2}, pages = {487-499}, doi = {10.1007/s00248-020-01501-0}, pmid = {32206831}, issn = {1432-184X}, support = {No.BT/PR9983/MED/97/194/2013//Department of Biotechnology, Government of India/ ; }, mesh = {Adult ; Bacteria/isolation &amp; purification ; Female ; Genome, Bacterial/*physiology ; Humans ; India ; Lactobacillus/genetics/*physiology ; *Microbiota ; Pregnancy ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Vagina/*microbiology ; Young Adult ; }, abstract = {The trillions of microorganisms residing in the human body display varying degrees of compositional and functional diversities within and between individuals and contribute significantly to host physiology and susceptibility to disease. Microbial species present in the vaginal milieu of reproductive age women showed a large personal component and varies widely in different ethnic groups at the taxonomic, genomic, and functional levels. Lactobacillus iners, L. crispatus, L. gasseri, L. jensenii, and L. johnsonii are most frequently detected bacterial species in the vaginal milieu of reproductive age women. However, we currently lack (i) an understanding of the baseline vaginal microbiota of reproductive age Indian women, (ii) the extent of taxonomic and functional variations of vaginal microbiota between individuals and (iii) the genomic repertoires of the dominant vaginal microbiota associated with the Indian subjects. In our study, we analyzed the metagenome of high vaginal swab (HVS) samples collected from 40 pregnant Indian women enrolled in the GARBH-Ini cohort. Composition and abundance of bacterial species was characterized by pyrosequencing 16S rRNA gene. We identified 3067 OTUs with ≥ 10 reads from four different bacterial phyla. Several species of lactobacilli were clustered into three community state types (CSTs). L. iners, L. crispatus, L. gasseri, and L. jensenii are the most frequently detected Lactobacillus species in the vaginal environment of Indian women. Other than Lactobacillus, several species of Halomonas were also identified in the vaginal environment of most of the women sampled. To gain genomic and functional insights, we isolated several Lactobacillus species from the HVS samples and explored their whole genome sequences by shotgun sequencing. We analyzed the genome of dominant Lactobacillus species, L. iners, L. crispatus, L. gasseri, and L. paragesseri to represent the CSTs and identify functions that may influence the composition of complex vaginal microbial ecology. This study reports for the first time the vaginal microbial ecology of Indian women and genomic insights into L. iners, L. crispatus, L. gasseri, and L. paragesseri commonly found in the genital tract of reproductive age women.}, }
@article {pmid32204538, year = {2020}, author = {Tsai, MC and Liu, YY and Lin, CC and Wang, CC and Wu, YJ and Yong, CC and Chen, KD and Chuah, SK and Yao, CC and Huang, PY and Chen, CH and Hu, TH and Chen, CL}, title = {Gut Microbiota Dysbiosis in Patients with Biopsy-Proven Nonalcoholic Fatty Liver Disease: A Cross-Sectional Study in Taiwan.}, journal = {Nutrients}, volume = {12}, number = {3}, pages = {}, pmid = {32204538}, issn = {2072-6643}, support = {CMRPG8H1111//Kaohsiung Chang Gung Memorial Hospital/ ; CMRPG8J1571//Kaohsiung Chang Gung Memorial Hospital/ ; CMRPG8K0661//Kaohsiung Chang Gung Memorial Hospital/ ; }, mesh = {Adolescent ; Adult ; Aged ; Biomarkers ; Biopsy ; Case-Control Studies ; Cross-Sectional Studies ; *Dysbiosis ; Female ; *Gastrointestinal Microbiome ; Humans ; Liver/metabolism/pathology ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; Non-alcoholic Fatty Liver Disease/diagnosis/*epidemiology/*etiology ; Public Health Surveillance ; Taiwan/epidemiology ; Young Adult ; }, abstract = {The gut microbiota plays a role in nonalcoholic fatty liver disease (NAFLD), but data about gut dysbiosis in Asians with NAFLD remains scarce. We analyzed the differences in fecal microbiota between adults with and without NAFLD. This cross-sectional study examined adults with histology-proven NAFLD (25 nonalcoholic fatty liver (NAFL) patients, 25 nonalcoholic steatohepatitis (NASH) patients, and 25 living liver donors (healthy controls)). The taxonomic composition of the gut microbiota was determined by 16S ribosomal RNA gene sequencing of stool samples. The NAFL and NASH groups showed lower total bacterial diversity and richness than the controls. NAFLD patients had higher levels of the phylum Bacteroidetes and lower levels of Firmicutes than controls. The genus RuminococcaceaeUCG-010, family Ruminococcaceae, order Clostridiales, and class Clostridia were less abundant in patients with NAFL or NASH than healthy individuals. The lipopolysaccharide biosynthesis pathway was differentially enriched in the NASH group. This study examined the largest number of Asian patients with biopsy-proven NAFL and NASH in terms of dysbiosis of the gut microbiota in NAFLD patients. NAFLD patients had higher levels of Bacteroidetes and lower levels of Firmicutes. These results are different from research from western countries and could provide different targets for therapies by region.}, }
@article {pmid32168729, year = {2020}, author = {Todorov, H and Kollar, B and Bayer, F and Brandão, I and Mann, A and Mohr, J and Pontarollo, G and Formes, H and Stauber, R and Kittner, JM and Endres, K and Watzer, B and Nockher, WA and Sommer, F and Gerber, S and Reinhardt, C}, title = {α-Linolenic Acid-Rich Diet Influences Microbiota Composition and Villus Morphology of the Mouse Small Intestine.}, journal = {Nutrients}, volume = {12}, number = {3}, pages = {}, pmid = {32168729}, issn = {2072-6643}, support = {Novel and neglected cardiovascular risk factors//Boehringer Ingelheim Stiftung/ ; RE 3450/5-2//Deutsche Forschungsgemeinschaft/ ; 01EO1003 and 01EO1503//Bundesministerium für Bildung und Forschung/ ; -//Naturwissenschaftlich-Medizinische Forschungszentrum (NMFZ)/ ; -//Inneruniversitäre Forschungsförderung (Stufe 1)/ ; }, mesh = {*Animal Feed/analysis ; Animals ; *Biodiversity ; Fatty Acids/metabolism ; Feces/microbiology ; Food Analysis ; *Gastrointestinal Microbiome ; Immunohistochemistry ; Intestinal Mucosa/cytology/*microbiology ; Intestine, Small/*metabolism/*microbiology ; Lipid Metabolism ; Male ; Metagenome ; Metagenomics/methods ; Mice ; alpha-Linolenic Acid/analysis/*metabolism ; }, abstract = {α-Linolenic acid (ALA) is well-known for its anti-inflammatory activity. In contrast, the influence of an ALA-rich diet on intestinal microbiota composition and its impact on small intestine morphology are not fully understood. In the current study, we kept adult C57BL/6J mice for 4 weeks on an ALA-rich or control diet. Characterization of the microbial composition of the small intestine revealed that the ALA diet was associated with an enrichment in Prevotella and Parabacteroides. In contrast, taxa belonging to the Firmicutes phylum, including Lactobacillus, Clostridium cluster XIVa, Lachnospiraceae and Streptococcus, had significantly lower abundance compared to control diet. Metagenome prediction indicated an enrichment in functional pathways such as bacterial secretion system in the ALA group, whereas the two-component system and ALA metabolism pathways were downregulated. We also observed increased levels of ALA and its metabolites eicosapentanoic and docosahexanoic acid, but reduced levels of arachidonic acid in the intestinal tissue of ALA-fed mice. Furthermore, intestinal morphology in the ALA group was characterized by elongated villus structures with increased counts of epithelial cells and reduced epithelial proliferation rate. Interestingly, the ALA diet reduced relative goblet and Paneth cell counts. Of note, high-fat Western-type diet feeding resulted in a comparable adaptation of the small intestine. Collectively, our study demonstrates the impact of ALA on the gut microbiome and reveals the nutritional regulation of gut morphology.}, }
@article {pmid32157805, year = {2020}, author = {Reñé, A and Auladell, A and Reboul, G and Moreira, D and López-García, P}, title = {Performance of the melting seawater-ice elution method on the metabarcoding characterization of benthic protist communities.}, journal = {Environmental microbiology reports}, volume = {12}, number = {3}, pages = {314-323}, doi = {10.1111/1758-2229.12834}, pmid = {32157805}, issn = {1758-2229}, support = {ProtistWorld Grant 322669//H2020 European Research Council/International ; COPAS CTM2017-86121-R//Ministerio de Economía y Competitividad/International ; José Castillejo Grant CAS17/00237//Ministerio de Educación, Cultura y Deporte/International ; }, mesh = {Biodiversity ; Ciliophora/genetics/isolation &amp; purification ; Dinoflagellida/genetics/isolation &amp; purification ; *Eukaryota/genetics/isolation &amp; purification ; Fungi/genetics/isolation &amp; purification ; Geologic Sediments/microbiology ; Metagenomics/*methods ; RNA, Ribosomal, 18S/genetics ; Seawater/*microbiology ; }, abstract = {Massive amplicon sequencing approaches to characterize the diversity of microbial eukaryotes in sediments are scarce and controls about the effects introduced by different methods to recover DNA are lacking. In this study, we compare the performance of the melting seawater-ice elution method on the characterization of benthic protist communities by 18S rRNA gene metabarcoding with results obtained by direct cell lysis and DNA purification from sediments. Even though the most abundant operational taxonomic units were recovered by both methods, eluted samples yielded higher richness than samples undergoing direct lysis. Both treatments allowed recovering the same taxonomic groups, although we observed significant differences in terms of relative abundance for some of them. Dinoflagellata and Ciliophora strongly dominated the community in eluted samples (> 80% reads). In directly lysed samples, they only represented 37%, while groups like Fungi and Ochrophytes were highly represented (> 20% reads respectively). Our results show that the elution process yields a higher protist richness estimation, most likely as a result of the higher sample volume used to recover organisms as compared to commonly used volumes for direct benthic DNA purification. Motile groups, like dinoflagellates and ciliates, are logically more enriched during the elution process.}, }
@article {pmid32090489, year = {2020}, author = {Villar, E and Cabrol, L and Heimbürger-Boavida, LE}, title = {Widespread microbial mercury methylation genes in the global ocean.}, journal = {Environmental microbiology reports}, volume = {12}, number = {3}, pages = {277-287}, doi = {10.1111/1758-2229.12829}, pmid = {32090489}, issn = {1758-2229}, support = {ANR-15-CE02-0011//Agence Nationale de la Recherche/International ; }, mesh = {*Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Chloroflexi/classification/genetics/isolation &amp; purification/metabolism ; Deltaproteobacteria/classification/genetics/isolation &amp; purification/metabolism ; Firmicutes/classification/genetics/isolation &amp; purification/metabolism ; Genes, Bacterial ; Mercury/metabolism ; Metagenomics ; Methylation ; Methylmercury Compounds/*metabolism ; Microbiota ; Oceans and Seas ; Phylogeny ; *Seawater/chemistry/microbiology ; Transcriptome ; }, abstract = {Methylmercury is a neurotoxin that bioaccumulates from seawater to high concentrations in marine fish, putting human and ecosystem health at risk. High methylmercury levels have been found in the oxic subsurface waters of all oceans, but only anaerobic microorganisms have been shown to efficiently produce methylmercury in anoxic environments. The microaerophilic nitrite-oxidizing bacteria Nitrospina have previously been suggested as possible mercury methylating bacteria in Antarctic sea ice. However, the microorganisms responsible for processing inorganic mercury into methylmercury in oxic seawater remain unknown. Here, we show metagenomic and metatranscriptomic evidence that the genetic potential for microbial methylmercury production is widespread in oxic seawater. We find high abundance and expression of the key mercury methylating genes hgcAB across all ocean basins, corresponding to the taxonomic relatives of known mercury methylating bacteria from Deltaproteobacteria, Firmicutes and Chloroflexi. Our results identify Nitrospina as the predominant and widespread microorganism carrying and actively expressing hgcAB. The highest hgcAB abundance and expression occurs in the oxic subsurface waters of the global ocean where the highest MeHg concentrations are typically observed.}, }
@article {pmid31933014, year = {2020}, author = {Aguirre-Garrido, JF and Martínez-Abarca, F and Montiel-Lugo, D and Hernández-Soto, LM and Ramírez-Saad, H}, title = {Metagenomic analyses uncover the differential effect of azide treatment on bacterial community structure by enriching a specific Cyanobacteria present in a saline-alkaline environmental sample.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {23}, number = {3}, pages = {467-474}, doi = {10.1007/s10123-020-00119-z}, pmid = {31933014}, issn = {1618-1905}, support = {BIO2017-82244-P//Ministerio de Ciencia, Innovación y Universidades/ ; 710228//Consejo Nacional de Ciencia y Tecnología/ ; 291062//Consejo Nacional de Ciencia y Tecnología/ ; }, mesh = {Bacteria/classification/genetics/isolation &amp; purification ; Cyanobacteria/genetics/*isolation &amp; purification ; DNA, Bacterial ; Environmental Microbiology ; Enzyme Inhibitors/adverse effects ; Genome, Bacterial ; Lakes/microbiology ; Metagenomics/*methods ; *Microbiota/genetics ; Salinity ; Sodium Azide/*adverse effects ; }, abstract = {Treatment of environmental samples under field conditions may require the application of chemical preservatives, although their use sometimes produces changes in the microbial communities. Sodium azide, a commonly used preservative, is known to differentially affect the growth of bacteria. Application of azide and darkness incubation to Isabel soda lake water samples induced changes in the structure of the bacterial community, as assessed by partial 16S rRNA gene pyrosequencing. Untreated water samples (WU) were dominated by gammaproteobacterial sequences accounting for 86%, while in the azide-treated (WA) samples, this group was reduced to 33% abundance, and cyanobacteria-related sequences became dominant with 53%. Shotgun sequencing and genome recruitment analyses pointed to Halomonas campanensis strain LS21 (genome size 4.07 Mbp) and Synechococcus sp. RS9917 (2.58 Mbp) as the higher recruiting genomes from the sequence reads of WA and WU environmental libraries, respectively, covering nearly the complete genomes. Combined treatment of water samples with sodium azide and darkness has proven effective on the selective enrichment of a cyanobacterial group. This approach may allow the complete (or almost-complete) genome sequencing of Cyanobacteria from metagenomic DNA of different origins, and thus increasing the number of the underrepresented cyanobacterial genomes in the databases.}, }
@article {pmid31933013, year = {2020}, author = {Xu, Y and Zhang, G and Ding, H and Ci, D and Dai, L and Zhang, Z}, title = {Influence of salt stress on the rhizosphere soil bacterial community structure and growth performance of groundnut (Arachis hypogaea L.).}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {23}, number = {3}, pages = {453-465}, doi = {10.1007/s10123-020-00118-0}, pmid = {31933013}, issn = {1618-1905}, support = {2018YFD1000906//the National Key R&amp;D Program of China/ ; CXGC2018E21//the Agricultural Scientific and the Technological Innovation Project of Shandong Academy of Agricultural Sciences/ ; }, mesh = {Actinobacteria/genetics/isolation &amp; purification ; Arachis/growth &amp; development/*microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Cyanobacteria/genetics/isolation &amp; purification ; DNA, Bacterial ; Metagenomics ; Microbiota/*genetics ; Phylogeny ; Plant Roots/microbiology ; RNA, Ribosomal, 16S ; *Rhizosphere ; Salinity ; *Salt Stress ; Soil/chemistry ; Soil Microbiology ; Sphingomonas/genetics/isolation &amp; purification ; }, abstract = {Soil salinity is regarded as severe environmental stress that can change the composition of rhizosphere soil bacterial community and import a plethora of harms to crop plants. However, relatively little is known about the relationship between salt stress and root microbial communities in groundnuts. The goal of this study was to assess the effect of salt stress on groundnut growth performance and rhizosphere microbial community structure. Statistical analysis exhibited that salt stress indeed affected groundnut growth and pod yield. Further taxonomic analysis showed that the bacterial community predominantly consisted of phyla Proteobacteria, Actinobacteria, Saccharibacteria, Chloroflexi, Acidobacteria, and Cyanobacteria. Among these bacteria, numbers of Cyanobacteria and Acidobacteria mainly increased, while that of Actinobacteria and Chloroflexi decreased after salt treatment via taxonomic and qPCR analysis. Moreover, Sphingomonas and Microcoleus as the predominant genera in salt-treated rhizosphere soils might enhance salt tolerance as plant growth-promoting rhizobacteria. Metagenomic profiling showed that series of sequences related to signaling transduction, posttranslational modification, and chaperones were enriched in the salt-treated soils, which may have implications for plant survival and salt tolerance. These data will help us better understand the symbiotic relationship between the dominant microbial community and groundnuts and form the foundation for further improvement of salt tolerance of groundnuts via modification of soil microbial community.}, }
@article {pmid31898031, year = {2020}, author = {Pi, S and Sun, J and Feng, L and Zhou, J}, title = {Performance and microbial diversity of denitrifying biofilms on polyurethane foam coupled with various solid carbon sources for nitrate-rich water purification.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {23}, number = {3}, pages = {405-413}, doi = {10.1007/s10123-019-00114-z}, pmid = {31898031}, issn = {1618-1905}, support = {51709236//National Natural Science Foundation of China/ ; }, mesh = {Bacteria/genetics/growth &amp; development/isolation &amp; purification/metabolism ; Biofilms/growth &amp; development ; Carbon/metabolism ; DNA, Bacterial ; *Denitrification ; Environmental Restoration and Remediation ; Metagenomics ; Microbiota/*genetics ; Nitrates/metabolism ; Polyurethanes ; RNA, Ribosomal, 16S/genetics ; Water Purification/*methods ; }, abstract = {This study investigated the performance and microbial communities of denitrifying biofilms on polyurethane foam coupled with various solid carbon sources of acid- and alkali-pretreated rice straw and rice husk. Results showed that acid and alkali-pretreated rice straw both had higher TOC release rates (0.041-0.685 mg g-1 day-1) than those of rice husk (0.019-0.160 mg g-1 day-1) over a month, while acid pretreatment of rice husk and rice straw had a much higher organics release rate than that of alkali pretreatment and non-pretreatment, respectively. Acid-pretreated rice straw achieved the most efficient TN removal performance (82.06 ± 3.65%) with the lower occurrences of NH4+-N during denitrification than that of alkali-pretreated rice straw (80.05 ± 4.12%) over more than a month operation. However, alkali pretreatment of rice husk demonstrated much more significantly efficient TN removal efficiency (80.39 ± 2.1%) than did acid pretreatment (69.59 ± 13.43%). MiSeq sequencing analysis showed that the four biofilm samples attached on polyurethane foam with the addition of pretreated rice straw or rice husk had a range of 13-15 differentially abundant phylum and 81-123 differentially abundant genera in comparison with biofilm without extra solid carbon sources, and a higher TN removal efficiency demonstrated more types of differentially abundant genera.}, }
@article {pmid31894501, year = {2020}, author = {Tiew, PY and Mac Aogain, M and Ali, NABM and Thng, KX and Goh, K and Lau, KJX and Chotirmall, SH}, title = {The Mycobiome in Health and Disease: Emerging Concepts, Methodologies and Challenges.}, journal = {Mycopathologia}, volume = {185}, number = {2}, pages = {207-231}, pmid = {31894501}, issn = {1573-0832}, support = {NMRC/Fellowship/0049/2017//National Medical Research Council Singapore/ ; MOH-000141//National Medical Research Council Singapore/ ; 2016-T1-001-050//Singapore Ministry of Education/ ; NIM/03/2018//Nanyang Technological University/ ; ARISE/2017/6//Nanyang Technological University (SG)/ ; }, mesh = {Computational Biology ; *Fungi/genetics/pathogenicity ; High-Throughput Nucleotide Sequencing ; Host Microbial Interactions ; Humans ; Metagenomics ; *Mycobiome ; *Mycoses/epidemiology/etiology/therapy/transmission ; Pathology, Molecular ; }, abstract = {Fungal disease is an increasingly recognised global clinical challenge associated with high mortality. Early diagnosis of fungal infection remains problematic due to the poor sensitivity and specificity of current diagnostic modalities. Advances in sequencing technologies hold promise in addressing these shortcomings and for improved fungal detection and identification. To translate such emerging approaches into mainstream clinical care will require refinement of current sequencing and analytical platforms, ensuring standardisation and consistency through robust clinical benchmarking and its validation across a range of patient populations. In this state-of-the-art review, we discuss current diagnostic and therapeutic challenges associated with fungal disease and provide key examples where the application of sequencing technologies has potential diagnostic application in assessing the human 'mycobiome'. We assess how ready access to fungal sequencing may be exploited in broadening our insight into host-fungal interaction, providing scope for clinical diagnostics and the translation of emerging mycobiome research into clinical practice.}, }
@article {pmid31726162, year = {2020}, author = {Guo, WL and Chen, M and Pan, WL and Zhang, Q and Xu, JX and Lin, YC and Li, L and Liu, B and Bai, WD and Zhang, YY and Ni, L and Rao, PF and Lv, XC}, title = {Hypoglycemic and hypolipidemic mechanism of organic chromium derived from chelation of Grifola frondosa polysaccharide-chromium (III) and its modulation of intestinal microflora in high fat-diet and STZ-induced diabetic mice.}, journal = {International journal of biological macromolecules}, volume = {145}, number = {}, pages = {1208-1218}, doi = {10.1016/j.ijbiomac.2019.09.206}, pmid = {31726162}, issn = {1879-0003}, mesh = {Animals ; Blood Glucose/metabolism ; Chelating Agents/*pharmacology ; Cholesterol/blood ; Chromium/*chemistry ; Diabetes Mellitus, Experimental ; Diet, High-Fat/adverse effects ; Dietary Carbohydrates/pharmacology ; Gastrointestinal Microbiome/*drug effects ; Glucose/metabolism ; Grifola/*chemistry ; Hyperglycemia/metabolism ; Hypoglycemic Agents/*pharmacology ; Hypolipidemic Agents/*pharmacology ; Lipid Metabolism/drug effects ; Liver/drug effects/metabolism ; Male ; Metagenomics ; Mice ; Polysaccharides/*pharmacology ; RNA, Messenger/metabolism ; Streptozocin/*pharmacology ; Triglycerides/blood ; }, abstract = {Polysaccharide from Grifola frondosa is an excellent metal-ion chelating agent owing to its distinctive structure and outstanding functional activities. Our previous research has successfully synthesized novel organic chromium derived from the chelation ofG. frondosapolysaccharide-chromium (III) [GFP-Cr(III)]. The purpose of present research was to reveal the hypoglycemic and hypolipidemic mechanism of GFP-Cr(III), and its relationship with the modulation of intestinal microflora. Successful fabrication of GFP-Cr(III) was verified by thermogravimetric analysis (TGA), powder X-ray diffraction (XRD) and 1H NMR spectrum.The hypoglycemic and hypolipidemic effects were examined using type 2 diabetic mice induced by a high-fat diet (HFD) and streptozocin (STZ). Results indicated that GFP-Cr(III) intervention improved abnormal serum biochemical indicators (triglyceride (TG), cholesterol (TC), low-density lipoprotein cholesterol (LDL-C) and glucose), inhibited lipid accumulation and steatosis in the liver. Metagenomic analysis revealed that GFP-Cr(III) treatment produced obvious changes on the intestinal microflora in T2DM mice. Thecorrelationnetwork analysis further revealed that the serum and hepatic lipid profiles were positively correlated with Streptococcus and Enterococcus, but negatively correlated with Enterorhabdus, Ruminococcaceae-UCG-011, Coriobacteriaceae and Micrococcaceae. Meanwhile, oral administration with GFP-Cr(III) regulated the mRNA expression related to glucose and lipid metabolism. These results of present study suggest that GFP-Cr(III) could be used as potential functional food ingredients for the amelioration of hyperglycemia and hyperlipidemia.}, }
@article {pmid31600863, year = {2020}, author = {Li, Y and Tremblay, J and Bainard, LD and Cade-Menun, B and Hamel, C}, title = {Long-term effects of nitrogen and phosphorus fertilization on soil microbial community structure and function under continuous wheat production.}, journal = {Environmental microbiology}, volume = {22}, number = {3}, pages = {1066-1088}, doi = {10.1111/1462-2920.14824}, pmid = {31600863}, issn = {1462-2920}, support = {PSS-1555//Agriculture and Agri-Food Canada/International ; //Natural Science and Engineering Research Council of Canada/International ; }, mesh = {Archaea/drug effects/physiology ; Bacterial Physiological Phenomena/drug effects ; Biodiversity ; Fertilizers ; Fungi/drug effects/physiology ; Longitudinal Studies ; Microbiota/*drug effects ; Nitrogen/*pharmacology ; Phosphorus/*pharmacology ; Soil/chemistry ; *Soil Microbiology ; Triticum/growth &amp; development/*microbiology ; }, abstract = {Soil microorganisms play a critical role in the biosphere, and the influence of cropland fertilization on the evolution of soil as a living entity is being actively documented. In this study, we used a shotgun metagenomics approach to globally expose the effects of 50-year N and P fertilization of wheat on soil microbial community structure and function, and their potential involvement in overall N cycling. Nitrogen (N) fertilization increased alpha diversity in archaea and fungi while reducing it in bacteria. Beta diversity of archaea, bacteria and fungi, as well as soil function, were also mainly driven by N fertilization. The abundance of archaea was negatively impacted by N fertilization while bacterial and fungal abundance was increased. The responses of N metabolism-related genes to fertilization differed in archaea, bacteria and fungi. All archaeal N metabolic processes were decreased by N fertilization, while denitrification, assimilatory nitrate reduction and organic-N metabolism were highly increased by N fertilization in bacteria. Nitrate assimilation was the main contribution of fungi to N cycling. Thaumarchaeota and Halobacteria in archaea; Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Deltaproteobacteria in bacteria; and Sordariomycetes in fungi participated dominantly and widely in soil N metabolic processes.}, }
@article {pmid31581017, year = {2020}, author = {Franzetti, A and Gandolfi, I and Bestetti, G and Padoa Schioppa, E and Canedoli, C and Brambilla, D and Cappelletti, D and Sebastiani, B and Federici, E and Papacchini, M and Ambrosini, R}, title = {Plant-microorganisms interaction promotes removal of air pollutants in Milan (Italy) urban area.}, journal = {Journal of hazardous materials}, volume = {384}, number = {}, pages = {121021}, doi = {10.1016/j.jhazmat.2019.121021}, pmid = {31581017}, issn = {1873-3336}, mesh = {Adsorption ; Air Pollutants/analysis/chemistry/*metabolism ; Bacteria/classification/genetics/*metabolism ; Biodegradation, Environmental ; Cedrus/chemistry/*microbiology ; Cities ; Italy ; Magnolia/chemistry/*microbiology ; Microbiota/genetics ; Particulate Matter/analysis/chemistry/*metabolism ; Plant Leaves/chemistry/microbiology ; Polycyclic Aromatic Hydrocarbons/analysis/chemistry/*metabolism ; RNA, Ribosomal, 16S ; }, abstract = {Plants and phyllosphere microorganisms may effectively contribute to reducing air pollution in cities through the adsorption and biodegradation of pollutants onto leaves. In this work, during all seasons, we sampled atmospheric particulate matter (PM10) and leaves of southern magnolia Magnolia grandiflora and deodar cedar Cedrus deodara, two evergreen plant species widespread in the urban area of Milan where the study was carried out. We then quantified Polycyclic Aromatic Hydrocarbons (PAHs) both in PM10 and on leaves and used sequencing of 16S rRNA gene, shotgun metagenomics and qPCR analyses to investigate the microbial communities hosted by the sampled leaves. Taxonomic and functional profiles of epiphytic bacterial communities differed between host plant species and seasons and the microbial communities on leaves harboured genes involved in the degradation of hydrocarbons. Evidence collected in this work also suggested that the abundance of hydrocarbon-degrading microorganisms on evergreen leaves increased with the concentration of hydrocarbons when atmospheric pollutants were deposited at high concentration on leaves, and that the biodegradation on the phyllosphere can contribute to the removal of PAHs from the urban air.}, }
@article {pmid30805695, year = {2020}, author = {Strain, CR and Collins, KC and Naughton, V and McSorley, EM and Stanton, C and Smyth, TJ and Soler-Vila, A and Rea, MC and Ross, PR and Cherry, P and Allsopp, PJ}, title = {Effects of a polysaccharide-rich extract derived from Irish-sourced Laminaria digitata on the composition and metabolic activity of the human gut microbiota using an in vitro colonic model.}, journal = {European journal of nutrition}, volume = {59}, number = {1}, pages = {309-325}, pmid = {30805695}, issn = {1436-6215}, support = {MFFRI/07/01//Sea Change Strategy, Department of Agriculture, Food and the Marine (IE)/ ; }, mesh = {Colon/*metabolism/microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects/physiology ; Humans ; In Vitro Techniques ; Laminaria/*metabolism/*microbiology ; Models, Biological ; Plant Extracts/metabolism/*pharmacology ; Polysaccharides/metabolism/*pharmacology ; }, abstract = {BACKGROUND: Brown seaweeds are known to be a rich source of fiber with the presence of several non-digestible polysaccharides including laminarin, fucoidan and alginate. These individual polysaccharides have previously been shown to favorably alter the gut microbiota composition and activity albeit the effect of the collective brown seaweed fiber component on the microbiota remains to be determined.<br><br>METHODS: This study investigated the effect of a crude polysaccharide-rich extract obtained from Laminaria digitata (CE) and a depolymerized CE extract (DE) on the gut microbiota composition and metabolism using an in vitro fecal batch culture model though metagenomic compositional analysis using 16S rRNA FLX amplicon pyrosequencing and short-chain fatty acid (SCFA) analysis using GC-FID.<br><br>RESULTS: Selective culture analysis showed no significant changes in cultured lactobacilli or bifidobacteria between the CE or DE and the cellulose-negative control at any time point measured (0, 5, 10, 24, 36, 48 h). Following metagenomic analysis, the CE and DE significantly altered the relative abundance of several families including Lachnospiraceae and genera including Streptococcus, Ruminococcus and Parabacteroides of human fecal bacterial populations in comparison to cellulose after 24 h. The concentrations of acetic acid, propionic acid, butyric acid and total SCFA were significantly higher for both the CE and DE compared to cellulose after 10, 24, 36 and 48 h fermentation (p < 0.05). Furthermore, the acetate:propionate ratio was significantly reduced (p < 0.05) for both CD and DE following 24, 36 and 48 h fermentation.<br><br>CONCLUSION: The microbiota-associated metabolic and compositional changes noted provide initial indication of putative beneficial health benefits of L. digitata in vitro; however, research is needed to clarify if L. digitata-derived fiber can favorably alter the gut microbiota and confer health benefits in vivo.}, }
@article {pmid33298993, year = {2020}, author = {Wong, MK and Nakao, M and Hyodo, S}, title = {Field application of an improved protocol for environmental DNA extraction, purification, and measurement using Sterivex filter.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {21531}, pmid = {33298993}, issn = {2045-2322}, abstract = {Environmental DNA (eDNA) is increasingly popular as a useful non-invasive method to monitor and study biodiversity and community structure in freshwater and marine environments. To effectively extract eDNA from the filter surface is a fundamental factor determining the representativeness of the samples. We improved the eDNA extraction efficiency of an established Sterivex method by 12- to 16-fold using a larger volume of lysis buffer mix coupled with backflushing the cartridges. The DNeasy extraction column could be overloaded when the environmental sample input is high, possibly due to a higher nonspecific binding present in environmental samples, thus resulting in a relatively lower quantity measured. Therefore, we included an internal control DNA in the extraction to monitor the extraction and purification efficiencies in field samples, which is crucial for quantification of original eDNA concentration. The use of Takara Probe qPCR Mix supplemented with protein-based additives improved the robustness of the real time PCR assay on inhibitor-rich environmental samples, but prior purification by Qiagen PowerClean Pro Cleanup kit could be essential for inhibitor-rich water samples, even though the recovery rate was unexpectedly low (average 33.0%). The improved extraction and quantification complement the qualitative analyses including metabarcoding and metagenomics in field application.}, }
@article {pmid33289802, year = {2020}, author = {Haro-Moreno, JM and Coutinho, FH and Zaragoza-Solas, A and Picazo, A and Almagro-Moreno, S and López-Pérez, M}, title = {Dysbiosis in marine aquaculture revealed through microbiome analysis: reverse ecology for environmental sustainability.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaa218}, pmid = {33289802}, issn = {1574-6941}, abstract = {The increasing demand of products for human consumption is leading to the fast-growing expansion of numerous food sectors such as marine aquaculture (mariculture). However, the excessive input of nutrients and pollutants modify marine ecosystems. Here, we applied a metagenomic approach to investigate these perturbations in samples from marine farms of gilthead seabream cultures. Results revealed dysbiosis and functional imbalance within the net cage with a unique structure with little interference with samples from the fish microbiota or those collected far away from the coast. Remarkable, below the cage the prokaryotic community was highly similar to the marine microbiome of photic offshore samples. We recovered 48 novel metagenome-assembled genomes. Metagenomic recruitment revealed a significant change of the microbial community which was dominated by several Proteobacteria orders (Sphingomonadales, Pseudomonadales, Caudobacterales and Rhizobiales). Genomic potential for bioremediation processes including nitrate removal through aerobic denitrification, degradation of aromatic compounds and other toxic products were enriched in these microbes. The detrimental side effects were the increased number of antimicrobial resistance genes and the presence of potentially emergent pathogens. Knowledge of this metabolic diversity and microbes involved in the ecological balance recovery can be used to reduce the environmental impact of these practices.}, }
@article {pmid33260452, year = {2020}, author = {Lattos, A and Giantsis, IA and Karagiannis, D and Theodorou, JA and Michaelidis, B}, title = {Gut Symbiotic Microbial Communities in the IUCN Critically Endangered Pinna nobilis Suffering from Mass Mortalities, Revealed by 16S rRNA Amplicon NGS.}, journal = {Pathogens (Basel, Switzerland)}, volume = {9}, number = {12}, pages = {}, doi = {10.3390/pathogens9121002}, pmid = {33260452}, issn = {2076-0817}, abstract = {Mass mortality events due to disease outbreaks have recently affected almost every healthy population of fan mussel, Pinna nobilis in Mediterranean Sea. The devastating mortality of the species has turned the interest of the research towards the causes of these events. After the haplosporidan infestation and the infection by Mycobacterium sp., new emerging pathogens have arisen based on the latest research. In the present study, a metagenomic approach of 16S rRNA next generation sequencing (NGS) was applied in order to assess the bacterial diversity within the digestive gland of diseased individuals as well as to carry out geographical correlations among the biodiversity of microbiome in the endangered species Pinna nobilis. The specimens originated from the mortalities occurred in 2019 in the region of Greece. Together with other bacterial genera, the results confirmed the presence of Vibrio spp., assuming synergistic effects in the mortality events of the species. Alongside with the presence of Vibrio spp., numerous bacterial genera were detected as well, including Aliivibrio spp., Photobacterium spp., Pseudoalteromonas spp., Psychrilyobacter spp. and Mycoplasma spp. Bacteria of the genus Mycoplasma were in high abundance particularly in the sample originated from Limnos island representing the first time recorded in Pinna nobilis. In conclusion, apart from exclusively the Haplosporidan and the Mycobacterium parasites, the presence of potentially pathogenic bacterial taxa detected, such as Vibrio spp., Photobactrium spp. and Alivibrio spp. lead us to assume that mortality events in the endangered Fan mussel, Pinna nobilis, may be attributed to synergistic effects of more pathogens.}, }
@article {pmid33256173, year = {2020}, author = {Truchado, DA and Llanos-Garrido, A and Oropesa-Olmedo, DA and Cerrada, B and Cea, P and Moens, MAJ and Gomez-Lucia, E and Doménech, A and Milá, B and Pérez-Tris, J and Cadar, D and Benítez, L}, title = {Comparative Metagenomics of Palearctic and Neotropical Avian Cloacal Viromes Reveal Geographic Bias in Virus Discovery.}, journal = {Microorganisms}, volume = {8}, number = {12}, pages = {}, doi = {10.3390/microorganisms8121869}, pmid = {33256173}, issn = {2076-2607}, support = {CGL2013-41642-P/BOS//Spanish National Research Agency/ ; CGL2017-82117-P//Spanish National Research Agency/ ; CEBA2015-TROCSYMB//ANR/ ; CEBA:ANR-10-LABX-25-01//ANR/ ; CT27/16-CT28/16//Complutense University of Madrid/ ; }, abstract = {Our understanding about viruses carried by wild animals is still scarce. The viral diversity of wildlife may be best described with discovery-driven approaches to the study of viral diversity that broaden research efforts towards non-canonical hosts and remote geographic regions. Birds have been key organisms in the transmission of viruses causing important diseases, and wild birds are threatened by viral spillovers associated with human activities. However, our knowledge of the avian virome may be biased towards poultry and highly pathogenic diseases. We describe and compare the fecal virome of two passerine-dominated bird assemblages sampled in a remote Neotropical rainforest in French Guiana (Nouragues Natural Reserve) and a Mediterranean forest in central Spain (La Herrería). We used metagenomic data to quantify the degree of functional and genetic novelty of viruses recovered by examining if the similarity of the contigs we obtained to reference sequences differed between both locations. In general, contigs from Nouragues were significantly less similar to viruses in databases than contigs from La Herrería using Blastn but not for Blastx, suggesting that pristine regions harbor a yet unknown viral diversity with genetically more singular viruses than more studied areas. Additionally, we describe putative novel viruses of the families Picornaviridae, Reoviridae and Hepeviridae. These results highlight the importance of wild animals and remote regions as sources of novel viruses that substantially broaden the current knowledge of the global diversity of viruses.}, }
@article {pmid33252655, year = {2020}, author = {Weißbecker, C and Schnabel, B and Heintz-Buschart, A}, title = {Dadasnake, a Snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology.}, journal = {GigaScience}, volume = {9}, number = {12}, pages = {}, doi = {10.1093/gigascience/giaa135}, pmid = {33252655}, issn = {2047-217X}, abstract = {BACKGROUND: Amplicon sequencing of phylogenetic marker genes, e.g., 16S, 18S, or ITS ribosomal RNA sequences, is still the most commonly used method to determine the composition of microbial communities. Microbial ecologists often have expert knowledge on their biological question and data analysis in general, and most research institutes have computational infrastructures to use the bioinformatics command line tools and workflows for amplicon sequencing analysis, but requirements of bioinformatics skills often limit the efficient and up-to-date use of computational resources.<br><br>RESULTS: We present dadasnake, a user-friendly, 1-command Snakemake pipeline that wraps the preprocessing of sequencing reads and the delineation of exact sequence variants by using the favorably benchmarked and widely used DADA2 algorithm with a taxonomic classification and the post-processing of the resultant tables, including hand-off in standard formats. The suitability of the provided default configurations is demonstrated using mock community data from bacteria and archaea, as well as fungi.<br><br>CONCLUSIONS: By use of Snakemake, dadasnake makes efficient use of high-performance computing infrastructures. Easy user configuration guarantees flexibility of all steps, including the processing of data from multiple sequencing platforms. It is easy to install dadasnake via conda environments. dadasnake is available at https://github.com/a-h-b/dadasnake.}, }
@article {pmid33240526, year = {2020}, author = {Porter, AF and Pettersson, JH and Chang, WS and Harvey, E and Rose, K and Shi, M and Eden, JS and Buchmann, J and Moritz, C and Holmes, EC}, title = {Novel hepaci- and pegi-like viruses in native Australian wildlife and non-human primates.}, journal = {Virus evolution}, volume = {6}, number = {2}, pages = {veaa064}, pmid = {33240526}, issn = {2057-1577}, abstract = {The Flaviviridae family of positive-sense RNA viruses contains important pathogens of humans and other animals, including Zika virus, dengue virus, and hepatitis C virus. The Flaviviridae are currently divided into four genera-Hepacivirus, Pegivirus, Pestivirus, and Flavivirus-each with a diverse host range. Members of the genus Hepacivirus are associated with an array of animal species, including humans, non-human primates, other mammalian species, as well as birds and fish, while the closely related pegiviruses have been identified in a variety of mammalian taxa, also including humans. Using a combination of total RNA and whole-genome sequencing we identified four novel hepaci-like viruses and one novel variant of a known hepacivirus in five species of Australian wildlife. The hosts infected comprised native Australian marsupials and birds, as well as a native gecko (Gehyra lauta). From these data we identified a distinct marsupial clade of hepaci-like viruses that also included an engorged Ixodes holocyclus tick collected while feeding on Australian long-nosed bandicoots (Perameles nasuta). Distinct lineages of hepaci-like viruses associated with geckos and birds were also identified. By mining the SRA database we similarly identified three new hepaci-like viruses from avian and primate hosts, as well as two novel pegi-like viruses associated with primates. The phylogenetic history of the hepaci- and pegi-like viruses as a whole, combined with co-phylogenetic analysis, provided support for virus-host co-divergence over the course of vertebrate evolution, although with frequent cross-species virus transmission. Overall, our work highlights the diversity of the Hepacivirus and Pegivirus genera as well as the uncertain phylogenetic distinction between.}, }
@article {pmid33214767, year = {2020}, author = {Das Kangabam, R and Silla, Y and Goswami, G and Barooah, M}, title = {Bacterial Operational Taxonomic Units Replace the Interactive Roles of Other Operational Taxonomic Units Under Strong Environmental Changes.}, journal = {Current genomics}, volume = {21}, number = {7}, pages = {512-524}, pmid = {33214767}, issn = {1389-2029}, abstract = {Background: Microorganisms are an important component of an aquatic ecosystem and play a critical role in the biogeochemical cycle which influences the circulation of the materials and maintains the balance in aquatic ecosystems.<br><br>Objective: The seasonal variation along with the impact of anthropogenic activities, water quality, bacterial community composition and dynamics in the Loktak Lake, the largest freshwater lake of North East India, located in the Indo-Burma hotspot region was assessed during post-monsoon and winter season through metagenome analysis.<br><br>Methods: Five soil samples were collected during Post-monsoon and winter season from the Loktak Lake that had undergone different anthropogenic impacts. The metagenomic DNA of the soil samples was extracted using commercial metagenomic DNA extraction kits following the manufacturer's instruction. The extracted DNA was used to prepare the NGS library and sequenced in the Illumina MiSeq platform.<br><br>Results: Metagenomics analysis reveals Proteobacteria as the predominant community followed by Acidobacteria and Actinobacteria. The presence of these groups of bacteria indicates nitrogen fixation, oxidation of iron, sulfur, methane, and source of novel antibiotic candidates. The bacterial members belonging to different groups were involved in various biogeochemical processes, including fixation of carbon and nitrogen, producing streptomycin, gramicidin and perform oxidation of sulfur, sulfide, ammonia, and methane.<br><br>Conclusion: The outcome of this study provides a valuable dataset representing a seasonal profile across various land use and analysis, targeting at establishing an understanding of how the microbial communities vary across the land use and the role of keystone taxa. The findings may contribute to searches for microbial bio-indicators as biodiversity markers for improving the aquatic ecosystem of the Loktak Lake.}, }
@article {pmid33195611, year = {2020}, author = {Himsworth, CG and Byers, KA and Fernando, C and Speerin, L and Lee, MJ and Hill, JE}, title = {When the Sum of the Parts Tells You More Than the Whole: The Advantage of Using Metagenomics to Characterize Bartonella spp. Infections in Norway Rats (Rattus norvegicus) and Their Fleas.}, journal = {Frontiers in veterinary science}, volume = {7}, number = {}, pages = {584724}, pmid = {33195611}, issn = {2297-1769}, abstract = {Urban Norway rats (Rattus norvegicus) are a reservoir for Bartonella spp. - a genus of zoonotic bacteria transmitted by hematophagous vectors, particularly fleas. Rats and fleas may be infected with more than one Bartonella species; however, mixed infections may be difficult to detect using culture and/or mono-locus PCR. We set out to characterize Bartonella spp. using gltA PCR and Sanger sequencing on blood (n = 480) and Nosopsyllus fasciatus flea pools (n = 200) obtained from a population of urban Norways rats from Vancouver, Canada. However, when contamination of a subset of flea pools necessitated the use of a second target (ssrA) and the results of gltA and ssrA were discordant, a metagenomic approach was used to better characterize the Bartonella spp. present in these samples and our objective transitioned to comparing data obtained via metagenomics to those from PCR/sequencing. Among the Bartonella spp.-positive rats (n = 95), 52 (55.3%), and 41 (43.6%) had Sanger sequences consistent with Bartonella tribocorum and Bartonella vinsonii, respectively. One rat had a mixed infection. All sequences from Bartonella spp.-positive flea pools (n = 85), were consistent with B. tribocorum, and re-analysis of 34 bloods of varying Bartonella spp. infection status (based gltA PCR and sequencing) using ssrA PCR showed that the assay was capable of identifying B. tribocorum but not B. vinsonii. Metagenomics analysis of a subset of PCR-positive blood samples (n = 70) and flea pools (n = 24) revealed that both B. tribocorum and B. vinsonii were circulating widely in the study population with 31/70 (44.3%) rats and 5/24 (2.1%) flea pools infected with both species. B. vinsonii, however, made up a smaller relative proportion of the reads for samples with mixed infections, which may be why it was generally not detected by genus-specific PCR and Sanger sequencing. Further analysis of 16S-23S ITS sequences amplified from a subset of samples identified the B. vinsonii strain as B. vinsonii subsp. berkhoffii type II. This demonstrates the value of a metagenomic approach for better characterizing the ecology and health risks associated with this bacterium, particularly given that the less dominant species, B. vinsonii is associated with greater pathogenicity in people.}, }
@article {pmid33194372, year = {2020}, author = {Busi, SB and Pramateftaki, P and Brandani, J and Fodelianakis, S and Peter, H and Halder, R and Wilmes, P and Battin, TJ}, title = {Optimised biomolecular extraction for metagenomic analysis of microbial biofilms from high-mountain streams.}, journal = {PeerJ}, volume = {8}, number = {}, pages = {e9973}, pmid = {33194372}, issn = {2167-8359}, abstract = {Glacier-fed streams (GFS) are harsh ecosystems dominated by microbial life organized in benthic biofilms, yet the biodiversity and ecosystem functions provided by these communities remain under-appreciated. To better understand the microbial processes and communities contributing to GFS ecosystems, it is necessary to leverage high throughput sequencing. Low biomass and high inorganic particle load in GFS sediment samples may affect nucleic acid extraction efficiency using extraction methods tailored to other extreme environments such as deep-sea sediments. Here, we benchmarked the utility and efficacy of four extraction protocols, including an up-scaled phenol-chloroform protocol. We found that established protocols for comparable sample types consistently failed to yield sufficient high-quality DNA, delineating the extreme character of GFS. The methods differed in the success of downstream applications such as library preparation and sequencing. An adapted phenol-chloroform-based extraction method resulted in higher yields and better recovered the expected taxonomic profile and abundance of reconstructed genomes when compared to commercially-available methods. Affordable and straight-forward, this method consistently recapitulated the abundance and genomes of a mock community, including eukaryotes. Moreover, by increasing the amount of input sediment, the protocol is readily adjustable to the microbial load of the processed samples without compromising protocol efficiency. Our study provides a first systematic and extensive analysis of the different options for extraction of nucleic acids from glacier-fed streams for high-throughput sequencing applications, which may be applied to other extreme environments.}, }
@article {pmid33188211, year = {2020}, author = {Michalak, L and Gaby, JC and Lagos, L and La Rosa, SL and Hvidsten, TR and Tétard-Jones, C and Willats, WGT and Terrapon, N and Lombard, V and Henrissat, B and Dröge, J and Arntzen, MØ and Hagen, LH and Øverland, M and Pope, PB and Westereng, B}, title = {Microbiota-directed fibre activates both targeted and secondary metabolic shifts in the distal gut.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {5773}, pmid = {33188211}, issn = {2041-1723}, mesh = {Acetylation/drug effects ; Animals ; Butyrates/metabolism ; Cecum/metabolism ; Diet ; Dietary Fiber/*pharmacology ; Feeding Behavior/drug effects ; Female ; *Gastrointestinal Microbiome/drug effects ; Gastrointestinal Tract/drug effects/*metabolism/*microbiology ; Genome ; Male ; Mannans/pharmacology ; Metabolic Networks and Pathways/drug effects ; Metagenomics ; Principal Component Analysis ; Proteome/metabolism ; RNA, Ribosomal, 16S/genetics ; *Secondary Metabolism/drug effects ; Swine ; Wood/chemistry ; }, abstract = {Beneficial modulation of the gut microbiome has high-impact implications not only in humans, but also in livestock that sustain our current societal needs. In this context, we have tailored an acetylated galactoglucomannan (AcGGM) fibre to match unique enzymatic capabilities of Roseburia and Faecalibacterium species, both renowned butyrate-producing gut commensals. Here, we test the accuracy of AcGGM within the complex endogenous gut microbiome of pigs, wherein we resolve 355 metagenome-assembled genomes together with quantitative metaproteomes. In AcGGM-fed pigs, both target populations differentially express AcGGM-specific polysaccharide utilization loci, including novel, mannan-specific esterases that are critical to its deconstruction. However, AcGGM-inclusion also manifests a &quot;butterfly effect&quot;, whereby numerous metabolic changes and interdependent cross-feeding pathways occur in neighboring non-mannanolytic populations that produce short-chain fatty acids. Our findings show how intricate structural features and acetylation patterns of dietary fibre can be customized to specific bacterial populations, with potential to create greater modulatory effects at large.}, }
@article {pmid33188179, year = {2020}, author = {Meyer-Cifuentes, IE and Werner, J and Jehmlich, N and Will, SE and Neumann-Schaal, M and Öztürk, B}, title = {Synergistic biodegradation of aromatic-aliphatic copolyester plastic by a marine microbial consortium.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {5790}, pmid = {33188179}, issn = {2041-1723}, mesh = {Aquatic Organisms/*metabolism ; Bacterial Proteins/metabolism ; Biodegradation, Environmental ; Carbon Dioxide/metabolism ; Gene Expression Regulation, Bacterial ; Genome, Bacterial ; *Microbial Consortia/genetics ; Minerals/chemistry ; Models, Biological ; Plastics/*metabolism ; Polyesters/*metabolism ; Protein Biosynthesis/genetics ; Time Factors ; }, abstract = {The degradation of synthetic polymers by marine microorganisms is not as well understood as the degradation of plastics in soil and compost. Here, we use metagenomics, metatranscriptomics and metaproteomics to study the biodegradation of an aromatic-aliphatic copolyester blend by a marine microbial enrichment culture. The culture can use the plastic film as the sole carbon source, reaching maximum conversion to CO2 and biomass in around 15 days. The consortium degrades the polymer synergistically, with different degradation steps being performed by different community members. We identify six putative PETase-like enzymes and four putative MHETase-like enzymes, with the potential to degrade aliphatic-aromatic polymers and their degradation products, respectively. Our results show that, although there are multiple genes and organisms with the potential to perform each degradation step, only a few are active during biodegradation.}, }
@article {pmid33178147, year = {2020}, author = {Behera, BK and Chakraborty, HJ and Patra, B and Rout, AK and Dehury, B and Das, BK and Sarkar, DJ and Parida, PK and Raman, RK and Rao, AR and Rai, A and Mohapatra, T}, title = {Metagenomic Analysis Reveals Bacterial and Fungal Diversity and Their Bioremediation Potential From Sediments of River Ganga and Yamuna in India.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {556136}, pmid = {33178147}, issn = {1664-302X}, abstract = {In this study, we report the presence of a microbial community of bioremediation potential in terms of relative abundance and taxonomic biodiversity in sediment samples of river Ganga and Yamuna, India at nine different sites. Metagenomic libraries were constructed using TruSeq Nano DNA Library Prep Kit and sequenced on NextSeq 500 by Illumina Next Generation Sequencing (NGS) technology. Bioremediation bacteria belong to 45 genera with 92 species and fungi belong to 13 genera with 24 species have been classified using Kaiju taxonomical classification. The study revealed that Proteobacteria was the most dominant bacterial flora, followed by Actinobacteria, Firmicutes, and Deinococcus-Thermus. PCA analysis revealed that bioremediation bacteria viz. Streptomyces bikiniensis, Rhodococcus qingshengii, Bacillus aerophilus, Pseudomonas veronii, etc., were more dominant in highly polluted river stretch as compared to less polluted river stretch. Similarly, the relative abundance of bioremediation fungi viz. Phanerochaete chrysosporium and Rhizopus oryzae, etc., were significantly correlated with the polluted Kanpur stretch of river Ganga. Several protein domains, which play a pivotal role in bioremediation in the polluted environments, including urea ABC transporter, UrtA, UrtD, UrtE, zinc/cadmium/mercury/lead-transporting ATPase, etc., were identified using protein domain analysis. The protein domains involved in pesticide biodegradation viz. P450, short-chain dehydrogenases/reductases (SDR), etc., were also discovered in river sediment metagenomics data. This is the first report on the richness of bioremediation microbial communities in the Ganga and Yamuna riverine ecosystems, highlighting their importance in aquatic pollution management.}, }
@article {pmid33171859, year = {2020}, author = {Webster, HJ and Emami-Khoyi, A and van Dyk, JC and Teske, PR and Jansen van Vuuren, B}, title = {Environmental DNA Metabarcoding as a Means of Estimating Species Diversity in an Urban Aquatic Ecosystem.}, journal = {Animals : an open access journal from MDPI}, volume = {10}, number = {11}, pages = {}, pmid = {33171859}, issn = {2076-2615}, abstract = {Adaptation to environments that are changing as a result of human activities is critical to species' survival. A large number of species are adapting to, and even thriving in, urban green spaces, but this diversity remains largely undocumented. In the current study, we explored the potential of environmental DNA (eDNA) to document species diversity in one of the largest green spaces in Johannesburg, South Africa. Using a novel metabarcoding approach that assembles short DNA fragments suitable for massively parallel sequencing platforms to the approximate standard ~710 bp COI barcoding fragment, we document the presence of 26 phyla, 52 classes, 134 orders, 289 families, 380 genera and 522 known species from the study site. Our results highlight the critical role that urban areas play in protecting the world's declining biodiversity.}, }
@article {pmid33162946, year = {2020}, author = {Barajas, HR and Martínez-Sánchez, S and Romero, MF and Álvarez, CH and Servín-González, L and Peimbert, M and Cruz-Ortega, R and García-Oliva, F and Alcaraz, LD}, title = {Testing the Two-Step Model of Plant Root Microbiome Acquisition Under Multiple Plant Species and Soil Sources.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {542742}, pmid = {33162946}, issn = {1664-302X}, abstract = {The two-step model for plant root microbiomes considers soil as the primary microbial source. Active selection of the plant's bacterial inhabitants results in a biodiversity decrease toward roots. We collected sixteen samples of in situ ruderal plant roots and their soils and used these soils as the main microbial input for single genotype tomatoes grown in a greenhouse. Our main goal was to test the soil influence in the structuring of rhizosphere microbiomes, minimizing environmental variability, while testing multiple plant species. We massively sequenced the 16S rRNA and shotgun metagenomes of the soils, in situ plants, and tomato roots. We identified a total of 271,940 bacterial operational taxonomic units (OTUs) within the soils, rhizosphere and endospheric microbiomes. We annotated by homology a total of 411,432 (13.07%) of the metagenome predicted proteins. Tomato roots did follow the two-step model with lower α-diversity than soil, while ruderal plants did not. Surprisingly, ruderal plants are probably working as a microenvironmental oasis providing moisture and plant-derived nutrients, supporting larger α-diversity. Ruderal plants and their soils are closer according to their microbiome community composition than tomato and its soil, based on OTUs and protein comparisons. We expected that tomato β-diversity clustered together with their soil, if it is the main rhizosphere microbiome structuring factor. However, tomato microbiome β-diversity was associated with plant genotype in most samples (81.2%), also supported by a larger set of enriched proteins in tomato rhizosphere than soil or ruderals. The most abundant bacteria found in soils was the Actinobacteria Solirubrobacter soli, ruderals were dominated by the Proteobacteria Sphingomonas sp. URGHD0057, and tomato mainly by the Bacteroidetes Ohtaekwangia koreensis, Flavobacterium terrae, Niastella vici, and Chryseolinea serpens. We calculated a metagenomic tomato root core of 51 bacterial genera and 2,762 proteins, which could be the basis for microbiome-oriented plant breeding programs. We attributed a larger diversity in ruderal plants roots exudates as an effect of the moisture and nutrient acting as a microbial harbor. The tomato and ruderal metagenomic differences are probably due to plant domestication trade-offs, impacting plant-bacteria interactions.}, }
@article {pmid33126925, year = {2020}, author = {Santos-Júnior, CD and Sarmento, H and de Miranda, FP and Henrique-Silva, F and Logares, R}, title = {Uncovering the genomic potential of the Amazon River microbiome to degrade rainforest organic matter.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {151}, doi = {10.1186/s40168-020-00930-w}, pmid = {33126925}, issn = {2049-2618}, support = {0050.0081178.13.9//Petrobras/ ; 141112/2016-6//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 311746/2017-9//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 309514/2017-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; RYC-2013-12554//Ministerio de Economía y Competitividad/ ; CTM2015-69936-P//Ministerio de Economía y Competitividad/ ; 240904//Norges Forskningsråd/ ; 2014/14139-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 88881.131637/2016-01//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, abstract = {BACKGROUND: The Amazon River is one of the largest in the world and receives huge amounts of terrestrial organic matter (TeOM) from the surrounding rainforest. Despite this TeOM is typically recalcitrant (i.e. resistant to degradation), only a small fraction of it reaches the ocean, pointing to a substantial TeOM degradation by the river microbiome. Yet, microbial genes involved in TeOM degradation in the Amazon River were barely known. Here, we examined the Amazon River microbiome by analysing 106 metagenomes from 30 sampling points distributed along the river.<br><br>RESULTS: We constructed the Amazon River basin Microbial non-redundant Gene Catalogue (AMnrGC) that includes ~ 3.7 million non-redundant genes, affiliating mostly to bacteria. We found that the Amazon River microbiome contains a substantial gene-novelty compared to other relevant known environments (rivers and rainforest soil). Genes encoding for proteins potentially involved in lignin degradation pathways were correlated to tripartite tricarboxylates transporters and hemicellulose degradation machinery, pointing to a possible priming effect. Based on this, we propose a model on how the degradation of recalcitrant TeOM could be modulated by labile compounds in the Amazon River waters. Our results also suggest changes of the microbial community and its genomic potential along the river course.<br><br>CONCLUSIONS: Our work contributes to expand significantly our comprehension of the world's largest river microbiome and its potential metabolism related to TeOM degradation. Furthermore, the produced gene catalogue (AMnrGC) represents an important resource for future research in tropical rivers. Video abstract.}, }
@article {pmid33126862, year = {2020}, author = {Zhang, X and Yi, N}, title = {NBZIMM: negative binomial and zero-inflated mixed models, with application to microbiome/metagenomics data analysis.}, journal = {BMC bioinformatics}, volume = {21}, number = {1}, pages = {488}, pmid = {33126862}, issn = {1471-2105}, mesh = {Algorithms ; *Data Analysis ; Humans ; Metagenome ; *Metagenomics ; Microbiota/*genetics ; *Models, Statistical ; Multilevel Analysis ; }, abstract = {BACKGROUND: Microbiome/metagenomic data have specific characteristics, including varying total sequence reads, over-dispersion, and zero-inflation, which require tailored analytic tools. Many microbiome/metagenomic studies follow a longitudinal design to collect samples, which further complicates the analysis methods needed. A flexible and efficient R package is needed for analyzing processed multilevel or longitudinal microbiome/metagenomic data.<br><br>RESULTS: NBZIMM is a freely available R package that provides functions for setting up and fitting negative binomial mixed models, zero-inflated negative binomial mixed models, and zero-inflated Gaussian mixed models. It also provides functions to summarize the results from fitted models, both numerically and graphically. The main functions are built on top of the commonly used R packages nlme and MASS, allowing us to incorporate the well-developed analytic procedures into the framework for analyzing over-dispersed and zero-inflated count or proportion data with multilevel structures (e.g., longitudinal studies). The statistical methods and their implementations in NBZIMM particularly address the data characteristics and the complex designs in microbiome/metagenomic studies. The package is freely available from the public GitHub repository https://github.com/nyiuab/NBZIMM .<br><br>CONCLUSION: The NBZIMM package provides useful tools for complex microbiome/metagenomics data analysis.}, }
@article {pmid33110490, year = {2020}, author = {Huang, C and Yu, Y and Du, W and Liu, Y and Dai, R and Tang, W and Wang, P and Zhang, C and Shi, G}, title = {Fungal and bacterial microbiome dysbiosis and imbalance of trans-kingdom network in asthma.}, journal = {Clinical and translational allergy}, volume = {10}, number = {}, pages = {42}, pmid = {33110490}, issn = {2045-7022}, abstract = {Background: Fungal and bacterial microbiota play an important role in development of asthma. We aim to characterize airway microbiome (mycobiome, bacteriome) and functional genes in asthmatics and controls.<br><br>Methods: Sputum microbiome of controls, untreated asthma patients and inhaled corticosteroid (ICS) receiving patients was detected using high throughput sequencing. Metagenomic sequencing was used to examine the functional genes of microbiome.<br><br>Results: 1. Mycobiome: α diversity was lower in untreated asthma group than that in controls. Mycobiome compositions differed among the three groups. Compared with controls, untreated asthma group has higher abundance of Wallemia, Mortierella and Fusarium. Compared with untreated asthma patients, ICS receiving patients has higher abundance of Fusarium and Mortierella, lower frequency of Wallemia, Alternaria and Aspergillus. 2. Bacteriome: α diversity was lower in untreated asthma group than that in controls. There are some overlaps of bacteriome compositions between controls and untreated asthma patients which were distinct from ICS receiving patients. Untreated asthma group has higher Streptococcus than controls. 3. Potential fungal and bacterial biomarkers of asthma: Trametes, Aspergillus, Streptococcus, Gemella, Neisseria, etc. 4. Correlation network: There are dense and homogenous correlations in controls but a dramatically unbalanced network in untreated asthma and ICS receiving patients, which suggested the existence of disease-specific inter-kingdom and intra-kingdom alterations. 5. Metagenomic analysis: functional pathways were associated with the status of asthma, microbiome and functional genes showed different correlations in different environment.<br><br>Conclusion: We showed mycobiome and bacteriome dysbiosis in asthma featured by alterations in biodiversity, community composition, inter-kingdom and intra-kingdom network. We also observed several functional genes associated with asthma.}, }
@article {pmid33108273, year = {2020}, author = {Kelly, L and Wolfson, SJ}, title = {Finding phenazine.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, pmid = {33108273}, issn = {2050-084X}, mesh = {Agriculture ; Bacteria/genetics ; *Microbiota ; Phenazines ; *Soil ; }, abstract = {Analysis of genetic information from soil samples provides insights into bacteria that help to protect crops from fungal diseases by producing chemicals called phenazines.}, }
@article {pmid33096423, year = {2020}, author = {Gurwara, S and Dai, A and Ajami, NJ and Graham, DY and White, DL and Chen, L and Jang, A and Chen, E and El-Serag, HB and Petrosino, JF and Jiao, L}, title = {Alcohol use alters the colonic mucosa-associated gut microbiota in humans.}, journal = {Nutrition research (New York, N.Y.)}, volume = {83}, number = {}, pages = {119-128}, pmid = {33096423}, issn = {1879-0739}, support = {I01 CX001430/CX/CSRD VA/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; R01 CA172880/CA/NCI NIH HHS/United States ; }, abstract = {Alcohol misuse is a risk factor for many adverse health outcomes. Alcohol misuse has been associated with an imbalance of gut microbiota in preclinical models and alcoholic diseases. We hypothesized that daily alcohol use would change the community composition and structure of the human colonic gut microbiota. Thirty-four polyp-free individuals donated 97 snap-frozen colonic biopsies. Microbial DNA was sequenced for the 16S ribosomal RNA gene hypervariable region 4. The SILVA database was used for operational taxonomic unit classification. Alcohol use was assessed using a food frequency questionnaire. We compared the biodiversity and relative abundance of the taxa among never drinkers (ND, n = 9), former drinkers (FD, n = 10), current light drinkers (LD, <2 drinks daily, n = 9), and current heavy drinkers (HD, ≥2 drinks daily, n = 6). False discovery rate-adjusted P values (q values) < .05 indicated statistical significance. HD had the lowest α diversity (Shannon index q value < 0.001), and HD's microbial composition differed the most from the other groups (P value = .002). LD had the highest relative abundance of Akkermansia (q values < 0.001). HD had the lowest relative abundance of Subdoligranulum, Roseburia, and Lachnospiraceaeunc91005 but the highest relative abundance of Lachnospiraceaeunc8895 (all q values < 0.05). The multivariable negative binomial regression model supported these observations. ND and FD had a similar microbial profile. Heavy alcohol use was associated with impaired gut microbiota that may partially mediate its effect on health outcomes.}, }
@article {pmid33093799, year = {2020}, author = {Jha, P and Singh, J and Vidyarthi, AS and Prasad, R}, title = {Unveiling the Biodiversity of Hyperthermophilic Archaea in Jharia Coal Mines: Potential Threat to Methanogenesis?.}, journal = {Current genomics}, volume = {21}, number = {5}, pages = {363-371}, pmid = {33093799}, issn = {1389-2029}, abstract = {Aim: To examine the biodiversity of archaeal sulfate reducers and methanogens present in the underground coal mines of Jharia using metagenomics and pyrosequencing.<br><br>Objectives: 1) Bioinformatical analysis of the metagenomic data related to a taxonomic analysis obtained from the coal to investigate complete archaeal taxonomic features of the coal bed methane (CBM) microbiome. 2) Bioinformatical analysis of the metagenomic data related to a functional analysis obtained from the coal to investigate functional features relating to taxonomic diversity of the CBM microbiome. 3) The functional attributes have been examined specifically for ORFs related to sulfite reduction and methanogenesis.The taxonomic and functional biodiversity related to euryarchaeota will help in a better understanding of the obstacles associated with methane production imposed by the sulfate reducers.<br><br>Background: The microbial methanogenesis in the coal microbiome is a resultant of substrate utilization by primarily fermentative bacteria and methanogens. The present work reveals the biodiversity of archaeal sulfate reducers and methanogens present in the underground coal mines of Jharia using metagenomics and pyrosequencing.<br><br>Methodology: Bioinformatical analysis for structural and functional attributes was accomplished using MG-RAST. The structural analysis was accomplished using RefSeq database, whereas the functional analysis was done via CoG database with a cut off value, a sequence percent identity, and sequence alignment length cut off of 1e-5, 60% and 45, respectively.<br><br>Results: Attained communities revealed the dominance of hyperthermophilic archaea Pyrococcus furiosus along with Thermococcus kodakarensis in the coal metagenome.The obtained results also suggest the presence of dissimilatory sulfite reductase and formylmethanofuran dehydrogenase, formylmethanofuran: tetrahydromethanopterin formyltransferase involved in sulfite reduction and methanogenesis, respectively, in the microbiome.<br><br>Conclusion: This report is the first attempt to showcase the existence of specific euryarchaeal diversity and their related functional attributes from Jharia coal mines through high throughput sequencing. The study helps in developing a better understanding of the presence of indigenous microbes (archaea) and their functions in the coal microbiome, which can be utilized further to resolve the energy crisis.}, }
@article {pmid33087062, year = {2020}, author = {Eng, A and Verster, AJ and Borenstein, E}, title = {MetaLAFFA: a flexible, end-to-end, distributed computing-compatible metagenomic functional annotation pipeline.}, journal = {BMC bioinformatics}, volume = {21}, number = {1}, pages = {471}, pmid = {33087062}, issn = {1471-2105}, support = {1R01GM124312/NH/NIH HHS/United States ; R01DK095869/NH/NIH HHS/United States ; 2435/19//Israel Science Foundation/ ; U19AG057377/NH/NIH HHS/United States ; }, mesh = {Humans ; Metagenomics/*methods ; Microbiota ; *Software ; }, abstract = {BACKGROUND: Microbial communities have become an important subject of research across multiple disciplines in recent years. These communities are often examined via shotgun metagenomic sequencing, a technology which can offer unique insights into the genomic content of a microbial community. Functional annotation of shotgun metagenomic data has become an increasingly popular method for identifying the aggregate functional capacities encoded by the community's constituent microbes. Currently available metagenomic functional annotation pipelines, however, suffer from several shortcomings, including limited pipeline customization options, lack of standard raw sequence data pre-processing, and insufficient capabilities for integration with distributed computing systems.<br><br>RESULTS: Here we introduce MetaLAFFA, a functional annotation pipeline designed to take unfiltered shotgun metagenomic data as input and generate functional profiles. MetaLAFFA is implemented as a Snakemake pipeline, which enables convenient integration with distributed computing clusters, allowing users to take full advantage of available computing resources. Default pipeline settings allow new users to run MetaLAFFA according to common practices while a Python module-based configuration system provides advanced users with a flexible interface for pipeline customization. MetaLAFFA also generates summary statistics for each step in the pipeline so that users can better understand pre-processing and annotation quality.<br><br>CONCLUSIONS: MetaLAFFA is a new end-to-end metagenomic functional annotation pipeline with distributed computing compatibility and flexible customization options. MetaLAFFA source code is available at https://github.com/borenstein-lab/MetaLAFFA and can be installed via Conda as described in the accompanying documentation.}, }
@article {pmid33082572, year = {2020}, author = {Kroeger, ME and Meredith, LK and Meyer, KM and Webster, KD and de Camargo, PB and de Souza, LF and Tsai, SM and van Haren, J and Saleska, S and Bohannan, BJM and Rodrigues, JLM and Berenguer, E and Barlow, J and Nüsslein, K}, title = {Rainforest-to-pasture conversion stimulates soil methanogenesis across the Brazilian Amazon.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-020-00804-x}, pmid = {33082572}, issn = {1751-7370}, support = {DEB 1442183//NSF | BIO | Division of Environmental Biology (DEB)/ ; 2009-447 35319-05186//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; 2014/50320-4//Fundação de Amparo à Pesquisa do Estado de São Paulo (São Paulo Research Foundation)/ ; }, abstract = {The Amazon rainforest is a biodiversity hotspot and large terrestrial carbon sink threatened by agricultural conversion. Rainforest-to-pasture conversion stimulates the release of methane, a potent greenhouse gas. The biotic methane cycle is driven by microorganisms; therefore, this study focused on active methane-cycling microorganisms and their functions across land-use types. We collected intact soil cores from three land use types (primary rainforest, pasture, and secondary rainforest) of two geographically distinct areas of the Brazilian Amazon (Santarém, Pará and Ariquemes, Rondônia) and performed DNA stable-isotope probing coupled with metagenomics to identify the active methanotrophs and methanogens. At both locations, we observed a significant change in the composition of the isotope-labeled methane-cycling microbial community across land use types, specifically an increase in the abundance and diversity of active methanogens in pastures. We conclude that a significant increase in the abundance and activity of methanogens in pasture soils could drive increased soil methane emissions. Furthermore, we found that secondary rainforests had decreased methanogenic activity similar to primary rainforests, and thus a potential to recover as methane sinks, making it conceivable for forest restoration to offset greenhouse gas emissions in the tropics. These findings are critical for informing land management practices and global tropical rainforest conservation.}, }
@article {pmid33077707, year = {2020}, author = {Herold, M and Martínez Arbas, S and Narayanasamy, S and Sheik, AR and Kleine-Borgmann, LAK and Lebrun, LA and Kunath, BJ and Roume, H and Bessarab, I and Williams, RBH and Gillece, JD and Schupp, JM and Keim, PS and Jäger, C and Hoopmann, MR and Moritz, RL and Ye, Y and Li, S and Tang, H and Heintz-Buschart, A and May, P and Muller, EEL and Laczny, CC and Wilmes, P}, title = {Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {5281}, pmid = {33077707}, issn = {2041-1723}, support = {R01 AI108888/AI/NIAID NIH HHS/United States ; R01 AI143254/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/classification/*genetics/isolation &amp; purification/*metabolism ; Bioreactors/microbiology ; Ecosystem ; Metabolomics ; Metagenome ; Metagenomics ; *Microbiota ; Proteomics ; Time Factors ; Waste Water/*microbiology ; }, abstract = {The development of reliable, mixed-culture biotechnological processes hinges on understanding how microbial ecosystems respond to disturbances. Here we reveal extensive phenotypic plasticity and niche complementarity in oleaginous microbial populations from a biological wastewater treatment plant. We perform meta-omics analyses (metagenomics, metatranscriptomics, metaproteomics and metabolomics) on in situ samples over 14 months at weekly intervals. Based on 1,364 de novo metagenome-assembled genomes, we uncover four distinct fundamental niche types. Throughout the time-series, we observe a major, transient shift in community structure, coinciding with substrate availability changes. Functional omics data reveals extensive variation in gene expression and substrate usage amongst community members. Ex situ bioreactor experiments confirm that responses occur within five hours of a pulse disturbance, demonstrating rapid adaptation by specific populations. Our results show that community resistance and resilience are a function of phenotypic plasticity and niche complementarity, and set the foundation for future ecological engineering efforts.}, }
@article {pmid33077235, year = {2020}, author = {Cissell, EC and McCoy, SJ}, title = {Shotgun metagenomic sequencing reveals the full taxonomic, trophic, and functional diversity of a coral reef benthic cyanobacterial mat from Bonaire, Caribbean Netherlands.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {142719}, doi = {10.1016/j.scitotenv.2020.142719}, pmid = {33077235}, issn = {1879-1026}, abstract = {Anthropogenic forcing is spurring cyanobacterial proliferation in aquatic ecosystems worldwide. While planktonic cyanobacterial blooms have received substantial research attention, benthic blooms of mat-forming cyanobacteria have received considerably less attention, especially benthic mat blooms on coral reefs. Resultingly, numerous aspects of coral reef benthic cyanobacterial bloom ecology remain unknown, including underlying biodiversity in the mat communities. Most previous characterizations of coral reef cyanobacterial mat composition have only considered the cyanobacterial component. Without an unbiased characterization of full community diversity, we cannot predict whole-community response to anthropogenic inputs or effectively determine appropriate mitigation strategies. Here, we advocate for the implementation of shotgun sequencing techniques to study coral reef cyanobacterial mats worldwide, utilizing a case study of a coral reef benthic cyanobacterial mat sampled from the island of Bonaire, Caribbean Netherlands. Read-based taxonomic profiling revealed that Cyanobacteria was present at only 47.57% relative abundance in a coral reef cyanobacterial mat, with non-cyanobacterial members of the sampled mat community, including diatoms (0.78%), fungi (0.25%), Archaea (0.34%), viruses (0.08%), and other bacteria (45.78%), co-dominating the community. We found numerous gene families for regulatory systems and for functional pathways (both aerobic and anaerobic). These gene families were involved in community coordination; photosynthesis; nutrient scavenging; and the cycling of sulfur, nitrogen, phosphorous, and iron. We also report bacteriophage (including prophage) sequences associated with this subtidal coral reef cyanobacterial mat, which could contribute to intra-mat nutrient cycling and bloom dynamics. Overall, our results suggest that Cyanobacteria-focused analysis of coral reef cyanobacterial mats underestimates mat diversity and fails to capture community members possessing broad metabolic potential for intra-mat nutrient scavenging, recycling, and retention that likely contribute to the contemporary success of cyanobacterial mats on reefs. We advocate for increased collaboration between microbiologists and coral reef ecologists to unite insights from each discipline and improve efforts to understand mat ecology.}, }
@article {pmid33063083, year = {2020}, author = {Liu, L and He, Y and Wang, K and Miao, J and Zheng, Z}, title = {Metagenomics approach to the intestinal microbiome structure and function in high fat diet-induced obesity in mice fed with conjugated linoleic acid (CLA).}, journal = {Food &amp; function}, volume = {11}, number = {11}, pages = {9729-9739}, doi = {10.1039/d0fo02112a}, pmid = {33063083}, issn = {2042-650X}, abstract = {In this study, a high fat diet induced obesity mouse model (DIO) was used to investigate the modulatory effect of high purity conjugated linoleic acid (CLA) on the intestinal microbiota. CLA was prepared by a simulated moving bed chromatography system and its influence on the gut microbes was analyzed by 16S amplicon V3-V4 region analysis. We observed a significant increase in the bacterial biodiversity and the abundance of genera of butyrate- and acetate-producing bacteria. After taking CLA for 6 weeks, the abundance of Bacteroides in the intestines of mice greatly increased, while the abundance of Firmicutes decreased. The corresponding decrease in the Firmicutes/Bacteroidetes ratio reflected a positive modulatory effect of CLA on the intestinal microbiota. In addition, KEGG pathways for the nucleotide metabolism, metabolism of terpenoids and polyketides and lipid metabolism were among the most differentially expressed genes after CLA intervention. The current study revealed that CLA can be used as a functional food component with potential therapeutic value to prevent obesity-related metabolic disorders by manipulating the intestinal microbiota.}, }
@article {pmid33059593, year = {2020}, author = {Golob, JL and Minot, SS}, title = {In silico benchmarking of metagenomic tools for coding sequence detection reveals the limits of sensitivity and precision.}, journal = {BMC bioinformatics}, volume = {21}, number = {1}, pages = {459}, pmid = {33059593}, issn = {1471-2105}, support = {AI134808//NIH / NIAID/ ; New Investigator Award//ASBMT/ ; }, mesh = {Algorithms ; *Benchmarking ; *Computer Simulation ; Humans ; *Metagenome ; Metagenomics ; Microbiota/genetics ; Open Reading Frames/*genetics ; Predictive Value of Tests ; }, abstract = {BACKGROUND: High-throughput sequencing can establish the functional capacity of a microbial community by cataloging the protein-coding sequences (CDS) present in the metagenome of the community. The relative performance of different computational methods for identifying CDS from whole-genome shotgun sequencing is not fully established.<br><br>RESULTS: Here we present an automated benchmarking workflow, using synthetic shotgun sequencing reads for which we know the true CDS content of the underlying communities, to determine the relative performance (sensitivity, positive predictive value or PPV, and computational efficiency) of different metagenome analysis tools for extracting the CDS content of a microbial community. Assembly-based methods are limited by coverage depth, with poor sensitivity for CDS at < 5X depth of sequencing, but have excellent PPV. Mapping-based techniques are more sensitive at low coverage depths, but can struggle with PPV. We additionally describe an expectation maximization based iterative algorithmic approach which we show to successfully improve the PPV of a mapping based technique while retaining improved sensitivity and computational efficiency.<br><br>CONCLUSION: Our benchmarking approach reveals the trade-offs of assembly versus alignment-based approaches and the relative performance of specific implementations when one wishes to extract the protein coding capacity of microbial communities.}, }
@article {pmid33037214, year = {2020}, author = {Pereira, FC and Wasmund, K and Cobankovic, I and Jehmlich, N and Herbold, CW and Lee, KS and Sziranyi, B and Vesely, C and Decker, T and Stocker, R and Warth, B and von Bergen, M and Wagner, M and Berry, D}, title = {Rational design of a microbial consortium of mucosal sugar utilizers reduces Clostridiodes difficile colonization.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {5104}, pmid = {33037214}, issn = {2041-1723}, mesh = {Acetylglucosamine/metabolism ; Animals ; Anti-Bacterial Agents ; Bacterial Proteins/metabolism ; Bacterial Toxins/metabolism ; Cell Separation/methods ; Clostridium Infections/microbiology ; Clostridium difficile/genetics/growth &amp; development/*pathogenicity ; Deuterium ; Female ; Gastric Mucins/chemistry/metabolism ; Gastrointestinal Microbiome/*physiology ; Intestinal Mucosa/drug effects/microbiology ; Metagenome ; Mice, Inbred C57BL ; Monosaccharides/*metabolism ; N-Acetylneuraminic Acid/metabolism ; Polysaccharides/chemistry/metabolism ; Spectrum Analysis, Raman ; }, abstract = {Many intestinal pathogens, including Clostridioides difficile, use mucus-derived sugars as crucial nutrients in the gut. Commensals that compete with pathogens for such nutrients are therefore ecological gatekeepers in healthy guts, and are attractive candidates for therapeutic interventions. Nevertheless, there is a poor understanding of which commensals use mucin-derived sugars in situ as well as their potential to impede pathogen colonization. Here, we identify mouse gut commensals that utilize mucus-derived monosaccharides within complex communities using single-cell stable isotope probing, Raman-activated cell sorting and mini-metagenomics. Sequencing of cell-sorted fractions reveals members of the underexplored family Muribaculaceae as major mucin monosaccharide foragers, followed by members of Lachnospiraceae, Rikenellaceae, and Bacteroidaceae families. Using this information, we assembled a five-member consortium of sialic acid and N-acetylglucosamine utilizers that impedes C. difficile's access to these mucosal sugars and impairs pathogen colonization in antibiotic-treated mice. Our findings underscore the value of targeted approaches to identify organisms utilizing key nutrients and to rationally design effective probiotic mixtures.}, }
@article {pmid33033250, year = {2020}, author = {Guo, W and Xin, M and Wang, Z and Yao, Y and Hu, Z and Song, W and Yu, K and Chen, Y and Wang, X and Guan, P and Appels, R and Peng, H and Ni, Z and Sun, Q}, title = {Origin and adaptation to high altitude of Tibetan semi-wild wheat.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {5085}, pmid = {33033250}, issn = {2041-1723}, mesh = {*Adaptation, Physiological/genetics ; *Altitude ; Domestication ; Ecotype ; Genome, Plant ; Geography ; Metagenomics ; Phenotype ; Principal Component Analysis ; Tibet ; Triticum/genetics/*physiology ; }, abstract = {Tibetan wheat is grown under environmental constraints at high-altitude conditions, but its underlying adaptation mechanism remains unknown. Here, we present a draft genome sequence of a Tibetan semi-wild wheat (Triticum aestivum ssp. tibetanum Shao) accession Zang1817 and re-sequence 245 wheat accessions, including world-wide wheat landraces, cultivars as well as Tibetan landraces. We demonstrate that high-altitude environments can trigger extensive reshaping of wheat genomes, and also uncover that Tibetan wheat accessions accumulate high-altitude adapted haplotypes of related genes in response to harsh environmental constraints. Moreover, we find that Tibetan semi-wild wheat is a feral form of Tibetan landrace, and identify two associated loci, including a 0.8-Mb deletion region containing Brt1/2 homologs and a genomic region with TaQ-5A gene, responsible for rachis brittleness during the de-domestication episode. Our study provides confident evidence to support the hypothesis that Tibetan semi-wild wheat is de-domesticated from local landraces, in response to high-altitude extremes.}, }
@article {pmid33032033, year = {2020}, author = {Suárez, N and Weckx, S and Minahk, C and Hebert, EM and Saavedra, L}, title = {Metagenomics-based approach for studying and selecting bioprotective strains from the bacterial community of artisanal cheeses.}, journal = {International journal of food microbiology}, volume = {335}, number = {}, pages = {108894}, doi = {10.1016/j.ijfoodmicro.2020.108894}, pmid = {33032033}, issn = {1879-3460}, mesh = {Animals ; Anti-Bacterial Agents/analysis/*biosynthesis ; Argentina ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Bacteriocins/analysis/*biosynthesis/genetics ; Cattle ; Cheese/analysis/*microbiology ; Metagenomics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {A metagenome-based approach was used to assess the taxonomic affiliation and functional potential for bacteriocin production of the bacterial community in cow's milk artisanal cheeses from Northwestern Argentina. Three different samples were analyzed by high-throughput sequencing of the V4 region of the 16S rRNA gene and shotgun metagenomics. Taxonomic analysis showed that cheese A and C were quite similar whereas cheese B displayed a rather different bacterial composition. Overall, two families, Streptococceae and Enterococceae, dominated the artisanal cheese microbiota, being the former family prevalent in cheese B and the later family the most important in samples A and C. Besides the usual species associated to cheeses, a number of bacterial taxa that have not been previously found in Argentinean artisanal cheeses were reported in the present work such as Macrococcus caseolyticus and Streptococcus macedonicus Functional metagenomics analysis using the bacteriocin mining software BAGEL3, identified 2 ORFs encoding antimicrobial peptides in cheese B and 42 different peptides in sample C. The bacteriocin genes found showed good correlation with taxonomy. Based on the microbial diversity and functional features found through shotgun metagenomic sequencing, a culture-dependent approach was applied aiming to isolate bacteriocin-producing bacteria able to inhibit the growth of the foodborne pathogen Listeria monocytogenes. From 151 bacterial colonies derived from the cheese samples, 10 were associated to high anti-Listeria activity. Based on partial 16S rRNA gene sequencing and RAPD-PCR analysis, all bacteriocinogenic isolates were identified as Enterococcus faecium. Finally, we carried out a pilot experiment with L. monocytogenes-contaminated cheese using one of the enterococcal isolates as a bioprotective adjunct culture. The use of E. faecium CRL1879 during artisanal cheese manufacturing did not alter the main organoleptic properties of the cheese and ensured an efficient control of the foodborne pathogen up to 30 days. This finding supports the use of E. faecium CRL1879 as an adjunct culture in the cheese-making process with a combination of both safety and minimal processing.}, }
@article {pmid33024120, year = {2020}, author = {Zhang, Y and Gu, Y and Ren, H and Wang, S and Zhong, H and Zhao, X and Ma, J and Gu, X and Xue, Y and Huang, S and Yang, J and Chen, L and Chen, G and Qu, S and Liang, J and Qin, L and Huang, Q and Peng, Y and Li, Q and Wang, X and Kong, P and Hou, G and Gao, M and Shi, Z and Li, X and Qiu, Y and Zou, Y and Yang, H and Wang, J and Xu, G and Lai, S and Li, J and Ning, G and Wang, W}, title = {Gut microbiome-related effects of berberine and probiotics on type 2 diabetes (the PREMOTE study).}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {5015}, pmid = {33024120}, issn = {2041-1723}, mesh = {Berberine/*pharmacology/therapeutic use ; Diabetes Mellitus, Type 2/*drug therapy/*microbiology ; Female ; Gastrointestinal Microbiome/*drug effects/physiology ; Glycated Hemoglobin A/metabolism ; Humans ; Hypoglycemic Agents/pharmacology/therapeutic use ; Male ; Metagenome/drug effects/genetics ; Middle Aged ; Placebos ; Probiotics/*therapeutic use ; Treatment Outcome ; }, abstract = {Human gut microbiome is a promising target for managing type 2 diabetes (T2D). Measures altering gut microbiota like oral intake of probiotics or berberine (BBR), a bacteriostatic agent, merit metabolic homoeostasis. We hence conducted a randomized, double-blind, placebo-controlled trial with newly diagnosed T2D patients from 20 centres in China. Four-hundred-nine eligible participants were enroled, randomly assigned (1:1:1:1) and completed a 12-week treatment of either BBR-alone, probiotics+BBR, probiotics-alone, or placebo, after a one-week run-in of gentamycin pretreatment. The changes in glycated haemoglobin, as the primary outcome, in the probiotics+BBR (least-squares mean [95% CI], -1.04[-1.19, -0.89]%) and BBR-alone group (-0.99[-1.16, -0.83]%) were significantly greater than that in the placebo and probiotics-alone groups (-0.59[-0.75, -0.44]%, -0.53[-0.68, -0.37]%, P < 0.001). BBR treatment induced more gastrointestinal side effects. Further metagenomics and metabolomic studies found that the hypoglycaemic effect of BBR is mediated by the inhibition of DCA biotransformation by Ruminococcus bromii. Therefore, our study reports a human microbial related mechanism underlying the antidiabetic effect of BBR on T2D. (Clinicaltrial.gov Identifier: NCT02861261).}, }
@article {pmid33020496, year = {2020}, author = {Natarajan, A and Bhatt, AS}, title = {Microbes and microbiomes in 2020 and beyond.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {4988}, pmid = {33020496}, issn = {2041-1723}, support = {R01 AI143757/AI/NIAID NIH HHS/United States ; R01 AI148623/AI/NIAID NIH HHS/United States ; }, mesh = {Environmental Microbiology ; Humans ; Metagenomics ; *Microbiota ; }, }
@article {pmid32994415, year = {2020}, author = {Guo, X and Gao, Q and Yuan, M and Wang, G and Zhou, X and Feng, J and Shi, Z and Hale, L and Wu, L and Zhou, A and Tian, R and Liu, F and Wu, B and Chen, L and Jung, CG and Niu, S and Li, D and Xu, X and Jiang, L and Escalas, A and Wu, L and He, Z and Van Nostrand, JD and Ning, D and Liu, X and Yang, Y and Schuur, EAG and Konstantinidis, KT and Cole, JR and Penton, CR and Luo, Y and Tiedje, JM and Zhou, J}, title = {Gene-informed decomposition model predicts lower soil carbon loss due to persistent microbial adaptation to warming.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {4897}, pmid = {32994415}, issn = {2041-1723}, mesh = {Acclimatization/genetics ; Archaea/genetics/isolation &amp; purification/metabolism ; Bacteria/genetics/isolation &amp; purification/metabolism ; Carbon/*analysis/metabolism ; Carbon Cycle ; Cellulose/metabolism ; Environmental DNA/genetics/isolation &amp; purification ; Fungi/genetics/isolation &amp; purification/metabolism ; Global Warming ; Grassland ; Hot Temperature/adverse effects ; Metagenome/*genetics ; Metagenomics ; Microbiota/*physiology ; Models, Genetic ; Plant Roots/chemistry ; Poaceae/chemistry ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Soil microbial respiration is an important source of uncertainty in projecting future climate and carbon (C) cycle feedbacks. However, its feedbacks to climate warming and underlying microbial mechanisms are still poorly understood. Here we show that the temperature sensitivity of soil microbial respiration (Q10) in a temperate grassland ecosystem persistently decreases by 12.0 ± 3.7% across 7 years of warming. Also, the shifts of microbial communities play critical roles in regulating thermal adaptation of soil respiration. Incorporating microbial functional gene abundance data into a microbially-enabled ecosystem model significantly improves the modeling performance of soil microbial respiration by 5-19%, and reduces model parametric uncertainty by 55-71%. In addition, modeling analyses show that the microbial thermal adaptation can lead to considerably less heterotrophic respiration (11.6 ± 7.5%), and hence less soil C loss. If such microbially mediated dampening effects occur generally across different spatial and temporal scales, the potential positive feedback of soil microbial respiration in response to climate warming may be less than previously predicted.}, }
@article {pmid32993188, year = {2020}, author = {Peng, M and Biswas, D}, title = {Environmental Influences of High-Density Agricultural Animal Operation on Human Forearm Skin Microflora.}, journal = {Microorganisms}, volume = {8}, number = {10}, pages = {}, pmid = {32993188}, issn = {2076-2607}, support = {20185110628809//National Institute of Food and Agriculture/ ; }, abstract = {The human forearm skin microbiome ecosystem contains rich and diverse microbes, which are influenced by environmental exposures. The microbial representatives can be exchanged between human and environment, specifically animals, by which they share certain or similar epidermal microbes. Livestock and poultry are the microbial sources that are associated with the transmission of community-based pathogenic infections. Here, in this study, we proposed investigating the environmental influences introduced by livestock/poultry operations on forearm skin microflora of on-site farm workers. A total of 30 human skin swab samples were collected from 20 animal workers in dairy or integrated farms and 10 healthy volunteer controls. The skin microbiome was 16S metagenomics that were sequenced with Illumina MiSeq system. For skin microbial community analysis, the abundance of major phyla and genera as well as alpha and beta diversities were compared across groups. We identified distinctive microbial compositional patterns on skin of workers in farm with different animal commodities. Workers in integrated farms containing various animals were associated with higher abundances of epidermal Proteobacteria, especially Pseudomonas and Acinetobacter, but lower Actinobacteria, especially Corynebacterium and Propionibacterium. For those workers with frequent dairy cattle operations, their Firmicutes in the forearm skin microbiota were enriched. Furthermore, farm animal operations also reduced Staphylococcus and Streptococcus, as well as modulated the microbial biodiversity in farm workers' skin microbiome. The alterations of forearm skin microflora in farm workers, influenced by their frequent farm animal operations, may increase their risk in skin infections with unusual pathogens and epidermal diseases.}, }
@article {pmid32992213, year = {2020}, author = {Hamood Altowayti, WA and Almoalemi, H and Shahir, S and Othman, N}, title = {Comparison of culture-independent and dependent approaches for identification of native arsenic-resistant bacteria and their potential use for arsenic bioremediation.}, journal = {Ecotoxicology and environmental safety}, volume = {205}, number = {}, pages = {111267}, doi = {10.1016/j.ecoenv.2020.111267}, pmid = {32992213}, issn = {1090-2414}, mesh = {Actinobacteria/cytology/*drug effects/genetics ; Arsenic/analysis/*toxicity ; Biodegradation, Environmental ; Culture Media/chemistry ; Drug Resistance, Bacterial/drug effects ; Firmicutes/cytology/*drug effects/genetics ; Gold ; Metagenomics/*methods ; Microbial Sensitivity Tests ; Microbiota/drug effects/genetics ; Mining ; Proteobacteria/cytology/*drug effects/genetics ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Soil Microbiology ; Soil Pollutants/analysis/*toxicity ; }, abstract = {Arsenic is a common contaminant in gold mine soil and tailings. Microbes present an opportunity for bio-treatment of arsenic, since it is a sustainable and cost-effective approach to remove arsenic from water. However, the development of existing bio-treatment approaches depends on isolation of arsenic-resistant microbes from arsenic contaminated samples. Microbial cultures are commonly used in bio-treatment; however, it is not established whether the structure of the cultured isolates resembles the native microbial community from arsenic-contaminated soil. In this milieu, a culture-independent approach using Illumina sequencing technology was used to profile the microbial community in situ. This was coupled with a culture-dependent technique, that is, isolation using two different growth media, to analyse the microbial population in arsenic laden tailing dam sludge based on the culture-independent sequencing approach, 4 phyla and 8 genera were identified in a sample from the arsenic-rich gold mine. Firmicutes (92.23%) was the dominant phylum, followed by Proteobacteria (3.21%), Actinobacteria (2.41%), and Bacteroidetes (1.49%). The identified genera included Staphylococcus (89.8%), Pseudomonas (1.25), Corynebacterium (0.82), Prevotella (0.54%), Megamonas (0.38%) and Sphingomonas (0.36%). The Shannon index value (3.05) and Simpson index value (0.1661) indicated low diversity in arsenic laden tailing. The culture dependent method exposed significant similarities with culture independent methods at the phylum level with Firmicutes, Proteobacteria and Actinobacteria, being common, and Firmicutes was the dominant phylum whereas, at the genus level, only Pseudomonas was presented by both methods. It showed high similarities between culture independent and dependent methods at the phylum level and large differences at the genus level, highlighting the complementarity between the two methods for identification of the native population bacteria in arsenic-rich mine. As a result, the present study can be a resource on microbes for bio-treatment of arsenic in mining waste.}, }
@article {pmid32987279, year = {2021}, author = {Zhang, W and Zhang, Q and Li, M and Wang, H and Li, Y and Peng, H and Feng, J}, title = {Microbial community and function evaluation in the start-up period of bioaugmented SBR fed with aniline wastewater.}, journal = {Bioresource technology}, volume = {319}, number = {}, pages = {124148}, doi = {10.1016/j.biortech.2020.124148}, pmid = {32987279}, issn = {1873-2976}, mesh = {Aniline Compounds ; Bioreactors ; Denitrification ; *Microbiota ; Nitrification ; Nitrogen ; Sewage ; Waste Disposal, Fluid ; *Waste Water ; }, abstract = {An enhanced sequencing batch reactor (SBR) system was developed to treat synthetic wastewater rich in 600 mg/L aniline. The aniline degradation efficiency was almost 100%, and the total nitrogen (TN) removal rate was more than 50%. Metagenomics technology revealed the community structure, functional genes and metabolic mechanism during the start-up of the enhanced reactor. Sequencing results showed that Proteobacteria, Bacteroidetes, Chloroflexi and Actinobacteria were dominant phylum. The proportion of degradation of aromatic compounds function increased gradually, but the proportion of nitrogen metabolism function changed little. Functional genes involved in aniline degradation including benA-xylX and dmpB/xylE were detected. The functional genes of nitrogen metabolism were involved in complete nitrification, traditional denitrification, assimilation nitrate reduction and dissimilation nitrate reduction. The functional contribution analysis and network analysis showed that the cooperation and competition of Thauera, Delftia, Diaphorobacter, Micavibrio and Azoarcus ensured the effective removal of aniline and nitrogen.}, }
@article {pmid32984078, year = {2020}, author = {Marazzato, M and Zicari, AM and Aleandri, M and Conte, AL and Longhi, C and Vitanza, L and Bolognino, V and Zagaglia, C and De Castro, G and Brindisi, G and Schiavi, L and De Vittori, V and Reddel, S and Quagliariello, A and Del Chierico, F and Putignani, L and Duse, M and Palamara, AT and Conte, MP}, title = {16S Metagenomics Reveals Dysbiosis of Nasal Core Microbiota in Children With Chronic Nasal Inflammation: Role of Adenoid Hypertrophy and Allergic Rhinitis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {458}, pmid = {32984078}, issn = {2235-2988}, abstract = {Allergic rhinitis (AR) and adenoid hypertrophy (AH) are, in children, the main cause of partial or complete upper airway obstruction and reduction in airflow. However, limited data exist about the impact of the increased resistance to airflow, on the nasal microbial composition of children with AR end AH. Allergic rhinitis (AR) as well as adenoid hypertrophy (AH), represent extremely common pathologies in this population. Their known inflammatory obstruction is amplified when both pathologies coexist. In our study, the microbiota of anterior nares of 75 pediatric subjects with AR, AH or both conditions, was explored by 16S rRNA-based metagenomic approach. Our data show for the first time, that in children, the inflammatory state is associated to similar changes in the microbiota composition of AR and AH subjects respect to the healthy condition. Together with such alterations, we observed a reduced variability in the between-subject biodiversity on the other hand, these same alterations resulted amplified by the nasal obstruction that could constitute a secondary risk factor for dysbiosis. Significant differences in the relative abundance of specific microbial groups were found between diseased phenotypes and the controls. Most of these taxa belonged to a stable and quantitatively dominating component of the nasal microbiota and showed marked potentials in discriminating the controls from diseased subjects. A pauperization of the nasal microbial network was observed in diseased status in respect to the number of involved taxa and connectivity. Finally, while stable co-occurrence relationships were observed within both control- and diseases-associated microbial groups, only negative correlations were present between them, suggesting that microbial subgroups potentially act as maintainer of the eubiosis state in the nasal ecosystem. In the nasal ecosystem, inflammation-associated shifts seem to impact the more intimate component of the microbiota rather than representing the mere loss of microbial diversity. The discriminatory potential showed by differentially abundant taxa provide a starting point for future research with the potential to improve patient outcomes. Overall, our results underline the association of AH and AR with the impairment of the microbial interplay leading to unbalanced ecosystems.}, }
@article {pmid32974807, year = {2020}, author = {Xu, AA and Hoffman, K and Gurwara, S and White, DL and Kanwal, F and El-Serag, HB and Petrosino, JF and Jiao, L}, title = {Oral Health and the Altered Colonic Mucosa-Associated Gut Microbiota.}, journal = {Digestive diseases and sciences}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10620-020-06612-9}, pmid = {32974807}, issn = {1573-2568}, support = {RP#140767//Cancer Prevention and Research Institute of Texas/ ; 001//Gillson Longenbaugh Foundation/ ; 001//Golfers Against Cancer/ ; CX001430//U.S. Department of Veterans Affairs/ ; P30 DK56338/DK/NIDDK NIH HHS/United States ; CIN13-413//U.S. Department of Veterans Affairs/ ; R01-CA172880//Division of Cancer Epidemiology and Genetics, National Cancer Institute/ ; }, abstract = {BACKGROUND: Systemic diseases have been associated with oral health and gut microbiota. We examined the association between oral health and the community composition and structure of the adherent colonic gut microbiota.<br><br>METHODS: We obtained 197 snap-frozen colonic biopsies from 62 colonoscopy-confirmed polyp-free individuals. Microbial DNA was sequenced for the 16S rRNA V4 region using the Illumina MiSeq, and the sequences were assigned to the operational taxonomic unit based on SILVA. We used a questionnaire to ascertain tooth loss, gum disease, and lifestyle factors. We compared biodiversity and relative abundance of bacterial taxa based on the amount of tooth loss and the presence of gum disease. The multivariable negative binomial regression model for panel data was used to estimate the association between the bacterial count and oral health. False discovery rate-adjusted P value (q value) < .05 indicated statistical significance.<br><br>RESULTS: More tooth loss and gum disease were associated with lower bacterial alpha diversity. The relative abundance of Faecalibacterium was lower (q values < .05) with more tooth loss. The association was significant after adjusting for age, ethnicity, obesity, smoking, alcohol use, hypertension, diabetes, and the colon segment. The relative abundance of Bacteroides was higher in those with gum disease.<br><br>CONCLUSIONS: Oral health was associated with alteration in the community composition and structure of the adherent gut bacteria in the colon. The reduced anti-inflammatory Faecalibacterium in participants with more tooth loss may indicate systemic inflammation. Future studies are warranted to confirm our findings and investigate the systemic role of Faecalibacterium.}, }
@article {pmid32960892, year = {2020}, author = {Crandall, SG and Gold, KM and Jiménez-Gasco, MDM and Filgueiras, CC and Willett, DS}, title = {A multi-omics approach to solving problems in plant disease ecology.}, journal = {PloS one}, volume = {15}, number = {9}, pages = {e0237975}, pmid = {32960892}, issn = {1932-6203}, mesh = {*Ecology ; Genomics/*methods ; Metabolomics/*methods ; Metagenomics/*methods ; Microbiota ; Plant Diseases/*etiology ; Plants/*immunology/metabolism ; Proteomics/*methods ; Systems Biology ; }, abstract = {The swift rise of omics-approaches allows for investigating microbial diversity and plant-microbe interactions across diverse ecological communities and spatio-temporal scales. The environment, however, is rapidly changing. The introduction of invasive species and the effects of climate change have particular impact on emerging plant diseases and managing current epidemics. It is critical, therefore, to take a holistic approach to understand how and why pathogenesis occurs in order to effectively manage for diseases given the synergies of changing environmental conditions. A multi-omics approach allows for a detailed picture of plant-microbial interactions and can ultimately allow us to build predictive models for how microbes and plants will respond to stress under environmental change. This article is designed as a primer for those interested in integrating -omic approaches into their plant disease research. We review -omics technologies salient to pathology including metabolomics, genomics, metagenomics, volatilomics, and spectranomics, and present cases where multi-omics have been successfully used for plant disease ecology. We then discuss additional limitations and pitfalls to be wary of prior to conducting an integrated research project as well as provide information about promising future directions.}, }
@article {pmid32957925, year = {2020}, author = {Zhao, Z and Cristian, A and Rosen, G}, title = {Keeping up with the genomes: efficient learning of our increasing knowledge of the tree of life.}, journal = {BMC bioinformatics}, volume = {21}, number = {1}, pages = {412}, pmid = {32957925}, issn = {1471-2105}, mesh = {Algorithms ; Bacteria/genetics ; Bayes Theorem ; Gastrointestinal Microbiome/*genetics ; *Genome, Bacterial ; Humans ; *Machine Learning ; Metagenome ; Metagenomics/*methods ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: It is a computational challenge for current metagenomic classifiers to keep up with the pace of training data generated from genome sequencing projects, such as the exponentially-growing NCBI RefSeq bacterial genome database. When new reference sequences are added to training data, statically trained classifiers must be rerun on all data, resulting in a highly inefficient process. The rich literature of &quot;incremental learning&quot; addresses the need to update an existing classifier to accommodate new data without sacrificing much accuracy compared to retraining the classifier with all data.<br><br>RESULTS: We demonstrate how classification improves over time by incrementally training a classifier on progressive RefSeq snapshots and testing it on: (a) all known current genomes (as a ground truth set) and (b) a real experimental metagenomic gut sample. We demonstrate that as a classifier model's knowledge of genomes grows, classification accuracy increases. The proof-of-concept naïve Bayes implementation, when updated yearly, now runs in 1/4th of the non-incremental time with no accuracy loss.<br><br>CONCLUSIONS: It is evident that classification improves by having the most current knowledge at its disposal. Therefore, it is of utmost importance to make classifiers computationally tractable to keep up with the data deluge. The incremental learning classifier can be efficiently updated without the cost of reprocessing nor the access to the existing database and therefore save storage as well as computation resources.}, }
@article {pmid32949366, year = {2020}, author = {Hemmat-Jou, MH and Safari-Sinegani, AA and Che, R and Mirzaie-Asl, A and Tahmourespour, A and Tahmasbian, I}, title = {Toxic trace element resistance genes and systems identified using the shotgun metagenomics approach in an Iranian mine soil.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11356-020-10824-x}, pmid = {32949366}, issn = {1614-7499}, abstract = {This study aimed to identify the microbial communities, resistance genes, and resistance systems in an Iranian mine soil polluted with toxic trace elements (TTE). The polluted soil samples were collected from a mining area and compared against non-polluted (control) collected soils from the vicinity of the mine. The soil total DNA was extracted and sequenced, and bioinformatic analysis of the assembled metagenomes was conducted to identify soil microbial biodiversity, TTE resistance genes, and resistance systems. The results of the employed shotgun approach indicated that the relative abundance of Proteobacteria, Firmicutes, Bacteroidetes, and Deinococcus-Thermus was significantly higher in the TTE-polluted soils compared with those in the control soils, while the relative abundance of Actinobacteria and Acidobacteria was significantly lower in the polluted soils. The high concentration of TTE increased the ratio of archaea to bacteria and decreased the alpha diversity in the polluted soils compared with the control soils. Canonical correspondence analysis (CCA) demonstrated that heavy metal pollution was the major driving factor in shaping microbial communities compared with any other soil characteristics. In the identified heavy metal resistome (HV-resistome) of TTE-polluted soils, major functional pathways were carbohydrates metabolism, stress response, amino acid and derivative metabolism, clustering-based subsystems, iron acquisition and metabolism, cell wall synthesis and capsulation, and membrane transportation. Ten TTE resistance systems were identified in the HV-resistome of TTE-polluted soils, dominated by &quot;P-type ATPases,&quot; &quot;cation diffusion facilitators,&quot; and &quot;heavy metal efflux-resistance nodulation cell division (HME-RND).&quot; Most of the resistance genes (69%) involved in resistance systems are affiliated to cell wall, outer membrane, periplasm, and cytoplasmic membrane. The finding of this study provides insight into the microbial community in Iranian TTE-polluted soils and their resistance genes and systems.}, }
@article {pmid32948523, year = {2020}, author = {Milani, C and Alessandri, G and Mancabelli, L and Mangifesta, M and Lugli, GA and Viappiani, A and Longhi, G and Anzalone, R and Duranti, S and Turroni, F and Ossiprandi, MC and van Sinderen, D and Ventura, M}, title = {Multi-omics Approaches To Decipher the Impact of Diet and Host Physiology on the Mammalian Gut Microbiome.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {23}, pages = {}, pmid = {32948523}, issn = {1098-5336}, mesh = {Animals ; Bacteria/classification/*isolation &amp; purification ; Diet/*veterinary ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Gene Expression Profiling/veterinary ; Mammals/*microbiology/*physiology ; Metagenomics ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Species Specificity ; }, abstract = {In recent years, various studies have demonstrated that the gut microbiota influences host metabolism. However, these studies were focused primarily on a single or a limited range of host species, thus preventing a full exploration of possible taxonomic and functional adaptations by gut microbiota members as a result of host-microbe coevolution events. In the current study, the microbial taxonomic profiles of 250 fecal samples, corresponding to 77 host species that cover the mammalian branch of the tree of life, were reconstructed by 16S rRNA gene-based sequence analysis. Moreover, shotgun metagenomics was employed to investigate the metabolic potential of the fecal microbiomes of 24 mammals, and subsequent statistical analyses were performed to assess the impact of host diet and corresponding physiology of the digestive system on gut microbiota composition and functionality. Functional data were confirmed and extended through metatranscriptome assessment of gut microbial populations of eight animals, thus providing insights into the transcriptional response of gut microbiota to specific dietary lifestyles. Therefore, the analyses performed in this study support the notion that the metabolic features of the mammalian gut microbiota have adapted to maximize energy extraction from the host's diet.IMPORTANCE Diet and host physiology have been recognized as main factors affecting both taxonomic composition and functional features of the mammalian gut microbiota. However, very few studies have investigated the bacterial biodiversity of mammals by using large sample numbers that correspond to multiple mammalian species, thus resulting in an incomplete understanding of the functional aspects of their microbiome. Therefore, we investigated the bacterial taxonomic composition of 250 fecal samples belonging to 77 host species distributed along the tree of life in order to assess how diet and host physiology impact the intestinal microbial community by selecting specific microbial players. Conversely, the application of shotgun metagenomics and metatranscriptomics approaches to a group of selected fecal samples allowed us to shed light on both metabolic features and transcriptional responses of the intestinal bacterial community based on different diets.}, }
@article {pmid32947654, year = {2020}, author = {Białasek, M and Miłobędzka, A}, title = {Revealing antimicrobial resistance in stormwater with MinION.}, journal = {Chemosphere}, volume = {258}, number = {}, pages = {127392}, pmid = {32947654}, issn = {1879-1298}, mesh = {Bacteria/drug effects ; Drug Resistance, Bacterial/*genetics ; Environmental Monitoring ; Feces/microbiology ; Genes, Bacterial/drug effects ; Humans ; Macrolides ; *Metagenome ; Metagenomics/methods ; Microbiota/drug effects ; Waste Water/microbiology ; beta-Lactams ; }, abstract = {Discharge of urban stormwater containing organic matter, heavy metals and sometime human feces, to the natural aquatic reservoirs without any treatment is not only an environmental problem. It can lead to prevalence of antibiotic resistant bacteria in stormwater systems and transmission of antibiotic resistance genes to the environment. We performed antibiotic resistome identification and virus detection in stormwater samples from Stockholm, using publicly available metagenomic sequencing MinION data. A MinION platform offers low-cost, precise environmental metagenomics analysis. 37 groups of antibiotic resistant bacteria (ARB), 11 resistance types with 26 resistance mechanisms - antibiotic resistance genes (ARGs) giving tolerance to the aminoglycoside, beta-lactams, fosmidomycin, MLS, multidrug and vancomycin were identified using ARGpore pipeline. The majority of the identified bacteria species were related to the natural environment such as soil and were not dangerous to human. Alarmingly, human pathogenic bacteria carrying resistance to antibiotics currently used against them (Bordetella resistant to macrolides and multidrug resistant Propionibacterium avidum) were also found in the samples. Most abundant viruses identified belonged to Caudovirales and Herpesvirales and they were not carrying ARGs. Unlike the virome, resistome and ARB were not unique for stormwater sampling points. This results underline the need for extensive monitoring of the microbial community structure in the urban stormwater systems to assess antimicrobial resistance spread.}, }
@article {pmid32947608, year = {2020}, author = {Søndertoft, NB and Vogt, JK and Arumugam, M and Kristensen, M and Gøbel, RJ and Fan, Y and Lyu, L and Bahl, MI and Eriksen, C and Ängquist, L and Frøkiær, H and Hansen, TH and Brix, S and Nielsen, HB and Hansen, T and Vestergaard, H and Gupta, R and Licht, TR and Lauritzen, L and Pedersen, O}, title = {The intestinal microbiome is a co-determinant of the postprandial plasma glucose response.}, journal = {PloS one}, volume = {15}, number = {9}, pages = {e0238648}, pmid = {32947608}, issn = {1932-6203}, mesh = {Algorithms ; Blood Glucose/*metabolism ; Fasting/blood ; Female ; *Gastrointestinal Microbiome ; Humans ; Life Style ; Male ; Middle Aged ; Models, Biological ; Phenomics ; *Postprandial Period ; }, abstract = {Elevated postprandial plasma glucose is a risk factor for development of type 2 diabetes and cardiovascular disease. We hypothesized that the inter-individual postprandial plasma glucose response varies partly depending on the intestinal microbiome composition and function. We analyzed data from Danish adults (n = 106), who were self-reported healthy and attended the baseline visit of two previously reported randomized controlled cross-over trials within the Gut, Grain and Greens project. Plasma glucose concentrations at five time points were measured before and during three hours after a standardized breakfast. Based on these data, we devised machine learning algorithms integrating bio-clinical, as well as shotgun-sequencing-derived taxa and functional potentials of the intestinal microbiome to predict individual postprandial glucose excursions. In this post hoc study, we found microbial and clinical features, which predicted up to 48% of the inter-individual variance of postprandial plasma glucose responses (Pearson correlation coefficient of measured vs. predicted values, R = 0.69, 95% CI: 0.45 to 0.84, p<0.001). The features were age, fasting serum triglycerides, systolic blood pressure, BMI, fasting total serum cholesterol, abundance of Bifidobacterium genus, richness of metagenomics species and abundance of a metagenomic species annotated to Clostridiales at order level. A model based only on microbial features predicted up to 14% of the variance in postprandial plasma glucose excursions (R = 0.37, 95% CI: 0.02 to 0.64, p = 0.04). Adding fasting glycaemic measures to the model including microbial and bio-clinical features increased the predictive power to R = 0.78 (95% CI: 0.59 to 0.89, p<0.001), explaining more than 60% of the inter-individual variance of postprandial plasma glucose concentrations. The outcome of the study points to a potential role of the taxa and functional potentials of the intestinal microbiome. If validated in larger studies our findings may be included in future algorithms attempting to develop personalized nutrition, especially for prediction of individual blood glucose excursions in dys-glycaemic individuals.}, }
@article {pmid32946440, year = {2020}, author = {Methe, BA and Hiltbrand, D and Roach, J and Xu, W and Gordon, SG and Goodner, BW and Stapleton, AE}, title = {Functional gene categories differentiate maize leaf drought-related microbial epiphytic communities.}, journal = {PloS one}, volume = {15}, number = {9}, pages = {e0237493}, pmid = {32946440}, issn = {1932-6203}, mesh = {Droughts ; Gene Regulatory Networks ; Genes, Plant ; Metagenomics ; Microbiota ; Molecular Sequence Annotation ; Plant Leaves/*genetics/*microbiology/physiology ; Stress, Physiological ; Water/metabolism ; Zea mays/*genetics/*microbiology/physiology ; }, abstract = {The phyllosphere epiphytic microbiome is composed of microorganisms that colonize the external aerial portions of plants. Relationships of plant responses to specific microorganisms-both pathogenic and beneficial-have been examined, but the phyllosphere microbiome functional and metabolic profile responses are not well described. Changing crop growth conditions, such as increased drought, can have profound impacts on crop productivity. Also, epiphytic microbial communities provide a new target for crop yield optimization. We compared Zea mays leaf microbiomes collected under drought and well-watered conditions by examining functional gene annotation patterns across three physically disparate locations each with and without drought treatment, through the application of short read metagenomic sequencing. Drought samples exhibited different functional sequence compositions at each of the three field sites. Maize phyllosphere functional profiles revealed a wide variety of metabolic and regulatory processes that differed in drought and normal water conditions and provide key baseline information for future selective breeding.}, }
@article {pmid32934151, year = {2020}, author = {Toivonen, L and Karppinen, S and Schuez-Havupalo, L and Waris, M and He, Q and Hoffman, KL and Petrosino, JF and Dumas, O and Camargo, CA and Hasegawa, K and Peltola, V}, title = {Longitudinal Changes in Early Nasal Microbiota and the Risk of Childhood Asthma.}, journal = {Pediatrics}, volume = {146}, number = {4}, pages = {}, doi = {10.1542/peds.2020-0421}, pmid = {32934151}, issn = {1098-4275}, mesh = {Aerococcaceae/isolation &amp; purification ; Age Factors ; Asthma/diagnosis/*etiology/microbiology ; Child ; Child, Preschool ; Female ; Finland ; Follow-Up Studies ; Gene Expression Profiling/methods ; Haemophilus/isolation &amp; purification ; Humans ; Incidence ; Infant ; Infant, Newborn ; Machine Learning ; Male ; *Microbiota/genetics ; Moraxella/isolation &amp; purification ; Multivariate Analysis ; Nose/*microbiology ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Respiratory Tract Infections/complications/epidemiology/microbiology ; Risk ; Streptococcus/isolation &amp; purification ; }, abstract = {OBJECTIVES: Although the airway microbiota is a highly dynamic ecology, the role of longitudinal changes in airway microbiota during early childhood in asthma development is unclear. We aimed to investigate the association of longitudinal changes in early nasal microbiota with the risk of developing asthma.<br><br>METHODS: In this prospective, population-based birth cohort study, we followed children from birth to age 7 years. The nasal microbiota was tested by using 16S ribosomal RNA gene sequencing at ages 2, 13, and 24 months. We applied an unsupervised machine learning approach to identify longitudinal nasal microbiota profiles during age 2 to 13 months (the primary exposure) and during age 2 to 24 months (the secondary exposure) and examined the association of these profiles with the risk of physician-diagnosed asthma at age 7 years.<br><br>RESULTS: Of the analytic cohort of 704 children, 57 (8%) later developed asthma. We identified 4 distinct longitudinal nasal microbiota profiles during age 2 to 13 months. In the multivariable analysis, compared with the persistent Moraxella dominance profile during age 2 to 13 months, the persistent Moraxella sparsity profile was associated with a significantly higher risk of asthma (adjusted odds ratio, 2.74; 95% confidence interval, 1.20-6.27). Similar associations were observed between the longitudinal changes in nasal microbiota during age 2 to 24 months and risk of asthma.<br><br>CONCLUSIONS: Children with an altered longitudinal pattern in the nasal microbiota during early childhood had a high risk of developing asthma. Our data guide the development of primary prevention strategies (eg, early identification of children at high risk and modification of microbiota) for childhood asthma. These observations present a new avenue for risk modification for asthma (eg, microbiota modification).}, }
@article {pmid32925939, year = {2020}, author = {Clark, JJ and Gilray, J and Orton, RJ and Baird, M and Wilkie, G and Filipe, ADS and Johnson, N and McInnes, CJ and Kohl, A and Biek, R}, title = {Population genomics of louping ill virus provide new insights into the evolution of tick-borne flaviviruses.}, journal = {PLoS neglected tropical diseases}, volume = {14}, number = {9}, pages = {e0008133}, pmid = {32925939}, issn = {1935-2735}, support = {BB/J013854/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MC_UU_12014/12/MRC_/Medical Research Council/United Kingdom ; MC_UU_12014/8/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Cell Line ; Cricetinae ; Encephalitis Viruses, Tick-Borne/classification/*genetics ; Encephalitis, Tick-Borne/virology ; *Evolution, Molecular ; Genetics, Population ; *Genome, Viral ; Metagenomics ; Phylogeny ; Sequence Analysis, RNA ; Sheep ; United Kingdom ; }, abstract = {The emergence and spread of tick-borne arboviruses pose an increased challenge to human and animal health. In Europe this is demonstrated by the increasingly wide distribution of tick-borne encephalitis virus (TBEV, Flavivirus, Flaviviridae), which has recently been found in the United Kingdom (UK). However, much less is known about other tick-borne flaviviruses (TBFV), such as the closely related louping ill virus (LIV), an animal pathogen which is endemic to the UK and Ireland, but which has been detected in other parts of Europe including Scandinavia and Russia. The emergence and potential spatial overlap of these viruses necessitates improved understanding of LIV genomic diversity, geographic spread and evolutionary history. We sequenced a virus archive composed of 22 LIV isolates which had been sampled throughout the UK over a period of over 80 years. Combining this dataset with published virus sequences, we detected no sign of recombination and found low diversity and limited evidence for positive selection in the LIV genome. Phylogenetic analysis provided evidence of geographic clustering as well as long-distance movement, including movement events that appear recent. However, despite genomic data and an 80-year time span, we found that the data contained insufficient temporal signal to reliably estimate a molecular clock rate for LIV. Additional analyses revealed that this also applied to TBEV, albeit to a lesser extent, pointing to a general problem with phylogenetic dating for TBFV. The 22 LIV genomes generated during this study provide a more reliable LIV phylogeny, improving our knowledge of the evolution of tick-borne flaviviruses. Our inability to estimate a molecular clock rate for both LIV and TBEV suggests that temporal calibration of tick-borne flavivirus evolution should be interpreted with caution and highlight a unique aspect of these viruses which may be explained by their reliance on tick vectors.}, }
@article {pmid32912302, year = {2020}, author = {Saary, P and Mitchell, AL and Finn, RD}, title = {Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {244}, pmid = {32912302}, issn = {1474-760X}, support = {BB/M011755/1, BB/R015228/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Microbial eukaryotes constitute a significant fraction of biodiversity and have recently gained more attention, but the recovery of high-quality metagenomic assembled eukaryotic genomes is limited by the current availability of tools. To help address this, we have developed EukCC, a tool for estimating the quality of eukaryotic genomes based on the automated dynamic selection of single copy marker gene sets. We demonstrate that our method outperforms current genome quality estimators, particularly for estimating contamination, and have applied EukCC to datasets derived from two different environments to enable the identification of novel eukaryote genomes, including one from the human skin.}, }
@article {pmid32899763, year = {2020}, author = {El-Hossary, EM and Abdel-Halim, M and Ibrahim, ES and Pimentel-Elardo, SM and Nodwell, JR and Handoussa, H and Abdelwahab, MF and Holzgrabe, U and Abdelmohsen, UR}, title = {Natural Products Repertoire of the Red Sea.}, journal = {Marine drugs}, volume = {18}, number = {9}, pages = {}, pmid = {32899763}, issn = {1660-3397}, abstract = {Marine natural products have achieved great success as an important source of new lead compounds for drug discovery. The Red Sea provides enormous diversity on the biological scale in all domains of life including micro- and macro-organisms. In this review, which covers the literature to the end of 2019, we summarize the diversity of bioactive secondary metabolites derived from Red Sea micro- and macro-organisms, and discuss their biological potential whenever applicable. Moreover, the diversity of the Red Sea organisms is highlighted as well as their genomic potential. This review is a comprehensive study that compares the natural products recovered from the Red Sea in terms of ecological role and pharmacological activities.}, }
@article {pmid32899230, year = {2020}, author = {Iacono, R and Cobucci-Ponzano, B and De Lise, F and Curci, N and Maurelli, L and Moracci, M and Strazzulli, A}, title = {Spatial Metagenomics of Three Geothermal Sites in Pisciarelli Hot Spring Focusing on the Biochemical Resources of the Microbial Consortia.}, journal = {Molecules (Basel, Switzerland)}, volume = {25}, number = {17}, pages = {}, pmid = {32899230}, issn = {1420-3049}, support = {ASI N. 2019-3-U.0//Agenzia Spaziale Italiana/ ; }, abstract = {Terrestrial hot springs are of great interest to the general public and to scientists alike due to their unique and extreme conditions. These have been sought out by geochemists, astrobiologists, and microbiologists around the globe who are interested in their chemical properties, which provide a strong selective pressure on local microorganisms. Drivers of microbial community composition in these springs include temperature, pH, in-situ chemistry, and biogeography. Microbes in these communities have evolved strategies to thrive in these conditions by converting hot spring chemicals and organic matter into cellular energy. Following our previous metagenomic analysis of Pisciarelli hot springs (Naples, Italy), we report here the comparative metagenomic study of three novel sites, formed in Pisciarelli as result of recent geothermal activity. This study adds comprehensive information about phylogenetic diversity within Pisciarelli hot springs by peeking into possible mechanisms of adaptation to biogeochemical cycles, and high applicative potential of the entire set of genes involved in the carbohydrate metabolism in this environment (CAZome). This site is an excellent model for the study of biodiversity on Earth and biosignature identification, and for the study of the origin and limits of life.}, }
@article {pmid32897356, year = {2020}, author = {Bandini, F and Misci, C and Taskin, E and Cocconcelli, PS and Puglisi, E}, title = {Biopolymers modulate microbial communities in municipal organic waste digestion.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {10}, pages = {}, doi = {10.1093/femsec/fiaa183}, pmid = {32897356}, issn = {1574-6941}, abstract = {The development of biopolymers has raised issues about their recalcitrance in the environment. Their disposal is mainly carried out with the organic fraction of municipal solid waste (OFMSW) through thermophilic anaerobic digestion and aerobic composting, bioprocesses aimed at turning organic matter into biogas and compost. However, the effects of biopolymers on OFMSW treatment, on the final compost and on the microbial communities involved are partly unexplored. In this study, the OFMSW treatment was reproduced on a laboratory-scale respecting real plant conditions and testing the impacts of mixing polylactic acid (PLA) and starch-based bioplastic (SBB) separately. The dynamics of bacterial, archaeal and fungal communities during the process was screened by high-throughput sequencing (HTS) of phylogenetic amplicons. Starch-based bioplastic showed a minor and heterogeneous microbial diversity between the anaerobic and aerobic phases. Contrariwise, PLA treatment resulted in wider and more diverse bacterial and fungal communities for the compost and the aerobic biofilm. Since the biodiversity in compost may play a crucial role in its stability and safety, the modulation of environmental microbial communities induced by higher concentrations of PLA in OFMSW treatment can pose relevant issues.}, }
@article {pmid32890633, year = {2020}, author = {Joulian, C and Fonti, V and Chapron, S and Bryan, CG and Guezennec, AG}, title = {Bioleaching of pyritic coal wastes: bioprospecting and efficiency of selected consortia.}, journal = {Research in microbiology}, volume = {171}, number = {7}, pages = {260-270}, doi = {10.1016/j.resmic.2020.08.002}, pmid = {32890633}, issn = {1769-7123}, abstract = {Pyrite-bearing coal wastes are responsible of the formation of acid mine drainage (AMD), and their management to mitigate environmental impacts is a challenge to the coal mine industry in Europe and worldwide. The European CEReS project sought to develop a generic co-processing strategy to reuse and recycle coal wastes, based on removal of AMD generating potential through bioleaching. Chemolitoautotrophic iron- and sulfur-oxidizing microbial consortia were enriched from a Polish coal waste at 30 °C and 48 °C, but not 42 °C. Pyrite leaching yield, determined from bioleaching tests in 2-L stirred bioreactors, was best with the 48 °C endogenous consortium (80%), then the 42 °C exogenous BRGM-KCC consortium (71%), and finally the 30 °C endogenous consortium (50%). 16S rRNA gene-targeted metagenomics from five surface locations on the dump waste revealed a microbial community adapted to the site context, composed of iron- and/or sulfur-oxidizing genera thriving in low pH and metal rich environments and involved in AMD generation. All together, the results confirmed the predisposition of the pyritic coal waste to bioleaching and the potential of endogenous microorganisms for efficient bioleaching at 48 °C. The good leaching yields open the perspective to optimize further and scale-up the bioleaching process.}, }
@article {pmid32884659, year = {2020}, author = {Saccò, M and Blyth, AJ and Humphreys, WF and Cooper, SJB and Austin, AD and Hyde, J and Mazumder, D and Hua, Q and White, NE and Grice, K}, title = {Refining trophic dynamics through multi-factor Bayesian mixing models: A case study of subterranean beetles.}, journal = {Ecology and evolution}, volume = {10}, number = {16}, pages = {8815-8826}, pmid = {32884659}, issn = {2045-7758}, abstract = {Food web dynamics are vital in shaping the functional ecology of ecosystems. However, trophic ecology is still in its infancy in groundwater ecosystems due to the cryptic nature of these environments. To unravel trophic interactions between subterranean biota, we applied an interdisciplinary Bayesian mixing model design (multi-factor BMM) based on the integration of faunal C and N bulk tissue stable isotope data (δ13C and δ15N) with radiocarbon data (Δ14C), and prior information from metagenomic analyses. We further compared outcomes from multi-factor BMM with a conventional isotope double proxy mixing model (SIA BMM), triple proxy (δ13C, δ15N, and Δ14C, multi-proxy BMM), and double proxy combined with DNA prior information (SIA + DNA BMM) designs. Three species of subterranean beetles (Paroster macrosturtensis, Paroster mesosturtensis, and Paroster microsturtensis) and their main prey items Chiltoniidae amphipods (AM1: Scutachiltonia axfordi and AM2: Yilgarniella sturtensis), cyclopoids and harpacticoids from a calcrete in Western Australia were targeted. Diet estimations from stable isotope only models (SIA BMM) indicated homogeneous patterns with modest preferences for amphipods as prey items. Multi-proxy BMM suggested increased-and species-specific-predatory pressures on amphipods coupled with high rates of scavenging/predation on sister species. SIA + DNA BMM showed marked preferences for amphipods AM1 and AM2, and reduced interspecific scavenging/predation on Paroster species. Multi-factorial BMM revealed the most precise estimations (lower overall SD and very marginal beetles' interspecific interactions), indicating consistent preferences for amphipods AM1 in all the beetles' diets. Incorporation of genetic priors allowed crucial refining of the feeding preferences, while integration of more expensive radiocarbon data as a third proxy (when combined with genetic data) produced more precise outcomes but close dietary reconstruction to that from SIA + DNA BMM. Further multidisciplinary modeling from other groundwater environments will help elucidate the potential behind these designs and bring light to the feeding ecology of one the most vital ecosystems worldwide.}, }
@article {pmid32867361, year = {2020}, author = {Xue, CX and Liu, J and Lea-Smith, DJ and Rowley, G and Lin, H and Zheng, Y and Zhu, XY and Liang, J and Ahmad, W and Todd, JD and Zhang, XH}, title = {Insights into the Vertical Stratification of Microbial Ecological Roles across the Deepest Seawater Column on Earth.}, journal = {Microorganisms}, volume = {8}, number = {9}, pages = {}, pmid = {32867361}, issn = {2076-2607}, abstract = {The Earth's oceans are a huge body of water with physicochemical properties and microbial community profiles that change with depth, which in turn influences their biogeochemical cycling potential. The differences between microbial communities and their functional potential in surface to hadopelagic water samples are only beginning to be explored. Here, we used metagenomics to investigate the microbial communities and their potential to drive biogeochemical cycling in seven different water layers down the vertical profile of the Challenger Deep (0-10,500 m) in the Mariana Trench, the deepest natural point in the Earth's oceans. We recovered 726 metagenome-assembled genomes (MAGs) affiliated to 27 phyla. Overall, biodiversity increased in line with increased depth. In addition, the genome size of MAGs at ≥4000 m layers was slightly larger compared to those at 0-2000 m. As expected, surface waters were the main source of primary production, predominantly from Cyanobacteria. Intriguingly, microbes conducting an unusual form of nitrogen metabolism were identified in the deepest waters (>10,000 m), as demonstrated by an enrichment of genes encoding proteins involved in dissimilatory nitrate to ammonia conversion (DNRA), nitrogen fixation and urea transport. These likely facilitate the survival of ammonia-oxidizing archaea α lineage, which are typically present in environments with a high ammonia concentration. In addition, the microbial potential for oxidative phosphorylation and the glyoxylate shunt was enhanced in >10,000 m waters. This study provides novel insights into how microbial communities and their genetic potential for biogeochemical cycling differs through the Challenger deep water column, and into the unique adaptive lifestyle of microbes in the Earth's deepest seawater.}, }
@article {pmid32867028, year = {2020}, author = {Marin-Gómez, W and Grande, MJ and Pérez-Pulido, R and Galvez, A and Lucas, R}, title = {Changes in the Bacterial Diversity of Human Milk during Late Lactation Period (Weeks 21 to 48).}, journal = {Foods (Basel, Switzerland)}, volume = {9}, number = {9}, pages = {}, pmid = {32867028}, issn = {2304-8158}, support = {RS-AGR230//Universidad de Jaén/ ; }, abstract = {Breast milk from a single mother was collected during a 28-week lactation period. Bacterial diversity was studied by amplicon sequencing analysis of the V3-V4 variable region of the 16S rRNA gene. Firmicutes and Proteobacteria were the main phyla detected in the milk samples, followed by Actinobacteria and Bacteroidetes. The proportion of Firmicutes to Proteobacteria changed considerably depending on the sampling week. A total of 411 genera or higher taxons were detected in the set of samples. Genus Streptococcus was detected during the 28-week sampling period, at relative abundances between 2.0% and 68.8%, and it was the most abundant group in 14 of the samples. Carnobacterium and Lactobacillus had low relative abundances. At the genus level, bacterial diversity changed considerably at certain weeks within the studied period. The weeks or periods with lowest relative abundance of Streptococcus had more diverse bacterial compositions including genera belonging to Proteobacteria that were poorly represented in the rest of the samples.}, }
@article {pmid32857738, year = {2020}, author = {Wang, J and Zhou, J}, title = {The effects of offshore petroleum exploitation on microbial community and antibiotic resistome of adjacent marine sediments.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {81}, number = {12}, pages = {2501-2510}, doi = {10.2166/wst.2020.289}, pmid = {32857738}, issn = {0273-1223}, mesh = {Anti-Bacterial Agents ; Bacteria/genetics ; Genes, Bacterial ; Geologic Sediments ; Humans ; *Microbiota ; *Petroleum ; }, abstract = {The exploitation of petroleum in offshore areas is becoming more prosperous due to the increasing human demand for oil. However, the effects of offshore petroleum exploitation on the microbial community in the surrounding environment are still not adequately understood. In the present study, variations in the composition, function, and antibiotic resistance of the microbial community in marine sediments adjacent to an offshore petroleum exploitation platform were analyzed by a metagenomics-based method. Significant shifts in the microbial community composition were observed in sediments impacted by offshore petroleum exploitation. Nitrosopumilales was enriched in marine sediments with the activities of offshore petroleum exploitation compared to the control sediments. The abundances of function genes involved in carbon, butanoate, methane, and fatty acid metabolism in sediment microbial communities also increased due to the offshore petroleum exploitation. Offshore petroleum exploitation resulted in the propagation of some antibiotic resistance genes (ARGs), including a multidrug transporter, smeE, and arnA, in marine sediments via horizontal gene transfer mediated by class I integrons. However, the total abundance and diversity of ARGs in marine sediments were not significantly affected by offshore petroleum exploitation. This study is the first attempt to analyze the impact of offshore petroleum exploitation on the spread of antibiotic resistance.}, }
@article {pmid32835181, year = {2020}, author = {Kirubakaran, R and ArulJothi, KN and Revathi, S and Shameem, N and Parray, JA}, title = {Emerging priorities for microbial metagenome research.}, journal = {Bioresource technology reports}, volume = {11}, number = {}, pages = {100485}, pmid = {32835181}, issn = {2589-014X}, abstract = {Overwhelming anthropogenic activities lead to deterioration of natural resources and the environment. The microorganisms are considered desirable, due to their suitability for easy genetic manipulation and handling. With the aid of modern biotechnological techniques, the culturable microorganisms have been widely exploited for the benefit of mankind. Metagenomics, a powerful tool to access the abundant biodiversity of the environmental samples including the unculturable microbes, to determine microbial diversity and population structure, their ecological roles and expose novel genes of interest. This review focuses on the microbial adaptations to the adverse environmental conditions, metagenomic techniques employed towards microbial biotechnology. Metagenomic approach helps to understand microbial ecology and to identify useful microbial derivatives like antibiotics, toxins, and enzymes with diverse and enhanced function. It also summarizes the application of metagenomics in clinical diagnosis, improving microbial ecology, therapeutics, xenobiotic degradation and impact on agricultural crops.}, }
@article {pmid32814564, year = {2020}, author = {Vidanaarachchi, R and Shaw, M and Tang, SL and Halgamuge, S}, title = {IMPARO: inferring microbial interactions through parameter optimisation.}, journal = {BMC molecular and cell biology}, volume = {21}, number = {Suppl 1}, pages = {34}, pmid = {32814564}, issn = {2661-8850}, abstract = {BACKGROUND: Microbial Interaction Networks (MINs) provide important information for understanding bacterial communities. MINs can be inferred by examining microbial abundance profiles. Abundance profiles are often interpreted with the Lotka Volterra model in research. However existing research fails to consider a biologically meaningful underlying mathematical model for MINs or to address the possibility of multiple solutions.<br><br>RESULTS: In this paper we present IMPARO, a method for inferring microbial interactions through parameter optimisation. We use biologically meaningful models for both the abundance profile, as well as the MIN. We show how multiple MINs could be inferred with similar reconstructed abundance profile accuracy, and argue that a unique solution is not always satisfactory. Using our method, we successfully inferred clear interactions in the gut microbiome which have been previously observed in in-vitro experiments.<br><br>CONCLUSIONS: IMPARO was used to successfully infer microbial interactions in human microbiome samples as well as in a varied set of simulated data. The work also highlights the importance of considering multiple solutions for MINs.}, }
@article {pmid32806340, year = {2020}, author = {Banchi, E and Ametrano, CG and Tordoni, E and Stanković, D and Ongaro, S and Tretiach, M and Pallavicini, A and Muggia, L and , }, title = {Environmental DNA assessment of airborne plant and fungal seasonal diversity.}, journal = {The Science of the total environment}, volume = {738}, number = {}, pages = {140249}, doi = {10.1016/j.scitotenv.2020.140249}, pmid = {32806340}, issn = {1879-1026}, mesh = {*DNA Barcoding, Taxonomic ; *Environmental DNA ; Fungi/genetics ; Italy ; Seasons ; }, abstract = {Environmental DNA (eDNA) metabarcoding and metagenomics analyses can improve taxonomic resolution in biodiversity studies. Only recently, these techniques have been applied in aerobiology, to target bacteria, fungi and plants in airborne samples. Here, we present a nine-month aerobiological study applying eDNA metabarcoding in which we analyzed simultaneously airborne diversity and variation of fungi and plants across five locations in North and Central Italy. We correlated species composition with the ecological characteristics of the sites and the seasons. The most abundant taxa among all sites and seasons were the fungal genera Cladosporium, Alternaria, and Epicoccum and the plant genera Brassica, Corylus, Cupressus and Linum, the latter being much more variable among sites. PERMANOVA and indicator species analyses showed that the plant diversity from air samples is significantly correlated with seasons, while that of fungi varied according to the interaction between seasons and sites. The results consolidate the performance of a new eDNA metabarcoding pipeline for the simultaneous amplification and analysis of airborne plant and fungal particles. They also highlight the promising complementarity of this approach with more traditional biomonitoring frameworks and routine reports of air quality provided by environmental agencies.}, }
@article {pmid32803809, year = {2020}, author = {Thompson, AR and Geisen, S and Adams, BJ}, title = {Shotgun metagenomics reveal a diverse assemblage of protists in a model Antarctic soil ecosystem.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15198}, pmid = {32803809}, issn = {1462-2920}, support = {#OPP-1637708//National Science Foundation/ ; NWO-VENI 016.Veni.181.078//Netherlands Organization for Scientific Research/ ; }, abstract = {The soils of the McMurdo Dry Valleys (MDV) of Antarctica are established models for understanding fundamental processes in soil ecosystem functioning (e.g. ecological tipping points, community structuring and nutrient cycling) because the extreme physical environment drastically reduces biodiversity and ecological complexity. Understanding the functioning of MDV soils requires in-depth knowledge of the diversity of MDV soil species. Protists, which contribute significantly to soil ecosystem functioning worldwide, remain poorly characterized in the MDV. To better assess the diversity of MDV protists, we performed shotgun metagenomics on 18 sites representing a variety of landscape features and edaphic variables. Our results show MDV soil protists are diverse at both the genus (155 of 281 eukaryote genera) and family (120) levels, but comprise only 6% of eukaryotic reads. Protists are structured by moisture, total N and distance from the local coast and possess limited richness in arid (< 5% moisture) and at high elevation sites, known drivers of communities in the MDV. High relative diversity and broad distribution of protists in our study promotes these organisms as key members of MDV soil microbiomes and the MDV as a useful system for understanding the contribution of soil protists to the structure of soil microbiomes.}, }
@article {pmid32803300, year = {2020}, author = {Wang, H and Huang, J and Wang, P and Li, T}, title = {Insights into the microbiota of larval and postlarval Pacific white shrimp (Penaeus vannamei) along early developmental stages: a case in pond level.}, journal = {Molecular genetics and genomics : MGG}, volume = {295}, number = {6}, pages = {1517-1528}, doi = {10.1007/s00438-020-01717-2}, pmid = {32803300}, issn = {1617-4623}, support = {QNLM201706//Pilot National Laboratory for Marine Science and Technology (Qingdao)/ ; CARS-48//China Agriculture Research System/ ; 2020TD39//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; 2018M640666//China Postdoctoral Science Foundation/ ; }, mesh = {Animals ; Bacteria/*classification/*genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Larva/growth &amp; development/*microbiology ; Metagenomics ; Microbiota/*genetics ; Penaeidae/growth &amp; development/*microbiology ; Ponds ; RNA, Ribosomal, 16S/*analysis/genetics ; }, abstract = {Increasing studies have revealed strong links among gut microbiota, health status, and shrimp development, but they mainly focus on the microbiota of Pacific white shrimp, Penaeus vannamei, during life stages from juveniles to adults. Little is known about shrimp microbiota dynamics at early developmental stages. In this study, with an aim to profile shrimp microbiota and its dynamics at stages nauplius, zoea, mysis, and early postlarva, we conducted a survey for the successful breeding processes in a commercial hatchery in China, sampled 33 samples including larval/postlarval shrimp, suspended substance in rearing water (SSRW), and nutrition supplements (i.e., algae and brine shrimp larvae) at stages N5, Z2, M2, and P2. The associated bacterial communities were sequenced and comparatively analyzed using high-throughput sequencing of bacterial 16S rRNA genes. Our case study results showed that bacterial community structures and compositions were strikingly different at stages N5, Z2, and P2, indicating the shift of microbiota at the three stages. Many taxa within Gamma-, Alphaproteobacteria, and Flavobacteriia classes were observed to be stage-specifically abundant and identified as taxonomic biomarkers potentially used to differentiate among shrimp at different early developmental stages. Summing up, these results shed light on larval/postlarval microbiota and its dynamics at different early developmental stages, highlighting the potential roles of shrimp development in microbiota formation and shifting.}, }
@article {pmid32791721, year = {2020}, author = {Butler, ÉM and Chiavaroli, V and Derraik, JGB and Grigg, CP and Wilson, BC and Walker, N and OʼSullivan, JM and Cutfield, WS}, title = {Maternal bacteria to correct abnormal gut microbiota in babies born by C-section.}, journal = {Medicine}, volume = {99}, number = {30}, pages = {e21315}, pmid = {32791721}, issn = {1536-5964}, mesh = {Adult ; Anthropometry/methods ; Asthma/epidemiology/etiology ; Bacterial Physiological Phenomena ; Body Composition ; Case-Control Studies ; Celiac Disease/epidemiology/etiology ; Cesarean Section/*adverse effects ; Delivery, Obstetric/trends ; Feces ; Female ; Humans ; Infant ; Infant, Newborn ; Male ; Metagenomics/methods ; Microbiota/genetics/*physiology ; New Zealand/epidemiology ; Pediatric Obesity/epidemiology/etiology ; Placebos/*administration &amp; dosage ; Pregnancy ; Vagina/*microbiology ; }, abstract = {INTRODUCTION: There is evidence that caesarean section (CS) is associated with increased risk of childhood obesity, asthma, and coeliac disease. The gut microbiota of CS-born babies differs to those born vaginally, possibly due to reduced exposure to maternal vaginal bacteria during birth. Vaginal seeding is a currently unproven practice intended to reduce such differences, so that the gut microbiota of CS-born babies is similar to that of babies born vaginally. Our pilot study, which uses oral administration as a novel form of vaginal seeding, will assess the degree of maternal strain transfer and overall efficacy of the procedure for establishing normal gut microbiota development.<br><br>METHODS AND ANALYSIS: Protocol for a single-blinded, randomized, placebo-controlled pilot study of a previously untested method of vaginal seeding (oral administration) in 30 CS-born babies. A sample of maternal vaginal bacteria is obtained prior to CS, and mixed with 5 ml sterile water to obtain a supernatant. Healthy babies are randomized at 1:1 to receive active treatment (3 ml supernatant) or placebo (3 ml sterile water). A reference group of 15 non-randomized vaginal-born babies are also being recruited. Babies' stool samples will undergo whole metagenomic shotgun sequencing to identify potential differences in community structure between CS babies receiving active treatment compared to those receiving placebo at age 1 month (primary outcome). Secondary outcomes include differences in overall gut community between CS groups (24 hours, 3 months); similarity of CS-seeded and placebo gut profiles to vaginally-born babies (24 hours, 1 and 3 months); degree of maternal vaginal strain transfer in CS-born babies (24 hours, 1 and 3 months); anthropometry (1 and 3 months) and body composition (3 months).<br><br>ETHICS AND DISSEMINATION: Ethics approval by the Northern A Health and Disability Ethics Committee (18/NTA/49). Results will be published in peer-reviewed journals and presented at international conferences.<br><br>REGISTRATION: Australian New Zealand Clinical Trials Registry (ACTRN12618000339257).}, }
@article {pmid32791454, year = {2020}, author = {Kim, DD and Park, D and Yoon, H and Yun, T and Song, MJ and Yoon, S}, title = {Quantification of nosZ genes and transcripts in activated sludge microbiomes with novel group-specific qPCR methods validated with metagenomic analyses.}, journal = {Water research}, volume = {185}, number = {}, pages = {116261}, doi = {10.1016/j.watres.2020.116261}, pmid = {32791454}, issn = {1879-2448}, mesh = {Denitrification ; Metagenome ; *Microbiota/genetics ; Nitrous Oxide/analysis ; Republic of Korea ; *Sewage ; }, abstract = {Substantial N2O emission results from activated sludge nitrogen removal processes. N2O-reducing organisms possessing NosZ-type N2O reductases have been recognized to play crucial roles in suppressing emission of N2O produced in anoxic activated sludge via denitrification; however, which of the diverse nosZ-possessing organisms function as the major N2O sink in situ remains largely unknown. Here, nosZ genes and transcripts in wastewater microbiomes were analyzed with the group-specific qPCR assays designed de novo combining culture-based and computational approaches. A sewage sample was enriched in a batch reactor fed continuous stream of N2 containing 20-10,000 ppmv N2O with excess amount (10 mM) of acetate as the source of carbon and electrons, where 14 genera of potential N2O-reducers were identified. All available amino acid sequences of NosZ affiliated to these taxa were grouped into five subgroups (two clade I and three clade II groups), and primers/probe sets exclusively and comprehensively targeting the subgroups were designed and validated with in silico PCR. Four distinct activated sludge samples from three different wastewater treatment plants in Korea were analyzed with the qPCR assays and the results were validated with the shotgun metagenome analysis results. With these group-specific qPCR assays, the nosZ genes and transcripts of six additional activated sludge samples were analyzed and the results of the analyses clearly indicated the dominance of two clade II nosZ subgroups (Flavobacterium-like and Dechloromonas-like) among both nosZ gene and transcript pools.}, }
@article {pmid32785287, year = {2020}, author = {Giddings, LA and Chlipala, G and Kunstman, K and Green, S and Morillo, K and Bhave, K and Peterson, H and Driscoll, H and Maienschein-Cline, M}, title = {Characterization of an acid rock drainage microbiome and transcriptome at the Ely Copper Mine Superfund site.}, journal = {PloS one}, volume = {15}, number = {8}, pages = {e0237599}, pmid = {32785287}, issn = {1932-6203}, support = {P20 GM103449/GM/NIGMS NIH HHS/United States ; UL1 TR002003/TR/NCATS NIH HHS/United States ; }, mesh = {Acids/*chemistry ; Copper/chemistry ; Genetic Markers ; *Metagenome ; *Microbiota ; Minerals/chemistry ; *Mining ; Proteobacteria/*genetics/growth &amp; development/*metabolism ; *Transcriptome ; }, abstract = {The microbial oxidation of metal sulfides plays a major role in the formation of acid rock drainage (ARD). We aimed to broadly characterize the ARD at Ely Brook, which drains the Ely Copper Mine Superfund site in Vermont, USA, using metagenomics and metatranscriptomics to assess the metabolic potential and seasonal ecological roles of microorganisms in water and sediment. Using Centrifuge against the NCBI &quot;nt&quot; database, ~25% of reads in sediment and water samples were classified as acid-tolerant Proteobacteria (61 ± 4%) belonging to the genera Pseudomonas (2.6-3.3%), Bradyrhizobium (1.7-4.1%), and Streptomyces (2.9-5.0%). Numerous genes (12%) were differentially expressed between seasons and played significant roles in iron, sulfur, carbon, and nitrogen cycling. The most abundant RNA transcript encoded the multidrug resistance protein Stp, and most expressed KEGG-annotated transcripts were involved in amino acid metabolism. Biosynthetic gene clusters involved in secondary metabolism (BGCs, 449) as well as metal- (133) and antibiotic-resistance (8501) genes were identified across the entire dataset. Several antibiotic and metal resistance genes were colocalized and coexpressed with putative BGCs, providing insight into the protective roles of the molecules BGCs produce. Our study shows that ecological stimuli, such as metal concentrations and seasonal variations, can drive ARD taxa to produce novel bioactive metabolites.}, }
@article {pmid32778056, year = {2020}, author = {Volant, S and Lechat, P and Woringer, P and Motreff, L and Campagne, P and Malabat, C and Kennedy, S and Ghozlane, A}, title = {SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis.}, journal = {BMC bioinformatics}, volume = {21}, number = {1}, pages = {345}, pmid = {32778056}, issn = {1471-2105}, mesh = {Body Fluids/microbiology ; Child, Preschool ; *Classification ; Feces/microbiology ; Humans ; *Internet ; Metagenome ; Metagenomics/*methods ; Microbiota ; RNA, Ribosomal, 16S/genetics ; *Software ; *Statistics as Topic ; *User-Computer Interface ; Workflow ; }, abstract = {BACKGROUND: Comparing the composition of microbial communities among groups of interest (e.g., patients vs healthy individuals) is a central aspect in microbiome research. It typically involves sequencing, data processing, statistical analysis and graphical display. Such an analysis is normally obtained by using a set of different applications that require specific expertise for installation, data processing and in some cases, programming skills.<br><br>RESULTS: Here, we present SHAMAN, an interactive web application we developed in order to facilitate the use of (i) a bioinformatic workflow for metataxonomic analysis, (ii) a reliable statistical modelling and (iii) to provide the largest panel of interactive visualizations among the applications that are currently available. SHAMAN is specifically designed for non-expert users. A strong benefit is to use an integrated version of the different analytic steps underlying a proper metagenomic analysis. The application is freely accessible at http://shaman.pasteur.fr/ , and may also work as a standalone application with a Docker container (aghozlane/shaman), conda and R. The source code is written in R and is available at https://github.com/aghozlane/shaman . Using two different datasets (a mock community sequencing and a published 16S rRNA metagenomic data), we illustrate the strengths of SHAMAN in quickly performing a complete metataxonomic analysis.<br><br>CONCLUSIONS: With SHAMAN, we aim at providing the scientific community with a platform that simplifies reproducible quantitative analysis of metagenomic data.}, }
@article {pmid32776951, year = {2020}, author = {Gschwind, R and Fournier, T and Kennedy, S and Tsatsaris, V and Cordier, AG and Barbut, F and Butel, MJ and Wydau-Dematteis, S}, title = {Evidence for contamination as the origin for bacteria found in human placenta rather than a microbiota.}, journal = {PloS one}, volume = {15}, number = {8}, pages = {e0237232}, pmid = {32776951}, issn = {1932-6203}, mesh = {Adult ; Bacteria/genetics/*isolation &amp; purification ; Cesarean Section ; Chorionic Villi/*microbiology ; Chorionic Villi Sampling ; DNA, Bacterial/analysis/genetics ; Delivery, Obstetric ; Extraembryonic Membranes/*microbiology ; Female ; Humans ; Microbiota ; Placenta/*microbiology ; Pregnancy ; Specimen Handling ; Umbilical Cord/*microbiology ; }, abstract = {Until recently the in utero environment of pregnant women was considered sterile. Recent high-sensitivity molecular techniques and high-throughput sequencing lead to some evidence for a low-biomass microbiome associated with the healthy placenta. Other studies failed to reveal evidence for a consistent presence of bacteria using either culture or molecular based techniques. Comparing conflicting &quot;placental microbiome&quot; studies is complicated by the use of varied and inconsistent protocols. Given this situation, we undertook an evaluation of the in utero environment sterility using several controlled methods, in the same study, to evaluate the presence or absence of bacteria and to explain contradictions present in the literature. Healthy pregnant women (n = 38) were recruited in three maternity wards. Placenta were collected after cesarean section with or without Alexis® and vaginal delivery births. For this study we sampled fetal membranes, umbilical cord and chorionic villi. Bacterial presence was analyzed using bacterial culture and qPCR on 34 fetal membranes, umbilical cord and chorionic villi samples. Shotgun metagenomics was performed on seven chorionic villi samples. We showed that the isolation of meaningful quantities of viable bacteria or bacterial DNA was possible only outside the placenta (fetal membranes and umbilical cords) highlighting the importance of sampling methods in studying the in utero environment. Bacterial communities described by metagenomics analysis were similar in chorionic villi samples and in negative controls and were dependent on the database chosen for the analysis. We conclude that the placenta does not harbor a specific, consistent and functional microbiota.}, }
@article {pmid32774330, year = {2020}, author = {Khamis, FM and Ombura, FLO and Akutse, KS and Subramanian, S and Mohamed, SA and Fiaboe, KKM and Saijuntha, W and Van Loon, JJA and Dicke, M and Dubois, T and Ekesi, S and Tanga, CM}, title = {Insights in the Global Genetics and Gut Microbiome of Black Soldier Fly, Hermetia illucens: Implications for Animal Feed Safety Control.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1538}, pmid = {32774330}, issn = {1664-302X}, abstract = {The utilization of the black soldier fly (BSF) Hermetia illucens L. for recycling organic waste into high-quality protein and fat biomass for animal feeds has gained momentum worldwide. However, information on the genetic diversity and environmental implications on safety of the larvae is limited. This study delineates genetic variability and unravels gut microbiome complex of wild-collected and domesticated BSF populations from six continents using mitochondrial COI gene and 16S metagenomics. All sequences generated from the study linked to H. illucens accessions KM967419.1, FJ794355.1, FJ794361.1, FJ794367.1, KC192965.1, and KY817115.1 from GenBank. Phylogenetic analyses of the sequences generated from the study and rooted by GenBank accessions of Hermetia albitarsis Fabricius and Hermetia sexmaculata Macquart separated all samples into three branches, with H. illucens and H. sexmaculata being closely related. Genetic distances between H. illucens samples from the study and GenBank accessions of H. illucens ranged between 0.0091 and 0.0407 while H. sexmaculata and H. albitarsis samples clearly separated from all H. illucens by distances of 0.1745 and 0.1903, respectively. Genetic distance matrix was used to generate a principal coordinate plot that further confirmed the phylogenetic clustering. Haplotype network map demonstrated that Australia, United States 1 (Rhode Island), United States 2 (Colorado), Kenya, and China shared a haplotype, while Uganda shared a haplotype with GenBank accession KC192965 BSF from United States. All other samples analyzed had individual haplotypes. Out of 481,695 reads analyzed from 16S metagenomics, four bacterial families (Enterobactereaceae, Dysgonomonadaceae, Wohlfahrtiimonadaceae, and Enterococcaceae) were most abundant in the BSF samples. Alpha-diversity, as assessed by Shannon index, showed that the Kenyan and Thailand populations had the highest and lowest microbe diversity, respectively; while microbial diversity assessed through Bray Curtis distance showed United States 3 (Maysville) and Netherlands populations to be the most dissimilar. Our findings on genetic diversity revealed slight phylogeographic variation between BSF populations across the globe. The 16S data depicted larval gut bacterial families with economically important genera that might pose health risks to both animals and humans. This study recommends pre-treatment of feedstocks and postharvest measures of the harvested BSF larvae to minimize risk of pathogen contamination along the insect-based feed value chain.}, }
@article {pmid32772242, year = {2020}, author = {Guilin, Z and Pengyu, Z and Wei, L and Fengqi, H and Chen, F and Yu, Y and Yue, H and Yuting, T}, title = {Reduction of gut microbial diversity and short chain fatty acids in BALB/c mice exposure to microcystin-LR.}, journal = {Ecotoxicology (London, England)}, volume = {29}, number = {9}, pages = {1347-1357}, doi = {10.1007/s10646-020-02254-9}, pmid = {32772242}, issn = {1573-3017}, mesh = {Animals ; Biodiversity ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome/*drug effects ; Mice ; Mice, Inbred BALB C ; Microcystins/*toxicity ; }, abstract = {Gut microbiota has been shown to play critical roles in host health. The present study was to determine the toxicological effects of microcystin-LR (MCLR) on gut microbial community and metabolites using 16S rDNA sequencing and gas chromatography-mass spectrometry (GC-MS). MCLR was administered to BALB/c mice by gavage for eight weeks. Results of the microbial alpha-diversity (Sobs, Chao1, ACE and Shannon indexes) decreased in MCLR-treated group versus controls. Phylum Candidatus Saccharibacteria decreased significantly in MCLR-treated group versus controls. Correspondingly, more than thirties genera in relative abundance decreased, especially short chain fatty acid (SCFA)-producing bacteria (e.g., Alistipes and Ruminococcus). These results indicated that the gut microbial community structure was remarkably changed by MCLR. Furthermore, concentrations of SCFAs were significantly decreased after MCLR exposure (P < 0.01), where butyrate decreased as high as 4.9-fold. Consequently, sub-chronic exposure to MCLR could not only alter the microbial composition but metabolites. This study offered novel insights into the toxic mechanism of MCs from gut microbiota, and facilitated further clarification of risks to human health from MCs exposure.}, }
@article {pmid32763595, year = {2020}, author = {Freitas, L and Appolinario, L and Calegario, G and Campeão, M and Tschoeke, D and Garcia, G and Venancio, IM and Cosenza, CAN and Leomil, L and Bernardes, M and Albuquerque, AL and Thompson, C and Thompson, F}, title = {Glacial-interglacial transitions in microbiomes recorded in deep-sea sediments from the western equatorial Atlantic.}, journal = {The Science of the total environment}, volume = {746}, number = {}, pages = {140904}, doi = {10.1016/j.scitotenv.2020.140904}, pmid = {32763595}, issn = {1879-1026}, mesh = {Geologic Sediments ; Metagenome ; *Microbiota ; Oceans and Seas ; Phytoplankton ; }, abstract = {In the late Quaternary, glacial-interglacial transitions are marked by major environmental changes. Glacial periods in the western equatorial Atlantic (WEA) are characterized by high continental terrigenous input, which increases the proportion of terrestrial organic matter (e.g. lignin, alkanes), nutrients (e.g. iron and sulphur), and lower primary productivity. On the other hand, interglacials are characterized by lower continental contribution and maxima in primary productivity. Microbes can serve as biosensors of past conditions, but scarce information is available on deep-sea sediments in the WEA. The hypothesis put forward in this study is that past changes in climate conditions modulated the taxonomic/functional composition of microbes from deep sediment layers. To address this hypothesis, we collected samples from a marine sediment core located in the WEA, which covered the last 130 kyr. This region is influenced by the presence of the Amazon River plume, which outputs dissolved and particulate nutrients in vast oceanic regions, as well as the Parnaiba river plume. Core GL-1248 was analysed by shotgun metagenomics and geochemical analyses (alkane, lignin, perylene, sulphur). Two clusters (glacial and interglacial-deglacial) were found based on taxonomic and functional profiles of metagenomes. The interglacial period had a higher abundance of genes belonging to several sub-systems (e.g. DNA, RNA metabolism, cell division, chemotaxis, and respiration) that are consistent with a past environment with enhanced primary productivity. On the other hand, the abundance of Alcanivorax, Marinobacter, Kangiella and aromatic compounds that may serve as energy sources for these bacteria were higher in the glacial. The glacial period was enriched in genes for the metabolism of aromatic compounds, lipids, isoprenoids, iron, and Sulphur, consistent with enhanced fluvial input during the last glacial period. In contrast, interglacials have increased contents of more labile materials originating from phytoplankton (e.g. Prochlorococcus). This study provides new insights into the microbiome as climatic archives at geological timescales.}, }
@article {pmid32763188, year = {2020}, author = {Easteal, S and Arkell, RM and Balboa, RF and Bellingham, SA and Brown, AD and Calma, T and Cook, MC and Davis, M and Dawkins, HJS and Dinger, ME and Dobbie, MS and Farlow, A and Gwynne, KG and Hermes, A and Hoy, WE and Jenkins, MR and Jiang, SH and Kaplan, W and Leslie, S and Llamas, B and Mann, GJ and McMorran, BJ and McWhirter, RE and Meldrum, CJ and Nagaraj, SH and Newman, SJ and Nunn, JS and Ormond-Parker, L and Orr, NJ and Paliwal, D and Patel, HR and Pearson, G and Pratt, GR and Rambaldini, B and Russell, LW and Savarirayan, R and Silcocks, M and Skinner, JC and Souilmi, Y and Vinuesa, CG and ,  and Baynam, G}, title = {Equitable Expanded Carrier Screening Needs Indigenous Clinical and Population Genomic Data.}, journal = {American journal of human genetics}, volume = {107}, number = {2}, pages = {175-182}, doi = {10.1016/j.ajhg.2020.06.005}, pmid = {32763188}, issn = {1537-6605}, mesh = {Australia ; Genetic Variation/genetics ; Humans ; Metagenomics/*methods ; Population Groups/*genetics ; }, abstract = {Expanded carrier screening (ECS) for recessive monogenic diseases requires prior knowledge of genomic variation, including DNA variants that cause disease. The composition of pathogenic variants differs greatly among human populations, but historically, research about monogenic diseases has focused mainly on people with European ancestry. By comparison, less is known about pathogenic DNA variants in people from other parts of the world. Consequently, inclusion of currently underrepresented Indigenous and other minority population groups in genomic research is essential to enable equitable outcomes in ECS and other areas of genomic medicine. Here, we discuss this issue in relation to the implementation of ECS in Australia, which is currently being evaluated as part of the national Government's Genomics Health Futures Mission. We argue that significant effort is required to build an evidence base and genomic reference data so that ECS can bring significant clinical benefit for many Aboriginal and/or Torres Strait Islander Australians. These efforts are essential steps to achieving the Australian Government's objectives and its commitment &quot;to leveraging the benefits of genomics in the health system for all Australians.&quot; They require culturally safe, community-led research and community involvement embedded within national health and medical genomics programs to ensure that new knowledge is integrated into medicine and health services in ways that address the specific and articulated cultural and health needs of Indigenous people. Until this occurs, people who do not have European ancestry are at risk of being, in relative terms, further disadvantaged.}, }
@article {pmid32745120, year = {2020}, author = {Hilderbrand, RH and Keller, SR and Laperriere, SM and Santoro, AE and Cessna, J and Trott, R}, title = {Microbial communities can predict the ecological condition of headwater streams.}, journal = {PloS one}, volume = {15}, number = {8}, pages = {e0236932}, pmid = {32745120}, issn = {1932-6203}, mesh = {Archaea/classification/genetics/isolation &amp; purification ; Bacteria/classification/genetics/isolation &amp; purification ; Ecological Parameter Monitoring/*methods ; Ecosystem ; Environmental Monitoring/methods ; Geologic Sediments/microbiology ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; }, abstract = {Humanity's reliance on clean water and the ecosystem services provided makes identifying efficient and effective ways to assess the ecological condition of streams ever more important. We used high throughput sequencing of the 16S rRNA region to explore relationships between stream microbial communities, environmental attributes, and assessments of stream ecological condition. Bacteria and archaea in microbial community samples collected from the water column and from stream sediments during spring and summer were used to replicate standard assessments of ecological condition performed with benthic macroinvertebrate collections via the Benthic Index of Biotic Integrity (BIBI). Microbe-based condition assessments were generated at different levels of taxonomic resolution from phylum to OTU (Operational Taxonomic Units) in order to understand appropriate levels of taxonomic aggregation. Stream sediment microbial communities from both spring and summer were much better than the water column at replicating BIBI condition assessment results. Accuracies were as high as 100% on training data used to build the models and up to 80% on validation data used to assess predictions. Assessments using all OTUs usually had the highest accuracy on training data, but were lower on validation data due to overfitting. In contrast, assessments at the order-level had similar performance accuracy for validation data, and a reduced subset of orders also performed well, suggesting the method could be generalized to other watersheds. Subsets of the important orders responded similarly to environmental gradients compared to the entire community, where strong shifts in community structure occurred for known aquatic stressors such as pH, dissolved organic carbon, and nitrate nitrogen. The results suggest the stream microbes may be useful for assessing the ecological condition of streams and especially useful for stream restorations where many eukaryotic taxa have been eliminated due to prior degradation and are unable to recolonize.}, }
@article {pmid32735609, year = {2020}, author = {Steinert, RE and Rehman, A and Souto Lima, EJ and Agamennone, V and Schuren, FHJ and Gero, D and Schreiner, P and Vonlanthen, R and Ismaeil, A and Tzafos, S and Hosa, H and Vetter, D and Misselwitz, B and Bueter, M}, title = {Roux-en-Y gastric bypass surgery changes fungal and bacterial microbiota in morbidly obese patients-A pilot study.}, journal = {PloS one}, volume = {15}, number = {7}, pages = {e0236936}, pmid = {32735609}, issn = {1932-6203}, mesh = {Adult ; Bacteria/classification/genetics/isolation &amp; purification ; DNA, Intergenic ; Feces/microbiology ; Female ; Fungi/classification/genetics/isolation &amp; purification ; *Gastric Bypass ; *Gastrointestinal Microbiome/genetics/physiology ; Genes, Bacterial ; Genes, Fungal ; Humans ; Male ; Metagenomics ; Microbiota ; Middle Aged ; Mycobiome ; *Obesity, Morbid/microbiology/surgery ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The Roux-en-Y gastric bypass (RYGB) remains the most effective treatment for morbidly obese patients to lower body weight and improve glycemic control. There is recent evidence that the mycobiome (fungal microbiome) can aggravate disease severity in a number of diseases including inflammatory bowel disease (IBD), irritable bowel syndrome (IBS) and hepatitis; moreover, a dysbiotic fungal microbiota has been reported in the obese. We characterized fungal and bacterial microbial composition in fecal samples of 16 morbidly obese patients before and three months after RYGB surgery and compared with nine healthy controls. We found that RYGB surgery induced a clear alteration in structure and composition of the gut fungal and bacterial microbiota. Beta diversity analysis revealed significant differences in bacterial microbiota between obese patients before surgery and healthy controls (P < 0.005) and a significant, unidirectional shift in RYGB patients after surgery (P < 0.001 vs. before surgery). In contrast, there was no significant difference in fungal microbiota between groups but individually specific changes after RYGB surgery. Interestingly, RYGB surgery induced a significant reduction in fungal alpha diversity namely Chao1, Sobs, and Shannon diversity index (P<0.05, respectively) which contrasts the trend for uniform changes in bacteria towards increased richness and diversity post-surgery. We did not observe any inter-kingdom relations in RYGB patients but in the healthy control cohort and there were several correlations between fungi and bacteria and clinical parameters (P<0.05, respectively) that warrant further research. Our study identifies changes in intestinal fungal communities in RYGB patients that are distinct to changes in the bacterial microbiota.}, }
@article {pmid32734321, year = {2020}, author = {Perlińska-Lenart, U and Piłsyk, S and Gryz, E and Turło, J and Hilszczańska, D and Kruszewska, JS}, title = {Identification of bacteria and fungi inhabiting fruiting bodies of Burgundy truffle (Tuber aestivum Vittad.).}, journal = {Archives of microbiology}, volume = {202}, number = {10}, pages = {2727-2738}, pmid = {32734321}, issn = {1432-072X}, support = {OR-271.3.5.2017//the State Forests National Forest Holding/ ; }, mesh = {Ascomycota/*physiology ; Bacillus/classification/genetics/*isolation &amp; purification ; Basidiomycota/classification/genetics/*isolation &amp; purification ; Bradyrhizobiaceae/classification/genetics/*isolation &amp; purification ; DNA, Ribosomal/genetics ; Fruiting Bodies, Fungal/*physiology ; High-Throughput Nucleotide Sequencing ; Microbiota ; }, abstract = {Tuber species may be regarded as complex microhabitats hosting diverse microorganisms inside their fruiting bodies. Here, we investigated the structure of microbial communities inhabiting the gleba of wild growing (in stands) T. aestivum, using Illumina sequencing and culture-based methods. The two methods used in combination allowed to extract more information on complex microbiota of Tuber aestivum gleba. Analysis of the V3-V4 region of 16S rDNA identified nine phyla of bacteria present in the gleba of T. aestivum ascomata, mostly Proteobacteria from the family Bradyrhizobiaceae. Our results ideally match the earlier data for other Tuber species where the family Bradyrhizobiaceae was the most represented. The ITS1 region of fungal rDNA represented six alien fungal species belonging to three phyla. To complement the metagenomic analysis, cultivable fungi and bacteria were obtained from the gleba of the same T. aestivum fruiting bodies. The identified fungi mostly belong to the phylum Basidiomycota and same to Ascomycota. Analysis of cultivable bacteria revealed that all the specimens were colonized by different strains of Bacillus. Fungal community inhabiting T. aestivum fruiting bodies was never shown before.}, }
@article {pmid32724224, year = {2020}, author = {Vu, D and Groenewald, M and Verkley, G}, title = {Convolutional neural networks improve fungal classification.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {12628}, pmid = {32724224}, issn = {2045-2322}, abstract = {Sequence classification plays an important role in metagenomics studies. We assess the deep neural network approach for fungal sequence classification as it has emerged as a successful paradigm for big data classification and clustering. Two deep learning-based classifiers, a convolutional neural network (CNN) and a deep belief network (DBN) were trained using our recently released barcode datasets. Experimental results show that CNN outperformed the traditional BLAST classification and the most accurate machine learning based Ribosomal Database Project (RDP) classifier on datasets that had many of the labels present in the training datasets. When classifying an independent dataset namely the &quot;Top 50 Most Wanted Fungi&quot;, CNN and DBN assigned less sequences than BLAST. However, they could assign much more sequences than the RDP classifier. In terms of efficiency, it took the machine learning classifiers up to two seconds to classify a test dataset while it was 53 s for BLAST. The result of the current study will enable us to speed up the taxonomic assignments for the fungal barcode sequences generated at our institute as ~ 70% of them still need to be validated for public release. In addition, it will help to quickly provide a taxonomic profile for metagenomics samples.}, }
@article {pmid32717520, year = {2020}, author = {Flores-Orozco, D and Patidar, R and Levin, DB and Sparling, R and Kumar, A and Çiçek, N}, title = {Effect of mesophilic anaerobic digestion on the resistome profile of dairy manure.}, journal = {Bioresource technology}, volume = {315}, number = {}, pages = {123889}, doi = {10.1016/j.biortech.2020.123889}, pmid = {32717520}, issn = {1873-2976}, mesh = {Anaerobiosis ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/drug effects ; Genes, Bacterial ; *Manure ; Microbiota/*drug effects ; }, abstract = {The effect of mesophilic anaerobic digestion (AD) on the resistome profile of manures from two different dairy farms was evaluated using a metagenomic approach. A total of 187 unique Antibiotic resistance genes (ARGs) for 17 different classes of antibiotics were detected in raw (undigested) manures. The results indicate that regardless of the origin of the dairy manure, mesophilic AD was capable of reducing or enriching the relative abundance of some ARGs. The main driver of these changes was strongly correlated with the evolution of the microbial community during the AD process. Putative ARG hosts were suggested by analyses of the co-occurrence of microbial groups and ARGs. Finally, network analyses revealed that mesophilic AD could also reduce the co-occurrence of different groups of ARGs potentially located in the same genetic elements. Our results provide valuable insights into the microbial mechanisms driving the diversity and abundance of ARGs during mesophilic AD.}, }
@article {pmid32706816, year = {2020}, author = {Wolfe, AE and Moskowitz, JE and Franklin, CL and Wiemken, TL and Ericsson, AC}, title = {Interactions of Segmented Filamentous Bacteria (Candidatus Savagella) and bacterial drivers in colitis-associated colorectal cancer development.}, journal = {PloS one}, volume = {15}, number = {7}, pages = {e0236595}, pmid = {32706816}, issn = {1932-6203}, support = {U42 OD010918/OD/NIH HHS/United States ; K01 OD019924/OD/NIH HHS/United States ; }, mesh = {Animals ; Clostridiaceae/genetics/*pathogenicity ; Colitis/complications/*pathology ; Colorectal Neoplasms/etiology/*pathology ; Disease Models, Animal ; Feces/microbiology ; Female ; Gastrointestinal Microbiome ; Helicobacter/physiology ; Male ; Mice ; Mice, Inbred BALB C ; Mice, Knockout ; Neoplasm Staging ; RNA, Ribosomal, 16S/genetics/metabolism ; Smad3 Protein/deficiency/genetics ; }, abstract = {Colorectal cancer (CRC) risk is influenced by host genetics, sex, and the gut microbiota. Using a genetically susceptible mouse model of CRC induced via inoculation with pathobiont Helicobacter spp. and demonstrating variable tumor incidence, we tested the ability of the Th17-enhancing commensal Candidatus Savagella, more commonly denoted as Segmented Filamentous Bacteria (SFB), to influence the incidence and severity of colitis-associated CRC in male and female mice. To document the composition of the gut microbiota during CRC development and identify taxa associated with disease, fecal samples were collected before and throughout disease development and characterized via 16S rRNA sequencing. While there were no significant SFB-dependent effects on disease incidence or severity, SFB was found to exert a sex-dependent protective effect in male mice. Furthermore, SFB stabilized the GM against Helicobacter-induced changes post-inoculation, resulting in a shift in disease association from Helicobacter spp. to Escherichia coli. These data support sex-dependent SFB-mediated effects on CRC risk, and highlight the complex community dynamics within the GM during exposure to inflammatory pathobionts.}, }
@article {pmid32706331, year = {2020}, author = {Pérez-Cobas, AE and Gomez-Valero, L and Buchrieser, C}, title = {Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses.}, journal = {Microbial genomics}, volume = {6}, number = {8}, pages = {}, pmid = {32706331}, issn = {2057-5858}, abstract = {Metagenomics and marker gene approaches, coupled with high-throughput sequencing technologies, have revolutionized the field of microbial ecology. Metagenomics is a culture-independent method that allows the identification and characterization of organisms from all kinds of samples. Whole-genome shotgun sequencing analyses the total DNA of a chosen sample to determine the presence of micro-organisms from all domains of life and their genomic content. Importantly, the whole-genome shotgun sequencing approach reveals the genomic diversity present, but can also give insights into the functional potential of the micro-organisms identified. The marker gene approach is based on the sequencing of a specific gene region. It allows one to describe the microbial composition based on the taxonomic groups present in the sample. It is frequently used to analyse the biodiversity of microbial ecosystems. Despite its importance, the analysis of metagenomic sequencing and marker gene data is quite a challenge. Here we review the primary workflows and software used for both approaches and discuss the current challenges in the field.}, }
@article {pmid32705341, year = {2020}, author = {Gupta, P and Vakhlu, J and Sharma, YP and Imchen, M and Kumavath, R}, title = {Metagenomic insights into the fungal assemblages of the northwest Himalayan cold desert.}, journal = {Extremophiles : life under extreme conditions}, volume = {24}, number = {5}, pages = {749-758}, doi = {10.1007/s00792-020-01191-z}, pmid = {32705341}, issn = {1433-4909}, support = {DST-SERB/2018/001085//Department science and technology/ ; BT/PR11727/BCE/08/720/2008//DBT-SRF/ ; CSIR (9/100/0177) 2K13-EMR-I//CSIR-SRF/ ; }, mesh = {Antarctic Regions ; Arctic Regions ; Biodiversity ; *Fungi/genetics ; *Metagenome ; *Mycobiome ; }, abstract = {Psychrophilic fungi are a critical biotic component in cold deserts that serves a central role in nutrient recycling and biogeochemical cycles. Despite their ecological significance, culture-independent studies on psychrophilic mycobiome are limited. In the present study, the fungal diversity patterns across the Drass, an Indian cold desert in the Himalaya, were indexed by targeted amplicon pyrosequencing (ITS). In the Drass dataset, Ascomycota was represented by 92 genera, while 22 genera represented Basidiomycota. The most abundant genus was Conocybe (20.46%). Most of the identified genera were reported in the literature to be prolific extracellular hydrolytic enzyme producers. To identify whether the Drass fungal assemblages share similarities to other cold deserts, these were further compared to Antarctic and Arctic cold deserts. Comparative analysis across the three cold deserts indicated the dominance of Dikarya (Ascomycota and Basidiomycota). The observed alpha diversity, Shannon index as well as Pielou's evenness was highest in the Antarctic followed by Drass and Arctic datasets. The genera Malassezia, Preussia, Pseudogymnoascus, Cadophora, Geopora, Monodictys, Tetracladium, Titaea, Mortierella, and Cladosporium were common to all the cold deserts. Furthermore, Conocybe was represented predominantly in Drass. Interestingly, the genus Conocybe has not been previously reported from any other studies on Antarctic or Arctic biomes. To the best of our knowledge, this is the first fungal metagenome study in Drass soil. Our analysis shows that despite the similarities of low temperature among the cold deserts, a significant differential abundance of fungal communities prevails in the global cold deserts.}, }
@article {pmid32703166, year = {2020}, author = {Kondratenko, Y and Korobeynikov, A and Lapidus, A}, title = {CDSnake: Snakemake pipeline for retrieval of annotated OTUs from paired-end reads using CD-HIT utilities.}, journal = {BMC bioinformatics}, volume = {21}, number = {Suppl 12}, pages = {303}, doi = {10.1186/s12859-020-03591-6}, pmid = {32703166}, issn = {1471-2105}, support = {19-16-00049//Russian Science Foundation/ ; }, mesh = {Databases, Genetic ; *High-Throughput Nucleotide Sequencing ; Humans ; Microbiota/genetics ; *Molecular Sequence Annotation ; RNA, Ribosomal, 16S/genetics ; *Software ; }, abstract = {BACKGROUND: Illumina paired-end reads are often used for 16S analysis in metagenomic studies. Since DNA fragment size is usually smaller than the sum of lengths of paired reads, reads can be merged for downstream analysis. In spite of development of several tools for merging of paired-end reads, poor quality at the 3' ends within the overlapping region prevents the accurate combining of significant portion of read pairs. Recently CD-HIT-OTU-Miseq was presented as a new approach for 16S analysis using the paired-end reads, it completely avoids the reads merging process due to separate clustering of paired reads. CD-HIT-OTU-Miseq is a set of tools which are supposed to be successively launched by auxiliary shell scripts. This launch mode is not suitable for processing of big amounts of data generated in modern omics experiments. To solve this issue we created CDSnake - Snakemake pipeline utilizing CD-HIT tools for easier consecutive launch of CD-HIT-OTU-Miseq tools for complete processing of paired end reads in metagenomic studies. Usage of pipeline make 16S analysis easier due to one-command launch and helps to yield reproducible results.<br><br>RESULTS: We benchmarked our pipeline against two commonly used pipelines for OTU retrieval, incorporated into popular workflow for microbiome analysis, QIIME2 - DADA2 and deblur. Three mock datasets having highly overlapping paired-end 2 × 250 bp reads were used for benchmarking - Balanced, HMP, and Extreme. CDSnake outputted less OTUs than DADA2 and deblur. However, on Balanced and HMP datasets number of OTUs outputted by CDSnake was closer to real number of strains which were used for mock community generation, than those outputted by DADA2 and deblur. Though generally slower than other pipelines, CDSnake outputted higher total counts, preserving more information from raw data. Inheriting this properties from original CD-HIT-OTU-MiSeq utilities, CDSnake made their usage handier due to simple scalability, easier automated runs and other Snakemake benefits.<br><br>CONCLUSIONS: We developed Snakemake pipeline for OTU-MiSeq utilities, which simplified and automated data analysis. Benchmarking showed that this approach is capable to outperform popular tools in certain conditions.}, }
@article {pmid32694124, year = {2020}, author = {Sieradzki, ET and Koch, BJ and Greenlon, A and Sachdeva, R and Malmstrom, RR and Mau, RL and Blazewicz, SJ and Firestone, MK and Hofmockel, KS and Schwartz, E and Hungate, BA and Pett-Ridge, J}, title = {Measurement Error and Resolution in Quantitative Stable Isotope Probing: Implications for Experimental Design.}, journal = {mSystems}, volume = {5}, number = {4}, pages = {}, pmid = {32694124}, issn = {2379-5077}, abstract = {Quantitative stable isotope probing (qSIP) estimates isotope tracer incorporation into DNA of individual microbes and can link microbial biodiversity and biogeochemistry in complex communities. As with any quantitative estimation technique, qSIP involves measurement error, and a fuller understanding of error, precision, and statistical power benefits qSIP experimental design and data interpretation. We used several qSIP data sets-from soil and seawater microbiomes-to evaluate how variance in isotope incorporation estimates depends on organism abundance and resolution of the density fractionation scheme. We assessed statistical power for replicated qSIP studies, plus sensitivity and specificity for unreplicated designs. As a taxon's abundance increases, the variance of its weighted mean density declines. Nine fractions appear to be a reasonable trade-off between cost and precision for most qSIP applications. Increasing the number of density fractions beyond that reduces variance, although the magnitude of this benefit declines with additional fractions. Our analysis suggests that, if a taxon has an isotope enrichment of 10 atom% excess, there is a 60% chance that this will be detected as significantly different from zero (with alpha 0.1). With five replicates, isotope enrichment of 5 atom% could be detected with power (0.6) and alpha (0.1). Finally, we illustrate the importance of internal standards, which can help to calibrate per sample conversions of %GC to mean weighted density. These results should benefit researchers designing future SIP experiments and provide a useful reference for metagenomic SIP applications where both financial and computational limitations constrain experimental scope.IMPORTANCE One of the biggest challenges in microbial ecology is correlating the identity of microorganisms with the roles they fulfill in natural environmental systems. Studies of microbes in pure culture reveal much about their genomic content and potential functions but may not reflect an organism's activity within its natural community. Culture-independent studies supply a community-wide view of composition and function in the context of community interactions but often fail to link the two. Quantitative stable isotope probing (qSIP) is a method that can link the identity and functional activity of specific microbes within a naturally occurring community. Here, we explore how the resolution of density gradient fractionation affects the error and precision of qSIP results, how they may be improved via additional experimental replication, and discuss cost-benefit balanced scenarios for SIP experimental design.}, }
@article {pmid32670226, year = {2020}, author = {Gubelit, YI and Grossart, HP}, title = {New Methods, New Concepts: What Can Be Applied to Freshwater Periphyton?.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1275}, pmid = {32670226}, issn = {1664-302X}, abstract = {Microbial interactions play an essential role in aquatic ecosystems and are of the great interest for both marine and freshwater ecologists. Recent development of new technologies and methods allowed to reveal many functional mechanisms and create new concepts. Yet, many fundamental aspects of microbial interactions have been almost exclusively studied for marine pelagic and benthic ecosystems. These studies resulted in a formulation of the Black Queen Hypothesis, a development of the phycosphere concept for pelagic communities, and a realization of microbial communication as a key mechanism for microbial interactions. In freshwater ecosystems, especially for periphyton communities, studies focus mainly on physiology, biodiversity, biological indication, and assessment, but the many aspects of microbial interactions are neglected to a large extent. Since periphyton plays a great role for aquatic nutrient cycling, provides the basis for water purification, and can be regarded as a hotspot of microbial biodiversity, we highlight that more in-depth studies on microbial interactions in periphyton are needed to improve our understanding on functioning of freshwater ecosystems. In this paper we first present an overview on recent concepts (e.g., the &quot;Black Queen Hypothesis&quot;) derived from state-of-the-art OMICS methods including metagenomics, metatranscriptomics, and metabolomics. We then point to the avenues how these methods can be applied for future studies on biodiversity and the ecological role of freshwater periphyton, a yet largely neglected component of many freshwater ecosystems.}, }
@article {pmid32648690, year = {2019}, author = {Deaton, J and Yu, FB and Quake, SR}, title = {Mini-Metagenomics and Nucleotide Composition Aid the Identification and Host Association of Novel Bacteriophage Sequences.}, journal = {Advanced biosystems}, volume = {3}, number = {11}, pages = {e1900108}, doi = {10.1002/adbi.201900108}, pmid = {32648690}, issn = {2366-7478}, mesh = {Bacteriophages/*genetics/isolation &amp; purification ; *Biodiversity ; *Genome, Viral ; *Metagenomics ; *Sequence Analysis, DNA ; }, abstract = {A broad spectrum of metagenomic and single cell sequencing techniques have become popular for dissecting environmental microbial diversity, leading to the characterization of thousands of novel microbial lineages. In addition to recovering bacterial and archaeal genomes, metagenomic assembly can also produce genomes of viruses that infect microbial cells. Because of their diversity, lack of marker genes, and small genome size, identifying novel bacteriophage sequences from metagenomic data is often challenging, especially when the objective is to establish phage-host relationships. The present work describes a computational approach that uses supervised learning to classify metagenomic contigs as phage or non-phage as well as assigning phage taxonomy based on tetranucleotide frequencies. Furthermore, the method assigns phage-host relationships using co-occurrence statistics derived from a recently developed mini-metagenomic experimental technique. This work evaluates method performance at identifying viral contigs and predicting taxonomic classification using publicly available references. Then, using two mini-metagenomic datasets, over 100 novel phage contigs from hot spring samples of Yellowstone National Park are identified and assigned to putative microbial hosts. Results of this work demonstrate the value of combining viral sequence identification with mini-metagenomic experimental methods to understand the microbial ecosystem.}, }
@article {pmid32645030, year = {2020}, author = {Vancuren, SJ and Dos Santos, SJ and Hill, JE and , }, title = {Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling.}, journal = {PloS one}, volume = {15}, number = {7}, pages = {e0235682}, pmid = {32645030}, issn = {1932-6203}, support = {//CIHR/Canada ; }, mesh = {Bacteria/genetics ; Chaperonin 60/*genetics ; DNA Barcoding, Taxonomic/*methods ; Female ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Vagina/microbiology ; }, abstract = {Amplification and sequencing of conserved genetic barcodes such as the cpn60 gene is a common approach to determining the taxonomic composition of microbiomes. Exact sequence variant calling has been proposed as an alternative to previously established methods for aggregation of sequence reads into operational taxonomic units (OTU). We investigated the utility of variant calling for cpn60 barcode sequences and determined the minimum sequence length required to provide species-level resolution. Sequence data from the 5´ region of the cpn60 barcode amplified from the human vaginal microbiome (n = 45), and a mock community were used to compare variant calling to de novo assembly of reads, and mapping to a reference sequence database in terms of number of OTU formed, and overall community composition. Variant calling resulted in microbiome profiles that were consistent in apparent composition to those generated with the other methods but with significant logistical advantages. Variant calling is rapid, achieves high resolution of taxa, and does not require reference sequence data. Our results further demonstrate that 150 bp from the 5´ end of the cpn60 barcode sequence is sufficient to provide species-level resolution of microbiota.}, }
@article {pmid32633756, year = {2020}, author = {Tovo, A and Menzel, P and Krogh, A and Cosentino Lagomarsino, M and Suweis, S}, title = {Taxonomic classification method for metagenomics based on core protein families with Core-Kaiju.}, journal = {Nucleic acids research}, volume = {48}, number = {16}, pages = {e93}, pmid = {32633756}, issn = {1362-4962}, mesh = {Bacteria/*classification/genetics ; Computational Biology ; DNA, Bacterial/genetics ; Databases, Protein ; Gastrointestinal Microbiome/*genetics ; Genetic Markers ; Humans ; *Metagenome ; Metagenomics/*methods ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {Characterizing species diversity and composition of bacteria hosted by biota is revolutionizing our understanding of the role of symbiotic interactions in ecosystems. Determining microbiomes diversity implies the assignment of individual reads to taxa by comparison to reference databases. Although computational methods aimed at identifying the microbe(s) taxa are available, it is well known that inferences using different methods can vary widely depending on various biases. In this study, we first apply and compare different bioinformatics methods based on 16S ribosomal RNA gene and shotgun sequencing to three mock communities of bacteria, of which the compositions are known. We show that none of these methods can infer both the true number of taxa and their abundances. We thus propose a novel approach, named Core-Kaiju, which combines the power of shotgun metagenomics data with a more focused marker gene classification method similar to 16S, but based on emergent statistics of core protein domain families. We thus test the proposed method on various mock communities and we show that Core-Kaiju reliably predicts both number of taxa and abundances. Finally, we apply our method on human gut samples, showing how Core-Kaiju may give more accurate ecological characterization and a fresh view on real microbiomes.}, }
@article {pmid32632193, year = {2020}, author = {Keohane, DM and Ghosh, TS and Jeffery, IB and Molloy, MG and O'Toole, PW and Shanahan, F}, title = {Microbiome and health implications for ethnic minorities after enforced lifestyle changes.}, journal = {Nature medicine}, volume = {26}, number = {7}, pages = {1089-1095}, doi = {10.1038/s41591-020-0963-8}, pmid = {32632193}, issn = {1546-170X}, mesh = {Adult ; Chronic Disease/*epidemiology ; Ethnic Groups/genetics ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics/immunology ; Genetics, Population ; Humans ; Immune System/*immunology/microbiology ; Ireland/epidemiology ; *Life Style ; Male ; Metagenomics/methods ; Microbiota/genetics/immunology ; Phylogeny ; Roma/genetics ; Transients and Migrants ; }, abstract = {Modern lifestyles increase the risk of chronic diseases, in part by modifying the microbiome, but the health effects of lifestyles enforced on ethnic minorities are understudied1-3. Lifestyle affects the microbiome early in life, when the microbiome is assembled and the immune system is undergoing maturation4-6. Moreover, the influence of lifestyle has been separated from genetic and geographic factors by studies of genetically similar populations and ethnically distinct groups living in the same geographic location7-11. The lifestyle of Irish Travellers, an ethnically distinct subpopulation, changed with legislation in 2002 that effectively ended nomadism and altered their living conditions. Comparative metagenomics of gut microbiomes shows that Irish Travellers retain a microbiota similar to that of non-industrialized societies. Their microbiota is associated with non-dietary factors and is proportionately linked with risk of microbiome-related metabolic disease. Our findings suggest there are microbiome-related public health implications when ethnic minorities are pressured to change lifestyles.}, }
@article {pmid32621033, year = {2020}, author = {Ramos, RT and Sodré, CS and de Sousa Rodrigues, PMGR and da Silva, AMP and Fuly, MS and Dos Santos, HF and Gonçalves, LS and de Carvalho Ferreira, D and Ribeiro, MG}, title = {High-throughput nucleotide sequencing for bacteriome studies in oral squamous cell carcinoma: a systematic review.}, journal = {Oral and maxillofacial surgery}, volume = {24}, number = {4}, pages = {387-401}, doi = {10.1007/s10006-020-00873-4}, pmid = {32621033}, issn = {1865-1569}, mesh = {*Carcinoma, Squamous Cell/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; *Microbiota/genetics ; *Mouth Neoplasms/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {PURPOSE: Dysbiosis has been identified in oral squamous cell carcinoma (OSCC). The aim of this study was to carry out a systematic review of an electronic research that was carried out on articles published between January 2008 and September 2018.<br><br>METHODS: Eight studies were selected after applying the inclusion and exclusion criteria.<br><br>RESULTS: All articles targeted the hypervariable regions of the 16S rRNA gene. At the phylum level, it was found reduction of Bacteroidetes (2/8 studies) and increase of Firmicutes (2/8 studies). At the genus level, Rothia increased (1/8 studies) and decreased (2/8 studies) in tumor samples, and Streptococcus also was found increased (3/8 studies) and reduced (3/8 studies). Fusobacterium only increased in OSCC samples (3/8 studies). At species level, an increase in F. nucleatum subsp. polymorphum was more associated to OSCC (2/8 studies) than with controls, as was P. aeruginosa (3/8 studies).<br><br>CONCLUSION: In summary, the results corroborated dysbiosis in OSCC patients, with enrichment of microbial taxa that are associated with inflammation and production of acetaldehyde. However, variations of study design and sample size were observed among the studies, as well as a shortage of more detailed analyses of possible correlations between risk habits and OSCC. This lack of more detailed analysis may be the cause of the inconsistencies in regard of the alterations reported for certain genera and species. In conclusion, there is an association between OSCC and oral microbiota dysbiosis, but its role in oral carcinogenesis needs to be clarified in more detail.}, }
@article {pmid32615432, year = {2020}, author = {Yang, L and Hou, K and Zhang, B and Ouyang, C and Lin, A and Xu, S and Ke, D and Fang, L and Chen, Q and Wu, J and Yan, C and Lian, Y and Jiang, T and He, J and Wang, H and Fu, Y and Xiao, C and Chen, Z}, title = {Preservation of the fecal samples at ambient temperature for microbiota analysis with a cost-effective and reliable stabilizer EffcGut.}, journal = {The Science of the total environment}, volume = {741}, number = {}, pages = {140423}, doi = {10.1016/j.scitotenv.2020.140423}, pmid = {32615432}, issn = {1879-1026}, mesh = {Cost-Benefit Analysis ; Feces ; Humans ; *Microbiota ; RNA, Ribosomal, 16S ; *Specimen Handling ; Temperature ; }, abstract = {With the increasing researches on the role of gut microbiota in human health and disease, appropriate storage method of fecal samples at ambient temperature would conveniently guarantee the precise and reliable microbiota results. Nevertheless, less choice of stabilizer that is cost-efficient and feasible to be used in longer preservation period obstructed the large-scale metagenomics studies. Here, we evaluated the efficacy of a guanidine isothiocyanate-based reagent method EffcGut and compared it with the other already used storage method by means of 16S rRNA gene sequencing technology. We found that guanidine isothiocyanate-based reagent method at ambient temperature was not inferior to OMNIgene·GUT OM-200 and it could retain the similar bacterial community as that of -80 °C within 24 weeks. Furthermore, bacterial diversity and community structure difference were compared among different sample fraction (supernatant, suspension and precipitate) preserved in EffcGut and -80 °C. We found that supernatant under the preservation of EffcGut retained the similar community structure and composition as that of the low temperature preservation method.}, }
@article {pmid32605604, year = {2020}, author = {Hou, J and Sievert, SM and Wang, Y and Seewald, JS and Natarajan, VP and Wang, F and Xiao, X}, title = {Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {102}, pmid = {32605604}, issn = {2049-2618}, support = {DY135-B2-12//China Ocean Mineral Resources Research and Development Association (CN)/International ; 91751205//National Natural Science Foundation of China/International ; 41530967//National Natural Science Foundation of China/International ; 41921006//National Natural Science Foundation of China/International ; KEXUE2019GZ06//Senior User Project of RV KEXUE/International ; OCE-1136727//US National Science Foundation/International ; }, abstract = {BACKGROUND: Deep-sea hydrothermal vents are highly productive biodiversity hotspots in the deep ocean supported by chemosynthetic microorganisms. Prominent features of these systems are sulfide chimneys emanating high-temperature hydrothermal fluids. While several studies have investigated the microbial diversity in both active and inactive sulfide chimneys that have been extinct for up to thousands of years, little is known about chimneys that have ceased activity more recently, as well as the microbial succession occurring during the transition from active to inactive chimneys.<br><br>RESULTS: Genome-resolved metagenomics was applied to an active and a recently extinct (~ 7 years) sulfide chimney from the 9-10° N hydrothermal vent field on the East Pacific Rise. Full-length 16S rRNA gene and a total of 173 high-quality metagenome assembled genomes (MAGs) were retrieved for comparative analysis. In the active chimney (L-vent), sulfide- and/or hydrogen-oxidizing Campylobacteria and Aquificae with the potential for denitrification were identified as the dominant community members and primary producers, fixing carbon through the reductive tricarboxylic acid (rTCA) cycle. In contrast, the microbiome of the recently extinct chimney (M-vent) was largely composed of heterotrophs from various bacterial phyla, including Delta-/Beta-/Alphaproteobacteria and Bacteroidetes. Gammaproteobacteria were identified as the main primary producers, using the oxidation of metal sulfides and/or iron oxidation coupled to nitrate reduction to fix carbon through the Calvin-Benson-Bassham (CBB) cycle. Further analysis revealed a phylogenetically distinct Nitrospirae cluster that has the potential to oxidize sulfide minerals coupled to oxygen and/or nitrite reduction, as well as for sulfate reduction, and that might serve as an indicator for the early stages of chimneys after venting has ceased.<br><br>CONCLUSIONS: This study sheds light on the composition, metabolic functions, and succession of microbial communities inhabiting deep-sea hydrothermal vent sulfide chimneys. Collectively, microbial succession during the life span of a chimney could be described to proceed from a &quot;fluid-shaped&quot; microbial community in newly formed and actively venting chimneys supported by the oxidation of reductants in the hydrothermal fluid to a &quot;mineral-shaped&quot; community supported by the oxidation of minerals after hydrothermal activity has ceased. Remarkably, the transition appears to occur within the first few years, after which the communities stay stable for thousands of years. Video Abstract.}, }
@article {pmid32601270, year = {2020}, author = {Fremin, BJ and Sberro, H and Bhatt, AS}, title = {MetaRibo-Seq measures translation in microbiomes.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {3268}, pmid = {32601270}, issn = {2041-1723}, support = {P50 AG047366/AG/NIA NIH HHS/United States ; }, mesh = {Metagenomics ; Microbiota/*genetics ; Protein Biosynthesis/genetics ; RNA-Seq/*methods ; }, abstract = {No method exists to measure large-scale translation of genes in uncultured organisms in microbiomes. To overcome this limitation, we develop MetaRibo-Seq, a method for simultaneous ribosome profiling of tens to hundreds of organisms in microbiome samples. MetaRibo-Seq was benchmarked against gold-standard Ribo-Seq in a mock microbial community and applied to five different human fecal samples. Unlike RNA-Seq, Ribo-Seq signal of a predicted gene suggests it encodes a translated protein. We demonstrate two applications of this technique: First, MetaRibo-Seq identifies small genes, whose identification until now has been challenging. For example, MetaRibo-Seq identifies 2,091 translated, previously unannotated small protein families from five fecal samples, more than doubling the number of small proteins predicted to exist in this niche. Second, the combined application of RNA-Seq and MetaRibo-Seq identifies differences in the translation of transcripts. In summary, MetaRibo-Seq enables comprehensive translational profiling in microbiomes and identifies previously unannotated small proteins.}, }
@article {pmid32598884, year = {2020}, author = {Zuo, T and Zhan, H and Zhang, F and Liu, Q and Tso, EYK and Lui, GCY and Chen, N and Li, A and Lu, W and Chan, FKL and Chan, PKS and Ng, SC}, title = {Alterations in Fecal Fungal Microbiome of Patients With COVID-19 During Time of Hospitalization until Discharge.}, journal = {Gastroenterology}, volume = {159}, number = {4}, pages = {1302-1310.e5}, doi = {10.1053/j.gastro.2020.06.048}, pmid = {32598884}, issn = {1528-0012}, mesh = {Adult ; Aged ; Aspergillus flavus/genetics/isolation &amp; purification ; Aspergillus niger/genetics/isolation &amp; purification ; Betacoronavirus ; Candida/genetics/isolation &amp; purification ; Candida albicans/genetics/isolation &amp; purification ; Case-Control Studies ; Community-Acquired Infections/microbiology ; Coronavirus Infections/*microbiology ; DNA, Fungal/analysis ; Feces/*microbiology ; Female ; Fungi/genetics/*isolation &amp; purification ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics ; Middle Aged ; *Mycobiome ; Nasopharynx/virology ; Pandemics ; Patient Discharge ; Pneumonia/microbiology ; Pneumonia, Viral/*microbiology ; Time Factors ; Young Adult ; }, abstract = {BACKGROUND &amp; AIMS: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects intestinal cells, and might affect the intestinal microbiota. We investigated changes in the fecal fungal microbiomes (mycobiome) of patients with SARS-CoV-2 infection during hospitalization and on recovery.<br><br>METHODS: We performed deep shotgun metagenomic sequencing analysis of fecal samples from 30 patients with coronavirus disease 2019 (COVID-19) in Hong Kong, from February 5 through May 12, 2020. Fecal samples were collected 2 to 3 times per week from time of hospitalization until discharge. We compared fecal mycobiome compositions of patients with COVID-19 with those from 9 subjects with community-acquired pneumonia and 30 healthy individuals (controls). We assessed fecal mycobiome profiles throughout time of hospitalization until clearance of SARS-CoV-2 from nasopharyngeal samples.<br><br>RESULTS: Patients with COVID-19 had significant alterations in their fecal mycobiomes compared with controls, characterized by enrichment of Candia albicans and a highly heterogeneous mycobiome configuration, at time of hospitalization. Although fecal mycobiomes of 22 patients with COVID-19 did not differ significantly from those of controls during times of hospitalization, 8 of 30 patients with COVID-19 had continued significant differences in fecal mycobiome composition, through the last sample collected. The diversity of the fecal mycobiome of the last sample collected from patients with COVID-19 was 2.5-fold higher than that of controls (P < .05). Samples collected at all timepoints from patients with COVID-19 had increased proportions of opportunistic fungal pathogens, Candida albicans, Candida auris, and Aspergillus flavus compared with controls. Two respiratory-associated fungal pathogens, A. flavus and Aspergillus niger, were detected in fecal samples from a subset of patients with COVID-19, even after clearance of SARS-CoV-2 from nasopharyngeal samples and resolution of respiratory symptoms.<br><br>CONCLUSIONS: In a pilot study, we found heterogeneous configurations of the fecal mycobiome, with enrichment of fungal pathogens from the genera Candida and Aspergillus, during hospitalization of 30 patients with COVID-19 compared with controls. Unstable gut mycobiomes and prolonged dysbiosis persisted in a subset of patients with COVID-19 up to 12 days after nasopharyngeal clearance of SARS-CoV-2. Studies are needed to determine whether alterations in intestinal fungi contribute to or result from SARS-CoV-2 infection, and the effects of these changes in disease progression.}, }
@article {pmid32589643, year = {2020}, author = {Ajene, IJ and Khamis, FM and van Asch, B and Pietersen, G and Rasowo, BA and Ombura, FL and Wairimu, AW and Akutse, KS and Sétamou, M and Mohamed, S and Ekesi, S}, title = {Microbiome diversity in Diaphorina citri populations from Kenya and Tanzania shows links to China.}, journal = {PloS one}, volume = {15}, number = {6}, pages = {e0235348}, pmid = {32589643}, issn = {1932-6203}, mesh = {Animals ; *Biodiversity ; China ; Drug Resistance, Microbial/genetics ; Hemiptera/*microbiology ; Insect Vectors/microbiology ; Kenya ; *Microbiota/drug effects/genetics ; *Phylogeny ; Plant Diseases/microbiology ; Sequence Analysis ; Symbiosis ; Tanzania ; }, abstract = {The Asian citrus psyllid (Diaphorina citri) is a key pest of Citrus spp. worldwide, as it acts as a vector for &quot;Candidatus Liberibacter asiaticus (Las)&quot;, the bacterial pathogen associated with the destructive Huanglongbing (HLB) disease. Recent detection of D. citri in Africa and reports of Las-associated HLB in Ethiopia suggest that the citrus industry on the continent is under imminent threat. Endosymbionts and gut bacteria play key roles in the biology of arthropods, especially with regards to vector-pathogen interactions and resistance to antibiotics. Thus, we aim to profile the bacterial genera and to identify antibiotic resistance genes within the microbiome of different populations worldwide of D. citri. The metagenome of D. citri was sequenced using the Oxford Nanopore full-length 16S metagenomics protocol, and the &quot;What's in my pot&quot; (WIMP) analysis pipeline. Microbial diversity within and between D. citri populations was assessed, and antibiotic resistance genes were identified using the WIMP-ARMA workflow. The most abundant genera were key endosymbionts of D. citri (&quot;Candidatus Carsonella&quot;, &quot;Candidatus Profftella&quot;, and Wolbachia). The Shannon diversity index showed that D. citri from Tanzania had the highest diversity of bacterial genera (1.92), and D. citri from China had the lowest (1.34). The Bray-Curtis dissimilarity showed that China and Kenya represented the most diverged populations, while the populations from Kenya and Tanzania were the least diverged. The WIMP-ARMA analyses generated 48 CARD genes from 13 bacterial species in each of the populations. Spectinomycin resistance genes were the most frequently found, with an average of 65.98% in all the populations. These findings add to the knowledge on the diversity of the African D. citri populations and the probable introduction source of the psyllid in these African countries.}, }
@article {pmid32588084, year = {2020}, author = {Zambounis, A and Ganopoulos, I and Tsaftaris, A and Valasiadis, D and Madesis, P}, title = {Metagenomics analysis of fungal communities associated with postharvest diseases in pear fruits under the effect of management practices.}, journal = {Archives of microbiology}, volume = {202}, number = {9}, pages = {2391-2400}, doi = {10.1007/s00203-020-01960-6}, pmid = {32588084}, issn = {1432-072X}, mesh = {*Food Microbiology ; Fruit/*microbiology ; *Fungi/classification/drug effects/genetics ; Fungicides, Industrial/pharmacology ; *Metagenomics ; *Mycobiome/drug effects/genetics ; Pyrus/*microbiology ; }, abstract = {An amplicon metagenomic approach based on the ITS1 region of fungal rDNA was employed to identify the composition of fungal communities associated with diseases of pear fruits during postharvest storage. The sampled fruits were harvested at an orchard using routine management practices involving treatments with various chemical fungicides and were transferred to a storage packinghouse. Effective tags of reading sequences clustered into 53 OTUs whereas Ascomycota was the dominant phylum (83.4%) followed by Basidiomycota (15.8%). Our results revealed that four genera, Penicillium, Rhodotorula, Alternaria and Cladosporium were the most abundant representing 59-95% of the relative abundance per sample. The interruption of chemical treatments during the last month before harvest altered the structure of the fungal community of fruits among untreated and treated samples, mainly in cases of relative abundance of Penicillium and Rhodotorula genera. We hypothesize that various antagonistic interactions might occur on fruit surfaces among the detected fungal genera whose relative abundances were affected by fungicide treatments. Interestingly, some common pre- and postharvest pear fungal pathogens were either less present (such as Moniliana), or undetected (such as Aspergillus, Venturia and Septoria) in untreated and treated samples.}, }
@article {pmid32556390, year = {2020}, author = {Khan, S and Chen, N and Zhang, C and Wang, L and Han, C and Lu, K and Li, Y and Rafiq, M and Iqbal, A and Zhao, C}, title = {Soil fungal taxonomic diversity along an elevation gradient on the semi-arid Xinglong Mountain, Northwest China.}, journal = {Archives of microbiology}, volume = {202}, number = {8}, pages = {2291-2302}, doi = {10.1007/s00203-020-01948-2}, pmid = {32556390}, issn = {1432-072X}, support = {31522013//National Natural Science Foundation of China/ ; }, mesh = {*Biodiversity ; China ; Fungi/*classification ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Elevation gradients, often regarded as &quot;natural experiments or laboratories&quot;, can be used to study changes in the distribution of microbial diversity related to changes in environmental conditions that typically occur over small geographical scales. We exploited this feature by characterizing fungal composition and diversity along an elevation gradient on Xinglong Mountain, northwest China. For this, we used MiSeq sequencing to obtain fungal sequences and clustered them into operational taxonomic units (OTUs). In total, we obtained 1,203,302 reads, 133,700 on average in each sample of soil collected at three selected elevations (2807, 3046, and 3536 m). The reads were assigned to 2192 OTUs. Inconsistent variations were observed in fungal alpha-diversity in samples from the three elevations. However, Principal Coordinate Analysis based on Bray-Curtis and UniFrac (weighted and unweighted) distance metrics revealed that fungal communities in soil samples from 3046 and 3536 m elevations were most similar. Principal Component Analysis based on relative abundances of shared OTUs confirmed that OTUs in samples from 3536 m elevation were more closely related to OTUs from 3046 m than samples from 2807 m elevation. Ascomycota, Basidiomycota, Glomeromycota, Cercozoa and Chytridiomycota were the most abundant fungal phyla across the elevation gradient. Our study also provides valuable indications of relations between fungal communities and an array of soil chemical properties, and variations in fungal taxonomic diversity across a substantial elevation gradient.}, }
@article {pmid32555605, year = {2020}, author = {Shamsaddini, A and Dadkhah, K and Gillevet, PM}, title = {BiomMiner: An advanced exploratory microbiome analysis and visualization pipeline.}, journal = {PloS one}, volume = {15}, number = {6}, pages = {e0234860}, pmid = {32555605}, issn = {1932-6203}, mesh = {Animals ; Bacteria/*classification/genetics ; Computational Biology/*methods ; Datasets as Topic ; *Gastrointestinal Microbiome ; Metagenomics/*methods ; Mice ; RNA, Ribosomal, 16S/genetics ; *Software ; }, abstract = {Current microbiome applications require substantial bioinformatics expertise to execute. As microbiome clinical diagnostics are being developed, there is a critical need to implement computational tools and applications that are user-friendly for the medical community to understand microbiome correlation with the health. To address this need, we have developed BiomMiner (pronounced as &quot;biominer&quot;), an automated pipeline that provides a comprehensive analysis of microbiome data. The pipeline finds taxonomic signatures of microbiome data and compiles actionable clinical report that allows clinicians and biomedical scientists to efficiently perform statistical analysis and data mining on the large microbiome datasets. BiomMiner generates web-enabled visualization of the analysis results and is specifically designed to facilitate the use of microbiome datasets in clinical applications.}, }
@article {pmid32554026, year = {2020}, author = {Appolinario, LR and Tschoeke, D and Calegario, G and Barbosa, LH and Moreira, MA and Albuquerque, ALS and Thompson, CC and Thompson, FL}, title = {Oil leakage induces changes in microbiomes of deep-sea sediments of Campos Basin (Brazil).}, journal = {The Science of the total environment}, volume = {740}, number = {}, pages = {139556}, doi = {10.1016/j.scitotenv.2020.139556}, pmid = {32554026}, issn = {1879-1026}, mesh = {Brazil ; Geologic Sediments ; Hydrocarbons ; Metagenomics ; *Microbiota ; *Petroleum ; }, abstract = {The Campos Basin (100,000 km2) is located on the continental shelf of southeastern Brazil. Despite the significant oil and gas industrial activities underway in the Campos Basin, scarce information is available regarding the hydrocarbon contents and microbial communities in the deep-sea sediments. To gain new insights on these aspects, we first obtained deep-sea sediment samples with different degrees of oil exposure. We obtained samples from a seabed fissure (N = 28), surroundings (250 m to 500 m from the fissure; N = 24), and a control area (N = 4). We used shotgun metagenomics to characterize the taxonomic and metabolic diversity and analyzed biogeochemical parameters (metal and oil concentration) of all samples. The high levels of unresolved complex mixture of hydrocarbons in the fissure indicate a potentially recent petrogenic contribution in these sediments. The fissure area was found to have a higher abundance of hydrocarbonoclastic bacterial genera and hydrocarbon degradation genes. These bacteria may be used as biosensors of sediment contamination. The effects of oil contamination, mainly around the fissure, are less clear at 250 m and 500 m, suggesting that the surroundings may not have been heavily affected by the oil leakage. Our study demonstrates that metagenomics can disclose biosensors for environmental monitoring.}, }
@article {pmid32535444, year = {2020}, author = {Barak, H and Brenner, A and Sivan, A and Kushmaro, A}, title = {Temporal distribution of microbial community in an industrial wastewater treatment system following crash and during recovery periods.}, journal = {Chemosphere}, volume = {258}, number = {}, pages = {127271}, doi = {10.1016/j.chemosphere.2020.127271}, pmid = {32535444}, issn = {1879-1298}, mesh = {Biodegradation, Environmental ; Bioreactors/*microbiology ; Gammaproteobacteria/drug effects/genetics ; Industrial Waste/analysis ; Membranes, Artificial ; Metagenomics ; Microbiota/*drug effects/genetics ; Sewage/microbiology ; *Waste Water/chemistry/microbiology ; Water Purification/*methods ; }, abstract = {Water and soil contamination by industrial wastes is a global concern. Biological treatment of industrial wastewater using bioreactors allows the removal of organic matter and nutrients and enables either reuse or safe discharge. Wastewater bioremediation depends in part on the microbial communities present in the bioreactor. To ascertain which communities may play a role in the remediation process, the present study investigates the microbial community structure and diversity of microorganisms found in a full-scale membrane bioreactor (MBR) for industrial wastewater treatment. The study was carried out using high-throughput data observations following a failure (crash) of the MBR and during the extended recovery of the process. Results revealed a positive correlation between the MBR's ability to remove organic matter and its microbial community richness. The significant changes in relative microbial abundance between crash and recovery periods of the MBR revealed the important role of specific bacterial genera in wastewater treatment processes. A whole-genome metagenomics based comparison showed a clear difference in microbial makeup between two functional periods of MBR activity. The crash period was characterized by abundance in bacteria belonging to Achromobacter, Acinetobacter, Halomonas, Pseudomonas and an uncultured MBAE14. The recovery period on the other hand was characterized by Aquamicrobium and by Wenzhouxiangella marina. Our study also revealed some interesting functional pathways characterizing the microbial communities from the two periods of bioreactor function, such as Nitrate and Sulfate reduction pathways. These differences indicate the connection between the bacterial diversity of the MBR and its efficiency to remove TOC.}, }
@article {pmid32534383, year = {2020}, author = {Muccee, F and Ejaz, S}, title = {Whole genome shotgun sequencing of POPs degrading bacterial community dwelling tannery effluents and petrol contaminated soil.}, journal = {Microbiological research}, volume = {238}, number = {}, pages = {126504}, doi = {10.1016/j.micres.2020.126504}, pmid = {32534383}, issn = {1618-0623}, abstract = {The present study involved identification of genes which are present in the genome of native bacteria to make them effective tools for bioremediation of persistent organic pollutants (POPs). During this study, forty-one POPs (naphthalene, toluene and petrol) metabolizing bacteria were isolated from tannery effluents and petrol contaminated soil samples by successive enrichment culturing. The taxonomic diversity and gene repertoire conferring POPs degradation ability to the isolated bacterial community were studied through whole genome shotgun sequencing of DNA consortium. The DNA consortium contained equimolar concentration of DNA extracted from each bacterial isolate using organic method. To add a double layer of confirmation the established DNA consortium was subjected to 16S rRNA metagenome sequencing and whole genome shotgun sequencing analysis. Biodiversity analysis revealed that the consortium was composed of phyla Firmicutes (80 %), Proteobacteria (12 %) and Actinobacteria (5%). Genera found included Bacillus (45 %), Burkholderia (25 %), Brevibacillus (9%) and Geobacillus (4%). Functional profiling of consortium helped us to identify genes associated with degradation pathways of a variety of organic compounds including toluene, naphthalene, caprolactam, benzoate, aminobenzoate, xylene, 4-hydroxyphenyl acetic acid, biphenyl, anthracene, aminobenzoate, chlorocyclohexane, chlorobenzene, n-phenylalkanoic acid, phenylpropanoid, salicylate, gentisate, central meta cleavage of aromatic compounds, cinnamic acid, catechol and procatechuate branch of β-ketoadipate pathway, phenyl-acetyl CoA and homogentisate catabolic pathway. The information thus generated has ensured not only biodegradation potential but also revealed many possible future applications of the isolated bacteria.}, }
@article {pmid32524948, year = {2020}, author = {Hinterwirth, A and Sié, A and Coulibaly, B and Ouermi, L and Dah, C and Tapsoba, C and Zhong, L and Chen, C and Lietman, TM and Keenan, JD and Doan, T and Oldenburg, CE}, title = {Rapid Reduction of Campylobacter Species in the Gut Microbiome of Preschool Children after Oral Azithromycin: A Randomized Controlled Trial.}, journal = {The American journal of tropical medicine and hygiene}, volume = {103}, number = {3}, pages = {1266-1269}, doi = {10.4269/ajtmh.19-0940}, pmid = {32524948}, issn = {1476-1645}, support = {R25 MH083620/MH/NIMH NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*therapeutic use ; Azithromycin/*therapeutic use ; Burkina Faso/epidemiology ; Campylobacter/genetics/*isolation &amp; purification ; Campylobacter Infections/epidemiology/microbiology/*mortality ; Child Mortality ; Child, Preschool ; *Gastrointestinal Microbiome ; Humans ; Infant ; Metagenomics ; Sequence Analysis, DNA ; }, abstract = {Campylobacter has emerged as a potential important cause of childhood morbidity in sub-Saharan Africa. Biannual mass azithromycin distribution has previously been shown to reduce all-cause child mortality in sub-Saharan Africa. We conducted a randomized controlled trial in Burkina Faso in which children were randomized in a 1:1 fashion to a 5-day course of azithromycin or placebo to investigate the effect of oral antibiotics on the gut microbiome. We evaluated the changes in the gut microbiome of preschool children treated with azithromycin using metagenomic DNA sequencing. We found that three Campylobacter species were reduced with azithromycin treatment compared with placebo. These results were consistent with other studies that have shown decreases in Campylobacter species after azithromycin treatment, generating the hypothesis that a decrease in Campylobacter may contribute to observations of reduction in mortality following azithromycin distribution.}, }
@article {pmid32524177, year = {2020}, author = {Dekaboruah, E and Suryavanshi, MV and Chettri, D and Verma, AK}, title = {Human microbiome: an academic update on human body site specific surveillance and its possible role.}, journal = {Archives of microbiology}, volume = {202}, number = {8}, pages = {2147-2167}, pmid = {32524177}, issn = {1432-072X}, mesh = {Computational Biology/*trends ; Disease ; *Human Body ; Humans ; Microbiota/*physiology ; }, abstract = {Human body is inhabited by vast number of microorganisms which form a complex ecological community and influence the human physiology, in the aspect of both health and diseases. These microbes show a relationship with the human immune system based on coevolution and, therefore, have a tremendous potential to contribute to the metabolic function, protection against the pathogen and in providing nutrients and energy. However, of these microbes, many carry out some functions that play a crucial role in the host physiology and may even cause diseases. The introduction of new molecular technologies such as transcriptomics, metagenomics and metabolomics has contributed to the upliftment on the findings of the microbiome linked to the humans in the recent past. These rapidly developing technologies are boosting our capacity to understand about the human body-associated microbiome and its association with the human health. The highlights of this review are inclusion of how to derive microbiome data and the interaction between human and associated microbiome to provide an insight on the role played by the microbiome in biological processes of the human body as well as the development of major human diseases.}, }
@article {pmid32521370, year = {2020}, author = {Kang, X and Cui, Y and Shen, T and Yan, M and Tu, W and Shoaib, M and Xiang, Q and Zhao, K and Gu, Y and Chen, Q and Li, S and Liang, Y and Ma, M and Zou, L and Yu, X}, title = {Changes of root microbial populations of natively grown plants during natural attenuation of V-Ti magnetite tailings.}, journal = {Ecotoxicology and environmental safety}, volume = {201}, number = {}, pages = {110816}, doi = {10.1016/j.ecoenv.2020.110816}, pmid = {32521370}, issn = {1090-2414}, mesh = {Biodegradation, Environmental ; China ; Ferrosoferric Oxide/analysis/*toxicity ; Metagenomics ; Microbiota/*drug effects/genetics ; Mining ; Plant Roots/*microbiology ; Poaceae/growth &amp; development/microbiology ; Rhizobium ; Rhizosphere ; Soil/chemistry ; Soil Microbiology ; Soil Pollutants/analysis/*toxicity ; Titanium/analysis/*toxicity ; Typhaceae/growth &amp; development/microbiology ; Vanadium/analysis/*toxicity ; }, abstract = {Mine tailings contain dangerously high levels of toxic metals which pose a constant threat to local ecosystems. Few naturally grown native plants can colonize tailings site and the existence of their root-associated microbial populations is poorly understood. The objective of this study was to give further insights into the interactions between native plants and their microbiota during natural attenuation of abandoned V-Ti magnetite mine tailings. In the present work, we first examined the native plants' potential for phytoremediation using plant/soil analytical methods and then investigated the root microbial communities and their inferred functions using 16 S rRNA-based metagenomics. It was found that in V-Ti magnetite mine tailings the two dominant plants Bothriochloa ischaemum and Typha angustifolia were able to increase available nitrogen in the rhizosphere soil by 23.3% and 53.7% respectively. The translocation factors (TF) for both plants indicated that B. ischaemum was able to accumulate Pb (TF = 1.212), while T. angustifolia was an accumulator of Mn (TF = 2.502). The microbial community structure was more complex in the soil associated with T. angustifolia than with B. ischaemum. The presence of both plants significantly reduced the population of Acinetobacter. Specifically, B. ischaemum enriched Massilia, Opitutus and Hydrogenophaga species while T. angustifolia significantly increased rhizobia species. Multivariate analyses revealed that among all tested soil variables Fe and total organic carbon (TOC) could be the key factors in shaping the microbial structure. The putative functional analysis indicated that soil sample of B. ischaemum was abundant with nitrate/nitrite reduction-related functions while that of T. angustifolia was rich in nitrogen fixing functions. The results indicate that these native plants host a diverse range of soil microbes, whose community structure can be shaped by plant types and soil variables. It is also possible that these plants can be used to improve soil nitrogen content and serve as bioaccumulators for Pb or Mn for phytoremediation purposes.}, }
@article {pmid32519746, year = {2020}, author = {Su, X and Zhao, Y and Li, Y and Ma, S and Wang, Z}, title = {Gut dysbiosis is associated with primary hypothyroidism with interaction on gut-thyroid axis.}, journal = {Clinical science (London, England : 1979)}, volume = {134}, number = {12}, pages = {1521-1535}, doi = {10.1042/CS20200475}, pmid = {32519746}, issn = {1470-8736}, mesh = {Adult ; Animals ; Case-Control Studies ; Dysbiosis/*complications ; Fatty Acids/metabolism ; Fecal Microbiota Transplantation ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*pathology ; Humans ; Hypothyroidism/*complications ; Male ; Metagenomics ; Mice, Inbred BALB C ; Phylogeny ; ROC Curve ; Thyroid Gland/*pathology ; }, abstract = {Background Previous studies have shown that the gut microbiome is associated with thyroid diseases, including Graves' disease, Hashimoto's disease, thyroid nodules, and thyroid cancer. However, the association between intestinal flora and primary hypothyroidism remains elusive. We aimed to characterize gut microbiome in primary hypothyroidism patients. Methods Fifty-two primary hypothyroidism patients and 40 healthy controls were recruited. The differences in gut microbiota between the two groups were analyzed by 16S rRNA sequencing technology. Fecal microbiota transplantation (FMT) was performed in mice using flora from both groups; changes in thyroid function were then assessed in the mice. Results There were significant differences in α and β diversities of gut microbiota between primary hypothyroidism patients and healthy individuals. The random forest analysis indicated that four intestinal bacteria (Veillonella, Paraprevotella, Neisseria, and Rheinheimera) could distinguish untreated primary hypothyroidism patients from healthy individuals with the highest accuracy; this was confirmed by receiver operator characteristic curve analysis. The short chain fatty acid producing ability of the primary hypothyroidism patients' gut was significantly decreased, which resulted in the increased serum lipopolysaccharide (LPS) levels. The FMT showed that mice receiving the transplant from primary hypothyroidism patients displayed decreased total thyroxine levels. Conclusions Our study suggests that primary hypothyroidism causes changes in gut microbiome. In turn, an altered flora can affect thyroid function in mice. These findings could help understand the development of primary hypothyroidism and might be further used to develop potential probiotics to facilitate the adjuvant treatment of this disease.}, }
@article {pmid32514171, year = {2020}, author = {Chng, KR and Li, C and Bertrand, D and Ng, AHQ and Kwah, JS and Low, HM and Tong, C and Natrajan, M and Zhang, MH and Xu, L and Ko, KKK and Ho, EXP and Av-Shalom, TV and Teo, JWP and Khor, CC and ,  and Chen, SL and Mason, CE and Ng, OT and Marimuthu, K and Ang, B and Nagarajan, N}, title = {Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment.}, journal = {Nature medicine}, volume = {26}, number = {6}, pages = {941-951}, doi = {10.1038/s41591-020-0894-4}, pmid = {32514171}, issn = {1546-170X}, mesh = {Beds/microbiology ; Biofilms ; Cross Infection/drug therapy/*microbiology/transmission ; Disinfection ; Drug Resistance, Bacterial/*genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Equipment Contamination ; Equipment and Supplies, Hospital/*microbiology ; Geographic Mapping ; Humans ; *Infection Control ; Metagenomics ; Microbiota/*genetics ; Opportunistic Infections/drug therapy/microbiology/transmission ; Patients' Rooms ; Singapore ; Spatio-Temporal Analysis ; Tertiary Care Centers ; }, abstract = {Although disinfection is key to infection control, the colonization patterns and resistomes of hospital-environment microbes remain underexplored. We report the first extensive genomic characterization of microbiomes, pathogens and antibiotic resistance cassettes in a tertiary-care hospital, from repeated sampling (up to 1.5 years apart) of 179 sites associated with 45 beds. Deep shotgun metagenomics unveiled distinct ecological niches of microbes and antibiotic resistance genes characterized by biofilm-forming and human-microbiome-influenced environments with corresponding patterns of spatiotemporal divergence. Quasi-metagenomics with nanopore sequencing provided thousands of high-contiguity genomes, phage and plasmid sequences (>60% novel), enabling characterization of resistome and mobilome diversity and dynamic architectures in hospital environments. Phylogenetics identified multidrug-resistant strains as being widely distributed and stably colonizing across sites. Comparisons with clinical isolates indicated that such microbes can persist in hospitals for extended periods (>8 years), to opportunistically infect patients. These findings highlight the importance of characterizing antibiotic resistance reservoirs in hospitals and establish the feasibility of systematic surveys to target resources for preventing infections.}, }
@article {pmid32497331, year = {2020}, author = {Mérot, C}, title = {Making the most of population genomic data to understand the importance of chromosomal inversions for adaptation and speciation.}, journal = {Molecular ecology}, volume = {29}, number = {14}, pages = {2513-2516}, doi = {10.1111/mec.15500}, pmid = {32497331}, issn = {1365-294X}, mesh = {Adaptation, Physiological ; *Chromosome Inversion ; Ecotype ; *Helianthus ; Humans ; Metagenomics ; }, abstract = {Chromosomal inversions are increasingly found to differentiate locally adapted populations. This adaptive role is predictable because reduced recombination protects allelic combinations from gene flow. However, we are far from understanding how frequently inversions contribute to local adaptation and how widespread this phenomenon is across species. In a &quot;From the Cover&quot; article in this issue of Molecular Ecology, Huang, Andrew, Owens, Ostevik, and Rieseberg (2020) provide an important step towards this goal not only by finding adaptive inversions in a sunflower ecotype, but also by reversing the approach used to investigate the link between adaptation and inversions. Most studies compare two phenotypes and uncover divergence at a few regions, of which some can subsequently be identified as inversions. In contrast, Huang et al first catalogue putative inversions and then test genotype-environment associations, which allows them to ask systematically whether inversions may be adaptive and in which ecological contexts. They achieve that by revisiting a previous reduced-representation sequencing (RAD-sequencing) data set, demonstrating the suitability of this method to detect inversions in species with limited genomic resources. As such, Huang et al pave the way for a better understanding of the evolutionary role of structural genomic variation and highlight that accounting for inversions in population genomics is now possible, and much needed, in a wider range of organisms.}, }
@article {pmid32497143, year = {2020}, author = {Wang, S and Yan, Z and Wang, P and Zheng, X and Fan, J}, title = {Comparative metagenomics reveals the microbial diversity and metabolic potentials in the sediments and surrounding seawaters of Qinhuangdao mariculture area.}, journal = {PloS one}, volume = {15}, number = {6}, pages = {e0234128}, pmid = {32497143}, issn = {1932-6203}, mesh = {Bacteria/classification/*genetics/*metabolism ; *Biodiversity ; China ; Geologic Sediments/*microbiology ; *Metagenomics ; Seawater/*microbiology ; }, abstract = {Qinhuangdao coastal area is an important mariculture area in North China. Microbial communities play an important role in driving biogeochemical cycle and energy flow. It is necessary to identify the microbial communities and their functions in the coastal mariculture area of Qinhuangdao. In this study, the microbial community compositions and their metabolic potentials in the sediments and their surrounding seawaters of Qinhuangdao mariculture area were uncovered by the 16S rRNA gene amplicon sequencing and metagenomic shotgun sequencing approaches. The results of amplicon sequencing showed that Gammaproteobacteria and Alphaproteobacteria were predominant classes. Our datasets showed a clear shift in microbial taxonomic groups and the metabolic pathways in the sediments and surrounding seawaters. Metagenomic analysis showed that purine metabolism, ABC transporters, and pyrimidine metabolism were the most abundant pathways. Genes related to two-component system, TCA cycle and nitrogen metabolism exhibited higher abundance in sediments compared with those in seawaters. The presence of cadmium-resistant genes and ABC transporters suggested the ability of microorganisms to resist the toxicity of cadmium. In summary, this study provides comprehensive and significant differential signatures in the microbial community and metabolic pathways in Qinhuangdao mariculture area, and can develop effective microbial indicators to monitor mariculture area in the future.}, }
@article {pmid32486022, year = {2020}, author = {Koike, Y and Kuwatsuka, S and Nishimoto, K and Motooka, D and Murota, H}, title = {Skin Mycobiome of Psoriasis Patients is Retained during Treatment with TNF and IL-17 Inhibitors.}, journal = {International journal of molecular sciences}, volume = {21}, number = {11}, pages = {}, pmid = {32486022}, issn = {1422-0067}, support = {KHKS20190401015//Kyowa Hakko Kirin/ ; }, abstract = {BACKGROUND: Biological treatment relieves refractory skin lesions in patients with psoriasis; however, changes in the fungal microbiome (the mycobiome) on the skin are unclear.<br><br>METHODS: The skin mycobiome of psoriasis patients treated with TNF inhibitors (TNFi, n = 5) and IL-17 inhibitors (IL-17i, n = 7) was compared with that of patients not receiving systemic therapy (n = 7). Skin swab samples were collected from non-lesional post-auricular areas. Fungal DNA was sequenced by ITS1 metagenomic analysis and taxonomic classification was performed.<br><br>RESULTS: An average of 37543 reads/sample were analyzed and fungi belonging to 31 genera were detected. The genus Malassezia accounted for >90% of reads in 7/7 samples from the no-therapy group, 4/5 from the TNFi group, and 5/7 from the IL-17i group. Biodiversity was low in those three groups. Few members of the genus trichophyton were detected; the genus Candida was not detected at all. Among the Malassezia species, M. restricta was the major species in 6/7 samples from the no-therapy group, 4/5 from the TNFi group, and 5/7 from the IL-17i group whose the other largest species revealed M. globosa.<br><br>CONCLUSIONS: The mycobiome is retained on post-auricular skin during systemic treatment with TNF and IL-17 inhibitors.}, }
@article {pmid32482859, year = {2020}, author = {Roach, TNF and Little, M and Arts, MGI and Huckeba, J and Haas, AF and George, EE and Quinn, RA and Cobián-Güemes, AG and Naliboff, DS and Silveira, CB and Vermeij, MJA and Kelly, LW and Dorrestein, PC and Rohwer, F}, title = {A multiomic analysis of in situ coral-turf algal interactions.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {24}, pages = {13588-13595}, pmid = {32482859}, issn = {1091-6490}, mesh = {Animals ; Anthozoa/chemistry/*metabolism/microbiology/parasitology ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Chlorophyta/chemistry/*metabolism ; Coral Reefs ; Ecosystem ; Metagenomics ; Microbiota ; }, abstract = {Viruses, microbes, and host macroorganisms form ecological units called holobionts. Here, a combination of metagenomic sequencing, metabolomic profiling, and epifluorescence microscopy was used to investigate how the different components of the holobiont including bacteria, viruses, and their associated metabolites mediate ecological interactions between corals and turf algae. The data demonstrate that there was a microbial assemblage unique to the coral-turf algae interface displaying higher microbial abundances and larger microbial cells. This was consistent with previous studies showing that turf algae exudates feed interface and coral-associated microbial communities, often at the detriment of the coral. Further supporting this hypothesis, when the metabolites were assigned a nominal oxidation state of carbon (NOSC), we found that the turf algal metabolites were significantly more reduced (i.e., have higher potential energy) compared to the corals and interfaces. The algae feeding hypothesis was further supported when the ecological outcomes of interactions (e.g., whether coral was winning or losing) were considered. For example, coral holobionts losing the competition with turf algae had higher Bacteroidetes-to-Firmicutes ratios and an elevated abundance of genes involved in bacterial growth and division. These changes were similar to trends observed in the obese human gut microbiome, where overfeeding of the microbiome creates a dysbiosis detrimental to the long-term health of the metazoan host. Together these results show that there are specific biogeochemical changes at coral-turf algal interfaces that predict the competitive outcomes between holobionts and are consistent with algal exudates feeding coral-associated microbes.}, }
@article {pmid32482169, year = {2020}, author = {Zhong, H and Lehtovirta-Morley, L and Liu, J and Zheng, Y and Lin, H and Song, D and Todd, JD and Tian, J and Zhang, XH}, title = {Novel insights into the Thaumarchaeota in the deepest oceans: their metabolism and potential adaptation mechanisms.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {78}, pmid = {32482169}, issn = {2049-2618}, support = {91751202//National Natural Science Foundation of China/International ; 41730530//National Natural Science Foundation of China/International ; 41476112//National Natural Science Foundation of China/International ; }, abstract = {BACKGROUND: Marine Group I (MGI) Thaumarchaeota, which play key roles in the global biogeochemical cycling of nitrogen and carbon (ammonia oxidizers), thrive in the aphotic deep sea with massive populations. Recent studies have revealed that MGI Thaumarchaeota were present in the deepest part of oceans-the hadal zone (depth > 6000 m, consisting almost entirely of trenches), with the predominant phylotype being distinct from that in the &quot;shallower&quot; deep sea. However, little is known about the metabolism and distribution of these ammonia oxidizers in the hadal water.<br><br>RESULTS: In this study, metagenomic data were obtained from 0-10,500 m deep seawater samples from the Mariana Trench. The distribution patterns of Thaumarchaeota derived from metagenomics and 16S rRNA gene sequencing were in line with that reported in previous studies: abundance of Thaumarchaeota peaked in bathypelagic zone (depth 1000-4000 m) and the predominant clade shifted in the hadal zone. Several metagenome-assembled thaumarchaeotal genomes were recovered, including a near-complete one representing the dominant hadal phylotype of MGI. Using comparative genomics, we predict that unexpected genes involved in bioenergetics, including two distinct ATP synthase genes (predicted to be coupled with H+ and Na+ respectively), and genes horizontally transferred from other extremophiles, such as those encoding putative di-myo-inositol-phosphate (DIP) synthases, might significantly contribute to the success of this hadal clade under the extreme condition. We also found that hadal MGI have the genetic potential to import a far higher range of organic compounds than their shallower water counterparts. Despite this trait, hadal MDI ammonia oxidation and carbon fixation genes are highly transcribed providing evidence they are likely autotrophic, contributing to the primary production in the aphotic deep sea.<br><br>CONCLUSIONS: Our study reveals potentially novel adaptation mechanisms of deep-sea thaumarchaeotal clades and suggests key functions of deep-sea Thaumarchaeota in carbon and nitrogen cycling. Video Abstract.}, }
@article {pmid32468578, year = {2020}, author = {Xie, J and Yu, R and Qi, J and Zhang, G and Peng, X and Luo, J}, title = {Pectin and inulin stimulated the mucus formation at a similar level: An omics-based comparative analysis.}, journal = {Journal of food science}, volume = {85}, number = {6}, pages = {1939-1947}, doi = {10.1111/1750-3841.15163}, pmid = {32468578}, issn = {1750-3841}, support = {31801543//National Natural Science Foundation of China/ ; 2018M643368//China Postdoctoral Science Foundation/ ; }, mesh = {Animals ; Bacteria/classification/genetics/metabolism ; Cecum/metabolism/microbiology ; Gastrointestinal Microbiome ; Inulin/*metabolism ; Male ; Mucin-2/metabolism ; Mucus/*metabolism/microbiology ; Pectins/*metabolism ; Polysaccharides/metabolism ; Rats ; Rats, Wistar ; }, abstract = {Mucin 2 (MUC2) is the skeleton of colonic mucus that comprises the physical intestinal barrier. Different dietary polysaccharides may affect colonic mucus at different extents. The effect of pectin on MUC2 production is contradictory. To investigate whether and how pectin affected hosts' colonic mucus, the amount of MUC2 in colon, the cecal, mucosal microbiota, and metabolites profiles were analyzed and compared with inulin. The results showed pectin stimulated the production of MUC2 at a similar level to inulin. Both interventions increased the abundance of cecal Lachnospira and Christensenellaceae_R-7_group, and enhanced the production of specific metabolites including soyasapogenol B 24-O-b-d-glucoside, lucyoside Q, trans-EKODE-(E)-Ib, and 1,26-dicaffeoylhexacosanediol. Additionally, pectin increased the relative abundance (RA) of cecal Lactobacillus, and induced less RA of potentially harmful bacteria such as Helicobacter in mucosal microbiota than inulin. In conclusion, we first reported that pectin and inulin stimulated the mucus formation at a similar level. Two genera of cecal bacteria and four metabolites may play an important role in enhancing the production of MUC2. Moreover, the MUC2 production may be unrelated to several traditional health-beneficial bacteria; pectin possibly performed as good as or better than the inulin in rats' gut.}, }
@article {pmid32461638, year = {2020}, author = {Polster, SP and Sharma, A and Tanes, C and Tang, AT and Mericko, P and Cao, Y and Carrión-Penagos, J and Girard, R and Koskimäki, J and Zhang, D and Stadnik, A and Romanos, SG and Lyne, SB and Shenkar, R and Yan, K and Lee, C and Akers, A and Morrison, L and Robinson, M and Zafar, A and Bittinger, K and Kim, H and Gilbert, JA and Kahn, ML and Shen, L and Awad, IA}, title = {Permissive microbiome characterizes human subjects with a neurovascular disease cavernous angioma.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {2659}, pmid = {32461638}, issn = {2041-1723}, support = {F30 NS100252/NS/NINDS NIH HHS/United States ; U54 NS065705/NS/NINDS NIH HHS/United States ; P01 NS092521/NS/NINDS NIH HHS/United States ; R01 NS100949/NS/NINDS NIH HHS/United States ; R01 HL094326/HL/NHLBI NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Biomarkers/blood ; Brain Neoplasms/complications/diagnosis/microbiology ; DNA, Bacterial/genetics ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Hemangioma, Cavernous/*complications/diagnosis ; Humans ; Intestines/microbiology/pathology ; Male ; Metagenomics ; Middle Aged ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {Cavernous angiomas (CA) are common vascular anomalies causing brain hemorrhage. Based on mouse studies, roles of gram-negative bacteria and altered intestinal homeostasis have been implicated in CA pathogenesis, and pilot study had suggested potential microbiome differences between non-CA and CA individuals based on 16S rRNA gene sequencing. We here assess microbiome differences in a larger cohort of human subjects with and without CA, and among subjects with different clinical features, and conduct more definitive microbial analyses using metagenomic shotgun sequencing. Relative abundance of distinct bacterial species in CA patients is shown, consistent with postulated permissive microbiome driving CA lesion genesis via lipopolysaccharide signaling, in humans as in mice. Other microbiome differences are related to CA clinical behavior. Weighted combinations of microbiome signatures and plasma inflammatory biomarkers enhance associations with disease severity and hemorrhage. This is the first demonstration of a sensitive and specific diagnostic microbiome in a human neurovascular disease.}, }
@article {pmid32442018, year = {2020}, author = {Ritchie, AI and Singanayagam, A}, title = {Metagenomic Characterization of the Respiratory Microbiome. A Pièce de Résistance.}, journal = {American journal of respiratory and critical care medicine}, volume = {202}, number = {3}, pages = {321-322}, pmid = {32442018}, issn = {1535-4970}, mesh = {Anti-Bacterial Agents ; Macrolides ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; }, }
@article {pmid32424337, year = {2020}, author = {Morris, RM and Cain, KR and Hvorecny, KL and Kollman, JM}, title = {Lysogenic host-virus interactions in SAR11 marine bacteria.}, journal = {Nature microbiology}, volume = {5}, number = {8}, pages = {1011-1015}, doi = {10.1038/s41564-020-0725-x}, pmid = {32424337}, issn = {2058-5276}, support = {R01 GM127648/GM/NIGMS NIH HHS/United States ; }, mesh = {Alphaproteobacteria/*virology ; Bacteriophages/*metabolism ; *Genome, Viral ; Heterotrophic Processes ; *Host Microbial Interactions ; *Lysogeny ; Metagenomics ; Microbiota ; Oceans and Seas ; Prophages/*metabolism ; Seawater/microbiology/virology ; Sequence Alignment ; Sequence Analysis, DNA ; Viral Proteins/*genetics/metabolism ; }, abstract = {Host-virus interactions structure microbial communities, drive biogeochemical cycles and enhance genetic diversity in nature1,2. Hypotheses proposed to explain the range of interactions that mediate these processes often invoke lysogeny3-6, a latent infection strategy used by temperate bacterial viruses to replicate in host cells until an induction event triggers the production and lytic release of free viruses. Most cultured bacteria harbour temperate viruses in their genomes (prophage)7. The absence of prophages in cultures of the dominant lineages of marine bacteria has contributed to an ongoing debate over the ecological significance of lysogeny and other viral life strategies in nature6,8-15. Here, we report the discovery of prophages in cultured SAR11, the ocean's most abundant clade of heterotrophic bacteria16,17. We show the concurrent production of cells and viruses, with enhanced virus production under carbon-limiting growth conditions. Evidence that related prophages are broadly distributed in the oceans suggests that similar interactions have contributed to the evolutionary success of SAR11 in nutrient-limited systems.}, }
@article {pmid32417556, year = {2020}, author = {Gallego, S and Barkay, T and Fahrenfeld, NL}, title = {Tagging the vanA gene in wastewater microbial communities for cell sorting and taxonomy of vanA carrying cells.}, journal = {The Science of the total environment}, volume = {732}, number = {}, pages = {138865}, doi = {10.1016/j.scitotenv.2020.138865}, pmid = {32417556}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents ; Bacterial Proteins ; Carbon-Oxygen Ligases ; In Situ Hybridization, Fluorescence ; Microbial Sensitivity Tests ; *Microbiota ; Phylogeny ; Waste Water ; }, abstract = {Failure to understand the microbial ecology driving the proliferation of antibiotic resistance in the environment prevents us from developing strategies to limit the spread of antibiotic resistant infectious disease. In this study, we developed for the first time a tyramide signal amplification-fluorescence in situ hybridization-fluorescence-activated cell sorting protocol (TSA-FISH-FACS) for the characterization of all vanA carrying bacteria in wastewater samples. Firstly, we validated the TSA-FISH protocol through microscopy in pure cultures and wastewater influent. Then, samples were sorted and quantified by FACS and qPCR. Significantly higher percentage tagging of cells was detected in vanA carrying pure cultures and wastewater samples spiked with vanA carrying cells as compared to vanA negative Gram positive strains and non-spiked wastewater samples respectively. qPCR analysis targeting vanZ, a regulating gene in the vanA cluster, showed its relative abundance was significantly greater in Enterococcus faecium ATCC 700221-spiked and positively sorted samples compared to the E. faecium spiked and negatively sorted samples. Phylogenetic analysis was then performed. Although further efforts are needed to overcome technical problems, we have, for the first time, demonstrated sorting bacterial-cells carrying antibiotic resistance genes from wastewater samples through a TSA-FISH-FACS protocol and provided insight into the microbial ecology of vancomycin resistant bacteria. Future potential applications using this approach will include the separation of members of an environmental microbial community (cultured and hard-to-culture) to allow for metagenomics on single cells or, in the case of clumping, targeting a smaller portion of the community with a priori knowledge that the target gene is present.}, }
@article {pmid32416615, year = {2020}, author = {Cordier, T and Alonso-Sáez, L and Apothéloz-Perret-Gentil, L and Aylagas, E and Bohan, DA and Bouchez, A and Chariton, A and Creer, S and Frühe, L and Keck, F and Keeley, N and Laroche, O and Leese, F and Pochon, X and Stoeck, T and Pawlowski, J and Lanzén, A}, title = {Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.15472}, pmid = {32416615}, issn = {1365-294X}, support = {//European Cross-Border Cooperation Programme/ ; RYC-2012-11404//'Ramón y Cajal' contract/ ; //Spanish Ministry of Economy and Competitiveness/ ; //Saudi Aramco-KAUST Center for Marine Environmental Observations/ ; ANR-17-CE32-011//French Agence Nationale de la Recherche/ ; //ERA-NET C-IPM BioAWARE/ ; //Office Français de la Biodiversité (OFB)/ ; NE/N003756/1//UK Natural Environment Research Council/ ; NE/N006216/1//UK Natural Environment Research Council/ ; STO414/15-1//German Science Foundation (DFG)/ ; CAWX1904//New Zealand Ministry for Business, Innovation and Employment/ ; C05X1707//New Zealand Ministry for Business, Innovation and Employment/ ; CA15219//DNAqua-Net COST Action/ ; //European Union/ ; //IKERBASQUE (Basque Foundation for Science)/ ; //Basque Government (project microgAMBI)/ ; 31003A_179125/SNSF_/Swiss National Science Foundation/Switzerland ; }, abstract = {A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, technical limitations and conceptual issues still stand in the way of its broad application by end-users. In addition, the multiplicity of potential implementation strategies may contribute to a perception that the routine application of this methodology is premature or &quot;in development&quot;, hence restraining regulators from binding these tools into legal frameworks. Here, we review recent implementations of environmental genomics-based methods, applied to the biomonitoring of ecosystems. By taking a general overview, without narrowing our perspective to particular habitats or groups of organisms, this paper aims to compare, review and discuss the strengths and limitations of four general implementation strategies of environmental genomics for monitoring: (a) Taxonomy-based analyses focused on identification of known bioindicators or described taxa; (b) De novo bioindicator analyses; (c) Structural community metrics including inferred ecological networks; and (d) Functional community metrics (metagenomics or metatranscriptomics). We emphasise the utility of the three latter strategies to integrate meiofauna and microorganisms that are not traditionally utilised in biomonitoring because of difficult taxonomic identification. Finally, we propose a roadmap for the implementation of environmental genomics into routine monitoring programmes that leverage recent analytical advancements, while pointing out current limitations and future research needs.}, }
@article {pmid32414048, year = {2020}, author = {Kuramae, EE and Derksen, S and Schlemper, TR and Dimitrov, MR and Costa, OYA and Silveira, APDD}, title = {Sorghum Growth Promotion by Paraburkholderia tropica and Herbaspirillum frisingense: Putative Mechanisms Revealed by Genomics and Metagenomics.}, journal = {Microorganisms}, volume = {8}, number = {5}, pages = {}, pmid = {32414048}, issn = {2076-2607}, support = {729.004.013//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 456420/2013-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {Bacteria from the genera Paraburkholderia and Herbaspirillum can promote the growth of Sorghum bicolor, but the underlying mechanisms are not yet known. In a pot experiment, sorghum plants grown on sterilized substrate were inoculated with Paraburkholderia tropica strain IAC/BECa 135 and Herbaspirillumfrisingense strain IAC/BECa 152 under phosphate-deficient conditions. These strains significantly increased Sorghum bicolor cultivar SRN-39 root and shoot biomass. Shotgun metagenomic analysis of the rhizosphere revealed successful colonization by both strains; however, the incidence of colonization was higher in plants inoculated with P. tropica strain IAC/BECa 135 than in those inoculated with H. frisingense strain IAC/BECa 152. Conversely, plants inoculated with H. frisingense strain IAC/BECa 152 showed the highest increase in biomass. Genomic analysis of the two inoculants implied a high degree of rhizosphere fitness of P. tropica strain IAC/BECa 135 through environmental signal processing, biofilm formation, and nutrient acquisition. Both genomes contained genes related to plant growth-promoting bacterial (PGPB) traits, including genes related to indole-3-acetate (IAA) synthesis, nitrogen fixation, nodulation, siderophore production, and phosphate solubilization, although the P. tropica strain IAC/BECa 135 genome contained a slightly more extensive repertoire. This study provides evidence that complementary mechanisms of growth promotion in Sorghum might occur, i.e., that P. tropica strain IAC/BECa 135 acts in the rhizosphere and increases the availability of nutrients, while H. frisingense strain IAC/BECa 152 influences plant hormone signaling. While the functional and taxonomic profiles of the rhizobiomes were similar in all treatments, significant differences in plant biomass were observed, indicating that the rhizobiome and the endophytic microbial community may play equally important roles in the complicated plant-microbial interplay underlying increased host plant growth.}, }
@article {pmid32391909, year = {2020}, author = {Cuadrat, RRC and Sorokina, M and Andrade, BG and Goris, T and Dávila, AMR}, title = {Global ocean resistome revealed: Exploring antibiotic resistance gene abundance and distribution in TARA Oceans samples.}, journal = {GigaScience}, volume = {9}, number = {5}, pages = {}, pmid = {32391909}, issn = {2047-217X}, abstract = {BACKGROUND: The rise of antibiotic resistance (AR) in clinical settings is of great concern. Therefore, the understanding of AR mechanisms, evolution, and global distribution is a priority for patient survival. Despite all efforts in the elucidation of AR mechanisms in clinical strains, little is known about its prevalence and evolution in environmental microorganisms. We used 293 metagenomic samples from the TARA Oceans project to detect and quantify environmental antibiotic resistance genes (ARGs) using machine learning tools.<br><br>RESULTS: After manual curation of ARGs, their abundance and distribution in the global ocean are presented. Additionally, the potential of horizontal ARG transfer by plasmids and their correlation with environmental and geographical parameters is shown. A total of 99,205 environmental open reading frames (ORFs) were classified as 1 of 560 different ARGs conferring resistance to 26 antibiotic classes. We found 24,567 ORFs in putative plasmid sequences, suggesting the importance of mobile genetic elements in the dynamics of environmental ARG transmission. Moreover, 4,804 contigs with >=2 putative ARGs were found, including 2 plasmid-like contigs with 5 different ARGs, highlighting the potential presence of multi-resistant microorganisms in the natural ocean environment. Finally, we identified ARGs conferring resistance to some of the most relevant clinical antibiotics, revealing the presence of 15 ARGs similar to mobilized colistin resistance genes (mcr) with high abundance on polar biomes. Of these, 5 are assigned to Psychrobacter, a genus including opportunistic human pathogens.<br><br>CONCLUSIONS: This study uncovers the diversity and abundance of ARGs in the global ocean metagenome. Our results are available on Zenodo in MySQL database dump format, and all the code used for the analyses, including a Jupyter notebook js avaliable on Github. We also developed a dashboard web application (http://www.resistomedb.com) for data visualization.}, }
@article {pmid32382098, year = {2020}, author = {Berlemont, R and Winans, N and Talamantes, D and Dang, H and Tsai, HW}, title = {MetaGeneHunt for protein domain annotation in short-read metagenomes.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {7712}, pmid = {32382098}, issn = {2045-2322}, support = {UL1 GM118979/GM/NIGMS NIH HHS/United States ; RL5 GM118978/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*genetics ; Computational Biology ; Databases, Genetic ; Genome, Microbial/genetics ; Metagenome/*genetics ; Metagenomics/methods ; Mice ; Microbiota/genetics ; Molecular Sequence Annotation ; Protein Domains/*genetics ; Sequence Analysis ; *Software ; }, abstract = {The annotation of short-reads metagenomes is an essential process to understand the functional potential of sequenced microbial communities. Annotation techniques based solely on the identification of local matches tend to confound local sequence similarity and overall protein homology and thus don't mirror the complex multidomain architecture and the shuffling of functional domains in many protein families. Here, we present MetaGeneHunt to identify specific protein domains and to normalize the hit-counts based on the domain length. We used MetaGeneHunt to investigate the potential for carbohydrate processing in the mouse gastrointestinal tract. We sampled, sequenced, and analyzed the microbial communities associated with the bolus in the stomach, intestine, cecum, and colon of five captive mice. Focusing on Glycoside Hydrolases (GHs) we found that, across samples, 58.3% of the 4,726,023 short-read sequences matching with a GH domain-containing protein were located outside the domain of interest. Next, before comparing the samples, the counts of localized hits matching the domains of interest were normalized to account for the corresponding domain length. Microbial communities in the intestine and cecum displayed characteristic GH profiles matching distinct microbial assemblages. Conversely, the stomach and colon were associated with structurally and functionally more diverse and variable microbial communities. Across samples, despite fluctuations, changes in the functional potential for carbohydrate processing correlated with changes in community composition. Overall MetaGeneHunt is a new way to quickly and precisely identify discrete protein domains in sequenced metagenomes processed with MG-RAST. In addition, using the sister program &quot;GeneHunt&quot; to create custom Reference Annotation Table, MetaGeneHunt provides an unprecedented way to (re)investigate the precise distribution of any protein domain in short-reads metagenomes.}, }
@article {pmid32381633, year = {2020}, author = {Ericsson, AC}, title = {Bronchopulmonary dysplasia: a crime of opportunity?.}, journal = {The European respiratory journal}, volume = {55}, number = {5}, pages = {}, doi = {10.1183/13993003.00551-2020}, pmid = {32381633}, issn = {1399-3003}, mesh = {*Bronchopulmonary Dysplasia/epidemiology/therapy ; Crime ; Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; Infant, Premature ; }, }
@article {pmid32380596, year = {2019}, author = {Francini-Filho, RB and Cordeiro, MC and Omachi, CY and Rocha, AM and Bahiense, L and Garcia, GD and Tschoeke, D and de Almeida, MG and Rangel, TP and De Oliveira, BCV and de Almeida, DQR and Menezes, R and Mazzei, EF and Joyeux, JC and Rezende, CE and Thompson, CC and Thompson, FL}, title = {Remote sensing, isotopic composition and metagenomics analyses revealed Doce River ore plume reached the southern Abrolhos Bank Reefs.}, journal = {The Science of the total environment}, volume = {697}, number = {}, pages = {134038}, doi = {10.1016/j.scitotenv.2019.134038}, pmid = {32380596}, issn = {1879-1026}, mesh = {Animals ; Anthozoa ; Brazil ; *Coral Reefs ; Ecosystem ; Isotopes/analysis ; *Metagenomics ; *Remote Sensing Technology ; Rivers/*chemistry ; Water Pollutants/*analysis ; }, abstract = {On November 5th, 2015, the Fundão dam rupture released >50 million m3 of ore tailings into the Doce River, Minas Gerais State, Brazil. The huge volume of mud spread along the river and reached the sea, 17 days after the disaster, in Regência, Espírito Santo State (ES). In 2018, after three years of the disaster, the impacts of the ore tailings in the marine environment are still unclear. This study aims to investigate possible short-term impacts in marine biodiversity caused by the ore tailings' mud over the reef ecosystems that are closest to the disaster area: i.e. recently discovered reefs in the southern Abrolhos Bank. A remote sensing surveillance including winds, sea surface temperature, total suspended material and watercolor (MODIS Aqua data) indicated that the iron tailings plume reached the southern portion of Abrolhos Bank on June 16th, 2016. Subsequently, to obtain further evidence of the presence of the tailings in the coral reefs, water samples were collected in a gradient spanning from the river estuary to the reefs in southern Abrolhos Bank, we also analyzed the isotopic and microbial composition of the samples, as well as the reef benthic composition. Despite no clues of negative impact on benthic (coral) communities, isotopic analysis confirmed the presence of the plume over the reefs area. This study serves as a baseline for future long-term impact assessments of the health of coral reefs in the Abrolhos Bank.}, }
@article {pmid32377002, year = {2020}, author = {Li, M and Liu, S and Wang, M and Hu, H and Yin, J and Liu, C and Huang, Y}, title = {Gut Microbiota Dysbiosis Associated with Bile Acid Metabolism in Neonatal Cholestasis Disease.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {7686}, pmid = {32377002}, issn = {2045-2322}, mesh = {Bile Acids and Salts/*metabolism ; Biomarkers ; Cholestasis/diagnosis/*etiology/*metabolism ; Disease Susceptibility ; *Dysbiosis ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; Liver/metabolism ; Liver Function Tests ; Metagenome ; Metagenomics/methods ; Prognosis ; }, abstract = {Neonatal cholestasis disease (NCD) is a complex and easily mis-diagnosed condition. We analyzed microbiota community structure in feces and measured short-chain fatty acids, bile acids (BAs) and liver function of 12 healthy, 13 NCD, and 13 treated infants after diagnosis. Based on 16S rRNA gene amplicon sequencing and gas-chromatographic-mass-spectrometric analysis of secondary BAs, we identified microbial genera and metabolites that associate with abnormal bile secretion. Streptococcus gallolyticus and Parabacteroides distasonis, and Lactobacillus gasseri had higher relative abundance in healthy and NCD infants respectively. Compared to NCD patients, healthy infants had higher LCA, CDCA and GCDCA fecal concentrations. The three microbial species and three secondary bile acids were selected as potential non-invasive combined biomarkers to diagnose NCD. We propose that microbiota-metabolite combined biomarkers could be used for diagnosis of NCD, and this may contribute to improved early clinical diagnosis of NCD in the future.}, }
@article {pmid32369006, year = {2020}, author = {Shah, S and Donze-Reiner, T and Shah, V}, title = {Diversity of navel microbiome in young adults.}, journal = {Journal of medical microbiology}, volume = {69}, number = {5}, pages = {721-727}, doi = {10.1099/jmm.0.001192}, pmid = {32369006}, issn = {1473-5644}, mesh = {Adolescent ; Adult ; Body Piercing ; Cluster Analysis ; DNA Barcoding, Taxonomic ; Female ; Humans ; Male ; Metagenomics/methods ; *Microbiota ; Opportunistic Infections/microbiology ; RNA, Ribosomal, 16S/genetics ; Sex Factors ; Skin/*microbiology ; Young Adult ; }, abstract = {Introduction. Human skin microbial communities represent a tremendous source of genetic diversity that evolves as a function of human age. Microbiota differs between regions of oily and moist skin, and appears to stabilize with age.Aim. We have a minimal understanding of the time frame required for the stabilization of skin microbiota, and the role played by gender. In the current study, we examined the microbiota present in the navel region of college-attending young adults in the age group of 18-25 years and investigated if diversity is associated with gender (male and female).Method. The study involved 16 female and six male subjects. Isolated DNA samples from navel swabs were processed using the Nextera XT library preparation kit and sequenced using the MiSeq platform. Data were analysed using QIIME and statistical analysis performed in R.Results. Microbiota of navel skin is dominated by Corynebacterium and Staphylococcus and includes opportunistic pathogens like Clostridium and Pseudomonas. Also present as the major component of the flora were the organisms normally associated with the gastrointestinal tract such as Acinetobacter, Campylobacter, Klebsiella and organisms from the Enterobacteriaceae and Moraxellaceae families. Comparison of alpha and beta diversity of the microbiota in the male and female navel regions suggests that the flora is not statistically different (P>0.05). However, pairwise comparison suggests that the abundance of 12 specific genera varied with gender, including higher abundance of Klebsiella and Enterobacter in females.Conclusion. Our findings indicate that the navel skin microbiota of young adults has a core microbiota of Corynebacterium and Staphylococcus. We also noted the presence of a significant number of opportunistic pathogens. A minor gender difference in the abundance of individual organisms was also observed.}, }
@article {pmid32354993, year = {2020}, author = {Chakraborty, A and Ruff, SE and Dong, X and Ellefson, ED and Li, C and Brooks, JM and McBee, J and Bernard, BB and Hubert, CRJ}, title = {Hydrocarbon seepage in the deep seabed links subsurface and seafloor biospheres.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {20}, pages = {11029-11037}, pmid = {32354993}, issn = {1091-6490}, mesh = {Alkanes/metabolism ; Archaea/classification/metabolism ; Bacteria/classification/metabolism ; Biodiversity ; Geologic Sediments/chemistry/*microbiology ; Gulf of Mexico ; Hydrocarbons/*metabolism ; Metagenome ; Metagenomics ; Microbiota/*physiology ; Petroleum/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry/*microbiology ; }, abstract = {Marine cold seeps transmit fluids between the subseafloor and seafloor biospheres through upward migration of hydrocarbons that originate in deep sediment layers. It remains unclear how geofluids influence the composition of the seabed microbiome and if they transport deep subsurface life up to the surface. Here we analyzed 172 marine surficial sediments from the deep-water Eastern Gulf of Mexico to assess whether hydrocarbon fluid migration is a mechanism for upward microbial dispersal. While 132 of these sediments contained migrated liquid hydrocarbons, evidence of continuous advective transport of thermogenic alkane gases was observed in 11 sediments. Gas seeps harbored distinct microbial communities featuring bacteria and archaea that are well-known inhabitants of deep biosphere sediments. Specifically, 25 distinct sequence variants within the uncultivated bacterial phyla Atribacteria and Aminicenantes and the archaeal order Thermoprofundales occurred in significantly greater relative sequence abundance along with well-known seep-colonizing members of the bacterial genus Sulfurovum, in the gas-positive sediments. Metabolic predictions guided by metagenome-assembled genomes suggested these organisms are anaerobic heterotrophs capable of nonrespiratory breakdown of organic matter, likely enabling them to inhabit energy-limited deep subseafloor ecosystems. These results point to petroleum geofluids as a vector for the advection-assisted upward dispersal of deep biosphere microbes from subsurface to surface environments, shaping the microbiome of cold seep sediments and providing a general mechanism for the maintenance of microbial diversity in the deep sea.}, }
@article {pmid32348348, year = {2020}, author = {Avila-Herrera, A and Thissen, J and Urbaniak, C and Be, NA and Smith, DJ and Karouia, F and Mehta, S and Venkateswaran, K and Jaing, C}, title = {Crewmember microbiome may influence microbial composition of ISS habitable surfaces.}, journal = {PloS one}, volume = {15}, number = {4}, pages = {e0231838}, pmid = {32348348}, issn = {1932-6203}, mesh = {*Astronauts ; DNA, Bacterial/genetics/isolation &amp; purification ; *Ecological Systems, Closed ; Environmental Monitoring/methods ; Humans ; Metagenome/genetics ; Microbiota/*genetics ; Saliva/microbiology ; Skin/microbiology ; Space Flight/*instrumentation ; *Spacecraft ; Time Factors ; }, abstract = {The International Space Station (ISS) is a complex built environment physically isolated from Earth. Assessing the interplay between the microbial community of the ISS and its crew is important for preventing biomedical and structural complications for long term human spaceflight missions. In this study, we describe one crewmember's microbial profile from body swabs of mouth, nose, ear, skin and saliva that were collected at eight different time points pre-, during and post-flight. Additionally, environmental surface samples from eight different habitable locations in the ISS were collected from two flights. Environmental samples from one flight were collected by the crewmember and samples from the next flight were collected after the crewmember departed. The microbial composition in both environment and crewmember samples was measured using shotgun metagenomic sequencing and processed using the Livermore Metagenomics Analysis Toolkit. Ordination of sample to sample distances showed that of the eight crew body sites analyzed, skin, nostril, and ear samples are more similar in microbial composition to the ISS surfaces than mouth and saliva samples; and that the microbial composition of the crewmember's skin samples are more closely related to the ISS surface samples collected by the crewmember on the same flight than ISS surface samples collected by other crewmembers on different flights. In these collections, species alpha diversity in saliva samples appears to decrease during flight and rebound after returning to Earth. This is the first study to compare the ISS microbiome to a crewmember's microbiome via shotgun metagenomic sequencing. We observed that the microbiome of the surfaces inside the ISS resemble those of the crew's skin. These data support future crew and ISS microbial surveillance efforts and the design of preventive measures to maintain crew habitat onboard spacecraft destined for long term space travel.}, }
@article {pmid32346574, year = {2020}, author = {Ajilogba, CF and Babalola, OO}, title = {Bambara groundnut soil metagenomics data.}, journal = {Data in brief}, volume = {30}, number = {}, pages = {105542}, pmid = {32346574}, issn = {2352-3409}, abstract = {Metagenomics analysis was carried out on extracted DNA of Rhizospheric soil samples from Bambara groundnut. This dataset presented reports on the bacterial communities at the different growth stages of Bambara groundnut and the bulk soil. Paired-end Illumina-Miseq sequencing of 16S rRNA genes was carried on the soil samples of the bacterial community with the phyla dominated by Actinobacteria (30.1%), Proteobacteria (22%), Acidobacteria (20.9%), Bacteroides (8.4%), Chloroflex (4.5%) and Firmicutes (4.4%) in all the soil samples. Samples from the bulk soil had the least average percent phyla, while samples at seed maturity stage had the highest average percent phyla. The alpha diversity at p = 0.05 was highest at this stage compared to the others and the control. Rubrobacter was the most predominant genera, after which is Acidobacterium and Skermanella. The biodiversity profile generated from the metagenomics analysis is useful in increasing knowledge of the drought-tolerance ability of Bambara groundnut. The data generated can be used to compare bacterial diversity at different growth stages of plants.}, }
@article {pmid32345218, year = {2020}, author = {Loo, EXL and Zain, A and Yap, GC and Purbojati, RW and Drautz-Moses, DI and Koh, YQ and Chong, YS and Tan, KH and Gluckman, PD and Yap, F and Eriksson, JG and Tham, E and Shek, LP and Kjelleberg, S and Schuster, SC and Banerjee, R and Lee, BW}, title = {Longitudinal assessment of antibiotic resistance gene profiles in gut microbiomes of infants at risk of eczema.}, journal = {BMC infectious diseases}, volume = {20}, number = {1}, pages = {312}, pmid = {32345218}, issn = {1471-2334}, support = {(R-178-000-222-511)//NMRC/ ; NMRC/TCR/004-NUS/2008; NMRC/TCR/012-NUHS/2014.//NMRC/ ; }, mesh = {Aminoglycosides/pharmacology ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics/metabolism ; Drug Resistance, Bacterial/*genetics ; Eczema/*diagnosis/etiology ; Escherichia coli/drug effects/enzymology/isolation &amp; purification ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Infant ; Infant, Newborn ; Klebsiella pneumoniae/drug effects/enzymology/isolation &amp; purification ; Longitudinal Studies ; Male ; Risk ; beta-Lactamases/genetics/metabolism ; beta-Lactams/pharmacology ; }, abstract = {BACKGROUND: While there is increasing knowledge about the gut microbiome, the factors influencing and the significance of the gut resistome are still not well understood. Infant gut commensals risk transferring multidrug-resistant antibiotic resistance genes (ARGs) to pathogenic bacteria. The rapid spread of multidrug-resistant pathogenic bacteria is a worldwide public health concern. Better understanding of the naïve infant gut resistome may build the evidence base for antimicrobial stewardship in both humans and in the food industry. Given the high carriage rate of extended spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae in Asia, we aimed to evaluate community prevalence, dynamics, and longitudinal changes in antibiotic resistance gene (ARG) profiles and prevalence of ESBL-producing E. coli and K. pneumoniae in the intestinal microbiome of infants participating in the Growing Up in Singapore Towards Healthy Outcomes (GUSTO) study, a longitudinal cohort study of pregnant women and their infants.<br><br>METHODS: We analysed ARGs in the first year of life among 75 infants at risk of eczema who had stool samples collected at multiple timepoints using metagenomics.<br><br>RESULTS: The mean number of ARGs per infant increased with age. The most common ARGs identified confer resistance to aminoglycoside, beta-lactam, macrolide and tetracycline antibiotics; all infants harboured these antibiotic resistance genes at some point in the first year of life. Few ARGs persisted throughout the first year of life. Beta-lactam resistant Escherichia coli and Klebsiella pneumoniae were detected in 4 (5.3%) and 32 (42.7%) of subjects respectively.<br><br>CONCLUSION: In this longitudinal cohort study of infants living in a region with high endemic antibacterial resistance, we demonstrate that majority of the infants harboured several antibiotic resistance genes in their gut and showed that the infant gut resistome is diverse and dynamic over the first year of life.}, }
@article {pmid32343737, year = {2020}, author = {Angebault, C and Payen, M and Woerther, PL and Rodriguez, C and Botterel, F}, title = {Combined bacterial and fungal targeted amplicon sequencing of respiratory samples: Does the DNA extraction method matter?.}, journal = {PloS one}, volume = {15}, number = {4}, pages = {e0232215}, pmid = {32343737}, issn = {1932-6203}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Biodiversity ; DNA, Bacterial/genetics/*isolation &amp; purification ; DNA, Fungal/genetics/*isolation &amp; purification ; France ; Fungi/classification/*genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/methods ; Microbiota/genetics ; Real-Time Polymerase Chain Reaction ; Respiratory System/*microbiology ; Sequence Analysis, DNA/methods ; Sputum/microbiology ; }, abstract = {BACKGROUND: High-throughput sequencing techniques are used to analyse the diversity of the respiratory microbiota in health and disease. Although extensive data are available regarding bacterial respiratory microbiota, its fungal component remains poorly studied. This is partly due to the technical issues associated with fungal metagenomics analyses. In this study, we compared two DNA extraction protocols and two fungal amplification targets for combined bacterial and fungal targeted amplicon sequencing analyses of the respiratory microbiota.<br><br>METHODS: Six sputa, randomly selected from routine samples in Mondor Hospital (Creteil, France) and treated anonymously, were tested after bacterial and fungal routine culture. Two of which were spiked with Aspergillus Fumigati and Aspergillus Nigri (105 conidia/mL). After mechanical lysis, DNA was extracted using automated QIAsymphony® extraction (AQE) or manual PowerSoil® MoBio extraction (MPE). DNA yield and purity were compared. DNA extracted from spiked sputa was subjected to (i) real-time PCR for Aspergillus DNA detection and (ii) combined metagenomic analyses targeting barcoded primers for fungal ITS1 and ITS2, and bacterial V1-V2 and V3-V4 16S regions. Amplicon libraries were prepared using MiSeq Reagent V3 kit on Illumina platform. Data were analysed using PyroMIC© and SHAMAN software, and compared with culture results.<br><br>RESULTS: AQE extraction provided a higher yield of DNA (AQE/MPE DNA ratio = 4.5 [1.3-11]) in a shorter time. The yield of Aspergillus DNA detected by qPCR was similar for spiked sputa regardless of extraction protocol. The extraction moderately impacted the diversity or relative abundances of bacterial communities using targeted amplicon sequencing (2/43 taxa impacted). For fungi, the relative abundances of 4/11 major taxa were impacted and AQE results were closer to culture results. The V1-V2 or V3-V4 and ITS1 or ITS2 targets assessed similarly the diversity of bacterial and fungal major taxa, but ITS2 and V3-V4 detected more minor taxa.<br><br>CONCLUSION: Our results showed the importance of DNA extraction for combined bacterial and fungal targeted metagenomics of respiratory samples. The extraction protocol can affect DNA yield and the relative abundances of few bacterial but more fungal taxa. For fungal analysis, ITS2 allowed the detection of a greater number of minor taxa compared with ITS1.}, }
@article {pmid32341166, year = {2020}, author = {Deboutte, W and Beller, L and Yinda, CK and Maes, P and de Graaf, DC and Matthijnssens, J}, title = {Honey-bee-associated prokaryotic viral communities reveal wide viral diversity and a profound metabolic coding potential.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {19}, pages = {10511-10519}, pmid = {32341166}, issn = {1091-6490}, mesh = {Animals ; Bacteria/genetics ; Bacteriophages/*genetics/metabolism ; Bees/genetics/*metabolism/*virology ; Biodiversity ; Ecosystem ; Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Phylogeny ; Pollination/genetics ; Symbiosis/genetics ; }, abstract = {Honey bees (Apis mellifera) produce an enormous economic value through their pollination activities and play a central role in the biodiversity of entire ecosystems. Recent efforts have revealed the substantial influence that the gut microbiota exert on bee development, food digestion, and homeostasis in general. In this study, deep sequencing was used to characterize prokaryotic viral communities associated with honey bees, which was a blind spot in research up until now. The vast majority of the prokaryotic viral populations are novel at the genus level, and most of the encoded proteins comprise unknown functions. Nevertheless, genomes of bacteriophages were predicted to infect nearly every major bee-gut bacterium, and functional annotation and auxiliary metabolic gene discovery imply the potential to influence microbial metabolism. Furthermore, undiscovered genes involved in the synthesis of secondary metabolic biosynthetic gene clusters reflect a wealth of previously untapped enzymatic resources hidden in the bee bacteriophage community.}, }
@article {pmid32340923, year = {2019}, author = {Gotschlich, EC and Colbert, RA and Gill, T}, title = {Methods in microbiome research: Past, present, and future.}, journal = {Best practice &amp; research. Clinical rheumatology}, volume = {33}, number = {6}, pages = {101498}, pmid = {32340923}, issn = {1532-1770}, support = {ZIA AR041184/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Dysbiosis ; Humans ; *Microbiota ; Research/trends ; }, abstract = {The human microbiome is impressively immense and participates in many aspects of our health and wellness, particularly involving the development and maintenance of a healthy immune system. Not only do our microbes teach the immune system to fight infection, they also teach immune tolerance and help maintain homeostasis. From this knowledge, we have learned that the loss of tolerance to microbiota in both innate and adaptive processes plays an important role in immune-mediated and autoimmune disease. In this chapter, we will be discussing about methods used to study the microbiome, both old and new methods, fundamental concepts that have taken hold within the field, and how these principles relate to rheumatology, including thoughts on how microbiome research may be focused in the next decade.}, }
@article {pmid32338757, year = {2020}, author = {Nagpal, S and Singh, R and Yadav, D and Mande, SS}, title = {MetagenoNets: comprehensive inference and meta-insights for microbial correlation networks.}, journal = {Nucleic acids research}, volume = {48}, number = {W1}, pages = {W572-W579}, pmid = {32338757}, issn = {1362-4962}, mesh = {Algorithms ; Humans ; Inflammatory Bowel Diseases/microbiology ; Metagenomics ; *Microbiota ; *Software ; }, abstract = {Microbial association networks are frequently used for understanding and comparing community dynamics from microbiome datasets. Inferring microbial correlations for such networks and obtaining meaningful biological insights, however, requires a lengthy data management workflow, choice of appropriate methods, statistical computations, followed by a different pipeline for suitably visualizing, reporting and comparing the associations. The complexity is further increased with the added dimension of multi-group 'meta-data' and 'inter-omic' functional profiles that are often associated with microbiome studies. This not only necessitates the need for categorical networks, but also integrated and bi-partite networks. Multiple options of network inference algorithms further add to the efforts required for performing correlation-based microbiome interaction studies. We present MetagenoNets, a web-based application, which accepts multi-environment microbial abundance as well as functional profiles, intelligently segregates 'continuous and categorical' meta-data and allows inference as well as visualization of categorical, integrated (inter-omic) and bi-partite networks. Modular structure of MetagenoNets ensures logical flow of analysis (inference, integration, exploration and comparison) in an intuitive and interactive personalized dashboard driven framework. Dynamic choice of filtration, normalization, data transformation and correlation algorithms ensures, that end-users get a one-stop solution for microbial network analysis. MetagenoNets is freely available at https://web.rniapps.net/metagenonets.}, }
@article {pmid32322441, year = {2020}, author = {Riley, NG and Goller, CC and Leggett, ZH and Lewis, DM and Ciccone, K and Dunn, RR}, title = {Catalyzing rapid discovery of gold-precipitating bacterial lineages with university students.}, journal = {PeerJ}, volume = {8}, number = {}, pages = {e8925}, pmid = {32322441}, issn = {2167-8359}, abstract = {Intriguing and potentially commercially useful microorganisms are found in our surroundings and new tools allow us to learn about their genetic potential and evolutionary history. Engaging students from different disciplines and courses in the search for microbes requires an exciting project with innovative but straightforward procedures and goals. Here we describe an interdisciplinary program to engage students from different courses in the sampling, identification and analysis of the DNA sequences of a unique yet common microbe, Delftia spp. A campus-wide challenge was created to identify the prevalence of this genus, able to precipitate gold, involving introductory level environmental and life science courses, upper-level advanced laboratory modules taken by undergraduate students (juniors and seniors), graduate students and staff from the campus. The number of participants involved allowed for extensive sampling while undergraduate researchers and students in lab-based courses participated in the sample processing and analyses, helping contextualize and solidify their learning of the molecular biology techniques. The results were shared at each step through publicly accessible websites and workshops. This model allows for the rapid discovery of Delftia presence and prevalence and is adaptable to different campuses and experimental questions.}, }
@article {pmid32320621, year = {2020}, author = {Mac Aogáin, M and Lau, KJX and Cai, Z and Kumar Narayana, J and Purbojati, RW and Drautz-Moses, DI and Gaultier, NE and Jaggi, TK and Tiew, PY and Ong, TH and Siyue Koh, M and Lim Yick Hou, A and Abisheganaden, JA and Tsaneva-Atanasova, K and Schuster, SC and Chotirmall, SH}, title = {Metagenomics Reveals a Core Macrolide Resistome Related to Microbiota in Chronic Respiratory Disease.}, journal = {American journal of respiratory and critical care medicine}, volume = {202}, number = {3}, pages = {433-447}, pmid = {32320621}, issn = {1535-4970}, mesh = {Adult ; Aged ; Aged, 80 and over ; Anti-Bacterial Agents ; Asthma/*microbiology ; Bronchiectasis/*microbiology ; Case-Control Studies ; Drug Resistance, Bacterial/*genetics ; Dysbiosis/*microbiology ; Female ; Fluoroquinolones ; Humans ; *Macrolides ; Male ; *Metagenomics ; Microbiota/*genetics ; Middle Aged ; Nebulizers and Vaporizers/microbiology ; Pulmonary Disease, Chronic Obstructive/*microbiology ; Severity of Illness Index ; Tetracycline Resistance/genetics ; beta-Lactam Resistance/genetics ; }, abstract = {Rationale: Long-term antibiotic use for managing chronic respiratory disease is increasing; however, the role of the airway resistome and its relationship to host microbiomes remains unknown.Objectives: To evaluate airway resistomes and relate them to host and environmental microbiomes using ultradeep metagenomic shotgun sequencing.Methods: Airway specimens from 85 individuals with and without chronic respiratory disease (severe asthma, chronic obstructive pulmonary disease, and bronchiectasis) were subjected to metagenomic sequencing to an average depth exceeding 20 million reads. Respiratory and device-associated microbiomes were evaluated on the basis of taxonomical classification and functional annotation including the Comprehensive Antibiotic Resistance Database to determine airway resistomes. Co-occurrence networks of gene-microbe association were constructed to determine potential microbial sources of the airway resistome. Paired patient-inhaler metagenomes were compared (n = 31) to assess for the presence of airway-environment overlap in microbiomes and/or resistomes.Measurements and Main Results: Airway metagenomes exhibit taxonomic and metabolic diversity and distinct antimicrobial resistance patterns. A &quot;core&quot; airway resistome dominated by macrolide but with high prevalence of β-lactam, fluoroquinolone, and tetracycline resistance genes exists and is independent of disease status or antibiotic exposure. Streptococcus and Actinomyces are key potential microbial reservoirs of macrolide resistance including the ermX, ermF, and msrD genes. Significant patient-inhaler overlap in airway microbiomes and their resistomes is identified where the latter may be a proxy for airway microbiome assessment in chronic respiratory disease.Conclusions: Metagenomic analysis of the airway reveals a core macrolide resistome harbored by the host microbiome.}, }
@article {pmid32317321, year = {2020}, author = {Price, TK and Wolff, B and Halverson, T and Limeira, R and Brubaker, L and Dong, Q and Mueller, ER and Wolfe, AJ}, title = {Temporal Dynamics of the Adult Female Lower Urinary Tract Microbiota.}, journal = {mBio}, volume = {11}, number = {2}, pages = {}, pmid = {32317321}, issn = {2150-7511}, support = {R01 DK104718/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Biodiversity ; Female ; Humans ; Metagenomics ; *Microbiota ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; Risk Factors ; Urinary Tract/*microbiology ; Urinary Tract Infections/microbiology ; }, abstract = {Temporal dynamics of certain human microbiotas have been described in longitudinal studies; variability often relates to modifiable factors or behaviors. Early studies of the urinary microbiota preferentially used samples obtained by transurethral catheterization to minimize vulvovaginal microbial contributions. Whereas voided specimens are preferred for longitudinal studies, the few studies that reported longitudinal data were limited to women with lower urinary tract (LUT) symptoms, due to ease of accessing a clinical population for sampling and the impracticality and risk of collecting repeated catheterized urine specimens in a nonclinical population. Here, we studied the microbiota of the LUT of nonsymptomatic, premenopausal women using midstream voided urine (MSU) specimens to investigate relationships between microbial dynamics and personal factors. Using 16S rRNA gene sequencing and a metaculturomics method called expanded quantitative urine culture (EQUC), we characterized the microbiotas of MSU and periurethral swab specimens collected daily for approximately 3 months from a small cohort of adult women. Participants were screened for eligibility, including the ability to self-collect paired urogenital specimens prior to enrollment. In this population, we found that measures of microbial dynamics related to specific participant-reported factors, particularly menstruation and vaginal intercourse. Further investigation of the trends revealed differences in the composition and diversity of LUT microbiotas within and across participants. These data, in combination with previous studies showing relationships between the LUT microbiota and LUT symptoms, suggest that personal factors relating to the genitourinary system may be an important consideration in the etiology, prevention, and/or treatment of LUT disorders.IMPORTANCE Following the discovery of the collective human urinary microbiota, important knowledge gaps remain, including the stability and variability of this microbial niche over time. Initial urinary studies preferentially utilized samples obtained by transurethral catheterization to minimize contributions from vulvovaginal microbes. However, catheterization has the potential to alter the urinary microbiota; therefore, voided specimens are preferred for longitudinal studies. In this report, we describe microbial findings obtained by daily assessment over 3 months in a small cohort of adult women. We found that, similarly to vaginal microbiotas, lower urinary tract (LUT) microbiotas are dynamic, with changes relating to several factors, particularly menstruation and vaginal intercourse. Our study results show that LUT microbiotas are both dynamic and resilient. They also offer novel opportunities to target LUT microbiotas by preventative or therapeutic means, through risk and/or protective factor modification.}, }
@article {pmid32307604, year = {2020}, author = {Jiang, T and Guo, C and Wang, M and Wang, M and You, S and Liu, Y and Zhang, X and Liu, H and Jiang, Y and Shao, H and Liang, Y and McMinn, A}, title = {Isolation and complete genome sequence of a novel cyanophage, S-B05, infecting an estuarine Synechococcus strain: insights into environmental adaptation.}, journal = {Archives of virology}, volume = {165}, number = {6}, pages = {1397-1407}, doi = {10.1007/s00705-020-04595-6}, pmid = {32307604}, issn = {1432-8798}, support = {No. 41906126//Natural Science Foundation of China/ ; No.41976117//Natural Science Foundation of China/ ; No.41676178//Natural Science Foundation of China/ ; LMB20091001//Open research fund of LMB/ ; }, mesh = {Base Composition ; Base Sequence ; China ; *Genome, Viral ; Host Specificity ; Metagenomics ; Myoviridae/*classification/*isolation &amp; purification/ultrastructure ; Open Reading Frames ; Pacific Ocean ; Phylogeny ; Seawater/*virology ; Synechococcus/*virology ; Water Microbiology ; Whole Genome Sequencing ; }, abstract = {A new cyanophage, S-B05, infecting a phycoerythrin-enriched (PE-type) Synechococcus strain was isolated by the liquid infection method, and its morphology and genetic features were examined. Phylogenetic analysis and morphological observation confirmed that S-B05 belongs to the family Myoviridae of the order Caudovirales. Its genome was fully sequenced, and found to be 208,857 bp in length with a G + C content of 39.9%. It contained 280 potential open reading frames and 123 conserved domains. Ninety-eight functional genes responsible for cyanophage structuring and packaging, DNA replication and regulation, and photosynthesis were identified, as well as genes encoding 172 hypothetical proteins. The genome of S-B05 is most similar to that of Prochlorococcus phage P-TIM68. Homologues of open reading frames of S-B05 can be found in various marine environments, as revealed by comparison of the S-B05 genome sequence to sequences in marine viral metagenomic databases. The presence of auxiliary metabolic genes (AMGs) related to photosynthesis, carbon metabolism, and phosphorus assimilation, as well as the phylogenetic relationships based on AMGs and the complete genome sequence, reflect the phage-host interaction mechanism or the specific adaptation strategy of the host to environmental conditions. The genome sequence information reported here will provide an important basis for further study of the adaptive evolution and ecological role of cyanophages and their hosts in the marine environment.}, }
@article {pmid32306993, year = {2020}, author = {Mejia, R and Damania, A and Jeun, R and Bryan, PE and Vargas, P and Juarez, M and Cajal, PS and Nasser, J and Krolewiecki, A and Lefoulon, E and Long, C and Drake, E and Cimino, RO and Slatko, B}, title = {Impact of intestinal parasites on microbiota and cobalamin gene sequences: a pilot study.}, journal = {Parasites &amp; vectors}, volume = {13}, number = {1}, pages = {200}, pmid = {32306993}, issn = {1756-3305}, support = {D34HP31024/HRSA/HRSA HHS/United States ; }, mesh = {Animals ; Child ; Child, Preschool ; *Coinfection/microbiology/parasitology ; Cross-Sectional Studies ; DNA, Helminth ; DNA, Protozoan ; Female ; Gastrointestinal Microbiome/*genetics ; Genes, Bacterial ; Giardia lamblia/classification/genetics/isolation &amp; purification ; Helminths/classification/genetics/isolation &amp; purification ; Humans ; *Intestines/microbiology/parasitology ; Male ; Metagenomics ; Parasites/classification/*genetics/isolation &amp; purification ; Pilot Projects ; Real-Time Polymerase Chain Reaction ; Vitamin B 12/*genetics/metabolism ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: Approximately 30% of children worldwide are infected with gastrointestinal parasites. Depending on the species, parasites can disrupt intestinal bacterial microbiota affecting essential vitamin biosynthesis.<br><br>METHODS: Stool samples were collected from 37 asymptomatic children from a previous cross-sectional Argentinian study. A multi-parallel real-time quantitative PCR was implemented for Ascaris lumbricoides, Ancylostoma duodenale, Necator americanus, Strongyloides stercoralis, Trichuris trichiura, Cryptosporidium spp., Entamoeba histolytica and Giardia duodenalis. In addition, whole-genome sequencing analysis was conducted for bacterial microbiota on all samples and analyzed using Livermore Metagenomic Analysis Toolkit and DIAMOND software. Separate analyses were carried out for uninfected, Giardia-only, Giardia + helminth co-infections, and helminth-only groups.<br><br>RESULTS: For Giardia-only infected children compared to uninfected children, DNA sequencing data showed a decrease in microbiota biodiversity that correlated with increasing Giardia burden and was statistically significant using Shannon's alpha diversity (Giardia-only > 1 fg/µl 2.346; non-infected group 3.253, P = 0.0317). An increase in diversity was observed for helminth-only infections with a decrease in diversity for Giardia + helminth co-infections (P = 0.00178). In Giardia-only infections, microbiome taxonomy changed from Firmicutes towards increasing proportions of Prevotella, with the degree of change related to the intensity of infection compared to uninfected (P = 0.0317). The abundance of Prevotella bacteria was decreased in the helminths-only group but increased for Giardia + helminth co-infections (P = 0.0262). Metagenomic analysis determined cobalamin synthesis was decreased in the Giardia > 1 fg/µl group compared to both the Giardia < 1 fg/µl and the uninfected group (P = 0.0369). Giardia + helminth group also had a decrease in cobalamin CbiM genes from helminth-only infections (P = 0.000754).<br><br>CONCLUSION: The study results may provide evidence for an effect of parasitic infections enabling the permissive growth of anaerobic bacteria such as Prevotella, suggesting an altered capacity of vitamin B12 (cobalamin) biosynthesis and potential impact on growth and development in children .}, }
@article {pmid32303552, year = {2020}, author = {Milani, C and Fontana, F and Alessandri, G and Mancabelli, L and Lugli, GA and Longhi, G and Anzalone, R and Viappiani, A and Duranti, S and Turroni, F and Ossiprandi, MC and van Sinderen, D and Ventura, M}, title = {Ecology of Lactobacilli Present in Italian Cheeses Produced from Raw Milk.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {12}, pages = {}, pmid = {32303552}, issn = {1098-5336}, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification ; Cheese/*microbiology ; Italy ; Lactobacillus/classification/genetics/isolation &amp; purification/*physiology ; Microbiota ; Milk/*microbiology ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; }, abstract = {Among the bacterial genera that are used for cheese production, Lactobacillus is a key taxon of high industrial relevance that is commonly present in commercial starter cultures for dairy fermentations. Certain lactobacilli play a defining role in the development of the organoleptic features during the ripening stages of particular cheeses. We performed an in-depth 16S rRNA gene-based microbiota analysis coupled with internally transcribed spacer-mediated Lactobacillus compositional profiling of 21 common Italian cheeses produced from raw milk in order to evaluate the ecological distribution of lactobacilli associated with this food matrix. Statistical analysis of the collected data revealed the existence of putative Lactobacillus community state types (LCSTs), which consist of clusters of Lactobacillus (sub)species. Each LCST is dominated by one or two taxa that appear to represent keystone elements of an elaborate network of positive and negative interactions with minor components of the cheese microbiota. The results obtained in this study reveal the existence of peculiar cheese microbiota assemblies that represent intriguing targets for further functional studies aimed at dissecting the species-specific role of bacteria in cheese manufacturing.IMPORTANCE The microbiota is known to play a key role in the development of the organoleptic features of dairy products. Lactobacilli have been reported to represent one of the main components of the nonstarter bacterial population, i.e., bacteria that are not deliberately added to the milk, harbored by cheese, although the species-level composition of this microbial population has never been assessed in detail. In the present study, we applied a recently developed metagenomic approach that employs an internally transcribed spacer to profile the Lactobacillus population harbored by cheese produced from raw milk at the (sub)species level. The obtained data revealed the existence of particular Lactobacillus community state types consisting of clusters of Lactobacillus (sub)species that tend to cooccur in the screened cheeses. Moreover, analysis of covariances between members of this genus indicate that these taxa form an elaborate network of positive and negative interactions that define specific clusters of covariant lactobacilli.}, }
@article {pmid32303546, year = {2020}, author = {Allaway, D and Haydock, R and Lonsdale, ZN and Deusch, OD and O'Flynn, C and Hughes, KR}, title = {Rapid Reconstitution of the Fecal Microbiome after Extended Diet-Induced Changes Indicates a Stable Gut Microbiome in Healthy Adult Dogs.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {13}, pages = {}, pmid = {32303546}, issn = {1098-5336}, mesh = {Animals ; Bacteria/classification/*isolation &amp; purification ; Diet/*veterinary ; Dogs ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Male ; Metagenome ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; }, abstract = {The gut microbiome has an important role in health, and diet represents a key lever for shaping the gut microbiome across all stages of life. Maternal milk consumption in neonates leads to long-term health effects, indicating that pliability in the infant gut microbiome in response to diet can drive enduring change. The ability of diet to drive lasting changes in the adult gut microbiome is less understood. We studied the effect of an extreme dietary shift on the fecal microbiome of 46 Labrador retriever dogs (mean age, 4.6 years) over 11 months. Dogs were fed a nutritionally complete, commercially available complex diet (CD) for a minimum of 5 weeks, followed by highly purified diets (PDs) for 36 weeks, and the initial CD for at least a further 4 weeks. Fecal samples were collected at regular intervals for DNA extraction. By analyzing 16S rRNA genes and the metagenomes, we observed minor effects on microbial diversity but significant changes in bacterial taxa and genetic potential when a PD was fed. Specifically, metagenomics identified an enrichment of quinone- and GABA-related pathways on PD, providing insights into dietary effects on cross-feeding strategies impacting community structure. When dogs returned to the CD, no significant differences were found with the initial time point. These findings are consistent with the gut microbiome being rapidly adaptable but capable of being reconstituted when provided with similar diets. These data highlight that long-term changes in the adult dog gut microbiome may only be achieved through long-term maintenance on a specified diet, rather than through feeding a transitionary diet.IMPORTANCE Diet can influence the adult gut microbiome (the community of bacteria) and health outcomes, but the ability to make changes persisting beyond feeding of a particular diet is poorly understood. We investigated whether feeding highly purified diets to adult dogs for 36 weeks would alter bacterial populations sufficiently to result in a persistent change following the dogs' return to a commercial diet. As expected, the microbiome changed when the purified diet was fed, but the original microbiome was reconstituted within weeks of the dogs returning to the commercial diet. The significance of these findings is in identifying an intrinsic stability of the host microbiome in healthy dogs, suggesting that dietary changes to support adult dog health through modifying the gut microbiome may be achieved only through maintenance on a specified diet, rather than through feeding transitionary diets.}, }
@article {pmid32284564, year = {2020}, author = {Bittinger, K and Zhao, C and Li, Y and Ford, E and Friedman, ES and Ni, J and Kulkarni, CV and Cai, J and Tian, Y and Liu, Q and Patterson, AD and Sarkar, D and Chan, SHJ and Maranas, C and Saha-Shah, A and Lund, P and Garcia, BA and Mattei, LM and Gerber, JS and Elovitz, MA and Kelly, A and DeRusso, P and Kim, D and Hofstaedter, CE and Goulian, M and Li, H and Bushman, FD and Zemel, BS and Wu, GD}, title = {Bacterial colonization reprograms the neonatal gut metabolome.}, journal = {Nature microbiology}, volume = {5}, number = {6}, pages = {838-847}, doi = {10.1038/s41564-020-0694-0}, pmid = {32284564}, issn = {2058-5276}, support = {P30 DK050306/DK/NIDDK NIH HHS/United States ; T32 CA009140/CA/NCI NIH HHS/United States ; UL1 TR001878/TR/NCATS NIH HHS/United States ; R01 GM080279/GM/NIGMS NIH HHS/United States ; R01 DK107565/DK/NIDDK NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {*Bacteria/classification/genetics ; Cohort Effect ; Computational Biology/methods ; Feces/microbiology ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Infant ; Infant, Newborn ; Metabolome ; Metabolomics/methods ; Metagenomics/methods ; Phylogeny ; Proteomics/methods ; }, abstract = {Initial microbial colonization and later succession in the gut of human infants are linked to health and disease later in life. The timing of the appearance of the first gut microbiome, and the consequences for the early life metabolome, are just starting to be defined. Here, we evaluated the gut microbiome, proteome and metabolome in 88 African-American newborns using faecal samples collected in the first few days of life. Gut bacteria became detectable using molecular methods by 16 h after birth. Detailed analysis of the three most common species, Escherichia coli, Enterococcus faecalis and Bacteroides vulgatus, did not suggest a genomic signature for neonatal gut colonization. The appearance of bacteria was associated with reduced abundance of approximately 50 human proteins, decreased levels of free amino acids and an increase in products of bacterial fermentation, including acetate and succinate. Using flux balance modelling and in vitro experiments, we provide evidence that fermentation of amino acids provides a mechanism for the initial growth of E. coli, the most common early colonizer, under anaerobic conditions. These results provide a deep characterization of the first microbes in the human gut and show how the biochemical environment is altered by their appearance.}, }
@article {pmid32275297, year = {2020}, author = {Simonin, M and Dasilva, C and Terzi, V and Ngonkeu, ELM and Diouf, D and Kane, A and Béna, G and Moulin, L}, title = {Influence of plant genotype and soil on the wheat rhizosphere microbiome: evidences for a core microbiome across eight African and European soils.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {6}, pages = {}, doi = {10.1093/femsec/fiaa067}, pmid = {32275297}, issn = {1574-6941}, mesh = {France ; Fungi ; Genotype ; Italy ; *Microbiota ; Plant Roots ; *Rhizosphere ; Soil ; Soil Microbiology ; Triticum ; }, abstract = {Here, we assessed the relative influence of wheat genotype, agricultural practices (conventional vs organic) and soil type on the rhizosphere microbiome. We characterized the prokaryotic (archaea and bacteria) and eukaryotic (fungi and protists) communities in soils from four different countries (Cameroon, France, Italy, Senegal) and determined if a rhizosphere core microbiome existed across these different countries. The wheat genotype had a limited effect on the rhizosphere microbiome (2% of variance) as the majority of the microbial taxa were consistently associated to multiple wheat genotypes grown in the same soil. Large differences in taxa richness and in community structure were observed between the eight soils studied (57% variance) and the two agricultural practices (10% variance). Despite these differences between soils, we observed that 177 taxa (2 archaea, 103 bacteria, 41 fungi and 31 protists) were consistently detected in the rhizosphere, constituting a core microbiome. In addition to being prevalent, these core taxa were highly abundant and collectively represented 50% of the reads in our data set. Based on these results, we identify a list of key taxa as future targets of culturomics, metagenomics and wheat synthetic microbiomes. Additionally, we show that protists are an integral part of the wheat holobiont that is currently overlooked.}, }
@article {pmid32273998, year = {2020}, author = {French, BJ and Lim, YW and Zgliczynski, BJ and Edwards, RA and Rohwer, F and Sandin, SA}, title = {Decoding diversity in a coral reef fish species complex with restricted range using metagenomic sequencing of gut contents.}, journal = {Ecology and evolution}, volume = {10}, number = {7}, pages = {3413-3423}, pmid = {32273998}, issn = {2045-7758}, abstract = {Aim: Identification of the processes that generate and maintain species diversity within the same region can provide insight into biogeographic patterns at broader spatiotemporal scales. Hawkfishes in the genus Paracirrhites are a unique taxon to explore with respect to niche differentiation, exhibiting diagnostic differences in coloration, and an apparent center of distribution outside of the Indo-Malay-Philippine (IMP) biodiversity hotspot for coral reef fishes. Our aim is to use next-generation sequencing methods to leverage samples of a taxon at their center of maximum diversity to explore phylogenetic relationships and a possible mechanism of coexistence.<br><br>Location: Flint Island, Southern Line Islands, Republic of Kiribati.<br><br>Methods: A comprehensive review of museum records, the primary literature, and unpublished field survey records was undertaken to determine ranges for four &quot;arc-eye&quot; hawkfish species in the Paracirrhites species complex and a potential hybrid. Fish from four Paracirrhites species were collected from Flint Island in the Southern Line Islands, Republic of Kiribati. Hindgut contents were sequenced, and subsequent metagenomic analyses were used to assess the phylogenetic relatedness of the host fish, the microbiome community structure, and prey remains for each species.<br><br>Results: Phylogenetic analyses conducted with recovered mitochondrial genomes revealed clustering of P. bicolor with P. arcatus and P. xanthus with P. nisus, which were unexpected on the basis of previous morphological work in this species complex. Differences in taxonomic composition of gut microbial communities and presumed prey remains indicate likely separation of foraging niches.<br><br>Main Conclusions: Our findings point toward previously unidentified relationships in this cryptic species complex at its proposed center of distribution. The three species endemic to the Polynesian province (P. nisus, P. xanthus, and P. bicolor) cluster separately from the more broadly distributed P. arcatus on the basis of relative abundance of metazoan sequences in the gut (presumed prey remains). Discordance between gut microbial communities and phylogeny of the host fish further reinforce the hypothesis of niche separation.}, }
@article {pmid32271799, year = {2020}, author = {Brumfield, KD and Hasan, NA and Leddy, MB and Cotruvo, JA and Rashed, SM and Colwell, RR and Huq, A}, title = {A comparative analysis of drinking water employing metagenomics.}, journal = {PloS one}, volume = {15}, number = {4}, pages = {e0231210}, pmid = {32271799}, issn = {1932-6203}, mesh = {Bacteria/genetics/pathogenicity ; Colony Count, Microbial ; DNA/genetics ; Drinking Water/*microbiology/*parasitology ; Genes, Bacterial ; *Metagenomics ; Microbiota/genetics ; Principal Component Analysis ; Virulence/genetics ; }, abstract = {The microbiological content of drinking water traditionally is determined by employing culture-dependent methods that are unable to detect all microorganisms, especially those that are not culturable. High-throughput sequencing now makes it possible to determine the microbiome of drinking water. Thus, the natural microbiota of water and water distribution systems can now be determined more accurately and analyzed in significantly greater detail, providing comprehensive understanding of the microbial community of drinking water applicable to public health. In this study, shotgun metagenomic analysis was performed to determine the microbiological content of drinking water and to provide a preliminary assessment of tap, drinking fountain, sparkling natural mineral, and non-mineral bottled water. Predominant bacterial species detected were members of the phyla Actinobacteria and Proteobacteria, notably the genera Alishewanella, Salmonella, and Propionibacterium in non-carbonated non-mineral bottled water, Methyloversatilis and Methylibium in sparkling natural mineral water, and Mycobacterium and Afipia in tap and drinking fountain water. Fecal indicator bacteria, i.e., Escherichia coli or enterococci, were not detected in any samples examined in this study. Bacteriophages and DNA encoding a few virulence-associated factors were detected but determined to be present only at low abundance. Antibiotic resistance markers were detected only at abundance values below our threshold of confidence. DNA of opportunistic plant and animal pathogens was identified in some samples and these included bacteria (Mycobacterium spp.), protozoa (Acanthamoeba mauritaniensis and Acanthamoeba palestinensis), and fungi (Melampsora pinitorqua and Chryosporium queenslandicum). Archaeal DNA (Candidatus Nitrosoarchaeum) was detected only in sparkling natural mineral water. This preliminary study reports the complete microbiome (bacteria, viruses, fungi, and protists) of selected types of drinking water employing whole-genome high-throughput sequencing and bioinformatics. Investigation into activity and function of the organisms detected is in progress.}, }
@article {pmid32267865, year = {2020}, author = {Kaur, K and Khatri, I and Akhtar, A and Subramanian, S and Ramya, TNC}, title = {Metagenomics analysis reveals features unique to Indian distal gut microbiota.}, journal = {PloS one}, volume = {15}, number = {4}, pages = {e0231197}, pmid = {32267865}, issn = {1932-6203}, mesh = {Adult ; Bifidobacterium/*genetics ; Body Mass Index ; Carbohydrate Metabolism/physiology ; DNA, Bacterial/genetics ; Diet ; Eating ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Healthy Volunteers ; Humans ; India ; Male ; Metagenomics/*methods ; Phylogeny ; Prevotella/*genetics ; Whole Genome Sequencing ; }, abstract = {Various factors including diet, age, geography, culture and socio-economic status have a role in determining the composition of the human gut microbiota. The human gut microbial composition is known to be altered in disease conditions. Considering the important role of the gut microbiome in maintaining homeostasis and overall health, it is important to understand the microbial diversity and the functional metagenome of the healthy gut. Here, we characterized the microbiota of 31 fecal samples from healthy individuals of Indian ethnic tribes from Ladakh, Jaisalmer and Khargone by shotgun metagenomic sequencing. Sequence analysis revealed that Bifidobacterium and Prevotella were the key microbes contributing to the differences among Jaisalmer, Khargone and Ladakh samples at the genus level. Our correlation network study identified carbohydrate-active enzymes and carbohydrate binding proteins that are associated with specific genera in the different Indian geographical regions studied. Network analysis of carbohydrate-active enzymes and genus abundance revealed that the presence of different carbohydrate-active enzymes is driven by differential abundance of genera. The correlation networks were different in the different geographical regions, and these interactions suggest the role of less abundant genera in shaping the gut environment. We compared our data with samples from different countries and found significant differences in taxonomic composition and abundance of carbohydrate-active enzymes in the gut microbiota as compared to the other countries.}, }
@article {pmid32259760, year = {2020}, author = {An, X and Chen, Y and Chen, G and Feng, L and Zhang, Q}, title = {Integrated metagenomic and metaproteomic analyses reveal potential degradation mechanism of azo dye-Direct Black G by thermophilic microflora.}, journal = {Ecotoxicology and environmental safety}, volume = {196}, number = {}, pages = {110557}, doi = {10.1016/j.ecoenv.2020.110557}, pmid = {32259760}, issn = {1090-2414}, mesh = {Azo Compounds/*analysis ; Biodegradation, Environmental ; Ecosystem ; Gene Expression Profiling ; Gene Library ; Gene Ontology ; Metagenome/*genetics ; Metagenomics ; Microbiota/*genetics ; Proteome/*genetics ; Water Pollutants, Chemical/*analysis ; }, abstract = {Direct Black G (DBG) is a typical toxic azo dye with extensive applications but it poses a serious threat to the aquatic ecosystem and humans. It is necessary to efficiently and safely remove DBG from environments by the application of various treatment technologies. A thermophilic microflora previously isolated from the soil can effectively metabolize DBG. However, the molecular basis of DBG degradation by this thermophilic microflora remains unknown. In this study, metagenomic sequencing technology and qRT-PCR have been used to elucidate the functional potential of genes and their modes of action on DBG. A quantitative metaproteomic method was further utilized to identify the relative functional proteins involved. Subsequently, the possible co-metabolic molecular mechanisms of DBG degradation by candidate genes and functional proteins of the thermophilic microflora were illustrated. The combination of metagenomics and metaproteomics to investigate the degradation of DBG by a microflora was reported for the first time in recent literature; this can further provide a deep insight into the molecular degradation mechanism of dye pollutants by natural microflora.}, }
@article {pmid32247981, year = {2020}, author = {Yue, Y and Shao, T and Long, X and He, T and Gao, X and Zhou, Z and Liu, Z and Rengel, Z}, title = {Microbiome structure and function in rhizosphere of Jerusalem artichoke grown in saline land.}, journal = {The Science of the total environment}, volume = {724}, number = {}, pages = {138259}, doi = {10.1016/j.scitotenv.2020.138259}, pmid = {32247981}, issn = {1879-1026}, mesh = {*Helianthus ; *Microbiota ; Rhizosphere ; Soil ; Soil Microbiology ; }, abstract = {The improvement and development of saline-alkali soils is currently a hot economic and scientific issue, and exploring the correlation between rhizosphere microorganisms of plants growing on saline-alkali soils and their salt tolerance has become the key point of related research. In our study, the community structure of microorganism and various properties of saline soils were characterized in which Jerusalem artichoke grown along a soil salinity gradient. A variety of basic soil properties were measured and the amplicon was performed as well as metagenomic sequencing on coastal saline soils using various techniques (such as RDA analysis and the assembly of genomes) to evaluate microbial functions. In addition, WGCNA (Weighted gene coexpression network analysis) method was used to identify the species related to salt stress and the sequence binning to assemble two enriched putative bacterial genomes. The research showed the cultivation of Jerusalem artichoke on saline soil changed soil physico-chemical and enzymatic properties; most of the rapidly changing as well as the long-term stable properties differed significantly between the rhizosphere and bulk soils. The amplicon and metagenomic sequencing revealed the function and structure of microorganisms varied between the rhizosphere and bulk soils, with greater microbial diversity in the rhizosphere. Catalase activity and the moisture content were the factors with the greatest impact on microorganisms. The putative genomes of two species of microorganisms (belong to Nitrospira and Gemmatimonas) were assembled, identified microbial species that were highly responsive to salt stress and that may play a key role in saline soil, stressed the important role of archaea in microbial communities in response to salt stress. The study provides a comprehensive understanding of the microbial community structure in the rhizosphere of Jerusalem artichoke to enable the improvement and economic development of saline land.}, }
@article {pmid32243481, year = {2020}, author = {Hess, MK and Rowe, SJ and Van Stijn, TC and Henry, HM and Hickey, SM and Brauning, R and McCulloch, AF and Hess, AS and Kirk, MR and Kumar, S and Pinares-Patiño, C and Kittelmann, S and Wood, GR and Janssen, PH and McEwan, JC}, title = {A restriction enzyme reduced representation sequencing approach for low-cost, high-throughput metagenome profiling.}, journal = {PloS one}, volume = {15}, number = {4}, pages = {e0219882}, pmid = {32243481}, issn = {1932-6203}, mesh = {Animals ; Bacteria/genetics ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing/economics/*methods ; Male ; Metagenome ; Metagenomics/economics/*methods ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Sheep/*microbiology ; }, abstract = {Microbial community profiles have been associated with a variety of traits, including methane emissions in livestock. These profiles can be difficult and expensive to obtain for thousands of samples (e.g. for accurate association of microbial profiles with traits), therefore the objective of this work was to develop a low-cost, high-throughput approach to capture the diversity of the rumen microbiome. Restriction enzyme reduced representation sequencing (RE-RRS) using ApeKI or PstI, and two bioinformatic pipelines (reference-based and reference-free) were compared to bacterial 16S rRNA gene sequencing using repeated samples collected two weeks apart from 118 sheep that were phenotypically extreme (60 high and 58 low) for methane emitted per kg dry matter intake (n = 236). DNA was extracted from freeze-dried rumen samples using a phenol chloroform and bead-beating protocol prior to RE-RRS. The resulting sequences were used to investigate the repeatability of the rumen microbial community profiles, the effect of laboratory and analytical method, and the relationship with methane production. The results suggested that the best method was PstI RE-RRS analyzed with the reference-free approach, which accounted for 53.3±5.9% of reads, and had repeatabilities of 0.49±0.07 and 0.50±0.07 for the first two principal components (PC1 and PC2), phenotypic correlations with methane yield of 0.43±0.06 and 0.46±0.06 for PC1 and PC2, and explained 41±8% of the variation in methane yield. These results were significantly better than for bacterial 16S rRNA gene sequencing of the same samples (p<0.05) except for the correlation between PC2 and methane yield. A Sensitivity study suggested approximately 2000 samples could be sequenced in a single lane on an Illumina HiSeq 2500, meaning the current work using 118 samples/lane and future proposed 384 samples/lane are well within that threshold. With minor adaptations, our approach could be used to obtain microbial profiles from other metagenomic samples.}, }
@article {pmid32235930, year = {2020}, author = {Basolo, A and Hohenadel, M and Ang, QY and Piaggi, P and Heinitz, S and Walter, M and Walter, P and Parrington, S and Trinidad, DD and von Schwartzenberg, RJ and Turnbaugh, PJ and Krakoff, J}, title = {Effects of underfeeding and oral vancomycin on gut microbiome and nutrient absorption in humans.}, journal = {Nature medicine}, volume = {26}, number = {4}, pages = {589-598}, doi = {10.1038/s41591-020-0801-z}, pmid = {32235930}, issn = {1546-170X}, support = {R01 HL122593/HL/NHLBI NIH HHS/United States ; R21 CA227232/CA/NCI NIH HHS/United States ; P30 DK098722/DK/NIDDK NIH HHS/United States ; }, mesh = {Administration, Oral ; Adolescent ; Adult ; Caloric Restriction ; Cross-Over Studies ; Diet ; Double-Blind Method ; Energy Metabolism/drug effects ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Intestinal Absorption/*drug effects ; Male ; Malnutrition/*metabolism/*microbiology ; Middle Aged ; Nutrients/*pharmacokinetics ; Vancomycin/*administration &amp; dosage/pharmacology ; Verrucomicrobia/isolation &amp; purification ; Young Adult ; }, abstract = {Direct evidence in humans for the impact of the microbiome on nutrient absorption is lacking. We conducted an extended inpatient study using two interventions that we hypothesized would alter the gut microbiome and nutrient absorption. In each, stool calorie loss, a direct proxy of nutrient absorption, was measured. The first phase was a randomized cross-over dietary intervention in which all participants underwent in random order 3 d of over- and underfeeding. The second was a randomized, double-blind, placebo-controlled pharmacologic intervention using oral vancomycin or matching placebo (NCT02037295). Twenty-seven volunteers (17 men and 10 women, age 35.1 ± 7.3, BMI 32.3 ± 8.0), who were healthy other than having impaired glucose tolerance and obesity, were enrolled and 25 completed the entire trial. The primary endpoints were the effects of dietary and pharmacological intervention on stool calorie loss. We hypothesized that stool calories expressed as percentage of caloric intake would increase with underfeeding compared with overfeeding and increase during oral vancomycin treatment. Both primary endpoints were met. Greater stool calorie loss was observed during underfeeding relative to overfeeding and during vancomycin treatment compared with placebo. Key secondary endpoints were to evaluate the changes in gut microbial community structure as evidenced by amplicon sequencing and metagenomics. We observed only a modest perturbation of gut microbial community structure with under- versus overfeeding but a more widespread change in community structure with reduced diversity with oral vancomycin. Increase in Akkermansia muciniphila was common to both interventions that resulted in greater stool calorie loss. These results indicate that nutrient absorption is sensitive to environmental perturbations and support the translational relevance of preclinical models demonstrating a possible causal role for the gut microbiome in dietary energy harvest.}, }
@article {pmid32235826, year = {2020}, author = {Zhu, F and Ju, Y and Wang, W and Wang, Q and Guo, R and Ma, Q and Sun, Q and Fan, Y and Xie, Y and Yang, Z and Jie, Z and Zhao, B and Xiao, L and Yang, L and Zhang, T and Feng, J and Guo, L and He, X and Chen, Y and Chen, C and Gao, C and Xu, X and Yang, H and Wang, J and Dang, Y and Madsen, L and Brix, S and Kristiansen, K and Jia, H and Ma, X}, title = {Metagenome-wide association of gut microbiome features for schizophrenia.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {1612}, pmid = {32235826}, issn = {2041-1723}, mesh = {Animals ; Bacteria/classification/genetics ; Behavior, Animal ; Disease Models, Animal ; Fecal Microbiota Transplantation ; Feces/microbiology ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Male ; *Metagenome ; Metagenomics/methods ; Mice ; Mice, Inbred C57BL ; RNA, Ribosomal, 16S ; ROC Curve ; Risk Factors ; Schizophrenia/*metabolism/*microbiology ; Social Behavior ; Streptococcus ; }, abstract = {Evidence is mounting that the gut-brain axis plays an important role in mental diseases fueling mechanistic investigations to provide a basis for future targeted interventions. However, shotgun metagenomic data from treatment-naïve patients are scarce hampering comprehensive analyses of the complex interaction between the gut microbiota and the brain. Here we explore the fecal microbiome based on 90 medication-free schizophrenia patients and 81 controls and identify a microbial species classifier distinguishing patients from controls with an area under the receiver operating characteristic curve (AUC) of 0.896, and replicate the microbiome-based disease classifier in 45 patients and 45 controls (AUC = 0.765). Functional potentials associated with schizophrenia include differences in short-chain fatty acids synthesis, tryptophan metabolism, and synthesis/degradation of neurotransmitters. Transplantation of a schizophrenia-enriched bacterium, Streptococcus vestibularis, appear to induces deficits in social behaviors, and alters neurotransmitter levels in peripheral tissues in recipient mice. Our findings provide new leads for further investigations in cohort studies and animal models.}, }
@article {pmid32231240, year = {2020}, author = {Chaudhari, DS and Dhotre, DP and Agarwal, DM and Gaike, AH and Bhalerao, D and Jadhav, P and Mongad, D and Lubree, H and Sinkar, VP and Patil, UK and Salvi, S and Bavdekar, A and Juvekar, SK and Shouche, YS}, title = {Gut, oral and skin microbiome of Indian patrilineal families reveal perceptible association with age.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {5685}, pmid = {32231240}, issn = {2045-2322}, mesh = {Adolescent ; Adult ; *Age Factors ; Aged ; Aged, 80 and over ; Bacteria/genetics ; Child ; Child, Preschool ; Family ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/genetics ; Humans ; India/epidemiology ; Male ; Metagenome/genetics ; Metagenomics/methods ; Microbiota/*genetics ; Middle Aged ; Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; Skin/microbiology ; }, abstract = {The human microbiome plays a key role in maintaining host homeostasis and is influenced by age, geography, diet, and other factors. Traditionally, India has an established convention of extended family arrangements wherein three or more generations, bound by genetic relatedness, stay in the same household. In the present study, we have utilized this unique family arrangement to understand the association of age with the microbiome. We characterized stool, oral and skin microbiome of 54 healthy individuals from six joint families by 16S rRNA gene-based metagenomics. In total, 69 (1.03%), 293 (2.68%) and 190 (8.66%) differentially abundant OTUs were detected across three generations in the gut, skin and oral microbiome, respectively. Age-associated changes in the gut and oral microbiome of patrilineal families showed positive correlations in the abundance of phyla Proteobacteria and Fusobacteria, respectively. Genera Treponema and Fusobacterium showed a positive correlation with age while Granulicatella and Streptococcus showed a negative correlation with age in the oral microbiome. Members of genus Prevotella illustrated high abundance and prevalence as a core OTUs in the gut and oral microbiome. In conclusion, this study highlights that precise and perceptible association of age with microbiome can be drawn when other causal factors are kept constant.}, }
@article {pmid32208434, year = {2020}, author = {Jangid, A and Fukuda, S and Seki, M and Horiuchi, T and Suzuki, Y and Taylor, TD and Ohno, H and Prakash, T}, title = {Association of colitis with gut-microbiota dysbiosis in clathrin adapter AP-1B knockout mice.}, journal = {PloS one}, volume = {15}, number = {3}, pages = {e0228358}, pmid = {32208434}, issn = {1932-6203}, mesh = {Adaptor Protein Complex 1/*deficiency/*genetics ; Animals ; Colitis/complications/*genetics/*microbiology ; Dysbiosis/complications/*microbiology ; *Gastrointestinal Microbiome ; Metagenomics ; Mice ; }, abstract = {Inflammatory bowel disease results from alterations in the immune system and intestinal microbiota. The role of intestinal epithelial cells (IECs) in maintaining gut homeostasis is well known and its perturbation often causes gastrointestinal disorders including IBD. The epithelial specific adaptor protein (AP)-1B is involved in the establishment of the polarity of IECs. Deficiency of the AP-1B μ subunit (Ap1m2-/-) leads to the development of chronic colitis in mice. However, how this deficiency affects the gut microbes and its potential functions remains elusive. To gain insights into the gut microbiome of Ap1m2-/- mice having the colitis phenotype, we undertook shotgun metagenomic sequencing analysis of knockout mice. We found important links to the microbial features involved in altering various physiological pathways, including carbohydrate metabolism, nutrient transportation, oxidative stress, and bacterial pathogenesis (cell motility). In addition, an increased abundance of sulfur-reducing and lactate-producing bacteria has been observed which may aggravate the colitis condition.}, }
@article {pmid32207614, year = {2020}, author = {Hu, W and Liang, J and Ju, F and Wang, Q and Liu, R and Bai, Y and Liu, H and Qu, J}, title = {Metagenomics Unravels Differential Microbiome Composition and Metabolic Potential in Rapid Sand Filters Purifying Surface Water Versus Groundwater.}, journal = {Environmental science &amp; technology}, volume = {54}, number = {8}, pages = {5197-5206}, doi = {10.1021/acs.est.9b07143}, pmid = {32207614}, issn = {1520-5851}, mesh = {Filtration ; *Groundwater ; Metagenomics ; *Microbiota ; Oxidation-Reduction ; Sand ; *Water Purification ; }, abstract = {Designed for retaining suspended particles, rapid sand filters (RSFs) are widely used in drinking water treatment. There is increasing evidence that microbial processes within RSFs contribute to the transformation and removal of organic carbon, nitrogen, and metal pollutants. Here, we linked microbial composition and functional profiles with the treatment performance of 12 different RSFs that significantly removed influent ammonium and manganese (Mn). Metagenomic analyses showed that chemoautotrophic or methanotrophic bacteria were prevalent in the groundwater filters, and chemoheterotrophic bacteria encoding more carbohydrate- and xenobiotic-metabolizing genes were more abundant in the surface water filters. Approximately 92% of ammonium was transformed into nitrate, with a critical contribution from comammox Nitrospira. The composition of comammox amoA differed between groundwater and surface water filters, with clade A dominating groundwater filters (78.0 ± 12.0%) and clade B dominating surface water filters (91.9 ± 8.9%). Further, we identified six bacterial genera encoding known Mn(II)-oxidizing genes in the RSFs, with Pseudomonas accounting for 71.1%. These Mn(II)-oxidizing bacteria might promote Mn(II) oxidation and thus increase the removal of influent Mn. Overall, our study gave a comprehensive investigation of microbiome in RSFs and highlighted the roles of comammox and Mn(II)-oxidizing bacteria in water purification.}, }
@article {pmid32203121, year = {2020}, author = {Campbell, TP and Sun, X and Patel, VH and Sanz, C and Morgan, D and Dantas, G}, title = {The microbiome and resistome of chimpanzees, gorillas, and humans across host lifestyle and geography.}, journal = {The ISME journal}, volume = {14}, number = {6}, pages = {1584-1599}, doi = {10.1038/s41396-020-0634-2}, pmid = {32203121}, issn = {1751-7370}, support = {DP2 DK098089/DK/NIDDK NIH HHS/United States ; R01 AI123394/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial ; Gastrointestinal Microbiome/drug effects ; Geography ; Gorilla gorilla/*microbiology ; Humans ; Life Style ; Metagenomics ; *Microbiota ; Pan troglodytes/*microbiology ; }, abstract = {The gut microbiome can vary across differences in host lifestyle, geography, and host species. By comparing closely related host species across varying lifestyles and geography, we can evaluate the relative contributions of these factors in structuring the composition and functions of the microbiome. Here we show that the gut microbial taxa, microbial gene family composition, and resistomes of great apes and humans are more related by host lifestyle than geography. We show that captive chimpanzees and gorillas are enriched for microbial genera commonly found in non-Westernized humans. Captive ape microbiomes also had up to ~34-fold higher abundance and up to ~5-fold higher richness of all antibiotic resistance genes compared with wild apes. Through functional metagenomics, we identified a number of novel antibiotic resistance genes, including a gene conferring resistance to colistin, an antibiotic of last resort. Finally, by comparing our study cohorts to human and ape gut microbiomes from a diverse range of environments and lifestyles, we find that the influence of host lifestyle is robust to various geographic locations.}, }
@article {pmid32200314, year = {2020}, author = {Wang, Y and Hu, Y and Liu, F and Cao, J and Lv, N and Zhu, B and Zhang, G and Gao, GF}, title = {Integrated metagenomic and metatranscriptomic profiling reveals differentially expressed resistomes in human, chicken, and pig gut microbiomes.}, journal = {Environment international}, volume = {138}, number = {}, pages = {105649}, doi = {10.1016/j.envint.2020.105649}, pmid = {32200314}, issn = {1873-6750}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Chickens ; China ; *Gastrointestinal Microbiome/genetics ; Genes, Bacterial ; Humans ; Metagenomics ; Swine ; }, abstract = {Gut microbiota is a reservoir of antibiotic resistance genes (ARGs). Yet, limited information is available regarding the presence (metagenomic DNA level) and expression profiles (metatranscriptomic RNA level) of ARGs in gut microbiota. Here, we used both metagenomic and metatranscriptomic approaches to comprehensively reveal the abundance, diversity, and expression of ARGs in human, chicken, and pig gut microbiomes in China. Based on deep sequencing data and ARG databases, a total of 330 ARGs associated with 21 antibiotic classes were identified in 18 human, chicken, and pig fecal samples. Metatranscriptomic analysis revealed that 49.4, 66.5, and 56.6% of ARGs identified in human, chicken, and pig gut microbiota, respectively, were expressed, indicating that a large proportion of ARGs were not transcriptionally active. Further analysis demonstrated that transcript abundance of tetracycline, aminoglycoside, and beta-lactam resistance genes was mainly contributed by acquired ARGs. We also found that various biocide, chemical, and metal resistance genes were actively transcribed in human and animal guts. The combination of metagenomic and metatranscriptomic analysis in this study allowed us to specifically link ARGs to their transcripts, providing a comprehensive view of the prevalence and expression of ARGs in gut microbiota. Taken together, these data deepen our understanding of the distribution, evolution, and dissemination of ARGs and metal resistance genes in human, chicken, and pig gut microbiota.}, }
@article {pmid32200249, year = {2020}, author = {Santos, A and Rachid, C and Pacheco, AB and Magalhães, V}, title = {Biotic and abiotic factors affect microcystin-LR concentrations in water/sediment interface.}, journal = {Microbiological research}, volume = {236}, number = {}, pages = {126452}, doi = {10.1016/j.micres.2020.126452}, pmid = {32200249}, issn = {1618-0623}, mesh = {Biodegradation, Environmental ; Cyanobacteria/*metabolism ; Genes, Bacterial ; Geologic Sediments/analysis/*microbiology ; *Harmful Algal Bloom ; Humans ; Hydrogen-Ion Concentration ; Lakes/microbiology ; Metagenomics ; Microbiota/*genetics ; *Microcystins/analysis ; RNA, Ribosomal, 16S/genetics ; Temperature ; Water/analysis ; Water Pollutants, Chemical/*analysis ; }, abstract = {Harmful cyanobacterial blooms are increasingly common in aquatic environments. This can lead to higher concentrations of cyanotoxins, such as microcystins (MCs), posing a great risk to diverse organisms, including humans. MCs are among the most commonly reported cyanotoxins in freshwater environments worldwide, where they may have different fates. MCs can adsorb to suspended particles into the water column and deposit onto the sediment where they can be affected by physical factors (e.g. winds in shallow lakes causing sediment resuspension) or biological factors (e.g. biodegradation). Here we focused on the conditions of a coastal shallow lagoon contaminated by MCs aiming to estimate the return of pre-existing MCs from the sediment to the water column, to evaluate the adsorption of dissolved MC-LR to the sediment and to verify the occurrence of biodegradation. In experiments with sediment, desorption and adsorption were tested under the influence of temperature, pH and aeration, reproducing conditions observed in the lagoon. MC-desorption was not detected under the tested conditions. Spiking MC-LR into lagoon water samples in the presence of sediment resulted in a 50 % reduction of soluble MC-LR concentration in control conditions (25 °C, pH 8.0, no aeration). Increasing temperature (45 °C) or introducing aeration further stimulated MC-LR removal from the water. Biodegradation was observed in sediment samples and interstitial water (even with tetracycline). The composition of the bacterial community differed in sediment and interstitial water: major phyla were Chloroflexi, Proteobacteria, Firmicutes, and OP3. From the assigned OTUs, we identified genera already described as MC degrading bacteria. Thus, the sediment is a key factor influencing the fate of MC-LR in this shallow coastal lake contributing to stable adsorption and biodegradation.}, }
@article {pmid32200181, year = {2020}, author = {Samson, R and Rajput, V and Shah, M and Yadav, R and Sarode, P and Dastager, SG and Dharne, MS and Khairnar, K}, title = {Deciphering taxonomic and functional diversity of fungi as potential bioindicators within confluence stretch of Ganges and Yamuna Rivers, impacted by anthropogenic activities.}, journal = {Chemosphere}, volume = {252}, number = {}, pages = {126507}, doi = {10.1016/j.chemosphere.2020.126507}, pmid = {32200181}, issn = {1879-1298}, mesh = {*Environmental Biomarkers ; Environmental Monitoring/*methods ; Fungi ; Metagenomics ; *Microbiota ; Rivers/chemistry/microbiology ; *Water Microbiology ; }, abstract = {River confluences are interesting ecological niche with limited information in respect of the structure and the functions of diverse microbial communities. Fungi are gaining global attention as promising biological spectacles for defining the trophic status of riverine systems. We condense existing knowledge in confluence diversity in two Indian rivers (i.e. Ganges and Yamuna), by combining sediment metagenomics using long read aided MinION nanopore sequencing. A total of 63 OTU's were observed, of which top 20 OTU's were considered based on relative abundance of each OTU at a particular location. Fungal genera such as Aspergillus, Penicillium, Kluveromyces, Lodderomyces, and Nakaseomyces were deciphered as potential bio indicators of river pollution and eutrophication in the confluent zone. In silico functional gene analysis uncovered hits for neurodegenerative diseases and xenobiotic degradation potential, supporting bioindication of river pollution in wake of anthropogenic intervention.}, }
@article {pmid32196510, year = {2020}, author = {Farhana, L and Sarkar, S and Nangia-Makker, P and Yu, Y and Khosla, P and Levi, E and Azmi, A and Majumdar, APN}, title = {Natural agents inhibit colon cancer cell proliferation and alter microbial diversity in mice.}, journal = {PloS one}, volume = {15}, number = {3}, pages = {e0229823}, pmid = {32196510}, issn = {1932-6203}, support = {R21 CA175916/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Biological Products/*pharmacology/therapeutic use ; Cell Proliferation/drug effects ; Colonic Neoplasms/*drug therapy/pathology ; Curcuma ; Curcumin/*pharmacology/therapeutic use ; Gastrointestinal Microbiome/*drug effects ; HCT116 Cells ; Humans ; Mice ; Mice, SCID ; Plant Extracts/*pharmacology/therapeutic use ; Tocotrienols/*pharmacology/therapeutic use ; Xenograft Model Antitumor Assays ; }, abstract = {The current study was undertaken to investigate the effect of differentially formulated polyphenolic compound Essential Turmeric Oil-Curcumin (ETO-Cur), and Tocotrienol-rich fraction (TRF) of vitamin E isomers on colorectal cancer (CRC) cells that produce aggressive tumors. Combinations of ETO-Cur and TRF were used to determine the combinatorial effects of ETO-Cur and TRF-mediated inhibition of growth of CRC cells in vitro and HCT-116 cells xenograft in SCID mice. 16S rRNA gene sequence profiling was performed to determine the outcome of gut microbial communities in mice feces between control and ETO-Cur-TRF groups. Bacterial identifications were validated by performing SYBR-based Real Time (RT) PCR. For metagenomics analysis to characterize the microbial communities, multiple software/tools were used, including Quantitative Insights into Microbial Ecology (QIIME) processing tool. We found ETO-Cur and TRF to synergize and that the combination of ETO-Cur-TRF significantly inhibited growth of HCT-116 xenografts in SCID mice. This was associated with a marked alteration in microbial communities and increased microbial OTU (operation taxonomic unit) number. The relative abundance of taxa was increased and the level of microbial diversity after 34 days of combinatorial treatment was found to be 44% higher over the control. Shifting of microbial family composition was observed in ETO-Cur-TRF treated mice as evidenced by marked reductions in Bacteroidaceae, Ruminococcaceae, Clostridiales, Firmicutes and Parabacteroids families, compared to controls. Interestingly, during the inhibition of tumor growth in ETO-Cur treated mice, probiotic Lactobacillaceae and Bifidobacteriaceae were increased by 20-fold and 6-fold, respectively. The relative abundance of anti-inflammatory Clostridium XIVa was also increased in ETO-Cur-TRF treated mice when compared with the control. Our data suggest that ETO-Cur-TRF show synergistic effects in inhibiting colorectal cancer cell proliferation in vitro and in mouse xenografts in vivo, and might induce changes in microbial diversity in mice.}, }
@article {pmid32196076, year = {2020}, author = {Deyett, E and Rolshausen, PE}, title = {Endophytic microbial assemblage in grapevine.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {5}, pages = {}, doi = {10.1093/femsec/fiaa053}, pmid = {32196076}, issn = {1574-6941}, mesh = {Bacteria/genetics ; *Microbiota ; Plant Roots ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; *Soil Microbiology ; }, abstract = {The plant vascular system has remained an underexplored niche despite its potential for hosting beneficial microbes. The aim of this work was to determine the origin of the microbial endophytes inhabiting grapevine. We focused on a single commercial vineyard in California over a two-year period and used an amplicon metagenomics approach to profile the bacterial (16S-V4) and fungal (ITS) communities of the microbiome across a continuum of six grapevine compartments: bulk soil, rhizosphere, root, cordon, cane and sap. Our data supported that roots are a bottleneck to microbial richness and that they are mostly colonized with soilborne microbes, including plant growth-promoting bacteria recruited by the host, but also saprophytic and pathogenic fungal invaders. A core group of taxa was identified throughout the vine; however, there was clear partitioning of the microbiome with niche adaptation of distinct taxonomic groups. Above- and belowground plant tissues displayed distinct microbial fingerprints and were intermixed in a limited capacity mostly by way of the plant sap. We discuss how cultural practices and human contact may shape the endosphere microbiome and identify potential channels for transmission of its residents.}, }
@article {pmid32193245, year = {2020}, author = {Valdés, N and Gonzalez, A and Garcia, V and Tello, M}, title = {Analysis of the Microbiome of Rainbow Trout (Oncorhynchus mykiss) Exposed to the Pathogen Flavobacterium psychrophilum 10094.}, journal = {Microbiology resource announcements}, volume = {9}, number = {12}, pages = {}, pmid = {32193245}, issn = {2576-098X}, abstract = {Rainbow trout that were resistant or susceptible to Flavobacterium psychrophilum infection were compared with respect to their microbial composition by using 16S rRNA V3-V4 sequencing. The differences occurred in gills, where resistant fish displayed a greater abundance of the phylum Proteobacteria and a smaller proportion of Firmicutes relative to those of susceptible fish.}, }
@article {pmid32185431, year = {2020}, author = {Pentimone, I and Colagiero, M and Rosso, LC and Ciancio, A}, title = {Omics applications: towards a sustainable protection of tomato.}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {10}, pages = {4185-4195}, doi = {10.1007/s00253-020-10500-7}, pmid = {32185431}, issn = {1432-0614}, abstract = {Transcriptome data and gene expression analysis have a huge potential in the study of multiple relationships involving plants, pathogens, and pests, including the interactions with beneficial microorganisms such as endophytes or other functional groups. Next-generation sequencing (NGS) and other recent long-read-based sequencing approaches (i.e., nanopore and others) provide unprecedented tools allowing the fast identification of plant information processing systems, in situ and in real time, fundamental for crop management and pest regulation. Other -omics approaches such as metagenomics and metatranscriptomics allow high-resolution insights on the rhizosphere ecology. They may highlight key factors affecting belowground biodiversity or processes, modulating the expression of stress-responsive pathways. The application of miRNAs and other small RNAs is a relatively new field of application, with enormous potential for the selective activation of defense pathways. However, limitations concerning the stability of the RNA molecules and their effective delivery must be overcome.}, }
@article {pmid32184999, year = {2020}, author = {Moore, G and Tessler, M and Cunningham, SW and Betancourt, J and Harbert, R}, title = {Paleo-metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA.}, journal = {Ecology and evolution}, volume = {10}, number = {5}, pages = {2530-2544}, pmid = {32184999}, issn = {2045-7758}, abstract = {Fossil rodent middens are powerful tools in paleoecology. In arid parts of western North America, packrat (Neotoma spp.) middens preserve plant and animal remains for tens of thousands of years. Midden contents are so well preserved that fragments of endogenous ancient DNA (aDNA) can be extracted and analyzed across millennia. Here, we explore the use of shotgun metagenomics to study the aDNA obtained from packrat middens up to 32,000 C14 years old. Eleven Illumina HiSeq 2500 libraries were successfully sequenced, and between 0.11% and 6.7% of reads were classified using Centrifuge against the NCBI &quot;nt&quot; database. Eukaryotic taxa identified belonged primarily to vascular plants with smaller proportions mapping to ascomycete fungi, arthropods, chordates, and nematodes. Plant taxonomic diversity in the middens is shown to change through time and tracks changes in assemblages determined by morphological examination of the plant remains. Amplicon sequencing of ITS2 and rbcL provided minimal data for some middens, but failed at amplifying the highly fragmented DNA present in others. With repeated sampling and deep sequencing, analysis of packrat midden aDNA from well-preserved midden material can provide highly detailed characterizations of past communities of plants, animals, bacteria, and fungi present as trace DNA fossils. The prospects for gaining more paleoecological insights from aDNA for rodent middens will continue to improve with optimization of laboratory methods, decreasing sequencing costs, and increasing computational power.}, }
@article {pmid32182280, year = {2020}, author = {Ivanova, AA and Zhelezova, AD and Chernov, TI and Dedysh, SN}, title = {Linking ecology and systematics of acidobacteria: Distinct habitat preferences of the Acidobacteriia and Blastocatellia in tundra soils.}, journal = {PloS one}, volume = {15}, number = {3}, pages = {e0230157}, pmid = {32182280}, issn = {1932-6203}, mesh = {*Acidobacteria/classification/genetics/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; Carbon/analysis ; Classification ; DNA, Bacterial ; Ecosystem ; Metagenomics ; Nitrogen/analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; *Tundra ; }, abstract = {The Acidobacteria is one of the major bacterial phyla in soils and peatlands. The currently explored diversity within this phylum is assigned to 15 class-level units, five of which contain described members. The ecologically relevant traits of acidobacteria from different classes remain poorly understood. Here, we compared the patterns of acidobacterial diversity in sandy soils of tundra, along a gradient of increasing vegetation-unfixed aeolian sand, semi-fixed surfaces with mosses and lichens, and mature soil under fully developed plant cover. The Acidobacteria-affiliated 16S rRNA gene sequences retrieved from these soils comprised 11 to 33% of total bacterial reads and belonged mostly to members of the classes Acidobacteriia and Blastocatellia, which displayed opposite habitat preferences. The relative abundance of the Blastocatellia was maximal in unfixed sands and declined in soils of vegetated plots, showing positive correlation with soil pH and negative correlation with carbon and nitrogen availability. An opposite tendency was characteristic for the Acidobacteriia. Most Blastocatellia-affiliated reads belonged to as-yet-undescribed members of the family Arenimicrobiaceae, which appears to be characteristic for dry, depleted in organic matter soil habitats. The pool of Acidobacteriia-affiliated sequences, apart from Acidobacteriaceae- and Bryobacteraceae-related reads, had a large proportion of sequences from as-yet-undescribed families, which seem to specialize in degrading plant-derived organic matter. This analysis reveals sandy soils of tundra as a source of novel acidobacterial diversity and provides an insight into the ecological preferences of different taxonomic groups within this phylum.}, }
@article {pmid32182269, year = {2020}, author = {Herren, GL and Habraken, J and Waeyenberge, L and Haegeman, A and Viaene, N and Cougnon, M and Reheul, D and Steel, H and Bert, W}, title = {Effects of synthetic fertilizer and farm compost on soil nematode community in long-term crop rotation plots: A morphological and metabarcoding approach.}, journal = {PloS one}, volume = {15}, number = {3}, pages = {e0230153}, pmid = {32182269}, issn = {1932-6203}, mesh = {Animals ; *Composting ; Crop Production/methods ; Ecosystem ; *Fertilizers ; Food Chain ; Metagenomics ; *Nematoda/anatomy &amp; histology/classification/genetics/growth &amp; development ; Nitrogen Compounds ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Soil biodiversity plays a key regulation role in the ecosystem services that underpin regenerative sustainable agriculture. It can be impacted by agricultural management techniques, both positively (through measures such as compost application) and negatively (through, for example, application of synthetic nitrogen). As one of the most numerous members of the soil biota, nematodes are well established as indicators for the soil food web. However, compost application also includes the addition of nematodes present in compost and their subsequent survival in soil is unknown. Nematode communities within the compost applied to soil, and nematode communities in the soil of a multi-year rotational cropping field trial in Melle (Belgium) were studied using morphological and metabarcoding techniques. Compost (C) and nitrogen fertilizer (NF) treated plots were compared. Three replicate plots were investigated for each of the following treatments: C application only; C and NF application; NF only; no C and no NF (control). Plots were sampled six times between 2015-2017, before and after C or NF were added each spring and after crop harvest (except for 2017). NF treatment resulted in a significant decrease of fungal feeding and predatory nematodes, while herbivorous nematodes were positively affected. Remarkably, we did not find compost addition to exert any noticeable effects on the soil nematode community. The morphological and metabarcoding data resulted in different results of the nematode community composition. However, trends and patterns in the two data sets were congruent when observed with NMDS plots and using the nematode maturity index. Metabarcoding of individual compost nematode taxa demonstrated that nematodes originating from compost did not persist in soil.}, }
@article {pmid32179734, year = {2020}, author = {Mas-Lloret, J and Obón-Santacana, M and Ibáñez-Sanz, G and Guinó, E and Pato, ML and Rodriguez-Moranta, F and Mata, A and García-Rodríguez, A and Moreno, V and Pimenoff, VN}, title = {Gut microbiome diversity detected by high-coverage 16S and shotgun sequencing of paired stool and colon sample.}, journal = {Scientific data}, volume = {7}, number = {1}, pages = {92}, pmid = {32179734}, issn = {2052-4463}, mesh = {*Colon ; Cross-Sectional Studies ; *Feces ; Female ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenomics ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {The gut microbiome has a fundamental role in human health and disease. However, studying the complex structure and function of the gut microbiome using next generation sequencing is challenging and prone to reproducibility problems. Here, we obtained cross-sectional colon biopsies and faecal samples from nine participants in our COLSCREEN study and sequenced them in high coverage using Illumina pair-end shotgun (for faecal samples) and IonTorrent 16S (for paired feces and colon biopsies) technologies. The metagenomes consisted of between 47 and 92 million reads per sample and the targeted sequencing covered more than 300 k reads per sample across seven hypervariable regions of the 16S gene. Our data is freely available and coupled with code for the presented metagenomic analysis using up-to-date bioinformatics algorithms. These results will add up to the informed insights into designing comprehensive microbiome analysis and also provide data for further testing for unambiguous gut microbiome analysis.}, }
@article {pmid32179689, year = {2020}, author = {Bonilla-Rosso, G and Steiner, T and Wichmann, F and Bexkens, E and Engel, P}, title = {Honey bees harbor a diverse gut virome engaging in nested strain-level interactions with the microbiota.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {13}, pages = {7355-7362}, pmid = {32179689}, issn = {1091-6490}, mesh = {Animals ; Bacteria/genetics ; Bacteriophages/genetics ; Bees/genetics/*microbiology/*virology ; Bifidobacterium/isolation &amp; purification/virology ; Gastrointestinal Microbiome ; Metagenome ; Microbiota ; Symbiosis/physiology ; }, abstract = {The honey bee gut microbiota influences bee health and has become an important model to study the ecology and evolution of microbiota-host interactions. Yet, little is known about the phage community associated with the bee gut, despite its potential to modulate bacterial diversity or to govern important symbiotic functions. Here we analyzed two metagenomes derived from virus-like particles, analyzed the prevalence of the identified phages across 73 bacterial metagenomes from individual bees, and tested the host range of isolated phages. Our results show that the honey bee gut virome is composed of at least 118 distinct clusters corresponding to both temperate and lytic phages and representing novel genera with a large repertoire of unknown gene functions. We find that the phage community is prevalent in honey bees across space and time and targets the core members of the bee gut microbiota. The large number and high genetic diversity of the viral clusters seems to mirror the high extent of strain-level diversity in the bee gut microbiota. We isolated eight lytic phages that target the core microbiota member Bifidobacterium asteroides, but that exhibited different host ranges at the strain level, resulting in a nested interaction network of coexisting phages and bacterial strains. Collectively, our results show that the honey bee gut virome consists of a complex and diverse phage community that likely plays an important role in regulating strain-level diversity in the bee gut and that holds promise as an experimental model to study bacteria-phage dynamics in natural microbial communities.}, }
@article {pmid32179266, year = {2020}, author = {Perez-Fernandez, C and Morales-Navas, M and Aguilera-Sáez, LM and Abreu, AC and Guardia-Escote, L and Fernández, I and Garrido-Cárdenas, JA and Colomina, MT and Giménez, E and Sánchez-Santed, F}, title = {Medium and long-term effects of low doses of Chlorpyrifos during the postnatal, preweaning developmental stage on sociability, dominance, gut microbiota and plasma metabolites.}, journal = {Environmental research}, volume = {184}, number = {}, pages = {109341}, doi = {10.1016/j.envres.2020.109341}, pmid = {32179266}, issn = {1096-0953}, mesh = {Adult ; Animals ; *Autism Spectrum Disorder/chemically induced ; *Chlorpyrifos/toxicity ; Female ; *Gastrointestinal Microbiome ; Humans ; *Insecticides/toxicity ; Mice ; Rats ; Social Behavior ; }, abstract = {Autism spectrum disorder (ASD) is a complex neurodevelopmental pathology characterized by altered verbalizations, reduced social interaction behavior, and stereotypies. Environmental factors have been associated with its development. Some researchers have focused on pesticide exposure. Chlorpyrifos (CPF) is the most used Organophosphate. Previous developmental studies with CPF showed decreased, enhanced or no effect on social outcomes eminently in mice. The study of CPF exposure during preweaning stages on social behavior is sparse in mice and non-existent in rats. d stressors could be at the basis of ASD development, and around postnatal day 10 in the rat is equivalent to the human birthday in neurodevelopmental terms. We explored the effects of exposure to low doses (1mg/kg/mL/day) of CPF during this stage regarding: sociability, dominance gut microbiome and plasma metabolomic profile, since alterations in these systems have also been linked to ASD. There was a modest influence of CPF on social behavior in adulthood, with null effects during adolescence. Dominance and hierarchical status were not affected by exposure. Dominance status explained the significant reduction in reaction to social novelty observed on the sociability test. CPF induced a significant gut microbiome dysbiosis and triggered a hyperlipidemic, hypoglycemic/hypogluconeogenesis and a general altered cell energy production in females. These behavioral results in rats extend and complement previous studies with mice and show novel influences on gut metagenomics and plasma lipid profile and metabolomics, but do not stablish a relation between the exposure to CPF and the ASD phenotype. The effects of dominance status on reaction to social novelty have an important methodological meaning for future research on sociability.}, }
@article {pmid32173258, year = {2019}, author = {Breban, M and Beaufrère, M and Glatigny, S}, title = {The microbiome in spondyloarthritis.}, journal = {Best practice &amp; research. Clinical rheumatology}, volume = {33}, number = {6}, pages = {101495}, doi = {10.1016/j.berh.2020.101495}, pmid = {32173258}, issn = {1532-1770}, mesh = {Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; *Spondylarthritis/microbiology ; *Spondylitis, Ankylosing ; }, abstract = {A causal link between the wealth of microbes that populate our body surfaces, designated as microbiota, and inflammatory disorders, including ankylosing spondylitis and the related spondyloarthritis (SpA) has been suspected for decades. This specially concerns the gut microbiota that became only recently accessible to thorough description thanks to massive sequencing methods or metagenomics. Here, we review evidences supporting the existence of microbiota imbalance or dysbiosis in the context of SpA. We also discuss currently existing evidences for a causal relationship between such dysbiosis and disease development, as well as putative therapeutic implications.}, }
@article {pmid32171248, year = {2020}, author = {Liu, T and Chen, CY and Chen-Deng, A and Chen, YL and Wang, JY and Hou, YI and Lin, MC}, title = {Joining Illumina paired-end reads for classifying phylogenetic marker sequences.}, journal = {BMC bioinformatics}, volume = {21}, number = {1}, pages = {105}, pmid = {32171248}, issn = {1471-2105}, support = {107-2221-E-006-198-MY2//Ministry of Science and Technology, Taiwan/ ; }, mesh = {Asthma/microbiology ; Bacteria/genetics ; Child ; Cluster Analysis ; Genetic Markers ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenome ; Metagenomics/methods ; Microbiota/genetics ; *Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: Illumina sequencing of a marker gene is popular in metagenomic studies. However, Illumina paired-end (PE) reads sometimes cannot be merged into single reads for subsequent analysis. When mergeable PE reads are limited, one can simply use only first reads for taxonomy annotation, but that wastes information in the second reads. Presumably, including second reads should improve taxonomy annotation. However, a rigorous investigation of how best to do this and how much can be gained has not been reported.<br><br>RESULTS: We evaluated two methods of joining as opposed to merging PE reads into single reads for taxonomy annotation using simulated data with sequencing errors. Our rigorous evaluation involved several top classifiers (RDP classifier, SINTAX, and two alignment-based methods) and realistic benchmark datasets. For most classifiers, read joining ameliorated the impact of sequencing errors and improved the accuracy of taxonomy predictions. For alignment-based top-hit classifiers, rearranging the reference sequences is recommended to avoid improper alignments of joined reads. For word-counting classifiers, joined reads could be compared to the original reference for classification. We also applied read joining to our own real MiSeq PE data of nasal microbiota of asthmatic children. Before joining, trimming low quality bases was necessary for optimizing taxonomy annotation and sequence clustering. We then showed that read joining increased the amount of effective data for taxonomy annotation. Using these joined trimmed reads, we were able to identify two promising bacterial genera that might be associated with asthma exacerbation.<br><br>CONCLUSIONS: When mergeable PE reads are limited, joining them into single reads for taxonomy annotation is always recommended. Reference sequences may need to be rearranged accordingly depending on the classifier. Read joining also relaxes the constraint on primer selection, and thus may unleash the full capacity of Illumina PE data for taxonomy annotation. Our work provides guidance for fully utilizing PE data of a marker gene when mergeable reads are limited.}, }
@article {pmid32169939, year = {2020}, author = {Props, R and Denef, VJ}, title = {Temperature and Nutrient Levels Correspond with Lineage-Specific Microdiversification in the Ubiquitous and Abundant Freshwater Genus Limnohabitans.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {10}, pages = {}, pmid = {32169939}, issn = {1098-5336}, mesh = {Comamonadaceae/classification/*genetics/*physiology ; *Gene Expression ; *Genes, Bacterial ; *Genetic Variation ; Lakes/microbiology ; Michigan ; Microbiota ; Nutrients ; Temperature ; }, abstract = {Most freshwater bacterial communities are characterized by a few dominant taxa that are often ubiquitous across freshwater biomes worldwide. Our understanding of the genomic diversity within these taxonomic groups is limited to a subset of taxa. Here, we investigated the genomic diversity that enables Limnohabitans, a freshwater genus key in funneling carbon from primary producers to higher trophic levels, to achieve abundance and ubiquity. We reconstructed eight putative Limnohabitans metagenome-assembled genomes (MAGs) from stations located along broad environmental gradients existing in Lake Michigan, part of Earth's largest surface freshwater system. De novo strain inference analysis resolved a total of 23 strains from these MAGs, which strongly partitioned into two habitat-specific clusters with cooccurring strains from different lineages. The largest number of strains belonged to the abundant LimB lineage, for which robust in situ strain delineation had not previously been achieved. Our data show that temperature and nutrient levels may be important environmental parameters associated with microdiversification within the Limnohabitans genus. In addition, strains predominant in low- and high-phosphorus conditions had larger genomic divergence than strains abundant under different temperatures. Comparative genomics and gene expression analysis yielded evidence for the ability of LimB populations to exhibit cellular motility and chemotaxis, a phenotype not yet associated with available Limnohabitans isolates. Our findings broaden historical marker gene-based surveys of Limnohabitans microdiversification and provide in situ evidence of genome diversity and its functional implications across freshwater gradients.IMPORTANCELimnohabitans is an important bacterial taxonomic group for cycling carbon in freshwater ecosystems worldwide. Here, we examined the genomic diversity of different Limnohabitans lineages. We focused on the LimB lineage of this genus, which is globally distributed and often abundant, and its abundance has shown to be largely invariant to environmental change. Our data show that the LimB lineage is actually comprised of multiple cooccurring populations for which the composition and genomic characteristics are associated with variations in temperature and nutrient levels. The gene expression profiles of this lineage suggest the importance of chemotaxis and motility, traits that had not yet been associated with the Limnohabitans genus, in adapting to environmental conditions.}, }
@article {pmid32167528, year = {2020}, author = {Mallawaarachchi, V and Wickramarachchi, A and Lin, Y}, title = {GraphBin: refined binning of metagenomic contigs using assembly graphs.}, journal = {Bioinformatics (Oxford, England)}, volume = {36}, number = {11}, pages = {3307-3313}, doi = {10.1093/bioinformatics/btaa180}, pmid = {32167528}, issn = {1367-4811}, mesh = {Algorithms ; *Metagenome ; Metagenomics ; *Microbiota ; Sequence Analysis, DNA ; Software ; }, abstract = {MOTIVATION: The field of metagenomics has provided valuable insights into the structure, diversity and ecology within microbial communities. One key step in metagenomics analysis is to assemble reads into longer contigs which are then binned into groups of contigs that belong to different species present in the metagenomic sample. Binning of contigs plays an important role in metagenomics and most available binning algorithms bin contigs using genomic features such as oligonucleotide/k-mer composition and contig coverage. As metagenomic contigs are derived from the assembly process, they are output from the underlying assembly graph which contains valuable connectivity information between contigs that can be used for binning.<br><br>RESULTS: We propose GraphBin, a new binning method that makes use of the assembly graph and applies a label propagation algorithm to refine the binning result of existing tools. We show that GraphBin can make use of the assembly graphs constructed from both the de Bruijn graph and the overlap-layout-consensus approach. Moreover, we demonstrate improved experimental results from GraphBin in terms of identifying mis-binned contigs and binning of contigs discarded by existing binning tools. To the best of our knowledge, this is the first time that the information from the assembly graph has been used in a tool for the binning of metagenomic contigs.<br><br>The source code of GraphBin is available at https://github.com/Vini2/GraphBin.<br><br>CONTACT: vijini.mallawaarachchi@anu.edu.au or yu.lin@anu.edu.au.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid32165294, year = {2020}, author = {Kieran, TJ}, title = {Mitochondrial, metagenomic, and phylogenetic analysis of the ground beetle Harpalus pensylvanicus (Coleoptera: Carabidae).}, journal = {Gene}, volume = {740}, number = {}, pages = {144540}, doi = {10.1016/j.gene.2020.144540}, pmid = {32165294}, issn = {1879-0038}, mesh = {Animals ; Coleoptera/classification/*genetics ; Genome, Mitochondrial/genetics ; *Metagenomics ; Microbiota/genetics ; }, abstract = {Harpalus pensylvanicus (Coloptera: Carabidae) is a weed seed predator common throughout the United States. While Carabidae is a very large group of beetles, limited genomic resources exist, especially mitochondrial genomes. This study expands research in this area by assembling and annotating the complete mitochondrial genome of H. pensylvanicus and performs phylogenetic analyses with closely related species. Further use of the metagenomic data was made to characterize microbial taxa and clusters of orthologous groups of proteins. The complete mitochondrial genome is 16,434 bp in length, AT rich, and consist of 13 protein coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a control region. Phylogenetic analyses were congruent with the Harpalinae and Pterostichinae clade together. Microbial classification shows a predominance of Gamma- (37.77%) and Alpha-proteobacteria (33.97%).}, }
@article {pmid32164527, year = {2020}, author = {Kobus, R and Abuín, JM and Müller, A and Hellmann, SL and Pichel, JC and Pena, TF and Hildebrandt, A and Hankeln, T and Schmidt, B}, title = {A big data approach to metagenomics for all-food-sequencing.}, journal = {BMC bioinformatics}, volume = {21}, number = {1}, pages = {102}, pmid = {32164527}, issn = {1471-2105}, support = {HySim//Deutsche Forschungsgemeinschaft/ ; RTI2018-093336-B-C21//Ministerio de Econom?a y Competitividad/ ; ED481B 2018/013 and ED431C 2018/19//Xunta de Galicia/ ; 2816503814//Federal O?ce for Agriculture and Food/ ; }, mesh = {*Big Data ; Biosurveillance ; Food Analysis/*methods ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing/*methods ; Metagenome ; Metagenomics/*methods ; Microbiota/genetics ; Software ; Whole Genome Sequencing/*methods ; }, abstract = {BACKGROUND: All-Food-Sequencing (AFS) is an untargeted metagenomic sequencing method that allows for the detection and quantification of food ingredients including animals, plants, and microbiota. While this approach avoids some of the shortcomings of targeted PCR-based methods, it requires the comparison of sequence reads to large collections of reference genomes. The steadily increasing amount of available reference genomes establishes the need for efficient big data approaches.<br><br>RESULTS: We introduce an alignment-free k-mer based method for detection and quantification of species composition in food and other complex biological matters. It is orders-of-magnitude faster than our previous alignment-based AFS pipeline. In comparison to the established tools CLARK, Kraken2, and Kraken2+Bracken it is superior in terms of false-positive rate and quantification accuracy. Furthermore, the usage of an efficient database partitioning scheme allows for the processing of massive collections of reference genomes with reduced memory requirements on a workstation (AFS-MetaCache) or on a Spark-based compute cluster (MetaCacheSpark).<br><br>CONCLUSIONS: We present a fast yet accurate screening method for whole genome shotgun sequencing-based biosurveillance applications such as food testing. By relying on a big data approach it can scale efficiently towards large-scale collections of complex eukaryotic and bacterial reference genomes. AFS-MetaCache and MetaCacheSpark are suitable tools for broad-scale metagenomic screening applications. They are available at https://muellan.github.io/metacache/afs.html (C++ version for a workstation) and https://github.com/jmabuin/MetaCacheSpark (Spark version for big data clusters).}, }
@article {pmid32157464, year = {2020}, author = {Casalone, E and Cavalieri, D and Daly, G and Vitali, F and Perito, B}, title = {Propolis hosts a diversemicrobial community.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {36}, number = {3}, pages = {50}, pmid = {32157464}, issn = {1573-0972}, support = {prot.2012RCEZWH_001//Programmi di Ricerca di Rilevante Interesse Nazionale (PRIN) 2012/ ; }, mesh = {Animals ; Anti-Infective Agents/pharmacology ; Bacteria/*classification/drug effects/isolation &amp; purification ; Bees ; DNA, Ribosomal/genetics ; Fungi/*classification/drug effects/isolation &amp; purification ; Gastrointestinal Microbiome ; Microbial Sensitivity Tests ; *Microbiota/drug effects ; Phylogeny ; Propolis/*pharmacology ; }, abstract = {Despite the deep knowledge of the honey bee (Apis mellifera) gut microbiome, information on the microbial communities of other hive components is still scarce. Propolis originates from a natural resinous mixture that honeybees collect from different plants sources and modify; it is used mainly to ensure the hygiene of the hive. By virtue of its antimicrobial properties, propolis has been considered relatively aseptic, yet its ability to harbor microorganisms has not been previously investigated. In this study we report the first description of the diversity of the microbial community of propolis by both targeted-metagenomics analysis and cultivation. We demonstrated that propolis hosts a variety of microbial strains belonging to taxa already described in other hive components. Some of them are cultivable in standard laboratory conditions, and show metabolic characteristics compatible with their persistence in different physiological states inside propolis. Isolated bacteria produce antimicrobials against Gram-negative and Gram-positive bacteria, and entomopathogenic fungi, with different spectra of inhibition. Metagenomics analysis shows the presence of bacteria and fungi with great potential to outcompete potentially harmful microorganisms. These findings suggest that the characterized microbiota could contribute to the overall antimicrobial properties of propolis and to its ecological role as &quot;disinfectant&quot; within the hive.}, }
@article {pmid32155560, year = {2020}, author = {Duan, JL and Sun, JW and Ji, MM and Ma, Y and Cui, ZT and Tian, RK and Xu, PC and Sun, WL and Yuan, XZ}, title = {Indicatory bacteria and chemical composition related to sulfur distribution in the river-lake systems.}, journal = {Microbiological research}, volume = {236}, number = {}, pages = {126453}, doi = {10.1016/j.micres.2020.126453}, pmid = {32155560}, issn = {1618-0623}, mesh = {*Bacteria/classification/genetics ; Biodiversity ; China ; Genes, Bacterial ; Geologic Sediments/chemistry/microbiology ; Lakes/*chemistry/microbiology ; Metagenomics ; Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S ; Rivers/*chemistry/microbiology ; *Sentinel Species/classification/genetics ; Sulfur/*analysis ; Water Pollutants, Chemical/analysis ; }, abstract = {Sulfate related water quality and trophic status are crucial to operation of water diversion. Though the sulfur geochemistry in the lake sediment have been well studied, the effective indicator of surrounding environment conditions related to sulfur in river-lake systems are still unknown. In this study, Dongping Lake (DPH), Weishan Lake (WSH), and Hanzhuang trunk canal (HZQ) were selected as the typical river-lake systems in the eastern of China. Different spatial variations in sedimentary sulfate, total sulfur, and elemental composition of sediments were investigated in these areas. The relatively high sulfate in surface water and sediments appeared in portions of WSH. The biodiversity of HZQ and WSH surface sediments was much higher than that of DPH. Pseudomonas, Acinetobacter, and Thiobacillus were the dominant genera of the river-lake systems. Among the different genera in distribution, genera such as Malikia, Sulfurovum and Lysinibacillus were significantly negatively correlated with sulfur related environmental factors. While the genera such as Pseudomonas, Vogesella and Acinetobacter were significantly positively correlated with these factors. Compared with connectivity in the largest interaction network, bacteria such as Proteus, Acidobacter and Chlorobacteria were identified as indicatory taxa to infer sulfate related conditions in the river-lake systems.}, }
@article {pmid32155146, year = {2020}, author = {Ramiro, RS and Durão, P and Bank, C and Gordo, I}, title = {Low mutational load and high mutation rate variation in gut commensal bacteria.}, journal = {PLoS biology}, volume = {18}, number = {3}, pages = {e3000617}, pmid = {32155146}, issn = {1545-7885}, mesh = {Adaptation, Physiological/genetics ; Animals ; Anti-Bacterial Agents/pharmacology ; DNA Polymerase III/genetics ; Escherichia coli/genetics ; Escherichia coli Proteins/genetics ; Gastrointestinal Microbiome/drug effects/*genetics ; Male ; Mice, Inbred C57BL ; Microorganisms, Genetically-Modified ; *Mutation Rate ; Selection, Genetic ; }, abstract = {Bacteria generally live in species-rich communities, such as the gut microbiota. Yet little is known about bacterial evolution in natural ecosystems. Here, we followed the long-term evolution of commensal Escherichia coli in the mouse gut. We observe the emergence of mutation rate polymorphism, ranging from wild-type levels to 1,000-fold higher. By combining experiments, whole-genome sequencing, and in silico simulations, we identify the molecular causes and explore the evolutionary conditions allowing these hypermutators to emerge and coexist within the microbiota. The hypermutator phenotype is caused by mutations in DNA polymerase III proofreading and catalytic subunits, which increase mutation rate by approximately 1,000-fold and stabilise hypermutator fitness, respectively. Strong mutation rate variation persists for >1,000 generations, with coexistence between lineages carrying 4 to >600 mutations. The in vivo molecular evolution pattern is consistent with fitness effects of deleterious mutations sd ≤ 10-4/generation, assuming a constant effect or exponentially distributed effects with a constant mean. Such effects are lower than typical in vitro estimates, leading to a low mutational load, an inference that is observed in in vivo and in vitro competitions. Despite large numbers of deleterious mutations, we identify multiple beneficial mutations that do not reach fixation over long periods of time. This indicates that the dynamics of beneficial mutations are not shaped by constant positive Darwinian selection but could be explained by other evolutionary mechanisms that maintain genetic diversity. Thus, microbial evolution in the gut is likely characterised by partial sweeps of beneficial mutations combined with hitchhiking of slightly deleterious mutations, which take a long time to be purged because they impose a low mutational load. The combination of these two processes could allow for the long-term maintenance of intraspecies genetic diversity, including mutation rate polymorphism. These results are consistent with the pattern of genetic polymorphism that is emerging from metagenomics studies of the human gut microbiota, suggesting that we have identified key evolutionary processes shaping the genetic composition of this community.}, }
@article {pmid32153535, year = {2020}, author = {Stokke, R and Reeves, EP and Dahle, H and Fedøy, AE and Viflot, T and Lie Onstad, S and Vulcano, F and Pedersen, RB and Eijsink, VGH and Steen, IH}, title = {Tailoring Hydrothermal Vent Biodiversity Toward Improved Biodiscovery Using a Novel in situ Enrichment Strategy.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {249}, pmid = {32153535}, issn = {1664-302X}, abstract = {Deep-sea hydrothermal vents are amongst the most extreme environments on Earth and represent interesting targets for marine bioprospecting and biodiscovery. The microbial communities in hydrothermal vents are often dominated by chemolithoautotrophs utilizing simple chemical compounds, though the full extent of their heterotrophic abilities is still being explored. In the bioprocessing industry, where degradation of complex organic materials often is a major challenge, new microbial solutions are heavily needed. To meet these needs, we have developed novel in situ incubators and tested if deployment of recalcitrant materials from fish farming and wood-pulping industries introduced changes in the microbial community structure in hot marine hydrothermal sediments. The incubation chambers were deployed in sediments at the Bruse vent site located within the Jan Mayen vent field for 1 year, after which the microbial populations in the chambers were profiled by 16S rRNA Ion Torrent amplicon sequencing. A total of 921 operational taxonomic units (OTUs) were assigned into 74 different phyla where differences in community structure were observed depending on the incubated material, chamber depth below the sea floor and/or temperature. A high fraction of putative heterotrophic microbial lineages related to cultivated members within the Thermotogales were observed. However, considerable fractions of previously uncultivated and novel Thermotogales and Bacteroidetes were also identified. Moreover, several novel lineages (e.g., members within the DPANN superphylum, unidentified archaeal lineages, unclassified Thermoplasmatales and Candidatus division BRC-1 bacterium) of as-yet uncultivated thermophilic archaea and bacteria were identified. Overall, our data illustrate that amendment of hydrothermal vent communities by in situ incubation of biomass induces shifts in community structure toward increased fractions of heterotrophic microorganisms. The technologies utilized here could aid in subsequent metagenomics-based enzyme discovery for diverse industries.}, }
@article {pmid32152478, year = {2020}, author = {Aron-Wisnewsky, J and Vigliotti, C and Witjes, J and Le, P and Holleboom, AG and Verheij, J and Nieuwdorp, M and Clément, K}, title = {Gut microbiota and human NAFLD: disentangling microbial signatures from metabolic disorders.}, journal = {Nature reviews. Gastroenterology &amp; hepatology}, volume = {17}, number = {5}, pages = {279-297}, doi = {10.1038/s41575-020-0269-9}, pmid = {32152478}, issn = {1759-5053}, mesh = {Animals ; Diabetes Mellitus, Type 2/microbiology ; Digestive System Diseases/microbiology ; Dysbiosis/immunology/microbiology ; Gastrointestinal Microbiome/*immunology ; Humans ; Non-alcoholic Fatty Liver Disease/immunology/*microbiology ; Obesity/microbiology ; Signal Transduction ; }, abstract = {Gut microbiota dysbiosis has been repeatedly observed in obesity and type 2 diabetes mellitus, two metabolic diseases strongly intertwined with non-alcoholic fatty liver disease (NAFLD). Animal studies have demonstrated a potential causal role of gut microbiota in NAFLD. Human studies have started to describe microbiota alterations in NAFLD and have found a few consistent microbiome signatures discriminating healthy individuals from those with NAFLD, non-alcoholic steatohepatitis or cirrhosis. However, patients with NAFLD often present with obesity and/or insulin resistance and type 2 diabetes mellitus, and these metabolic confounding factors for dysbiosis have not always been considered. Patients with different NAFLD severity stages often present with heterogeneous lesions and variable demographic characteristics (including age, sex and ethnicity), which are known to affect the gut microbiome and have been overlooked in most studies. Finally, multiple gut microbiome sequencing tools and NAFLD diagnostic methods have been used across studies that could account for discrepant microbiome signatures. This Review provides a broad insight into microbiome signatures for human NAFLD and explores issues with disentangling these signatures from underlying metabolic disorders. More advanced metagenomics and multi-omics studies using system biology approaches are needed to improve microbiome biomarkers.}, }
@article {pmid32144387, year = {2020}, author = {De Angelis, M and Ferrocino, I and Calabrese, FM and De Filippis, F and Cavallo, N and Siragusa, S and Rampelli, S and Di Cagno, R and Rantsiou, K and Vannini, L and Pellegrini, N and Lazzi, C and Turroni, S and Lorusso, N and Ventura, M and Chieppa, M and Neviani, E and Brigidi, P and O'Toole, PW and Ercolini, D and Gobbetti, M and Cocolin, L}, title = {Diet influences the functions of the human intestinal microbiome.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {4247}, pmid = {32144387}, issn = {2045-2322}, mesh = {Cell Line, Tumor ; Computational Biology/methods ; *Diet ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Metabolic Networks and Pathways ; Metagenome ; Metagenomics/methods ; Nitrogen/metabolism ; }, abstract = {Gut microbes programme their metabolism to suit intestinal conditions and convert dietary components into a panel of small molecules that ultimately affect host physiology. To unveil what is behind the effects of key dietary components on microbial functions and the way they modulate host-microbe interaction, we used for the first time a multi-omic approach that goes behind the mere gut phylogenetic composition and provides an overall picture of the functional repertoire in 27 fecal samples from omnivorous, vegan and vegetarian volunteers. Based on our data, vegan and vegetarian diets were associated to the highest abundance of microbial genes/proteins responsible for cell motility, carbohydrate- and protein-hydrolyzing enzymes, transport systems and the synthesis of essential amino acids and vitamins. A positive correlation was observed when intake of fiber and the relative fecal abundance of flagellin were compared. Microbial cells and flagellin extracted from fecal samples of 61 healthy donors modulated the viability of the human (HT29) colon carcinoma cells and the host response through the stimulation of the expression of Toll-like receptor 5, lectin RegIIIα and three interleukins (IL-8, IL-22 and IL-23). Our findings concretize a further and relevant milestone on how the diet may prevent/mitigate disease risk.}, }
@article {pmid32135180, year = {2020}, author = {Gordon, CA and Krause, L and McManus, DP and Morrison, M and Weerakoon, KG and Connor, MC and Olveda, RM and Ross, AG and Gobert, GN}, title = {Helminths, polyparasitism, and the gut microbiome in the Philippines.}, journal = {International journal for parasitology}, volume = {50}, number = {3}, pages = {217-225}, doi = {10.1016/j.ijpara.2019.12.008}, pmid = {32135180}, issn = {1879-0135}, mesh = {Adolescent ; Adult ; Albendazole/therapeutic use ; Ancylostoma/isolation &amp; purification ; Ancylostomatoidea/isolation &amp; purification ; Animals ; Ascaris/isolation &amp; purification ; Bacteria/classification/genetics/isolation &amp; purification ; Child ; Child, Preschool ; Cohort Studies ; *Coinfection/microbiology/parasitology ; Feces/microbiology/parasitology ; Female ; Gastrointestinal Microbiome/*genetics ; Genes, Bacterial ; Helminthiasis/drug therapy/*epidemiology ; Helminths/genetics/*isolation &amp; purification ; Host-Parasite Interactions ; Humans ; Male ; Metagenomics ; Microbial Interactions ; Middle Aged ; Pathology, Molecular ; Philippines/epidemiology ; Schistosoma/isolation &amp; purification ; Schistosomiasis/drug therapy/*epidemiology ; Soil/parasitology ; Trichuris/isolation &amp; purification ; Young Adult ; }, abstract = {Polyparasitism, involving soil-transmitted helminths. and Schistosoma blood flukes, is common in low to middle income countries. These helminths impact on the gut environment and can cause changes to the gut microbiome composition. Here we examined the gut microbiome in individuals with polyparasitism from two human cohorts in the Philippines utilising DNA sequencing-based profiling. Multiple helminth species infections were high with 70.3% of study participants harbouring at least two parasite species, and 16% harbouring at least five species. Increased numbers of helminth co-infections, in particular with the gut-resident soil-transmitted helminths, were significantly associated with increased bacterial diversity; however no significant parasite-gut microbiome associations were evident for individuals infected only with Schistosoma japonicum. In general, a healthy gut is associated with high bacterial diversity, which in these human cohorts may be the result of helminth-mediated immune modulation, or due to changes in the gut environment caused by these parasitic helminths.}, }
@article {pmid32132981, year = {2020}, author = {Song, D and Zhang, Y and Liu, J and Zhong, H and Zheng, Y and Zhou, S and Yu, M and Todd, JD and Zhang, XH}, title = {Metagenomic Insights Into the Cycling of Dimethylsulfoniopropionate and Related Molecules in the Eastern China Marginal Seas.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {157}, pmid = {32132981}, issn = {1664-302X}, abstract = {The microbial cycling of dimethylsulfoniopropionate (DMSP) and its gaseous catabolites dimethylsulfide (DMS) and methanethiol (MeSH) are important processes in the global sulfur cycle, marine microbial food webs, signaling pathways, atmospheric chemistry, and potentially climate regulation. Many functional genes have been identified and used to study the genetic potential of microbes to produce and catabolize these organosulfur compounds in different marine environments. Here, we sampled seawater, marine sediment and hydrothermal sediment, and polymetallic sulfide in the eastern Chinese marginal seas and analyzed their microbial communities for the genetic potential to cycle DMSP, DMS, and MeSH using metagenomics. DMSP was abundant in all sediment samples, but was fivefold less prominent in those from hydrothermal samples. Indeed, Yellow Sea (YS) sediment samples had DMSP concentrations two orders of magnitude higher than in surface water samples. Bacterial genetic potential to synthesize DMSP (mainly in Rhodobacteraceae bacteria) was far higher than for phytoplankton in all samples, but particularly in the sediment where no algal DMSP synthesis genes were detected. Thus, we propose bacteria as important DMSP producers in these marine sediments. DMSP catabolic pathways mediated by the DMSP lyase DddP (prominent in Pseudomonas and Mesorhizobium bacteria) and DMSP demethylase DmdA enzymes (prominent in Rhodobacteraceae bacteria) and MddA-mediated MeSH S-methylation were very abundant in Bohai Sea and Yellow Sea sediments (BYSS) samples. In contrast, the genetic potential for DMSP degradation was very low in the hydrothermal sediment samples-dddP was the only catabolic gene detected and in only one sample. However, the potential for DMS production from MeSH (mddA) and DMS oxidation (dmoA and ddhA) was relatively abundant. This metagenomics study does not provide conclusive evidence for DMSP cycling; however, it does highlight the potential importance of bacteria in the synthesis and catabolism of DMSP and related compounds in diverse sediment environments.}, }
@article {pmid32130435, year = {2020}, author = {Tikariha, H and Purohit, HJ}, title = {Unfolding microbial community intelligence in aerobic and anaerobic biodegradation processes using metagenomics.}, journal = {Archives of microbiology}, volume = {202}, number = {6}, pages = {1269-1274}, doi = {10.1007/s00203-020-01839-6}, pmid = {32130435}, issn = {1432-072X}, mesh = {Aerobiosis ; Anaerobiosis ; *Biodegradation, Environmental ; Bioreactors/*microbiology ; *Metagenomics ; Microbiota/*physiology ; Sewage/*microbiology ; Waste Water/*microbiology ; }, abstract = {Environmental factors and available nutrients influence microbial communities, and with that, there exists a dynamic shift in community structure and hierarchy in wastewater treatment systems. Of the various factors, the availability and gradient of oxygen selectively enrich a typical microbial community and also form the community stratification which could be established through metagenomics studies. In recent years, metagenomics with various sets of bioinformatics tools has assisted in exploration and better insight into the organization and relation of the taxonomical and functional composition and associate physiological intelligence of the microbial communities. The microbial communities, under defined conditions acquire a typical hierarchy with flexible but active network of the metabolic route, which ensures the survival needs of every member residing in that community and their abundance. This knowledge of community functional organization defines the rule in designing and improving biodegradation processes in case of both aerobic and anaerobic systems.}, }
@article {pmid32123204, year = {2020}, author = {Lo Sasso, G and Phillips, BW and Sewer, A and Battey, JND and Kondylis, A and Talikka, M and Titz, B and Guedj, E and Peric, D and Bornand, D and Dulize, R and Merg, C and Corciulo, M and Ouadi, S and Yanuar, R and Tung, CK and Ivanov, NV and Peitsch, MC and Hoeng, J}, title = {The reduction of DSS-induced colitis severity in mice exposed to cigarette smoke is linked to immune modulation and microbial shifts.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {3829}, pmid = {32123204}, issn = {2045-2322}, mesh = {Animals ; Colitis/chemically induced/*immunology/*microbiology ; Dextran Sulfate/*pharmacology ; Male ; Mice ; Mice, Inbred C57BL ; Microbiota/drug effects ; Smoke/*adverse effects ; Tobacco Products/*adverse effects ; }, abstract = {Exposure to cigarette smoke (CS) causes detrimental health effects, increasing the risk of cardiovascular, pulmonary diseases and carcinogenesis in exposed individuals. The impact of CS on Inflammatory Bowel Disease (IBD) has been established by a number of epidemiological and clinical studies. In fact, CS is associated with a higher risk of developing Crohn's disease (CD) while inversely correlates with the development, disease risks, and relapse rate of ulcerative colitis (UC). To investigate the effect of CS exposure on experimental colitis, we performed a comprehensive and integrated comparative analysis of colon transcriptome and microbiome in mice exposed to dextran sodium sulfate (DSS) and CS. Colon transcriptome analysis revealed that CS downregulated specific pathways in a concentration-dependent manner, affecting both the inflammatory state and composition of the gut microbiome. Metagenomics analysis demonstrated that CS can modulate DSS-induced dysbiosis of specific bacterial genera, contributing to resolve the inflammation or accelerate recovery. The risks of smoking far outweigh any possible benefit, thus smoking cessation must always be encouraged because of its significant health benefits. However, the inverse association between active smoking and the development of UC cannot be ignored and the present study lays the foundation for investigating potential molecular mechanisms responsible for the attenuation of colitis by certain compounds of tobacco when decoupled from combustion.}, }
@article {pmid32111593, year = {2020}, author = {Li, X and Islam, MM and Chen, L and Wang, L and Zheng, X}, title = {Metagenomics-Guided Discovery of Potential Bacterial Metallothionein Genes from the Soil Microbiome That Confer Cu and/or Cd Resistance.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {9}, pages = {}, pmid = {32111593}, issn = {1098-5336}, mesh = {Bacteria/drug effects/*genetics ; Cadmium/*adverse effects ; Copper/*adverse effects ; Drug Resistance, Bacterial/*genetics ; Genes, Bacterial ; *Metagenome ; Metagenomics ; Metallothionein/*genetics/metabolism ; Microbiota/drug effects/*genetics ; Soil Microbiology ; Soil Pollutants/adverse effects ; }, abstract = {Metallothionein (MT) genes are valuable genetic materials for developing metal bioremediation tools. Currently, a limited number of prokaryotic MTs have been experimentally identified, which necessitates the expansion of bacterial MT diversity. In this study, we conducted a metagenomics-guided analysis for the discovery of potential bacterial MT genes from the soil microbiome. More specifically, we combined resistance gene enrichment through diversity loss, metagenomic mining with a dedicated MT database, evolutionary trace analysis, DNA chemical synthesis, and functional genomic validation to identify novel MTs. Results showed that Cu stress induced a compositional change in the soil microbiome, with an enrichment of metal-resistant bacteria in soils with higher Cu concentrations. Shotgun metagenomic sequencing was performed to obtain the gene pool of environmental DNA (eDNA), which was subjected to a local BLAST search against an MT database for detecting putative MT genes. Evolutional trace analysis led to the identification of 27 potential MTs with conserved cysteine/histidine motifs different from those of known prokaryotic MTs. Following chemical synthesis of these 27 potential MT genes and heterologous expression in Escherichia coli, six of them were found to improve the hosts' growth substantially and enhanced the hosts' sorption of Cu, Cd, and Zn, among which MT5 led to a 13.7-fold increase in Cd accumulation. Furthermore, four of them restored Cu and/or Cd resistance in two metal-sensitive E. coli strains.IMPORTANCE The metagenomics-guided procedure developed here bypasses the difficulties encountered in classic PCR-based approaches and led to the discovery of novel MT genes, which may be useful in developing bioremediation tools. The procedure used here expands our knowledge on the diversity of bacterial MTs in the environment and may also be applicable to identify other functional genes from eDNA.}, }
@article {pmid32109809, year = {2020}, author = {Zhang, L and Zhang, Y and Patterson, J and Arslan, M and Zhang, Y and Gamal El-Din, M}, title = {Biofiltration of oil sands process water in fixed-bed biofilm reactors shapes microbial community structure for enhanced degradation of naphthenic acids.}, journal = {The Science of the total environment}, volume = {718}, number = {}, pages = {137028}, doi = {10.1016/j.scitotenv.2020.137028}, pmid = {32109809}, issn = {1879-1026}, mesh = {Biodegradation, Environmental ; Biofilms ; Carboxylic Acids ; Filtration ; *Microbiota ; Oil and Gas Fields ; Ozone ; Water Pollutants, Chemical ; }, abstract = {Naphthenic acids (NAs) are a complex mixture of carboxylic acids present in oil sands process water (OSPW). Their recalcitrant nature makes them difficult to be removed from the environment using conventional remediation strategies. This study hypothesized that, upon continuous operation, biofiltration of OSPW in fixed-bed biofilm reactors would allow the development of NA-degrading microbial community within the biofilter following successful removal. Both raw and ozonated OSPW were treated in the biofilters and changes in microbial community were tested via 16S/18S amplicon sequencing and metatranscriptomics. Through switch from suspended growth to attached growth, a shift in indigenous microbial community was seen following by an increase in alpha diversity. Concomitantly, improved degradation of NAs was monitored, i.e., 35.8% and 69.4% of NAs were removed from raw and ozonated OSPW, respectively. Metatranscriptomics analysis suggested the presence of genes involved in the degradation of organic acids and petroleum-related compounds. Specifically, functional abundance of aromatic compounds' metabolism improved from 0.05% to 0.76%; whereas abundance of benzoate transport and degradation pathway increased from 0.04% to 0.64%. These changes conclude that continuous operation of OSPW in the bioreactors was in favor of shaping the overall microbiome towards better NA degradation.}, }
@article {pmid32108314, year = {2020}, author = {Jo, J and Oh, J and Park, C}, title = {Microbial community analysis using high-throughput sequencing technology: a beginner's guide for microbiologists.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {58}, number = {3}, pages = {176-192}, pmid = {32108314}, issn = {1976-3794}, mesh = {Animals ; *Bacteria/classification/genetics ; Computational Biology/methods ; Datasets as Topic ; High-Throughput Nucleotide Sequencing/*methods ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Programmed Instructions as Topic ; Seawater/microbiology ; Sequence Analysis, DNA/*methods ; *Software ; Soil Microbiology ; Stichopus/microbiology ; }, abstract = {Microbial communities present in diverse environments from deep seas to human body niches play significant roles in the complex ecosystem and human health. Characterizing their structural and functional diversities is indispensable, and many approaches, such as microscopic observation, DNA fingerprinting, and PCR-based marker gene analysis, have been successfully applied to identify microorganisms. Since the revolutionary improvement of DNA sequencing technologies, direct and high-throughput analysis of genomic DNA from a whole environmental community without prior cultivation has become the mainstream approach, overcoming the constraints of the classical approaches. Here, we first briefly review the history of environmental DNA analysis applications with a focus on profiling the taxonomic composition and functional potentials of microbial communities. To this end, we aim to introduce the shotgun metagenomic sequencing (SMS) approach, which is used for the untargeted (&quot;shotgun&quot;) sequencing of all (&quot;meta&quot;) microbial genomes (&quot;genomic&quot;) present in a sample. SMS data analyses are performed in silico using various software programs; however, in silico analysis is typically regarded as a burden on wet-lab experimental microbiologists. Therefore, in this review, we present microbiologists who are unfamiliar with in silico analyses with a basic and practical SMS data analysis protocol. This protocol covers all the bioinformatics processes of the SMS analysis in terms of data preprocessing, taxonomic profiling, functional annotation, and visualization.}, }
@article {pmid32105997, year = {2020}, author = {Dias, MF and da Rocha Fernandes, G and Cristina de Paiva, M and Christina de Matos Salim, A and Santos, AB and Amaral Nascimento, AM}, title = {Exploring the resistome, virulome and microbiome of drinking water in environmental and clinical settings.}, journal = {Water research}, volume = {174}, number = {}, pages = {115630}, doi = {10.1016/j.watres.2020.115630}, pmid = {32105997}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents ; *Drinking Water ; Drug Resistance, Microbial ; Genes, Bacterial ; Humans ; Metagenomics ; *Microbiota ; }, abstract = {Aquatic ecosystems harbor a vast pool of antibiotic resistance genes (ARGs), which can suffer mutation, recombination and selection events. Here, we explored the diversity of ARGs, virulence factors and the bacterial community composition in water samples before (surface raw water, RW) and after (disinfected water, DW) drinking water conventional treatment, as well as in tap water (TW) and ultrafiltration membranes (UM, recovered from hemodialysis equipment) through metagenomics. A total of 852 different ARGs were identified, 21.8% of them only in RW, which might reflect the impact of human activities on the river at the sampling point. Although a similar resistance profile has been observed between the samples, significant differences in the frequency of clinically relevant antibiotic classes (penam and peptide) were identified. Resistance determinants to last resort antibiotics, including sequences related to mcr, optrA and poxtA and clinically relevant beta-lactamase genes (i.e. blaKPC, blaGES, blaIMP, blaVIM, blaSPM and blaNDM) were detected. 830 coding sequences (CDSs - related to 217 different ARGs) were embedded in contigs associated with mobile genetic elements, specially plasmids, of which 68% in RW, DW and TW, suggesting the importance of water environments in resistance dissemination. Shifts in bacterial pathogens genera were observed, such as a significant increase in Mycobacterium after treatment and distribution. In UM, the potentially pathogenic genus Halomonas predominated. Its draft genome was closely related to H. stevensii, hosting mainly multidrug efflux pumps. These results broaden our understanding of the global ARGs diversity and stress the importance of tracking the ever-expanding environmental resistome.}, }
@article {pmid32103130, year = {2020}, author = {Xu, P and Shi, Y and Liu, P and Yang, Y and Zhou, C and Li, G and Luo, J and Zhang, C and Cao, H and Hu, G and Guo, X}, title = {16S rRNA gene sequencing reveals an altered composition of the gut microbiota in chickens infected with a nephropathogenic infectious bronchitis virus.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {3556}, pmid = {32103130}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; Chickens ; Computational Biology/methods ; Coronavirus Infections/*veterinary ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; *Infectious bronchitis virus/physiology ; Intestinal Mucosa/metabolism/microbiology/pathology ; *Metagenome ; *Metagenomics/methods ; Poultry Diseases/*etiology ; *RNA, Ribosomal, 16S ; Viral Load ; }, abstract = {Infectious bronchitis virus (IBV), a member of the Coronaviridae family, causes serious losses to the poultry industry. Intestinal microbiota play an important role in chicken health and contribute to the defence against colonization by invading pathogens. The aim of this study was to investigate the link between the intestinal microbiome and nephropathogenic IBV (NIBV) infection. Initially, chickens were randomly distributed into 2 groups: the normal group (INC) and the infected group (IIBV). The ilea were collected for morphological assessment, and the ileal contents were collected for 16S rRNA gene sequencing analysis. The results of the IIBV group analyses showed a significant decrease in the ratio of villus height to crypt depth (P < 0.05), while the goblet cells increased compared to those in the INC group. Furthermore, the microbial diversity in the ilea decreased and overrepresentation of Enterobacteriaceae and underrepresentation of Chloroplast and Clostridia was found in the NIBV-infected chickens. In conclusion, these results showed that the significant separation of the two groups and the characterization of the gut microbiome profiles of the chickens with NIBV infection may provide valuable information and promising biomarkers for the diagnosis of this disease.}, }
@article {pmid32099013, year = {2020}, author = {Fidler, G and Tolnai, E and Stagel, A and Remenyik, J and Stundl, L and Gal, F and Biro, S and Paholcsek, M}, title = {Tendentious effects of automated and manual metagenomic DNA purification protocols on broiler gut microbiome taxonomic profiling.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {3419}, pmid = {32099013}, issn = {2045-2322}, mesh = {Animals ; Chickens/*microbiology ; *DNA, Bacterial/chemistry/genetics/isolation &amp; purification ; *Gastrointestinal Microbiome ; *Gram-Negative Bacteria/classification/genetics ; *Metagenome ; *Metagenomics ; }, abstract = {Here, we developed protocols to improve sensitivity, rigor and comparability of 16S rRNA gene amplification-based next-generation sequencing (NGS) results. A thorough study was performed by evaluating extraction efficiency with respect to the yield, purity, fragmentation of the purified DNA, and sequencing metrics considering the number of quality reads, amplicon sequence variants (ASVs), community structure and biodiversity. We identified batch-effects that significantly bias broiler gastrointestinal tract (GIT) community compositions and made recommendations to improve sensitivity, consistency, and cross-study comparability. We found that the purity of the extracted nucleic acid had a strong effect on the success rate of downstream library preparations. The preparation of stool bacterial suspensions from feces showed a significant positive influence on community biodiversity by enriching Gram-negative bacteria and cataloguing low abundant taxa with greater success than direct processing of fecal material. Applications relying on the automated Roche MagNa Pure 24 magnetic-bead based method provided results with high consistency therefore it seems to be the optimal choice in large-scale studies for investigating broiler GIT microbiota.}, }
@article {pmid32098813, year = {2020}, author = {Waterworth, SC and Flórez, LV and Rees, ER and Hertweck, C and Kaltenpoth, M and Kwan, JC}, title = {Horizontal Gene Transfer to a Defensive Symbiont with a Reduced Genome in a Multipartite Beetle Microbiome.}, journal = {mBio}, volume = {11}, number = {1}, pages = {}, pmid = {32098813}, issn = {2150-7511}, mesh = {Animals ; Bacteria/genetics ; Biological Products ; Burkholderia/genetics ; Coleoptera/*microbiology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome Size ; Genome, Bacterial/*genetics ; Metagenomics ; Microbiota/*genetics ; Multigene Family ; Symbiosis/*genetics/physiology ; }, abstract = {Symbiotic mutualisms of bacteria and animals are ubiquitous in nature, running a continuum from facultative to obligate from the perspectives of both partners. The loss of functions required for living independently but not within a host gives rise to reduced genomes in many symbionts. Although the phenomenon of genome reduction can be explained by existing evolutionary models, the initiation of the process is not well understood. Here, we describe the microbiome associated with the eggs of the beetle Lagria villosa, consisting of multiple bacterial symbionts related to Burkholderia gladioli, including a reduced-genome symbiont thought to be the exclusive producer of the defensive compound lagriamide. We show that the putative lagriamide-producing symbiont is the only member of the microbiome undergoing genome reduction and that it has already lost the majority of its primary metabolism and DNA repair pathways. The key step preceding genome reduction in the symbiont was likely the horizontal acquisition of the putative lagriamide lga biosynthetic gene cluster. Unexpectedly, we uncovered evidence of additional horizontal transfers to the symbiont's genome while genome reduction was occurring and despite a current lack of genes needed for homologous recombination. These gene gains may have given the genome-reduced symbiont a selective advantage in the microbiome, especially given the maintenance of the large lga gene cluster despite ongoing genome reduction.IMPORTANCE Associations between microorganisms and an animal, plant, or fungal host can result in increased dependence over time. This process is due partly to the bacterium not needing to produce nutrients that the host provides, leading to loss of genes that it would need to live independently and to a consequent reduction in genome size. It is often thought that genome reduction is aided by genetic isolation-bacteria that live in monocultures in special host organs, or inside host cells, have less access to other bacterial species from which they can obtain genes. Here, we describe exposure of a genome-reduced beetle symbiont to a community of related bacteria with nonreduced genomes. We show that the symbiont has acquired genes from other bacteria despite going through genome reduction, suggesting that isolation has not yet played a major role in this case of genome reduction, with horizontal gene gains still offering a potential route for adaptation.}, }
@article {pmid32093685, year = {2020}, author = {Fernández, J and de la Fuente, VG and García, MTF and Sánchez, JG and Redondo, BI and Villar, CJ and Lombó, F}, title = {A diet based on cured acorn-fed ham with oleic acid content promotes anti-inflammatory gut microbiota and prevents ulcerative colitis in an animal model.}, journal = {Lipids in health and disease}, volume = {19}, number = {1}, pages = {28}, pmid = {32093685}, issn = {1476-511X}, support = {IDI/2018/000120//Gobierno del Principado de Asturias/ ; FUO-222-16//Cárnicas Joselito/ ; }, mesh = {*Animal Feed ; Animals ; Anti-Inflammatory Agents/chemistry/*therapeutic use ; Colitis, Ulcerative/*drug therapy/microbiology ; Colon/microbiology ; Cytokines/blood ; Disease Models, Animal ; Gas Chromatography-Mass Spectrometry ; Gastrointestinal Microbiome/*drug effects ; Intestinal Mucosa/microbiology ; Male ; Oleic Acid/chemistry/*therapeutic use ; Phylogeny ; RNA, Ribosomal, 16S/metabolism ; Rats ; Rats, Inbred F344 ; }, abstract = {BACKGROUND: Diets based on meat products are not recommended in the case of ulcerative colitis (UC). The objective here is to test if some traditional cured meat products, as acorn-fed ham (high levels of oleic acid), may be useful for controlling inflammatory diseases as UC in animal models, which could represent a new dietary complementary intervention in the prevention of this inflammatory disease in humans.<br><br>METHODS: Two rat cohorts have been used: conventional vegetable rat feed and acorn-fed ham. UC was induced with DSS in drinking water ad libitum for 1 week. Short-chain fatty acids (SCFAs) and 16S rRNA metagenomics from bacterial populations were analyzed in cecum samples. Colon samples were analyzed for histological parameters.<br><br>RESULTS: Acorn-fed ham diet induced changes in gut microbiota composition, with pronounced enrichments in anti-inflammatory bacterial genera (Alistipes, Blautia, Dorea, Parabacteroides). The animals with this diet showed a strong reduction in most parameters associated to ulcerative colitis: disease activity index, macroscopic score of colitis, epitelium alteration in colon mucosa, inflammatory cell density in colon, myeloperoxidase titers in colon, proinflammatory cytokines (IL-17, IFN-γ). Also, acorn-fed ham diet animals showed increased total antioxidant activity an oleic acid levels in plasma, as well as higher short-chain fatty acid concentrations in cecum (isobutyric, isovaleric and valeric).<br><br>CONCLUSIONS: In the acorn-fed ham cohort, as a result of the dietary intake of oleic acid and low intake of omega-6 fatty acids, a strong preventive effect against UC symptoms was observed.}, }
@article {pmid32092934, year = {2020}, author = {Mohanty, I and Podell, S and Biggs, JS and Garg, N and Allen, EE and Agarwal, V}, title = {Multi-Omic Profiling of Melophlus Sponges Reveals Diverse Metabolomic and Microbiome Architectures that Are Non-overlapping with Ecological Neighbors.}, journal = {Marine drugs}, volume = {18}, number = {2}, pages = {}, pmid = {32092934}, issn = {1660-3397}, support = {R01 ES030316/ES/NIEHS NIH HHS/United States ; R01-ES030316/NH/NIH HHS/United States ; R00-ES026620/NH/NIH HHS/United States ; OCE-1837116//National Science Foundation/ ; }, mesh = {Animals ; *Ecosystem ; *Metabolomics ; *Microbiota ; Phylogeny ; Porifera/genetics/*metabolism/*microbiology ; }, abstract = {Marine sponge holobionts, defined as filter-feeding sponge hosts together with their associated microbiomes, are prolific sources of natural products. The inventory of natural products that have been isolated from marine sponges is extensive. Here, using untargeted mass spectrometry, we demonstrate that sponges harbor a far greater diversity of low-abundance natural products that have evaded discovery. While these low-abundance natural products may not be feasible to isolate, insights into their chemical structures can be gleaned by careful curation of mass fragmentation spectra. Sponges are also some of the most complex, multi-organismal holobiont communities in the oceans. We overlay sponge metabolomes with their microbiome structures and detailed metagenomic characterization to discover candidate gene clusters that encode production of sponge-derived natural products. The multi-omic profiling strategy for sponges that we describe here enables quantitative comparison of sponge metabolomes and microbiomes to address, among other questions, the ecological relevance of sponge natural products and for the phylochemical assignment of previously undescribed sponge identities.}, }
@article {pmid32071370, year = {2020}, author = {Kim, DJ and Yang, J and Seo, H and Lee, WH and Ho Lee, D and Kym, S and Park, YS and Kim, JG and Jang, IJ and Kim, YK and Cho, JY}, title = {Colorectal cancer diagnostic model utilizing metagenomic and metabolomic data of stool microbial extracellular vesicles.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {2860}, pmid = {32071370}, issn = {2045-2322}, mesh = {Bacteria/classification/genetics ; Colorectal Neoplasms/*diagnosis/genetics/microbiology/pathology ; Dysbiosis/genetics/microbiology/pathology ; Extracellular Vesicles/*genetics ; Feces/*microbiology ; Gastrointestinal Microbiome/genetics ; Gene Expression Regulation, Neoplastic/genetics ; Humans ; *Metabolomics ; Metagenome/genetics ; Metagenomics ; }, abstract = {Colorectal cancer (CRC) is the most common type cancers in the world. CRC occurs sporadically in the majority of cases, indicating the predominant cause of the disease are environmental factors. Diet-induced changes in gut-microbiome are recently supposed to contribute on epidemics of CRC. This study was aimed to investigate the association of metagenomics and metabolomics in gut extracellular vesicles (EVs) of CRC and healthy subjects. A total of 40 healthy volunteers and 32 patients with CRC were enrolled in this study. Metagenomic profiling by sequencing 16 S rDNA was performed for assessing microbial codiversity. We explored the small molecule metabolites using gas chromatography-time-of-flight mass spectrometry. In total, stool EVs were prepared from 40 healthy volunteers and 32 patients with CRC. Metagenomic profiling demonstrated that bacterial phyla, particularly of Firmicutes and Proteobacteria, were significantly altered in patients with colorectal cancer. Through metabolomics profiling, we determined seven amino acids, four carboxylic acids, and four fatty acids; including short-chain to long chain fatty acids that altered in the disease group. Binary logistic regression was further tested to evaluate the diagnostic performance. In summary, the present findings suggest that gut flora dysbiosis may result in alternation of amino acid metabolism, which may be correlated with the pathogenesis of CRC.}, }
@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}, mesh = {Animals ; Biodiversity ; Europe ; *Soil ; Soil Microbiology ; }, 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 metabarcoding.}, journal = {Molecular ecology resources}, volume = {20}, number = {3}, pages = {}, doi = {10.1111/1755-0998.13148}, pmid = {32065512}, issn = {1755-0998}, support = {ICI150100041//ARC Centre for Mine Site Restoration/ ; }, 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, probably 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 {pmid32062353, year = {2020}, author = {Trøseid, M and Andersen, GØ and Broch, K and Hov, JR}, title = {The gut microbiome in coronary artery disease and heart failure: Current knowledge and future directions.}, journal = {EBioMedicine}, volume = {52}, number = {}, pages = {102649}, doi = {10.1016/j.ebiom.2020.102649}, pmid = {32062353}, issn = {2352-3964}, mesh = {Animals ; Butyrates/metabolism ; Coronary Artery Disease/*etiology/*metabolism ; Diet ; *Disease Susceptibility ; Dysbiosis/metabolism ; Fatty Acids, Volatile/biosynthesis ; *Gastrointestinal Microbiome ; Heart Failure/*etiology/*metabolism ; Humans ; Intestinal Mucosa/immunology/metabolism/pathology ; Lipopolysaccharides/metabolism ; Metagenome ; Metagenomics ; Signal Transduction ; }, abstract = {Host-microbiota interactions involving inflammatory and metabolic pathways have been linked to the pathogenesis of multiple immune-mediated diseases and metabolic conditions like diabetes and obesity. Accumulating evidence suggests that alterations in the gut microbiome could play a role in cardiovascular disease. This review focuses on recent advances in our understanding of the interplay between diet, gut microbiota and cardiovascular disease, with emphasis on heart failure and coronary artery disease. Whereas much of the literature has focused on the circulating levels of the diet- and microbiota-dependent metabolite trimethylamine-N-oxide (TMAO), several recent sequencing-based studies have demonstrated compositional and functional alterations in the gut microbiomes in both diseases. Some microbiota characteristics are consistent across several study cohorts, such as a decreased abundance of microbes with capacity for producing butyrate. However, the published gut microbiota studies generally lack essential covariates like diet and clinical data, are too small to capture the substantial variation in the gut microbiome, and lack parallel plasma samples, limiting the ability to translate the functional capacity of the gut microbiomes to actual function reflected by circulating microbiota-related metabolites. This review attempts to give directions for future studies in order to demonstrate clinical utility of the gut-heart axis.}, }
@article {pmid32062351, year = {2020}, author = {Loughman, A and Ponsonby, AL and O'Hely, M and Symeonides, C and Collier, F and Tang, MLK and Carlin, J and Ranganathan, S and Allen, K and Pezic, A and Saffery, R and Jacka, F and Harrison, LC and Sly, PD and Vuillermin, P and , }, title = {Gut microbiota composition during infancy and subsequent behavioural outcomes.}, journal = {EBioMedicine}, volume = {52}, number = {}, pages = {102640}, doi = {10.1016/j.ebiom.2020.102640}, pmid = {32062351}, issn = {2352-3964}, mesh = {Adult ; Age Factors ; Anti-Bacterial Agents/pharmacology ; Australia ; Biodiversity ; Brain/physiology ; Child ; *Child Behavior ; Child, Preschool ; Cohort Studies ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/drug effects ; Humans ; Infant ; *Infant Behavior ; Male ; Metagenome ; Metagenomics/methods ; *Neurogenesis ; RNA, Ribosomal, 16S ; Risk Factors ; }, abstract = {BACKGROUND: Despite intense interest in the relationship between gut microbiota and brain development, longitudinal data from human studies are lacking. This study aimed to investigate the relationship between the composition of gut microbiota during infancy and subsequent behavioural outcomes.<br><br>METHODS: A subcohort of 201 children with behavioural outcome measures was identified within a longitudinal, Australian birth-cohort study. The faecal microbiota were analysed at 1, 6, and 12 months of age. Behavioural outcomes were measured at 2 years of age.<br><br>FINDINGS: In an unselected birth cohort, we found a clear association between decreased normalised abundance of Prevotella in faecal samples collected at 12 months of age and increased behavioural problems at 2 years, in particular Internalizing Problem scores. This association appeared independent of multiple potentially confounding variables, including maternal mental health. Recent exposure to antibiotics was the best predictor of decreased Prevotella.<br><br>INTERPRETATION: Our findings demonstrate a strong association between the composition of the gut microbiota in infancy and subsequent behavioural outcomes; and support the importance of responsible use of antibiotics during early life.<br><br>FUNDING: This study was funded by the National Health and Medical Research Council of Australia (1082307, 1147980, 1129813), The Murdoch Children's Research Institute, Barwon Health, Deakin University, Perpetual Trustees, and The Shepherd Foundation. The funders had no involvement in the data collection, analysis or interpretation, trial design, recruitment or any other aspect pertinent to the study.}, }
@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 {pmid32054085, year = {2020}, author = {Langan, EA and Recke, A and Bokor-Billmann, T and Billmann, F and Kahle, BK and Zillikens, D}, title = {The Role of the Cutaneous Microbiome in Hidradenitis Suppurativa-Light at the End of the Microbiological Tunnel.}, journal = {International journal of molecular sciences}, volume = {21}, number = {4}, pages = {}, pmid = {32054085}, issn = {1422-0067}, mesh = {Animals ; Bacteria/genetics/isolation &amp; purification ; Dysbiosis/complications/microbiology/physiopathology ; Hidradenitis Suppurativa/complications/*microbiology/physiopathology ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; Microbiota ; Skin/*microbiology/physiopathology ; }, abstract = {The development of next generation sequencing, coupled with advances in bio-informatics, has provided new insights into the role of the cutaneous microbiome in the pathophysiology of a range of inflammatory skin diseases. In fact, it has even been suggested that the identification of specific skin microbial signatures may not only be useful in terms of diagnosis of skin diseases but they may also ultimately help inform personalised treatment strategies. To date, research investigating the role of microbiota in the development of inflammatory skin diseases has largely focused on atopic eczema and psoriasis vulgaris. The role of the microbiome in Hidradenits suppurativa (HS)-also known as acne inversa-a chronic auto-inflammatory skin disease associated with significant morbidity, has received comparatively little attention. This is despite the fact that antimicrobial therapy plays a central role in the treatment of HS. After briefly outlining the clinical features of HS and current treatment strategies, we move on to review the evidence of microbial dysbiosis in HS pathophysiology. We conclude by outlining the potential for metagenomic studies to deepen our understanding of HS biology but more importantly to identify novel and much needed treatment strategies.}, }
@article {pmid32053789, year = {2020}, author = {Khan Mirzaei, M and Khan, MAA and Ghosh, P and Taranu, ZE and Taguer, M and Ru, J and Chowdhury, R and Kabir, MM and Deng, L and Mondal, D and Maurice, CF}, title = {Bacteriophages Isolated from Stunted Children Can Regulate Gut Bacterial Communities in an Age-Specific Manner.}, journal = {Cell host &amp; microbe}, volume = {27}, number = {2}, pages = {199-212.e5}, pmid = {32053789}, issn = {1934-6069}, mesh = {Age Factors ; Bacteria/classification/genetics/isolation &amp; purification/virology ; Bacteriophages/classification/genetics/*isolation &amp; purification ; Child, Preschool ; Female ; *Gastrointestinal Microbiome/genetics/physiology ; Genes, Bacterial ; Genes, Viral ; Growth Disorders/*microbiology/*virology ; Host Microbial Interactions ; Humans ; Infant ; Male ; Metagenomics ; Proteobacteria/classification/genetics/isolation &amp; purification/virology ; RNA, Ribosomal, 16S ; }, abstract = {Stunting, a severe and multigenerational growth impairment, globally affects 22% of children under the age of 5 years. Stunted children have altered gut bacterial communities with higher proportions of Proteobacteria, a phylum with several known human pathogens. Despite the links between an altered gut microbiota and stunting, the role of bacteriophages, highly abundant bacterial viruses, is unknown. Here, we describe the gut bacterial and bacteriophage communities of Bangladeshi stunted children younger than 38 months. We show that these children harbor distinct gut bacteriophages relative to their non-stunted counterparts. In vitro, these gut bacteriophages are infectious and can regulate bacterial abundance and composition in an age-specific manner, highlighting their possible role in the pathophysiology of child stunting. Specifically, Proteobacteria from non-stunted children increased in the presence of phages from younger stunted children, suggesting that phages could contribute to the bacterial community changes observed in child stunting.}, }
@article {pmid32046772, year = {2020}, author = {Chen, HL and Zhao, XY and Zhao, GX and Huang, HB and Li, HR and Shi, CW and Yang, WT and Jiang, YL and Wang, JZ and Ye, LP and Zhao, Q and Wang, CF and Yang, GL}, title = {Dissection of the cecal microbial community in chickens after Eimeria tenella infection.}, journal = {Parasites &amp; vectors}, volume = {13}, number = {1}, pages = {56}, pmid = {32046772}, issn = {1756-3305}, support = {2017YFD0500400//The National Key Research and Development Program of China/ ; 2017YFD0501200//The National Key Research and Development Program of China/ ; 31672528//the National Natural Science Foundation of China/ ; }, mesh = {Animals ; Bacteria/classification/isolation &amp; purification ; Cecum/microbiology/parasitology/pathology ; *Chickens/microbiology/parasitology ; Coccidiosis/therapy/*veterinary ; *Eimeria tenella/genetics/parasitology ; Gastrointestinal Microbiome/*genetics ; Metagenomics ; Poultry Diseases/*parasitology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Eimeria spp. are responsible for chicken coccidiosis which is the most important enteric protozoan disease resulting in tremendous economic losses in the poultry industry. Understanding the interaction between the avian cecal microbiota and coccidia is of interest in the development of alternative treatments that do not rely on chemotherapeutics and do not lead to drug resistance.<br><br>METHODS: We utilized 16S rRNA gene sequencing to detect the dynamics of the cecal microbial community in AA broilers challenged with Eimeria tenella. Histopathological analysis of the cecum was also conducted.<br><br>RESULTS: We found that microbial shifts occur during the infection. Lactobacillus, Faecalibacterium, Ruminococcaceae UCG-013, Romboutsia and Shuttleworthia decreased in abundance. However, the opportunistic pathogens Enterococcus and Streptococcus increased in abundance over time in response to the infection.<br><br>CONCLUSIONS: Eimeria tenella disrupts the integrity of the cecal microbiota and could promote the establishment and growth of potentially pathogenic bacteria. Defining bacterial populations affected by coccidial infection might help identify bacterial markers for intestinal disease as well as populations or species that could be beneficial in maintaining and restoring gut homeostasis during and after infection with E. tenella.}, }
@article {pmid32043695, year = {2020}, author = {He, Z and Pan, L and Zhang, M and Zhang, M and Huang, F and Gao, S}, title = {Metagenomic comparison of structure and function of microbial community between water, effluent and shrimp intestine of higher place Litopenaeus vannamei ponds.}, journal = {Journal of applied microbiology}, volume = {129}, number = {2}, pages = {243-255}, doi = {10.1111/jam.14610}, pmid = {32043695}, issn = {1365-2672}, support = {KLM2017005//Key Laboratory of Mariculture, Ministry Education, Ocean University of China (OUC)/ ; 20160359//Bio-Form Biotechnology Co. LTD/ ; }, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification ; Intestines/*microbiology ; Metagenome ; Microbiota/genetics/*physiology ; Penaeidae/*microbiology ; Ponds/*microbiology ; RNA, Ribosomal, 16S/genetics ; Shellfish/*microbiology ; Waste Water/microbiology ; }, abstract = {AIMS: The present study aimed to reveal microbial relationship between shrimp intestine and ambient in higher place shrimp ponds from the aspects of composition and function.<br><br>METHODS AND RESULTS: Metagenome and 16S rRNA gene sequencing were used to compare microbial compositions and functions of water, effluent and shrimp intestine in higher place Litopenaeus vannamei ponds. Although the three groups had similar dominant phyla, such as Proteobacteria, Bacteroidetes and Tenericutes, their bacterial compositions at the genus level were obviously different. Compared to effluent and intestine, the relative abundance of Vibrio as common opportunistic pathogen for shrimp was significantly higher in water. However, cluster analysis showed that intestinal microbial composition was more similar to that of effluent than water. Metagenomic data showed that the predominant microbial functions in the three groups were mostly related to energy production and biosynthesis, while carbohydrate metabolism was relatively enriched in intestinal microbiota. More importantly, Proteobacteria played a critical role in carbon metabolism and biosynthesis of amino acids in the three habitats, and Vibrio had the most functions related to bacterial virulence and infection.<br><br>CONCLUSIONS: Shrimp intestinal microbiota had a close correlation with the ambient microbiota in both structure and function. As the most dominant phylum, Proteobacteria was very important for microbiota communication and nutrient cycling in higher place shrimp ponds. Moreover, due to the pathogenicity, it was necessary to monitor the abundant changes of Vibrio in water to decrease the risk of shrimp disease outbreaks.<br><br>These above results may be helpful to comprehensively understand the characteristics and functions of microbiota in higher place shrimp ponds, thereby providing basic information for developing the management strategies of entire microbiota to sustain shrimp health.}, }
@article {pmid32042169, year = {2020}, author = {Moss, EL and Maghini, DG and Bhatt, AS}, title = {Complete, closed bacterial genomes from microbiomes using nanopore sequencing.}, journal = {Nature biotechnology}, volume = {38}, number = {6}, pages = {701-707}, doi = {10.1038/s41587-020-0422-6}, pmid = {32042169}, issn = {1546-1696}, support = {R01 AI148623/AI/NIAID NIH HHS/United States ; P50 AG047366/AG/NIA NIH HHS/United States ; T32 HG000044/HG/NHGRI NIH HHS/United States ; P30 CA124435/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Animals ; DNA, Bacterial/analysis/genetics ; Dogs ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Genome, Bacterial/*genetics ; Humans ; Metagenomics/*methods ; Mice ; Nanopore Sequencing/*methods ; Sequence Analysis, DNA/*methods ; }, abstract = {Microbial genomes can be assembled from short-read sequencing data, but the assembly contiguity of these metagenome-assembled genomes is constrained by repeat elements. Correct assignment of genomic positions of repeats is crucial for understanding the effect of genome structure on genome function. We applied nanopore sequencing and our workflow, named Lathe, which incorporates long-read assembly and short-read error correction, to assemble closed bacterial genomes from complex microbiomes. We validated our approach with a synthetic mixture of 12 bacterial species. Seven genomes were completely assembled into single contigs and three genomes were assembled into four or fewer contigs. Next, we used our methods to analyze metagenomics data from 13 human stool samples. We assembled 20 circular genomes, including genomes of Prevotella copri and a candidate Cibiobacter sp. Despite the decreased nucleotide accuracy compared with alternative sequencing and assembly approaches, our methods improved assembly contiguity, allowing for investigation of the role of repeat elements in microbial function and adaptation.}, }
@article {pmid32041654, year = {2020}, author = {Cheaib, B and Seghouani, H and Ijaz, UZ and Derome, N}, title = {Community recovery dynamics in yellow perch microbiome after gradual and constant metallic perturbations.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {14}, doi = {10.1186/s40168-020-0789-0}, pmid = {32041654}, issn = {2049-2618}, mesh = {Animals ; Bacteria/*classification/drug effects/pathogenicity ; Bioaccumulation ; Cadmium Chloride/*pharmacology ; High-Throughput Nucleotide Sequencing ; Liver/metabolism ; Metagenomics ; Microbiota/*drug effects ; Perches/metabolism/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Stress, Physiological ; }, abstract = {BACKGROUND: The eco-evolutionary processes ruling post-disturbance microbial assembly remain poorly studied, particularly in host-microbiome systems. The community recovery depends not only on the type, duration, intensity, and gradient of disturbance, but also on the initial community structure, phylogenetic composition, legacy, and habitat (soil, water, host). In this study, yellow perch (Perca flavescens) juveniles were exposed over 90 days to constant and gradual sublethal doses of cadmium chloride. Afterward, the exposure of aquaria tank system to cadmium was ceased for 60 days. The skin, gut and water tank microbiomes in control and treatment groups, were characterized before, during and after the cadmium exposure using 16s rDNA libraries and high throughput sequencing technology (Illumina, Miseq).<br><br>RESULTS: Our data exhibited long-term bioaccumulation of cadmium salts in the liver even after two months since ceasing the exposure. The gradient of cadmium disturbance had differential effects on the perch microbiota recovery, including increases in evenness, taxonomic composition shifts, as well as functional and phylogenetic divergence. The perch microbiome reached an alternative stable state in the skin and nearly complete recovery trajectories in the gut communities. The recovery of skin communities showed a significant proliferation of opportunistic fish pathogens (i.e., Flavobacterium). Our findings provide evidence that neutral processes were a much more significant contributor to microbial community turnover in control treatments than in those treated with cadmium, suggesting the role of selective processes in driving community recovery.<br><br>CONCLUSIONS: The short-term metallic disturbance of fish development has important long-term implications for host health. The recovery of microbial communities after metallic exposure depends on the magnitude of exposure (constant, gradual), and the nature of the ecological niche (water, skin, and gut). The skin and gut microbiota of fish exposed to constant concentrations of cadmium (CC) were closer to the control negative than those exposed to the gradual concentrations (CV). Overall, our results show that the microbial assembly during the community recovery were both orchestrated by neutral and deterministic processes. Video Abtract.}, }
@article {pmid32039051, year = {2019}, author = {Tong, Y and Zheng, L and Qing, P and Zhao, H and Li, Y and Su, L and Zhang, Q and Zhao, Y and Luo, Y and Liu, Y}, title = {Oral Microbiota Perturbations Are Linked to High Risk for Rheumatoid Arthritis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {475}, pmid = {32039051}, issn = {2235-2988}, mesh = {Arthritis, Rheumatoid/*epidemiology ; Bacteria/classification/genetics ; Biodiversity ; Case-Control Studies ; China ; Dysbiosis/*complications ; Female ; *Host Microbial Interactions ; Humans ; Male ; Metagenomics ; Middle Aged ; Mouth/*microbiology ; RNA, Ribosomal, 16S/genetics ; Risk Assessment ; }, abstract = {Oral microbial dysbiosis is known to increase susceptibility of an individual to develop rheumatoid arthritis (RA). Individuals at-risk of RA may undergo different phases of disease progression. In this study, we aim to investigate whether and whereby the oral microbiome communities alter prior to symptoms of RA. Seventy-nine saliva samples were collected from 29 high-risk individuals, who were positive for anti-citrullinated protein antibodies (ACPA) and have no clinical arthritis, 27 RA patients and 23 healthy controls (HCs). The salivary microbiome was examined using 16S ribosomal RNA gene sequencing. Alpha and beta diversity analysis and the linear discriminant analysis were applied to examine the bacterial diversity, community structure and discriminatory taxa between three groups, respectively. The correlation between salivary bacteria and autoantibodies were analyzed. In the &quot;pre-clinical&quot; stages, salivary microbial diversity was significantly reduced comparing to RA patients and HCs. In contrast to HCs, like RA patients, individuals at high-risk for RA showed a reduction in the abundance of genus Defluviitaleaceae_UCG-011 and the species Neisseria oralis, but an expansion of Prevotella_6. Unexpectedly, the relative abundance of Porphyromonas gingivalis, reported as opportunistic pathogens for RA development, was significantly decreased in high-risk individuals. Additionally, we identified four genera in the saliva from high-risk individuals positively correlated with serum ACPA titers, and the other two genera inversely displayed. In summary, we observed a characteristic compositional change of salivary microbes in individuals at high-risk for RA, suggesting that oral microbiota dysbiosis occurs in the &quot;pre-clinical&quot; stage of RA and are correlated with systemic autoimmune features.}, }
@article {pmid32031212, year = {2020}, author = {Fenske, GJ and Ghimire, S and Antony, L and Christopher-Hennings, J and Scaria, J}, title = {Integration of culture-dependent and independent methods provides a more coherent picture of the pig gut microbiome.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {3}, pages = {}, doi = {10.1093/femsec/fiaa022}, pmid = {32031212}, issn = {1574-6941}, mesh = {Animals ; Bacteroidetes/genetics ; *Gastrointestinal Microbiome ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Swine ; }, abstract = {Bacterial communities resident in the hindgut of pigs, have profound impacts on health and disease. Investigations into the pig microbiome have utilized either culture-dependent, or far more commonly, culture-independent techniques using next generation sequencing. We contend that a combination of both approaches generates a more coherent view of microbiome composition. In this study, we surveyed the microbiome of Tamworth breed and feral pigs through the integration high throughput culturing and shotgun metagenomics. A single culture medium was used for culturing. Selective screens were added to the media to increase culture diversity. In total, 46 distinct bacterial species were isolated from the Tamworth and feral samples. Selective screens successfully shifted the diversity of bacteria on agar plates. Tamworth pigs are highly dominated by Bacteroidetes primarily composed of the genus Prevotella whereas feral samples were more diverse with almost equal proportions of Firmicutes and Bacteroidetes. The combination of metagenomics and culture techniques facilitated a greater retrieval of annotated genes than either method alone. The single medium based pig microbiota library we report is a resource to better understand pig gut microbial ecology and function. It allows for assemblage of defined bacterial communities for studies in bioreactors or germfree animal models.}, }
@article {pmid32024572, year = {2020}, author = {Newbold, CJ and Ramos-Morales, E}, title = {Review: Ruminal microbiome and microbial metabolome: effects of diet and ruminant host.}, journal = {Animal : an international journal of animal bioscience}, volume = {14}, number = {S1}, pages = {s78-s86}, doi = {10.1017/S1751731119003252}, pmid = {32024572}, issn = {1751-732X}, mesh = {Animals ; Diet/veterinary ; Fermentation ; *Gastrointestinal Microbiome ; Gene Expression Profiling/veterinary ; *Metabolome ; Metabolomics ; *Metagenome ; Metagenomics ; Methane/*metabolism ; Nitrogen/metabolism ; Phylogeny ; Plant Extracts/metabolism ; *Proteome ; Proteomics ; Rumen/metabolism ; Ruminants/metabolism/*microbiology ; *Transcriptome ; }, abstract = {The rumen contains a great diversity of prokaryotic and eukaryotic microorganisms that allow the ruminant to utilize ligno-cellulose material and to convert non-protein nitrogen into microbial protein to obtain energy and amino acids. However, rumen fermentation also has potential deleterious consequences associated with the emissions of greenhouse gases, excessive nitrogen excreted in manure and may also adversely influence the nutritional value of ruminant products. While several strategies for optimizing the energy and nitrogen use by ruminants have been suggested, a better understanding of the key microorganisms involved and their activities is essential to manipulate rumen processes successfully. Diet is the most obvious factor influencing the rumen microbiome and fermentation. Among dietary interventions, the ban of antimicrobial growth promoters in animal production systems has led to an increasing interest in the use of plant extracts to manipulate the rumen. Plant extracts (e.g. saponins, polyphenol compounds, essential oils) have shown potential to decrease methane emissions and improve the efficiency of nitrogen utilization; however, there are limitations such as inconsistency, transient and adverse effects for their use as feed additives for ruminants. It has been proved that the host animal may also influence the rumen microbial population both as a heritable trait and through the effect of early-life nutrition on microbial population structure and function in adult ruminants. Recent developments have allowed phylogenetic information to be upscaled to metabolic information; however, research effort on cultivation of microorganisms for an in-depth study and characterization is needed. The introduction and integration of metagenomic, transcriptomic, proteomic and metabolomic techniques is offering the greatest potential of reaching a truly systems-level understanding of the rumen; studies have been focused on the prokaryotic population and a broader approach needs to be considered.}, }
@article {pmid32023487, year = {2020}, author = {Wang, GH and Berdy, BM and Velasquez, O and Jovanovic, N and Alkhalifa, S and Minbiole, KPC and Brucker, RM}, title = {Changes in Microbiome Confer Multigenerational Host Resistance after Sub-toxic Pesticide Exposure.}, journal = {Cell host &amp; microbe}, volume = {27}, number = {2}, pages = {213-224.e7}, doi = {10.1016/j.chom.2020.01.009}, pmid = {32023487}, issn = {1934-6069}, mesh = {Animals ; Atrazine/metabolism/toxicity ; Bacteria/genetics/isolation &amp; purification/metabolism ; Directed Molecular Evolution ; Drug Resistance/genetics ; *Gastrointestinal Microbiome/drug effects/genetics ; Genes, Bacterial ; Maternal Inheritance ; Metagenomics ; Pesticides/metabolism/*toxicity ; Pseudomonas/genetics/isolation &amp; purification/metabolism ; Serratia marcescens/genetics/isolation &amp; purification/metabolism ; Wasps/drug effects/*microbiology ; Xenobiotics/metabolism/toxicity ; }, abstract = {The gut is a first point of contact with ingested xenobiotics, where chemicals are metabolized directly by the host or microbiota. Atrazine is a widely used pesticide, but the role of the microbiome metabolism of this xenobiotic and the impact on host responses is unclear. We exposed successive generations of the wasp Nasonia vitripennis to subtoxic levels of atrazine and observed changes in the structure and function of the gut microbiome that conveyed atrazine resistance. This microbiome-mediated resistance was maternally inherited and increased over successive generations, while also heightening the rate of host genome selection. The rare gut bacteria Serratia marcescens and Pseudomonas protegens contributed to atrazine metabolism. Both of these bacteria contain genes that are linked to atrazine degradation and were sufficient to confer resistance in experimental wasp populations. Thus, pesticide exposure causes functional, inherited changes in the microbiome that should be considered when assessing xenobiotic exposure and as potential countermeasures to toxicity.}, }
@article {pmid32015529, year = {2020}, author = {Dion, MB and Oechslin, F and Moineau, S}, title = {Phage diversity, genomics and phylogeny.}, journal = {Nature reviews. Microbiology}, volume = {18}, number = {3}, pages = {125-138}, doi = {10.1038/s41579-019-0311-5}, pmid = {32015529}, issn = {1740-1534}, mesh = {Bacteriophages/*classification/*genetics/ultrastructure ; *Biodiversity ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Viral ; Host Microbial Interactions ; Metagenomics ; *Phylogeny ; Recombination, Genetic ; Viral Proteins/genetics ; Virion/ultrastructure ; }, abstract = {Recent advances in viral metagenomics have enabled the rapid discovery of an unprecedented catalogue of phages in numerous environments, from the human gut to the deep ocean. Although these advances have expanded our understanding of phage genomic diversity, they also revealed that we have only scratched the surface in the discovery of novel viruses. Yet, despite the remarkable diversity of phages at the nucleotide sequence level, the structural proteins that form viral particles show strong similarities and conservation. Phages are uniquely interconnected from an evolutionary perspective and undergo multiple events of genetic exchange in response to the selective pressure of their hosts, which drives their diversity. In this Review, we explore phage diversity at the structural, genomic and community levels as well as the complex evolutionary relationships between phages, moulded by the mosaicity of their genomes.}, }
@article {pmid32013116, year = {2020}, author = {Han, Y and Park, H and Choi, BR and Ji, Y and Kwon, EY and Choi, MS}, title = {Alteration of Microbiome Profile by D-Allulose in Amelioration of High-Fat-Diet-Induced Obesity in Mice.}, journal = {Nutrients}, volume = {12}, number = {2}, pages = {}, pmid = {32013116}, issn = {2072-6643}, support = {NRF-2016R1A2B4011329//National Research Foundation of Korea/ ; 22A20130000161//National Research Foundation of Korea/ ; }, mesh = {Animals ; Diet, High-Fat/*adverse effects ; Dietary Supplements ; Fructose/*administration &amp; dosage/*pharmacology ; Gastrointestinal Microbiome/*drug effects ; Male ; Mice ; Mice, Inbred C57BL ; Obesity/*chemically induced/*drug therapy ; }, abstract = {Recently, there has been a global shift in diet towards an increased intake of energy-dense foods that are high in sugars. D-allulose has received attention as a sugar substitute and has been reported as one of the anti-obesity food components; however, its correlation with the intestinal microbial community is not yet completely understood. Thirty-six C57BL/6J mice were divided in to four dietary groups and fed a normal diet (ND), a high-fat diet (HFD, 20% fat, 1% cholesterol, w/w), and a HFD with 5% erythritol (ERY) and D-allulose (ALL) supplement for 16 weeks. A pair-feeding approach was used so that all groups receiving the high-fat diet would have the same calorie intake. As a result, body weight and body fat mass in the ALL group were significantly decreased toward the level of the normal group with a simultaneous decrease in plasma leptin and resistin. Fecal short-chain fatty acid (SCFA) production analysis revealed that ALL induced elevated total SCFA production compared to the other groups. Also, ALL supplement induced the change in the microbial community that could be responsible for improving the obesity based on 16S rRNA gene sequence analysis, and ALL significantly increased the energy expenditure in Day(6a.m to 6pm). Taken together, our findings suggest that 5% dietary ALL led to an improvement in HFD-induced obesity by altering the microbiome community.}, }
@article {pmid32007292, year = {2020}, author = {Santos-Cortez, RLP and Bhutta, MF and Earl, JP and Hafrén, L and Jennings, M and Mell, JC and Pichichero, ME and Ryan, AF and Tateossian, H and Ehrlich, GD}, title = {Panel 3: Genomics, precision medicine and targeted therapies.}, journal = {International journal of pediatric otorhinolaryngology}, volume = {130 Suppl 1}, number = {}, pages = {109835}, doi = {10.1016/j.ijporl.2019.109835}, pmid = {32007292}, issn = {1872-8464}, support = {R01 DC015688/DC/NIDCD NIH HHS/United States ; R01 DC012595/DC/NIDCD NIH HHS/United States ; R01 DC002148/DC/NIDCD NIH HHS/United States ; R01 DC000129/DC/NIDCD NIH HHS/United States ; MC_UP_1503/1/MRC_/Medical Research Council/United Kingdom ; R01 DC015004/DC/NIDCD NIH HHS/United States ; R01 AI080935/AI/NIAID NIH HHS/United States ; R13 DC017389/DC/NIDCD NIH HHS/United States ; }, mesh = {Animals ; Ear, Middle/*microbiology ; Genetic Predisposition to Disease/*genetics ; Genomics ; Humans ; Microbiota/genetics ; Otitis Media/drug therapy/*genetics/*microbiology/prevention &amp; control ; Precision Medicine ; }, abstract = {OBJECTIVE: To review the most recent advances in human and bacterial genomics as applied to pathogenesis and clinical management of otitis media.<br><br>DATA SOURCES: PubMed articles published since the last meeting in June 2015 up to June 2019.<br><br>REVIEW METHODS: A panel of experts in human and bacterial genomics of otitis media was formed. Each panel member reviewed the literature in their respective fields and wrote draft reviews. The reviews were shared with all panel members, and a merged draft was created. The panel met at the 20th International Symposium on Recent Advances in Otitis Media in June 2019, discussed the review and refined the content. A final draft was made, circulated, and approved by the panel members.<br><br>CONCLUSION: Trans-disciplinary approaches applying pan-omic technologies to identify human susceptibility to otitis media and to understand microbial population dynamics, patho-adaptation and virulence mechanisms are crucial to the development of novel, personalized therapeutics and prevention strategies for otitis media.<br><br>IMPLICATIONS FOR PRACTICE: In the future otitis media prevention strategies may be augmented by mucosal immunization, combination vaccines targeting multiple pathogens, and modulation of the middle ear microbiome. Both treatment and vaccination may be tailored to an individual's otitis media phenotype as defined by molecular profiles obtained by using rapidly developing techniques in microbial and host genomics.}, }
@article {pmid32005736, year = {2020}, author = {Alessandri, G and Milani, C and Mancabelli, L and Longhi, G and Anzalone, R and Lugli, GA and Duranti, S and Turroni, F and Ossiprandi, MC and van Sinderen, D and Ventura, M}, title = {Deciphering the Bifidobacterial Populations within the Canine and Feline Gut Microbiota.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {7}, pages = {}, pmid = {32005736}, issn = {1098-5336}, mesh = {Animals ; Bifidobacterium/*isolation &amp; purification ; Cats/*microbiology ; DNA, Ribosomal Spacer/analysis ; Dogs/*microbiology ; *Gastrointestinal Microbiome ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; }, abstract = {During the course of evolution, dogs and cats have been subjected to extensive domestication, becoming the principal companion animals for humans. For this reason, their health care, including their intestinal microbiota, is considered of considerable importance. However, the canine and feline gut microbiota still represent a largely unexplored research area. In the present work, we profiled the microbiota of 23 feline fecal samples by 16S rRNA gene and bifidobacterial internally transcribed spacer (ITS) approaches and compared this information with previously reported data from 138 canine fecal samples. The obtained data allowed the reconstruction of the core gut microbiota of the above-mentioned samples coupled with their classification into distinct community state types at both genus and species levels, identifying Bacteroides, Fusobacterium, and Prevotella 9 as the main bacterial components of the canine and feline gut microbiota. At the species level, the intestinal bifidobacterial gut communities of dogs and cats differed in terms of both species number and composition, as emphasized by a covariance analysis. Together, our findings show that the intestinal populations of cats and dogs are similar in terms of genus-level taxonomical composition, while at the bifidobacterial species level, clear differences were observed, indicative of host-specific colonization behavior by particular bifidobacterial taxa.IMPORTANCE Currently, domesticated dogs and cats are the most cherished companion animals for humans, and concerns about their health and well-being are therefore important. In this context, the gut microbiota plays a crucial role in maintaining and promoting host health. However, despite the social relevance of domesticated dogs and cats, their intestinal microbial communities are still far from being completely understood. In this study, the taxonomical composition of canine and feline gut microbiota was explored at genus and bifidobacterial species levels, allowing classification of these microbial populations into distinct gut community state types at either of the two investigated taxonomic levels. Furthermore, the reconstruction of core gut microbiota coupled with covariance network analysis based on bifidobacterial internally transcribed spacer (ITS) profiling revealed differences in the bifidobacterial compositions of canine and feline gut microbiota, suggesting that particular bifidobacterial species have developed a selective ability to colonize a specific host.}, }
@article {pmid32005194, year = {2020}, author = {Crusell, MKW and Brink, LR and Nielsen, T and Allin, KH and Hansen, T and Damm, P and Lauenborg, J and Hansen, TH and Pedersen, O}, title = {Gestational diabetes and the human salivary microbiota: a longitudinal study during pregnancy and postpartum.}, journal = {BMC pregnancy and childbirth}, volume = {20}, number = {1}, pages = {69}, pmid = {32005194}, issn = {1471-2393}, support = {13-4608//Augustinus Fonden/ ; 10-001605//Aase og Ejnar Danielsens Fond/ ; }, mesh = {Adult ; Blood Glucose ; Body Mass Index ; Diabetes, Gestational/*microbiology ; Female ; Glucose Tolerance Test ; Humans ; Longitudinal Studies ; *Microbiota ; Postpartum Period/*blood ; Pregnancy ; Pregnancy Trimester, Third/*blood ; RNA, Ribosomal, 16S ; Saliva/*microbiology ; }, abstract = {BACKGROUND: An aberrant composition of the salivary microbiota has been found in individuals with type 2 diabetes, and in pregnant women salivary microbiota composition has been associated with preeclampsia and pre-term birth. Pregnant women, who develop gestational diabetes (GDM), have a high risk of developing type 2 diabetes after pregnancy. In the present study we assessed whether GDM is linked to variation in the oral microbial community by examining the diversity and composition of the salivary microbiota.<br><br>METHOD: In this observational study the salivary microbiota of pregnant women with GDM (n = 50) and normal glucose regulation (n = 160) in third trimester and 9 months postpartum was assessed by 16S rRNA gene amplicon sequencing of the V1-V3 region. GDM was diagnosed in accordance with the International Association of the Diabetes and Pregnancy Study Groups (IADPSG) criteria. Cross-sectional difference in alpha diversity was assessed using Student's t-test and longitudinal changes were assessed by mixed linear regression. Cross-sectional and longitudinal difference in beta diversity was assessed by permutational multivariate analyses of variance. Differentially abundant genera and OTUs were identified by negative binomial regression.<br><br>RESULTS: In the third trimester, two species-level operational taxonomic units (OTUs), while eight OTUs postpartum were differentially abundant in women with GDM compared with normoglycaemic women. OTU richness, Shannon diversity and Pielou evenness decreased from late pregnancy to 9 months after delivery regardless of glycaemic status.<br><br>CONCLUSION: GDM is associated with a minor aberration of the salivary microbiota during late pregnancy and postpartum. For unknown reasons richness of the salivary microbiota decreased from late pregnancy to postpartum, which might be explained by the physiological changes of the immune system during human pregnancy.}, }
@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}, mesh = {Animals ; Bacteria/*classification/metabolism ; DNA Barcoding, Taxonomic ; Dysbiosis ; Environmental Pollution/analysis ; Fishes/*microbiology ; Fresh Water/microbiology ; Genetic Variation ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Salinity ; Skin/*microbiology ; Temperature ; }, 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 {pmid32004459, year = {2020}, author = {Zhou, W and Spoto, M and Hardy, R and Guan, C and Fleming, E and Larson, PJ and Brown, JS and Oh, J}, title = {Host-Specific Evolutionary and Transmission Dynamics Shape the Functional Diversification of Staphylococcus epidermidis in Human Skin.}, journal = {Cell}, volume = {180}, number = {3}, pages = {454-470.e18}, pmid = {32004459}, issn = {1097-4172}, support = {DP2 GM126893/GM/NIGMS NIH HHS/United States ; F30 DE027870/DE/NIDCR NIH HHS/United States ; K22 AI119231/AI/NIAID NIH HHS/United States ; T90 DE021989/DE/NIDCR NIH HHS/United States ; U54 NS105539/NS/NINDS NIH HHS/United States ; U19 AI142733/AI/NIAID NIH HHS/United States ; R21 AR075174/AR/NIAMS NIH HHS/United States ; R43 AR073562/AR/NIAMS NIH HHS/United States ; }, mesh = {Adult ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; *Evolution, Molecular ; Female ; *Gene Transfer, Horizontal ; Healthy Volunteers ; Host Microbial Interactions/*genetics ; Humans ; Male ; Microbiota/*genetics ; Middle Aged ; Phylogeny ; *Polymorphism, Single Nucleotide ; Skin/*microbiology ; Staphylococcus epidermidis/*genetics/isolation &amp; purification/pathogenicity ; Virulence/genetics ; Young Adult ; }, abstract = {Metagenomic inferences of bacterial strain diversity and infectious disease transmission studies largely assume a dominant, within-individual haplotype. We hypothesize that within-individual bacterial population diversity is critical for homeostasis of a healthy microbiome and infection risk. We characterized the evolutionary trajectory and functional distribution of Staphylococcus epidermidis-a keystone skin microbe and opportunistic pathogen. Analyzing 1,482 S. epidermidis genomes from 5 healthy individuals, we found that skin S. epidermidis isolates coalesce into multiple founder lineages rather than a single colonizer. Transmission events, natural selection, and pervasive horizontal gene transfer result in population admixture within skin sites and dissemination of antibiotic resistance genes within-individual. We provide experimental evidence for how admixture can modulate virulence and metabolism. Leveraging data on the contextual microbiome, we assess how interspecies interactions can shape genetic diversity and mobile gene elements. Our study provides insights into how within-individual evolution of human skin microbes shapes their functional diversification.}, }
@article {pmid32002757, year = {2020}, author = {Galloway-Peña, J and Hanson, B}, title = {Tools for Analysis of the Microbiome.}, journal = {Digestive diseases and sciences}, volume = {65}, number = {3}, pages = {674-685}, pmid = {32002757}, issn = {1573-2568}, support = {K01 AI143881/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Computational Biology/*methods/trends ; High-Throughput Nucleotide Sequencing/*methods/trends ; Humans ; Machine Learning/trends ; Metagenomics/*methods/trends ; Microbiota/*physiology ; Sequence Analysis, DNA/*methods/trends ; }, abstract = {Over the past decade, it has become exceedingly clear that the microbiome is a critical factor in human health and disease and thus should be investigated to develop innovative treatment strategies. The field of metagenomics has come a long way in leveraging the advances of next-generation sequencing technologies resulting in the capability to identify and quantify all microorganisms present in human specimens. However, the field of metagenomics is still in its infancy, specifically in regard to the limitations in computational analysis, statistical assessments, standardization, and validation due to vast variability in the cohorts themselves, experimental design, and bioinformatic workflows. This review summarizes the methods, technologies, computational tools, and model systems for characterizing and studying the microbiome. We also discuss important considerations investigators must make when interrogating the involvement of the microbiome in health and disease in order to establish robust results and mechanistic insights before moving into therapeutic design and intervention.}, }
@article {pmid31998300, year = {2019}, author = {Montassier, E and Al-Ghalith, GA and Mathé, C and Le Bastard, Q and Douillard, V and Garnier, A and Guimon, R and Raimondeau, B and Touchefeu, Y and Duchalais, E and Vince, N and Limou, S and Gourraud, PA and Laplaud, DA and Nicot, AB and Soulillou, JP and Berthelot, L}, title = {Distribution of Bacterial α1,3-Galactosyltransferase Genes in the Human Gut Microbiome.}, journal = {Frontiers in immunology}, volume = {10}, number = {}, pages = {3000}, pmid = {31998300}, issn = {1664-3224}, mesh = {Bacteria/*classification/*genetics ; Galactosyltransferases/*genetics ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; Microbiota ; Open Reading Frames ; Phylogeny ; }, abstract = {Because of a loss-of-function mutation in the GGTA1 gene, humans are unable to synthetize α1,3-Galactose (Gal) decorated glycans and develop high levels of circulating anti-α1,3-Galactose antibodies (anti-Gal Abs). Anti-Gal Abs have been identified as a major obstacle of organ xenotransplantation and play a role in several host-pathogen relationships including potential susceptibility to infection. Anti-Gal Abs are supposed to stem from immunization against the gut microbiota, an assumption derived from the observation that some pathogens display α1,3-Gal and that antibiotic treatment decreases the level of anti-Gal. However, there is little information to date concerning the microorganisms producing α1,3-Gal in the human gut microbiome. Here, available α1,3-Galactosyltransferase (GT) gene sequences from gut bacteria were selectively quantified for the first time in the gut microbiome shotgun sequences of 163 adult individuals from three published population-based metagenomics analyses. We showed that most of the gut microbiome of adult individuals contained a small set of bacteria bearing α1,3-GT genes. These bacteria belong mainly to the Enterobacteriaceae family, including Escherichia coli, but also to Pasteurellaceae genera, Haemophilus influenza and Lactobacillus species. α1,3-Gal antigens and α1,3-GT activity were detected in healthy stools of individuals exhibiting α1,3-GT bacterial gene sequences in their shotgun data.}, }
@article {pmid31993987, year = {2020}, author = {Farukh, M}, title = {Comparative genomic analysis of selenium utilization traits in different marine environments.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {58}, number = {2}, pages = {113-122}, doi = {10.1007/s12275-020-9250-0}, pmid = {31993987}, issn = {1976-3794}, mesh = {Ecosystem ; Genes, Bacterial/genetics ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; *Oceans and Seas ; Phosphotransferases/*genetics ; Proteobacteria/metabolism ; Selenium/metabolism ; }, abstract = {Selenium (Se) is an essential trace element for many organisms, which is required in the biosynthesis of proteins with selenocysteine, tRNAs with selenouridine, and certain enzymes with Se as a cofactor. Recent large-scale metagenomics projects provide a unique opportunity for studying the global trends of Se utilization in marine environments. Here, we analyzed samples from different marine microbial communities, revealed by the Tara Oceans project, to characterize the Se utilization traits. We found that the selenophosphate synthetase gene, which defines the overall Se utilization, and Se utilization traits are present in all samples. Regions with samples rich and poor in Se utilization traits were categorized. From the analysis of environmental factors, the mesopelagic zone and high temperature (> 15°C) of water are favorable, while geographical location has little influence on Se utilization. All Se utilization traits showed a relatively independent occurrence. The taxonomic classification of Se traits shows that most of the sequences corresponding to Se utilization traits belong to the phylum Proteobacteria. Overall, our study provides useful insights into the general features of Se utilization in ocean samples and may help to understand the evolutionary dynamics of Se utilization in different marine environments.}, }
@article {pmid31990924, year = {2020}, author = {Ericsson, AC and Personett, AR and Rindt, H and Grobman, ME and Reinero, CR}, title = {Respiratory dysbiosis and population-wide temporal dynamics in canine chronic bronchitis and non-inflammatory respiratory disease.}, journal = {PloS one}, volume = {15}, number = {1}, pages = {e0228085}, pmid = {31990924}, issn = {1932-6203}, support = {K01 OD019924/OD/NIH HHS/United States ; }, mesh = {Animals ; Bacterial Typing Techniques ; Bronchitis, Chronic/*microbiology/pathology ; Bronchoalveolar Lavage Fluid/microbiology ; Case-Control Studies ; Climate ; Dogs ; Dysbiosis/*microbiology/pathology ; Feces/microbiology ; Female ; Humans ; Lung/*microbiology/pathology ; Male ; Microbiota/*genetics ; Pets ; Principal Component Analysis ; RNA, Ribosomal, 16S/classification/*genetics ; }, abstract = {The lungs of people and companion animals are now recognized to harbor diverse, low biomass bacterial communities. While these communities are difficult to characterize using culture-based approaches, targeted molecular methods such as 16S rRNA amplicon sequencing can do so using DNA extracted from samples such as bronchoalveolar lavage fluid (BALF). Previous studies identified a surprisingly uniform composition of the microbiota in the lungs of healthy research dogs living in a controlled environment, however there are no reports of the lung microbiota of client-owned dogs. Moreover, compositional changes in the lung microbiota depending on disease status have been reported in people, suggesting that similar events may occur in dogs, a species subject to several respiratory disease mechanisms analogous to those seen in people. To address these knowledge gaps, BALF samples from client-owned dogs presenting to the University of Missouri Veterinary Health Center for respiratory signs between 2014 and 2017 were processed for and subjected to 16S rRNA sequencing. Based on specific diagnostic criteria, dogs were categorized as Chronic Bronchitis (CB, n = 53) or non-CB (n = 11). Community structure was compared between groups, as well as to historical data from healthy research dogs (n = 16) of a uniform breed and environment. The lung microbiota detected in all client-owned dogs was markedly different in composition from that previously detected in research dogs and contained increased relative abundance of multiple canine fecal and environmental bacteria, likely due to aspiration associated with their clinical signs. While inter-sample diversity differed significantly between samples from CB and non-CB dogs, the variability within both groups made it difficult to discern reproducible bacterial classifiers of disease. During subsequent analyses to identify other sources of variability within the data however, population-wide temporal dynamics in community structure were observed, with substantial changes occurring in late 2015 and again in early 2017. A review of regional climate data indicated that the first change occurred during a historically warm and wet period, suggesting that changes in environmental conditions may be associated with changes in the respiratory microbiota in the context of respiratory disease. As the lung microbiota in humans and other animals is believed to result from repetitive micro-aspirations during health and in certain disease states associated with dyspnea and laryngeal dysfunction, these data support the increased colonization of the lower airways during compromised airway function, and the potential for temporal effects due to putative factors such as climate.}, }
@article {pmid31990909, year = {2020}, author = {Kordy, K and Gaufin, T and Mwangi, M and Li, F and Cerini, C and Lee, DJ and Adisetiyo, H and Woodward, C and Pannaraj, PS and Tobin, NH and Aldrovandi, GM}, title = {Contributions to human breast milk microbiome and enteromammary transfer of Bifidobacterium breve.}, journal = {PloS one}, volume = {15}, number = {1}, pages = {e0219633}, pmid = {31990909}, issn = {1932-6203}, support = {K12 HD052954/HD/NICHD NIH HHS/United States ; }, mesh = {Acinetobacter/genetics/isolation &amp; purification ; Adolescent ; Adult ; *Bacterial Translocation ; Bifidobacterium breve/genetics/*isolation &amp; purification ; Enterobacter/genetics/isolation &amp; purification ; Female ; Gastrointestinal Microbiome/genetics ; Humans ; Infant ; Infant, Newborn ; Intestines/*microbiology ; Mammary Glands, Human/*microbiology ; Metagenomics/methods ; Milk, Human/*microbiology ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; Staphylococcus/genetics/isolation &amp; purification ; Streptococcus/genetics/isolation &amp; purification ; }, abstract = {Increasing evidence supports the importance of the breast milk microbiome in seeding the infant gut. However, the origin of bacteria in milk and the process of milk microbe-mediated seeding of infant intestine need further elucidation. Presumed sources of bacteria in milk include locations of mother-infant and mother-environment interactions. We investigate the role of mother-infant interaction on breast milk microbes. Shotgun metagenomics and 16S rRNA gene sequencing identified milk microbes of mother-infant pairs in breastfed infants and in infants that have never latched. Although breast milk has low overall biomass, milk microbes play an important role in seeding the infant gut. Breast milk bacteria were largely comprised of Staphylococcus, Streptococcus, Acinetobacter, and Enterobacter primarily derived from maternal areolar skin and infant oral sites in breastfeeding pairs. This suggests that the process of breastfeeding is a potentially important mechanism for propagation of breast milk microbes through retrograde flux via infant oral and areolar skin contact. In one infant delivered via Caesarian section, a distinct strain of Bifidobacteria breve was identified in maternal rectum, breast milk and the infant's stool potentially suggesting direct transmission. This may support the existence of microbial translocation of this anaerobic bacteria via the enteromammary pathway in humans, where maternal bacteria translocate across the maternal gut and are transferred to the mammary glands. Modulating sources of human milk microbiome seeding potentially imply opportunities to ultimately influence the development of the infant microbiome and health.}, }
@article {pmid31989644, year = {2020}, author = {Osei Sekyere, J and Maningi, NE and Fourie, PB}, title = {Mycobacterium tuberculosis, antimicrobials, immunity, and lung-gut microbiota crosstalk: current updates and emerging advances.}, journal = {Annals of the New York Academy of Sciences}, volume = {1467}, number = {1}, pages = {21-47}, doi = {10.1111/nyas.14300}, pmid = {31989644}, issn = {1749-6632}, mesh = {Animals ; Anti-Infective Agents/*therapeutic use ; Gastrointestinal Microbiome/*immunology ; Humans ; Lung/*microbiology ; Mice ; *Mycobacterium tuberculosis ; Tuberculosis/*drug therapy/microbiology ; }, abstract = {Increasingly, gut microbiota distortions are being implicated in the pathogenesis of several infectious and noninfectious diseases. Specifically, in the absence of an eubiotic microbiota, mice are more prone to colonization and infection by Mycobacterium tuberculosis (Mtb). In this qualitative analysis, the following were observed: (1) antimicrobials cause long-term gut microbiota perturbations; (2) Mtb causes limited and transient disturbances to the lung-gut microbiota; (3) pathogens (e.g., Helicobacter hepaticus) affect microbiota integrity and reduce resistance to Mtb; (4) dysbiosis depletes bacterial species regulating proper immune functioning, reducing resistance to Mtb; (5) dysregulated immune cells fail to express important pathogen-recognition receptors (e.g., macrophage-inducible C-type lectin; MINCLE) and Mtb-killing cytokines (e.g., IFN-γ, TNF-α, and IL-17), with hampered phagocytic capability; (6) autophagy is central to the immune system's clearance of Mtb, control of inflammation, and immunity-microbiome balance; (7) microbiota-produced short-chain fatty acids, which are reduced by dysbiosis, affect immune cells and increase Mtb proliferation; (8) commensal species (e.g., Lactobacillus plantarum) and microbiota metabolites (e.g., indole propionic acid) reduce tuberculosis progression; and (9) fecal transplants mostly restored eubiosis, increased immune resistance to Mtb, restricted dissemination of Mtb, and reduced tuberculosis-associated organ pathologies. Overuse of antimicrobials, as shown in mice, is a risk factor for reactivating latent or treated tuberculosis.}, }
@article {pmid31988585, year = {2020}, author = {Lv, XY and Ding, HG and Zheng, JF and Fan, CL and Li, L}, title = {Rifaximin improves survival in cirrhotic patients with refractory ascites: A real-world study.}, journal = {World journal of gastroenterology}, volume = {26}, number = {2}, pages = {199-218}, pmid = {31988585}, issn = {2219-2840}, mesh = {Aged ; Anti-Bacterial Agents/pharmacology/*therapeutic use ; Ascites/*drug therapy/immunology/microbiology/mortality ; Bacterial Infections/*drug therapy/immunology/microbiology/mortality ; Drug Resistance ; Female ; Gastrointestinal Microbiome/drug effects/immunology ; Humans ; Liver Cirrhosis/complications/*drug therapy/microbiology/mortality ; Male ; Middle Aged ; Peritonitis/*drug therapy/immunology/microbiology/mortality ; Rifaximin/pharmacology/*therapeutic use ; Treatment Outcome ; }, abstract = {BACKGROUND: Rifaximin has been shown to reduce the incidence of hepatic encephalopathy and other complications in patients with cirrhosis. However, few studies have investigated the effect of rifaximin in cirrhotic patients with refractory ascites.<br><br>AIM: To evaluate the effects of rifaximin in the treatment of refractory ascites and to preliminarily explore its possible mechanism.<br><br>METHODS: A total of 75 cirrhotic patients with refractory ascites were enrolled in the study (50 in a rifaximin and 25 in a control group). Patients in the rifaximin group were divided into two subgroups according to the presence of spontaneous bacterial peritonitis and treatment with or without other antibiotics (19 patients treated with rifaximin and 31 patients treated with rifaximin plus intravenous antibiotics). All patients received conventional treatment for refractory ascites, while patients in the rifaximin group received oral rifaximin-α 200 mg four times daily for at least 2 wk. The ascites grade, fasting weight, liver and kidney function, and inflammatory factors in the plasma were evaluated before and after treatment. In addition, the gut microbiota was determined by metagenomics sequencing to analyse the changes in the characteristics of the gut microbiota before and after rifaximin treatment. The patients were followed for 6 mo.<br><br>RESULTS: Compared with the control group, the fasting weight of patients significantly decreased and the ascites significantly subsided after treatment with rifaximin (P = 0.011 and 0.009, respectively). The 6-mo survival rate of patients in the rifaximin group was significantly higher than that in the control group (P = 0.048). The concentration of interferon-inducible protein 10 decreased significantly in the rifaximin group compared with that in the control group (P = 0.024). The abundance of Roseburia, Haemophilus, and Prevotella was significantly reduced after rifaximin treatment, while the abundance of Lachnospiraceae_noname, Subdoligranulum, and Dorea decreased and the abundance of Coprobacillus increased after treatment with rifaximin plus intravenous antibiotics. The gene expression of virulence factors was significantly reduced after treatment in both subgroups treated with rifaximin or rifaximin plus intravenous antibiotics.<br><br>CONCLUSION: Rifaximin mitigates ascites and improves survival of cirrhotic patients with refractory ascites. A possible mechanism is that rifaximin regulates the structure and function of intestinal bacteria, thus improving the systemic inflammatory state.}, }
@article {pmid31987960, year = {2020}, author = {Mitra, A and Grossman Biegert, GW and Delgado, AY and Karpinets, TV and Solley, TN and Mezzari, MP and Yoshida-Court, K and Petrosino, JF and Mikkelson, MD and Lin, L and Eifel, P and Zhang, J and Ramondetta, LM and Jhingran, A and Sims, TT and Schmeler, K and Okhuysen, P and Colbert, LE and Klopp, AH}, title = {Microbial Diversity and Composition Is Associated with Patient-Reported Toxicity during Chemoradiation Therapy for Cervical Cancer.}, journal = {International journal of radiation oncology, biology, physics}, volume = {107}, number = {1}, pages = {163-171}, doi = {10.1016/j.ijrobp.2019.12.040}, pmid = {31987960}, issn = {1879-355X}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Aged ; Biodiversity ; Chemoradiotherapy/*adverse effects ; Cohort Studies ; Female ; Gastrointestinal Microbiome/*radiation effects ; Gastrointestinal Tract/*microbiology/*radiation effects ; Humans ; Middle Aged ; Patient Reported Outcome Measures ; *Safety ; Uterine Cervical Neoplasms/drug therapy/*microbiology/radiotherapy/*therapy ; }, abstract = {PURPOSE: Patients receiving pelvic radiation for cervical cancer experience high rates of acute gastrointestinal (GI) toxicity. The association of changes in the gut microbiome with bowel toxicity from radiation is not well characterized.<br><br>METHODS AND MATERIALS: Thirty-five patients undergoing definitive chemoradiation therapy (CRT) underwent longitudinal sampling (baseline and weeks 1, 3, and 5) of the gut microbiome and prospective assessment of patient-reported GI toxicity. DNA was isolated from stool obtained at rectal examination and analyzed with 16S rRNA sequencing. GI toxicity was assessed with the Expanded Prostate Cancer Index Composite instrument to evaluate frequency, urgency, and discomfort associated with bowel function. Shannon diversity index was used to characterize alpha (within sample) diversity. Weighted UniFrac principle coordinates analysis was used to compare beta (between sample) diversity between samples using permutational multivariate analysis of variance. Linear discriminant analysis effect size highlighted microbial features that best distinguish categorized patient samples.<br><br>RESULTS: Gut microbiome diversity continuously decreased over the course of CRT, with the largest decrease at week 5. Expanded Prostate Cancer Index Composite bowel function scores also declined over the course of treatment, reflecting increased symptom burden. At all individual time points, higher diversity of the gut microbiome was linearly correlated with better patient-reported GI function, but baseline diversity was not predictive of eventual outcome. Patients with high toxicity demonstrated different compositional changes during CRT in addition to compositional differences in Clostridia species.<br><br>CONCLUSIONS: Over time, increased radiation toxicity is associated with decreased gut microbiome diversity. Baseline diversity is not predictive of end-of-treatment bowel toxicity, but composition may identify patients at risk for developing high toxicity.}, }
@article {pmid31984532, year = {2020}, author = {Liou, JM and Lee, YC and Wu, MS}, title = {Treatment of Helicobacter pylori infection and its long-term impacts on gut microbiota.}, journal = {Journal of gastroenterology and hepatology}, volume = {35}, number = {7}, pages = {1107-1116}, doi = {10.1111/jgh.14992}, pmid = {31984532}, issn = {1440-1746}, support = {NTU-107L9014-1//Ministry of Education, Taiwan/ ; MOHW107-TDU-B-211-123002//Ministry of Health and Welfare, Taiwan/ ; TCTC 108-2321-B-002-040//Ministry of Science and Technology of Taiwan/ ; MOST 108-2314-B-002-187//Ministry of Science and Technology of Taiwan/ ; MOST 108-2314-B-002-209//Ministry of Science and Technology of Taiwan/ ; NTUH 106-P06//National Taiwan University Hospital/ ; NTUH 107-P05//National Taiwan University Hospital/ ; //Liver Disease Prevention &amp; Treatment Research Foundation, Taiwan/ ; }, mesh = {Anti-Bacterial Agents/*administration &amp; dosage/adverse effects/pharmacology ; Asia ; Bismuth/administration &amp; dosage ; Drug Resistance, Bacterial ; Drug Therapy, Combination ; Gastritis/*drug therapy/*microbiology ; *Gastrointestinal Microbiome/drug effects ; *Helicobacter Infections ; *Helicobacter pylori/drug effects ; Humans ; Levofloxacin/administration &amp; dosage ; }, abstract = {The rising prevalence of antibiotic resistance and the long-term safety following eradication therapy are important issues in the management of Helicobacter pylori infection. The prevalence of clarithromycin, levofloxacin, and metronidazole resistance of H. pylori has increased to 21%, 27%, and 45%, respectively, in the Asia-Pacific region. Personalized treatment guided by susceptibility testing may provide a reliably excellent eradication rate in the first-line treatment but is costly and not widely available. Population-specific empirical therapy according to the local prevalence of antibiotic resistance may be an alternative strategy. Levofloxacin-based therapy and bismuth quadruple therapy are the recommended second-line rescue therapy. Susceptibility testing or genotypic resistance-guided therapy is the preferred treatment for refractory H. pylori infection, but empirical therapy may be an acceptable alternative. Eradication of H. pylori leads to short-term perturbation of gut microbiota. The diversity of gut microbiota can be restored months after eradication therapy, but the speed of recovery varies with regimens. The short-term increases of antibiotic resistance of Escherichia coli and Klebsiella pneumoniae may be restored to basal states months after H. pylori eradication. Future studies that apply in-depth sequencing, such as shotgun metagenomics sequencing, are needed to clarify whether the compositions of gut microbiota at the species level are fully restored.}, }
@article {pmid31982498, year = {2020}, author = {Pan, HW and Du, LT and Li, W and Yang, YM and Zhang, Y and Wang, CX}, title = {Biodiversity and richness shifts of mucosa-associated gut microbiota with progression of colorectal cancer.}, journal = {Research in microbiology}, volume = {171}, number = {3-4}, pages = {107-114}, doi = {10.1016/j.resmic.2020.01.001}, pmid = {31982498}, issn = {1769-7123}, mesh = {Aged ; *Biodiversity ; Colorectal Neoplasms/etiology/*pathology ; Computational Biology/methods ; *Dysbiosis ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Metagenomics ; Middle Aged ; }, abstract = {The host-associated gut microbiota is considered critical for the occurrence and progression of colorectal cancer (CRC); however, systematic evaluations of the changes in the biodiversity and richness of mucosa-associated gut microbiota with the development of CRC have been limited. Twenty-three paired samples from colorectal tumor sites and the surrounding non-tumor tissues were collected from stage I to IV CRC patients. The microbial compositions of the samples were analyzed by Illumina MiSeq sequencing of the V4 region of the 16S rRNA gene. Gut bacterial alterations at the tumor sites and surrounding healthy tissue sites collected from the different stages of CRC patients were analyzed. No significant differences were observed in the overall microbial richness and biodiversity between the CRC tissue and surrounding non-CRC tissue samples, however, composition and community segregation of the gut microbiota with the progression of CRC were observed. A general increasing trend of Bacteroidetes, Firmicutes, and Fusobacteria and decreasing trend of Proteobacteria were observed at the phylum level with the development of CRC. Further analysis revealed that thirty-four taxa differed significantly with the progression of CRC. Conclusively, our findings provide a comprehensive view of the human mucosa-associated gut microbiota, in association with the different stages of CRC.}, }
@article {pmid31978162, year = {2020}, author = {Chung, YW and Gwak, HJ and Moon, S and Rho, M and Ryu, JH}, title = {Functional dynamics of bacterial species in the mouse gut microbiome revealed by metagenomic and metatranscriptomic analyses.}, journal = {PloS one}, volume = {15}, number = {1}, pages = {e0227886}, pmid = {31978162}, issn = {1932-6203}, mesh = {Animals ; Bacteria/classification/*genetics ; Bacteroidetes/genetics ; Feces/microbiology ; Firmicutes/genetics ; Gastrointestinal Microbiome/*genetics ; Metagenome/*genetics ; *Metagenomics ; Mice ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Transcriptome/genetics ; }, abstract = {BACKGROUND: Microbial communities of the mouse gut have been extensively studied; however, their functional roles and regulation are yet to be elucidated. Metagenomic and metatranscriptomic analyses may allow us a comprehensive profiling of bacterial composition and functions of the complex gut microbiota. The present study aimed to investigate the active functions of the microbial communities in the murine cecum by analyzing both metagenomic and metatranscriptomic data on specific bacterial species within the microbial communities, in addition to the whole microbiome.<br><br>RESULTS: Bacterial composition of the healthy mouse gut microbiome was profiled using the following three different approaches: 16S rRNA-based profiling based on amplicon and shotgun sequencing data, and genome-based profiling based on shotgun sequencing data. Consistently, Bacteroidetes, Firmicutes, and Deferribacteres emerged as the major phyla. Based on NCBI taxonomy, Muribaculaceae, Lachnospiraceae, and Deferribacteraceae were the predominant families identified in each phylum. The genes for carbohydrate metabolism were upregulated in Muribaculaceae, while genes for cofactors and vitamin metabolism and amino acid metabolism were upregulated in Deferribacteraceae. The genes for translation were commonly enhanced in all three families. Notably, combined analysis of metagenomic and metatranscriptomic sequencing data revealed that the functions of translation and metabolism were largely upregulated in all three families in the mouse gut environment. The ratio of the genes in the metagenome and their expression in the metatranscriptome indicated higher expression of carbohydrate metabolism in Muribaculum, Duncaniella, and Mucispirillum.<br><br>CONCLUSIONS: We demonstrated a fundamental methodology for linking genomic and transcriptomic datasets to examine functional activities of specific bacterial species in a complicated microbial environment. We investigated the normal flora of the mouse gut using three different approaches and identified Muribaculaceae, Lachnospiraceae, and Deferribacteraceae as the predominant families. The functional distribution of these families was reflected in the entire microbiome. By comparing the metagenomic and metatranscriptomic data, we found that the expression rates differed for different functional categories in the mouse gut environment. Application of these methods to track microbial transcription in individuals over time, or before and after administration of a specific stimulus will significantly facilitate future development of diagnostics and treatments.}, }
@article {pmid31978143, year = {2020}, author = {De Cesare, A and Sala, C and Castellani, G and Astolfi, A and Indio, V and Giardini, A and Manfreda, G}, title = {Effect of Lactobacillus acidophilus D2/CSL (CECT 4529) supplementation in drinking water on chicken crop and caeca microbiome.}, journal = {PloS one}, volume = {15}, number = {1}, pages = {e0228338}, pmid = {31978143}, issn = {1932-6203}, mesh = {Animals ; Bacteria/*classification/drug effects/genetics ; Cecum/microbiology ; Chickens/*microbiology ; Crop, Avian/microbiology ; Drinking Water/*chemistry ; Lactobacillus acidophilus/*physiology ; Male ; Metagenomics ; Microbiota/drug effects ; Phylogeny ; Probiotics/*administration &amp; dosage/pharmacology ; Sequence Analysis, DNA ; }, abstract = {In this study we gained insights into the effects of the supplementation with Lactobacillus acidophilus D2/CSL (CECT 4529) in the chicken drinking water on crop and caeca microbiomes. The probiotic was supplemented at the concentrations of 0.2 g Lactobacillus acidophilus/day/bird and 0.02 g Lactobacillus acidophilus/day/bird and its effect on the crop and caeca microbiomes was assessed at 14 and 35 days of rearing. The results showed that mean relative abundance of Lactobacillus acidophilus in the caeca did not show significative differences in the treated and control birds, although Lactobacillus acidophilus as well as Faecalibacterium prausnitzii, Lactobacillus crispatus and Lactobacillus reuteri significantly increased over time. Moreover, the treatment with the high dose of probiotic significantly increased the abundance of Clostridium asparagiforme, Clostridium hathewayi and Clostridium saccharolyticum producing butyrate and other organic acids supporting the chicken health. Finally, at 35 days, the Cell division protein FtsH (EC 3.4.24.-) and the Site-specific recombinase genes were significantly increased in the caeca of birds treated with the high dose of probiotic in comparison to the control group. The results of this study showed that Lactobacillus acidophilus D2/CSL (CECT 4529) supplementation in the drinking water at the concentrations of 0.2 and 0.02 g Lactobacillus acidophilus/day/bird improved beneficial microbes and functional genes in broiler crops and caeca. Nevertheless, the main site of action of the probiotic is the crop, at least in the early stage of the chicken life. Indeed, at 14 days Lactobacillus acidophilus was significantly higher in the crops of chickens treated with the high dose of LA in comparison to the control (14.094 vs 1.741%, p = 0.036).}, }
@article {pmid31977194, year = {2020}, author = {Chevrette, MG and Handelsman, J}, title = {From Metagenomes to Molecules: Innovations in Functional Metagenomics Unlock Hidden Chemistry in the Human Microbiome.}, journal = {Biochemistry}, volume = {59}, number = {6}, pages = {729-730}, doi = {10.1021/acs.biochem.0c00033}, pmid = {31977194}, issn = {1520-4995}, mesh = {Humans ; Metagenome ; *Metagenomics ; *Microbiota ; }, }
@article {pmid31971995, year = {2020}, author = {Ben Maamar, S and Glawe, AJ and Brown, TK and Hellgeth, N and Hu, J and Wang, JP and Huttenhower, C and Hartmann, EM}, title = {Mobilizable antibiotic resistance genes are present in dust microbial communities.}, journal = {PLoS pathogens}, volume = {16}, number = {1}, pages = {e1008211}, pmid = {31971995}, issn = {1553-7374}, mesh = {*Air Pollution, Indoor ; Drug Resistance, Microbial/*genetics ; *Dust ; Environmental Microbiology ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome, Bacterial ; Metagenomics ; Microbiota/*genetics ; }, abstract = {The decades-long global trend of urbanization has led to a population that spends increasing amounts of time indoors. Exposure to microbes in buildings, and specifically in dust, is thus also increasing, and has been linked to various health outcomes and to antibiotic resistance genes (ARGs). These are most efficiently screened using DNA sequencing, but this method does not determine which microbes are viable, nor does it reveal whether their ARGs can actually disseminate to other microbes. We have thus performed the first study to: 1) examine the potential for ARG dissemination in indoor dust microbial communities, and 2) validate the presence of detected mobile ARGs in viable dust bacteria. Specifically, we integrated 166 dust metagenomes from 43 different buildings. Sequences were assembled, annotated, and screened for potential integrons, transposons, plasmids, and associated ARGs. The same dust samples were further investigated using cultivation and isolate genome and plasmid sequencing. Potential ARGs were detected in dust isolate genomes, and we confirmed their placement on mobile genetic elements using long-read sequencing. We found 183 ARGs, of which 52 were potentially mobile (associated with a putative plasmid, transposon or integron). One dust isolate related to Staphylococcus equorum proved to contain a plasmid carrying an ARG that was detected metagenomically and confirmed through whole genome and plasmid sequencing. This study thus highlights the power of combining cultivation with metagenomics to assess the risk of potentially mobile ARGs for public health.}, }
@article {pmid31968354, year = {2020}, author = {Schulz, F and Roux, S and Paez-Espino, D and Jungbluth, S and Walsh, DA and Denef, VJ and McMahon, KD and Konstantinidis, KT and Eloe-Fadrosh, EA and Kyrpides, NC and Woyke, T}, title = {Giant virus diversity and host interactions through global metagenomics.}, journal = {Nature}, volume = {578}, number = {7795}, pages = {432-436}, pmid = {31968354}, issn = {1476-4687}, mesh = {Animals ; *Biodiversity ; Capsid Proteins/genetics ; DNA Viruses/*classification/*genetics ; Eukaryotic Cells/*metabolism/*virology ; Gene Transfer, Horizontal ; Genome, Viral/genetics ; Giant Viruses/classification/genetics ; Host Microbial Interactions/*genetics ; *Metagenomics ; Phylogeny ; }, abstract = {Our current knowledge about nucleocytoplasmic large DNA viruses (NCLDVs) is largely derived from viral isolates that are co-cultivated with protists and algae. Here we reconstructed 2,074 NCLDV genomes from sampling sites across the globe by building on the rapidly increasing amount of publicly available metagenome data. This led to an 11-fold increase in phylogenetic diversity and a parallel 10-fold expansion in functional diversity. Analysis of 58,023 major capsid proteins from large and giant viruses using metagenomic data revealed the global distribution patterns and cosmopolitan nature of these viruses. The discovered viral genomes encoded a wide range of proteins with putative roles in photosynthesis and diverse substrate transport processes, indicating that host reprogramming is probably a common strategy in the NCLDVs. Furthermore, inferences of horizontal gene transfer connected viral lineages to diverse eukaryotic hosts. We anticipate that the global diversity of NCLDVs that we describe here will establish giant viruses-which are associated with most major eukaryotic lineages-as important players in ecosystems across Earth's biomes.}, }
@article {pmid31967575, year = {2020}, author = {Probst, AJ and Vaishampayan, P}, title = {Are we There Yet? Understanding Interplanetary Microbial Hitchhikers using Molecular Methods.}, journal = {Current issues in molecular biology}, volume = {38}, number = {}, pages = {33-52}, doi = {10.21775/cimb.038.033}, pmid = {31967575}, issn = {1467-3045}, mesh = {Adenosine Triphosphate/chemistry ; Bacteria/growth &amp; development/*isolation &amp; purification ; Cell Survival ; *Ecological Systems, Closed ; *Environmental Microbiology ; Extraterrestrial Environment/*chemistry ; Genomics ; Metagenomics ; Microbiota ; RNA, Ribosomal/chemistry/isolation &amp; purification ; *Space Flight ; Spacecraft/standards ; Spores/isolation &amp; purification ; Sterilization ; United States ; United States National Aeronautics and Space Administration ; Weightlessness ; }, abstract = {Since the early time of space travel, planetary bodies undergoing chemical or biological evolution have been of particular interest for life detection missions. NASA's and ESA's Planetary Protection offices ensure responsible exploration of the solar system and aim at avoiding inadvertent contamination of celestial bodies with biomolecules or even living organisms. Life forms that have the potential to colonize foreign planetary bodies could be a threat to the integrity of science objectives of life detection missions. While standard requirements for assessing the cleanliness of spacecraft are still based on cultivation approaches, several molecular methods have been applied in the past to elucidate the full breadth of (micro)organisms that can be found on spacecraft and in cleanrooms, where the hardware is assembled. Here, we review molecular assays that have been applied in Planetary Protection research and list their significant advantages and disadvantages. By providing a comprehensive summary of the latest molecular methods yet to be applied in this research area, this article will not only aid in designing technological roadmaps for future Planetary Protection endeavors but also help other disciplines in environmental microbiology that deal with low biomass samples.}, }
@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 = {12}, number = {2}, pages = {185-194}, doi = {10.1111/1758-2229.12822}, pmid = {31965701}, issn = {1758-2229}, support = {Ciencia Básica 256096//Consejo Nacional de Ciencia y Tecnología/International ; Cátedras CONACyT 883//Consejo Nacional de Ciencia y Tecnología/International ; Infraestructura 253217//Consejo Nacional de Ciencia y Tecnología/International ; }, 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 10-25% 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.}, }
@article {pmid31964729, year = {2020}, author = {Flannery, JE and Stagaman, K and Burns, AR and Hickey, RJ and Roos, LE and Giuliano, RJ and Fisher, PA and Sharpton, TJ}, title = {Gut Feelings Begin in Childhood: the Gut Metagenome Correlates with Early Environment, Caregiving, and Behavior.}, journal = {mBio}, volume = {11}, number = {1}, pages = {}, pmid = {31964729}, issn = {2150-7511}, support = {T32 ES007060/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; *Caregivers ; Child ; *Child Behavior ; *Environment ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Models, Theoretical ; Socioeconomic Factors ; }, abstract = {Psychosocial environments impact normative behavioral development in children, increasing the risk of problem behaviors and psychiatric disorders across the life span. Converging evidence demonstrates that early normative development is affected by the gut microbiome, which itself can be altered by early psychosocial environments. However, much of our understanding of the gut microbiome's role in early development stems from nonhuman animal models and predominately focuses on the first years of life, during peri- and postnatal microbial colonization. As a first step to identify if these findings translate to humans and the extent to which these relationships are maintained after initial microbial colonization, we conducted a metagenomic investigation among a cross-sectional sample of early school-aged children with a range of adverse experiences and caregiver stressors and relationships. Our results indicate that the taxonomic and functional composition of the gut microbiome correlates with behavior during a critical period of child development. Furthermore, our analysis reveals that both socioeconomic risk exposure and child behaviors associate with the relative abundances of specific taxa (e.g., Bacteroides and Bifidobacterium species) as well as functional modules encoded in their genomes (e.g., monoamine metabolism) that have been linked to cognition and health. While we cannot infer causality within this study, these findings suggest that caregivers may moderate the gut microbiome's link to environment and behaviors beyond the first few years of life.IMPORTANCE Childhood is a formative period of behavioral and biological development that can be modified, for better or worse, by the psychosocial environment that is in part determined by caregivers. Not only do our own genes and the external environment influence such developmental trajectories, but the community of microbes living in, on, and around our bodies-the microbiome-plays an important role as well. By surveying the gut microbiomes of a cross-sectional cohort of early school-aged children with a range of psychosocial environments and subclinical mental health symptoms, we demonstrated that caregiving behaviors modified the child gut microbiome's association to socioeconomic risk and behavioral dysregulation.}, }
@article {pmid31964728, year = {2020}, author = {Carini, P and Delgado-Baquerizo, M and Hinckley, ES and Holland-Moritz, H and Brewer, TE and Rue, G and Vanderburgh, C and McKnight, D and Fierer, N}, title = {Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities.}, journal = {mBio}, volume = {11}, number = {1}, pages = {}, pmid = {31964728}, issn = {2150-7511}, mesh = {*Metagenome ; *Metagenomics/methods ; Microbial Interactions ; *Microbiota ; RNA, Ribosomal, 16S ; Seasons ; Soil/chemistry ; *Soil Microbiology ; Spatio-Temporal Analysis ; }, abstract = {Few studies have comprehensively investigated the temporal variability in soil microbial communities despite widespread recognition that the belowground environment is dynamic. In part, this stems from the challenges associated with the high degree of spatial heterogeneity in soil microbial communities and because the presence of relic DNA (DNA from dead cells or secreted extracellular DNA) may dampen temporal signals. Here, we disentangle the relationships among spatial, temporal, and relic DNA effects on prokaryotic and fungal communities in soils collected from contrasting hillslopes in Colorado, USA. We intensively sampled plots on each hillslope over 6 months to discriminate between temporal variability, intraplot spatial heterogeneity, and relic DNA effects on the soil prokaryotic and fungal communities. We show that the intraplot spatial variability in microbial community composition was strong and independent of relic DNA effects and that these spatial patterns persisted throughout the study. When controlling for intraplot spatial variability, we identified significant temporal variability in both plots over the 6-month study. These microbial communities were more dissimilar over time after relic DNA was removed, suggesting that relic DNA hinders the detection of important temporal dynamics in belowground microbial communities. We identified microbial taxa that exhibited shared temporal responses and show that these responses were often predictable from temporal changes in soil conditions. Our findings highlight approaches that can be used to better characterize temporal shifts in soil microbial communities, information that is critical for predicting the environmental preferences of individual soil microbial taxa and identifying linkages between soil microbial community composition and belowground processes.IMPORTANCE Nearly all microbial communities are dynamic in time. Understanding how temporal dynamics in microbial community structure affect soil biogeochemistry and fertility are key to being able to predict the responses of the soil microbiome to environmental perturbations. Here, we explain the effects of soil spatial structure and relic DNA on the determination of microbial community fluctuations over time. We found that intensive spatial sampling was required to identify temporal effects in microbial communities because of the high degree of spatial heterogeneity in soil and that DNA from nonliving sources masks important temporal patterns. We identified groups of microbes with shared temporal responses and show that these patterns were predictable from changes in soil characteristics. These results provide insight into the environmental preferences and temporal relationships between individual microbial taxa and highlight the importance of considering relic DNA when trying to detect temporal dynamics in belowground communities.}, }
@article {pmid31963239, year = {2020}, author = {Burton, KJ and Krüger, R and Scherz, V and Münger, LH and Picone, G and Vionnet, N and Bertelli, C and Greub, G and Capozzi, F and Vergères, G}, title = {Trimethylamine-N-Oxide Postprandial Response in Plasma and Urine Is Lower After Fermented Compared to Non-Fermented Dairy Consumption in Healthy Adults.}, journal = {Nutrients}, volume = {12}, number = {1}, pages = {}, pmid = {31963239}, issn = {2072-6643}, support = {14/JP-HDHL/B3076//Joint Programming Initiative A healthy diet for a healthy life/ ; 170280//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; }, mesh = {Adolescent ; Adult ; Bacteria/*metabolism ; Biomarkers/blood/urine ; Cross-Over Studies ; *Cultured Milk Products ; *Dairy Products ; Double-Blind Method ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Methylamines/*blood/*urine ; *Postprandial Period ; Switzerland ; Young Adult ; }, abstract = {Trimethylamine-N-oxide (TMAO) can be produced by the gut microbiota from dietary substrates and is associated with cardiovascular disease. While dairy products contain TMAO precursors, the effect of fermented dairy on TMAO metabolism remains unclear. We used plasma and urine samples collected for two randomised cross-over studies to evaluate the effects of fermented dairy consumption on TMAO metabolism. In Study 1, thirteen healthy young men tested a yogurt and an acidified milk during postprandial tests and a two-week daily intervention. In Study 2, ten healthy adults tested milk and cheese during postprandial tests. TMAO and five related metabolites were measured in plasma and urine by LC-MS/MS and NMR. Faecal microbiota composition was assessed in Study 1 (16S rRNA metagenomics sequencing). Fermented milk products were associated with lower postprandial TMAO responses than non-fermented milks in urine (Study 1, p = 0.01; Study 2, p = 0.02) and in plasma, comparing yogurt and acidified milk (Study 1, p = 0.04). Daily consumption of dairy products did not differentially affect fasting TMAO metabolites. Significant correlations were observed between microbiota taxa and circulating or urinary TMAO concentrations. Fermentation of dairy products appear, at least transiently, to affect associations between dairy products and circulating TMAO levels.}, }
@article {pmid31959969, year = {2020}, author = {Whelan, FJ and Waddell, B and Syed, SA and Shekarriz, S and Rabin, HR and Parkins, MD and Surette, MG}, title = {Culture-enriched metagenomic sequencing enables in-depth profiling of the cystic fibrosis lung microbiota.}, journal = {Nature microbiology}, volume = {5}, number = {2}, pages = {379-390}, doi = {10.1038/s41564-019-0643-y}, pmid = {31959969}, issn = {2058-5276}, support = {//CIHR/Canada ; }, mesh = {Algorithms ; Cystic Fibrosis/*microbiology ; High-Throughput Nucleotide Sequencing ; Humans ; Lung/*microbiology ; Metagenome ; Metagenomics/methods ; Microbiological Techniques ; Microbiota/*genetics ; Sequence Analysis, DNA ; }, abstract = {Amplicon sequencing (for example, of the 16S rRNA gene) identifies the presence and relative abundance of microbial community members. However, metagenomic sequencing is needed to identify the genetic content and functional potential of a community. Metagenomics is challenging in samples dominated by host DNA, such as those from the skin, tissue and respiratory tract. Here, we combine advances in amplicon and metagenomic sequencing with culture-enriched molecular profiling to study the human microbiota. Using the cystic fibrosis lung as an example, we cultured an average of 82.13% of the operational taxonomic units representing 99.3% of the relative abundance identified in direct sequencing of sputum samples; importantly, culture enrichment identified 63.3% more operational taxonomic units than direct sequencing. We developed the PLate Coverage Algorithm (PLCA) to determine a representative subset of culture plates on which to conduct culture-enriched metagenomics, resulting in the recovery of greater taxonomic diversity-including of low-abundance taxa-with better metagenome-assembled genomes, longer contigs and better functional annotations when compared to culture-independent methods. The PLCA is also applied as a proof of principle to a previously published gut microbiota dataset. Culture-enriched molecular profiling can be used to better understand the role of the human microbiota in health and disease.}, }
@article {pmid31959785, year = {2020}, author = {Moreno-Pino, M and Cristi, A and Gillooly, JF and Trefault, N}, title = {Characterizing the microbiomes of Antarctic sponges: a functional metagenomic approach.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {645}, pmid = {31959785}, issn = {2045-2322}, mesh = {Animals ; Antarctic Regions ; Carbon/metabolism ; Carbon Dioxide/metabolism ; Chemoautotrophic Growth ; Light ; Marine Biology/*methods ; Metagenomics/*methods ; *Microbiota/genetics/physiology ; Nitrogen/metabolism ; Nutrients/metabolism ; Porifera/*genetics/metabolism/*microbiology/physiology ; Seawater/microbiology ; Symbiosis ; }, abstract = {Relatively little is known about the role of sponge microbiomes in the Antarctic marine environment, where sponges may dominate the benthic landscape. Specifically, we understand little about how taxonomic and functional diversity contributes to the symbiotic lifestyle and aids in nutrient cycling. Here we use functional metagenomics to investigate the community composition and metabolic potential of microbiomes from two abundant Antarctic sponges, Leucetta antarctica and Myxilla sp. Genomic and taxonomic analyses show that both sponges harbor a distinct microbial community with high fungal abundance, which differs from the surrounding seawater. Functional analyses reveal both sponge-associated microbial communities are enriched in functions related to the symbiotic lifestyle (e.g., CRISPR system, Eukaryotic-like proteins, and transposases), and in functions important for nutrient cycling. Both sponge microbiomes possessed genes necessary to perform processes important to nitrogen cycling (i.e., ammonia oxidation, nitrite oxidation, and denitrification), and carbon fixation. The latter indicates that Antarctic sponge microorganisms prefer light-independent pathways for CO2 fixation mediated by chemoautotrophic microorganisms. Together, these results show how the unique metabolic potential of two Antarctic sponge microbiomes help these sponge holobionts survive in these inhospitable environments, and contribute to major nutrient cycles of these ecosystems.}, }
@article {pmid31959775, year = {2020}, author = {Cooper, RO and Cressler, CE}, title = {Characterization of key bacterial species in the Daphnia magna microbiota using shotgun metagenomics.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {652}, pmid = {31959775}, issn = {2045-2322}, mesh = {Amino Acids ; Animals ; Comamonadaceae ; Daphnia/metabolism/*microbiology ; Flagella/physiology ; High-Throughput Nucleotide Sequencing ; *Host Microbial Interactions ; Metagenomics/*methods ; Microbiota/*genetics/physiology ; Nitrates/metabolism ; Oxidation-Reduction ; RNA, Ribosomal, 16S ; Sulfur/metabolism ; Vitamins/biosynthesis ; }, abstract = {The keystone zooplankton Daphnia magna has recently been used as a model system for understanding host-microbiota interactions. However, the bacterial species present and functions associated with their genomes are not well understood. In order to understand potential functions of these species, we combined 16S rRNA sequencing and shotgun metagenomics to characterize the whole-organism microbiota of Daphnia magna. We assembled five potentially novel metagenome-assembled genomes (MAGs) of core bacteria in Daphnia magna. Genes involved in host colonization and immune system evasion were detected across the MAGs. Some metabolic pathways were specific to some MAGs, including sulfur oxidation, nitrate reduction, and flagellar assembly. Amino acid exporters were identified in MAGs identified as important for host fitness, and pathways for key vitamin biosynthesis and export were identified across MAGs. In total, our examination of functions in these MAGs shows a diversity of nutrient acquisition and metabolism pathways present that may benefit the host, as well as genomic signatures of host association and immune system evasion.}, }
@article {pmid31957879, year = {2020}, author = {Arıkan, M and Mitchell, AL and Finn, RD and Gürel, F}, title = {Microbial composition of Kombucha determined using amplicon sequencing and shotgun metagenomics.}, journal = {Journal of food science}, volume = {85}, number = {2}, pages = {455-464}, pmid = {31957879}, issn = {1750-3841}, support = {215Z672//Türkiye Bilimsel ve Teknolojik Araştirma Kurumu/ ; 20138//Bilimsel Araştirma Projeleri Birimi, Istanbul Üniversitesi/ ; BB/M011755/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R015228/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //European Molecular Biology Laboratory/ ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Beverages/*microbiology ; Fermentation ; Fermented Foods and Beverages/*microbiology ; Metagenome ; Metagenomics ; *Microbiota ; Sequence Analysis, DNA ; Yeasts/classification/genetics/*isolation &amp; purification/metabolism ; }, abstract = {Kombucha, a fermented tea generated from the co-culture of yeasts and bacteria, has gained worldwide popularity in recent years due to its potential benefits to human health. As a result, many studies have attempted to characterize both its biochemical properties and microbial composition. Here, we have applied a combination of whole metagenome sequencing (WMS) and amplicon (16S rRNA and Internal Transcribed Spacer 1 [ITS1]) sequencing to investigate the microbial communities of homemade Kombucha fermentations from day 3 to day 15. We identified the dominant bacterial genus as Komagataeibacter and dominant fungal genus as Zygosaccharomyces in all samples at all time points. Furthermore, we recovered three near complete Komagataeibacter genomes and one Zygosaccharomyces bailii genome and then predicted their functional properties. Also, we determined the broad taxonomic and functional profile of plasmids found within the Kombucha microbial communities. Overall, this study provides a detailed description of the taxonomic and functional systems of the Kombucha microbial community. Based on this, we conject that the functional complementarity enables metabolic cross talks between Komagataeibacter species and Z. bailii, which helps establish the sustained a relatively low diversity ecosystem in Kombucha.}, }
@article {pmid31956324, year = {2019}, author = {Rinaldi, E and Consonni, A and Cordiglieri, C and Sacco, G and Crasà, C and Fontana, A and Morelli, L and Elli, M and Mantegazza, R and Baggi, F}, title = {Therapeutic Effect of Bifidobacterium Administration on Experimental Autoimmune Myasthenia Gravis in Lewis Rats.}, journal = {Frontiers in immunology}, volume = {10}, number = {}, pages = {2949}, pmid = {31956324}, issn = {1664-3224}, mesh = {Animals ; Autoimmunity ; *Bifidobacterium ; Cell Movement ; Dendritic Cells/immunology/metabolism ; Disease Models, Animal ; Female ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/methods ; Myasthenia Gravis, Autoimmune, Experimental/*etiology ; Probiotics/*administration &amp; dosage ; RNA, Ribosomal, 16S ; Rats ; Rats, Inbred Lew ; }, abstract = {Beneficial effects of probiotics on gut microbiota homeostasis and inflammatory immune responses suggested the investigation of their potential clinical efficacy in experimental models of autoimmune diseases. Indeed, administration of two bifidobacteria and lactobacilli probiotic strains prevented disease manifestations in the Lewis rat model of Myasthenia Gravis (EAMG). Here, we demonstrate the clinical efficacy of therapeutic administration of vital bifidobacteria (i.e., from EAMG onset). The mechanisms involved in immunomodulation were investigated with ex vivo and in vitro experiments. Improvement of EAMG symptoms was associated to decreased anti-rat AChR antibody levels, and differential expression of TGFβ and FoxP3 immunoregulatory transcripts in draining lymph nodes and spleen of treated-EAMG rats. Exposure of rat bone marrow-derived dendritic cells to bifidobacteria or lactobacilli strains upregulated toll-like receptor 2 mRNA expression, a key molecule involved in bacterium recognition via lipotheicoic acid. Live imaging experiments of AChR-specific effector T cells, co-cultured with BMDCs pre-exposed to bifidobacteria, demonstrated increased percentages of motile effector T cells, suggesting a hindered formation of TCR-peptide-MHC complex. Composition of gut microbiota was studied by 16S rRNA gene sequencing, and α and β diversity were determined in probiotic treated EAMG rats, with altered ratios between Tenericutes and Verrucomicrobia (phylum level), and Ruminococcaceae and Lachnospiraceae (family level). Moreover, the relative abundance of Akkermansia genus was found increased compared to healthy and probiotic treated EAMG rats. In conclusion, our findings confirms that the administration of vital bifidobacteria at EAMG onset has beneficial effects on disease progression; this study further supports preclinical research in human MG to evaluate probiotic efficacy as supplementary therapy in MG.}, }
@article {pmid31953381, year = {2020}, author = {Vich Vila, A and Collij, V and Sanna, S and Sinha, T and Imhann, F and Bourgonje, AR and Mujagic, Z and Jonkers, DMAE and Masclee, AAM and Fu, J and Kurilshikov, A and Wijmenga, C and Zhernakova, A and Weersma, RK}, title = {Impact of commonly used drugs on the composition and metabolic function of the gut microbiota.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {362}, pmid = {31953381}, issn = {2041-1723}, mesh = {Adult ; Anti-Bacterial Agents/pharmacology ; Antidepressive Agents/pharmacology ; Bacteria/*classification/*drug effects/*metabolism ; Body Mass Index ; Case-Control Studies ; Cohort Studies ; Computational Biology ; Ecosystem ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects/*physiology ; Humans ; Irritable Bowel Syndrome/drug therapy/microbiology ; Laxatives/pharmacology ; Male ; *Metagenomics ; Metformin/pharmacology ; Microbial Interactions/drug effects ; Middle Aged ; Proton Pump Inhibitors/pharmacology ; }, abstract = {The human gut microbiota has now been associated with drug responses and efficacy, while chemical compounds present in these drugs can also impact the gut bacteria. However, drug-microbe interactions are still understudied in the clinical context, where polypharmacy and comorbidities co-occur. Here, we report relations between commonly used drugs and the gut microbiome. We performed metagenomics sequencing of faecal samples from a population cohort and two gastrointestinal disease cohorts. Differences between users and non-users were analysed per cohort, followed by a meta-analysis. While 19 of 41 drugs are found to be associated with microbial features, when controlling for the use of multiple medications, proton-pump inhibitors, metformin, antibiotics and laxatives show the strongest associations with the microbiome. We here provide evidence for extensive changes in taxonomy, metabolic potential and resistome in relation to commonly used drugs. This paves the way for future studies and has implications for current microbiome studies by demonstrating the need to correct for multiple drug use.}, }
@article {pmid31953333, year = {2020}, author = {Riiser, ES and Haverkamp, THA and Varadharajan, S and Borgan, Ø and Jakobsen, KS and Jentoft, S and Star, B}, title = {Metagenomic Shotgun Analyses Reveal Complex Patterns of Intra- and Interspecific Variation in the Intestinal Microbiomes of Codfishes.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {6}, pages = {}, pmid = {31953333}, issn = {1098-5336}, mesh = {Animals ; Bacteria/*genetics/isolation &amp; purification ; *Ecotype ; Female ; Gadiformes/*microbiology ; Gadus morhua/microbiology ; Gastrointestinal Microbiome/*genetics ; Male ; *Metagenome ; Norway ; }, abstract = {The relative importance of host-specific selection or environmental factors in determining the composition of the intestinal microbiome in wild vertebrates remains poorly understood. Here, we used metagenomic shotgun sequencing of individual specimens to compare the levels of intra- and interspecific variation of intestinal microbiome communities in two ecotypes (NEAC and NCC) of Atlantic cod (Gadus morhua) that have distinct behavior and habitats and three Gadidae species that occupy a range of ecological niches. Interestingly, we found significantly diverged microbiomes among the two Atlantic cod ecotypes. Interspecific patterns of variation are more variable, with significantly diverged communities for most species' comparisons, apart from the comparison between coastal cod (NCC) and Norway pout (Trisopterus esmarkii), whose community compositions are not significantly diverged. The absence of consistent species-specific microbiomes suggests that external environmental factors, such as temperature, diet, or a combination thereof, comprise major drivers of the intestinal community composition of codfishes.IMPORTANCE The composition of the intestinal microbial community associated with teleost fish is influenced by a diversity of factors, ranging from internal factors (such as host-specific selection) to external factors (such as niche occupation). These factors are often difficult to separate, as differences in niche occupation (e.g., diet, temperature, or salinity) may correlate with distinct evolutionary trajectories. Here, we investigate four gadoid species with contrasting levels of evolutionary separation and niche occupation. Using metagenomic shotgun sequencing, we observed distinct microbiomes among two Atlantic cod (Gadus morhua) ecotypes (NEAC and NCC) with distinct behavior and habitats. In contrast, interspecific patterns of variation were more variable. For instance, we did not observe interspecific differentiation between the microbiomes of coastal cod (NCC) and Norway pout (Trisopterus esmarkii), whose lineages underwent evolutionary separation over 20 million years ago. The observed pattern of microbiome variation in these gadoid species is therefore most parsimoniously explained by differences in niche occupation.}, }
@article {pmid31950303, year = {2020}, author = {Queiroz, LL and Bendia, AG and Duarte, RTD and das Graças, DA and da Costa da Silva, AL and Nakayama, CR and Sumida, PY and Lima, AOS and Nagano, Y and Fujikura, K and Kitazato, H and Pellizari, VH}, title = {Bacterial diversity in deep-sea sediments under influence of asphalt seep at the São Paulo Plateau.}, journal = {Antonie van Leeuwenhoek}, volume = {113}, number = {5}, pages = {707-717}, doi = {10.1007/s10482-020-01384-8}, pmid = {31950303}, issn = {1572-9699}, support = {2013/09159-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 311010/2015-6//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, mesh = {Alphaproteobacteria/classification/genetics/isolation &amp; purification ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; DNA, Bacterial/genetics ; Deltaproteobacteria/classification/genetics/isolation &amp; purification ; Gammaproteobacteria/classification/genetics/isolation &amp; purification ; Geologic Sediments/*microbiology ; High-Throughput Nucleotide Sequencing/methods ; Hydrocarbons/metabolism ; *Metagenome ; Metagenomics/methods ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Water Microbiology ; }, abstract = {Here we investigated the diversity of bacterial communities from deep-sea surface sediments under influence of asphalt seeps at the Sao Paulo Plateau using next-generation sequencing method. Sampling was performed at North São Paulo Plateau using the human occupied vehicle Shinkai 6500 and her support vessel Yokosuka. The microbial diversity was studied at two surficial sediment layers (0-1 and 1-4 cm) of five samples collected in cores in water depths ranging from 2456 to 2728 m. Bacterial communities were studied through sequencing of 16S rRNA gene on the Ion Torrent platform and clustered in operational taxonomic units. We observed high diversity of bacterial sediment communities as previously described by other studies. When we considered community composition, the most abundant classes were Alphaproteobacteria (27.7%), Acidimicrobiia (20%), Gammaproteobacteria (11.3%) and Deltaproteobacteria (6.6%). Most abundant OTUs at family level were from two uncultured bacteria from Actinomarinales (5.95%) and Kiloniellaceae (3.17%). The unexpected high abundance of Alphaproteobacteria and Acidimicrobiia in our deep-sea microbial communities may be related to the presence of asphalt seep at North São Paulo Plateau, since these bacterial classes contain bacteria that possess the capability of metabolizing hydrocarbon compounds.}, }
@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 &amp; 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 {pmid31942082, year = {2020}, author = {Chong, J and Liu, P and Zhou, G and Xia, J}, title = {Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data.}, journal = {Nature protocols}, volume = {15}, number = {3}, pages = {799-821}, doi = {10.1038/s41596-019-0264-1}, pmid = {31942082}, issn = {1750-2799}, mesh = {DNA, Bacterial ; Databases, Genetic ; Meta-Analysis as Topic ; Metagenomics/methods ; Microbiota/*genetics/*physiology ; Models, Statistical ; RNA, Bacterial ; *Software ; }, abstract = {MicrobiomeAnalyst is an easy-to-use, web-based platform for comprehensive analysis of common data outputs generated from current microbiome studies. It enables researchers and clinicians with little or no bioinformatics training to explore a wide variety of well-established methods for microbiome data processing, statistical analysis, functional profiling and comparison with public datasets or known microbial signatures. MicrobiomeAnalyst currently contains four modules: Marker-gene Data Profiling (MDP), Shotgun Data Profiling (SDP), Projection with Public Data (PPD), and Taxon Set Enrichment Analysis (TSEA). This protocol will first introduce the MDP module by providing a step-wise description of how to prepare, process and normalize data; perform community profiling; identify important features; and conduct correlation and classification analysis. We will then demonstrate how to perform predictive functional profiling and introduce several unique features of the SDP module for functional analysis. The last two sections will describe the key steps involved in using the PPD and TSEA modules for meta-analysis and visual exploration of the results. In summary, MicrobiomeAnalyst offers a one-stop shop that enables microbiome researchers to thoroughly explore their preprocessed microbiome data via intuitive web interfaces. The complete protocol can be executed in ~70 min.}, }
@article {pmid31936703, year = {2020}, author = {Kang, S and You, HJ and Lee, YG and Jeong, Y and Johnston, TV and Baek, NI and Ku, S and Ji, GE}, title = {Production, Structural Characterization, and In Vitro Assessment of the Prebiotic Potential of Butyl-Fructooligosaccharides.}, journal = {International journal of molecular sciences}, volume = {21}, number = {2}, pages = {}, pmid = {31936703}, issn = {1422-0067}, support = {2017R1A2B2012390//National Research Foundation of Korea/ ; NRF-2017M3A9F3041747//National Research Foundation of Korea/ ; }, mesh = {Adult ; Ammonia/analysis ; Bacteria/classification/metabolism ; Biodiversity ; Butyrates/*metabolism ; Dietary Fiber ; Fatty Acids, Volatile/metabolism ; Feces/chemistry/microbiology ; Female ; Fermentation ; Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Oligosaccharides/*chemistry/*metabolism ; Prebiotics/*analysis ; Spectroscopy, Fourier Transform Infrared ; Young Adult ; }, abstract = {Short-chain fatty acids (SCFAs), especially butyrate, produced in mammalian intestinal tracts via fermentation of dietary fiber, are known biofunctional compounds in humans. However, the variability of fermentable fiber consumed on a daily basis and the diversity of gut microbiota within individuals often limits the production of short-chain fatty acids in the human gut. In this study, we attempted to enhance the butyrate levels in human fecal samples by utilizing butyl-fructooligosaccharides (B-FOS) as a novel prebiotic substance. Two major types of B-FOS (GF3-1B and GF3-2B), composed of short-chain fructooligosaccharides (FOS) bound to one or two butyric groups by ester bonds, were synthesized. Qualitative analysis of these B-FOS using Fourier transform infrared (FT-IR) spectroscopy, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), nuclear magnetic resonance (NMR) and low-resolution fast-atom bombardment mass spectra (LR-FAB-MS), showed that the chemical structure of GF3-1B and GF3-2B were [O-(1-buty-β-D-fru-(2→1)-O-β-D-fru-(2→1)-O-β-D-fru-O-α-D-glu] and [O-(1-buty)-β-D-fru-(2→1)-O-β-D-fru-(2→1)-O-(4-buty)-β-D-fru-O-α-D-glu], respectively. The ratio of these two compounds was approximately 5:3. To verify their biofunctionality as prebiotic oligosaccharides, proliferation and survival patterns of human fecal microbiota were examined in vitro via 16S rRNA metagenomics analysis compared to a positive FOS control and a negative control without a carbon source. B-FOS treatment showed different enrichment patterns on the fecal microbiota community during fermentation, and especially stimulated the growth of major butyrate producing bacterial consortia and modulated specific butyrate producing pathways with significantly enhanced butyrate levels. Furthermore, the relative abundance of Fusobacterium and ammonia production with related metabolic genes were greatly reduced with B-FOS and FOS treatment compared to the control group. These findings indicate that B-FOS differentially promotes butyrate production through the enhancement of butyrate-producing bacteria and their metabolic genes, and can be applied as a novel prebiotic compound in vivo.}, }
@article {pmid31930986, year = {2020}, author = {Casals-Pascual, C and González, A and Vázquez-Baeza, Y and Song, SJ and Jiang, L and Knight, R}, title = {Microbial Diversity in Clinical Microbiome Studies: Sample Size and Statistical Power Considerations.}, journal = {Gastroenterology}, volume = {158}, number = {6}, pages = {1524-1528}, doi = {10.1053/j.gastro.2019.11.305}, pmid = {31930986}, issn = {1528-0012}, mesh = {Bacteria/*genetics/isolation &amp; purification ; Biomarkers/analysis ; Feces/microbiology ; Gastrointestinal Diseases/*diagnosis/microbiology/therapy ; Gastrointestinal Microbiome/*genetics ; Genetic Heterogeneity ; Humans ; Intestinal Mucosa/microbiology ; Metagenomics/*standards ; Observational Studies as Topic/standards ; Phylogeny ; Randomized Controlled Trials as Topic/standards ; Sample Size ; Treatment Outcome ; }, }
@article {pmid31927597, year = {2020}, author = {Sun, F and Wang, C and Chen, H and Zheng, Z}, title = {Metagenomic Analysis of the Effect of Enteromorpha prolifera Bloom on Microbial Community and Function in Aquaculture Environment.}, journal = {Current microbiology}, volume = {77}, number = {5}, pages = {816-825}, pmid = {31927597}, issn = {1432-0991}, support = {2017A020216008//Guangdong Science and Technology Department/ ; 2016I1002//Fujian Provincial Department of Science and Technology/ ; 2017T3010//Fujian Provincial Department of Science and Technology/ ; }, mesh = {Actinomycetales/classification ; *Aquaculture ; *Eutrophication ; Flavobacteriaceae/classification ; *Metagenome ; Metagenomics ; *Microbiota ; Sequence Analysis, DNA ; Ulva/growth &amp; development/*metabolism ; Viruses/classification ; }, abstract = {Enteromorpha prolifera blooms considerably affected coastal environments in recent years. However, the effects of E. prolifera on microbial ecology and function remained unknown. In this study, metagenomic sequencing was used to investigate the effect of E. prolifera bloom on the microbial communities and functional genes in an aquaculture environment. Results showed that E. prolifera bloom could significantly alter the microbial composition and abundance, and heterotrophic bacteria comprised the major groups in the E. prolifera bloom pond, which was dominated by Actinomycetales and Flavobacteriales. The study indicated that viruses played an important role in shaping the microbial community and diversity during E. prolifera bloom. These viruses affected various dominant microbial taxa (such as Rhodobacteraceae, Synechococcus, and Prochlorococcus), which produced an obvious impact on potential nutrient transformation. Functional annotation analysis indicated that E. prolifera bloom would considerably shift the metabolism function by altering the structure and abundance of the microbial community. E. prolifera bloom pond had the low ability of potential metabolic capabilities of nitrogen, sulfur, and phosphate, whereas promoted gene abundance of genetic information processing. These changes in the microbial community and function could produce serious effect on aquaculture ecosystem.}, }
@article {pmid31926407, year = {2020}, 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}, mesh = {Animals ; Biodiversity ; Canada ; Fresh Water ; Humans ; *Metagenomics ; *Soil ; }, 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 {pmid31924616, year = {2020}, author = {Jnana, A and Muthuraman, V and Varghese, VK and Chakrabarty, S and Murali, TS and Ramachandra, L and Shenoy, KR and Rodrigues, GS and Prasad, SS and Dendukuri, D and Morschhauser, A and Nestler, J and Peter, H and Bier, FF and Satyamoorthy, K}, title = {Microbial Community Distribution and Core Microbiome in Successive Wound Grades of Individuals with Diabetic Foot Ulcers.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {6}, pages = {}, pmid = {31924616}, issn = {1098-5336}, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/classification/*isolation &amp; purification ; Diabetic Foot/*microbiology ; Female ; Humans ; Male ; *Microbiota ; Middle Aged ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Sex Factors ; Young Adult ; }, abstract = {Diabetic foot ulcer (DFU) is a major complication of diabetes with high morbidity and mortality rates. The pathogenesis of DFUs is governed by a complex milieu of environmental and host factors. The empirical treatment is initially based on wound severity since culturing and profiling the antibiotic sensitivity of wound-associated microbes is time-consuming. Hence, a thorough and rapid analysis of the microbial landscape is a major requirement toward devising evidence-based interventions. Toward this, 122 wound (100 diabetic and 22 nondiabetic) samples were sampled for their bacterial community structure using both culture-based and next-generation 16S rRNA-based metagenomics approach. Both the approaches showed that the Gram-negative microbes were more abundant in the wound microbiome. The core microbiome consisted of bacterial genera, including Alcaligenes, Pseudomonas, Burkholderia, and Corynebacterium in decreasing order of average relative abundance. Despite the heterogenous nature and extensive sharing of microbes, an inherent community structure was apparent, as revealed by a cluster analysis based on Euclidean distances. Facultative anaerobes (26.5%) were predominant in Wagner grade 5, while strict anaerobes were abundant in Wagner grade 1 (26%). A nonmetric dimensional scaling analysis could not clearly discriminate samples based on HbA1c levels. Sequencing approach revealed the presence of major culturable species even in samples with no bacterial growth in culture-based approach. Our study indicates that (i) the composition of core microbial community varies with wound severity, (ii) polymicrobial species distribution is individual specific, and (iii) antibiotic susceptibility varies with individuals. Our study suggests the need to evolve better-personalized care for better wound management therapies.IMPORTANCE Chronic nonhealing diabetic foot ulcers (DFUs) are a serious complication of diabetes and are further exacerbated by bacterial colonization. The microbial burden in the wound of each individual displays diverse morphological and physiological characteristics with unique patterns of host-pathogen interactions, antibiotic resistance, and virulence. Treatment involves empirical decisions until definitive results on the causative wound pathogens and their antibiotic susceptibility profiles are available. Hence, there is a need for rapid and accurate detection of these polymicrobial communities for effective wound management. Deciphering microbial communities will aid clinicians to tailor their treatment specifically to the microbes prevalent in the DFU at the time of assessment. This may reduce DFUs associated morbidity and mortality while impeding the rise of multidrug-resistant microbes.}, }
@article {pmid31922546, year = {2020}, author = {Morris, MM and Frixione, NJ and Burkert, AC and Dinsdale, EA and Vannette, RL}, title = {Microbial abundance, composition, and function in nectar are shaped by flower visitor identity.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {3}, pages = {}, doi = {10.1093/femsec/fiaa003}, pmid = {31922546}, issn = {1574-6941}, mesh = {Animals ; Bees ; Birds ; Flowers ; *Microbiota ; *Plant Nectar ; Pollination ; }, abstract = {Microbial dispersal is essential for establishment in new habitats, but the role of vector identity is poorly understood in community assembly and function. Here, we compared microbial assembly and function in floral nectar visited by legitimate pollinators (hummingbirds) and nectar robbers (carpenter bees). We assessed effects of visitation on the abundance and composition of culturable bacteria and fungi and their taxonomy and function using shotgun metagenomics and nectar chemistry. We also compared metagenome-assembled genomes (MAGs) of Acinetobacter, a common and highly abundant nectar bacterium, among visitor treatments. Visitation increased microbial abundance, but robbing resulted in 10× higher microbial abundance than pollination. Microbial communities differed among visitor treatments: robbed flowers were characterized by predominant nectar specialists within Acetobacteraceae and Metschnikowiaceae, with a concurrent loss of rare taxa, and these resulting communities harbored genes relating to osmotic stress, saccharide metabolism and specialized transporters. Gene differences were mirrored in function: robbed nectar contained a higher percentage of monosaccharides. Draft genomes of Acinetobacter revealed distinct amino acid and saccharide utilization pathways in strains isolated from robbed versus pollinated flowers. Our results suggest an unrecognized cost of nectar robbing for pollination and distinct effects of visitor type on interactions between plants and pollinators. Overall, these results suggest vector identity is an underappreciated factor structuring microbial community assembly and function.}, }
@article {pmid31917273, year = {2020}, author = {Yuan, X and Wang, L and Meng, D and Wu, L and Wang, X and Zhang, D and Luo, Z and Pang, Y and Liu, G}, title = {The impact of NBUVB on microbial community profiling in the lesional skin of vitiligo subjects.}, journal = {Microbial pathogenesis}, volume = {140}, number = {}, pages = {103943}, doi = {10.1016/j.micpath.2019.103943}, pmid = {31917273}, issn = {1096-1208}, mesh = {Actinobacteria/classification/genetics/isolation &amp; purification ; Bacteria/classification/genetics/isolation &amp; purification ; Female ; Firmicutes/classification/genetics/isolation &amp; purification ; Humans ; Male ; Metagenomics ; Microbiota/*genetics ; Proteobacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S ; Skin/*microbiology/pathology ; *Ultraviolet Therapy ; Vitiligo/*microbiology ; }, abstract = {BACKGROUND: The impact of NBUVB on the cutaneous microbiota of vitiligo patients remains to be fully elucidated.<br><br>METHODS: To characterize the cutaneous microbiota in vitiligo patients, cutaneous samples from 60 patients with vitiligo and after NBUVB irradiation were profiled using the Illumina MiSeq platform. Alpha diversity estimations revealed higher microbiota diversity in samples from patients with lesional skin. Beta diversity (Principal Component Analysis (PCA)) analysis showed that the bacterial community structure segregated differently between different groups.<br><br>RESULTS: There was a statistically significant increase in the Sobs, ACE, and Chao indices in the NB group compared with NF group, as determined by t-test. The alpha diversity have no significant difference between NF and DB group. At the phylum level, Firmicutes, Proteobacteria and Actinobacteria were the most predominant phyla. Propionibacterium and Pseudomonas were the most predominant genera in each group. In addition, Staphylococcus, Bacillus and Prevotella were enriched in DF group compared to DB group. Propionibacterium was enriched in DB group compared to DF group.<br><br>CONCLUSIONS: Our studies indicate differences in microbial community dynamics of the lesional and non-lesional sites of vitiligo subjects, with greater diversity and higher association between microbial communities of the unaffected site. And NBUVB irradiation might eliminate these differences.}, }
@article {pmid31911493, year = {2020}, author = {Saw, JHW and Nunoura, T and Hirai, M and Takaki, Y and Parsons, R and Michelsen, M and Longnecker, K and Kujawinski, EB and Stepanauskas, R and Landry, Z and Carlson, CA and Giovannoni, SJ}, title = {Pangenomics Analysis Reveals Diversification of Enzyme Families and Niche Specialization in Globally Abundant SAR202 Bacteria.}, journal = {mBio}, volume = {11}, number = {1}, pages = {}, pmid = {31911493}, issn = {2150-7511}, mesh = {Biodiversity ; Chloroflexi/*enzymology/*genetics ; Computational Biology/methods ; *Genome, Bacterial ; Metabolic Networks and Pathways ; Metabolomics/methods ; *Metagenome ; *Metagenomics ; *Multigene Family ; Phylogeny ; Phylogeography ; }, abstract = {It has been hypothesized that the abundant heterotrophic ocean bacterioplankton in the SAR202 clade of the phylum Chloroflexi evolved specialized metabolisms for the oxidation of organic compounds that are resistant to microbial degradation via common metabolic pathways. Expansions of paralogous enzymes were reported and implicated in hypothetical metabolism involving monooxygenase and dioxygenase enzymes. In the proposed metabolic schemes, the paralogs serve the purpose of diversifying the range of organic molecules that cells can utilize. To further explore SAR202 evolution and metabolism, we reconstructed single amplified genomes and metagenome-assembled genomes from locations around the world that included the deepest ocean trenches. In an analysis of 122 SAR202 genomes that included seven subclades spanning SAR202 diversity, we observed additional evidence of paralog expansions that correlated with evolutionary history, as well as further evidence of metabolic specialization. Consistent with previous reports, families of flavin-dependent monooxygenases were observed mainly in the group III SAR202 genomes, and expansions of dioxygenase enzymes were prevalent in those of group VII. We found that group I SAR202 genomes encode expansions of racemases in the enolase superfamily, which we propose evolved for the degradation of compounds that resist biological oxidation because of chiral complexity. Supporting the conclusion that the paralog expansions indicate metabolic specialization, fragment recruitment and fluorescent in situ hybridization (FISH) with phylogenetic probes showed that SAR202 subclades are indigenous to different ocean depths and geographical regions. Surprisingly, some of the subclades were abundant in surface waters and contained rhodopsin genes, altering our understanding of the ecological role of SAR202 species in stratified water columns.IMPORTANCE The oceans contain an estimated 662 Pg C in the form of dissolved organic matter (DOM). Information about microbial interactions with this vast resource is limited, despite broad recognition that DOM turnover has a major impact on the global carbon cycle. To explain patterns in the genomes of marine bacteria, we propose hypothetical metabolic pathways for the oxidation of organic molecules that are resistant to oxidation via common pathways. The hypothetical schemes we propose suggest new metabolic pathways and classes of compounds that could be important for understanding the distribution of organic carbon throughout the biosphere. These genome-based schemes will remain hypothetical until evidence from experimental cell biology can be gathered to test them. Our findings also fundamentally change our understanding of the ecology of SAR202 bacteria, showing that metabolically diverse variants of these cells occupy niches spanning all depths and are not relegated to the dark ocean.}, }
@article {pmid31911491, year = {2020}, author = {Song, SJ and Sanders, JG and Delsuc, F and Metcalf, J and Amato, K and Taylor, MW and Mazel, F and Lutz, HL and Winker, K and Graves, GR and Humphrey, G and Gilbert, JA and Hackett, SJ and White, KP and Skeen, HR and Kurtis, SM and Withrow, J and Braile, T and Miller, M and McCracken, KG and Maley, JM and Ezenwa, VO and Williams, A and Blanton, JM and McKenzie, VJ and Knight, R}, title = {Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats.}, journal = {mBio}, volume = {11}, number = {1}, pages = {}, pmid = {31911491}, issn = {2150-7511}, mesh = {Animals ; *Biological Evolution ; *Birds ; *Chiroptera ; Computational Biology/methods ; *Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; *Vertebrates ; }, abstract = {Diet and host phylogeny drive the taxonomic and functional contents of the gut microbiome in mammals, yet it is unknown whether these patterns hold across all vertebrate lineages. Here, we assessed gut microbiomes from ∼900 vertebrate species, including 315 mammals and 491 birds, assessing contributions of diet, phylogeny, and physiology to structuring gut microbiomes. In most nonflying mammals, strong correlations exist between microbial community similarity, host diet, and host phylogenetic distance up to the host order level. In birds, by contrast, gut microbiomes are only very weakly correlated to diet or host phylogeny. Furthermore, while most microbes resident in mammalian guts are present in only a restricted taxonomic range of hosts, most microbes recovered from birds show little evidence of host specificity. Notably, among the mammals, bats host especially bird-like gut microbiomes, with little evidence for correlation to host diet or phylogeny. This suggests that host-gut microbiome phylosymbiosis depends on factors convergently absent in birds and bats, potentially associated with physiological adaptations to flight. Our findings expose major variations in the behavior of these important symbioses in endothermic vertebrates and may signal fundamental evolutionary shifts in the cost/benefit framework of the gut microbiome.IMPORTANCE In this comprehensive survey of microbiomes of >900 species, including 315 mammals and 491 birds, we find a striking convergence of the microbiomes of birds and animals that fly. In nonflying mammals, diet and short-term evolutionary relatedness drive the microbiome, and many microbial species are specific to a particular kind of mammal, but flying mammals and birds break this pattern with many microbes shared across different species, with little correlation either with diet or with relatedness of the hosts. This finding suggests that adaptation to flight breaks long-held relationships between hosts and their microbes.}, }
@article {pmid31904815, year = {2020}, author = {Zhang, X and Yi, N}, title = {Fast zero-inflated negative binomial mixed modeling approach for analyzing longitudinal metagenomics data.}, journal = {Bioinformatics (Oxford, England)}, volume = {36}, number = {8}, pages = {2345-2351}, doi = {10.1093/bioinformatics/btz973}, pmid = {31904815}, issn = {1367-4811}, mesh = {Humans ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; Models, Statistical ; RNA, Ribosomal, 16S/genetics ; }, abstract = {MOTIVATION: Longitudinal metagenomics data, including both 16S rRNA and whole-metagenome shotgun sequencing data, enhanced our abilities to understand the dynamic associations between the human microbiome and various diseases. However, analytic tools have not been fully developed to simultaneously address the main challenges of longitudinal metagenomics data, i.e. high-dimensionality, dependence among samples and zero-inflation of observed counts.<br><br>RESULTS: We propose a fast zero-inflated negative binomial mixed modeling (FZINBMM) approach to analyze high-dimensional longitudinal metagenomic count data. The FZINBMM approach is based on zero-inflated negative binomial mixed models (ZINBMMs) for modeling longitudinal metagenomic count data and a fast EM-IWLS algorithm for fitting ZINBMMs. FZINBMM takes advantage of a commonly used procedure for fitting linear mixed models, which allows us to include various types of fixed and random effects and within-subject correlation structures and quickly analyze many taxa. We found that FZINBMM remarkably outperformed in computational efficiency and was statistically comparable with two R packages, GLMMadaptive and glmmTMB, that use numerical integration to fit ZINBMMs. Extensive simulations and real data applications showed that FZINBMM outperformed other previous methods, including linear mixed models, negative binomial mixed models and zero-inflated Gaussian mixed models.<br><br>FZINBMM has been implemented in the R package NBZIMM, available in the public GitHub repository http://github.com//nyiuab//NBZIMM.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid31901868, year = {2020}, author = {Gurung, M and Li, Z and You, H and Rodrigues, R and Jump, DB and Morgun, A and Shulzhenko, N}, title = {Role of gut microbiota in type 2 diabetes pathophysiology.}, journal = {EBioMedicine}, volume = {51}, number = {}, pages = {102590}, doi = {10.1016/j.ebiom.2019.11.051}, pmid = {31901868}, issn = {2352-3964}, support = {R01 DK103761/DK/NIDDK NIH HHS/United States ; R01 DK112360/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/metabolism ; Diabetes Mellitus, Type 2/drug therapy/*microbiology/*physiopathology ; *Gastrointestinal Microbiome ; Humans ; }, abstract = {A substantial body of literature has provided evidence for the role of gut microbiota in metabolic diseases including type 2 diabetes. However, reports vary regarding the association of particular taxonomic groups with disease. In this systematic review, we focused on the potential role of different bacterial taxa affecting diabetes. We have summarized evidence from 42 human studies reporting microbial associations with disease, and have identified supporting preclinical studies or clinical trials using treatments with probiotics. Among the commonly reported findings, the genera of Bifidobacterium, Bacteroides, Faecalibacterium, Akkermansia and Roseburia were negatively associated with T2D, while the genera of Ruminococcus, Fusobacterium, and Blautia were positively associated with T2D. We also discussed potential molecular mechanisms of microbiota effects in the onset and progression of T2D.}, }
@article {pmid31901572, year = {2020}, author = {Aagaard, KM}, title = {Mode of delivery and pondering potential sources of the neonatal microbiome.}, journal = {EBioMedicine}, volume = {51}, number = {}, pages = {102554}, doi = {10.1016/j.ebiom.2019.11.015}, pmid = {31901572}, issn = {2352-3964}, mesh = {Bacteria/genetics ; Cesarean Section ; *Delivery, Obstetric ; Humans ; Infant, Newborn ; *Microbiota/genetics ; Odds Ratio ; RNA, Ribosomal, 16S/genetics ; }, }
@article {pmid31900552, year = {2020}, author = {Cai, X and Mao, Y and Xu, J and Tian, L and Wang, Y and Iqbal, W and Yang, B and Liu, C and Zhao, X and Wang, Y}, title = {Characterizing community dynamics and exploring bacterial assemblages in two activated sludge systems.}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {4}, pages = {1795-1808}, doi = {10.1007/s00253-019-10279-2}, pmid = {31900552}, issn = {1432-0614}, support = {51608329; 51708358//National Natural Science Foundation of China/ ; 41907214//National Natural Science Foundation of China/ ; 2017A030313315//Natural Science Foundation of Guangdong Province/ ; JCYJ20160520165135743, JCYJ20170412171918012//Shenzhen Science and Technology Projects/ ; 2017ZX07202//National Major Science and Technology Program for Water Pollution Control and Treatment (CN)/ ; 827-000223//Natural Science Foundation of Shenzhen University/ ; 2019M653053//Postdoctoral Research Foundation of China/ ; }, mesh = {Animals ; Bacteria/*classification ; Feces/microbiology ; Genetic Variation ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenomics ; *Microbiota ; Sewage/*microbiology ; }, abstract = {Bacterial communities in the activated sludge (AS) determine the wastewater treatment performance in the municipal wastewater treatment plants (WWTPs). Aiming at identifying the affecting factors and the variation patterns of the bacterial assemblages in AS, a 2-year time-series AS samples were collected from two separated WWTPs and metagenomic sequencing was conducted. Obvious seasonal shift and succession of the bacterial community were observed in both WWTPs on the genus and species levels, especially for the persistent taxa, implying that temperature was a decisive factor for maintaining bacterial assemblage patterns in long-term period. Taxa abundance distribution (TAD) concerning occurrence frequency and average abundance were found fitting for exponential formulations, and the approximately equal total abundance of persistent taxa suggested that stable and high abundance (~ 90%) of core functional bacterial groups would help to maintain wastewater treatment performance. Drastic changes of environmental factors were found causing temporally significant bacterial structure variation, while the innate correlations between bacterial species could recover the community gradually and maintain relative stability of the AS system. Delayed correlations between environmental factors and abundant (persistent or intermittent) bacterial species were observed widely, while synchronous biotic interactions were identified more frequently. Besides, bacterial species with similar functions were prone to cluster together and shared the same seasonal variation pattern, implicating that the cooperation of functional correlated taxa played the most dominant role in shaping the bacterial assemblages. Furthermore, rare bacterial groups were to be explored for removing emerging pollutants with lower concentrations. The results of this study would assist dealing with operational defect and optimize the treatment system in WWTPs.}, }
@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 {pmid31896059, year = {2020}, author = {Vargas, JE and Andrés, S and López-Ferreras, L and López, S}, title = {Effects of supplemental plant oils on rumen bacterial community profile and digesta fatty acid composition in a continuous culture system (RUSITEC).}, journal = {Anaerobe}, volume = {61}, number = {}, pages = {102143}, doi = {10.1016/j.anaerobe.2019.102143}, pmid = {31896059}, issn = {1095-8274}, mesh = {Animal Feed/analysis ; Animals ; Bacteriological Techniques ; *Dietary Supplements ; Fatty Acids/*metabolism ; *Fermentation ; Metagenomics/methods ; *Microbiota ; *Plant Oils ; Rumen/*microbiology ; }, abstract = {Lipid supplementation of ruminant diets may trigger changes in the ruminal microbiota and in anaerobic digestion. Changes in the bacterial community composition and in the fatty acid hydrogenation caused by the addition of different supplemental plant oils to a high concentrate diet were investigated in vitro using RUSITEC (rumen simulation technique) fermenters. The control (CTR) diet was a high-concentrate total mixed ration for dairy sheep, with no supplementary oil. The other experimental diets were supplemented with olive (OLV), sunflower (SFL) or linseed (LNS) oils at 6% (dry matter basis). Four RUSITEC fermenters were used for each experimental diet, all inoculated with rumen digesta of sheep. Extent of dry matter and fat degradation, composition of the bacterial community and long-chain fatty acids in digesta were determined. The addition of plant oils increased (P < 0.001) apparent degradation of fat in the fermenters, whereas fermentation kinetics (gas production and average fermentation rate) were lower (P < 0.05) with the LNS than with the CTR diet. Hydrogenation of C18 unsaturated fatty acids (P < 0.05), in particular that of oleic acid (P < 0.001), and stearic acid proportion (P < 0.001) were reduced, and oleic acid proportion was increased (P < 0.001) with all oil supplements. Addition of OLV decreased linoleic and LNS increased α-linolenic (P < 0.001), whereas conjugated linoleic was increased with SFL oil (P = 0.025) and vaccenic increased with both SFL and LNS oils (P = 0.008). Addition of 6% OLV and LNS reduced (P < 0.05) microbial community diversity and quantity of total bacteria relative to the control. Some specific microbial groups were affected (P < 0.001) by oil addition, with less relative abundance of Clostridiales and Actinobacteria and increased Bacteroidales, Aeromonadales and Lactobacillales species. In conclusion, the supplementation of high-concentrate ruminant diets with plant oils, in particular from sunflower or linseed, causes shifts in the rumen microbiota and fatty acid hydrogenation in the rumen increasing the formation of vaccenic and conjugated linoleic acids.}, }
@article {pmid31894129, year = {2019}, author = {Bhat, AH and Prabhu, P and Balakrishnan, K}, title = {A critical analysis of state-of-the-art metagenomics OTU clustering algorithms.}, journal = {Journal of biosciences}, volume = {44}, number = {6}, pages = {}, pmid = {31894129}, issn = {0973-7138}, mesh = {Algorithms ; Cluster Analysis ; *Computational Biology ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/*trends ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Software ; }, abstract = {Taxonomic profiling, using hyper-variable regions of 16S rRNA, is one of the important goals in metagenomics analysis. Operational taxonomic unit (OTU) clustering algorithms are the important tools to perform taxonomic profiling by grouping 16S rRNA sequence reads into OTU clusters. Presently various OTU clustering algorithms are available within different pipelines, even some pipelines have implemented more than one clustering algorithms, but there is less literature available for the relative performance and features of these algorithms. This makes the choice of using these methods unclear. In this study five current state-of-the-art OTU clustering algorithms (CDHIT, Mothur's Average Neighbour, SUMACLUST, Swarm, and UCLUST) have been comprehensively evaluated on the metagenomics sequencing data. It was found that in all the datasets, Mothur's average neighbour and Swarm created more number of OTU clusters. Based on normalized mutual information (NMI) and normalized information difference (NID), Swarm and Mothur's average neighbour showed better clustering qualities than others. But in terms of time complexity the greedy algorithms (SUMACLUST, CDHIT, and UCLUST) performed well. So there is a trade-off between quality and time, and it is necessary while analysing large size of 16S rRNA gene sequencing data.}, }
@article {pmid31892851, year = {2020}, author = {Liang, S and Mao, Y and Liao, M and Xu, Y and Chen, Y and Huang, X and Wei, C and Wu, C and Wang, Q and Pan, X and Tang, W}, title = {Gut microbiome associated with APC gene mutation in patients with intestinal adenomatous polyps.}, journal = {International journal of biological sciences}, volume = {16}, number = {1}, pages = {135-146}, pmid = {31892851}, issn = {1449-2288}, mesh = {Adenomatous Polyps/*genetics ; Aged ; Colorectal Neoplasms/*genetics/*microbiology ; Faecalibacterium prausnitzii/genetics/physiology ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Genes, APC/physiology ; Humans ; Male ; Metagenomics ; Middle Aged ; Mutation/*genetics ; }, abstract = {Background: The 'adenoma-carcinoma sequence' is a well-recognized model of colorectal cancer (CRC) development. However, the interaction between gut microbiota and genetic variation in the initiation of CRC is not clear. Our study attempts to demonstrate the relationship between gut microbiota and host genetics in patients with intestinal adenomatous polyps. Method: The entire exon region of the APC gene was sequenced in 35 patients with pathologically diagnosed adenomatous polyps. Patients with highly pathogenic APC mutation were classified as the case group, while the others were classified as the control group. The patients'stool and serum samples were respectively collected for metagenomics and metabolomics measurements. Results: In the analysis of gut microbiome, there were three most important species, in which Fusobacterium_mortiferum was significantly increased while Faecalibacterium_prausnitzii and Bifidobacterium_pseudocatenulatum were significantly decreased in the case group. The significantly low abundance of the Photosynthesis pathway in patients with APC mutation was due to the low abundance of species Faecalibacterium_prausnitzii and Bifidobacterium_pseudocatenulatum. Moreover, there were two clusters of KEGG pathways correlated with two clusters of species characterized by Faecalibacterium_prausnitzii and Fusobacterium_mortiferum. As to serum metabolomics, the abundance of (R)-3-Hydroxybutyric acid and 2-Hydroxyphenethylamine were significantly higher in patients with APC mutation, while the abundance of 1-Aminocyclopropanecarboxylic acid,7-Ketocholesterol, DL-lactate, and L-Pyroglutamic acid were significantly higher in controlgroup. After analyzing the metabolome and microbiome data by sparCCmethod, we found that there was a significantly negative correlation between the abundance of Faecalibacterium_prausnitzii and Fusobacterium_mortiferum, and a significantly positive correlation between Faecalibacterium_prausnitzii abundance and the steroid hormone Hydrocortisone (Cortisol) in serum. Conclusions: Host's APC mutation was closely related to the changes of gut microbiota and serum metabolites, and some species of gut microbiome like Faecalibacterium_prausnitzii and Fusobacterium_mortiferum might have the potential to predict the development of CRC from intestinal adenomatous polyps.}, }
@article {pmid31888470, year = {2019}, author = {Goloshchapov, OV and Olekhnovich, EI and Sidorenko, SV and Moiseev, IS and Kucher, MA and Fedorov, DE and Pavlenko, AV and Manolov, AI and Gostev, VV and Veselovsky, VA and Klimina, KM and Kostryukova, ES and Bakin, EA and Shvetcov, AN and Gumbatova, ED and Klementeva, RV and Shcherbakov, AA and Gorchakova, MV and Egozcue, JJ and Pawlowsky-Glahn, V and Suvorova, MA and Chukhlovin, AB and Govorun, VM and Ilina, EN and Afanasyev, BV}, title = {Long-term impact of fecal transplantation in healthy volunteers.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {312}, pmid = {31888470}, issn = {1471-2180}, mesh = {Adult ; *Fecal Microbiota Transplantation ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Healthy Volunteers ; Humans ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Time Factors ; }, abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) has been recently approved by FDA for the treatment of refractory recurrent clostridial colitis (rCDI). Success of FTM in treatment of rCDI led to a number of studies investigating the effectiveness of its application in the other gastrointestinal diseases. However, in the majority of studies the effects of FMT were evaluated on the patients with initially altered microbiota. The aim of our study was to estimate effects of FMT on the gut microbiota composition in healthy volunteers and to monitor its long-term outcomes.<br><br>RESULTS: We have performed a combined analysis of three healthy volunteers before and after capsule FMT by evaluating their general condition, adverse clinical effects, changes of basic laboratory parameters, and several immune markers. Intestinal microbiota samples were evaluated by 16S rRNA gene and shotgun sequencing. The data analysis demonstrated profound shift towards the donor microbiota taxonomic composition in all volunteers. Following FMT, all the volunteers exhibited gut colonization with donor gut bacteria and persistence of this effect for almost ∼1 year of observation. Transient changes of immune parameters were consistent with suppression of T-cell cytotoxicity. FMT was well tolerated with mild gastrointestinal adverse events, however, one volunteer developed a systemic inflammatory response syndrome.<br><br>CONCLUSIONS: The FMT leads to significant long-term changes of the gut microbiota in healthy volunteers with the shift towards donor microbiota composition and represents a relatively safe procedure to the recipients without long-term adverse events.}, }
@article {pmid31888048, year = {2019}, author = {Sakanaka, M and Gotoh, A and Yoshida, K and Odamaki, T and Koguchi, H and Xiao, JZ and Kitaoka, M and Katayama, T}, title = {Varied Pathways of Infant Gut-Associated Bifidobacterium to Assimilate Human Milk Oligosaccharides: Prevalence of the Gene Set and Its Correlation with Bifidobacteria-Rich Microbiota Formation.}, journal = {Nutrients}, volume = {12}, number = {1}, pages = {}, pmid = {31888048}, issn = {2072-6643}, support = {18K14379; 19K15732; 19K22277; 201860637; 17J08530//Japan Society for the Promotion of Science/ ; }, mesh = {*Bifidobacterium/enzymology/genetics/metabolism ; Breast Feeding ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/genetics/physiology ; Genome, Bacterial/genetics ; Humans ; Infant ; Metagenomics ; *Milk, Human/chemistry/metabolism ; Oligosaccharides/*metabolism ; }, abstract = {The infant's gut microbiome is generally rich in the Bifidobacterium genus. The mother's milk contains natural prebiotics, called human milk oligosaccharides (HMOs), as the third most abundant solid component after lactose and lipids, and of the different gut microbes, infant gut-associated bifidobacteria are the most efficient in assimilating HMOs. Indeed, the fecal concentration of HMOs was found to be negatively correlated with the fecal abundance of Bifidobacterium in infants. Given these results, two HMO molecules, 2'-fucosyllactose and lacto-N-neotetraose, have recently been industrialized to fortify formula milk. As of now, however, our knowledge about the HMO consumption pathways in infant gut-associated bifidobacteria is still incomplete. The recent studies indicate that HMO assimilation abilities significantly vary among different Bifidobacterium species and strains. Therefore, to truly maximize the effects of prebiotic and probiotic supplementation in commercialized formula, we need to understand HMO consumption behaviors of bifidobacteria in more detail. In this review, we summarized how different Bifidobacterium species/strains are equipped with varied gene sets required for HMO assimilation. We then examined the correlation between the abundance of the HMO-related genes and bifidobacteria-rich microbiota formation in the infant gut through data mining analysis of a deposited fecal microbiome shotgun sequencing dataset. Finally, we shortly described future perspectives on HMO-related studies.}, }
@article {pmid31885873, year = {2019}, author = {Pareek, S and Kurakawa, T and Das, B and Motooka, D and Nakaya, S and Rongsen-Chandola, T and Goyal, N and Kayama, H and Dodd, D and Okumura, R and Maeda, Y and Fujimoto, K and Nii, T and Ogawa, T and Iida, T and Bhandari, N and Kida, T and Nakamura, S and Nair, GB and Takeda, K}, title = {Comparison of Japanese and Indian intestinal microbiota shows diet-dependent interaction between bacteria and fungi.}, journal = {NPJ biofilms and microbiomes}, volume = {5}, number = {1}, pages = {37}, pmid = {31885873}, issn = {2055-5008}, support = {K08 DK110335/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/*growth &amp; development/*metabolism ; Diet/*methods ; Feces/microbiology ; Fungi/classification/*growth &amp; development/*metabolism ; *Gastrointestinal Microbiome ; Humans ; India ; Japan ; Mice ; *Microbial Interactions ; Models, Animal ; Polysaccharides/metabolism ; }, abstract = {The bacterial species living in the gut mediate many aspects of biological processes such as nutrition and activation of adaptive immunity. In addition, commensal fungi residing in the intestine also influence host health. Although the interaction of bacterium and fungus has been shown, its precise mechanism during colonization of the human intestine remains largely unknown. Here, we show interaction between bacterial and fungal species for utilization of dietary components driving their efficient growth in the intestine. Next generation sequencing of fecal samples from Japanese and Indian adults revealed differential patterns of bacterial and fungal composition. In particular, Indians, who consume more plant polysaccharides than Japanese, harbored increased numbers of Prevotella and Candida. Candida spp. showed strong growth responses to the plant polysaccharide arabinoxylan in vitro. Furthermore, the culture supernatants of Candida spp. grown with arabinoxylan promoted rapid proliferation of Prevotella copri. Arabinose was identified as a potential growth-inducing factor in the Candida culture supernatants. Candida spp. exhibited a growth response to xylose, but not to arabinose, whereas P. copri proliferated in response to both xylose and arabinose. Candida spp., but not P. copri, colonized the intestine of germ-free mice. However, P. copri successfully colonized mouse intestine already harboring Candida. These findings demonstrate a proof of concept that fungal members of gut microbiota can facilitate a colonization of the intestine by their bacterial counterparts, potentially mediated by a dietary metabolite.}, }
@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}, mesh = {Africa ; *Gastrointestinal Microbiome ; Humans ; Metagenomics/*methods ; }, 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}, pmid = {31884971}, issn = {1741-7007}, mesh = {Archaea/*virology ; Bacteria/*virology ; Bacteriophages/*genetics ; *Genome, Viral ; *Microbiota ; Phylogeny ; }, 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 {pmid31882580, year = {2019}, author = {Griffen, AL and Thompson, ZA and Beall, CJ and Lilly, EA and Granada, C and Treas, KD and DuBois, KR and Hashmi, SB and Mukherjee, C and Gilliland, AE and Vazquez, JA and Hagensee, ME and Leys, EJ and Fidel, PL}, title = {Significant effect of HIV/HAART on oral microbiota using multivariate analysis.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {19946}, pmid = {31882580}, issn = {2045-2322}, support = {R01 DE022815/DE/NIDCR NIH HHS/United States ; U54 GM104940/GM/NIGMS NIH HHS/United States ; }, mesh = {Adult ; Anti-Retroviral Agents/pharmacology ; Antiretroviral Therapy, Highly Active/methods ; CD4 Lymphocyte Count/methods ; Dental Caries/*microbiology ; Female ; HIV Infections/drug therapy/*microbiology ; HIV-1/drug effects/pathogenicity ; Humans ; Male ; Metagenomics/methods ; Microbiota/*drug effects ; Multivariate Analysis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Persons infected with HIV are particularly vulnerable to a variety of oral microbial diseases. Although various study designs and detection approaches have been used to compare the oral microbiota of HIV-negative and HIV-positive persons, both with and without highly active antiretroviral therapy (HAART), methods have varied, and results have not been consistent or conclusive. The purpose of the present study was to compare the oral bacterial community composition in HIV-positive persons under HAART to an HIV-negative group using 16S rRNA gene sequence analysis. Extensive clinical data was collected, and efforts were made to balance the groups on clinical variables to minimize confounding. Multivariate analysis was used to assess the independent contribution of HIV status. Eighty-nine HIV-negative participants and 252 HIV-positive participants under HAART were sampled. The independent effect of HIV under HAART on the oral microbiome was statistically significant, but smaller than the effect of gingivitis, periodontal disease, smoking, caries, and other clinical variables. In conclusion, a multivariate comparison of a large sample of persons with HIV under HAART to an HIV-negative control group showed a complex set of clinical features that influenced oral bacterial community composition, including the presence of HIV under HAART.}, }
@article {pmid31882572, year = {2019}, author = {Wang, Z and Yang, Y and Xia, Y and Wu, T and Zhu, J and Yang, J and Li, Z}, title = {Time-course relationship between environmental factors and microbial diversity in tobacco soil.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {19969}, pmid = {31882572}, issn = {2045-2322}, mesh = {Bacteria/classification/genetics ; *Biodiversity ; Chemical Phenomena ; *Environment ; Environmental Microbiology ; Fungi/classification/genetics ; Metagenome ; Metagenomics/methods ; *Microbiota ; Soil/chemistry ; *Soil Microbiology ; Time Factors ; *Tobacco/growth &amp; development ; }, abstract = {Soil physicochemical properties and microbial diversity both play equally important roles in tobacco cultivation. However, the relationship between these factors remains unclear. In this study, we investigated their correlations through the whole tobacco growth period, including the pretransplanting (YX-p), root extending (R), flourishing (F), and mature (M) stages in the Yuxi region of the Yunnan-Guizhou Plateau by measuring physicochemical properties and conducting 16S/18S rRNA analysis. The analysis demonstrated that the microbial community richness and diversity continuously changed along with the growth course of the tobacco. Multiple environmental factors showed a certain correlation with the diversity of microbial communities. Some bacteria could accumulate nitrogen during the growth stages, and the diversity of the bacterial community also increased when the content of organic matter rose. In addition, the water content and available K also influenced the diversity of the microbial community. The dynamic changes in soil physicochemical properties and enzyme activities gave rise to differences in the microbial community composition and structure, all of which affected the growth of tobacco. This study revealed the time-course relationship between environmental factors and microbial diversity in tobacco soil. An understanding of this relationship provides guidance for research on the interaction system of plants, soil and microbes and on improving plant yield and quality.}, }
@article {pmid31879084, year = {2020}, author = {Marsh, RL and Aho, C and Beissbarth, J and Bialasiewicz, S and Binks, M and Cervin, A and Kirkham, LS and Lemon, KP and Slack, MPE and Smith-Vaughan, HC}, title = {Panel 4: Recent advances in understanding the natural history of the otitis media microbiome and its response to environmental pressures.}, journal = {International journal of pediatric otorhinolaryngology}, volume = {130 Suppl 1}, number = {}, pages = {109836}, doi = {10.1016/j.ijporl.2019.109836}, pmid = {31879084}, issn = {1872-8464}, support = {R01 GM117174/GM/NIGMS NIH HHS/United States ; R13 DC017389/DC/NIDCD NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Bacteria ; Disease Models, Animal ; Ear, Middle/*microbiology ; Humans ; *Microbiota/drug effects ; Nasopharynx/microbiology ; Otitis Media/*microbiology ; Smoking ; Vaccines/pharmacology ; }, abstract = {OBJECTIVE: To perform a comprehensive review of otitis media microbiome literature published between 1st July 2015 and 30th June 2019.<br><br>DATA SOURCES: PubMed database, National Library of Medicine.<br><br>REVIEW METHODS: Key topics were assigned to each panel member for detailed review. Draft reviews were collated and circulated for discussion when the panel met at the 20th International Symposium on Recent Advances in Otitis Media in June 2019. The final draft was prepared with input from all panel members.<br><br>CONCLUSIONS: Much has been learned about the different types of bacteria (including commensals) present in the upper respiratory microbiome, but little is known about the virome and mycobiome. A small number of studies have investigated the middle ear microbiome; however, current data are often limited by small sample sizes and methodological heterogeneity between studies. Furthermore, limited reporting of sample collection methods mean that it is often difficult to determine whether bacteria detected in middle ear fluid specimens originated from the middle ear or the external auditory canal. Recent in vitro studies suggest that bacterial interactions in the nasal/nasopharyngeal microbiome may affect otitis media pathogenesis by modifying otopathogen behaviours. Impacts of environmental pressures (e.g. smoke, nutrition) and clinical interventions (e.g. vaccination, antibiotics) on the upper respiratory and middle ear microbiomes remain poorly understood as there are few data.<br><br>IMPLICATIONS FOR PRACTICE: Advances in understanding bacterial dynamics in the upper airway microbiome are driving development of microbiota-modifying therapies to prevent or treat disease (e.g. probiotics). Further advances in otitis media microbiomics will likely require technological improvements that overcome the current limitations of OMICs technologies when applied to low volume and low biomass specimens that potentially contain high numbers of host cells. Improved laboratory models are needed to elucidate mechanistic interactions among the upper respiratory and middle ear microbiomes. Minimum reporting standards are critically needed to improve inter-study comparisons and enable future meta-analyses.}, }
@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 {pmid31876912, year = {2020}, author = {Bartolomaeus, TUP and Forslund, SK}, title = {Hitchhiker's guide to microbiome studies.}, journal = {Cardiovascular research}, volume = {116}, number = {3}, pages = {e44-e47}, doi = {10.1093/cvr/cvz316}, pmid = {31876912}, issn = {1755-3245}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; DNA, Bacterial/classification/*genetics/isolation &amp; purification ; Feces/microbiology ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Host-Pathogen Interactions ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; Ribotyping ; Skin/*microbiology ; }, }
@article {pmid31876614, year = {2020}, author = {Lees, EA and Carrol, ED and Ellaby, NAF and Roberts, P and Corless, CE and Lenzi, L and Darby, A and O'Brien, SJ and Cunliffe, NA and Turner, MA and Miyajima, F and Pirmohamed, M}, title = {Characterization of Circulating Clostridium difficile Strains, Host Response and Intestinal Microbiome in Hospitalized Children With Diarrhea.}, journal = {The Pediatric infectious disease journal}, volume = {39}, number = {3}, pages = {221-228}, doi = {10.1097/INF.0000000000002559}, pmid = {31876614}, issn = {1532-0987}, support = {/DH_/Department of Health/United Kingdom ; MR/K000551/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adolescent ; *Bacteremia ; Bacterial Toxins/genetics ; Biomarkers ; Child ; Child, Preschool ; Clostridium difficile/classification ; Cytokines/metabolism ; Diarrhea/*epidemiology/*etiology ; Enterocolitis, Pseudomembranous/*epidemiology/*microbiology ; Feces/chemistry/microbiology ; Female ; *Gastrointestinal Microbiome ; Hospitalization ; *Host-Pathogen Interactions ; Humans ; Incidence ; Infant ; Infant, Newborn ; Male ; Metagenomics/methods ; Molecular Typing ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Clostridium difficile is capable of causing severe enterocolitis in adults. The significance of toxin-producing C. difficile in children with diarrhea is unclear and practice differs on whether to institute treatment. We aimed to characterize the microbiome in relation to the presence of C. difficile and co-infection with other pathogens and to describe host response to infection.<br><br>METHODS: Participants were children with acute diarrhea, 0-16 years of age, from whom stool samples had been submitted to the hospital laboratory for routine microbiology/virology. Convenience sampling was used for 50 prospective and 150 retrospective samples. No participants were treated for C. difficile. Rates of culture positivity for C. difficile, presence of toxin and PCR-ribotype were compared between age groups. Presence of other potential pathogens, comorbidities and complications were recorded. Microbiotal diversity was measured by 16S profiling.<br><br>RESULTS: Nineteen of 77 (25%) children <2 years of age and 13 of 119 (11%) children >2 years of age were C. difficile positive, of whom 10 (53%) and 9 (69%), respectively, carried toxigenic strains. Increased Shannon diversity was seen in children carrying C. difficile, with altered milieu. Presence of C. difficile was not associated with adverse clinical outcomes. In stools containing both Norovirus and C. difficile, there was increased relative abundance of verrucomicrobia.<br><br>CONCLUSIONS: Children with diarrhea regularly carried toxigenic and non-toxigenic strains of C. difficile, demonstrating enhanced microbiotal diversity, and change in milieu, without apparent morbidity. This unexpected finding is contrary to that seen in adults with C. difficile disease.}, }
@article {pmid31875016, year = {2019}, author = {Passaro, N and Casagrande, A and Chiara, M and Fosso, B and Manzari, C and D'Erchia, AM and Iesari, S and Pisani, F and Famulari, A and Tulissi, P and Mastrosimone, S and Maresca, MC and Mercante, G and Spriano, G and Corrado, G and Vizza, E and Garbuglia, AR and Capobianchi, MR and Mottini, C and Cenci, A and Tartaglia, M and Costa, AN and Pesole, G and Crescenzi, M}, title = {No metagenomic evidence of tumorigenic viruses in cancers from a selected cohort of immunosuppressed subjects.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {19815}, pmid = {31875016}, issn = {2045-2322}, mesh = {Computational Biology/methods ; Humans ; *Immunocompromised Host ; Immunosuppression/adverse effects ; Metagenome ; Metagenomics/*methods ; Microbiota ; Neoplasms/*virology ; Oncogenic Viruses/*genetics ; Probability ; Sequence Analysis, RNA ; Viruses/genetics ; }, abstract = {The possible existence of yet undiscovered human tumorigenic viruses is still under scrutiny. The development of large-scale sequencing technologies, coupled with bioinformatics techniques for the characterization of metagenomic sequences, have provided an invaluable tool for the detection of unknown, infectious, tumorigenic agents, as demonstrated by several recent studies. However, discoveries of novel viruses possibly associated with tumorigenesis are scarce at best. Here, we apply a rigorous bioinformatics workflow to investigate in depth tumor metagenomes from a small but carefully selected cohort of immunosuppressed patients. While a variegated bacterial microbiome was associated with each tumor, no evidence of the presence of putative oncoviruses was found. These results are consistent with the major findings of several recent papers and suggest that new human tumorigenic viruses are not common even in immunosuppressed populations.}, }
@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}, pmid = {31873124}, issn = {2045-2322}, mesh = {Animals ; DNA, Ancient/*analysis ; Dental Calculus/*microbiology ; Egypt ; Humans ; *Metagenome ; Microbiota/*genetics ; Neanderthals ; Pan troglodytes ; Papio ; }, 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 {pmid31870316, year = {2019}, author = {Deutscher, AT and Chapman, TA and Shuttleworth, LA and Riegler, M and Reynolds, OL}, title = {Tephritid-microbial interactions to enhance fruit fly performance in sterile insect technique programs.}, journal = {BMC microbiology}, volume = {19}, number = {Suppl 1}, pages = {287}, pmid = {31870316}, issn = {1471-2180}, mesh = {Animals ; *Bacterial Physiological Phenomena ; Domestication ; Female ; Gastrointestinal Microbiome ; Insect Control ; Male ; Pest Control, Biological ; Sexual Behavior, Animal/*physiology ; Tephritidae/microbiology/*physiology ; }, abstract = {BACKGROUND: The Sterile Insect Technique (SIT) is being applied for the management of economically important pest fruit flies (Diptera: Tephritidae) in a number of countries worldwide. The success and cost effectiveness of SIT depends upon the ability of mass-reared sterilized male insects to successfully copulate with conspecific wild fertile females when released in the field.<br><br>METHODS: We conducted a critical analysis of the literature about the tephritid gut microbiome including the advancement of methods for the identification and characterization of microbiota, particularly next generation sequencing, the impacts of irradiation (to induce sterility of flies) and fruit fly rearing, and the use of probiotics to manipulate the fruit fly gut microbiota.<br><br>RESULTS: Domestication, mass-rearing, irradiation and handling, as required in SIT, may change the structure of the fruit flies' gut microbial community compared to that of wild flies under field conditions. Gut microbiota of tephritids are important in their hosts' development, performance and physiology. Knowledge of how mass-rearing and associated changes of the microbial community impact the functional role of the bacteria and host biology is limited. Probiotics offer potential to encourage a gut microbial community that limits pathogens, and improves the quality of fruit flies.<br><br>CONCLUSIONS: Advances in technologies used to identify and characterize the gut microbiota will continue to expand our understanding of tephritid gut microbial diversity and community composition. Knowledge about the functions of gut microbes will increase through the use of gnotobiotic models, genome sequencing, metagenomics, metatranscriptomics, metabolomics and metaproteomics. The use of probiotics, or manipulation of the gut microbiota, offers significant opportunities to enhance the production of high quality, performing fruit flies in operational SIT programs.}, }
@article {pmid31866425, year = {2020}, author = {Liu, Q and Liu, Q and Meng, H and Lv, H and Liu, Y and Liu, J and Wang, H and He, L and Qin, J and Wang, Y and Dai, Y and Otto, M and Li, M}, title = {Staphylococcus epidermidis Contributes to Healthy Maturation of the Nasal Microbiome by Stimulating Antimicrobial Peptide Production.}, journal = {Cell host &amp; microbe}, volume = {27}, number = {1}, pages = {68-78.e5}, doi = {10.1016/j.chom.2019.11.003}, pmid = {31866425}, issn = {1934-6069}, support = {ZIA AI000904/AI/NIAID NIH HHS/United States ; }, mesh = {Adult ; Aged, 80 and over ; Antimicrobial Cationic Peptides/*biosynthesis ; Biofilms/growth &amp; development ; Cell Line ; Child ; Child, Preschool ; Epidermal Cells ; Female ; High-Throughput Nucleotide Sequencing ; Host Microbial Interactions ; Humans ; Immunity, Innate ; Male ; Metagenomics ; Microbiota/*immunology ; Nasal Cavity/*microbiology ; RNA, Ribosomal, 16S ; *Staphylococcus epidermidis/isolation &amp; purification/metabolism ; Symbiosis ; Young Adult ; }, abstract = {The composition of the human microbiome profoundly impacts human well-being. However, the mechanisms underlying microbiome maturation are poorly understood. The nasal microbiome is of particular importance as a source of many respiratory infections. Here, we performed a large sequencing and culture-based analysis of the human nasal microbiota from different age groups. We observed a significant decline of pathogenic bacteria before adulthood, with an increase of the commensal Staphylococcus epidermidis. In seniors, this effect was partially reversed. In vitro, many S. epidermidis isolates stimulated nasal epithelia to produce antimicrobial peptides, killing pathogenic competitors, while S. epidermidis itself proved highly resistant owing to its exceptional capacity to form biofilms. Furthermore, S. epidermidis isolates with high antimicrobial peptide-inducing and biofilm-forming capacities outcompeted pathogenic bacteria during nasal colonization in vivo. Our study identifies a pivotal role of S. epidermidis in healthy maturation of the nasal microbiome, which is achieved at least in part by symbiotic cooperation with innate host defense.}, }
@article {pmid31863999, year = {2020}, 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}, mesh = {Bacteria ; Biodiversity ; *Lakes ; *Metagenomics ; Nitrification ; Phylogeny ; }, 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}, pmid = {31856722}, issn = {1471-2180}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/classification/*isolation &amp; purification ; Disease Reservoirs/*microbiology ; *Equipment Contamination ; *Housing ; Metagenome ; Microbial Consortia ; Microbial Sensitivity Tests ; *Rubber ; *Water Microbiology ; }, 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 {pmid31855786, year = {2020}, author = {Moreno-Mesonero, L and Hortelano, I and Moreno, Y and Ferrús, MA}, title = {Evidence of viable Helicobacter pylori and other bacteria of public health interest associated with free-living amoebae in lettuce samples by next generation sequencing and other molecular techniques.}, journal = {International journal of food microbiology}, volume = {318}, number = {}, pages = {108477}, doi = {10.1016/j.ijfoodmicro.2019.108477}, pmid = {31855786}, issn = {1879-3460}, mesh = {Amoeba/*microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Food Microbiology ; Food Parasitology ; Helicobacter pylori/genetics/*isolation &amp; purification ; Humans ; Lettuce/*microbiology/*parasitology ; Microbiota/genetics ; Public Health ; Real-Time Polymerase Chain Reaction ; }, abstract = {Vegetables are one of the sources from which Helicobacter pylori can be acquired. This bacterium infects >50% of the global population and is a recognized type I human carcinogen. H. pylori enters into the viable but non-culturable state when it is in the environment, and therefore the use of molecular techniques is much convenient for its detection. Free-living amoebae (FLA) are protozoans found in vegetables. They are transmission vehicles for amoeba-resistant bacteria, among which H. pylori is included. The aim of this study is to study the occurrence and viability of H. pylori from lettuce samples, H. pylori internalized into FLA and the microbiome of FLA isolated from these samples. Special focus was pointed to human pathogenic bacteria. H. pylori was not directly detected in any lettuce sample by means of molecular techniques and neither by culture. However, intra-amoebic H. pylori DNA was detected by means of PMA-qPCR in 55% of the samples and viable intra-amoebic H. pylori cells in 25% of the samples by means of DVC-FISH technique. When FLA microbiome was studied, 21 bacterial genera were part of FLA microbiome in all samples. Helicobacter genus was detected as part of the FLA microbiome in two samples. Other bacteria of public health interest such as Aeromonas sp., Arcobacter sp., Legionella sp., Mycobacterium sp., Pseudomonas sp. and Salmonella sp. were detected as part of FLA microbiome along the analysed samples. This study demonstrates for the first time that H. pylori is internalized as well as alive inside FLA isolated from vegetables. Moreover, this study shows that FLA promote H. pylori detection in environmental samples. In addition, as far as we are aware, this is the first study which studies the microbiome of FLA isolated from vegetables. Among the FLA microbiome, bacteria of public health interest were detected, pointing out that FLA are carriers of these pathogens which can reach humans and cause a public health concern.}, }
@article {pmid31855753, year = {2020}, author = {Wang, L and Yin, Z and Jing, C}, title = {Metagenomic insights into microbial arsenic metabolism in shallow groundwater of Datong basin, China.}, journal = {Chemosphere}, volume = {245}, number = {}, pages = {125603}, doi = {10.1016/j.chemosphere.2019.125603}, pmid = {31855753}, issn = {1879-1298}, mesh = {Arsenic/*metabolism ; Carbon/analysis ; China ; Groundwater/*microbiology ; Metagenome/genetics ; Metagenomics/*methods ; Microbiota/genetics ; Oxidation-Reduction ; Sulfates/analysis ; Temperature ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Elevated arsenic (As) in groundwater is an urgent environmental problem that has caused serious endemic diseases in Datong basin, China. The fate and toxicity of As are generally regulated by microbial As metabolic processes. However, little is known about the microbial community and As metabolism in Datong basin. Herein, the microbial community structure and As metabolism genes in four wells with different levels of As concentration in Shanyin county were investigated using metagenomics approach. The results showed that the presence of As influenced the microbial communities, and Rhodococcus genus was significantly enriched in elevated As wells. As resistance genes were dominant from low to high As containing wells, and As efflux genes such as arsB and acr3 were positively correlated with As concentrations, suggesting that microbes tend to pump As out of the cell as a strategy for As detoxification. Other environmental factors including oxidation-reduction potential (ORP), total organic carbon (TOC), sulfate, and temperature also played a role in shaping the microbial community structure and As metabolic processes.}, }
@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 {pmid31852805, year = {2019}, author = {Engel, K and Ford, SE and Coyotzi, S and McKelvie, J and Diomidis, N and Slater, G and Neufeld, JD}, title = {Stability of Microbial Community Profiles Associated with Compacted Bentonite from the Grimsel Underground Research Laboratory.}, journal = {mSphere}, volume = {4}, number = {6}, pages = {}, pmid = {31852805}, issn = {2379-5042}, mesh = {Bacteria/chemistry/*classification/genetics ; *Bentonite ; Cluster Analysis ; Cytosol/chemistry ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Environmental Microbiology ; Fatty Acids/analysis ; Metagenomics ; *Microbiota ; Phospholipids/analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Switzerland ; }, abstract = {To assess the microbiology and corrosion potential of engineered components of a deep geological repository for long-term storage of high-level nuclear waste, the Materials Corrosion Test is being conducted at the Underground Research Laboratory in Grimsel, Switzerland. Modules containing metal coupons surrounded by highly compacted MX-80 bentonite, at two dry densities (1.25 and 1.50 g/cm3), were emplaced within 9-m-deep boreholes, and the first modules were retrieved after 13 months of exposure. Bentonite and associated module materials were sampled, and microbial communities and their distributions were assessed using 16S rRNA gene sequencing and phospholipid fatty acid (PLFA) analysis. Borehole fluid was dominated by amplicon sequence variants (ASVs) affiliated with Desulfosporosinus and Desulfovibrio, which are putatively involved in sulfate reduction. The relative abundance of these ASVs was lower for samples from inside the borehole module, and they were almost undetectable in samples of the inner bentonite layer. The dominant ASV in case and filter sample sequence data was affiliated with Pseudomonas stutzeri, yet its relative abundance decreased in the inner layer samples. Streptomyces sp. ASVs were relatively abundant in all bentonite core sample data both prior to emplacement and after 13 months of exposure, presumably as metabolically inactive spores or extracellular &quot;relic&quot; DNA. PLFA concentrations in outer and inner layer bentonite samples suggested cellular abundances of 1 × 106 to 3 × 106 cells/g, with similar PLFA distributions within all bentonite samples. Our results demonstrate consistent microbial communities inside the saturated borehole module, providing the first evidence for microbial stability under conditions that mimic a deep geological repository.IMPORTANCE The Materials Corrosion Test in Grimsel Underground Research Laboratory, Switzerland, enables an evaluation of microbiological implications of bentonite clay at densities relevant for a deep geological repository. Our research demonstrates that after 13 months of exposure within a granitic host rock, the microbial 16S rRNA gene signatures of saturated bentonite clay within the modules were consistent with the profiles in the original clay used to pack the modules. Such results provide evidence that densities chosen for this emplacement test are refractory to microbial activity, at least on the relatively short time frame leading to the first time point sampling event, which will help inform in situ engineered barrier system science. This study has important implications for the design of deep geological repository sites under consideration for the Canadian Shield.}, }
@article {pmid31852462, year = {2019}, author = {Zhang, X and Browman, G and Siu, W and Basen-Engquist, KM and Hanash, SM and Hoffman, KL and Okhuysen, PC and Scheet, P and Petrosino, JF and Kopetz, S and Daniel, CR}, title = {The BE GONE trial study protocol: a randomized crossover dietary intervention of dry beans targeting the gut microbiome of overweight and obese patients with a history of colorectal polyps or cancer.}, journal = {BMC cancer}, volume = {19}, number = {1}, pages = {1233}, pmid = {31852462}, issn = {1471-2407}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; Institutional Research Grant//University of Texas MD Anderson Cancer Center/ ; 5P30 CA016672-37/CA/NCI NIH HHS/United States ; RSG-17-049-01-NEC//American Cancer Society/ ; RP160097//Cancer Prevention and Research Institute of Texas/ ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Colonic Neoplasms/*diet therapy/microbiology/pathology/prevention &amp; control ; Colonic Polyps/*diet therapy/microbiology/pathology/prevention &amp; control ; Cross-Over Studies ; Female ; *Gastrointestinal Microbiome ; Humans ; Life Style ; Male ; Middle Aged ; Obesity/microbiology/*physiopathology ; Overweight/microbiology/*physiopathology ; Progression-Free Survival ; Risk Factors ; }, abstract = {BACKGROUND: Mouse and human studies support the promise of dry beans to improve metabolic health and to lower cancer risk. In overweight/obese patients with a history of colorectal polyps or cancer, the Beans to Enrich the Gut microbiome vs. Obesity's Negative Effects (BE GONE) trial will test whether and how an increase in the consumption of pre-cooked, canned dry beans within the context of usual diet and lifestyle can enhance the gut landscape to improve metabolic health and reduce cancer risk.<br><br>METHODS/DESIGN: This randomized crossover trial is designed to characterize changes in (1) host markers spanning lipid metabolism, inflammation, and obesity-related cancer risk; (2) compositional and functional profiles of the fecal microbiome; and (3) host and microbial metabolites. With each subject serving as their own control, the trial will compare the participant's usual diet with (intervention) and without (control) dry beans. Canned, pre-cooked dry beans are provided to participants and the usual diet continually assessed and monitored. Following a 4-week run-in and equilibration period, each participant provides a total of 5 fasting blood and 6 stool samples over a total period of 16 weeks. The intervention consists of a 2-week ramp-up of dry bean intake to 1 cup/d, which is then continued for an additional 6 weeks. Intra- and inter-individual outcomes are assessed across each crossover period with consideration of the joint or modifying effects of the usual diet and baseline microbiome.<br><br>DISCUSSION: The BE GONE trial is evaluating a scalable dietary prevention strategy targeting the gut microbiome of high-risk patients to mitigate the metabolic and inflammatory effects of adiposity that influence colorectal cancer risk, recurrence, and survival. The overarching scientific goal is to further elucidate interactions between diet, the gut microbiome, and host metabolism. Improved understanding of the diet-microbiota interplay and effective means to target these relationships will be key to the future of clinical and public health approaches to cancer and other major diet- and obesity-related diseases.<br><br>TRIAL REGISTRATION: This protocol is registered with the U.S. National Institutes of Health trial registry, ClinicalTrials.gov, under the identifier NCT02843425. First posted July 25, 2016; last verified January 25, 2019.}, }
@article {pmid31850241, year = {2019}, author = {Wang, J and Gu, X and Yang, J and Wei, Y and Zhao, Y}, title = {Gut Microbiota Dysbiosis and Increased Plasma LPS and TMAO Levels in Patients With Preeclampsia.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {409}, pmid = {31850241}, issn = {2235-2988}, mesh = {Adult ; Biomarkers ; Case-Control Studies ; *Dysbiosis ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Lipopolysaccharides/*blood ; Metagenome ; Metagenomics/methods ; Methylamines/*blood ; Pre-Eclampsia/*blood/*etiology ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Objective: To characterize the gut microbiota in patients with preeclampsia (PE) compared with healthy controls. Methods: We analyzed and compared the microbiota communities in the feces of 48 PE patients with 48 age-, gestational weeks-, and pre-pregnancy body mass index-matched healthy controls using 16S rRNA gene sequencing, and also we tested fecal and plasma lipopolysaccharide (LPS) and plasma trimethylamine-N-oxide (TMAO) concentration levels in the two groups. Results: Compared with the control group, microbial alpha diversity was lower in the PE group, but there was no statistically significant difference between the two groups. At the phylum level, Firmicutes (51.64% PE vs. 59.62% Control, P < 0.05), Bacteroidetes (40.51% PE vs. 34.81% Control, P< 0.05), Proteobacteria (4.51% PE vs. 2.56% Control, P < 0.05), and Actinobacteria (2.90% PE vs. 1.77% Control, P < 0.05), exhibited significant differences between the PE group and the control group. LEfSe analysis found 17 differentially abundant taxa between the two groups. PICRUSt analysis found that in the KEGG pathways, the microbial gene functions related to LPS biosynthesis were higher in the fecal microbiome of the PE group. The fecal and plasma LPS concentrations and plasma TMAO concentrations of PE patients were higher than those of the healthy controls. Conclusion: PE patients had gut microbiota dysbiosis and increased plasma LPS and TMAO levels, which will lead to a better understanding of the relationship between the gut microbiota and PE.}, }
@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}, 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 {pmid31848793, year = {2020}, author = {Firmino, FC and Porcellato, D and Cox, M and Suen, G and Broadbent, JR and Steele, JL}, title = {Characterization of microbial communities in ethanol biorefineries.}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {47}, number = {2}, pages = {183-195}, pmid = {31848793}, issn = {1476-5535}, mesh = {Bioreactors ; Ethanol/*metabolism ; Fermentation ; Firmicutes/genetics/metabolism ; Lactobacillus/genetics/metabolism ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Bacterial contamination of corn-based ethanol biorefineries can reduce their efficiency and hence increase their carbon footprint. To enhance our understanding of these bacterial contaminants, we temporally sampled four biorefineries in the Midwestern USA that suffered from chronic contamination and characterized their microbiomes using both 16S rRNA sequencing and shotgun metagenomics. These microbiotas were determined to be relatively simple, with 13 operational taxonomic units (OTUs) accounting for 90% of the bacterial population. They were dominated by Firmicutes (89%), with Lactobacillus comprising 80% of the OTUs from this phylum. Shotgun metagenomics confirmed our 16S rRNA data and allowed us to characterize bacterial succession at the species level, with the results of this analysis being that Lb. helveticus was the dominant contaminant in this fermentation. Taken together, these results provide insights into the microbiome of ethanol biorefineries and identifies a species likely to be commonly responsible for chronic contamination of these facilities.}, }
@article {pmid31844663, year = {2019}, author = {Olm, MR and Bhattacharya, N and Crits-Christoph, A and Firek, BA and Baker, R and Song, YS and Morowitz, MJ and Banfield, JF}, title = {Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria.}, journal = {Science advances}, volume = {5}, number = {12}, pages = {eaax5727}, pmid = {31844663}, issn = {2375-2548}, support = {R01 AI092531/AI/NIAID NIH HHS/United States ; R01 GM109454/GM/NIGMS NIH HHS/United States ; S10 OD018174/OD/NIH HHS/United States ; }, mesh = {Enterobacteriaceae/genetics ; Enterocolitis, Necrotizing/*genetics/microbiology ; Feces/microbiology ; Fimbriae, Bacterial/*genetics/microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; Infant, Newborn ; Infant, Premature ; Infant, Premature, Diseases/genetics/microbiology ; Klebsiella/genetics ; *Metagenomics ; Multigene Family/genetics ; }, abstract = {Necrotizing enterocolitis (NEC) is a devastating intestinal disease that occurs primarily in premature infants. We performed genome-resolved metagenomic analysis of 1163 fecal samples from premature infants to identify microbial features predictive of NEC. Features considered include genes, bacterial strain types, eukaryotes, bacteriophages, plasmids, and growth rates. A machine learning classifier found that samples collected before NEC diagnosis harbored significantly more Klebsiella, bacteria encoding fimbriae, and bacteria encoding secondary metabolite gene clusters related to quorum sensing and bacteriocin production. Notably, replication rates of all bacteria, especially Enterobacteriaceae, were significantly higher 2 days before NEC diagnosis. The findings uncover biomarkers that could lead to early detection of NEC and targets for microbiome-based therapeutics.}, }
@article {pmid31843867, year = {2020}, author = {Schlaberg, R}, title = {Microbiome Diagnostics.}, journal = {Clinical chemistry}, volume = {66}, number = {1}, pages = {68-76}, doi = {10.1373/clinchem.2019.303248}, pmid = {31843867}, issn = {1530-8561}, mesh = {Bacteria/genetics/isolation &amp; purification ; Drug Resistance/genetics ; Fungi/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/*methods/standards ; Microbiota/*genetics ; Mitochondria/genetics ; Quality Control ; RNA, Ribosomal, 16S/chemistry/metabolism ; }, abstract = {BACKGROUND: During the past decade, breakthroughs in sequencing technology and computational biology have provided the basis for studies of the myriad ways in which microbial communities (&quot;microbiota&quot;) in and on the human body influence human health and disease. In almost every medical specialty, there is now a growing interest in accurate and replicable profiling of the microbiota for use in diagnostic and therapeutic application.<br><br>CONTENT: This review provides an overview of approaches, challenges, and considerations for diagnostic applications borrowing from other areas of molecular diagnostics, including clinical metagenomics. Methodological considerations and evolving approaches for microbiota profiling from mitochondrially encoded 16S rRNA-based amplicon sequencing to metagenomics and metatranscriptomics are discussed. To improve replicability, at least the most vulnerable steps in testing workflows will need to be standardized and continuous efforts needed to define QC standards. Challenges such as purity of reagents and consumables, improvement of reference databases, and availability of diagnostic-grade data analysis solutions will require joint efforts across disciplines and with manufacturers.<br><br>SUMMARY: The body of literature supporting important links between the microbiota at different anatomic sites with human health and disease is expanding rapidly and therapeutic manipulation of the intestinal microbiota is becoming routine. The next decade will likely see implementation of microbiome diagnostics in diagnostic laboratories to fully capitalize on technological and scientific advances and apply them in routine medical practice.}, }
@article {pmid31837260, year = {2019}, author = {Duan, J and Yin, B and Li, W and Chai, T and Liang, W and Huang, Y and Tan, X and Zheng, P and Wu, J and Li, Y and Li, Y and Zhou, W and Xie, P}, title = {Age-related changes in microbial composition and function in cynomolgus macaques.}, journal = {Aging}, volume = {11}, number = {24}, pages = {12080-12096}, pmid = {31837260}, issn = {1945-4589}, mesh = {Aging/*physiology ; Amino Acids/metabolism ; Animals ; Bacteria/*classification/enzymology/genetics ; Carbohydrates/chemistry ; Female ; *Gastrointestinal Microbiome ; Macaca fascicularis/*microbiology ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Age can significantly affect human physiology and disease risk. Recent studies have shown that age may affect the composition and function of the gut microbiota, but the underlying mechanisms remain largely unknown. Non-human primates are an ideal model for uncovering how age shapes the gut microbiota, as their microbial composition is highly similar to that of humans and is not easily affected by confounding factors. Here, using the 16S rRNA and metagenomic sequencing methods, we characterized the microbial phenotypes of 16 female cynomolgus macaques from three age groups (young, adult and old). Our findings revealed significant differences in microbial composition among the three groups. With increased age, the relative abundances of Veillonellaceae, Coriobacteriaceae and Succinivibrionaceae were significantly increased, Ruminococcaceae and Rikenellaceae were significantly decreased at the family level. Functional enrichment showed that genes that differed among the three groups were mainly involved in arginine biosynthesis, purine metabolism and microbial polysaccharides metabolism. Moreover, CAZymes corresponding to polysaccharide degrading activities were also observed among the three groups. In conclusion, we characterized the composition and function of the gut microbiota at different ages, and our findings provide a new entry point for understanding the effects of age on the human body.}, }
@article {pmid31836758, year = {2019}, author = {Ting, CH and Pan, CY and Chen, YC and Lin, YC and Chen, TY and Rajanbabu, V and Chen, JY}, title = {Impact of Tilapia hepcidin 2-3 dietary supplementation on the gut microbiota profile and immunomodulation in the grouper (Epinephelus lanceolatus).}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {19047}, pmid = {31836758}, issn = {2045-2322}, mesh = {Animal Feed ; Animals ; Anti-Infective Agents/pharmacology ; Bacteria/drug effects ; Bass/genetics/growth &amp; development/*immunology/*microbiology ; *Dietary Supplements ; Feeding Behavior/drug effects ; Fermentation ; Gastrointestinal Microbiome/*drug effects ; Gene Expression Regulation/drug effects ; Hepcidins/*pharmacology ; Immunomodulation/*drug effects ; Metagenomics ; Microbial Sensitivity Tests ; Protein Stability/drug effects ; Recombinant Proteins/metabolism ; Spleen/metabolism ; Temperature ; Tilapia/*metabolism ; }, abstract = {Hepcidin regulates iron homeostasis and host-defense mechanisms, while the hepcidin-like protein, Tilapia hepcidin (TH)2-3, functions as an antimicrobial peptide (AMP). Since AMP dietary supplements may be used as alternatives to antibiotics in livestock, we tested the effects of recombinant (r)TH2-3 as a dietary supplement in grouper aquaculture. rTH2-3 was produced by a Pichia pastoris expression system and exhibited thermostability and broad-spectrum antimicrobial activity. The feed conversion ratio and feed efficiency were determined in Epinephelus lanceolatus (grouper) fed with rTH2-3-supplemented diet for 28 days. In addition, grouper showed enhanced superoxide dismutase (SOD) activity after rTH2-3 feeding compared to regular-diet-fed fish. Gut microbiota analysis revealed that microbial diversity was enhanced by feeding grouper with 1% rTH2-3. After challenging grouper with Vibrio alginolyticus, differential regulation of immune-related genes in the liver and spleen was observed between the TH2-3 and regular-diet groups, including for genes associated with antimicrobial and pro-inflammatory functions, complement components, and major histocompatibility complex (Mhc). These findings suggest that overall immunity was improved. Thus, our results suggest long-term supplementation with rTH2-3 may be beneficial for aquacultured grouper. The beneficial effects of the supplement are likely based on changes in the commensal microbial community as well as immunomodulation.}, }
@article {pmid31836579, year = {2020}, author = {Ouyang, Y and Norton, JM}, title = {Short-Term Nitrogen Fertilization Affects Microbial Community Composition and Nitrogen Mineralization Functions in an Agricultural Soil.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {5}, pages = {}, pmid = {31836579}, issn = {1098-5336}, mesh = {Agriculture ; *Fertilizers ; *Microbiota ; Nitrogen/administration &amp; dosage/*metabolism ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Soil/*chemistry ; *Soil Microbiology ; Utah ; }, abstract = {Soil extracellular enzymes play a significant role in the N mineralization process. However, few studies have documented the linkage between enzyme activity and the microbial community that performs the function. This study examined the effects of inorganic and organic N fertilization on soil microbial communities and their N mineralization functions over 4 years. Soils were collected from silage corn field plots with four contrasting N treatments: control (no additional N), ammonium sulfate (AS; 100 and 200 kg of N ha-1), and compost (200 kg of N ha-1). Illumina amplicon sequencing was used to comprehensively assess the overall bacterial community (16S rRNA genes), bacterial ureolytic community (ureC), and bacterial chitinolytic community (chiA). Selected genes involved in N mineralization were also examined using quantitative real-time PCR and metagenomics. Enzymes (and marker genes) included protease (npr and sub), chitinase (chiA), urease (ureC), and arginase (rocF). Compost significantly increased diversity of overall bacterial communities even after one application, while ammonium fertilizers had no influence on the overall bacterial communities over four seasons. Bacterial ureolytic and chitinolytic communities were significantly changed by N fertilization. Compost treatment strongly elevated soil enzyme activities after 4 years of repeated application. Functional gene abundances were not significantly affected by N treatments, and they were not correlated with corresponding enzyme activities. N mineralization genes were recovered from soil metagenomes based on a gene-targeted assembly. Understanding how the structure and function of soil microbial communities involved with N mineralization change in response to fertilization practices may indicate suitable agricultural management practices that improve ecosystem services while reducing negative environmental consequences.IMPORTANCE Agricultural N management practices influence the enzymatic activities involved in N mineralization. However, specific enzyme activities do not identify the microbial species directly involved in the measured process, leaving the link between the composition of the microbial community and the production of key enzymes poorly understood. In this study, the application of high-throughput sequencing, real-time PCR, and metagenomics shed light on how the abundance and diversity of microorganisms involved in N mineralization respond to N management. We suggest that N fertilization has significantly changed bacterial ureolytic and chitinolytic communities.}, }
@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 = {}, pmid = {31835740}, issn = {1999-4915}, mesh = {Animals ; Birds/*virology ; Circoviridae Infections/*veterinary ; Computational Biology/methods ; French Guiana ; *Genome, Viral ; *Genomics/methods ; Gyrovirus/*classification/*genetics ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Phylogeny ; Prevalence ; *Rainforest ; }, 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 {pmid31835036, year = {2019}, author = {Pachiadaki, MG and Brown, JM and Brown, J and Bezuidt, O and Berube, PM and Biller, SJ and Poulton, NJ and Burkart, MD and La Clair, JJ and Chisholm, SW and Stepanauskas, R}, title = {Charting the Complexity of the Marine Microbiome through Single-Cell Genomics.}, journal = {Cell}, volume = {179}, number = {7}, pages = {1623-1635.e11}, doi = {10.1016/j.cell.2019.11.017}, pmid = {31835036}, issn = {1097-4172}, support = {R21 AI134037/AI/NIAID NIH HHS/United States ; }, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; Energy Metabolism ; *Metagenome ; Metagenomics/methods ; *Microbiota ; Phylogeography ; Plankton ; Seawater/*microbiology ; Single-Cell Analysis/methods ; Transcriptome ; }, abstract = {Marine bacteria and archaea play key roles in global biogeochemistry. To improve our understanding of this complex microbiome, we employed single-cell genomics and a randomized, hypothesis-agnostic cell selection strategy to recover 12,715 partial genomes from the tropical and subtropical euphotic ocean. A substantial fraction of known prokaryoplankton coding potential was recovered from a single, 0.4 mL ocean sample, which indicates that genomic information disperses effectively across the globe. Yet, we found each genome to be unique, implying limited clonality within prokaryoplankton populations. Light harvesting and secondary metabolite biosynthetic pathways were numerous across lineages, highlighting the value of single-cell genomics to advance the identification of ecological roles and biotechnology potential of uncultured microbial groups. This genome collection enabled functional annotation and genus-level taxonomic assignments for >80% of individual metagenome reads from the tropical and subtropical surface ocean, thus offering a model to improve reference genome databases for complex microbiomes.}, }
@article {pmid31832698, year = {2020}, author = {Huang, CL and Sarkar, R and Hsu, TW and Yang, CF and Chien, CH and Chang, WC and Chiang, TY}, title = {Endophytic Microbiome of Biofuel Plant Miscanthus sinensis (Poaceae) Interacts with Environmental Gradients.}, journal = {Microbial ecology}, volume = {80}, number = {1}, pages = {133-144}, doi = {10.1007/s00248-019-01467-8}, pmid = {31832698}, issn = {1432-184X}, support = {106-2621-B-006-001-MY3//Ministry of Science and Technology, Taiwan/ ; }, mesh = {Bacteria/classification/*isolation &amp; purification ; Biofuels ; Ecosystem ; *Ecotype ; *Endophytes ; Metagenomics ; *Microbiota ; Poaceae/*microbiology ; *Rhizosphere ; }, abstract = {Miscanthus in Taiwan occupies a cline along altitude and adapts to diverse environments, e.g., habitats of high salinity and volcanoes. Rhizospheric and endophytic bacteria may help Miscanthus acclimate to those stresses. The relative contributions of rhizosphere vs. endosphere compartments to the adaptation remain unknown. Here, we used targeted metagenomics to compare the microbial communities in the rhizosphere and endosphere among ecotypes of M. sinensis that dwell habitats under different stresses. Proteobacteria and Actinobacteria predominated in the endosphere. Diverse phyla constituted the rhizosphere microbiome, including a core microbiome found consistently across habitats. In endosphere, the predominance of the bacteria colonizing from the surrounding soil suggests that soil recruitment must have subsequently determined the endophytic microbiome in Miscanthus roots. In endosphere, the bacterial diversity decreased with the altitude, likely corresponding to rising limitation to microorganisms according to the species-energy theory. Specific endophytes were associated with different environmental stresses, e.g., Pseudomonas spp. for alpine and Agrobacterium spp. for coastal habitats. This suggests Miscanthus actively recruits an endosphere microbiome from the rhizosphere it influences.}, }
@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 {pmid31830070, year = {2019}, author = {Khilyas, IV and Sorokina, AV and Elistratova, AA and Markelova, MI and Siniagina, MN and Sharipova, MR and Shcherbakova, TA and D'Errico, ME and Cohen, MF}, title = {Microbial diversity and mineral composition of weathered serpentine rock of the Khalilovsky massif.}, journal = {PloS one}, volume = {14}, number = {12}, pages = {e0225929}, pmid = {31830070}, issn = {1932-6203}, mesh = {Asbestos, Serpentine/*analysis ; Biodiversity ; Computational Biology/methods ; Geologic Sediments/*chemistry/*microbiology ; Metagenome ; Metagenomics/methods ; *Microbiota ; Minerals/*analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Russia ; *Soil Microbiology ; Spectrum Analysis ; }, abstract = {Endolithic microbial communities survive nutrient and energy deficient conditions while contributing to the weathering of their mineral substrate. This study examined the mineral composition and microbial communities of fully serpentinized weathered rock from 0.1 to 6.5 m depth at a site within the Khalilovsky massif, Orenburg Region, Southern Ural Mountains, Russia. The mineral composition includes a major content of serpentinite family (mostly consisting of lizardite and chrysotile), magnesium hydrocarbonates (hydromagnesite with lesser amounts of hydrotalcite and pyroaurite) concentrated in the upper layers, and clay minerals. We found that the deep-seated weathered serpentinites are chrysotile-type minerals, while the middle and surface serpentinites mostly consist of lizardite and chrysotile types. Microbial community analysis, based on 16S rRNA gene sequencing, showed a similar diversity of phyla throughout the depth profile. The dominant bacterial phyla were the Actinobacteria (of which unclassified genera in the orders Acidimicrobiales and Actinomycetales were most numerous), Chloroflexi (dominated by an uncultured P2-11E order) and the Proteobacteria (predominantly class Betaproteobacteria). Densities of several groups of bacteria were negatively correlated with depth. Occurrence of the orders Actinomycetales, Gaiellales, Solirubrobacterales, Rhizobiales and Burkholderiales were positively correlated with depth. Our findings show that endolithic microbial communities of the Khalilovsky massif have similar diversity to those of serpentine soils and rocks, but are substantially different from those of the aqueous environments of actively serpentinizing systems.}, }
@article {pmid31830061, year = {2019}, author = {Masha, SC and Owuor, C and Ngoi, JM and Cools, P and Sanders, EJ and Vaneechoutte, M and Crucitti, T and de Villiers, EP}, title = {Comparative analysis of the vaginal microbiome of pregnant women with either Trichomonas vaginalis or Chlamydia trachomatis.}, journal = {PloS one}, volume = {14}, number = {12}, pages = {e0225545}, pmid = {31830061}, issn = {1932-6203}, mesh = {Adolescent ; Adult ; Chlamydia Infections/immunology/*microbiology ; Chlamydia trachomatis/genetics/immunology/isolation &amp; purification ; DNA, Bacterial/isolation &amp; purification ; Female ; Humans ; Microbiota/genetics/*immunology ; Pregnancy ; Pregnancy Complications, Infectious/immunology/*microbiology ; RNA, Ribosomal, 16S/genetics ; Trichomonas Vaginitis/immunology/*microbiology ; Trichomonas vaginalis/genetics/immunology/isolation &amp; purification ; Vagina/*microbiology ; Young Adult ; }, abstract = {BACKGROUND: Although the significance of the human vaginal microbiome for health and disease is increasingly acknowledged, there is paucity of data on the differences in the composition of the vaginal microbiome upon infection with different sexually transmitted pathogens.<br><br>METHOD: The composition of the vaginal bacterial community of women with Trichomonas vaginalis (TV, N = 18) was compared to that of women with Chlamydia trachomatis (CT, N = 14), and to that of controls (N = 21) (women negative for TV, CT and bacterial vaginosis). The vaginal bacterial composition was determined using high throughput sequencing with the Ion 16S metagenomics kit of the variable regions 2, 4 and 8 of the bacterial 16S ribosomal RNA gene from the vaginal swab DNA extract of the women. QIIME and R package &quot;Phyloseq&quot; were used to assess the α- and β-diversity and absolute abundance of the 16S rRNA gene per sample in the three groups. Differences in taxa at various levels were determined using the independent T-test.<br><br>RESULTS: A total of 545 operational taxonomic units (OTUs) were identified in all the three groups of which 488 occurred in all three groups (core OTUs). Bacterial α-diversity, by both Simpson's and Shannon's indices, was significantly higher, (p = 0.056) and (p = 0.001) respectively, among women with either TV or CT than among controls (mean α-diversity TV-infected > CT-infected > Controls). At the genus level, women infected with TV had a significantly (p < 0.01) higher abundance of Parvimonas and Prevotella species compared to both controls and CT-infected women, whereas women infected with CT had a significantly (p < 0.05) higher abundance of Anaerococcus, Collinsella, Corynebacterium and Dialister.<br><br>CONCLUSION: The vaginal microbiomes of TV and CT-infected women were markedly different from each other and from women without TV and CT. Future studies should determine whether the altered microbiomes are merely markers of disease, or whether they actively contribute to the pathology of the two genital infections.}, }
@article {pmid31828407, year = {2020}, author = {Paddock, MB and Fernández-Bayo, JD and VanderGheynst, JS}, title = {The effect of the microalgae-bacteria microbiome on wastewater treatment and biomass production.}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {2}, pages = {893-905}, doi = {10.1007/s00253-019-10246-x}, pmid = {31828407}, issn = {1432-0614}, support = {1438211//National Science Foundation/ ; ARV-15-008//California Energy Commission/ ; }, mesh = {Ammonium Compounds/analysis ; Bacteria/classification/*growth &amp; development/*metabolism ; Biological Oxygen Demand Analysis ; Bioreactors/microbiology ; Metagenomics ; Microalgae/classification/*growth &amp; development/*metabolism ; *Microbiota ; Nitrogen/analysis ; Waste Water/chemistry/*microbiology ; Water Pollutants/metabolism ; Water Purification/*methods ; }, abstract = {The use of microalgae for wastewater treatment has been proposed as a cost-effective method to produce biofuels while remediating waste streams. This study examined the microalgae biomass production rate, wastewater treatment efficiency, and prokaryotic organism microbiome associated with microalgae Chlorella sorokiniana cultivated on anaerobic digestate effluent. Final microalgae biomass concentrations from nine photobioreactors were highly variable and had values that ranged between 0.14 g/L and 0.90 g/L. Nutrient removal efficiencies for TN (total nitrogen), N-NH4 (ammonium nitrogen), and COD (chemical oxygen demand) ranged from 34% to 67%, 65% to 97%, and-60% to 14%, respectively. Analysis of individual OTUs (operational taxonomic units) from the microbial community revealed that microalgae biomass concentrations were significantly correlated with the relative abundance of OTUs in the genus Pusillimonas. Predictive metagenomic analyses identified additional correlations associated with biomass production and nutrient removal. These results suggest that the microbial community present during microalgae cultivation on wastewater can impact the performance of the system for biomass production and wastewater treatment.}, }
@article {pmid31828159, year = {2019}, author = {Nuli, R and Azhati, J and Cai, J and Kadeer, A and Zhang, B and Mohemaiti, P}, title = {Metagenomics and Faecal Metabolomics Integrative Analysis towards the Impaired Glucose Regulation and Type 2 Diabetes in Uyghur-Related Omics.}, journal = {Journal of diabetes research}, volume = {2019}, number = {}, pages = {2893041}, pmid = {31828159}, issn = {2314-6753}, mesh = {Actinobacteria ; Adult ; Bacteroides ; Case-Control Studies ; China/epidemiology ; Diabetes Mellitus, Type 2/epidemiology/metabolism/*microbiology ; Dysbiosis/epidemiology/metabolism/*microbiology ; Feces/chemistry/microbiology ; Female ; Firmicutes ; Gastrointestinal Microbiome/*genetics ; Glucose Intolerance/epidemiology/metabolism/*microbiology ; Humans ; Male ; *Metabolomics ; *Metagenomics ; Middle Aged ; }, abstract = {Objective: Gut microbiota and their metabolites play an important role in the development of type 2 diabetes mellitus (T2DM). This research was designed to study the relationship between gut microbiota and faecal metabolites of Uyghur newly onset T2DM and impaired glucose regulation (IGR) patients.<br><br>Materials and Methods: A total of 60 different glycemic Uyghur subjects were enrolled and divided into T2DM, IGR, and normal glucose tolerance (NGT) groups. Metagenomics and LC-MS-based untargeted faecal metabolomics were employed. Correlations between bacterial composition and faecal metabolomics were evaluated.<br><br>Results: We discovered that the composition and diversity of gut microbiota in newly onset T2DM and IGR were different from those in NGT. The α-diversity was higher in NGT than in T2DM and IGR; β-diversity analysis revealed apparent differences in the bacterial community structures between patients with T2DM, IGR, and NGT. LC-MS faecal metabolomics analysis discovered different metabolomics features in the three groups. Alchornoic acid, PE (14 : 0/20 : 3), PI, L-tyrosine, LysoPC (15 : 0), protorifamycin I, pimelic acid, epothilone A, 7-dehydro-desmosterol, L-lysine, LysoPC (14 : 1), and teasterone are the most significant differential enriched metabolites. Most of the differential enriched metabolites were involved in metabolic processes, including carbohydrate metabolism, starch and sucrose metabolism, phenylpropanoid biosynthesis, and biosynthesis of amino acids. Procrustes analysis and correlation analysis identified correlations between gut microbiota and faecal metabolites. Matricin was positively correlated with Bacteroides and negatively correlated with Actinobacteria; protorifamycin I was negatively correlated with Actinobacteria; epothilone A was negatively correlated with Actinobacteria and positively correlated with Firmicutes; PA was positively correlated with Bacteroides and negatively correlated with Firmicutes; and cristacarpin was positively correlated with Actinobacteria; however, this correlation relationship does not imply causality.<br><br>Conclusions: This study used joint metagenomics and metabolomics analyses to elucidate the relationship between gut microbiota and faecal metabolites in different glycemic groups, and the result suggested that metabolic disorders and gut microbiota dysbiosis occurred in Uyghur T2DM and IGR. The results provide a theoretical basis for studying the pathological mechanism for further research.}, }
@article {pmid31826972, year = {2019}, author = {Pierce, ML and Ward, JE}, title = {Gut Microbiomes of the Eastern Oyster (Crassostrea virginica) and the Blue Mussel (Mytilus edulis): Temporal Variation and the Influence of Marine Aggregate-Associated Microbial Communities.}, journal = {mSphere}, volume = {4}, number = {6}, pages = {}, pmid = {31826972}, issn = {2379-5042}, mesh = {Animals ; Bacteria/*classification/genetics ; Cluster Analysis ; Connecticut ; Crassostrea/*microbiology ; DNA, Ribosomal/chemistry/genetics ; *Gastrointestinal Microbiome ; Metagenomics ; Mytilus edulis/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seasons ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Gut microbial community structure was evaluated for two species of bivalve molluscs, the eastern oyster (Crassostrea virginica) and the blue mussel (Mytilus edulis) collected from Long Island Sound, Connecticut, over the course of a year. These bivalves utilize a shared feeding mechanism, which may result in similar gut microbial communities. Their particle diet, marine aggregates, and surrounding environment, aggregate-free seawater (AFSW), were also collected for comparison. Due to the suspension-feeding activities of bivalves, the potential for aggregate- and AFSW-associated microbiota to influence their microbial communities may be significant. Both taxonomic and functional diversity of the samples were assessed. 16S rRNA gene amplicon sequencing indicated that oysters and mussels maintained similar, but not identical, gut microbiomes, with some temporal variation. Throughout the year, bivalve species had gut microbial community compositions that were more similar to one another than to aggregates. Within a month, bivalves shared on average a quarter of their total operational taxonomic units (OTUs) with each other and a 10th of their total OTUs with aggregates. During months with warm water temperatures, individuals within each of the four sample types had similar alpha diversity, but again, temporal variation was observed. On a functional level, bivalve gut microbial communities exhibited variation attributed to host species and season. Unlike oysters, mussel gut bacterial communities maintained high richness and evenness values throughout the year, even when values for the particle diet and AFSW were reduced. Overall, a core gut bivalve microbiome was present, and it was partially influenced by the marine aggregate microbial community.IMPORTANCE This work investigates the influence that extrinsic factors, diet, and the environment can have on the microbiomes of shellfish. Over the course of a year, the gut microbial communities of two species of bivalves, oysters and mussels, held under identical conditions in coastal marine waters were compared. While the mussels and oysters harbored gut microbial communities with similar composition, on a functional level, they exhibited species and temporal variation. These results indicate that intrinsic factors influence the bivalve microbiome, resulting in species variability, even when environmental conditions, feeding mechanism, and particle diet are constant. Seasonal and multispecies comparisons for bivalve-associated microbial communities are rare, and we believe this research represents an important contribution. The results presented here advance our understanding of the symbiotic interactions between marine invertebrates, the microbial communities they harbor, and the environment.}, }
@article {pmid31826833, year = {2020}, author = {Tomita, S and Watanabe, J and Nakamura, T and Endo, A and Okada, S}, title = {Characterisation of the bacterial community structures of sunki, a traditional unsalted pickle of fermented turnip leaves.}, journal = {Journal of bioscience and bioengineering}, volume = {129}, number = {5}, pages = {541-551}, doi = {10.1016/j.jbiosc.2019.11.010}, pmid = {31826833}, issn = {1347-4421}, mesh = {Brassica napus/*microbiology ; Fermentation ; Fermented Foods and Beverages/analysis/microbiology ; Food Microbiology ; Japan ; Lactobacillus/classification/genetics/*isolation &amp; purification/metabolism ; *Microbiota ; Phylogeny ; Plant Leaves/microbiology ; }, abstract = {The bacterial community structure in 29 naturally fermented samples of sunki, an unsalted lactic-fermented pickle in Japan, was determined by 16S rRNA gene-targeted metagenomic analysis. The data revealed that genus Lactobacillus was dominant in all samples and various bacterial species, related to Lactobacillus delbrueckii, Lactobacillus plantarum, Lactobacillus buchneri, Lactobacillus fermentum, Lactobacillus reuteri, Lactobacillus crispatus, Lactobacillus intestinalis, and Lactobacillus gasseri, showed a range of dominance depending on the samples. Comparative analysis of the bacterial composition by principal coordinate analysis and hierarchical clustering classified the varied bacterial composition of the 29 samples into three types of bacterial community structure. These types comprised lactobacilli belonging to different phylogenetic groups: type A had a certain ratio of Lactobacillus fermentum (70.3-22.1%, average 41.2%) in combination with several species belonging to Lactobacillus delbrueckii-phylogenetic group, type B comprised remarkably high levels of species Lactobacillus delbrueckii (average 89.5%), and type C had combinations of species belonging to Lactobacillus plantarum- and Lactobacillus buchneri-phylogenetic groups. Interestingly, these types differed in the compositional profiles of water-soluble and volatile compounds, and statistically significant differences were observed in the levels of acetic acid, succinic acid, ethanol, ethyl acetate, glutamic acid, γ-aminobutyric acid, and isovaleraldehyde. Furthermore, metabolomic analysis revealed a correlation of Lactobacillus fermentum dominance with pH value and lactic and acetic acid levels, with high R values of 0.643, -0.642, and 0.528, respectively. The data reported in this study showed the characteristics of the bacterial composition in the unsalted sunki pickle and its potential relationship with the compositional profile.}, }
@article {pmid31825995, year = {2019}, author = {Woloszynek, S and Mell, JC and Zhao, Z and Simpson, G and O'Connor, MP and Rosen, GL}, title = {Exploring thematic structure and predicted functionality of 16S rRNA amplicon data.}, journal = {PloS one}, volume = {14}, number = {12}, pages = {e0219235}, pmid = {31825995}, issn = {1932-6203}, mesh = {Bacteria/*classification/*genetics ; *Biodiversity ; Crohn Disease/*microbiology ; Humans ; Metagenomics/*methods ; Microbiota ; Mouth Neoplasms/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Software ; Time Factors ; }, abstract = {Analysis of microbiome data involves identifying co-occurring groups of taxa associated with sample features of interest (e.g., disease state). Elucidating such relations is often difficult as microbiome data are compositional, sparse, and have high dimensionality. Also, the configuration of co-occurring taxa may represent overlapping subcommunities that contribute to sample characteristics such as host status. Preserving the configuration of co-occurring microbes rather than detecting specific indicator species is more likely to facilitate biologically meaningful interpretations. Additionally, analyses that use taxonomic relative abundances to predict the abundances of different gene functions aggregate predicted functional profiles across taxa. This precludes straightforward identification of predicted functional components associated with subsets of co-occurring taxa. We provide an approach to explore co-occurring taxa using &quot;topics&quot; generated via a topic model and link these topics to specific sample features (e.g., disease state). Rather than inferring predicted functional content based on overall taxonomic relative abundances, we instead focus on inference of functional content within topics, which we parse by estimating interactions between topics and pathways through a multilevel, fully Bayesian regression model. We apply our methods to three publicly available 16S amplicon sequencing datasets: an inflammatory bowel disease dataset, an oral cancer dataset, and a time-series dataset. Using our topic model approach to uncover latent structure in 16S rRNA amplicon surveys, investigators can (1) capture groups of co-occurring taxa termed topics; (2) uncover within-topic functional potential; (3) link taxa co-occurrence, gene function, and environmental/host features; and (4) explore the way in which sets of co-occurring taxa behave and evolve over time. These methods have been implemented in a freely available R package: https://cran.r-project.org/package=themetagenomics, https://github.com/EESI/themetagenomics.}, }
@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 {pmid31823916, year = {2019}, author = {Singh, S and Verma, N and Taneja, N}, title = {The human gut resistome: Current concepts &amp; future prospects.}, journal = {The Indian journal of medical research}, volume = {150}, number = {4}, pages = {345-358}, pmid = {31823916}, issn = {0971-5916}, mesh = {Databases, Genetic ; Drug Resistance, Microbial/*genetics ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; }, abstract = {The human gut is home to a myriad of organisms. While some are harmless commensals, others are transient, pathogenic flora. The gut microbiome is composed of diverse bacterial flora, and apart from playing a major role in protecting from various infectious and non-infectious diseases, it plays an important role in resistance to antimicrobials. The collection of genes or genetic material that confers antimicrobial resistance constitutes the gut resistome, and it may involve the pathogens or commensals of the intestinal tract. The diversity of this gut resistome is influenced by various environmental factors including the diet and antibiotic exposure. This review highlights the recent concepts pertaining to the human gut resistome, factors affecting it, how it impacts human health and diseases, methods to study the resistome and potential therapeutic approaches.}, }
@article {pmid31822775, year = {2019}, author = {Chen, S and Zheng, Y and Zhou, Y and Guo, W and Tang, Q and Rong, G and Hu, W and Tang, J and Luo, H}, title = {Gut Dysbiosis with Minimal Enteritis Induced by High Temperature and Humidity.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {18686}, pmid = {31822775}, issn = {2045-2322}, mesh = {Animals ; Bacterial Translocation ; Body Weight ; Diarrhea/metabolism ; Dysbiosis/*physiopathology ; Enteritis/*microbiology ; Enzyme-Linked Immunosorbent Assay ; *Gastrointestinal Microbiome ; *Hot Temperature ; *Humidity ; Inflammation ; Intestinal Mucosa/metabolism ; Intestines/microbiology ; Male ; Mice ; Mice, Inbred C57BL ; Organ Size ; Probiotics/administration &amp; dosage ; RNA, Ribosomal, 16S/metabolism ; Signal Transduction ; }, abstract = {High temperature and humidity (HTH) can cause diarrhea owing to food and drinking water contamination. However, their direct effects on gut microbiota and gastrointestinal inflammation are unknown. This study aimed to investigate the effects of HTH and probiotics on the microbiome. Twenty-one male mice were randomly assigned to normal control (NC), HTH, and broad-spectrum probiotic-treated (PR) groups. HTH and PR groups were regularly housed at 30 ± 0.5 °C with humidity of 85-90% for eight consecutive weeks. A broad-spectrum probiotic was administrated to PR-group mice from day 50 to 56. Clinical signs were observed and gut microbiota were analyzed via 16 S rRNA-based functional metagenomics. Intestinal pathology and the expression of defensins and pro-inflammatory cytokines were also assessed. Mice in the HTH and PR groups gradually developed sticky or loose feces. The HTH group developed a distinct microbiota profile associated with augmented metabolism and human-like pathophysiologies upon suppression of environmental sensing. Pathological assays indicated minimal enteritis, increased bacterial translocation, and elevated intestinal pro-inflammatory cytokine levels. Thus, ambient HTH directly contributes to gut dysbiosis and minimal enteritis, whereas probiotics partially normalized the microbiota and ameliorated gut inflammation. This study provides novel insights into the pathogenesis of environment-associated diseases and offers a potential therapeutic approach.}, }
@article {pmid31821372, year = {2019}, author = {Osimani, A and Milanović, V and Roncolini, A and Riolo, P and Ruschioni, S and Isidoro, N and Loreto, N and Franciosi, E and Tuohy, K and Olivotto, I and Zarantoniello, M and Cardinali, F and Garofalo, C and Aquilanti, L and Clementi, F}, title = {Hermetia illucens in diets for zebrafish (Danio rerio): A study of bacterial diversity by using PCR-DGGE and metagenomic sequencing.}, journal = {PloS one}, volume = {14}, number = {12}, pages = {e0225956}, pmid = {31821372}, issn = {1932-6203}, mesh = {*Animal Feed ; Animals ; Bacteria/classification/genetics ; *Diptera/microbiology ; Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; Microbial Viability ; RNA, Ribosomal, 16S ; Zebrafish/*physiology ; }, abstract = {In the present research, bacterial diversity was studied during a 6-month feeding trial utilizing zebrafish (Danio rerio) fed Hermetia illucens reared on different substrates with an emphasis on fish gut bacterial diversity. A polyphasic approach based on viable counting, PCR-DGGE and metagenomic 16S rRNA gene amplicon target sequencing was applied. Two different H. illucens groups were reared on coffee by-products (C) or a mixture of vegetables (S). Viable counts showed a wide variability based on substrate. PCR-DGGE and Illumina sequencing allowed the major and minor bacterial taxa to be detected. Both samples of larvae and their frass reared on the S substrate showed the highest richness and evenness of bacterial communities, whereas zebrafish (ZHC) fed H. illucens reared on substrate C and zebrafish (ZHS) fed H. illucens reared on substrate S had the lowest bacterial richness and evenness. A stimulating effect of bioactive compounds from coffee by-products on the occurrence of Lactobacillaceae and Leuconostoccaceae in H. illucens reared on substrate C has been hypothesized. Zebrafish gut samples originating from the two feeding trials showed complex microbial patterns in which Actinobacteria and Alteromonadales were always detected, irrespective of the diet used. Enterobacteriaceae in fish guts were more abundant in ZHS than in ZHC, thus suggesting an influence of the bioactive compounds (chlorogenic and caffeic acids) in the substrate on Enterobacteriaceae in fish guts. ZHC showed a higher abundance of Clostridia than did ZHS, which was likely explained by stimulating activity on the bacteria in this class by the bioactive compounds contained in H. illucens reared on substrate C. An influence of the microbiota of H. illucens or insect-derived bioactive compounds on the gut microbiota of zebrafish has been suggested. The presence of bacteria consistently associated with zebrafish guts has been found irrespective of the diet, thus attesting to the likely stability of the core fish microbiota.}, }
@article {pmid31820070, year = {2020}, author = {Tyx, RE and Rivera, AJ and Keong, LM and Stanfill, SB}, title = {An exploration of smokeless tobacco product nucleic acids: a combined metagenome and metatranscriptome analysis.}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {2}, pages = {751-763}, doi = {10.1007/s00253-019-10232-3}, pmid = {31820070}, issn = {1432-0614}, support = {CC999999/ImCDC/Intramural CDC HHS/United States ; }, mesh = {Bacteria/metabolism ; Biotransformation ; DNA, Bacterial/genetics ; *Gene Expression Profiling ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; *Microbiota ; Nitrates/metabolism ; Nitrites/metabolism ; RNA, Bacterial/analysis/genetics ; RNA, Viral/analysis/genetics ; Tobacco, Smokeless/*microbiology ; }, abstract = {Smokeless tobacco (ST) products are used worldwide and are a major public health concern. In addition to harmful chemicals found in these products, microbes found in ST products are believed to be responsible for generating harmful tobacco-specific nitrosamines (TSNAs), the most abundant carcinogens in ST. These microbes also contribute endotoxins and other pro-inflammatory components. A greater understanding of the microbial constituents in these products is sought in order to potentially link select design aspects or manufacturing processes to avoidable increases in harmful constituents. Previous studies looked primarily at bacterial constituents and had not differentiated between viable vs nonviable organisms, so in this study, we sought to use a dual metatranscriptomic and metagenomic analysis to see if differences exist. Using high-throughput sequencing, we observed that there were differences in taxonomic abundances between the metagenome and metatranscriptome, and in the metatranscriptome, we also observed an abundance of plant virus RNA not previously reported in DNA-only studies. We also found in the product tested, that there were no viable bacteria capable of metabolizing nitrate to nitrite. Therefore, the product tested would not be likely to increase TSNAs during shelf storage. We tested only a single product to date using the strategy presented here, but succeeded in demonstrating the value of using of these methods in tobacco products. These results present novel findings from the first combined metagenome and metatranscriptome of a commercial tobacco product.}, }
@article {pmid31818595, year = {2020}, author = {Brereton, NJB and Gonzalez, E and Desjardins, D and Labrecque, M and Pitre, FE}, title = {Co-cropping with three phytoremediation crops influences rhizosphere microbiome community in contaminated soil.}, journal = {The Science of the total environment}, volume = {711}, number = {}, pages = {135067}, doi = {10.1016/j.scitotenv.2019.135067}, pmid = {31818595}, issn = {1879-1026}, mesh = {Biodegradation, Environmental ; *Microbiota ; Plant Roots ; RNA, Ribosomal, 16S ; Rhizosphere ; Soil ; *Soil Microbiology ; Soil Pollutants ; }, abstract = {Human industrial activities have left millions of hectares of land polluted with trace element metals and persistent organic pollutants (POPs) around the world. Although contaminated sites are environmentally damaging, high economic costs often discourage soil remediation efforts. Phytoremediation is a potential green technology solution but can be challenging due to the diversity of anthropogenic contaminants. Co-cropping could provide improved tolerance to diverse soil challenges by taking advantage of distinct crop capabilities. Co-cropping of three species with potentially complementary functions, Festuca arundinacea, Salix miyabeana and Medicago sativa, perform well on diversely contaminated soils. Here, rhizosphere microbiomes of each crop in monoculture and in all co-cropping combinations were compared using 16S rRNA gene amplification, sequencing and differential abundance analysis. The hyperaccumulating F. arundinacea rhizosphere microbiome included putative plant growth promoting bacteria (PGPB) and metal tolerance species, such as Rhizorhapis suberifaciens, Cellvibrio fibrivorans and Pseudomonas lini. The rhizosphere microbiome of the fast-growing tree S. miyabeana included diverse taxa involved in POP degradation, including the species Phenylobacterium panacis. The well-characterised nitrogen-fixing M. sativa microbiome species, Sinorhizobium meliloti, was identified alongside others involved in nutrient acquisition and putative yet-to-be-cultured Candidatus saccharibacteria (TM7-1 group). The majority of differentially abundant rhizosphere-associated bacterial species were maintained in co-cropping pairs, with pairs having higher numbers of differentially abundant taxa than monocultures in all cases. This was not the case when all three crops were co-cropped, where most host-specific bacterial species were not detected as differentially abundant, indicating the potential for reduced rhizosphere functionality. The crops cultivated in pairs here retained rhizosphere microbiome bacteria involved in these monoculture ecosystem services of plant growth promotion, POP tolerance and degradation, and improved nutrient acquisition. These findings provide a promising outlook of the potential for complementary co-cropping strategies for phytoremediation of the multifaceted anthropogenic pollution which can disastrously affect soils around the world.}, }
@article {pmid31818246, year = {2019}, author = {Shelomi, M and Lin, SS and Liu, LY}, title = {Transcriptome and microbiome of coconut rhinoceros beetle (Oryctes rhinoceros) larvae.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {957}, pmid = {31818246}, issn = {1471-2164}, support = {MOST 106-2311-B-002-002-MY3//Ministry of Science and Technology (TW)/ ; MOST 108-2313-B-002-050//Ministry of Science and Technology, Taiwan/ ; MOST 108-2311-B-002-018-MY3//Ministry of Science and Technology, Taiwan/ ; }, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification ; Coleoptera/*genetics/*microbiology ; Female ; Gastrointestinal Tract/metabolism/microbiology ; Gene Expression ; Insect Proteins/genetics ; Isoptera/microbiology ; Larva/genetics/microbiology ; Male ; Metagenomics ; *Microbiota/genetics ; Phylogeny ; Transcriptome ; }, abstract = {BACKGROUND: The coconut rhinoceros beetle, Oryctes rhinoceros, is a major pest of palm crops in tropical Asia and the Pacific Islands. Little molecular data exists for this pest, impeding our ability to develop effective countermeasures and deal with the species' growing resistance to viral biocontrols. We present the first molecular biology analyses of this species, including a metagenomic assay to understand the microbiome of different sections of its digestive tract, and a transcriptomics assay to complement the microbiome data and to shed light on genes of interest like plant cell wall degrading enzymes and immunity and xenobiotic resistance genes.<br><br>RESULTS: The gut microbiota of Oryctes rhinoceros larvae is quite similar to that of the termite gut, as both species feed on decaying wood. We found the first evidence for endogenous beta-1,4-endoglucanase in the beetle, plus evidence for microbial cellobiase, suggesting the beetle can degrade cellulose together with its gut microfauna. A number of antimicrobial peptides are expressed, particularly by the fat body but also by the midgut and hindgut.<br><br>CONCLUSIONS: This transcriptome provides a wealth of data about the species' defense against chemical and biological threats, has uncovered several potentially new species of microbial symbionts, and significantly expands our knowledge about this pest.}, }
@article {pmid31810497, year = {2019}, author = {Zhang, X and Li, L and Butcher, J and Stintzi, A and Figeys, D}, title = {Advancing functional and translational microbiome research using meta-omics approaches.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {154}, pmid = {31810497}, issn = {2049-2618}, mesh = {Gastrointestinal Microbiome/*drug effects/*physiology ; Host Microbial Interactions ; Humans ; Metabolomics/*methods ; Metagenomics/*methods ; Precision Medicine/*methods ; Proteomics/*methods ; }, abstract = {The gut microbiome has emerged as an important factor affecting human health and disease. The recent development of -omics approaches, including phylogenetic marker-based microbiome profiling, shotgun metagenomics, metatranscriptomics, metaproteomics, and metabolomics, has enabled efficient characterization of microbial communities. These techniques can provide strain-level taxonomic resolution of the taxa present in microbiomes, assess the potential functions encoded by the microbial community and quantify the metabolic activities occurring within a complex microbiome. The application of these meta-omics approaches to clinical samples has identified microbial species, metabolic pathways, and metabolites that are associated with the development and treatment of human diseases. These findings have further facilitated microbiome-targeted drug discovery and efforts to improve human health management. Recent in vitro and in vivo investigations have uncovered the presence of extensive drug-microbiome interactions. These interactions have also been shown to be important contributors to the disparate patient responses to treatment that are often observed during disease therapy. Therefore, developing techniques or frameworks that enable rapid screening, detailed evaluation, and accurate prediction of drug/host-microbiome interactions is critically important in the modern era of microbiome research and precision medicine. Here we review the current status of meta-omics techniques, including integrative multi-omics approaches, for characterizing the microbiome's functionality in the context of health and disease. We also summarize and discuss new frameworks for applying meta-omics approaches and microbiome assays to study drug-microbiome interactions. Lastly, we discuss and exemplify strategies for implementing microbiome-based precision medicines using these meta-omics approaches and high throughput microbiome assays.}, }
@article {pmid31802337, year = {2020}, author = {Cleary, DFR and Polónia, ARM and Huang, YM and Swierts, T}, title = {Compositional variation between high and low prokaryotic diversity coral reef biotopes translates to different predicted metagenomic gene content.}, journal = {Antonie van Leeuwenhoek}, volume = {113}, number = {4}, pages = {563-587}, doi = {10.1007/s10482-019-01364-7}, pmid = {31802337}, issn = {1572-9699}, support = {PTDC/AAC-AMB/115304/2009//Fundação para a Ciência e a Tecnologia/ ; SFRH/BPD/117563/2016//Fundação para a Ciência e a Tecnologia/ ; }, mesh = {Animals ; Bacteria/*classification/*genetics ; *Coral Reefs ; Invertebrates/*microbiology ; Metagenomics ; Species Specificity ; }, abstract = {In a previous study, we identified host species that housed high and low diversity prokaryotic communities. In the present study, we expand on this and assessed the prokaryotic communities associated with seawater, sediment and 11 host species from 7 different phyla in a Taiwanese coral reef setting. The host taxa sampled included hard, octo- and black corals, molluscs, bryozoans, flatworms, fish and sea urchins. There were highly significant differences in composition among host species and all host species housed distinct communities from those found in seawater and sediment. In a hierarchical clustering analysis, samples from all host species, with the exception of the coral Galaxea astreata, formed significantly supported clusters. In addition to this, the coral G. astreata and the bryozoan Triphyllozoon inornatum on the one hand and the coral Tubastraea coccinea, the hermit crab Calcinus laevimanus and the flatworm Thysanozoon nigropapillosum on the other formed significantly supported clusters. In addition to composition, there were highly pronounced differences in richness and evenness among host species from the most diverse species, the bryozoan T. inornatum at 2518 ± 240 OTUs per 10,000 sequences to the least diverse species, the octocoral Cladiella sp. at 142 ± 14 OTUs per 10,000 sequences. In line with the differences in composition, there were significant differences in predicted metagenomic gene counts among host species. Furthermore, there were pronounced compositional and predicted functional differences between high diversity hosts (Liolophura japonica, G. astreata, T. coccinea, C. laevimanus, T. inornatum) and low diversity hosts (Antipathes sp., Pomacentrus coelestis, Modiolus auriculatus, T. nigropapillosum, Cladiella sp. and Diadema savigny). In particular, we found that all tested low diversity hosts were predicted to be enriched for the phosphotransferase system compared to high diversity hosts.}, }
@article {pmid31800638, year = {2019}, author = {Choi, S and Lee, JG and Lee, AR and Eun, CS and Han, DS and Park, CH}, title = {Helicobacter pylori antibody and pepsinogen testing for predicting gastric microbiome abundance.}, journal = {PloS one}, volume = {14}, number = {12}, pages = {e0225961}, pmid = {31800638}, issn = {1932-6203}, mesh = {Adult ; Antibodies, Bacterial/*immunology ; Bacterial Load ; Comorbidity ; Female ; Helicobacter Infections/diagnosis/*immunology/*metabolism/*microbiology ; Helicobacter pylori/*immunology ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Pepsinogen A/*metabolism ; Prognosis ; Serologic Tests ; Stomach Neoplasms/etiology ; }, abstract = {BACKGROUND: Although the high-throughput sequencing technique is useful for evaluating gastric microbiome, it is difficult to use clinically. We aimed to develop a predictive model for gastric microbiome based on serologic testing.<br><br>METHODS: This study was designed to analyze sequencing data obtained from the Hanyang University Gastric Microbiome Cohort, which was established initially to investigate gastric microbial composition according to the intragastric environment. We evaluated the relationship between the relative abundance of potential gastric cancer-associated bacteria (nitrosating/nitrate-reducing bacteria or type IV secretion system [T4SS] protein gene-contributing bacteria) and serologic markers (IgG anti-Helicobacter pylori [HP] antibody or pepsinogen [PG] levels).<br><br>RESULTS: We included 57 and 26 participants without and with HP infection, respectively. The relative abundance of nitrosating/nitrate-reducing bacteria was 4.9% and 3.6% in the HP-negative and HP-positive groups, respectively, while that of T4SS protein gene-contributing bacteria was 20.5% and 6.5% in the HP-negative and HP-positive groups, respectively. The relative abundance of both nitrosating/nitrate-reducing bacteria and T4SS protein gene-contributing bacteria increased exponentially as PG levels decreased. Advanced age (only for nitrosating/nitrate-reducing bacteria), a negative result of IgG anti-HP antibody, low PG levels, and high Charlson comorbidity index were associated with a high relative abundance of nitrosating/nitrate-reducing bacteria and T4SS protein gene-contributing bacteria. The adjusted coefficient of determination (R2) was 53.7% and 70.0% in the model for nitrosating/nitrate-reducing bacteria and T4SS protein gene-contributing bacteria, respectively.<br><br>CONCLUSION: Not only the negative results of IgG anti-HP antibody but also low PG levels were associated with a high abundance of nitrosating/nitrate-reducing bacteria and T4SS protein gene-contributing bacteria.}, }
@article {pmid31798840, year = {2019}, author = {Bich, VTN and Thanh, LV and Thai, PD and Van Phuong, TT and Oomen, M and Driessen, C and Beuken, E and Hoang, TH and van Doorn, HR and Penders, J and Wertheim, HFL}, title = {An exploration of the gut and environmental resistome in a community in northern Vietnam in relation to antibiotic use.}, journal = {Antimicrobial resistance and infection control}, volume = {8}, number = {}, pages = {194}, pmid = {31798840}, issn = {2047-2994}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Adolescent ; Adult ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/genetics ; Child ; Child, Preschool ; Drug Resistance, Multiple, Bacterial/*genetics ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; *Genes, Bacterial ; Humans ; Infant ; Infant, Newborn ; Longitudinal Studies ; Male ; Metagenomics ; Middle Aged ; Pets/microbiology ; Prospective Studies ; Vietnam ; Young Adult ; }, abstract = {Background: Antibiotic resistance is a major global public health threat. Antibiotic use can directly impact the antibiotic resistant genes (ARGs) profile of the human intestinal microbiome and consequently the environment through shedding.<br><br>Methods: We determined the resistome of human feces, animal stools, human food and environmental (rain, well, and irrigative water) samples (n = 304) in 40 households within a community cohort and related the data to antibiotic consumption. Metagenomic DNA was isolated and qPCR was used to determine presence of mobile colistin resistance (mcr) genes, genes encoding extended-spectrum β-lactamases (ESBL), carbapenemases and quinolone resistance genes.<br><br>Results: Nearly 40 % (39.5%, 120/304) of samples contained ESBL genes (most frequent were CTX-M-9 (23.7% [72/304]), CTX-M-1 (18.8% [57/304]). Quinolone resistance genes (qnrS) were detected in all human and 91% (41/45) of animal stool samples. Mcr-1 and mcr-3 were predominantly detected in human feces at 88% (82/93) and 55% (51/93) and animal feces at 93% (42/45) and 51% (23/45), respectively. Mcr-2, mrc-4 and mcr-5 were not detected in human feces, and only sporadically (< 6%) in other samples. Carbapenemase-encoding genes were most common in water (15% [14/91]) and cooked food (13% [10/75]) samples, while their prevalence in human and animal stools was lower at 4% in both human (4/93) and animal (2/45) samples. We did not find an association between recent antibiotic consumption and ARGs in human stools. Principal component analysis showed that the resistome differs between ecosystems with a strong separation of ARGs profiles of human and animal stools on the one hand versus cooked food and water samples on the other.<br><br>Conclusions: Our study indicated that ARGs were abundant in human and animal stools in a rural Vietnamese community, including ARGs targeting last resort antibiotics. The resistomes of animal and human stools were similar as opposed to the resistomes from water and food sources. No association between antibiotic use and ARG profiles was found in a setting of high background rates of AMR.}, }
@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}, pmid = {31795935}, issn = {1471-2164}, mesh = {Agriculture ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Biodiversity ; Ecosystem ; Genotype ; India ; Metabolic Networks and Pathways ; *Microbiota ; Myanmar ; Oryza/genetics/*microbiology ; Phenotype ; Seeds/microbiology ; }, 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 {pmid31793046, year = {2020}, author = {Liu, G and Chen, F and Cai, Y and Chen, Z and Luan, Q and Yu, X}, title = {Measuring the subgingival microbiota in periodontitis patients: Comparison of the surface layer and the underlying layers.}, journal = {Microbiology and immunology}, volume = {64}, number = {2}, pages = {99-112}, doi = {10.1111/1348-0421.12759}, pmid = {31793046}, issn = {1348-0421}, support = {81470740//National Natural Science Foundation of China/ ; }, mesh = {Actinobacteria/classification/genetics/isolation &amp; purification ; Actinomyces/isolation &amp; purification ; Adult ; Bacteria/classification/genetics/*isolation &amp; purification ; Classification ; Dental Plaque/*microbiology ; Female ; Fusobacteria/classification/genetics/isolation &amp; purification ; Fusobacterium/isolation &amp; purification ; Fusobacterium nucleatum/isolation &amp; purification ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Male ; Metagenomics ; *Microbiota/genetics ; Periodontitis/*microbiology ; Phylogeny ; Porphyromonas gingivalis/isolation &amp; purification ; Prevotella intermedia/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Spirochaetales/classification/genetics/isolation &amp; purification ; Streptococcus intermedius/isolation &amp; purification ; Treponema/isolation &amp; purification ; Young Adult ; }, abstract = {Periodontitis is a major cause of tooth loss in adults that initially results from dental plaque. Subgingival plaque pathogenesis is affected by both community composition and plaque structures, although limited data are available concerning the latter. To bridge this knowledge gap, subgingival plaques were obtained using filter paper (the fourth layer) and curette (the first-third layers) sequentially and the phylogenetic differences between the first-third layers and the fourth layer were characterized by sequencing the V3-V4 regions of 16S rRNA. A total of 11 phyla, 148 genera, and 308 species were obtained by bioinformatic analysis, and no significant differences between the operational taxonomic unit numbers were observed for these groups. In both groups, the most abundant species were Porphyromonas gingivalis and Fusobacterium nucleatum. Actinomyces naeslundii, Streptococcus intermedius, and Prevotella intermedia possessed relatively high proportions in the first-third layers; while in the fourth layer, both traditional pathogens (Treponema denticola and Campylobacter rectus) and novel pathobionts (Eubacterium saphenum, Filifactor alocis, Treponema sp. HOT238) were prominent. Network analysis showed that either of them exhibited a scale-free property and was constructed by two negatively correlated components (the pathogen component and the nonpathogen component), while the synergy in the nonpathogen component was lower in the first-third layers than that in the fourth layer. After merging these two parts into a whole plaque group, the negative/positive correlation ratio increased. With potential connections, the first-third layers and the fourth layer showed characteristic key nodes in bacterial networks.}, }
@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}, support = {T32 HG000044/HG/NHGRI NIH HHS/United States ; }, 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 {pmid31785113, year = {2020}, author = {Hagan, RW and Hofman, CA and Hübner, A and Reinhard, K and Schnorr, S and Lewis, CM and Sankaranarayanan, K and Warinner, CG}, title = {Comparison of extraction methods for recovering ancient microbial DNA from paleofeces.}, journal = {American journal of physical anthropology}, volume = {171}, number = {2}, pages = {275-284}, doi = {10.1002/ajpa.23978}, pmid = {31785113}, issn = {1096-8644}, support = {EXC 2051 #390713860//Deutsche Forschungsgemeinschaft/International ; //Max-Planck-Gesellschaft/International ; R01 GM089886/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Anthropology, Physical/*methods ; Archaeology/methods ; DNA, Ancient/*analysis/*isolation &amp; purification ; Dogs ; Feces/*chemistry ; Gastrointestinal Microbiome ; Metagenomics ; Sequence Analysis, DNA/*methods/veterinary ; }, abstract = {OBJECTIVES: Paleofeces are valuable to archeologists and evolutionary biologists for their potential to yield health, dietary, and host information. As a rich source of preserved biomolecules from host-associated microorganisms, they can also provide insights into the recent evolution and changing ecology of the gut microbiome. However, there is currently no standard method for DNA extraction from paleofeces, which combine the dual challenges of complex biological composition and degraded DNA. Due to the scarcity and relatively poor preservation of paleofeces when compared with other archeological remains, it is important to use efficient methods that maximize ancient DNA (aDNA) recovery while also minimizing downstream taxonomic biases.<br><br>METHODS: In this study, we use shotgun metagenomics to systematically compare the performance of five DNA extraction methods on a set of well-preserved human and dog paleofeces from Mexico (~1,300 BP).<br><br>RESULTS: Our results show that all tested DNA extraction methods yield a consistent microbial taxonomic profile, but that methods optimized for ancient samples recover significantly more DNA.<br><br>CONCLUSIONS: These results show promise for future studies that seek to explore the evolution of the human gut microbiome by comparing aDNA data with those generated in modern studies.}, }
@article {pmid31782201, year = {2020}, author = {Wille, M}, title = {Unravelling virus community ecology in bats through the integration of metagenomics and community ecology.}, journal = {Molecular ecology}, volume = {29}, number = {1}, pages = {23-25}, doi = {10.1111/mec.15306}, pmid = {31782201}, issn = {1365-294X}, mesh = {Animals ; *Biota ; Chiroptera/*virology ; *Ecology ; Humans ; *Metagenomics ; Rabies virus/genetics ; Viruses/*genetics ; }, abstract = {The spillover of viruses from wildlife into agricultural animals or humans has profound socioeconomic and public health impact. Vampire bats, found throughout South America, feed directly on humans and other animals and are an important reservoir for zoonotic viruses, including rabies virus. This has resulted in considerable effort in understanding both the ecology of bat-borne viruses and the composition and associated correlates of the structure of entire virus communities in wildlife, particularly in the context of disease control interventions. In a From the Cover article in this issue of Molecular Ecology, Bergner et al. (2019) set out to reveal virus community dynamics in vampire bats by interrogating factors that affect the structure, diversity and richness of these communities. Due to the linkage of metagenomic sequence data with community ecology, this study represents an important advance in the field of virus ecology.}, }
@article {pmid31781816, year = {2020}, author = {Sun, F and Wang, C and Chen, L and Weng, G and Zheng, Z}, title = {The intestinal bacterial community of healthy and diseased animals and its association with the aquaculture environment.}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {2}, pages = {775-783}, doi = {10.1007/s00253-019-10236-z}, pmid = {31781816}, issn = {1432-0614}, support = {2017A020216008//Project of Guangdong Science and Technology Department/ ; 2016I1002//Project of Fujian Science and Technology Department/ ; 2017T3010//Project of Fujian Science and Technology Department/ ; }, mesh = {Animals ; Aquaculture ; Bacteria/*classification/*genetics ; Crustacea/*microbiology ; *Gastrointestinal Microbiome ; Geologic Sediments/*microbiology ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Water Microbiology ; }, abstract = {Although increasing levels of attention have been targeted towards aquaculture-associated bacteria, the bacterial community of animal intestines and its relationship with the aquaculture environment need to be further investigated. In this study, we used high-throughput sequencing to analyze the bacterial community of pond water, sediment, and the intestines of diseased and healthy animals. Our data showed that Proteobacteria, Firmicutes, Cyanobacteria, and Bacteroidetes were the dominant taxa of bacteria across all samples and accounted for more than 90% of the total sequence. Difference analysis and Venn diagrams showed that most of the intestinal bacterial OTUs (operational taxonomic units) of diseased and healthy animals were the same as those of sediment and water, indicating that the aquaculture environment was the main source of intestinal bacteria. Compared with healthy animals, a considerable reduction of OTUs was evident in diseased animals. Welch's t test showed that the dominant bacterial taxa in sediment, water, and animal intestine were significantly different (p < 0.05) and each had its own unique dominant microorganisms. In addition, differences between the intestinal bacteria of healthy and diseased animals were represented by potential probiotics and pathogens, such as Bacillus, Vibrio, Oceanobacillus, and Lactococcus. Principal component analysis (PcoA) showed that a similar environment shaped a similar microbial structure. There was a large difference in the spectrum of intestinal bacteria in diseased animals; furthermore, the spectrum of intestinal bacteria in diseased animals was very different from the environment than in healthy animals. This study provides a theoretical basis for a relationship between the intestinal bacteria of healthy and diseased animals and the environment and provides guidance for environmental regulation and disease prevention in aquaculture areas.}, }
@article {pmid31781106, year = {2019}, author = {Pessoa, L and Aleti, G and Choudhury, S and Nguyen, D and Yaskell, T and Zhang, Y and Li, W and Nelson, KE and Neto, LLS and Sant'Ana, ACP and Freire, M}, title = {Host-Microbial Interactions in Systemic Lupus Erythematosus and Periodontitis.}, journal = {Frontiers in immunology}, volume = {10}, number = {}, pages = {2602}, pmid = {31781106}, issn = {1664-3224}, support = {R00 DE023584/DE/NIDCR NIH HHS/United States ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Autoimmunity ; Computational Biology/methods ; Cytokines/metabolism ; *Disease Susceptibility ; Female ; *Host-Pathogen Interactions ; Humans ; Inflammation Mediators/metabolism ; Lupus Erythematosus, Systemic/*etiology/metabolism ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota/immunology ; Middle Aged ; Periodontitis/*etiology/metabolism ; Phylogeny ; }, abstract = {Background: Systemic lupus erythematosus (SLE) is a potentially fatal complex autoimmune disease, that is characterized by widespread inflammation manifesting tissue damage and comorbidities across the human body including heart, blood vessels, joints, skin, liver, kidneys, and periodontal tissues. The etiology of SLE is partially attributed to a deregulated inflammatory response to microbial dysbiosis and environmental changes. In the mouth, periodontal environment provides an optimal niche for local and systemic inflammation. Our aim was to evaluate the reciprocal impact of periodontal subgingival microbiome on SLE systemic inflammation. Methods: Ninety-one female subjects were recruited, including healthy (n = 31), SLE-inactive (n = 29), and SLE-active (n = 31). Patients were screened for probing depth, bleeding on probing, clinical attachment level, and classified according to CDC/AAP criteria with or without periodontal dysbiosis. Serum inflammatory cytokines were measured by human cytokine panel and a targeted pathogenic subgingival biofilm panel was examined by DNA-DNA checkerboard from subgingival plaque samples. Results: The results showed significant upregulation of serum proinflammatory cytokines in individuals with SLE when compared to controls. Stratification of subject's into SLE-inactive (I) and SLE-active (A) phenotypes or periodontitis and non-periodontitis groups provided new insights into SLE pathophysiology. Ten proinflammatory cytokines were upregulated in serum of SLE-I only and one in SLE-A only. Four molecules overlapped in SLE-A and SLE-I. Anti-inflammatory cytokines included IL-4 IL-10, which were upregulated in SLE-I sera (but not SLE-A), controlling clinical phenotypes. Out of 24 significant differential oral microbial abundances found in SLE, 14 unique subgingival bacteria profiles were found to be elevated in SLE. The most severe oral pathogens (Treponema denticola and Tannerella forsythia) showed increase abundances on SLE-A periodontal sites when compared to SLE-I and healthy controls. Inflammation as measured by cytokine-microbial correlations showed that periodontal pathogens dominating the environment increased proinflammatory cytokines systemically. Conclusions: Altogether, low-grade systemic inflammation that influenced SLE disease activity and severity was correlated to dysbiotic changes of the oral microbiota present in periodontal diseases.}, }
@article {pmid31779234, year = {2019}, author = {Leoni, C and Ceci, O and Manzari, C and Fosso, B and Volpicella, M and Ferrari, A and Fiorella, P and Pesole, G and Cicinelli, E and Ceci, LR}, title = {Human Endometrial Microbiota at Term of Normal Pregnancies.}, journal = {Genes}, volume = {10}, number = {12}, pages = {}, pmid = {31779234}, issn = {2073-4425}, mesh = {Adult ; Bacteria/*classification/genetics ; Cesarean Section ; DNA Barcoding, Taxonomic/*methods ; Endometrium/*microbiology ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Microbiota ; Phylogeny ; Pilot Projects ; Pregnancy ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {The endometrium is a challenging site for metagenomic analysis due to difficulties in obtaining uncontaminated samples and the limited abundance of the bacterial population. Indeed, solid correlations between endometrial physio-pathologic conditions and bacteria compositions have not yet been firmly established. Nevertheless, the study of the endometrial microbiota is of great interest due to the close correlations between microbiota profiles, women's health, and successful pregnancies. In this study, we decided to tackle the study of the endometrial microbiota through analysis of bacterial population in women subjected to elective caesarean delivery. As a pilot study, a cohort of 19 Caucasian women at full term of normal pregnancy and with a prospection of elective caesarean delivery was enrolled for endometrium sampling at the time of caesarean section. Sampling was carried out by endometrial biopsy soon after the delivery of the newborn and the discharge of the placenta and fetal membranes from the uterus. Bacterial composition was established by a deep metabarcoding next generation sequencing (NGS) procedure addressing the V5-V6 hypervariable region of the 16S rRNA gene. Amplicon sequences were analysed by bioinformatic procedures for denoising and taxonomic classification. The RDP database was used as 16S rRNA reference collection. Metabarcoding analysis showed the presence of a common bacterial composition, including six genera classifiable within the human microbiota (Cutibacterium, Escherichia, Staphylococcus, Acinetobacter, Streptococcus, Corynebacterium), that could be part of the core endometrial microbiota under the specific conditions examined. These results can provide useful information for future studies on the correlations between bacteria and successful pregnancies.}, }
@article {pmid31778179, year = {2019}, author = {Megaw, J and Kelly, SA and Thompson, TP and Skvortsov, T and Gilmore, BF}, title = {Profiling the microbial community of a Triassic halite deposit in Northern Ireland: an environment with significant potential for biodiscovery.}, journal = {FEMS microbiology letters}, volume = {366}, number = {22}, pages = {}, doi = {10.1093/femsle/fnz242}, pmid = {31778179}, issn = {1574-6968}, support = {BB/L017083/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Archaea/*classification/genetics/*isolation &amp; purification ; Bacteria/*classification/genetics/*isolation &amp; purification ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Geologic Sediments/*microbiology ; Metagenomics ; Microbiological Techniques ; *Microbiota ; Northern Ireland ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Kilroot salt mine, a Triassic halite deposit located in County Antrim, Northern Ireland, is the only permanent hypersaline environment on the island of Ireland. In this study, the microbiome of this unstudied environment was profiled for the first time using conventional and enhanced culturing techniques, and culture independent metagenomic approaches. Using both conventional isolation plates and iChip devices, 89 halophilic archaeal isolates from six known genera, and 55 halophilic or halotolerant bacterial isolates from 18 genera were obtained, based on 16S rRNA gene sequencing. The archaeal isolates were similar to those previously isolated from other ancient halite deposits, and as expected, numerous genera were identified in the metagenome which were not represented among the culturable isolates. Preliminary screening of a selection of isolates from this environment identified antimicrobial activities against a panel of clinically important bacterial pathogens from 15 of the bacterial isolates and one of the archaea. This, alongside previous studies reporting the discovery of novel biocatalysts from the Kilroot mine microbiome, suggests that this environment may be a new, untapped source of of chemical diversity with high biodiscovery potential.}, }
@article {pmid31775777, year = {2019}, author = {Yang, L and Haidar, G and Zia, H and Nettles, R and Qin, S and Wang, X and Shah, F and Rapport, SF and Charalampous, T and Methé, B and Fitch, A and Morris, A and McVerry, BJ and O'Grady, J and Kitsios, GD}, title = {Metagenomic identification of severe pneumonia pathogens in mechanically-ventilated patients: a feasibility and clinical validity study.}, journal = {Respiratory research}, volume = {20}, number = {1}, pages = {265}, pmid = {31775777}, issn = {1465-993X}, support = {U01 HL098962/HL/NHLBI NIH HHS/United States ; R01 HL097376/HL/NHLBI NIH HHS/United States ; MR/N013956/1//UK Antimicrobial Resistance Cross Council Initiative/ ; K23 HL139987/HL/NHLBI NIH HHS/United States ; MR/N013956/1/MRC_/Medical Research Council/United Kingdom ; K24 HL123342/HL/NHLBI NIH HHS/United States ; BBS/E/F/000PR10348/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012504/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; RP-PG-0514-20018/DH_/Department of Health/United Kingdom ; BBS/E/F/000PR10349/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; RP-PG-0514-20018//National Institute for Health Research/ ; K23 GM122069/GM/NIGMS NIH HHS/United States ; A749//Rosetrees Trust/ ; P01 HL114453/HL/NHLBI NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/administration &amp; dosage ; Case-Control Studies ; DNA, Bacterial/*genetics ; Feasibility Studies ; Female ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Male ; Metagenomics/methods ; Microbiota/*genetics ; *Nanopores ; Pneumonia/diagnosis/*genetics/*therapy ; Reference Values ; Respiration, Artificial/methods ; Respiratory Insufficiency/diagnosis/genetics/therapy ; Risk Factors ; Sensitivity and Specificity ; Severity of Illness Index ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: Metagenomic sequencing of respiratory microbial communities for pathogen identification in pneumonia may help overcome the limitations of culture-based methods. We examined the feasibility and clinical validity of rapid-turnaround metagenomics with Nanopore™ sequencing of clinical respiratory specimens.<br><br>METHODS: We conducted a case-control study of mechanically-ventilated patients with pneumonia (nine culture-positive and five culture-negative) and without pneumonia (eight controls). We collected endotracheal aspirates and applied a microbial DNA enrichment method prior to metagenomic sequencing with the Oxford Nanopore MinION device. For reference, we compared Nanopore results against clinical microbiologic cultures and bacterial 16S rRNA gene sequencing.<br><br>RESULTS: Human DNA depletion enabled in depth sequencing of microbial communities. In culture-positive cases, Nanopore revealed communities with high abundance of the bacterial or fungal species isolated by cultures. In four cases with resistant clinical isolates, Nanopore detected antibiotic resistance genes corresponding to the phenotypic resistance in antibiograms. In culture-negative pneumonia, Nanopore revealed probable bacterial pathogens in 1/5 cases and Candida colonization in 3/5 cases. In controls, Nanopore showed high abundance of oral bacteria in 5/8 subjects, and identified colonizing respiratory pathogens in other subjects. Nanopore and 16S sequencing showed excellent concordance for the most abundant bacterial taxa.<br><br>CONCLUSIONS: We demonstrated technical feasibility and proof-of-concept clinical validity of Nanopore metagenomics for severe pneumonia diagnosis, with striking concordance with positive microbiologic cultures, and clinically actionable information obtained from sequencing in culture-negative samples. Prospective studies with real-time metagenomics are warranted to examine the impact on antimicrobial decision-making and clinical outcomes.}, }
@article {pmid31772206, year = {2019}, author = {Orellana, LH and Hatt, JK and Iyer, R and Chourey, K and Hettich, RL and Spain, JC and Yang, WH and Chee-Sanford, JC and Sanford, RA and Löffler, FE and Konstantinidis, KT}, title = {Comparing DNA, RNA and protein levels for measuring microbial dynamics in soil microcosms amended with nitrogen fertilizer.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {17630}, doi = {10.1038/s41598-019-53679-0}, pmid = {31772206}, issn = {2045-2322}, mesh = {Ammonium Compounds/*pharmacology ; Archaea/drug effects/genetics/isolation &amp; purification ; Archaeal Proteins/*analysis ; Bacteria/drug effects/genetics/isolation &amp; purification ; Bacterial Proteins/*analysis ; DNA, Archaeal/*analysis ; DNA, Bacterial/*analysis ; *Fertilizers ; Gene Expression Regulation, Archaeal/drug effects ; Gene Expression Regulation, Bacterial/drug effects ; Gene Ontology ; Metagenomics ; Microbiota/*drug effects ; Nitrates/analysis ; *Nitrification/genetics ; Nitrogen Isotopes/analysis ; Oxidation-Reduction ; Phylogeny ; Proteomics ; RNA, Archaeal/*analysis ; RNA, Bacterial/*analysis ; RNA, Ribosomal, 16S/analysis ; Soil/chemistry ; *Soil Microbiology ; Urea/*pharmacology ; }, abstract = {To what extent multi-omic techniques could reflect in situ microbial process rates remains unclear, especially for highly diverse habitats like soils. Here, we performed microcosm incubations using sandy soil from an agricultural site in Midwest USA. Microcosms amended with isotopically labeled ammonium and urea to simulate a fertilization event showed nitrification (up to 4.1 ± 0.87 µg N-NO3- g-1 dry soil d-1) and accumulation of N2O after 192 hours of incubation. Nitrification activity (NH4+ → NH2OH → NO → NO2- → NO3-) was accompanied by a 6-fold increase in relative expression of the 16S rRNA gene (RNA/DNA) between 10 and 192 hours of incubation for ammonia-oxidizing bacteria Nitrosomonas and Nitrosospira, unlike archaea and comammox bacteria, which showed stable gene expression. A strong relationship between nitrification activity and betaproteobacterial ammonia monooxygenase and nitrite oxidoreductase transcript abundances revealed that mRNA quantitatively reflected measured activity and was generally more sensitive than DNA under these conditions. Although peptides related to housekeeping proteins from nitrite-oxidizing microorganisms were detected, their abundance was not significantly correlated with activity, revealing that meta-proteomics provided only a qualitative assessment of activity. Altogether, these findings underscore the strengths and limitations of multi-omic approaches for assessing diverse microbial communities in soils and provide new insights into nitrification.}, }
@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 = {}, pmid = {31766550}, issn = {1999-4915}, support = {639707/ERC_/European Research Council/International ; }, mesh = {Bacteriophages/*genetics ; Bacteroides/*virology ; *Biodiversity ; Evolution, Molecular ; Gastrointestinal Microbiome/*genetics ; Genome, Viral/*genetics ; Genomics ; Humans ; Metagenomics ; Phylogeny ; Protein Domains ; Tandem Repeat Sequences/genetics ; Viral Proteins/genetics ; }, 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 {pmid31761556, year = {2020}, author = {Sousa, STP and Cabral, L and Lacerda-Júnior, GV and Noronha, MF and Ottoni, JR and Sartoratto, A and Oliveira, VM}, title = {Exploring the genetic potential of a fosmid metagenomic library from an oil-impacted mangrove sediment for metabolism of aromatic compounds.}, journal = {Ecotoxicology and environmental safety}, volume = {189}, number = {}, pages = {109974}, doi = {10.1016/j.ecoenv.2019.109974}, pmid = {31761556}, issn = {1090-2414}, mesh = {Bacteria/genetics/metabolism ; Biodegradation, Environmental ; Dioxygenases/genetics ; Gene Library ; Geologic Sediments/*microbiology ; Hydrocarbons, Aromatic/*metabolism ; *Metagenome ; Metagenomics ; Microbiota ; Mixed Function Oxygenases/genetics ; *Petroleum Pollution ; }, abstract = {Aromatic hydrocarbons (AH) are widely distributed in nature, and many of them have been reported as relevant environmental pollutants and valuable carbon sources for different microorganisms. In this work, high-throughput sequencing of a metageno