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

Animals
Bifidobacterium/genetics/*isolation & purification
Callimico
Callithrix
Cattle
Gastrointestinal Microbiome
Metagenomics

@article {pmid30411190,
year = {2019},
author = {Rossi, A and Bellone, A and Fokin, SI and Boscaro, V and Vannini, C},
title = {Detecting Associations Between Ciliated Protists and Prokaryotes with Culture-Independent Single-Cell Microbiomics: a Proof-of-Concept Study.},
journal = {Microbial ecology},
volume = {78},
number = {1},
pages = {232-242},
doi = {10.1007/s00248-018-1279-9},
pmid = {30411190},
issn = {1432-184X},
support = {565-60%2016//University of Pisa/ ; 565-60%2017//University of Pisa/ ; 565-FFABR 2017//Ministero dell'Istruzione, dell'Università e della Ricerca/ ; },
mesh = {Bacteria/classification/genetics/*isolation & purification ; Bacterial Physiological Phenomena ; Biological Evolution ; Ciliophora/genetics/isolation & purification/*microbiology/physiology ; Ecosystem ; Metagenomics/*methods ; *Microbiota ; Phylogeny ; Pilot Projects ; Sequence Analysis, DNA ; Symbiosis ; },
abstract = {Symbioses between prokaryotes and microbial eukaryotes, particularly ciliated protists, have been studied for a long time. Nevertheless, researchers have focused only on a few host genera and species, mainly due to difficulties in cultivating the hosts, and usually have considered a single symbiont at a time. Here, we present a pilot study using a single-cell microbiomic approach to circumvent these issues. Unicellular ciliate isolation followed by simultaneous amplification of eukaryotic and prokaryotic markers was used. Our preliminary test gave reliable and satisfactory results both on samples collected from different habitats (marine and freshwater) and on ciliates belonging to different taxonomic groups. Results suggest that, as already assessed for many macro-organisms like plants and metazoans, ciliated protists harbor distinct microbiomes. The applied approach detected new potential symbionts as well as new hosts for previously described ones, with relatively low time and cost effort and without culturing. When further developed, single-cell microbiomics for ciliates could be applied to a large number of studies aiming to unravel the evolutionary and ecological meaning of these symbiotic systems.},
}

Bacteria/classification/genetics/*isolation & purification
Bacterial Physiological Phenomena
Biological Evolution
Ciliophora/genetics/isolation & purification/*microbiology/physiology
Ecosystem
Metagenomics/*methods
*Microbiota
Phylogeny
Pilot Projects
Sequence Analysis, DNA
Symbiosis

@article {pmid30397794,
year = {2019},
author = {Lau, NS and Zarkasi, KZ and Md Sah, ASR and Shu-Chien, AC},
title = {Diversity and Coding Potential of the Microbiota in the Photic and Aphotic Zones of Tropical Man-Made Lake with Intensive Aquaculture Activities: a Case Study on Temengor Lake, Malaysia.},
journal = {Microbial ecology},
volume = {78},
number = {1},
pages = {20-32},
doi = {10.1007/s00248-018-1283-0},
pmid = {30397794},
issn = {1432-184X},
mesh = {Aquaculture ; Bacteria/classification/genetics/*isolation & purification/metabolism ; Biodiversity ; DNA, Bacterial/genetics ; Ecosystem ; Lakes/chemistry/*microbiology ; Malaysia ; Metagenomics ; *Microbiota ; Nitrogen/analysis/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfur/analysis/metabolism ; },
abstract = {Although freshwater biomes cover less than 1% of the Earth's surface, they have disproportionate ecological significances. Attempts to study the taxonomy and function of freshwater microbiota are currently limited to samples collected from temperate lakes. In this study, we investigated samples from the photic and aphotic of an aquaculture site (disturbed) of Temengor Lake, a tropical lake in comparison with the undisturbed site of the lake using 16S rRNA amplicon and shotgun metagenomic approaches. Vertical changes in bacterial community composition and function of the Temengor Lake metagenomes were observed. The photic water layer of Temengor Lake was dominated by typical freshwater assemblages consisting of Proteobacteria, Actinobacteria, Bacteroidetes, Verrucomicrobia, and Cyanobacteria lineages. On the other hand, the aphotic water featured in addition to Proteobacteria, Bacteroidetes, Verrucomicrobia, and two more abundant bacterial phyla that are typically ubiquitous in anoxic habitats (Chloroflexi and Firmicutes). The aphotic zone of Temengor Lake exhibited genetic potential for nitrogen and sulfur metabolisms for which terminal electron acceptors other than oxygen are used in the reactions. The aphotic water of the disturbed site also showed an overrepresentation of genes associated with the metabolism of carbohydrates, likely driven by the enrichment of nutrient resulting from aquaculture activities at the site. The results presented in this study can serve as a basis for understanding the structure and functional capacity of the microbial communities in the photic and aphotic zones/water layers of tropical man-made lakes.},
}

Aquaculture
Bacteria/classification/genetics/*isolation & purification/metabolism
Biodiversity
DNA, Bacterial/genetics
Ecosystem
Lakes/chemistry/*microbiology
Malaysia
Metagenomics
*Microbiota
Nitrogen/analysis/metabolism
Phylogeny
RNA, Ribosomal, 16S/genetics
Sulfur/analysis/metabolism

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

Animals
Bacteria/enzymology/genetics
*Diet
Fungi/*growth & development
*Gastrointestinal Microbiome
Gastrointestinal Tract/enzymology/microbiology
Isoptera/*enzymology/*microbiology
Metagenome
Phylogeny
Plant Cells/metabolism
Sequence Analysis, DNA
Symbiosis
Wood/metabolism

@article {pmid30918994,
year = {2019},
author = {Klima, CL and Holman, DB and Ralston, BJ and Stanford, K and Zaheer, R and Alexander, TW and McAllister, TA},
title = {Lower Respiratory Tract Microbiome and Resistome of Bovine Respiratory Disease Mortalities.},
journal = {Microbial ecology},
volume = {78},
number = {2},
pages = {446-456},
doi = {10.1007/s00248-019-01361-3},
pmid = {30918994},
issn = {1432-184X},
support = {2015R025R//Alberta Livestock and Meat Agency/ ; 001//Growing Forward II/ ; 001//Genomics Research Initiative/ ; },
mesh = {Alberta ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/classification/drug effects/genetics/*isolation & purification ; Bacterial Infections/microbiology/mortality/*veterinary ; Cattle ; Cattle Diseases/*microbiology/mortality ; *Drug Resistance, Bacterial ; *Microbiota ; Respiratory System/*microbiology ; Respiratory Tract Diseases/microbiology/mortality/*veterinary ; },
abstract = {Bovine respiratory disease (BRD) continues to be a serious health problem in beef cattle production. A multifactorial condition, BRD encompasses several types of pneumonia that are associated with multiple viral and bacterial agents. Comprehensive identification of microbes associated with BRD fatalities could enhance our understanding of the range of pathogens that contribute to the disease and identify new therapeutic targets. This study used metagenomic analysis to describe the lower respiratory tract microbiome and resistome of 15 feedlot cattle BRD and 3 non-BRD mortalities along with any affiliated integrative and conjugative elements (ICEs). Known bacterial pathogens associated with BRD, including Histophilus somni, Mannheimia haemolytica, and Mycoplasma bovis, were relatively abundant (> 5%) in most, but not all samples. Other relatively abundant genera (> 1%) included Acinetobacter, Bacillus, Bacteroides, Clostridium, Enterococcus, and Pseudomonas. Antimicrobial resistance genes (ARGs) comprised up to 0.5% of sequences and many of these genes were associated with ICEs previously described within the Pasteurellaceae family. A total of 20 putative ICEs were detected among 16 samples. These results document the wide diversity of microorganisms in the lower respiratory tract of cattle that have succumbed to BRD. The data also strongly suggest that antimicrobial-resistant Pasteurellaceae strains are prevalent in BRD cases in Alberta and that the resistance observed is associated with ICEs. The presence of ICEs harboring a wide array of ARGs holds significant consequence for the effectiveness of drug therapies for the control of BRD in beef cattle.},
}

Alberta
Animals
Anti-Bacterial Agents/pharmacology
Bacteria/classification/drug effects/genetics/*isolation & purification
Bacterial Infections/microbiology/mortality/*veterinary
Cattle
Cattle Diseases/*microbiology/mortality
*Drug Resistance, Bacterial
*Microbiota
Respiratory System/*microbiology
Respiratory Tract Diseases/microbiology/mortality/*veterinary

@article {pmid30698687,
year = {2019},
author = {Dhakan, DB and Maji, A and Sharma, AK and Saxena, R and Pulikkan, J and Grace, T and Gomez, A and Scaria, J and Amato, KR and Sharma, VK},
title = {The unique composition of Indian gut microbiome, gene catalogue, and associated fecal metabolome deciphered using multi-omics approaches.},
journal = {GigaScience},
volume = {8},
number = {3},
pages = {},
doi = {10.1093/gigascience/giz004},
pmid = {30698687},
issn = {2047-217X},
mesh = {Adolescent ; Adult ; Child ; Child, Preschool ; Cluster Analysis ; Discriminant Analysis ; Feces/*microbiology ; Gastrointestinal Microbiome/*genetics ; *Genes ; Humans ; India ; Infant ; Least-Squares Analysis ; Membrane Transport Proteins/metabolism ; *Metabolome ; Metabolomics/*methods ; Metagenome ; Metagenomics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Statistics, Nonparametric ; Young Adult ; },
abstract = {BACKGROUND: Metagenomic studies carried out in the past decade have led to an enhanced understanding of the gut microbiome in human health; however, the Indian gut microbiome has not been well explored. We analyzed the gut microbiome of 110 healthy individuals from two distinct locations (North-Central and Southern) in India using multi-omics approaches, including 16S rRNA gene amplicon sequencing, whole-genome shotgun metagenomic sequencing, and metabolomic profiling of fecal and serum samples.

RESULTS: The gene catalogue established in this study emphasizes the uniqueness of the Indian gut microbiome in comparison to other populations. The gut microbiome of the cohort from North-Central India, which was primarily consuming a plant-based diet, was found to be associated with Prevotella and also showed an enrichment of branched chain amino acid (BCAA) and lipopolysaccharide biosynthesis pathways. In contrast, the gut microbiome of the cohort from Southern India, which was consuming an omnivorous diet, showed associations with Bacteroides, Ruminococcus, and Faecalibacterium and had an enrichment of short chain fatty acid biosynthesis pathway and BCAA transporters. This corroborated well with the metabolomics results, which showed higher concentration of BCAAs in the serum metabolome of the North-Central cohort and an association with Prevotella. In contrast, the concentration of BCAAs was found to be higher in the fecal metabolome of the Southern-India cohort and showed a positive correlation with the higher abundance of BCAA transporters.

CONCLUSIONS: The study reveals the unique composition of the Indian gut microbiome, establishes the Indian gut microbial gene catalogue, and compares it with the gut microbiome of other populations. The functional associations revealed using metagenomic and metabolomic approaches provide novel insights on the gut-microbe-metabolic axis, which will be useful for future epidemiological and translational researches.},
}

Adolescent
Adult
Child
Child, Preschool
Cluster Analysis
Discriminant Analysis
Feces/*microbiology
Gastrointestinal Microbiome/*genetics
*Genes
Humans
India
Infant
Least-Squares Analysis
Membrane Transport Proteins/metabolism
*Metabolome
Metabolomics/*methods
Metagenome
Metagenomics
Middle Aged
RNA, Ribosomal, 16S/genetics
Statistics, Nonparametric
Young Adult

@article {pmid30509871,
year = {2019},
author = {Kozyrskyj, AL and Bourque, SL and Ospina, MB},
title = {Microbiota be nimble.},
journal = {EBioMedicine},
volume = {39},
number = {},
pages = {21-22},
doi = {10.1016/j.ebiom.2018.11.058},
pmid = {30509871},
issn = {2352-3964},
mesh = {Dietary Carbohydrates/metabolism ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; Metagenome ; Metagenomics/methods ; Pregnancy ; },
}

Dietary Carbohydrates/metabolism
Female
*Gastrointestinal Microbiome
Humans
Infant, Newborn
Metagenome
Metagenomics/methods
Pregnancy

@article {pmid30418043,
year = {2018},
author = {Muleviciene, A and D'Amico, F and Turroni, S and Candela, M and Jankauskiene, A},
title = {Iron deficiency anemia-related gut microbiota dysbiosis in infants and young children: A pilot study.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {65},
number = {4},
pages = {551-564},
doi = {10.1556/030.65.2018.045},
pmid = {30418043},
issn = {1217-8950},
mesh = {Anemia, Iron-Deficiency/*complications ; Bacteria/classification/genetics ; Child ; Child, Preschool ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Dysbiosis ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Male ; Metagenomics ; *Microbiota ; Phylogeny ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Nutritional iron deficiency (ID) causes not only anemia but also malfunction of the entire human organism. Recently, a role of the gut microbiota has been hypothesized, but limited data are available especially in infants. Here, we performed a pilot study to explore the gut microbiota in 10 patients with iron deficiency anemia (IDA) and 10 healthy controls aged 6-34 months. Fresh stool samples were collected from diapers, and the fecal microbiota was profiled by next-generation sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. Except for diet diversity, the breastfeeding status at the enrollment, the exclusive breastfeeding duration, and the introduction of complementary foods did not differ between groups. Distinct microbial signatures were found in IDA patients, with increased relative abundance of Enterobacteriaceae (mean relative abundance, patients vs. controls, 4.4% vs. 3.0%) and Veillonellaceae (13.7% vs. 3.6%), and reduced abundance of Coriobacteriaceae (3.5% vs. 8.8%) compared to healthy controls. A decreased Bifidobacteriaceae/Enterobacteriaceae ratio was observed in IDA patients. Notwithstanding the low sample size, our data highlight microbiota dysbalance in IDA worth for further investigations, aimed at unraveling the ID impact on the microbiome trajectory in early life, and the possible long-term consequences.},
}

Anemia, Iron-Deficiency/*complications
Bacteria/classification/genetics
Child
Child, Preschool
Cluster Analysis
DNA, Bacterial/chemistry/genetics
DNA, Ribosomal/chemistry/genetics
*Dysbiosis
Feces/microbiology
Female
*Gastrointestinal Microbiome
Humans
Infant
Male
Metagenomics
*Microbiota
Phylogeny
Pilot Projects
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA

@article {pmid29471692,
year = {2018},
author = {Knáb, M and Szili-Kovács, T and Márialigeti, K and Móga, J and Borsodi, AK},
title = {Bacterial diversity in soils of different Hungarian karst areas.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {65},
number = {4},
pages = {439-458},
doi = {10.1556/030.65.2018.002},
pmid = {29471692},
issn = {1217-8950},
mesh = {Bacteria/*classification/*isolation & purification ; Bacteriological Techniques ; *Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Geography ; Humans ; Hungary ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; },
abstract = {Karst areas have great environmental importance as sources of subsurface water and often maintain very sensitive ecosystems. In recent years, increasing number of microbiological studies focused on the bacterial communities of karst soils. In this study, diversity examinations on two distinct Hungarian karst areas, Aggtelek and Tapolca, were performed using parallel cultivation and molecular cloning methods. The phylogenetic affiliation of bacterial strains and molecular clones was determined based on their 16S rRNA gene sequences. Bacterial isolates were identified as members of the phyla Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes. Besides the taxa identified by cultivation, members of the phyla Chloroflexi, Cyanobacteria, Acidobacteria, Verrucomicrobia, and Gemmatimonadetes were detected by the cloning. The difference in the composition of soil bacterial communities was related to geographic locations and soil types. Both the highest and the lowest bacterial diversities were detected in samples from Aggtelek National Park, characterized by Leptic Luvisol and Rendzic Leptosol soil types. The difference in the composition of bacterial communities between Rendzic Leptosol and Leptic Phaeozem soil types at Tapolca could be the result of human impacts.},
}

Bacteria/*classification/*isolation & purification
Bacteriological Techniques
*Biota
Cluster Analysis
DNA, Bacterial/chemistry/genetics
DNA, Ribosomal/chemistry/genetics
Geography
Humans
Hungary
Metagenomics
Phylogeny
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
*Soil Microbiology

@article {pmid29093477,
year = {2017},
author = {Zhang, L and Fu, Q and Li, W and Wang, B and Yin, X and Liu, S and Xu, Z and Niu, Q},
title = {Identification and characterization of a novel β-glucosidase via metagenomic analysis of Bursaphelenchus xylophilus and its microbial flora.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {14850},
pmid = {29093477},
issn = {2045-2322},
mesh = {Animals ; Cellulose/metabolism ; Glucosides/metabolism ; Metagenomics/*methods ; Microbiota/genetics ; Nematoda/*enzymology/microbiology ; Pinus/parasitology ; beta-Glucosidase/*isolation & purification/metabolism ; },
abstract = {β-glucosidases catalyze the final step of cellulose hydrolysis and are essential in cellulose degradation. A β-glucosidase gene, cen502, was identified and isolated from a metagenomic library from Bursaphelenchus xylophilus via functional screening. Analyses indicated that cen502 encodes a 465 amino acid polypeptide that contains a catalytic domain belonging to the glycoside hydrolase family 1 (GH1). Cen502 was heterologously expressed, purified, and biochemically characterized. Recombinant Cen502 displayed optimum enzymatic activity at pH 8.0 and 38 °C. The enzyme had highest specific activity to p-nitrophenyl-β-D-glucopyranoside (pNPG; 180.3 U/mg) and had K m and V max values of 2.334 mol/ml and 9.017 μmol/min/mg, respectively. The addition of Fe2+ and Mn2+ significantly increased Cen502 β-glucosidase activity by 60% and 50%, respectively, while 10% and 25% loss of β-glucosidase activity was induced by addition of Pb2+ and K+, respectively. Cen502 exhibited activity against a broad array of substrates, including cellobiose, lactose, salicin, lichenan, laminarin, and sophorose. However, Cen502 displayed a preference for the hydrolysis of β-1,4 glycosidic bonds rather than β-1,3, β-1,6, or β-1,2 bonds. Our results indicate that Cen502 is a novel β-glucosidase derived from bacteria associated with B. xylophilus and may represent a promising target to enhance the efficiency of cellulose bio-degradation in industrial applications.},
}

Animals
Cellulose/metabolism
Glucosides/metabolism
Metagenomics/*methods
Microbiota/genetics
Nematoda/*enzymology/microbiology
Pinus/parasitology
beta-Glucosidase/*isolation & purification/metabolism

@article {pmid31307536,
year = {2019},
author = {Chen, J and McIlroy, SE and Archana, A and Baker, DM and Panagiotou, G},
title = {A pollution gradient contributes to the taxonomic, functional, and resistome diversity of microbial communities in marine sediments.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {104},
doi = {10.1186/s40168-019-0714-6},
pmid = {31307536},
issn = {2049-2618},
support = {2016-67//Environment and Conservation Fund/ ; },
abstract = {BACKGROUND: Coastal marine environments are one of the most productive ecosystems on Earth. However, anthropogenic impacts exert significant pressure on coastal marine biodiversity, contributing to functional shifts in microbial communities and human health risk factors. However, relatively little is known about the impact of eutrophication-human-derived nutrient pollution-on the marine microbial biosphere.

RESULTS: Here, we tested the hypothesis that benthic microbial diversity and function varies along a pollution gradient, with a focus on human pathogens and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG annotation revealed that zinc, lead, total volatile solids, and ammonia nitrogen were correlated with microbial diversity and function. We propose several microbes, including Planctomycetes and sulfate-reducing microbes as candidates to reflect pollution concentration. Annotation of antibiotic resistance genes showed that the highest abundance of efflux pumps was found at the most polluted site, corroborating the relationship between pollution and human health risk factors. This result suggests that sediments at polluted sites harbor microbes with a higher capacity to reduce intracellular levels of antibiotics, heavy metals, or other environmental contaminants.

CONCLUSIONS: Our findings suggest a correlation between pollution and the marine sediment microbiome and provide insight into the role of high-turnover microbial communities as well as potential pathogenic organisms as real-time indicators of water quality, with implications for human health and demonstrate the inner functional shifts contributed by the microcommunities.},
}

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

Chromatography, High Pressure Liquid
*Fermentation
Fermented Foods/*microbiology
Gas Chromatography-Mass Spectrometry
*Metagenomics
*Microbiota/genetics
Taste

@article {pmid31051396,
year = {2019},
author = {Cabral, L and Noronha, MF and de Sousa, STP and Lacerda-Júnior, GV and Richter, L and Fostier, AH and Andreote, FD and Hess, M and Oliveira, VM},
title = {The metagenomic landscape of xenobiotics biodegradation in mangrove sediments.},
journal = {Ecotoxicology and environmental safety},
volume = {179},
number = {},
pages = {232-240},
doi = {10.1016/j.ecoenv.2019.04.044},
pmid = {31051396},
issn = {1090-2414},
mesh = {Biodegradation, Environmental ; Drug Resistance, Microbial/genetics ; Gene Library ; *Geologic Sediments/chemistry/microbiology ; Hydrolases/genetics ; Metagenomics/*methods ; Metals, Heavy/*analysis/toxicity ; Microbiota/drug effects/*genetics ; Petroleum/analysis/toxicity ; *Wetlands ; Xenobiotics/*analysis/toxicity ; },
abstract = {Metagenomics is a powerful approach to study microorganisms present in any given environment and their potential to maintain and improve ecosystem health without the need of cultivating these microorganisms in the laboratory. In this study, we combined a cultivation-independent metagenomics approach with functional assays to identify the detoxification potential of microbial genes evaluating their potential to contribute to xenobiotics resistance in oil-impacted mangrove sediments. A metagenomic fosmid library containing 12,960 clones from highly contaminated mangrove sediment was used in this study. For assessment of metal resistance, clones were grown in culture medium with increasing concentrations of mercury. The analyses metagenomic library sequences revealed the presence of genes related to heavy metals and antibiotics resistance in the oil-impacted mangrove microbiome. The taxonomic profiling of these sequences suggests that at the genus level, Geobacter was the most abundant genus in our dataset. A functional screening assessment of the metagenomic library successfully detected 24 potential heavy metal tolerant clones, six of which were capable of growing with increased concentrations of mercury. The genetic characterization of selected clones allowed the detection of genes related to detoxification processes, such as chromate transport protein ChrA, haloacid dehalogenase-like hydrolase, lipopolysaccharide transport system, and 3-oxoacyl-[acyl-carrier-protein] reductase. Clones were capable of growing in medium containing increased concentrations of metals and antibiotics, but none manifested strong mercury removal from culture medium characteristic of mercuric reductase activity. These results suggest that resistance to xenobiotic stress varies greatly and that additional studies to elucidate the potential of metal biotransformation need to be carried out with the goal of improving bioremediation application.},
}

Biodegradation, Environmental
Drug Resistance, Microbial/genetics
Gene Library
*Geologic Sediments/chemistry/microbiology
Hydrolases/genetics
Metagenomics/*methods
Metals, Heavy/*analysis/toxicity
Microbiota/drug effects/*genetics
Petroleum/analysis/toxicity
*Wetlands
Xenobiotics/*analysis/toxicity

@article {pmid30901843,
year = {2019},
author = {Cortes, L and Wopereis, H and Tartiere, A and Piquenot, J and Gouw, JW and Tims, S and Knol, J and Chelsky, D},
title = {Metaproteomic and 16S rRNA Gene Sequencing Analysis of the Infant Fecal Microbiome.},
journal = {International journal of molecular sciences},
volume = {20},
number = {6},
pages = {},
doi = {10.3390/ijms20061430},
pmid = {30901843},
issn = {1422-0067},
mesh = {Anti-Bacterial Agents/pharmacology ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome/drug effects ; Humans ; Infant ; Informatics/methods ; Male ; Metagenome ; *Metagenomics/methods ; Proteome ; *Proteomics/methods ; *RNA, Ribosomal, 16S ; },
abstract = {A metaproteomic analysis was conducted on the fecal microbiome of eight infants to characterize global protein and pathway expression. Although mass spectrometry-based proteomics is now a routine tool, analysis of the microbiome presents specific technical challenges, including the complexity and dynamic range of member taxa, the need for well-annotated metagenomic databases, and high inter-protein sequence redundancy and similarity. In this study, an approach was developed for assessment of biological phenotype and metabolic status, as a functional complement to DNA sequence analysis. Fecal samples were prepared and analysed by tandem mass spectrometry and a homology-based meta-clustering strategy was used to combine peptides from multiple species into representative proteins. In total, 15,250 unique peptides were sequenced and assigned to 2154 metaclusters, which were then assigned to pathways and functional groups. Differences were noted in several pathways, consistent with the dominant genera observed in different subjects. Although this study was not powered to draw conclusions from the comparisons, the results obtained demonstrate the applicability of this approach and provide the methods needed for performing semi-quantitative comparisons of human fecal microbiome composition, physiology and metabolism, as well as a more detailed assessment of microbial composition in comparison to 16S rRNA gene sequencing.},
}

Anti-Bacterial Agents/pharmacology
Feces/*microbiology
Female
*Gastrointestinal Microbiome/drug effects
Humans
Infant
Informatics/methods
Male
Metagenome
*Metagenomics/methods
Proteome
*Proteomics/methods
*RNA, Ribosomal, 16S

@article {pmid29196717,
year = {2017},
author = {Hamad, I and Ranque, S and Azhar, EI and Yasir, M and Jiman-Fatani, AA and Tissot-Dupont, H and Raoult, D and Bittar, F},
title = {Culturomics and Amplicon-based Metagenomic Approaches for the Study of Fungal Population in Human Gut Microbiota.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {16788},
pmid = {29196717},
issn = {2045-2322},
mesh = {Ascomycota/classification/genetics/isolation & purification ; Basidiomycota/classification/genetics/isolation & purification ; Case-Control Studies ; DNA, Fungal/analysis ; DNA, Ribosomal Spacer/*analysis ; Feces/microbiology ; Fungi/*classification/genetics/isolation & purification ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; Microbiological Techniques ; Mycobiome ; Mycoses/*microbiology ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Herein, the mycobiota was characterized in fecal samples from sick patients and healthy subjects, collected from different geographical locations and using both culturomics and amplicon-based metagenomics approaches. Using the culturomics approach, a total of 17,800 fungal colonies were isolated from 14 fecal samples, and resulted in the isolation of 41 fungal species, of which 10 species had not been previously reported in the human gut. Deep sequencing of fungal-directed ITS1 and ITS2 amplicons led to the detection of a total of 142 OTUs and 173 OTUs from the ITS1 and ITS2 regions, respectively. Ascomycota composed the largest fraction of the total OTUs analyzed (78.9% and 68.2% of the OTUs from the ITS1 and ITS2 regions, respectively), followed by Basidiomycota (16.9% and 30.1% of the OTUs from the ITS1 and ITS2 regions, respectively). Interestingly, the results demonstrate that the ITS1/ITS2 amplicon sequencing provides different information about gut fungal communities compared to culturomics, though both approaches complete each other in assessing fungal diversity in fecal samples. We also report higher fungal diversity and abundance in patients compared to healthy subjects. In conclusion, combining both culturomic and amplicon-based metagenomic approaches may be a novel strategy towards analyzing fungal compositions in the human gut.},
}

Ascomycota/classification/genetics/isolation & purification
Basidiomycota/classification/genetics/isolation & purification
Case-Control Studies
DNA, Fungal/analysis
DNA, Ribosomal Spacer/*analysis
Feces/microbiology
Fungi/*classification/genetics/isolation & purification
Gastrointestinal Microbiome
High-Throughput Nucleotide Sequencing/*methods
Humans
Metagenomics/*methods
Microbiological Techniques
Mycobiome
Mycoses/*microbiology
Phylogeny
Sequence Analysis, DNA

@article {pmid28947833,
year = {2017},
author = {Thomas, M and Webb, M and Ghimire, S and Blair, A and Olson, K and Fenske, GJ and Fonder, AT and Christopher-Hennings, J and Brake, D and Scaria, J},
title = {Metagenomic characterization of the effect of feed additives on the gut microbiome and antibiotic resistome of feedlot cattle.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {12257},
pmid = {28947833},
issn = {2045-2322},
mesh = {*Animal Feed ; Animals ; Anti-Bacterial Agents/*administration & dosage ; Bacteria/classification/genetics ; Cattle ; *Dietary Supplements ; Drug Resistance, Bacterial/*drug effects ; Gastrointestinal Microbiome/*drug effects ; Genes, Bacterial ; Metagenomics ; North America ; },
abstract = {In North America, antibiotic feed additives such as monensin and tylosin are added to the finishing diets of feedlot cattle to counter the ill-effects of feeding diets with rapidly digestible carbohydrates. While these feed additives have been proven to improve feed efficiency and reduce liver abscess incidence, how these products impact the gastrointestinal microbiota is not completely understood. In this study, we analyzed the impact of providing antibiotic feed additives to feedlot cattle using metagenome sequencing of treated and control animals. Our results indicate that use of antibiotic feed additives does not produce discernable changes at the phylum level. However, treated cattle had reduced abundance of gram-positive bacteria at the genus level. The abundance of Ruminococcus, Erysipelotrichaceae and Lachnospiraceae in the gut of treated steers was reduced. Functional analysis of the data indicates that there was only minimal impact due to the treatment in the rumen. Genes involved in detoxification were significantly increased in the rumen of AB steers. But the relative abundance of these genes was < 0.3%. However, our results did not show any correlation between the presence of antimicrobial resistance genes in the gut microbiota and the administration of antibiotic feed additives.},
}

*Animal Feed
Animals
Anti-Bacterial Agents/*administration & dosage
Bacteria/classification/genetics
Cattle
*Dietary Supplements
Drug Resistance, Bacterial/*drug effects
Gastrointestinal Microbiome/*drug effects
Genes, Bacterial
Metagenomics
North America

@article {pmid28947818,
year = {2017},
author = {Stat, M and Huggett, MJ and Bernasconi, R and DiBattista, JD and Berry, TE and Newman, SJ and Harvey, ES and Bunce, M},
title = {Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {12240},
pmid = {28947818},
issn = {2045-2322},
mesh = {Animals ; Aquatic Organisms/*classification/*genetics ; DNA/analysis/genetics ; Environmental Monitoring/*methods ; Metagenomics/*methods ; Seawater/chemistry ; Sensitivity and Specificity ; Sequence Analysis, DNA ; Tropical Climate ; },
abstract = {Effective marine management requires comprehensive data on the status of marine biodiversity. However, efficient methods that can document biodiversity in our oceans are currently lacking. Environmental DNA (eDNA) sourced from seawater offers a new avenue for investigating the biota in marine ecosystems. Here, we investigated the potential of eDNA to inform on the breadth of biodiversity present in a tropical marine environment. Directly sequencing eDNA from seawater using a shotgun approach resulted in only 0.34% of 22.3 million reads assigning to eukaryotes, highlighting the inefficiency of this method for assessing eukaryotic diversity. In contrast, using 'tree of life' (ToL) metabarcoding and 20-fold fewer sequencing reads, we could detect 287 families across the major divisions of eukaryotes. Our data also show that the best performing 'universal' PCR assay recovered only 44% of the eukaryotes identified across all assays, highlighting the need for multiple metabarcoding assays to catalogue biodiversity. Lastly, focusing on the fish genus Lethrinus, we recovered intra- and inter-specific haplotypes from seawater samples, illustrating that eDNA can be used to explore diversity beyond taxon identifications. Given the sensitivity and low cost of eDNA metabarcoding we advocate this approach be rapidly integrated into biomonitoring programs.},
}

Animals
Aquatic Organisms/*classification/*genetics
DNA/analysis/genetics
Environmental Monitoring/*methods
Metagenomics/*methods
Seawater/chemistry
Sensitivity and Specificity
Sequence Analysis, DNA
Tropical Climate

@article {pmid31171880,
year = {2019},
author = {Yachida, S and Mizutani, S and Shiroma, H and Shiba, S and Nakajima, T and Sakamoto, T and Watanabe, H and Masuda, K and Nishimoto, Y and Kubo, M and Hosoda, F and Rokutan, H and Matsumoto, M and Takamaru, H and Yamada, M and Matsuda, T and Iwasaki, M and Yamaji, T and Yachida, T and Soga, T and Kurokawa, K and Toyoda, A and Ogura, Y and Hayashi, T and Hatakeyama, M and Nakagama, H and Saito, Y and Fukuda, S and Shibata, T and Yamada, T},
title = {Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer.},
journal = {Nature medicine},
volume = {25},
number = {6},
pages = {968-976},
doi = {10.1038/s41591-019-0458-7},
pmid = {31171880},
issn = {1546-170X},
mesh = {Adult ; Aged ; Case-Control Studies ; Colorectal Neoplasms/genetics/*metabolism/*microbiology ; Disease Progression ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Male ; Metabolomics ; Metagenomics ; Middle Aged ; Neoplasm Staging ; Young Adult ; },
abstract = {In most cases of sporadic colorectal cancers, tumorigenesis is a multistep process, involving genomic alterations in parallel with morphologic changes. In addition, accumulating evidence suggests that the human gut microbiome is linked to the development of colorectal cancer. Here we performed fecal metagenomic and metabolomic studies on samples from a large cohort of 616 participants who underwent colonoscopy to assess taxonomic and functional characteristics of gut microbiota and metabolites. Microbiome and metabolome shifts were apparent in cases of multiple polypoid adenomas and intramucosal carcinomas, in addition to more advanced lesions. We found two distinct patterns of microbiome elevations. First, the relative abundance of Fusobacterium nucleatum spp. was significantly (P < 0.005) elevated continuously from intramucosal carcinoma to more advanced stages. Second, Atopobium parvulum and Actinomyces odontolyticus, which co-occurred in intramucosal carcinomas, were significantly (P < 0.005) increased only in multiple polypoid adenomas and/or intramucosal carcinomas. Metabolome analyses showed that branched-chain amino acids and phenylalanine were significantly (P < 0.005) increased in intramucosal carcinomas and bile acids, including deoxycholate, were significantly (P < 0.005) elevated in multiple polypoid adenomas and/or intramucosal carcinomas. We identified metagenomic and metabolomic markers to discriminate cases of intramucosal carcinoma from the healthy controls. Our large-cohort multi-omics data indicate that shifts in the microbiome and metabolome occur from the very early stages of the development of colorectal cancer, which is of possible etiological and diagnostic importance.},
}

Adult
Aged
Case-Control Studies
Colorectal Neoplasms/genetics/*metabolism/*microbiology
Disease Progression
Female
*Gastrointestinal Microbiome/genetics
Humans
Male
Metabolomics
Metagenomics
Middle Aged
Neoplasm Staging
Young Adult

@article {pmid31142849,
year = {2019},
author = {Fettweis, JM and Serrano, MG and Brooks, JP and Edwards, DJ and Girerd, PH and Parikh, HI and Huang, B and Arodz, TJ and Edupuganti, L and Glascock, AL and Xu, J and Jimenez, NR and Vivadelli, SC and Fong, SS and Sheth, NU and Jean, S and Lee, V and Bokhari, YA and Lara, AM and Mistry, SD and Duckworth, RA and Bradley, SP and Koparde, VN and Orenda, XV and Milton, SH and Rozycki, SK and Matveyev, AV and Wright, ML and Huzurbazar, SV and Jackson, EM and Smirnova, E and Korlach, J and Tsai, YC and Dickinson, MR and Brooks, JL and Drake, JI and Chaffin, DO and Sexton, AL and Gravett, MG and Rubens, CE and Wijesooriya, NR and Hendricks-Muñoz, KD and Jefferson, KK and Strauss, JF and Buck, GA},
title = {The vaginal microbiome and preterm birth.},
journal = {Nature medicine},
volume = {25},
number = {6},
pages = {1012-1021},
doi = {10.1038/s41591-019-0450-2},
pmid = {31142849},
issn = {1546-170X},
mesh = {Adult ; African Americans ; Biodiversity ; Cohort Studies ; Cytokines/metabolism ; Female ; Host Microbial Interactions/immunology ; Humans ; Infant, Newborn ; Inflammation Mediators/metabolism ; Longitudinal Studies ; Metagenomics ; *Microbiota/genetics/immunology ; Premature Birth/etiology/immunology/*microbiology ; Risk Factors ; United States ; Vagina/immunology/*microbiology ; Young Adult ; },
abstract = {The incidence of preterm birth exceeds 10% worldwide. There are significant disparities in the frequency of preterm birth among populations within countries, and women of African ancestry disproportionately bear the burden of risk in the United States. In the present study, we report a community resource that includes 'omics' data from approximately 12,000 samples as part of the integrative Human Microbiome Project. Longitudinal analyses of 16S ribosomal RNA, metagenomic, metatranscriptomic and cytokine profiles from 45 preterm and 90 term birth controls identified harbingers of preterm birth in this cohort of women predominantly of African ancestry. Women who delivered preterm exhibited significantly lower vaginal levels of Lactobacillus crispatus and higher levels of BVAB1, Sneathia amnii, TM7-H1, a group of Prevotella species and nine additional taxa. The first representative genomes of BVAB1 and TM7-H1 are described. Preterm-birth-associated taxa were correlated with proinflammatory cytokines in vaginal fluid. These findings highlight new opportunities for assessment of the risk of preterm birth.},
}

Adult
African Americans
Biodiversity
Cohort Studies
Cytokines/metabolism
Female
Host Microbial Interactions/immunology
Humans
Infant, Newborn
Inflammation Mediators/metabolism
Longitudinal Studies
Metagenomics
*Microbiota/genetics/immunology
Premature Birth/etiology/immunology/*microbiology
Risk Factors
United States
Vagina/immunology/*microbiology
Young Adult

@article {pmid30719705,
year = {2019},
author = {Cheng, L and Chen, Y and Zhang, X and Zheng, X and Cao, J and Wu, Z and Qin, W and Cheng, K},
title = {A metagenomic analysis of the modulatory effect of Cyclocarya paliurus flavonoids on the intestinal microbiome in a high-fat diet-induced obesity mouse model.},
journal = {Journal of the science of food and agriculture},
volume = {99},
number = {8},
pages = {3967-3975},
doi = {10.1002/jsfa.9622},
pmid = {30719705},
issn = {1097-0010},
support = {//K. C. Wong Magna Fund of Ningbo University/ ; 2017C02039//Key Research and Development Project of Zhejiang Province/ ; 2018C02047//Key Research and Development Project of Zhejiang Province/ ; LY19C200006//Zhejiang Provincial Natural Science Foundation of China/ ; },
mesh = {Adult ; Animals ; Bacteria/classification/drug effects/*genetics/isolation & purification ; Diet, High-Fat/adverse effects ; Disease Models, Animal ; Dysbiosis/drug therapy/metabolism/microbiology ; Female ; Flavonoids/*administration & dosage/analysis ; Gastrointestinal Microbiome/*drug effects ; Humans ; Intestines/*microbiology ; Juglandaceae/*chemistry ; Male ; Metagenomics ; Mice ; Mice, Inbred C57BL ; Obesity/*drug therapy/microbiology ; Plant Extracts/*administration & dosage/analysis ; },
abstract = {BACKGROUND: As a result of a low bioavailability, the majority of Cyclocarya paliurus flavonoids (CPF) remain in the large intestine where they accumulate to exert a modulatory effect on the intestinal micro-ecology. Therefore, the present study investigated the modulatory effect of CPF on intestinal microbiota.

RESULTS: CPF dramatically ameliorated the obesity-induced gut dysbiosis. A significant decrease (P < 0.05) was observed in the ratio of Firmicutes/Bacteroidetes after CPF treatment for 8 weeks. Moreover, Kyoto Encyclopedia of Genes and Genomes pathways of biosynthesis of amino acids, the two-component system and ATP-binding cassette transporters enriched the most differentially expressed genes after CPF intervention.

CONCLUSION: The results of the present study indicate that CPF might have prebiotic-like activity and could be used as a functional food component with potential therapeutic utility to prevent obesity-related metabolic disorders by manipulating the gut flora and affecting certain metabolic pathways, thus contributing to the improvement of human health. © 2019 Society of Chemical Industry.},
}

Adult
Animals
Bacteria/classification/drug effects/*genetics/isolation & purification
Diet, High-Fat/adverse effects
Disease Models, Animal
Dysbiosis/drug therapy/metabolism/microbiology
Female
Flavonoids/*administration & dosage/analysis
Gastrointestinal Microbiome/*drug effects
Humans
Intestines/*microbiology
Juglandaceae/*chemistry
Male
Metagenomics
Mice
Mice, Inbred C57BL
Obesity/*drug therapy/microbiology
Plant Extracts/*administration & dosage/analysis

@article {pmid29539432,
year = {2018},
author = {Fujisaka, S and Avila-Pacheco, J and Soto, M and Kostic, A and Dreyfuss, JM and Pan, H and Ussar, S and Altindis, E and Li, N and Bry, L and Clish, CB and Kahn, CR},
title = {Diet, Genetics, and the Gut Microbiome Drive Dynamic Changes in Plasma Metabolites.},
journal = {Cell reports},
volume = {22},
number = {11},
pages = {3072-3086},
pmid = {29539432},
issn = {2211-1247},
support = {P30 DK040561/DK/NIDDK NIH HHS/United States ; U01 CA210171/CA/NCI NIH HHS/United States ; P30 DK036836/DK/NIDDK NIH HHS/United States ; R01 DK033201/DK/NIDDK NIH HHS/United States ; R37 DK031036/DK/NIDDK NIH HHS/United States ; R01 DK031036/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; Diet, High-Fat/*methods ; Gastrointestinal Microbiome/*genetics ; Humans ; Metabolomics/*methods ; Mice ; Obesity/*genetics/pathology ; },
abstract = {Diet, genetics, and the gut microbiome are determinants of metabolic status, in part through production of metabolites by the gut microbiota. To understand the mechanisms linking these factors, we performed LC-MS-based metabolomic analysis of cecal contents and plasma from C57BL/6J, 129S1/SvImJ, and 129S6/SvEvTac mice on chow or a high-fat diet (HFD) and HFD-treated with vancomycin or metronidazole. Prediction of the functional metagenome of gut bacteria by PICRUSt analysis of 16S sequences revealed dramatic differences in microbial metabolism. Cecal and plasma metabolites showed multifold differences reflecting the combined and integrated effects of diet, antibiotics, host background, and the gut microbiome. Eighteen plasma metabolites correlated positively or negatively with host insulin resistance across strains and diets. Over 1,000 still-unidentified metabolite peaks were also highly regulated by diet, antibiotics, and genetic background. Thus, diet, host genetics, and the gut microbiota interact to create distinct responses in plasma metabolites, which can contribute to regulation of metabolism and insulin resistance.},
}

Animals
Diet, High-Fat/*methods
Gastrointestinal Microbiome/*genetics
Humans
Metabolomics/*methods
Mice
Obesity/*genetics/pathology

@article {pmid29463537,
year = {2018},
author = {Ajami, NJ and Cope, JL and Wong, MC and Petrosino, JF and Chesnel, L},
title = {Impact of Oral Fidaxomicin Administration on the Intestinal Microbiota and Susceptibility to Clostridium difficile Colonization in Mice.},
journal = {Antimicrobial agents and chemotherapy},
volume = {62},
number = {5},
pages = {},
pmid = {29463537},
issn = {1098-6596},
mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Clostridium Infections/*drug therapy/prevention & control ; Clostridium difficile/*drug effects ; Cross Infection/drug therapy/microbiology/prevention & control ; Disease Models, Animal ; Feces/microbiology ; Female ; Fidaxomicin/*pharmacology ; Gastrointestinal Microbiome/*drug effects ; Mice ; Mice, Inbred C57BL ; RNA, Ribosomal, 16S/genetics ; Vancomycin/*pharmacology ; },
abstract = {Clostridium difficile infection (CDI), a common cause of hospital-acquired infections, typically occurs after disruption of the normal gut microbiome by broad-spectrum antibiotics. Fidaxomicin is a narrow-spectrum antibiotic that demonstrates a reduced impact on the normal gut microbiota and is approved for the treatment of CDI. To further explore the benefits of this property, we used a murine model to examine the effects of fidaxomicin versus vancomycin on gut microbiota and susceptibility to C. difficile colonization while tracking microbiota recovery over time. Mice were exposed to fidaxomicin or vancomycin by oral gavage for 3 days and subsequently challenged with C. difficile spores at predetermined time points up to 21 days postexposure to antibiotics. Fecal samples were subsequently collected for analysis. Twenty-four hours postchallenge, mice were euthanized and the colon contents harvested. The microbiota was characterized using 16S rRNA gene sequencing. All fidaxomicin-exposed mice (except for one at day 8) were resistant to C. difficile colonization. However, 9 of 15 vancomycin-exposed mice were susceptible to C. difficile colonization until day 12. All vancomycin-exposed mice recovered colonization resistance by day 16. Bacterial diversity was similar prior to antibiotic exposure in both arms and decreased substantially after exposure. A shift in taxonomic structure and composition occurred after both exposures; however, the shift was greater in vancomycin-exposed than in fidaxomicin-exposed mice. In summary, compared with vancomycin, fidaxomicin exposure had less impact on microbiota composition, promoted faster microbial recovery, and had less impact on the loss of C. difficile colonization resistance.},
}

Animals
Anti-Bacterial Agents/*pharmacology
Clostridium Infections/*drug therapy/prevention & control
Clostridium difficile/*drug effects
Cross Infection/drug therapy/microbiology/prevention & control
Disease Models, Animal
Feces/microbiology
Female
Fidaxomicin/*pharmacology
Gastrointestinal Microbiome/*drug effects
Mice
Mice, Inbred C57BL
RNA, Ribosomal, 16S/genetics
Vancomycin/*pharmacology

@article {pmid29194524,
year = {2018},
author = {Zhu, C and Miller, M and Marpaka, S and Vaysberg, P and Rühlemann, MC and Wu, G and Heinsen, FA and Tempel, M and Zhao, L and Lieb, W and Franke, A and Bromberg, Y},
title = {Functional sequencing read annotation for high precision microbiome analysis.},
journal = {Nucleic acids research},
volume = {46},
number = {4},
pages = {e23},
pmid = {29194524},
issn = {1362-4962},
mesh = {Algorithms ; Bacterial Proteins/physiology ; Child ; Crohn Disease/microbiology ; Humans ; Metagenomics/*methods ; *Microbiota ; Molecular Sequence Annotation/*methods ; Prader-Willi Syndrome/microbiology ; Sequence Alignment ; },
abstract = {The vast majority of microorganisms on Earth reside in often-inseparable environment-specific communities-microbiomes. Meta-genomic/-transcriptomic sequencing could reveal the otherwise inaccessible functionality of microbiomes. However, existing analytical approaches focus on attributing sequencing reads to known genes/genomes, often failing to make maximal use of available data. We created faser (functional annotation of sequencing reads), an algorithm that is optimized to map reads to molecular functions encoded by the read-correspondent genes. The mi-faser microbiome analysis pipeline, combining faser with our manually curated reference database of protein functions, accurately annotates microbiome molecular functionality. mi-faser's minutes-per-microbiome processing speed is significantly faster than that of other methods, allowing for large scale comparisons. Microbiome function vectors can be compared between different conditions to highlight environment-specific and/or time-dependent changes in functionality. Here, we identified previously unseen oil degradation-specific functions in BP oil-spill data, as well as functional signatures of individual-specific gut microbiome responses to a dietary intervention in children with Prader-Willi syndrome. Our method also revealed variability in Crohn's Disease patient microbiomes and clearly distinguished them from those of related healthy individuals. Our analysis highlighted the microbiome role in CD pathogenicity, demonstrating enrichment of patient microbiomes in functions that promote inflammation and that help bacteria survive it.},
}

Algorithms
Bacterial Proteins/physiology
Child
Crohn Disease/microbiology
Humans
Metagenomics/*methods
*Microbiota
Molecular Sequence Annotation/*methods
Prader-Willi Syndrome/microbiology
Sequence Alignment

@article {pmid29142285,
year = {2017},
author = {Mehrpouya-Bahrami, P and Chitrala, KN and Ganewatta, MS and Tang, C and Murphy, EA and Enos, RT and Velazquez, KT and McCellan, J and Nagarkatti, M and Nagarkatti, P},
title = {Blockade of CB1 cannabinoid receptor alters gut microbiota and attenuates inflammation and diet-induced obesity.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {15645},
pmid = {29142285},
issn = {2045-2322},
support = {K01 AT007824/AT/NCCIH NIH HHS/United States ; P01 AT003961/AT/NCCIH NIH HHS/United States ; P20 GM103641/GM/NIGMS NIH HHS/United States ; R01 AT006888/AT/NCCIH NIH HHS/United States ; R01 ES019313/ES/NIEHS NIH HHS/United States ; R01 MH094755/MH/NIMH NIH HHS/United States ; },
mesh = {Adipose Tissue/metabolism/pathology ; Animals ; Cannabinoid Receptor Antagonists/*pharmacology ; Cell Movement/drug effects ; Cytokines/metabolism ; Gastrointestinal Microbiome/*drug effects ; Inflammation/drug therapy/metabolism/pathology ; Macrophages/metabolism ; Male ; Mice ; Obesity/*drug therapy/etiology/metabolism ; Receptor, Cannabinoid, CB1/*antagonists & inhibitors/metabolism ; Rimonabant/*pharmacology ; },
abstract = {Obesity is characterized by chronic low-grade, systemic inflammation, altered gut microbiota, and gut barrier disruption. Additionally, obesity is associated with increased activity of endocannabinoid system (eCB). However, the clear connection between gut microbiota and the eCB system in the regulation of energy homeostasis and adipose tissue inflammation and metabolism, remains to be established. We investigated the effect of treatment of mice with a cannabinoid receptor 1 (CB1) antagonist on Diet-Induced Obesity (DIO), specifically whether such a treatment that blocks endocannabinoid activity can induce changes in gut microbiota and anti-inflammatory state in adipose tissue. Blockade of CB1 attenuated DIO, inflammatory cytokines and trafficking of M1 macrophages into adipose tissue. Decreased inflammatory tone was associated with a lower intestinal permeability and decreased metabolic endotoxemia as evidenced by reduced plasma LPS level, and improved hyperglycemia and insulin resistance. 16S rRNA metagenomics sequencing revealed that CB1 blockade dramatically increased relative abundance of Akkermansia muciniphila and decreased Lanchnospiraceae and Erysipelotrichaceae in the gut. Together, the current study suggests that blocking of CB1 ameliorates Diet-Induced Obesity and metabolic disorder by modulating macrophage inflammatory mediators, and that this effect is associated with alterations in gut microbiota and their metabolites.},
}

Adipose Tissue/metabolism/pathology
Animals
Cannabinoid Receptor Antagonists/*pharmacology
Cell Movement/drug effects
Cytokines/metabolism
Gastrointestinal Microbiome/*drug effects
Inflammation/drug therapy/metabolism/pathology
Macrophages/metabolism
Male
Mice
Obesity/*drug therapy/etiology/metabolism
Receptor, Cannabinoid, CB1/*antagonists & inhibitors/metabolism
Rimonabant/*pharmacology

@article {pmid29097759,
year = {2017},
author = {Meiser, A and Otte, J and Schmitt, I and Grande, FD},
title = {Sequencing genomes from mixed DNA samples - evaluating the metagenome skimming approach in lichenized fungi.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {14881},
pmid = {29097759},
issn = {2045-2322},
mesh = {DNA, Fungal/*genetics ; *Genome, Fungal ; Lichens/classification/*genetics ; Metagenomics ; Sequence Analysis, DNA ; Transcriptome ; },
abstract = {The metagenome skimming approach, i.e. low coverage shotgun sequencing of multi-species assemblages and subsequent reconstruction of individual genomes, is increasingly used for in-depth genomic characterization of ecological communities. This approach is a promising tool for reconstructing genomes of facultative symbionts, such as lichen-forming fungi, from metagenomic reads. However, no study has so far tested accuracy and completeness of assemblies based on metagenomic sequences compared to assemblies based on pure culture strains of lichenized fungi. Here we assembled the genomes of Evernia prunastri and Pseudevernia furfuracea based on metagenomic sequences derived from whole lichen thalli. We extracted fungal contigs using two different taxonomic binning methods, and performed gene prediction on the fungal contig subsets. We then assessed quality and completeness of the metagenome-based assemblies using genome assemblies as reference which are based on pure culture strains of the two fungal species. Our comparison showed that we were able to reconstruct fungal genomes from uncultured lichen thalli, and also cover most of the gene space (86-90%). Metagenome skimming will facilitate genome mining, comparative (phylo)genomics, and population genetics of lichen-forming fungi by circumventing the time-consuming, sometimes unfeasible, step of aposymbiotic cultivation.},
}

DNA, Fungal/*genetics
*Genome, Fungal
Lichens/classification/*genetics
Metagenomics
Sequence Analysis, DNA
Transcriptome

@article {pmid31301473,
year = {2019},
author = {Bengtsson-Palme, J and Milakovic, M and Švecová, H and Ganjto, M and Jonsson, V and Grabic, R and Udikovic-Kolic, N},
title = {Industrial wastewater treatment plant enriches antibiotic resistance genes and alters the structure of microbial communities.},
journal = {Water research},
volume = {162},
number = {},
pages = {437-445},
doi = {10.1016/j.watres.2019.06.073},
pmid = {31301473},
issn = {1879-2448},
abstract = {Antibiotic resistance is an emerging global health crisis, driven largely by overuse and misuse of antibiotics. However, there are examples in which the production of these antimicrobial agents has polluted the environment with active antibiotic residues, selecting for antibiotic resistant bacteria and the genes they carry. In this work, we have used shotgun metagenomics to investigate the taxonomic structure and resistance gene composition of sludge communities in a treatment plant in Croatia receiving wastewater from production of the macrolide antibiotic azithromycin. We found that the total abundance of antibiotic resistance genes was three times higher in sludge from the treatment plant receiving wastewater from pharmaceutical production than in municipal sludge from a sewage treatment plant in Zagreb. Surprisingly, macrolide resistance genes did not have higher abundances in the industrial sludge, but genes associated with mobile genetic elements such as integrons had. We conclude that at high concentrations of antibiotics, selection may favor taxonomic shifts towards intrinsically resistant species or strains harboring chromosomal resistance mutations rather than acquisition of mobile resistance determinants. Our results underscore the need for regulatory action also within Europe to avoid release of antibiotics into the environment.},
}

@article {pmid30826606,
year = {2019},
author = {Bai, Y and Ruan, X and Xie, X and Yan, Z},
title = {Antibiotic resistome profile based on metagenomics in raw surface drinking water source and the influence of environmental factor: A case study in Huaihe River Basin, China.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {248},
number = {},
pages = {438-447},
doi = {10.1016/j.envpol.2019.02.057},
pmid = {30826606},
issn = {1873-6424},
mesh = {Anti-Bacterial Agents/pharmacology ; Bacitracin/pharmacology ; Burkholderiaceae/drug effects/*genetics ; China ; Drinking Water/*microbiology ; Drug Resistance, Microbial/*genetics ; Flavobacterium/drug effects/*genetics ; Genes, Bacterial/genetics ; Humans ; Metagenomics ; Microbiota/drug effects ; Rivers/*microbiology ; Tetracyclines/pharmacology ; Verrucomicrobia/drug effects/*genetics ; beta-Lactams/pharmacology ; },
abstract = {The contamination with antibiotic resistance genes (ARGs) in raw drinking water source may pose a direct threat to human health. In this study, metagenomics sequencing and analysis were applied to investigate the ARG pattern in 12 drinking water sources in upper and middle reach of Huaihe River Basin, China. Based on the redundant analysis and multi-linear regression model, location, specific microbial taxa, number of livestock and health facilities significantly influenced the ARG profile in drinking water sources. Besides the cluster effect of ARG in samples from plain and bedrock mountain areas, the samples from fracture aquifer areas also showed a distinctive biogeographic pattern with that from porous aquifer areas. Putative ARGs host Opitutus and Flavobacterium were the enriched biomarkers in plain and fracture aquifer area respectively, which mainly carried bacitracin, multidrug, beta-lactam and tetracycline ARGs. This result illuminated that both natural background and anthropogenic activities in the watershed influenced the ARG profile in natural freshwater system significantly. The low MGEs abundance and absence of pathogen revealed a low ARG dissemination risk in sampled drinking water sources, while Polynucleobacter was an abundant ARGs host and was significantly related to the ARG profile, which indicated that specific bacteria was responsible for ARGs propagation and accumulation in surface freshwater system. Further researches are needed to assess human exposure to raw drinking water source and the potential risk, as well as the species interaction in microbial community and its impact on ARG propagation under oligotrophic condition.},
}

Anti-Bacterial Agents/pharmacology
Bacitracin/pharmacology
Burkholderiaceae/drug effects/*genetics
China
Drinking Water/*microbiology
Drug Resistance, Microbial/*genetics
Flavobacterium/drug effects/*genetics
Genes, Bacterial/genetics
Humans
Metagenomics
Microbiota/drug effects
Rivers/*microbiology
Tetracyclines/pharmacology
Verrucomicrobia/drug effects/*genetics
beta-Lactams/pharmacology

@article {pmid30311571,
year = {2018},
author = {Shillitoe, EJ},
title = {The Microbiome of Oral Cancer.},
journal = {Critical reviews in oncogenesis},
volume = {23},
number = {3-4},
pages = {153-160},
doi = {10.1615/CritRevOncog.2018027422},
pmid = {30311571},
issn = {0893-9675},
mesh = {Animals ; Bacterial Infections/complications/microbiology ; Cell Transformation, Neoplastic ; Disease Susceptibility ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; Mouth Neoplasms/*etiology ; Mycoses/complications/microbiology ; Virus Diseases/complications/virology ; },
abstract = {The pathogenesis of oral cancer is complex, and not all relevant factors involved in it have been determined. In particular, the role of the microbiota is not well understood because of difficulties in isolating and culturing its organisms. However, the recent development of metagenomic sequencing allows the discovery of all the DNA sequences in a specimen, and thus, the microbiome is now under intensive investigation. Studies of the bacteriome, the mycobiome, and the virome have revealed new organisms and have uncovered various differences between healthy persons and patients with oral cancer. In addition, sequencing of human samples shows the existence of DNA sequences that may be from novel microbes but are actually of unknown origin and so are referred to as the dark matter. The large volumes of data that are being produced by sequencing projects must be studied further to reveal novel pathogens and new pathways in the development of oral cancer.},
}

Animals
Bacterial Infections/complications/microbiology
Cell Transformation, Neoplastic
Disease Susceptibility
Humans
Metagenome
Metagenomics/methods
*Microbiota
Mouth Neoplasms/*etiology
Mycoses/complications/microbiology
Virus Diseases/complications/virology

@article {pmid30257633,
year = {2018},
author = {White, LS and Van den Bogaerde, J and Kamm, M},
title = {The gut microbiota: cause and cure of gut diseases.},
journal = {The Medical journal of Australia},
volume = {209},
number = {7},
pages = {312-317},
pmid = {30257633},
issn = {1326-5377},
mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Diseases/microbiology/physiopathology/therapy ; *Gastrointestinal Microbiome/drug effects/genetics/physiology ; Humans ; Inflammatory Bowel Diseases/microbiology/physiopathology/therapy ; Liver Diseases/microbiology/physiopathology/therapy ; Metabolic Syndrome/microbiology/physiopathology/therapy ; Metagenomics ; Mice ; *Obesity/microbiology/physiopathology/therapy ; },
abstract = {The gastrointestinal microbiota is emerging as a central factor in the pathogenesis of a range of gastrointestinal and hepatic disorders. Epidemiological studies, and experimental studies in animals and humans, have highlighted a likely causative role of this microbial community in the modern global epidemics of inflammatory bowel disease, non-alcoholic fatty liver disease, non-alcoholic steato-hepatitis, obesity and metabolic syndrome. New techniques for microbial culture and gene sequencing are enabling the identification of specific pathogens and protective organisms in these conditions. Factors that change the microbiota are being defined: dietary pattern, specific foods, food additives in processed food and drinks, such as emulsifiers and non-sugar sweeteners, and antibiotics. Microbiota changes in early life appear critical to the later development of a range of inflammatory disorders. For many of these conditions, the treatment paradigm will change, at least in part, from immune suppression and drug therapy to treatments that reshape the microbiota or restore its integrity. These treatments include dietary changes, specific microbial manipulation and faecal microbiota transplantation. A dialogue is needed regarding population strategies that target disease prevention. This will include how food is produced, what additives it contains, and how it is processed. Widespread use of antibiotics, from agricultural and veterinary to medicinal settings, needs more attention. At the individual level, microbial profiles may be able to predict who is at risk of disease when subjected to particular environmental influences, and what microbial restoration is needed to minimise risk.},
}

Animals
Anti-Bacterial Agents/pharmacology
*Gastrointestinal Diseases/microbiology/physiopathology/therapy
*Gastrointestinal Microbiome/drug effects/genetics/physiology
Humans
Inflammatory Bowel Diseases/microbiology/physiopathology/therapy
Liver Diseases/microbiology/physiopathology/therapy
Metabolic Syndrome/microbiology/physiopathology/therapy
Metagenomics
Mice
*Obesity/microbiology/physiopathology/therapy

@article {pmid30250051,
year = {2019},
author = {Ju, F and Beck, K and Yin, X and Maccagnan, A and McArdell, CS and Singer, HP and Johnson, DR and Zhang, T and Bürgmann, H},
title = {Wastewater treatment plant resistomes are shaped by bacterial composition, genetic exchange, and upregulated expression in the effluent microbiomes.},
journal = {The ISME journal},
volume = {13},
number = {2},
pages = {346-360},
doi = {10.1038/s41396-018-0277-8},
pmid = {30250051},
issn = {1751-7370},
mesh = {Anti-Bacterial Agents/analysis ; Bacteria/drug effects/genetics/metabolism ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Metagenome ; Metagenomics ; *Microbiota ; Transcriptome ; Up-Regulation ; Waste Disposal, Fluid ; Waste Water/chemistry/*microbiology ; },
abstract = {Wastewater treatment plants (WWTPs) are implicated as hotspots for the dissemination of antibacterial resistance into the environment. However, the in situ processes governing removal, persistence, and evolution of resistance genes during wastewater treatment remain poorly understood. Here, we used quantitative metagenomic and metatranscriptomic approaches to achieve a broad-spectrum view of the flow and expression of genes related to antibacterial resistance to over 20 classes of antibiotics, 65 biocides, and 22 metals. All compartments of 12 WWTPs share persistent resistance genes with detectable transcriptional activities that were comparatively higher in the secondary effluent, where mobility genes also show higher relative abundance and expression ratios. The richness and abundance of resistance genes vary greatly across metagenomes from different treatment compartments, and their relative and absolute abundances correlate with bacterial community composition and biomass concentration. No strong drivers of resistome composition could be identified among the chemical stressors analyzed, although the sub-inhibitory concentration (hundreds of ng/L) of macrolide antibiotics in wastewater correlates with macrolide and vancomycin resistance genes. Contig-based analysis shows considerable co-localization between resistance and mobility genes and implies a history of substantial horizontal resistance transfer involving human bacterial pathogens. Based on these findings, we propose future inclusion of mobility incidence (M%) and host pathogenicity of antibiotic resistance genes in their quantitative health risk ranking models with an ultimate goal to assess the biological significance of wastewater resistomes with regard to disease control in humans or domestic livestock.},
}

Anti-Bacterial Agents/analysis
Bacteria/drug effects/genetics/metabolism
Drug Resistance, Bacterial/*genetics
Gene Transfer, Horizontal
Genes, Bacterial
Metagenome
Metagenomics
*Microbiota
Transcriptome
Up-Regulation
Waste Disposal, Fluid
Waste Water/chemistry/*microbiology

@article {pmid30158571,
year = {2018},
author = {Caussy, C and Loomba, R},
title = {Gut microbiome, microbial metabolites and the development of NAFLD.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {15},
number = {12},
pages = {719-720},
doi = {10.1038/s41575-018-0058-x},
pmid = {30158571},
issn = {1759-5053},
mesh = {Female ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; *Non-alcoholic Fatty Liver Disease ; Obesity ; },
}

Female
*Gastrointestinal Microbiome
Humans
Metagenomics
*Non-alcoholic Fatty Liver Disease
Obesity

@article {pmid30136922,
year = {2018},
author = {Cornet, L and Bertrand, AR and Hanikenne, M and Javaux, EJ and Wilmotte, A and Baurain, D},
title = {Metagenomic assembly of new (sub)polar Cyanobacteria and their associated microbiome from non-axenic cultures.},
journal = {Microbial genomics},
volume = {4},
number = {9},
pages = {},
pmid = {30136922},
issn = {2057-5858},
mesh = {Antarctic Regions ; Arctic Regions ; Cyanobacteria/*classification/*genetics/isolation & purification ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Cyanobacteria form one of the most diversified phyla of Bacteria. They are important ecologically as primary producers, for Earth evolution and biotechnological applications. Yet, Cyanobacteria are notably difficult to purify and grow axenically, and most strains in culture collections contain heterotrophic bacteria that were probably associated with Cyanobacteria in the environment. Obtaining cyanobacterial DNA without contaminant sequences is thus a challenging and time-consuming task. Here, we describe a metagenomic pipeline that enables the easy recovery of genomes from non-axenic cultures. We tested this pipeline on 17 cyanobacterial cultures from the BCCM/ULC public collection and generated novel genome sequences for 12 polar or subpolar strains and three temperate ones, including three early-branching organisms that will be useful for phylogenomics. In parallel, we assembled 31 co-cultivated bacteria (12 nearly complete) from the same cultures and showed that they mostly belong to Bacteroidetes and Proteobacteria, some of them being very closely related in spite of geographically distant sampling sites.},
}

Antarctic Regions
Arctic Regions
Cyanobacteria/*classification/*genetics/isolation & purification
*Metagenome
Metagenomics
Microbiota/*genetics
Phylogeny
RNA, Ribosomal, 16S/genetics

@article {pmid29184122,
year = {2017},
author = {Lee, WH and Chen, HM and Yang, SF and Liang, C and Peng, CY and Lin, FM and Tsai, LL and Wu, BC and Hsin, CH and Chuang, CY and Yang, T and Yang, TL and Ho, SY and Chen, WL and Ueng, KC and Huang, HD and Huang, CN and Jong, YJ},
title = {Bacterial alterations in salivary microbiota and their association in oral cancer.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {16540},
pmid = {29184122},
issn = {2045-2322},
mesh = {Biodiversity ; Carcinoma, Squamous Cell/diagnosis/epidemiology/etiology ; Computational Biology/methods ; Disease Susceptibility ; Female ; Humans ; Male ; Metagenomics ; *Microbiota ; Mouth Mucosa/microbiology/pathology ; Mouth Neoplasms/diagnosis/*epidemiology/*etiology ; RNA, Ribosomal, 16S ; Saliva/*microbiology ; Taiwan/epidemiology ; },
abstract = {Oral squamous cell carcinoma (OSCC) is the most common malignant neoplasm of the oral cavity and the fourth leading malignancy and cause of cancer-related death in the male population of Taiwan. Most cases are detected at advanced stages, resulting in poor prognosis. Therefore, improved detection of early oral health disorders is indispensable. The involvement of oral bacteria in inflammation and their association with OSCC progression provide a feasible target for diagnosis. Due to the nature of oral neoplasms, the diagnosis of epithelial precursor lesions is relatively easy compared with that of other types of cancer. However, the transition from an epithelial precursor lesion to cancer is slow and requires further and continuous follow-up. In this study, we investigated microbiota differences between normal individuals, epithelial precursor lesion patients, and cancer patients with different lifestyle habits, such as betel chewing and smoking, using next-generation sequencing. Overall, the oral microbiome compositions of five genera, Bacillus, Enterococcus, Parvimonas, Peptostreptococcus, and Slackia, revealed significant differences between epithelial precursor lesion and cancer patients and correlated with their classification into two clusters. These composition changes might have the potential to constitute a biomarker to help in monitoring the oral carcinogenesis transition from epithelial precursor lesion to cancer.},
}

Biodiversity
Carcinoma, Squamous Cell/diagnosis/epidemiology/etiology
Computational Biology/methods
Disease Susceptibility
Female
Humans
Male
Metagenomics
*Microbiota
Mouth Mucosa/microbiology/pathology
Mouth Neoplasms/diagnosis/*epidemiology/*etiology
RNA, Ribosomal, 16S
Saliva/*microbiology
Taiwan/epidemiology

@article {pmid29184093,
year = {2017},
author = {Stearns, JC and Simioni, J and Gunn, E and McDonald, H and Holloway, AC and Thabane, L and Mousseau, A and Schertzer, JD and Ratcliffe, EM and Rossi, L and Surette, MG and Morrison, KM and Hutton, EK},
title = {Intrapartum antibiotics for GBS prophylaxis alter colonization patterns in the early infant gut microbiome of low risk infants.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {16527},
pmid = {29184093},
issn = {2045-2322},
support = {MSH-136665//CIHR/Canada ; },
mesh = {Adult ; Anti-Bacterial Agents/*administration & dosage ; *Antibiotic Prophylaxis ; Bifidobacterium/drug effects ; Delivery, Obstetric ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Infant ; Infant, Newborn ; Male ; *Maternal Exposure ; Metagenome ; Metagenomics ; Pregnancy ; Streptococcal Infections/*microbiology/*prevention & control ; Streptococcus agalactiae/*drug effects/physiology ; },
abstract = {Early life microbial colonization and succession is critically important to healthy development with impacts on metabolic and immunologic processes throughout life. A longitudinal prospective cohort was recruited from midwifery practices to include infants born at full term gestation to women with uncomplicated pregnancies. Here we compare bacterial community succession in infants born vaginally, with no exposure to antibiotics (n = 53), with infants who were exposed to intrapartum antibiotic prophylaxis (IAP) for Group B Streptococcus (GBS; n = 14), and infants born by C-section (n = 7). Molecular profiles of the 16 S rRNA genes indicate that there is a delay in the expansion of Bifidobacterium, which was the dominate infant gut colonizer, over the first 12 weeks and a persistence of Escherichia when IAP for GBS exposure is present during vaginal labour. Longer duration of IAP exposure increased the magnitude of the effect on Bifidobacterium populations, suggesting a longer delay in microbial community maturation. As with prior studies, we found altered gut colonisation following C-section that included a notable lack of Bacteroidetes. This study found that exposure of infants to IAP for GBS during vaginal birth affected aspects of gut microbial ecology that, although dramatic at early time points, disappeared by 12 weeks of age in most infants.},
}

Adult
Anti-Bacterial Agents/*administration & dosage
*Antibiotic Prophylaxis
Bifidobacterium/drug effects
Delivery, Obstetric
Female
Gastrointestinal Microbiome/*drug effects
Humans
Infant
Infant, Newborn
Male
*Maternal Exposure
Metagenome
Metagenomics
Pregnancy
Streptococcal Infections/*microbiology/*prevention & control
Streptococcus agalactiae/*drug effects/physiology

@article {pmid29463904,
year = {2018},
author = {Lavelle, A and Sokol, H},
title = {Gut microbiota: Beyond metagenomics, metatranscriptomics illuminates microbiome functionality in IBD.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {15},
number = {4},
pages = {193-194},
pmid = {29463904},
issn = {1759-5053},
mesh = {*Gastrointestinal Microbiome ; Humans ; *Inflammatory Bowel Diseases ; Metagenomics ; *Microbiota ; },
}

*Gastrointestinal Microbiome
Humans
*Inflammatory Bowel Diseases
Metagenomics
*Microbiota

@article {pmid29018275,
year = {2017},
author = {Ray, K},
title = {Gut microbiota: Human faecal sample processing in metagenomic studies: striving for standards.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {14},
number = {11},
pages = {631},
pmid = {29018275},
issn = {1759-5053},
mesh = {Feces ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; },
}

Feces
*Gastrointestinal Microbiome
Humans
Metagenomics

@article {pmid28513633,
year = {2017},
author = {Thomas, H},
title = {NAFLD: A gut microbiome signature for advanced fibrosis diagnosis in NAFLD.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {14},
number = {7},
pages = {388},
pmid = {28513633},
issn = {1759-5053},
mesh = {Dysbiosis ; Fibrosis ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; *Non-alcoholic Fatty Liver Disease ; },
}

Dysbiosis
Fibrosis
*Gastrointestinal Microbiome
Humans
Metagenomics
*Non-alcoholic Fatty Liver Disease

@article {pmid28406159,
year = {2017},
author = {Hatzenbuhler, C and Kelly, JR and Martinson, J and Okum, S and Pilgrim, E},
title = {Sensitivity and accuracy of high-throughput metabarcoding methods for early detection of invasive fish species.},
journal = {Scientific reports},
volume = {7},
number = {},
pages = {46393},
pmid = {28406159},
issn = {2045-2322},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; Fish Proteins/genetics ; Fishes/*classification/embryology/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Introduced Species ; Limit of Detection ; Metagenomics ; Sequence Analysis, DNA/methods ; },
abstract = {High-throughput DNA metabarcoding has gained recognition as a potentially powerful tool for biomonitoring, including early detection of aquatic invasive species (AIS). DNA based techniques are advancing, but our understanding of the limits to detection for metabarcoding complex samples is inadequate. For detecting AIS at an early stage of invasion when the species is rare, accuracy at low detection limits is key. To evaluate the utility of metabarcoding in future fish community monitoring programs, we conducted several experiments to determine the sensitivity and accuracy of routine metabarcoding methods. Experimental mixes used larval fish tissue from multiple "common" species spiked with varying proportions of tissue from an additional "rare" species. Pyrosequencing of genetic marker, COI (cytochrome c oxidase subunit I) and subsequent sequence data analysis provided experimental evidence of low-level detection of the target "rare" species at biomass percentages as low as 0.02% of total sample biomass. Limits to detection varied interspecifically and were susceptible to amplification bias. Moreover, results showed some data processing methods can skew sequence-based biodiversity measurements from corresponding relative biomass abundances and increase false absences. We suggest caution in interpreting presence/absence and relative abundance in larval fish assemblages until metabarcoding methods are optimized for accuracy and precision.},
}

Animals
DNA Barcoding, Taxonomic/*methods
Electron Transport Complex IV/*genetics
Fish Proteins/genetics
Fishes/*classification/embryology/genetics
High-Throughput Nucleotide Sequencing/*methods
Introduced Species
Limit of Detection
Metagenomics
Sequence Analysis, DNA/methods

@article {pmid27876768,
year = {2017},
author = {Dickson, I},
title = {Gut microbiota: Culturomics: illuminating microbial dark matter.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {14},
number = {1},
pages = {3},
pmid = {27876768},
issn = {1759-5053},
mesh = {*Gastrointestinal Microbiome ; *Gastrointestinal Tract ; Humans ; Metagenomics ; },
}

*Gastrointestinal Microbiome
*Gastrointestinal Tract
Humans
Metagenomics

@article {pmid31178526,
year = {2019},
author = {Wang, N and Guo, Y and Li, G and Xia, Y and Ma, M and Zang, J and Ma, Y and Yin, X and Han, W and Lv, J and Cao, H},
title = {Geochemical-Compositional-Functional Changes in Arctic Soil Microbiomes Post Land Submergence Revealed by Metagenomics.},
journal = {Microbes and environments},
volume = {34},
number = {2},
pages = {180-190},
doi = {10.1264/jsme2.ME18091},
pmid = {31178526},
issn = {1347-4405},
mesh = {Archaea/classification/genetics ; Archaeal Proteins/genetics/metabolism ; Arctic Regions ; Bacteria/classification/genetics ; Bacterial Proteins/genetics/metabolism ; Biodiversity ; Geologic Sediments/chemistry/*microbiology ; Lakes ; *Metagenomics ; Methane/metabolism ; *Microbiota/genetics ; Nitrogen/metabolism ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {Lakes of meltwater in the Artic have become one of the transforming landscape changes under global warming. We herein compared microbial communities between sediments and bank soils at an arctic lake post land submergence using geochemistry, 16S rRNA amplicons, and metagenomes. The results obtained showed that each sample had approximately 2,609 OTUs on average and shared 1,716 OTUs based on the 16S rRNA gene V3-V4 region. Dominant phyla in sediments and soils included Proteobacteria, Acidobacteria, Actinobacteria, Gemmatimonadetes, and Nitrospirae; sediments contained a unique phylum, Euryarchaeota, with the phylum Thaumarchaeota being primarily present in bank soils. Among the top 35 genera across all sites, 17 were more abundant in sediments, while the remaining 18 were more abundant in bank soils; seven out of the top ten genera across all sites were only from sediments. A redundancy analysis separated sediment samples from soil samples based on the components of nitrite and ammonium. Metagenome results supported the role of nitrite because most of the genes for denitrification and methane metabolic genes were more abundant in sediments than in soils, while the abundance of phosphorus-utilizing genes was similar and, thus, was not a significant explanatory factor. We identified several modules from the global networks of OTUs that were closely related to some geochemical factors, such as pH and nitrite. Collectively, the present results showing consistent changes in geochemistry, microbiome compositions, and functional genes suggest an ecological mechanism across molecular and community levels that structures microbiomes post land submergence.},
}

Archaea/classification/genetics
Archaeal Proteins/genetics/metabolism
Arctic Regions
Bacteria/classification/genetics
Bacterial Proteins/genetics/metabolism
Biodiversity
Geologic Sediments/chemistry/*microbiology
Lakes
*Metagenomics
Methane/metabolism
*Microbiota/genetics
Nitrogen/metabolism
RNA, Ribosomal, 16S/genetics
Soil/chemistry
*Soil Microbiology

@article {pmid30871224,
year = {2019},
author = {Gurwara, S and Ajami, NJ and Jang, A and Hessel, FC and Chen, L and Plew, S and Wang, Z and Graham, DY and Hair, C and White, DL and Kramer, J and Kourkoumpetis, T and Hoffman, K and Cole, R and Hou, J and Husain, N and Jarbrink-Sehgal, M and Hernaez, R and Kanwal, F and Ketwaroo, G and Shah, R and Velez, M and Natarajan, Y and El-Serag, HB and Petrosino, JF and Jiao, L},
title = {Dietary Nutrients Involved in One-Carbon Metabolism and Colonic Mucosa-Associated Gut Microbiome in Individuals with an Endoscopically Normal Colon.},
journal = {Nutrients},
volume = {11},
number = {3},
pages = {},
doi = {10.3390/nu11030613},
pmid = {30871224},
issn = {2072-6643},
support = {RP#140767//Cancer Prevention and Research Institute of Texas/ ; 1000//Gillson Longenbaugh Foundation/ ; 0000//Golfers Against Cancer/ ; },
mesh = {Aged ; Bacteria/*metabolism ; Colon/*microbiology ; Cross-Sectional Studies ; *Diet ; Food Analysis ; Gastrointestinal Microbiome/*drug effects/physiology ; Humans ; Intestinal Mucosa/*microbiology ; Male ; Middle Aged ; Prospective Studies ; },
abstract = {One carbon (1C) metabolism nutrients influence epigenetic regulation and they are supplied by diet and synthesized by gut microbiota. We examined the association between dietary consumption of methyl donors (methionine, betaine and choline) and B vitamins (folate, B2, B6, and B12) and the community composition and structure of the colonic mucosa-associated gut microbiota determined by 16S rRNA gene sequencing in 97 colonic biopsies of 35 men. We used the food frequency questionnaire to assess daily consumption of nutrients, and the UPARSE and SILVA databases for operational taxonomic unit classification. The difference in bacterial diversity and taxonomic relative abundance were compared between low versus high consumption of these nutrients. False discover rate (FDR) adjusted p value < 0.05 indicated statistical significance. The bacterial richness and composition differed significantly by the consumption of folate and B vitamins (p < 0.001). Compared with higher consumption, a lower consumption of these nutrients was associated with a lower abundance of Akkermansia (folate), Roseburia (vitamin B2), and Faecalibacterium (vitamins B2, B6, and B12) but a higher abundance of Erysipelatoclostridium (vitamin B2) (FDR p values < 0.05). The community composition and structure of the colonic bacteria differed significantly by dietary consumption of folate and B vitamins.},
}

Aged
Bacteria/*metabolism
Colon/*microbiology
Cross-Sectional Studies
*Diet
Food Analysis
Gastrointestinal Microbiome/*drug effects/physiology
Humans
Intestinal Mucosa/*microbiology
Male
Middle Aged
Prospective Studies

@article {pmid30763538,
year = {2019},
author = {Gogokhia, L and Buhrke, K and Bell, R and Hoffman, B and Brown, DG and Hanke-Gogokhia, C and Ajami, NJ and Wong, MC and Ghazaryan, A and Valentine, JF and Porter, N and Martens, E and O'Connell, R and Jacob, V and Scherl, E and Crawford, C and Stephens, WZ and Casjens, SR and Longman, RS and Round, JL},
title = {Expansion of Bacteriophages Is Linked to Aggravated Intestinal Inflammation and Colitis.},
journal = {Cell host & microbe},
volume = {25},
number = {2},
pages = {285-299.e8},
doi = {10.1016/j.chom.2019.01.008},
pmid = {30763538},
issn = {1934-6069},
support = {//Wellcome Trust/United Kingdom ; DP2 GM111099/GM/NIGMS NIH HHS/United States ; R00 HL102228/HL/NHLBI NIH HHS/United States ; R01 GM114817/GM/NIGMS NIH HHS/United States ; R01 DK114252/DK/NIDDK NIH HHS/United States ; DP2 AT008746/AT/NCCIH NIH HHS/United States ; },
mesh = {Animals ; Bacteria/*virology ; *Bacteriophages ; CD4-Positive T-Lymphocytes/metabolism ; Colitis, Ulcerative/*immunology/*microbiology/pathology ; Colorectal Neoplasms/*immunology/*microbiology/pathology ; Disease Models, Animal ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; Humans ; Interferon-gamma/metabolism ; Intestinal Mucosa/*immunology/*microbiology/pathology ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Pilot Projects ; Prospective Studies ; Specific Pathogen-Free Organisms ; },
abstract = {Bacteriophages are the most abundant members of the microbiota and have the potential to shape gut bacterial communities. Changes to bacteriophage composition are associated with disease, but how phages impact mammalian health remains unclear. We noted an induction of host immunity when experimentally treating bacterially driven cancer, leading us to test whether bacteriophages alter immune responses. Treating germ-free mice with bacteriophages leads to immune cell expansion in the gut. Lactobacillus, Escherichia, and Bacteroides bacteriophages and phage DNA stimulated IFN-γ via the nucleotide-sensing receptor TLR9. The resultant immune responses were both phage and bacteria specific. Additionally, increasing bacteriophage levels exacerbated colitis via TLR9 and IFN-γ. Similarly, ulcerative colitis (UC) patients responsive to fecal microbiota transplantation (FMT) have reduced phages compared to non-responders, and mucosal IFN-γ positively correlates with bacteriophage levels. Bacteriophages from active UC patients induced more IFN-γ compared to healthy individuals. Collectively, these results indicate that bacteriophages can alter mucosal immunity to impact mammalian health.},
}

Animals
Bacteria/*virology
*Bacteriophages
CD4-Positive T-Lymphocytes/metabolism
Colitis, Ulcerative/*immunology/*microbiology/pathology
Colorectal Neoplasms/*immunology/*microbiology/pathology
Disease Models, Animal
Fecal Microbiota Transplantation
*Gastrointestinal Microbiome
Humans
Interferon-gamma/metabolism
Intestinal Mucosa/*immunology/*microbiology/pathology
Mice
Mice, Inbred C57BL
Mice, Knockout
Pilot Projects
Prospective Studies
Specific Pathogen-Free Organisms

@article {pmid29176730,
year = {2017},
author = {Junqueira, ACM and Ratan, A and Acerbi, E and Drautz-Moses, DI and Premkrishnan, BNV and Costea, PI and Linz, B and Purbojati, RW and Paulo, DF and Gaultier, NE and Subramanian, P and Hasan, NA and Colwell, RR and Bork, P and Azeredo-Espin, AML and Bryant, DA and Schuster, SC},
title = {The microbiomes of blowflies and houseflies as bacterial transmission reservoirs.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {16324},
pmid = {29176730},
issn = {2045-2322},
mesh = {Animals ; Feces/microbiology ; Helicobacter pylori/isolation & purification ; Houseflies/*microbiology ; Metagenomics ; Microbiota/physiology ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Blowflies and houseflies are mechanical vectors inhabiting synanthropic environments around the world. They feed and breed in fecal and decaying organic matter, but the microbiome they harbour and transport is largely uncharacterized. We sampled 116 individual houseflies and blowflies from varying habitats on three continents and subjected them to high-coverage, whole-genome shotgun sequencing. This allowed for genomic and metagenomic analyses of the host-associated microbiome at the species level. Both fly host species segregate based on principal coordinate analysis of their microbial communities, but they also show an overlapping core microbiome. Legs and wings displayed the largest microbial diversity and were shown to be an important route for microbial dispersion. The environmental sequencing approach presented here detected a stochastic distribution of human pathogens, such as Helicobacter pylori, thereby demonstrating the potential of flies as proxies for environmental and public health surveillance.},
}

Animals
Feces/microbiology
Helicobacter pylori/isolation & purification
Houseflies/*microbiology
Metagenomics
Microbiota/physiology
Phylogeny
Sequence Analysis, DNA

@article {pmid29138475,
year = {2017},
author = {Lin, JJ and Wang, FY and Li, WH and Wang, TY},
title = {The rises and falls of opsin genes in 59 ray-finned fish genomes and their implications for environmental adaptation.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {15568},
pmid = {29138475},
issn = {2045-2322},
mesh = {Animals ; *Evolution, Molecular ; Fishes/*genetics ; Genome/genetics ; Metagenomics ; Opsins/classification/*genetics ; Phylogeny ; Rod Opsins/classification/*genetics ; Synteny/genetics ; },
abstract = {We studied the evolution of opsin genes in 59 ray-finned fish genomes. We identified the opsin genes and adjacent genes (syntenies) in each genome. Then we inferred the changes in gene copy number (N), syntenies, and tuning sites along each phylogenetic branch during evolution. The Exorh (rod opsin) gene has been retained in 56 genomes. Rh1, the intronless rod opsin gene, first emerged in ancestral Actinopterygii, and N increased to 2 by the teleost-specific whole genome duplication, but then decreased to 1 in the ancestor of Neoteleostei fishes. For cone opsin genes, the rhodopsin-like (Rh2) and long-wave-sensitive (LWS) genes showed great variation in N among species, ranging from 0 to 5 and from 0 to 4, respectively. The two short-wave-sensitive genes, SWS1 and SWS2, were lost in 23 and 6 species, respectively. The syntenies involving LWS, SWS2 and Rh2 underwent complex changes, while the evolution of the other opsin gene syntenies was much simpler. Evolutionary adaptation in tuning sites under different living environments was discussed. Our study provides a detailed view of opsin gene gains and losses, synteny changes and tuning site changes during ray-finned fish evolution.},
}

Animals
*Evolution, Molecular
Fishes/*genetics
Genome/genetics
Metagenomics
Opsins/classification/*genetics
Phylogeny
Rod Opsins/classification/*genetics
Synteny/genetics

@article {pmid29123168,
year = {2017},
author = {Zheng, S and Shao, S and Qiao, Z and Chen, X and Piao, C and Yu, Y and Gao, F and Zhang, J and Du, J},
title = {Clinical Parameters and Gut Microbiome Changes Before and After Surgery in Thoracic Aortic Dissection in Patients with Gastrointestinal Complications.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {15228},
pmid = {29123168},
issn = {2045-2322},
mesh = {Aneurysm, Dissecting/*surgery ; Bacteria/*classification/genetics ; Blood Chemical Analysis ; Cytokines/blood ; Gastrointestinal Diseases/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; *Microbiota ; Postoperative Complications/*microbiology ; },
abstract = {Thoracic aortic dissection (TAAD) is one of the most common types of aortic diseases. Although surgery remains the main method of treatment, the high rate of postoperative gastrointestinal complications significantly influences the effects of surgery and the recovery process. Moreover, the mechanisms underlying this disease remain unclear. To address these problems, we examined changes in the gut microbiota in 40 thoracic aortic dissection patients with abdominal complications after surgery. Levels of white blood cells (WBC), neutrophile granulocytes (NE), alanine aminotransferase (ALT), and aspartate aminotransferase (AST) were higher in all patients after surgery. Levels of inflammatory cytokines, including interleukin (IL)-2, IL-6, IL-8, and IL-10, were also higher after surgery. A metagenome analysis revealed that levels of Oscillibacter, Anaerotruncus, Alistipes, and Clostridium difficile were higher after the operation. The abundance of functional genes, such as the spermidine/putrescine transport system permease protein, the flagellar motor switch protein, and branched-chain amino acid transport system proteins, was also higher post-surgery. These changes likely contribute to diarrhea, bloating, gastrointestinal bleeding, and other abdominal complications after surgery, and our research opens up new treatment possibilities for patients suffering from abdominal complications after surgical treatment.},
}

Aneurysm, Dissecting/*surgery
Bacteria/*classification/genetics
Blood Chemical Analysis
Cytokines/blood
Gastrointestinal Diseases/*microbiology
*Gastrointestinal Microbiome
Humans
Metagenomics
*Microbiota
Postoperative Complications/*microbiology

@article {pmid29042583,
year = {2017},
author = {Xie, K and Deng, Y and Zhang, S and Zhang, W and Liu, J and Xie, Y and Zhang, X and Huang, H},
title = {Prokaryotic Community Distribution along an Ecological Gradient of Salinity in Surface and Subsurface Saline Soils.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {13332},
pmid = {29042583},
issn = {2045-2322},
mesh = {Biodiversity ; Environment ; Geologic Sediments/*chemistry/*microbiology ; Metagenome ; Metagenomics/methods ; Microbiota ; *Prokaryotic Cells ; RNA, Ribosomal, 16S/genetics ; *Salinity ; Soil/*chemistry ; *Soil Microbiology ; },
abstract = {Salinity effects on microbial communities in saline soils is still unclear, and little is known about subsurface soil microbial communities especially in saline or hypersaline ecosystems. Here we presented the survey of the prokaryotic community in saline soils along a salinity gradient (17.3-148.3 dS/m) in surface (0-10 cm) and subsurface (15-30 cm) saline soils of Qarhan Salt Lake, China. Moreover, we compared them with three paired nonsaline normal soils. Using the high-throughput sequencing technology and several statistical methods, we observed no significant community difference between surface soils and subsurface soils. For environmental factors, we found that TOC was the primary driver of the prokaryotic community distribution in surface saline soils, so was pH in subsurface saline soils. Salinity had more effects on the prokaryotic community in subsurface saline soils than in surface saline soils and played a less important role in saline soils than in saline waters or saline sediments. Our research provided references for the prokaryotic community distribution along a salinity gradient in both surface and subsurface saline soils of arid playa areas.},
}

Biodiversity
Environment
Geologic Sediments/*chemistry/*microbiology
Metagenome
Metagenomics/methods
Microbiota
*Prokaryotic Cells
RNA, Ribosomal, 16S/genetics
*Salinity
Soil/*chemistry
*Soil Microbiology

@article {pmid29026883,
year = {2017},
author = {Martinez, KA and Devlin, JC and Lacher, CR and Yin, Y and Cai, Y and Wang, J and Dominguez-Bello, MG},
title = {Increased weight gain by C-section: Functional significance of the primordial microbiome.},
journal = {Science advances},
volume = {3},
number = {10},
pages = {eaao1874},
pmid = {29026883},
issn = {2375-2548},
support = {P30 CA016087/CA/NCI NIH HHS/United States ; T32 AI007180/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Biodiversity ; Body Weight ; *Cesarean Section ; Feces/microbiology ; Female ; Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; Mice ; *Microbiota ; Obesity/etiology ; *Weight Gain ; },
abstract = {Epidemiological evidence supports a direct association between early microbiota impact-including C-section-and obesity. We performed antibiotic-free, fostered C-sections and determined the impact on the early microbiota and body weight during development. Mice in the C-section group gained more body mass after weaning, with a stronger phenotype in females. C-section-born mice lacked the dynamic developmental gut microbiota changes observed in control mice. The results demonstrate a causal relationship between C-section and increased body weight, supporting the involvement of maternal vaginal bacteria in normal metabolic development.},
}

Animals
Biodiversity
Body Weight
*Cesarean Section
Feces/microbiology
Female
Gastrointestinal Microbiome
Metagenome
Metagenomics/methods
Mice
*Microbiota
Obesity/etiology
*Weight Gain

@article {pmid30470178,
year = {2018},
author = {Griffith, BC and Weiss, BL and Aksoy, E and Mireji, PO and Auma, JE and Wamwiri, FN and Echodu, R and Murilla, G and Aksoy, S},
title = {Analysis of the gut-specific microbiome from field-captured tsetse flies, and its potential relevance to host trypanosome vector competence.},
journal = {BMC microbiology},
volume = {18},
number = {Suppl 1},
pages = {146},
pmid = {30470178},
issn = {1471-2180},
support = {D43 TW007391/TW/FIC NIH HHS/United States ; R01 AI051584/AI/NIAID NIH HHS/United States ; R01 AI068932/AI/NIAID NIH HHS/United States ; U01 AI115648/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Bacteria/*classification ; *Gastrointestinal Microbiome ; Geography ; High-Throughput Nucleotide Sequencing ; Insect Vectors/*microbiology/parasitology ; Kenya ; Symbiosis ; Trypanosoma/*physiology ; Tsetse Flies/*microbiology/parasitology ; Uganda ; },
abstract = {BACKGROUND: The tsetse fly (Glossina sp.) midgut is colonized by maternally transmitted and environmentally acquired bacteria. Additionally, the midgut serves as a niche in which pathogenic African trypanosomes reside within infected flies. Tsetse's bacterial microbiota impacts many aspects of the fly's physiology. However, little is known about the structure of tsetse's midgut-associated bacterial communities as they relate to geographically distinct fly habitats in east Africa and their contributions to parasite infection outcomes. We utilized culture dependent and independent methods to characterize the taxonomic structure and density of bacterial communities that reside within the midgut of tsetse flies collected at geographically distinct locations in Kenya and Uganda.

RESULTS: Using culture dependent methods, we isolated 34 strains of bacteria from four different tsetse species (G. pallidipes, G. brevipalpis, G. fuscipes and G. fuscipleuris) captured at three distinct locations in Kenya. To increase the depth of this study, we deep sequenced midguts from individual uninfected and trypanosome infected G. pallidipes captured at two distinct locations in Kenya and one in Uganda. We found that tsetse's obligate endosymbiont, Wigglesworthia, was the most abundant bacterium present in the midgut of G. pallidipes, and the density of this bacterium remained largely consistent regardless of whether or not its tsetse host was infected with trypanosomes. These fly populations also housed the commensal symbiont Sodalis, which was found at significantly higher densities in trypanosome infected compared to uninfected flies. Finally, midguts of field-captured G. pallidipes were colonized with distinct, low density communities of environmentally acquired microbes that differed in taxonomic structure depending on parasite infection status and the geographic location from which the flies were collected.

CONCLUSIONS: The results of this study will enhance our understanding of the tripartite relationship between tsetse, its microbiota and trypanosome vector competence. This information may be useful for developing novel disease control strategies or enhancing the efficacy of those already in use.},
}

Animals
Bacteria/*classification
*Gastrointestinal Microbiome
Geography
High-Throughput Nucleotide Sequencing
Insect Vectors/*microbiology/parasitology
Kenya
Symbiosis
Trypanosoma/*physiology
Tsetse Flies/*microbiology/parasitology
Uganda

@article {pmid30427574,
year = {2019},
author = {Barnes, RC and Kim, H and Fang, C and Bennett, W and Nemec, M and Sirven, MA and Suchodolski, JS and Deutz, N and Britton, RA and Mertens-Talcott, SU and Talcott, ST},
title = {Body Mass Index as a Determinant of Systemic Exposure to Gallotannin Metabolites during 6-Week Consumption of Mango (Mangifera indica L.) and Modulation of Intestinal Microbiota in Lean and Obese Individuals.},
journal = {Molecular nutrition & food research},
volume = {63},
number = {2},
pages = {e1800512},
doi = {10.1002/mnfr.201800512},
pmid = {30427574},
issn = {1613-4133},
mesh = {Adult ; *Body Mass Index ; Fatty Acids, Volatile/biosynthesis ; Feces/chemistry ; Female ; *Gastrointestinal Microbiome ; Humans ; Hydrolyzable Tannins/*metabolism ; Male ; *Mangifera/chemistry ; Obesity/*metabolism/microbiology ; Phenols/analysis ; Polymerase Chain Reaction ; },
abstract = {SCOPE: This human clinical pilot trial investigated pharmacokinetics of gallotannin-metabolites and modulation of intestinal microbiota in healthy lean and obese individuals after 6 weeks of daily mango consumption.

METHODS AND RESULTS: Participants are divided into three groups: Lean Mango (LM: n = 12; BMI = 22.9 kg m-2), Obese Mango (OM: n = 9; BMI = 34.6 kg m-2), and Lean Control (LC: n = 11; BMI = 22.1 kg m-2). LM and OM consumed 400 g of mango per day for 6 weeks. LC consumed mango only on Days 0 and 42. After 6 weeks, LM experienced increased systemic exposure (AUC0-8h) to gallotannin-metabolites, 1.4-fold (p = 0.043). The greatest increase is 4-O-methyl-gallic acid, 3.3-fold (p = 0.0026). Cumulative urinary excretion of gallotannin-metabolites significantly increased in LM and OM, but not LC. For OM, qPCR data show increased levels of tannase-producing Lactococcus lactis and decreased levels of Clostridium leptum and Bacteroides thetaiotaomicron, bacteria associated with obesity. LM experienced an increased trend of fecal levels of butyric (1.3-fold; p = 0.09) and valeric acids (1.5-fold; p = 0.056). Plasma endotoxins showed a decreased trend in LM and OM.

CONCLUSION: Continuous mango intake significantly increased systemic exposure to gallotannin- metabolites and induced an increased trend for fecal short-chain fatty acids in lean but not obese individuals. This pharmacokinetic discrepancy may result in BMI-associated reduced gallotannin-derived health benefits.},
}

Adult
*Body Mass Index
Fatty Acids, Volatile/biosynthesis
Feces/chemistry
Female
*Gastrointestinal Microbiome
Humans
Hydrolyzable Tannins/*metabolism
Male
*Mangifera/chemistry
Obesity/*metabolism/microbiology
Phenols/analysis
Polymerase Chain Reaction

@article {pmid30355340,
year = {2018},
author = {Mailhe, M and Ricaboni, D and Vitton, V and Gonzalez, JM and Bachar, D and Dubourg, G and Cadoret, F and Robert, C and Delerce, J and Levasseur, A and Fournier, PE and Angelakis, E and Lagier, JC and Raoult, D},
title = {Repertoire of the gut microbiota from stomach to colon using culturomics and next-generation sequencing.},
journal = {BMC microbiology},
volume = {18},
number = {1},
pages = {157},
pmid = {30355340},
issn = {1471-2180},
mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/*classification/isolation & purification ; Colon/*microbiology ; Colonoscopy ; Colony Count, Microbial ; DNA, Bacterial/genetics ; Endoscopy, Digestive System ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Hydrogen-Ion Concentration ; Male ; *Metagenomics ; Middle Aged ; Proton Pump Inhibitors/administration & dosage ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Stomach/*microbiology ; Young Adult ; },
abstract = {BACKGROUND: Most studies on the human microbiota have analyzed stool samples, although a large proportion of the absorption of nutrients takes place in upper gut tract. We collected samples from different locations along the entire gastrointestinal tract from six patients who had simultaneously undergone upper endoscopy and colonoscopy, to perform a comprehensive analysis using culturomics with matrix assisted laser desorption ionisation - time of flight (MALDI-TOF) identification and by metagenomics targeting the 16S ribosomal ribonucleic acid (rRNA) gene.

RESULTS: Using culturomics, we isolated 368 different bacterial species, including 37 new species. Fewer species were isolated in the upper gut: 110 in the stomach and 106 in the duodenum, while 235 were isolated from the left colon (p < 0.02). We isolated fewer aero-intolerant species in the upper gut: 37 from the stomach and 150 from the left colon (p < 0.004). Using metagenomics, 1,021 species were identified. The upper gut microbiota was revealed to be less rich than the lower gut microbiota, with 37,622 reads from the stomach, 28,390 from the duodenum, and 79,047 from the left colon (p < 0.009). There were fewer reads for aero-intolerant species in the upper gut (8,656 in the stomach, 5,188 in the duodenum and 72,262 in the left colon, p < 0.02). Patients taking proton pump inhibitors (PPI) were then revealed to have a higher stomach pH and a greater diversity of species in the upper digestive tract than patients not receiving treatment (p < 0.001).

CONCLUSION: Significant modifications in bacterial composition and diversity exist throughout the gastrointestinal tract. We suggest that the upper gut may be key to understanding the relationship between the gut microbiota and health.},
}

Adult
Aged
Aged, 80 and over
Bacteria/*classification/isolation & purification
Colon/*microbiology
Colonoscopy
Colony Count, Microbial
DNA, Bacterial/genetics
Endoscopy, Digestive System
Female
*Gastrointestinal Microbiome
High-Throughput Nucleotide Sequencing
Humans
Hydrogen-Ion Concentration
Male
*Metagenomics
Middle Aged
Proton Pump Inhibitors/administration & dosage
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Stomach/*microbiology
Young Adult

@article {pmid28125344,
year = {2017},
author = {Walsh, AM and Crispie, F and Claesson, MJ and Cotter, PD},
title = {Translating Omics to Food Microbiology.},
journal = {Annual review of food science and technology},
volume = {8},
number = {},
pages = {113-134},
doi = {10.1146/annurev-food-030216-025729},
pmid = {28125344},
issn = {1941-1413},
mesh = {*Food Microbiology ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenomics ; Probiotics ; *Transcriptome ; },
abstract = {This review examines the applications of omics technologies in food microbiology, with a primary focus on high-throughput sequencing (HTS) technologies. We discuss the different sequencing approaches applicable to the study of food-related microbial isolates and mixed microbial communities in foods, and we provide an overview of the sequencing platforms suitable for each approach. We highlight the potential for genomics, metagenomics, and metatranscriptomics to guide efforts to optimize food fermentations. Additionally, we explore the use of comparative and functional genomics to further our understanding of the mechanisms of probiotic action and we describe the applicability of HTS as a food safety measure. Finally, we consider the use of HTS to investigate the effects that ingested microbes have on the human gut microbiota.},
}

*Food Microbiology
Gastrointestinal Microbiome
High-Throughput Nucleotide Sequencing
Humans
*Metagenomics
Probiotics
*Transcriptome

@article {pmid31126262,
year = {2019},
author = {Ke, S and Fang, S and He, M and Huang, X and Yang, H and Yang, B and Chen, C and Huang, L},
title = {Age-based dynamic changes of phylogenetic composition and interaction networks of health pig gut microbiome feeding in a uniformed condition.},
journal = {BMC veterinary research},
volume = {15},
number = {1},
pages = {172},
doi = {10.1186/s12917-019-1918-5},
pmid = {31126262},
issn = {1746-6148},
support = {31772579//National Natural Science Foundation of China/ ; 31472071//National Natural Science Foundation of China/ ; },
mesh = {*Age Factors ; Animals ; Bacteria/*classification/genetics ; Bacterial Typing Techniques ; Female ; Gastrointestinal Microbiome/*physiology ; Male ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sus scrofa/*microbiology ; },
abstract = {BACKGROUND: The gut microbiota impacts on a range of host biological processes, and the imbalances in its composition are associated with pathology. Though the understanding of contribution of the many factors, e.g. gender, diet and age, in the development of gut microbiota has been well established, the dynamic changes of the phylogenetic composition and the interaction networks along with the age remain unclear in pigs.

RESULTS: Here we applied 16S ribosomal RNA gene sequencing, enterotype-like clustering (Classification of the gut microbiome into distinct types) and phylogenetic co-occurrence network to explore the dynamic changes of pig gut microbiome following the ages with a successive investigation at four ages in a cohort of 953 pigs. We found that Firmicutes and Bacteroidetes are two predominant phyla throughout the experimental period. The richness of gut microbiota was significantly increased from 25 to 240 days of age. Principal coordinates analysis showed a clear difference in the gut microbial community compositions between pre-weaning piglets and the pigs at the other three age groups. The gut microbiota of pre-weaning piglets was clearly classified into two enterotypes, which were dominated by Fusobacterium and p-75-a5, respectively. However, Prevotella and Treponema were the main drivers of the enterotypes for pigs at the age of 80, 120 and 240 days. Besides the piglets, even some adult pigs switched putative enterotypes between ages. We confirmed that the topological features of phylogenetic co-occurrence networks, including scale, stability and complexity were increased along with the age. The biological significance for modules in the network of piglets were mainly associated with the utilization of simple carbohydrate and lactose, whereas the sub-networks identified at the ages of 80, 120 and 240 days may be involved in the digestion of complex dietary polysaccharide. The modules related to the metabolism of protein and amino acids could be identified in the networks at 120 and 240 days. This dynamic change of the functional capacities of gut microbiome was further supported by functional prediction analysis.

CONCLUSIONS: The present study provided meaningful biological insights into the age-based dynamic shifts of ecological community of porcine gut microbiota.},
}

*Age Factors
Animals
Bacteria/*classification/genetics
Bacterial Typing Techniques
Female
Gastrointestinal Microbiome/*physiology
Male
Metagenomics
Phylogeny
RNA, Ribosomal, 16S/genetics
Sus scrofa/*microbiology

@article {pmid30298261,
year = {2018},
author = {Adeolu, M and Parkinson, J and Xiong, X},
title = {Analyzing Metabolic Pathways in Microbiomes.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1849},
number = {},
pages = {291-307},
doi = {10.1007/978-1-4939-8728-3_18},
pmid = {30298261},
issn = {1940-6029},
mesh = {High-Throughput Nucleotide Sequencing/*methods ; Humans ; *Metabolic Networks and Pathways ; Metagenomics ; *Microbiota ; *Transcriptome ; },
abstract = {Understanding the metabolic activity of a microbial community, at both the level of the individual microbe and the whole microbiome, provides fundamental biological, biochemical, and clinical insights into the nature of the microbial community and interactions with their hosts in health and disease. Here, we discuss a method to examine the expression of metabolic pathways in microbial communities using data from metatranscriptomic next-generation sequencing data. The methodology described here encompasses enzyme function annotation, differential enzyme expression and pathway enrichment analyses, and visualization of metabolic networks with differential enzyme expression levels.},
}

High-Throughput Nucleotide Sequencing/*methods
Humans
*Metabolic Networks and Pathways
Metagenomics
*Microbiota
*Transcriptome

@article {pmid30298260,
year = {2018},
author = {Dunn, KA and Andrews, K and Bashwih, RO and Bielawski, JP},
title = {Bayesian Inference of Microbial Community Structure from Metagenomic Data Using BioMiCo.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1849},
number = {},
pages = {267-289},
doi = {10.1007/978-1-4939-8728-3_17},
pmid = {30298260},
issn = {1940-6029},
mesh = {*Algorithms ; *Bayes Theorem ; Computational Biology/*methods ; Metagenomics/*methods ; *Microbiota ; },
abstract = {Microbial samples taken from an environment often represent mixtures of communities, where each community is composed of overlapping assemblages of species. Such data represent a serious analytical challenge, as the community structures will be present as complex mixtures, there will be very large numbers of component species, and the species abundance will often be sparse over samples. The structure and complexity of these samples will vary according to both biotic and abiotic factors, and classical methods of data analysis will have a limited value in this setting. A novel Bayesian modeling framework, called BioMiCo, was developed to meet this challenge. BioMiCo takes abundance data derived from environmental DNA, and models each sample by a two-level mixture, where environmental OTUs contribute community structures, and those structures are related to the known biotic and abiotic features of each sample. The model is constrained by Dirichlet priors, which induces compact structures, minimizes variance, and maximizes model interpretability. BioMiCo is trained on a portion of the data, and once trained a BioMiCo model can be employed to make predictions about the features of new samples. This chapter provides a set of protocols that illustrate the application of BioMiCo to real inference problems. Each protocol is designed around the analysis of a real dataset, which was carefully chosen to illustrate specific aspects of real data analysis. With these protocols, users of BioMiCo will be able to undertake basic research into the properties of complex microbial systems, as well as develop predictive models for applied microbiomics.},
}

*Algorithms
*Bayes Theorem
Computational Biology/*methods
Metagenomics/*methods
*Microbiota

@article {pmid30298257,
year = {2018},
author = {Hug, LA},
title = {Subsampled Assemblies and Hybrid Nucleotide Composition/Differential Coverage Binning for Genome-Resolved Metagenomics.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1849},
number = {},
pages = {215-225},
doi = {10.1007/978-1-4939-8728-3_14},
pmid = {30298257},
issn = {1940-6029},
mesh = {Algorithms ; *Genome, Microbial ; Metagenomics/*methods ; *Microbiota ; Nucleotides/*genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {Metagenomic analyses for reconstruction of genomes from mixed microbial community datasets now routinely allow rapid, accurate genome recovery for tens to hundreds of organisms from environmental samples. This chapter provides a step-by-step protocol for reconstructing genomes from metagenomic datasets, with a focus on the most abundant community members. Subsampling assembly approaches are implemented to improve assembly of abundant genome sequences, an iterative process that targets progressively less abundant populations and improves total community representation in the final merged assembly. A hybrid approach to genome binning is described, combining differential coverage information from a series of metagenomic samples with nucleotide composition information. This approach strengthens binning through application of multiple independent variables for contig clustering. Genome curation through error correction and gap closure leads to high-quality draft genomes, and, for some community members, closed and complete genome sequences reconstructed directly from environmental samples.},
}

Algorithms
*Genome, Microbial
Metagenomics/*methods
*Microbiota
Nucleotides/*genetics
Sequence Analysis, DNA/*methods

@article {pmid30298255,
year = {2018},
author = {Zhang, Q},
title = {Metagenome Assembly and Contig Assignment.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1849},
number = {},
pages = {179-192},
doi = {10.1007/978-1-4939-8728-3_12},
pmid = {30298255},
issn = {1940-6029},
mesh = {Bacteria/classification/*genetics/isolation & purification ; Computational Biology/methods ; DNA Barcoding, Taxonomic/*methods ; High-Throughput Nucleotide Sequencing/*methods ; *Metagenome ; Microbiota ; Molecular Sequence Annotation ; *Software ; },
abstract = {The recent development of metagenomic assembly has revolutionized metagenomic data analysis, thanks to the improvement of sequencing techniques, more powerful computational infrastructure and the development of novel algorithms and methods. Using longer assembled contigs rather than raw reads improves the process of metagenomic binning and annotation significantly, ultimately resulting in a deeper understanding of the microbial dynamics of the metagenomic samples being analyzed. In this chapter, we demonstrate a typical metagenomic analysis pipeline including raw read quality evaluation and trimming, assembly and contig binning. Alternative tools that can be used for each step are also discussed.},
}

Bacteria/classification/*genetics/isolation & purification
Computational Biology/methods
DNA Barcoding, Taxonomic/*methods
High-Throughput Nucleotide Sequencing/*methods
*Metagenome
Microbiota
Molecular Sequence Annotation
*Software

@article {pmid30298253,
year = {2018},
author = {McMurdie, PJ},
title = {Normalization of Microbiome Profiling Data.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1849},
number = {},
pages = {143-168},
doi = {10.1007/978-1-4939-8728-3_10},
pmid = {30298253},
issn = {1940-6029},
mesh = {Bacteria/classification/*genetics/isolation & purification ; Computational Biology/*methods ; Data Analysis ; High-Throughput Nucleotide Sequencing/*methods ; *Metagenome ; *Microbiota ; Phylogeny ; *Software ; },
abstract = {Normalization is a term that is often used but rarely defined and poorly understood. The number of choices of normalization procedure is large-some are inappropriate or inadmissible-and all are narrowly relevant to a specific analysis that depends on both the nature of the data and the question being asked. This chapter describes key definitions of normalization as they apply in metagenomics, mainly for taxonomic profiling data; while also demonstrating specific, reproducible examples of normalization procedures in the context of analysis techniques for which they were intended. The analysis and graphics code is distributed as a supplemental companion to this chapter so that the motivated reader can re-use it on new data.},
}

Bacteria/classification/*genetics/isolation & purification
Computational Biology/*methods
Data Analysis
High-Throughput Nucleotide Sequencing/*methods
*Metagenome
*Microbiota
Phylogeny
*Software

@article {pmid30298244,
year = {2018},
author = {Daly, RA and Wrighton, KC and Wilkins, MJ},
title = {Characterizing the Deep Terrestrial Subsurface Microbiome.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1849},
number = {},
pages = {1-15},
doi = {10.1007/978-1-4939-8728-3_1},
pmid = {30298244},
issn = {1940-6029},
mesh = {Bacteria/*classification/*genetics ; Biomass ; DNA, Bacterial/*analysis ; Gene Library ; Geologic Sediments/*microbiology ; Metagenomics ; *Microbiota ; Soil Microbiology ; Water Microbiology ; },
abstract = {A large portion of the earth's biomass resides in the subsurface and recent studies have expanded our knowledge of indigenous microbial life. Advances in the field of metagenomics now allow analysis of microbial communities from low-biomass samples such as deep (>2.5 km) shale core samples. Here we present protocols for the best practices in contamination control, handling core material, extraction of nucleic acids, and low-input library preparation for subsequent metagenomic sequencing.},
}

Bacteria/*classification/*genetics
Biomass
DNA, Bacterial/*analysis
Gene Library
Geologic Sediments/*microbiology
Metagenomics
*Microbiota
Soil Microbiology
Water Microbiology

@article {pmid31267680,
year = {2019},
author = {Taubert, M and Grob, C and Crombie, A and Howat, AM and Burns, OJ and Weber, M and Lott, C and Kaster, AK and Vollmers, J and Jehmlich, N and von Bergen, M and Chen, Y and Murrell, JC},
title = {Communal metabolism by Methylococcaceae and Methylophilaceae is driving rapid aerobic methane oxidation in sediments of a shallow seep near Elba, Italy.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.14728},
pmid = {31267680},
issn = {1462-2920},
abstract = {Release of abiotic methane from marine seeps into the atmosphere is a major source of this potent greenhouse gas. Methanotrophic microorganisms in methane seeps use methane as carbon and energy source, thus significantly mitigating global methane emissions. Here we investigated microbial methane oxidation at the sediment-water interface of a shallow marine methane seep. Metagenomics and metaproteomics, combined with 13 C-methane stable isotope probing, demonstrated that various members of the gammaproteobacterial family Methylococcaceae were the key players for methane oxidation, catalyzing the first reaction step to methanol. We observed a transfer of carbon to methanol-oxidizing methylotrophs of the betaproteobacterial family Methylophilaceae, suggesting an interaction between methanotrophic and methylotrophic microorganisms that allowed for rapid methane oxidation. From our microcosms, we estimated methane oxidation rates of up to 871 nmol of methane per gram sediment and day. This implies that more than 50% of methane at the seep is removed by microbial oxidation at the sediment-water interface, based on previously reported in situ methane fluxes. The organic carbon produced was further assimilated by different heterotrophic microbes, demonstrating that the methane-oxidizing community supported a complex trophic network. Our results provide valuable eco-physiological insights into this specialized microbial community performing an ecosystem function of global relevance. This article is protected by copyright. All rights reserved.},
}

@article {pmid31266971,
year = {2019},
author = {Fernández-Correa, I and Truchado, DA and Gomez-Lucia, E and Doménech, A and Pérez-Tris, J and Schmidt-Chanasit, J and Cadar, D and Benítez, L},
title = {A novel group of avian astroviruses from Neotropical passerine birds broaden the diversity and host range of Astroviridae.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {9513},
doi = {10.1038/s41598-019-45889-3},
pmid = {31266971},
issn = {2045-2322},
support = {CGL2017-82117-P//Ministry of Economy and Competitiveness | Agencia Estatal de Investigaci&#x00F3;n (Spanish Agencia Estatal de Investigaci&#x00F3;n)/ ; CGL2017-82117-P//Ministry of Economy and Competitiveness | Agencia Estatal de Investigaci&#x00F3;n (Spanish Agencia Estatal de Investigaci&#x00F3;n)/ ; CT27/16-CT28/16//Universidad Complutense de Madrid (Complutense University of Madrid)/ ; },
abstract = {Metagenomics is helping to expand the known diversity of viruses, especially of those with poorly studied hosts in remote areas. The Neotropical region harbors a considerable diversity of avian species that may play a role as both host and short-distance vectors of unknown viruses. Viral metagenomics of cloacal swabs from 50 Neotropical birds collected in French Guiana revealed the presence of four complete astrovirus genomes. They constitute an early diverging novel monophyletic clade within the Avastrovirus phylogeny, representing a putative new astrovirus species (provisionally designated as Avastrovirus 5) according to the International Committee on Taxonomy of Viruses (ICTV) classification criteria. Their genomic organization shares some characteristics with Avastrovirus but also with Mamastrovirus. The pan-astrovirus RT-PCR analysis of the cloacal samples of 406 wild Neotropical birds showed a community-level prevalence of 4.9% (5.1% in passerines, the highest described so far in this order of birds). By screening birds of a remote region, we expanded the known host range of astroviruses to the avian families Cardinalidae, Conopophagidae, Furnariidae, Thamnophilidae, Turdidae and Tyrannidae. Our results provide important first insights into the unexplored viral communities, the ecology, epidemiology and features of host-pathogen interactions that shape the evolution of avastroviruses in a remote Neotropical rainforest.},
}

@article {pmid31036930,
year = {2019},
author = {Zhang, J and Liu, YX and Zhang, N and Hu, B and Jin, T and Xu, H and Qin, Y and Yan, P and Zhang, X and Guo, X and Hui, J and Cao, S and Wang, X and Wang, C and Wang, H and Qu, B and Fan, G and Yuan, L and Garrido-Oter, R and Chu, C and Bai, Y},
title = {NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice.},
journal = {Nature biotechnology},
volume = {37},
number = {6},
pages = {676-684},
doi = {10.1038/s41587-019-0104-4},
pmid = {31036930},
issn = {1546-1696},
mesh = {Alleles ; Anion Transport Proteins/chemistry/*genetics ; Bacteria/classification/*genetics ; Genotype ; Metagenomics ; Microbiota/*genetics ; Nitrogen/metabolism ; Oryza/*genetics/growth & development/metabolism/microbiology ; Phylogeny ; Plant Breeding ; Plant Roots/genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Nitrogen-use efficiency of indica varieties of rice is superior to that of japonica varieties. We apply 16S ribosomal RNA gene profiling to characterize root microbiota of 68 indica and 27 japonica varieties grown in the field. We find that indica and japonica recruit distinct root microbiota. Notably, indica-enriched bacterial taxa are more diverse, and contain more genera with nitrogen metabolism functions, than japonica-enriched taxa. Using genetic approaches, we provide evidence that NRT1.1B, a rice nitrate transporter and sensor, is associated with the recruitment of a large proportion of indica-enriched bacteria. Metagenomic sequencing reveals that the ammonification process is less abundant in the root microbiome of the nrt1.1b mutant. We isolated 1,079 pure bacterial isolates from indica and japonica roots and derived synthetic communities (SynComs). Inoculation of IR24, an indica variety, with an indica-enriched SynCom improved rice growth in organic nitrogen conditions compared with a japonica-enriched SynCom. The links between plant genotype and root microbiota membership established in this study will inform breeding strategies to improve nitrogen use in crops.},
}

Alleles
Anion Transport Proteins/chemistry/*genetics
Bacteria/classification/*genetics
Genotype
Metagenomics
Microbiota/*genetics
Nitrogen/metabolism
Oryza/*genetics/growth & development/metabolism/microbiology
Phylogeny
Plant Breeding
Plant Roots/genetics/microbiology
RNA, Ribosomal, 16S/genetics

@article {pmid31264806,
year = {2019},
author = {Pereira, O and Hochart, C and Auguet, JC and Debroas, D and Galand, PE},
title = {Genomic ecology of Marine Group II, the most common marine planktonic Archaea across the surface ocean.},
journal = {MicrobiologyOpen},
volume = {},
number = {},
pages = {e852},
doi = {10.1002/mbo3.852},
pmid = {31264806},
issn = {2045-8827},
support = {ANR-14-CE02-0004-01//Agence Nationale de la Recherche/ ; },
abstract = {Planktonic Archaea have been detected in all the world's oceans and are found from surface waters to the deep sea. The two most common Archaea phyla are Thaumarchaeota and Euryarchaeota. Euryarchaeota are generally more common in surface waters, but very little is known about their ecology and their potential metabolisms. In this study, we explore the genomic ecology of the Marine Group II (MGII), the main marine planktonic Euryarchaeota, and test if it is composed of different ecologically relevant units. We re-analyzed Tara Oceans metagenomes from the photic layer and the deep ocean by annotating sequences against a custom MGII database and by mapping gene co-occurrences. Our data provide a global view of the distribution of Euryarchaeota, and more specifically of MGII subgroups, and reveal their association to a number of gene-coding sequences. In particular, we show that MGII proteorhodopsins were detected in both the surface and the deep chlorophyll maximum layer and that different clusters of these light harvesting proteins were present. Our approach helped describing the set of genes found together with specific MGII subgroups. We could thus define genomic environments that could theoretically describe ecologically meaningful units and the ecological niche that they occupy.},
}

@article {pmid30606403,
year = {2019},
author = {Gong, J and Noel, S and Pluznick, JL and Hamad, ARA and Rabb, H},
title = {Gut Microbiota-Kidney Cross-Talk in Acute Kidney Injury.},
journal = {Seminars in nephrology},
volume = {39},
number = {1},
pages = {107-116},
doi = {10.1016/j.semnephrol.2018.10.009},
pmid = {30606403},
issn = {1558-4488},
support = {R01 DK111209/DK/NIDDK NIH HHS/United States ; },
mesh = {Acute Kidney Injury/immunology/*microbiology ; Animals ; Blood Pressure ; Dysbiosis/*complications ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*immunology ; Humans ; Methylamines/metabolism ; Prebiotics ; Probiotics/therapeutic use ; Uremia/microbiology ; },
abstract = {The recent surge in research on the intestinal microbiota has greatly changed our understanding of human biology. Significant technical advances in DNA sequencing analysis and its application to metagenomics and metatranscriptomics has profoundly enhanced our ability to quantify and track complex microbial communities and to begin understanding their impact on human health and disease. This has led to a better understanding of the relationships between the intestinal microbiome and renal physiology/pathophysiology. In this review, we discuss the interactions between intestinal microbiota and kidney. We focus on select aspects including the intestinal barrier, immunologic and soluble mediators of microbiome effects, and effects of dysbiosis on acute kidney injury. Relevant studies on microbiome changes in other renal diseases are highlighted. We also introduce potential mechanisms of intervention with regard to gut microbiota in renal diseases.},
}

Acute Kidney Injury/immunology/*microbiology
Animals
Blood Pressure
Dysbiosis/*complications
Fatty Acids, Volatile/metabolism
Gastrointestinal Microbiome/*physiology
Gastrointestinal Tract/*immunology
Humans
Methylamines/metabolism
Prebiotics
Probiotics/therapeutic use
Uremia/microbiology

@article {pmid31034867,
year = {2019},
author = {Tsiaoussis, J and Antoniou, MN and Koliarakis, I and Mesnage, R and Vardavas, CI and Izotov, BN and Psaroulaki, A and Tsatsakis, A},
title = {Effects of single and combined toxic exposures on the gut microbiome: Current knowledge and future directions.},
journal = {Toxicology letters},
volume = {312},
number = {},
pages = {72-97},
doi = {10.1016/j.toxlet.2019.04.014},
pmid = {31034867},
issn = {1879-3169},
mesh = {Environmental Pollutants/*toxicity ; Gastrointestinal Microbiome/*drug effects ; Hazardous Substances/*toxicity ; Humans ; },
abstract = {Human populations are chronically exposed to mixtures of toxic chemicals. Predicting the health effects of these mixtures require a large amount of information on the mode of action of their components. Xenobiotic metabolism by bacteria inhabiting the gastrointestinal tract has a major influence on human health. Our review aims to explore the literature for studies looking to characterize the different modes of action and outcomes of major chemical pollutants, and some components of cosmetics and food additives, on gut microbial communities in order to facilitate an estimation of their potential mixture effects. We identified good evidence that exposure to heavy metals, pesticides, nanoparticles, polycyclic aromatic hydrocarbons, dioxins, furans, polychlorinated biphenyls, and non-caloric artificial sweeteners affect the gut microbiome and which is associated with the development of metabolic, malignant, inflammatory, or immune diseases. Answering the question 'Who is there?' is not sufficient to define the mode of action of a toxicant in predictive modeling of mixture effects. Therefore, we recommend that new studies focus to simulate real-life exposure to diverse chemicals (toxicants, cosmetic/food additives), including as mixtures, and which combine metagenomics, metatranscriptomics and metabolomic analytical methods achieving in that way a comprehensive evaluation of effects on human health.},
}

Environmental Pollutants/*toxicity
Gastrointestinal Microbiome/*drug effects
Hazardous Substances/*toxicity
Humans

@article {pmid30866822,
year = {2019},
author = {Lee, Y and Schmidt, H and Collier, TC and Conner, WR and Hanemaaijer, MJ and Slatkin, M and Marshall, JM and Chiu, JC and Smartt, CT and Lanzaro, GC and Mulligan, FS and Cornel, AJ},
title = {Genome-wide divergence among invasive populations of Aedes aegypti in California.},
journal = {BMC genomics},
volume = {20},
number = {1},
pages = {204},
doi = {10.1186/s12864-019-5586-4},
pmid = {30866822},
issn = {1471-2164},
support = {U01CK000516//ACL HHS/United States ; HR0011-17-2-0047//Defense Sciences Office, DARPA/ ; 1U01CK000516//Centers for Disease Control and Prevention/ ; },
mesh = {Aedes/*classification/genetics ; Animals ; California ; Evolution, Molecular ; Genetic Variation ; Genetics, Population ; Genome Size ; *Genome, Insect ; Introduced Species ; Metagenomics ; Mosquito Vectors/classification/genetics ; Phylogeny ; Phylogeography ; Whole Genome Sequencing/*veterinary ; },
abstract = {BACKGROUND: In the summer of 2013, Aedes aegypti Linnaeus was first detected in three cities in central California (Clovis, Madera and Menlo Park). It has now been detected in multiple locations in central and southern CA as far south as San Diego and Imperial Counties. A number of published reports suggest that CA populations have been established from multiple independent introductions.

RESULTS: Here we report the first population genomics analyses of Ae. aegypti based on individual, field collected whole genome sequences. We analyzed 46 Ae. aegypti genomes to establish genetic relationships among populations from sites in California, Florida and South Africa. Based on 4.65 million high quality biallelic SNPs, we identified 3 major genetic clusters within California; one that includes all sample sites in the southern part of the state (South of Tehachapi mountain range) plus the town of Exeter in central California and two additional clusters in central California.

CONCLUSIONS: A lack of concordance between mitochondrial and nuclear genealogies suggests that the three founding populations were polymorphic for two main mitochondrial haplotypes prior to being introduced to California. One of these has been lost in the Clovis populations, possibly by a founder effect. Genome-wide comparisons indicate extensive differentiation between genetic clusters. Our observations support recent introductions of Ae. aegypti into California from multiple, genetically diverged source populations. Our data reveal signs of hybridization among diverged populations within CA. Genetic markers identified in this study will be of great value in pursuing classical population genetic studies which require larger sample sizes.},
}

Aedes/*classification/genetics
Animals
California
Evolution, Molecular
Genetic Variation
Genetics, Population
Genome Size
*Genome, Insect
Introduced Species
Metagenomics
Mosquito Vectors/classification/genetics
Phylogeny
Phylogeography
Whole Genome Sequencing/*veterinary

@article {pmid30866812,
year = {2019},
author = {Das, P and Babaei, P and Nielsen, J},
title = {Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome.},
journal = {BMC genomics},
volume = {20},
number = {1},
pages = {208},
doi = {10.1186/s12864-019-5591-7},
pmid = {30866812},
issn = {1471-2164},
support = {HEALTH-F4-2012-305312//METACARDIS/ ; },
mesh = {Bacteria/*classification/genetics/isolation & purification/metabolism ; Bacterial Proteins/*genetics ; China ; Feces/microbiology ; Gastrointestinal Microbiome ; Gene Expression Profiling ; Humans ; Metagenomics/*methods ; Phylogeny ; Phylogeography ; United States ; Vitamins/*metabolism ; Whole Genome Sequencing ; },
abstract = {BACKGROUND: Human gut microbial communities have been known to produce vitamins, which are subsequently absorbed by the host in the large intestine. However, the relationship between species with vitamin pathway associated functional features or their gene abundance in different states of health and disease is lacking. Here, we analyzed shotgun fecal metagenomes of individuals from four different countries for genes that are involved in vitamin biosynthetic pathways and transport mechanisms and corresponding species' abundance.

RESULTS: We found that the prevalence of these genes were found to be distributed across the dominant phyla of gut species. The number of positive correlations were high between species harboring genes related to vitamin biosynthetic pathways and transporter mechanisms than that with either alone. Although, the range of total gene abundances remained constant across healthy populations at the global level, species composition and their presence for metabolic pathway related genes determine the abundance and functional genetic content of vitamin metabolism. Based on metatranscriptomics data, the equation between abundance of vitamin-biosynthetic enzymes and vitamin-dependent enzymes suggests that the production and utilization potential of these enzymes seems way more complex usage allocations than just mere direct linear associations.

CONCLUSIONS: Our findings provide a rationale to examine and disentangle the interrelationship between B-vitamin dosage (dietary or microbe-mediated) on gut microbial members and the host, in the gut microbiota of individuals with under- or overnutrition.},
}

Bacteria/*classification/genetics/isolation & purification/metabolism
Bacterial Proteins/*genetics
China
Feces/microbiology
Gastrointestinal Microbiome
Gene Expression Profiling
Humans
Metagenomics/*methods
Phylogeny
Phylogeography
United States
Vitamins/*metabolism
Whole Genome Sequencing

@article {pmid30452938,
year = {2018},
author = {Bilal, T and Malik, B and Hakeem, KR},
title = {Metagenomic analysis of uncultured microorganisms and their enzymatic attributes.},
journal = {Journal of microbiological methods},
volume = {155},
number = {},
pages = {65-69},
doi = {10.1016/j.mimet.2018.11.014},
pmid = {30452938},
issn = {1872-8359},
mesh = {Bioengineering/methods ; Biofuels ; Biotechnology ; Enzyme Activation ; *Enzymes/genetics/metabolism ; Extremophiles/*enzymology/*genetics ; Genome, Microbial/*genetics ; Genomics ; Metagenomics/*methods ; Microbiological Techniques/methods ; Microbiota/genetics ; },
abstract = {Although second generation biofuel technology is a sustainable route for bioethanol production it is not currently a robust technology because of certain hindrances viz., unavailability of potential enzyme resources, low efficiency of enzymes and restricted availability of potent enzymes that work under harsh conditions in industrial processes. Therefore, bioprospecting of extremophilic microorganisms using metagenomics is a promising alternative to discover novel microbes and enzymes with efficient tolerance to unfavourable conditions and thus could revolutionize the energy sector. Metagenomics a recent field in "omics" technology enables the genomic study of uncultured microorganisms with the goal of better understanding microbial dynamics. Metagenomics in conjunction with NextGen Sequencing technology facilitates the sequencing of microbial DNA directly from environmental samples and has expanded, and transformed our knowledge of the microbial world. However, filtering the meaningful information from the millions of genomic sequences offers a serious challenge to bioinformaticians. The current review holds the opinion tool 'know- how' to unravel the secrets of nature while expediting the bio-industrial world. We also discuss the novel biocatalytic agents discovered through metagenomics and how bioengineering plays a pivotal role to enhance their efficiency.},
}

Bioengineering/methods
Biofuels
Biotechnology
Enzyme Activation
*Enzymes/genetics/metabolism
Extremophiles/*enzymology/*genetics
Genome, Microbial/*genetics
Genomics
Metagenomics/*methods
Microbiological Techniques/methods
Microbiota/genetics

@article {pmid30287354,
year = {2018},
author = {Staley, C and Sadowsky, MJ},
title = {Practical considerations for sampling and data analysis in contemporary metagenomics-based environmental studies.},
journal = {Journal of microbiological methods},
volume = {154},
number = {},
pages = {14-18},
doi = {10.1016/j.mimet.2018.09.020},
pmid = {30287354},
issn = {1872-8359},
mesh = {Algorithms ; Biodiversity ; Biostatistics/methods ; Computational Biology/methods ; DNA/analysis/isolation & purification ; *Data Analysis ; Ecology ; Ecosystem ; Environment ; *Environmental Microbiology ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Metagenome ; Metagenomics/*methods ; Microbiota/genetics ; Phylogeography ; Sequence Analysis, DNA/methods ; Specimen Handling/*methods ; },
abstract = {Recent advancements in metagenomic-based studies, especially analyses of amplicon-based DNA sequencing targeting taxonomic marker genes, has led to an unprecedented characterization of microbial communities from diverse ecosystems around the world. While originally constrained by a lack of appropriate analytical tools and sequencing depth, new technologies and computational and statistical algorithms have been developed to handle highly dimensional, next-generation sequencing datasets. Both these tools allow for the robust analysis of structural and distributional patterns of microbiota essential for the understanding of microbial ecology and biogeography. Furthermore, consortia of individual laboratories working on large interdisciplinary research programs, like the Human and Earth Microbiome Projects, have developed standardized protocols for DNA extraction, sequencing pipelines, and bioinformatics. These approaches provide large repositories of publicly available data to serve as references for on-going and future, hypothesis-driven studies to better characterize the roles of microbial communities in diverse ecosystems. In this review, we outline the currently available statistical approaches and tools to aid in statistically powered study designs and analyses. Given what is now known about the enormous diversity and variability of the microbial communities in aquatic and terrestrial habitats, we also discuss practical considerations for sample collection. Due to the extensive advances made in the field of metagenomics over the last decade, rigorous, well replicated, hypothesis-driven studies are: 1) needed, 2) now possible, and 3) essential to make best use of sequencing-based technologies to characterize the roles of microbial communities in the structure and function of diverse ecosystems.},
}

Algorithms
Biodiversity
Biostatistics/methods
Computational Biology/methods
DNA/analysis/isolation & purification
*Data Analysis
Ecology
Ecosystem
Environment
*Environmental Microbiology
High-Throughput Nucleotide Sequencing/methods
Humans
*Metagenome
Metagenomics/*methods
Microbiota/genetics
Phylogeography
Sequence Analysis, DNA/methods
Specimen Handling/*methods

@article {pmid29770137,
year = {2018},
author = {Stanisavljević, S and Dinić, M and Jevtić, B and Đedović, N and Momčilović, M and Đokić, J and Golić, N and Mostarica Stojković, M and Miljković, Đ},
title = {Gut Microbiota Confers Resistance of Albino Oxford Rats to the Induction of Experimental Autoimmune Encephalomyelitis.},
journal = {Frontiers in immunology},
volume = {9},
number = {},
pages = {942},
pmid = {29770137},
issn = {1664-3224},
mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Cytokines/metabolism ; Disease Models, Animal ; *Disease Resistance/immunology ; Encephalomyelitis, Autoimmune, Experimental/*etiology/metabolism/therapy ; Fecal Microbiota Transplantation/methods ; Female ; *Gastrointestinal Microbiome/drug effects/immunology ; Lymph Nodes/immunology/metabolism ; Metagenome ; Metagenomics/methods ; Peyer's Patches/immunology/metabolism ; Rats ; },
abstract = {Albino Oxford (AO) rats are extremely resistant to induction of experimental autoimmune encephalomyelitis (EAE). EAE is an animal model of multiple sclerosis, a chronic inflammatory disease of the central nervous system (CNS), with established autoimmune pathogenesis. The autoimmune response against the antigens of the CNS is initiated in the peripheral lymphoid tissues after immunization of AO rats with CNS antigens. Subsequently, limited infiltration of the CNS occurs, yet without clinical sequels. It has recently become increasingly appreciated that gut-associated lymphoid tissues (GALT) and gut microbiota play an important role in regulation and propagation of encephalitogenic immune response. Therefore, modulation of AO gut microbiota by antibiotics was performed in this study. The treatment altered composition of gut microbiota in AO rats and led to a reduction in the proportion of regulatory T cells in Peyer's patches, mesenteric lymph nodes, and in lymph nodes draining the site of immunization. Upregulation of interferon-γ and interleukin (IL)-17 production was observed in the draining lymph nodes. The treatment led to clinically manifested EAE in AO rats with more numerous infiltrates and higher production of IL-17 observed in the CNS. Importantly, transfer of AO gut microbiota into EAE-prone Dark Agouti rats ameliorated the disease. These results clearly imply that gut microbiota is an important factor in AO rat resistance to EAE and that gut microbiota transfer is an efficacious way to treat CNS autoimmunity. These findings also support the idea that gut microbiota modulation has a potential as a future treatment of multiple sclerosis.},
}

Animals
Anti-Bacterial Agents/pharmacology
Cytokines/metabolism
Disease Models, Animal
*Disease Resistance/immunology
Encephalomyelitis, Autoimmune, Experimental/*etiology/metabolism/therapy
Fecal Microbiota Transplantation/methods
Female
*Gastrointestinal Microbiome/drug effects/immunology
Lymph Nodes/immunology/metabolism
Metagenome
Metagenomics/methods
Peyer's Patches/immunology/metabolism
Rats

@article {pmid28125788,
year = {2017},
author = {Yang, Y and Chen, N and Chen, T},
title = {Inference of Environmental Factor-Microbe and Microbe-Microbe Associations from Metagenomic Data Using a Hierarchical Bayesian Statistical Model.},
journal = {Cell systems},
volume = {4},
number = {1},
pages = {129-137.e5},
doi = {10.1016/j.cels.2016.12.012},
pmid = {28125788},
issn = {2405-4712},
mesh = {Algorithms ; Animals ; Bacteria/classification/genetics ; Bayes Theorem ; Computational Biology/methods ; Computer Simulation ; Gene-Environment Interaction ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Models, Statistical ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; },
abstract = {The inference of associations between environmental factors and microbes and among microbes is critical to interpreting metagenomic data, but compositional bias, indirect associations resulting from common factors, and variance within metagenomic sequencing data limit the discovery of associations. To account for these problems, we propose metagenomic Lognormal-Dirichlet-Multinomial (mLDM), a hierarchical Bayesian model with sparsity constraints, to estimate absolute microbial abundance and simultaneously infer both conditionally dependent associations among microbes and direct associations between microbes and environmental factors. We empirically show the effectiveness of the mLDM model using synthetic data, data from the TARA Oceans project, and a colorectal cancer dataset. Finally, we apply mLDM to 16S sequencing data from the western English Channel and report several associations. Our model can be used on both natural environmental and human metagenomic datasets, promoting the understanding of associations in the microbial community.},
}

Algorithms
Animals
Bacteria/classification/genetics
Bayes Theorem
Computational Biology/methods
Computer Simulation
Gene-Environment Interaction
High-Throughput Nucleotide Sequencing/methods
Humans
Metagenomics/*methods
Microbiota/*genetics
Models, Statistical
RNA, Ribosomal, 16S
Sequence Analysis, DNA

@article {pmid31250077,
year = {2019},
author = {Goss-Souza, D and Mendes, LW and Rodrigues, JLM and Tsai, SM},
title = {Ecological Processes Shaping Bulk Soil and Rhizosphere Microbiome Assembly in a Long-Term Amazon Forest-to-Agriculture Conversion.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-019-01401-y},
pmid = {31250077},
issn = {1432-184X},
support = {2008/58114-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2014/50320-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 140317/2014-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico (BR)/ ; 311008/2016-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
abstract = {Forest-to-agriculture conversion has been identified as a major threat to soil biodiversity and soil processes resilience, although the consequences of long-term land use change to microbial community assembly and ecological processes have been often neglected. Here, we combined metagenomic approach with a large environmental dataset, to (i) identify the microbial assembly patterns and, (ii) to evaluate the ecological processes governing microbial assembly, in bulk soil and soybean rhizosphere, along a long-term forest-to-agriculture conversion chronosequence, in Eastern Amazon. We hypothesized that (i) microbial communities in bulk soil and rhizosphere have different assembly patterns and (ii) the weight of the four ecological processes governing assembly differs between bulk soil and rhizosphere and along the chronosequence in the same fraction. Community assembly in bulk soil fitted most the zero-sum multinomial (ZSM) neutral-based model, regardless of time. Low to intermediate dispersal was observed. Decreasing influence of abiotic factors was counterbalanced by increasing influence of biotic factors, as the chronosequence advanced. Undominated ecological processes of dispersal limitation and variable selection governing community assembly were observed in this soil fraction. For soybean rhizosphere, community assembly fitted most the lognormal niche-based model in all chronosequence areas. High dispersal and an increasing influence of abiotic factors coupled with a decreasing influence of biotic factors were found along the chronosequence. Thus, we found a dominant role of dispersal process governing microbial assembly with a secondary effect of homogeneous selection process, mainly driven by decreasing aluminum and increased cations saturation in soil solution, due to long-term no-till cropping. Together, our results indicate that long-term no-till lead community abundances in bulk soil to be in a transient and conditional state, while for soybean rhizosphere, community abundances reach a periodic and permanent distribution state. Dominant dispersal process in rhizosphere, coupled with homogeneous selection, brings evidences that soybean root system selects microbial taxa via trade-offs in order to keep functional resilience of soil processes.},
}

@article {pmid30838598,
year = {2019},
author = {Divaris, K and Shungin, D and Rodríguez-Cortés, A and Basta, PV and Roach, J and Cho, H and Wu, D and Ferreira Zandoná, AG and Ginnis, J and Ramamoorthy, S and Kinchen, JM and Kwintkiewicz, J and Butz, N and Ribeiro, AA and Azcarate-Peril, MA},
title = {The Supragingival Biofilm in Early Childhood Caries: Clinical and Laboratory Protocols and Bioinformatics Pipelines Supporting Metagenomics, Metatranscriptomics, and Metabolomics Studies of the Oral Microbiome.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1922},
number = {},
pages = {525-548},
doi = {10.1007/978-1-4939-9012-2_40},
pmid = {30838598},
issn = {1940-6029},
mesh = {Bacteria/*genetics/isolation & purification/metabolism ; *Biofilms ; Child, Preschool ; DNA, Bacterial/genetics ; Dental Caries/etiology/*microbiology ; Gene Expression Profiling/methods ; Gingiva/microbiology ; Humans ; Metabolomics/*methods ; Metagenomics/*methods ; Microbiota ; RNA, Bacterial/genetics ; Sequence Analysis, DNA/methods ; Sequence Analysis, RNA/methods ; Software ; Specimen Handling/methods ; Tooth, Deciduous/*microbiology ; Transcriptome ; },
abstract = {Early childhood caries (ECC) is a biofilm-mediated disease. Social, environmental, and behavioral determinants as well as innate susceptibility are major influences on its incidence; however, from a pathogenetic standpoint, the disease is defined and driven by oral dysbiosis. In other words, the disease occurs when the natural equilibrium between the host and its oral microbiome shifts toward states that promote demineralization at the biofilm-tooth surface interface. Thus, a comprehensive understanding of dental caries as a disease requires the characterization of both the composition and the function or metabolic activity of the supragingival biofilm according to well-defined clinical statuses. However, taxonomic and functional information of the supragingival biofilm is rarely available in clinical cohorts, and its collection presents unique challenges among very young children. This paper presents a protocol and pipelines available for the conduct of supragingival biofilm microbiome studies among children in the primary dentition, that has been designed in the context of a large-scale population-based genetic epidemiologic study of ECC. The protocol is being developed for the collection of two supragingival biofilm samples from the maxillary primary dentition, enabling downstream taxonomic (e.g., metagenomics) and functional (e.g., transcriptomics and metabolomics) analyses. The protocol is being implemented in the assembly of a pediatric precision medicine cohort comprising over 6000 participants to date, contributing social, environmental, behavioral, clinical, and biological data informing ECC and other oral health outcomes.},
}

Bacteria/*genetics/isolation & purification/metabolism
*Biofilms
Child, Preschool
DNA, Bacterial/genetics
Dental Caries/etiology/*microbiology
Gene Expression Profiling/methods
Gingiva/microbiology
Humans
Metabolomics/*methods
Metagenomics/*methods
Microbiota
RNA, Bacterial/genetics
Sequence Analysis, DNA/methods
Sequence Analysis, RNA/methods
Software
Specimen Handling/methods
Tooth, Deciduous/*microbiology
Transcriptome

@article {pmid29523365,
year = {2017},
author = {Lagier, JC and Dubourg, G and Amrane, S and Raoult, D},
title = {Koch Postulate: Why Should we Grow Bacteria?.},
journal = {Archives of medical research},
volume = {48},
number = {8},
pages = {774-779},
doi = {10.1016/j.arcmed.2018.02.003},
pmid = {29523365},
issn = {1873-5487},
mesh = {Anti-Bacterial Agents/therapeutic use ; Bacteria/drug effects/genetics/*isolation & purification ; *Bacterial Infections/diagnosis/drug therapy/microbiology ; *Bacteriological Techniques ; *Cell Culture Techniques ; Humans ; Metagenomics ; Microbial Sensitivity Tests ; Microbiota/*physiology ; },
}

Anti-Bacterial Agents/therapeutic use
Bacteria/drug effects/genetics/*isolation & purification
*Bacterial Infections/diagnosis/drug therapy/microbiology
*Bacteriological Techniques
*Cell Culture Techniques
Humans
Metagenomics
Microbial Sensitivity Tests
Microbiota/*physiology

@article {pmid28835919,
year = {2017},
author = {Dickson, LB and Jiolle, D and Minard, G and Moltini-Conclois, I and Volant, S and Ghozlane, A and Bouchier, C and Ayala, D and Paupy, C and Moro, CV and Lambrechts, L},
title = {Carryover effects of larval exposure to different environmental bacteria drive adult trait variation in a mosquito vector.},
journal = {Science advances},
volume = {3},
number = {8},
pages = {e1700585},
pmid = {28835919},
issn = {2375-2548},
mesh = {Animals ; Antibiosis ; *Bacteria ; *Biological Variation, Population ; Breeding ; Dengue/transmission ; Ecosystem ; Environment ; *Environmental Microbiology ; Gastrointestinal Microbiome ; Host-Pathogen Interactions ; Humans ; Larva ; Life Cycle Stages ; Metagenome ; Metagenomics ; Microbiota ; Mosquito Vectors/*growth & development/*microbiology/virology ; *Quantitative Trait, Heritable ; },
abstract = {Conditions experienced during larval development of holometabolous insects can affect adult traits, but whether differences in the bacterial communities of larval development sites contribute to variation in the ability of insect vectors to transmit human pathogens is unknown. We addressed this question in the mosquito Aedes aegypti, a major arbovirus vector breeding in both sylvatic and domestic habitats in Sub-Saharan Africa. Targeted metagenomics revealed differing bacterial communities in the water of natural breeding sites in Gabon. Experimental exposure to different native bacterial isolates during larval development resulted in significant differences in pupation rate and adult body size but not life span. Larval exposure to an Enterobacteriaceae isolate resulted in decreased antibacterial activity in adult hemolymph and reduced dengue virus dissemination titer. Together, these data provide the proof of concept that larval exposure to different bacteria can drive variation in adult traits underlying vectorial capacity. Our study establishes a functional link between larval ecology, environmental microbes, and adult phenotypic variation in a holometabolous insect vector.},
}

Animals
Antibiosis
*Bacteria
*Biological Variation, Population
Breeding
Dengue/transmission
Ecosystem
Environment
*Environmental Microbiology
Gastrointestinal Microbiome
Host-Pathogen Interactions
Humans
Larva
Life Cycle Stages
Metagenome
Metagenomics
Microbiota
Mosquito Vectors/*growth & development/*microbiology/virology
*Quantitative Trait, Heritable

@article {pmid30725462,
year = {2019},
author = {Morales, E and Chen, J and Greathouse, KL},
title = {Compositional Analysis of the Human Microbiome in Cancer Research.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1928},
number = {},
pages = {299-335},
doi = {10.1007/978-1-4939-9027-6_16},
pmid = {30725462},
issn = {1940-6029},
mesh = {Biological Evolution ; Gastrointestinal Microbiome ; Humans ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S ; *Research ; },
abstract = {Gut microbial composition has shown to be associated with obesity, diabetes mellitus, inflammatory bowel disease, colitis, autoimmune disorders, and cancer, among other diseases. Microbiome research has significantly evolved through the years and continues to advance as we develop new and better strategies to more accurately measure its composition and function. Careful selection of study design, inclusion and exclusion criteria of participants, and methodology are paramount to accurately analyze microbial structure. Here we present the most up-to-date available information on methods for gut microbial collection and analysis.},
}

Biological Evolution
Gastrointestinal Microbiome
Humans
*Metagenome
*Metagenomics/methods
*Microbiota
Polymerase Chain Reaction
RNA, Ribosomal, 16S
*Research

@article {pmid30685386,
year = {2019},
author = {Liu, J and Johnson, R and Dillon, S and Kroehl, M and Frank, DN and Tuncil, YE and Zhang, X and Ir, D and Robertson, CE and Seifert, S and Higgins, J and Hamaker, B and Wilson, CC and Erlandson, KM},
title = {Among older adults, age-related changes in the stool microbiome differ by HIV-1 serostatus.},
journal = {EBioMedicine},
volume = {40},
number = {},
pages = {583-594},
doi = {10.1016/j.ebiom.2019.01.033},
pmid = {30685386},
issn = {2352-3964},
support = {K23 AG050260/AG/NIA NIH HHS/United States ; P30 DK048520/DK/NIDDK NIH HHS/United States ; T32 AG000279/AG/NIA NIH HHS/United States ; UL1 TR002535/TR/NCATS NIH HHS/United States ; },
mesh = {Age Factors ; Aged ; Aged, 80 and over ; Biomarkers ; Case-Control Studies ; Computational Biology/methods ; Diet ; Dysbiosis ; Fatty Acids, Volatile/metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome ; HIV Infections/*epidemiology/*virology ; HIV Seropositivity ; *HIV-1 ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; },
abstract = {BACKGROUND: HIV-1 infection and physiological aging are independently linked to elevated systemic inflammation and changes in enteric microbial communities (dysbiosis). However, knowledge of the direct effect of HIV infection on the aging microbiome and potential links to systemic inflammation is lacking.

METHODS: In a cross-sectional study of older people living with HIV (PLWH) (median age 61.5 years, N = 14) and uninfected controls (median 58 years, n = 22) we compared stool microbiota, levels of microbial metabolites (short-chain fatty acid levels, SCFA) and systemic inflammatory biomarkers by HIV serostatus and age.

FINDINGS: HIV and age were independently associated with distinct changes in the stool microbiome. For example, abundances of Enterobacter and Paraprevotella were higher and Eggerthella and Roseburia lower among PLWH compared to uninfected controls. Age-related microbiome changes also differed by HIV serostatus. Some bacteria with inflammatory potential (e.g. Escherichia) increased with age among PLWH, but not controls. Stool SCFA levels were similar between the two groups yet patterns of associations between individual microbial taxa and SCFA levels differed. Abundance of various genera including Escherichia and Bifidobacterium positively associated with inflammatory biomarkers (e.g. soluble Tumor Necrosis Factor Receptors) among PLWH, but not among controls.

INTERPRETATION: The age effect on the gut microbiome and associations between microbiota and microbial metabolites or systemic inflammation differed based on HIV serostatus, raising important implications for the impact of therapeutic interventions, dependent on HIV serostatus or age.},
}

Age Factors
Aged
Aged, 80 and over
Biomarkers
Case-Control Studies
Computational Biology/methods
Diet
Dysbiosis
Fatty Acids, Volatile/metabolism
Feces/microbiology
*Gastrointestinal Microbiome
HIV Infections/*epidemiology/*virology
HIV Seropositivity
*HIV-1
Humans
Male
Metagenome
Metagenomics/methods
Middle Aged

@article {pmid30584008,
year = {2019},
author = {Liu, X and Shao, L and Liu, X and Ji, F and Mei, Y and Cheng, Y and Liu, F and Yan, C and Li, L and Ling, Z},
title = {Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer.},
journal = {EBioMedicine},
volume = {40},
number = {},
pages = {336-348},
doi = {10.1016/j.ebiom.2018.12.034},
pmid = {30584008},
issn = {2352-3964},
mesh = {Aged ; Biodiversity ; Cohort Studies ; Combined Modality Therapy ; Computational Biology/methods ; Dysbiosis ; Female ; Gastric Mucosa/*microbiology/pathology ; Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Neoplasm Grading ; Neoplasm Staging ; RNA, Ribosomal, 16S ; Stomach Neoplasms/*etiology/pathology/therapy ; },
abstract = {BACKGROUND: As part of the tumor microenvironment, the gastric microbiota play vital roles in tumor initiation, progression and metastasis, but stomach microhabitats are not always uniform. We aimed to characterize differences of gastric microbiota in stomach microhabitats associated with gastric cancer (GC) development.

METHODS: A cohort of 276 GC patients without preoperative chemotherapy was enrolled retrospectively, and 230 normal, 247 peritumoral and 229 tumoral tissues were obtained for gastric microbiota analysis targeting the 16S rRNA gene by MiSeq sequencing. The microbial diversity and composition, bacterial co-occurrence correlations and predictive functional profiles were compared across different microhabitats.

FINDINGS: GC-specific stomach microhabitats, not GC stages or types, determine the composition and diversity of the gastric microbiota. Most notably, bacterial richness was decreased in peritumoral and tumoral microhabitats, and the correlation network of abundant gastric bacteria was simplified in tumoral microhabitat. Helicobacter pylori (HP), Prevotella copri and Bacteroides uniformis were significantly decreased, whereas Prevotella melaninogenica, Streptococcus anginosus and Propionibacterium acnes were increased in tumoral microhabitat. Higher HP colonisation influenced the overall structure of the gastric microbiota in normal and peritumoral microhabitats. PiCRUSt analysis revealed that genes associated with nucleotide transport and metabolism and amino acid transport and metabolism were significantly enriched in tumoral microbiota, while gastric acid secretion was significantly higher in HP positive group of the tumoral microbiota.

INTERPRETATION: Our present study provided new insights into the roles of gastric microbiota in different stomach microhabitats in gastric carcinogenesis, especially the pathogenesis of HP. FUND: National Natural Science Foundation of China.},
}

Aged
Biodiversity
Cohort Studies
Combined Modality Therapy
Computational Biology/methods
Dysbiosis
Female
Gastric Mucosa/*microbiology/pathology
Gastrointestinal Microbiome
Humans
Male
Metagenome
Metagenomics/methods
*Microbiota
Middle Aged
Neoplasm Grading
Neoplasm Staging
RNA, Ribosomal, 16S
Stomach Neoplasms/*etiology/pathology/therapy

@article {pmid30155556,
year = {2019},
author = {Ma, ZS},
title = {Sketching the Human Microbiome Biogeography with DAR (Diversity-Area Relationship) Profiles.},
journal = {Microbial ecology},
volume = {77},
number = {3},
pages = {821-838},
doi = {10.1007/s00248-018-1245-6},
pmid = {30155556},
issn = {1432-184X},
mesh = {Bacteria/classification/genetics/*isolation & purification ; *Biodiversity ; Humans ; Metagenomics ; *Microbiota ; Models, Biological ; },
abstract = {SAR (species area relationship) is a classic ecological theory that has been extensively investigated and applied in the studies of global biogeography and biodiversity conservation in macro-ecology. It has also found important applications in microbial ecology in recent years thanks to the breakthroughs in metagenomic sequencing technology. Nevertheless, SAR has a serious limitation for practical applications-ignoring the species abundance and treating all species as equally abundant. This study aims to explore the biogeography discoveries of human microbiome over 18 sites of 5 major microbiome habitats, establish the baseline DAR (diversity-area scaling relationship) parameters, and perform comparisons with the classic SAR. The extension from SAR to DAR by adopting the Hill numbers as diversity measures not only overcomes the previously mentioned flaw of SAR but also allows for obtaining a series of important findings on the human microbiome biodiversity and biogeography. Specifically, two types of DAR models were built, the traditional power law (PL) and power law with exponential cutoff (PLEC), using comprehensive datasets from the HMP (human microbiome project). Furthermore, the biogeography "maps" for 18 human microbiome sites using their DAR profiles for assessing and predicting the diversity scaling across individuals, PDO profiles (pair-wise diversity overlap) for measuring diversity overlap (similarity), and MAD profile (for predicting the maximal accrual diversity in a population) were sketched out. The baseline biogeography maps for the healthy human microbiome diversity can offer guidelines for conserving human microbiome diversity and investigating the health implications of the human microbiome diversity and heterogeneity.},
}

Bacteria/classification/genetics/*isolation & purification
*Biodiversity
Humans
Metagenomics
*Microbiota
Models, Biological

@article {pmid30068938,
year = {2018},
author = {Hoedt, EC and Parks, DH and Volmer, JG and Rosewarne, CP and Denman, SE and McSweeney, CS and Muir, JG and Gibson, PR and Cuív, PÓ and Hugenholtz, P and Tyson, GW and Morrison, M},
title = {Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size.},
journal = {The ISME journal},
volume = {12},
number = {12},
pages = {2942-2953},
pmid = {30068938},
issn = {1751-7370},
mesh = {Animals ; Cattle ; Feces/microbiology ; *Gastrointestinal Microbiome ; Genome Size/*genetics ; Humans ; *Metagenomics ; Methanobacteriaceae/*genetics/physiology ; Methanobrevibacter/genetics/physiology ; Phylogeny ; Rumen/microbiology ; },
abstract = {The genus Methanosphaera is a well-recognized but poorly characterized member of the mammalian gut microbiome, and distinctive from Methanobrevibacter smithii for its ability to induce a pro-inflammatory response in humans. Here we have used a combination of culture- and metagenomics-based approaches to expand the representation and information for the genus, which has supported the examination of their phylogeny and physiological capacity. Novel isolates of the genus Methanosphaera were recovered from bovine rumen digesta and human stool, with the bovine isolate remarkable for its large genome size relative to other Methanosphaera isolates from monogastric hosts. To substantiate this observation, we then recovered seven high-quality Methanosphaera-affiliated population genomes from ruminant and human gut metagenomic datasets. Our analyses confirm a monophyletic origin of Methanosphaera spp. and that the colonization of monogastric and ruminant hosts favors representatives of the genus with different genome sizes, reflecting differences in the genome content needed to persist in these different habitats.},
}

Animals
Cattle
Feces/microbiology
*Gastrointestinal Microbiome
Genome Size/*genetics
Humans
*Metagenomics
Methanobacteriaceae/*genetics/physiology
Methanobrevibacter/genetics/physiology
Phylogeny
Rumen/microbiology

@article {pmid30050163,
year = {2018},
author = {Ishii, S and Suzuki, S and Tenney, A and Nealson, KH and Bretschger, O},
title = {Comparative metatranscriptomics reveals extracellular electron transfer pathways conferring microbial adaptivity to surface redox potential changes.},
journal = {The ISME journal},
volume = {12},
number = {12},
pages = {2844-2863},
pmid = {30050163},
issn = {1751-7370},
mesh = {Carbon/metabolism ; Cytochrome c Group/genetics/metabolism ; Electric Conductivity ; Electrodes ; Electron Transport ; Geobacter/*genetics/metabolism ; Heme ; *Metabolic Networks and Pathways ; Metagenomics ; *Microbiota ; Oxidation-Reduction ; *Transcriptome ; },
abstract = {Some microbes can capture energy through redox reactions with electron flow to solid-phase electron acceptors, such as metal-oxides or poised electrodes, via extracellular electron transfer (EET). While diverse oxide minerals, exhibiting different surface redox potentials, are widely distributed on Earth, little is known about how microbes sense and use the minerals. Here we show electrochemical, metabolic, and transcriptional responses of EET-active microbial communities established on poised electrodes to changes in the surface redox potentials (as electron acceptors) and surrounding substrates (as electron donors). Combination of genome-centric stimulus-induced metatranscriptomics and metabolic pathway investigation revealed that nine Geobacter/Pelobacter microbes performed EET activity differently according to their preferable surface potentials and substrates. While the Geobacter/Pelobacter microbes coded numerous numbers of multi-heme c-type cytochromes and conductive e-pili, wide variations in gene expression were seen in response to altering surrounding substrates and surface potentials, accelerating EET via poised electrode or limiting EET via an open circuit system. These flexible responses suggest that a wide variety of EET-active microbes utilizing diverse EET mechanisms may work together to provide such EET-active communities with an impressive ability to handle major changes in surface potential and carbon source availability.},
}

Carbon/metabolism
Cytochrome c Group/genetics/metabolism
Electric Conductivity
Electrodes
Electron Transport
Geobacter/*genetics/metabolism
Heme
*Metabolic Networks and Pathways
Metagenomics
*Microbiota
Oxidation-Reduction
*Transcriptome

@article {pmid28924190,
year = {2017},
author = {Cornejo-Granados, F and Lopez-Zavala, AA and Gallardo-Becerra, L and Mendoza-Vargas, A and Sánchez, F and Vichido, R and Brieba, LG and Viana, MT and Sotelo-Mundo, RR and Ochoa-Leyva, A},
title = {Microbiome of Pacific Whiteleg shrimp reveals differential bacterial community composition between Wild, Aquacultured and AHPND/EMS outbreak conditions.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {11783},
pmid = {28924190},
issn = {2045-2322},
mesh = {Animals ; *Aquaculture ; *Bacteria/classification/genetics ; *Gastrointestinal Microbiome ; Metagenomics ; Penaeidae/growth & development/*microbiology ; },
abstract = {Crustaceans form the second largest subphylum on Earth, which includes Litopeneaus vannamei (Pacific whiteleg shrimp), one of the most cultured shrimp worldwide. Despite efforts to study the shrimp microbiota, little is known about it from shrimp obtained from the open sea and the role that aquaculture plays in microbiota remodeling. Here, the microbiota from the hepatopancreas and intestine of wild type (wt) and aquacultured whiteleg shrimp and pond sediment from hatcheries were characterized using sequencing of seven hypervariable regions of the 16S rRNA gene. Cultured shrimp with AHPND/EMS disease symptoms were also included. We found that (i) microbiota and their predicted metagenomic functions were different between wt and cultured shrimp; (ii) independent of the shrimp source, the microbiota of the hepatopancreas and intestine was different; (iii) the microbial diversity between the sediment and intestines of cultured shrimp was similar; and (iv) associated to an early development of AHPND/EMS disease, we found changes in the microbiome and the appearance of disease-specific bacteria. Notably, under cultured conditions, we identified bacterial taxa enriched in healthy shrimp, such as Faecalibacterium prausnitzii and Pantoea agglomerans, and communities enriched in diseased shrimp, such as Aeromonas taiwanensis, Simiduia agarivorans and Photobacterium angustum.},
}

Animals
*Aquaculture
*Bacteria/classification/genetics
*Gastrointestinal Microbiome
Metagenomics
Penaeidae/growth & development/*microbiology

@article {pmid31012060,
year = {2019},
author = {Lorenzi, AS and Chia, MA and Lopes, FAC and Silva, GGZ and Edwards, RA and Bittencourt-Oliveira, MDC},
title = {Cyanobacterial biodiversity of semiarid public drinking water supply reservoirs assessed via next-generation DNA sequencing technology.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {57},
number = {6},
pages = {450-460},
doi = {10.1007/s12275-019-8349-7},
pmid = {31012060},
issn = {1976-3794},
mesh = {Bacterial Toxins/analysis/genetics/isolation & purification ; *Biodiversity ; Brazil ; Cyanobacteria/*classification/genetics/*isolation & purification ; DNA, Bacterial/analysis ; Drinking Water/*microbiology ; Environmental Monitoring/methods ; Genes, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Microcystis/genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Saxitoxin/genetics ; Seasons ; Sequence Analysis, DNA/*methods ; Uracil/analogs & derivatives ; *Water Microbiology ; *Water Supply ; },
abstract = {Next-generation DNA sequencing technology was applied to generate molecular data from semiarid reservoirs during well-defined seasons. Target sequences of 16S-23S rRNA ITS and cpcBA-IGS were used to reveal the taxonomic groups of cyanobacteria present in the samples, and genes coding for cyanotoxins such as microcystins (mcyE), saxitoxins (sxtA), and cylindrospermopsins (cyrJ) were investigated. The presence of saxitoxins in the environmental samples was evaluated using ELISA kit. Taxonomic analyses of high-throughput DNA sequencing data showed the dominance of the genus Microcystis in Mundaú reservoir. Furthermore, it was the most abundant genus in the dry season in Ingazeira reservoir. In the rainy season, 16S-23S rRNA ITS analysis revealed that Cylindrospermopsis raciborskii comprised 46.8% of the cyanobacterial community in Ingazeira reservoir, while the cpcBAIGS region revealed that C. raciborskii (31.8%) was the most abundant taxon followed by Sphaerospermopsis aphanizomenoides (17.3%) and Planktothrix zahidii (16.6%). Despite the presence of other potential toxin-producing genera, the detected sxtA gene belonged to C. raciborskii, while the mcyE gene belonged to Microcystis in both reservoirs. The detected mcyE gene had good correlation with MC content, while the amplification of the sxtA gene was related to the presence of STX. The cyrJ gene was not detected in these samples. Using DNA analyses, our results showed that the cyanobacterial composition of Mundaú reservoir was similar in successive dry seasons, and it varied between seasons in Ingazeira reservoir. In addition, our data suggest that some biases of analysis influenced the cyanobacterial communities seen in the NGS output of Ingazeira reservoir.},
}

Bacterial Toxins/analysis/genetics/isolation & purification
*Biodiversity
Brazil
Cyanobacteria/*classification/genetics/*isolation & purification
DNA, Bacterial/analysis
Drinking Water/*microbiology
Environmental Monitoring/methods
Genes, Bacterial/genetics
High-Throughput Nucleotide Sequencing/methods
Metagenomics/methods
Microcystis/genetics
RNA, Ribosomal, 16S/genetics
RNA, Ribosomal, 23S/genetics
Saxitoxin/genetics
Seasons
Sequence Analysis, DNA/*methods
Uracil/analogs & derivatives
*Water Microbiology
*Water Supply

@article {pmid30992350,
year = {2019},
author = {Cobián Güemes, AG and Lim, YW and Quinn, RA and Conrad, DJ and Benler, S and Maughan, H and Edwards, R and Brettin, T and Cantú, VA and Cuevas, D and Hamidi, R and Dorrestein, P and Rohwer, F},
title = {Cystic Fibrosis Rapid Response: Translating Multi-omics Data into Clinically Relevant Information.},
journal = {mBio},
volume = {10},
number = {2},
pages = {},
doi = {10.1128/mBio.00431-19},
pmid = {30992350},
issn = {2150-7511},
mesh = {Adult ; Case-Control Studies ; Coinfection/complications ; Cystic Fibrosis/*complications/microbiology ; Disease Management ; *Disease Progression ; Escherichia coli Infections/*diagnosis ; Fatal Outcome ; Gene Expression Profiling ; *Genomics ; Humans ; Lung/*microbiology/physiopathology ; Male ; Metabolome ; *Metabolomics ; Metagenome ; Microbiota ; Shiga Toxin/genetics ; Shiga-Toxigenic Escherichia coli/genetics/pathogenicity ; },
abstract = {Pulmonary exacerbations are the leading cause of death in cystic fibrosis (CF) patients. To track microbial dynamics during acute exacerbations, a CF rapid response (CFRR) strategy was developed. The CFRR relies on viromics, metagenomics, metatranscriptomics, and metabolomics data to rapidly monitor active members of the viral and microbial community during acute CF exacerbations. To highlight CFRR, a case study of a CF patient is presented, in which an abrupt decline in lung function characterized a fatal exacerbation. The microbial community in the patient's lungs was closely monitored through the multi-omics strategy, which led to the identification of pathogenic shigatoxigenic Escherichia coli (STEC) expressing Shiga toxin. This case study illustrates the potential for the CFRR to deconstruct complicated disease dynamics and provide clinicians with alternative treatments to improve the outcomes of pulmonary exacerbations and expand the life spans of individuals with CF.IMPORTANCE Proper management of polymicrobial infections in patients with cystic fibrosis (CF) has extended their life span. Information about the composition and dynamics of each patient's microbial community aids in the selection of appropriate treatment of pulmonary exacerbations. We propose the cystic fibrosis rapid response (CFRR) as a fast approach to determine viral and microbial community composition and activity during CF pulmonary exacerbations. The CFRR potential is illustrated with a case study in which a cystic fibrosis fatal exacerbation was characterized by the presence of shigatoxigenic Escherichia coli The incorporation of the CFRR within the CF clinic could increase the life span and quality of life of CF patients.},
}

Adult
Case-Control Studies
Coinfection/complications
Cystic Fibrosis/*complications/microbiology
Disease Management
*Disease Progression
Escherichia coli Infections/*diagnosis
Fatal Outcome
Gene Expression Profiling
*Genomics
Humans
Lung/*microbiology/physiopathology
Male
Metabolome
*Metabolomics
Metagenome
Microbiota
Shiga Toxin/genetics
Shiga-Toxigenic Escherichia coli/genetics/pathogenicity

@article {pmid28912589,
year = {2017},
author = {Naghoni, A and Emtiazi, G and Amoozegar, MA and Cretoiu, MS and Stal, LJ and Etemadifar, Z and Shahzadeh Fazeli, SA and Bolhuis, H},
title = {Microbial diversity in the hypersaline Lake Meyghan, Iran.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {11522},
pmid = {28912589},
issn = {2045-2322},
mesh = {Archaea/*classification/genetics/growth & development ; Bacteria/*classification/genetics/growth & development ; *Biota ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Iran ; Lakes/chemistry/*microbiology ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Saline Waters ; Sequence Analysis, DNA ; },
abstract = {Lake Meyghan is one of the largest and commercially most important salt lakes in Iran. Despite its inland location and high altitude, Lake Meyghan has a thalassohaline salt composition suggesting a marine origin. Inputs of fresh water by rivers and rainfall formed various basins characterized by different salinities. We analyzed the microbial community composition of three basins by isolation and culturing of microorganisms and by analysis of the metagenome. The basins that were investigated comprised a green ~50 g kg-1 salinity brine, a red ~180 g kg-1 salinity brine and a white ~300 g kg-1 salinity brine. Using different growth media, 57 strains of Bacteria and 48 strains of Archaea were isolated. Two bacterial isolates represent potential novel species with less than 96% 16S rRNA gene sequence identity to known species. Abundant isolates were also well represented in the metagenome. Bacteria dominated the low salinity brine, with Alteromonadales (Gammaproteobacteria) as a particularly important taxon, whereas the high salinity brines were dominated by haloarchaea. Although the brines of Lake Meyghan differ in geochemical composition, their ecosystem function appears largely conserved amongst each other while being driven by different microbial communities.},
}

Archaea/*classification/genetics/growth & development
Bacteria/*classification/genetics/growth & development
*Biota
Cluster Analysis
DNA, Archaeal/chemistry/genetics
DNA, Bacterial/chemistry/genetics
DNA, Ribosomal/chemistry/genetics
Iran
Lakes/chemistry/*microbiology
Metagenomics
Phylogeny
RNA, Ribosomal, 16S/genetics
*Saline Waters
Sequence Analysis, DNA

@article {pmid30915691,
year = {2019},
author = {Akyol, Ç and Ozbayram, EG and Demirel, B and Onay, TT and Ince, O and Ince, B},
title = {Linking nano-ZnO contamination to microbial community profiling in sanitary landfill simulations.},
journal = {Environmental science and pollution research international},
volume = {26},
number = {13},
pages = {13580-13591},
doi = {10.1007/s11356-019-04906-8},
pmid = {30915691},
issn = {1614-7499},
support = {112Y322//TUBITAK/ ; 13081//Boğaziçi University Research Fund Project/ ; },
mesh = {Archaea ; Bacteria ; Biofuels ; Bioreactors/*microbiology ; Microbiota ; RNA, Ribosomal, 16S/*chemistry ; Refuse Disposal/methods ; Solid Waste/*analysis ; Waste Disposal Facilities ; Zinc Oxide/*analysis/chemistry ; },
abstract = {Nanomaterials (NMs) commercially used for various activities mostly end up in landfills. Reduced biogas productions reported in landfill reactors create a need for more comprehensive research on these greatly-diverse microbial pools. In order to evaluate the impact of one of the most widely-used NMs, namely nano-zinc oxide (nano-ZnO), simulated bioreactor and conventional landfills were operated using real municipal solid waste (MSW) for 300 days with addition nano-ZnO. Leachate samples were taken at different phases and analyzed by 16S rRNA gene amplicon sequencing. The bacterial communities were distinctly characterized by Cloacamonaceae (phylum WWE1), Rhodocyclaceae (phylum Proteobacteria), Porphyromonadaceae (phylum Bacteroidetes), and Synergistaceae (phylum Synergistetes). The bacterial community in the bioreactors shifted at the end of the operation and was dominated by Rhodocyclaceae. There was not a major change in the bacterial community in the conventional reactors. The methanogenic archaeal diversity highly differed between the bioreactors and conventional reactors. The dominance of Methanomicrobiaceae was observed in the bioreactors during the peak methane-production period; however, their prominence shifted to WSA2 in the nano-ZnO-added bioreactor and to Methanocorpusculaceae in the control bioreactor towards the end. Methanocorpusculaceae was the most abundant family in both conventional control and nano-ZnO-containing reactors.},
}

Archaea
Bacteria
Biofuels
Bioreactors/*microbiology
Microbiota
RNA, Ribosomal, 16S/*chemistry
Refuse Disposal/methods
Solid Waste/*analysis
Waste Disposal Facilities
Zinc Oxide/*analysis/chemistry

@article {pmid30526624,
year = {2018},
author = {Wu, G and Niu, M and Tang, W and Hu, J and Wei, G and He, Z and Chen, Y and Jiang, Y and Chen, P},
title = {L-Fucose ameliorates high-fat diet-induced obesity and hepatic steatosis in mice.},
journal = {Journal of translational medicine},
volume = {16},
number = {1},
pages = {344},
pmid = {30526624},
issn = {1479-5876},
support = {2016A030306043//Natural Science Foundation of Guangdong Province/International ; 2017B030314034//Natural Science Foundation of Guangdong Province/International ; 2016A020216015//China Association for Science and Technology/International ; },
mesh = {Adiposity/drug effects ; Animals ; Cecum/drug effects/microbiology ; *Diet, High-Fat ; Dysbiosis/complications/microbiology/pathology ; Feeding Behavior ; Fucose/pharmacology/*therapeutic use ; Gastrointestinal Microbiome/drug effects ; Glucose Tolerance Test ; Insulin ; Metagenomics ; Mice, Inbred C57BL ; Non-alcoholic Fatty Liver Disease/*complications/*drug therapy/microbiology ; Obesity/*complications/*drug therapy/microbiology ; Weight Gain/drug effects ; },
abstract = {BACKGROUND: L-Fucose (Fuc), a six-deoxy hexose monosaccharide, is present endogenously in humans and animals and has a wide range of biological functions. In the present study, we aimed to examine the effect of Fuc on obesity and hepatic steatosis in mice fed a high-fat diet (HFD).

METHODS: C57BL/6 mice were fed a normal chow (NC) or HFD for 18 weeks to induce obesity and fatty liver. Fuc was administered intragastrically from the 8th week to the end of the experiment (18 weeks).

RESULTS: Metagenomic analysis showed that HFD altered the genomic profile of gut microbiota in the mice; specifically, expression of alpha-L-fucosidase, the gene responsible for Fuc generation, was markedly reduced in the HFD group compared with that in the NC group. Fuc treatment decreased body weight gain, fat accumulation, and hepatic triglyceride elevation in HFD-fed mice. In addition, Fuc decreased the levels of endotoxin-producing bacteria of the Desulfovibrionaceae family and restored HFD-induced enteric dysbiosis at both compositional and functional levels.

CONCLUSION: Our findings suggest that Fuc might be a novel strategy to treat HFD-induced obesity and fatty liver.},
}

Adiposity/drug effects
Animals
Cecum/drug effects/microbiology
*Diet, High-Fat
Dysbiosis/complications/microbiology/pathology
Feeding Behavior
Fucose/pharmacology/*therapeutic use
Gastrointestinal Microbiome/drug effects
Glucose Tolerance Test
Insulin
Metagenomics
Mice, Inbred C57BL
Non-alcoholic Fatty Liver Disease/*complications/*drug therapy/microbiology
Obesity/*complications/*drug therapy/microbiology
Weight Gain/drug effects

@article {pmid30449316,
year = {2018},
author = {Guerin, E and Shkoporov, A and Stockdale, SR and Clooney, AG and Ryan, FJ and Sutton, TDS and Draper, LA and Gonzalez-Tortuero, E and Ross, RP and Hill, C},
title = {Biology and Taxonomy of crAss-like Bacteriophages, the Most Abundant Virus in the Human Gut.},
journal = {Cell host & microbe},
volume = {24},
number = {5},
pages = {653-664.e6},
doi = {10.1016/j.chom.2018.10.002},
pmid = {30449316},
issn = {1934-6069},
mesh = {Bacteriophages/*classification/*genetics/*physiology/ultrastructure ; Base Sequence ; Capsid Proteins/genetics ; DNA Viruses ; Feces/virology ; Fermentation ; *Gastrointestinal Microbiome ; Genome, Viral/genetics ; Genomics ; Humans ; Metagenomics/methods ; *Phylogeny ; Sequence Analysis ; Viral Proteins/genetics ; },
abstract = {CrAssphages represent the most abundant virus in the human gut microbiota, but the lack of available genome sequences for comparison has kept them enigmatic. Recently, sequence-based classification of distantly related crAss-like phages from multiple environments was reported, leading to a proposed familial-level taxonomic group. Here, we assembled the metagenomic sequencing reads from 702 human fecal virome/phageome samples and analyzed 99 complete circular crAss-like phage genomes and 150 contigs ≥70 kb. In silico comparative genomics and taxonomic analysis enabled a classification scheme of crAss-like phages from human fecal microbiomes into four candidate subfamilies composed of ten candidate genera. Laboratory analysis was performed on fecal samples from an individual harboring seven distinct crAss-like phages. We achieved crAss-like phage propagation in ex vivo human fecal fermentations and visualized short-tailed podoviruses by electron microscopy. Mass spectrometry of a crAss-like phage capsid protein could be linked to metagenomic sequencing data, confirming crAss-like phage structural annotations.},
}

Bacteriophages/*classification/*genetics/*physiology/ultrastructure
Base Sequence
Capsid Proteins/genetics
DNA Viruses
Feces/virology
Fermentation
*Gastrointestinal Microbiome
Genome, Viral/genetics
Genomics
Humans
Metagenomics/methods
*Phylogeny
Sequence Analysis
Viral Proteins/genetics

@article {pmid29961061,
year = {2018},
author = {Lee, J and Lim, JH and Park, J and Kim, IN},
title = {Temporal and Vertical Variation in Microbial Community Composition in Response to Physicochemical Characteristics in a Water Column of Highly Eutrophied Jinhae Bay, South Korea.},
journal = {Journal of molecular microbiology and biotechnology},
volume = {28},
number = {2},
pages = {65-77},
doi = {10.1159/000489633},
pmid = {29961061},
issn = {1660-2412},
mesh = {Bacteroidetes/genetics/isolation & purification ; Bays/*microbiology ; Cyanobacteria/genetics/isolation & purification ; DNA, Bacterial/genetics/isolation & purification ; *Eutrophication ; *Microbiota ; Proteobacteria/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics/isolation & purification ; Republic of Korea ; Seasons ; Sequence Analysis, DNA ; Water Microbiology ; },
abstract = {Microbial communities play an essential role in marine biogeochemical cycles. Physical and biogeochemical changes in Jinhae Bay, the most anthropogenically eutrophied bay on the coasts of South Korea, are well described, but less is known about the associated changes in microbial communities. Temporal and vertical variation in microbial communities at three depths (surface, middle, and bottom) at seven time points (June to December) at the J1 sampling site were investigated on the MiSeq platform based on the 16S rRNA gene. Overall, the microbial community was dominated by Proteobacteria, Cyanobacteria, and Bacteroidetes from June to November, whereas Firmicutes were dominant in December, especially in the middle and bottom layers. The results indicate that the microbial community composition strongly varied with temporal changes in the physicochemical water properties. Moreover, the community composition differed markedly between the surface and middle layers and the bottom layer in the summer, when the water column was strongly stratified and bottom water hypoxia developed. A redundancy analysis suggested a significant correlation between physicochemical variables (i.e., temperature, salinity, and oxygen concentration) and microbial community composition. This study indicates that temporal changes in water conditions and eutrophication-induced hypoxia effectively shape the structure of the microbial community.},
}

Bacteroidetes/genetics/isolation & purification
Bays/*microbiology
Cyanobacteria/genetics/isolation & purification
DNA, Bacterial/genetics/isolation & purification
*Eutrophication
*Microbiota
Proteobacteria/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics/isolation & purification
Republic of Korea
Seasons
Sequence Analysis, DNA
Water Microbiology

@article {pmid29715508,
year = {2018},
author = {Lamichhane, S and Sen, P and Dickens, AM and Orešič, M and Bertram, HC},
title = {Gut metabolome meets microbiome: A methodological perspective to understand the relationship between host and microbe.},
journal = {Methods (San Diego, Calif.)},
volume = {149},
number = {},
pages = {3-12},
doi = {10.1016/j.ymeth.2018.04.029},
pmid = {29715508},
issn = {1095-9130},
mesh = {Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/immunology/metabolism ; Host Microbial Interactions/*physiology ; Humans ; Metabolome/*physiology ; Metabolomics/*methods/trends ; },
abstract = {It is well established that gut microbes and their metabolic products regulate host metabolism. The interactions between the host and its gut microbiota are highly dynamic and complex. In this review we present and discuss the metabolomic strategies to study the gut microbial ecosystem. We highlight the metabolic profiling approaches to study faecal samples aimed at deciphering the metabolic product derived from gut microbiota. We also discuss how metabolomics data can be integrated with metagenomics data derived from gut microbiota and how such approaches may lead to better understanding of the microbial functions. Finally, the emerging approaches of genome-scale metabolic modelling to study microbial co-metabolism and host-microbe interactions are highlighted.},
}

Gastrointestinal Microbiome/*physiology
Gastrointestinal Tract/immunology/metabolism
Host Microbial Interactions/*physiology
Humans
Metabolome/*physiology
Metabolomics/*methods/trends

@article {pmid28912574,
year = {2017},
author = {Purcell, RV and Visnovska, M and Biggs, PJ and Schmeier, S and Frizelle, FA},
title = {Distinct gut microbiome patterns associate with consensus molecular subtypes of colorectal cancer.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {11590},
pmid = {28912574},
issn = {2045-2322},
mesh = {Adult ; Aged ; Aged, 80 and over ; *Biomarkers, Tumor ; Colorectal Neoplasms/*etiology/metabolism/*pathology ; Computational Biology ; Female ; *Gastrointestinal Microbiome ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Humans ; Male ; Metagenome ; Metagenomics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Transcriptome ; },
abstract = {Colorectal cancer (CRC) is a heterogeneous disease and recent advances in subtype classification have successfully stratified the disease using molecular profiling. The contribution of bacterial species to CRC development is increasingly acknowledged, and here, we sought to analyse CRC microbiomes and relate them to tumour consensus molecular subtypes (CMS), in order to better understand the relationship between bacterial species and the molecular mechanisms associated with CRC subtypes. We classified 34 tumours into CRC subtypes using RNA-sequencing derived gene expression and determined relative abundances of bacterial taxonomic groups using 16S rRNA amplicon metabarcoding. 16S rRNA analysis showed enrichment of Fusobacteria and Bacteroidetes, and decreased levels of Firmicutes and Proteobacteria in CMS1. A more detailed analysis of bacterial taxa using non-human RNA-sequencing reads uncovered distinct bacterial communities associated with each molecular subtype. The most highly enriched species associated with CMS1 included Fusobacterium hwasookii and Porphyromonas gingivalis. CMS2 was enriched for Selenomas and Prevotella species, while CMS3 had few significant associations. Targeted quantitative PCR validated these findings and also showed an enrichment of Fusobacterium nucleatum, Parvimonas micra and Peptostreptococcus stomatis in CMS1. In this study, we have successfully associated individual bacterial species to CRC subtypes for the first time.},
}

Adult
Aged
Aged, 80 and over
*Biomarkers, Tumor
Colorectal Neoplasms/*etiology/metabolism/*pathology
Computational Biology
Female
*Gastrointestinal Microbiome
Gene Expression Profiling
Gene Expression Regulation, Neoplastic
Humans
Male
Metagenome
Metagenomics
Middle Aged
RNA, Ribosomal, 16S/genetics
Reproducibility of Results
Transcriptome

@article {pmid28900280,
year = {2017},
author = {Zhang, J and Mao, L and Zhang, L and Loh, KC and Dai, Y and Tong, YW},
title = {Metagenomic insight into the microbial networks and metabolic mechanism in anaerobic digesters for food waste by incorporating activated carbon.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {11293},
pmid = {28900280},
issn = {2045-2322},
mesh = {*Anaerobiosis ; Computational Biology/methods ; *Energy Metabolism ; Fermentation ; Food ; Metabolic Networks and Pathways ; *Metagenome ; *Metagenomics/methods ; Methane/biosynthesis ; *Microbiota ; Waste Disposal, Fluid ; },
abstract = {Powdered activated carbon (AC) is commonly used as an effective additive to enhance anaerobic digestion (AD), but little is known about how the metabolic pathways resulting from adding AC change the microbial association network and enhance food waste treatment. In this work, the use of AC in an anaerobic digestion system for food waste was explored. Using bioinformatics analysis, taxonomic trees and the KEGG pathway analysis, changes in microbial network and biometabolic pathways were tracked. The overall effect of these changes were used to explain and validate improved digestion performance. The results showed that AC accelerated the decomposition of edible oil in food waste, enhancing the conversion of food waste to methane with the optimized dosage of 12 g AC per reactor. Specifically, when AC was added, the proponoate metabolic pathway that converts propanoic acid to acetic acid became more prominent, as measured by 16S rRNA in the microbial community. The other two metabolic pathways, Lipid Metabolism and Methane Metabolism, were also enhanced. Bioinformatics analysis revealed that AC promoted the proliferation of syntrophic microorganisms such as Methanosaeta and Geobacter, forming a highly intensive syntrophic microbial network.},
}

*Anaerobiosis
Computational Biology/methods
*Energy Metabolism
Fermentation
Food
Metabolic Networks and Pathways
*Metagenome
*Metagenomics/methods
Methane/biosynthesis
*Microbiota
Waste Disposal, Fluid

@article {pmid28900257,
year = {2017},
author = {Potter, C and Freeman, C and Golyshin, PN and Ackermann, G and Fenner, N and McDonald, JE and Ehbair, A and Jones, TG and Murphy, LM and Creer, S},
title = {Subtle shifts in microbial communities occur alongside the release of carbon induced by drought and rewetting in contrasting peatland ecosystems.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {11314},
pmid = {28900257},
issn = {2045-2322},
support = {BB/M029085/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Biodiversity ; Carbon/*metabolism ; *Droughts ; *Ecosystem ; Environment ; Metagenome ; Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Soil/*chemistry ; *Soil Microbiology ; },
abstract = {Peat represents a globally significant pool of sequestered carbon. However, peatland carbon stocks are highly threatened by anthropogenic climate change, including drought, which leads to a large release of carbon dioxide. Although the enzymatic mechanisms underlying drought-driven carbon release are well documented, the effect of drought on peatland microbial communities has been little studied. Here, we carried out a replicated and controlled drought manipulation using intact peat 'mesocosm cores' taken from bog and fen habitats, and used a combination of community fingerprinting and sequencing of marker genes to identify community changes associated with drought. Community composition varied with habitat and depth. Moreover, community differences between mesocosm cores were stronger than the effect of the drought treatment, emphasising the importance of replication in microbial marker gene studies. While the effect of drought on the overall composition of prokaryotic and eukaryotic communities was weak, a subset of the microbial community did change in relative abundance, especially in the fen habitat at 5 cm depth. 'Drought-responsive' OTUs were disproportionately drawn from the phyla Bacteroidetes and Proteobacteria. Collectively, the data provide insights into the microbial community changes occurring alongside drought-driven carbon release from peatlands, and suggest a number of novel avenues for future research.},
}

*Biodiversity
Carbon/*metabolism
*Droughts
*Ecosystem
Environment
Metagenome
Metagenomics/methods
*Microbiota
RNA, Ribosomal, 16S/genetics
RNA, Ribosomal, 18S/genetics
Soil/*chemistry
*Soil Microbiology