@article {pmid30420843,
year = {2018},
author = {Alves, LF and Meleiro, LP and Silva, RN and Westmann, CA and Guazzaroni, ME},
title = {Novel Ethanol- and 5-Hydroxymethyl Furfural-Stimulated β-Glucosidase Retrieved From a Brazilian Secondary Atlantic Forest Soil Metagenome.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2556},
doi = {10.3389/fmicb.2018.02556},
pmid = {30420843},
issn = {1664-302X},
abstract = {Beta-glucosidases are key enzymes involved in lignocellulosic biomass degradation for bioethanol production, which complete the final step during cellulose hydrolysis by converting cellobiose into glucose. Currently, industry requires enzymes with improved catalytic performance or tolerance to process-specific parameters. In this sense, metagenomics has become a powerful tool for accessing and exploring the biochemical biodiversity present in different natural environments. Here, we report the identification of a novel β-glucosidase from metagenomic DNA isolated from soil samples enriched with decaying plant matter from a Secondary Atlantic Forest region. For this, we employed a functional screening approach using an optimized and synthetic broad host-range vector for library production. The novel β-glucosidase - named Lfa2 - displays three GH3-family conserved domains and conserved catalytic amino acids D283 and E487. The purified enzyme was most active in pH 5.5 and at 50°C, and showed hydrolytic activity toward several pNP synthetic substrates containing β-glucose, β-galactose, β-xylose, β-fucose, and α-arabinopyranose, as well as toward cellobiose. Lfa2 showed considerable glucose tolerance, exhibiting an IC50 of 300 mM glucose and 30% of remaining activity in 600 mM glucose. In addition, Lfa2 retained full or slightly enhanced activity in the presence of several metal ions. Further, β-glucosidase activity was increased by 1.7-fold in the presence of 10% (v/v) ethanol, a concentration that can be reached in conventional fermentation processes. Similarly, Lfa2 showed 1.7-fold enhanced activity at high concentrations of 5-hydroxymethyl furfural, one of the most important cellulase inhibitors in pretreated sugarcane bagasse hydrolysates. Moreover, the synergistic effect of Lfa2 on Bacillus subtilis GH5-CBM3 endoglucanase activity was demonstrated by the increased production of glucose (1.6-fold). Together, these results indicate that β-glucosidase Lfa2 is a promissory enzyme candidate for utilization in diverse industrial applications, such as cellulosic biomass degradation or flavor enhancement in winemaking and grape processing.},
}

@article {pmid30346155,
year = {2018},
author = {Pérez-Burillo, S and Pastoriza, S and Jiménez-Hernández, N and D'Auria, G and Francino, MP and Rufián-Henares, JA},
title = {Effect of Food Thermal Processing on the Composition of the Gut Microbiota.},
journal = {Journal of agricultural and food chemistry},
volume = {66},
number = {43},
pages = {11500-11509},
doi = {10.1021/acs.jafc.8b04077},
pmid = {30346155},
issn = {1520-5118},
mesh = {Bacteria/classification ; *Cooking ; Edible Grain ; Fabaceae ; Fatty Acids, Volatile/analysis ; Fermentation ; Fruit ; Furaldehyde/analogs & derivatives/analysis ; *Gastrointestinal Microbiome ; *Hot Temperature ; Humans ; Lysine/analogs & derivatives/analysis ; Maillard Reaction ; Meat ; RNA, Ribosomal, 16S/genetics ; Vegetables ; },
abstract = {Cooking modifies food composition due to chemical reactions. Additionally, food composition shapes the human gut microbiota. Thus, the objective of this research was to unravel the effect of different food cooking methods on the structure and functionality of the gut microbiota. Common culinary techniques were applied to five foods, which were submitted to in vitro digestion-fermentation. Furosine, 5-(hydroxymethyl)furfural, and furfural were used as Maillard reaction indicators to control the heat treatment. Short-chain fatty acids production was quantified as indicator of healthy metabolic output. Gut microbial community structure was analyzed through 16S rRNA. Both food composition and cooking methods modified the microbiota composition and released short-chain fatty acids. In general, intense cooking technologies (roasting and grilling) increased the abundance of beneficial bacteria like Ruminococcus spp. or Bifidobacterium spp. compared to milder treatments (boiling). However, for some foods (banana or bread), intense cooking decreased the levels of healthy bacteria.},
}

Bacteria/classification
*Cooking
Edible Grain
Fabaceae
Fatty Acids, Volatile/analysis
Fermentation
Fruit
Furaldehyde/analogs & derivatives/analysis
*Gastrointestinal Microbiome
*Hot Temperature
Humans
Lysine/analogs & derivatives/analysis
Maillard Reaction
Meat
RNA, Ribosomal, 16S/genetics
Vegetables

@article {pmid29788417,
year = {2018},
author = {Patil, RD and Ellison, MJ and Wolff, SM and Shearer, C and Wright, AM and Cockrum, RR and Austin, KJ and Lamberson, WR and Cammack, KM and Conant, GC},
title = {Poor feed efficiency in sheep is associated with several structural abnormalities in the community metabolic network of their ruminal microbes.},
journal = {Journal of animal science},
volume = {96},
number = {6},
pages = {2113-2124},
doi = {10.1093/jas/sky096},
pmid = {29788417},
issn = {1525-3163},
mesh = {Animal Feed/*analysis ; Animals ; Female ; *Gastrointestinal Microbiome ; *Metabolic Networks and Pathways ; *Metagenomics ; Rumen/metabolism/microbiology ; Sheep/microbiology/*physiology ; },
abstract = {Ruminant animals have a symbiotic relationship with the microorganisms in their rumens. In this relationship, rumen microbes efficiently degrade complex plant-derived compounds into smaller digestible compounds, a process that is very likely associated with host animal feed efficiency. The resulting simpler metabolites can then be absorbed by the host and converted into other compounds by host enzymes. We used a microbial community metabolic network inferred from shotgun metagenomics data to assess how this metabolic system differs between animals that are able to turn ingested feedstuffs into body mass with high efficiency and those that are not. We conducted shotgun sequencing of microbial DNA from the rumen contents of 16 sheep that differed in their residual feed intake (RFI), a measure of feed efficiency. Metagenomic reads from each sheep were mapped onto a database-derived microbial metabolic network, which was linked to the sheep metabolic network by interface metabolites (metabolites transferred from microbes to host). No single enzyme was identified as being significantly different in abundance between the low and high RFI animals (P > 0.05, Wilcoxon test). However, when we analyzed the metabolic network as a whole, we found several differences between efficient and inefficient animals. Microbes from low RFI (efficient) animals use a suite of enzymes closer in network space to the host's reactions than those of the high RFI (inefficient) animals. Similarly, low RFI animals have microbial metabolic networks that, on average, contain reactions using shorter carbon chains than do those of high RFI animals, potentially allowing the host animals to extract metabolites more efficiently. Finally, the efficient animals possess community networks with greater Shannon diversity among their enzymes than do inefficient ones. Thus, our system approach to the ruminal microbiome identified differences attributable to feed efficiency in the structure of the microbes' community metabolic network that were undetected at the level of individual microbial taxa or reactions.},
}

Animal Feed/*analysis
Animals
Female
*Gastrointestinal Microbiome
*Metabolic Networks and Pathways
*Metagenomics
Rumen/metabolism/microbiology
Sheep/microbiology/*physiology

@article {pmid28349946,
year = {2017},
author = {Yan, W and Sun, C and Yuan, J and Yang, N},
title = {Gut metagenomic analysis reveals prominent roles of Lactobacillus and cecal microbiota in chicken feed efficiency.},
journal = {Scientific reports},
volume = {7},
number = {},
pages = {45308},
doi = {10.1038/srep45308},
pmid = {28349946},
issn = {2045-2322},
mesh = {Amino Acids/metabolism ; Animal Feed ; Animals ; Bacteria/genetics/isolation & purification ; Biodiversity ; Cecum/microbiology ; Chickens ; Duodenum/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Lactobacillus/genetics/*isolation & purification ; *Metagenomics ; Phenotype ; RNA, Ribosomal, 16S/chemistry/genetics/metabolism ; Sequence Analysis, DNA ; },
abstract = {Interactions between the host and gut microbiota can affect gut metabolism. In this study, the individual performances of 252 hens were recorded to evaluate feed efficiency. Hens with contrasting feed efficiencies (14 birds per group) were selected to investigate their duodenal, cecal and fecal microbial composition by sequencing the 16S rRNA gene V4 region. The results showed that the microbial community in the cecum was quite different from those in the duodenum and feces. The highest biodiversity and all differentially abundant taxa between the different efficiency groups were observed in the cecal microbial community with false discovery rate (FDR) <0.05. Of these differentially abundant cecal microbes, Lactobacillus accounted for a greater proportion than the others. The abundances of Lactobacillus and Akkermansia were significantly higher while that of Faecalibacterium was lower (FDR < 0.05) in the better feed efficiency (BFE) group. Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis revealed that the functions relating to glycometabolism and amino acid metabolism were enriched in the cecal microbiota of the BFE group. These results indicated the prominent role of cecal microbiota in the feed efficiency of chickens and suggested plausible uses of Lactobacillus to improve the feed efficiency of host.},
}

Amino Acids/metabolism
Animal Feed
Animals
Bacteria/genetics/isolation & purification
Biodiversity
Cecum/microbiology
Chickens
Duodenum/microbiology
Feces/microbiology
*Gastrointestinal Microbiome
Lactobacillus/genetics/*isolation & purification
*Metagenomics
Phenotype
RNA, Ribosomal, 16S/chemistry/genetics/metabolism
Sequence Analysis, DNA

@article {pmid28112173,
year = {2017},
author = {Ji, P and Zhang, Y and Wang, J and Zhao, F},
title = {MetaSort untangles metagenome assembly by reducing microbial community complexity.},
journal = {Nature communications},
volume = {8},
number = {},
pages = {14306},
doi = {10.1038/ncomms14306},
pmid = {28112173},
issn = {2041-1723},
mesh = {Bacteria/*genetics ; Computational Biology ; Genome, Bacterial ; Genome, Microbial ; Kelp/*microbiology ; *Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA/methods ; *Software ; },
abstract = {Most current approaches to analyse metagenomic data rely on reference genomes. Novel microbial communities extend far beyond the coverage of reference databases and de novo metagenome assembly from complex microbial communities remains a great challenge. Here we present a novel experimental and bioinformatic framework, metaSort, for effective construction of bacterial genomes from metagenomic samples. MetaSort provides a sorted mini-metagenome approach based on flow cytometry and single-cell sequencing methodologies, and employs new computational algorithms to efficiently recover high-quality genomes from the sorted mini-metagenome by the complementary of the original metagenome. Through extensive evaluations, we demonstrated that metaSort has an excellent and unbiased performance on genome recovery and assembly. Furthermore, we applied metaSort to an unexplored microflora colonized on the surface of marine kelp and successfully recovered 75 high-quality genomes at one time. This approach will greatly improve access to microbial genomes from complex or novel communities.},
}

Bacteria/*genetics
Computational Biology
Genome, Bacterial
Genome, Microbial
Kelp/*microbiology
*Metagenome
Metagenomics/*methods
Microbiota/*genetics
Sequence Analysis, DNA/methods
*Software

@article {pmid30205462,
year = {2018},
author = {Hidalgo-Cantabrana, C and Sanozky-Dawes, R and Barrangou, R},
title = {Insights into the Human Virome Using CRISPR Spacers from Microbiomes.},
journal = {Viruses},
volume = {10},
number = {9},
pages = {},
doi = {10.3390/v10090479},
pmid = {30205462},
issn = {1999-4915},
support = {support//North Carolina Agricultural Foundation/International ; internal support//North Carolina State University/International ; },
mesh = {*Biodiversity ; Clustered Regularly Interspaced Short Palindromic Repeats ; Humans ; Metagenomics ; *Microbiota ; Viruses/*classification/genetics/*isolation & purification ; },
abstract = {Due to recent advances in next-generation sequencing over the past decade, our understanding of the human microbiome and its relationship to health and disease has increased dramatically. Yet, our insights into the human virome, and its interplay with important microbes that impact human health, is relatively limited. Prokaryotic and eukaryotic viruses are present throughout the human body, comprising a large and diverse population which influences several niches and impacts our health at various body sites. The presence of prokaryotic viruses like phages, has been documented at many different body sites, with the human gut being the richest ecological niche. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and associated proteins constitute the adaptive immune system of bacteria, which prevents attack by invasive nucleic acid. CRISPR-Cas systems function by uptake and integration of foreign genetic element sequences into the CRISPR array, which constitutes a genomic archive of iterative vaccination events. Consequently, CRISPR spacers can be investigated to reconstruct interplay between viruses and bacteria, and metagenomic sequencing data can be exploited to provide insights into host-phage interactions within a niche. Here, we show how the CRISPR spacer content of commensal and pathogenic bacteria can be used to determine the evidence of their phage exposure. This framework opens new opportunities for investigating host-virus dynamics in metagenomic data, and highlights the need to dedicate more efforts for virome sampling and sequencing.},
}

*Biodiversity
Clustered Regularly Interspaced Short Palindromic Repeats
Humans
Metagenomics
*Microbiota
Viruses/*classification/genetics/*isolation & purification

@article {pmid28696003,
year = {2018},
author = {Malanoski, AP and Lin, B and Eddie, BJ and Wang, Z and Hervey, WJ and Glaven, SM},
title = {Relative abundance of 'Candidatus Tenderia electrophaga' is linked to cathodic current in an aerobic biocathode community.},
journal = {Microbial biotechnology},
volume = {11},
number = {1},
pages = {98-111},
doi = {10.1111/1751-7915.12757},
pmid = {28696003},
issn = {1751-7915},
mesh = {*Bioelectric Energy Sources ; *Biota ; Carbon Dioxide/metabolism ; Chromatiaceae/classification/genetics/*isolation & purification/*metabolism ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Electrodes/*microbiology ; Metagenomics ; Oxidation-Reduction ; Oxygen/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Biocathode microbial communities are proposed to catalyse a range of useful reactions. Unlike bioanodes, model biocathode organisms have not yet been successfully cultivated in isolation highlighting the need for culture-independent approaches to characterization. Biocathode MCL (Marinobacter, Chromatiaceae, Labrenzia) is a microbial community proposed to couple CO2 fixation to extracellular electron transfer and O2 reduction. Previous metagenomic analysis of a single MCL bioelectrochemical system (BES) resulted in resolution of 16 bin genomes. To further resolve bin genomes and compare community composition across replicate MCL BES, we performed shotgun metagenomic and 16S rRNA gene (16S) sequencing at steady-state current. Clustering pooled reads from replicate BES increased the number of resolved bin genomes to 20, over half of which were > 90% complete. Direct comparison of unassembled metagenomic reads and 16S operational taxonomic units (OTUs) predicted higher community diversity than the assembled/clustered metagenome and the predicted relative abundances did not match. However, when 16S OTUs were mapped to bin genomes and genome abundance was scaled by 16S gene copy number, estimated relative abundance was more similar to metagenomic analysis. The relative abundance of the bin genome representing 'Ca. Tenderia electrophaga' was correlated with increasing current, further supporting the hypothesis that this organism is the electroautotroph.},
}

*Bioelectric Energy Sources
*Biota
Carbon Dioxide/metabolism
Chromatiaceae/classification/genetics/*isolation & purification/*metabolism
Cluster Analysis
DNA, Bacterial/chemistry/genetics
DNA, Ribosomal/chemistry/genetics
Electrodes/*microbiology
Metagenomics
Oxidation-Reduction
Oxygen/metabolism
Phylogeny
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA

@article {pmid30122883,
year = {2018},
author = {Zhao, Y and Mao, YF and Tang, YS and Ni, MZ and Liu, QH and Wang, Y and Feng, Q and Peng, JH and Hu, YY},
title = {Altered oral microbiota in chronic hepatitis B patients with different tongue coatings.},
journal = {World journal of gastroenterology},
volume = {24},
number = {30},
pages = {3448-3461},
doi = {10.3748/wjg.v24.i30.3448},
pmid = {30122883},
issn = {2219-2840},
mesh = {Adult ; Bacteria/genetics/*isolation & purification/metabolism ; Case-Control Studies ; DNA, Viral/isolation & purification ; Female ; Gastrointestinal Microbiome/*physiology ; Healthy Volunteers ; Hepatitis B virus/genetics/*isolation & purification ; Hepatitis B, Chronic/diagnosis/metabolism/*microbiology ; Humans ; Male ; Medicine, Chinese Traditional/methods ; Metagenomics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Tongue/*microbiology ; },
abstract = {AIM: To elucidate tongue coating microbiota and metabolic differences in chronic hepatitis B (CHB) patients with yellow or white tongue coatings.

METHODS: Tongue coating samples were collected from 53 CHB patients (28 CHB yellow tongue coating patients and 25 CHB white tongue coating patients) and 22 healthy controls. Microbial DNA was extracted from the tongue samples, and the bacterial 16S ribosomal RNA gene V3 region was amplified from all samples and sequenced with the Ion Torrent PGM™ sequencing platform according to the standard protocols. The metabolites in the tongue coatings were evaluated using a liquid chromatography-mass spectrometry (LC-MS) platform. Statistical analyses were then performed.

RESULTS: The relative compositions of the tongue coating microbiotas and metabolites in the CHB patients were significantly different from those of the healthy controls, but the tongue coating microbiota abundances and diversity levels were not significantly different. Compared with the CHB white tongue coating patients, the CHB yellow tongue coating patients had higher hepatitis B viral DNA (HBV-DNA) titers (median 21210 vs 500, respectively, P = 0.03) and a significantly lower level of Bacteroidetes (20.14% vs 27.93%, respectively, P = 0.013) and higher level of Proteobacteria (25.99% vs 18.17%, respectively, P = 0.045) in the microbial compositions at the phylum level. The inferred metagenomic pathways enriched in the CHB yellow tongue coating patients were mainly those involved in amino acid metabolism, which was consistent with the metabolic disorder. The abundances of bacteria from Bacteroidales at the order level were higher in the CHB white tongue coating patients (19.2% vs 27.22%, respectively, P = 0.011), whereas Neisseriales were enriched in the yellow tongue coating patients (21.85% vs 13.83%, respectively, P = 0.029). At the family level, the abundance of Neisseriaceae in the yellow tongue patients was positively correlated with the HBV-DNA level but negatively correlated with the S-adenosyl-L-methionine level.

CONCLUSION: This research illustrates specific clinical features and bacterial structures in CHB patients with different tongue coatings, which facilitates understanding of the traditional tongue diagnosis.},
}

Adult
Bacteria/genetics/*isolation & purification/metabolism
Case-Control Studies
DNA, Viral/isolation & purification
Female
Gastrointestinal Microbiome/*physiology
Healthy Volunteers
Hepatitis B virus/genetics/*isolation & purification
Hepatitis B, Chronic/diagnosis/metabolism/*microbiology
Humans
Male
Medicine, Chinese Traditional/methods
Metagenomics
Middle Aged
RNA, Ribosomal, 16S/genetics
Tongue/*microbiology

@article {pmid30405577,
year = {2018},
author = {Bertelli, C and Courtois, S and Rosikiewicz, M and Piriou, P and Aeby, S and Robert, S and Loret, JF and Greub, G},
title = {Reduced Chlorine in Drinking Water Distribution Systems Impacts Bacterial Biodiversity in Biofilms.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2520},
doi = {10.3389/fmicb.2018.02520},
pmid = {30405577},
issn = {1664-302X},
abstract = {In drinking water distribution systems (DWDS), a disinfectant residual is usually applied to limit bacterial regrowth. However, delivering water with no or reduced chlorine residual could potentially decrease the selection for antimicrobial resistant microorganisms, favor bacterial regrowth and result in changes in bacterial populations. To evaluate the feasibility of water reduction in local DWDS while ensuring water safety, water quality was measured over 2 months in two different networks, each of them harboring sub-areas with normal and reduced chlorine. Water quality remained good in chlorine reduced samples, with limited development of total flora and absence of coliforms. Furthermore, 16S rRNA amplicon-based metagenomics was used to investigate the diversity and the composition of microbial communities in the sub-networks. Taxonomic classification of sequence reads showed a reduced bacterial diversity in sampling points with higher chlorine residuals. Chlorine disinfection created more homogeneous bacterial population, dominated by Pseudomonas, a genus that contains some major opportunistic pathogens such as P. aeruginosa. In the absence of chlorine, a larger and unknown biodiversity was unveiled, also highlighted by a decreased rate of taxonomic classification to the genus and species level. Overall, this experiment in a functional DWDS will facilitate the move toward potable water delivery systems without residual disinfectants and will improve water taste for consumers.},
}

@article {pmid28255158,
year = {2017},
author = {Jandhyala, SM and Madhulika, A and Deepika, G and Rao, GV and Reddy, DN and Subramanyam, C and Sasikala, M and Talukdar, R},
title = {Altered intestinal microbiota in patients with chronic pancreatitis: implications in diabetes and metabolic abnormalities.},
journal = {Scientific reports},
volume = {7},
number = {},
pages = {43640},
doi = {10.1038/srep43640},
pmid = {28255158},
issn = {2045-2322},
mesh = {Adult ; Biodiversity ; Case-Control Studies ; Diabetes Mellitus, Type 2/diagnosis/*etiology ; Disease Progression ; *Dysbiosis ; Energy Metabolism ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metabolic Diseases/diagnosis/*etiology ; Metagenome ; Metagenomics/methods ; Middle Aged ; Pancreatitis, Chronic/*complications/diagnosis ; },
abstract = {Intestinal dysbiosis and its functional implications in chronic pancreatitis (CP) have not been elaborately studied. We evaluated the taxonomic and functional alterations in intestinal microbiota in 30 well-characterised patients with CP (16 without, 14 with diabetes) and 10 healthy controls. The patients with CP and diabetes had significantly longer disease duration and greater degree of malnutrition. There was increase in plasma endotoxin concentrations from controls to CP non-diabetics to CP diabetics. We observed significant differences in richness and alpha diversity between the groups. We also observed increase in the Firmicutes:Bacteroidetes ratio in CP patients without and with diabetes. There was reduction in abundance of Faecalibacterium prausnitzii and Ruminococcus bromii from controls to CP non-diabetics to CP diabetics. On the other hand, there was increase in LPS (endotoxin) synthetic pathways (KEGG orthology) in the groups. Faecalibacterium prausnitzii abundance correlated negatively with plasma endotoxin and glycemic status; while plasma endotoxin correlated positively with blood glucose and negatively with plasma insulin. Our results have important implications for future studies exploring mechanistic insights on secondary diabetes in CP.},
}

Adult
Biodiversity
Case-Control Studies
Diabetes Mellitus, Type 2/diagnosis/*etiology
Disease Progression
*Dysbiosis
Energy Metabolism
Female
*Gastrointestinal Microbiome
Humans
Male
Metabolic Diseases/diagnosis/*etiology
Metagenome
Metagenomics/methods
Middle Aged
Pancreatitis, Chronic/*complications/diagnosis

@article {pmid28240318,
year = {2017},
author = {Lee, ST and Davy, SK and Tang, SL and Kench, PS},
title = {Water flow buffers shifts in bacterial community structure in heat-stressed Acropora muricata.},
journal = {Scientific reports},
volume = {7},
number = {},
pages = {43600},
doi = {10.1038/srep43600},
pmid = {28240318},
issn = {2045-2322},
mesh = {Animals ; Anthozoa/*microbiology/*physiology ; Bacteria/*classification/genetics ; *Biodiversity ; Environment ; *Hot Temperature ; Metagenome ; Metagenomics/methods ; Seasons ; Seawater ; *Stress, Physiological ; *Symbiosis ; Temperature ; Vibrio/classification/genetics ; },
abstract = {Deterioration of coral health and associated change in the coral holobiont's bacterial community are often a result of different environmental stressors acting synergistically. There is evidence that water flow is important for a coral's resistance to elevated seawater temperature, but there is no information on how water flow affects the coral-associated bacterial community under these conditions. In a laboratory cross-design experiment, Acropora muricata nubbins were subjected to interactive effects of seawater temperature (27 °C to 31 °C) and water flow (0.20 m s-1 and 0.03 m s-1). In an in situ experiment, water flow manipulation was conducted with three colonies of A. muricata during the winter and summer, by partially enclosing each colony in a clear plastic mesh box. 16S rRNA amplicon pyrosequencing showed an increase in the relative abundance of Flavobacteriales and Rhodobacterales in the laboratory experiment, and Vibrio spp. in the in situ experiment when corals were exposed to elevated temperature and slow water flow. In contrast, corals that were exposed to faster water flow under laboratory and in situ conditions had a stable bacterial community. These findings indicate that water flow plays an important role in the maintenance of specific coral-bacteria associations during times of elevated thermal stress.},
}

Animals
Anthozoa/*microbiology/*physiology
Bacteria/*classification/genetics
*Biodiversity
Environment
*Hot Temperature
Metagenome
Metagenomics/methods
Seasons
Seawater
*Stress, Physiological
*Symbiosis
Temperature
Vibrio/classification/genetics

@article {pmid29076296,
year = {2017},
author = {de la Calle, F},
title = {Marine microbiome as source of natural products.},
journal = {Microbial biotechnology},
volume = {10},
number = {6},
pages = {1293-1296},
doi = {10.1111/1751-7915.12882},
pmid = {29076296},
issn = {1751-7915},
mesh = {Biological Products/*metabolism ; Biotechnology/methods ; Data Mining/methods ; Metabolic Networks and Pathways/genetics ; Metagenomics ; *Microbiota ; Seawater/*microbiology ; },
}

Biological Products/*metabolism
Biotechnology/methods
Data Mining/methods
Metabolic Networks and Pathways/genetics
Metagenomics
*Microbiota
Seawater/*microbiology

@article {pmid30041354,
year = {2018},
author = {Tiralerdpanich, P and Sonthiphand, P and Luepromchai, E and Pinyakong, O and Pokethitiyook, P},
title = {Potential microbial consortium involved in the biodegradation of diesel, hexadecane and phenanthrene in mangrove sediment explored by metagenomics analysis.},
journal = {Marine pollution bulletin},
volume = {133},
number = {},
pages = {595-605},
doi = {10.1016/j.marpolbul.2018.06.015},
pmid = {30041354},
issn = {1879-3363},
mesh = {Alkanes/*metabolism ; Bacteria/genetics/metabolism ; Biodegradation, Environmental ; Environmental Pollutants/metabolism ; Gasoline ; Geologic Sediments/*microbiology ; Metagenomics/methods ; Microbial Consortia/genetics/*physiology ; Phenanthrenes/*metabolism ; RNA, Ribosomal, 16S/metabolism ; Thailand ; Wetlands ; },
abstract = {Hydrocarbon contamination is a serious problem that degrades the quality of mangrove ecosystems, and bioremediation using autochthonous bacteria is a promising technology to recover an impacted environment. This research investigates the biodegradation rates of diesel, hexadecane and phenanthrene, by conducting a microcosm study and survey of the autochthonous microbial community in contaminated mangrove sediment, using an Illumina MiSeq platform. The biodegradation rates of diesel, hexadecane and phenanthrene were 82, 86 and 8 mg kg-1 sediment day-1, respectively. The removal efficiencies of hexadecane and phenanthrene were >99%, whereas the removal efficiency of diesel was 88%. A 16S rRNA gene amplicon sequence analysis revealed that the major bacterial assemblages detected were Gammaproteobacteria, Deltaproteobacteria, Alphaproteobacteria. The bacterial compositions were relatively constant, while reductions of the supplemented hydrocarbons were observed. The results imply that the autochthonous microorganisms in the mangrove sediment were responsible for the degradation of the respective hydrocarbons. Diesel-, hexadecane- and phenanthrene-degrading bacteria, namely Bacillus sp., Pseudomonas sp., Acinetobacter sp. and Staphylococcus sp., were also isolated from the mangrove sediment. The mangrove sediment provides a potential resource of effective hydrocarbon-degrading bacteria that can be used as an inoculum or further developed as a ready-to-use microbial consortium for the purpose of bioremediation.},
}

Alkanes/*metabolism
Bacteria/genetics/metabolism
Biodegradation, Environmental
Environmental Pollutants/metabolism
Gasoline
Geologic Sediments/*microbiology
Metagenomics/methods
Microbial Consortia/genetics/*physiology
Phenanthrenes/*metabolism
RNA, Ribosomal, 16S/metabolism
Thailand
Wetlands

@article {pmid28252037,
year = {2017},
author = {Aoki, R and Kamikado, K and Suda, W and Takii, H and Mikami, Y and Suganuma, N and Hattori, M and Koga, Y},
title = {A proliferative probiotic Bifidobacterium strain in the gut ameliorates progression of metabolic disorders via microbiota modulation and acetate elevation.},
journal = {Scientific reports},
volume = {7},
number = {},
pages = {43522},
doi = {10.1038/srep43522},
pmid = {28252037},
issn = {2045-2322},
mesh = {Acetates/*metabolism ; Animals ; Bifidobacterium/*metabolism ; Disease Models, Animal ; *Gastrointestinal Microbiome ; Glucose/metabolism ; Glucose Intolerance/metabolism/therapy ; Male ; Metabolic Diseases/etiology/*metabolism/therapy ; Metagenome ; Metagenomics/methods ; Mice ; *Probiotics ; },
abstract = {The gut microbiota is an important contributor to the worldwide prevalence of metabolic syndrome (MS), which includes obesity and diabetes. The anti-MS effects exerted by Bifidobacterium animalis ssp. lactis GCL2505 (BlaG), a highly proliferative Bifidobacterium strain in the gut, and B. longum ssp. longum JCM1217T (BloJ) were comparatively examined. BlaG treatment reduced visceral fat accumulation and improved glucose tolerance, whereas BloJ had no effect on these parameters. Gut microbial analysis revealed that BlaG exerted stronger effects on the overall bacterial structure of the gut microbiota than BloJ, including enrichment of the genus Bifidobacterium. The levels of acetate and glucagon-like peptide-1 were increased by BlaG treatment in both the gut and plasma, but not by BloJ treatment. Correlation analysis suggested that the elevation of gut acetate levels by BlaG treatment plays a pivotal role in the BlaG-induced anti-MS effects. These findings indicated that BlaG, a highly viable and proliferative probiotic, improves metabolic disorders by modulating gut microbiota, which results in the elevation of SCFAs, especially acetate.},
}

Acetates/*metabolism
Animals
Bifidobacterium/*metabolism
Disease Models, Animal
*Gastrointestinal Microbiome
Glucose/metabolism
Glucose Intolerance/metabolism/therapy
Male
Metabolic Diseases/etiology/*metabolism/therapy
Metagenome
Metagenomics/methods
Mice
*Probiotics

@article {pmid30166168,
year = {2018},
author = {Li, Z and Feng, C and Luo, X and Yao, H and Zhang, D and Zhang, T},
title = {Revealing the influence of microbiota on the quality of Pu-erh tea during fermentation process by shotgun metagenomic and metabolomic analysis.},
journal = {Food microbiology},
volume = {76},
number = {},
pages = {405-415},
doi = {10.1016/j.fm.2018.07.001},
pmid = {30166168},
issn = {1095-9998},
mesh = {Aspergillus/classification/genetics/isolation & purification/metabolism ; Bacteria/classification/genetics/isolation & purification/*metabolism ; Camellia sinensis/chemistry/*microbiology ; Fermentation ; Flavoring Agents/chemistry/metabolism ; Metabolomics ; Metagenomics ; *Microbiota ; Phenols/chemistry/metabolism ; Quality Control ; Tea/*chemistry/microbiology ; },
abstract = {Multispecies microbial community in natural solid-state fermentation (SSF) is crucial for the formation of Chinese Pu-erh tea's unique quality. However, the association between microbiota and tea quality are still poorly understood. Herein, shotgun metagenomic and metabolomic analysis showed that significant variations in composition of microbiota, collective functional genes, and flavour compounds occurred during SSF process. Furthermore, the formation pathways of the dominant flavours including theabrownin, methoxy-phenolic compound, alcohol and carvone were proposed. Moreover, biological interaction networks analysis among functional core microbiota, functional genes, and dominant flavours indicated Aspergillus was the main flavour-producing microorganism in the early SSF, while many other genera including Bacillus, Rasamsonia, Lichtheimia, Debaryomyces were determined as the functional core microorganism for flavours production in the late SSF. This study provides a perspective for bridging the gap between the microbiota and quality in Pu-erh tea, and benefited for further optimizing production efficiency and product quality.},
}

Aspergillus/classification/genetics/isolation & purification/metabolism
Bacteria/classification/genetics/isolation & purification/*metabolism
Camellia sinensis/chemistry/*microbiology
Fermentation
Flavoring Agents/chemistry/metabolism
Metabolomics
Metagenomics
*Microbiota
Phenols/chemistry/metabolism
Quality Control
Tea/*chemistry/microbiology

@article {pmid29471863,
year = {2018},
author = {Petrosino, JF},
title = {The microbiome in precision medicine: the way forward.},
journal = {Genome medicine},
volume = {10},
number = {1},
pages = {12},
doi = {10.1186/s13073-018-0525-6},
pmid = {29471863},
issn = {1756-994X},
support = {R01 AI108588/AI/NIAID NIH HHS/United States ; HHSN267200700014C/DK/NIDDK NIH HHS/United States ; R01 MH112356/MH/NIMH NIH HHS/United States ; U19 AI116497/AI/NIAID NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; },
mesh = {Disease ; Humans ; *Microbiota ; Phenotype ; *Precision Medicine ; },
abstract = {Novel associations between the human microbiome and health and disease are routinely emerging, and important host-microbiome interactions are targets for new diagnostics and therapeutics. Understanding how broadly host-microbe associations are maintained across populations is revealing individualized host-microbiome phenotypes that can be integrated with other 'omics' data sets to enhance precision medicine.},
}

Disease
Humans
*Microbiota
Phenotype
*Precision Medicine

@article {pmid28396267,
year = {2017},
author = {Puehler, A and Kalinowski, J},
title = {Microbial genomics and metagenomics in human health and disease.},
journal = {Journal of biotechnology},
volume = {250},
number = {},
pages = {1},
doi = {10.1016/j.jbiotec.2017.04.007},
pmid = {28396267},
issn = {1873-4863},
mesh = {Bacteria/genetics ; Bacterial Infections/*genetics ; Bacteriophages/genetics ; *Genome, Bacterial ; Genomics ; Humans ; Microbiota ; Sequence Analysis, DNA ; },
}

Bacteria/genetics
Bacterial Infections/*genetics
Bacteriophages/genetics
*Genome, Bacterial
Genomics
Humans
Microbiota
Sequence Analysis, DNA

@article {pmid28785417,
year = {2016},
author = {Jameson, E and Doxey, AC and Airs, R and Purdy, KJ and Murrell, JC and Chen, Y},
title = {Metagenomic data-mining reveals contrasting microbial populations responsible for trimethylamine formation in human gut and marine ecosystems.},
journal = {Microbial genomics},
volume = {2},
number = {9},
pages = {e000080},
doi = {10.1099/mgen.0.000080},
pmid = {28785417},
issn = {2057-5858},
mesh = {Actinobacteria/enzymology/*genetics ; *Data Mining ; *Ecosystem ; Gastrointestinal Microbiome/*genetics ; Geologic Sediments/microbiology ; Humans ; *Metagenomics ; Methylamines/*metabolism ; Oxidoreductases, N-Demethylating/genetics ; Proteobacteria/enzymology/*genetics ; },
abstract = {Existing metagenome datasets from many different environments contain untapped potential for understanding metabolic pathways and their biological impact. Our interest lies in the formation of trimethylamine (TMA), a key metabolite in both human health and climate change. Here, we focus on bacterial degradation pathways for choline, carnitine, glycine betaine and trimethylamine N-oxide (TMAO) to TMA in human gut and marine metagenomes. We found the TMAO reductase pathway was the most prevalent pathway in both environments. Proteobacteria were found to contribute the majority of the TMAO reductase pathway sequences, except in the stressed gut, where Actinobacteria dominated. Interestingly, in the human gut metagenomes, a high proportion of the Proteobacteria hits were accounted for by the genera Klebsiella and Escherichia. Furthermore Klebsiella and Escherichia harboured three of the four potential TMA-production pathways (choline, carnitine and TMAO), suggesting they have a key role in TMA cycling in the human gut. In addition to the intensive TMAO-TMA cycling in the marine environment, our data suggest that carnitine-to-TMA transformation plays an overlooked role in aerobic marine surface waters, whereas choline-to-TMA transformation is important in anaerobic marine sediments. Our study provides new insights into the potential key microbes and metabolic pathways for TMA formation in two contrasting environments.},
}

Actinobacteria/enzymology/*genetics
*Data Mining
*Ecosystem
Gastrointestinal Microbiome/*genetics
Geologic Sediments/microbiology
Humans
*Metagenomics
Methylamines/*metabolism
Oxidoreductases, N-Demethylating/genetics
Proteobacteria/enzymology/*genetics

@article {pmid28211884,
year = {2017},
author = {Li, Z and Lu, L and Guo, J and Yang, J and Zhang, J and He, B and Xu, L},
title = {Responses of spatial-temporal dynamics of bacterioplankton community to large-scale reservoir operation: a case study in the Three Gorges Reservoir, China.},
journal = {Scientific reports},
volume = {7},
number = {},
pages = {42469},
doi = {10.1038/srep42469},
pmid = {28211884},
issn = {2045-2322},
mesh = {*Bacteroidetes ; *Biodiversity ; China ; Chlorophyll/analysis ; Environment ; Geography ; Metagenome ; Metagenomics/methods ; *Plankton ; Rivers/*microbiology ; Spatio-Temporal Analysis ; *Water Microbiology ; },
abstract = {Large rivers are commonly regulated by damming, yet the effects of such disruption on bacterioplankton community structures have not been adequately studied. The aim of this study was to explore the biogeographical patterns present under dam regulation and to uncover the major drivers structuring bacterioplankton communities. Bacterioplankton assemblages in the Three Gorges Reservoir (TGR) were analyzed using Illumina Miseq sequencing by comparing seven sites located within the TGR before and after impoundment. This approach revealed ecological and spatial-temporal variations in bacterioplankton community composition along the longitudinal axis. The community was dynamic and dominated by Proteobacteria and Actinobacteria phyla, encompassing 39.26% and 37.14% of all sequences, respectively, followed by Bacteroidetes (8.67%) and Cyanobacteria (3.90%). The Shannon-Wiener index of the bacterioplankton community in the flood season (August) was generally higher than that in the impoundment season (November). Principal Component Analysis of the bacterioplankton community compositions showed separation between different seasons and sampling sites. Results of the relationship between bacterioplankton community compositions and environmental variables highlighted that ecological processes of element cycling and large dam disturbances are of prime importance in driving the assemblages of riverine bacterioplankton communities.},
}

*Bacteroidetes
*Biodiversity
China
Chlorophyll/analysis
Environment
Geography
Metagenome
Metagenomics/methods
*Plankton
Rivers/*microbiology
Spatio-Temporal Analysis
*Water Microbiology

@article {pmid28198425,
year = {2017},
author = {Leite, MF and Pan, Y and Bloem, J and Berge, HT and Kuramae, EE},
title = {Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank.},
journal = {Scientific reports},
volume = {7},
number = {},
pages = {42634},
doi = {10.1038/srep42634},
pmid = {28198425},
issn = {2045-2322},
mesh = {Bacteria ; Carbon/chemistry/metabolism ; Fungi ; Metagenome ; Metagenomics/methods ; Microbiota ; Nitrogen/*chemistry/*metabolism ; *Soil Microbiology ; },
abstract = {Use of organic amendments is a valuable strategy for crop production. However, it remains unclear how organic amendments shape both soil microbial community structure and activity, and how these changes impact nutrient mineralization rates. We evaluated the effect of various organic amendments, which range in Carbon/Nitrogen (C/N) ratio and degradability, on the soil microbiome in a mesocosm study at 32, 69 and 132 days. Soil samples were collected to determine community structure (assessed by 16S and 18S rRNA gene sequences), microbial biomass (fungi and bacteria), microbial activity (leucine incorporation and active hyphal length), and carbon and nitrogen mineralization rates. We considered the microbial soil DNA as the microbial seedbank. High C/N ratio favored fungal presence, while low C/N favored dominance of bacterial populations. Our results suggest that organic amendments shape the soil microbial community structure through a feedback mechanism by which microbial activity responds to changing organic inputs and rearranges composition of the microbial seedbank. We hypothesize that the microbial seedbank composition responds to changing organic inputs according to the resistance and resilience of individual species, while changes in microbial activity may result in increases or decreases in availability of various soil nutrients that affect plant nutrient uptake.},
}

Bacteria
Carbon/chemistry/metabolism
Fungi
Metagenome
Metagenomics/methods
Microbiota
Nitrogen/*chemistry/*metabolism
*Soil Microbiology

@article {pmid28198423,
year = {2017},
author = {Montella, S and Ventorino, V and Lombard, V and Henrissat, B and Pepe, O and Faraco, V},
title = {Discovery of genes coding for carbohydrate-active enzyme by metagenomic analysis of lignocellulosic biomasses.},
journal = {Scientific reports},
volume = {7},
number = {},
pages = {42623},
doi = {10.1038/srep42623},
pmid = {28198423},
issn = {2045-2322},
mesh = {Biodegradation, Environmental ; *Biomass ; Biotransformation ; Carbohydrate Metabolism/*genetics ; Cellulases/*genetics/*metabolism ; Computational Biology/methods ; Crops, Agricultural ; Gene Expression Profiling ; Glycoside Hydrolases/genetics/metabolism ; High-Throughput Nucleotide Sequencing ; Hydrolysis ; Lignin/*metabolism ; *Metagenome ; *Metagenomics/methods ; Microbiota ; Open Reading Frames ; Polysaccharides/metabolism ; },
abstract = {In this study, a high-throughput sequencing approach was applied to discover novel biocatalysts for lignocellulose hydrolysis from three dedicated energy crops, Arundo donax, Eucalyptus camaldulensis and Populus nigra, after natural biodegradation. The microbiomes of the three lignocellulosic biomasses were dominated by bacterial species (approximately 90%) with the highest representation by the Streptomyces genus both in the total microbial community composition and in the microbial diversity related to GH families of predicted ORFs. Moreover, the functional clustering of the predicted ORFs showed a prevalence of poorly characterized genes, suggesting these lignocellulosic biomasses are potential sources of as yet unknown genes. 1.2%, 0.6% and 3.4% of the total ORFs detected in A. donax, E. camaldulensis and P. nigra, respectively, were putative Carbohydrate-Active Enzymes (CAZymes). Interestingly, the glycoside hydrolases abundance in P. nigra (1.8%) was higher than that detected in the other biomasses investigated in this study. Moreover, a high percentage of (hemi)cellulases with different activities and accessory enzymes (mannanases, polygalacturonases and feruloyl esterases) was detected, confirming that the three analyzed samples were a reservoir of diversified biocatalysts required for an effective lignocellulose saccharification.},
}

Biodegradation, Environmental
*Biomass
Biotransformation
Carbohydrate Metabolism/*genetics
Cellulases/*genetics/*metabolism
Computational Biology/methods
Crops, Agricultural
Gene Expression Profiling
Glycoside Hydrolases/genetics/metabolism
High-Throughput Nucleotide Sequencing
Hydrolysis
Lignin/*metabolism
*Metagenome
*Metagenomics/methods
Microbiota
Open Reading Frames
Polysaccharides/metabolism

@article {pmid29660711,
year = {2018},
author = {Kotoky, R and Rajkumari, J and Pandey, P},
title = {The rhizosphere microbiome: Significance in rhizoremediation of polyaromatic hydrocarbon contaminated soil.},
journal = {Journal of environmental management},
volume = {217},
number = {},
pages = {858-870},
doi = {10.1016/j.jenvman.2018.04.022},
pmid = {29660711},
issn = {1095-8630},
mesh = {Biodegradation, Environmental ; Hydrocarbons/*metabolism ; Microbiota ; Plant Roots ; *Rhizosphere ; Soil ; *Soil Microbiology ; Soil Pollutants ; },
abstract = {Microbial communities are an essential part of plant rhizosphere and participate in the functioning of plants, including rhizoremediation of petroleum contaminants. Rhizoremediation is a promising technology for removal of polyaromatic hydrocarbons based on interactions between plants and microbiome in the rhizosphere. Root exudation in the rhizosphere provides better nutrient uptake for rhizosphere microbiome, and therefore it is considered to be one of the major factors of microbial community function in the rhizosphere that plays a key role in the enhanced PAH biodegradation. Although the importance of the rhizosphere microbiome for plant growth has been widely recognized, the interactions between microbiome and plant roots in the process of rhizosphere mediated remediation of PAH still needs attention. Most of the current researches target PAH degradation by plant or single microorganism, separately, whereas the interactions between plants and whole microbiome are overlooked and its role has been ignored. This review summarizes recent knowledge of PAH degradation in the rhizosphere in the process of plant-microbiome interactions based on emerging omics approaches such as metagenomics, metatranscriptomics, metabolomics and metaproteomics. These omics approaches with combinations to bioinformatics tools provide us a better understanding in integrated activity patterns between plants and rhizosphere microbes, and insight into the biochemical and molecular modification of the meta-organisms (plant-microbiome) to maximize rhizoremediation activity. Moreover, a better understanding of the interactions could lead to the development of techniques to engineer rhizosphere microbiome for better hydrocarbon degradation.},
}

Biodegradation, Environmental
Hydrocarbons/*metabolism
Microbiota
Plant Roots
*Rhizosphere
Soil
*Soil Microbiology
Soil Pollutants

@article {pmid29032502,
year = {2018},
author = {Santoro, A and Ostan, R and Candela, M and Biagi, E and Brigidi, P and Capri, M and Franceschi, C},
title = {Gut microbiota changes in the extreme decades of human life: a focus on centenarians.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {75},
number = {1},
pages = {129-148},
doi = {10.1007/s00018-017-2674-y},
pmid = {29032502},
issn = {1420-9071},
mesh = {Aged ; Aged, 80 and over ; Aging/genetics/*physiology ; *Diet ; Female ; Gastrointestinal Microbiome/*physiology ; Genetics, Population ; Humans ; Longevity/genetics/*physiology ; Male ; },
abstract = {The gut microbiota (GM) is a complex, evolutionarily molded ecological system, which contributes to a variety of physiological functions. The GM is highly dynamic, being sensitive to environmental stimuli, and its composition changes over the host's entire lifespan. However, the basic question of how much these changes may be ascribed to variables such as population, diet, genetics and gender, and/or to the aging process per se is still largely unanswered. We argue that comparison among studies on centenarians-the best model of healthy aging and longevity-recruited from different geographical areas/populations (different genetics and dietary habits) can help to disentangle the contribution of aging and non-aging-related variables to GM remodeling with age. The current review focuses on the role of population, gender and host genetics as possible drivers of GM modification along the human aging process. The feedback impact of age-associated GM variation on the GM-brain axis and GM metabolomics is also discussed. We likewise address the role of GM in neurodegenerative diseases such as Parkinson's and Alzheimer's, and its possible therapeutic use, taking advantage of the fact that centenarians are characterized by an extreme (healthy) phenotype versus patients suffering from age-related pathologies. Finally, it is argued that longitudinal studies combining metagenomics sequencing and in-depth phylogenetic analysis with a comprehensive phenotypic characterization of centenarians and patients using up-to-date omics (metabolomics, transcriptomics and meta-transcriptomics) are urgently needed.},
}

Aged
Aged, 80 and over
Aging/genetics/*physiology
*Diet
Female
Gastrointestinal Microbiome/*physiology
Genetics, Population
Humans
Longevity/genetics/*physiology
Male

@article {pmid28983638,
year = {2018},
author = {Turroni, F and Milani, C and Duranti, S and Ferrario, C and Lugli, GA and Mancabelli, L and van Sinderen, D and Ventura, M},
title = {Bifidobacteria and the infant gut: an example of co-evolution and natural selection.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {75},
number = {1},
pages = {103-118},
doi = {10.1007/s00018-017-2672-0},
pmid = {28983638},
issn = {1420-9071},
mesh = {Bifidobacterium/genetics/*physiology ; Evolution, Molecular ; Gastrointestinal Microbiome/genetics/*physiology ; Gastrointestinal Tract/metabolism/*microbiology ; Humans ; Infant ; Microbial Interactions/genetics/*physiology ; Polysaccharides/metabolism ; Selection, Genetic ; Time Factors ; },
abstract = {Throughout the human life, the gut microbiota interacts with us in a number of different ways, thereby influencing our health status. The acquisition of such an interactive gut microbiota commences at birth. Medical and environmental factors including diet, antibiotic exposure and mode of delivery are major factors that shape the composition of the microbial communities in the infant gut. Among the most abundant members of the infant microbiota are species belonging to the Bifidobacterium genus, which are believed to confer beneficial effects upon their host. Bifidobacteria may be acquired directly from the mother by vertical transmission and their persistence in the infant gut is associated with their saccharolytic activity toward glycans that are abundant in the infant gut. Here, we discuss the establishment of the infant gut microbiota and the contribution of bifidobacteria to this early life microbial consortium.},
}

Bifidobacterium/genetics/*physiology
Evolution, Molecular
Gastrointestinal Microbiome/genetics/*physiology
Gastrointestinal Tract/metabolism/*microbiology
Humans
Infant
Microbial Interactions/genetics/*physiology
Polysaccharides/metabolism
Selection, Genetic
Time Factors

@article {pmid28176868,
year = {2017},
author = {Yergeau, E and Michel, C and Tremblay, J and Niemi, A and King, TL and Wyglinski, J and Lee, K and Greer, CW},
title = {Metagenomic survey of the taxonomic and functional microbial communities of seawater and sea ice from the Canadian Arctic.},
journal = {Scientific reports},
volume = {7},
number = {},
pages = {42242},
doi = {10.1038/srep42242},
pmid = {28176868},
issn = {2045-2322},
mesh = {Arctic Regions ; Canada ; Databases, Genetic ; Geography ; Ice Cover/*microbiology ; Metagenomics/*methods ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; },
abstract = {Climate change has resulted in an accelerated decline of Arctic sea ice since 2001 resulting in primary production increases and prolongation of the ice-free season within the Northwest Passage. The taxonomic and functional microbial community composition of the seawater and sea ice of the Canadian Arctic is not very well known. Bacterial communities from the bottom layer of sea ice cores and surface water from 23 locations around Cornwallis Island, NU, Canada, were extensively screened. The bacterial 16S rRNA gene was sequenced for all samples while shotgun metagenomics was performed on selected samples. Bacterial community composition showed large variation throughout the sampling area both for sea ice and seawater. Seawater and sea ice samples harbored significantly distinct microbial communities, both at different taxonomic levels and at the functional level. A key difference between the two sample types was the dominance of algae in sea ice samples, as visualized by the higher relative abundance of algae and photosynthesis-related genes in the metagenomic datasets and the higher chl a concentrations. The relative abundance of various OTUs and functional genes were significantly correlated with multiple environmental parameters, highlighting many potential environmental drivers and ecological strategies.},
}

Arctic Regions
Canada
Databases, Genetic
Geography
Ice Cover/*microbiology
Metagenomics/*methods
Microbiota/*genetics
Phylogeny
RNA, Ribosomal, 16S/genetics
Seawater/*microbiology

@article {pmid28169321,
year = {2017},
author = {Xu, J and Wei, Y and Jia, H and Xiao, L and Gong, D},
title = {A new perspective on studying burial environment before archaeological excavation: analyzing bacterial community distribution by high-throughput sequencing.},
journal = {Scientific reports},
volume = {7},
number = {},
pages = {41691},
doi = {10.1038/srep41691},
pmid = {28169321},
issn = {2045-2322},
mesh = {*Archaeology ; Bacteria/classification/genetics ; Biodiversity ; *Burial ; High-Throughput Nucleotide Sequencing ; Hydrogen-Ion Concentration ; Metagenome ; Metagenomics/methods ; Microbiota ; Phylogeny ; Salinity ; Soil/chemistry ; *Soil Microbiology ; Water/chemistry ; },
abstract = {Burial conditions play a crucial role in archaeological heritage preservation. Especially, the microorganisms were considered as the leading causes which incurred degradation and vanishment of historic materials. In this article, we analyzed bacterial diversity and community structure from M1 of Wangshanqiao using 16 S rRNA gene amplicon sequencing. The results indicated that microbial communities in burial conditions were diverse among four different samples. The samples from the robber hole varied most obviously in community structure both in Alpha and Beta diversity. In addition, the dominant phylum in different samples were Proteobacteria, Actinobacteria and Bacteroidetes, respectively. Moreover, the study implied that historical materials preservation conditions had connections with bacterial community distribution. At the genus level, Acinetobacter might possess high ability in degrading organic culture heritage in burial conditions, while Bacteroides were associated closely with favorable preservation conditions. This method contributes to fetch information which would never recover after excavation, and it will help to explore microbial degradation on precious organic culture heritage and further our understanding of archaeological burial environment. The study also indicates that robbery has a serious negative impact on burial remains.},
}

*Archaeology
Bacteria/classification/genetics
Biodiversity
*Burial
High-Throughput Nucleotide Sequencing
Hydrogen-Ion Concentration
Metagenome
Metagenomics/methods
Microbiota
Phylogeny
Salinity
Soil/chemistry
*Soil Microbiology
Water/chemistry

@article {pmid28150710,
year = {2017},
author = {Nguyen, D and Boberg, J and Cleary, M and Bruelheide, H and Hönig, L and Koricheva, J and Stenlid, J},
title = {Foliar fungi of Betula pendula: impact of tree species mixtures and assessment methods.},
journal = {Scientific reports},
volume = {7},
number = {},
pages = {41801},
doi = {10.1038/srep41801},
pmid = {28150710},
issn = {2045-2322},
mesh = {Betula/classification/*microbiology ; Biodiversity ; Ecosystem ; Fungi/*classification/*genetics ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/methods ; Plant Leaves/microbiology ; },
abstract = {Foliar fungi of silver birch (Betula pendula) in an experimental Finnish forest were investigated across a gradient of tree species richness using molecular high-throughput sequencing and visual macroscopic assessment. We hypothesized that the molecular approach detects more fungal taxa than visual assessment, and that there is a relationship among the most common fungal taxa detected by both techniques. Furthermore, we hypothesized that the fungal community composition, diversity, and distribution patterns are affected by changes in tree diversity. Sequencing revealed greater diversity of fungi on birch leaves than the visual assessment method. One species showed a linear relationship between the methods. Species-specific variation in fungal community composition could be partially explained by tree diversity, though overall fungal diversity was not affected by tree diversity. Analysis of specific fungal taxa indicated tree diversity effects at the local neighbourhood scale, where the proportion of birch among neighbouring trees varied, but not at the plot scale. In conclusion, both methods may be used to determine tree diversity effects on the foliar fungal community. However, high-throughput sequencing provided higher resolution of the fungal community, while the visual macroscopic assessment detected functionally active fungal species.},
}

Betula/classification/*microbiology
Biodiversity
Ecosystem
Fungi/*classification/*genetics
High-Throughput Nucleotide Sequencing
Metagenome
Metagenomics/methods
Plant Leaves/microbiology

@article {pmid28139751,
year = {2017},
author = {Jia, HR and Dai, PL and Geng, LL and Jack, CJ and Li, YH and Wu, YY and Diao, QY and Ellis, JD},
title = {No effect of Bt Cry1Ie toxin on bacterial diversity in the midgut of the Chinese honey bees, Apis cerana cerana (Hymenoptera, Apidae).},
journal = {Scientific reports},
volume = {7},
number = {},
pages = {41688},
doi = {10.1038/srep41688},
pmid = {28139751},
issn = {2045-2322},
mesh = {Animals ; Bacillus thuringiensis ; Bacterial Toxins/*pharmacology ; Bees/*drug effects/*microbiology ; *Biodiversity ; Cluster Analysis ; Gastrointestinal Microbiome/*drug effects ; Metagenome ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Cry1Ie protein derived from Bacillus thuringiensis (Bt) has been proposed as a promising candidate for the development of a new Bt-maize variety to control maize pests in China. We studied the response of the midgut bacterial community of Apis cerana cerana to Cry1Ie toxin under laboratory conditions. Newly emerged bees were fed one of the following treatments for 15 and 30 days: three concentrations of Cry1Ie toxin (20 ng/mL, 200 ng/mL, and 20 μg/mL) in sugar syrup, pure sugar syrup as a negative control and 48 ng/mL imidacloprid as a positive control. The relative abundance of 16S rRNA genes was measured by Quantitative Polymerase Chain Reaction and no apparent differences were found among treatments for any of these counts at any time point. Furthermore, the midgut bacterial structure and compositions were determined using high-throughput sequencing targeting the V3-V4 regions of the 16S rDNA. All core honey bee intestinal bacterial genera such as Lactobacillus, Bifidobacterium, Snodgrassella, and Gilliamella were detected, and no significant changes were found in the species diversity and richness for any bacterial taxa among treatments at different time points. These results suggest that Cry1Ie toxin may not affect gut bacterial communities of Chinese honey bees.},
}

Animals
Bacillus thuringiensis
Bacterial Toxins/*pharmacology
Bees/*drug effects/*microbiology
*Biodiversity
Cluster Analysis
Gastrointestinal Microbiome/*drug effects
Metagenome
Metagenomics/methods
RNA, Ribosomal, 16S/genetics

@article {pmid28091525,
year = {2017},
author = {Patrascu, O and Béguet-Crespel, F and Marinelli, L and Le Chatelier, E and Abraham, AL and Leclerc, M and Klopp, C and Terrapon, N and Henrissat, B and Blottière, HM and Doré, J and Béra-Maillet, C},
title = {A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic.},
journal = {Scientific reports},
volume = {7},
number = {},
pages = {40248},
doi = {10.1038/srep40248},
pmid = {28091525},
issn = {2045-2322},
support = {322820//European Research Council/International ; },
mesh = {Bacteroides/metabolism ; Carbohydrate Metabolism ; Carboxymethylcellulose Sodium/metabolism ; Chromosome Mapping ; Clostridiales/metabolism ; Dietary Fiber/*metabolism/*microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Ileum/*microbiology ; Metagenome ; Metagenomics ; Xylans/metabolism ; },
abstract = {The digestion of dietary fibers is a major function of the human intestinal microbiota. So far this function has been attributed to the microorganisms inhabiting the colon, and many studies have focused on this distal part of the gastrointestinal tract using easily accessible fecal material. However, microbial fermentations, supported by the presence of short-chain fatty acids, are suspected to occur in the upper small intestine, particularly in the ileum. Using a fosmid library from the human ileal mucosa, we screened 20,000 clones for their activities against carboxymethylcellulose and xylans chosen as models of the major plant cell wall (PCW) polysaccharides from dietary fibres. Eleven positive clones revealed a broad range of CAZyme encoding genes from Bacteroides and Clostridiales species, as well as Polysaccharide Utilization Loci (PULs). The functional glycoside hydrolase genes were identified, and oligosaccharide break-down products examined from different polysaccharides including mixed-linkage β-glucans. CAZymes and PULs were also examined for their prevalence in human gut microbiome. Several clusters of genes of low prevalence in fecal microbiome suggested they belong to unidentified strains rather specifically established upstream the colon, in the ileum. Thus, the ileal mucosa-associated microbiota encompasses the enzymatic potential for PCW polysaccharide degradation in the small intestine.},
}

Bacteroides/metabolism
Carbohydrate Metabolism
Carboxymethylcellulose Sodium/metabolism
Chromosome Mapping
Clostridiales/metabolism
Dietary Fiber/*metabolism/*microbiology
Feces/microbiology
*Gastrointestinal Microbiome
Humans
Ileum/*microbiology
Metagenome
Metagenomics
Xylans/metabolism

@article {pmid29439741,
year = {2018},
author = {Xiong, W and Wang, Y and Sun, Y and Ma, L and Zeng, Q and Jiang, X and Li, A and Zeng, Z and Zhang, T},
title = {Antibiotic-mediated changes in the fecal microbiome of broiler chickens define the incidence of antibiotic resistance genes.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {34},
doi = {10.1186/s40168-018-0419-2},
pmid = {29439741},
issn = {2049-2618},
support = {31702290//the National Natural Science Foundation of China/International ; 31672608//the National Natural Science Foundation of China/International ; GRF7201/11E//Hong Kong/International ; },
mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*classification/drug effects/genetics/isolation & purification ; Bacterial Proteins/*genetics ; Bifidobacterium/classification/drug effects/genetics/isolation & purification ; Chickens ; Chlortetracycline/pharmacology ; *Drug Resistance, Bacterial ; Escherichia/classification/drug effects/genetics/isolation & purification ; Feces/*microbiology ; Gene Regulatory Networks ; Klebsiella/classification/drug effects/genetics/isolation & purification ; Metagenomics ; Microbiota/drug effects ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Antimicrobial agents have been widely used in animal farms to prevent and treat animal diseases and to promote growth. Antimicrobial agents may change the bacterial community and enhance the resistome in animal feces. We used metagenome-wide analysis to investigate the changes in bacterial community, variations in antibiotic resistance genes (ARGs), and their bacterial hosts in the feces of broiler chickens over a full-treatment course of chlortetracycline at low and therapeutic dose levels.

RESULTS: The effects of chlortetracycline on resistome were dependent on the specific ARG subtypes and not simply the overall community-level ARGs. Therapeutic dose of chlortetracycline promoted the abundance of tetracycline resistance genes (tetA and tetW) and inhibited multidrug resistance genes (mdtA, mdtC, mdtK, ompR, and TolC). The therapeutic dose of chlortetracycline led to loss of Proteobacteria mainly due to the decrease of Escherichia/Shigella (from 72 to 58%). Inhibition of Escherichia by chlortetracycline was the primary reason for the decrease of genes resistant to multiple drugs in the therapeutic dose group. The ARG host Bifidobacterium were enriched due to tetW harbored by Bifidobacterium under chlortetracycline treatment. Escherichia was always the major host for multidrug resistance genes, whereas the primary host was changed from Escherichia to Klebsiella for aminoglycoside resistance genes with the treatment of therapeutic dose of chlortetracycline.

CONCLUSIONS: We provided the first metagenomic insights into antibiotic-mediated alteration of ARG-harboring bacterial hosts at community-wide level in chicken feces. These results indicated that the changes in the structure of antibiotic-induced feces microbial communities accompany changes in the abundance of bacterial hosts carrying specific ARGs in the feces microbiota. These findings will help to optimize therapeutic schemes for the effective treatment of antibiotic resistant pathogens in poultry farms. Resistome variations in faecal microbiome of chickens exposed to chlortetracycline.},
}

Animals
Anti-Bacterial Agents/*pharmacology
Bacteria/*classification/drug effects/genetics/isolation & purification
Bacterial Proteins/*genetics
Bifidobacterium/classification/drug effects/genetics/isolation & purification
Chickens
Chlortetracycline/pharmacology
*Drug Resistance, Bacterial
Escherichia/classification/drug effects/genetics/isolation & purification
Feces/*microbiology
Gene Regulatory Networks
Klebsiella/classification/drug effects/genetics/isolation & purification
Metagenomics
Microbiota/drug effects
RNA, Ribosomal, 16S/genetics

@article {pmid29347966,
year = {2018},
author = {Zhou, W and Gay, N and Oh, J},
title = {ReprDB and panDB: minimalist databases with maximal microbial representation.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {15},
doi = {10.1186/s40168-018-0399-2},
pmid = {29347966},
issn = {2049-2618},
support = {K22 AI119231/AI/NIAID NIH HHS/United States ; },
mesh = {Access to Information ; Algorithms ; Computational Biology/methods ; *Databases, Genetic ; *Gastrointestinal Microbiome ; Humans ; Metagenomics/*methods ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Skin/*microbiology ; },
abstract = {BACKGROUND: Profiling of shotgun metagenomic samples is hindered by a lack of unified microbial reference genome databases that (i) assemble genomic information from all open access microbial genomes, (ii) have relatively small sizes, and (iii) are compatible to various metagenomic read mapping tools. Moreover, computational tools to rapidly compile and update such databases to accommodate the rapid increase in new reference genomes do not exist. As a result, database-guided analyses often fail to profile a substantial fraction of metagenomic shotgun sequencing reads from complex microbiomes.

RESULTS: We report pipelines that efficiently traverse all open access microbial genomes and assemble non-redundant genomic information. The pipelines result in two species-resolution microbial reference databases of relatively small sizes: reprDB, which assembles microbial representative or reference genomes, and panDB, for which we developed a novel iterative alignment algorithm to identify and assemble non-redundant genomic regions in multiple sequenced strains. With the databases, we managed to assign taxonomic labels and genome positions to the majority of metagenomic reads from human skin and gut microbiomes, demonstrating a significant improvement over a previous database-guided analysis on the same datasets.

CONCLUSIONS: reprDB and panDB leverage the rapid increases in the number of open access microbial genomes to more fully profile metagenomic samples. Additionally, the databases exclude redundant sequence information to avoid inflated storage or memory space and indexing or analyzing time. Finally, the novel iterative alignment algorithm significantly increases efficiency in pan-genome identification and can be useful in comparative genomic analyses.},
}

Access to Information
Algorithms
Computational Biology/methods
*Databases, Genetic
*Gastrointestinal Microbiome
Humans
Metagenomics/*methods
Phylogeny
Sequence Alignment
Sequence Analysis, DNA
Skin/*microbiology

@article {pmid29298732,
year = {2018},
author = {Luna, PN and Hasegawa, K and Ajami, NJ and Espinola, JA and Henke, DM and Petrosino, JF and Piedra, PA and Sullivan, AF and Camargo, CA and Shaw, CA and Mansbach, JM},
title = {The association between anterior nares and nasopharyngeal microbiota in infants hospitalized for bronchiolitis.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {2},
doi = {10.1186/s40168-017-0385-0},
pmid = {29298732},
issn = {2049-2618},
support = {R01 AI-114552/NH/NIH HHS/United States ; UG3 OD-023253/NH/NIH HHS/United States ; R01 AI-108588/NH/NIH HHS/United States ; R01 AI108588/AI/NIAID NIH HHS/United States ; UG3 OD023253/OD/NIH HHS/United States ; U01 AI-087881/NH/NIH HHS/United States ; },
mesh = {Bronchiolitis/*microbiology ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Female ; Hospitalization ; Humans ; Infant ; Longitudinal Studies ; Male ; Microbiota ; Nasal Cavity/*microbiology ; Nasopharynx/*microbiology ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; Staphylococcus/classification/genetics/*isolation & purification ; },
abstract = {BACKGROUND: The airway microbiome is a subject of great interest for the study of respiratory disease. Anterior nare samples are more accessible than samples from deeper within the nasopharynx. However, the correlation between the microbiota found in the anterior nares and the microbiota found within the nasopharynx is unknown. We assessed the anterior nares and nasopharyngeal microbiota to determine (1) the relation of the microbiota from these two upper airway sites and (2) if associations were maintained between the microbiota from these two sites and two bronchiolitis severity outcomes.

RESULTS: Among 815 infants hospitalized at 17 US centers for bronchiolitis with optimal 16S rRNA gene sequence reads from both nasal swab and nasopharyngeal aspirate samples, there were strong intra-individual correlations in the microbial communities between the two sample types, especially relating to Haemophilus and Moraxella genera. By contrast, we found a high abundance of Staphylococcus genus in the nasal swabs-a pattern not found in the nasopharyngeal samples and not informative when predicting the dominant nasopharyngeal genera. While these disparities may have been due to sample processing differences (i.e., nasal swabs were mailed at ambient temperature to emulate processing of future parent collected swabs while nasopharyngeal aspirates were mailed on dry ice), a previously reported association between Haemophilus-dominant nasopharyngeal microbiota and the increased severity of bronchiolitis was replicated utilizing the nasal swab microbiota and the same outcome measures: intensive care use (adjusted OR 6.43; 95% CI 2.25-20.51; P < 0.001) and hospital length-of-stay (adjusted OR 4.31; 95% CI, 1.73-11.11; P = 0.002). Additionally, Moraxella-dominant nasopharyngeal microbiota was previously identified as protective against intensive care use, a result that was replicated when analyzing the nasal swab microbiota (adjusted OR 0.30; 95% CI, 0.11-0.64; P = 0.01).

CONCLUSIONS: While the microbiota of the anterior nares and the nasopharynx are distinct, there is considerable overlap between the bacterial community compositions from these two anatomic sites. Despite processing differences between the samples, these results indicate that microbiota severity associations from the nasopharynx are recapitulated in the anterior nares, suggesting that nasal swab samples not only are effective sample types, but also can be used to detect microbial risk markers.},
}

Bronchiolitis/*microbiology
DNA, Bacterial/genetics
DNA, Ribosomal/genetics
Female
Hospitalization
Humans
Infant
Longitudinal Studies
Male
Microbiota
Nasal Cavity/*microbiology
Nasopharynx/*microbiology
RNA, Ribosomal, 16S/*genetics
Sequence Analysis, DNA/*methods
Staphylococcus/classification/genetics/*isolation & purification

@article {pmid28323391,
year = {2018},
author = {Martinez-Sañudo, I and Simonato, M and Squartini, A and Mori, N and Marri, L and Mazzon, L},
title = {Metagenomic analysis reveals changes of the Drosophila suzukii microbiota in the newly colonized regions.},
journal = {Insect science},
volume = {25},
number = {5},
pages = {833-846},
doi = {10.1111/1744-7917.12458},
pmid = {28323391},
issn = {1744-7917},
support = {613678//European Union's Seventh Framework Programme/ ; },
mesh = {*Animal Distribution ; Animals ; Bacteria/*classification ; China ; Drosophila/*microbiology ; Europe ; *Gastrointestinal Microbiome ; *Introduced Species ; Japan ; *Metagenome ; Metagenomics ; United States ; },
abstract = {The spotted wing drosophila, Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) is a highly polyphagous pest of a wide variety of wild or cultivated berry and stone fruit. Originating from Southeast Asia, it has recently invaded a wide range of regions in Europe and North America. It is well known that insect microbiotas may significantly influence several aspects of the host biology and play an important role in invasive species introduction into new areas. However, in spite of the great economic importance of D. suzukii, a limited attention has been given so far to its microbiota. In this study, we present the first in-depth characterization of gut bacterial diversity from field (native and invasive range) and lab-reared populations of this insect. The gut bacterial communities of field insects were dominated, regardless of their origin, by 2 families of the phylum Proteobacteria: Acetobacteraceae and Enterobacteriaceae, while Firmicutes, mainly represented by the family Staphylococcaceae, prevailed in lab-reared population. Locality was the most significant factor in shaping the microbiota of wild flies. Moreover, a negative correlation between diversity and abundance of Enterobacteriaceae and the time elapsed since the establishment of D. suzukii in a new region was observed. Altogether our results indicate that habitat, food resources as well as the colonization phase of a new region contribute to shape the bacterial communities of the invasive species which, in turn, by evolving more quickly, could influence host adaptation in a new environment.},
}

*Animal Distribution
Animals
Bacteria/*classification
China
Drosophila/*microbiology
Europe
*Gastrointestinal Microbiome
*Introduced Species
Japan
*Metagenome
Metagenomics
United States

@article {pmid30356699,
year = {2018},
author = {Weißbecker, C and Wubet, T and Lentendu, G and Kühn, P and Scholten, T and Bruelheide, H and Buscot, F},
title = {Experimental Evidence of Functional Group-Dependent Effects of Tree Diversity on Soil Fungi in Subtropical Forests.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2312},
doi = {10.3389/fmicb.2018.02312},
pmid = {30356699},
issn = {1664-302X},
abstract = {Deconvoluting the relative contributions made by specific biotic and abiotic drivers to soil fungal community compositions facilitates predictions about the functional responses of ecosystems to environmental changes, such as losses of plant diversity, but it is hindered by the complex interactions involved. Experimental assembly of tree species allows separation of the respective effects of plant community composition (biotic components) and soil properties (abiotic components), enabling much greater statistical power than can be achieved in observational studies. We therefore analyzed these contributions by assessing, via pyrotag sequencing of the internal transcribed spacer (ITS2) rDNA region, fungal communities in young subtropical forest plots included in a large experiment on the effects of tree species richness. Spatial variables and soil properties were the main drivers of soil fungal alpha and beta-diversity, implying strong early-stage environmental filtering and dispersal limitation. Tree related variables, such as tree community composition, significantly affected arbuscular mycorrhizal and pathogen fungal community structure, while differences in tree host species and host abundance affected ectomycorrhizal fungal community composition. At this early stage of the experiment, only a limited amount of carbon inputs (rhizodeposits and leaf litter) was being provided to the ecosystem due to the size of the tree saplings, and persisting legacy effects were observed. We thus expect to find increasing tree related effects on fungal community composition as forest development proceeds.},
}

@article {pmid29555111,
year = {2018},
author = {Pandit, RJ and Hinsu, AT and Patel, SH and Jakhesara, SJ and Koringa, PG and Bruno, F and Psifidi, A and Shah, SV and Joshi, CG},
title = {Microbiota composition, gene pool and its expression in Gir cattle (Bos indicus) rumen under different forage diets using metagenomic and metatranscriptomic approaches.},
journal = {Systematic and applied microbiology},
volume = {41},
number = {4},
pages = {374-385},
doi = {10.1016/j.syapm.2018.02.002},
pmid = {29555111},
issn = {1618-0984},
mesh = {Animal Feed/*analysis ; Animals ; Bacteria/*classification/genetics ; Cattle ; *Diet ; Metagenome/genetics ; Metagenomics/methods ; Microbiota/genetics ; Rumen/*microbiology ; },
abstract = {Zebu (Bos indicus) is a domestic cattle species originating from the Indian subcontinent and now widely domesticated on several continents. In this study, we were particularly interested in understanding the functionally active rumen microbiota of an important Zebu breed, the Gir, under different dietary regimes. Metagenomic and metatranscriptomic data were compared at various taxonomic levels to elucidate the differential microbial population and its functional dynamics in Gir cattle rumen under different roughage dietary regimes. Different proportions of roughage rather than the type of roughage (dry or green) modulated microbiome composition and the expression of its gene pool. Fibre degrading bacteria (i.e. Clostridium, Ruminococcus, Eubacterium, Butyrivibrio, Bacillus and Roseburia) were higher in the solid fraction of rumen (P<0.01) compared to the liquid fraction, whereas bacteria considered to be utilizers of the degraded product (i.e. Prevotella, Bacteroides, Parabacteroides, Paludibacter and Victivallis) were dominant in the liquid fraction (P<0.05). Likewise, expression of fibre degrading enzymes and related carbohydrate binding modules (CBMs) occurred in the solid fraction. When metagenomic and metatranscriptomic data were compared, it was found that some genera and species were transcriptionally more active, although they were in low abundance, making an important contribution to fibre degradation and its further metabolism in the rumen. This study also identified some of the transcriptionally active genera, such as Caldicellulosiruptor and Paludibacter, whose potential has been less-explored in rumen. Overall, the comparison of metagenomic shotgun and metatranscriptomic sequencing appeared to be a much richer source of information compared to conventional metagenomic analysis.},
}

Animal Feed/*analysis
Animals
Bacteria/*classification/genetics
Cattle
*Diet
Metagenome/genetics
Metagenomics/methods
Microbiota/genetics
Rumen/*microbiology

@article {pmid28134326,
year = {2017},
author = {Liu, H and Carvalhais, LC and Schenk, PM and Dennis, PG},
title = {Effects of jasmonic acid signalling on the wheat microbiome differ between body sites.},
journal = {Scientific reports},
volume = {7},
number = {},
pages = {41766},
doi = {10.1038/srep41766},
pmid = {28134326},
issn = {2045-2322},
mesh = {Biodiversity ; Biomass ; Cyclopentanes/*metabolism ; Metagenome ; Metagenomics/methods ; Microbiota/*genetics ; Oxylipins/*metabolism ; Plant Roots/metabolism/microbiology ; Plant Shoots/metabolism/microbiology ; Rhizosphere ; *Signal Transduction ; Soil Microbiology ; Triticum/genetics/*metabolism/*microbiology ; },
abstract = {Jasmonic acid (JA) signalling helps plants to defend themselves against necrotrophic pathogens and herbivorous insects and has been shown to influence the root microbiome of Arabidopsis thaliana. In this study, we determined whether JA signalling influences the diversity and functioning of the wheat (Triticum aestivum) microbiome and whether these effects are specific to particular parts of the plant. Activation of the JA pathway was achieved via exogenous application of methyl jasmonate and was confirmed by significant increases in the abundance of 10 JA-signalling-related gene transcripts. Phylogenetic marker gene sequencing revealed that JA signalling reduced the diversity and changed the composition of root endophytic but not shoot endophytic or rhizosphere bacterial communities. The total enzymatic activity and substrate utilisation profiles of rhizosphere bacterial communities were not affected by JA signalling. Our findings indicate that the effects of JA signalling on the wheat microbiome are specific to individual plant compartments.},
}

Biodiversity
Biomass
Cyclopentanes/*metabolism
Metagenome
Metagenomics/methods
Microbiota/*genetics
Oxylipins/*metabolism
Plant Roots/metabolism/microbiology
Plant Shoots/metabolism/microbiology
Rhizosphere
*Signal Transduction
Soil Microbiology
Triticum/genetics/*metabolism/*microbiology

@article {pmid28134269,
year = {2017},
author = {Zhou, X and Zhang, J and Gao, D and Gao, H and Guo, M and Li, L and Zhao, M and Wu, F},
title = {Conversion from long-term cultivated wheat field to Jerusalem artichoke plantation changed soil fungal communities.},
journal = {Scientific reports},
volume = {7},
number = {},
pages = {41502},
doi = {10.1038/srep41502},
pmid = {28134269},
issn = {2045-2322},
mesh = {Agriculture ; Biodiversity ; *Fungi/classification/genetics ; Helianthus/growth & development/*microbiology ; Metagenome ; Metagenomics/methods ; *Soil Microbiology ; *Triticum/growth & development/microbiology ; },
abstract = {Understanding soil microbial communities in agroecosystems has the potential to contribute to the improvement of agricultural productivity and sustainability. Effects of conversion from long-term wheat plantation to Jerusalem artichoke (JA) plantation on soil fungal communities were determined by amplicon sequencing of total fungal ITS regions. Quantitative PCR and PCR-denaturing gradient gel electrophoresis were also used to analyze total fungal and Trichoderma spp. ITS regions and Fusarium spp. Ef1α genes. Results showed that soil organic carbon was higher in the first cropping of JA and Olsen P was lower in the third cropping of JA. Plantation conversion changed soil total fungal and Fusarium but not Trichoderma spp. community structures and compositions. The third cropping of JA had the lowest total fungal community diversity and Fusarium spp. community abundance, but had the highest total fungal and Trichoderma spp. community abundances. The relative abundances of potential fungal pathogens of wheat were higher in the wheat field. Fungal taxa with plant growth promoting, plant pathogen or insect antagonistic potentials were enriched in the first and second cropping of JA. Overall, short-term conversion from wheat to JA plantation changed soil fungal communities, which is related to changes in soil organic carbon and Olsen P contents.},
}

Agriculture
Biodiversity
*Fungi/classification/genetics
Helianthus/growth & development/*microbiology
Metagenome
Metagenomics/methods
*Soil Microbiology
*Triticum/growth & development/microbiology

@article {pmid29273717,
year = {2017},
author = {Albanese, D and Donati, C},
title = {Strain profiling and epidemiology of bacterial species from metagenomic sequencing.},
journal = {Nature communications},
volume = {8},
number = {1},
pages = {2260},
doi = {10.1038/s41467-017-02209-5},
pmid = {29273717},
issn = {2041-1723},
mesh = {Bacteria/*genetics ; Bifidobacterium longum/genetics ; *Computational Biology ; Databases, Genetic ; Enterococcus faecalis/genetics ; Escherichia coli/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome/*genetics ; *Metagenomics ; Microbiota/*genetics ; Neisseria meningitidis/genetics ; Polymorphism, Single Nucleotide ; Propionibacterium acnes/genetics ; Staphylococcus aureus/genetics ; Staphylococcus epidermidis/genetics ; Streptococcus pneumoniae/genetics ; },
abstract = {Microbial communities are often composed by complex mixtures of multiple strains of the same species, characterized by a wide genomic and phenotypic variability. Computational methods able to identify, quantify and classify the different strains present in a sample are essential to fully exploit the potential of metagenomic sequencing in microbial ecology, with applications that range from the epidemiology of infectious diseases to the characterization of the dynamics of microbial colonization. Here we present a computational approach that uses the available genomic data to reconstruct complex strain profiles from metagenomic sequencing, quantifying the abundances of the different strains and cataloging them according to the population structure of the species. We validate the method on synthetic data sets and apply it to the characterization of the strain distribution of several important bacterial species in real samples, showing how its application provides novel insights on the structure and complexity of the microbiota.},
}

Bacteria/*genetics
Bifidobacterium longum/genetics
*Computational Biology
Databases, Genetic
Enterococcus faecalis/genetics
Escherichia coli/genetics
High-Throughput Nucleotide Sequencing
Humans
Metagenome/*genetics
*Metagenomics
Microbiota/*genetics
Neisseria meningitidis/genetics
Polymorphism, Single Nucleotide
Propionibacterium acnes/genetics
Staphylococcus aureus/genetics
Staphylococcus epidermidis/genetics
Streptococcus pneumoniae/genetics

@article {pmid29950381,
year = {2018},
author = {Jenior, ML and Leslie, JL and Young, VB and Schloss, PD},
title = {Clostridium difficile Alters the Structure and Metabolism of Distinct Cecal Microbiomes during Initial Infection To Promote Sustained Colonization.},
journal = {mSphere},
volume = {3},
number = {3},
pages = {},
doi = {10.1128/mSphere.00261-18},
pmid = {29950381},
issn = {2379-5042},
mesh = {Animals ; Anti-Bacterial Agents/*administration & dosage/adverse effects ; Cecum/*chemistry/*microbiology ; Clostridium Infections/*microbiology ; Clostridium difficile/*growth & development ; Disease Models, Animal ; *Gastrointestinal Microbiome ; Gene Expression Profiling ; Metabolomics ; Metagenomics ; Mice ; },
abstract = {Susceptibility to Clostridium difficile infection (CDI) is primarily associated with previous exposure to antibiotics, which compromise the structure and function of the gut bacterial community. Specific antibiotic classes correlate more strongly with recurrent or persistent C. difficile infection. As such, we utilized a mouse model of infection to explore the effect of distinct antibiotic classes on the impact that infection has on community-level transcription and metabolic signatures shortly following pathogen colonization and how those changes may associate with persistence of C. difficile Untargeted metabolomic analysis revealed that C. difficile infection had significantly larger impacts on the metabolic environment across cefoperazone- and streptomycin-pretreated mice, which became persistently colonized compared to clindamycin-pretreated mice, where infection quickly became undetectable. Through metagenome-enabled metatranscriptomics, we observed that transcripts for genes associated with carbon and energy acquisition were greatly reduced in infected animals, suggesting that those niches were instead occupied by C. difficile Furthermore, the largest changes in transcription were seen in the least abundant species, indicating that C. difficile may "attack the loser" in gut environments where sustained infection occurs more readily. Overall, our results suggest that C. difficile is able to restructure the nutrient-niche landscape in the gut to promote persistent infection.IMPORTANCEClostridium difficile has become the most common single cause of hospital-acquired infection over the last decade in the United States. Colonization resistance to the nosocomial pathogen is primarily provided by the gut microbiota, which is also involved in clearing the infection as the community recovers from perturbation. As distinct antibiotics are associated with different risk levels for CDI, we utilized a mouse model of infection with 3 separate antibiotic pretreatment regimens to generate alternative gut microbiomes that each allowed for C. difficile colonization but varied in clearance rate. To assess community-level dynamics, we implemented an integrative multi-omics approach that revealed that infection significantly changed many aspects of the gut community. The degree to which the community changed was inversely correlated with clearance during the first 6 days of infection, suggesting that C. difficile differentially modifies the gut environment to promote persistence. This is the first time that metagenome-enabled metatranscriptomics have been employed to study the behavior of a host-associated microbiota in response to an infection. Our results allow for a previously unseen understanding of the ecology associated with C. difficile infection and provide the groundwork for identification of context-specific probiotic therapies.},
}

Animals
Anti-Bacterial Agents/*administration & dosage/adverse effects
Cecum/*chemistry/*microbiology
Clostridium Infections/*microbiology
Clostridium difficile/*growth & development
Disease Models, Animal
*Gastrointestinal Microbiome
Gene Expression Profiling
Metabolomics
Metagenomics
Mice

@article {pmid29898983,
year = {2018},
author = {Zhu, L and Yang, Z and Yao, R and Xu, L and Chen, H and Gu, X and Wu, T and Yang, X},
title = {Potential Mechanism of Detoxification of Cyanide Compounds by Gut Microbiomes of Bamboo-Eating Pandas.},
journal = {mSphere},
volume = {3},
number = {3},
pages = {},
doi = {10.1128/mSphere.00229-18},
pmid = {29898983},
issn = {2379-5042},
mesh = {Ailuridae/*microbiology/*physiology ; Animals ; Bacteria/classification/genetics/metabolism ; Biotransformation ; Cyanides/*metabolism ; *Gastrointestinal Microbiome ; Metagenomics ; Ursidae/*microbiology/*physiology ; },
abstract = {Gut microbes can enhance the ability of hosts to consume secondary plant compounds and, therefore, expand the dietary niche breadth of mammalian herbivores. The giant and red pandas are bamboo-eating specialists within the mammalian order Carnivora. Bamboo contains abundant plant secondary metabolites (e.g., cyanide-containing compounds). However, Carnivora species, including the giant panda, have deficient levels of rhodanese (one of the essential cyanide detoxification enzymes) in their tissues compared with the same tissues of herbivores. Here, we make a comparative analysis of 94 gut metagenomes, including 25 from bamboo-eating pandas (19 from giant pandas and 6 from red pandas), 30 from Père David's deer, and 39 from published data for other mammals. The bamboo-eating pandas' gut microbiomes had some common features, such as high proportions of Pseudomonas bacteria. The results revealed that bamboo-eating pandas' gut microbiomes were significantly enriched in putative genes coding for enzymes related to cyanide degradation (e.g., rhodanese) compared with the gut microbiomes of typical herbivorous mammals, which might have coevolved with their special bamboo diets. The enrichment of putative cyanide-digesting gut microbes, in combination with adaptations related to morphology (e.g., pseudothumbs) and genomic signatures, show that the giant panda and red panda have evolved some common traits to adapt to their bamboo diet.IMPORTANCE The giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens), two obligate bamboo feeders, have distinct phylogenetic positions in the order Carnivora. Bamboo is extraordinarily rich in plant secondary metabolites, such as allied phenolic and polyphenolic compounds and even toxic cyanide compounds. Here, the enrichment of putative cyanide-digesting gut microbes, in combination with adaptations related to morphology (e.g., pseudothumbs) and genomic signatures, show that the giant panda and red panda have evolved some common traits to adapt to their bamboo diet. Thus, here is another story of diet-driven gut microbiota in nature.},
}

Ailuridae/*microbiology/*physiology
Animals
Bacteria/classification/genetics/metabolism
Biotransformation
Cyanides/*metabolism
*Gastrointestinal Microbiome
Metagenomics
Ursidae/*microbiology/*physiology

@article {pmid29848762,
year = {2018},
author = {Garcia, SL and Buck, M and Hamilton, JJ and Wurzbacher, C and Grossart, HP and McMahon, KD and Eiler, A},
title = {Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria.},
journal = {mSphere},
volume = {3},
number = {3},
pages = {},
doi = {10.1128/mSphere.00202-18},
pmid = {29848762},
issn = {2379-5042},
mesh = {Bacteria/*metabolism ; Fresh Water/*microbiology ; *Metabolism ; *Microbial Consortia ; Microbial Interactions ; },
abstract = {Genome streamlining is frequently observed in free-living aquatic microorganisms and results in physiological dependencies between microorganisms. However, we know little about the specificity of these microbial associations. In order to examine the specificity and extent of these associations, we established mixed cultures from three different freshwater environments and analyzed the cooccurrence of organisms using a metagenomic time series. Free-living microorganisms with streamlined genomes lacking multiple biosynthetic pathways showed no clear recurring pattern in their interaction partners. Free-living freshwater bacteria form promiscuous cooperative associations. This notion contrasts with the well-documented high specificities of interaction partners in host-associated bacteria. Considering all data together, we suggest that highly abundant free-living bacterial lineages are functionally versatile in their interactions despite their distinct streamlining tendencies at the single-cell level. This metabolic versatility facilitates interactions with a variable set of community members.},
}

Bacteria/*metabolism
Fresh Water/*microbiology
*Metabolism
*Microbial Consortia
Microbial Interactions

@article {pmid29687353,
year = {2018},
author = {Allali, I and Boukhatem, N and Bouguenouch, L and Hardi, H and Boudouaya, HA and Cadenas, MB and Ouldim, K and Amzazi, S and Azcarate-Peril, MA and Ghazal, H},
title = {Gut microbiome of Moroccan colorectal cancer patients.},
journal = {Medical microbiology and immunology},
volume = {207},
number = {3-4},
pages = {211-225},
doi = {10.1007/s00430-018-0542-5},
pmid = {29687353},
issn = {1432-1831},
mesh = {Adult ; Aged ; Cluster Analysis ; Colorectal Neoplasms/*complications/*microbiology ; Cytosol/chemistry ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Dysbiosis ; Fatty Acids/analysis ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics ; *Microbiota ; Middle Aged ; Morocco ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Surveys and Questionnaires ; Young Adult ; },
abstract = {Although colorectal cancer is the third leading cause of death in Morocco, there are no studies of the microbiome changes associated with the disease in the Moroccan population. The aim of our study was to compare the stool microbiome of Moroccan cancer patients with healthy individuals. We analyzed the microbiome composition of samples from 11 CRC patients and 12 healthy individuals by 16S rRNA amplicon sequencing. Principal coordinate analysis of samples revealed defined cancer versus healthy clusters. Our findings showed that cancer samples had higher proportions of Firmicutes (T = 50.5%; N = 28.4%; p = 0.04), specifically of Clostridia (T = 48.3%; N = 19.0%; p = 0.002), and Fusobacteria (T = 0.1%; N = 0.0%; p = 0.02), especially of Fusobacteriia (T = 0.1%; N = 0.0%; p = 0.02), while Bacteroidetes were enriched in healthy samples (T = 35.1%; N = 62.8%; p = 0.06), particularly the class Bacteroidia (T = 35.1%; N = 62.6%; p = 0.06). Porphyromonas, Clostridium, Ruminococcus, Selenomonas, and Fusobacterium were significantly overrepresented in diseased patients, similarly to other studies. Predicted functional information showed that bacterial motility proteins, flagellar assembly, and fatty acid biosynthesis metabolism were significantly overrepresented in cancer patients, while amino acid metabolism and glycan biosynthesis were overrepresented in controls. This suggests that involvement of these functional metagenomes is similar and relevant in the carcinogenesis process, independent of the origin of the samples. Results from this study allowed identification of bacterial taxa relevant to the Moroccan population and encourages larger studies to facilitate population-directed therapeutic approaches.},
}

Adult
Aged
Cluster Analysis
Colorectal Neoplasms/*complications/*microbiology
Cytosol/chemistry
DNA, Bacterial/chemistry/genetics
DNA, Ribosomal/chemistry/genetics
*Dysbiosis
Fatty Acids/analysis
Female
*Gastrointestinal Microbiome
Humans
Male
Metagenomics
*Microbiota
Middle Aged
Morocco
Phylogeny
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
Surveys and Questionnaires
Young Adult

@article {pmid29079861,
year = {2018},
author = {Velásquez-Mejía, EP and de la Cuesta-Zuluaga, J and Escobar, JS},
title = {Impact of DNA extraction, sample dilution, and reagent contamination on 16S rRNA gene sequencing of human feces.},
journal = {Applied microbiology and biotechnology},
volume = {102},
number = {1},
pages = {403-411},
doi = {10.1007/s00253-017-8583-z},
pmid = {29079861},
issn = {1432-0614},
mesh = {DNA/genetics/*isolation & purification ; *DNA Contamination ; DNA, Bacterial/genetics ; Feces/*microbiology ; Gastrointestinal Microbiome/*genetics ; *High-Throughput Nucleotide Sequencing ; Humans ; Indicators and Reagents ; Metagenomics/methods ; Microbial Consortia/genetics ; Microbiota/genetics ; RNA, Ribosomal, 16S/chemistry/*genetics ; Sequence Analysis, DNA ; },
abstract = {Culture-independent methods have granted the possibility to study microbial diversity in great detail, but technical issues pose a threat to the accuracy of new findings. Biases introduced during DNA extraction can result in erroneous representations of the microbial community, particularly in samples with low microbial biomass. We evaluated the DNA extraction method, initial sample biomass, and reagent contamination on the assessment of the human gut microbiota. Fecal samples of 200 mg were subjected to 1:10 serial dilutions; total DNA was obtained using two commercial kits and the microbiota assessed by 16S ribosomal RNA (rRNA) gene sequencing. In addition, we sequenced multiple technical controls. The two kits were efficient in extracting DNA from samples with as low as 2 mg of feces. However, in instances of lower biomass, only one kit performed well. The number of reads from negative controls was negligible. Both DNA extraction kits allowed inferring microbial consortia with similar membership but different abundances. Furthermore, we found differences in the taxonomic profile of the microbial community. Unexpectedly, the effect of sample dilution was moderate and did not introduce severe bias into the microbial inference. Indeed, the microbiota inferred from fecal samples was distinguishable from that of negative controls. In most cases, samples as low as 2 mg did not result in a dissimilar representation of the microbial community compared with the undiluted sample. Our results indicate that the gut microbiota inference is not much affected by contamination with laboratory reagents but largely impacted by the protocol to extract DNA.},
}

DNA/genetics/*isolation & purification
*DNA Contamination
DNA, Bacterial/genetics
Feces/*microbiology
Gastrointestinal Microbiome/*genetics
*High-Throughput Nucleotide Sequencing
Humans
Indicators and Reagents
Metagenomics/methods
Microbial Consortia/genetics
Microbiota/genetics
RNA, Ribosomal, 16S/chemistry/*genetics
Sequence Analysis, DNA

@article {pmid27530840,
year = {2016},
author = {Jitwasinkul, T and Suriyaphol, P and Tangphatsornruang, S and Hansen, MA and Hansen, LH and Sørensen, SJ and Permpikul, C and Rongrungruang, Y and Tribuddharat, C},
title = {Plasmid metagenomics reveals multiple antibiotic resistance gene classes among the gut microbiomes of hospitalised patients.},
journal = {Journal of global antimicrobial resistance},
volume = {6},
number = {},
pages = {57-66},
doi = {10.1016/j.jgar.2016.03.001},
pmid = {27530840},
issn = {2213-7173},
mesh = {Animals ; Anti-Bacterial Agents ; Cattle ; Drug Resistance, Multiple, Bacterial/*genetics ; *Gastrointestinal Microbiome ; *Genes, Bacterial ; Humans ; Inpatients ; Metagenomics ; Microbial Sensitivity Tests ; Plasmids/*genetics ; Sequence Analysis, DNA ; Thailand ; },
abstract = {Antibiotic resistance genes are rapidly spread between pathogens and the normal flora, with plasmids playing an important role in their circulation. This study aimed to investigate antibiotic resistance plasmids in the gut microbiome of hospitalised patients. Stool samples were collected from seven inpatients at Siriraj Hospital (Bangkok, Thailand) and were compared with a sample from a healthy volunteer. Plasmids from the gut microbiomes extracted from the stool samples were subjected to high-throughput DNA sequencing (GS Junior). Newbler-assembled DNA reads were categorised into known and unknown sequences (using >80% alignment length as the cut-off), and ResFinder was used to classify the antibiotic resistance gene pools. Plasmid replicon modules were used for plasmid typing. Forty-six genes conferring resistance to several classes of antibiotics were identified in the stool samples. Several antibiotic resistance genes were shared by the patients; interestingly, most were reported previously in food animals and healthy humans. Four antibiotic resistance genes were found in the healthy subject. One gene (aph3-III) was identified in the patients and the healthy subject and was related to that in cattle. Uncommon genes of hospital origin such as blaTEM-124-like and fosA, which confer resistance to extended-spectrum β-lactams and fosfomycin, respectively, were identified. The resistance genes did not match the patients' drug treatments. In conclusion, several plasmid types were identified in the gut microbiome; however, it was difficult to link these to the antibiotic resistance genes identified. That the antibiotic resistance genes came from hospital and community environments is worrying.},
}

Animals
Anti-Bacterial Agents
Cattle
Drug Resistance, Multiple, Bacterial/*genetics
*Gastrointestinal Microbiome
*Genes, Bacterial
Humans
Inpatients
Metagenomics
Microbial Sensitivity Tests
Plasmids/*genetics
Sequence Analysis, DNA
Thailand

@article {pmid29934497,
year = {2018},
author = {Ji, Y and Zhang, F and Zhang, R and Shen, Y and Liu, L and Wang, J and Yang, J and Tang, Q and Xun, J and Qi, T and Wang, Z and Song, W and Tang, Y and Chen, J and Lu, H},
title = {Changes in intestinal microbiota in HIV-1-infected subjects following cART initiation: influence of CD4+ T cell count.},
journal = {Emerging microbes & infections},
volume = {7},
number = {1},
pages = {113},
doi = {10.1038/s41426-018-0117-y},
pmid = {29934497},
issn = {2222-1751},
support = {81571977//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Adult ; Antiretroviral Therapy, Highly Active ; Biodiversity ; Biomarkers ; *CD4 Lymphocyte Count ; CD4-CD8 Ratio ; Computational Biology/methods ; Female ; *Gastrointestinal Microbiome/drug effects ; HIV Infections/drug therapy/*immunology/virology ; HIV-1/*immunology ; Humans ; Male ; Metagenome ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Viral Load ; },
abstract = {The roles of immunodeficiency and combined antiretroviral therapy (cART) in shaping the gut microbiota in HIV-1-infected subjects (HISs) have not been described thoroughly by time-series investigations. In this study, 36 antiretroviral-naïve HISs were enrolled to prospectively assess alterations in the fecal microbiota and plasma markers of microbial translocation and inflammation with cART. At baseline, the species α-diversity of the fecal microbiota was significantly lower in HISs with a CD4+ T cell count <300/mm3 than in HISs with a CD4+ T cell count >300/mm3 (Shannon index: Median 2.557 vs. 2.981, P = 0.006; Simpson index: Median 0.168 vs. 0.096, P = 0.004). Additionally, the baseline α-diversity indices correlated with CD4+ T cell counts (Shannon index: r = 0.474, P = 0.004; Simpson index: r = -0.467, P = 0.004) and the specific plasma biomarkers for microbial translocation and inflammation. After cART introduction, the species α-diversity of fecal microbiota in HISs with CD4+ T cell counts <300/mm3 was significantly restored (Shannon index: Median 2.557 vs. 2.791, P = 0.007; Simpson index: Median 0.168 vs. 0.112, P = 0.004), while the variances were insignificant among HISs with CD4+ T cell counts >300/mm3 (Shannon index: Median 2.981 vs. 2.934, P = 0.179; Simpson index: Median 0.096 vs. 0.119, P = 0.082). Meanwhile, with cART introduction, alterations in the gut microbial composition were more significant in the subgroup with CD4+ T cell counts >300/mm3, corresponding to increases in the specific plasma inflammatory markers. These findings implicated the interactive roles of immunodeficiency and cART for affecting gut microbiota in HIV-1-infected individuals, providing new insights into intestinal microbiome dysbiosis related to HIV-1 infection.},
}

Adult
Antiretroviral Therapy, Highly Active
Biodiversity
Biomarkers
*CD4 Lymphocyte Count
CD4-CD8 Ratio
Computational Biology/methods
Female
*Gastrointestinal Microbiome/drug effects
HIV Infections/drug therapy/*immunology/virology
HIV-1/*immunology
Humans
Male
Metagenome
Metagenomics
RNA, Ribosomal, 16S/genetics
Viral Load

@article {pmid29800328,
year = {2018},
author = {Birkl, P and Bharwani, A and Kjaer, JB and Kunze, W and McBride, P and Forsythe, P and Harlander-Matauschek, A},
title = {Differences in cecal microbiome of selected high and low feather-pecking laying hens.},
journal = {Poultry science},
volume = {97},
number = {9},
pages = {3009-3014},
doi = {10.3382/ps/pey167},
pmid = {29800328},
issn = {1525-3171},
mesh = {*Aggression ; Animals ; Bacteria/classification ; Cecum/*microbiology ; Chickens/genetics/*microbiology/*physiology ; Feathers ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; *Selection, Genetic ; Sequence Analysis, RNA/veterinary ; },
abstract = {In mammals, it has become increasingly clear that the gut microbiota influences not only gastrointestinal physiology but also modulates behavior. In domestic birds, ceca have the greatest gastrointestinal microbial population. Feather-pecking (FP) behavior in laying hens is one of the most important unsolved behavioral issues in modern agriculture. The aim of the present study was to assess the cecal microbial community of divergently selected high (HFP; n = 20) and low (LFP; n = 20) feather-pecking birds at 60 wk of age. The cecal samples were subjected to community profiling of 16S rRNA and in silico metagenomics using a modified bar-coded Illumina sequencing method on a MiSeq Illumina sequencer. Our results revealed that compared to HFP birds, LFP birds are characterized by an increased overall microbial diversity (beta diversity) shown by a difference in the Bray-Curtis index (R2 = 0.171, P < 0.05). Furthermore, operational taxonomic unit comparisons showed an increased presence of Clostridiae and decreased presence of Lactobaccillacae in HFP birds when compared to LFP birds (False Discovery Rate < 0.05, Mann-Whitney comparisons). Our data indicate that there may be differences in the cecal profile between these 2 lines of laying hens. More research, building on this first study using sequencing technology for profiling the chicken cecal microbiome, will be needed in order to reveal if and how there exists a functional link between the performance of FP and the cecal microbial community.},
}

*Aggression
Animals
Bacteria/classification
Cecum/*microbiology
Chickens/genetics/*microbiology/*physiology
Feathers
Feces/microbiology
Female
*Gastrointestinal Microbiome
RNA, Bacterial/analysis
RNA, Ribosomal, 16S/analysis
*Selection, Genetic
Sequence Analysis, RNA/veterinary

@article {pmid28094284,
year = {2017},
author = {Murphy, K and Curley, D and O'Callaghan, TF and O'Shea, CA and Dempsey, EM and O'Toole, PW and Ross, RP and Ryan, CA and Stanton, C},
title = {The Composition of Human Milk and Infant Faecal Microbiota Over the First Three Months of Life: A Pilot Study.},
journal = {Scientific reports},
volume = {7},
number = {},
pages = {40597},
doi = {10.1038/srep40597},
pmid = {28094284},
issn = {2045-2322},
mesh = {Biodiversity ; Feces/*microbiology ; Humans ; Infant ; Infant, Newborn ; Metagenome ; Metagenomics/methods ; *Microbiota ; Milk, Human/*microbiology ; Pilot Projects ; },
abstract = {Human milk contains a diverse array of bioactives and is also a source of bacteria for the developing infant gut. The aim of this study was to characterize the bacterial communities in human milk and infant faeces over the first 3 months of life, in 10 mother-infant pairs. The presence of viable Bifidobacterium and Lactobacillus in human milk was also evaluated. MiSeq sequencing revealed a large diversity of the human milk microbiota, identifying over 207 bacterial genera in milk samples. The phyla Proteobacteria and Firmicutes and the genera Pseudomonas, Staphylococcus and Streptococcus were the predominant bacterial groups. A core of 12 genera represented 81% of the microbiota relative abundance in milk samples at week 1, 3 and 6, decreasing to 73% at week 12. Genera shared between infant faeces and human milk samples accounted for 70-88% of the total relative abundance in infant faecal samples, supporting the hypothesis of vertical transfer of bacteria from milk to the infant gut. In addition, identical strains of Bifidobacterium breve and Lactobacillus plantarum were isolated from the milk and faeces of one mother-infant pair. Vertical transfer of bacteria via breastfeeding may contribute to the initial establishment of the microbiota in the developing infant intestine.},
}

Biodiversity
Feces/*microbiology
Humans
Infant
Infant, Newborn
Metagenome
Metagenomics/methods
*Microbiota
Milk, Human/*microbiology
Pilot Projects

@article {pmid29028897,
year = {2018},
author = {Guo, X and Li, Z and Yao, Q and Mueller, RS and Eng, JK and Tabb, DL and Hervey, WJ and Pan, C},
title = {Sipros Ensemble improves database searching and filtering for complex metaproteomics.},
journal = {Bioinformatics (Oxford, England)},
volume = {34},
number = {5},
pages = {795-802},
doi = {10.1093/bioinformatics/btx601},
pmid = {29028897},
issn = {1367-4811},
abstract = {Motivation: Complex microbial communities can be characterized by metagenomics and metaproteomics. However, metagenome assemblies often generate enormous, and yet incomplete, protein databases, which undermines the identification of peptides and proteins in metaproteomics. This challenge calls for increased discrimination of true identifications from false identifications by database searching and filtering algorithms in metaproteomics.

Results: Sipros Ensemble was developed here for metaproteomics using an ensemble approach. Three diverse scoring functions from MyriMatch, Comet and the original Sipros were incorporated within a single database searching engine. Supervised classification with logistic regression was used to filter database searching results. Benchmarking with soil and marine microbial communities demonstrated a higher number of peptide and protein identifications by Sipros Ensemble than MyriMatch/Percolator, Comet/Percolator, MS-GF+/Percolator, Comet & MyriMatch/iProphet and Comet & MyriMatch & MS-GF+/iProphet. Sipros Ensemble was computationally efficient and scalable on supercomputers.

Freely available under the GNU GPL license at http://sipros.omicsbio.org.

Contact: cpan@utk.edu.

Supplementary information: Supplementary data are available at Bioinformatics online.},
}

@article {pmid30325092,
year = {2018},
author = {Zhang, SY and Tsementzi, D and Hatt, JK and Bivins, A and Khelurkar, N and Brown, J and Tripathi, SN and Konstantinidis, KT},
title = {Intensive allochthonous inputs along the Ganges River and their effect on microbial community composition and dynamics.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.14439},
pmid = {30325092},
issn = {1462-2920},
abstract = {Little is known about microbial communities in the Ganges River, India and how they respond to intensive anthropogenic inputs. Here we applied shotgun metagenomics sequencing to study microbial community dynamics and function in planktonic samples collected along a ~700 km river transect, including urban cities and rural settings in upstream waters, before and after the monsoon rainy season. Our results showed that 11-32% of the microbes represented terrestrial, sewage and human inputs (allochthonous). Sewage inputs significantly contributed to the higher abundance, by 13-fold of human gut microbiome (HG) associated sequences and 2-fold of antibiotic resistance genes (ARGs) in the Ganges relative to other riverine ecosystems in Europe, North and South America. Metagenome-assembled genome sequences (MAGs) representing allochthonous populations were detectable and tractable across the river after 1-2 days of (downstream) transport (>200 km apart). Only ~8% of these MAGs were abundant in U.S. freshwater ecosystems, revealing distinct biodiversity for the Ganges. Microbial communities in the rainy season exhibited increased alpha-diversity and spatial heterogeneity and showed significantly weaker distance-decay patterns compared to the dry season. These results advance our understanding of the Ganges microbial communities and how they respond to anthropogenic pollution. This article is protected by copyright. All rights reserved.},
}

@article {pmid29524068,
year = {2018},
author = {Wang, C and Li, Q and Li, J},
title = {Gut microbiota and its implications in small bowel transplantation.},
journal = {Frontiers of medicine},
volume = {12},
number = {3},
pages = {239-248},
doi = {10.1007/s11684-018-0617-0},
pmid = {29524068},
issn = {2095-0225},
mesh = {Biomarkers ; *Gastrointestinal Microbiome ; Graft Rejection/*immunology ; Humans ; Immunity, Mucosal ; Intestine, Small/*microbiology/*transplantation ; Metagenomics ; Transplantation Tolerance/*immunology ; },
abstract = {The gut microbiota is mainly composed of a diverse population of commensal bacterial species and plays a pivotal role in the maintenance of intestinal homeostasis, immune modulation and metabolism. The influence of the gut microbiota on solid organ transplantation has recently been recognized. In fact, several studies indicated that acute and chronic allograft rejection in small bowel transplantation (SBT) is closely associated with the alterations in microbial patterns in the gut. In this review, we focused on the recent findings regarding alterations in the microbiota following SBTand the potential roles of these alterations in the development of acute and chronic allograft rejection. We also reviewed important advances with respect to the interplays between the microbiota and host immune systems in SBT. Furthermore, we explored the potential of the gut microbiota as a microbial marker and/or therapeutic target for the predication and intervention of allograft rejection and chronic dysfunction. Given that current research on the gut microbiota has become increasingly sophisticated and comprehensive, large cohort studies employing metagenomic analysis and multivariate linkage should be designed for the characterization of host-microbe interaction and causality between microbiota alterations and clinical outcomes in SBT. The findings are expected to provide valuable insights into the role of gut microbiota in the development of allograft rejection and other transplant-related complications and introduce novel therapeutic targets and treatment approaches in clinical practice.},
}

Biomarkers
*Gastrointestinal Microbiome
Graft Rejection/*immunology
Humans
Immunity, Mucosal
Intestine, Small/*microbiology/*transplantation
Metagenomics
Transplantation Tolerance/*immunology

@article {pmid29433401,
year = {2018},
author = {Alex, CE and Kubiski, SV and Li, L and Sadeghi, M and Wack, RF and McCarthy, MA and Pesavento, JB and Delwart, E and Pesavento, PA},
title = {Amdoparvovirus Infection in Red Pandas (Ailurus fulgens).},
journal = {Veterinary pathology},
volume = {55},
number = {4},
pages = {552-561},
doi = {10.1177/0300985818758470},
pmid = {29433401},
issn = {1544-2217},
mesh = {Ailuridae/*virology ; Animals ; Endangered Species ; Feces/virology ; Female ; *Genetic Variation ; Genome, Viral/*genetics ; In Situ Hybridization/veterinary ; Male ; Metagenomics ; Microscopy, Electron/veterinary ; Parvoviridae Infections/diagnostic imaging/pathology/*veterinary/virology ; Parvovirinae/genetics/*isolation & purification ; Phylogeny ; Polymerase Chain Reaction/veterinary ; Virus Shedding ; },
abstract = {Aleutian mink disease virus is the type species in the genus Amdoparvovirus, and in mink and other Mustelidae can cause either subclinical disease or fatal chronic immune stimulation and immune complex disease. The authors describe a novel amdoparvovirus in the endangered red panda (Ailurus fulgens), discovered using viral metagenomics. The authors analyzed the prevalence, tissue distribution, and disease association by PCR, in situ hybridization, electron microscopy, and histology in a group of 6 red pandas from a single zoological collection. The study incorporates a fecal shedding survey and analysis of tissues from 4 necropsied animals over a 12-year span. The tentatively named red panda amdoparvovirus (RpAPV) was detected in the feces and/or tissues of all animals tested. At necropsy of 1 geriatric animal, infection was associated with pyogranulomatous peritonitis, pancreatitis, and myocarditis. Other animals had detectable low-level viral nucleic acid in lymph nodes and both oral and intestinal epithelium at the time of necropsy. Full-length genome sequences of RpAPV strains from 2 animals had 12% sequence divergence, demonstrating genetic diversity even among in-contact animals. RpAPV is a persistent infection in this cohort of red pandas, and has variable clinical expression.},
}

Ailuridae/*virology
Animals
Endangered Species
Feces/virology
Female
*Genetic Variation
Genome, Viral/*genetics
In Situ Hybridization/veterinary
Male
Metagenomics
Microscopy, Electron/veterinary
Parvoviridae Infections/diagnostic imaging/pathology/*veterinary/virology
Parvovirinae/genetics/*isolation & purification
Phylogeny
Polymerase Chain Reaction/veterinary
Virus Shedding

@article {pmid29346588,
year = {2018},
author = {Cridland, JM and Ramirez, SR and Dean, CA and Sciligo, A and Tsutsui, ND},
title = {Genome Sequencing of Museum Specimens Reveals Rapid Changes in the Genetic Composition of Honey Bees in California.},
journal = {Genome biology and evolution},
volume = {10},
number = {2},
pages = {458-472},
doi = {10.1093/gbe/evy007},
pmid = {29346588},
issn = {1759-6653},
support = {S10 RR027303/RR/NCRR NIH HHS/United States ; S10 RR029668/RR/NCRR NIH HHS/United States ; },
mesh = {Animals ; Bees/*genetics ; California ; Chromosome Mapping ; *Evolution, Molecular ; Genetics, Population ; *Genome, Insect ; Introduced Species ; Metagenomics ; Pollination ; Polymorphism, Single Nucleotide ; Population Dynamics ; },
abstract = {The western honey bee, Apis mellifera, is an enormously influential pollinator in both natural and managed ecosystems. In North America, this species has been introduced numerous times from a variety of different source populations in Europe and Africa. Since then, feral populations have expanded into many different environments across their broad introduced range. Here, we used whole genome sequencing of historical museum specimens and newly collected modern populations from California (USA) to analyze the impact of demography and selection on introduced populations during the past 105 years. We find that populations from both northern and southern California exhibit pronounced genetic changes, but have changed in different ways. In northern populations, honey bees underwent a substantial shift from western European to eastern European ancestry since the 1960s, whereas southern populations are dominated by the introgression of Africanized genomes during the past two decades. Additionally, we identify an isolated island population that has experienced comparatively little change over a large time span. Fine-scale comparison of different populations and time points also revealed SNPs that differ in frequency, highlighting a number of genes that may be important for recent adaptations in these introduced populations.},
}

Animals
Bees/*genetics
California
Chromosome Mapping
*Evolution, Molecular
Genetics, Population
*Genome, Insect
Introduced Species
Metagenomics
Pollination
Polymorphism, Single Nucleotide
Population Dynamics

@article {pmid29242367,
year = {2017},
author = {Costea, PI and Coelho, LP and Sunagawa, S and Munch, R and Huerta-Cepas, J and Forslund, K and Hildebrand, F and Kushugulova, A and Zeller, G and Bork, P},
title = {Subspecies in the global human gut microbiome.},
journal = {Molecular systems biology},
volume = {13},
number = {12},
pages = {960},
pmid = {29242367},
issn = {1744-4292},
mesh = {Escherichia coli/physiology ; *Gastrointestinal Microbiome/genetics ; Genes, Bacterial ; Humans ; *Microbiota/genetics ; Phenotype ; Phylogeography ; Species Specificity ; },
abstract = {Population genomics of prokaryotes has been studied in depth in only a small number of primarily pathogenic bacteria, as genome sequences of isolates of diverse origin are lacking for most species. Here, we conducted a large-scale survey of population structure in prevalent human gut microbial species, sampled from their natural environment, with a culture-independent metagenomic approach. We examined the variation landscape of 71 species in 2,144 human fecal metagenomes and found that in 44 of these, accounting for 72% of the total assigned microbial abundance, single-nucleotide variation clearly indicates the existence of sub-populations (here termed subspecies). A single subspecies (per species) usually dominates within each host, as expected from ecological theory. At the global scale, geographic distributions of subspecies differ between phyla, with Firmicutes subspecies being significantly more geographically restricted. To investigate the functional significance of the delineated subspecies, we identified genes that consistently distinguish them in a manner that is independent of reference genomes. We further associated these subspecies-specific genes with properties of the microbial community and the host. For example, two of the three Eubacterium rectale subspecies consistently harbor an accessory pro-inflammatory flagellum operon that is associated with lower gut community diversity, higher host BMI, and higher blood fasting insulin levels. Using an additional 676 human oral samples, we further demonstrate the existence of niche specialized subspecies in the different parts of the oral cavity. Taken together, we provide evidence for subspecies in the majority of abundant gut prokaryotes, leading to a better functional and ecological understanding of the human gut microbiome in conjunction with its host.},
}

Escherichia coli/physiology
*Gastrointestinal Microbiome/genetics
Genes, Bacterial
Humans
*Microbiota/genetics
Phenotype
Phylogeography
Species Specificity

@article {pmid28079128,
year = {2017},
author = {Jing, G and Sun, Z and Wang, H and Gong, Y and Huang, S and Ning, K and Xu, J and Su, X},
title = {Parallel-META 3: Comprehensive taxonomical and functional analysis platform for efficient comparison of microbial communities.},
journal = {Scientific reports},
volume = {7},
number = {},
pages = {40371},
doi = {10.1038/srep40371},
pmid = {28079128},
issn = {2045-2322},
support = {R34 AA021502/AA/NIAAA NIH HHS/United States ; },
mesh = {Adult ; Base Sequence ; Biodiversity ; Biomarkers/metabolism ; Child ; Computer Simulation ; Databases, Genetic ; Humans ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Time Factors ; },
abstract = {The number of metagenomes is increasing rapidly. However, current methods for metagenomic analysis are limited by their capability for in-depth data mining among a large number of microbiome each of which carries a complex community structure. Moreover, the complexity of configuring and operating computational pipeline also hinders efficient data processing for the end users. In this work we introduce Parallel-META 3, a comprehensive and fully automatic computational toolkit for rapid data mining among metagenomic datasets, with advanced features including 16S rRNA extraction for shotgun sequences, 16S rRNA copy number calibration, 16S rRNA based functional prediction, diversity statistics, bio-marker selection, interaction network construction, vector-graph-based visualization and parallel computing. Application of Parallel-META 3 on 5,337 samples with 1,117,555,208 sequences from diverse studies and platforms showed it could produce similar results as QIIME and PICRUSt with much faster speed and lower memory usage, which demonstrates its ability to unravel the taxonomical and functional dynamics patterns across large datasets and elucidate ecological links between microbiome and the environment. Parallel-META 3 is implemented in C/C++ and R, and integrated into an executive package for rapid installation and easy access under Linux and Mac OS X. Both binary and source code packages are available at http://bioinfo.single-cell.cn/parallel-meta.html.},
}

Adult
Base Sequence
Biodiversity
Biomarkers/metabolism
Child
Computer Simulation
Databases, Genetic
Humans
*Metagenome
Metagenomics
Microbiota/*genetics
RNA, Ribosomal, 16S/genetics
Time Factors

@article {pmid30308887,
year = {2019},
author = {Coble, AA and Flinders, CA and Homyack, JA and Penaluna, BE and Cronn, RC and Weitemier, K},
title = {eDNA as a tool for identifying freshwater species in sustainable forestry: A critical review and potential future applications.},
journal = {The Science of the total environment},
volume = {649},
number = {},
pages = {1157-1170},
doi = {10.1016/j.scitotenv.2018.08.370},
pmid = {30308887},
issn = {1879-1026},
abstract = {Environmental DNA (eDNA) is an emerging biological monitoring tool that can aid in assessing the effects of forestry and forest manufacturing activities on biota. Monitoring taxa across broad spatial and temporal scales is necessary to ensure forest management and forest manufacturing activities meet their environmental goals of maintaining biodiversity. Our objectives are to describe potential applications of eDNA across the wood products supply chain extending from regenerating forests, harvesting, and wood transport, to manufacturing facilities, and to review the current state of the science in this context. To meet our second objective, we summarize the taxa examined with targeted (PCR, qPCR or ddPCR) or metagenomic eDNA methods (eDNA metabarcoding), evaluate how estimated species richness compares between traditional field sampling and eDNA metabarcoding approaches, and compare the geographical representation of prior eDNA studies in freshwater ecosystems to global wood baskets. Potential applications of eDNA include evaluating the effects of forestry and forest manufacturing activities on aquatic biota, delineating fish-bearing versus non fish-bearing reaches, evaluating effectiveness of constructed road crossings for freshwater organism passage, and determining the presence of at-risk species. Studies using targeted eDNA approaches focused on fish, amphibians, and invertebrates, while metagenomic studies focused on fish, invertebrates, and microorganisms. Rare, threatened, or endangered species received the least attention in targeted eDNA research, but are arguably of greatest interest to sustainable forestry and forest manufacturing that seek to preserve freshwater biodiversity. Ultimately, using eDNA methods will enable forestry and forest manufacturing managers to have data-driven prioritization for conservation actions for all freshwater species.},
}

@article {pmid29476620,
year = {2018},
author = {Chappell, CR and Fukami, T},
title = {Nectar yeasts: a natural microcosm for ecology.},
journal = {Yeast (Chichester, England)},
volume = {35},
number = {6},
pages = {417-423},
doi = {10.1002/yea.3311},
pmid = {29476620},
issn = {1097-0061},
mesh = {Animals ; Bacteria ; Biota ; Flowers ; Models, Biological ; *Plant Nectar ; Pollination ; *Social Behavior ; *Social Environment ; *Yeasts ; },
abstract = {The species of yeasts that colonize floral nectar can modify the mutualistic relationships between plants and pollinators by changing the chemical properties of nectar. Recent evidence supporting this possibility has led to increased interest among ecologists in studying these fungi as well as the bacteria that interact with them in nectar. Although not fully explored, nectar yeasts also constitute a promising natural microcosm that can be used to facilitate development of general ecological theory. We discuss the methodological and conceptual advantages of using nectar yeasts from this perspective, including simplicity of communities, tractability of dispersal, replicability of community assembly, and the ease with which the mechanisms of species interactions can be studied in complementary experiments conducted in the field and the laboratory. To illustrate the power of nectar yeasts as a study system, we discuss several topics in community ecology, including environmental filtering, priority effects, and metacommunity dynamics. An exciting new direction is to integrate metagenomics and comparative genomics into nectar yeast research to address these fundamental ecological topics.},
}

Animals
Bacteria
Biota
Flowers
Models, Biological
*Plant Nectar
Pollination
*Social Behavior
*Social Environment
*Yeasts

@article {pmid29773467,
year = {2018},
author = {Daliri, EB and Tango, CN and Lee, BH and Oh, DH},
title = {Human microbiome restoration and safety.},
journal = {International journal of medical microbiology : IJMM},
volume = {308},
number = {5},
pages = {487-497},
doi = {10.1016/j.ijmm.2018.05.002},
pmid = {29773467},
issn = {1618-0607},
mesh = {Anti-Bacterial Agents ; Bacteria/classification/isolation & purification ; Diet ; Dysbiosis/*therapy ; Fecal Microbiota Transplantation/*adverse effects/methods ; Gastrointestinal Microbiome/*physiology ; Humans ; Probiotics/*administration & dosage ; },
abstract = {The human gut microbiome consists of many bacteria which are in symbiotic relationship with human beings. The gut microbial metabolism, as well as the microbial-host co-metabolism, has been found to greatly influence health and disease. Factors such as diet, antibiotic use and lifestyle have been associated with alterations in the gut microbial community and may result in several pathological conditions. For this reason, several strategies including fecal microbiota transplant and probiotic administration have been applied and proven to be feasible and effective in restoring the gut microbiota in humans. Yet, safety concerns such as potential health risks that may arise from such interventions and how these strategies are regulated need to be addressed. Also, it will be important to know if these microbiome restoration strategies can have a profound impact on health. This review provides an overview of our current knowledge of the microbiome restoration strategies and safety issues on how these strategies are regulated.},
}

Anti-Bacterial Agents
Bacteria/classification/isolation & purification
Diet
Dysbiosis/*therapy
Fecal Microbiota Transplantation/*adverse effects/methods
Gastrointestinal Microbiome/*physiology
Humans
Probiotics/*administration & dosage

@article {pmid29588360,
year = {2018},
author = {Corvelo, A and Clarke, WE and Robine, N and Zody, MC},
title = {taxMaps: comprehensive and highly accurate taxonomic classification of short-read data in reasonable time.},
journal = {Genome research},
volume = {28},
number = {5},
pages = {751-758},
doi = {10.1101/gr.225276.117},
pmid = {29588360},
issn = {1549-5469},
mesh = {Bacteria/classification/genetics ; Computational Biology/*methods ; Databases, Nucleic Acid ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; Microbiota/genetics ; Reproducibility of Results ; Rivers/microbiology ; *Software ; Species Specificity ; Water Microbiology ; },
abstract = {High-throughput sequencing is a revolutionary technology for the analysis of metagenomic samples. However, querying large volumes of reads against comprehensive DNA/RNA databases in a sensitive manner can be compute-intensive. Here, we present taxMaps, a highly efficient, sensitive, and fully scalable taxonomic classification tool. Using a combination of simulated and real metagenomics data sets, we demonstrate that taxMaps is more sensitive and more precise than widely used taxonomic classifiers and is capable of delivering classification accuracy comparable to that of BLASTN, but at up to three orders of magnitude less computational cost.},
}

Bacteria/classification/genetics
Computational Biology/*methods
Databases, Nucleic Acid
High-Throughput Nucleotide Sequencing/*methods
Humans
Metagenomics/*methods
Microbiota/genetics
Reproducibility of Results
Rivers/microbiology
*Software
Species Specificity
Water Microbiology

@article {pmid29083504,
year = {2018},
author = {Puri, P and Liangpunsakul, S and Christensen, JE and Shah, VH and Kamath, PS and Gores, GJ and Walker, S and Comerford, M and Katz, B and Borst, A and Yu, Q and Kumar, DP and Mirshahi, F and Radaeva, S and Chalasani, NP and Crabb, DW and Sanyal, AJ and , },
title = {The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis.},
journal = {Hepatology (Baltimore, Md.)},
volume = {67},
number = {4},
pages = {1284-1302},
doi = {10.1002/hep.29623},
pmid = {29083504},
issn = {1527-3350},
support = {U01 AA021883/AA/NIAAA NIH HHS/United States ; U01 AA021840/AA/NIAAA NIH HHS/United States ; R01 AA021171/AA/NIAAA NIH HHS/United States ; U01 AA021788/AA/NIAAA NIH HHS/United States ; K23 AA021179/AA/NIAAA NIH HHS/United States ; U01 AA021891/AA/NIAAA NIH HHS/United States ; },
mesh = {Adult ; Alcohol Drinking/adverse effects ; DNA, Bacterial/*blood/genetics ; Endotoxins/blood ; Female ; Hepatitis, Alcoholic/*microbiology ; Humans ; Liver/microbiology/pathology ; Liver Diseases, Alcoholic/*microbiology ; Male ; Metagenomics/*methods ; Microbiota/*genetics ; Middle Aged ; Monocytes/pathology ; },
abstract = {Intestinal dysbiosis is implicated in alcoholic hepatitis (AH). However, changes in the circulating microbiome, its association with the presence and severity of AH, and its functional relevance in AH is unknown. Qualitative and quantitative assessment of changes in the circulating microbiome were performed by sequencing bacterial DNA in subjects with moderate AH (MAH) (n = 18) or severe AH (SAH) (n = 19). These data were compared with heavy drinking controls (HDCs) without obvious liver disease (n = 19) and non-alcohol-consuming controls (NACs, n = 20). The data were related to endotoxin levels and markers of monocyte activation. Linear discriminant analysis effect size (LEfSe) analysis, inferred metagenomics, and predictive functional analysis using PICRUSt were performed. There was a significant increase in 16S copies/ng DNA both in MAH (P < 0.01) and SAH (P < 0.001) subjects. Compared with NACs, the relative abundance of phylum Bacteroidetes was significantly decreased in HDCs, MAH, and SAH (P < 0.001). In contrast, all alcohol-consuming groups had enrichment with Fusobacteria; this was greatest for HDCs and decreased progressively in MAH and SAH. Subjects with SAH had significantly higher endotoxemia (P = 0.01). Compared with alcohol-consuming groups, predictive functional metagenomics indicated an enrichment of bacteria with genes related to methanogenesis and denitrification. Furthermore, both HDCs and SAH showed activation of a type III secretion system that has been linked to gram-negative bacterial virulence. Metagenomics in SAH versus NACs predicted increased isoprenoid synthesis via mevalonate and anthranilate degradation, known modulators of gram-positive bacterial growth and biofilm production, respectively.

CONCLUSION: Heavy alcohol consumption appears to be the primary driver of changes in the circulating microbiome associated with a shift in its inferred metabolic functions. (Hepatology 2018;67:1284-1302).},
}

Adult
Alcohol Drinking/adverse effects
DNA, Bacterial/*blood/genetics
Endotoxins/blood
Female
Hepatitis, Alcoholic/*microbiology
Humans
Liver/microbiology/pathology
Liver Diseases, Alcoholic/*microbiology
Male
Metagenomics/*methods
Microbiota/*genetics
Middle Aged
Monocytes/pathology

@article {pmid28232956,
year = {2017},
author = {Marbouty, M and Baudry, L and Cournac, A and Koszul, R},
title = {Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay.},
journal = {Science advances},
volume = {3},
number = {2},
pages = {e1602105},
doi = {10.1126/sciadv.1602105},
pmid = {28232956},
issn = {2375-2548},
mesh = {Animals ; *Bacteria/genetics/metabolism/virology ; *Bacteriophages/genetics/metabolism ; *Gastrointestinal Microbiome ; *Genome, Bacterial ; *Genome, Viral ; Male ; Mice ; },
abstract = {The biochemical activities of microbial communities, or microbiomes, are essential parts of environmental and animal ecosystems. The dynamics, balance, and effects of these communities are strongly influenced by phages present in the population. Being able to characterize bacterium-phage relationships is therefore essential to investigate these ecosystems to the full extent of their complexity. However, this task is currently limited by (i) the ability to characterize complete bacterial and viral genomes from a complex mix of species and (ii) the difficulty to assign phage sequences to their bacterial hosts. We show that both limitations can be circumvented using meta3C, an experimental and computational approach that exploits the physical contacts between DNA molecules to infer their proximity. In a single experiment, dozens of bacterial and phage genomes present in a complex mouse gut microbiota were assembled and scaffolded de novo. The phage genomes were then assigned to their putative bacterial hosts according to the physical contacts between the different DNA molecules, opening new perspectives for a comprehensive picture of the genomic structure of the gut flora. Therefore, this work holds far-reaching implications for human health studies aiming to bridge the virome to the microbiome.},
}

Animals
*Bacteria/genetics/metabolism/virology
*Bacteriophages/genetics/metabolism
*Gastrointestinal Microbiome
*Genome, Bacterial
*Genome, Viral
Male
Mice

@article {pmid30149004,
year = {2018},
author = {Kim, JY and Kim, EM and Yi, MH and Lee, J and Lee, S and Hwang, Y and Yong, D and Sohn, WM and Yong, TS},
title = {Intestinal fluke Metagonimus yokogawai infection increases probiotic Lactobacillus in mouse cecum.},
journal = {Experimental parasitology},
volume = {193},
number = {},
pages = {45-50},
doi = {10.1016/j.exppara.2018.08.002},
pmid = {30149004},
issn = {1090-2449},
mesh = {Animals ; Bacteria/classification/growth & development ; Cecum/*microbiology ; Fish Diseases/parasitology ; Gastrointestinal Microbiome ; Heterophyidae/*physiology ; *Lactobacillus ; Mice ; Mice, Inbred ICR ; Osmeriformes/parasitology ; *Probiotics ; Trematode Infections/*microbiology ; },
abstract = {Helminth infection can alleviate immune-mediated disorders such as allergies and autoimmune diseases, by altering the gut microbiome. However, changes in gut microbiome due to intestinal trematodes remain unelucidated. Here, we evaluated the changes in the gut microbiome of ICR mice infected with Metagonimus yokogawai, a hypo-virulent intestinal trematode. Four weeks after infection, mouse cecal content was analyzed by 16S rRNA amplicon analysis. Although there was no apparent difference in species richness and diversity, the microbiome composition was different in the infected and control groups. Furthermore, several Lactobacillus species with known immunomodulatory role in immune-mediated diseases were increased in the infected group.},
}

Animals
Bacteria/classification/growth & development
Cecum/*microbiology
Fish Diseases/parasitology
Gastrointestinal Microbiome
Heterophyidae/*physiology
*Lactobacillus
Mice
Mice, Inbred ICR
Osmeriformes/parasitology
*Probiotics
Trematode Infections/*microbiology

@article {pmid29654556,
year = {2018},
author = {Jung, DH and Seo, DH and Kim, GY and Nam, YD and Song, EJ and Yoon, S and Park, CS},
title = {The effect of resistant starch (RS) on the bovine rumen microflora and isolation of RS-degrading bacteria.},
journal = {Applied microbiology and biotechnology},
volume = {102},
number = {11},
pages = {4927-4936},
doi = {10.1007/s00253-018-8971-z},
pmid = {29654556},
issn = {1432-0614},
support = {no. 2017R1A2B4004218//National Research Foundation of Korea/ ; },
mesh = {Animals ; Bacteria/isolation & purification/metabolism ; Cattle ; Feces/microbiology ; Fermentation ; Gastrointestinal Microbiome/*drug effects ; Humans ; Rumen/*microbiology ; Starch/*metabolism/*pharmacology ; },
abstract = {Resistant starch (RS) in the diet reaches the large intestine without degradation, where it is decomposed by the commensal microbiota. The fermentation of RS produces secondary metabolites including short-chain fatty acids (SCFAs), which have been linked to a variety of physiological and health effects. Therefore, the availability of RS as a prebiotic is a current issue. The objectives of this study were (1) to use metagenomics to observe microbial flora changes in Bos taurus coreanae rumen fluid in the presence of RS and (2) to isolate RS-degrading microorganisms. The major microbial genus in a general rumen fluid was Succiniclasticum sp., whereas Streptococcus sp. immediately predominated after the addition of RS into the culture medium and was then drastically replaced by Lactobacillus sp. The presence of Bifidobacterium sp. was also observed continuously. Several microorganisms with high RS granule-degrading activity were identified and isolated, including B. choerinum FMB-1 and B. pseudolongum FMB-2. B. choerinum FMB-1 showed the highest RS-hydrolyzing activity and degraded almost 60% of all substrates tested. Coculture experiments demonstrated that Lactobacillus brevis ATCC 14869, which was isolated from human feces, could grow using reducing sugars generated from RS by B. choerinum FMB-1. These results suggest that Bifidobacterium spp., especially B. choerinum FMB-1, are the putative primary degrader of RS in rumen microbial flora and could be further studied as probiotic candidates.},
}

Animals
Bacteria/isolation & purification/metabolism
Cattle
Feces/microbiology
Fermentation
Gastrointestinal Microbiome/*drug effects
Humans
Rumen/*microbiology
Starch/*metabolism/*pharmacology

@article {pmid30271256,
year = {2018},
author = {Anslan, S and Nilsson, RH and Wurzbacher, C and Baldrian, P and Leho Tedersoo, and Bahram, M},
title = {Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding.},
journal = {MycoKeys},
volume = {},
number = {39},
pages = {29-40},
doi = {10.3897/mycokeys.39.28109},
pmid = {30271256},
issn = {1314-4049},
abstract = {Along with recent developments in high-throughput sequencing (HTS) technologies and thus fast accumulation of HTS data, there has been a growing need and interest for developing tools for HTS data processing and communication. In particular, a number of bioinformatics tools have been designed for analysing metabarcoding data, each with specific features, assumptions and outputs. To evaluate the potential effect of the application of different bioinformatics workflow on the results, we compared the performance of different analysis platforms on two contrasting high-throughput sequencing data sets. Our analysis revealed that the computation time, quality of error filtering and hence output of specific bioinformatics process largely depends on the platform used. Our results show that none of the bioinformatics workflows appears to perfectly filter out the accumulated errors and generate Operational Taxonomic Units, although PipeCraft, LotuS and PIPITS perform better than QIIME2 and Galaxy for the tested fungal amplicon dataset. We conclude that the output of each platform requires manual validation of the OTUs by examining the taxonomy assignment values.},
}

@article {pmid30165813,
year = {2018},
author = {Rotimi, AM and Pierneef, R and Reva, ON},
title = {Selection of marker genes for genetic barcoding of microorganisms and binning of metagenomic reads by Barcoder software tools.},
journal = {BMC bioinformatics},
volume = {19},
number = {1},
pages = {309},
doi = {10.1186/s12859-018-2320-1},
pmid = {30165813},
issn = {1471-2105},
support = {93664//National Research Foundation/ ; },
mesh = {Algorithms ; Bacteria/*genetics ; Base Sequence ; DNA Barcoding, Taxonomic/*methods ; *Genes, Bacterial ; Genetic Markers ; Humans ; Metagenome/genetics ; Metagenomics/*methods ; Microbiota/genetics ; Phylogeny ; ROC Curve ; Reproducibility of Results ; Sample Size ; *Software ; Species Specificity ; Whole Genome Sequencing ; },
abstract = {BACKGROUND: Metagenomic approaches have revealed the complexity of environmental microbiomes with the advancement in whole genome sequencing displaying a significant level of genetic heterogeneity on the species level. It has become apparent that patterns of superior bioactivity of bacteria applicable in biotechnology as well as the enhanced virulence of pathogens often requires distinguishing between closely related species or sub-species. Current methods for binning of metagenomic reads usually do not allow for identification below the genus level and generally stops at the family level.

RESULTS: In this work, an attempt was made to improve metagenomic binning resolution by creating genome specific barcodes based on the core and accessory genomes. This protocol was implemented in novel software tools available for use and download from http://bargene.bi.up.ac.za /. The most abundant barcode genes from the core genomes were found to encode for ribosomal proteins, certain central metabolic genes and ABC transporters. Performance of metabarcode sequences created by this package was evaluated using artificially generated and publically available metagenomic datasets. Furthermore, a program (Barcoding 2.0) was developed to align reads against barcode sequences and thereafter calculate various parameters to score the alignments and the individual barcodes. Taxonomic units were identified in metagenomic samples by comparison of the calculated barcode scores to set cut-off values. In this study, it was found that varying sample sizes, i.e. number of reads in a metagenome and metabarcode lengths, had no significant effect on the sensitivity and specificity of the algorithm. Receiver operating characteristics (ROC) curves were calculated for different taxonomic groups based on the results of identification of the corresponding genomes in artificial metagenomic datasets. The reliability of distinguishing between species of the same genus or family by the program was nearly perfect.

CONCLUSIONS: The results showed that the novel online tool BarcodeGenerator (http://bargene.bi.up.ac.za /) is an efficient approach for generating barcode sequences from a set of complete genomes provided by users. Another program, Barcoder 2.0 is available from the same resource to enable an efficient and practical use of metabarcodes for visualization of the distribution of organisms of interest in environmental and clinical samples.},
}

Algorithms
Bacteria/*genetics
Base Sequence
DNA Barcoding, Taxonomic/*methods
*Genes, Bacterial
Genetic Markers
Humans
Metagenome/genetics
Metagenomics/*methods
Microbiota/genetics
Phylogeny
ROC Curve
Reproducibility of Results
Sample Size
*Software
Species Specificity
Whole Genome Sequencing

@article {pmid30128756,
year = {2018},
author = {Mukhtar, S and Mirza, BS and Mehnaz, S and Mirza, MS and Mclean, J and Malik, KA},
title = {Impact of soil salinity on the microbial structure of halophyte rhizosphere microbiome.},
journal = {World journal of microbiology & biotechnology},
volume = {34},
number = {9},
pages = {136},
doi = {10.1007/s11274-018-2509-5},
pmid = {30128756},
issn = {1573-0972},
support = {Project # HEC (FD/2012/1843)//Higher Education Commission, Pakistan/ ; Project # 5-9/PAS/2012/969//Pakistan Academy of Sciences/ ; },
mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; DNA, Bacterial ; Ecosystem ; Metagenomics ; Microbiota/genetics/*physiology ; Pakistan ; Phylogeny ; Plant Roots/microbiology ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; *Salinity ; Salt-Tolerant Plants/classification/*microbiology ; Soil/*chemistry ; *Soil Microbiology ; },
abstract = {The rhizosphere microbiome plays a significant role in the life of plants in promoting plant survival under adverse conditions. However, limited information is available about microbial diversity in saline environments. In the current study, we compared the composition of the rhizosphere microbiomes of the halophytes Urochloa, Kochia, Salsola, and Atriplex living in moderate and high salinity environments (Khewra salt mines; Pakistan) with that of the non-halophyte Triticum. Soil microbiomes analysis using pyrosequencing of 16S rRNA gene indicated that Actinobacteria were dominant in saline soil samples whereas Proteobacteria predominated in non-saline soil samples. Firmicutes, Acidobacteria, Bacteriodetes and Thaumarchaeota were predominant phyla in saline and non-saline soils, whereas Cyanobacteria, Verrucomicrobia, Gemmatimonadetes and the unclassified WPS-2 were less abundant. Sequences from Euryarchaeota, Ignavibacteriae, and Nanohaloarchaeota were identified only from the rhizosphere of halophytes. Dominant halophilic bacteria and archaea identified in this study included Agrococcus, Armatimonadetes gp4, Halalkalicoccus, Haloferula and Halobacterium. Our analysis showed that increases in soil salinity correlated with significant differences in the alpha and beta diversity of the microbial communities across saline and non-saline soil samples. Having a complete inventory of the soil bacteria from different saline environments in Pakistan will help in the discovery of potential inoculants for crops growing on salt-affected land.},
}

Archaea/*classification/genetics
Bacteria/*classification/genetics
DNA, Bacterial
Ecosystem
Metagenomics
Microbiota/genetics/*physiology
Pakistan
Phylogeny
Plant Roots/microbiology
RNA, Ribosomal, 16S/genetics
Rhizosphere
*Salinity
Salt-Tolerant Plants/classification/*microbiology
Soil/*chemistry
*Soil Microbiology

@article {pmid29704757,
year = {2018},
author = {Campanaro, S and Treu, L and Kougias, PG and Luo, G and Angelidaki, I},
title = {Metagenomic binning reveals the functional roles of core abundant microorganisms in twelve full-scale biogas plants.},
journal = {Water research},
volume = {140},
number = {},
pages = {123-134},
doi = {10.1016/j.watres.2018.04.043},
pmid = {29704757},
issn = {1879-2448},
mesh = {Anaerobiosis ; *Biofuels ; Bioreactors/*microbiology ; Manure ; *Metagenome ; Metagenomics/methods ; Microbiota/*physiology ; Sewage/microbiology ; Waste Disposal, Fluid ; Waste Water ; },
abstract = {The aim of this work was to elucidate the microbial ecology in twelve mesophilic and thermophilic full-scale biogas plants using a genome-centric metagenomic approach. In this study both biogas plants treating manure and those treating sludge from waste water treatment plants were considered. The identification of 132 Metagenome-Assembled Genomes (MAGs) and analysis of their abundance profile in different samples allowed the identification of the most abundant core members of the anaerobic digestion microbiome. Canonical correspondence analysis was used to determine the influence of biotic and environmental factors on MAGs abundance and to investigate the methanogenic performance of the biogas plants. Prediction of the functional properties of MAGs was obtained analyzing their KEGG pathways and their carbohydrate active domains. Network analysis allowed investigation of species-species associations and shed light on syntrophic interactions between members belonging to the anaerobic digestion dark matter (phylum Fermentibacteria). By stratifying and comparing different levels of information, it was predicted that some MAGs have a crucial role in the manure-supplemented thermophilic biogas plants and it was highlighted the importance of the glycine cleavage system in complementing the "truncated" Wood-Ljungdahl pathway.},
}

Anaerobiosis
*Biofuels
Bioreactors/*microbiology
Manure
*Metagenome
Metagenomics/methods
Microbiota/*physiology
Sewage/microbiology
Waste Disposal, Fluid
Waste Water

@article {pmid29676472,
year = {2018},
author = {Hao, DC and Zhang, CR and Xiao, PG},
title = {The first Taxus rhizosphere microbiome revealed by shotgun metagenomic sequencing.},
journal = {Journal of basic microbiology},
volume = {58},
number = {6},
pages = {501-512},
doi = {10.1002/jobm.201700663},
pmid = {29676472},
issn = {1521-4028},
mesh = {Archaea/classification/genetics/isolation & purification ; Bacteria/classification/genetics/isolation & purification ; Biodegradation, Environmental ; Environmental Pollutants/adverse effects ; Fungi/classification/genetics/isolation & purification ; Genes, Archaeal/genetics ; Genes, Bacterial/genetics ; Genes, Fungal/genetics ; Genes, Viral/genetics ; Metagenomics/*methods ; *Microbiota ; Phylogeny ; Plant Roots/*microbiology ; *Rhizosphere ; *Soil Microbiology ; Taxus/*microbiology ; Viruses/classification/genetics/isolation & purification ; },
abstract = {In the present study, the shotgun high throughput metagenomic sequencing was implemented to globally capture the features of Taxus rhizosphere microbiome. Total reads could be assigned to 6925 species belonging to 113 bacteria phyla and 301 species of nine fungi phyla. For archaea and virus, 263 and 134 species were for the first time identified, respectively. More than 720,000 Unigenes were identified by clean reads assembly. The top five assigned phyla were Actinobacteria (363,941 Unigenes), Proteobacteria (182,053), Acidobacteria (44,527), Ascomycota (fungi; 18,267), and Chloroflexi (15,539). KEGG analysis predicted numerous functional genes; 7101 Unigenes belong to "Xenobiotics biodegradation and metabolism." A total of 12,040 Unigenes involved in defense mechanisms (e.g., xenobiotic metabolism) were annotated by eggNOG. Talaromyces addition could influence not only the diversity and structure of microbial communities of Taxus rhizosphere, but also the relative abundance of functional genes, including metabolic genes, antibiotic resistant genes, and genes involved in pathogen-host interaction, bacterial virulence, and bacterial secretion system. The structure and function of rhizosphere microbiome could be sensitive to non-native microbe addition, which could impact on the pollutant degradation. This study, complementary to the amplicon sequencing, more objectively reflects the native microbiome of Taxus rhizosphere and its response to environmental pressure, and lays a foundation for potential combination of phytoremediation and bioaugmentation.},
}

Archaea/classification/genetics/isolation & purification
Bacteria/classification/genetics/isolation & purification
Biodegradation, Environmental
Environmental Pollutants/adverse effects
Fungi/classification/genetics/isolation & purification
Genes, Archaeal/genetics
Genes, Bacterial/genetics
Genes, Fungal/genetics
Genes, Viral/genetics
Metagenomics/*methods
*Microbiota
Phylogeny
Plant Roots/*microbiology
*Rhizosphere
*Soil Microbiology
Taxus/*microbiology
Viruses/classification/genetics/isolation & purification

@article {pmid29567298,
year = {2018},
author = {Stensvold, CR and van der Giezen, M},
title = {Associations between Gut Microbiota and Common Luminal Intestinal Parasites.},
journal = {Trends in parasitology},
volume = {34},
number = {5},
pages = {369-377},
doi = {10.1016/j.pt.2018.02.004},
pmid = {29567298},
issn = {1471-5007},
mesh = {Blastocystis/*physiology ; Dientamoeba/*physiology ; *Environmental Biomarkers ; Gastrointestinal Microbiome/*physiology ; Host-Parasite Interactions/*physiology ; Humans ; Intestinal Diseases, Parasitic/*microbiology ; Intestines/microbiology/parasitology ; },
abstract = {The development and integration of DNA-based methods in research and clinical microbiology laboratories have enabled standardised and comprehensive detection and differentiation of the microbes colonising our guts. For instance, the single-celled parasites Blastocystis and Dientamoeba appear to be much more common than previously thought, especially so in healthy individuals. While increasing evidence appears to suggest limited pathogenicity of these parasites, next-generation-sequencing-based studies have helped us to appreciate links between parasite colonisation and certain host phenotypical characteristics and gut microbial profiles. The fundamental question remains as to whether such parasites are merely indicators or active manipulators of gut microbiota structure and function. In this article, we collate existing evidence that these parasites are, at minimum, indicators of intestinal microbiota structure.},
}

Blastocystis/*physiology
Dientamoeba/*physiology
*Environmental Biomarkers
Gastrointestinal Microbiome/*physiology
Host-Parasite Interactions/*physiology
Humans
Intestinal Diseases, Parasitic/*microbiology
Intestines/microbiology/parasitology

@article {pmid29500689,
year = {2018},
author = {Xia, H and Wang, Y and Shi, C and Atoni, E and Zhao, L and Yuan, Z},
title = {Comparative Metagenomic Profiling of Viromes Associated with Four Common Mosquito Species in China.},
journal = {Virologica Sinica},
volume = {33},
number = {1},
pages = {59-66},
doi = {10.1007/s12250-018-0015-4},
pmid = {29500689},
issn = {1995-820X},
mesh = {Animals ; *Biodiversity ; China ; Culicidae/*virology ; Host Specificity ; *Metagenomics ; Mosquito Vectors/*virology ; Viral Tropism ; Viruses/*classification/genetics/*isolation & purification ; },
abstract = {Vast viruses are thought to be associated with mosquitoes. Anopheles sinensis, Armigeres subalbatus, Culex quinquefasciatus, and Culex tritaeniorhynchus are very common mosquito species in China, and whether the virome structure in each species is species-specific has not been evaluated. In this study, a total of 2222 mosquitoes were collected from the same geographic location, and RNAs were sequenced using the Illumina Miseq platform. After querying to the Refseq database, a total of 3,435,781, 2,223,509, 5,727,523, and 6,387,867 paired-end reads were classified under viral sequences from An. sinensis, Ar. subalbatus, Cx. quinquefasciatus, and Cx. tritaeniorhynchus, respectively, with the highest prevalence of virus-associated reads being observed in Cx. quinquefasciatus. The metagenomic comparison analysis showed that the virus-related reads were distributed across 26 virus families, together with an unclassified group of viruses. Anelloviridae, Circoviridae, Genomoviridae, Iridoviridae, Mesoniviridae, Microviridae, Myoviridae, Parvoviridae, Phenuiviridae, and Podoviridae were the top ten significantly different viral families among the four species. Further analysis reveals that the virome is species-specific in four mosquito samples, and several viral sequences which maybe belong to novel viruses are discovered for the first time in those mosquitoes. This investigation provides a basis for a comprehensive knowledge on the mosquito virome status in China.},
}

Animals
*Biodiversity
China
Culicidae/*virology
Host Specificity
*Metagenomics
Mosquito Vectors/*virology
Viral Tropism
Viruses/*classification/genetics/*isolation & purification

@article {pmid29171095,
year = {2018},
author = {Barko, PC and McMichael, MA and Swanson, KS and Williams, DA},
title = {The Gastrointestinal Microbiome: A Review.},
journal = {Journal of veterinary internal medicine},
volume = {32},
number = {1},
pages = {9-25},
doi = {10.1111/jvim.14875},
pmid = {29171095},
issn = {1939-1676},
mesh = {Animals ; Dysbiosis/*veterinary ; *Gastrointestinal Microbiome ; Mammals ; Metabolomics ; Metagenomics ; },
abstract = {The gastrointestinal microbiome is a diverse consortium of bacteria, archaea, fungi, protozoa, and viruses that inhabit the gut of all mammals. Studies in humans and other mammals have implicated the microbiome in a range of physiologic processes that are vital to host health including energy homeostasis, metabolism, gut epithelial health, immunologic activity, and neurobehavioral development. The microbial genome confers metabolic capabilities exceeding those of the host organism alone, making the gut microbiome an active participant in host physiology. Recent advances in DNA sequencing technology and computational biology have revolutionized the field of microbiomics, permitting mechanistic evaluation of the relationships between an animal and its microbial symbionts. Changes in the gastrointestinal microbiome are associated with diseases in humans and animals including inflammatory bowel disease, asthma, obesity, metabolic syndrome, cardiovascular disease, immune-mediated conditions, and neurodevelopmental conditions such as autism spectrum disorder. While there remains a paucity of data regarding the intestinal microbiome in small animals, recent studies have helped to characterize its role in host animal health and associated disease states. This review is intended to familiarize small animal veterinarians with recent advances in the field of microbiomics and to prime them for a future in which diagnostic tests and therapies will incorporate these developments into clinical practice.},
}

Animals
Dysbiosis/*veterinary
*Gastrointestinal Microbiome
Mammals
Metabolomics
Metagenomics

@article {pmid28891744,
year = {2018},
author = {Fraumene, C and Manghina, V and Cadoni, E and Marongiu, F and Abbondio, M and Serra, M and Palomba, A and Tanca, A and Laconi, E and Uzzau, S},
title = {Caloric restriction promotes rapid expansion and long-lasting increase of Lactobacillus in the rat fecal microbiota.},
journal = {Gut microbes},
volume = {9},
number = {2},
pages = {104-114},
doi = {10.1080/19490976.2017.1371894},
pmid = {28891744},
issn = {1949-0984},
mesh = {Animals ; Bacteria/classification/genetics/*growth & development ; *Caloric Restriction ; Cluster Analysis ; DNA, Bacterial/genetics ; Diet ; Feces/*microbiology ; Gastrointestinal Microbiome/*physiology ; Lactobacillus/classification/*growth & development ; Models, Animal ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Inbred F344 ; },
abstract = {Previous studies indicated that caloric restricted diet enables to lower significantly the risk of cardiovascular and metabolic diseases. In experimental animal models, life-long lasting caloric restriction (CR) was demonstrated to induce changes of the intestinal microbiota composition, regardless of fat content and/or exercise. To explore the potential impact of short and long-term CR treatment on the gut microbiota, we conducted an analysis of fecal microbiota composition in young and adult Fisher 344 rats treated with a low fat feed under ad libitum (AL) or CR conditions (70%). We report here significant changes of the rat fecal microbiota that arise rapidly in young growing animals after short-term administration of a CR diet. In particular, Lactobacillus increased significantly after 8 weeks of CR treatment and its relative abundance was significantly higher in CR vs AL fed animals after 36 weeks of dietary intervention. Taken together, our data suggest that Lactobacillus intestinal colonization is hampered in AL fed young rats compared to CR fed ones, while health-promoting CR diet intervention enables the expansion of this genus rapidly and persistently up to adulthood.},
}

Animals
Bacteria/classification/genetics/*growth & development
*Caloric Restriction
Cluster Analysis
DNA, Bacterial/genetics
Diet
Feces/*microbiology
Gastrointestinal Microbiome/*physiology
Lactobacillus/classification/*growth & development
Models, Animal
RNA, Ribosomal, 16S/genetics
Rats
Rats, Inbred F344

@article {pmid29453765,
year = {2018},
author = {Mahajan, R and Attri, S and Sharma, K and Singh, N and Sharma, D and Goel, G},
title = {Statistical assessment of DNA extraction methodology for culture-independent analysis of microbial community associated with diverse environmental samples.},
journal = {Molecular biology reports},
volume = {45},
number = {3},
pages = {297-308},
doi = {10.1007/s11033-018-4162-3},
pmid = {29453765},
issn = {1573-4978},
support = {INT/RUS/RFBR/P-175//Department of Science and Technology, Ministry of Science and Technology/ ; },
mesh = {Animals ; DNA/genetics/*isolation & purification ; DNA, Bacterial/genetics/isolation & purification ; Feces/chemistry ; Humans ; Metagenomics/methods ; Microbiota/genetics ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA/methods ; Soil/chemistry ; },
abstract = {Cost-effectiveness, quality, time-effectiveness and ease of the methodology are the most crucial factors in isolating quality DNA from wide variety of samples. Thus, research efforts focusing on the development of an efficient DNA extraction protocol is the need of the hour. The present study therefore, focuses on development of an efficient, rapid and free of inhibitory substances based methodology for extracting metagenomic DNA from diverse environmental samples viz. anaerobic biogas digesta, ruminant stomach, human feces, soil, and microbial starter cultures used for preparation of fermented food. PCR-DGGE based analysis and quality metagenomic library preparation, using DNA extraction methodology, validates the developed protocol. The developed protocol is cost effective, capable of isolating DNA from small sample size (100-1000 µl), time efficient (1.5-2.0 h protocol) and results in significantly higher DNA yield (4-8 times increased yield) when compared to previously available DNA extraction method and a commercial DNA extraction kit. The DNA extracted from the samples using different protocols was evaluated based on its ability to identify diverse microbial species using PCR-DGGE profiles targeting variable region within the 16S rRNA gene. The results of microbial community analysis revealed comparability of the developed protocol to commercial kits, in effectively identifying dominant representatives of the microbial community in different samples. Using the DNA extracted from the presented methodology, metagenomic libraries were prepared, which were found suitable for sequencing on Illumina platform.},
}

Animals
DNA/genetics/*isolation & purification
DNA, Bacterial/genetics/isolation & purification
Feces/chemistry
Humans
Metagenomics/methods
Microbiota/genetics
Polymerase Chain Reaction/methods
Sequence Analysis, DNA/methods
Soil/chemistry

@article {pmid28612429,
year = {2017},
author = {Tanner, K and Vilanova, C and Porcar, M},
title = {Bioprospecting challenges in unusual environments.},
journal = {Microbial biotechnology},
volume = {10},
number = {4},
pages = {671-673},
doi = {10.1111/1751-7915.12723},
pmid = {28612429},
issn = {1751-7915},
mesh = {Bacteria/classification/genetics/isolation & purification/*metabolism ; Biodiversity ; Bioprospecting/*trends ; Biotechnology ; *Environmental Microbiology ; Metagenomics ; },
}

Bacteria/classification/genetics/isolation & purification/*metabolism
Biodiversity
Bioprospecting/*trends
Biotechnology
*Environmental Microbiology
Metagenomics

@article {pmid29858829,
year = {2018},
author = {Gupta, SK and Shin, H and Han, D and Hur, HG and Unno, T},
title = {Metagenomic analysis reveals the prevalence and persistence of antibiotic- and heavy metal-resistance genes in wastewater treatment plant.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {56},
number = {6},
pages = {408-415},
doi = {10.1007/s12275-018-8195-z},
pmid = {29858829},
issn = {1976-3794},
mesh = {Anti-Bacterial Agents/*toxicity ; Bacteria/*classification/drug effects/*genetics/isolation & purification ; DNA, Bacterial/genetics ; Drug Resistance, Microbial/*genetics ; Genes, Bacterial ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; Metals, Heavy/*toxicity ; Microbial Consortia/genetics ; Phylogeny ; Republic of Korea ; Sequence Analysis ; Sewage/microbiology ; Waste Water/*microbiology ; Water Purification ; },
abstract = {The increased antibiotic resistance among microorganisms has resulted into growing interest for investigating the wastewater treatment plants (WWTPs) as they are reported to be the major source in the dissemination of antibiotic resistance genes (ARGs) and heavy metal resistance genes (HMRGs) in the environment. In this study, we investigated the prevalence and persistence of ARGs and HMRGs as well as bacterial diversity and mobile genetic elements (MGEs) in influent and effluent at the WWTP in Gwangju, South Korea, using high-throughput sequencing based metagenomic approach. A good number of broad-spectrum of resistance genes (both ARG and HMRG) were prevalent and likely persistent, although large portion of them were successfully removed at the wastewater treatment process. The relative abundance of ARGs and MGEs was higher in effluent as compared to that of influent. Our results suggest that the resistance genes with high abundance and bacteria harbouring ARGs and MGEs are likely to persist more through the treatment process. On analyzing the microbial community, the phylum Proteobacteria, especially potentially pathogenic species belonging to the genus Acinetobacter, dominated in WWTP. Overall, our study demonstrates that many ARGs and HMRGs may persist the treatment processes in WWTPs and their association to MGEs may contribute to the dissemination of resistance genes among microorganisms in the environment.},
}

Anti-Bacterial Agents/*toxicity
Bacteria/*classification/drug effects/*genetics/isolation & purification
DNA, Bacterial/genetics
Drug Resistance, Microbial/*genetics
Genes, Bacterial
High-Throughput Nucleotide Sequencing
Metagenomics/*methods
Metals, Heavy/*toxicity
Microbial Consortia/genetics
Phylogeny
Republic of Korea
Sequence Analysis
Sewage/microbiology
Waste Water/*microbiology
Water Purification

@article {pmid29587819,
year = {2018},
author = {Dickson, LB and Ghozlane, A and Volant, S and Bouchier, C and Ma, L and Vega-Rúa, A and Dusfour, I and Jiolle, D and Paupy, C and Mayanja, MN and Kohl, A and Lutwama, JJ and Duong, V and Lambrechts, L},
title = {Diverse laboratory colonies of Aedes aegypti harbor the same adult midgut bacterial microbiome.},
journal = {Parasites & vectors},
volume = {11},
number = {1},
pages = {207},
doi = {10.1186/s13071-018-2780-1},
pmid = {29587819},
issn = {1756-3305},
support = {ANR-16-CE35-0004-01//Agence Nationale de la Recherche/International ; ANR-17-ERC2-0016-01//Agence Nationale de la Recherche/International ; ANR-10-LABX-62-IBEID//Investissement d'Avenir program Laboratoire d'Excellence Integrative Biology of Emerging Infectious Diseases/International ; 734584//European Union's Horizon 2020 research and innovation programme under ZikaPLAN/International ; 2015-FED-192//Programme Opérationnel FEDER-Guadeloupe-Conseil Régional/International ; MC_UU_12014//Medical Research Council/United Kingdom ; ANR10-INBS-09-08//France Génomique consortium/International ; },
mesh = {Aedes/*microbiology ; Animals ; Bacteria/*classification/*genetics ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Host-associated microbes, collectively known as the microbiota, play an important role in the biology of multicellular organisms. In mosquito vectors of human pathogens, the gut bacterial microbiota influences vectorial capacity and has become the subject of intense study. In laboratory studies of vector biology, genetic effects are often inferred from differences between geographically and genetically diverse colonies of mosquitoes that are reared in the same insectary. It is unclear, however, to what extent genetic effects can be confounded by uncontrolled differences in the microbiota composition among mosquito colonies. To address this question, we used 16S metagenomics to compare the midgut bacterial microbiome of six laboratory colonies of Aedes aegypti recently derived from wild populations representing the geographical range and genetic diversity of the species.

RESULTS: We found that the diversity, abundance, and community structure of the midgut bacterial microbiome was remarkably similar among the six different colonies of Ae. aegypti, regardless of their geographical origin. We also confirmed the relatively low complexity of bacterial communities inhabiting the mosquito midgut.

CONCLUSIONS: Our finding that geographically diverse colonies of Ae. aegypti reared in the same insectary harbor a similar gut bacterial microbiome supports the conclusion that the gut microbiota of adult mosquitoes is environmentally determined regardless of the host genotype. Thus, uncontrolled differences in microbiota composition are unlikely to represent a significant confounding factor in genetic studies of vector biology.},
}

Aedes/*microbiology
Animals
Bacteria/*classification/*genetics
Cluster Analysis
DNA, Ribosomal/chemistry/genetics
*Gastrointestinal Microbiome
Gastrointestinal Tract/microbiology
Metagenomics
Phylogeny
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA

@article {pmid29497869,
year = {2018},
author = {Tan, Z and Wang, Y and Yang, T and Ao, H and Chen, S and Xing, K and Zhang, F and Zhao, X and Liu, J and Wang, C},
title = {Differences in gut microbiota composition in finishing Landrace pigs with low and high feed conversion ratios.},
journal = {Antonie van Leeuwenhoek},
volume = {111},
number = {9},
pages = {1673-1685},
doi = {10.1007/s10482-018-1057-1},
pmid = {29497869},
issn = {1572-9699},
support = {BAIC02-2016//Beijing Innovation Consortium of Agriculture Research System/ ; },
mesh = {Amino Acids/metabolism ; Animal Feed/*analysis ; Animals ; Bacteria/*classification/genetics ; *Biodiversity ; Carbohydrate Metabolism ; Cecum/microbiology ; Colon/microbiology ; DNA, Bacterial/genetics ; Discriminant Analysis ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Intestine, Small/microbiology ; Metabolic Networks and Pathways ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Swine ; },
abstract = {The goal of this study was to evaluate the microbial communities in the gut and feces from female finishing Landrace pigs with high and low feed conversion ratio (FCR) by 16S rRNA gene amplicon sequencing. Many potential biomarkers can distinguish between high and low FCR groups in the duodenum, ileum, cecum, colon, and rectum, according to linear discriminant analysis effect sizes. The relative abundance of microbes were tested by Mann-Whitney test between the high and low FCR groups in different organs: Campylobacter, Prevotella and Sphaerochaeta were different in the duodenum (P < 0.05); Sanguibacter, Kingella and Anaeroplasma in jejunum; Anaeroplasma, Arthrobacter, Kingella, Megasphaera and SMB53 in the ileum; Butyricicoccus, Campylobacter, Mitsuokella, and Coprobacillus in the cecum; Lactococcus and Peptococcus in the colon; Staphylococcus in the rectum; and Rothia in feces. The prevalence of microbial genera in certain locations could potentially be used as biomarkers to distinguish between high and low FCR. Functional prediction clustering analysis suggested that bacteria in the hindgut mainly participated in carbohydrate metabolism and amino acid metabolism, and different in the relative abundance of metabolic pathways, as predicted from the microbial taxa present, were identified by comparing the high and low groups of each location. The results may provide insights for the alteration of the intestinal microbial communities to improve the growth rate of pigs.},
}

Amino Acids/metabolism
Animal Feed/*analysis
Animals
Bacteria/*classification/genetics
*Biodiversity
Carbohydrate Metabolism
Cecum/microbiology
Colon/microbiology
DNA, Bacterial/genetics
Discriminant Analysis
Feces/microbiology
Female
*Gastrointestinal Microbiome
Intestine, Small/microbiology
Metabolic Networks and Pathways
Metagenomics
RNA, Ribosomal, 16S/genetics
*Swine

@article {pmid29268781,
year = {2017},
author = {Carda-Diéguez, M and Ghai, R and Rodríguez-Valera, F and Amaro, C},
title = {Wild eel microbiome reveals that skin mucus of fish could be a natural niche for aquatic mucosal pathogen evolution.},
journal = {Microbiome},
volume = {5},
number = {1},
pages = {162},
doi = {10.1186/s40168-017-0376-1},
pmid = {29268781},
issn = {2049-2618},
support = {BES-2012-052361//Secretaría de Estado de Investigación, Desarrollo e Innovación/International ; AGL2014-58933-P (cofunded with FEDER funds)//Secretaría de Estado de Investigación, Desarrollo e Innovación/International ; 17-04828S//Grantová Agentura České Republiky/International ; CGL2016-76273-P [AEI/FEDER, EU]//AEI/FEDER/EU/International ; CGL2015-71523-REDC (Acciones de dinamización "REDES DE EXCELENCIA" CONSOLIDER)//Dirección General de Investigación Científica y Técnica/International ; Prometeo II/2014/012 "AQUAMET"//Generalitat Valenciana/International ; },
mesh = {Anguilla/anatomy & histology/*microbiology ; Animals ; Animals, Wild/microbiology ; Bacteria/genetics/isolation & purification/*pathogenicity ; DNA, Bacterial ; Evolution, Molecular ; Genomic Islands ; Genomics ; Humans ; Metagenomics ; Microbiota/*genetics ; Mucus/*microbiology ; Skin/*microbiology ; Vibrio/genetics/isolation & purification/pathogenicity ; *Water Microbiology ; },
abstract = {BACKGROUND: Fish skin mucosal surfaces (SMS) are quite similar in composition and function to some mammalian MS and, in consequence, could constitute an adequate niche for the evolution of mucosal aquatic pathogens in natural environments. We aimed to test this hypothesis by searching for metagenomic and genomic evidences in the SMS-microbiome of a model fish species (Anguilla Anguilla or eel), from different ecosystems (four natural environments of different water salinity and one eel farm) as well as the water microbiome (W-microbiome) surrounding the host.

RESULTS: Remarkably, potentially pathogenic Vibrio monopolized wild eel SMS-microbiome from natural ecosystems, Vibrio anguillarum/Vibrio vulnificus and Vibrio cholerae/Vibrio metoecus being the most abundant ones in SMS from estuary and lake, respectively. Functions encoded in the SMS-microbiome differed significantly from those in the W-microbiome and allowed us to predict that successful mucus colonizers should have specific genes for (i) attachment (mainly by forming biofilms), (ii) bacterial competence and communication, and (iii) resistance to mucosal innate immunity, predators (amoeba), and heavy metals/drugs. In addition, we found several mobile genetic elements (mainly integrative conjugative elements) as well as a series of evidences suggesting that bacteria exchange DNA in SMS. Further, we isolated and sequenced a V. metoecus strain from SMS. This isolate shares pathogenicity islands with V. cholerae O1 from intestinal infections that are absent in the rest of sequenced V. metoecus strains, all of them from water and extra-intestinal infections.

CONCLUSIONS: We have obtained metagenomic and genomic evidence in favor of the hypothesis on the role of fish mucosal surfaces as a specialized habitat selecting microbes capable of colonizing and persisting on other comparable mucosal surfaces, e.g., the human intestine.},
}

Anguilla/anatomy & histology/*microbiology
Animals
Animals, Wild/microbiology
Bacteria/genetics/isolation & purification/*pathogenicity
DNA, Bacterial
Evolution, Molecular
Genomic Islands
Genomics
Humans
Metagenomics
Microbiota/*genetics
Mucus/*microbiology
Skin/*microbiology
Vibrio/genetics/isolation & purification/pathogenicity
*Water Microbiology

@article {pmid29246178,
year = {2017},
author = {Razavi, M and Marathe, NP and Gillings, MR and Flach, CF and Kristiansson, E and Joakim Larsson, DG},
title = {Discovery of the fourth mobile sulfonamide resistance gene.},
journal = {Microbiome},
volume = {5},
number = {1},
pages = {160},
doi = {10.1186/s40168-017-0379-y},
pmid = {29246178},
issn = {2049-2618},
support = {942-2015-750//Svenska Forskningsrådet Formas/ ; 521-2013-8633//Vetenskapsrådet/ ; 2015-02492//Vetenskapsrådet (SE)/ ; },
mesh = {Aminoglycosides/pharmacology ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics ; Bioprospecting ; Cross Infection/microbiology ; Dihydropteroate Synthase/genetics/isolation & purification ; Drug Resistance, Microbial/*genetics ; Escherichia coli/drug effects/genetics ; Genes, Bacterial ; Humans ; India ; *Integrons/genetics ; Metagenomics ; Microbial Consortia/genetics ; Microbial Sensitivity Tests ; RNA, Ribosomal, 16S/genetics ; Rivers/microbiology ; Sulfonamides/*pharmacology ; beta-Lactams/pharmacology ; },
abstract = {BACKGROUND: Over the past 75 years, human pathogens have acquired antibiotic resistance genes (ARGs), often from environmental bacteria. Integrons play a major role in the acquisition of antibiotic resistance genes. We therefore hypothesized that focused exploration of integron gene cassettes from microbial communities could be an efficient way to find novel mobile resistance genes. DNA from polluted Indian river sediments were amplified using three sets of primers targeting class 1 integrons and sequenced by long- and short-read technologies to maintain both accuracy and context.

RESULTS: Up to 89% of identified open reading frames encode known resistance genes, or variations thereof (> 1000). We identified putative novel ARGs to aminoglycosides, beta-lactams, trimethoprim, rifampicin, and chloramphenicol, including several novel OXA variants, providing reduced susceptibility to carbapenems. One dihydropteroate synthase gene, with less than 34% amino acid identity to the three known mobile sulfonamide resistance genes (sul1-3), provided complete resistance when expressed in Escherichia coli. The mobilized gene, here named sul4, is the first mobile sulfonamide resistance gene discovered since 2003. Analyses of adjacent DNA suggest that sul4 has been decontextualized from a set of chromosomal genes involved in folate synthesis in its original host, likely within the phylum Chloroflexi. The presence of an insertion sequence common region element could provide mobility to the entire integron. Screening of 6489 metagenomic datasets revealed that sul4 is already widespread in seven countries across Asia and Europe.

CONCLUSIONS: Our findings show that exploring integrons from environmental communities with a history of antibiotic exposure can provide an efficient way to find novel, mobile resistance genes. The mobilization of a fourth sulfonamide resistance gene is likely to provide expanded opportunities for sulfonamide resistance to spread, with potential impacts on both human and animal health.},
}

Aminoglycosides/pharmacology
Animals
Anti-Bacterial Agents/*pharmacology
Bacteria/*drug effects/genetics
Bioprospecting
Cross Infection/microbiology
Dihydropteroate Synthase/genetics/isolation & purification
Drug Resistance, Microbial/*genetics
Escherichia coli/drug effects/genetics
Genes, Bacterial
Humans
India
*Integrons/genetics
Metagenomics
Microbial Consortia/genetics
Microbial Sensitivity Tests
RNA, Ribosomal, 16S/genetics
Rivers/microbiology
Sulfonamides/*pharmacology
beta-Lactams/pharmacology

@article {pmid29228991,
year = {2017},
author = {Auffret, MD and Dewhurst, RJ and Duthie, CA and Rooke, JA and John Wallace, R and Freeman, TC and Stewart, R and Watson, M and Roehe, R},
title = {The rumen microbiome as a reservoir of antimicrobial resistance and pathogenicity genes is directly affected by diet in beef cattle.},
journal = {Microbiome},
volume = {5},
number = {1},
pages = {159},
doi = {10.1186/s40168-017-0378-z},
pmid = {29228991},
issn = {2049-2618},
support = {BB/N01720X/1 and BB/N016742/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animal Feed/adverse effects/*analysis ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacteriocins/pharmacology ; Bacteroidetes/drug effects/genetics/pathogenicity ; Cattle/*microbiology ; Chloramphenicol/pharmacology ; Drug Resistance, Multiple, Bacterial/*genetics ; Firmicutes/drug effects/genetics/pathogenicity ; *Genes, Bacterial ; Humans ; Metagenomics/methods ; *Microbiota ; Proteobacteria/drug effects/genetics/pathogenicity ; Red Meat/analysis ; Rumen/*microbiology ; Virulence ; },
abstract = {BACKGROUND: The emergence and spread of antimicrobial resistance is the most urgent current threat to human and animal health. An improved understanding of the abundance of antimicrobial resistance genes and genes associated with microbial colonisation and pathogenicity in the animal gut will have a major role in reducing the contribution of animal production to this problem. Here, the influence of diet on the ruminal resistome and abundance of pathogenicity genes was assessed in ruminal digesta samples taken from 50 antibiotic-free beef cattle, comprising four cattle breeds receiving two diets containing different proportions of concentrate.

RESULTS: Two hundred and four genes associated with antimicrobial resistance (AMR), colonisation, communication or pathogenicity functions were identified from 4966 metagenomic genes using KEGG identification. Both the diversity and abundance of these genes were higher in concentrate-fed animals. Chloramphenicol and microcin resistance genes were dominant in samples from forage-fed animals (P < 0.001), while aminoglycoside and streptomycin resistances were enriched in concentrate-fed animals. The concentrate-based diet also increased the relative abundance of Proteobacteria, which includes many animal and zoonotic pathogens. A high ratio of Proteobacteria to (Firmicutes + Bacteroidetes) was confirmed as a good indicator for rumen dysbiosis, with eight cases all from concentrate-fed animals. Finally, network analysis demonstrated that the resistance/pathogenicity genes are potentially useful as biomarkers for health risk assessment of the ruminal microbiome.

CONCLUSIONS: Diet has important effects on the complement of AMR genes in the rumen microbial community, with potential implications for human and animal health.},
}

Animal Feed/adverse effects/*analysis
Animals
Anti-Bacterial Agents/pharmacology
Bacteriocins/pharmacology
Bacteroidetes/drug effects/genetics/pathogenicity
Cattle/*microbiology
Chloramphenicol/pharmacology
Drug Resistance, Multiple, Bacterial/*genetics
Firmicutes/drug effects/genetics/pathogenicity
*Genes, Bacterial
Humans
Metagenomics/methods
*Microbiota
Proteobacteria/drug effects/genetics/pathogenicity
Red Meat/analysis
Rumen/*microbiology
Virulence

@article {pmid29197424,
year = {2017},
author = {Cheng, K and Ning, Z and Zhang, X and Li, L and Liao, B and Mayne, J and Stintzi, A and Figeys, D},
title = {MetaLab: an automated pipeline for metaproteomic data analysis.},
journal = {Microbiome},
volume = {5},
number = {1},
pages = {157},
doi = {10.1186/s40168-017-0375-2},
pmid = {29197424},
issn = {2049-2618},
support = {217066//Natural Sciences and Engineering Research Council of Canada/ ; 9408//Genome Canada/Ontario Genomics/ ; },
mesh = {*Computational Biology ; Databases, Protein ; Gastrointestinal Microbiome ; *Metagenomics ; Microbiota ; *Proteomics ; *Software ; Statistics as Topic ; },
abstract = {BACKGROUND: Research involving microbial ecosystems has drawn increasing attention in recent years. Studying microbe-microbe, host-microbe, and environment-microbe interactions are essential for the understanding of microbial ecosystems. Currently, metaproteomics provide qualitative and quantitative information of proteins, providing insights into the functional changes of microbial communities. However, computational analysis of large-scale data generated in metaproteomic studies remains a challenge. Conventional proteomic software have difficulties dealing with the extreme complexity and species diversity present in microbiome samples leading to lower rates of peptide and protein identification. To address this issue, we previously developed the MetaPro-IQ approach for highly efficient microbial protein/peptide identification and quantification.

RESULT: Here, we developed an integrated software platform, named MetaLab, providing a complete and automated, user-friendly pipeline for fast microbial protein identification, quantification, as well as taxonomic profiling, directly from mass spectrometry raw data. Spectral clustering adopted in the pre-processing step dramatically improved the speed of peptide identification from database searches. Quantitative information of identified peptides was used for estimating the relative abundance of taxa at all phylogenetic ranks. Taxonomy result files exported by MetaLab are fully compatible with widely used metagenomics tools. Herein, the potential of MetaLab is evaluated by reanalyzing a metaproteomic dataset from mouse gut microbiome samples.

CONCLUSION: MetaLab is a fully automatic software platform enabling an integrated data-processing pipeline for metaproteomics. The function of sample-specific database generation can be very advantageous for searching peptides against huge protein databases. It provides a seamless connection between peptide determination and taxonomic profiling; therefore, the peptide abundance is readily used for measuring the microbial variations. MetaLab is designed as a versatile, efficient, and easy-to-use tool which can greatly simplify the procedure of metaproteomic data analysis for researchers in microbiome studies.},
}

*Computational Biology
Databases, Protein
Gastrointestinal Microbiome
*Metagenomics
Microbiota
*Proteomics
*Software
Statistics as Topic

@article {pmid29036588,
year = {2018},
author = {Liu, X and Yu, Y and Liu, J and Elliott, CF and Qian, C and Liu, J},
title = {A novel data structure to support ultra-fast taxonomic classification of metagenomic sequences with k-mer signatures.},
journal = {Bioinformatics (Oxford, England)},
volume = {34},
number = {1},
pages = {171-178},
doi = {10.1093/bioinformatics/btx432},
pmid = {29036588},
issn = {1367-4811},
support = {P30 CA177558/CA/NCI NIH HHS/United States ; R01 HG006272/HG/NHGRI NIH HHS/United States ; },
mesh = {Algorithms ; Bacteria/genetics ; *Genome, Microbial ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA/*methods ; *Software ; },
abstract = {Motivation: Metagenomic read classification is a critical step in the identification and quantification of microbial species sampled by high-throughput sequencing. Although many algorithms have been developed to date, they suffer significant memory and/or computational costs. Due to the growing popularity of metagenomic data in both basic science and clinical applications, as well as the increasing volume of data being generated, efficient and accurate algorithms are in high demand.

Results: We introduce MetaOthello, a probabilistic hashing classifier for metagenomic sequencing reads. The algorithm employs a novel data structure, called l-Othello, to support efficient querying of a taxon using its k-mer signatures. MetaOthello is an order-of-magnitude faster than the current state-of-the-art algorithms Kraken and Clark, and requires only one-third of the RAM. In comparison to Kaiju, a metagenomic classification tool using protein sequences instead of genomic sequences, MetaOthello is three times faster and exhibits 20-30% higher classification sensitivity. We report comparative analyses of both scalability and accuracy using a number of simulated and empirical datasets.

MetaOthello is a stand-alone program implemented in C ++. The current version (1.0) is accessible via https://doi.org/10.5281/zenodo.808941.

Contact: liuj@cs.uky.edu.

Supplementary information: Supplementary data are available at Bioinformatics online.},
}

Algorithms
Bacteria/genetics
*Genome, Microbial
High-Throughput Nucleotide Sequencing/*methods
Humans
Metagenomics/*methods
Microbiota/*genetics
Sequence Analysis, DNA/*methods
*Software

@article {pmid28597254,
year = {2017},
author = {Gopal, M and Bhute, SS and Gupta, A and Prabhu, SR and Thomas, GV and Whitman, WB and Jangid, K},
title = {Changes in structure and function of bacterial communities during coconut leaf vermicomposting.},
journal = {Antonie van Leeuwenhoek},
volume = {110},
number = {10},
pages = {1339-1355},
doi = {10.1007/s10482-017-0894-7},
pmid = {28597254},
issn = {1572-9699},
support = {BT/PR/0054/NDB/52/94/2007//Department of Biotechnology , Ministry of Science and Technology/ ; },
mesh = {Animals ; Bacteria/classification/genetics ; Bacterial Proteins/metabolism ; *Biodiversity ; *Cocos ; *Composting ; DNA, Bacterial/genetics ; Metagenomics/methods ; *Microbiota ; Oligochaeta/*metabolism/microbiology ; Plant Leaves/*metabolism ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {To understand bacterial community dynamics during the vermicomposting of lignin-rich coconut leaves using an indigenous isolate of an epigeic earthworm, Eudrilus sp., we employed amplicon-based pyrosequencing of the V1 to V3 region of the 16S rRNA genes. Total community DNA was isolated from two separate vermicomposting tanks in triplicate at four different stages of the process: pre-decomposition (15th day), initial vermicomposting (45th day), 50-70% vermicomposting (75th day) and mature vermicompost (105th day). Alpha diversity measurements revealed an increase in bacterial diversity till the 75th day, which then declined in the mature vermicompost. Beta diversity comparisons showed formation of distinct, stage-specific communities. In terms of relative abundance, the Acidobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes, Nitrospirae, Planctomycetes, TM7 and WS3 groups increased until the 50-70% vermicomposting stage (p = 0.05). During the same time, the abundance of Bacteroidetes and Proteobacteria decreased. In contrast, the levels of Firmicutes increased throughout the 105-day vermicomposting process. The distribution of the most abundant OTUs revealed that each stage of the vermicomposting process possessed its own unique microbiome. Predictions based on the OTUs present by PICRUSt suggested a functional shift in the microbiome during vermicomposting. Enzymes and pathways of lipid and lignin metabolism were predicted to be initially abundant, but by the end of the process, biosynthesis of secondary metabolites and plant beneficial properties were enriched. The study revealed that bacterial communities undergo a continuous change throughout the vermicomposting process and that certain OTUs associated with specific stages could be targets for further improvements in the process.},
}

Animals
Bacteria/classification/genetics
Bacterial Proteins/metabolism
*Biodiversity
*Cocos
*Composting
DNA, Bacterial/genetics
Metagenomics/methods
*Microbiota
Oligochaeta/*metabolism/microbiology
Plant Leaves/*metabolism
RNA, Ribosomal, 16S/genetics
Reproducibility of Results
Soil/chemistry
*Soil Microbiology

@article {pmid29540507,
year = {2018},
author = {Succurro, A and Ebenhöh, O},
title = {Review and perspective on mathematical modeling of microbial ecosystems.},
journal = {Biochemical Society transactions},
volume = {46},
number = {2},
pages = {403-412},
doi = {10.1042/BST20170265},
pmid = {29540507},
issn = {1470-8752},
mesh = {*Ecosystem ; Metagenomics ; *Microbiota ; *Models, Biological ; },
abstract = {Understanding microbial ecosystems means unlocking the path toward a deeper knowledge of the fundamental mechanisms of life. Engineered microbial communities are also extremely relevant to tackling some of today's grand societal challenges. Advanced meta-omics experimental techniques provide crucial insights into microbial communities, but have been so far mostly used for descriptive, exploratory approaches to answer the initial 'who is there?'

QUESTION: An ecosystem is a complex network of dynamic spatio-temporal interactions among organisms as well as between organisms and the environment. Mathematical models with their abstraction capability are essential to capture the underlying phenomena and connect the different scales at which these systems act. Differential equation models and constraint-based stoichiometric models are deterministic approaches that can successfully provide a macroscopic description of the outcome from microscopic behaviors. In this mini-review, we present classical and recent applications of these modeling methods and illustrate the potential of their integration. Indeed, approaches that can capture multiple scales are needed in order to understand emergent patterns in ecosystems and their dynamics regulated by different spatio-temporal phenomena. We finally discuss promising examples of methods proposing the integration of differential equations with constraint-based stoichiometric models and argue that more work is needed in this direction.},
}

*Ecosystem
Metagenomics
*Microbiota
*Models, Biological

@article {pmid30242595,
year = {2018},
author = {Hemmat-Jou, MH and Safari-Sinegani, AA and Mirzaie-Asl, A and Tahmourespour, A},
title = {Analysis of microbial communities in heavy metals-contaminated soils using the metagenomic approach.},
journal = {Ecotoxicology (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10646-018-1981-x},
pmid = {30242595},
issn = {1573-3017},
abstract = {Soil pollution occurring at mining sites has adverse impacts on soil microbial diversity. New approaches, such as metagenomics approach, have become a powerful tool to investigate biodiversity of soil microbial communities. In the current study, metagenomics approach was used to investigate the microbial diversity of soils contaminated with different concentrations of lead (Pb) and zinc (Zn). The contaminated soils were collected from a Pb and Zn mine. The soil total DNA was extracted and 16S rDNA genes were amplified using universal primers. The PCR amplicons were sequenced and bioinformatic analysis of metagenomes was conducted to identify prokaryotic diversity in the Pb- and Zn-contaminated soils. The results indicated that the ten most abundant bacteria in all samples were Solirubrobacter (Actinobacteria), Geobacter (Proteobacteria), Edaphobacter (Acidobacteria), Pseudomonas (Proteobacteria), Gemmatiomonas (Gemmatimonadetes), Nitrosomonas, Xanthobacter, and Sphingomonas (Proteobacteria), Pedobacter (Bacterioidetes), and Ktedonobacter (Chloroflexi), descendingly. Archaea were also numerous, and Nitrososphaerales which are important in the nitrogen cycle had the highest abundance in the samples. Although, alpha and beta diversity showed negative effects of Pb and Zn contamination on soil microbial communities, microbial diversity of the contaminated soils was not subjected to a significant change. This study provided valuable insights into microbial composition in heavy metals-contaminated soils.},
}

@article {pmid30240114,
year = {2018},
author = {Bergner, LM and Orton, RJ and da Silva Filipe, A and Shaw, AE and Becker, DJ and Tello, C and Biek, R and Streicker, DG},
title = {Using non-invasive metagenomics to characterize viral communities from wildlife.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.12946},
pmid = {30240114},
issn = {1755-0998},
abstract = {Microbial communities play an important role in organismal and ecosystem health. While high throughput metabarcoding has revolutionized the study of bacterial communities, generating comparable viral communities has proven elusive, particularly in wildlife samples where the diversity of viruses present and limited quantities of viral nucleic acid present distinctive challenges. Metagenomic sequencing is a promising solution for studying viral communities, but the lack of standardized methods currently precludes comparisons across host taxa or localities. Here we developed an untargeted shotgun metagenomic sequencing protocol to generate comparable viral communities from non-invasively collected fecal and oropharyngeal swabs. Using samples from common vampire bats (Desmodus rotundus), a key species for virus transmission to humans and domestic animals, we tested how different storage media, nucleic acid extraction procedures and enrichment steps affect viral community detection. Based on finding viral contamination in fetal bovine serum, we recommend storing swabs in RNALater or another non-biological medium. We recommend extracting nucleic acid directly from swabs rather than from supernatant or pelleted material, which had undetectable levels of viral RNA. Results from a low-input RNA library preparation protocol suggest that ribosomal RNA depletion and light DNAse treatment reduce host and bacterial nucleic acid, and improve virus detection. Finally, applying our approach to twelve pooled samples from seven localities in Peru, we showed that detected viral communities saturated at the attained sequencing depth, allowing unbiased comparisons of viral community composition. Future studies using the methods outlined here will elucidate the determinants of viral communities across host species, environments and time. This article is protected by copyright. All rights reserved.},
}

@article {pmid30231921,
year = {2018},
author = {Vavourakis, CD and Andrei, AS and Mehrshad, M and Ghai, R and Sorokin, DY and Muyzer, G},
title = {A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {168},
doi = {10.1186/s40168-018-0548-7},
pmid = {30231921},
issn = {2049-2618},
support = {322551//European Research Council/International ; 322551//European Research Council/International ; L200961651//Czech Academy of Science/ ; 16-14-00121//Russian Science Support Foundation/ ; 24002002//Dutch Ministry of Education and Science/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; 17-04828S//Grant Agency of the Czech Republic/ ; 17-04828S//Grant Agency of the Czech Republic/ ; },
abstract = {BACKGROUND: Hypersaline soda lakes are characterized by extreme high soluble carbonate alkalinity. Despite the high pH and salt content, highly diverse microbial communities are known to be present in soda lake brines but the microbiome of soda lake sediments received much less attention of microbiologists. Here, we performed metagenomic sequencing on soda lake sediments to give the first extensive overview of the taxonomic diversity found in these complex, extreme environments and to gain novel physiological insights into the most abundant, uncultured prokaryote lineages.

RESULTS: We sequenced five metagenomes obtained from four surface sediments of Siberian soda lakes with a pH 10 and a salt content between 70 and 400 g L-1. The recovered 16S rRNA gene sequences were mostly from Bacteria, even in the salt-saturated lakes. Most OTUs were assigned to uncultured families. We reconstructed 871 metagenome-assembled genomes (MAGs) spanning more than 45 phyla and discovered the first extremophilic members of the Candidate Phyla Radiation (CPR). Five new species of CPR were among the most dominant community members. Novel dominant lineages were found within previously well-characterized functional groups involved in carbon, sulfur, and nitrogen cycling. Moreover, key enzymes of the Wood-Ljungdahl pathway were encoded within at least four bacterial phyla never previously associated with this ancient anaerobic pathway for carbon fixation and dissimilation, including the Actinobacteria.

CONCLUSIONS: Our first sequencing effort of hypersaline soda lake sediment metagenomes led to two important advances. First, we showed the existence and obtained the first genomes of haloalkaliphilic members of the CPR and several hundred other novel prokaryote lineages. The soda lake CPR is a functionally diverse group, but the most abundant organisms in this study are likely fermenters with a possible role in primary carbon degradation. Second, we found evidence for the presence of the Wood-Ljungdahl pathway in many more taxonomic groups than those encompassing known homo-acetogens, sulfate-reducers, and methanogens. Since only few environmental metagenomics studies have targeted sediment microbial communities and never to this extent, we expect that our findings are relevant not only for the understanding of haloalkaline environments but can also be used to set targets for future studies on marine and freshwater sediments.},
}

@article {pmid29180750,
year = {2017},
author = {Brooks, B and Olm, MR and Firek, BA and Baker, R and Thomas, BC and Morowitz, MJ and Banfield, JF},
title = {Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome.},
journal = {Nature communications},
volume = {8},
number = {1},
pages = {1814},
doi = {10.1038/s41467-017-02018-w},
pmid = {29180750},
issn = {2041-1723},
support = {R01 AI092531/AI/NIAID NIH HHS/United States ; S10 OD018174/OD/NIH HHS/United States ; },
mesh = {Cross Infection/*microbiology ; Environmental Exposure ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/microbiology/*physiology ; Humans ; Infant ; Infant, Newborn ; Infant, Premature/*physiology ; *Intensive Care Units, Neonatal ; Metagenomics/methods ; },
abstract = {Preterm infants exhibit different microbiome colonization patterns relative to full-term infants, and it is speculated that the hospital room environment may contribute to infant microbiome development. Here, we present a genome-resolved metagenomic study of microbial genotypes from the gastrointestinal tracts of infants and from the neonatal intensive care unit (NICU) room environment. Some strains detected in hospitalized infants also occur in sinks and on surfaces, and belong to species such as Staphylococcus epidermidis, Enterococcus faecalis, Pseudomonas aeruginosa, and Klebsiella pneumoniae, which are frequently implicated in nosocomial infection and preterm infant gut colonization. Of the 15 K. pneumoniae strains detected in the study, four were detected in both infant gut and room samples. Time series experiments showed that nearly all strains associated with infant gut colonization can be detected in the room after, and often before, detection in the gut. Thus, we conclude that a component of premature infant gut colonization is the cycle of microbial exchange between the room and the occupant.},
}

Cross Infection/*microbiology
Environmental Exposure
Feces/microbiology
Female
Gastrointestinal Microbiome/*genetics
Gastrointestinal Tract/microbiology/*physiology
Humans
Infant
Infant, Newborn
Infant, Premature/*physiology
*Intensive Care Units, Neonatal
Metagenomics/methods

@article {pmid29404836,
year = {2018},
author = {Boers, SA and de Zeeuw, M and Jansen, R and van der Schroeff, MP and van Rossum, AMC and Hays, JP and Verhaegh, SJC},
title = {Characterization of the nasopharyngeal and middle ear microbiota in gastroesophageal reflux-prone versus gastroesophageal reflux non-prone children.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {37},
number = {5},
pages = {851-857},
doi = {10.1007/s10096-017-3178-2},
pmid = {29404836},
issn = {1435-4373},
mesh = {Bacterial Typing Techniques ; Biodiversity ; Child ; Child, Preschool ; Ear, Middle/*microbiology ; Female ; Gastroesophageal Reflux/*complications ; Humans ; Infant ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Nasopharyngitis/diagnosis/*etiology ; Nasopharynx/*microbiology ; Otitis Media/diagnosis/*etiology ; RNA, Ribosomal, 16S ; },
abstract = {Otitis media (OM) is one of the most common pediatric infections worldwide, but the complex microbiology associated with OM is poorly understood. Previous studies have shown an association between OM and gastroesophageal reflux (GER) in children. Therefore, in order to bridge the gap in our current understanding of the interaction between GER and OM, we investigated the nasopharyngeal and middle ear microbiota of children suffering from GER-associated OM and OM only, using culture-independent 16S rRNA gene sequencing. Middle ear fluid, nasopharyngeal swabs, and clinical data were collected as part of a prospective pilot study conducted at the Department of Otorhinolaryngology of the Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands. A total of 30 children up to 12 years of age who suffered from recurrent acute otitis media (AOM) (5), chronic otitis media with effusion (OME) (23), or both (2), and who were listed for tympanostomy tube placement, were included in the study. Nine children were included in the GER-associated OM cohort and 21 in the OM-only cohort. We found no obvious effect of GER on the nasopharyngeal and middle ear microbiota between the two groups of children. However, our results highlight the need to assess the true role of Alloiococcus spp. and Turicella spp. in children presenting with a high prevalence of recurrent AOM and chronic OME.},
}

Bacterial Typing Techniques
Biodiversity
Child
Child, Preschool
Ear, Middle/*microbiology
Female
Gastroesophageal Reflux/*complications
Humans
Infant
Male
Metagenome
Metagenomics/methods
*Microbiota
Nasopharyngitis/diagnosis/*etiology
Nasopharynx/*microbiology
Otitis Media/diagnosis/*etiology
RNA, Ribosomal, 16S