Sequencing and Understanding 16s analysis with MR DNA

How To sequence the 16s and ITS fungal gene affordably  MR DNA 16s sequencing microbiome and metagenome low prices

16s rRNA Sequencing with MR DNA

16S ribosomal  (rRNA) sequencing using next generation sequencing is a method used to identify and compare bacteria and archaea present within almost any type of sample. 16S rRNA gene sequencing is a well-established method for studying phylogeny and taxonomy of samples from complex microbiomes or environments that are difficult or impossible to study.

 

 

 

 

16s sequencing illumina or PGM low cost prices with MR DNA

MR DNA is a next generation sequencing provider with low cost 16s sequencing services.

 

 

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Select item 27585943

 

21.

Clin Microbiol Infect. 2016 Aug 29. pii: S1198-743X(16)30330-5. doi: 10.1016/j.cmi.2016.08.010. [Epub ahead of print]

Outbreak investigation for toxigenic Corynebacterium diphtheriae wound infections in refugees from Northeast Africa and Syria in Switzerland and Germany by whole genome sequencing.

Meinel DM1, Kuehl R2, Zbinden R3, Boskova V4, Garzoni C5, Fadini D6, Dolina M7, Blümel B8, Weibel T9, Tschudin-Sutter S2, Widmer AF2, Bielicki JA10, Dierig A10, Heininger U10, Konrad R11, Berger A11, Hinic V12, Goldenberger D12, Blaich A12, Stadler T4, Battegay M13, Sing A11, Egli A14.

Author information

 

 

Abstract

OBJECTIVES:

Toxigenic Corynebacterium diphtheriae is an important and potential fatal threat to patients and public health. During the current dramatic influx of refugees in Europe, our objective was to use whole genome sequencing for the characterisation of a suspected outbreak of C. diphtheriae wound infections among refugees.

METHODS:

After conventional culture, we identified C. diphtheriae using MALDI-TOF mass-spectrometry and investigated toxigenicity by PCR. Whole genome sequencing was performed on a MiSeq Illumina with >70x coverage, 2x250bp read length, and mapping against a reference genome.

RESULTS:

Twenty cases of cutaneous C. diphtheriae in refugees from East African countries and Syria identified between April and August 2015 were included. Patients presented with wound infections shortly after arrival in Switzerland and Germany. Toxin production was detected in 9/20 (45%) isolates. Whole genome sequencing-based typing revealed relatedness between isolates using Neighbour joining algorithms. We detected three separate clusters among epidemiologically related refugees. Although the isolates within a cluster showed strong relatedness, isolates differed by >50 nucleotide polymorphisms.

CONCLUSIONS:

Toxigenic C. diphtheriae associated wound infections are currently observed more frequently in Europe, due to refugees travelling under poor hygienic conditions. Close genetic relatedness of C. diphtheriae isolates from 20 refugees with wound infections indicates likely transmission between patients. However, the diversity within each cluster and phylogenetic time-tree analysis suggest that transmissions happened several months ago, most likely outside Europe. Whole genome sequencing offers the potential to describe outbreaks in very high resolution and is a helpful tool in infection tracking and identification of transmission routes.

Copyright © 2016. Published by Elsevier Ltd.

KEYWORDS:

Corynebacterium diphtheriae; emerging diseases; outbreak investigation; refugee; toxin-production; typing; whole genome sequencing

PMID: 27585943 DOI: 10.1016/j.cmi.2016.08.010

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Select item 27585642

 

22.

Mod Rheumatol. 2016 Sep 1:1-7. [Epub ahead of print]

Genome-wide DNA methylation patterns in CD4+ T cells from Chinese Han patients with rheumatoid arthritis.

Guo S1, Zhu Q1, Jiang T1,2, Wang R1,2, Shen Y1,2, Zhu X3, Wang Y1, Bai F1,2, Ding Q1,2, Zhou X4, Chen G5, He DY1,2.

Author information

 

 

Abstract

INTRODUCTION:

Rheumatoid arthritis (RA) is an autoimmune disease that causes chronic inflammation of the joints. Recent evidence indicated the epigenetic changes may contribute to the pathogenesis of RA.

METHOD:

To understand the extent and nature of dysregulated DNA methylation in RA CD4T cells, we performed a genome-wide DNA methylation study in CD4 + T cells in 12 RA patients compared to 12 matched normal healthy controls. Cytosine methylation status was quantified with Illumina methylation 450K microarray.

RESULT:

The DNA methylation profiling showed 383 hyper- and 785 hypo-methylated genes in the CD4 + T cells of the RA patients (p < 3.4 × 10-7). Gene ontology analysis indicated transcript alternative splicing and protein modification mediated by DNA methylation might play an important role in the pathogenesis of RA. In addition, the result showed that human leukocyte antigen (HLA) region including HLA-DRB6, HLA-DQA1 and HLA-E was frequently hypomethylated, but HLA-DQB1 hypermethylated in CpG island region and hypomethylated in CpG shelf region in RA patients. Outside the MHC region, HDAC4, NXN, TBCD and TMEM61 were the most hypermethylated genes, while ITIH3, TCN2, PRDM16, SLC1A5 and GALNT9 are the most hypomethylated genes.

CONCLUSION:

Genome-wide DNA methylation profile revealed significant DNA methylation change in CD4 + T cells from patients with RA.

KEYWORDS:

CD4 + T cells; DNA Methylation; Genome-wide; Illumina methylation 450k microarray; Rheumatoid arthritis

PMID: 27585642 DOI: 10.1080/14397595.2016.1218595

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Select item 27570972

 

23.

PLoS One. 2016 Aug 29;11(8):e0161008. doi: 10.1371/journal.pone.0161008. eCollection 2016.

Genomic Analyses of Cladophialophora bantiana, a Major Cause of Cerebral Phaeohyphomycosis Provides Insight into Its Lifestyle, Virulence and Adaption in Host.

Kuan CS1, Cham CY2,3, Singh G2, Yew SM1, Tan YC4, Chong PS4, Toh YF1, Atiya N1, Na SL1, Lee KW4, Hoh CC4, Yee WY4, Ng KP1.

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Abstract

Cladophialophora bantiana is a dematiaceous fungus with a predilection for causing central nervous system (CNS) infection manifesting as brain abscess in both immunocompetent and immunocompromised patients. In this paper, we report comprehensive genomic analyses of C. bantiana isolated from the brain abscess of an immunocompetent man, the first reported case in Malaysia and Southeast Asia. The identity of the fungus was determined using combined morphological analysis and multilocus phylogeny. The draft genome sequence of a neurotrophic fungus, C. bantiana UM 956 was generated using Illumina sequencing technology to dissect its genetic fundamental and basic biology. The assembled 37.1 Mb genome encodes 12,155 putative coding genes, of which, 1.01% are predicted transposable elements. Its genomic features support its saprophytic lifestyle, renowned for its versatility in decomposing hemicellulose and pectin components. The C. bantiana UM 956 was also found to carry some important putative genes that engaged in pathogenicity, iron uptake and homeostasis as well as adaptation to various stresses to enable the organism to survive in hostile microenvironment. This wealth of resource will further catalyse more downstream functional studies to provide better understanding on how this fungus can be a successful and persistent pathogen in human.

PMID: 27570972 PMCID: PMC5003357 DOI: 10.1371/journal.pone.0161008

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Select item 27558013

 

24.

HLA. 2016 Sep;88(3):87-99. doi: 10.1111/tan.12852. Epub 2016 Aug 24.

HLA class I variation in Iranian Lur and Kurd populations: high haplotype and allotype diversity with an abundance of KIR ligands.

Ashouri E1,2,3, Norman PJ1,2, Guethlein LA1,2, Han AS1,2, Nemat-Gorgani N1,2, Norberg SJ4, Ghaderi A5, Parham P1,2.

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Abstract

HLA-A, -B and -C alleles of 285 individuals, representing three Iranian Lur populations and one Iranian Kurd population were sequenced completely, yielding human leukocyte antigen (HLA) class I genotypes at high resolution and filling four fields of the official HLA nomenclature. Each population has 87-99 alleles, evenly distributed between the three HLA class I genes, 145 alleles being identified in total. These alleles were already known, named and deposited in the HLA database. The alleles form 316 different HLA A-B-C haplotypes, with each population having between 80 and 112 haplotypes. The four Iranian populations form a related group that is distinguished from other populations, including other Iranians. All four KIR ligands - the A3/11, Bw4, C1 and C2 epitopes - are well represented, particularly Bw4, which is carried by three high-frequency allotypes: HLA-A*24:02, HLA-A*32:01 and HLA-B*51:01. In the Lur and Kurd populations, between 82% and 94% of individuals have the Bw4 epitope, the ligand for KIR3DL1. HLA-B*51:01 is likely of Neandertal origin and associated with Behcet's disease, also known as the Silk Road disease. The Lordegan Lur have the highest frequency of HLA-B*51:01 in the world. This allele is present on 46 Lur and Kurd haplotypes. Present at lower frequency is HLA-B*51:08, which is also associated with Behcet's disease. In the four Iranian populations, 31 haplotypes encode both Bw4(+) HLA-A and Bw4(+) HLA-B, a dual combination of Bw4 epitopes that is relatively rare in other populations, worldwide. This study both demonstrates and emphasizes the value of studying HLA class I polymorphism at highest resolution in anthropologically well-defined populations.

© 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

KEYWORDS:

Bw4 epitope; HLA class I polymorphism; HLA-B*51:01; Lur and Kurd populations; high-throughput sequencing

PMID: 27558013 DOI: 10.1111/tan.12852

[PubMed - in process]

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24.

PLoS One. 2016 Apr 7;11(4):e0153215. doi: 10.1371/journal.pone.0153215. eCollection 2016.

Age-Related Differences in the Gastrointestinal Microbiota of Chinstrap Penguins (Pygoscelis antarctica).

Barbosa A1, Balagué V2, Valera F3, Martínez A4, Benzal J3, Motas M5, Diaz JI6, Mira A7, Pedrós-Alió C2.

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Abstract

The gastrointestinal tract microbiota is known to play very important roles in the well being of animals. It is a complex community composed by hundreds of microbial species interacting closely among them and with their host, that is, a microbial ecosystem. The development of high throughput sequencing techniques allows studying the diversity of such communities in a realistic way and considerable work has been carried out in mammals and some birds such as chickens. Wild birds have received less attention and in particular, in the case of penguins, only a few individuals of five species have been examined with molecular techniques. We collected cloacal samples from Chinstrap penguins in the Vapour Col rookery in Deception Island, Antarctica, and carried out pyrosequencing of the V1-V3 region of the 16S rDNA in samples from 53 individuals, 27 adults and 26 chicks. This provided the first description of the Chinstrap penguin gastrointestinal tract microbiota and the most extensive in any penguin species. Firmicutes, Bacteoridetes, Proteobacteria, Fusobacteria, Actinobacteria, and Tenericutes were the main components. There were large differences between chicks and adults. The former had more Firmicutes and the latter more Bacteroidetes and Proteobacteria. In addition, adults had richer and more diverse bacterial communities than chicks. These differences were also observed between parents and their offspring. On the other hand, nests explained differences in bacterial communities only among chicks. We suggest that environmental factors have a higher importance than genetic factors in the microbiota composition of chicks. The results also showed surprisingly large differences in community composition with other Antarctic penguins including the congeneric Adélie and Gentoo penguins.

PMID: 27055030 PMCID: PMC4824521 DOI: 10.1371/journal.pone.0153215

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Select item 27052710

 

25.

Food Microbiol. 2016 Aug;57:116-27. doi: 10.1016/j.fm.2016.02.004. Epub 2016 Feb 18.

Metagenomic analysis of a Mexican ripened cheese reveals a unique complex microbiota.

Escobar-Zepeda A1, Sanchez-Flores A2, Quirasco Baruch M3.

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Abstract

Cotija cheese is a Mexican handcrafted product made from raw cow milk whose ripening process occurs spontaneously and, presumably, it is influenced by environmental conditions. Its sensory characteristics and safety are probably the result of the balance between microbial populations and their metabolic capacity. In this work, we studied the dominance and richness of the bacteria in the Cotija cheese microbiome, as well as their metabolic potential by high-throughput sequencing. By the analysis of 16S ribosomal sequences, it was found that this metagenome is composed mainly of three dominant genera: Lactobacillus, Leuconostoc and Weissella, and more than 500 of non-dominant genera grouped in 31 phyla of both bacteria and archaea. The analysis of single-copy marker genes reported a similar result for dominant genera, although with greater resolution that reached the species level. Pathogenic bacteria such as Salmonella, Listeria monocytogenes, Brucella or Mycobacterium were not found. The Cotija cheese microbiome has the metabolic capacity for the synthesis of a wide range of flavor compounds, mainly involved with the metabolism of branched chain amino acids and free fatty acids. Genes associated with bacteriocin production and immunity were also found. Arguably, this is one of the most diverse metagenomes among the microbial communities related to fermented products.

Copyright © 2016 Elsevier Ltd. All rights reserved.

KEYWORDS:

Bacteriocins; Fermented food metagenomics; High-throughput sequencing; Lactic acid bacteria; Raw-milk ripened cheese

PMID: 27052710 DOI: 10.1016/j.fm.2016.02.004

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Select item 27048805

 

26.

MBio. 2016 Apr 5;7(2):e02234-15. doi: 10.1128/mBio.02234-15.

Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community.

Hemme CL1, Green SJ2, Rishishwar L3, Prakash O4, Pettenato A5, Chakraborty R5, Deutschbauer AM6, Van Nostrand JD7, Wu L7, He Z7, Jordan IK8, Hazen TC9, Arkin AP10, Kostka JE3, Zhou J11.

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Abstract

Unraveling the drivers controlling the response and adaptation of biological communities to environmental change, especially anthropogenic activities, is a central but poorly understood issue in ecology and evolution. Comparative genomics studies suggest that lateral gene transfer (LGT) is a major force driving microbial genome evolution, but its role in the evolution of microbial communities remains elusive. To delineate the importance of LGT in mediating the response of a groundwater microbial community to heavy metal contamination, representative Rhodanobacter reference genomes were sequenced and compared to shotgun metagenome sequences. 16S rRNA gene-based amplicon sequence analysis indicated that Rhodanobacter populations were highly abundant in contaminated wells with low pHs and high levels of nitrate and heavy metals but remained rare in the uncontaminated wells. Sequence comparisons revealed that multiple geochemically important genes, including genes encoding Fe(2+)/Pb(2+) permeases, most denitrification enzymes, and cytochrome c553, were native to Rhodanobacter and not subjected to LGT. In contrast, the Rhodanobacter pangenome contained a recombinational hot spot in which numerous metal resistance genes were subjected to LGT and/or duplication. In particular, Co(2+)/Zn(2+)/Cd(2+) efflux and mercuric resistance operon genes appeared to be highly mobile within Rhodanobacter populations. Evidence of multiple duplications of a mercuric resistance operon common to most Rhodanobacter strains was also observed. Collectively, our analyses indicated the importance of LGT during the evolution of groundwater microbial communities in response to heavy metal contamination, and a conceptual model was developed to display such adaptive evolutionary processes for explaining the extreme dominance of Rhodanobacter populations in the contaminated groundwater microbiome.

IMPORTANCE:

Lateral gene transfer (LGT), along with positive selection and gene duplication, are the three main mechanisms that drive adaptive evolution of microbial genomes and communities, but their relative importance is unclear. Some recent studies suggested that LGT is a major adaptive mechanism for microbial populations in response to changing environments, and hence, it could also be critical in shaping microbial community structure. However, direct evidence of LGT and its rates in extant natural microbial communities in response to changing environments is still lacking. Our results presented in this study provide explicit evidence that LGT played a crucial role in driving the evolution of a groundwater microbial community in response to extreme heavy metal contamination. It appears that acquisition of genes critical for survival, growth, and reproduction via LGT is the most rapid and effective way to enable microorganisms and associated microbial communities to quickly adapt to abrupt harsh environmental stresses.

Copyright © 2016 Hemme et al.

PMID: 27048805 PMCID: PMC4817265 DOI: 10.1128/mBio.02234-15

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17.

Colorectal Dis. 2016 Sep 27. doi: 10.1111/codi.13534. [Epub ahead of print]

A collaborative study of the current concepts and challenges for treatment of anastomotic leakage in colorectal surgery.

Vallance A1,2, Wexner S3, Berho M4, Cahill R5, Coleman M6, Haboubi N7, Heald RJ8, Kennedy RH9, Moran B8, Mortensen N2, Motson RW10, Novell R11, O'Connell PR5, Ris F12, Rockall T13, Senapati A14, Windsor A15, Jayne DG16.

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Abstract

The reduction of the incidence, detection, and treatment of anastomotic leakage (AL) continues to challenge the colorectal surgical community. AL is not consistently defined and reported in clinical studies, its occurrence is variably reported and its impact on long-term morbidity and healthcare resources has received relatively little attention. Controversy continues about the best strategies to reduce the risk. Diagnostic tests lack sensitivity and specificity, resulting in delayed diagnosis and increased morbidity. Intraoperative fluorescence angiography has recently been introduced as a means of real-time assessment of anastomotic perfusion with preliminary evidence suggesting that it may reduce the rate of AL. In addition, concepts are emerging about the role of the rectal mucosal microbiome in AL and the possible role of new prophylactic therapies. In January 2016 a meeting of expert colorectal surgeons and pathologists was held in London, UK to identify the ongoing controversies surrounding AL in colorectal surgery. The outcome of the meeting is presented in the form of research challenges that need to be addressed. This article is protected by copyright. All rights reserved.

This article is protected by copyright. All rights reserved.

PMID: 27671222 DOI: 10.1111/codi.13534

 

16s rRNA Sequencing with MR DNA

16S ribosomal  (rRNA) sequencing using next generation sequencing is a method used to identify and compare bacteria and archaea present within almost any type of sample. 16S rRNA gene sequencing is a well-established method for studying phylogeny and taxonomy of samples from complex microbiomes or environments that are difficult or impossible to study.

 

 

 

 

16s sequencing illumina or PGM low cost prices with MR DNA

MR DNA is a next generation sequencing provider with low cost 16s sequencing services.

Select item 27670882

 

19.

Sci Rep. 2016 Sep 27;6:33965. doi: 10.1038/srep33965.

Probiotic legacy effects on gut microbial assembly in tilapia larvae.

Giatsis C1, Sipkema D2, Ramiro-Garcia J2,3,4, Bacanu GM2, Abernathy J5, Verreth J1, Smidt H2, Verdegem M1.

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Abstract

The exposure of fish to environmental free-living microbes and its effect on early colonization in the gut have been studied in recent years. However, little is known regarding how the host and environment interact to shape gut communities during early life. Here, we tested whether the early microbial exposure of tilapia larvae affects the gut microbiota at later life stages. The experimental period was divided into three stages: axenic, probiotic and active suspension. Axenic tilapia larvae were reared either under conventional conditions (active suspension systems) or exposed to a single strain probiotic (Bacillus subtilis) added to the water. Microbial characterization by Illumina HiSeq sequencing of 16S rRNA gene amplicons showed the presence of B. subtilis in the gut during the seven days of probiotic application. Although B. subtilis was no longer detected in the guts of fish exposed to the probiotic after day 7, gut microbiota of the exposed tilapia larvae remained significantly different from that of the control treatment. Compared with the control, fish gut microbiota under probiotic treatment was less affected by spatial differences resulting from tank replication, suggesting that the early probiotic contact contributed to the subsequent observation of low inter-individual variation.

PMID: 27670882 DOI: 10.1038/srep33965

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Select item 27670644

 

20.

Mol Nutr Food Res. 2016 Sep 27. doi: 10.1002/mnfr.201600552. [Epub ahead of print]

Reduction in cardiometabolic risk factors by a multifunctional diet is mediated via several branches of metabolism as evidenced by non-targeted metabolite profiling approach.

Tovar J1, de Mello VD2, Nilsson A3, Johansson M3, Paananen J2, Lehtonen M4, Hanhineva K2, Björck I3.

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Abstract

SCOPE:

MFD, a diet based on multiple functional concepts and ingredients with antiinflammatory activity, was previously shown to improve different cardiometabolic risk-associated markers in healthy subjects. Here, we assessed the impact of MFD on plasma metabolome and explored associations of the differential metabolites with clinical parameters, searching for metabolic determinants related to the effects of MFD.

METHODS AND RESULTS:

Forty-four overweight healthy volunteers completed a randomized crossover intervention comparing MFD with a control diet devoid of the active components of MFD. Fasting plasma samples were analyzed with non-targeted metabolite profiling at baseline and at the end (4 wk) of each diet period by liquid chromatography coupled to quadrupole-time of flight-MS system, revealing a vast impact of MFD on metabolic homeostasis. Main metabolite classes affected included acylcarnitines, furan fatty acids, phospholipids (plasmalogens, phosphatidylcholines, phosphatidylethanolamines), and various low-molecular weight products from the bioactivity of gut microbiota. Circulating levels of several of these metabolites correlated with changes in clinical blood lipid biomarkers.

CONCLUSIONS:

The metabolomics approach revealed that consumption of MFD affected different areas of metabolism, highlighting the impact of a healthy diet on plasma metabolome. This seems linked to reduced cardiometabolic risk and provides mechanistic insight into the effects of MFD. This article is protected by copyright. All rights reserved.

This article is protected by copyright. All rights reserved.

KEYWORDS:

Cardiometabolic diseases; Dietary prevention; Functional foods; Metabolic syndrome; Plasma metabolomics

PMID: 27670644 DOI: 10.1002/mnfr.201600552

[PubMed - as supplied by publisher]

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16s rRNA Sequencing with MR DNA

16S ribosomal  (rRNA) sequencing using next generation sequencing is a method used to identify and compare bacteria and archaea present within almost any type of sample. 16S rRNA gene sequencing is a well-established method for studying phylogeny and taxonomy of samples from complex microbiomes or environments that are difficult or impossible to study.

 

 

 

 

16s sequencing illumina or PGM low cost prices with MR DNA

MR DNA is a next generation sequencing provider with low cost 16s sequencing services.

 

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1.
PLoS One. 2016 Sep 21;11(9):e0161836. doi: 10.1371/journal.pone.0161836.

Microbial Characterization of Qatari Barchan Sand Dunes.

Author information

  • 1Department of Research, Weill Cornell Medical Qatar, Qatar Foundation, Doha, Qatar.
  • 2Department of Microbiology, Cornell University, Ithaca, New York, United States of America.
  • 3Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York, United States of America.
  • 4Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America.

Abstract

This study represents the first characterization of sand microbiota in migrating barchan sand dunes. Bacterial communities were studied through direct counts and cultivation, as well as 16S rRNA gene and metagenomic sequence analysis to gain an understanding of microbial abundance, diversity, and potential metabolic capabilities. Direct on-grain cell counts gave an average of 5.3 ± 0.4 x 105 cells g-1 of sand. Cultured isolates (N = 64) selected for 16S rRNA gene sequencing belonged to the phyla Actinobacteria (58%), Firmicutes (27%) and Proteobacteria (15%). Deep-sequencing of 16S rRNA gene amplicons from 18 dunes demonstrated a high relative abundance of Proteobacteria, particularly enteric bacteria, and a dune-specific-pattern of bacterial community composition that correlated with dune size. Shotgun metagenome sequences of two representative dunes were analyzed and found to have similar relative bacterial abundance, though the relative abundances of eukaryotic, viral and enterobacterial sequences were greater in sand from the dune closer to a camel-pen. Functional analysis revealed patterns similar to those observed in desert soils; however, the increased relative abundance of genes encoding sporulation and dormancy are consistent with the dune microbiome being well-adapted to the exceptionally hyper-arid Qatari desert.

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2.
Hepatology. 2016 Sep 17. doi: 10.1002/hep.28829. [Epub ahead of print]

Changes in blood microbiota profiles associated with liver fibrosis in obese patients: A pilot analysis.

Author information

  • 1Vaiomer SAS, Labège, France. benjamin.lelouvier@vaiomer.com.
  • 2Vaiomer SAS, Labège, France.
  • 3IMT, Université Paul Sabatier, Toulouse, France.
  • 4INSERM U1048, I2MC, Toulouse, France.
  • 5Department of Diabetes, Endocrinology, and Nutrition, IDIBGI, Girona, Spain.
  • 6Department of Radiology, IDI, IDIBGI, Girona, Spain.
  • 7Department of Systems Medicine and Center for Atherosclerosis, University of Rome "Tor Vergata", Rome, Italy.
  • 8Vaiomer SAS, Labège, France. amar.j@chu-toulouse.fr.
  • 9INSERM U1048, I2MC, Toulouse, France. amar.j@chu-toulouse.fr.
  • 10Department of Therapeutics, Rangueil Hospital, Toulouse, France. amar.j@chu-toulouse.fr.

Abstract

OBJECTIVE:

The early detection of liver fibrosis among patients with nonalcoholic fatty liver disease (NAFLD) is an important clinical need. In view of the suggested role played by bacterial translocation in liver disease and obesity, we sought to investigate the relationship between blood microbiota and liver fibrosis in European cohorts of patients with severe obesity.

DESIGN:

We carried out a cross-sectional study of obese patients, well-characterized with respect to the severity of the NAFLD, in the cohort FLORINASH. This cohort has been divided into a discovery cohort comprising 50 Spanish patients and then in a validation cohort of 71 Italian patients. Blood bacterial DNA was analyzed both quantitatively by 16S rDNA qPCR and qualitatively by 16S rDNA targeted metagenomic sequencing and functional metagenome prediction. Spanish plasma bile acid contents were analyzed by LC/MS.

RESULTS:

The 16S rDNA concentration was significantly higher in patients of the discovery cohort with liver fibrosis. By 16S sequencing, we found specific differences in the proportion of several bacterial taxa in both blood and feces that correlate with the presence of liver fibrosis thus defining a specific signature of the liver disease. Several secondary/primary bile acids ratios were also decreased with liver fibrosis in the discovery cohort. We confirmed in the validation cohort the correlation between blood 16S rDNA concentration and liver fibrosis whereas we did not confirm the specific bacterial taxa signature, despite a similar trend in patients with more severe fibrosis.

CONCLUSIONS:

We have shown that changes in blood microbiota are associated with liver fibrosis in obese patients. Blood microbiota analysis provides potential biomarkers for the detection of liver fibrosis in this population. This article is protected by copyright. All rights reserved.

© 2016 by the American Association for the Study of Liver Diseases.

KEYWORDS:

16S metagenomic sequencing; bile acids; biomarker; tissue microbiota

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3.
Front Microbiol. 2016 Aug 25;7:1341. doi: 10.3389/fmicb.2016.01341. eCollection 2016.

Bacterial Abilities and Adaptation Toward the Rhizosphere Colonization.

Author information

  • 1Soil Microbiology Lab, Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo Piracicaba, Brazil.

Abstract

The rhizosphere harbors one of the most complex, diverse, and active plant-associated microbial communities. This community can be recruited by the plant host to either supply it with nutrients or to help in the survival under stressful conditions. Although selection for the rhizosphere community is evident, the specific bacterial traits that make them able to colonize this environment are still poorly understood. Thus, here we used a combination of community level physiological profile (CLPP) analysis and 16S rRNA gene quantification and sequencing (coupled with in silico analysis and metagenome prediction), to get insights on bacterial features and processes involved in rhizosphere colonization of sugarcane. CLPP revealed a higher metabolic activity in the rhizosphere compared to bulk soil, and suggested that D-galacturonic acid plays a role in bacterial selection by the plant roots (supported by results of metagenome prediction). Quantification of the 16S rRNA gene confirmed the higher abundance of bacteria in the rhizosphere. Sequence analysis showed that of the 252 classified families sampled, 24 were significantly more abundant in the bulk soil and 29 were more abundant in the rhizosphere. Furthermore, metagenomes predicted from the 16S rRNA gene sequences revealed a significant higher abundance of predicted genes associated with biofilm formation and with horizontal gene transfer (HGT) processes. In sum, this study identified major bacterial groups and their potential abilities to occupy the sugarcane rhizosphere, and indicated that polygalacturonase activity and HGT events may be important features for rhizosphere colonization.

KEYWORDS:

horizontal gene transfer; metagenome prediction; microbiome; plant selection; sugarcane

4.
Environ Sci Technol. 2016 Sep 20;50(18):9807-15. doi: 10.1021/acs.est.6b00262. Epub 2016 Sep 7.

Antimicrobial Chemicals Are Associated with Elevated Antibiotic Resistance Genes in the Indoor Dust Microbiome.

Author information

  • 1Department of Biostatistics, Harvard T.H. Chan School of Public Health , Boston, Massachusetts 02115, United States.
  • 2Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States.
  • 3Biodesign Center for Environmental Security and Global Security Initiative, The Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States.

Abstract

Antibiotic resistance is increasingly widespread, largely due to human influence. Here, we explore the relationship between antibiotic resistance genes and the antimicrobial chemicals triclosan, triclocarban, and methyl-, ethyl-, propyl-, and butylparaben in the dust microbiome. Dust samples from a mixed-use athletic and educational facility were subjected to microbial and chemical analyses using a combination of 16S rRNA amplicon sequencing, shotgun metagenome sequencing, and liquid chromatography tandem mass spectrometry. The dust resistome was characterized by identifying antibiotic resistance genes annotated in the Comprehensive Antibiotic Resistance Database (CARD) from the metagenomes of each sample using the Short, Better Representative Extract Data set (ShortBRED). The three most highly abundant antibiotic resistance genes were tet(W), blaSRT-1, and erm(B). The complete dust resistome was then compared against the measured concentrations of antimicrobial chemicals, which for triclosan ranged from 0.5 to 1970 ng/g dust. We observed six significant positive associations between the concentration of an antimicrobial chemical and the relative abundance of an antibiotic resistance gene, including one between the ubiquitous antimicrobial triclosan and erm(X), a 23S rRNA methyltransferase implicated in resistance to several antibiotics. This study is the first to look for an association between antibiotic resistance genes and antimicrobial chemicals in dust.

5.
FEMS Microbiol Ecol. 2016 Nov;92(11). pii: fiw182. doi: 10.1093/femsec/fiw182. Epub 2016 Aug 23.

Taxonomic and predicted metabolic profiles of the human gut microbiome in pre-Columbian mummies.

Author information

  • 1Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA Department of Biology, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
  • 2Department of Translational Research on New Technologies in Medicine and Surgery, Division of Paleopathology, University of Pisa, Pisa 56126, Italy Center for Anthropological, Paleopathological and Historical Studies of the Sardinian and Mediterranean Populations, Department of Biomedical Sciences, University of Sassari, Sassari 07100, Italy.
  • 3Laboratory of Molecular Archaeo-Anthropology/ancient DNA, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino 62032, Italy.
  • 4Molecular Research LP (MR DNA), Shallowater, Texas 79363, USA.
  • 5Department of Biology, University of Puerto Rico, Julio Garcia Diaz Building, San Juan 00931, Puerto Rico.
  • 6Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA Department of Biology, California Polytechnic State University, San Luis Obispo, CA 93407, USA rcano@calpoly.edu.

Abstract

Characterization of naturally mummified human gut remains could potentially provide insights into the preservation and evolution of commensal and pathogenic microorganisms, and metabolic profiles. We characterized the gut microbiome of two pre-Columbian Andean mummies dating to the 10-15th centuries using 16S rRNA gene high-throughput sequencing and metagenomics, and compared them to a previously characterized gut microbiome of an 11th century AD pre-Columbian Andean mummy. Our previous study showed that the Clostridiales represented the majority of the bacterial communities in the mummified gut remains, but that other microbial communities were also preserved during the process of natural mummification, as shown with the metagenomics analyses. The gut microbiome of the other two mummies were mainly comprised by Clostridiales or Bacillales, as demonstrated with 16S rRNA gene amplicon sequencing, many of which are facultative anaerobes, possibly consistent with the process of natural mummification requiring low oxygen levels. Metagenome analyses showed the presence of other microbial groups that were positively or negatively correlated with specific metabolic profiles. The presence of sequences similar to both Trypanosoma cruzi and Leishmania donovani could suggest that these pathogens were prevalent in pre-Columbian individuals. Taxonomic and functional profiling of mummified human gut remains will aid in the understanding of the microbial ecology of the process of natural mummification.

© FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

KEYWORDS:

Chagas’ disease; Firmicutes; ancient gut microbiomes; leishmaniasis; mummies

[PubMed - in process]
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6.
Biotechnol Biofuels. 2016 Aug 11;9:171. doi: 10.1186/s13068-016-0581-3. eCollection 2016.

Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates.

Author information

  • 1Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany.
  • 2Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany.
  • 3Institute of Microbiology and Wine Research, Johannes Gutenberg-University, Becherweg 15, 55128 Mainz, Germany.
  • 4Dept. Bioengineering, Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V. (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany.
  • 5Faculty Life Sciences/Research Center ''Biomass Utilization Hamburg', University of Applied Sciences Hamburg (HAW), Ulmenliet 20, 21033 Hamburg-Bergedorf, Germany.
  • 6RIPAC-LABOR GmbH, Am Mühlenberg 11, 14476 Potsdam-Golm, Germany.
  • 7Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany ; Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
  • 8Department of Bioinformatics and Systems Biology, Justus-Liebig University Gießen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany.

Abstract

BACKGROUND:

One of the most promising technologies to sustainably produce energy and to mitigate greenhouse gas emissions from combustion of fossil energy carriers is the anaerobic digestion and biomethanation of organic raw material and waste towards biogas by highly diverse microbial consortia. In this context, the microbial systems ecology of thermophilic industrial-scale biogas plants is poorly understood.

RESULTS:

The microbial community structure of an exemplary thermophilic biogas plant was analyzed by a comprehensive approach comprising the analysis of the microbial metagenome and metatranscriptome complemented by the cultivation of hydrolytic and acido-/acetogenic Bacteria as well as methanogenic Archaea. Analysis of metagenome-derived 16S rRNA gene sequences revealed that the bacterial genera Defluviitoga (5.5 %), Halocella (3.5 %), Clostridium sensu stricto (1.9 %), Clostridium cluster III (1.5 %), and Tepidimicrobium (0.7 %) were most abundant. Among the Archaea, Methanoculleus (2.8 %) and Methanothermobacter (0.8 %) were predominant. As revealed by a metatranscriptomic 16S rRNA analysis, Defluviitoga (9.2 %), Clostridium cluster III (4.8 %), and Tepidanaerobacter (1.1 %) as well as Methanoculleus (5.7 %) mainly contributed to these sequence tags indicating their metabolic activity, whereas Hallocella (1.8 %), Tepidimicrobium (0.5 %), and Methanothermobacter (<0.1 %) were transcriptionally less active. By applying 11 different cultivation strategies, 52 taxonomically different microbial isolates representing the classes Clostridia, Bacilli, Thermotogae, Methanomicrobia and Methanobacteria were obtained. Genome analyses of isolates support the finding that, besides Clostridium thermocellum and Clostridium stercorarium, Defluviitoga tunisiensis participated in the hydrolysis of hemicellulose producing ethanol, acetate, and H2/CO2. The latter three metabolites are substrates for hydrogentrophic and acetoclastic archaeal methanogenesis.

CONCLUSIONS:

Obtained results showed that high abundance of microorganisms as deduced from metagenome analysis does not necessarily indicate high transcriptional or metabolic activity, and vice versa. Additionally, it appeared that the microbiome of the investigated thermophilic biogas plant comprised a huge number of up to now unknown and insufficiently characterized species.

KEYWORDS:

Acetogenic Bacteria; Acidogenic Bacteria; Anaerobic digestion; Biomethanation; Cellulolytic Bacteria; Culturomics; Fragment recruitment; Methanogenic Archaea; Microbial community structure; Polyphasic characterization

7.
Transl Res. 2016 Jul 25. pii: S1931-5244(16)30127-X. doi: 10.1016/j.trsl.2016.07.012. [Epub ahead of print]

High-resolution characterization of the human microbiome.

Author information

  • 1Department of Genome Sciences, University of Washington, Seattle, WA.
  • 2Department of Genome Sciences, University of Washington, Seattle, WA; Department of Computer Science and Engineering, University of Washington, Seattle, WA; Santa Fe Institute, Santa Fe, NM. Electronic address: elbo@uw.edu.

Abstract

The human microbiome plays an important and increasingly recognized role in human health. Studies of the microbiome typically use targeted sequencing of the 16S rRNA gene, whole metagenome shotgun sequencing, or other meta-omic technologies to characterize the microbiome's composition, activity, and dynamics. Processing, analyzing, and interpreting these data involve numerous computational tools that aim to filter, cluster, annotate, and quantify the obtained data and ultimately provide an accurate and interpretable profile of the microbiome's taxonomy, functional capacity, and behavior. These tools, however, are often limited in resolution and accuracy and may fail to capture many biologically and clinically relevant microbiome features, such as strain-level variation or nuanced functional response to perturbation. Over the past few years, extensive efforts have been invested toward addressing these challenges and developing novel computational methods for accurate and high-resolution characterization of microbiome data. These methods aim to quantify strain-level composition and variation, detect and characterize rare microbiome species, link specific genes to individual taxa, and more accurately characterize the functional capacity and dynamics of the microbiome. These methods and the ability to produce detailed and precise microbiome information are clearly essential for informing microbiome-based personalized therapies. In this review, we survey these methods, highlighting the challenges each method sets out to address and briefly describing methodological approaches.

Copyright © 2016 Elsevier Inc. All rights reserved.

[PubMed - as supplied by publisher]
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8.
Biotechnol Biofuels. 2016 Jul 26;9:156. doi: 10.1186/s13068-016-0565-3. eCollection 2016.

Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants.

Author information

  • 1Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany.
  • 2Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany ; Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany.

Abstract

BACKGROUND:

Biofuel production from conversion of biomass is indispensable in the portfolio of renewable energies. Complex microbial communities are involved in the anaerobic digestion process of plant material, agricultural residual products and food wastes. Analysis of the genetic potential and microbiology of communities degrading biomass to biofuels is considered to be the key to develop process optimisation strategies. Hence, due to the still incomplete taxonomic and functional characterisation of corresponding communities, new and unknown species are of special interest.

RESULTS:

Three mesophilic and one thermophilic production-scale biogas plants (BGPs) were taxonomically profiled using high-throughput 16S rRNA gene amplicon sequencing. All BGPs shared a core microbiome with the thermophilic BGP featuring the lowest diversity. However, the phyla Cloacimonetes and Spirochaetes were unique to BGPs 2 and 3, Fusobacteria were only found in BGP3 and members of the phylum Thermotogae were present only in the thermophilic BGP4. Taxonomic analyses revealed that these distinctive taxa mostly represent so far unknown species. The only exception is the dominant Thermotogae OTU featuring 16S rRNA gene sequence identity to Defluviitoga tunisiensis L3, a sequenced and characterised strain. To further investigate the genetic potential of the biogas communities, corresponding metagenomes were sequenced in a deepness of 347.5 Gbp in total. A combined assembly comprised 80.3 % of all reads and resulted in the prediction of 1.59 million genes on assembled contigs. Genome binning yielded genome bins comprising the prevalent distinctive phyla Cloacimonetes, Spirochaetes, Fusobacteria and Thermotogae. Comparative genome analyses between the most dominant Thermotogae bin and the very closely related Defluviitoga tunisiensis L3 genome originating from the same BGP revealed high genetic similarity. This finding confirmed applicability and reliability of the binning approach. The four highly covered genome bins of the other three distinct phyla showed low or very low genetic similarities to their closest phylogenetic relatives, and therefore indicated their novelty.

CONCLUSIONS:

In this study, the 16S rRNA gene sequencing approach and a combined metagenome assembly and binning approach were used for the first time on different production-scale biogas plants and revealed insights into the genetic potential and functional role of so far unknown species.

KEYWORDS:

16S rRNA gene; Anaerobic digestion; Biogas; Cloacimonetes (WWE1); Fusobacteria; Genome binning; Metagenomics; Microbial community; Spirochaetes; Thermotogae

9.
Front Microbiol. 2016 Jul 11;7:1081. doi: 10.3389/fmicb.2016.01081. eCollection 2016.

The Gut Microbiota in Immune-Mediated Inflammatory Diseases.

Author information

  • 1Department of Medical Microbiology and Infectious Diseases, University of Manitoba, WinnipegMB, Canada; National Microbiology Laboratory, Public Health Agency of Canada, WinnipegMB, Canada.
  • 2Department of Internal Medicine and the IBD Clinical and Research Centre, University of Manitoba, Winnipeg MB, Canada.

Abstract

The collection of microbes and their genes that exist within and on the human body, collectively known as the microbiome has emerged as a principal factor in human health and disease. Humans and microbes have established a symbiotic association over time, and perturbations in this association have been linked to several immune-mediated inflammatory diseases (IMID) including inflammatory bowel disease, rheumatoid arthritis, and multiple sclerosis. IMID is a term used to describe a group of chronic, highly disabling diseases that affect different organ systems. Though a cornerstone commonality between IMID is the idiopathic nature of disease, a considerable portion of their pathobiology overlaps including epidemiological co-occurrence, genetic susceptibility loci and environmental risk factors. At present, it is clear that persons with an IMID are at an increased risk for developing comorbidities, including additional IMID. Advancements in sequencing technologies and a parallel explosion of 16S rDNA and metagenomics community profiling studies have allowed for the characterization of microbiomes throughout the human body including the gut, in a myriad of human diseases and in health. The main challenge now is to determine if alterations of gut flora are common between IMID or, if particular changes in the gut community are in fact specific to a single disease. Herein, we review and discuss the relationships between the gut microbiota and IMID.

KEYWORDS:

chronic immune mediated inflammatory diseases; dysbiosis; metagenome; microbiome; systems microbiology

Publication Types

Publication Types

10.
ACS Synth Biol. 2016 Aug 9. [Epub ahead of print]

A Cell-Cell Communication-Based Screening System for Novel Microbes with Target Enzyme Activities.

Author information

  • 1Synthetic Biology & Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology , 125 Gwahak-ro, Yuseong-gu, Daejeon, South Korea.
  • 2Biosystems and Bioengineering Program, University of Science and Technology , 217 Gajung-ro, Yuseong-gu, Daejeon, South Korea.

Abstract

The development of synthetic biological devices has increased rapidly in recent years and the practical benefits of such biological devices are becoming increasingly clear. Here, we further improved the design of a previously reported high-throughput genetic enzyme screening system by investigating device-compatible biological components and phenol-mediated cell-cell communication, both of which increased the efficiency and practicality of the screening device without requiring the use of flow cytometry analysis. A sensor cell was designed to detect novel microbes with target enzyme activities on solid media by forming clear, circular colonies with fluorescence around the unknown microbes producing target enzymes. This mechanism of detection was enabled by the combination of pre-effector phenolic substrate treatment in the presence of target enzyme-producing microbes and control of the growth and fluorescence of remote sensor cells via phenol-mediated cell-cell communication. The sensor cells were applied to screen soil bacteria with phosphatase activity using phenyl phosphate as phenolic substrates. The sensor cells facilitated successful visualization of phosphatase activity in unknown microbes, which were identified by 16S rRNA analysis. Enzyme activity assays confirmed that the proposed screening technique was able to find 23 positive clones out of 33 selected colonies. Since many natural enzymatic reactions produce phenolic compounds from phenol-derived substrates, we anticipate that the proposed technique may have broad applications in the assessment and screening of novel microbes with target enzymes of interest. This method also can provide insights into the identification of novel enzymes for which screening assays are not yet available.

KEYWORDS:

cell−cell communication; enzyme; genetic circuit; high-throughput screening; metagenome; microbiome; phenol

[PubMed - as supplied by publisher]
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11.
PLoS One. 2016 Jul 18;11(7):e0159066. doi: 10.1371/journal.pone.0159066. eCollection 2016.

Metagenome and Metatranscriptome Profiling of Moderate and Severe COPD Sputum in Taiwanese Han Males.

Author information

  • 1Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan.
  • 2Department of Life Sciences, National Central University, Taoyuan, Taiwan.
  • 3Department of Computer Science and Engineering, Yuan Ze University, Taoyuan, Taiwan.
  • 4Institute of Medical Sciences, Tzu Chi University, Hualien, Taiwan.
  • 5Innovation Center for Big Data and Digital Convergence, Yuan Ze University, Taoyuan, Taiwan.

Abstract

Chronic obstructive pulmonary disease (COPD) is an inflammatory lung disorder characterized by the progressive obstruction of airflow and is currently the fourth leading cause of death in the world. The pathogenesis of COPD is thought to involve bacterial infections and inflammations. Owing to advancement in sequencing technology, evidence is emerging that supports an association between the lung microbiome and COPD. However, few studies have looked into the expression profile of the bacterial communities in the COPD lungs. In this study, we analyzed the sputum microbiome of four moderate and four severe COPD male patients both at the DNA and RNA level, using next generation sequencing technology. We found that bacterial composition determined by 16S rRNA gene sequencing may not directly translate to the set of actively expressing bacteria as defined by transcriptome sequencing. The two sequencing data agreed on Prevotella, Rothia, Neisseria, Porphyromonas, Veillonella, Fusobacterium and Streptococcus being among the most differentially abundant genera between the moderate and severe COPD samples, supporting their association with COPD severity. However, the two sequencing analyses disagreed on the relative abundance of these bacteria in the two COPD groups, implicating the importance of studying the actively expressing bacteria for enriching our understanding of COPD. Though we have described the metatranscriptome profiles of the lung microbiome in moderate and severe COPD, further investigations are required to determine the functional basis underlying the relationship between the microbial species in the lungs and pathogenesis of COPD.

12.
Sci Data. 2016 Jul 5;3:160050. doi: 10.1038/sdata.2016.50.

A catalogue of 136 microbial draft genomes from Red Sea metagenomes.

Author information

  • 1Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
  • 2Department of Pediatrics, University of California, San Diego, California 92037, USA.
  • 3Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072, Australia.
  • 4Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.

Abstract

Earth is expected to continue warming and the Red Sea is a model environment for understanding the effects of global warming on ocean microbiomes due to its unusually high temperature, salinity and solar irradiance. However, most microbial diversity analyses of the Red Sea have been limited to cultured representatives and single marker gene analyses, hence neglecting the substantial uncultured majority. Here, we report 136 microbial genomes (completion minus contamination is ≥50%) assembled from 45 metagenomes from eight stations spanning the Red Sea and taken from multiple depths between 10 to 500 m. Phylogenomic analysis showed that most of the retrieved genomes belong to seven different phyla of known marine microbes, but more than half representing currently uncultured species. The open-access data presented here is the largest number of Red Sea representative microbial genomes reported in a single study and will help facilitate future studies in understanding the physiology of these microorganisms and how they have adapted to the relatively harsh conditions of the Red Sea.

[PubMed - indexed for MEDLINE]
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13.
J Allergy Clin Immunol. 2016 May 10. pii: S0091-6749(16)30268-8. doi: 10.1016/j.jaci.2016.03.041. [Epub ahead of print]

Early-life gut microbiome composition and milk allergy resolution.

Author information

  • 1Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY; Division of Pediatric Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY. Electronic address: supinda@post.harvard.edu.
  • 2Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY.
  • 3Division of Pediatric Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY.
  • 4Department of Pediatrics, Johns Hopkins University, Baltimore, Md.
  • 5Department of Pediatrics, University of North Carolina, Chapel Hill, NC.
  • 6Emmes Corporation, Rockville, Md.
  • 7Department of Pediatrics, University of Arkansas for Medical Sciences and Arkansas Children's Hospital, Little Rock, Ark.
  • 8Department of Pediatrics, National Jewish Health, Denver, Colo.
  • 9Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Medicine, Division of Clinical Immunology and Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY.

Abstract

BACKGROUND:

Gut microbiota may play a role in the natural history of cow's milk allergy.

OBJECTIVE:

We sought to examine the association between early-life gut microbiota and the resolution of cow's milk allergy.

METHODS:

We studied 226 children with milk allergy who were enrolled at infancy in the Consortium of Food Allergy observational study of food allergy. Fecal samples were collected at age 3 to 16 months, and the children were followed longitudinally with clinical evaluation, milk-specific IgE levels, and milk skin prick test performed at enrollment, 6 months, 12 months, and yearly thereafter up until age 8 years. Gut microbiome was profiled by 16s rRNA sequencing and microbiome analyses performed using Quantitative Insights into Microbial Ecology (QIIME), Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt), and Statistical Analysis of Metagenomic Profiles (STAMP).

RESULTS:

Milk allergy resolved by age 8 years in 128 (56.6%) of the 226 children. Gut microbiome composition at age 3 to 6 months was associated with milk allergy resolution by age 8 years (PERMANOVA P = .047), with enrichment of Clostridia and Firmicutes in the infant gut microbiome of subjects whose milk allergy resolved. Metagenome functional prediction supported decreased fatty acid metabolism in the gut microbiome of subjects whose milk allergy resolved (η2 = 0.43; ANOVA P = .034).

CONCLUSIONS:

Early infancy is a window during which gut microbiota may shape food allergy outcomes in childhood. Bacterial taxa within Clostridia and Firmicutes could be studied as probiotic candidates for milk allergy therapy.

Copyright © 2016 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

KEYWORDS:

16s rRNA sequencing; Bacteroidetes; Clostridia; Cow's milk allergy; Firmicutes; fatty acid; food allergy; metagenome; microbiome; microbiota

[PubMed - as supplied by publisher]
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14.
Chem Res Toxicol. 2016 Jun 20;29(6):949-51. doi: 10.1021/acs.chemrestox.6b00066. Epub 2016 Jun 9.

Sex-Specific Effects of Arsenic Exposure on the Trajectory and Function of the Gut Microbiome.

Author information

  • 1Department of Environmental Health Science, University of Georgia , Athens, Georgia 30602, United States.

Abstract

The gut microbiome is deeply involved in numerous aspects of human health; however, it can be readily perturbed by environmental toxicants, such as arsenic. Meanwhile, the interaction among host, gut microbiome, and xenobiotics is a very complex dynamic process. Previously, we have demonstrated that gut microbiome phenotypes driven by host genetics and bacterial infection affect the responses to arsenic exposure. The role of host sex in shaping the gut microbiome raises the question whether sex plays a role in exposure-induced microbiome responses. To examine this, we used 16S rRNA sequencing and metagenomics sequencing to analyze the changes of the gut microbiome and its associated functional metagenome in both female and male C57/BL6 mice. Our results clearly demonstrated that arsenic exposure perturbed the trajectory and function of the gut microbiome in a sex-specific manner.

[PubMed - in process]
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15.
Gut Microbes. 2016 Sep 2;7(5):384-96. doi: 10.1080/19490976.2016.1190073. Epub 2016 May 23.

Composition and function of the pediatric colonic mucosal microbiome in untreated patients with ulcerative colitis.

Author information

  • 1a Department of Medicine , Baylor College of Medicine , Houston , TX , USA.
  • 2b Department of Pathology and Immunology , Baylor College of Medicine , Houston , TX , USA.
  • 3c Texas Children's Microbiome Center, Texas Children's Hospital , Houston , TX , USA.
  • 4d Department of Pediatrics , Baylor College of Medicine , Houston , TX , USA.
  • 5e USDA/ARS Children's Nutrition Research Center, Texas Children's Hospital , Houston , TX , USA.
  • 6f Molecular Research (MR DNA) , Shallowater , TX , USA.

Abstract

Inflammatory bowel diseases (IBD) are chronic intestinal inflammatory disorders characterized by a complex disruption of the physiologic interaction between the host immune system and intestinal microbes precipitated by environmental factors. Numerous observations indicate the altered composition and function of the intestinal microbiome of patients with ulcerative colitis (UC), a subtype of IBD. The accuracy of these results may be limited by confounding factors, such as concurrent medication use. To address these limitations, we examined the colonic mucosal microbiome of pediatric patients with UC prior to initiating treatment. Based on bacterial 16S rRNA gene sequencing, we identified a significant decrease in the phylum Verrucomicrobia in patients with UC. At the genus level, we observed a significant decrease in the short chain fatty acid producer Roseburia. Despite these compositional changes, we did not identify inferred gene content differences between the UC and control groups. To determine if microbial taxa may be associated with clinical outcomes, we retrospectively assessed the clinical course of the UC patients. Despite similar metrics of OTU richness and diversity, multiple OTU differences were observed between patients who responded to therapy and those who did not. Our observations regarding the mucosal microbiome and the associations with differential clinical outcomes support the contributions of gut microbes to disease onset and modulation.

KEYWORDS:

Inflammatory bowel disease; metagenome; microbiome; microbiota; ulcerative colitis

[PubMed - in process]
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16.
Environ Health Perspect. 2016 May 20. [Epub ahead of print]

Gender-Specific Effects of Organophosphate Diazinon on the Gut Microbiome and Its Metabolic Functions.

Author information

  • 1Department of Environmental Health Science, University of Georgia, Athens, Georgia, USA.

Abstract

BACKGROUND:

There is growing recognition of the significance of the gut microbiome to human health, and the association between a perturbed gut microbiome with human diseases has been established. Previous studies also show the role of environmental toxicants in perturbing the gut microbiome and its metabolic functions. The wide agricultural use of diazinon, an organophosphate insecticide, has raised serious environmental health concerns since it is a potent neurotoxicant. With studies demonstrating the presence of a microbiome-gut-brain axis, it is possible that gut microbiome perturbation may also contribute to diazinon toxicity.

OBJECTIVES:

We investigated the impact of diazinon exposure on the gut microbiome composition and its metabolic functions in C57BL/6 mice.

METHODS:

We used a combination of 16S rRNA gene sequencing, metagenomics sequencing, and mass spectrometry-based metabolomics profiling in a mouse model to examine the functional impact of diazinon on the gut microbiome.

RESULTS:

16S rRNA gene sequencing revealed that diazinon exposure significantly perturbed the gut microbiome, and metagenomic sequencing found that diazinon exposure altered the functional metagenome. Moreover, metabolomics profiling revealed an altered metabolic profile arising from exposure. Of particular significance, these changes were more pronounced for male mice than females.

CONCLUSIONS:

Diazinon exposure perturbed the gut microbiome community structure, functional metagenome, and associated metabolic profiles in a gender-specific manner. These findings may provide novel insights regarding perturbations of the gut microbiome and its functions as a potential new mechanism contributing to diazinon neurotoxicity and, in particular, its sex-selective effects.

[PubMed - as supplied by publisher]
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17.
Genetika. 2016 Jan;52(1):47-58.

[Distinctive Features of the Microbial Diversity and the Polyketide Synthase GenesSpectrum in the Community of the Endemic Baikal Sponge Swartschewskia papyracea].

[Article in Russian]

Abstract

The diversity of the symbiotic community of the endemic Baikal sponge Swartschewskia papyracea was studied, and an analysis of the polyketide synthases genes spectrum in sponge-associated microorganisms was carried out. Six bacterial phyla were detected in the S. papyracea microbiome, namely, Verrucomicrobia, Cyanobacteria, Actinobacteria, Bacteroidetes, Proteobacteria, and Planctomycetes. Unlike the microbial associations of other freshwater sponges, the community under study was dominated by the Verrucomicrobia (42.1%) and Cyanobacteria (17.5%) phyla, while the proportion of the Proteobacteria was unusually low (9.7%). In the S. papyracea community metagenome, there were identified 18 polyketide synthases genes fragments, the closest homologs of which included the polyketide synthases of the microorganisms belonging to the bacterial phyla Cyanobacteria, Proteobacteria (Betaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria classes), and Acidobacteria and to the eukaryotic algae of the Heterokonta phylum (Eustigmatophyceae class). Polyketide synthase sequences from S. papyracea formed three groups on the phylogenetic tree: a group of hybrid NRPS/PKS complexes, a group of cyanobacterial polyketide synthases, and a group of homologs of the eukaryotic alga Nannochloropsis galiana. Notably, the identified polyketide synthase genes fragments showed only a 57-88% similarity to the sequences in the databases, which implies the presence of genes controlling the synthesis of the novel, still unstudied, polyketide compounds in the S. papyracea community. It was proposed that the habitation conditions of S. papyracea affect the taxonomic composition of the microorganisms associated with the sponge, including the diversity of the producers of secondary metabolites.

PMID:
27183792
[PubMed - indexed for MEDLINE]
18.
PLoS One. 2016 May 12;11(5):e0155362. doi: 10.1371/journal.pone.0155362. eCollection 2016.

Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing.

Author information

  • 1Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America.
  • 2Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland, United States of America.
  • 3Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
  • 4Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.
  • 5Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
  • 6Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany.
  • 7Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany.
  • 8Max Delbrück Centre for Molecular Medicine, Berlin, Germany.
  • 9Department of Bioinformatics Biocenter, University of Würzburg, Würzburg, Germany.

Abstract

Accumulating evidence indicates that the gut microbiota affects colorectal cancer development, but previous studies have varied in population, technical methods, and associations with cancer. Understanding these variations is needed for comparisons and for potential pooling across studies. Therefore, we performed whole-genome shotgun sequencing on fecal samples from 52 pre-treatment colorectal cancer cases and 52 matched controls from Washington, DC. We compared findings from a previously published 16S rRNA study to the metagenomics-derived taxonomy within the same population. In addition, metagenome-predicted genes, modules, and pathways in the Washington, DC cases and controls were compared to cases and controls recruited in France whose specimens were processed using the same platform. Associations between the presence of fecal Fusobacteria, Fusobacterium, and Porphyromonas with colorectal cancer detected by 16S rRNA were reproduced by metagenomics, whereas higher relative abundance of Clostridia in cancer cases based on 16S rRNA was merely borderline based on metagenomics. This demonstrated that within the same sample set, most, but not all taxonomic associations were seen with both methods. Considering significant cancer associations with the relative abundance of genes, modules, and pathways in a recently published French metagenomics dataset, statistically significant associations in the Washington, DC population were detected for four out of 10 genes, three out of nine modules, and seven out of 17 pathways. In total, colorectal cancer status in the Washington, DC study was associated with 39% of the metagenome-predicted genes, modules, and pathways identified in the French study. More within and between population comparisons are needed to identify sources of variation and disease associations that can be reproduced despite these variations. Future studies should have larger sample sizes or pool data across studies to have sufficient power to detect associations that are reproducible and significant after correction for multiple testing.

19.
Bioinform Biol Insights. 2016 Apr 20;10:19-25. doi: 10.4137/BBI.S34610. eCollection 2016.

Use of Metatranscriptomics in Microbiome Research.

Author information

  • 1Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.

Abstract

The human intestinal microbiome is a microbial ecosystem that expresses as many as 100 times more genes than the human host, thereby constituting an important component of the human holobiome, which contributes to multiple health and disease processes. As most commensal species are difficult or impossible to culture, genomic characterization of microbiome composition and function, under various environmental conditions, comprises a central tool in understanding its roles in health and disease. The first decade of microbiome research was mainly characterized by usage of DNA sequencing-based 16S rDNA and shotgun metagenome sequencing, allowing for the elucidation of microbial composition and genome structure. Technological advances in RNA-seq have recently provided us with an ability to gain insight into the genes that are actively expressed in complex bacterial communities, enabling the elucidation of the functional changes that dictate the microbiome functions at given contexts, its interactions with the host, and functional alterations that accompany the conversion of a healthy microbiome toward a disease-driving configuration. Here, we highlight some of the key metatranscriptomics strategies that are implemented to determine microbiota gene expression and its regulation and discuss the advantages and potential challenges associated with these approaches.

KEYWORDS:

RNA-Seq; bacteria; gut; microbiome; next generation sequencing; transcriptome

Publication Types

Publication Types

20.
Sci Rep. 2016 Apr 29;6:25271. doi: 10.1038/srep25271.

Role of Fusobacteria in the serrated pathway of colorectal carcinogenesis.

Author information

  • 1Department of Internal Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri 11923, Korea.
  • 2Department of Pathology, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri 11923, Korea.

Abstract

Fusobacteria are associated with colorectal cancer (CRC) and are amplified during colorectal carcinogenesis. Compared to the adenoma-carcinoma sequence of carcinogenesis, serrated neoplasm has distinct clinical features and a different molecular background. We aimed to compare the gut microbiome between tubular adenoma (TA) and sessile serrated adenoma/polyp (SSA/P). Patients with TA, SSA/P, or CRC were recruited. Three pieces of colorectal mucosal tissue were obtained from each patient by endoscopic biopsy. 16S rRNA gene pyrosequencing and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) were performed. Among 26 enrolled patients, 8, 10, and 8 had TA, SSA/P, and CRC, respectively. The relative abundance of Fusobacteria did not differ significantly between the TA and SSA/P groups (4.3% and 1.9%, P = 0.739) but was higher in the CRC group (33.8%) than in the TA or SSA/P group, respectively (TA vs. CRC, P = 0.002, false discovery rate [FDR] = 0.023; SSA/P vs. CRC, P < 0.001, FDR = 0.001). PICRUSt revealed that most functions in the TA metagenome were similar to those in the SSA/P metagenome. The gut microbiome, including relative abundance of Fusobacteria, did not differ between TA and SSA/P, suggesting that Fusobacteria may contribute to both the serrated pathway and the adenoma-carcinoma sequence.

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