27 research outputs found
Gene sets for utilization of primary and secondary nutrition supplies in the distal gut of endangered iberian lynx
Recent studies have indicated the existence of an extensive trans-genomic trans-mural co-metabolism between gut microbes and animal hosts that is diet-, host phylogeny- and provenance-influenced. Here, we analyzed the biodiversity at the level of small subunit rRNA gene sequence and the metabolic composition of 18 Mbp of consensus metagenome sequences and activity characteristics of bacterial intra-cellular extracts, in wild Iberian lynx (Lynx pardinus) fecal samples. Bacterial signatures (14.43% of all of the Firmicutes reads and 6.36% of total reads) related to the uncultured anaerobic commensals Anaeroplasma spp., which are typically found in ovine and bovine rumen, were first identified. The lynx gut was further characterized by an over-representation of ‘presumptive’ aquaporin aqpZ genes and genes encoding ‘active’ lysosomal-like digestive enzymes that are possibly needed to acquire glycerol, sugars and amino acids from glycoproteins, glyco(amino)lipids, glyco(amino)glycans and nucleoside diphosphate sugars. Lynx gut was highly enriched (28% of the total glycosidases) in genes encoding α-amylase and related enzymes, although it exhibited low rate of enzymatic activity indicative of starch degradation. The preponderance of β-xylosidase activity in protein extracts further suggests lynx gut microbes being most active for the metabolism of β-xylose containing plant N-glycans, although β-xylosidases sequences constituted only 1.5% of total glycosidases. These collective and unique bacterial, genetic and enzymatic activity signatures suggest that the wild lynx gut microbiota not only harbors gene sets underpinning sugar uptake from primary animal tissues (with the monotypic dietary profile of the wild lynx consisting of 80–100% wild rabbits) but also for the hydrolysis of prey-derived plant biomass. Although, the present investigation corresponds to a single sample and some of the statements should be considered qualitative, the data most likely suggests a tighter, more coordinated and complex evolutionary and nutritional ecology scenario of carnivore gut microbial communities than has been previously assumed
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The ocean sampling day consortium.
Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world's oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits
The ocean sampling day consortium
Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits
The Ocean Sampling Day Consortium
Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits
Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica
M.K. and P.N.G. designed the work; T.N.C. performed physiological studies; M.K., M.F.,
Y.A.-R., A.B., N.L.-C., M.E.G., O.R.K., T.Y.N., S.K., I.L., O.V.G., M.M.Y. R.R. and P.N.G.
were associated with genome annotation; H.J.H. performed lipids and FAME analysis;
M.F., M-l.F., S.J., S.C. and J.P.A performed chaperonin anti-proteome analysis; A.-x. S.,
O.K., O.E., P.A.P., P.S. and Y.K. were associated with structural proteomics; A.T. and R.F.
were associated with functional proteomics; H.L. performed electron microscopy; R.D.
performed real-time PCR; M.M.-G. and M.F. performed DIGE proteome analysis;
M.G. was involved in siderophore production; O.N.R. performed genomic islands’
analysis; H.T. performed storage lipid compounds’ analysis; P.N.G. coordinated
manuscript writing.Accession Codes: The genome sequence of Oleispira antarctica RB-8 has been deposited
in GenBank under accession core FO203512. Protein structures have deposited in PDB
under accession codes 3QVM (a/b hydrolase, OLEAN_C08020), 3QVQ (phosphodiesterase,
OLEAN_C20330), 3M16 (transaldolase, OLEAN_C18160), 3LQY (isochorismatase,
OLEAN_C07660), 3LNP (amidohydrolase, OLEAN_C13880), 3V77/3L53 (fumarylacetoacetate isomerase/hydrolase, OLEAN_C35840), 3VCR/3LAB
(2-keto-3-deoxy-6-phosphogluconate aldolase, OLEAN_C25130), 3IRU (phoshonoacetaldehyde
hydrolase, OLEAN_C33610), 3I4Q (inorganic pyrophosphatase,
OLEAN_C30460), 3LMB (protein with unknown function, OLEAN_C10530).Ubiquitous bacteria from the genus Oleispira drive oil degradation in the largest environment
on Earth, the cold and deep sea. Here we report the genome sequence of Oleispira antarctica
and show that compared with Alcanivorax borkumensis—the paradigm of mesophilic
hydrocarbonoclastic bacteria—O. antarctica has a larger genome that has witnessed massive
gene-transfer events. We identify an array of alkane monooxygenases, osmoprotectants,
siderophores and micronutrient-scavenging pathways. We also show that at low temperatures,
the main protein-folding machine Cpn60 functions as a single heptameric barrel that
uses larger proteins as substrates compared with the classical double-barrel structure
observed at higher temperatures. With 11 protein crystal structures, we further report the
largest set of structures from one psychrotolerant organism. The most common structural
feature is an increased content of surface-exposed negatively charged residues compared to
their mesophilic counterparts. Our findings are relevant in the context of microbial
cold-adaptation mechanisms and the development of strategies for oil-spill mitigation in cold
environments.We acknowledge the funding from the EU Framework Program 7 to support Projects
MAMBA (226977), ULIXES (266473), MAGIC PAH (245226) and MICROB3 (287589)
This work received the support of the Government of Canada through Genome Canada
and the Ontario Genomics Institute (grant 2009-OGI-ABC-1405 to A.F.Y. and A.S.), and
the U.S. Government National Institutes of Health (grants GM074942 and GM094585
(to A.S. through Midwest Center for Structural Genomics). The study was supported by
the Max Planck Society and the Deutsche Forschungsgemeinschaft through project KU
2679/2-1 and BU 890/21-1. We thank the sequencing team of the AG Reinhardt for
technical assistance and Alfred Beck for computational support. The skilful work of
electron microscopic sample preparation by Mrs. Ingeborg Kristen (Dept. VAM, HZI
Braunschweig) is gratefully acknowledged. Authors thank Professor Ken Timmis for his
critical reading the manuscript and useful comments.http://www.nature.com/naturecommunicationsam201
Hepatotoxic potential of Therapeutic Oligonucleotides can be predicted from their sequence and modification pattern
Antisense oligonucleotides that recruit RNase H and thereby cleave complementary messenger RNAs are being developed as therapeutics. Dose-dependent hepatic changes associated with hepatocyte necrosis and increases in serum alanine-aminotransferase levels have been observed after treatment with certain oligonucleotides. Although general mechanisms for drug-induced hepatic injury are known, the characteristics of oligonucleotides that determine their hepatotoxic potential are not well understood. Here, we present a comprehensive analysis of the hepatotoxic potential of locked nucleic acid-modified oligonucleotides in mice. We developed a random forests classifier, in which oligonucleotides are regarded as being composed of dinucleotide units, which distinguished between 206 oligonucleotides with high and low hepatotoxic potential with 80% accuracy as estimated by out-of-bag validation. In a validation set, 17 out of 23 oligonucleotides were correctly predicted (74% accuracy). In isolation, some dinucleotide units increase, and others decrease, the hepatotoxic potential of the oligonucleotides within which they are found. However, a complex interplay between all parts of an oligonucleotide can influence the hepatotoxic potential. Using the classifier, we demonstrate how an oligonucleotide with otherwise high hepatotoxic potential can be efficiently redesigned to abate hepatotoxic potential. These insights establish analysis of sequence and modification patterns as a powerful tool in the preclinical discovery process for oligonucleotide-based medicines
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Overview of the relative abundance of phylogenetic prokaryotic groups recovered from the lynx distal gut based on SSU rRNA tag sequences extracted from the pyrosequences.
All reads belonging to phylum Proteobacteria identified related to Betaproteobacteria, which is only cited in the Figure.</
Astrobiology of life on Earth
Astrobiology is often regarded as the study of life beyond Earth, but here we consider life
on Earth through an astrobiological lens. Microbiology has historically focused on
various anthropocentric sub-fields (such as fermented foods or commensals and
pathogens of crop plants, livestock, and humans), but addressing key biological
questions via astrobiological approaches can further our understanding of all life on
Earth. We highlight potential implications of this approach through the articles in this
Environmental Microbiology special issue “Ecophysiology of extremophiles". They
report on the microbiology of places/processes including low-temperature environments
and chemically diverse saline- and hypersaline habitats; aspects of sulphur metabolism
in dysoxic marine waters; thermal acidic springs; biology of extremophile viruses; the
survival of terrestrial extremophiles on the surface of Mars; rock-associated microbes
and biological soils crusts of deserts; the deep biosphere; and interactions of microbes
with igneous and sedimentary rocks. These studies, some of which we highlight here,
contribute towards our understanding of the biotic activities and tenacity of terrestrial
life. Their findings will help set the stage for future work focused on the constraints for
life, and how organisms adapt and evolve to circumvent these constraints