Non-human microbiome, August 5, 2014

Microbiome papers on giraffes, sheeps, sponges and corals, soybean, soil, seawater, and fungi found in vacuum cleaner dust.

Mammal microbiome

The giraffe (Giraffa camelopardalis) rumen microbiome – Michael Roggenbuck, Cathrine Sauer, Morten Poulsen, Mads F. Bertelsen, Søren Johannes Sørensen – FEMS Microbiology Ecology

“Here we investigated the microbial community of 7 wild-caught giraffes (Giraffa camelopardalis), 3 of which were fed natural browse and 4 were fed Boskos pellets, leafy alfalfa hay and cut savanna browse, by characterizing the 16S rRNA gene diversity using 454 FLX high throughput sequencing. “

Two Different Bacterial Community Types Are Linked with the Low-Methane Emission Trait in Sheep – Sandra Kittelmann – PLOS ONE

“Bacterial community structures in 236 rumen samples from 118 high- and low-CH4 emitting sheep formed gradual transitions between three ruminotypes. Two of these (Q and S) were linked to significantly lower CH4 yields”

Invertebrate microbiome

Host-specific microbial communities in three sympatric North Sea sponges – Mohd Azrul Naim, Jose A. Morillo, Søren J. Sørensen, Waleed Abu Al-Soud, Hauke Smidt and Detmer Sipkema – FEMS Microbiology Ecology

“In this study we assessed the diversity of the microbial communities hosted by three sympatric sponges living in a semi-enclosed North-Sea environment using pyrosequencing of bacterial and archaeal 16S ribosomal RNA gene fragments.”

Host-specific microbial communities in three sympatric North Sea sponges– Mohd Azrul Naim – FEMS Microbiology Ecology

“In this study we assessed the diversity of the microbial communities hosted by three sympatric sponges living in a semi-enclosed North-Sea environment using pyrosequencing of bacterial and archaeal 16S ribosomal RNA gene fragments. “

Disturbance to conserved bacterial communities in the cold water gorgonian coral Eunicella verrucosa – Emma Ransome – FEMS Microbial Ecology

“The bacterial communities associated with healthy and diseased colonies of the cold water gorgonian coral Eunicella verrucosa at three sites off the south-west coast of England were compared using denaturing gradient gel electrophoresis (DGGE) and clone libraries. “

Application of a new cultivation technology, I-tip, for studying microbial diversity in freshwater sponges of Lake Baikal, Russia – Dawoon Jung – FEMS Microbial Ecology

“The I-tip was developed as an in situ cultivation device that allows microorganisms to enter and natural chemical compounds to diffuse, thereby permitting the microorganisms to grow utilizing chemical compounds in their natural environment. “

Plant microbiome

Comparison of the Rhizosphere Bacterial Communities of Zigongdongdou Soybean and a High-Methionine Transgenic Line of This Cultivar – Jingang Liang – PLOS ONE

“Using 16S rRNA gene-based pyrosequencing analysis of the V4 region and DNA extracted from bacterial consortia collected from the rhizosphere of soybean plants grown in an agricultural field at the pod-setting stage, we characterized the populational structure of the bacterial community involved.”

Soil microbiome

Exploring the immediate and long-term impact on bacterial communities in soil amended with animal and urban organic waste fertilizers using pyrosequencing and screening for horizontal transfer of antibiotic resistance – Leise Riber, Pernille Hasse Busk Poulsen, Waleed Abu Al-Soud, Lea Benedicte Skov Hansen, Lasse Bergmark, Asker Brejnrod, Anders Norman, Lars Hestbjerg Hansen, Jakob Magid andSøren Johannes Sørensen – FEMS Microbiology Immunology

“Soils were sampled in weeks 0, 3, 9 and 29 after fertilizer application. Pseudomonas isolates were enumerated, and the impact on soil-bacterial community structure was investigated using 16S-rRNA amplicon pyrosequencing.”

Microbial Diversity in Hummock and Hollow Soils of Three Wetlands on the Qinghai-Tibetan Plateau Revealed by 16S rRNA Pyrosequencing – Yongcui Deng – PLOS ONE

“Principal coordinate analysis (PCoA) indicated that the microbial community structure differed between locations and microtopographies and canonical correspondence analysis indicated an association between microbial community structure and soil properties or geography. “

Seawater microbiome

Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes – Alyse K. Hawley, Heather M. Brewer, Angela D. Norbeck, Ljiljana Paša-Tolić, and Steven J. Hallam – PNAS USA

“Here we use metagenomic and metaproteomic methods to chart in situ metabolic networks linking key microbial players driving carbon and nutrient cycling in a seasonally stratified fjord, Saanich Inlet”

Sequencing on the Seven Seas – Rina Shaikh-Lesko – The Scientist

“Researchers have installed an advanced genomics lab facility aboard a boat to create a floating molecular testing facility for marine life sciences”

Microbiome of the Built Environment

Characterization of Fungal Communities in House Dust Samples Collected From Central Portugal—A Preliminary Survey – Ana C.A. Sousa – Journal of Toxicology and Environmental Health

“A total of 28 samples were obtained from vacuum cleaner deposits from households located in central Portugal. DNA was extracted from dust samples and fungal communities were analyzed using a culture-independent polymerase chain reaction (PCR)– denaturing gradient gel electrophoresis (DGGE) approach. “

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General microbiology and science, July 7

Metagenomics binning based on co-abundance, bias in Illumina sequencing, and lots of metabolomics.

Phages and viruses

Bacteriophage-based synthetic biology for the study of infectious diseases – Robert J Citorik – Current Opinion in Microbiology

“Here, we discuss bacteriophage-based technologies and their application to the study of infectious diseases. “

Sequencing and Metagenomics

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes – H Bjørn Nielsen (and 142 other authors) – Nature Biotechnology

“Here we present a method, based on binning co-abundant genes across a series of metagenomic samples, that enables comprehensive discovery of new microbial organisms, viruses and co-inherited genetic entities and aids assembly of microbial genomes without the need for reference sequences.”

Evaluating bias of Illumina-based bacterial 16S rRNA gene profiles – Katherine Kennedy – Applied and Environmental Microbiology

“In this study, we tested the effects of template concentration, pooling of PCR amplicons, and sample preparation/inter-lane sequencing on the reproducibility associated with paired-end Illumina sequencing of bacterial 16S rRNA genes.”

Next generation sequencing technology: Advances and applications – HPJ Buermans, JT den Dunnen – Biochimica et Biophysica Acta (BBA) – Molecular Basis of Disease

“In this chapter we review the technical background of the different commercially available NGS platforms with respect to template generation and the sequencing reaction and take a small step towards what the upcoming NGS technologies will bring.”

Systems biology as an approach for deciphering microbial interactions – Puneet Kumar Singh – Briefings in Functional Genomics

“Here, we endeavor to summarize, epigrammatic description of sophisticated techniques and software that provides an enhanced understanding of metagenomics data analysis. “

Metabolomics

Stronger findings for metabolomics through Bayesian modeling of multiple peaks and compound correlations – Tommi Suvitaival – Bioinformatics

“We propose a hierarchical Bayesian model for inferring
differences between groups of samples more accurately in
metabolomic studies, where the observed compounds are collinear.”

Emergent Biosynthetic Capacity in Simple Microbial Communities – Hsuan-Chao Chiu – PLOS Computational Biology

“Here we present a comprehensive computational framework, integrating high-quality metabolic models of multiple species, temporal dynamics, and flux variability analysis, to study the metabolic capacity and dynamics of simple two-species microbial ecosystems.”

Metabolomics Analysis Identifies Intestinal Microbiota-Derived Biomarkers of Colonization Resistance in Clindamycin-Treated Mice – Robin L. P. Jump – PLOS ONE

“Clindamycin treatment caused marked changes in metabolites present in fecal specimens. Of 484 compounds analyzed, 146 (30%) exhibited a significant increase or decrease in concentration during clindamycin treatment followed by recovery to baseline that coincided with restoration of in vivo colonization resistance.”

Volatile Organic Compounds as Novel Markers for the Detection of Bacterial
Infections – Mohsen Sohrabi – Clinical Microbiology

“The possibility of using VOCs markers as one of the largest groups of bacterial metabolites would open a new frontier for developing more efficient techniques in the diagnosis of bacterial infections.”

The importance of sulfur-containing metabolites in discriminating fecal extracts between normal and type 2 diabetic mice – Alesia Walker – Journal of Proteome Research

“We demonstrate that a metabolic disorder such as T2DM affects the gastrointestinal tract environment thereby influencing different metabolic pathways and their respective metabolites in diabetic mice. “

Microarrrays

Applications of Phylogenetic Microarrays to Profiling of Human Microbiomes (PDF) -Oleg Paliy and Vijay Shankar – Book chapter

“This chapter will focus on currently available phylogenetic microarrays for the inter- rogation of human-associated microbiota, the technologies used to construct the arrays, as well as several key features that distinguish them from other approaches. “

Arsenic metabolism

Infant toenails as a biomarker of in utero arsenic exposure – Matthew A Davis – Journal of Exposure Science and Environmental Epidemiology

“In a sample of 170 mother–infant pairs from New Hampshire, we determined infant exposure to in utero arsenic by evaluating infant toenails as a biomarker using inductively coupled plasma mass spectrometry. “

Chromosomal organization

Spatial confinement is a major determinant of the folding landscape of human chromosomes – Gamze Gürsoy – Nucleic Acids Research

“Here we describe a model called constrained self-avoiding chromatin (C-SAC) for studying spatial structures of chromosomes, as the available space is a key determinant of chromosome folding. “

Bacteria in the news

The bacteria has been decimated: how much should we care what words used to mean? – By Tom Chivers – Telegraph

“Much amusement this morning on the Today programme, as John Humphrys shamefacedly confessed to having said “a bacteria” on the previous day’s episode.”

Yoghurt industry blamed for encouraging bacteria – The Daily Mash

“One day massive cow-sized bacteria will rule the world and they will kill everyone who doesn’t like special yoghurts.”

When Scientists Experiment on Themselves: H. pylori and Ulcers – By Hanno Charisius – Scientific American

“With his famous self-experiment, Marshall was able to demonstrate that Helicobacter pylori bacteria can cause acute gastritis which in turn may cause ulcers. He had asked neither an ethics commission nor his wife for permission to conduct this experiment. “

In rental cars, dangerous bacteria may come along for the ride – Jeff Rossen and Josh Davis, Today

“Armed with gloves and goggles, they swabbed every car from top to bottom: the steering wheels, gearshifts, door handles, even the GPS units.”

Bacteria that ‘eats’ odour could bring end to smelly toilets in China – Stephen Chen – South China Morning Post

“Mainland scientists have developed a “bioweapon” that can wipe out the notorious bad smell in public toilets. Up to 75 per cent of the odour can be removed, with the rest suppressed by a natural, pleasant fragrance, according to researchers with the Chinese Academy of Sciences.”

Marine Mammals

Some SeaWorld mammals survive longer in captivity – Mike Schneider – Associated Press

“Breakthroughs in training and medicine that allow the parks’ medical staffs to perform far fewer stressful or invasive procedures are partly responsible for those successes, SeaWorld officials said.”

Science and publishing

Highly cited Researchers 2014 – Thomson Reuters

“Over three thousand researchers earned the distinction by writing the greatest numbers of reports officially designated by Essential Science Indicators℠ as Highly Cited Papers—ranking among the top 1% most cited for their subject field and year of publication, earning them the mark of exceptional impact.”

Dr. Bik’s Picks

Rats use their whiskers in a similar way to how humans use their hands and fingers – Science Daily

“Rats deliberately change how they sense their environment using their facial whiskers depending on whether the environment is novel, if there is a risk of collision and whether or not they can see where they are going.”

Giraffe legs’ strong, skinny secret – Victoria Gill – BBC Science

“Scientists have worked out the anatomical secret to giraffes’ long and spindly – but strong – legs.”

Environmentalists Almost Killed My Friend – Josh Bloom – Science 2.0

“It is hysteria-producing nonsense like this that leads any non-scientist to conclude that we are systematically being poisoned every day. “

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