Tag Archives: beer

Animal microbiome digest, September 16, 2014

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Microbiomes of baby elephants, baby macaques, cows, mice, honey bees, oysters, Panama forest trees, yoghurt, air, beer, and clothes. We also learn that oregano has no effect on piglet microbiome. Just in case you wondered.

Mammal microbiome

A Comparative Metagenome Survey of the Fecal Microbiota of a Breast- and a Plant-Fed Asian Elephant Reveals an Unexpectedly High Diversity of Glycoside Hydrolase Family Enzymes – Nele Ilmberger – PLOS ONE

“A phylogenetic and metagenomic study of elephant feces samples (derived from a three-weeks-old and a six-years-old Asian elephant) was conducted in order to describe the microbiota inhabiting this large land-living animal.”

Breast-fed and bottle-fed infant rhesus macaques develop distinct gut microbiotas and immune systems – Amir Ardeshir – Science Translational Medicine

“We show that breast-fed and bottle-fed infant rhesus macaques develop markedly different immune systems, which remain different 6 months after weaning when the animals begin receiving identical diets.”

Characterization of the rumen lipidome and microbiome of steers fed a diet supplemented with flax and echium oil – Sharon Ann Huws – Microbial Biotechnology

“Microbiome pyrosequences showed that 50% of the bacterial genera were core to all diets (found at least once under each dietary intervention)”

Metagenome of Mehsani Buffalo Rumen Microbiota: An Assessment of Variation in Feed-Dependent Phylogenetic and Functional Classification – Parmar N.R. – Journal of Molecular Microbiology and Biotechnology

“Diet composed of varying proportion of green and dry roughages along with grains was given to 8 Mehsani buffaloes, and rumen metagenome was sketched using shotgun semiconductor sequencing.”

Gastrointestinal microbiota of wild and inbred individuals of two house mouse subspecies assessed using high throughput parallel pyrosequencing – Jakub Kreisinger – Molecular Ecology

“Using 454 pyrosequencing, we performed 16S rDNA GTM barcoding for 30 wild house mice (Mus musculus) and wild-derived inbred strain mice belonging to two subspecies (M.m.musculus and M.m. domesticus).”

The Use of Restriction Fragment Length Polymorphism and Fluorescence in Situ Hybridization to Investigate Microbiota of Piglets after Feeding Oregano – Katrin Stelter – Food and Nutrition Sciences

“The results showed no significant changes in microbiota in response to oregano. “

Insect microbiome

Buzz off, that’s my bee! – Gemma Langridge – Nature Reviews Microbiology

“These newly sequenced bee gut symbionts have revealed multiple genes that are candidates for determining host specificity. “

Hidden Diversity in Honey Bee Gut Symbionts Detected by Single-Cell Genomics – Philipp Engel – PLOS Genetics

“In both species, the divergence of 16S rRNA loci appears to have been curtailed by frequent recombination within populations, while other genomic regions have continuously diverged. “

Bacterial Communities in the Gut and Reproductive Organs of Bactrocera minax (Diptera: Tephritidae) Based on 454 Pyrosequencing – Ailin Wang – PLOS ONE

“We used a 454 pyrosequencing technology to study in depth the microbial communities associated with gut and reproductive organs of Bactrocera minax.”

Invertebrate microbiome

Hemolymph microbiome of Pacific oysters in response to temperature, temperature stress and infection – Ana Lokmer and Karl Mathias Wegner – ISME Journal

“We monitored oyster survival and repeatedly collected hemolymph of dead and alive animals to determine the microbiome composition by 16s rRNA gene amplicon pyrosequencing. “

Plant microbiome

Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest – Steven W. Kembel – PNAS

“In this study we sequenced bacterial communities present on tree leaves in a neotropical forest in Panama, to quantify the poorly understood relationships between bacterial biodiversity on leaves (the phyllosphere) vs. host tree attributes. “

Litter decomposition and soil microbial community composition in three Korean pine (Pinus koraiensis) forests along an altitudinal gradient – Yong Zhou – Plant and Soil

“Single- and mixed-species litter decomposition rates were determined by the litterbag method and soil microbial community composition was characterized by PLFAs.”

Soil microbiome

Pyrosequencing assessment of rhizosphere fungal communities from a soybean field – Akifumi Sugiyama – Canadian Journal of Microbiology

“This study utilized 454 pyrosequencing to analyze rhizosphere fungal communities during soybean growth.”

Water microbiome

Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years – Jacob A Cram – ISME Journal

“Biodiversity appeared to be driven partially by exchange of microbes between depths and was highest when communities were changing slowly over time.”

Long-term effects of the antibacterial agent triclosan on marine periphyton communities – Martin Eriksson – PeerJ PrePrints

“Pollution-Induced Community Tolerance (PICT) was observed for algae and cyanobacteria at 100 nM TCS and higher.”

Review: Master recyclers: features and functions of bacteria associated with phytoplankton blooms – Alison Buchan – Nature Reviews Microbiology

“In this Review, we discuss the central role that these bacteria have in transforming phytoplankton-derived organic matter and thus in biogeochemical nutrient cycling.”

Built environment microbiome

Diversity and dynamics of the indoor air microbiome in an urban subway network – Marcus H. Y. Leung – Applied and Environmental Microbiology

“Targeting the 16S rDNA V4 region, extensive taxonomic diversity was found, with the most common bacterial genera in the subway environment among those seen associated on skin.”

Microbial Odor Profile of Polyester and cotton clothes after a fitness session – Chris Callewaert – Applied and Environmental Microbiology

“A dissimilar bacterial growth was found in cotton versus synthetic clothing textiles. Micrococci were isolated in almost all synthetic shirts and were detected almost solely on synthetic shirts by means of DGGE fingerprinting. “

Food microbiology

Vegetable microbiomes: is there a connection among opportunistic infections, human health and our ‘gut feeling’? – Gabriele Berg – Microbial Biotechnology

“Based on these results, we discuss the question if vegetables can serve as a source of infection for immunocompromised individuals as well as possible solutions to avoid outbreaks. “

Assessment of the bacterial and fungal diversity in home-made yoghurts of Xinjiang of China by pyrosequencing – Haiyan Xu – Journal of the Science of Food and Agriculture

“The bacterial and fungal community diversity of 22 home-made yoghurt samples from Zhaosu and Tekesi counties of Xinjiang in China were analyzed with pyrosequencing. “

Victory, life-sciences firm team up to detect bacteria that can spoil beer’s taste – Diane Mastrull – Philly.com

“The list is long of the perfect accompaniments to beer: hot dogs, pizza, peanuts, and pretzels, to name just a few. Most definitely not on that list: pediococcus and lactobacillus. Consider them beer buzzkills.”

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General microbiology and science, September 15, 2014

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Biodiversity and evolution in microbial communities, metabolomics, swabbing, DNA extraction, ITS approaches, marine viruses, and Bik’s Picks.

Microbial Ecology

The cryptic role of biodiversity in the emergence of host–microbial mutualisms – Pradeep Pillai – Ecology Letters

“Using a metacommunity model, we show that competition between multiple cheaters within the host’s microbiome, when combined with the spatial structure of host–microbial interactions, can have a constructive rather than a disruptive effect by allowing the emergence and maintenance of mutualistic microorganisms within the host.”

Microbial communities evolve faster in extreme environments – Sheng-Jin Li – Nature Scientific Reports

“Here we report a relative evolutionary rates (rERs) analysis of microbial communities from six diverse natural environments based on 40 metagenomic samples. “

Metabolomics

Mapping the Inner Workings of the Microbiome: Genomic- and Metagenomic-Based Study of Metabolism and Metabolic Interactions in the Human Microbiome – Ohad Manor, Roie Levy, Elhanan Borenstein – Cell Metabolism

“Here, we discuss recent efforts to study the metabolic inner workings of this complex ecosystem. “

Techniques

Comparison of seven methods for extraction of bacterial DNA from fecal and cecal samples of mice – Janina Ferrand – Journal of Microbiological Methods

“DNA quantity and quality were assessed by fluorometry, spectrophotometry, gel electrophoresis and qPCR….For both feces and intestinal contents, the most efficient extraction method was the FastDNA® SPIN Kit for Soil.”

Swab Sample Transfer for Point-Of-Care Diagnostics: Characterization of Swab Types and Manual Agitation Methods – Nuttada Panpradist – PLOS ONE

“In this study, we compared bacterial release efficiency of seven swab types using manual-agitation methods typical of POC devices.”

Improved resolution of bacteria by high throughput sequence analysis of the rRNA internal transcribed spacer – Paul M. Ruegger – Journal of Microbiological Methods

“Comparisons of the ITS region and two SSU regions using annotated bacterial genomes in GenBank showed much greater resolving power is possible with the ITS region. “

Pyroprinting: A rapid and flexible genotypic fingerprinting method for typing bacterial strains – Michael W. Black – Journal of Microbiological Methods

“Pyroprinting relies on the simultaneous pyrosequencing of polymorphic multicopy loci, such as the intergenic transcribed spacer regions of rRNA operons in bacterial genomes.”

Bioinformatics

OrthoClust: an orthology-based network framework for clustering data across multiple species – Koon-Kiu Yan – Genome Biology

“We demonstrate the application of OrthoClust using the RNA-Seq expression profiles of Caenorhabditis elegans and Drosophila melanogaster from the modENCODE consortium.”

Viruses and Phages

Review: Factors affecting virus dynamics and microbial host–virus interactions in marine environments – Kristina D.A. Mojica and Corina P.D. Brussaard – FEMS Microbiology Ecology

“The goal of the present minireview was to contribute to the evolution of marine viral ecology, through the assimilation of available data regarding the manner and degree to which environmental factors affect viral decay and infectivity as well as influence latent period and production.”

More Microbes

Dead or Alive: Molecular Assessment of Microbial Viability – Gerard A. Cangelosi and John S. Meschke – Applied and Environmental Microbiology

“This article reviews molecular viability analysis in that context and discusses future opportunities for these strategies in genetic, metagenomic, and single-cell microbiology.”

Bacteria in the news

Is your body mostly microbes? Actually, we have no idea – Peter Andrey Smith – The Boston Globe

“There’s only one problem: The oft-cited 10-to-1 figure is almost certainly inaccurate.”

The Death Microbiome Could Inform Forensic Science And Medicine – Randall Mayes – Design & Trend

“For pathologists working out the time of death, research has focused on the way that insects and microbes from a corpse’ environment take up residence in the flesh.”

Tiny hitchhikers, big health impact: Studying the microbiome to learn about disease – Krista Conger – ScopeBlog Stanford

Got microbes? Meet some of the tiny life forms that call you home and may make antibiotics for you (with annoying 5 questions if you want to read the whole article) – Susannah Bodman – Oregon Live

Fighting Poisons With Bacteria – Going Inside the Rice Microbiome – Carina Storrs – NY Times

“Dr. Bais is working to develop rice plants that take up less arsenic, a common contaminant in the fields of his native India and other Asian countries.”

Possum faeces may cause flesh-eating ulcers in humans, Victorian researchers say – ABC Australia

“Infectious disease researchers at Victoria’s Barwon Health have found that possums can carry the buruli bacteria, which can cause major skin ulcers in humans.”

Scientific publishing

Ten Simple Rules for Better Figures – Nicolas P. Rougier – PLOS Computational Biology

“we aim to provide a basic set of rules to improve figure design and to explain some of the common pitfalls.”

The digital toolbox – Nature Editorial

“A new section of Nature examines the software and websites that make research easier.”

Scientific career

There is life after academia – Nature Editorial

“With high numbers of postdocs emerging from universities, prospective PhD students must be prepared for the fact that they will probably not end up with a career in research.”

Bik’s Picks

PBS: Video on the science behind brewing beer hops to it – CNET

“PBS series “It’s Okay To Be Smart” takes a look at how beer is made, and what external factors influence the final product.”

The coffee genome provides insight into the convergent evolution of caffeine biosynthesis -France Denoeud – Science

“We generated a high-quality draft genome of the species Coffea canephora, which displays a conserved chromosomal gene order among asterid angiosperms. “

On the Other Hand – Bob Grant – The Scientist

“Handedness, a conspicuous but enigmatic human trait, may be shared by other animals. What does it mean for evolution and brain function?”

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