May 14, 2019

Good morning microbe lovers! This digest presents papers for everyone taste, plus some really nice general microbiology and science papers. Check out cool snow algae microbiome in Antarctica, soil aggregates microbiome, DNA extraction methods in studying animal microbiomes and more.

Don’t forget to spread MD with friends, colleges and others- it really helps us knowing our hard work is actually being read.

General microbiology

Into the wild: microbiome transplant studies need broader ecological reality , Christopher J. Greyson-Gaito, EcoEcoRxiv

Predicting the decision making chemicals used for bacterial growth, Kazuha Ashino, Scientific Reports

A longitudinal big data approach for precision health, Sophia Miryam Schussler-Fiorenza Rose, Nature Medicine

Human Microbiome

Mammographic breast density and its association with urinary estrogens and the fecal microbiota in postmenopausal women, Gieira S. Jones, PLOS One

Periodontal Health and Oral Microbiota in Patients with Rheumatoid Arthritis, K. Erikkson, Journal of Clinical Medicine

Animal Microbiome

Habitat fragmentation is associated with dietary shifts and microbiota variability in common vampire bats, Melissa R. Ingala, Ecology and Evolution

Fungal disease and temperature alter skin microbiome structure in an experimental salamander system, CR Muletz-Wolz, Molecular Ecology

Variations of the intestinal gut microbiota of farmed rainbow trout, Oncorhynchus mykiss (Walbaum), depending on the infection status of the fish, A.N Parshukov, Journal of Applied Microbiology

Responses of microbial community structure in turbot (Scophthalmus maximus) larval intestine to the regulation of probiotic introduced through live feed, Yan Jiang, PLOS One

Assessment of microbial communities on freshly killed wild boar meat by MALDI-TOF MS and 16S rRNA amplicon sequencing, M.F. Peruzy, Int. Food Microbiology

**Methods Impact of DNA extraction methods on the observed microbial communities from the intestinal flora of the penaeid shrimp Litopenaeus vannamei, Boyun Jiang, FEMS Microbiology Letters

Air Microbiome

** Snow algae communities in Antarctica: metabolic and taxonomic composition, Matthew P. Davey, The New Phytologist

Soil and Plants Microbiome

**Minireview Soil aggregate microbial communities: Towards understanding microbiome interactions at biologically relevant scales, Regina L. Wilpiszeski, App. Env. Microbiology

Comparative microbiome analysis of two different long-term pesticide contaminated soils revealed the anthropogenic influence on functional potential of microbial communities, Raj Kumar Regar, Science of the Total Environment

Interpreting distance‐decay pattern of soil bacteria via quantifying the assembly processes at multiple spatial scales, Maomao Feng, MicrobiologyOpen

Complex microbial communities drive iron and sulfur cycling in Arctic fjord sediments, J. Buongiorno, App. Env. Microbiology

Defining the root endosphere and rhizosphere microbiomes from the World Olive Germplasm Collection, Antonio Jose Fernandez-Gonzales, bioRxiv

Microbiome in the news

Human gut microbiome physiology can now be studied in vitro using Organ Chip technology, Phys.org

Inspirotec Inc and Argonne National Laboratory Collaborate on Largest Study to Date of Airborne Allergens and Microbiome in Same Homes, Globenewswire

Advertisements

General microbiology and science, September 29, 2014

Metabolomics, metagenomics, OTU binning, DNA extraction for metagenomics, RNAseq, life without water, microbes and art, and Bik’s Picks.

Metabolomics

A Peptide-Based Method for 13C Metabolic Flux Analysis in Microbial Communities – Amit Ghosh – PLOS Computational Biology

“Here we propose a new type of 13C MFA that infers fluxes based on peptide labeling, instead of amino acid labeling. “

Metabolic fingerprint of dimethyl sulfone (DMSO2) in microbial-mammalian co-metabolism – Xuan He and Carolyn Marie Slupsky – Journal of Proteome Research

“Here, we review a metabolic pathway that integrates the microbial catabolism of methionine with mammalian metabolism of methanethiol (MT), dimethyl sulfide (DMS) and dimethyl sulfoxide (DMSO)”

Metagenomics

Metagenomic epidemiology: a new frontier – Stephen S Francis, Lee W Riley – Journal of Epidemiology and Community Health

“In this commentary we hope to briefly summarise studies into the bacterial and viral microbiome and how this shifting paradigm affects epidemiology.“

Phages and viruses

Viral attack exacerbates the susceptibility of a bloom-forming alga to ocean acidification – Shanwen Chen – Global Change Biology

“..when the harmful bloom alga Phaeocystis globosa is infected with viruses under future ocean conditions, its photosynthetic performance further decreased and cells became more susceptible to stressful light levels..”

Ecology / Bioinformatics

Limits to robustness and reproducibility in the demarcation of operational taxonomic units – Thomas S. B. Schmidt – Environmental Microbiology

“Using a global data set of 887 870 bacterial 16S rRNA gene sequences, we objectively quantified biases introduced by several widely employed sequence clustering algorithms. “

Techniques

* DNA extraction protocols cause differences in 16S rRNA amplicon sequencing efficiency but not in community profile composition or structure – Benjamin E. R. Rubin – MicrobiologyOpen

“While bacterial community composition recovered using Illumina 16S rRNA amplicon sequencing was not detectably biased by any method, the quantity of bacterial DNA varied drastically, reducing the number of samples that could be amplified and sequenced. “

Protocols for metagenomic DNA extraction and Illumina amplicon library preparation for faecal and swab samples – A.-T. E. Vo1 and J. A. Jedlicka – Molecular Ecology Resources

“We developed and tested a novel metagenomic DNA extraction approach using solid phase reversible immobilization (SPRI) beads on Western Bluebird (Sialia mexicana) samples stored in RNAlater.”

Caught in the act: RNA-Seq provides novel insights into mRNA degradation – Jan Gerwig and Jörg Stülke – Molecular Microbiology

“In MolecularMicrobiology, Liu et al. (2014) have analysed RNA processing by polynucleotide phosphorylase, the major 3′–5′ exonuclease in Bacillus subtilis.”

3D genome reconstruction from chromosomal contacts – Annick Lesne – Nature Methods

“We propose a two-step algorithm, ShRec3D, and assess its accuracy using both in silico data and human genome-wide 3C (Hi-C) data.”

More microbiology

Multiplication of microbes below 0.690 water activity: implications for terrestrial and extraterrestrial life – Andrew Stevenson – Environmental Microbiology

“We discuss water activity in relation to the limits of Earth’s present-day biosphere; the possibility of microbial multiplication by utilizing water from thin, aqueous films or non-liquid sources;”

Microbes in the News

Scientists sniffing out the Western allergy epidemic – BBC News

“Both families gamely agreed to provide bacterial swabs of their skin, guts and even their homes in the hope they might offer clues about why they suffer from allergies.”

Study looks at bacteria on a plane – CNN Wire

“A study by Auburn University looked at how long two potentially deadly bacteria, e-coli and MRSA, can live on airline surfaces. They checked things like toilet handles, tray tables and seat pockets.”

Bacteria in wine may bring health benefits – LiveScience – Agata Blaszczak Boxe

“In the study, researchers in Spain isolated 11 strains of bacteria from wine, including strains of Lactobacillus, which are also found in yogurt, as well as Oenococcus and Pediococcus bacteria, which are associated with the wine-making process.”

A gut feeling: Bacteria like that found in yoghurt may have helped shape our personalities and made us who we are – Alex Finnis – Daily Mail UK

“Bacteria in our stomachs can affect our brain chemistry, scientists have discovered – which means eating yoghurt could help us be happier.

Science and Art

Should Silicon Valley Hire Microbes? – Glenn McDonald – Discovery

“It’s an art installation slated to launch October 21 at San Francisco’s Modernism Gallery. The event will feature the official certification of approximately 100 billion bacteria in areas including product development and finance. “

Octopus bacteria lights up this installation – Liat Clark – Wired UK

“A designer has harvested bacteria from an octopus to create a bioluminescent installation that lights up when it is moved.”

Photographer Immerses His Film in Live Bacteria for Years to Create Unique Portraits – Gannon Burgett – PetaPixel

“Over the course of a few weeks, months or years, the microbes destabilize and eat away at the silver halide particles in the emulsion.”

Bik’s Picks

Dolphins are attracted to magnets: Add dolphins to the list of magnetosensitive animals, French researchers say – Science Daily

“Dolphins are indeed sensitive to magnetic stimuli, as they behave differently when swimming near magnetized objects.”

Science explains why volcanoes are erupting all over the place right now – Robin Wylie – Washington Post

“The Earth seems to have been smoking a lot recently. Volcanoes are erupting in Iceland, Hawaii, Indonesia, Ecuador and Mexico right now. “

Scientists find tiny, poisonous new mystery frog – Andrew Griffin – Independent

“Scientists have discovered a new species of poison dart frog, small enough to fit on a fingernail but still bearing the toxic poison that gives the frogs their name.”

[hr]

General microbiology and science, September 15, 2014

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?”

[hr]

Microbiome Digest, August 1, 2014

Microbiome composition and vaccine response or chemotherapy, cassava beer, two nice articles about metagenomics tools and contamination, and the weekend picks.

Human gut microbiome

Stool Microbiota and Vaccine Responses of Infants – M. Nazmul Huda – Pediatrics

“Actinobacteria abundance was positively associated with T-cell responses to BCG, OPV, and TT; with the delayed-type hypersensitivity response; with immunoglobulin G responses; and with TI. B longum subspecies infantis correlated positively with TI and several vaccine responses. “

Systematic review: the role of the gut microbiota in chemotherapy- or radiation-induced gastrointestinal mucositis – current evidence and potential clinical applications – Y. Touchefeu – Alimentary Pharmacology & Therapeutics

“Search of the literature published in English using Medline, Scopus and the Cochrane Library, with main search terms ‘intestinal microbiota’, ‘bacteremia’, ‘mucositis’, ‘chemotherapy-induced diarrhoea’, ‘chemotherapy-induced mucositis’, ‘radiotherapy-induced mucositis’.”

Food microbiology

Local domestication of lactic acid bacteria via cassava beer fermentation – Alese M. Colehour – PeerJ

“Bacteria responsible for chicha fermentation could be a source of microbes for the human microbiome, but little is known regarding the microbiology of chicha. “

Microbes in the News

It’s a bit – eh – graphic, but a nice overview of science and the people working in this field. I wish it would have contained a couple of pictures of non-pregnant women though. It feels as if we are only a vessel:  The Body’s Ecosystem – The Scientist

“Research on the human microbiome is booming, and scientists have moved from simply taking stock of gut flora to understanding the influence of microbes throughout the body.”

‘I’m not fat, it’s viral’ – Phage found in gut bacteria may aid obesity – Dan Stanton 0 Biopharma Reporter

“A newly discovered virus which infects intestinal bacteria might be a cause of obesity, but could increasing interest in bacteriophages drive new personalised medicines and alternatives to antibiotics?”

Diet Must be Different for Men and Women: Study – Soumo Ghosh – International Business Times

“The researchers found that the microscopic bacteria, or other such organism housed inside the human stomach are different in the case of men and women. Hence, they believe that the same diet for both may not have the same effect in them.”

Metabolomics

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.”

Metagenomics

Metagenomics Mash-Up – Kelly Rae Chi – The Scientist

“The Scientist spoke with developers of tools for parsing genomic data from diverse communities of microorganisms. Here are some of the newest strategies and programs for taxonomic, functional, and comparative analyses.”

Microbial detection

Who are the contaminants in your sequencing project? – Jonathan Eisen – MicrobeNet

“Such amplification is alas pretty common – due to contamination occurring in some other material added to the PCR reaction. “

Science and publishing

The Self-Edited Woman – Paige Brown – SciLogs International

“Un-prompted, several young female science bloggers I’ve interviewed mention having blogged anonymously in the past, being self-conscious about expressing their expertise on a topic, or avoiding certain topics because of the nasty comments they might receive. “

Bik’s Picks

We have the science to build an Ebola vaccine. So why hasn’t it happened? – Sarah Kliff – Vox

“This isn’t how an Ebola outbreak has to work. Researchers have devoted lots of time to building a vaccine that could stop the disease altogether — and according to Daniel Bausch, a Tulane professor who researches Ebola and other infectious diseases, they’re making really significant progress.”

Littering and Following the Crowd – Vivian Wagner – The Atlantic

“Why it’s so tempting to throw trash on the ground, and how environmentalists are using psychology to change that”

F.D.A. Acts on Lab Tests Developed In-House – Andrew Pollack – The New York Times

“The Food and Drug Administration announced on Thursday that it would start regulating medical laboratory testing, saying that tests used to make important treatment decisions must be vetted and validated before they go into use.”

Grad Student Freed By Police After Three Years Trapped In The Same Experiment – The Allium

“He is thought to have survived by eating printouts of PloS One papers and drinking his own tears.”

[hr]

Microbiome Digest, July 25

A year worth of oral/stool samples shows relative stability, antibiotics and preterm infants, reagent contamination, and 42. Have a great weekend!

 

Oral and gut microbiome

Screen Shot 2014-07-25 at 9.45.01 PMHost lifestyle affects human microbiota on daily timescales – Lawrence A David – Genome Biology

“Here, we link over 10,000 longitudinal measurements of human wellness and action to the daily gut and salivary microbiota dynamics of two individuals over the course of one year. These time series show overall microbial communities to be stable for months. However, rare events in each subjects’ life rapidly and broadly impacted microbiota dynamics. “

Pregnancy and Birth

Screen Shot 2014-07-25 at 9.44.20 PMThe impact of postnatal antibiotics on the preterm intestinal microbiome – Majd Dardas – Pediatric Research

“Rectal (fecal) swabs were collected at 10 and 30 d and analyzed by 16S rRNA pyrosequencing. At both time points, we examined the rectal microbiome from infants who received only 2 d of antibiotics and those who received at least 7 d of antibiotics.”

Techniques

Screen Shot 2014-07-25 at 9.45.50 PMReagent contamination can critically impact sequence-based microbiome analyses – Susannah Salter – BioRxiv (preprint)

“In this study we demonstrate that contaminating DNA is ubiquitous in commonly used DNA extraction kits, varies greatly in composition between different kits and kit batches, and that this contamination critically impacts results obtained from samples containing a low microbial biomass. “

Dengue

Speaking about “matter of timing”, seems like this paper came out a bit too late.
Screen Shot 2014-07-25 at 9.46.14 PMDengue and the World Football Cup: A Matter of Timing – Christovam Barcellos, Rachel Lowe – PLOS Neglected Tropical Diseases

“We provide a nationwide risk map, averaging June dengue incidence rates for 2001–2012. The areas along the Amazonian rivers and in the inner portions of southernmost states are actually low-risk areas, while elevated dengue risk is found in the central Brazilian plateau.”

Infection and host response

Don’t forget your towel! Even the issue number, 1004201, contains the “The Answer to the Ultimate Question of Life, the Universe, and Everything”. Perfection.
Screen Shot 2014-07-25 at 9.46.22 PMMicrobial Egress: A Hitchhiker’s Guide to Freedom – Ana Traven, Thomas Naderer – PLOS Pathogens

“The Restaurant at the End of the Infection — Macrophages as Host Cells”
“So Long and Thanks for All the Inflammatory Cell Death”

Dr. Bik’s Picks

crowSmarter than a first-grader? Crows can perform as well as 7- to 10-year-olds on cause-and-effect water displacement tasks

“New research conducted by UC Santa Barbara’s Corina Logan, with her collaborators at the University of Auckland in New Zealand, demonstrates the birds’ intellectual prowess may be more fact than fiction.”

JBC Journal of Biological ChemistryFour billion-year-old chemistry in cells today – Phys.org

“Parts of the primordial soup in which life arose have been maintained in our cells today according to scientists at the University of East Anglia.”

Screen Shot 2014-07-25 at 9.47.50 PMDustup Over Lionfish Science Fair Project – Bob Grant – The Scientist

A former graduate student says he feels slighted by a failure to attribute his contributions to a line of research regarding the salinity tolerances of an invasive species. “I’m not sure what happened, but my main issue is that the national media has presented a story that is sensationalized, and has left me out of the picture.”

[hr]

General microbiology and science, July 15

Dengue virus replication, poliovirus transmission, marine viral communities, primer choice, and CRISPRs systems and antibiotic resistance.

Dengue virus

Letter: Are viral small RNA regulating Dengue virus replication beyond serotype 2? – Esteban Finol – PNAS

Letter: Reply to Finol: Viral small RNA from Dengue virus and its egulatory role in different serotypes – Mazhar Hussain and Sassan Asgari – PNAS

Poliovirus

Screen shot 2014-07-15 at 06.00PM, Jul 15The role of older children and adults in wild poliovirus transmission – Isobel M. Blake – PNAS

“We fit a mathematical model of poliovirus transmission to time series data from two large outbreaks that affected adults (Tajikistan 2010, Republic of Congo 2010) using maximum-likelihood estimation based on iterated particle-filtering methods. “

Phages and viruses

Screen shot 2014-07-15 at 06.01PM, Jul 15Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses – Bonnie L. Hurwitz – PNAS

“Here we combine advances in bioinformatics (shared k-mer analyses) and social networking (regression modeling) to develop an annotation- and assembly-free visualization and analytical strategy for comparative metagenomics that uses all the data in a unified statistical framework. “

Screen shot 2014-07-15 at 06.02PM, Jul 15Contrasted coevolutionary dynamics between a bacterial pathogen and its bacteriophages – Alex Betts – PNAS

“We used experimental evolution between Pseudomonas aeruginosa and a panel of its lytic phages and found the full known range of coevolutionary dynamics.”

CRISPRs and antibiotic resistance

Screen shot 2014-07-15 at 06.03PM, Jul 15A CRISPR-Cas system enhances envelope integrity mediating antibiotic resistance and inflammasome evasion – Timothy R. Sampson – PNAS

“We demonstrate that components of a clustered, regularly interspaced, short palindromic repeats–CRISPR associated (CRISPR-Cas) system, a prokaryotic defense against viruses and foreign nucleic acid, act to regulate the permeability of the bacterial envelope, ultimately providing these cells with the capability to resist membrane damage caused by antibiotics. “

Extraction and amplification techniques

The Influence of DNA Extraction Procedure and Primer Set on the Bacterial Community Analysis by Pyrosequencing of Barcoded 16S rRNA Gene Amplicons – Ingo C. Starke – Molecular Biology International

“In this study, the effect of different DNA extraction procedures and primer sets on pyrosequencing results regarding the composition of bacterial communities in the ileum of piglets was investigated. “

Metagenomics general

Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution – Mikhail Tikhonov – ISME Journal

“We present a clustering-free approach to multi-sample Illumina data sets that can identify independent bacterial subpopulations regardless of the similarity of their 16S tag sequences. “

 

General Microbiology

Screen shot 2014-07-15 at 06.04PM, Jul 15Recovery of a Medieval Brucella melitensis Genome Using Shotgun Metagenomics – Gemma L. Kay – mBio

“We sequenced the metagenome of a calcified nodule from the skeleton of a 14th-century middle-aged male excavated from the medieval Sardinian settlement of Geridu. We obtained 6.5-fold coverage of a Brucella melitensis genome”

Screen shot 2014-07-15 at 06.05PM, Jul 15Review: The Ins and Outs of Bacterial Iron Metabolism – Elaine R. Frawley and Ferric C. Fang – Molecular Microbiology

“The recent discovery of putative iron efflux transporters in Salmonella enterica serovar Typhimurium is discussed in the context of cellular iron homeostasis.”

Screen shot 2014-07-15 at 06.05PM, Jul 15 1Genetic information transfer promotes cooperation in bacteria – Tatiana Dimitriu – PNAS

“Our experiments and models converge to show that when both cheating and cooperative genes are transferred, cooperators win against cheaters because transfer increases assortment among alleles, favoring cooperation.”

Challenges and Opportunities of Integrative Taxonomy for Research and Society – Taxonomic Research in the Era of OMICS Technologies (PDF)  (Herausforderungen und Chancen der integrativen Taxonomie für Forschung und Gesellschaft) – Deutsche Akademie der Naturforscher Leopoldina e.V.

Microbiomes and metagenomes in need of professional classification – Rudolf Amann
The intestinal microbiome and human health: a new challenge for taxonomy of metagenomic data – Bärbel Stecher
Characterizing species boundaries and species histories in closely related fungi using comparative population genomic approaches – Eva H. Stukenbrock

Coming of ageThe coming of age of microbial ecology – Ana E. Escalante and Silvia Pajares – Chapter in Open Access book: Frontiers in Ecology, Evolution and Complexity

“Despite major challenges, new technological advances in genomic sciences have prompted microbial ecology into a revolution in data generation that has allowed us to move beyond studies of single isolates to the study of entire microbial communities without reliance on culture-dependent methods.”

Review: The Dynamic Interactions between Salmonella and the Microbiota, within the Challenging Niche of the Gastrointestinal Tract – C. M. Anjam Khan – International Scholarly Research Notices

“This gastrointestinal pathogen not only faces the hostile defenses of the host’s immune system, but also faces fierce competition from the large and diverse community of microbiota for space and nutrients.”

 

Science and publishing

Screen shot 2014-07-15 at 05.59PM, Jul 15Is Social Media Saving Science? – Michael White – Pacific Standard

“Why do editors and expert reviewers, whose primary job is to vet manuscripts, miss major flaws that are so obvious to readers after the papers are published?”

Dr. Bik’s Picks

Screen shot 2014-07-15 at 06.07PM, Jul 15Effect of sleep deprivation on the human metabolome – Sarah K. Davies – PNAS

“Clear daily rhythms were observed in most metabolites, with 24 h wakefulness mainly reducing the amplitude of these rhythms.”

Screen shot 2014-07-15 at 06.06PM, Jul 15Comparison of five different RNA sources to examine the lactating bovine mammary gland transcriptome using RNA-Sequencing – Angela Cánovas – Nature Scientific Reports

“Our results provide a comparison between different sampling methods (invasive and non-invasive) to define the transcriptome of mammary gland tissue and milk cells.’

Screen shot 2014-07-15 at 06.07PM, Jul 15 1Superior time perception for lower musical pitch explains why bass-ranged instruments lay down musical rhythms – Michael J. Hove – PNAS

“Here, we show that, when two streams of tones are presented simultaneously, the brain better detects timing deviations in the lower-pitched than in the higher-pitched stream and that tapping synchronization to the tones is more influenced by the lower-pitched stream. “

[hr]

Non-human microbiomes, June 9

Phages in cow dung, genome of a bumble-bee symbiont, and the microbiome of beach sand.

Mammal microbiomes

Screen shot 2014-06-09 at 02.43PM, Jun 09Differing Populations of Endemic Bacteriophages in Cattle Shedding High and Low Numbers of Escherichia coli O157:H7 Bacteria in Feces – J. Hallewell – Applied and Environmental Microbiology

“Based on genome size estimated by pulsed-field gel electrophoresis and morphology determined by transmission electron microscopy, T4- and O1-like phages of Myoviridae and T1-like phage of Siphoviridae were isolated. “

Insect microbiomes

Screen shot 2014-06-09 at 02.59PM, Jun 09Genomic Features of a Bumble Bee Symbiont Reflect Its Host Environment – Vincent G. Martinson – Applied and Environmental Microbiology

“Here, we report the genome of one gammaproteobacterial member of the gut microbiota, for which we propose the name “Candidatus Schmidhempelia bombi,” that was inadvertently sequenced alongside the genome of its host, the bumble bee, Bombus impatiens.”

Plant microbiomes

Screen shot 2014-06-09 at 02.52PM, Jun 09In Situ Evaluation of Paenibacillus alvei in Reducing Carriage of Salmonella enterica Serovar Newport on Whole Tomato Plants – Sarah Allard – Applied and Environmental Microbiology

“Long-term intervention measures to reduce Salmonella prevalence on tomatoes remain elusive for growing and postharvest environments. A naturally occurring bacterium identified by 16S rRNA gene sequencing as Paenibacillus alvei was isolated epiphytically from plants native to the Virginia Eastern Shore tomato-growing region. “

Screen shot 2014-06-09 at 03.20PM, Jun 09Streptomyces sp. strain PGPA39 alleviates salt stress and promotes growth of ‘Micro Tom’ tomato plants – Sasikumar Arunachalam Palaniyandi – Journal of Applied Microbiology

“A significant increase in plant biomass and chlorophyll content, and a reduction in leaf proline content were observed in PGPA39-inoculated tomato plants under salt stress compared to control and salt stressed non-inoculated plants.”

Screen shot 2014-06-09 at 02.54PM, Jun 09Microscopy, Culture, and Quantitative Real-Time PCR Examination Confirm Internalization of Mycobacteria in Plants – M. Kaevska – Applied and Environmental Microbiology

” The substrate into which plants were seeded was previously contaminated with different strains of Mycobacterium avium (108to 1010 cells/g of soil) and feces from animals with paratuberculosis. We detected M.avium subsp. aviumhominissuis, and paratuberculosis in the stems and leaves of the plants by both culture and real-time quantitative PCR. “

Environmental microbiomes

Screen shot 2014-06-09 at 02.40PM, Jun 09

Soil and groundwater microbiomes

Use of Silicate Minerals for pH Control during Reductive Dechlorination of Chloroethenes in Batch Cultures of Different Microbial Consortia  – Elsa Lacroix – Applied and Environmental Microbiology

“The consortia showed significant differences in sensitivities toward acidic pH for the different dechlorination steps. Molecular analysis indicated that Dehalococcoides spp. that were present in all consortia were the most pH-sensitive organohalide-respiring guild members compared to Sulfurospirillum spp. and Dehalobacter spp.”

Screen shot 2014-06-09 at 03.01PM, Jun 09Variables Influencing Extraction of Nucleic Acids from Microbial Plankton (Viruses, Bacteria, and Protists) Collected on Nanoporous Aluminum Oxide Filters – Jaclyn A. Mueller – Applied and Environmental Microbiology

“Anodic aluminum oxide (AAO) filters have high porosity and can be manufactured with a pore size that is small enough to quantitatively capture viruses. These properties make the filters potentially useful for harvesting total microbial communities from water samples for molecular analyses, but their performance for nucleic acid extraction has not been systematically or quantitatively evaluated. “

Screen shot 2014-06-09 at 03.08PM, Jun 09MS2 Bacteriophage Reduction and Microbial Communities in Biosand Filters – Hanting Wang – Environmental Science & Technology

” In the upper layers, “CandidatusNitrosopumilus maritimus” and “Ca. Nitrospira defluvii” were found as dominant populations, while significant amounts of Thiobacillus-related OTUs were detected in the lower layers. “

Ponds, lakes, and ocean microbiomes

Screen shot 2014-06-09 at 02.48PM, Jun 09Diversity and Transport of Microorganisms in Intertidal Sands of the California Coast – Alexandria B. Boehm – Applied and Environmental Microbiology

“The present study uses next-generation massively parallel sequencing to characterize the microbial community present at 49 beaches along the coast of California. In addition, we characterize the transport of microorganisms within intertidal sands using laboratory column experiments. We identified extensive diversity in the beach sands.”

Screen shot 2014-06-09 at 02.46PM, Jun 09From Metagenomics to Pure Culture: Isolation and Characterization of the Moderately Halophilic Bacterium Spiribacter salinus gen. nov., sp. nov. – María José León – Applied and Environmental Microbiology

“We report the isolation and taxonomic characterization of this new, never before cultured microorganism, designated M19-40T, isolated from a saltern located in Isla Cristina, Spain, using a medium with a mixture of 15% salts, yeast extract, and pyruvic acid as the carbon source. “

Screen shot 2014-06-09 at 03.05PM, Jun 09The Pattern of Change in the Abundances of Specific Bacterioplankton Groups Is Consistent across Different Nutrient-Enriched Habitats in Crete – Stilianos Fodelianakis – Applied and Environmental Microbiology

“Here, we investigated the bacterial community changes at three different nutrient-enriched and adjacent undisturbed habitats along the north coast of Crete, Greece: a fish farm, a closed bay within a town with low water renewal rates, and a city port where the level of nutrient enrichment and the trophic status of the habitat were different. “

[hr]