Microbiome digest, October 21, 2014

Human oral microbiome

Abstract 4834: Microbiome in Oral Epithelial Dysplasia and Squamous Cell Carcinoma
Deepak Saxena – Cancer Research

“PCR amplicons targeting V3-V5 region of 16S rRNA gene were sequenced by 454 pyrosequencing. “

Human respiratory microbiome

Microbial Communities in the Upper Respiratory Tract of Patients with Asthma and Chronic Obstructive Pulmonary Disease – HeeKuk Park – PLOS ONE

“To account for the qualitative and quantitative diversity of the 16S rRNA gene in the oropharynx, the microbiomes of 18 asthma patients, 17 COPD patients, and 12 normal individuals were assessed using a high-throughput next-generation sequencing analysis.”

Human gut microbiome

Decreased bacterial diversity characterizes an altered gut microbiota in psoriatic arthritis and resembles dysbiosis of inflammatory bowel disease – Jose U. Scher – Arthritis & Rheumatology

“High-throughput 16S rRNA pyrosequencing was utilized to compare community composition of gut microbiota in PsA patients, subjects with psoriasis of the skin and healthy, matched-controls. “

Pregnancy and birth

The Salivary Scavenger and Agglutinin in Early Life: Diverse Roles in Amniotic Fluid and in the Infant Intestine – Martin Parnov Reichhardt – Journal of Immunology

“The present study revealed that SALSA was present in the amniotic fluid (AF) and exceptionally enriched in both meconium and feces of infants. “

Animal microbiome

* Unique and shared responses of the gut microbiota to prolonged fasting: a comparative study across five classes of vertebrate hosts – Kevin D. Kohl – FEMS Microbiology Ecology

“We used 16S rRNA sequencing to document changes in colonic and cecal microbiomes of animals representing five classes of vertebrates at four time points through prolonged fasting: tilapia, toads, geckos, quail, and mice. “

GeoChip-based insights into the microbial functional gene repertoire of marine sponges (HMA, LMA) and seawater – Kristina Bayer – FEMS Microbiology Ecology

“By use of GeoChip, altogether 20,273 probes encoding for 627 functional genes and representing 16 gene categories were identified”

Natural volcanic CO2 seeps reveal future trajectories for host–microbial associations in corals and sponges – Kathleen M Morrow – ISME Journal

“The corals Acropora millepora and Porites cylindrica were less abundant and hosted significantly different microbial communities at the CO2 seep than at nearby control sites <500 m away.”
Plant microbiome

Phylogenetic conservatism in plant-soil feedback and its implications for plant abundance – Brian L. Anacke – Ecology Letters

“We conclude that soil biota influence the abundance of close plant relatives in nature.”

Bioreactor microbiome

Influence of Acidic pH on Hydrogen and Acetate Production by an Electrosynthetic Microbiome – Edward V. LaBelle – PLOS ONE

“Production of hydrogen and organic compounds by an electrosynthetic microbiome using electrodes and carbon dioxide as sole electron donor and carbon source, respectively, was examined after exposure to acidic pH (~5). “

Metagenomics / Transcriptomics / Bioinformatics

Census-based rapid and accurate metagenome taxonomic profiling – Amirhossein Shamsaddini – BMC Genomics

“We have developed a robust subsampling-based algorithm implemented in a tool called CensuScope meant to take a ‘sneak peak’ into the population distribution and estimate taxonomic composition as if a census was taken of the metagenomic landscape. “

Metatranscriptomes from diverse microbial communities: assessment of data reduction techniques for rigorous annotation – Andrew Toseland – BMC Genomics

“To investigate the effect of such techniques on the annotation of metatranscriptome data we assess two commonly employed methods: clustering and de-novo assembly. To do this, we also developed an approach to simulate 454 and Illumina metatranscriptome data sets with varying degrees of taxonomic diversity. “

Microbial Ecology

Mathematical Modeling of Microbial Community Dynamics: A Methodological Review – Hyun-Seob Song – Processes

“In this article, we provide an overview of mathematical tools that include not only current mainstream approaches, but also less traditional approaches that, in our opinion, can be potentially useful. “

A phylogenetic perspective on species diversity, β-diversity, and biogeography for the microbial world – Albert Barberán† and Emilio O. Casamayor – Molecular Ecology

“We explored links between evolution/phylogeny and community ecology using bacterial 16S rRNA gene information from a high altitude lakes district dataset to describe phylogenetic community composition, spatial distribution, and β-diversity and biogeographical patterns applying evolutionary relatedness without relying on any particular operational taxonomic unit definition.”

Distance-Decay and Taxa-Area Relationships for Bacteria, Archaea and Methanogenic Archaea in a Tropical Lake Sediment – Davi Pedroni Barreto – PLOS ONE

“The samples were analyzed using T-RFLP (Terminal restriction fragment length polymorphism) targeting mcrA (coding for a subunit of methyl-coenzyme M reductase) and the genes of Archaeal and Bacterial 16S rRNA.”

More microbiology

From Denise Monack’s lab: Role of disease-associated tolerance in infectious superspreaders – Smita Gopinath – PNAS USA

“Using a mouse model of Salmonella infection, we show that levels of Salmonella are equivalent between antibiotic-treated superspreader and nonsuperspreader hosts; however, superspreader hosts are uniquely able to tolerate antibiotic treatment, unlike nonsuperspreader hosts. “

*Also see:  Antibiotics may help Salmonella spread in infected animals, scientists learn – Stanford Medicine News

Spatial organization of bacterial chromosomes – Xindan Wang, David Z Rudner – Current Opinion in Microbiology

“Here, we summarize these different patterns highlighting similarities and differences and discuss the protein factors that help establish and maintain them.”

Bacterial healers: Microbes can redeem themselves to fight disease – Susan Gaidos – Science News

“It’s just a matter of time before bacterial-based treatments become a routine part of a doctor’s toolkit, says microbiologist Robert Britton of the Baylor College of Medicine in Houston, who is studying the relationship between microbes and human health. “

Techniques

Rapid fingerprinting of methanogenic communities by high-resolution melting analysis – Jaai Kim, Changsoo Lee – Bioresource Technology

“The new method produced robust community clustering and ordination results comparable to the results from the commonly used denaturing gradient gel electrophoresis (DGGE) performed in parallel.”

Microbes in the news

Our unique ‘microbial aura’ travels with us wherever we go – Science Friday – PRI

“Unless you lived exactly the same life as me, you would not have the same microbiome. You are, in essence, microbially unique,” explains Jack Gilbert

We’re making a Microbiome Documentary Series and could use your Help – Jamie – Reddit

“My name’s Jamie and I’m part of a team trying to crowdfund a documentary series on the human microbiome titled: ‘Redefining Human’.”

Building houses with bacteria – Euronews

“Houses of the future could be partially built with bacteria. It sounds like science fiction but researchers involved in an EU-backed project in Madrid are working towards making this a concrete reality.”

Bik’s Picks

The Role of Surface Chemistry in Adhesion and Wetting of Gecko Toe Pads – Ila Badge – Scientific Reports

“As expected, under wet conditions, adhesion on a hydrophilic surface (glass) was lower than that on a hydrophobic surface (alkyl-silane monolayer on glass).”

Scientists prepare for an 8-month mission to Mars – on Earth soil- BetaWired

“There’s a new experiment commencing in Hawaii, and the results will help NASA better prepare its astronauts for a lengthy mission to Mars.”

White rhino subspecies is down to one breeding male – Andrea James – BoingBoing

“Sad news from Kenya: the northern white rhino subspecies is down to one breeding male with the death of Suni this month. Only six remain.”

Scientists restore hearing in noise-deafened mice, pointing way to new therapies – ScienceDirect

“Scientists have restored the hearing of mice partly deafened by noise, using advanced tools to boost the production of a key protein in their ears.”

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General microbiology and science, August 5, 2014

Antibiotic resistance, phages, bioinformatics tools, and how to present your research in 3 minutes.

Antibiotic resistance

The Natural Environment May Be the Most Important Source of Antibiotic Resistance Genes – Desmond Keith O’Toole – mBio

“I found the recent paper by Wichmann et al. (1) of great interest, and it illustrates an aspect of antibiotic resistance that has concerned me for a long time, namely, the origin of that resistance.”

Phages and viruses

Pervasive domestication of defective prophages by bacteria – Louis-Marie Bobay, Marie Touchon, and Eduardo P. C. Rocha – PNAS USA

“We identified over 300 vertically inherited prophages within enterobacterial genomes. Some of these elements are very old and might predate the split between Escherichia coli and Salmonella enterica. “

Bioinformatics tools

MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm – Yu-Wei Wu, Yung-Hsu Tang, Susannah G Tringe, Blake A Simmons and Steven W Singer – Microbiome

“We have developed a binning algorithm, MaxBin, which automates the binning of assembled metagenomic scaffolds using an expectation-maximization algorithm after the assembly of metagenomic sequencing reads.”

Fast and Sensitive Alignment of Microbial Whole Genome Sequencing Reads to Large Sequence Datasets on a Desktop PC: Application to Metagenomic Datasets and Pathogen Identification – Lőrinc S. Pongor – PLOS ONE

“We have developed Taxoner, an open source, taxon assignment pipeline that includes a fast aligner (e.g. Bowtie2) and a comprehensive DNA sequence database. “

More microbes

Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever – Zhemin Zhou, Angela McCann, François-Xavier Weill, Camille Blin, Satheesh Nair, John Wain, Gordon Dougan, and Mark Achtman – PNAS

“We identified seven modern lineages among 149 genomes on the basis of 4,584 SNPs in the core genome and estimated that Paratyphi A originated 450 y ago. “

Bacillus subtilis chromosome organization oscillates between two distinct patterns – Xindan Wang, Paula Montero Llopis, and David Z. Rudner – PNAS USA

“We propose that the distinct organization patterns observed for bacterial chromosomes reflect a common organization–segregation mechanism, and that simple modifications to it underlie the unique patterns observed in different species.”

Microbes in the news

Researchers Find Surprises in Human Microbiome – Carol Potera – BioScience

But “some forms of autism may have an etiology that lies in the gut, not the brain,” says Sarkis Mazmanian of the California Institute of Technology.

Science and publishing

Science Speak – Rina Shaikh-Lesko – The Scientist

“Contests that challenge young scientists to explain their research without jargon are turning science communication into a competitive sport.”

Researcher’s death shocks Japan – David Cyranoski – Nature Newsblog

“Yoshiki Sasai, one of Japan’s top stem-cell researchers, died this morning (5 August) in an apparent suicide. “

Bik’s Picks

The color red distorts time perception for men, but not for women – Masahiro Shibasaki & Nobuo Masataka – Nature Scientific Reports

“The results showed that the perceived duration of a red screen was longer than was that of a blue screen. However, the results reflected sex differences; men, but not women, overestimated the duration of the red screen. “

Gray’s paradox: A fluid mechanical perspective – Rahul Bale, Max Hao, Amneet Pal Singh Bhalla, Namrata Patel & Neelesh A. Patankar – Nature Scientific Reports

“Nearly eighty years ago, Gray reported that the drag power experienced by a dolphin was larger than the estimated muscle power – this is termed as Gray’s paradox. We provide a fluid mechanical perspective of this paradox.”

 

Total darkness at night key to success of breast cancer therapy, study shows – Science Daily

“Exposure to light at night, which shuts off nighttime production of the hormone melatonin, renders breast cancer completely resistant to tamoxifen, a widely used breast cancer drug, says a new study. “

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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. “

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General microbiology and science digest, July 2

Genome assembly, metabolomics of Salmonella infection, a brief history of women in science (but in Nature!), and Nature’s retraction of the STAP papers.

Metagenomics

Screen Shot 2014-07-02 at 10.13.28 PMBayesian Genome Assembly and Assessment by Markov Chain Monte Carlo Sampling – Mark Howison – PLOS ONE

“We present a Markov chain Monte Carlo approach to sequence assembly that instead generates distributions of assembly hypotheses with posterior probabilities, providing an explicit statistical framework for evaluating alternative hypotheses and assessing assembly uncertainty. “

Infection and host response

Screen Shot 2014-07-02 at 10.14.12 PMSalmonella Typhi and Salmonella Paratyphi – A elaborate distinct systemic metabolite signatures during enteric fever – Elin Näsström – eLife

“To investigate metabolite signals associated with enteric fever we performed two dimensional gas chromatography with time-of-flight mass spectrometry (GCxGC/TOFMS) on plasma from patients with S. Typhi and S. Paratyphi A infections and asymptomatic controls, identifying 695 individual metabolite peaks.”

and: Host-pathogen interactions: Honing in on enteric fever – Lyle R McKinnon, Quarraisha Abdool Karim – eLife

“The use of metabolomics could lead to improved diagnostics for enteric fever. “

Screen Shot 2014-07-02 at 10.14.58 PMHuman Genetic Variation and Yellow Fever Mortality during 19th Century U.S. Epidemics – Lauren E Blake, Mariano A Garcia-Blanco – mBio

“Caucasians diagnosed with YF were 6.8 times more likely to succumb than non-Caucasians with the disease. No other major causes of death during the 19th century demonstrated a similar mortality skew toward Caucasians. “

Bacterial and viral detection in clinical samples

Screen Shot 2014-07-02 at 10.15.58 PMThe Microbial Detection Array for Detection of Emerging Viruses in Clinical Samples – A Useful Panmicrobial Diagnostic Tool – Maiken W. Rosenstierne – PLOS ONE

“We report a modified Whole Transcriptome Amplification (WTA) method that increases unbiased amplification, particular of RNA viruses.”

The Sooner, The Better – Nicholette Zeliadt – The Scientist

“New approaches to diagnosing bacterial infections may one day allow the identification of pathogens and their antibiotic susceptibility in a matter of hours or minutes.”

Screen Shot 2014-07-02 at 10.16.45 PMReview: Biosensors for Whole-Cell Bacterial Detection – Asif Ahmed – Clinical Microbiology Reviews

” In this review, we discuss recent progress in the use of biosensors for the detection of whole bacterial cells for sensitive and earlier identification of bacteria without the need for sample processing.”

Screen Shot 2014-07-02 at 10.17.23 PMIsolation of Microorganisms Using Sub-Micrometer Constrictions – Nil Tandogan – PLOS ONE

“We present an automated method for isolating pure bacterial cultures from samples containing multiple species that exploits the cell’s own physiology to perform the separation.”

Phages and viruses

Screen Shot 2014-07-02 at 10.18.17 PMFour Escherichia coli O157:H7 Phages: A New Bacteriophage Genus and Taxonomic Classification of T1-Like Phages – Yan D. Niu – PLOS ONE

“Comparative genomic, proteomic and phylogenetic analysis suggested that the four phages along with 17 T1-like phage genomes from database of National Center for Biotechnology Information (NCBI) can be assigned into a proposed subfamily “Tunavirinae” with further classification into five genera”

Dengue

Screen Shot 2014-07-02 at 10.18.45 PMClinical and Virological Descriptive Study in the 2011 Outbreak of Dengue in the Amazonas, Brazil – Valquiria do Carmo Alves Martins – PLOS ONE

“The aim of the study was to describe the clinical epidemiology of dengue in Manaus, the capital city of the state of the Amazonas, where all the four DENV serotypes were co-circulating simultaneously.”

Phylogeny and taxonomy

Screen Shot 2014-07-02 at 10.12.14 PMComparative Genomics of the Bacterial Genus Streptococcus Illuminates Evolutionary Implications of Species Groups – Xiao-Yang Gao – PLOS ONE

“We use comparative genomic approaches to yield a better understanding of the evolution of Streptococcus through genome dynamics, population structure, phylogenies and virulence factor distribution of species groups. “

Screen Shot 2014-07-02 at 10.12.46 PMLivestock-Associated MRSA Carriage in Patients without Direct Contact with Livestock – Miranda M. L. van Rijen – PLOS ONE

“Fifty-six individuals (20.7%) without animal contact carried MC398. In hospitals with high pig-densities in the adherence area, the proportion of MC398 of all MUO was higher than this proportion in hospitals without pigs in the surroundings.”

 Arsenic metabolism

Screen Shot 2014-07-02 at 10.02.56 PMMichigan’s arsenic problem is among the worst in the nation. Here’s why that matters – Rebecca Williams – Michigan Radio

“If you’re on city water, your drinking water has to comply with a federal regulation that limits the amount of arsenic in it, but if you’re on a private well, the federal and state governments do not limit the amount of arsenic in your well.”

Women in Science

Screen Shot 2014-07-02 at 9.59.45 PMWomen in science: A temporary liberation – Patricia Fara – Nature

“The First World War ushered women into laboratories and factories. In Britain, it may have won them the vote, argues Patricia Fara, but not the battle for equality.”

Science and Ethics

Nature Editorial: STAP retracted – Nature

“This week, Nature publishes retractions of two high-profile papers that claimed a major advance in the field of stem cells… We — research funders, research practitioners, institutions and journals — need to put quality assurance and laboratory professionalism ever higher on our agendas, to ensure that the money entrusted by governments is not squandered, and that citizens’ trust in science is not betrayed.”

Dr. Bik’s Picks

Screen Shot 2014-07-02 at 10.11.31 PMPLOS ONE Publishes its 100,000th Article – Damian Pattinson – PLOS Blogs

“PLOS ONE publishes its 100,000th article – a pretty major milestone for a journal that has seen its fair share of momentous events, and a perfect opportunity to reflect on this journey.”

Screen Shot 2014-07-02 at 10.08.37 PMLeprosy, Still Claiming Victims – Natalie Angier, New York Times

““I’m absolutely convinced that leprosy must be thought of as a genetic disease as well as an infectious one,” Dr. Schurr said. In the end, he added wryly, “understanding it may help cure diseases of rich people, too.””

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