Tag Archives: phages

Microbiome digest, October 10, 2014

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A quiet day in microbiome literature. Some general microbiome reviews, a phage commonly found in insect symbionts, and an unusual fecal transplant.

General microbiome

Viruses and the Microbiota – Christopher M. Robinson and Julie K. Pfeiffer – Annual Review of Virology

“This review examines the known effects and mechanisms by which microbiota influence mammalian virus infections.”

Review: The Microbiota, Chemical Symbiosis, and Human Disease – Matthew R. Redinbo – Journal of Molecular Biology

“Here, the recent literature linking the microbiota to diseases of three of the key mammalian mucosal epithelial compartments – nasal, lung and gastrointestinal (GI) tract – is reviewed with a focus on new knowledge about the taxa, species, proteins and chemistry that promote health and impact progression toward disease.”

Human gut microbiome

Alien Invasions and Gut “Island Biogeography” – Edward F. DeLong – Cell

“Now, Seedorf et al. show that microbiota from a variety of disparate habitats can successfully colonize and compete in the mammalian gut environment.”

Review: The small intestine microbiota, nutritional modulation and relevance for health – Sahar El Aidy – Current Opinion in Biotechnology (April 2015 issue!)

“This review highlights the recent advances made in the study of the human small intestine microbiota”

The Opposing Forces of the Intestinal Microbiome and the Emerging Pathobiome – Jennifer Defazio – Surgical Clinics of North America

Insect microbiome

Arsenophonus insect symbionts are commonly infected with APSE, a bacteriophage involved in protective symbiosis – Olivier Duron – FEMS Microbiology Ecology

“APSE was found in association with two-thirds of the Arsenophonus strains examined and from a variety of insect groups such as aphids, white flies, parasitoid wasps, triatomine bugs, louse flies, and bat flies.”

Microbes in the news

Beyond the call: Scientist self-administers fecal transplant in search for healthy microbiome – Helen Clark – GizMag

“Jeff Leach’s first-person narrative bookends a fascinating discussion on the changing nature of gut bacteria in many Western societies”

Dr. Raphael Kellman’s Microbiome Diet – Faith Middleton, Lori Mack, Jonathan McNicol – WNPR News

“Repair and boost the bacteria in the gut with the right food, prebiotics and probiotics, and you’ll feel better and lose weight. That’s the theory of Dr. Raphael Kellman of New York, author of The Microbiome Diet.”

The Mad Science Behind OMSI’s Greatest Exhibits – Nathan Tucker

“During my visit, the primary focus is on the shop’s next big traveling exhibition, an NSF-funded exploration of the human microbiome called The Zoo in You. “

Study Shows Rebiotix Microbiota-based Drug Candidate Targeted at Recurrent C. difficile Infection is Highly Effective – PR Newswire – SysCon

“Results for groundbreaking multi-center study of lead drug candidate RBX2660 (microbiota suspension) presented at IDWeek 2014”

Bik’s Picks

Gross! Or is it? University pushes peeing in the shower to save water – Megan Holohan – Today

“The campaign, aptly titled “Go with the Flow,” claims that if every student peed in the shower once daily, the university would save about $230,000 a year on water.”

‘Giant leap’ to type 1 diabetes cure – James Gallagher – BBC News Healthy

“A team at Harvard University used stem cells to produce hundreds of millions of the cells in the laboratory.”

Want to stay thin? Strap ice packs around body – Kounteya Sinha – Times of India

“Exposure to cold temperatures can convert white fat tissue from the thighs and belly to beige fat that burns calories for heat.“

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General microbiology and science digest, October 6, 2014

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Phages to reduce biofilms or monitor virus outbreaks, binning metagenomic reads, lots of microbes in the news. In Bik’s Picks, we have the 2014 Nobel Prize for Medicine and a giant ant nest.

 

More Microbes

Combined Use of Bacteriophage K and a Novel Bacteriophage To Reduce Staphylococcus aureus Biofilm Formation – D. R. Alves – Applied and Environmental Microbiology

“DRA88 was mixed with phage K to produce a high-titer mixture that showed strong lytic activity against a wide range of S. aureus isolates, including representatives of the major international MRSA clones and coagulase-negative Staphylococcus. “

Detection of Pathogenic Viruses in Sewage Provided Early Warnings of Hepatitis A Virus and Norovirus Outbreaks – Maria Hellmér – Applied and Environmental Microbiology

“ In this study, the presence of eight pathogenic viruses (norovirus, astrovirus, rotavirus, adenovirus, Aichi virus, parechovirus, hepatitis A virus [HAV], and hepatitis E virus) was investigated in sewage to explore whether their identification could be used as an early warning of outbreaks. “

Bioinformatics

New software aims to improve sorting the microbiome – The Cherry Creek News

“MaxBin automates the binning of assembled metagenomic scaffolds using an expectation-maximization algorithm after the assembly of metagenomic sequencing reads,” says Singer, a chemist who also holds an appointment with Berkeley Lab’s Earth Sciences Division. “

Microbes in the news

* King’s launches British Gut – King’s College London

“British Gut – the UK’s largest open-source science project to understand the microbial diversity of the human gut – has been launched today by the Department of Twin Research at King’s College London, in collaboration with American Gut.”

Pay attention to your gut bacteria – Charles Wallace – Financial Times

“A number of organisations, such as Mr Leach’s own American Gut project and the commercial venture uBiome, offer an analysis of the bacteria in your gut for about $100. “

Home sweet microbiome – By Scott LaFee – UT San Diego

“The University of Chicago recently published findings from its Home Microbiome Project, which surveyed the domiciles of seven families: 18 people, three dogs and one cat.”

Medical superbugs: Antibiotic-resistant bacteria carried by more than a third of nursing home residents, study – ABC Australia

“Scientists from Monash University swabbed more than a 100 residents from four high-care facilities across the city.”

Special bacteria, 13000 cleaners to clean Dhaka – Rezaul Hoque – BDNews

“This special kind of microorganism will be sprayed on waste dumps. The spray has been developed in Thailand. We have introduced it here in Bangladesh with the aid of a Malaysian company.””

Yogurt bacteria could replace colonoscopies for cancer detection – Billy Steele – EnGadget

“MIT professor Sangeeta Bhatia is working on engineered bacteria that detects colorectal cancer. After the nanoparticles pass through the digestive system, a urine sample shows results on a reactive paper — similar to that of a pregnancy test.”

Science and Publishing

Adjudicating “misbehavior”: how can scientists respond when they don’t get fair credit? –  Janet D. Stemwedel – Scientific American

“Denying someone of fair credit for the contribution they made to a piece of research is not a good thing. But who can you turn to if someone does it to you? “

Twitter’s science stars, the sequel – John Travis – Science

“We listed. You tweeted (often in outrage). We listened (mostly). And now we’re doubling down on our recent list of Twitter’s 50 most popular researchers with a revision that names 100 of the most followed scientists on the social media platform. “

Bik’s Picks

2014 Nobel Prize in Physiology or Medicine: Cells that constitute a positioning system in the brain – Science Daily

“The 2014 Nobel Prize in Physiology or Medicine has been awarded to John O´Keefe, May-Britt Moser and Edvard I. Moser for their discoveries of cells that constitute a positioning system in the brain.”

Concrete Cast of Ant Nest Reveals Huge Underground Metropolis – Lisa Winter – IFL Science

“Through a process that took a few months, researchers made a cast of an anthill by pumping it full of concrete, allowing it to cure and dry, then excavating it out to explore the intricacies of the ant civilization. “

Tall tale: scientists unravel the genetics of human height – Will Dunham – Daily Mail

“Researchers on Sunday unveiled what they called the biggest such study to date, analyzing genome data from more than a quarter million people to identify nearly 700 genetic variants and more than 400 genome regions relating to height.”

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General microbiology and science digest, October 2, 2014

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Viruses and metagenomics, the soil of Central Park, and sweat eating bacteria.

Ecology

Loops and autonomy promote evolvability of ecosystem networks – Jianxi Luo – Scientific Reports

“To correlate ecosystem structure and evolvability, we adopt the NK model originally from evolutionary biology to generate and assess the ruggedness of fitness landscapes of a wide spectrum of model food webs with gradual variation in the amount of feeding loops and link density. “

Erosion of functional independence early in the evolution of a microbial mutualism
Kristina L. Hillesland – PNAS USA

“We show that as the bacterium Desulfovibrio vulgaris evolved for 1,000 generations in conditions forcing cooperation with the archaeon Methanococcus maripaludis, it lost a key metabolic trait that would be required for it to grow alone in most environments.”

Tree diversity does not always improve resistance of forest ecosystems to drought – Charlotte Grossiord – PNAS USA

“Within our study network of 160 forest stands across Europe, we found that mixed species forests are less exposed to drought stress in some regions only. “

Phages, viruses, and metagenomics

Dynamics of CRISPR Loci in Microevolutionary Process of Yersinia pestis Strains – Maria Paloma S. Barros – PLOS ONE

“This study allowed observing a microevolutionary process in a group of Y. pestis isolated from Brazil. “

Metagenomic approaches for direct and cell culture evaluation of the virological quality of wastewater – Tiong Gim Aw – Journal of Virological Methods

“In this study, NGS and bioinformatics have been employed for the direct detection and characterization of viruses in wastewater and of viruses isolated after cell culture. “

Metagenomics / Bioinformatics

Analysis of the Relationship between Genomic GC Content and Patterns of Base Usage, Codon Usage and Amino Acid Usage in Prokaryotes: Similar GC Content Adopts Similar Compositional Frequencies Regardless of the Phylogenetic Lineages – Hui-Qi Zhou – PLOS ONE

“The GC contents of 2670 prokaryotic genomes that belong to diverse phylogenetic lineages were analyzed in this paper. “

Benchmarking Undedicated Cloud Computing Providers for Analysis of Genomic Datasets
Seyhan Yazar – PLOS ONE

“We benchmarked two established cloud computing services, Amazon Web Services Elastic MapReduce (EMR) on Amazon EC2 instances and Google Compute Engine (GCE), using publicly available genomic datasets”

SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation – Brejnev Muhizi Muhire – PLOS ONE

“Here we present Sequence Demarcation Tool (SDT), …that aims to provide a robust and highly reproducible means of objectively using pairwise genetic identity calculations to classify any set of nucleotide or amino acid sequences.”

A two-stage statistical procedure for feature selection and comparison in functional analysis of metagenomes – Naruekamol Pookhao – Bioinformatics

“We propose a two-stage statistical procedure for selecting informative features and identifying differentially abundant features between two or more groups of microbial communities.”

FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus – Emmanuel Prestat – Nucleic Acids Research

“A new functional gene database, FOAM (Functional Ontology Assignments for Metagenomes), was developed to screen environmental metagenomic sequence datasets. “

Microbes in the News

Soil Microbiome of Central Park – Jef Akst – The Scientist

“The soil of New York City’s Central Park is bursting with biodiversity spanning all three domains of life, according to a study published today”

Supporting the “Good” Gut Microbes – Anna Azvolinksy – The Scientist

“During systemic infection, mice kick-start the production of a specific sugar to feed and protect the beneficial bacteria in their guts while fighting pathogenic strains.”

Sweat-Eating Bacteria: Acne Miracle Cure? – Discovery News

“A new, small study has shown that applying a topical creme containing the bacteria leads to healthier skin and could be used to treat acne and promote healing in wounds.”

Women in Science

* Sexism in Science – sbhatnagar3 – Phylogenomics Blogspot

“Please don’t treat these seminars as a fashion show. It distracts the people away from your work”.”

Bik’s Picks

Behavior of bats at wind turbines – Paul. M. Cryan – PNAS USA

“Bats are dying in unprecedented numbers at wind turbines, but causes of their susceptibility are unknown. “

Flexible energetics of cheetah hunting strategies provide resistance against kleptoparasitism – David M. Scantlebury – Science

“We show that daily energy expenditure (DEE) of cheetahs was similar to size-based predictions and positively related to distance traveled.”

Previously unseen details of seafloor exposed in new map – Science Daily

“Twice as accurate as the previous version, the new map features a much more vivid picture of seafloor structures, including thousands of previously uncharted mountains.”

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Microbiome Digest, August 29, 2014

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@MicrobiomDigest will be enjoying vacation for the next two weeks, so I won’t be able to post as much as usual. I might occasionally have some time and internet access at the same time, and post something, but don’t rely on this blog during that time for your daily Microbiome fix. But I will be back! Enjoy this last (short) one for now:
Human oral microbiome

Bacterial community composition of chronic periodontitis and novel oral sampling sites for detecting disease indicators – Vaia Galimanas – Microbiome

Human gut microbiome

Immunoglobulin A Coating Identifies Colitogenic Bacteria in Inflammatory Bowel Disease – Noah W Palm – Cell

Modulation of immune development and function by intestinal microbiota – Agnieszka M. Kabat – Trends in Immunology

 

Worms, bacteria, and micronutrients: an elegant model of our diet – Lutfu Safak Yilmaz, Albertha J.M. Walhout – Trends in Genetics

 

Mammal microbiome

Spatial heterogeneity of gut microbiota reveals multiple bacterial communities with distinct characteristics (in flying squirrels) – Hsiao-Pei Lu – Scientific Reports

Social influences on the gut microbiome of developing monkeys – W.Z. Amaral – Brain, Behavior, and Immunity

 

Do Rumen Bacteroidetes Utilize an Alternative Mechanism for Cellulose Degradation? – AE Naas – mBio

 

Characterization of the Fecal Microbiota of Pigs before and after Inoculation with “Brachyspira hampsonii” – Matheus O. Costa – PLOS ONE

 

Sponges and corals

The versatile nature of coral-associated viruses – Bettarel Yvan – Environmental Microbiology

Onset and establishment of diazotrophs and other bacterial associates in the early life history stages of the coral Acropora millepora – Kimberley A. Lema – Molecular Ecology

Rocks and Water Microbiome

Microbial Colonization of Bare Rocks: Laboratory Biofilm Enhances Mineral Weathering – F. Seiffert – Procedia Earth and Planetary Science

Microbial diversity and biogeochemical cycling in soda lakes – Dimitry Y. Sorokin – Extremophiles

Food microbiome

Switzerland Puts Secret Bacteria In Cheese To Catch Knockoffs – Sarah Zhang – Gizmodo

Bioinformatics

A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data – Yuan Zhang – PLOS Computational Biology

Metabolomics

Taking your breath away: metabolomics breathes life in to personalized medicine
Nicholas J.W. Rattray – Trends in Biotechnology

Phages and Viruses

Identifying and analyzing bacteriophages in human fecal samples: what could we discover? – Maite Muniesa1 & Juan Jofre – Future Medicine

Microbes in the news

Hotel rooms aren’t yucky – you colonize them with your own personal bacteria within hours — Rachel Feltman – Washington Post

A touching story: The ancient conversation between plants, fungi and bacteria – David Tenenbaum – News UW Madison

Bik’s Picks

The universal ‘anger face’: Each element makes you look physically stronger and more formidable – Science Daily

Zombie Bacteria Invasion? Nothing To Worry About – Science 2.0

Report: Ice Bucket Challenge Causing Ecological Mayhem in California – The Allium (Satire)

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Non-human microbiome, August 19, 2014

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A very diverse mix today: kangaroo, rumen, Daphnia, ticks, corals, rice, switchgrass, drinking water, acid mine drainage, rocks, soil microbiomes.

Mammal microbiome

* Investigation of the microbial metabolism of carbon dioxide and hydrogen in the kangaroo foregut by stable isotope probing – Scott Godwin – ISME Journal

“Our results clearly demonstrate that the activity of bacterial reductive acetogens is a key factor in the reduced methane output of kangaroos”

Temporal dynamics of fibrolytic and methanogenic rumen microorganisms during in situ incubation of switchgrass determined by 16S rRNA gene profiling – Hailan Piao – Frontiers in Microbiology

“Here we investigated the temporal succession of microbial taxa and its effect on fiber composition during rumen incubation using 16S rRNA amplicon sequencing.”

Arthropod microbiome

Bacterial epibionts of Daphnia: a potential route for the transfer of dissolved organic carbon in freshwater food webs – Ester M Eckert and Jakob Pernthaler – ISME Journal

“We analysed the activity and identity of bacterial epibionts in cultures of Daphnia galeata and of natural daphnid populations.”

Evaluation of microbial communities and symbionts in Ixodes ricinus and ungulate hosts (Cervus elaphus and Ovis aries) from shared habitats on the west coast of Norway
Erik G. Granquist – Ticks and Tick-borne Diseases

“Five different species; M. mitochondrii, W. pipientis, Borrelia spp., Rickettia spp. and A. phagocytophilum, were analyzed on a 7500 Fast Real-time PCR system (Life Technologies, Carlsbad, CA), and carried out in separate 96-wells reaction plates. “

Coral microbiome

New insights into Oculina patagonica coral diseases and their associated Vibrio spp. communities – Esther Rubio-Portillo – ISME Journal

“….we have analysed the seasonal patterns of the culturable Vibrio spp. assemblages associated with healthy and diseased O. patagonica colonies. “

Bloom of the cyanobacterium Moorea bouillonii on the gorgonian coral Annella reticulata in Japan – Hideyuki Yamashiro – Nature Scientific Reports

“In addition to the cyanobacterium–shrimp interaction, the new trait of anchoring by the cyanobacterium into gorgonian coral may contribute to persistence of this bloom.”

* Not just who, but how many: the importance of partner abundance in reef coral symbioses – Ross Cunning and Andrew C. Baker – Frontiers in Microbiology

“…we generate testable hypotheses regarding the importance of symbiont abundance by first discussing different metrics and their potential links to symbiosis performance and breakdown, and then describing how natural variability and dynamics of symbiont communities may help explain ecological patterns on coral reefs and predict responses to environmental change.”

Plant microbiome

Phylogeny and Functions of Bacterial Communities Associated with Field-Grown Rice Shoots – Takashi Okubo – Microbes and Environments

“Metagenomic analysis was applied to bacterial communities associated with the shoots of two field-grown rice cultivars, Nipponbare and Kasalath.”

Reviving of the endophytic bacterial community as a putative mechanism of plant resistance – Olga Podolich – Plant and Soil

“Based on the published results, we suggest that the endophyte-mediated stress tolerance or disease resistance can develop, if the plant hosts a sufficient diversity of ‘protective’ endophytes. “

The rhizosphere microbiota of plant invaders: an overview of recent advances in the microbiomics of invasive plants – Vanessa C. Coats, Mary E. Rumpho – Frontiers in Microbiology

“This review discusses recent advances in invasive plant biology that have resulted from microbiome analyses as well as the microbial factors that direct plant fitness and adaptability in natural systems.”

Kelp forest size alters microbial community structure and function on Vancouver Island, Canada – Jessica Liz Clasen and Jonathan B. Shurin – Ecology

“We investigated the response of microbial communities to variation in kelp abundance between regions with and without sea otter populations along the west coast of Vancouver Island, British Columbia, Canada”

Soil, sediments, rocks

* Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest – Neslihan Taş – ISME Journal

“We measured geochemistry, GHG fluxes, potential soil enzyme activities and microbial community structure via 16SrRNA gene and metagenome sequencing.”

Integrated Metagenomics and Metatranscriptomics Analyses of Root-Associated Soil from Transgenic Switchgrass – Archana Chauhan – Genome Announcements

“Here we report metagenomic and metatranscriptomic analyses of root-associated soil from COMT switchgrass compared with nontransgenic counterparts.”

Abiotic stress tolerance and competition-related traits underlie phylogenetic clustering in soil bacterial communities – Marta Goberna – Ecology Letters

“We examined the distribution of 15 traits and 3290 bacterial taxa in 28 plots. Communities showed a marked functional response to the environment. “

Elevated nitrate enriches microbial functional genes for potential bioremediation of complexly contaminated sediments – Meiying Xu – ISME Journal

“Here we analyzed sediment microbial communities from a field-scale in situ bioremediation site, a creek in Pearl River Delta containing a variety of contaminants “

Occurrence and expression of bacterial human virulence gene homologues in natural soil bacteria – Ditte A. Søborg – FEMS Microbiology Ecology

“The presence and in vitro expression of homologues to 22 bacterial human virulence determinants amongst culturable soil bacteria was investigated.”

Endolithic bacterial communities in rock coatings from Kärkevagge, Swedish Lapland – Cassandra L. Marnocha – FEMS Microbiology Ecology

“Using 454 Roche pyrosequencing of the 16S rDNA gene, nine rock coating samples from three different coating mineralogies were sequenced.”

Biodegradation Potential of Organically Enriched Sediments under Sulfate- and Iron-Reducing Conditions as Revealed by the 16S rRNA Deep Sequencing – Tomoyuki Hori – Journal of Water and Environment Technology

“The effects of supplementation with sulfate and lepidocrocite (a crystalline Fe[III] oxide) on the structure and activity of the slurry microorganisms were examined by the combined physicochemical analyses and 16S rRNA deep sequencing. “

Soil bacterial diversity in degraded and restored lands of Northeast Brazil – Ademir Sérgio Ferreira Araújo – Antonie van Leeuwenhoek

“In this study we compare the structure and diversity of bacterial communities in degraded and restored lands in Northeast Brazil and determine the soil biological and chemical properties influencing bacterial communities. “

* Biogeochemical environments of streambed-sediment pore waters with and without arsenic enrichment in a sedimentary rock terrain, New Jersey Piedmont, USA
A.C. Mumford – Science of the Total Environment

“The 16S rRNA gene and the As(V) respiratory reductase gene, arrA, were amplified from DNA extracted from streambed pore water at both sites and analyzed, revealing that distinct bacterial communities that corresponded to the redox conditions were present at each site. “

Water, wastewater, sludge microbiome

* A comprehensive insight into bacterial virulence in drinking water using 454 pyrosequencing and Illumina high-throughput sequencing – Kailong Huang – Ecotoxicology and Environmental Safety

“In order to comprehensively investigate bacterial virulence in drinking water, 454 pyrosequencing and Illumina high-throughput sequencing were used to detect potential pathogenic bacteria and virulence factors (VFs) in a full-scale drinking water treatment and distribution system. “

A high-throughput sequencing ecotoxicology study of freshwater bacterial communities and their responses to tebuconazole – Pascault Noémie – FEMS Microbiology Ecology

“Pyrosequencing revealed that bacterial diversity was higher in the river than in the lakes and in previously-exposed sites than in pristine sites.”

Disturbance and temporal partitioning of the activated sludge metacommunity – David C Vuono – ISME Journal

“Bacterial small subunit (SSU) rRNA genes were surveyed from sludge samples resulting in a sequence library of >417 000 SSU rRNA genes. “

Review: Environmental bacteriophages: viruses of microbes in aquatic ecosystems – Télesphore Sime-Ngando – Frontiers in Microbiology

“The present chapter sought to review the literature on the diversity and functional roles of viruses of microbes in environmental microbiology,”

* Inter-species interconnections in acid mine drainage microbial communities
Luis R. Comolli and Jill F. Banfield – Frontiers in Microbiology

“Here, we present cryogenic transmission electron microscope (cryo-TEM) 2D images and 3D tomographic datasets for archaeal species from natural acid mine drainage (AMD) microbial communities. “

A study on the microbial community structure in oil reservoirs developed by water flooding – Lin Junzhang – Journal of Petroleum Science and Engineering

“This study was performed to identify the microbial community structures in 10 different types of water-flooded oil reservoirs on Sinopec Shengli Oil Field. “

Microbes of the built environment

* Microbial Existence in Controlled Habitats and Their Resistance to Space Conditions – Kasthuri Venkateswaran – Microbes and Environments

“In this review, we discussed the presence of microbes in space research-related closed habitats and the resistance of some microbial species to the extreme environmental conditions of space.”

Microbial Monitoring of Crewed Habitats in Space—Current Status and Future Perspectives – Nobuyasu Yamaguchi – Microbes and Environments

“In this review, the current status of microbial monitoring conducted in the International Space Station (ISS) as well as the results of recent microbial spaceflight experiments have been summarized and future perspectives are discussed.”

Food microbiology

Investigation of bacterial and fungal diversity in tarag using high-throughput sequencing
Zhihong Sun – Journal of Dairy Science

“This is the first study on the bacterial and fungal community diversity in 17 tarag samples (naturally fermented dairy products) through a metagenomic approach involving high-throughput pyrosequencing. “

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General microbiology and science, July 15

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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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Non-human microbiome, June 30

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Primate vaginal microbiome, birds painting eggs with bacteria, MHC and microbiota in fish, onions and tomato, bacteria on the beach, and (#BacteriaHysteria alert) “fecal veneer on climbing walls”.

Primate microbiome (also see Human digest)

Screen Shot 2014-06-30 at 11.23.32 PMPrimate vaginal microbiomes exhibit species specificity without universal Lactobacillus dominance – Suleyman Yildirim – ISME J (uncorrected proof, link to Chapman Research)

“Our results indicated that all primates exhibited host-specific vaginal microbiota and that humans were distinct from other primates in both microbiome composition and extent of diversity”

Bird microbiome

Screen Shot 2014-06-30 at 11.43.49 PMSpecial structures of hoopoe eggshells enhance the adhesion of symbiont-carrying uropygial secretion that increase hatching success – Manuel Martín-Vivaldi – Journal of Animal Ecology

“The findings of specialized crypts on the eggshells of hoopoes, and of video-recorded females smearing secretion containing symbiotic bacteria at a high density onto the eggshells strongly support a link between secretion and bacteria on eggs. “

and:  The Bird That Paints Its Eggs With Bacteria – Ed Yong – National Geographic

“Now, they’ve found evidence that these birds use the same bacteria to protect their young before they’re even born. By filming nesting females, they confirmed that the birds actively paint their eggs with their uropygial secretions.”

Fish microbiology

Screen Shot 2014-06-30 at 11.45.12 PMMajor Histocompatibility Complex class II polymorphism influences gut microbiota composition and diversity – Daniel I. Bolnick – Molecular Ecology

“Here, we show that MHC II polymorphism is associated with among-individual variation in gut microbiota within a single wild vertebrate population of a small fish, the threespine stickleback. “

Insect microbiome

WolbachiaThe Coevolutionary Period of Wolbachia pipientis Infecting Drosophila ananassae and its Impact on the Evolution of the Host Germline Stem Cell Regulating Genes – Jae Young Choi and Charles F. Aquadro – Molecular Biology and Evolution

“Phylogenetic analysis of D. ananassae mitochondrial DNA and W. pipientis DNA sequence diversity revealed the current W. pipientis infection is not recent. In addition, we examined the population genetics and molecular evolution of several Germline Stem Cell (GSC) regulating genes of D. ananassae”

Plant microbiome

Screen Shot 2014-06-30 at 11.43.01 PMIdentification of bacteria pathogenic to or associated with onion (Allium cepa) based on sequence differences in a portion of the conserved gyrase B gene – Jean M. Bonasera – Journal of Microbiological Methods

“We have developed a method for the identification of Gram-negative bacteria, particularly members of the Enterobacteriaceae, based on sequence variation in a portion of the gyrB gene. Thus, we identified, in most cases to species level, over 1000 isolates from onion bulbs and leaves and soil in which onions were grown.”

Occurrence and distribution of tomato seed-borne mycoflora in Saudi Arabia and its correlation with the climatic variables – Abdulaziz A. Al-Askar – Microbial Biotechnology

“One hundred samples of tomato seeds were collected in 2011 and 2012 from tomato-cultivated fields in Saudi Arabia and screened for their seed-borne mycoflora. A total of 30 genera and 57 species of fungi were recovered from the collected seed samples using agar plate and deep-freezing blotter methods. “

WasabiManagement of Meloidogyne incognita on tomato with endophytic bacteria and fresh residue of Wasabia japonica – Guang-Ju Li – Journal of Applied Microbiology

“By in vitro bioassay, 53 NEB strains showing nematicidal efficacies of >50% against J2 of M. incognita were isolated from wasabi. Basing on 16S rRNA gene sequences, these NEB were identified into 18 species of 11 genera.”

Lichen and fungi

Screen Shot 2014-06-30 at 11.46.20 PMA single macrolichen constitutes hundreds of unrecognized species – Robert Lücking – PNAS

“This lichen was long believed to represent a single species, but after revising this number to 16 in two genera (Cora and Corella), here we show that at least 126 phylogenetically and morphologically distinct species are contained within this group, with statistical analysis predicting more than 400. “

Soil, sand, and slurry microbiome

The Ecological Controls on the Prevalence of Candidate Division TM7 in Polar Regions – Tristrom Winsley – Frontiers in Microbiology

“We correlated chemical, physical and biological parameters of each soil with the relative abundance of the two major classes of the phylum to deduce factors that influence the groups’ seemingly ubiquitous nature. “

Review: Present status of effect of microorganisms from sand beach on public
health – Emmanuel Velonakis – Journal of Coastal Life Medicine

“Relatively, recent epidemiological studies in the USA revealed positive correlation between time spent at the beach and gastroenteritis. New parameters such as wind blowing and beach users’ density are also introduced for discussion in association with the sand microbial load”

Crusts slurryMethanotrophs, methanogens, and microbial community structure in livestock slurry surface crusts – Yun-Feng Duan – Journal of Applied Microbiology

“Microbial communities in four crusts from cattle and swine slurries were investigated using DGGE and tag-encoded amplicon pyrosequencing. All crusts had distinct compositions of bacteria and archaea.”

Water microbiology

Biosynthesis of polybrominated aromatic organic compounds by marine bacteria
Vinayak Agarwal – Nature Chemical Biology

“Herein we report the discovery of a conserved biosynthetic gene cluster in marine bacteria responsible for the synthesis of widespread polybrominated aromatic compounds”

Environmental bacteriophages : viruses of microbes in aquatic ecosystems – Télesphore Sime – Ngando – Frontiers in Microbiology

“The present chapter sought to review the literature on the diversity and functional roles of viruses of microbes in environmental microbiology, focusing primarily on prokaryotic viruses (i.e. phages) in aquatic ecosystems, which form the bulk of our knowledge in modern environmental viral ecology.”

Built Environment

I really dislike this title …
Screen Shot 2014-06-30 at 11.47.38 PMMicrobial Sequencing Analyses Suggest the Presence of a Fecal Veneer on Indoor Climbing Wall Holds – S. L. Bräuer – Current Microbiology

“In contrast to many other studies of built environments, the majority of microorganisms on holds were most closely related to microbes annotated as being recovered from environmental sources, such as soil, with human skin also representing an important source.”

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General microbiology and science, June 24

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Metabolomics, metagenomics, phages in the human gut, arsenic poisoning in China, and a big award for Dengue research.

Metabolomics

Metaproteomics: Extracting and Mining Proteome Information to Characterize Metabolic Activities in Microbial Communities – Paul E. Abraham – Current Protocols in Bioinformatics

“In this article, we provide an overview of current bioinformatic approaches and software implementations in metaproteome studies in order to highlight the key considerations needed for successful implementation of this powerful community-biology tool. “

Review: The human volatilome: volatile organic compounds (VOCs) in exhaled breath, skin emanations, urine, feces and saliva – Anton Amann – Journal of Breath Research

“Fecal volatiles have been implicated in differentiating certain infectious bowel diseases such as Clostridium difficile, Campylobacter, Salmonella and Cholera. They have also been used to differentiate other non-infectious conditions such as irritable bowel syndrome and inflammatory bowel disease.”

Metagenomics and DNA structure

Sequencing the Strange Communities: Taking on Metagenomics – Aaron Krol – Bio-IT World

““Communities are made up of organisms that interact,” says Jonathan Eisen, a professor at the School of Medicine and the College of Biological Sciences at the University of California, Davis. “They’re not made up of short reads of Illumina sequences. And we need to stitch those together into organisms in order to make useful predictions, and interpretation of experimental data.””

Gene positioning and genome function – Nidhi Vishnoi, Jie Yao – Frontiers in Biology

” In this review, we discuss some recent findings as well as experimental tools to investigate subnuclear gene positioning and to explore its implications in genome functions.”

Phages and viruses

Classification and quantification of bacteriophage taxa in human gut metagenomes – Alison S Waller – ISME Journal 

“Using taxon-specific marker genes, we identified and monitored 20 viral taxa in 252 human gut metagenomic samples, mostly at the level of genera. “

Techniques

Enzymatic Treatment of Specimens before DNA Extraction Directly Influences Molecular Detection of Infectious Agents – Pablo Goldschmidt – PLOS ONE

“The goal of the present work was to assess the efficiency of enzymatic pretreatments on infectious agents to make DNA available for further extraction and amplification.”

Dengue

Sustainable Sciences Institute (SSI) Awarded $1 Million to Battle Growing Threat to Global Public Health: Mosquito-borne Dengue Virus – PR Web

“SSI, a San Francisco nonprofit founded by Eva Harris, UC Berkeley Professor of Infectious Disease and Vaccinology and former MacArthur “Genius” award winner, has worked to minimize the threat of potentially fatal Dengue disease for 15 years. With the latest award of $1 million dollars, Harris and other SSI investigators will be able to extend their reach and speed up their efforts.”

Infection and host response

Early MicroRNA Expression Profile as a Prognostic Biomarker for the Development of Pelvic Inflammatory Disease in a Mouse Model of Chlamydial Genital Infection – Laxmi Yeruva – mBio

“To determine if chemokine and cytokine production within 24 h of infection is associated with the outcome of pathology, levels of 15 chemokines and cytokines were measured. “

Immunity to gastrointestinal nematodes: mechanisms and myths – Richard K. Grencis – Immunological Reviews

“This review aims to discuss the recent discoveries in both host protection and immunoregulation against gastrointestinal nematodes, placing the data in context of the specific life cycles imposed by the different parasites studied and the future challenges of considering the mucosal/immune axis to encompass host, parasite, and microbiome in its widest sense.”

Tailored immunity at mucosae – Yasmine Belkaid – Immunological Reviews

“This issue of Immunological Reviews presents articles from investigators involved in the exploration of the mechanisms by which mucosal barrier sites induce and control innate and adaptive immune responses.”

Detection of bacteria in blood and other sites

Rapid Detection of Enterobacteriaceae Producing Extended Spectrum Beta-Lactamases Directly From Positive Blood Cultures by Matrix-Assisted Laser-Desorption-Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF-MS) – Marina Oviaño – Clinical Microbiology and Infection

“In the assay, 141 blood cultures were tested, 13 out of them were real bacteremias and 128 corresponded to blood culture bottles seeded with bacterial clinical isolates. Bacteremias were analyzed by MALDI-TOF after a positive growth result and the 128 remaining blood cultures 24 hours after the bacterial seeding. “

General microbiology and ecology

The quest for a unified view of bacterial land colonization – Hao Wu – ISME Journal

“Here, we perform comprehensive analyses based on a large variety of bacteria by integrating taxonomic, phylogenetic and metagenomic data, in the quest for a unified view that elucidates genomic, evolutionary and ecological dynamics of the marine progenitors in adapting to nonaquatic environments. “

Lateral transfer of eukaryotic ribosomal RNA genes: an emerging concern for molecular ecology of microbial eukaryotes – Akinori Yabuki – ISME Journal

“Two distinct sequences of the 18S rRNA gene were detected from a clonal culture of the stramenopile, Ciliophrys infusionum. One was clearly derived from Ciliophrys, but the other gene originated from a perkinsid alveolate.”

Arsenic metabolism

Arsenic Pollution Sows Despair in Chinese Cancer Village (slideshow)- Yahoo News

“Xiong Demin could not have foreseen that the mine he worked at for 32 years would leave his home village poisoned and hundreds of residents, including himself and his wife, stricken with cancer.”

Dr. Bik’s Picks – Evolution Edition

Molecular Phylogeny, Biogeography, and Habitat Preference Evolution of Marsupials – Kieren J. Mitchell – Molecular Biology and Evolution

“We use 101 mitochondrial genomes and data from 26 nuclear loci to reconstruct a dated phylogeny including 97% of extant genera and 58% of modern marsupial species”

Parallel sites implicate functional convergence of the hearing gene prestin among echolocating mammals – Zhen Liu – Molecular Biology and Evolution

“By functional assays, we show that a key parameter of prestin function, 1/α, is increased in all echolocating mammals and that the N7T parallel substitution accounted for this functional convergence. Moreover, another parameter, V1/2, was shifted toward the depolarization direction in a toothed whale, the bottlenose dolphin (Tursiops truncatus) and a constant-frequency bat, Stoliczka’s trident bat (Aselliscus stoliczkanus). “

Evolutionary developmental transcriptomics reveals a gene network module regulating interspecific diversity in plant leaf shape – Yasunori Ichihashi – PNAS

“Utilizing the natural variation in leaf morphology between tomato and two related wild species, we identified a gene network module that leads to a dynamic rewiring of interactions in the whole leaf developmental gene regulatory network. “

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Human and cell phone microbiome, June 24

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The PhoneBiome has finally been characterized. Effect of maltodextrin on gut microbiome, and obesity and risk for preterm birth.

Skin and phone microbiome

Mobile phones carry the personal microbiome of their owners – James F. Meadow – Peer J

“We found that about 22% of the bacterial taxa on participants’ fingers were also present on their own phones, as compared to 17% they shared on average with other people’s phones. “

Gut microbiome

The Metabolizable Energy of Dietary Resistant Maltodextrin Is Variable and Alters Fecal Microbiota Composition in Adult Men – David J. Baer – The Journal of Nutrition

“RM intake was associated with statistically significant increases (P < 0.001) in various operational taxonomic units matching closest to ruminococcus, eubacterium, lachnospiraceae, bacteroides, holdemania, and faecalibacterium, implicating RM in their growth in the gut. “

B cells as a critical node in the microbiota–host immune system network –
Emma Slack – Immunological Reviews

“In this review, we address how B-cell responses to members of the intestinal microbiota form a robust network with mucus, epithelial integrity, follicular helper T cells, innate immunity, and gut-associated lymphoid tissues to maintain host–microbiota mutualism.”

Classification and quantification of bacteriophage taxa in human gut metagenomes – Alison S Waller – ISME Journal 

“Using taxon-specific marker genes, we identified and monitored 20 viral taxa in 252 human gut metagenomic samples, mostly at the level of genera. “

Cesarean delivery and risk of inflammatory bowel disease: a systematic review and meta-analysis – Yi Li – Scandinavian Journal of Gastroenterology

“Results of this meta-analysis support the hypothesis that cesarean delivery was associated with the risk of CD but not of UC. The total rate of cesarean delivery of IBD patients was similar with that of control subjects.

Intestinal microbiota in pathophysiology and management of irritable bowel syndrome – Lee KN – World Journal of Gastroenterology

“…the role of the intestinal microbiota in the pathophysiology and management of IBS is not clear. This review provides the accumulating evidence on it.”

Pregnancy and Birth

Maternal Prepregnancy Body Mass Index and Risk of Spontaneous Preterm Birth – Gary M. Shaw – Paediatric and Perinatal Epidemiology

“Analyses of mothers without hypertension and diabetes, adjusted for age, education, height, and prenatal care initiation, showed obesity categories I–III to be associated with increased risk of spontaneous preterm birth at 20–23 and 24–27 weeks among those of parity 1 in each race/ethnic group.”

and

Obesity before pregnancy linked to earliest preterm births, Stanford/Packard study finds – Erin Digitale – Stanford Medicine News Center

“Women who are obese before they become pregnant face an increased risk of delivering their babies before 28 weeks of pregnancy, a new study of nearly 1 million California births has found.”

Maturation of the enteric mucosal innate immune system during the postnatal period – Marcus Fulde and Mathias W. Hornef – Immunological Reviews

“Here, we discuss both adaptive and developmental mechanisms of the mucosal innate immune system that prevent inappropriate stimulation and facilitate establishment of a stable homeostatic host–microbial interaction after birth.”

Early Infant Nutrition and Metabolic Programming: What Are the Potential Molecular Mechanisms? – Stephanie-May Ruchat – Current Nutrition Reports

“This review will present potential molecular mechanisms through which early postnatal nutrition may influence health and disease programming, focusing on research that used “-omics” approaches (i.e., epigenomics, transcriptomics, proteomics, and metabolomics).”

Oral presentation: Serum beta defensin concentration in the first trimester is related to genotype, and is higher in women who develop PPROM and deliver before 34 weeks – CP James – Arch Dis Child Fetal Neonatal Ed

“Serum hBD2 expression is higher in women who have PPROM and PTB. Women with PPROM and PTB have a distinct innate immune profile evident in their serum in the first trimester, which may provide the basis for a predictive test.”

Animal models of human microbiota and disease

Modulation of gut microbiota during probiotic-mediated attenuation of metabolic syndrome in high fat diet-fed mice – Jingjing Wang – ISME Journal

“Weighted UniFrac principal coordinate analysis based on 454 pyrosequencing of fecal bacterial 16S rRNA genes showed that the probiotic strains shifted the overall structure of the HFD-disrupted gut microbiota toward that of lean mice fed a normal (chow) diet. “

Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission – Michelle G Rooks – ISME Journal

“Here, we surveyed the gut microbiome of the T-bet−/− Rag2−/− mouse model of colitis during active disease and treatment-induced remission. “

Early-Life Environmental Variation Affects Intestinal Microbiota and Immune Development in New-Born Piglets – Dirkjan Schokker – PLOS ONE

” We observed that the applied antibiotic treatment affected the composition and diversity of gut microbiota and reduced the expression of a large number of immune-related processes. The effect of management procedures on top of the use of an antibiotic was limited.”

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Non-human microbiomes, June 9

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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. avium, hominissuis, 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. “

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