Author Archives: eliesbik

Microbiome digest, October 30, 2014

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Bacteriocins in human metagenomic libraries, freezing/thawing effects on community composition, microbiome of preterm neonates, and bacteria in soil.
Multiple-site human microbiome

Diversity and dynamics of bacteriocins from human microbiome – Jinshui Zheng – Environmental Microbiology

“We employed bioinformatic analyses to identify putative bacteriocin sequences in metagenomic sequences obtained from different human body sites. “

Human respiratory microbiome

* Implications of multiple freeze-thawing on respiratory samples for culture-independent analyses – Leah Cuthbertson – Journal of Cystic Fibrosis

“Following each cycle, an aliquot was removed and treated with propidium monoazide (PMA) prior to DNA extraction and 16S rRNA gene pyrosequencing.”

Human gut microbiome

Immune Homeostasis, Dysbiosis and Therapeutic Modulation of the Gut Microbiota – Christine T. Peterson – Clinical & Experimental Immunology

“This review discusses host-microbiota homeostasis, consequences of its perturbation, and the associated challenges in therapeutic developments that lie ahead.”

Microbiome of pregnancy and birth

* Intestinal Microbiota Development in Preterm Neonates and Effect of Perinatal Antibiotics – Silvia Arboleya – The Journal of Pediatrics

“We used 16S ribosomal RNA gene sequence-based microbiota analysis and quantitative polymerase chain reaction to evaluate the establishment of the intestinal microbiota. “

Animal microbiome

Hidden Population Structure and Cross-species Transmission of Whipworms (Trichuris sp.) in Humans and Non-human Primates in Uganda – Ria R. Ghai – PLOS Neglected Tropical Diseases

“We examined the phylogenetic structure of whipworms in a multi-species community of non-human primates and humans in Western Uganda, using both traditional microscopy and molecular methods.”

Soil microbiome

Metagenomic analysis reveals microbial functional redundancies and specificities in a soil under different tillage and crop-management regimes – Renata Carolini Souza – Applied Soil Ecology

“in this study we used a shotgun metagenomic approach to compare different soil…, and crop … managements in a 13-year-old field experiment in southern Brazil. “

Evaluating T-RFLP protocols to sensitively analyze the genetic diversity and community changes of soil alkane degrading bacteria – Julia Giebler – European Journal of Soil Biology

“This study aimed at identifying a reliable, highly resolving fingerprinting method to monitor alkane degrading communities in soil.”

Contrasting land uses in Mediterranean agro-silvo-pastoral systems generated patchy diversity patterns of vascular plants and below-ground microorganisms – Simonetta Bagella – Comptes Rendus Biologies

“Species richness decreased with increasing land use intensity, the Shannon index showed the highest values in grasslands and hay crops.”

Food microbiology

Characterization and use of microbial communities in Doenjang to control the unpleasant odor of Ginkgo epicarp – Sunhyun Park – Food Science and Biotechnology

“Microbes in doenjang were probably responsible for the reduction in the butyric acid content. Microbial communities were analyzed during fermentation.”

Bioreactor microbiology

Thermophilic anaerobic digestion of thermal pretreated sludge: role of microbial community structure and correlation with process performances – M.C. Gagliano – Water Research

“16S rRNA gene clonal analysis and Fluorescence In Situ Hybridization (FISH) analyses allowed us to identify the majority of bacterial and archaeal populations. “

Bioinformatics

Fast dendrogram-based OTU clustering using sequence embedding – Thuy-Diem Nguyen – Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics

“In this paper, we introduce a new hierarchical clustering method called CRiSPy-Embed which aims to produce high-quality clustering results at a low computational cost. “

Focus: a new multilayer graph model for short read analysis and extraction of biologically relevant features – Julia Warnke – Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics

“We present Focus, a new multilayer graph model for short read analysis and extraction of biologically relevant features. “

The UniFrac significance test generates different outputs given semantically equivalent inputs – Jeffrey Long – Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics

“We identify a discrepancy in the UniFrac methodology that causes semantically equivalent inputs to produce different outputs in tests of statistical significance.”

Microbes in the news

SpaceX 4 splashes down, returns bacteria samples to Earth – Josh Barrett – WaayTV

“HudsonAlpha’s Genomic Sciences Lab will be sequencing the genomes of E. coli bacteria that were aboard the ISS. For some reason, bacteria are not as susceptible to antibiotics in space.”

Bik’s Picks

Why Millennials &%#@! Love Science – Alexandra Ossola – The Atlantic

“Today’s young adults see new discoveries both as a source of awe and a means for innovation.”

1,000 Flavors of Banana: the New Science of Food Additives – Annie Gasparro – The Wall Street Journal

“Rather than sourcing the jalapeño or poblano pepper, you can create it with a flavor house, and just apply it over a corn chip,” said Jared Simon, marketing director for Hain Celestial Group Inc. ’s snacks and bakery division, which uses natural flavors for its foods such as Terra vegetable chips.”

Spooky Science: The Sounds of Halloween – Science Buddies – Scientific American

“In this science activity, you will investigate what goes into the composition of a perfect creepy soundtrack. “

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Microbiome Digest, October 29, 2014

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The genome of Mycoplasma Mnola, helminths in wild rats, fungi in strawberry roots, and the top 100 most cited papers of all time. Can you guess which one is #1?

Human genital microbiome

An Emerging Mycoplasma Associated with Trichomoniasis, Vaginal Infection and Disease – Jennifer M. Fettweis – PLOS ONE

“In this study, the mycoplasma was found almost exclusively in women infected with the sexually transmitted pathogen Trichomonas vaginalis, but rarely observed in women with no diagnosed disease.”

Human gut microbiome

Bacteriology and Changes in Antibiotic Susceptibility in Adults with Community-Acquired Perforated Appendicitis – Hong Gil Jeon – PLOS ONE

“We retrospectively reviewed records of adult patients diagnosed with perforated appendicitis at an 800-bed teaching hospital between January 2000 and December 2011. “

Animal microbiome

Changes in the intestinal bacterial community during the growth of white shrimp, Litopenaeus vannamei – Zhaobin Huang – Aquaculture Research

“In this study, we documented the changes in the intestinal bacterial community at four stages in Litopenaeus vannamei…, using 454 pyrosequencing techniques. “

* Assessment of Helminth Biodiversity in Wild Rats Using 18S rDNA Based Metagenomics – Ryusei Tanaka – PLOS ONE

“In this study, we assessed parasite diversity in wild rats using 18S rDNA-based metagenomics. 18S rDNA PCR products were sequenced using an Illumina MiSeq sequencer and the analysis of the sequences using the QIIME software successfully classified them into several parasite groups.”

Soil microbiome

Linking soil microbial communities to vascular plant abundance along a climate gradient – Luca Bragazza – New Phytologist

“Microbial community structure and function were measured seasonally in four peatlands located along an altitude gradient representing a natural gradient of climate and associated vascular plant abundance.”

* Influence of Soil Type, Cultivar and Verticillium dahliae on the Structure of the Root and Rhizosphere Soil Fungal Microbiome of Strawberry – Srivathsa Nallanchakravarthula – PLOS ONE

“In this study we examined the effects of different soils and cultivars, and the presence of a soil-borne fungal pathogen, Verticillium dahliae, on the fungal microbiome of the rhizosphere soil and roots of strawberry plants, using high-throughput pyrosequencing.”

Metagenomics / Bioinformatics

* Evaluation of a Hybrid Approach Using UBLAST and BLASTX for Metagenomic Sequences Annotation of Specific Functional Genes – Ying Yang – PLOS ONE

“A hybrid annotation pipeline proposed previously for taxonomic assignments was evaluated in this study for metagenomic sequences annotation of specific functional genes, such as antibiotic resistance genes, arsenic resistance genes and key genes in nitrogen metabolism. “

Metabolomics

Long-term phenotypic evolution of bacteria – Germán Plata – Nature

“Here we perform a comparative analysis of bacterial growth and gene deletion phenotypes using hundreds of genome-scale metabolic models. “

Phages and viruses

Conditional tolerance of temperate phages via transcription-dependent CRISPR-Cas targeting – Gregory W. Goldberg – Nature

“Here we show that the Staphylococcus epidermidis CRISPR-Cas system can prevent lytic infection but tolerate lysogenization by temperate phages. “

Science, publishing and career

The top 100 papers – Richard Van Noorden – Nature

“To mark the anniversary, Nature asked Thomson Reuters, which now owns the SCI, to list the 100 most highly cited papers of all time.”

Bibliometrics: Is your most cited work your best? – John P. A. Ioannidis – Nature

“John P. A. Ioannidis and colleagues asked the most highly cited biomedical scientists to score their top-ten papers in six ways.”

Recommendations for the Role of Publishers in Access to Data – Jennifer Lin, Carly Strasser – PLOS Biology

“As appeals for public access of research data continue to proliferate, many scholarly publishers—alongside funders, institutions, and libraries—are expanding their role to address this need. “

How to Make More Published Research True – John P. A. Ioannidis – PLOS ONE

“Currently, many published research findings are false or exaggerated, and an estimated 85% of research resources are wasted.”

* Prominent Geomicrobiologist Dies – Tracy Vence – The Scientist

“Katrina Edwards, whose research focus was on discovering life beneath the ocean floor, has passed away at age 46.”

Bik’s Picks

* The Art of Science: Popsicles Go Viral – The Finch and Pea

“Lick a virus? Probably not a good idea, unless it’s a Dangerous Popsicle, a sweet treat created by artist and designer Wei Li. “

Dozens of genes associated with autism in new research – Science Direct

“Two major genetic studies of autism, involving more than 50 laboratories worldwide, have newly implicated dozens of genes in the disorder. “

Antares Rocket Explosion Destroyed These Kids’ Science Projects – Rheana Murray – ABC News

“Students across the nation watched their science projects go up in flames as the rocket bound for the International Space Station exploded moments after takeoff.”

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General microbiology and science digest, October 28, 2014

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Viruses in humans and caribous, metabolomics of losing weight, and microbes on rough surfaces.
Metabolomics

Impact of a 6-week very low-calorie diet and weight reduction on the serum and fecal metabolome of overweight subjects – Mette S. Schmedes – European Food Research and Technology

“NMR-based metabolomics was carried out on serum and fecal samples obtained from healthy female subjects pre- and post-weight reduction. “

Book with lots of plagiarized text (in at least 3 chapters), so not worth the $25 for the physical book, or even the free download:
Metabonomics and Gut Microbiota in Nutrition and Disease – Springer Link

Metagenomics

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes – Donovan H. Parks – PeerJ Preprints

“Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree along with information about the collocation of these genes. “

Viruses and phages

Expanding the Conversation on High-Throughput Virome Sequencing Standards To Include Consideration of Microbial Contamination Sources – Michael J. Strong, Zhen Lin, Erik K. Flemington – mBio

“We thank Ladner and colleagues for their conversation about standardizing viral genome sequences derived from high-throughput (HT) sequencing technology.”

Chlorovirus ATCV-1 is part of the human oropharyngeal virome and is associated with changes in cognitive functions in humans and mice – Robert H. Yolken – PNAS USA

“Unexpectedly, we identified DNA sequences homologous to virus ATCV-1, an algal virus not previously known to infect humans, in oropharyngeal samples obtained from healthy adults. “

* Preservation of viral genomes in 700-y-old caribou feces from a subarctic ice patch – Terry Fei Fan Ng – PNAS USA

“Using a viral particle-associated nucleic acid enrichment approach, we genetically characterized one complete DNA and one partial RNA viral genome from a 700-y-old fecal sample preserved in ice. “

Microbial Ecology

Trophic interactions induce spatial self-organization of microbial consortia on rough surfaces – Gang Wang, Dani Or – Scientific Reports

“A mechanistic model of cell-level interactions among multispecies microbial populations grown on hydrated rough surfaces facilitated systematic evaluation of how trophic dependencies shape spatial self-organization of microbial consortia in complex diffusion fields.”

Scaling laws governing stochastic growth and division of single bacterial cells – Srividya Iyer-Biswas – PNAS USA

“Now, by using a unique combination of measurement and analysis technologies, together with mathematical modeling, we discover quantitative features that are conserved across physiological conditions. “

Microbes in the news

Gut feelings – Microbiome and mental health – Fabio Piccini – Wall Street International

“Might people suffering from certain forms of mental health problems benefit from a fecal transplant from someone with more happy-go-lucky bacteria? “

Small Things Considered: Bacteria Allow Woodrats to Eat Poison – Anne A. Madden – ASM blog

“Despite such dire consequences, woodrats ingest enough of these plant toxins to kill a lab rat. Every day. But the desert is not littered with woodrat corpses, so clearly they are able to detoxify this poisonous salad somehow. “

Saving The Bees Using Microscopic Bugs – RedOrbit

“Phages are the most abundant life form on the planet and each phage has a unique bacteria that it will attack,” said Sandra Burnett, BYU professor of microbiology and molecular biology. “This makes phage an ideal treatment for bacterial disease because it can target specific bacteria while leaving all other cells alone.”

Science, publishing, and career

Reputation and impact in academic careers – Alexander Michael Petersen – PNAS USA

“Here, we develop a framework for quantifying the influence author reputation has on a publication’s future impact.”

NPRs All Things Considered (Podcast, 5 min): Is ‘Leaning In’ The Only Formula For Women’s Success In Science? – Kelly McEvers – NPR

“Don’t wait to be invited or encouraged to make a career in science, engineering or technology, Frances Arnold advises the young women she teaches at the California Institute of Technology. “

Bik’s Picks

Doctors Making Housecalls: Better, Cheaper Care at Home? – Jennifer Ferris – MedPageToday

“In a little over a decade the practice has exploded in popularity — with Taavoni and more than 40 other providers in North Carolina innovating new ways to bring healthcare home.”

Oil platforms off California are among the most productive marine fish habitats globally –
Jeremy T. Claisse – PNAS USA

“Here, we find that fish communities living on the complex hardscape habitat created throughout the water column by the structure of oil and gas platforms off California have the highest secondary production per unit area of seafloor of any marine ecosystem for which similar estimates exist.”

Can Science Perfect Food? – Daniela Galarza – Eater.com

“A research team in Japan is blowing past molecular gastronomy to discover new ways of perfecting already flawless dishes.”

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Non-human microbiome digest, October 28, 2014

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Microbiome of rodent blood, oysters, sponges, hydras, Eucalyptus, soil, and a very deep location.

Animal microbiome

* Association of Host and Microbial Species Diversity across Spatial Scales in Desert Rodent Communities – Yoni Gavish – PLOS ONE

“Following pyrosequencing of rodent blood samples, bacterial communities were found to be comprised primarily of broad niche lineages. “

Metagenomic Assessment of the Eastern Oyster-Associated Microbiota – Ashvini Chauhan – ASM Genome Announcements

“Bacteria associated with the Eastern oysters (Crassostrea virginica) native to Apalachicola Bay, FL, were investigated using 16S rRNA gene amplicon metagenomic sequencing”

Temporal changes in the diazotrophic bacterial communities associated with Caribbean sponges Ircinia stroblina and Mycale laxissima – Fan Zhang, Jan Vicente and Russell T. Hill – Frontiers in Microbiology

“Diazotrophic communities associated with two Caribbean sponges, Ircinia strobilina and Mycale laxissima were studied in a time series during which three individuals of each sponge were collected in four time points “

Species-Specific Viromes in the Ancestral Holobiont Hydra – Juris A. Grasis – PLOS ONE

“We sought to determine the viral communities associating with different Hydra species, whether these viral communities were altered with environmental stress, and whether these viruses affect the Hydra-associated holobiont.”

Plant microbiome

* Microbial Cargo: Do bacteria on symbiotic propagules reinforce the microbiome of lichens? – Ines Aline Aschenbrenner – Environmental Microbiology

“The lung lichen was sampled from three localities in eastern Austria to analyze their associated bacterial communities by bar-coded pyrosequencing, network analysis and fluorescence in situ hybridization.”

Soil microbial properties in Eucalyptus grandis plantations of different ages – C.T. Cortez – Journal of soil science and plant nutrition

“We investigated the soil microbial properties (soil microbial C, N, respiration, carbon use efficiency, and microbial C-to-N ratio) among Eucalyptus grandis plantations of differing ages (1 to 4 years) in Northeast Brazil. “

Soil, rocks, and sediments microbiome

* In-depth analyses of deep subsurface sediments using 454-pyrosequencing reveals a reservoir of buried fungal communities at record-breaking depths – Vanessa Rédou – FEMS Microbiology Ecology

“Here, we investigated the vertical distribution of DNA and RNA fungal signatures within subseafloor sediments of the Canterbury basin (New Zealand) by 454 pyrotag sequencing of fungal genetic markers.”

* Just in time for Halloween: RNA-based molecular survey of biodiversity of limestone tombstone microbiota in response to atmospheric sulfur pollution – Federica Villa – Letters in Applied Microbiology

“In this study, the biofilm microflora of historic limestone tombstones located in a highly polluted urban environment (Cambridge, MA) and in a less polluted location (Lexington, MA), were compared using comprehensive RNA-based molecular analyses of 16S rRNA gene sequences as well as sequences of genes for different pathways of sulfur metabolism (soxB, apsA, dsrA).”

Methane dynamics regulated by microbial community response to permafrost thaw – Carmody K. McCalley – Nature

“Here we show that changes in vegetation and increasing methane emissions with permafrost thaw are associated with a switch from hydrogenotrophic to partly acetoclastic methanogenesis”

Land use and seasonal effects on a Mediterranean soil bacterial community – D. Franciolia – Journal of soil science and plant nutrition

“We compared the fingerprints from both independent replicates and pooled samples to ascertain the best approach for studying the environmental effects on bacterial composition. “

Environmental controls on microbial communities in continental serpentinite fluids
Melitza Crespo-Medina – Frontiers in Microbiology

“Growth was monitored by direct microscopic counts; DNA yield and community composition was assessed at the end of the three month incubation”

Water microbiome

* Microbial transformation of the Deepwater Horizon oil spill – past, present, and future perspectives – Nikole E. Kimes – Frontiers in Microbiology

“In this review, we summarize the microbial response to the oil spill as described by studies performed during the past four years”

Diversity and geochemical structuring of bacterial communities along a salinity gradient in a carbonate aquifer subject to sea water intrusion – Marina Héry – FEMS Microbiology Ecology

“The objective of this study was to characterize and compare bacterial community diversity and composition along a vertical saline gradient in a carbonate coastal aquifer using high throughput sequencing of 16S rRNA genes”

The Variation of Microbial Communities in a Depth Profile of an Acidic, Nutrient-Poor Boreal Bog in Southwestern Finland – Irina Tsitko – OJE

“High throughput sequencing was used to characterize the bacterial communities throughout the bog’s depth profile.”

Spatial distribution patterns of benthic microbial communities along the Pearl Estuary, China – Jiwen Liu – Systematic and Applied Microbiology

“In the present study, benthic microbial communities along the Pearl Estuary, a typical subtropical estuary in China subjected to extensive anthropogenic disturbance, were investigated using 16S rRNA gene-based pyrosequencing.”

Microbes of the built environment

* Bacterial biogeographical patterns in a cooking centre for hospital foodservice – Giuseppina Stellato – International Journal of Food Microbiology

“In this study, the bacterial biogeographical patterns in a hospital cooking centre was studied by 16S rRNA – based culture-independent high-throughput amplicon sequencing in order to provide a comprehensive mapping of the surfaces and tools that come in contact with foods during preparation.”

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Human microbiome digest, October 28, 2014

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Oral microbiome and hyposalivation or caries, COPD, nasal microbiome, and bacterial communities in human semen.
Human oral microbiome

Book chapter: Xerostomia and the Oral Microflora – Antoon J. M. Ligtenberg PhD, Annica Almståhl – SpringerLink

“Hyposalivation changes the oral microbiome with the most dramatic changes after radiation therapy.”

Metatranscriptomics reveals overall active bacterial composition in caries lesions – Aurea Simón-Soro – Journal of Oral Microbiology

“A mean of 4,900 sequences of the 16S rRNA gene with an average read length of 661 bp was obtained per sample, giving a comprehensive view of the active bacterial communities in caries lesions. “

Comparison of bacterial culture and 16S rRNA community profiling by clonal analysis and and pyrosequencing for the characterisation of the caries-associated microbiome – Kathrin Schulze-Schweifing – Frontiers in Microbiology

“In this study, five pairs of broad range primers targeting 16S rRNA genes were used in clonal analysis of 6 samples collected from tooth lesions involving dentine in subjects with active caries. Samples were also subjected to cultural analysis and pyrosequencing by means of the 454 platform. “

Human respiratory microbiome

Review: The potential impact of the pulmonary microbiome on immunopathogenesis of Aspergillus-related lung disease – Eva Kolwijck and Frank L. van de Veerdonk – European Journal of Immunology

“In this perspective, we review this emerging area of research and discuss the role of the microbiome in aspergillosis, role of Aspergillus in the microbiome, and the influence of the microbiome on anti-Aspergillus host defense and its role in preventing aspergillosis.”

Novosphingobium and Its Potential Role in Chronic Obstructive Pulmonary Diseases: Insights from Microbiome Studies – Alleluiah Rutebemberwa – PLOS ONE

“We sought to elucidate the presence and types of lung bacterial populations in different stages of COPD, aimed at revealing important insights into the pathobiology of the disease”

The Nasal and Sinus Microbiome in Health and Disease – Michael T. Wilson and Daniel L. Hamilos – Current Allergy and Asthma Reports

“This review will focus on recent advances in the appreciation and understanding of these relationships in terms of the upper respiratory tract, specifically the nose and paranasal sinuses.”

Human genital microbiome

Bacterial Communities in Semen from Men of Infertile Couples: Metagenomic Sequencing Reveals Relationships of Seminal Microbiota to Semen Quality – Shun-Long Weng – PLOS ONE

“Ninety-six semen samples collected were examined for bacterial communities, measuring seven clinical criteria for semen quality”

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General microbiology and science digest, October 27, 2014

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A new Shiny R tool for microbial communities, virus-like pictures in human distal gut, interaction between oral bacteria, dancing your PhD, and X-ray movies of human joints in action.

Bioinformatics

* Seed: a user-friendly tool for exploring and visualizing microbial community data –
Daniel Beck – Bioinformatics

“Seed is written in R using the Shiny library. This provides access to powerful R based functions and libraries through a simple user interface. “

Viruses and phages

With cool pictures: Characterization of virus-like particles associated with the human faecal and caecal microbiota – Lesley Hoyles – Research in Microbiology

“Various methodologies for the recovery of VLPs from faeces were tested and optimized, including successful down-stream processing of such samples for the purpose of an in-depth electron microscopic analysis, pulsed-field gel electrophoresis and efficient DNA recovery.”

Transcriptomics / Proteomics / Metabolomics

Thermophilic microbial cellulose decomposition and methanogenesis pathways recharacterized by metatranscriptomic and metagenomic analysis – Yu Xia – Scientific Reports

“The metatranscriptomic recharacterization in the present study captured microbial enzymes at the unprecedented scale of 40,000 active genes belonged to 2,269 KEGG functions were identified.”

Proteomic and transcriptional analysis of interaction between oral microbiota Porphyromonas gingivalis and Streptococcus oralis – Kazuhiko Maeda – Journal of Proteome Research

“Here, using shotgun proteomics we examined the molecular basis of mixed-biofilm formation by P. gingivalis with Streptococcus oralis.”

Review: Toward the comprehensive understanding of the gut ecosystem via metabolomics-based integrated omics approach – Wanping Aw, Shinji Fukuda – Seminars in Immunopathology

“In this review, we discuss in detail the relationship between gut microbiota and its metabolites … in the host health and etiopathogenesis of various pathological states such as multiple sclerosis, autism, obesity, diabetes, and chronic kidney disease. “

More Microbiology

Biofilms: Five-Star Accommodations for the Aerobically Challenged – Robert A. Cramer – Current Biology

“A recent study finds that fungal biofilms are capable of supporting growth of anaerobic bacteria, suggesting that these fungi can promote bacterial growth in otherwise toxic environments.”

Microbes in the news

* Sorry, Your Gut Bacteria Are Not the Answer to All Your Health Problems – Gabrielle Canon – Mother Jones

“We’re told that tweaks to the microbiome can cure everything from allergies to Ebola. Not exactly, say experts. …despite the optimism, some researchers caution that much of what we hear about microbiome science isn’t always, well, science. “

* Orthopedic surgeon studies bear bacteria to aid bear attack victims – Healio

“Working with the Montana Fish, Wildlife & Parks, Iwersen has been collecting cultures of bacteria from the mouths of grizzly bears and correlating them with the types of bacteria found in the bear bites on patients. “

Mexican scientist investigates intestinal bacteria – BetaWired

“Recent findings of the investigator Xicotencatl Gracida Canales…at Harvard University in Cambridge, USA, suggest that in the absence of an intestinal shield, variations in bacterial metabolism can affect reproductive cells and cause infertility in an animal model called C. Elegans.”

Algae-Based Material Takes On Body Odor – Dana Dovey – NewsWeek

“A team of Swedish researchers from the KTH Royal Institute of Technology has found a way to eliminate the growth of this smell-inducing bacteria using one of nature’s best antimicrobials, algae.”

MoBE Postdoctoral Fellowship: From Source to Tap: Linking the Drinking Water Microbiome to Human Health – Sarah Haig – MicroBEnet

“We hypothesize that the microbial communities in municipally treated drinking water are a source of opportunistic pathogens, posing a risk to people with cystic fibrosis”

Science, publishing, career

Is NIH policy the best way to sex equality in studies? – Bethany Brookshire – Science News

“The end goal will be to make sure that NIH-funded scientists “balance male and female cells and animals in preclinical studies in all future [grant] applications” to the NIH.”

Some suggestions for having diverse speakers at meetings – Jonathan Eisen – The Tree of Life

“Some people were asking what one can do to improve gender diversity at meetings so I thought I would post this which I was meaning to do anyway “

‘Dance Your Ph.D.’ finalists announced – John Bohannon – Science

“Rather than reading a paper about it, why not watch a dance? A ballet and a modern dance on those very topics have made it into the finals of this year’s “Dance Your Ph.D.” contest.”

Bik’s Picks

Interactive world map of vaccine-preventable outbreaks – Council for Foreign Relations

“This interactive map visually plots global outbreaks of measles, mumps, whooping cough, polio, rubella, and other diseases that are easily preventable by inexpensive and effective vaccines.”

Dietary cocoa flavanols reverse age-related memory decline in mice – Science Daily

“Dietary cocoa flavanols —- naturally occurring bioactives found in cocoa —- reversed age-related memory decline in healthy older adults, according to a new study. Flavanols are also found naturally in tea leaves and in certain fruits and vegetables”

Amazing X-ray GIFs Show Joints In Motion – Lisa Winter – IFL Science

“Cameron Drake of San Francisco has created a collection of magnificent images showing joints in motion. He was aided by orthopedic physician Dr. Noah Weiss and the finished product is completely amazing. “

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Non-human microbiome digest, October 27, 2014

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Microbiomes of camels, cheetahs, jackals, birds and reptiles, limpets, corals, plant roots, soils, and sea water.

Animal microbiome

* In-depth diversity analysis of the bacterial community resident in the camel rumen – Javad Gharechahi – Systematic and Applied Microbiology

“In this study, 16S rRNA gene amplicon pyrosequencing was applied in order to explore the structure of the bacterial community inhabiting the camel rumen.”

Oligotyping reveals differences between gut microbiomes of free-ranging sympatric Namibian carnivores (Acinonyx jubatus, Canis mesomelas) on a bacterial species-like level – Sebastian Menke – Frontiers in Microbiology

“Here, we used Illumina MiSeq to sequence amplicons generated from the V4 region of the 16S rRNA gene to investigate the gut microbiome of two free-ranging sympatric Namibian carnivore species, the cheetah (Acinonyx jubatus) and the black-backed jackal (Canis mesomelas).”

Diet is a major factor governing the fecal butyrate-producing community structure across Mammalia, Aves and Reptilia – Marius Vital – ISME Journal

“We investigated the butyrate-producing community in hindgut-fermenting Mammalia (n=38), Aves (n=8) and Reptilia (n=8) using a gene-targeted pyrosequencing approach of the terminal genes of the main butyrate-synthesis pathways”

Decadal changes in common reef coral populations and their associations with algal symbionts (Symbiodinium spp.) – Timothy R. McClanahan – Marine Ecology

“Decadal populations changes in four coral taxa and their patterns of association with algal symbionts (Symbiodinium spp. – 10 years of sampling) were examined on Kenyan back reefs over a period of climatic disturbances (1991−2009). “

Metaphylogenomic and Potential Functionality of the Limpet Patella pellucida’s Gastrointestinal Tract Microbiome – Magda Dudek – International Journal of Molecular Sciences

“This study investigated the microbial diversity associated with the digestive tract of the seaweed grazing marine limpet Patella pellucida.”

Plant microbiome

* Distinct root-associated bacterial communities on three wild plant species growing in a common field – Kristin Aleklett – PeerJ Preprints

“We sampled endophytic and epiphytic bacteria in root tissues from a population of a wild, clonal plant… as well as two neighboring plant species … to determine if plant species hosted unique root microbiota”

The fungal leaf endophyte Paraconiothyrium variabile specifically metabolizes the host-plant metabolome for its own benefit – Yuan Tian – Phytochemistry

“..we have investigated the action of the endophytic fungus Paraconiothyrium variabile, isolated from the leaves of Cephalotaxus harringtonia, on the secondary metabolome of the host-plant. “

Soil microbiome

Late winter under ice pelagic microbial communities in the high Arctic Ocean and the impact of short-term exposure to elevated CO2 levels – Adam Monier – Frontiers in Microbiology

“Phylogenetic diversity was greater in the attached fraction compared to the free-living fraction in situ, in the controls and in the treatments.”

The ecological dichotomy of ammonia-oxidizing archaea and bacteria in the hyper-arid soils of the Antarctic Dry Valleys – Catarina M. Magalhães – Frontiers in Microbiology

“Here we showed that AOB and AOA amoA gene diversity was generally low; only four AOA and three AOB operational taxonomic units (OTUs) were identified from a total of 420 AOA and AOB amoA clones.”

Soil bacterial community composition altered by increased nutrient availability in Arctic tundra soils – Akihiro Koyama – Frontiers in Microbiology

“Fertilization significantly altered overall bacterial community composition and reduced evenness, to a greater degree in organic than mineral soils, and in the 1989 compared to the 2006 site.”

Effect of volatile organic compounds absorbed to fresh biochar on survival of Bacillus mucilaginosus and structure of soil microbial communities – Daquan Sun – Journal of Soils and Sediments

“The structure of a soil microbial community incubated in biochar was examined via denaturing gradient gel electrophoresis (DGGE). “

Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community – Uli Klümper – ISME Journal

“We identified transfer to many different recipients belonging to 11 different bacterial phyla. “

Water microbiome

* Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities – Chris L Dupont – ISME Journal

“Relative to surface waters, bacterial SCM communities displayed greater genetic diversity and enrichment in putative sulfur oxidizers, multiple actinomycetes, low-light-adapted Prochlorococcus and cell-associated viruses.”

Aerobic methanotrophic communities at the Red Sea brine-seawater interface – Rehab Z. Abdallah – Frontiers in Microbiology

“The current study analyzed the aerobic free–living methane-oxidizing bacterial communities that potentially contribute to methane oxidation at the brine-seawater interfaces of the three aforementioned brine pools, using metagenomic pyrosequencing, 16S rRNA pyrotags and pmoA library constructs. “

Bacterial community structure is indicative of chemical inputs in the Upper Mississippi River – Christopher Staley – Frontiers in Microbiology

“Bacterial communities were characterized by Illumina sequencing of the V6 region of 16S rDNA and compared to >40 chemical and nutrient concentrations. “

Semiconductor Sequencing Reveals the Diversity of Bacterial Communities in an Amazonian Reservoir – Diego Assis das Graças – Aquatic Science and Technology

“In this study, we used a next-generation sequencing platform, the Ion Torrent Personal Genome Machine, and employed a barcode library to investigate the bacterial diversity along a 70-m deep water column in the proximity of the dam. “

Seasonal changes of microbial communities in two shallow peat bog lakes – Sylwia Lew – Folia Microbiologica

“We investigated the seasonal dynamics of the microbial community in two small peat bog lakes, Kuźnik Olsowy and Kuźnik Bagienny, located in western Poland.”

Bioreactor microbiome

Methane-fed microbial microcosms show differential community dynamics and pinpoint taxa involved in communal response – Igor Y Oshkin – ISME Journal

“We report observations on the dynamics of bacterial communities in response to methane stimulus in laboratory microcosm incubations prepared with lake sediment samples.”

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Human microbiome digest, October 27, 2014

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Development of gut microbiome in infants, understanding oral microbiome through high-throughput sequencing, gut bacteria in deceased alcoholics, and bacteria after stroke.

Microbiome general

The symbiont side of symbiosis: do microbes really benefit? – Justine R. Garcia and Nicole M. Gerardo – Frontiers in Microbiology

“We evaluate these hypotheses based on available evidence, which indicate reduced competition and predation are not universal benefits for symbionts. “

Pregnancy and birth microbiome

Review: Diet and the development of the human intestinal microbiome – Noah Voreades – Frontiers in Microbiology

“This review focuses primarily on diet, as it is one of the most pivotal factors in the development of the human gut microbiome from infancy to the elderly.”

Human oral microbiome

Review: Application of high-throughput sequencing in understanding human oral microbiome related with health and disease – Hui Chen and Wen Jiang – Frontiers in Microbiology

“This review describes the application of high-throughput sequencing for characterization of oral microbiota and analyzing the changes of the microbiome in the states of health or disease.”

Human gut microbiome

Cellular and molecular pathways through which commensal bacteria modulate sensitization to dietary antigens – Taylor Feehley, Cathryn R Nagler – Current Opinion in Immunology

“This review will discuss the cellular and molecular pathways activated by commensal bacteria to protect against allergic sensitization.”

Microbial Therapy in Liver Disease: Probiotics Probe the Microbiome–Gut–Liver–Brain Axis – David W. Victor 3rd, Eamonn M.M. Quigley – Gastroenterology

“It is timely, therefore, that Dhiman et al should embark on an ambitious study, reported in this issue of Gastroenterology, designed to assess the efficacy of the probiotic cocktail, VSL#3, as secondary prophylaxis in patients with OHE.”

Changes in gut bacterial populations and their translocation into liver and ascites in alcoholic liver cirrhotics – Sari Tuomisto – BMC Gastroenterology

“Relative ratios of major commensal bacterial communities (Bacteroides spp., Bifidobacterium spp., Clostridium leptum group, Enterobactericaea and Lactobacillus spp.) were determined in faecal samples from post mortem examinations performed on 42 males”

Animal models of microbiome research

Age-related changes in intestinal permeability and gut microbiota after ischemic stroke – Joshua Crapser – Journal of Neuroimmunology

“This study aimed to elucidate the role of systemic factors, such as intestinal stress, underlying the poor outcomes of aging mice after stroke.”

Spatial and temporal colonization dynamics of segmented filamentous bacteria is influenced by gender, age and experimental infection with Helicobacter hepaticus in Swiss Webster mice – Zhongming Ge – Microbes and Infection

“Hh infection in both genders did not alter SFB levels in the jejunum and ileum, but increased SFB levels in the cecum and colon of males compared to the controls”

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Microbiome digest, October 24, 2014

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Microbiome of placentas, infant respiratory microbiome, metabolomics, mutipartite genomes, microbes in the news, and some weekend picks.
Human microbiome general

Microbiome/microbiota and allergies – Yuzaburo Inoue, Naoki Shimojo – Seminars in Immunopathology

“In this review, we summarize the recent findings regarding the importance of the microbiome/microbiota in the development of allergic diseases and also the results of interventional studies using probiotics or prebiotics to prevent allergies.”

Pregnancy and birth

Term and preterm labour are associated with distinct microbial community structures in placental membranes which are independent of mode of delivery – Ronan M. Doyle – Placenta

“In this study, 16S rDNA pyrosequencing was used to identify bacteria in placental membranes. Caesarean sections and vaginal deliveries at term were found to harbour common genera”

Early Respiratory Microbiota Composition Determines Bacterial Succession Patterns and Respiratory Health in Children – Giske Biesbroek – Am J Respir Crit Care Med.

“Upper respiratory microbiota profiles of 60 healthy children at the ages of 1.5, 6, 12 and 24 months were characterized by 16S-based pyrosequencing”

From the “old NEC” to the “new NECs” – Melania Puddu – Journal of Pediatric and Neonatal Individualized Medicine

“This review describes in detail the new NECs especially those which affect preterm infants: contagion or lymphocytosis associated, transfusion associated and cow’s milk allergy associated.”

Metagenomics

The effects of variable sample biomass on comparative metagenomics – Meghan Chafee – Environmental Microbiology

“We investigated the interacting effects of DNA input and library amplification by PCR on comparative metagenomic analysis using dilutions of a single complex template from an Arabidopsis-associated microbial community.”

Metabolomics 

The nexus of syntrophy-associated microbiota in anaerobic digestion revealed by long-term enrichment and community survey – Takashi Narihiro – Environmental Microbiology

“16S pyrotag analysis revealed core populations of known syntrophs (six clades) and methanogens (nine clades) associated with acid degradation, and evidence for substrate- and/or inoculum-dependent specificity in syntrophic partnerships.”

In Vitro Fermentation of Lactulose by Human Gut Bacteria – Bingyong Mao – Journal of Agricultural and Food Chemistry

“This study aimed to identify lactulose-metabolizing bacteria in the human gut, using in-silico and traditional culture methods. “

Epigenomic regulation of host–microbiota interactions – Theresa Alenghat, David Artis – Trends in Immunology

“We review recent advances in understanding the interplay between the microbiota and mammalian epigenomic pathways, and highlight emerging findings that implicate a central role for histone deacetylases (HDACs) in orchestrating host–microbiota interactions.”

More microbiology

Examination of Prokaryotic Multipartite Genome Evolution through Experimental Genome Reduction – George C. diCenzo – PLOS Genetics

“To gain insight into the role and evolutionary history of these replicons, we have ‘reversed evolution’ by constructing a S. meliloti strain consisting solely of the chromosome and lacking the pSymB chromid and pSymA megaplasmid.”

Microbes in the news

How An Antibiotic Gene Jumped All Over The Tree of Life – Ed Yong – National Geographic

“Metcalf showed that it has also jumped from bacteria into every other major branch of life. It’s in animals, plants, fungi, archaea, and even some viruses.”

Research investigates bacteria on banknotes – Harper Adams University

“This study investigates how easy it is for bacteria and pathogens to survive on currency and whether the material the notes are made of, has an effect on the transfer.”

How millennials will save us all – Jennifer Block – Quartz

“Millennials get a bad rap for loading up on debt, mooching off their parents, and hiding behind technology. But there’s one problem that they may be particularly suited to tackling: our shrinking microbiome.“

Bik’s Picks

World’s Most Asked Questions: How Much Water Should I Drink a Day? – SciShow – Youtube

“People ask Google everything under the sun. One of the most commonly searched questions in the world is “How much water should I drink a day?” SciShow has the answer!”

Ten Simple Rules for Writing a PLOS Ten Simple Rules Article – Harriet Dashnow – PLOS Computational Biology

“This search left us wanting, until we discovered the PLOS Ten Simple Rules collection. We have found them to be a series of concise articles that capture the professional zeitgeist of being a scientist in an approachable manner.”

Satire: Ambitious New High-Speed Rail Plan Will Fly Americans To Japan To Use Their Trains – The Onion

“The transit system that the U.S. has needed for so long is now just a 7,000-mile plane journey to Tokyo’s Narita International Airport and a brief passage through Japanese customs away,” Obama continued.”

Microbiome Digest, October 23, 2014

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Not much microbiome news today – which was good because I got time to watch the solar eclipse and a huge solar storm at the same time.  Enjoy the read!

Animal models of microbiome research

Lyn Deficiency Leads to Increased Microbiota-Dependent Intestinal Inflammation and Susceptibility to Enteric Pathogens – Morgan E. Roberts – Journal of Immunology

“Lyn2/2 mice exhibited profound cecal inflammation, bacterial dissemination, and morbidity following S. Typhimurium challenge and greater colonic inflammation throughout the course of C. rodentium infection.”

Rock microbiome

* Halophilic Archaea Cultivated from Surface Sterilized Middle-Late Eocene Rock Salt Are Polyploid – Salla T. Jaakkola – PLOS ONE

“We used real-time PCR to show that our isolates are polyploid, with genome copy numbers of 11–14 genomes per cell in exponential growth phase.”

More Microbiology

Zooming in to see the bigger picture: Microfluidic and nanofabrication tools to study bacteria – Felix J. H. Hol, Cees Dekker – Science

“Here, we review the new scientific insights gained by using a diverse set of nanofabrication and microfluidic techniques to study individual bacteria and multispecies communities.”

Review: Theory and Empiricism in Virulence Evolution – James J. Bull, Adam S. Lauring – PLOS Pathogens

“Our purpose here is to offer a brief introduction to virulence theory, explain some of its strengths and weaknesses, and suggest how theory might be united with empiric data”

Techniques

Comparing the new 16S rRNA V4 and ITS primers to the old primers-RESULTS! – Embriette Hyde – MicroBEnet

“The Knight lab has been working hard testing new primers for 16S rRNA amplicon production and its time to share our progress.”

Microbes in the News

As permafrost soils thaw, soil microbes amplify global climate change – Science Daily

“Now, research by an international team of scientists from the U.S., Sweden and Australia, led by University of Arizona scientists, shows that a single species of microbe, discovered only very recently, is an unexpected key player in climate change.”

* The Scientist: Prof. Esther Angert Studies Extreme Bacteria – Siddesh Ramesh – Cornell Sun

“While the majority of bacteria cannot be seen without a microscope, there exists a group of bacterial species that is visible to the naked eye. Known as Epulopiscium, they are “an extreme on the spectrum of diversity of bacterial life in existence,” according to Prof. Esther Angert, microbiology.”

Bik’s Picks

Flare Alert: Monster Sunspot Turns Toward Earth – Ian O’Neill – Discovery

“Amateur astronomers have been wowed by a vast sunspot that has rotated to face Earth, the largest since this solar cycle began in 2008, and solar observatories (on the ground and orbiting Earth) are closely monitoring the region.“

Watch cell division with new, remarkable resolution: Nobel winner Betzig strikes again – Tech Times

“Just weeks after sharing the Nobel Prize in chemistry for his work involving high-resolution microscopes, a U.S. researcher has again stunned the scientific world with a new technique that peers deeply into living cells.”

Ancient Europeans do not drink milk according to new study – BetaWired

“Almost everyone drinks milk today but a new study shows that ancient Europeans were not milk lovers back in the old days. According to a DNA analysis result, ancient Europeans are lactose intolerant.”

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